sites cluster analysis: Topics by Science.gov

Sample records for sites cluster analysis

Applied anatomic site study of palatal anchorage implants using cone beam computed tomography.

PubMed

Lai, Ren-fa; Zou, Hui; Kong, Wei-dong; Lin, Wei

2010-06-01

The purpose of this study was to conduct quantitative research on bone height and bone mineral density of palatal implant sites for implantation, and to provide reference sites for safe and stable palatal implants. Three-dimensional reformatting images were reconstructed by cone beam computed tomography (CBCT) in 34 patients, aged 18 to 35 years, using EZ Implant software. Bone height was measured at 20 sites of interest on the palate. Bone mineral density was measured at the 10 sites with the highest implantation rate, classified using K-mean cluster analysis based on bone height and bone mineral density. According to the cluster analysis, 10 sites were classified into three clusters. Significant differences in bone height and bone mineral density were detected between these three clusters (P<0.05). The greatest bone height was obtained in cluster 2, followed by cluster 1 and cluster 3. The highest bone mineral density was found in cluster 3, followed by cluster 1 and cluster 2. CBCT plays an important role in pre-surgical treatment planning. CBCT is helpful in identifying safe and stable implantation sites for palatal anchorage.
Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering.

PubMed

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor; Essex, M

2015-05-01

To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.
Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering

PubMed Central

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor

2015-01-01

Abstract To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice. PMID:25560745
A framework to spatially cluster air pollution monitoring sites in US based on the PM2.5 composition

PubMed Central

Austin, Elena; Coull, Brent A.; Zanobetti, Antonella; Koutrakis, Petros

2013-01-01

Background Heterogeneity in the response to PM2.5 is hypothesized to be related to differences in particle composition across monitoring sites which reflect differences in source types as well as climatic and topographic conditions impacting different geographic locations. Identifying spatial patterns in particle composition is a multivariate problem that requires novel methodologies. Objectives Use cluster analysis methods to identify spatial patterns in PM2.5 composition. Verify that the resulting clusters are distinct and informative. Methods 109 monitoring sites with 75% reported speciation data during the period 2003–2008 were selected. These sites were categorized based on their average PM2.5 composition over the study period using k-means cluster analysis. The obtained clusters were validated and characterized based on their physico-chemical characteristics, geographic locations, emissions profiles, population density and proximity to major emission sources. Results Overall 31 clusters were identified. These include 21 clusters with 2 or more sites which were further grouped into 4 main types using hierarchical clustering. The resulting groupings are chemically meaningful and represent broad differences in emissions. The remaining clusters, encompassing single sites, were characterized based on their particle composition and geographic location. Conclusions The framework presented here provides a novel tool which can be used to identify and further classify sites based on their PM2.5 composition. The solution presented is fairly robust and yielded groupings that were meaningful in the context of air-pollution research. PMID:23850585
An application of bioassessment metrics and multivariate techniques to evaluate central Nebraska streams

USGS Publications Warehouse

Frenzel, S.A.

1996-01-01

Ninety-one stream sites in central Nebraska were classified into four clusters on the basis of a cluster analysis (TWINSPAN) of macroinvertebrate data. Rapid bioassessment protocol scores for macroinvertebrate species were significantly different among sites grouped by teh first division into two clusters. This division may have distinguished sites on the basis of water-quality imparement. Individual metrics that differed between clusters of sites were the Hilsenhoff Biotic Index, the number of Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa, and the ratio of individuals in EPT to Chironomidae taxa. Canonical correspondence analysis of 57 of 91 sites showed that stream width, site altitude, latitude, soil permeability, water temperature, and mean annual precipitation were the most important environmental variables describing variance in the species-environment relation. Stream width and soil permeability reflected streamflow characteristics of a site, whereas site altitude and latitude were factors related to general climatic conditions. Mean annual precipitation related to both streamflow and climatic conditions.
Efficacy of GPS cluster analysis for predicting carnivory sites of a wide-ranging omnivore: the American black bear

USGS Publications Warehouse

Kindschuh, Sarah R.; Cain, James W.; Daniel, David; Peyton, Mark A.

2016-01-01

The capacity to describe and quantify predation by large carnivores expanded considerably with the advent of GPS technology. Analyzing clusters of GPS locations formed by carnivores facilitates the detection of predation events by identifying characteristics which distinguish predation sites. We present a performance assessment of GPS cluster analysis as applied to the predation and scavenging of an omnivore, the American black bear (Ursus americanus), on ungulate prey and carrion. Through field investigations of 6854 GPS locations from 24 individual bears, we identified 54 sites where black bears formed a cluster of locations while predating or scavenging elk (Cervus elaphus), mule deer (Odocoileus hemionus), or cattle (Bos spp.). We developed models for three data sets to predict whether a GPS cluster was formed at a carnivory site vs. a non-carnivory site (e.g., bed sites or non-ungulate foraging sites). Two full-season data sets contained GPS locations logged at either 3-h or 30-min intervals from April to November, and a third data set contained 30-min interval data from April through July corresponding to the calving period for elk. Longer fix intervals resulted in the detection of fewer carnivory sites. Clusters were more likely to be carnivory sites if they occurred in open or edge habitats, if they occurred in the early season, if the mean distance between all pairs of GPS locations within the cluster was less, and if the cluster endured for a longer period of time. Clusters were less likely to be carnivory sites if they were initiated in the morning or night compared to the day. The top models for each data set performed well and successfully predicted 71–96% of field-verified carnivory events, 55–75% of non–carnivory events, and 58–76% of clusters overall. Refinement of this method will benefit from further application across species and ecological systems.
Computational identification of developmental enhancers:conservation and function of transcription factor binding-site clustersin drosophila melanogaster and drosophila psedoobscura

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berman, Benjamin P.; Pfeiffer, Barret D.; Laverty, Todd R.

2004-08-06

The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayedmore » embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. Measuring conservation of sequence features closely linked to function--such as binding-site clustering--makes better use of comparative sequence data than commonly used methods that examine only sequence identity.« less
Evaluation of Potential Locations for Siting Small Modular Reactors near Federal Energy Clusters to Support Federal Clean Energy Goals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belles, Randy J.; Omitaomu, Olufemi A.

2014-09-01

Geographic information systems (GIS) technology was applied to analyze federal energy demand across the contiguous US. Several federal energy clusters were previously identified, including Hampton Roads, Virginia, which was subsequently studied in detail. This study provides an analysis of three additional diverse federal energy clusters. The analysis shows that there are potential sites in various federal energy clusters that could be evaluated further for placement of an integral pressurized-water reactor (iPWR) to support meeting federal clean energy goals.
Analysis of Rainfall and PM2.5 Data Using Clustered Trajectory Analysis for National Park Sites in the Western U.S.

NASA Astrophysics Data System (ADS)

Solorzano, N. N.; Hafner, W.; Jaffe, D.

2005-12-01

We calculated daily kinematic back-trajectories using the NOAA-HYSPLIT model to analyze 7 years of PM2.5 data from National Park sites in the Western U.S. (Glacier N.P., Mount Rainier N.P., Sequoia N.P., Rocky Mountain N.P. and Denali N.P.) The back-trajectories were clustered using a k-means clustering algorithm to segregate the trajectories into 6 main transport patterns. We calculated trajectory clusters for 1, 5 and 10 days to represent short, medium and long-range flow patterns. Some trajectory types and clusters show marked seasonality. Generally faster flow patterns are more prevalent in winter and slower/stagnant patterns are more prevalent in summer. In addition, we found significant inter-annual variability that may be important for explaining variations in rainfall and/or pollutant concentrations. The 5 and 10-day analyses revealed that, for the 4 non-Alaskan sites, trajectories from Asia tend to be less frequent in the summer, compared to the rest of the year. The clusters of different duration show very different predictive power for rainfall and PM2.5. We found that the 1-day clusters are a better predictor for precipitation and PM2.5 concentrations, as compared to the 5 and 10-day clusters. At each of the sites, there is at least one cluster with an average PM2.5 concentration that is different than the average for the site, indicating distinctive transport patterns. The same is true for 5 and 10-day clusters. Interestingly, only one site, Mount Rainier N.P., shows seasonal differences in PM2.5 concentrations between the clusters that differ from the average.
An approach to functionally relevant clustering of the protein universe: Active site profile‐based clustering of protein structures and sequences

PubMed Central

Knutson, Stacy T.; Westwood, Brian M.; Leuthaeuser, Janelle B.; Turner, Brandon E.; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D.; Harper, Angela F.; Brown, Shoshana D.; Morris, John H.; Ferrin, Thomas E.; Babbitt, Patricia C.

2017-01-01

Abstract Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification—amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two‐Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure‐Function Linkage Database, SFLD) self‐identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self‐identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well‐curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP‐identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F‐measure and performance analysis on the enolase search results and comparison to GEMMA and SCI‐PHY demonstrate that TuLIP avoids the over‐division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. PMID:28054422
An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.

PubMed

Knutson, Stacy T; Westwood, Brian M; Leuthaeuser, Janelle B; Turner, Brandon E; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D; Harper, Angela F; Brown, Shoshana D; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C; Fetrow, Jacquelyn S

2017-04-01

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.
Computational identification of developmental enhancers:conservation and function of transcription factor binding-site clustersin drosophila melanogaster and drosophila psedoobscura

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berman, Benjamin P.; Pfeiffer, Barret D.; Laverty, Todd R.

2004-08-06

Background The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. Results We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene,more » and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. Conclusions Measuring conservation of sequence features closely linked to function - such as binding-site clustering - makes better use of comparative sequence data than commonly used methods that examine only sequence identity.« less
Identification of PM10 air pollution origins at a rural background site

NASA Astrophysics Data System (ADS)

Reizer, Magdalena; Orza, José A. G.

2018-01-01

Trajectory cluster analysis and concentration weighted trajectory (CWT) approach have been applied to investigate the origins of PM10 air pollution recorded at a rural background site in North-eastern Poland (Diabla Góra). Air mass back-trajectories used in this study have been computed with the Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model for a 10-year period of 2006-2015. A cluster analysis grouped back-trajectories into 7 clusters. Most of the trajectories correspond to fast and moderately moving westerly and northerly flows (45% and 25% of the cases, respectively). However, significantly higher PM10 concentrations were observed for slow moving easterly (11%) and southerly (20%) air masses. The CWT analysis shows that high PM10 levels are observed at Diabla Góra site when air masses are originated and passed over the heavily industrialized areas in Central-Eastern Europe located to the south and south-east of the site.
The adiposity of children is associated with their lifestyle behaviours: a cluster analysis of school-aged children from 12 nations.

PubMed

Dumuid, Dorothea; Olds, T; Lewis, L K; Martin-Fernández, J A; Barreira, T; Broyles, S; Chaput, J-P; Fogelholm, M; Hu, G; Kuriyan, R; Kurpad, A; Lambert, E V; Maia, J; Matsudo, V; Onywera, V O; Sarmiento, O L; Standage, M; Tremblay, M S; Tudor-Locke, C; Zhao, P; Katzmarzyk, P; Gillison, F; Maher, C

2018-02-01

The relationship between children's adiposity and lifestyle behaviour patterns is an area of growing interest. The objectives of this study are to identify clusters of children based on lifestyle behaviours and compare children's adiposity among clusters. Cross-sectional data from the International Study of Childhood Obesity, Lifestyle and the Environment were used. the participants were children (9-11 years) from 12 nations (n = 5710). 24-h accelerometry and self-reported diet and screen time were clustering input variables. Objectively measured adiposity indicators were waist-to-height ratio, percent body fat and body mass index z-scores. sex-stratified analyses were performed on the global sample and repeated on a site-wise basis. Cluster analysis (using isometric log ratios for compositional data) was used to identify common lifestyle behaviour patterns. Site representation and adiposity were compared across clusters using linear models. Four clusters emerged: (1) Junk Food Screenies, (2) Actives, (3) Sitters and (4) All-Rounders. Countries were represented differently among clusters. Chinese children were over-represented in Sitters and Colombian children in Actives. Adiposity varied across clusters, being highest in Sitters and lowest in Actives. Children from different sites clustered into groups of similar lifestyle behaviours. Cluster membership was linked with differing adiposity. Findings support the implementation of activity interventions in all countries, targeting both physical activity and sedentary time. © 2016 World Obesity Federation.
Characterization and analysis of temporal and spatial variations in habitat and macroinvertebrate community structure, Fountain Creek basin, Colorado Springs and vicinity, Colorado, 1998-2001

USGS Publications Warehouse

Bruce, James F.

2002-01-01

The Fountain Creek Basin in and around Colorado Springs, Colorado, is affected by various land- and water-use activities. Biological, hydrological, water-quality, and land-use data were collected at 10 sites in the Fountain Creek Basin from April 1998 through April 2001 to provide a baseline characterization of macroinvertebrate communities and habitat conditions for comparison in subsequent studies; and to assess variation in macroinvertebrate community structure relative to habitat quality. Analysis of variance results indicated that instream and riparian variables were not affected by season, but significant differences were found among sites. Nine metrics were used to describe and evaluate macroinvertebrate community structure. Statistical analysis indicated that for six of the nine metrics, significant variability occurred between spring and fall seasons for 60 percent of the sites. Cluster analysis (unweighted pair group method average) using macroinvertebrate presence-absence data showed a well-defined separation between spring and fall samples. Six of the nine metrics had significant spatial variation. Cluster analysis using Sorenson?s Coefficient of Community values computed from macroinvertebrate density (number of organisms per square meter) data showed that macroinvertebrate community structure was more similar among tributary sites than main-stem sites. Canonical correspondence analysis identified a substrate particle-size gradient from site-specific species-abundance data and environmental correlates that decreased the 10 sites to 5 site clusters and their associated taxa.
The Influence of the Host Plant Is the Major Ecological Determinant of the Presence of Nitrogen-Fixing Root Nodule Symbiont Cluster II Frankia Species in Soil

PubMed Central

Battenberg, Kai; Wren, Jannah A.; Hillman, Janell; Edwards, Joseph; Huang, Liujing

2016-01-01

ABSTRACT The actinobacterial genus Frankia establishes nitrogen-fixing root nodule symbioses with specific hosts within the nitrogen-fixing plant clade. Of four genetically distinct subgroups of Frankia, cluster I, II, and III strains are capable of forming effective nitrogen-fixing symbiotic associations, while cluster IV strains generally do not. Cluster II Frankia strains have rarely been detected in soil devoid of host plants, unlike cluster I or III strains, suggesting a stronger association with their host. To investigate the degree of host influence, we characterized the cluster II Frankia strain distribution in rhizosphere soil in three locations in northern California. The presence/absence of cluster II Frankia strains at a given site correlated significantly with the presence/absence of host plants on the site, as determined by glutamine synthetase (glnA) gene sequence analysis, and by microbiome analysis (16S rRNA gene) of a subset of host/nonhost rhizosphere soils. However, the distribution of cluster II Frankia strains was not significantly affected by other potential determinants such as host-plant species, geographical location, climate, soil pH, or soil type. Rhizosphere soil microbiome analysis showed that cluster II Frankia strains occupied only a minute fraction of the microbiome even in the host-plant-present site and further revealed no statistically significant difference in the α-diversity or in the microbiome composition between the host-plant-present or -absent sites. Taken together, these data suggest that host plants provide a factor that is specific for cluster II Frankia strains, not a general growth-promoting factor. Further, the factor accumulates or is transported at the site level, i.e., beyond the host rhizosphere. IMPORTANCE Biological nitrogen fixation is a bacterial process that accounts for a major fraction of net new nitrogen input in terrestrial ecosystems. Transfer of fixed nitrogen to plant biomass is especially efficient via root nodule symbioses, which represent evolutionarily and ecologically specialized mutualistic associations. Frankia spp. (Actinobacteria), especially cluster II Frankia spp., have an extremely broad host range, yet comparatively little is known about the soil ecology of these organisms in relation to the host plants and their rhizosphere microbiomes. This study reveals a strong influence of the host plant on soil distribution of cluster II Frankia spp. PMID:27795313
Temporal and spatial assessment of river surface water quality using multivariate statistical techniques: a study in Can Tho City, a Mekong Delta area, Vietnam.

PubMed

Phung, Dung; Huang, Cunrui; Rutherford, Shannon; Dwirahmadi, Febi; Chu, Cordia; Wang, Xiaoming; Nguyen, Minh; Nguyen, Nga Huy; Do, Cuong Manh; Nguyen, Trung Hieu; Dinh, Tuan Anh Diep

2015-05-01

The present study is an evaluation of temporal/spatial variations of surface water quality using multivariate statistical techniques, comprising cluster analysis (CA), principal component analysis (PCA), factor analysis (FA) and discriminant analysis (DA). Eleven water quality parameters were monitored at 38 different sites in Can Tho City, a Mekong Delta area of Vietnam from 2008 to 2012. Hierarchical cluster analysis grouped the 38 sampling sites into three clusters, representing mixed urban-rural areas, agricultural areas and industrial zone. FA/PCA resulted in three latent factors for the entire research location, three for cluster 1, four for cluster 2, and four for cluster 3 explaining 60, 60.2, 80.9, and 70% of the total variance in the respective water quality. The varifactors from FA indicated that the parameters responsible for water quality variations are related to erosion from disturbed land or inflow of effluent from sewage plants and industry, discharges from wastewater treatment plants and domestic wastewater, agricultural activities and industrial effluents, and contamination by sewage waste with faecal coliform bacteria through sewer and septic systems. Discriminant analysis (DA) revealed that nephelometric turbidity units (NTU), chemical oxygen demand (COD) and NH₃ are the discriminating parameters in space, affording 67% correct assignation in spatial analysis; pH and NO₂ are the discriminating parameters according to season, assigning approximately 60% of cases correctly. The findings suggest a possible revised sampling strategy that can reduce the number of sampling sites and the indicator parameters responsible for large variations in water quality. This study demonstrates the usefulness of multivariate statistical techniques for evaluation of temporal/spatial variations in water quality assessment and management.
Interstitial telomeric sequences in human chromosomes cluster with common fragile sites, mutagen sensitive sites, viral integration sites, cancer breakpoints, proto-oncogenes and breakpoints involved in primate evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adekunle, S.S.A.; Wyandt, H.; Mark, H.F.L.

1994-09-01

Recently we mapped the telomeric repeat sequences to 111 interstitial sites in the human genome and to sites of gaps and breaks induced by aphidicolin and sister chromatid exchange sites detected by BrdU. Many of these sites correspond to conserved fragile sites in man, gorilla and chimpazee, to sites of conserved sister chromatid exchange in the mammalian X chromosome, to mutagenic sensitive sites, mapped locations of proto-oncogenes, breakpoints implicated in primate evolution and to breakpoints indicated as the sole anomaly in neoplasia. This observation prompted us to investigate if the interstitial telomeric sites cluster with these sites. An extensive literaturemore » search was carried out to find all the available published sites mentioned above. For comparison, we also carried out a statistical analysis of the clustering of the sites of the telomeric repeats with the gene locations where only nucleotide mutations have been observed as the only chromosomal abnormality. Our results indicate that the telomeric repeats cluster most with fragile sites, mutagenic sensitive sites and breakpoints implicated in primate evolution and least with cancer breakpoints, mapped locations of proto-oncogenes and other genes with nucleotide mutations.« less
Cluster analysis of S. Cerevisiae nucleosome binding sites

NASA Astrophysics Data System (ADS)

Suvorova, Y.; Korotkov, E.

2017-12-01

It is well known that major part of a eukaryotic genome is wrapped around histone proteins forming nucleosomes. It was also demonstrated that the DNA sequence itself is playing an important role in the nucleosome positioning process. In this work, a cluster analysis of 67 517 nucleosome binding sites from the S. Cerevisiae genome was carried out. The classification method is based on the self-adjusting dinucleotides position weight matrix. As a result, 135 significant clusters were discovered that contain 43225 sequences (which constitutes 64% of the initial set). The meaning of the found classes is discussed, as well as the possibility of the further usage.
Symptom Clusters in Advanced Cancer Patients: An Empirical Comparison of Statistical Methods and the Impact on Quality of Life.

PubMed

Dong, Skye T; Costa, Daniel S J; Butow, Phyllis N; Lovell, Melanie R; Agar, Meera; Velikova, Galina; Teckle, Paulos; Tong, Allison; Tebbutt, Niall C; Clarke, Stephen J; van der Hoek, Kim; King, Madeleine T; Fayers, Peter M

2016-01-01

Symptom clusters in advanced cancer can influence patient outcomes. There is large heterogeneity in the methods used to identify symptom clusters. To investigate the consistency of symptom cluster composition in advanced cancer patients using different statistical methodologies for all patients across five primary cancer sites, and to examine which clusters predict functional status, a global assessment of health and global quality of life. Principal component analysis and exploratory factor analysis (with different rotation and factor selection methods) and hierarchical cluster analysis (with different linkage and similarity measures) were used on a data set of 1562 advanced cancer patients who completed the European Organization for the Research and Treatment of Cancer Quality of Life Questionnaire-Core 30. Four clusters consistently formed for many of the methods and cancer sites: tense-worry-irritable-depressed (emotional cluster), fatigue-pain, nausea-vomiting, and concentration-memory (cognitive cluster). The emotional cluster was a stronger predictor of overall quality of life than the other clusters. Fatigue-pain was a stronger predictor of overall health than the other clusters. The cognitive cluster and fatigue-pain predicted physical functioning, role functioning, and social functioning. The four identified symptom clusters were consistent across statistical methods and cancer types, although there were some noteworthy differences. Statistical derivation of symptom clusters is in need of greater methodological guidance. A psychosocial pathway in the management of symptom clusters may improve quality of life. Biological mechanisms underpinning symptom clusters need to be delineated by future research. A framework for evidence-based screening, assessment, treatment, and follow-up of symptom clusters in advanced cancer is essential. Copyright © 2016 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

Combined Analyses of Bacterial, Fungal and Nematode Communities in Andosolic Agricultural Soils in Japan

PubMed Central

Bao, Zhihua; Ikunaga, Yoko; Matsushita, Yuko; Morimoto, Sho; Takada-Hoshino, Yuko; Okada, Hiroaki; Oba, Hirosuke; Takemoto, Shuhei; Niwa, Shigeru; Ohigashi, Kentaro; Suzuki, Chika; Nagaoka, Kazunari; Takenaka, Makoto; Urashima, Yasufumi; Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Toyota, Koki; Saito, Masanori; Tsushima, Seiya

2012-01-01

We simultaneously examined the bacteria, fungi and nematode communities in Andosols from four agro-geographical sites in Japan using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and statistical analyses to test the effects of environmental factors including soil properties on these communities depending on geographical sites. Statistical analyses such as Principal component analysis (PCA) and Redundancy analysis (RDA) revealed that the compositions of the three soil biota communities were strongly affected by geographical sites, which were in turn strongly associated with soil characteristics such as total C (TC), total N (TN), C/N ratio and annual mean soil temperature (ST). In particular, the TC, TN and C/N ratio had stronger effects on bacterial and fungal communities than on the nematode community. Additionally, two-way cluster analysis using the combined DGGE profile also indicated that all soil samples were classified into four clusters corresponding to the four sites, showing high site specificity of soil samples, and all DNA bands were classified into four clusters, showing the coexistence of specific DGGE bands of bacteria, fungi and nematodes in Andosol fields. The results of this study suggest that geography relative to soil properties has a simultaneous impact on soil microbial and nematode community compositions. This is the first combined profile analysis of bacteria, fungi and nematodes at different sites with agricultural Andosols. PMID:22223474
Combined analyses of bacterial, fungal and nematode communities in andosolic agricultural soils in Japan.

PubMed

Bao, Zhihua; Ikunaga, Yoko; Matsushita, Yuko; Morimoto, Sho; Takada-Hoshino, Yuko; Okada, Hiroaki; Oba, Hirosuke; Takemoto, Shuhei; Niwa, Shigeru; Ohigashi, Kentaro; Suzuki, Chika; Nagaoka, Kazunari; Takenaka, Makoto; Urashima, Yasufumi; Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Toyota, Koki; Saito, Masanori; Tsushima, Seiya

2012-01-01

We simultaneously examined the bacteria, fungi and nematode communities in Andosols from four agro-geographical sites in Japan using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and statistical analyses to test the effects of environmental factors including soil properties on these communities depending on geographical sites. Statistical analyses such as Principal component analysis (PCA) and Redundancy analysis (RDA) revealed that the compositions of the three soil biota communities were strongly affected by geographical sites, which were in turn strongly associated with soil characteristics such as total C (TC), total N (TN), C/N ratio and annual mean soil temperature (ST). In particular, the TC, TN and C/N ratio had stronger effects on bacterial and fungal communities than on the nematode community. Additionally, two-way cluster analysis using the combined DGGE profile also indicated that all soil samples were classified into four clusters corresponding to the four sites, showing high site specificity of soil samples, and all DNA bands were classified into four clusters, showing the coexistence of specific DGGE bands of bacteria, fungi and nematodes in Andosol fields. The results of this study suggest that geography relative to soil properties has a simultaneous impact on soil microbial and nematode community compositions. This is the first combined profile analysis of bacteria, fungi and nematodes at different sites with agricultural Andosols.
Quantifying site-specific physical heterogeneity within an estuarine seascape

USGS Publications Warehouse

Kennedy, Cristina G.; Mather, Martha E.; Smith, Joseph M.

2017-01-01

Quantifying physical heterogeneity is essential for meaningful ecological research and effective resource management. Spatial patterns of multiple, co-occurring physical features are rarely quantified across a seascape because of methodological challenges. Here, we identified approaches that measured total site-specific heterogeneity, an often overlooked aspect of estuarine ecosystems. Specifically, we examined 23 metrics that quantified four types of common physical features: (1) river and creek confluences, (2) bathymetric variation including underwater drop-offs, (3) land features such as islands/sandbars, and (4) major underwater channel networks. Our research at 40 sites throughout Plum Island Estuary (PIE) provided solutions to two problems. The first problem was that individual metrics that measured heterogeneity of a single physical feature showed different regional patterns. We solved this first problem by combining multiple metrics for a single feature using a within-physical feature cluster analysis. With this approach, we identified sites with four different types of confluences and three different types of underwater drop-offs. The second problem was that when multiple physical features co-occurred, new patterns of total site-specific heterogeneity were created across the seascape. This pattern of total heterogeneity has potential ecological relevance to structure-oriented predators. To address this second problem, we identified sites with similar types of total physical heterogeneity using an across-physical feature cluster analysis. Then, we calculated an additive heterogeneity index, which integrated all physical features at a site. Finally, we tested if site-specific additive heterogeneity index values differed for across-physical feature clusters. In PIE, the sites with the highest additive heterogeneity index values were clustered together and corresponded to sites where a fish predator, adult striped bass (Morone saxatilis), aggregated in a related acoustic tracking study. In summary, we have shown general approaches to quantifying site-specific heterogeneity.
Cluster analysis of intradiurnal holm oak pollen cycles at peri-urban and rural sampling sites in southwestern Spain

NASA Astrophysics Data System (ADS)

Hernández-Ceballos, M. A.; García-Mozo, H.; Galán, C.

2015-08-01

The impact of regional and local weather and of local topography on intradiurnal variations in airborne pollen levels was assessed by analysing bi-hourly holm oak ( Quercus ilex subsp. ballota (Desf.) Samp.) pollen counts at two sampling stations located 40 km apart, in southwestern Spain (Cordoba city and El Cabril nature reserve) over the period 2010-2011. Pollen grains were captured using Hirst-type volumetric spore traps. Analysis of regional weather conditions was based on the computation of backward trajectories using the HYSPLIT model. Sampling days were selected on the basis of phenological data; rainy days were eliminated, as were days lying outside a given range of percentiles (P95-P5). Analysis of cycles for the study period, as a whole, revealed differences between sampling sites, with peak bi-hourly pollen counts at night in Cordoba and at midday in El Cabril. Differences were also noted in the influence of surface weather conditions (temperature, relative humidity and wind). Cluster analysis of diurnal holm oak pollen cycles revealed the existence of five clusters at each sampling site. Analysis of backward trajectories highlighted specific regional air-flow patterns associated with each site. Findings indicated the contribution of both nearby and distant pollen sources to diurnal cycles. The combined use of cluster analysis and meteorological analysis proved highly suitable for charting the impact of local weather conditions on airborne pollen-count patterns. This method, and the specific tools used here, could be used not only to study diurnal variations in counts for other pollen types and in other biogeographical settings, but also in a number of other research fields involving airborne particle transport modelling, e.g. radionuclide transport in emergency preparedness exercises.
Cluster analysis of intradiurnal holm oak pollen cycles at peri-urban and rural sampling sites in southwestern Spain.

PubMed

Hernández-Ceballos, M A; García-Mozo, H; Galán, C

2015-08-01

The impact of regional and local weather and of local topography on intradiurnal variations in airborne pollen levels was assessed by analysing bi-hourly holm oak (Quercus ilex subsp. ballota (Desf.) Samp.) pollen counts at two sampling stations located 40 km apart, in southwestern Spain (Cordoba city and El Cabril nature reserve) over the period 2010-2011. Pollen grains were captured using Hirst-type volumetric spore traps. Analysis of regional weather conditions was based on the computation of backward trajectories using the HYSPLIT model. Sampling days were selected on the basis of phenological data; rainy days were eliminated, as were days lying outside a given range of percentiles (P95-P5). Analysis of cycles for the study period, as a whole, revealed differences between sampling sites, with peak bi-hourly pollen counts at night in Cordoba and at midday in El Cabril. Differences were also noted in the influence of surface weather conditions (temperature, relative humidity and wind). Cluster analysis of diurnal holm oak pollen cycles revealed the existence of five clusters at each sampling site. Analysis of backward trajectories highlighted specific regional air-flow patterns associated with each site. Findings indicated the contribution of both nearby and distant pollen sources to diurnal cycles. The combined use of cluster analysis and meteorological analysis proved highly suitable for charting the impact of local weather conditions on airborne pollen-count patterns. This method, and the specific tools used here, could be used not only to study diurnal variations in counts for other pollen types and in other biogeographical settings, but also in a number of other research fields involving airborne particle transport modelling, e.g. radionuclide transport in emergency preparedness exercises.
Health-Related Quality of Life and Lifestyle Behavior Clusters in School-Aged Children from 12 Countries.

PubMed

Dumuid, Dorothea; Olds, Timothy; Lewis, Lucy K; Martin-Fernández, Josep Antoni; Katzmarzyk, Peter T; Barreira, Tiago; Broyles, Stephanie T; Chaput, Jean-Philippe; Fogelholm, Mikael; Hu, Gang; Kuriyan, Rebecca; Kurpad, Anura; Lambert, Estelle V; Maia, José; Matsudo, Victor; Onywera, Vincent O; Sarmiento, Olga L; Standage, Martyn; Tremblay, Mark S; Tudor-Locke, Catrine; Zhao, Pei; Gillison, Fiona; Maher, Carol

2017-04-01

To evaluate the relationship between children's lifestyles and health-related quality of life and to explore whether this relationship varies among children from different world regions. This study used cross-sectional data from the International Study of Childhood Obesity, Lifestyle and the Environment. Children (9-11 years) were recruited from sites in 12 nations (n = 5759). Clustering input variables were 24-hour accelerometry and self-reported diet and screen time. Health-related quality of life was self-reported with KIDSCREEN-10. Cluster analyses (using compositional analysis techniques) were performed on a site-wise basis. Lifestyle behavior cluster characteristics were compared between sites. The relationship between cluster membership and health-related quality of life was assessed with the use of linear models. Lifestyle behavior clusters were similar across the 12 sites, with clusters commonly characterized by (1) high physical activity (actives); (2) high sedentary behavior (sitters); (3) high screen time/unhealthy eating pattern (junk-food screenies); and (4) low screen time/healthy eating pattern and moderate physical activity/sedentary behavior (all-rounders). Health-related quality of life was greatest in the all-rounders cluster. Children from different world regions clustered into groups of similar lifestyle behaviors. Cluster membership was related to differing health-related quality of life, with children from the all-rounders cluster consistently reporting greatest health-related quality of life at sites around the world. Findings support the importance of a healthy combination of lifestyle behaviors in childhood: low screen time, healthy eating pattern, and balanced daily activity behaviors (physical activity and sedentary behavior). ClinicalTrials.gov: NCT01722500. Copyright © 2016 Elsevier Inc. All rights reserved.
SU-F-R-33: Can CT and CBCT Be Used Simultaneously for Radiomics Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, R; Wang, J; Zhong, H

2016-06-15

Purpose: To investigate whether CBCT and CT can be used in radiomics analysis simultaneously. To establish a batch correction method for radiomics in two similar image modalities. Methods: Four sites including rectum, bladder, femoral head and lung were considered as region of interest (ROI) in this study. For each site, 10 treatment planning CT images were collected. And 10 CBCT images which came from same site of same patient were acquired at first radiotherapy fraction. 253 radiomics features, which were selected by our test-retest study at rectum cancer CT (ICC>0.8), were calculated for both CBCT and CT images in MATLAB.more » Simple scaling (z-score) and nonlinear correction methods were applied to the CBCT radiomics features. The Pearson Correlation Coefficient was calculated to analyze the correlation between radiomics features of CT and CBCT images before and after correction. Cluster analysis of mixed data (for each site, 5 CT and 5 CBCT data are randomly selected) was implemented to validate the feasibility to merge radiomics data from CBCT and CT. The consistency of clustering result and site grouping was verified by a chi-square test for different datasets respectively. Results: For simple scaling, 234 of the 253 features have correlation coefficient ρ>0.8 among which 154 features haveρ>0.9 . For radiomics data after nonlinear correction, 240 of the 253 features have ρ>0.8 among which 220 features have ρ>0.9. Cluster analysis of mixed data shows that data of four sites was almost precisely separated for simple scaling(p=1.29 * 10{sup −7}, χ{sup 2} test) and nonlinear correction (p=5.98 * 10{sup −7}, χ{sup 2} test), which is similar to the cluster result of CT data (p=4.52 * 10{sup −8}, χ{sup 2} test). Conclusion: Radiomics data from CBCT can be merged with those from CT by simple scaling or nonlinear correction for radiomics analysis.« less
RSAT 2015: Regulatory Sequence Analysis Tools

PubMed Central

Medina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragon, Jaime A.; Delerce, Jeremy; Jaeger, Sébastien; Blanchet, Christophe; Vincens, Pierre; Caron, Christophe; Staines, Daniel M.; Contreras-Moreira, Bruno; Artufel, Marie; Charbonnier-Khamvongsa, Lucie; Hernandez, Céline; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2015-01-01

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/. PMID:25904632
Compositional variability in Mediterranean archaeofaunas from Upper Paleolithic Southwest Europe

NASA Astrophysics Data System (ADS)

Jones, Emily Lena

2018-03-01

Recent meta-analyses of Upper Paleolithic Southwestern European archaeofaunas (Jones, 2015, 2016) have identified a consistent "Mediterranean" cluster from the Last Glacial Maximum through the early Holocene, suggesting similarities in environment and/or consistency in hunting strategy across this region through time despite radical changes in climate. However, while these archaeofaunas from this cluster all derive from sites located within today's Mediterranean bioclimatic region, many of them are from locations far from the Mediterranean Sea - Atlantic Portugal, the Spanish Meseta - which today differ significantly from each other in biotic composition. In this paper, I explore clustering (through cluster analysis and non-metric multidimensional scaling) within the Mediterranean archaeofaunal group. I test for the influence of sample size as well as the geographic variables of site elevation, latitude, and longitude on variability in the large mammal portions of archaeofaunal assemblages. ANOVA shows no relationship between cluster-defined groups and site elevation or longitude; instead, site latitude appears to be a primary contributor to patterning. However, the overall compositional similarity of the Mediterranean archaeofaunas in this dataset suggests more consistency than variability in Upper Paleolithic hunting strategy in this region.
Investigation of Spatial and Temporal Trends in Water Quality in Daya Bay, South China Sea

PubMed Central

Wu, Mei-Lin; Wang, You-Shao; Dong, Jun-De; Sun, Cui-Ci; Wang, Yu-Tu; Sun, Fu-Lin; Cheng, Hao

2011-01-01

The objective is to identify the spatial and temporal variability of the hydrochemical quality of the water column in a subtropical coastal system, Daya Bay, China. Water samples were collected in four seasons at 12 monitoring sites. The Southeast Asian monsoons, northeasterly from October to the next April and southwesterly from May to September have also an important influence on water quality in Daya Bay. In the spatial pattern, two groups have been identified, with the help of multidimensional scaling analysis and cluster analysis. Cluster I consisted of the sites S3, S8, S10 and S11 in the west and north coastal parts of Daya Bay. Cluster I is mainly related to anthropogenic activities such as fish-farming. Cluster II consisted of the rest of the stations in the center, east and south parts of Daya Bay. Cluster II is mainly related to seawater exchange from South China Sea. PMID:21776234
The Antenatal Corticosteroids Trial (ACT): a secondary analysis to explore site differences in a multi-country trial.

PubMed

Klein, Karen; McClure, Elizabeth M; Colaci, Daniela; Thorsten, Vanessa; Hibberd, Patricia L; Esamai, Fabian; Garces, Ana; Patel, Archana; Saleem, Sarah; Pasha, Omrana; Chomba, Elwyn; Carlo, Waldemar A; Krebs, Nancy F; Goudar, Shivaprasad; Derman, Richard J; Liechty, Edward A; Koso-Thomas, Marion; Buekens, Pierre M; Belizán, José M; Goldenberg, Robert L; Althabe, Fernando

2016-05-24

The Antenatal Corticosteroid Trial (ACT) assessed the feasibility, effectiveness, and safety of a multifaceted intervention to increase the use of antenatal corticosteroids (ACS) in mothers at risk of preterm birth at all levels of care in low and middle-income countries. The intervention effectively increased the use of ACS but had no overall impact on neonatal mortality in the targeted <5(th) percentile birth weight infants. Being in the intervention clusters was also associated with an overall increase in neonatal deaths. We sought to explore plausible pathways through which this intervention increased neonatal mortality. We conducted secondary analyses to assess site differences in outcome and potential explanations for the differences in outcomes if found. By site, and in the intervention and control clusters, we evaluated characteristics of the mothers and care systems, the proportion of the <5(th) percentile infants and the overall population that received ACS, the rates of possible severe bacterial infection (pSBI), determined from clinical signs, and neonatal mortality rates. There were substantial differences between the sites in both participant and health system characteristics, with Guatemala and Argentina generally having the highest levels of care. In some sites there were substantial differences in the health system characteristics between the intervention and control clusters. The increase in ACS in the intervention clusters was similar among the sites. While overall, there was no difference in neonatal mortality among <5(th) percentile births between the intervention and control clusters, Guatemala and Pakistan both had significant reductions in neonatal mortality in the <5(th) percentile infants in the intervention clusters. The improvement in neonatal mortality in the Guatemalan site in the <5(th) percentile infants was associated with a higher level of care at the site and an improvement in care in the intervention clusters. There was a significant increase overall in neonatal mortality in the intervention clusters compared to the control. Across sites, this increase in neonatal mortality was statistically significant and most apparent in the African sites. This increase in neonatal mortality was accompanied by a significant increase in pSBI in the African sites. The improvement in neonatal mortality in the Guatemalan site in the <5(th) percentile infants was associated with a higher level of care and an improvement in care in the intervention clusters. The increase in neonatal mortality in the intervention clusters across all sites was largely driven by the poorer outcomes in the African sites, which also had an increase in pSBI in the intervention clusters. We emphasize that these results come from secondary analyses. Additional prospective studies are needed to assess the effectiveness and safety of ACS on neonatal health in low resource settings. clinicaltrials.gov (NCT01084096).
Distribution-based fuzzy clustering of electrical resistivity tomography images for interface detection

NASA Astrophysics Data System (ADS)

Ward, W. O. C.; Wilkinson, P. B.; Chambers, J. E.; Oxby, L. S.; Bai, L.

2014-04-01

A novel method for the effective identification of bedrock subsurface elevation from electrical resistivity tomography images is described. Identifying subsurface boundaries in the topographic data can be difficult due to smoothness constraints used in inversion, so a statistical population-based approach is used that extends previous work in calculating isoresistivity surfaces. The analysis framework involves a procedure for guiding a clustering approach based on the fuzzy c-means algorithm. An approximation of resistivity distributions, found using kernel density estimation, was utilized as a means of guiding the cluster centroids used to classify data. A fuzzy method was chosen over hard clustering due to uncertainty in hard edges in the topography data, and a measure of clustering uncertainty was identified based on the reciprocal of cluster membership. The algorithm was validated using a direct comparison of known observed bedrock depths at two 3-D survey sites, using real-time GPS information of exposed bedrock by quarrying on one site, and borehole logs at the other. Results show similarly accurate detection as a leading isosurface estimation method, and the proposed algorithm requires significantly less user input and prior site knowledge. Furthermore, the method is effectively dimension-independent and will scale to data of increased spatial dimensions without a significant effect on the runtime. A discussion on the results by automated versus supervised analysis is also presented.
Somatosensory nociceptive characteristics differentiate subgroups in people with chronic low back pain: a cluster analysis.

PubMed

Rabey, Martin; Slater, Helen; OʼSullivan, Peter; Beales, Darren; Smith, Anne

2015-10-01

The objectives of this study were to explore the existence of subgroups in a cohort with chronic low back pain (n = 294) based on the results of multimodal sensory testing and profile subgroups on demographic, psychological, lifestyle, and general health factors. Bedside (2-point discrimination, brush, vibration and pinprick perception, temporal summation on repeated monofilament stimulation) and laboratory (mechanical detection threshold, pressure, heat and cold pain thresholds, conditioned pain modulation) sensory testing were examined at wrist and lumbar sites. Data were entered into principal component analysis, and 5 component scores were entered into latent class analysis. Three clusters, with different sensory characteristics, were derived. Cluster 1 (31.9%) was characterised by average to high temperature and pressure pain sensitivity. Cluster 2 (52.0%) was characterised by average to high pressure pain sensitivity. Cluster 3 (16.0%) was characterised by low temperature and pressure pain sensitivity. Temporal summation occurred significantly more frequently in cluster 1. Subgroups were profiled on pain intensity, disability, depression, anxiety, stress, life events, fear avoidance, catastrophizing, perception of the low back region, comorbidities, body mass index, multiple pain sites, sleep, and activity levels. Clusters 1 and 2 had a significantly greater proportion of female participants and higher depression and sleep disturbance scores than cluster 3. The proportion of participants undertaking <300 minutes per week of moderate activity was significantly greater in cluster 1 than in clusters 2 and 3. Low back pain, therefore, does not appear to be homogeneous. Pain mechanisms relating to presentations of each subgroup were postulated. Future research may investigate prognoses and interventions tailored towards these subgroups.
Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

PubMed Central

2012-01-01

Background Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. Results The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Conclusions Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family. PMID:22793672
Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.

PubMed

Durston, Kirk K; Chiu, David Ky; Wong, Andrew Kc; Li, Gary Cl

2012-07-13

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Our results demonstrate that the method we present here using a k-modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.
Tropospheric Ozonesonde Profiles at Long-term U.S. Monitoring Sites: 1. A Climatology Based on Self-Organizing Maps

NASA Technical Reports Server (NTRS)

Stauffer, Ryan M.; Thompson, Anne M.; Young, George S.

2016-01-01

Sonde-based climatologies of tropospheric ozone (O3) are vital for developing satellite retrieval algorithms and evaluating chemical transport model output. Typical O3 climatologies average measurements by latitude or region, and season. A recent analysis using self-organizing maps (SOM) to cluster ozonesondes from two tropical sites found that clusters of O3 mixing ratio profiles are an excellent way to capture O3variability and link meteorological influences to O3 profiles. Clusters correspond to distinct meteorological conditions, e.g., convection, subsidence, cloud cover, and transported pollution. Here the SOM technique is extended to four long-term U.S. sites (Boulder, CO; Huntsville, AL; Trinidad Head, CA; and Wallops Island, VA) with4530 total profiles. Sensitivity tests on k-means algorithm and SOM justify use of 3 3 SOM (nine clusters). Ateach site, SOM clusters together O3 profiles with similar tropopause height, 500 hPa height temperature, and amount of tropospheric and total column O3. Cluster means are compared to monthly O3 climatologies.For all four sites, near-tropopause O3 is double (over +100 parts per billion by volume; ppbv) the monthly climatological O3 mixing ratio in three clusters that contain 1316 of profiles, mostly in winter and spring.Large midtropospheric deviations from monthly means (6 ppbv, +710 ppbv O3 at 6 km) are found in two of the most populated clusters (combined 3639 of profiles). These two clusters contain distinctly polluted(summer) and clean O3 (fall-winter, high tropopause) profiles, respectively. As for tropical profiles previously analyzed with SOM, O3 averages are often poor representations of U.S. O3 profile statistics.
Tropospheric ozonesonde profiles at long-term U.S. monitoring sites: 1. A climatology based on self-organizing maps

PubMed Central

Stauffer, Ryan M.; Thompson, Anne M.; Young, George S.

2018-01-01

Sonde-based climatologies of tropospheric ozone (O3) are vital for developing satellite retrieval algorithms and evaluating chemical transport model output. Typical O3 climatologies average measurements by latitude or region, and season. Recent analysis using self-organizing maps (SOM) to cluster ozonesondes from two tropical sites found clusters of O3 mixing ratio profiles are an excellent way to capture O3 variability and link meteorological influences to O3 profiles. Clusters correspond to distinct meteorological conditions, e.g. convection, subsidence, cloud cover, and transported pollution. Here, the SOM technique is extended to four long-term U.S. sites (Boulder, CO; Huntsville, AL; Trinidad Head, CA; Wallops Island, VA) with 4530 total profiles. Sensitivity tests on k-means algorithm and SOM justify use of 3×3 SOM (nine clusters). At each site, SOM clusters together O3 profiles with similar tropopause height, 500 hPa height/temperature, and amount of tropospheric and total column O3. Cluster means are compared to monthly O3 climatologies. For all four sites, near-tropopause O3 is double (over +100 parts per billion by volume; ppbv) the monthly climatological O3 mixing ratio in three clusters that contain 13 – 16% of profiles, mostly in winter and spring. Large mid-tropospheric deviations from monthly means (−6 ppbv, +7 – 10 ppbv O3 at 6 km) are found in two of the most populated clusters (combined 36 – 39% of profiles). These two clusters contain distinctly polluted (summer) and clean O3 (fall-winter, high tropopause) profiles, respectively. As for tropical profiles previously analyzed with SOM, O3 averages are often poor representations of U.S. O3 profile statistics. PMID:29619288
Tropospheric ozonesonde profiles at long-term U.S. monitoring sites: 1. A climatology based on self-organizing maps.

PubMed

Stauffer, Ryan M; Thompson, Anne M; Young, George S

2016-02-16

Sonde-based climatologies of tropospheric ozone (O 3 ) are vital for developing satellite retrieval algorithms and evaluating chemical transport model output. Typical O 3 climatologies average measurements by latitude or region, and season. Recent analysis using self-organizing maps (SOM) to cluster ozonesondes from two tropical sites found clusters of O 3 mixing ratio profiles are an excellent way to capture O 3 variability and link meteorological influences to O 3 profiles. Clusters correspond to distinct meteorological conditions, e.g. convection, subsidence, cloud cover, and transported pollution. Here, the SOM technique is extended to four long-term U.S. sites (Boulder, CO; Huntsville, AL; Trinidad Head, CA; Wallops Island, VA) with 4530 total profiles. Sensitivity tests on k-means algorithm and SOM justify use of 3×3 SOM (nine clusters). At each site, SOM clusters together O 3 profiles with similar tropopause height, 500 hPa height/temperature, and amount of tropospheric and total column O 3 . Cluster means are compared to monthly O 3 climatologies. For all four sites, near-tropopause O 3 is double (over +100 parts per billion by volume; ppbv) the monthly climatological O 3 mixing ratio in three clusters that contain 13 - 16% of profiles, mostly in winter and spring. Large mid-tropospheric deviations from monthly means (-6 ppbv, +7 - 10 ppbv O 3 at 6 km) are found in two of the most populated clusters (combined 36 - 39% of profiles). These two clusters contain distinctly polluted (summer) and clean O 3 (fall-winter, high tropopause) profiles, respectively. As for tropical profiles previously analyzed with SOM, O 3 averages are often poor representations of U.S. O 3 profile statistics.
Molecular Analysis of Bacterial Community Dynamics During Bioaugmentation Studies in a Soil Column and at a Field Test Site

DTIC Science & Technology

2004-06-03

82 4.14 A GelComparII-generated UPGMA clustering dendrogram and corresponding normalized restriction...A GelComparII-generated UPGMA clustering dendrogram and corresponding normalized restriction profiles from the community...A GelComparII-generated UPGMA clustering dendrogram and corresponding normalized restriction profiles from the community
How Japanese students characterize information from web-sites.

PubMed

Iwahara, A; Yamada, M; Hatta, T; Kawakami, A; Okamoto, M

2000-12-01

How 352 Japanese university students regard web-site information was investigated by two kinds of survey. Application of correspondence analysis and cluster analysis to the questionnaire responses to the web-site advertisement showed students regarded a web-site as a new alien medium which is different from current media. Students regarded web-sites as simply complicated, intellectual, and impermanent, or not memorable. Students got precise information from web-sites but they did not use it in making decisions to purchase goods.

The impact of on-site wastewater from high density cluster developments on groundwater quality

NASA Astrophysics Data System (ADS)

Morrissey, P. J.; Johnston, P. M.; Gill, L. W.

2015-11-01

The net impact on groundwater quality from high density clusters of unsewered housing across a range of hydro(geo)logical settings has been assessed. Four separate cluster development sites were selected, each representative of different aquifer vulnerability categories. Groundwater samples were collected on a monthly basis over a two year period for chemical and microbiological analysis from nested multi-horizon sampling boreholes upstream and downstream of the study sites. The field results showed no statistically significant difference between upstream and downstream water quality at any of the study areas, although there were higher breakthroughs in contaminants in the High and Extreme vulnerability sites linked to high intensity rainfall events; these however, could not be directly attributed to on-site effluent. Linked numerical models were then built for each site using HYDRUS 2D to simulate the attenuation of contaminants through the unsaturated zone from which the resulting hydraulic and contaminant fluxes at the water table were used as inputs into MODFLOW MT3D models to simulate the groundwater flows. The results of the simulations confirmed the field observations at each site, indicating that the existing clustered on-site wastewater discharges would only cause limited and very localised impacts on groundwater quality, with contaminant loads being quickly dispersed and diluted downstream due to the relatively high groundwater flow rates. Further simulations were then carried out using the calibrated models to assess the impact of increasing cluster densities revealing little impact at any of the study locations up to a density of 6 units/ha with the exception of the Extreme vulnerability site.
Archeological Survey of the Proposed Charity Lake Hydroelectric Project, Upper Smith River Basin, Patrick and Franklin Counties, Virginia.

DTIC Science & Technology

1986-04-01

Chapel Hill. Oosting, H.J. 1942 An Ecological Analysis of the Plant Communities of Piedmont North Carolina. The American Midland Naturalist 28:1-126...sites and 3 sites were recommeded for furthework. / ,. ’-’ / .!A I 17. Document Analysis a. Descriptors i b. Identifior/Open-Ended Terms I Archeology...maintained at USRB is a Woodland community pattern of small satellite sites clustering near the large sites, and the ceramic analysis reported here suggests
β-globin gene cluster haplotypes in ethnic minority populations of southwest China

PubMed Central

Sun, Hao; Liu, Hongxian; Huang, Kai; Lin, Keqin; Huang, Xiaoqin; Chu, Jiayou; Ma, Shaohui; Yang, Zhaoqing

2017-01-01

The genetic diversity and relationships among ethnic minority populations of southwest China were investigated using seven polymorphic restriction enzyme sites in the β-globin gene cluster. The haplotypes of 1392 chromosomes from ten ethnic populations living in southwest China were determined. Linkage equilibrium and recombination hotspot were found between the 5′ sites and 3′ sites of the β-globin gene cluster. 5′ haplotypes 2 (+−−−), 6 (−++−+), 9 (−++++) and 3′ haplotype FW3 (−+) were the predominant haplotypes. Notably, haplotype 9 frequency was significantly high in the southwest populations, indicating their difference with other Chinese. The interpopulation differentiation of southwest Chinese minority populations is less than those in populations of northern China and other continents. Phylogenetic analysis shows that populations sharing same ethnic origin or language clustered to each other, indicating current β-globin cluster diversity in the Chinese populations reflects their ethnic origin and linguistic affiliations to a great extent. This study characterizes β-globin gene cluster haplotypes in southwest Chinese minorities for the first time, and reveals the genetic variability and affinity of these populations using β-globin cluster haplotype frequencies. The results suggest that ethnic origin plays an important role in shaping variations of the β-globin gene cluster in the southwestern ethnic populations of China. PMID:28205625
RSAT 2015: Regulatory Sequence Analysis Tools.

PubMed

Medina-Rivera, Alejandra; Defrance, Matthieu; Sand, Olivier; Herrmann, Carl; Castro-Mondragon, Jaime A; Delerce, Jeremy; Jaeger, Sébastien; Blanchet, Christophe; Vincens, Pierre; Caron, Christophe; Staines, Daniel M; Contreras-Moreira, Bruno; Artufel, Marie; Charbonnier-Khamvongsa, Lucie; Hernandez, Céline; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

2015-07-01

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
A Framework for Designing Cluster Randomized Trials with Binary Outcomes

ERIC Educational Resources Information Center

Spybrook, Jessaca; Martinez, Andres

2011-01-01

The purpose of this paper is to provide a frame work for approaching a power analysis for a CRT (cluster randomized trial) with a binary outcome. The authors suggest a framework in the context of a simple CRT and then extend it to a blocked design, or a multi-site cluster randomized trial (MSCRT). The framework is based on proportions, an…
Diversity in aconitine alkaloid profile of Aconitum plants in Hokkaido contrasts with their genetic similarity.

PubMed

Kakiuchi, Nobuko; Atsumi, Toshiyuki; Higuchi, Mari; Kamikawa, Shohei; Miyako, Haruka; Wakita, Yuriko; Ohtsuka, Isao; Hayashi, Shigeki; Hishida, Atsuyuki; Kawahara, Nobuo; Nishizawa, Makoto; Yamagishi, Takashi; Kadota, Yuichi

2015-01-01

Aconite tuber is a representative crude drug for warming the body internally in Japanese Kampo medicine and Chinese traditional medicine. The crude drug is used in major prescriptions for the aged. Varieties of Aconitum plants are distributed throughout the Japanese Islands, especially Hokkaido. With the aim of identifying the medicinal potential of Aconitum plants from Hokkaido, 107 specimens were collected from 36 sites in the summer of 2011 and 2012. Their nuclear DNA region, internal transcribed spacer (ITS), and aconitine alkaloid contents were analyzed. Phylogenic analysis of ITS by maximum parsimony analysis showed that the majority of the specimens were grouped into one cluster (cluster I), separated from the other cluster (cluster II) consisting of alpine specimens. The aconitine alkaloid content of the tuberous roots of 76 specimens showed 2 aspects-specimens from the same collection site showed similar aconitine alkaloid profiles, and cluster I specimens from different habitats showed various alkaloid profiles. Environmental pressure of each habitat is presumed to have caused the morphology and aconitine alkaloid profile of these genetically similar specimens to diversify.
Spatio-Temporal Clustering of Monitoring Network

NASA Astrophysics Data System (ADS)

Hussain, I.; Pilz, J.

2009-04-01

Pakistan has much diversity in seasonal variation of different locations. Some areas are in desserts and remain very hot and waterless, for example coastal areas are situated along the Arabian Sea and have very warm season and a little rainfall. Some areas are covered with mountains, have very low temperature and heavy rainfall; for instance Karakoram ranges. The most important variables that have an impact on the climate are temperature, precipitation, humidity, wind speed and elevation. Furthermore, it is hard to find homogeneous regions in Pakistan with respect to climate variation. Identification of homogeneous regions in Pakistan can be useful in many aspects. It can be helpful for prediction of the climate in the sub-regions and for optimizing the number of monitoring sites. In the earlier literature no one tried to identify homogeneous regions of Pakistan with respect to climate variation. There are only a few papers about spatio-temporal clustering of monitoring network. Steinhaus (1956) presented the well-known K-means clustering method. It can identify a predefined number of clusters by iteratively assigning centriods to clusters based. Castro et al. (1997) developed a genetic heuristic algorithm to solve medoids based clustering. Their method is based on genetic recombination upon random assorting recombination. The suggested method is appropriate for clustering the attributes which have genetic characteristics. Sap and Awan (2005) presented a robust weighted kernel K-means algorithm incorporating spatial constraints for clustering climate data. The proposed algorithm can effectively handle noise, outliers and auto-correlation in the spatial data, for effective and efficient data analysis by exploring patterns and structures in the data. Soltani and Modarres (2006) used hierarchical and divisive cluster analysis to categorize patterns of rainfall in Iran. They only considered rainfall at twenty-eight monitoring sites and concluded that eight clusters existed. Soltani and Modarres (2006) classified the sites by using only average rainfall of sites, they did not consider time replications and spatial coordinates. Kerby et.al (2007) purposed spatial clustering method based on likelihood. They took account of the geographic locations through the variance covariance matrix. Their purposed method works like hierarchical clustering methods. Moreovere, it is inappropiriate for time replication data and could not perform well for large number of sites. Tuia.et.al (2008) used scan statistics for identifying spatio-temporal clusters for fire sequences in the Tuscany region in Italy. The scan statistics clustering method was developed by Kulldorff et al. (1997) to detect spatio-temporal clusters in epidemiology and assessing their significance. The purposed scan statistics method is used only for univariate discrete stochastic random variables. In this paper we make use of a very simple approach for spatio-temporal clustering which can create separable and homogeneous clusters. Most of the clustering methods are based on Euclidean distances. It is well known that geographic coordinates are spherical coordinates and estimating Euclidean distances from spherical coordinates is inappropriate. As a transformation from geographic coordinates to rectangular (D-plane) coordinates we use the Lambert projection method. The partition around medoids clustering method is incorporated on the data including D-plane coordinates. Ordinary kriging is taken as validity measure for the precipitation data. The kriging results for clusters are more accurate and have less variation compared to complete monitoring network precipitation data. References Casto.V.E and Murray.A.T (1997). Spatial Clustering with Data Mining with Genetic Algorithms. http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.56.8573 Kaufman.L and Rousseeuw.P.J (1990). Finding Groups in Data: An Introduction to Cluster Analysis. Wiley series of Probability and Mathematical Statistics, New York. Kulldorf.M (1997). A spatial scan statistic. Commun. Stat.-Theor. Math. 26(6), 1481-1496 Kerby. A , Marx. D, Samal. A and Adamchuck. V. (2007). Spatial Clustering Using the Likelihood Function. Seventh IEEE International Conference on Data Mining - Workshops Steinhaus.H (1956). Sur la division des corp materiels en parties. Bull. Acad. Polon. Sci., C1. III vol IV:801- 804 Snyder, J. P. (1987). Map Projection: A Working Manual. U. S. Geological Survey Professional Paper 1395. Washington, DC: U. S. Government Printing Office, pp. 104-110 Sap.M.N and Awan. A.M (2005). Finding Spatio-Temporal Patterns in Climate Data Using Clustering. Proceedings of the International Conference on Cyberworlds (CW'05) Soltani.S and Modarres.R (2006). Classification of Spatio -Temporal Pattern of Rainfall in Iran: Using Hierarchical and Divisive Cluster Analysis. Journal of Spatial Hydrology Vol.6, No.2 Tuia.D, Ratle.F, Lasaponara.R, Telesca.L and Kanevski.M (2008). Scan Statistics Analysis for Forest Fire Clusters. Commun. in Nonlinear science and numerical simulation 13,1689-1694.
Indexing method for assessment of pollution potential of leachate from non-engineered landfill sites and its effect on ground water quality.

PubMed

Rana, Rishi; Ganguly, Rajiv; Gupta, Ashok Kumar

2017-12-26

Dumping of solid waste in a non-engineered landfill site often leads to contamination of ground water due to leachate percolation into ground water. The present paper assesses the pollution potential of leachate generated from three non-engineered landfill sites located in the Tricity region (one each in cities of Chandigarh, Mohali and Panchkula) of Northern India and its possible effects of contamination of groundwater. Analysis of physico-chemical properties of leachate from all the three landfill sites and the surrounding groundwater samples from five different downwind distances from each of the landfill sites were collected and tested to determine the leachate pollution index (LPI) and the water quality index (WQI). The Leachate Pollution Index values of 26.1, 27 and 27.8 respectively for landfill sites of Chandigarh (CHD), Mohali (MOH) and Panchkula (PKL) cities showed that the leachate generated are contaminated. The average pH values of the leachate samples over the sampling period (9.2 for CHD, 8.97 for MOH and 8.9 for PKL) show an alkaline nature indicating that all the three landfill sites could be classified as mature to old stage. The WQI calculated over the different downwind distances from the contamination sites showed that the quality of the groundwater improved with an increase in the downwind distance. Principal component analysis (PCA) carried out established major components mainly from natural and anthropogenic sources with cumulative variance of 88% for Chandigarh, 87.1% for Mohali and 87.8% for Panchkula. Hierarchical cluster analysis (HCA) identifies three distinct cluster types for the groundwater samples. These clusters corresponds to a relatively low pollution, moderate pollution and high pollution regions. It is suggested that all the three non-engineered landfill sites be converted to engineered landfill sites to prevent groundwater contamination and also new sites be considered for construction of these engineered landfill sites as the present dumpsites are nearing the end of their lifespan capacity.
Carbon Fibers Conductivity Studies

NASA Technical Reports Server (NTRS)

Yang, C. Y.; Butkus, A. M.

1980-01-01

In an attempt to understand the process of electrical conduction in polyacrylonitrile (PAN)-based carbon fibers, calculations were carried out on cluster models of the fiber consisting of carbon, nitrogen, and hydrogen atoms using the modified intermediate neglect of differential overlap (MINDO) molecular orbital (MO) method. The models were developed based on the assumption that PAN carbon fibers obtained with heat treatment temperatures (HTT) below 1000 C retain nitrogen in a graphite-like lattice. For clusters modeling an edge nitrogen site, analysis of the occupied MO's indicated an electron distribution similar to that of graphite. A similar analysis for the somewhat less stable interior nitrogen site revealed a partially localized II electron distribution around the nitrogen atom. The differences in bonding trends and structural stability between edge and interior nitrogen clusters led to a two-step process proposed for nitrogen evolution with increasing HTT.
Spatial characterization of dissolved trace elements and heavy metals in the upper Han River (China) using multivariate statistical techniques.

PubMed

Li, Siyue; Zhang, Quanfa

2010-04-15

A data matrix (4032 observations), obtained during a 2-year monitoring period (2005-2006) from 42 sites in the upper Han River is subjected to various multivariate statistical techniques including cluster analysis, principal component analysis (PCA), factor analysis (FA), correlation analysis and analysis of variance to determine the spatial characterization of dissolved trace elements and heavy metals. Our results indicate that waters in the upper Han River are primarily polluted by Al, As, Cd, Pb, Sb and Se, and the potential pollutants include Ba, Cr, Hg, Mn and Ni. Spatial distribution of trace metals indicates the polluted sections mainly concentrate in the Danjiang, Danjiangkou Reservoir catchment and Hanzhong Plain, and the most contaminated river is in the Hanzhong Plain. Q-model clustering depends on geographical location of sampling sites and groups the 42 sampling sites into four clusters, i.e., Danjiang, Danjiangkou Reservoir region (lower catchment), upper catchment and one river in headwaters pertaining to water quality. The headwaters, Danjiang and lower catchment, and upper catchment correspond to very high polluted, moderate polluted and relatively low polluted regions, respectively. Additionally, PCA/FA and correlation analysis demonstrates that Al, Cd, Mn, Ni, Fe, Si and Sr are controlled by natural sources, whereas the other metals appear to be primarily controlled by anthropogenic origins though geogenic source contributing to them. 2009 Elsevier B.V. All rights reserved.
A meadow site classification for the Sierra Nevada, California

Treesearch

Raymond D. Ratliff

1982-01-01

This report describes 14 meadow site classes derived through techniques of agglomerative cluster analysis. The class names are: Carex rostrata (beaked sedge), Poa (Kentucky bluegrass), Heleocharis/Heleocharis (ephemeral-lake), Hypericum/Polygonum/ Viola (hillside bog), Trifolium/...
Three sympatric clusters of the malaria vector Anopheles culicifacies E (Diptera: Culicidae) detected in Sri Lanka.

PubMed

Harischandra, Iresha Nilmini; Dassanayake, Ranil Samantha; De Silva, Bambaranda Gammacharige Don Nissanka Kolitha

2016-01-04

The disease re-emergence threat from the major malaria vector in Sri Lanka, Anopheles culicifacies, is currently increasing. To predict malaria vector dynamics, knowledge of population genetics and gene flow is required, but this information is unavailable for Sri Lanka. This study was carried out to determine the population structure of An. culicifacies E in Sri Lanka. Eight microsatellite markers were used to examine An. culicifacies E collected from six sites in Sri Lanka during 2010-2012. Standard population genetic tests and analyses, genetic differentiation, Hardy-Weinberg equilibrium, linkage disequilibrium, Bayesian cluster analysis, AMOVA, SAMOVA and isolation-by-distance were conducted using five polymorphic loci. Five microsatellite loci were highly polymorphic with high allelic richness. Hardy-Weinberg Equilibrium (HWE) was significantly rejected for four loci with positive F(IS) values in the pooled population (p < 0.0100). Three loci showed high deviations in all sites except Kataragama, which was in agreement with HWE for all loci except one locus (p < 0.0016). Observed heterozygosity was less than the expected values for all sites except Kataragama, where reported negative F(IS) values indicated a heterozygosity excess. Genetic differentiation was observed for all sampling site pairs and was not supported by the isolation by distance model. Bayesian clustering analysis identified the presence of three sympatric clusters (gene pools) in the studied population. Significant genetic differentiation was detected in cluster pairs with low gene flow and isolation by distance was not detected between clusters. Furthermore, the results suggested the presence of a barrier to gene flow that divided the populations into two parts with the central hill region of Sri Lanka as the dividing line. Three sympatric clusters were detected among An. culicifacies E specimens isolated in Sri Lanka. There was no effect of geographic distance on genetic differentiation and the central mountain ranges in Sri Lanka appeared to be a barrier to gene flow.
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

PubMed

Harper, Angela F; Leuthaeuser, Janelle B; Babbitt, Patricia C; Morris, John H; Ferrin, Thomas E; Poole, Leslie B; Fetrow, Jacquelyn S

2017-02-01

Peroxiredoxins (Prxs or Prdxs) are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx superfamily identified using a novel method called MISST (Multi-level Iterative Sequence Searching Technique). MISST is an iterative search process developed to be both agglomerative, to add sequences containing similar functional site features, and divisive, to split groups when functional site features suggest distinct functionally-relevant clusters. Superfamily members need not be identified initially-MISST begins with a minimal representative set of known structures and searches GenBank iteratively. Further, the method's novelty lies in the manner in which isofunctional groups are selected; rather than use a single or shifting threshold to identify clusters, the groups are deemed isofunctional when they pass a self-identification criterion, such that the group identifies itself and nothing else in a search of GenBank. The method was preliminarily validated on the Prxs, as the Prxs presented challenges of both agglomeration and division. For example, previous sequence analysis clustered the Prx functional families Prx1 and Prx6 into one group. Subsequent expert analysis clearly identified Prx6 as a distinct functionally relevant group. The MISST process distinguishes these two closely related, though functionally distinct, families. Through MISST search iterations, over 38,000 Prx sequences were identified, which the method divided into six isofunctional clusters, consistent with previous expert analysis. The results represent the most complete computational functional analysis of proteins comprising the Prx superfamily. The feasibility of this novel method is demonstrated by the Prx superfamily results, laying the foundation for potential functionally relevant clustering of the universe of protein sequences.
An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins

PubMed Central

Babbitt, Patricia C.; Ferrin, Thomas E.

2017-01-01

Peroxiredoxins (Prxs or Prdxs) are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx superfamily identified using a novel method called MISST (Multi-level Iterative Sequence Searching Technique). MISST is an iterative search process developed to be both agglomerative, to add sequences containing similar functional site features, and divisive, to split groups when functional site features suggest distinct functionally-relevant clusters. Superfamily members need not be identified initially—MISST begins with a minimal representative set of known structures and searches GenBank iteratively. Further, the method’s novelty lies in the manner in which isofunctional groups are selected; rather than use a single or shifting threshold to identify clusters, the groups are deemed isofunctional when they pass a self-identification criterion, such that the group identifies itself and nothing else in a search of GenBank. The method was preliminarily validated on the Prxs, as the Prxs presented challenges of both agglomeration and division. For example, previous sequence analysis clustered the Prx functional families Prx1 and Prx6 into one group. Subsequent expert analysis clearly identified Prx6 as a distinct functionally relevant group. The MISST process distinguishes these two closely related, though functionally distinct, families. Through MISST search iterations, over 38,000 Prx sequences were identified, which the method divided into six isofunctional clusters, consistent with previous expert analysis. The results represent the most complete computational functional analysis of proteins comprising the Prx superfamily. The feasibility of this novel method is demonstrated by the Prx superfamily results, laying the foundation for potential functionally relevant clustering of the universe of protein sequences. PMID:28187133
Periorbital melasma: Hierarchical cluster analysis of clinical features in Asian patients.

PubMed

Jung, Y S; Bae, J M; Kim, B J; Kang, J-S; Cho, S B

2017-11-01

Studies have shown melasma lesions to be distributed across the face in centrofacial, malar, and mandibular patterns. Meanwhile, however, melasma lesions of the periorbital area have yet to be thoroughly described. We analyzed normal and ultraviolet light-exposed photographs of patients with melasma. The periorbital melasma lesions were measured according to anatomical reference points and a hierarchical cluster analysis was performed. The periorbital melasma lesions showed clinical features of fine and homogenous melasma pigmentation, involving both the upper and lower eyelids that extended to other anatomical sites with a darker and coarser appearance. The hierarchical cluster analysis indicated that patients with periorbital melasma can be categorized into two clusters according to the surface anatomy of the face. Significant differences between cluster 1 and cluster 2 were found in lateral distance and inferolateral distance, but not in medial distance and superior distance. Comparing the two clusters, patients in cluster 2 were found to be significantly older and more commonly accompanied by melasma lesions of the temple and medial cheek. Our hierarchical cluster analysis of periorbital melasma lesions demonstrated that Asian patients with periorbital melasma can be categorized into two clusters according to the surface anatomy of the face. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Dialing in single-site reactivity of a supported calixarene-protected tetrairidium cluster catalyst† †Electronic supplementary information (ESI) available: Detailed characterization of Ir4 clusters, raw kinetic data, time scale analysis, experimental methods, and sample preparation. See DOI: 10.1039/c7sc00686a Click here for additional data file.

PubMed Central

Palermo, Andrew; Solovyov, Andrew; Ertler, Daniel

2017-01-01

A closed Ir4 carbonyl cluster, 1, comprising a tetrahedral metal frame and three sterically bulky tert-butyl-calix[4]arene(OPr)3(OCH2PPh2) (Ph = phenyl; Pr = propyl) ligands at the basal plane, was characterized with variable-temperature 13C NMR spectroscopy, which show the absence of scrambling of the CO ligands at temperatures up to 313 K. This demonstration of distinct sites for the CO ligands was found to extend to the reactivity and catalytic properties, as shown by selective decarbonylation in a reaction with trimethylamine N-oxide (TMAO) as an oxidant, which, reacting in the presence of ethylene, leads to the selective bonding of an ethyl ligand at the apical Ir site. These clusters were supported intact on porous silica and found to catalyze ethylene hydrogenation, and a comparison of the kinetics of the single-hydrogenation reaction and steady-state hydrogenation catalysis demonstrates a unique single-site catalyst—with each site having the same catalytic activity. Reaction orders in the catalytic ethylene hydrogenation reaction of approximately 1/2 and 0 for H2 and C2H4, respectively, nearly match those for conventional noble-metal catalysts. In contrast to oxidative decarbonylation, thermal desorption of CO from silica-supported cluster 1 occurred exclusively at the basal plane, giving rise to sites that do not react with ethylene and are catalytically inactive for ethylene hydrogenation. The evidence of distinctive sites on the cluster catalyst leads to a model that links to hydrogen-transfer catalysis on metals—involving some surface sites that bond to both hydrocarbon and hydrogen and are catalytically engaged (so-called “*” sites) and others, at the basal plane, which bond hydrogen and CO but not hydrocarbon and are reservoir sites (so-called “S” sites). PMID:28959418
Improved airfield damage assessment System (IADAS) capstone

DTIC Science & Technology

2017-09-01

96 Figure C-1. Russian RBK-500 BetAB Cluster Bomb . Sources: Jane’s Air Launched Weapons (2007) and Flankers Site (2017...127 Figure C-2. Russian RBK-500RTM AO Cluster Bomb . Sources: International Campaign to Ban Landmines (2012) and The Fighter...AFCEC Air Force Civil Engineer Center AoA analysis of alternatives CBU cluster bomb unit CCDR combatant commanders COCOMO II Constructive Cost Model
Quantifying clustered DNA damage induction and repair by gel electrophoresis, electronic imaging and number average length analysis

NASA Technical Reports Server (NTRS)

Sutherland, Betsy M.; Georgakilas, Alexandros G.; Bennett, Paula V.; Laval, Jacques; Sutherland, John C.; Gewirtz, A. M. (Principal Investigator)

2003-01-01

Assessing DNA damage induction, repair and consequences of such damages requires measurement of specific DNA lesions by methods that are independent of biological responses to such lesions. Lesions affecting one DNA strand (altered bases, abasic sites, single strand breaks (SSB)) as well as damages affecting both strands (clustered damages, double strand breaks) can be quantified by direct measurement of DNA using gel electrophoresis, gel imaging and number average length analysis. Damage frequencies as low as a few sites per gigabase pair (10(9)bp) can be quantified by this approach in about 50ng of non-radioactive DNA, and single molecule methods may allow such measurements in DNA from single cells. This review presents the theoretical basis, biochemical requirements and practical aspects of this approach, and shows examples of their applications in identification and quantitation of complex clustered damages.
Genetic analysis reveals the identity of the photoreceptor for phototaxis in hormogonium filaments of Nostoc punctiforme.

PubMed

Campbell, Elsie L; Hagen, Kari D; Chen, Rui; Risser, Douglas D; Ferreira, Daniela P; Meeks, John C

2015-02-15

In cyanobacterial Nostoc species, substratum-dependent gliding motility is confined to specialized nongrowing filaments called hormogonia, which differentiate from vegetative filaments as part of a conditional life cycle and function as dispersal units. Here we confirm that Nostoc punctiforme hormogonia are positively phototactic to white light over a wide range of intensities. N. punctiforme contains two gene clusters (clusters 2 and 2i), each of which encodes modular cyanobacteriochrome-methyl-accepting chemotaxis proteins (MCPs) and other proteins that putatively constitute a basic chemotaxis-like signal transduction complex. Transcriptional analysis established that all genes in clusters 2 and 2i, plus two additional clusters (clusters 1 and 3) with genes encoding MCPs lacking cyanobacteriochrome sensory domains, are upregulated during the differentiation of hormogonia. Mutational analysis determined that only genes in cluster 2i are essential for positive phototaxis in N. punctiforme hormogonia; here these genes are designated ptx (for phototaxis) genes. The cluster is unusual in containing complete or partial duplicates of genes encoding proteins homologous to the well-described chemotaxis elements CheY, CheW, MCP, and CheA. The cyanobacteriochrome-MCP gene (ptxD) lacks transmembrane domains and has 7 potential binding sites for bilins. The transcriptional start site of the ptx genes does not resemble a sigma 70 consensus recognition sequence; moreover, it is upstream of two genes encoding gas vesicle proteins (gvpA and gvpC), which also are expressed only in the hormogonium filaments of N. punctiforme. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
Gastrointestinal Fibroblasts Have Specialized, Diverse Transcriptional Phenotypes: A Comprehensive Gene Expression Analysis of Human Fibroblasts

PubMed Central

Ishii, Genichiro; Aoyagi, Kazuhiko; Sasaki, Hiroki; Ochiai, Atsushi

2015-01-01

Background Fibroblasts are the principal stromal cells that exist in whole organs and play vital roles in many biological processes. Although the functional diversity of fibroblasts has been estimated, a comprehensive analysis of fibroblasts from the whole body has not been performed and their transcriptional diversity has not been sufficiently explored. The aim of this study was to elucidate the transcriptional diversity of human fibroblasts within the whole body. Methods Global gene expression analysis was performed on 63 human primary fibroblasts from 13 organs. Of these, 32 fibroblasts from gastrointestinal organs (gastrointestinal fibroblasts: GIFs) were obtained from a pair of 2 anatomical sites: the submucosal layer (submucosal fibroblasts: SMFs) and the subperitoneal layer (subperitoneal fibroblasts: SPFs). Using hierarchical clustering analysis, we elucidated identifiable subgroups of fibroblasts and analyzed the transcriptional character of each subgroup. Results In unsupervised clustering, 2 major clusters that separate GIFs and non-GIFs were observed. Organ- and anatomical site-dependent clusters within GIFs were also observed. The signature genes that discriminated GIFs from non-GIFs, SMFs from SPFs, and the fibroblasts of one organ from another organ consisted of genes associated with transcriptional regulation, signaling ligands, and extracellular matrix remodeling. Conclusions GIFs are characteristic fibroblasts with specific gene expressions from transcriptional regulation, signaling ligands, and extracellular matrix remodeling related genes. In addition, the anatomical site- and organ-dependent diversity of GIFs was also discovered. These features of GIFs contribute to their specific physiological function and homeostatic maintenance, and create a functional diversity of the gastrointestinal tract. PMID:26046848

Nonlinear dynamics of the cellular-automaton ``game of Life''

NASA Astrophysics Data System (ADS)

Garcia, J. B. C.; Gomes, M. A. F.; Jyh, T. I.; Ren, T. I.; Sales, T. R. M.

1993-11-01

A statistical analysis of the ``game of Life'' due to Conway [Berlekamp, Conway, and Guy, Winning Ways for Your Mathematical Plays (Academic, New York, 1982), Vol. 2] is reported. The results are based on extensive computer simulations starting with uncorrelated distributions of live sites at t=0. The number n(s,t) of clusters of s live sites at time t, the mean cluster size s¯(t), and the diversity of sizes among other statistical functions are obtained. The dependence of the statistical functions with the initial density of live sites is examined. Several scaling relations as well as static and dynamic critical exponents are found.
Diversity and evolution analysis of glycoprotein GP85 from avian leukosis virus subgroup J isolates from chickens of different genetic backgrounds during 1989-2016: Coexistence of five extremely different clusters.

PubMed

Wang, Peikun; Lin, Lulu; Li, Haijuan; Yang, Yongli; Huang, Teng; Wei, Ping

2018-02-01

ALV-J has caused the most serious losses to the poultry industry in China. The gp85-coding sequence of ALV-J is known to be prone to mutation, but any association between the gp85 gene and breed of chicken remains unclear. A comprehensive and systematic study of the evolutionary process of ALV-J in China is needed. In this study, we compared and analyzed gp85 gene sequences from 198 ALV-J isolates, originating from China, USA, UK and France during 1989-2016. These were sorted into five clusters. Cluster 1, 2, 3, 4 and 5 included isolates from chicken types of different genetic backgrounds, e.g. white-feather broiler, Guangxi indigenous chicken breeds, Yellow chickens and layer chickens respectively. A correlation comparison of amino acid sequence similarities in the gp85 protein among the five clusters showed significant differences (P < 0.01) with the exception being when the third and fifth cluster were compared (P > 0.05). Results of entropy analysis of the gp85 sequences revealed that cluster 3 had the largest variation and cluster 1 had the least variation. The N-glycosylation sites in the majority of isolates numbered 14, 16, 17, 16 and 16, respectively, with regards to clusters 1-5. In addition, 5 isolates from cluster 3 had one more glycosylation site than the other isolates from cluster 3. Our study provides evidence that there were five extremely different ALV-J clusters during 1989-2016 and that the gp85 genes isolated from indigenous chicken breed isolates had the largest variation.
The effectiveness of an aged care specific leadership and management program on workforce, work environment, and care quality outcomes: design of a cluster randomised controlled trial.

PubMed

Jeon, Yun-Hee; Simpson, Judy M; Chenoweth, Lynn; Cunich, Michelle; Kendig, Hal

2013-10-25

A plethora of observational evidence exists concerning the impact of management and leadership on workforce, work environment, and care quality. Yet, no randomised controlled trial has been conducted to test the effectiveness of leadership and management interventions in aged care. An innovative aged care clinical leadership program (Clinical Leadership in Aged Care--CLiAC) was developed to improve managers' leadership capacities to support the delivery of quality care in Australia. This paper describes the study design of the cluster randomised controlled trial testing the effectiveness of the program. Twenty-four residential and community aged care sites were recruited as managers at each site agreed in writing to participate in the study and ensure that leaders allocated to the control arm would not be offered the intervention program. Sites undergoing major managerial or structural changes were excluded. The 24 sites were randomly allocated to receive the CLiAC program (intervention) or usual care (control), stratified by type (residential vs. community, six each for each arm). Treatment allocation was masked to assessors and staff of all participating sites. The objective is to establish the effectiveness of the CLiAC program in improving work environment, workforce retention, as well as care safety and quality, when compared to usual care. The primary outcomes are measures of work environment, care quality and safety, and staff turnover rates. Secondary outcomes include manager leadership capacity, staff absenteeism, intention to leave, stress levels, and job satisfaction. Differences between intervention and control groups will be analysed by researchers blinded to treatment allocation using linear regression of individual results adjusted for stratification and clustering by site (primary analysis), and additionally for baseline values and potential confounders (secondary analysis). Outcomes measured at the site level will be compared by cluster-level analysis. The overall costs and benefits of the program will also be assessed. The outcomes of the trial have the potential to inform actions to enhance leadership and management capabilities of the aged care workforce, address pressing issues about workforce shortages, and increase the quality of aged care services. Australian New Zealand Clinical Trials Registry (ACTRN12611001070921).
Craniometric relationships among medieval Central European populations: implications for Croat migration and expansion.

PubMed

Slaus, Mario; Tomicić, Zeljko; Uglesić, Ante; Jurić, Radomir

2004-08-01

To determine the ethnic composition of the early medieval Croats, the location from which they migrated to the east coast of the Adriatic, and to separate early medieval Croats from Bijelo brdo culture members, using principal components analysis and discriminant function analysis of craniometric data from Central and South-East European medieval archaeological sites. Mean male values for 8 cranial measurements from 39 European and 5 Iranian sites were analyzed by principal components analysis. Raw data for 17 cranial measurements for 103 female and 112 male skulls were used to develop discriminant functions. The scatter-plot of the analyzed sites on the first 2 principal components showed a pattern of intergroup relationships consistent with geographical and archaeological information not included in the data set. The first 2 principal components separated the sites into 4 distinct clusters: Avaroslav sites west of the Danube, Avaroslav sites east of the Danube, Bijelo brdo sites, and Polish sites. All early medieval Croat sites were located in the cluster of Polish sites. Two discriminant functions successfully differentiated between early medieval Croats and Bijelo brdo members. Overall accuracies were high -- 89.3% for males, and 97.1% for females. Early medieval Croats seem to be of Slavic ancestry, and at one time shared a common homeland with medieval Poles. Application of unstandardized discriminant function coefficients to unclassified crania from 18 sites showed an expansion of early medieval Croats into continental Croatia during the 10th to 13th century.
Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.

PubMed

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-09-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. © 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.
Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

PubMed Central

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-01-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. PMID:26073648
Analysis of Transcriptional Regulation of the Human miR-17-92 Cluster; Evidence for Involvement of Pim-1

PubMed Central

Thomas, Maren; Lange-Grünweller, Kerstin; Hartmann, Dorothee; Golde, Lara; Schlereth, Julia; Streng, Dennis; Aigner, Achim; Grünweller, Arnold; Hartmann, Roland K.

2013-01-01

The human polycistronic miRNA cluster miR-17-92 is frequently overexpressed in hematopoietic malignancies and cancers. Its transcription is in part controlled by an E2F-regulated host gene promoter. An intronic A/T-rich region directly upstream of the miRNA coding region also contributes to cluster expression. Our deletion analysis of the A/T-rich region revealed a strong dependence on c-Myc binding to the functional E3 site. Yet, constructs lacking the 5′-proximal ~1.3 kb or 3′-distal ~0.1 kb of the 1.5 kb A/T-rich region still retained residual specific promoter activity, suggesting multiple transcription start sites (TSS) in this region. Furthermore, the protooncogenic kinase, Pim-1, its phosphorylation target HP1γ and c-Myc colocalize to the E3 region, as inferred from chromatin immunoprecipitation. Analysis of pri-miR-17-92 expression levels in K562 and HeLa cells revealed that silencing of E2F3, c-Myc or Pim-1 negatively affects cluster expression, with a synergistic effect caused by c-Myc/Pim-1 double knockdown in HeLa cells. Thus, we show, for the first time, that the protooncogene Pim-1 is part of the network that regulates transcription of the human miR-17-92 cluster. PMID:23749113
Methanogenic pathways in Alaskan peatlands at different trophic levels with evidence from stable isotope ratios and metagenomics

NASA Astrophysics Data System (ADS)

Zhang, L.; Liu, X.; Langford, L.; Chanton, J.; Roth, S.; Schaefer, J.; Barkay, T.; Hines, M. E.

2017-12-01

To better constrain the large uncertainties in emission fluxes, it is necessary to improve the understanding of methanogenic pathways in northern peatlands with heterogeneous surface vegetation and pH. Surface vegetation is an excellent indicator of porewater pH, which heavily influences the microbial communities in peatlands. Stable C isotope ratios (d13C) have been used as a robust tool to distinguish methanogenic pathways, especially in conjunction with metagenomic analysis of the microbial communities. To link surface vegetation species compositions, pH, microbial communities, and methanogenic pathways, 15 peatland sites were studied in Fairbanks and Anchorage, Alaska in the summer of 2014. These sites were ordinated using multiple factor analysis into 3 clusters based on pH, temp, CH4 and volatile fatty acid production rates, d13C values, and surface vegetation composition. In the ombrotrophic group (pH 3.3), various Sphagna species dominanted, but included shrubs Ledum decumbens and Eriophorum vaginatum. Primary fermentation rates were slow with no CH4 detected. The fen cluster (pH 5.3) was dominated by various Carex species, and CH4 production rates were lower than those in the intermediate cluster but more enriched in 13C (-49‰). Methanosaeta and Methanosarcina were the dominant methanogens. In the intermediate trophic level (pH 4.7), Sphagnum squarrosum and Carex aquatilis were abundant. The same methanogens as in fen cluster also dominated this group, but with higher abundances, which, in part, lead to the higher CH4 production rates in this cluster. The syntrophs Syntrophobacter and Pelobacter were also more abundant than the fen sites, which may explain the d13CH4 values that were the lighetest among the three clusters (-54‰). The high methanogenic potential in the intermediate trophic sites warrant further study since they are not only present in large areas currently, but also represent the transient stage during the evolution from bog to fen in projected climate change scenarios.
Environmental factors influence on chemical polymorphism of the essential oils of Lychnophora ericoides.

PubMed

Curado, Marco A; Oliveira, Carolina B A; Jesus, José G; Santos, Suzana C; Seraphin, José C; Ferri, Pedro H

2006-11-01

Lychnophora ericoides is a Brazilian medicinal plant used in folk medicine as an anti-inflammatory and analgesic agent. The essential oils from leaves of two populations with and without scent, collected at 2-month intervals during an 1-year period, were analysed by GC-MS. The results were submitted to principal component and cluster analysis which allowed two groups of essential oils to be distinguished with respect to sampling site and scent: cluster I (Vianópolis site, with specimens exhibiting an aromatic scent) containing a high percentage of alpha-bisabolol (44.7-76.4%) and alpha-cadinol (10.9-23.5%), and cluster II (Cristalina site, with specimens without scent) characterised by a high content of (E)-nerolidol (31.3-47.1%) and ar-dihydro-turmerone (4.8-15.4%). The canonical discriminant analysis showed that using the data set of the seven sampling months and (E)-nerolidol and alpha-bisabolol as predictable variables, it was possible to distinguish between the samples harvested according to Cerrado seasons, dry winter (May-September) and humid summer (November-March). In addition, canonical correlation analysis between the soil sampling sites and the populations revealed a significant relationship between oil components and edaphic factors. Oxygenated sesquiterpenes and potential acidity, Al saturation, cationic exchange capacity, silt, and sand load as the first canonical variate were fairly strongly related to samples collected in Vianópolis site. On the other hand, monoterpenes and sesquiterpene hydrocarbons were strongly related to chemical balance in soils (organic matter, P and base saturation), which is related to samples at the Cristalina site. The chemovariation observed appears to be environmentally determined.
Source attribution of poly- and perfluoroalkyl substances (PFASs) in surface waters from Rhode Island and the New York Metropolitan Area

PubMed Central

Zhang, Xianming; Lohmann, Rainer; Dassuncao, Clifton; Hu, Xindi C.; Weber, Andrea K.; Vecitis, Chad D.; Sunderland, Elsie M.

2017-01-01

Exposure to poly and perfluoroalkyl substances (PFASs) has been associated with adverse health effects in humans and wildlife. Understanding pollution sources is essential for environmental regulation but source attribution for PFASs has been confounded by limited information on industrial releases and rapid changes in chemical production. Here we use principal component analysis (PCA), hierarchical clustering, and geospatial analysis to understand source contributions to 14 PFASs measured across 37 sites in the Northeastern United States in 2014. PFASs are significantly elevated in urban areas compared to rural sites except for perfluorobutane sulfonate (PFBS), N-methyl perfluorooctanesulfonamidoacetic acid (N-MeFOSAA), perfluoroundecanate (PFUnDA) and perfluorododecanate (PFDoDA). The highest PFAS concentrations across sites were for perfluorooctanate (PFOA, 56 ng L−1) and perfluorohexane sulfonate (PFOS, 43 ng L−1) and PFOS levels are lower than earlier measurements of U.S. surface waters. PCA and cluster analysis indicates three main statistical groupings of PFASs. Geospatial analysis of watersheds reveals the first component/cluster originates from a mixture of contemporary point sources such as airports and textile mills. Atmospheric sources from the waste sector are consistent with the second component, and the metal smelting industry plausibly explains the third component. We find this source-attribution technique is effective for better understanding PFAS sources in urban areas. PMID:28217711
Managing for desired experiences and site preferences: the case of fee-fishing anglers.

PubMed

Schuett, Michael A; Pierskalla, Chad D

2007-02-01

Fee-fishing involves paying a fee for the privilege of fishing a body of water where fish populations are enhanced by stocking fish. Past literature on this activity has focused more on the operation of the enterprise and management of the fish than the people and site characteristics. The objectives of the study were to profile anglers and describe their site/management preferences. This study utilized an on-site interview and mail-back questionnaire at fee-fishing establishments in West Virginia (n = 212). Factor analysis of desired recreation experiences yielded five factors: Experience nature & adventure, Stress release & relaxation, Trophy fishing, Escape, and Family time. Cluster analysis showed that these anglers can be segmented into two distinct clusters, differing by sociodemographic characteristics, fishing behavior, and site/management preferences. The findings from this study provide baseline data to aid public resource managers and fee-fishing business owners in determining how to provide satisfying outdoor experiences and deliver desired services on-site. Future research will be needed from additional fee-fishing sites to obtain more detail about this outdoor recreation cohort and be able to generalize to a larger population of participants.
Managing for Desired Experiences and Site Preferences: The Case of Fee-Fishing Anglers

NASA Astrophysics Data System (ADS)

Schuett, Michael A.; Pierskalla, Chad D.

2007-02-01

Fee-fishing involves paying a fee for the privilege of fishing a body of water where fish populations are enhanced by stocking fish. Past literature on this activity has focused more on the operation of the enterprise and management of the fish than the people and site characteristics. The objectives of the study were to profile anglers and describe their site/management preferences. This study utilized an on-site interview and mail-back questionnaire at fee-fishing establishments in West Virginia ( n = 212). Factor analysis of desired recreation experiences yielded five factors: Experience nature & adventure, Stress release & relaxation, Trophy fishing, Escape, and Family time. Cluster analysis showed that these anglers can be segmented into two distinct clusters, differing by sociodemographic characteristics, fishing behavior, and site/management preferences. The findings from this study provide baseline data to aid public resource managers and fee-fishing business owners in determining how to provide satisfying outdoor experiences and deliver desired services on-site. Future research will be needed from additional fee-fishing sites to obtain more detail about this outdoor recreation cohort and be able to generalize to a larger population of participants.
What is living on your dog's skin? Characterization of the canine cutaneous mycobiota and fungal dysbiosis in canine allergic dermatitis.

PubMed

Meason-Smith, Courtney; Diesel, Alison; Patterson, Adam P; Older, Caitlin E; Mansell, Joanne M; Suchodolski, Jan S; Rodrigues Hoffmann, Aline

2015-12-01

To characterize the skin-associated fungal microbiota (mycobiota) in dogs, and to evaluate the influence of body site, individual dog or health status on the distribution of fungi, next-generation sequencing was performed targeting the internal transcribed spacer region. A total of 10 dogs with no history of skin disease were sampled at 10 distinct body sites consisting of haired and mucosal skin, and 8 dogs with diagnosed skin allergies were sampled at six body sites commonly affected by allergic disease. Analysis of similarities revealed that body site was not an influencing factor on membership or structure of fungal communities in healthy skin; however, the mucosal sites were significantly reduced in fungal richness. The mycobiota from body sites in healthy dogs tended to be similar within a dog, which was visualized in principle coordinates analysis (PCoA) by clustering of all sites from one dog separate from other dogs. The mycobiota of allergic skin was significantly less rich than that of healthy skin, and all sites sampled clustered by health status in PCoA. Interestingly, the most abundant fungi present on canine skin, across all body sites and health statuses, were Alternaria and Cladosporium--two of the most common fungal allergens in human environmental allergies. © FEMS 2015.
What is living on your dog's skin? Characterization of the canine cutaneous mycobiota and fungal dysbiosis in canine allergic dermatitis

PubMed Central

Meason-Smith, Courtney; Diesel, Alison; Patterson, Adam P.; Older, Caitlin E.; Mansell, Joanne M.; Suchodolski, Jan S.; Rodrigues Hoffmann, Aline

2015-01-01

To characterize the skin-associated fungal microbiota (mycobiota) in dogs, and to evaluate the influence of body site, individual dog or health status on the distribution of fungi, next-generation sequencing was performed targeting the internal transcribed spacer region. A total of 10 dogs with no history of skin disease were sampled at 10 distinct body sites consisting of haired and mucosal skin, and 8 dogs with diagnosed skin allergies were sampled at six body sites commonly affected by allergic disease. Analysis of similarities revealed that body site was not an influencing factor on membership or structure of fungal communities in healthy skin; however, the mucosal sites were significantly reduced in fungal richness. The mycobiota from body sites in healthy dogs tended to be similar within a dog, which was visualized in principle coordinates analysis (PCoA) by clustering of all sites from one dog separate from other dogs. The mycobiota of allergic skin was significantly less rich than that of healthy skin, and all sites sampled clustered by health status in PCoA. Interestingly, the most abundant fungi present on canine skin, across all body sites and health statuses, were Alternaria and Cladosporium—two of the most common fungal allergens in human environmental allergies. PMID:26542075
Temporary disaster debris management site identification using binomial cluster analysis and GIS.

PubMed

Grzeda, Stanislaw; Mazzuchi, Thomas A; Sarkani, Shahram

2014-04-01

An essential component of disaster planning and preparation is the identification and selection of temporary disaster debris management sites (DMS). However, since DMS identification is a complex process involving numerous variable constraints, many regional, county and municipal jurisdictions initiate this process during the post-disaster response and recovery phases, typically a period of severely stressed resources. Hence, a pre-disaster approach in identifying the most likely sites based on the number of locational constraints would significantly contribute to disaster debris management planning. As disasters vary in their nature, location and extent, an effective approach must facilitate scalability, flexibility and adaptability to variable local requirements, while also being generalisable to other regions and geographical extents. This study demonstrates the use of binomial cluster analysis in potential DMS identification in a case study conducted in Hamilton County, Indiana. © 2014 The Author(s). Disasters © Overseas Development Institute, 2014.
The properties of small Ag clusters bound to DNA bases.

PubMed

Soto-Verdugo, Víctor; Metiu, Horia; Gwinn, Elisabeth

2010-05-21

We study the binding of neutral silver clusters, Ag(n) (n=1-6), to the DNA bases adenine (A), cytosine (C), guanine (G), and thymine (T) and the absorption spectra of the silver cluster-base complexes. Using density functional theory (DFT), we find that the clusters prefer to bind to the doubly bonded ring nitrogens and that binding to T is generally much weaker than to C, G, and A. Ag(3) and Ag(4) make the stronger bonds. Bader charge analysis indicates a mild electron transfer from the base to the clusters for all bases, except T. The donor bases (C, G, and A) bind to the sites on the cluster where the lowest unoccupied molecular orbital has a pronounced protrusion. The site where cluster binds to the base is controlled by the shape of the higher occupied states of the base. Time-dependent DFT calculations show that different base-cluster isomers may have very different absorption spectra. In particular, we find new excitations in base-cluster molecules, at energies well below those of the isolated components, and with strengths that depend strongly on the orientations of planar clusters with respect to the base planes. Our results suggest that geometric constraints on binding, imposed by designed DNA structures, may be a feasible route to engineering the selection of specific cluster-base assemblies.
Photoelectron spectroscopy and density functional theory studies of (FeS)mH- (m = 2-4) cluster anions: effects of the single hydrogen.

PubMed

Yin, Shi; Bernstein, Elliot R

2017-12-20

Single hydrogen containing iron hydrosulfide cluster anions (FeS) m H - (m = 2-4) are studied by photoelectron spectroscopy (PES) at 3.492 eV (355 nm) and 4.661 eV (266 nm) photon energies, and by Density Functional Theory (DFT) calculations. The structural properties, relative energies of different spin states and isomers, and the first calculated vertical detachment energies (VDEs) of different spin states for these (FeS) m H - (m = 2-4) cluster anions are investigated at various reasonable theory levels. Two types of structural isomers are found for these (FeS) m H - (m = 2-4) clusters: (1) the single hydrogen atom bonds to a sulfur site (SH-type); and (2) the single hydrogen atom bonds to an iron site (FeH-type). Experimental and theoretical results suggest such available different SH- and FeH-type structural isomers should be considered when evaluating the properties and behavior of these single hydrogen containing iron sulfide clusters in real chemical and biological systems. Compared to their related, respective pure iron sulfur (FeS) m - clusters, the first VDE trend of the diverse type (FeS) m H 0,1 - (m = 1-4) clusters can be understood through (1) the different electron distribution properties of their highest singly occupied molecular orbital employing natural bond orbital analysis (NBO/HSOMO), and (2) the partial charge distribution on the NBO/HSOMO localized sites of each cluster anion. Generally, the properties of the NBO/HSOMOs play the principal role with regard to the physical and chemical properties of all the anions. The change of cluster VDE from low to high is associated with the change in nature of their NBO/HSOMO from a dipole bound and valence electron mixed character, to a valence p orbital on S, to a valence d orbital on Fe, and to a valence p orbital on Fe or an Fe-Fe delocalized valence bonding orbital. For clusters having the same properties for NBO/HSOMOs, the partial charge distributions at the NBO/HSOMO localized sites additionally affect their VDEs: a more negative or less positive localized charge distribution is correlated with a lower first VDE. The single hydrogen in these (FeS) m H - (m = 2-4) cluster anions is suggested to affect their first VDEs through the different structure types (SH- or FeH-), the nature of the NBO/HSOMOs at the local site, and the value of partial charge number at the local site of the NBO/HSOMO.
Community composition and cellulase activity of cellulolytic bacteria from forest soils planted with broad-leaved deciduous and evergreen trees.

PubMed

Yang, Jiang-Ke; Zhang, Jing-Jing; Yu, Heng-Yu; Cheng, Jian-Wen; Miao, Li-Hong

2014-02-01

Cellulolytic bacteria in forest soil provide carbon sources to improve the soil fertility and sustain the nutrient balance of the forest ecological system through the decomposition of cellulosic remains. These bacteria can also be utilized for the biological conversion of biomass into renewable biofuels. In this study, the community compositions and activities of cellulolytic bacteria in the soils of forests planted with broad-leaved deciduous (Chang Qing Garden, CQG) and broad-leaved evergreen (Forest Park, FP) trees in Wuhan, China were resolved through restriction fragment length polymorphism (RFLP) and sequencing analysis of the 16S rRNA gene. All of the isolates exhibited 35 RFLP fingerprint patterns and were clustered into six groups at a similarity level of 50 %. The phylogeny analysis based on the 16S rRNA gene sequence revealed that these RFLP groups could be clustered into three phylogenetic groups and further divided into six subgroups at a higher resolution. Group I consists of isolates from Bacillus cereus, Bacillus subtilis complex (I-A) and from Paenibacillus amylolyticus-related complex (I-B) and exhibited the highest cellulase activity among all of the cellulolytic bacteria isolates. Cluster II consists of isolates belonging to Microbacterium testaceum (II-A), Chryseobacterium indoltheticum (II-B), and Flavobacterium pectinovorum and the related complex (II-C). Cluster III consists of isolates belonging to Pseudomonas putida-related species. The community shift with respect to the plant species and the soil properties was evidenced by the phylogenetic composition of the communities. Groups I-A and I-B, which account for 36.0 % of the cellulolytic communities in the CQG site, are the dominant groups (88.4 %) in the FP site. Alternatively, the ratio of the bacteria belonging to group III (P. putida-related isolates) shifted from 28.0 % in CQG to 4.0 % in FP. The soil nutrient analysis revealed that the CQG site planted with deciduous broad-leaved trees has a richer organic nutrient (total organic carbon and total nitrogen) than the FP site planted with evergreen broad-leaved trees. Against this background, the population density and the diversity of cellulolytic bacteria in the CQG site are clearly higher than those in the FP site, and the latter was dominated with high-cellulase-activity Bacillus- and Paenibacillus-related bacteria. The canonical correspondence analysis further indicated that the distribution of these groups is correlated with the FP site, whereas groups II and III are correlated with the organic nutrient-rich CQG site.
Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi.

PubMed

Slot, Jason C; Rokas, Antonis

2011-01-25

Genes involved in intermediary and secondary metabolism in fungi are frequently physically linked or clustered. For example, in Aspergillus nidulans the entire pathway for the production of sterigmatocystin (ST), a highly toxic secondary metabolite and a precursor to the aflatoxins (AF), is located in a ∼54 kb, 23 gene cluster. We discovered that a complete ST gene cluster in Podospora anserina was horizontally transferred from Aspergillus. Phylogenetic analysis shows that most Podospora cluster genes are adjacent to or nested within Aspergillus cluster genes, although the two genera belong to different taxonomic classes. Furthermore, the Podospora cluster is highly conserved in content, sequence, and microsynteny with the Aspergillus ST/AF clusters and its intergenic regions contain 14 putative binding sites for AflR, the transcription factor required for activation of the ST/AF biosynthetic genes. Examination of ∼52,000 Podospora expressed sequence tags identified transcripts for 14 genes in the cluster, with several expressed at multiple life cycle stages. The presence of putative AflR-binding sites and the expression evidence for several cluster genes, coupled with the recent independent discovery of ST production in Podospora [1], suggest that this HGT event probably resulted in a functional cluster. Given the abundance of metabolic gene clusters in fungi, our finding that one of the largest known metabolic gene clusters moved intact between species suggests that such transfers might have significantly contributed to fungal metabolic diversity. PAPERFLICK: Copyright Â© 2011 Elsevier Ltd. All rights reserved.
Delayed repair of radiation induced clustered DNA damage: Friend or foe?

PubMed Central

Eccles, Laura J.; O’Neill, Peter; Lomax, Martine E.

2011-01-01

A signature of ionizing radiation exposure is the induction of DNA clustered damaged sites, defined as two or more lesions within one to two helical turns of DNA by passage of a single radiation track. Clustered damage is made up of double strand breaks (DSB) with associated base lesions or abasic (AP) sites, and non-DSB clusters comprised of base lesions, AP sites and single strand breaks. This review will concentrate on the experimental findings of the processing of non-DSB clustered damaged sites. It has been shown that non-DSB clustered damaged sites compromise the base excision repair pathway leading to the lifetime extension of the lesions within the cluster, compared to isolated lesions, thus the likelihood that the lesions persist to replication and induce mutation is increased. In addition certain non-DSB clustered damaged sites are processed within the cell to form additional DSB. The use of E. coli to demonstrate that clustering of DNA lesions is the major cause of the detrimental consequences of ionizing radiation is also discussed. The delayed repair of non-DSB clustered damaged sites in humans can be seen as a “friend”, leading to cell killing in tumour cells or as a “foe”, resulting in the formation of mutations and genetic instability in normal tissue. PMID:21130102

Activation of CO2 by supported Cu clusters.

PubMed

Iyemperumal, Satish Kumar; Deskins, N Aaron

2017-11-01

Catalytic reduction of carbon dioxide to useful chemicals is a potent way to mitigate this greenhouse gas, but the challenge lies in finding active reduction catalysts. Using density functional theory we studied CO 2 activation over TiO 2 -supported Cu clusters of size 1-4 atoms. The linear to bent transformation of CO 2 is necessary for activation, and we found that all the clusters stabilized bent CO 2 , along with a significant gain of electrons on the CO 2 (indicative of activation). On all the TiO 2 supported Cu clusters, the interfacial sites were found to stabilize the bent CO 2 adsorption, where the active site of adsorption on Cu dimer, trimer and tetramer was on the Cu atom farthest away from the TiO 2 surface. Particularly, the Cu dimer stabilized bent CO 2 very strongly, although this species was found to be unstable on the surface. A synthesis technique that could stabilize the Cu dimer could therefore lead to a very active catalyst. Furthermore we found (using vibrational and charge analysis) that the active sites for the CO 2 activation predominantly had 0 and +1 oxidation states; the oxidation state of Cu is known to directly affect CO 2 reduction activity. Our study shows TiO 2 -supported small Cu clusters can be active catalysts for CO 2 reduction and also provides further motivation for theoretical and experimental studies of metal clusters.
[Spatial distribution characteristics of the physical and chemical properties of water in the Kunes River after the supply of snowmelt during spring].

PubMed

Liu, Xiang; Guo, Ling-Peng; Zhang, Fei-Yun; Ma, Jie; Mu, Shu-Yong; Zhao, Xin; Li, Lan-Hai

2015-02-01

Eight physical and chemical indicators related to water quality were monitored from nineteen sampling sites along the Kunes River at the end of snowmelt season in spring. To investigate the spatial distribution characteristics of water physical and chemical properties, cluster analysis (CA), discriminant analysis (DA) and principal component analysis (PCA) are employed. The result of cluster analysis showed that the Kunes River could be divided into three reaches according to the similarities of water physical and chemical properties among sampling sites, representing the upstream, midstream and downstream of the river, respectively; The result of discriminant analysis demonstrated that the reliability of such a classification was high, and DO, Cl- and BOD5 were the significant indexes leading to this classification; Three principal components were extracted on the basis of the principal component analysis, in which accumulative variance contribution could reach 86.90%. The result of principal component analysis also indicated that water physical and chemical properties were mostly affected by EC, ORP, NO3(-) -N, NH4(+) -N, Cl- and BOD5. The sorted results of principal component scores in each sampling sites showed that the water quality was mainly influenced by DO in upstream, by pH in midstream, and by the rest of indicators in downstream. The order of comprehensive scores for principal components revealed that the water quality degraded from the upstream to downstream, i.e., the upstream had the best water quality, followed by the midstream, while the water quality at downstream was the worst. This result corresponded exactly to the three reaches classified using cluster analysis. Anthropogenic activity and the accumulation of pollutants along the river were probably the main reasons leading to this spatial difference.
Water quality analysis of the Rapur area, Andhra Pradesh, South India using multivariate techniques

NASA Astrophysics Data System (ADS)

Nagaraju, A.; Sreedhar, Y.; Thejaswi, A.; Sayadi, Mohammad Hossein

2017-10-01

The groundwater samples from Rapur area were collected from different sites to evaluate the major ion chemistry. The large number of data can lead to difficulties in the integration, interpretation, and representation of the results. Two multivariate statistical methods, hierarchical cluster analysis (HCA) and factor analysis (FA), were applied to evaluate their usefulness to classify and identify geochemical processes controlling groundwater geochemistry. Four statistically significant clusters were obtained from 30 sampling stations. This has resulted two important clusters viz., cluster 1 (pH, Si, CO3, Mg, SO4, Ca, K, HCO3, alkalinity, Na, Na + K, Cl, and hardness) and cluster 2 (EC and TDS) which are released to the study area from different sources. The application of different multivariate statistical techniques, such as principal component analysis (PCA), assists in the interpretation of complex data matrices for a better understanding of water quality of a study area. From PCA, it is clear that the first factor (factor 1), accounted for 36.2% of the total variance, was high positive loading in EC, Mg, Cl, TDS, and hardness. Based on the PCA scores, four significant cluster groups of sampling locations were detected on the basis of similarity of their water quality.
Percolation of the site random-cluster model by Monte Carlo method

NASA Astrophysics Data System (ADS)

Wang, Songsong; Zhang, Wanzhou; Ding, Chengxiang

2015-08-01

We propose a site random-cluster model by introducing an additional cluster weight in the partition function of the traditional site percolation. To simulate the model on a square lattice, we combine the color-assignation and the Swendsen-Wang methods to design a highly efficient cluster algorithm with a small critical slowing-down phenomenon. To verify whether or not it is consistent with the bond random-cluster model, we measure several quantities, such as the wrapping probability Re, the percolating cluster density P∞, and the magnetic susceptibility per site χp, as well as two exponents, such as the thermal exponent yt and the fractal dimension yh of the percolating cluster. We find that for different exponents of cluster weight q =1.5 , 2, 2.5 , 3, 3.5 , and 4, the numerical estimation of the exponents yt and yh are consistent with the theoretical values. The universalities of the site random-cluster model and the bond random-cluster model are completely identical. For larger values of q , we find obvious signatures of the first-order percolation transition by the histograms and the hysteresis loops of percolating cluster density and the energy per site. Our results are helpful for the understanding of the percolation of traditional statistical models.
Researching for sustained translation from site cluster permeability into building courtyard and interior atrium

NASA Astrophysics Data System (ADS)

Teddy Badai Samodra, FX; Defiana, Ima; Setyawan, Wahyu

2018-03-01

Many previous types of research have discussed the permeability of site cluster. Because of interaction and interconnected attribute, it will be better that there is its translation into lower context such as building and interior scale. In this paper, the sustainability design performance of both similar designs of courtyard and atrium are investigated continuing the recommendation of site space permeability. By researching related literature review and study through Ecotect Analysis and Ansys Fluent simulations, the pattern transformation and optimum courtyard and atrium design could comply the requirement. The results highlighted that the air movement from the site could be translated at the minimum of 50% higher to the building and indoor environment. Thus, it has potency for energy efficiency when grid, loop, and cul-de-sac site clusters, with 25% of ground coverage, have connectivity with building courtyard compared to the atrium. Energy saving is higher when using low thermal transmittance of transparent material and its lower area percentages for the courtyard walls. In general, it was more energy efficient option as part of a low rise building, while the courtyard building performed better with increasing irregular building height more than 90% of the difference.
Computational lymphatic node models in pediatric and adult hybrid phantoms for radiation dosimetry

NASA Astrophysics Data System (ADS)

Lee, Choonsik; Lamart, Stephanie; Moroz, Brian E.

2013-03-01

We developed models of lymphatic nodes for six pediatric and two adult hybrid computational phantoms to calculate the lymphatic node dose estimates from external and internal radiation exposures. We derived the number of lymphatic nodes from the recommendations in International Commission on Radiological Protection (ICRP) Publications 23 and 89 at 16 cluster locations for the lymphatic nodes: extrathoracic, cervical, thoracic (upper and lower), breast (left and right), mesentery (left and right), axillary (left and right), cubital (left and right), inguinal (left and right) and popliteal (left and right), for different ages (newborn, 1-, 5-, 10-, 15-year-old and adult). We modeled each lymphatic node within the voxel format of the hybrid phantoms by assuming that all nodes have identical size derived from published data except narrow cluster sites. The lymph nodes were generated by the following algorithm: (1) selection of the lymph node site among the 16 cluster sites; (2) random sampling of the location of the lymph node within a spherical space centered at the chosen cluster site; (3) creation of the sphere or ovoid of tissue representing the node based on lymphatic node characteristics defined in ICRP Publications 23 and 89. We created lymph nodes until the pre-defined number of lymphatic nodes at the selected cluster site was reached. This algorithm was applied to pediatric (newborn, 1-, 5-and 10-year-old male, and 15-year-old males) and adult male and female ICRP-compliant hybrid phantoms after voxelization. To assess the performance of our models for internal dosimetry, we calculated dose conversion coefficients, called S values, for selected organs and tissues with Iodine-131 distributed in six lymphatic node cluster sites using MCNPX2.6, a well validated Monte Carlo radiation transport code. Our analysis of the calculations indicates that the S values were significantly affected by the location of the lymph node clusters and that the values increased for smaller phantoms due to the shorter inter-organ distances compared to the bigger phantoms. By testing sensitivity of S values to random sampling and voxel resolution, we confirmed that the lymph node model is reasonably stable and consistent for different random samplings and voxel resolutions.
Light absorption, optical and microphysical properties of trajectory-clustered aerosols at two AERONET sites in West Africa

NASA Astrophysics Data System (ADS)

Fawole, O. G.; Cai, X.; MacKenzie, A. R.

2015-12-01

Aerosol remote sensing techniques and back-trajectory modeling can be combined to identify aerosol types. We have clustered 7 years of AERONET aerosol signals using trajectory analysis to identify dominant aerosol sources at two AERONET sites in West Africa: Ilorin (4.34 oE, 8.32 oN) and Djougou (1.60 oE, 9.76 oN). Of particular interest are air masses that have passed through the gas flaring region in the Niger Delta area, of Nigeria, en-route the AERONET sites. 7-day back trajectories were calculated using the UK UGAMP trajectory model driven by ECMWF wind analyses data. Dominant sources identified, using literature classifications, are desert dust (DD), Biomass burning (BB) and Urban-Industrial (UI). Below, we use a combination of synoptic trajectories and aerosol optical properties to distinguish a fourth source: that due to gas flaring. Gas flaring, (GF) the disposal of gas through stack in an open-air flame, is believed to be a prominent source of black carbon (BC) and greenhouse gases. For these different aerosol source signatures, single scattering albedo (SSA), refractive index , extinction Angstrom exponent (EEA) and absorption Angstrom exponent (AAE) were used to classify the light absorption characteristics of the aerosols for λ = 440, 675, 870 and1020 nm. A total of 1625 daily averages of aerosol data were collected for the two sites. Of which 245 make up the GF cluster for both sites. For GF cluster, the range of fine-mode fraction is 0.4 - 0.7. Average values SSA(λ), for the total and GF clusters are 0.90(440), 0.93(675), 0.95(870) and 0.96(1020), and 0.93(440), 0.92(675), 0.9(870) and 0.9(1020), respectively. Values of for the GF clusters for both sites are 0.62 - 1.11, compared to 1.28 - 1.66 for the remainder of the clusters, which strongly indicates the dominance of carbonaceous particles (BC), typical of a highly industrial area. An average value of 1.58 for the real part of the refractive index at low SSA for aerosol in the GF cluster is also an indicator of high BC content. Extinction Angstrom exponent, is an indicator of the particle size. EAE values of 0.95-1.32 for aerosol in the GF cluster shows that the aerosols are mainly fine or accumulation mode while values of EAE (0.36-0.6) for the other cluster indicate coarse mode domination of the aerosol. See table 1 for a summary of result.
Descriptive analysis and spatial epidemiology of porcine reproductive and respiratory syndrome (PRRS) for swine sites participating in area regional control and elimination programs from 3 regions of Ontario

PubMed Central

Arruda, Andreia G.; Poljak, Zvonimir; Friendship, Robert; Carpenter, Jane; Hand, Karen

2015-01-01

The objectives of this study were to describe demographics, basic biosecurity practices, ownership structure, and prevalence of porcine reproductive and respiratory syndrome (PRRS) in swine sites located in 3 regions in Ontario, and investigate the presence of spatial clustering and clusters of PRRS positive sites in the 3 regions. A total of 370 swine sites were enrolled in Area Regional Control and Elimination projects in Niagara, Watford, and Perth from 2010 to 2013. Demographics, biosecurity, and site ownership data were collected using a standardized questionnaire and site locations were obtained from an industry organization. Status was assigned on the basis of available diagnostic tests and/or assessment by site veterinarians. Spatial dependence was investigated using the D-function, the spatial scan statistic test and the spatial relative risk method. Results showed that the use of strict all-in all-out (AIAO) pig flow and shower before entry are uncommon biosecurity practices in swine sites, but a larger proportion of sites reported having a Danish entry. The prevalence of PRRS in the 3 regions ranged from 17% to 48% and localized high and low risk clusters were detected. Sites enrolled in the PRRS control projects were characterized by membership in multiple and overlapping ownership structures and networks, which complicates the way the results of monitoring and disease management measures are communicated to the target population. PMID:26424906
A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

PubMed

Rajan, Vaibhav

2013-03-01

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.
Sputum neutrophil counts are associated with more severe asthma phenotypes using cluster analysis.

PubMed

Moore, Wendy C; Hastie, Annette T; Li, Xingnan; Li, Huashi; Busse, William W; Jarjour, Nizar N; Wenzel, Sally E; Peters, Stephen P; Meyers, Deborah A; Bleecker, Eugene R

2014-06-01

Clinical cluster analysis from the Severe Asthma Research Program (SARP) identified 5 asthma subphenotypes that represent the severity spectrum of early-onset allergic asthma, late-onset severe asthma, and severe asthma with chronic obstructive pulmonary disease characteristics. Analysis of induced sputum from a subset of SARP subjects showed 4 sputum inflammatory cellular patterns. Subjects with concurrent increases in eosinophil (≥2%) and neutrophil (≥40%) percentages had characteristics of very severe asthma. To better understand interactions between inflammation and clinical subphenotypes, we integrated inflammatory cellular measures and clinical variables in a new cluster analysis. Participants in SARP who underwent sputum induction at 3 clinical sites were included in this analysis (n = 423). Fifteen variables, including clinical characteristics and blood and sputum inflammatory cell assessments, were selected using factor analysis for unsupervised cluster analysis. Four phenotypic clusters were identified. Cluster A (n = 132) and B (n = 127) subjects had mild-to-moderate early-onset allergic asthma with paucigranulocytic or eosinophilic sputum inflammatory cell patterns. In contrast, these inflammatory patterns were present in only 7% of cluster C (n = 117) and D (n = 47) subjects who had moderate-to-severe asthma with frequent health care use despite treatment with high doses of inhaled or oral corticosteroids and, in cluster D, reduced lung function. The majority of these subjects (>83%) had sputum neutrophilia either alone or with concurrent sputum eosinophilia. Baseline lung function and sputum neutrophil percentages were the most important variables determining cluster assignment. This multivariate approach identified 4 asthma subphenotypes representing the severity spectrum from mild-to-moderate allergic asthma with minimal or eosinophil-predominant sputum inflammation to moderate-to-severe asthma with neutrophil-predominant or mixed granulocytic inflammation. Published by Mosby, Inc.
Sputum neutrophils are associated with more severe asthma phenotypes using cluster analysis

PubMed Central

Moore, Wendy C.; Hastie, Annette T.; Li, Xingnan; Li, Huashi; Busse, William W.; Jarjour, Nizar N.; Wenzel, Sally E.; Peters, Stephen P.; Meyers, Deborah A.; Bleecker, Eugene R.

2013-01-01

Background Clinical cluster analysis from the Severe Asthma Research Program (SARP) identified five asthma subphenotypes that represent the severity spectrum of early onset allergic asthma, late onset severe asthma and severe asthma with COPD characteristics. Analysis of induced sputum from a subset of SARP subjects showed four sputum inflammatory cellular patterns. Subjects with concurrent increases in eosinophils (≥2%) and neutrophils (≥40%) had characteristics of very severe asthma. Objective To better understand interactions between inflammation and clinical subphenotypes we integrated inflammatory cellular measures and clinical variables in a new cluster analysis. Methods Participants in SARP at three clinical sites who underwent sputum induction were included in this analysis (n=423). Fifteen variables including clinical characteristics and blood and sputum inflammatory cell assessments were selected by factor analysis for unsupervised cluster analysis. Results Four phenotypic clusters were identified. Cluster A (n=132) and B (n=127) subjects had mild-moderate early onset allergic asthma with paucigranulocytic or eosinophilic sputum inflammatory cell patterns. In contrast, these inflammatory patterns were present in only 7% of Cluster C (n=117) and D (n=47) subjects who had moderate-severe asthma with frequent health care utilization despite treatment with high doses of inhaled or oral corticosteroids, and in Cluster D, reduced lung function. The majority these subjects (>83%) had sputum neutrophilia either alone or with concurrent sputum eosinophilia. Baseline lung function and sputum neutrophils were the most important variables determining cluster assignment. Conclusion This multivariate approach identified four asthma subphenotypes representing the severity spectrum from mild-moderate allergic asthma with minimal or eosinophilic predominant sputum inflammation to moderate-severe asthma with neutrophilic predominant or mixed granulocytic inflammation. PMID:24332216
Assessment of Social Vulnerability Identification at Local Level around Merapi Volcano - A Self Organizing Map Approach

NASA Astrophysics Data System (ADS)

Lee, S.; Maharani, Y. N.; Ki, S. J.

2015-12-01

The application of Self-Organizing Map (SOM) to analyze social vulnerability to recognize the resilience within sites is a challenging tasks. The aim of this study is to propose a computational method to identify the sites according to their similarity and to determine the most relevant variables to characterize the social vulnerability in each cluster. For this purposes, SOM is considered as an effective platform for analysis of high dimensional data. By considering the cluster structure, the characteristic of social vulnerability of the sites identification can be fully understand. In this study, the social vulnerability variable is constructed from 17 variables, i.e. 12 independent variables which represent the socio-economic concepts and 5 dependent variables which represent the damage and losses due to Merapi eruption in 2010. These variables collectively represent the local situation of the study area, based on conducted fieldwork on September 2013. By using both independent and dependent variables, we can identify if the social vulnerability is reflected onto the actual situation, in this case, Merapi eruption 2010. However, social vulnerability analysis in the local communities consists of a number of variables that represent their socio-economic condition. Some of variables employed in this study might be more or less redundant. Therefore, SOM is used to reduce the redundant variable(s) by selecting the representative variables using the component planes and correlation coefficient between variables in order to find the effective sample size. Then, the selected dataset was effectively clustered according to their similarities. Finally, this approach can produce reliable estimates of clustering, recognize the most significant variables and could be useful for social vulnerability assessment, especially for the stakeholder as decision maker. This research was supported by a grant 'Development of Advanced Volcanic Disaster Response System considering Potential Volcanic Risk around Korea' [MPSS-NH-2015-81] from the Natural Hazard Mitigation Research Group, National Emergency Management Agency of Korea. Keywords: Self-organizing map, Component Planes, Correlation coefficient, Cluster analysis, Sites identification, Social vulnerability, Merapi eruption 2010
The effectiveness of an aged care specific leadership and management program on workforce, work environment, and care quality outcomes: design of a cluster randomised controlled trial

PubMed Central

2013-01-01

Background A plethora of observational evidence exists concerning the impact of management and leadership on workforce, work environment, and care quality. Yet, no randomised controlled trial has been conducted to test the effectiveness of leadership and management interventions in aged care. An innovative aged care clinical leadership program (Clinical Leadership in Aged Care − CLiAC) was developed to improve managers’ leadership capacities to support the delivery of quality care in Australia. This paper describes the study design of the cluster randomised controlled trial testing the effectiveness of the program. Methods Twenty-four residential and community aged care sites were recruited as managers at each site agreed in writing to participate in the study and ensure that leaders allocated to the control arm would not be offered the intervention program. Sites undergoing major managerial or structural changes were excluded. The 24 sites were randomly allocated to receive the CLiAC program (intervention) or usual care (control), stratified by type (residential vs. community, six each for each arm). Treatment allocation was masked to assessors and staff of all participating sites. The objective is to establish the effectiveness of the CLiAC program in improving work environment, workforce retention, as well as care safety and quality, when compared to usual care. The primary outcomes are measures of work environment, care quality and safety, and staff turnover rates. Secondary outcomes include manager leadership capacity, staff absenteeism, intention to leave, stress levels, and job satisfaction. Differences between intervention and control groups will be analysed by researchers blinded to treatment allocation using linear regression of individual results adjusted for stratification and clustering by site (primary analysis), and additionally for baseline values and potential confounders (secondary analysis). Outcomes measured at the site level will be compared by cluster-level analysis. The overall costs and benefits of the program will also be assessed. Discussion The outcomes of the trial have the potential to inform actions to enhance leadership and management capabilities of the aged care workforce, address pressing issues about workforce shortages, and increase the quality of aged care services. Trial registration Australian New Zealand Clinical Trials Registry (ACTRN12611001070921) PMID:24160714
Relationship between Trophic Status and Methanogenic Pathways in Alaskan Peatlands

NASA Astrophysics Data System (ADS)

Zhang, L.; Liu, X.; Sidelinger, W.; Wang, Y.; Hines, M. E.; Langford, L.; Chanton, J.

2015-12-01

To improve predictions of naturally emitted CH4 from northern wetlands, it is necessary to further examine the methanogenic pathways in these wetlands. Stable isotope C ratios (δ13C) have been used as a robust tool to distinguish different pathways, but different sources of parent compounds (acetate and CO2) with unique δ13C may add complexity to previously established criteria. Large portions of peatlands accommodate a mixture of different sphagna and sedges. Plant species may look very similar and belong to the same genus but are different morphologically and physiologically. To better understand the relationships between surface vegetation patterns and methanogenic pathways, 26 peatland sites were studied in Fairbanks and Anchorage, Alaska in summers of 2014 and 2015. These sites were ordinated using multiple factor analysis into 3 clusters based on pH, temp, CH4 and volatile fatty acids production rates, δ13C values, and surface vegetation species/pattern. In the low-pH trophic cluster (pH~3.5), non-vascular/vascular plant ratios (NV/V) were ~ 0.87 and dominated by diverse Sphagnum species and specific sedges (Eriophorum vaginatum), and fermentation was the dominant end-point in decomposition with no CH4 detected. Although NV/V is about the same in the intermediate cluster (0.74) (pH~4.5), and Sphagnum squarrosum was largely present, both hydrogenotrophic (HM) and acetoclastic methanogenesis (AM) were very active. Syntrophy was present at certain sites, which may provide CO2 with unique δ13C for CH4 production. At the highest pH trophic cluster examined in this study (pH~5), non-vascular plants were almost not existent and Carex aquatilis dominated. CH4 production rates (mainly HM) were slower than those in the intermediate cluster and the apparent fractionation factor a was lower than in the sites with syntrophy, which warrants further investigation of the position and compound specific δ13C analysis of volatile fatty acids.
From Points to Patterns - Functional Relations between Groundwater Connectivity and Catchment-scale Streamflow Response

NASA Astrophysics Data System (ADS)

Rinderer, M.; McGlynn, B. L.; van Meerveld, I. H. J.

2016-12-01

Groundwater measurements can help us to improve our understanding of runoff generation at the catchment-scale but typically only provide point-scale data. These measurements, therefore, need to be interpolated or upscaled in order to obtain information about catchment scale groundwater dynamics. Our approach used data from 51 spatially distributed groundwater monitoring sites in a Swiss pre-alpine catchment and time series clustering to define six groundwater response clusters. Each of the clusters was characterized by distinctly different site characteristics (i.e., Topographic Wetness Index and curvature), which allowed us to assign all unmonitored locations to one of these clusters. Time series modeling and the definition of response thresholds (i.e., the depth of more transmissive soil layers) allowed us to derive maps of the spatial distribution of active (i.e., responding) locations across the catchment at 15 min time intervals. Connectivity between all active locations and the stream network was determined using a graph theory approach. The extent of the active and connected areas differed during events and suggests that not all active locations directly contributed to streamflow. Gate keeper sites prevented connectivity of upslope locations to the channel network. Streamflow dynamics at the catchment outlet were correlated to catchment average connectivity dynamics. In a sensitivity analysis we tested six different groundwater levels for a site to be considered "active", which showed that the definition of the threshold did not significantly influence the conclusions drawn from our analysis. This study is the first one to derive patterns of groundwater dynamics based on empirical data (rather than interpolation) and provides insight into the spatio-temporal evolution of the active and connected runoff source areas at the catchment-scale that is critical to understanding the dynamics of water quantity and quality in streams.
A Zn(II)2Cys6 DNA binding protein regulates the sirodesmin PL biosynthetic gene cluster in Leptosphaeria maculans

PubMed Central

Fox, Ellen M.; Gardiner, Donald M.; Keller, Nancy P.; Howlett, Barbara J.

2008-01-01

A gene, sirZ, encoding a Zn(II)2Cys6 DNA binding protein is present in a cluster of genes responsible for the biosynthesis of the epipolythiodioxopiperazine (ETP) toxin, sirodesmin PL in the ascomycete plant pathogen, Leptosphaeria maculans. RNA-mediated silencing of sirZ gives rise to transformants that produce only residual amounts of sirodesmin PL and display a decrease in the transcription of several sirodesmin PL biosynthetic genes. This indicates that SirZ is a major regulator of this gene cluster. Proteins similar to SirZ are encoded in the gliotoxin biosynthetic gene cluster of Aspergillus fumigatus (gliZ) and in an ETP-like cluster in Penicillium lilacinoechinulatum (PlgliZ). Despite its high level of sequence similarity to gliZ, PlgliZ is unable to complement the gliotoxin-deficiency of a mutant of gliZ in A. fumigatus. Putative binding sites for these regulatory proteins in the promoters of genes in these clusters were predicted using bioinformatic analysis. These sites are similar to those commonly bound by other proteins with Zn(II)2Cys6 DNA binding domains. PMID:18023597
Dual effects of water vapor on ceria-supported gold clusters.

PubMed

Li, Zhimin; Li, Weili; Abroshan, Hadi; Ge, Qingjie; Li, Gao; Jin, Rongchao

2018-04-05

Atomically precise nanocatalysts are currently being intensely pursued in catalysis research. Such nanocatalysts can serve as model catalysts for gaining fundamental insights into catalytic processes. In this work we report a discovery that water vapor provokes the mild removal of surface long-chain ligands on 25-atom Au25(SC12H25)18 nanoclusters in a controlled manner. Using the resultant Au25(SC12H25)18-x/CeO2 catalyst and CO oxidation as a probe reaction, we found that the catalytic activity of cluster/CeO2 is enhanced from nearly zero conversion of CO (in the absence of water) to 96.2% (in the presence of 2.3 vol% H2O) at the same temperature (100 °C). The cluster catalysts exhibit high stability during the CO oxidation process under moisture conditions (up to 20 vol% water vapor). Water vapor plays a dual role in gold cluster-catalyzed CO oxidation. FT-IR and XPS analyses in combination with density functional theory (DFT) simulations suggest that the "-SC12H25" ligands are easier to be removed under a water vapor atmosphere, thus generating highly active sites. Moreover, the O22- peroxide species constitutes the active oxygen species in CO oxidation, evidenced by Raman spectroscopy analysis and isotope experiments on the CeO2 and cluster/CeO2. The results also indicate the perimeter sites of the interface of Au25(SC12H25)18-x/CeO2 to be active sites for catalytic CO oxidation. The controlled exposure of active sites under mild conditions is of critical importance for the utilization of clusters in catalysis.
Combined multivariate statistical techniques, Water Pollution Index (WPI) and Daniel Trend Test methods to evaluate temporal and spatial variations and trends of water quality at Shanchong River in the Northwest Basin of Lake Fuxian, China.

PubMed

Wang, Quan; Wu, Xianhua; Zhao, Bin; Qin, Jie; Peng, Tingchun

2015-01-01

Understanding spatial and temporal variations in river water quality and quantitatively evaluating the trend of changes are important in order to study and efficiently manage water resources. In this study, an analysis of Water Pollution Index (WPI), Daniel Trend Test, Cluster Analysis and Discriminant Analysis are applied as an integrated approach to quantitatively explore the spatial and temporal variations and the latent sources of water pollution in the Shanchong River basin, Northwest Basin of Lake Fuxian, China. We group all field surveys into 2 clusters (dry season and rainy season). Moreover, 14 sampling sites have been grouped into 3 clusters for the rainy season (highly polluted, moderately polluted and less polluted sites) and 2 clusters for the dry season (highly polluted and less polluted sites) based on their similarities and the level of pollution during the two seasons. The results show that the main trend of pollution was aggravated during the transition from the dry to the rainy season. The Water Pollution Index of Total Nitrogen is the highest of all pollution parameters, whereas the Chemical Oxygen Demand (Chromium) is the lowest. Our results also show that the main sources of pollution are farming activities alongside the Shanchong River, soil erosion and fish culture at Shanchong River reservoir area and domestic sewage from scattered rural residential area. Our results suggest that strategies to prevent water pollutionat the Shanchong River basin need to focus on non-point pollution control by employing appropriate fertilizer formulas in farming, and take the measures of soil and water conservation at Shanchong reservoir area, and purifying sewage from scattered villages.
Combined Multivariate Statistical Techniques, Water Pollution Index (WPI) and Daniel Trend Test Methods to Evaluate Temporal and Spatial Variations and Trends of Water Quality at Shanchong River in the Northwest Basin of Lake Fuxian, China

PubMed Central

Wang, Quan; Wu, Xianhua; Zhao, Bin; Qin, Jie; Peng, Tingchun

2015-01-01

Understanding spatial and temporal variations in river water quality and quantitatively evaluating the trend of changes are important in order to study and efficiently manage water resources. In this study, an analysis of Water Pollution Index (WPI), Daniel Trend Test, Cluster Analysis and Discriminant Analysis are applied as an integrated approach to quantitatively explore the spatial and temporal variations and the latent sources of water pollution in the Shanchong River basin, Northwest Basin of Lake Fuxian, China. We group all field surveys into 2 clusters (dry season and rainy season). Moreover, 14 sampling sites have been grouped into 3 clusters for the rainy season (highly polluted, moderately polluted and less polluted sites) and 2 clusters for the dry season (highly polluted and less polluted sites) based on their similarities and the level of pollution during the two seasons. The results show that the main trend of pollution was aggravated during the transition from the dry to the rainy season. The Water Pollution Index of Total Nitrogen is the highest of all pollution parameters, whereas the Chemical Oxygen Demand (Chromium) is the lowest. Our results also show that the main sources of pollution are farming activities alongside the Shanchong River, soil erosion and fish culture at Shanchong River reservoir area and domestic sewage from scattered rural residential area. Our results suggest that strategies to prevent water pollutionat the Shanchong River basin need to focus on non-point pollution control by employing appropriate fertilizer formulas in farming, and take the measures of soil and water conservation at Shanchong reservoir area, and purifying sewage from scattered villages. PMID:25837673
Large Data at Small Universities: Astronomical processing using a computer classroom

NASA Astrophysics Data System (ADS)

Fuller, Nathaniel James; Clarkson, William I.; Fluharty, Bill; Belanger, Zach; Dage, Kristen

2016-06-01

The use of large computing clusters for astronomy research is becoming more commonplace as datasets expand, but access to these required resources is sometimes difficult for research groups working at smaller Universities. As an alternative to purchasing processing time on an off-site computing cluster, or purchasing dedicated hardware, we show how one can easily build a crude on-site cluster by utilizing idle cycles on instructional computers in computer-lab classrooms. Since these computers are maintained as part of the educational mission of the University, the resource impact on the investigator is generally low.By using open source Python routines, it is possible to have a large number of desktop computers working together via a local network to sort through large data sets. By running traditional analysis routines in an “embarrassingly parallel” manner, gains in speed are accomplished without requiring the investigator to learn how to write routines using highly specialized methodology. We demonstrate this concept here applied to 1. photometry of large-format images and 2. Statistical significance-tests for X-ray lightcurve analysis. In these scenarios, we see a speed-up factor which scales almost linearly with the number of cores in the cluster. Additionally, we show that the usage of the cluster does not severely limit performance for a local user, and indeed the processing can be performed while the computers are in use for classroom purposes.

Influence of atmospheric transport on ozone and trace- level toxic air contaminants over the northeastern United States

NASA Astrophysics Data System (ADS)

Brankov, Elvira

This thesis presents a methodology for examining the relationship between synoptic-scale atmospheric transport patterns and observed pollutant concentration levels. It involves calculating a large number of back-trajectories from the observational site and subjecting them to cluster analysis. The pollutant concentration data observed at that site are then segregated according to the back-trajectory clusters. If the pollutant observations extend over several seasons, it is important to filter out seasonal and long-term components from the time series data before pollutant cluster-segregation, because only the short-term component of the time series data is related to the synoptic-scale transport. Multiple comparison procedures are used to test for significant differences in the chemical composition of pollutant data associated with each cluster. This procedure is useful in indicating potential pollutant source regions and isolating meteorological regimes associated with pollutant transport from those regions. If many observational sites are available, the spatial and temporal scales of the pollution transport from a given direction can be extracted through the time-lagged inter- site correlation analysis of pollutant concentrations. The proposed methodology is applicable to any pollutant at any site if sufficiently abundant data set is available. This is illustrated through examination of five-year long time series data of ozone concentrations at several sites in the Northeast. The results provide evidence of ozone transport to these sites, revealing the characteristic spatial and temporal scales involved in the transport and identifying source regions for this pollutant. Problems related to statistical analyses of censored data are addressed in the second half of this thesis. Although censoring (reporting concentrations in a non-quantitative way) is typical for trace-level measurements, methods for statistical analysis, inference and interpretation of such data are complex and still under development. In this study, multiple comparison of censored data sets was required in order to examine the influence of synoptic- scale circulations on concentration levels of several trace-level toxic pollutants observed in the Northeast (e.g., As, Se, Mn, V, etc.). Since the traditional multiple comparison procedures are not readily applicable to such data sets, a Monte Carlo simulation study was performed to assess several nonparametric methods for multiple comparison of censored data sets. Application of an appropriate comparison procedure to clusters of toxic trace elements observed in the Northeast led to the identification of potential source regions and atmospheric patterns associated with the long-range transport of these pollutants. A method for comparison of proportions and elemental ratio calculations were used to confirm/clarify these inferences with a greater degree of confidence.
An Enhanced K-Means Algorithm for Water Quality Analysis of The Haihe River in China.

PubMed

Zou, Hui; Zou, Zhihong; Wang, Xiaojing

2015-11-12

The increase and the complexity of data caused by the uncertain environment is today's reality. In order to identify water quality effectively and reliably, this paper presents a modified fast clustering algorithm for water quality analysis. The algorithm has adopted a varying weights K-means cluster algorithm to analyze water monitoring data. The varying weights scheme was the best weighting indicator selected by a modified indicator weight self-adjustment algorithm based on K-means, which is named MIWAS-K-means. The new clustering algorithm avoids the margin of the iteration not being calculated in some cases. With the fast clustering analysis, we can identify the quality of water samples. The algorithm is applied in water quality analysis of the Haihe River (China) data obtained by the monitoring network over a period of eight years (2006-2013) with four indicators at seven different sites (2078 samples). Both the theoretical and simulated results demonstrate that the algorithm is efficient and reliable for water quality analysis of the Haihe River. In addition, the algorithm can be applied to more complex data matrices with high dimensionality.
Igs expressed by chronic lymphocytic leukemia B cells show limited binding-site structure variability.

PubMed

Marcatili, Paolo; Ghiotto, Fabio; Tenca, Claudya; Chailyan, Anna; Mazzarello, Andrea N; Yan, Xiao-Jie; Colombo, Monica; Albesiano, Emilia; Bagnara, Davide; Cutrona, Giovanna; Morabito, Fortunato; Bruno, Silvia; Ferrarini, Manlio; Chiorazzi, Nicholas; Tramontano, Anna; Fais, Franco

2013-06-01

Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated.
Soil chemistry and pollution study of a closed landfill site at Ampar Tenang, Selangor, Malaysia.

PubMed

Mohd Adnan, Siti Nur Syahirah Binti; Yusoff, Sumiani; Piaw, Chua Yan

2013-06-01

A total of 20 landfills are located in State of Selangor, Malaysia. This includes the Ampar Tenang landfill site, which was closed on 26 January 2010. It was reported that the landfill has been upgraded to a level I type of sanitary classification. However, the dumpsite area is not being covered according to the classification. In addition, municipal solid waste was dumped directly on top of the unlined natural alluvium formation. This does not only contaminate surface and subsurface soils, but also initiates the potential risk of groundwater pollution. Based on previous studies, the Ampar Tenang soil has been proven to no longer be capable of preventing pollution migration. In this study, metal concentrations of soil samples up to 30 m depth were analyzed based on statistical analysis. It is very significant because research of this type has not been carried out before. The subsurface soils were significantly polluted by arsenic (As), lead (Pb), iron (Fe), copper (Cu) and aluminium (Al). As and Pb exceeded the safe limit values of 5.90 mg/kg and 31.00 mg/kg, respectively, based on Provincial Sediment Quality Guidelines for Metals and the Interim Sediment Quality Values. Furthermore, only Cu concentrations showed a significantly decreasing trend with increasing depth. Most metals were found on clay-type soils based on the cluster analysis method. Moreover, the analysis also differentiates two clusters: cluster I-Pb, As, zinc, Cu, manganese, calcium, sodium, magnesium, potassium and Fe; cluster II-Al. Different clustering may suggest a different contamination source of metals.
Transcriptomic analysis of neuregulin-1 regulated genes following ischemic stroke by computational identification of promoter binding sites: A role for the ETS-1 transcription factor.

PubMed

Surles-Zeigler, Monique C; Li, Yonggang; Distel, Timothy J; Omotayo, Hakeem; Ge, Shaokui; Ford, Byron D

2018-01-01

Ischemic stroke is a major cause of mortality in the United States. We previously showed that neuregulin-1 (NRG1) was neuroprotective in rat models of ischemic stroke. We used gene expression profiling to understand the early cellular and molecular mechanisms of NRG1's effects after the induction of ischemia. Ischemic stroke was induced by middle cerebral artery occlusion (MCAO). Rats were allocated to 3 groups: (1) control, (2) MCAO and (3) MCAO + NRG1. Cortical brain tissues were collected three hours following MCAO and NRG1 treatment and subjected to microarray analysis. Data and statistical analyses were performed using R/Bioconductor platform alongside Genesis, Ingenuity Pathway Analysis and Enrichr software packages. There were 2693 genes differentially regulated following ischemia and NRG1 treatment. These genes were organized by expression patterns into clusters using a K-means clustering algorithm. We further analyzed genes in clusters where ischemia altered gene expression, which was reversed by NRG1 (clusters 4 and 10). NRG1, IRS1, OPA3, and POU6F1 were central linking (node) genes in cluster 4. Conserved Transcription Factor Binding Site Finder (CONFAC) identified ETS-1 as a potential transcriptional regulator of NRG1 suppressed genes following ischemia. A transcription factor activity array showed that ETS-1 activity was increased 2-fold, 3 hours following ischemia and this activity was attenuated by NRG1. These findings reveal key early transcriptional mechanisms associated with neuroprotection by NRG1 in the ischemic penumbra.
Pollen assemblages as paleoenvironmental proxies in the Florida Everglades

USGS Publications Warehouse

Willard, D.A.; Weimer, L.M.; Riegel, W.L.

2001-01-01

Analysis of 170 pollen assemblages from surface samples in eight vegetation types in the Florida Everglades indicates that these wetland sub-environments are distinguishable from the pollen record and that they are useful proxies for hydrologic and edaphic parameters. Vegetation types sampled include sawgrass marshes, cattail marshes, sloughs with floating aquatics, wet prairies, brackish marshes, tree islands, cypress swamps, and mangrove forests. The distribution of these vegetation types is controlled by specific environmental parameters, such as hydrologic regime, nutrient availability, disturbance level, substrate type, and salinity; ecotones between vegetation types may be sharp. Using R-mode cluster analysis of pollen data, we identified diagnostic species groupings; Q-mode cluster analysis was used to differentiate pollen signatures of each vegetation type. Cluster analysis and the modern analog technique were applied to interpret vegetational and environmental trends over the last two millennia at a site in Water Conservation Area 3A. The results show that close modern analogs exist for assemblages in the core and indicate past hydrologic changes at the site, correlated with both climatic and land-use changes. The ability to differentiate marshes with different hydrologic and edaphic requirements using the pollen record facilitates assessment of relative impacts of climatic and anthropogenic changes on this wetland ecosystem on smaller spatial and temporal scales than previously were possible. ?? 2001 Elsevier Science B.V.
An analysis of cluster headache information provided on internet websites.

PubMed

Peterlin, B Lee; Gambini-Suarez, Eduardo; Lidicker, Jeffrey; Levin, Morris

2008-03-01

To evaluate the quality of websites providing cluster headache information for patients and healthcare providers. The Internet has become an increasingly important source of healthcare information. However, limited data exist regarding the quality of websites providing headache information. This was a cross-sectional study conducted in February 2007. Websites providing cluster headache information were determined on the search engine MetaCrawler and classified as either patient oriented or healthcare provider oriented. The overall quality of each site was evaluated using a score system. Readability was evaluated using the Flesch-Kincaid Grade Level Readability Score (FKRS). Website quality was analyzed based on ownership, purpose, authorship, author qualifications, attribution, interactivity, and currency. The technical quality of the cluster headache information was analyzed based on content specific to cluster headache. The final ranking, based on the sum of the ranks of all 3 categories, was determined and then contrasted between the patient-oriented and healthcare professional-oriented websites using 2-sample t-tests. Of the first 40 websites found on MetaCrawler, 72.5% were advertisements, unrelated to headache, or repeated websites. Although the standard US writing averages are at a seventh to eighth grade level, the mean FKRS of all sites was at a 12th grade level of difficulty, with no significant difference between the patient-oriented or healthcare provider-oriented websites (P = .54). Of a total possible 14 points, the overall mean quality component score was 9.9 for all sites; and of a total possible 23 points, the overall mean technical component score was 13.9. There was no significant difference for either the quality or technical component scores between patient-oriented or healthcare provider-oriented websites (P = .45 and P = .80, respectively). There are numerous cluster headache websites that can be found on the Internet. The quality of most of the websites dedicated to cluster headache is mediocre, and although there are some excellent cluster headache websites, these sites may be challenging for many users to locate. There was no significant difference in the overall quality of websites oriented for patients or healthcare providers providing cluster headache information evaluated in this study. In addition, websites providing high-quality cluster headache information are written at an educational level too high for a significant portion of the general population to fully utilize. Physicians should strongly consider providing lists of quality websites on cluster headache for their patients.
Groundwater source contamination mechanisms: Physicochemical profile clustering, risk factor analysis and multivariate modelling

NASA Astrophysics Data System (ADS)

Hynds, Paul; Misstear, Bruce D.; Gill, Laurence W.; Murphy, Heather M.

2014-04-01

An integrated domestic well sampling and "susceptibility assessment" programme was undertaken in the Republic of Ireland from April 2008 to November 2010. Overall, 211 domestic wells were sampled, assessed and collated with local climate data. Based upon groundwater physicochemical profile, three clusters have been identified and characterised by source type (borehole or hand-dug well) and local geological setting. Statistical analysis indicates that cluster membership is significantly associated with the prevalence of bacteria (p = 0.001), with mean Escherichia coli presence within clusters ranging from 15.4% (Cluster-1) to 47.6% (Cluster-3). Bivariate risk factor analysis shows that on-site septic tank presence was the only risk factor significantly associated (p < 0.05) with bacterial presence within all clusters. Point agriculture adjacency was significantly associated with both borehole-related clusters. Well design criteria were associated with hand-dug wells and boreholes in areas characterised by high permeability subsoils, while local geological setting was significant for hand-dug wells and boreholes in areas dominated by low/moderate permeability subsoils. Multivariate susceptibility models were developed for all clusters, with predictive accuracies of 84% (Cluster-1) to 91% (Cluster-2) achieved. Septic tank setback was a common variable within all multivariate models, while agricultural sources were also significant, albeit to a lesser degree. Furthermore, well liner clearance was a significant factor in all models, indicating that direct surface ingress is a significant well contamination mechanism. Identification and elucidation of cluster-specific contamination mechanisms may be used to develop improved overall risk management and wellhead protection strategies, while also informing future remediation and maintenance efforts.
Analysis of correlated mutations in HIV-1 protease using spectral clustering.

PubMed

Liu, Ying; Eyal, Eran; Bahar, Ivet

2008-05-15

The ability of human immunodeficiency virus-1 (HIV-1) protease to develop mutations that confer multi-drug resistance (MDR) has been a major obstacle in designing rational therapies against HIV. Resistance is usually imparted by a cooperative mechanism that can be elucidated by a covariance analysis of sequence data. Identification of such correlated substitutions of amino acids may be obscured by evolutionary noise. HIV-1 protease sequences from patients subjected to different specific treatments (set 1), and from untreated patients (set 2) were subjected to sequence covariance analysis by evaluating the mutual information (MI) between all residue pairs. Spectral clustering of the resulting covariance matrices disclosed two distinctive clusters of correlated residues: the first, observed in set 1 but absent in set 2, contained residues involved in MDR acquisition; and the second, included those residues differentiated in the various HIV-1 protease subtypes, shortly referred to as the phylogenetic cluster. The MDR cluster occupies sites close to the central symmetry axis of the enzyme, which overlap with the global hinge region identified from coarse-grained normal-mode analysis of the enzyme structure. The phylogenetic cluster, on the other hand, occupies solvent-exposed and highly mobile regions. This study demonstrates (i) the possibility of distinguishing between the correlated substitutions resulting from neutral mutations and those induced by MDR upon appropriate clustering analysis of sequence covariance data and (ii) a connection between global dynamics and functional substitution of amino acids.
Quantitative methylation level of the EPHX1 promoter in peripheral blood DNA is associated with polycystic ovary syndrome.

PubMed

Sang, Qing; Li, Xin; Wang, Haojue; Wang, Huan; Zhang, Shaozhen; Feng, Ruizhi; Xu, Yao; Li, Qiaoli; Zhao, Xinzhi; Xing, Qinghe; Jin, Li; He, Lin; Wang, Lei

2014-01-01

Steroid synthesis and metabolic pathways play important roles in the pathophysiology of PCOS, but until now there have been no studies on the methylation profiles of specific genes in steroid synthesis pathways that are known to be associated with PCOS. Here we used MassARRAY quantitative methylation analysis to determine the methylation levels of each CpG site or cluster in the promoters of EPHX1, SRD5A1, and CYP11A1 in 64 peripheral blood samples. We further examined the methylation level of EPHX1 in an independent cohort consisting of 116 people. Finally, we investigated the role of EPHX1 in steroidogenesis in the KGN cell line. For SRD5A1 and CYP11A1, there was no significant difference in methylation level between patients and controls. For EPHX1, however, the methylation levels of a few consecutive CpG sites and clusters were found to be significantly associated with PCOS. The methylation levels of a number of CpG clusters or sites were significantly lower in patients than in controls in the first cohort consisting of 64 people, such as clusters 13-14 (P<0.05), 15-16 (P<0.001), and 19-24 (P<0.001) and sites CpG_53 (P<0.01) and CpG_54 (P<0.05). Among differentiated methylation sites and clusters, the methylation levels of the CpG cluster 13-14 and CpG cluster 19-24 in PCOS patients were significantly lower than in controls in the second cohort of 116 people (P<0.05 for both). In addition, knockdown and overexpression experiments in KGN cells showed that EPHX1 can regulate estradiol concentrations, and this indicates a role for EPHX1 in steroidogenesis. Our study has demonstrated that methylation of the EPHX1 promoter might be associated with PCOS. This study provides direct evidence that methylation plays an important role in PCOS and demonstrates a novel role for EPHX1 in female reproduction.
Quantitative Methylation Level of the EPHX1 Promoter in Peripheral Blood DNA Is Associated with Polycystic Ovary Syndrome

PubMed Central

Wang, Huan; Zhang, Shaozhen; Feng, Ruizhi; Xu, Yao; Li, Qiaoli; Zhao, Xinzhi; Xing, Qinghe; Jin, Li; He, Lin; Wang, Lei

2014-01-01

Steroid synthesis and metabolic pathways play important roles in the pathophysiology of PCOS, but until now there have been no studies on the methylation profiles of specific genes in steroid synthesis pathways that are known to be associated with PCOS. Here we used MassARRAY quantitative methylation analysis to determine the methylation levels of each CpG site or cluster in the promoters of EPHX1, SRD5A1, and CYP11A1 in 64 peripheral blood samples. We further examined the methylation level of EPHX1 in an independent cohort consisting of 116 people. Finally, we investigated the role of EPHX1 in steroidogenesis in the KGN cell line. For SRD5A1 and CYP11A1, there was no significant difference in methylation level between patients and controls. For EPHX1, however, the methylation levels of a few consecutive CpG sites and clusters were found to be significantly associated with PCOS. The methylation levels of a number of CpG clusters or sites were significantly lower in patients than in controls in the first cohort consisting of 64 people, such as clusters 13–14 (P<0.05), 15–16 (P<0.001), and 19–24 (P<0.001) and sites CpG_53 (P<0.01) and CpG_54 (P<0.05). Among differentiated methylation sites and clusters, the methylation levels of the CpG cluster 13–14 and CpG cluster 19–24 in PCOS patients were significantly lower than in controls in the second cohort of 116 people (P<0.05 for both). In addition, knockdown and overexpression experiments in KGN cells showed that EPHX1 can regulate estradiol concentrations, and this indicates a role for EPHX1 in steroidogenesis. Our study has demonstrated that methylation of the EPHX1 promoter might be associated with PCOS. This study provides direct evidence that methylation plays an important role in PCOS and demonstrates a novel role for EPHX1 in female reproduction. PMID:24505354
Convex Clustering: An Attractive Alternative to Hierarchical Clustering

PubMed Central

Chen, Gary K.; Chi, Eric C.; Ranola, John Michael O.; Lange, Kenneth

2015-01-01

The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics.ucla.edu/software/ PMID:25965340
Convex clustering: an attractive alternative to hierarchical clustering.

PubMed

Chen, Gary K; Chi, Eric C; Ranola, John Michael O; Lange, Kenneth

2015-05-01

The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics.ucla.edu/software/.
Analysis of NFU-1 metallocofactor binding-site substitutions-impacts on iron-sulfur cluster coordination and protein structure and function.

PubMed

Wesley, Nathaniel A; Wachnowsky, Christine; Fidai, Insiya; Cowan, J A

2017-11-01

Iron-sulfur (Fe/S) clusters are ancient prosthetic groups found in numerous metalloproteins and are conserved across all kingdoms of life due to their diverse, yet essential functional roles. Genetic mutations to a specific subset of mitochondrial Fe/S cluster delivery proteins are broadly categorized as disease-related under multiple mitochondrial dysfunction syndrome (MMDS), with symptoms indicative of a general failure of the metabolic system. Multiple mitochondrial dysfunction syndrome 1 (MMDS1) arises as a result of the missense mutation in NFU1, an Fe/S cluster scaffold protein, which substitutes a glycine near the Fe/S cluster-binding pocket to a cysteine (p.Gly208Cys). This substitution has been shown to promote protein dimerization such that cluster delivery to NFU1 is blocked, preventing downstream cluster trafficking. However, the possibility of this additional cysteine, located adjacent to the cluster-binding site, serving as an Fe/S cluster ligand has not yet been explored. To fully understand the consequences of this Gly208Cys replacement, complementary substitutions at the Fe/S cluster-binding pocket for native and Gly208Cys NFU1 were made, along with six other variants. Herein, we report the results of an investigation on the effect of these substitutions on both cluster coordination and NFU1 structure and function. The data suggest that the G208C substitution does not contribute to cluster binding. Rather, replacement of the glycine at position 208 changes the oligomerization state as a result of global structural alterations that result in the downstream effects manifest as MMDS1, but does not perturb the coordination chemistry of the Fe-S cluster. © 2017 Federation of European Biochemical Societies.
Assembling the Tat protein translocase

PubMed Central

Alcock, Felicity; Stansfeld, Phillip J; Basit, Hajra; Habersetzer, Johann; Baker, Matthew AB; Palmer, Tracy; Wallace, Mark I; Berks, Ben C

2016-01-01

The twin-arginine protein translocation system (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membranes of plant chloroplasts. The Tat transporter is assembled from multiple copies of the membrane proteins TatA, TatB, and TatC. We combine sequence co-evolution analysis, molecular simulations, and experimentation to define the interactions between the Tat proteins of Escherichia coli at molecular-level resolution. In the TatBC receptor complex the transmembrane helix of each TatB molecule is sandwiched between two TatC molecules, with one of the inter-subunit interfaces incorporating a functionally important cluster of interacting polar residues. Unexpectedly, we find that TatA also associates with TatC at the polar cluster site. Our data provide a structural model for assembly of the active Tat translocase in which substrate binding triggers replacement of TatB by TatA at the polar cluster site. Our work demonstrates the power of co-evolution analysis to predict protein interfaces in multi-subunit complexes. DOI: http://dx.doi.org/10.7554/eLife.20718.001 PMID:27914200
Complex time series analysis of PM10 and PM2.5 for a coastal site using artificial neural network modelling and k-means clustering

NASA Astrophysics Data System (ADS)

Elangasinghe, M. A.; Singhal, N.; Dirks, K. N.; Salmond, J. A.; Samarasinghe, S.

2014-09-01

This paper uses artificial neural networks (ANN), combined with k-means clustering, to understand the complex time series of PM10 and PM2.5 concentrations at a coastal location of New Zealand based on data from a single site. Out of available meteorological parameters from the network (wind speed, wind direction, solar radiation, temperature, relative humidity), key factors governing the pattern of the time series concentrations were identified through input sensitivity analysis performed on the trained neural network model. The transport pathways of particulate matter under these key meteorological parameters were further analysed through bivariate concentration polar plots and k-means clustering techniques. The analysis shows that the external sources such as marine aerosols and local sources such as traffic and biomass burning contribute equally to the particulate matter concentrations at the study site. These results are in agreement with the results of receptor modelling by the Auckland Council based on Positive Matrix Factorization (PMF). Our findings also show that contrasting concentration-wind speed relationships exist between marine aerosols and local traffic sources resulting in very noisy and seemingly large random PM10 concentrations. The inclusion of cluster rankings as an input parameter to the ANN model showed a statistically significant (p < 0.005) improvement in the performance of the ANN time series model and also showed better performance in picking up high concentrations. For the presented case study, the correlation coefficient between observed and predicted concentrations improved from 0.77 to 0.79 for PM2.5 and from 0.63 to 0.69 for PM10 and reduced the root mean squared error (RMSE) from 5.00 to 4.74 for PM2.5 and from 6.77 to 6.34 for PM10. The techniques presented here enable the user to obtain an understanding of potential sources and their transport characteristics prior to the implementation of costly chemical analysis techniques or advanced air dispersion models.
75 FR 39278 - Notice of Lodging of Settlement Agreement Under the Comprehensive Environmental Response...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-08

... Cluster Superfund Site located in Chicago, Illinois. In addition, Ringier, A.G. has agreed to make a cash payment to EPA, in the amount of $38,617.58, in connection with the Lake Calumet Cluster Superfund Site..., with respect to the Lake Calumet Cluster Site or the Lenz Oil Services Site, with respect to conduct of...
Theory for electron transfer from a mixed-valence dimer with paramagnetic sites to a mononuclear acceptor

NASA Astrophysics Data System (ADS)

Bominaar, E. L.; Achim, C.; Borshch, S. A.

1999-06-01

Polynuclear transition-metal complexes, such as Fe-S clusters, are the prosthetic groups in a large number of metalloproteins and serve as temporary electron storage units in a number of important redox-based biological processes. Polynuclearity distinguishes clusters from mononuclear centers and confers upon them unique properties, such as spin ordering and the presence of thermally accessible excited spin states in clusters with paramagnetic sites, and fractional valencies in clusters of the mixed-valence type. In an earlier study we presented an effective-mode (EM) analysis of electron transfer from a binuclear mixed-valence donor with paramagnetic sites to a mononuclear acceptor which revealed that the cluster-specific attributes have an important impact on the kinetics of long-range electron transfer. In the present study, the validity of these results is tested in the framework of more detailed theories which we have termed the multimode semiclassical (SC) model and the quantum-mechanical (QM) model. It is found that the qualitative trends in the rate constant are the same in all treatments and that the semiclassical models provide a good approximation of the more rigorous quantum-mechanical description of electron transfer under physiologically relevant conditions. In particular, the present results corroborate the importance of electron transfer via excited spin states in reactions with a low driving force and justify the use of semiclassical theory in cases in which the QM model is computationally too demanding. We consider cases in which either one or two donor sites of a dimer are electronically coupled to the acceptor. In the case of multiconnectivity, the rate constant for electron transfer from a valence-delocalized (class-III) donor is nonadditive with respect to transfer from individual metal sites of the donor and undergoes an order-of-magnitude change by reversing the sign of the intradimer metal-metal resonance parameter (β). In the case of single connectivity, the rate constant for electron transfer from a valence-localized (class-II) donor can readily be tuned over several orders of magnitude by introducing differences in the electronic potentials at the two metal sites of the donor. These results indicate that theories of cluster-based electron transfer, in order to be realistic, need to consider both intrinsic electronic structure and extrinsic interactions of the cluster with the protein environment.
Trophic Status Controls Mercury Methylation Pathways in Northern Peats

NASA Astrophysics Data System (ADS)

Hines, M. E.; Zhang, L.; Barkay, T.; Krabbenhoft, D. P.; Schaefer, J.; Hu, H.; Sidelinger, W.; Liu, X.; Wang, Y.

2015-12-01

Methyl mercury (MeHg) can be produced by a variety of microbes including syntrophs, methanogens, acetogens, and fermenters, besides sulfate (SO42-, SRB) and iron- reducing bacteria. Many freshwater wetlands are deficient in electron acceptors that support the traditional respiratory pathways of methylation, yet they accumulate high levels of MeHg. To investigate methylation in these wetlands and to connect these pathways with vegetation and microbial communities, incubation experiments were conducted using peats from 26 sites in Alaska. The sites were clustered using multiple factor analysis based on pH, temp, CH4 and volatile fatty acids production rates, and surface vegetation composition. Three clusters were generated and corresponded to three trophic levels that were manifested by three pH levels (3.5, 4.5, and 5). Hg methylation activity in laboratory incubations was determined using the short-lived radioisotope 197Hg. In the low pH, Sphagnum-dominated cluster, methylation rates were less than 1% day-1 and likely conducted by primary fermenters. Conversely, the high pH trophic cluster dominated by Carex aquatilis and active syntrophy exhibited Hg methylation rates as high as 12% day-1. In intermediate sites, rich in Sphagnum magellanicum with less Carex, a gradient in syntrophy and Hg methylation paths was observed. Amendments with process-stimulators and inhibitors revealed no evidence of SO42- reduction, but suggested that SRB, metabolizing either syntrophically with methanogens and/or by fermentation, likely methylated Hg. While on going metatranscriptomics studies are required to verify the role of syntrophs, fermenters, and methanogens as methylators, these results revealed that Hg methylation pathways change greatly along trophic gradients with a dominance of respiratory pathways in mineral-rich sites, syntrophy dominance in intermediate sites, and fermentation dominance in nutrient-poor sites.
Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O 2-tolerant NAD +-reducing [NiFe] hydrogenase

DOE PAGES

Lauterbach, Lars; Wang, Hongxin; Horch, Marius; ...

2014-10-30

Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD+-reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H 2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function of the various metal cofactors present in the enzyme. Here, all iron-containing cofactors of the SH were investigated by 57Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters,more » which is consistent with the amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD+-reducing hydrogenases. For the first time, Fe–CO and Fe–CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe–CO modes. The present approach explores the complex vibrational signature of the Fe–S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.« less

Nuclear resonance vibrational spectroscopy reveals the FeS cluster composition and active site vibrational properties of an O2-tolerant NAD+-reducing [NiFe] hydrogenase.

PubMed

Lauterbach, Lars; Wang, Hongxin; Horch, Marius; Gee, Leland B; Yoda, Yoshitaka; Tanaka, Yoshihito; Zebger, Ingo; Lenz, Oliver; Cramer, Stephen P

Hydrogenases are complex metalloenzymes that catalyze the reversible splitting of molecular hydrogen into protons and electrons essentially without overpotential. The NAD + -reducing soluble hydrogenase (SH) from Ralstonia eutropha is capable of H 2 conversion even in the presence of usually toxic dioxygen. The molecular details of the underlying reactions are largely unknown, mainly because of limited knowledge of the structure and function the various metal cofactors present in the enzyme. Here all iron-containing cofactors of the SH were investigated by 57 Fe specific nuclear resonance vibrational spectroscopy (NRVS). Our data provide experimental evidence for one [2Fe2S] center and four [4Fe4S] clusters, which is consistent with amino acid sequence composition. Only the [2Fe2S] cluster and one of the four [4Fe4S] clusters were reduced upon incubation of the SH with NADH. This finding explains the discrepancy between the large number of FeS clusters and the small amount of FeS cluster-related signals as detected by electron paramagnetic resonance spectroscopic analysis of several NAD + -reducing hydrogenases. For the first time, Fe-CO and Fe-CN modes derived from the [NiFe] active site could be distinguished by NRVS through selective 13 C labeling of the CO ligand. This strategy also revealed the molecular coordinates that dominate the individual Fe-CO modes. The present approach explores the complex vibrational signature of the Fe-S clusters and the hydrogenase active site, thereby showing that NRVS represents a powerful tool for the elucidation of complex biocatalysts containing multiple cofactors.
A comparative analysis of clustering algorithms: O{sub 2} migration in truncated hemoglobin I from transition networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cazade, Pierre-André; Berezovska, Ganna; Meuwly, Markus, E-mail: m.meuwly@unibas.ch

2015-01-14

The ligand migration network for O{sub 2}–diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k–means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of themore » major differences between k–means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.« less
A comparative analysis of clustering algorithms: O2 migration in truncated hemoglobin I from transition networks.

PubMed

Cazade, Pierre-André; Zheng, Wenwei; Prada-Gracia, Diego; Berezovska, Ganna; Rao, Francesco; Clementi, Cecilia; Meuwly, Markus

2015-01-14

The ligand migration network for O2-diffusion in truncated Hemoglobin N is analyzed based on three different clustering schemes. For coordinate-based clustering, the conventional k-means and the kinetics-based Markov Clustering (MCL) methods are employed, whereas the locally scaled diffusion map (LSDMap) method is a collective-variable-based approach. It is found that all three methods agree well in their geometrical definition of the most important docking site, and all experimentally known docking sites are recovered by all three methods. Also, for most of the states, their population coincides quite favourably, whereas the kinetics of and between the states differs. One of the major differences between k-means and MCL clustering on the one hand and LSDMap on the other is that the latter finds one large primary cluster containing the Xe1a, IS1, and ENT states. This is related to the fact that the motion within the state occurs on similar time scales, whereas structurally the state is found to be quite diverse. In agreement with previous explicit atomistic simulations, the Xe3 pocket is found to be a highly dynamical site which points to its potential role as a hub in the network. This is also highlighted in the fact that LSDMap cannot identify this state. First passage time distributions from MCL clusterings using a one- (ligand-position) and two-dimensional (ligand-position and protein-structure) descriptor suggest that ligand- and protein-motions are coupled. The benefits and drawbacks of the three methods are discussed in a comparative fashion and highlight that depending on the questions at hand the best-performing method for a particular data set may differ.
Analysis of the Structures and Properties of (GaSb)n (n = 4-9) Clusters through Density Functional Theory.

PubMed

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De; Wan, Jian Guo

2016-07-07

An optimization strategy combining global semiempirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (GaSb)n clusters up to n = 9. The growth pattern of the clusters differed from those of previously reported group III-V binary clusters. A cagelike configuration was found for cluster sizes n ≤ 7. The structure of (GaSb)6 deviated from that of other III-V clusters. Competition existed between core-shell and hollow cage structures of (GaSb)7. Novel noncagelike structures were energetically preferred over the cages for the (GaSb)8 and (GaSb)9 clusters. Electronic properties, such as vertical ionization potential, adiabatic electron affinities, HOMO-LUMO gaps, and average on-site charges on Ga or Sb atoms, as well as binding energies, were computed.
Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

PubMed Central

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-01-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. PMID:24920327
Functional evolution of PLP-dependent enzymes based on active-site structural similarities.

PubMed

Catazaro, Jonathan; Caprez, Adam; Guru, Ashu; Swanson, David; Powers, Robert

2014-10-01

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5'-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the comparison of protein active site structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional-fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS. © 2014 Wiley Periodicals, Inc.
75 FR 41521 - Delphi Corporation, Automotive Holding Group, Instrument Cluster Plant, Currently Known as...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-16

..., Automotive Holding Group, Instrument Cluster Plant, Currently Known as General Motors Corporation, Including... Corporation, Automotive Holding Group, Instrument Cluster Plant, including on-site leased workers from... Material Management working on-site at Delphi Corporation, Automotive Holding Group, Instrument Cluster...
Groundwater quality assessment of urban Bengaluru using multivariate statistical techniques

NASA Astrophysics Data System (ADS)

Gulgundi, Mohammad Shahid; Shetty, Amba

2018-03-01

Groundwater quality deterioration due to anthropogenic activities has become a subject of prime concern. The objective of the study was to assess the spatial and temporal variations in groundwater quality and to identify the sources in the western half of the Bengaluru city using multivariate statistical techniques. Water quality index rating was calculated for pre and post monsoon seasons to quantify overall water quality for human consumption. The post-monsoon samples show signs of poor quality in drinking purpose compared to pre-monsoon. Cluster analysis (CA), principal component analysis (PCA) and discriminant analysis (DA) were applied to the groundwater quality data measured on 14 parameters from 67 sites distributed across the city. Hierarchical cluster analysis (CA) grouped the 67 sampling stations into two groups, cluster 1 having high pollution and cluster 2 having lesser pollution. Discriminant analysis (DA) was applied to delineate the most meaningful parameters accounting for temporal and spatial variations in groundwater quality of the study area. Temporal DA identified pH as the most important parameter, which discriminates between water quality in the pre-monsoon and post-monsoon seasons and accounts for 72% seasonal assignation of cases. Spatial DA identified Mg, Cl and NO3 as the three most important parameters discriminating between two clusters and accounting for 89% spatial assignation of cases. Principal component analysis was applied to the dataset obtained from the two clusters, which evolved three factors in each cluster, explaining 85.4 and 84% of the total variance, respectively. Varifactors obtained from principal component analysis showed that groundwater quality variation is mainly explained by dissolution of minerals from rock water interactions in the aquifer, effect of anthropogenic activities and ion exchange processes in water.
Chromatin-Specific Regulation of Mammalian rDNA Transcription by Clustered TTF-I Binding Sites

PubMed Central

Diermeier, Sarah D.; Németh, Attila; Rehli, Michael; Grummt, Ingrid; Längst, Gernot

2013-01-01

Enhancers and promoters often contain multiple binding sites for the same transcription factor, suggesting that homotypic clustering of binding sites may serve a role in transcription regulation. Here we show that clustering of binding sites for the transcription termination factor TTF-I downstream of the pre-rRNA coding region specifies transcription termination, increases the efficiency of transcription initiation and affects the three-dimensional structure of rRNA genes. On chromatin templates, but not on free rDNA, clustered binding sites promote cooperative binding of TTF-I, loading TTF-I to the downstream terminators before it binds to the rDNA promoter. Interaction of TTF-I with target sites upstream and downstream of the rDNA transcription unit connects these distal DNA elements by forming a chromatin loop between the rDNA promoter and the terminators. The results imply that clustered binding sites increase the binding affinity of transcription factors in chromatin, thus influencing the timing and strength of DNA-dependent processes. PMID:24068958
Aerosol Models for the CALIPSO Lidar Inversion Algorithms

NASA Technical Reports Server (NTRS)

Omar, Ali H.; Winker, David M.; Won, Jae-Gwang

2003-01-01

We use measurements and models to develop aerosol models for use in the inversion algorithms for the Cloud Aerosol Lidar and Imager Pathfinder Spaceborne Observations (CALIPSO). Radiance measurements and inversions of the AErosol RObotic NETwork (AERONET1, 2) are used to group global atmospheric aerosols using optical and microphysical parameters. This study uses more than 105 records of radiance measurements, aerosol size distributions, and complex refractive indices to generate the optical properties of the aerosol at more 200 sites worldwide. These properties together with the radiance measurements are then classified using classical clustering methods to group the sites according to the type of aerosol with the greatest frequency of occurrence at each site. Six significant clusters are identified: desert dust, biomass burning, urban industrial pollution, rural background, marine, and dirty pollution. Three of these are used in the CALIPSO aerosol models to characterize desert dust, biomass burning, and polluted continental aerosols. The CALIPSO aerosol model also uses the coarse mode of desert dust and the fine mode of biomass burning to build a polluted dust model. For marine aerosol, the CALIPSO aerosol model uses measurements from the SEAS experiment 3. In addition to categorizing the aerosol types, the cluster analysis provides all the column optical and microphysical properties for each cluster.
Chemometric expertise of the quality of groundwater sources for domestic use.

PubMed

Spanos, Thomas; Ene, Antoaneta; Simeonova, Pavlina

2015-01-01

In the present study 49 representative sites have been selected for the collection of water samples from central water supplies with different geographical locations in the region of Kavala, Northern Greece. Ten physicochemical parameters (pH, electric conductivity, nitrate, chloride, sodium, potassium, total alkalinity, total hardness, bicarbonate and calcium) were analyzed monthly, in the period from January 2010 to December 2010. Chemometric methods were used for monitoring data mining and interpretation (cluster analysis, principal components analysis and source apportioning by principal components regression). The clustering of the chemical indicators delivers two major clusters related to the water hardness and the mineral components (impacted by sea, bedrock and acidity factors). The sampling locations are separated into three major clusters corresponding to the spatial distribution of the sites - coastal, lowland and semi-mountainous. The principal components analysis reveals two latent factors responsible for the data structures, which are also an indication for the sources determining the groundwater quality of the region (conditionally named "mineral" factor and "water hardness" factor). By the apportionment approach it is shown what the contribution is of each of the identified sources to the formation of the total concentration of each one of the chemical parameters. The mean values of the studied physicochemical parameters were found to be within the limits given in the 98/83/EC Directive. The water samples are appropriate for human consumption. The results of this study provide an overview of the hydrogeological profile of water supply system for the studied area.
A taxonomy of epithelial human cancer and their metastases

PubMed Central

2009-01-01

Background Microarray technology has allowed to molecularly characterize many different cancer sites. This technology has the potential to individualize therapy and to discover new drug targets. However, due to technological differences and issues in standardized sample collection no study has evaluated the molecular profile of epithelial human cancer in a large number of samples and tissues. Additionally, it has not yet been extensively investigated whether metastases resemble their tissue of origin or tissue of destination. Methods We studied the expression profiles of a series of 1566 primary and 178 metastases by unsupervised hierarchical clustering. The clustering profile was subsequently investigated and correlated with clinico-pathological data. Statistical enrichment of clinico-pathological annotations of groups of samples was investigated using Fisher exact test. Gene set enrichment analysis (GSEA) and DAVID functional enrichment analysis were used to investigate the molecular pathways. Kaplan-Meier survival analysis and log-rank tests were used to investigate prognostic significance of gene signatures. Results Large clusters corresponding to breast, gastrointestinal, ovarian and kidney primary tissues emerged from the data. Chromophobe renal cell carcinoma clustered together with follicular differentiated thyroid carcinoma, which supports recent morphological descriptions of thyroid follicular carcinoma-like tumors in the kidney and suggests that they represent a subtype of chromophobe carcinoma. We also found an expression signature identifying primary tumors of squamous cell histology in multiple tissues. Next, a subset of ovarian tumors enriched with endometrioid histology clustered together with endometrium tumors, confirming that they share their etiopathogenesis, which strongly differs from serous ovarian tumors. In addition, the clustering of colon and breast tumors correlated with clinico-pathological characteristics. Moreover, a signature was developed based on our unsupervised clustering of breast tumors and this was predictive for disease-specific survival in three independent studies. Next, the metastases from ovarian, breast, lung and vulva cluster with their tissue of origin while metastases from colon showed a bimodal distribution. A significant part clusters with tissue of origin while the remaining tumors cluster with the tissue of destination. Conclusion Our molecular taxonomy of epithelial human cancer indicates surprising correlations over tissues. This may have a significant impact on the classification of many cancer sites and may guide pathologists, both in research and daily practice. Moreover, these results based on unsupervised analysis yielded a signature predictive of clinical outcome in breast cancer. Additionally, we hypothesize that metastases from gastrointestinal origin either remember their tissue of origin or adapt to the tissue of destination. More specifically, colon metastases in the liver show strong evidence for such a bimodal tissue specific profile. PMID:20017941
Using Self-Organizing Map (SOM) Clusters of Ozonesonde Profiles to Evaluate Climatologies and Create Linkages between Meteorology and Pollution

NASA Astrophysics Data System (ADS)

Stauffer, R. M.; Thompson, A. M.; Young, G. S.; Oltmans, S. J.; Johnson, B.

2016-12-01

Ozone (O3) climatologies are typically created by averaging ozonesonde profiles on a monthly or seasonal basis, either for specific regions or zonally. We demonstrate the advantages of using a statistical clustering technique, self-organizing maps (SOM), over this simple averaging, through analysis of more than 4500 sonde profiles taken from the long-term US sites at Boulder, CO; Huntsville, AL; Trinidad Head, CA; and Wallops Island, VA. First, we apply SOM to O3 mixing ratios from surface to 12 km amsl. At all four sites, profiles in SOM clusters exhibit similar tropopause height, 500 hPa height and temperature, and total and tropospheric column O3. Second, when profiles from each SOM cluster are compared to monthly O3 means, near-tropopause O3 in three of the clusters is double (over +100 ppbv) the climatological O3 mixing ratio. The three clusters include 13-16% of all profiles, mostly from winter and spring. Large mid-tropospheric deviations from monthly means are found in two highly-populated clusters that represent either distinctly polluted (summer) or clean O3 (fall-winter, high tropopause) profiles. Thus, SOM indeed appear to represent US O3 profile statistics better than conventional climatologies. In the case of Trinidad Head, SOM clusters of O3 profile data from the lower troposphere (surface-6 km amsl) can discriminate background vs polluted O3 and the meteorology associated with each. Two of nine O3 clusters exhibit thin layers ( 100s of m thick) of high O3, typically between 1 and 4 km. Comparisons between clusters and downwind, high-altitude surface O3 measurements display a marked impact of the elevated tropospheric O3. Days corresponding to the high O3 clusters exhibit hourly surface O3 anomalies at surface sites of +5 -10 ppbv compared to a climatology; the anomalies can last up to four days. We also explore applications of SOM to tropical ozonesonde profiles, where tropospheric O3 variability is generally smaller.
Classification of typical and atypical antipsychotic drugs on the basis of dopamine D-1, D-2 and serotonin2 pKi values.

PubMed

Meltzer, H Y; Matsubara, S; Lee, J C

1989-10-01

The pKi values of 13 reference typical and 7 reference atypical antipsychotic drugs (APDs) for rat striatal dopamine D-1 and D-2 receptor binding sites and cortical serotonin (5-HT2) receptor binding sites were determined. The atypical antipsychotics had significantly lower pKi values for the D-2 but not 5-HT2 binding sites. There was a trend for a lower pKi value for the D-1 binding site for the atypical APD. The 5-HT2 and D-1 pKi values were correlated for the typical APD whereas the 5-HT2 and D-2 pKi values were correlated for the atypical APD. A stepwise discriminant function analysis to determine the independent contribution of each pKi value for a given binding site to the classification as a typical or atypical APD entered the D-2 pKi value first, followed by the 5-HT2 pKi value. The D-1 pKi value was not entered. A discriminant function analysis correctly classified 19 of 20 of these compounds plus 14 of 17 additional test compounds as typical or atypical APD for an overall correct classification rate of 89.2%. The major contributors to the discriminant function were the D-2 and 5-HT2 pKi values. A cluster analysis based only on the 5-HT2/D2 ratio grouped 15 of 17 atypical + one typical APD in one cluster and 19 of 20 typical + two atypical APDs in a second cluster, for an overall correct classification rate of 91.9%. When the stepwise discriminant function was repeated for all 37 compounds, only the D-2 and 5-HT2 pKi values were entered into the discriminant function.(ABSTRACT TRUNCATED AT 250 WORDS)
Site-specific estimation of peak-streamflow frequency using generalized least-squares regression for natural basins in Texas

USGS Publications Warehouse

Asquith, William H.; Slade, R.M.

1999-01-01

The U.S. Geological Survey, in cooperation with the Texas Department of Transportation, has developed a computer program to estimate peak-streamflow frequency for ungaged sites in natural basins in Texas. Peak-streamflow frequency refers to the peak streamflows for recurrence intervals of 2, 5, 10, 25, 50, and 100 years. Peak-streamflow frequency estimates are needed by planners, managers, and design engineers for flood-plain management; for objective assessment of flood risk; for cost-effective design of roads and bridges; and also for the desin of culverts, dams, levees, and other flood-control structures. The program estimates peak-streamflow frequency using a site-specific approach and a multivariate generalized least-squares linear regression. A site-specific approach differs from a traditional regional regression approach by developing unique equations to estimate peak-streamflow frequency specifically for the ungaged site. The stations included in the regression are selected using an informal cluster analysis that compares the basin characteristics of the ungaged site to the basin characteristics of all the stations in the data base. The program provides several choices for selecting the stations. Selecting the stations using cluster analysis ensures that the stations included in the regression will have the most pertinent information about flooding characteristics of the ungaged site and therefore provide the basis for potentially improved peak-streamflow frequency estimation. An evaluation of the site-specific approach in estimating peak-streamflow frequency for gaged sites indicates that the site-specific approach is at least as accurate as a traditional regional regression approach.
Characterization of spatial and temporal variability in hydrochemistry of Johor Straits, Malaysia.

PubMed

Abdullah, Pauzi; Abdullah, Sharifah Mastura Syed; Jaafar, Othman; Mahmud, Mastura; Khalik, Wan Mohd Afiq Wan Mohd

2015-12-15

Characterization of hydrochemistry changes in Johor Straits within 5 years of monitoring works was successfully carried out. Water quality data sets (27 stations and 19 parameters) collected in this area were interpreted subject to multivariate statistical analysis. Cluster analysis grouped all the stations into four clusters ((Dlink/Dmax) × 100<90) and two clusters ((Dlink/Dmax) × 100<80) for site and period similarities. Principal component analysis rendered six significant components (eigenvalue>1) that explained 82.6% of the total variance of the data set. Classification matrix of discriminant analysis assigned 88.9-92.6% and 83.3-100% correctness in spatial and temporal variability, respectively. Times series analysis then confirmed that only four parameters were not significant over time change. Therefore, it is imperative that the environmental impact of reclamation and dredging works, municipal or industrial discharge, marine aquaculture and shipping activities in this area be effectively controlled and managed. Copyright © 2015 Elsevier Ltd. All rights reserved.
Landsat-TM identification of Amblyomma variegatum (Acari: Ixodidae) habitats in Guadeloupe

NASA Technical Reports Server (NTRS)

Hugh-Jones, M.; Barre, N.; Nelson, G.; Wehnes, K.; Warner, J.; Garvin, J.; Garris, G.

1992-01-01

The feasibility of identifying specific habitats of the African bont tick, Amblyomma variegatum, from Landsat-TM images was investigated by comparing remotely sensed images of visible farms in Grande Terre (Guadeloupe) with field observations made in the same period of time (1986-1987). The different tick habitates could be separated using principal component analysis. The analysis clustered the sites by large and small variance of band values, and by vegetation and moisture indexes. It was found that herds in heterogeneous sites with large variances had more ticks than those in homogeneous or low variance sites. Within the heterogeneous sites, those with high vegetation and moisture indexes had more ticks than those with low values.
A pyrosequencing assay for the quantitative methylation analysis of the PCDHB gene cluster, the major factor in neuroblastoma methylator phenotype.

PubMed

Banelli, Barbara; Brigati, Claudio; Di Vinci, Angela; Casciano, Ida; Forlani, Alessandra; Borzì, Luana; Allemanni, Giorgio; Romani, Massimo

2012-03-01

Epigenetic alterations are hallmarks of cancer and powerful biomarkers, whose clinical utilization is made difficult by the absence of standardization and of common methods of data interpretation. The coordinate methylation of many loci in cancer is defined as 'CpG island methylator phenotype' (CIMP) and identifies clinically distinct groups of patients. In neuroblastoma (NB), CIMP is defined by a methylation signature, which includes different loci, but its predictive power on outcome is entirely recapitulated by the PCDHB cluster only. We have developed a robust and cost-effective pyrosequencing-based assay that could facilitate the clinical application of CIMP in NB. This assay permits the unbiased simultaneous amplification and sequencing of 17 out of 19 genes of the PCDHB cluster for quantitative methylation analysis, taking into account all the sequence variations. As some of these variations were at CpG doublets, we bypassed the data interpretation conducted by the methylation analysis software to assign the corrected methylation value at these sites. The final result of the assay is the mean methylation level of 17 gene fragments in the protocadherin B cluster (PCDHB) cluster. We have utilized this assay to compare the methylation levels of the PCDHB cluster between high-risk and very low-risk NB patients, confirming the predictive value of CIMP. Our results demonstrate that the pyrosequencing-based assay herein described is a powerful instrument for the analysis of this gene cluster that may simplify the data comparison between different laboratories and, in perspective, could facilitate its clinical application. Furthermore, our results demonstrate that, in principle, pyrosequencing can be efficiently utilized for the methylation analysis of gene clusters with high internal homologies.
An Enhanced K-Means Algorithm for Water Quality Analysis of The Haihe River in China

PubMed Central

Zou, Hui; Zou, Zhihong; Wang, Xiaojing

2015-01-01

The increase and the complexity of data caused by the uncertain environment is today’s reality. In order to identify water quality effectively and reliably, this paper presents a modified fast clustering algorithm for water quality analysis. The algorithm has adopted a varying weights K-means cluster algorithm to analyze water monitoring data. The varying weights scheme was the best weighting indicator selected by a modified indicator weight self-adjustment algorithm based on K-means, which is named MIWAS-K-means. The new clustering algorithm avoids the margin of the iteration not being calculated in some cases. With the fast clustering analysis, we can identify the quality of water samples. The algorithm is applied in water quality analysis of the Haihe River (China) data obtained by the monitoring network over a period of eight years (2006–2013) with four indicators at seven different sites (2078 samples). Both the theoretical and simulated results demonstrate that the algorithm is efficient and reliable for water quality analysis of the Haihe River. In addition, the algorithm can be applied to more complex data matrices with high dimensionality. PMID:26569283
Detection of Tuberculosis Infection Hotspots Using Activity Spaces Based Spatial Approach in an Urban Tokyo, from 2003 to 2011.

PubMed

Izumi, Kiyohiko; Ohkado, Akihiro; Uchimura, Kazuhiro; Murase, Yoshiro; Tatsumi, Yuriko; Kayebeta, Aya; Watanabe, Yu; Ishikawa, Nobukatsu

2015-01-01

Identifying ongoing tuberculosis infection sites is crucial for breaking chains of transmission in tuberculosis-prevalent urban areas. Previous studies have pointed out that detection of local accumulation of tuberculosis patients based on their residential addresses may be limited by a lack of matching between residences and tuberculosis infection sites. This study aimed to identify possible tuberculosis hotspots using TB genotype clustering statuses and a concept of "activity space", a place where patients spend most of their waking hours. We further compared the spatial distribution by different residential statuses and describe urban environmental features of the detected hotspots. Culture-positive tuberculosis patients notified to Shinjuku city from 2003 to 2011 were enrolled in this case-based cross-sectional study, and their demographic and clinical information, TB genotype clustering statuses, and activity space were collected. Spatial statistics (Global Moran's I and Getis-Ord Gi* statistics) identified significant hotspots in 152 census tracts, and urban environmental features and tuberculosis patients' characteristics in these hotspots were assessed. Of the enrolled 643 culture-positive tuberculosis patients, 416 (64.2%) were general inhabitants, 42 (6.5%) were foreign-born people, and 184 were homeless people (28.6%). The percentage of overall genotype clustering was 43.7%. Genotype-clustered general inhabitants and homeless people formed significant hotspots around a major railway station, whereas the non-clustered general inhabitants formed no hotspots. This suggested the detected hotspots of activity spaces may reflect ongoing tuberculosis transmission sites and were characterized by smaller residential floor size and a higher proportion of non-working households. Activity space-based spatial analysis suggested possible TB transmission sites around the major railway station and it can assist in further comprehension of TB transmission dynamics in an urban setting in Japan.

Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone

PubMed Central

Ullrich, Alexander; Böhme, Mathias A.; Schöneberg, Johannes; Depner, Harald; Sigrist, Stephan J.; Noé, Frank

2015-01-01

Synaptic vesicle fusion is mediated by SNARE proteins forming in between synaptic vesicle (v-SNARE) and plasma membrane (t-SNARE), one of which is Syntaxin-1A. Although exocytosis mainly occurs at active zones, Syntaxin-1A appears to cover the entire neuronal membrane. By using STED super-resolution light microscopy and image analysis of Drosophila neuro-muscular junctions, we show that Syntaxin-1A clusters are more abundant and have an increased size at active zones. A computational particle-based model of syntaxin cluster formation and dynamics is developed. The model is parametrized to reproduce Syntaxin cluster-size distributions found by STED analysis, and successfully reproduces existing FRAP results. The model shows that the neuronal membrane is adjusted in a way to strike a balance between having most syntaxins stored in large clusters, while still keeping a mobile fraction of syntaxins free or in small clusters that can efficiently search the membrane or be traded between clusters. This balance is subtle and can be shifted toward almost no clustering and almost complete clustering by modifying the syntaxin interaction energy on the order of only 1 kBT. This capability appears to be exploited at active zones. The larger active-zone syntaxin clusters are more stable and provide regions of high docking and fusion capability, whereas the smaller clusters outside may serve as flexible reserve pool or sites of spontaneous ectopic release. PMID:26367029
Regional Frequency Analysis of Annual Maximum Streamflow in Gipuzkoa (Spain)

NASA Astrophysics Data System (ADS)

Erro, J.; López, J. J.

2012-04-01

Extreme streamflow events have been an important cause of recent flooding in Gipuzkoa, and any change in the magnitude of such events may have severe impacts upon urban structures such as dams, urban drainage systems and flood defences, and cause failures to occur. So a regional frequency analysis of annual maximum streamflow was developed for Gipuzkoa, using the well known L-moments approach together with the index-flood procedure, and following the four steps that characterize it: initial screening of the data, identification of homogeneous regions, choice of the appropriate frequency distribution and estimation of quantiles for different return periods. The preliminary study, completed in 2009, was based on the observations recorded at 22 stations distributed throughout the area. A primary filtering of the data revealed the absence of jumps, inconsistencies and changes in trends within the series, and the discordancy measures showed that none of the sites used in the analysis had to be considered discordant with the others. Regionalization was performed by cluster analysis, grouping the stations according to eight physical site characteristics: latitude, longitude, drainage basin area, elevation, main channel length of the basin, slope, annual mean rainfall and annual maximum rainfall. It resulted in two groups - one cluster with the 18 sites of small-medium basin area, and a second cluster with the 4 remaining sites of major basin area - in which the homogeneity criteria were tested and satisfied. However, the short lenght of the series together with the introduction of the observations of 2010 and the inclusion of a historic extreme streamflow event occurred in northern Spain in November 2011, completely changed the results. With this consideration and adjustment, all Gipuzkoa could be treated as a homogeneus region. The goodness-of-fit measures indicated that Generalized Logistic (GLO) is the only suitable distribution to characterize Gipuzkoa. Using the regional L-moment algorithm, quantiles associated with return periods of interest were estimated, and Monte Carlo simulation was used to compute RMSE, bias and error bounds for the estimates.
Admixture in Humans of Two Divergent Plasmodium knowlesi Populations Associated with Different Macaque Host Species

PubMed Central

Divis, Paul C. S.; Singh, Balbir; Anderios, Fread; Hisam, Shamilah; Matusop, Asmad; Kocken, Clemens H.; Assefa, Samuel A.; Duffy, Craig W.; Conway, David J.

2015-01-01

Human malaria parasite species were originally acquired from other primate hosts and subsequently became endemic, then spread throughout large parts of the world. A major zoonosis is now occurring with Plasmodium knowlesi from macaques in Southeast Asia, with a recent acceleration in numbers of reported cases particularly in Malaysia. To investigate the parasite population genetics, we developed sensitive and species-specific microsatellite genotyping protocols and applied these to analysis of samples from 10 sites covering a range of >1,600 km within which most cases have occurred. Genotypic analyses of 599 P. knowlesi infections (552 in humans and 47 in wild macaques) at 10 highly polymorphic loci provide radical new insights on the emergence. Parasites from sympatric long-tailed macaques (Macaca fascicularis) and pig-tailed macaques (M. nemestrina) were very highly differentiated (FST = 0.22, and K-means clustering confirmed two host-associated subpopulations). Approximately two thirds of human P. knowlesi infections were of the long-tailed macaque type (Cluster 1), and one third were of the pig-tailed-macaque type (Cluster 2), with relative proportions varying across the different sites. Among the samples from humans, there was significant indication of genetic isolation by geographical distance overall and within Cluster 1 alone. Across the different sites, the level of multi-locus linkage disequilibrium correlated with the degree of local admixture of the two different clusters. The widespread occurrence of both types of P. knowlesi in humans enhances the potential for parasite adaptation in this zoonotic system. PMID:26020959
Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

PubMed

Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

2018-01-01

Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.
Broad DNA methylation changes of spermatogenesis, inflammation and immune response-related genes in a subgroup of sperm samples for assisted reproduction.

PubMed

Schütte, B; El Hajj, N; Kuhtz, J; Nanda, I; Gromoll, J; Hahn, T; Dittrich, M; Schorsch, M; Müller, T; Haaf, T

2013-11-01

Aberrant sperm DNA methylation patterns, mainly in imprinted genes, have been associated with male subfertility and oligospermia. Here, we performed a genome-wide methylation analysis in sperm samples representing a wide range of semen parameters. Sperm DNA samples of 38 males attending a fertility centre were analysed with Illumina HumanMethylation27 BeadChips, which quantify methylation of >27 000 CpG sites in cis-regulatory regions of almost 15 000 genes. In an unsupervised analysis of methylation of all analysed sites, the patient samples clustered into a major and a minor group. The major group clustered with samples from normozoospermic healthy volunteers and, thus, may more closely resemble the normal situation. When correlating the clusters with semen and clinical parameters, the sperm counts were significantly different between groups with the minor group exhibiting sperm counts in the low normal range. A linear model identified almost 3000 CpGs with significant methylation differences between groups. Functional analysis revealed a broad gain of methylation in spermatogenesis-related genes and a loss of methylation in inflammation- and immune response-related genes. Quantitative bisulfite pyrosequencing validated differential methylation in three of five significant candidate genes on the array. Collectively, we identified a subgroup of sperm samples for assisted reproduction with sperm counts in the low normal range and broad methylation changes (affecting approximately 10% of analysed CpG sites) in specific pathways, most importantly spermatogenesis-related genes. We propose that epigenetic analysis can supplement traditional semen parameters and has the potential to provide new insights into the aetiology of male subfertility. © 2013 American Society of Andrology and European Academy of Andrology.
A comparison of regional flood frequency analysis approaches in a simulation framework

NASA Astrophysics Data System (ADS)

Ganora, D.; Laio, F.

2016-07-01

Regional frequency analysis (RFA) is a well-established methodology to provide an estimate of the flood frequency curve at ungauged (or scarcely gauged) sites. Different RFA approaches exist, depending on the way the information is transferred to the site of interest, but it is not clear in the literature if a specific method systematically outperforms the others. The aim of this study is to provide a framework wherein carrying out the intercomparison by building up a virtual environment based on synthetically generated data. The considered regional approaches include: (i) a unique regional curve for the whole region; (ii) a multiple-region model where homogeneous subregions are determined through cluster analysis; (iii) a Region-of-Influence model which defines a homogeneous subregion for each site; (iv) a spatially smooth estimation procedure where the parameters of the regional model vary continuously along the space. Virtual environments are generated considering different patterns of heterogeneity, including step change and smooth variations. If the region is heterogeneous, with the parent distribution changing continuously within the region, the spatially smooth regional approach outperforms the others, with overall errors 10-50% lower than the other methods. In the case of a step-change, the spatially smooth and clustering procedures perform similarly if the heterogeneity is moderate, while clustering procedures work better when the step-change is severe. To extend our findings, an extensive sensitivity analysis has been performed to investigate the effect of sample length, number of virtual stations, return period of the predicted quantile, variability of the scale parameter of the parent distribution, number of predictor variables and different parent distribution. Overall, the spatially smooth approach appears as the most robust approach as its performances are more stable across different patterns of heterogeneity, especially when short records are considered.
Perturbation of the quinone-binding site of complex II alters the electronic properties of the proximal [3Fe-4S] iron-sulfur cluster.

PubMed

Ruprecht, Jonathan; Iwata, So; Rothery, Richard A; Weiner, Joel H; Maklashina, Elena; Cecchini, Gary

2011-04-08

Succinate-ubiquinone oxidoreductase (SQR) and menaquinol-fumarate oxidoreductase (QFR) from Escherichia coli are members of the complex II family of enzymes. SQR and QFR catalyze similar reactions with quinones; however, SQR preferentially reacts with higher potential ubiquinones, and QFR preferentially reacts with lower potential naphthoquinones. Both enzymes have a single functional quinone-binding site proximal to a [3Fe-4S] iron-sulfur cluster. A difference between SQR and QFR is that the redox potential of the [3Fe-4S] cluster in SQR is 140 mV higher than that found in QFR. This may reflect the character of the different quinones with which the two enzymes preferentially react. To investigate how the environment around the [3Fe-4S] cluster affects its redox properties and catalysis with quinones, a conserved amino acid proximal to the cluster was mutated in both enzymes. It was found that substitution of SdhB His-207 by threonine (as found in QFR) resulted in a 70-mV lowering of the redox potential of the cluster as measured by EPR. The converse substitution in QFR raised the redox potential of the cluster. X-ray structural analysis suggests that placing a charged residue near the [3Fe-4S] cluster is a primary reason for the alteration in redox potential with the hydrogen bonding environment having a lesser effect. Steady state enzyme kinetic characterization of the mutant enzymes shows that the redox properties of the [3Fe-4S] cluster have only a minor effect on catalysis.
The Energy Landscape Analysis of Cancer Mutations in Protein Kinases

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2011-01-01

The growing interest in quantifying the molecular basis of protein kinase activation and allosteric regulation by cancer mutations has fueled computational studies of allosteric signaling in protein kinases. In the present study, we combined computer simulations and the energy landscape analysis of protein kinases to characterize the interplay between oncogenic mutations and locally frustrated sites as important catalysts of allostetric kinase activation. While structurally rigid kinase core constitutes a minimally frustrated hub of the catalytic domain, locally frustrated residue clusters, whose interaction networks are not energetically optimized, are prone to dynamic modulation and could enable allosteric conformational transitions. The results of this study have shown that the energy landscape effect of oncogenic mutations may be allosteric eliciting global changes in the spatial distribution of highly frustrated residues. We have found that mutation-induced allosteric signaling may involve a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. The presented study has demonstrated that activation cancer mutations may affect the thermodynamic equilibrium between kinase states by allosterically altering the distribution of locally frustrated sites and increasing the local frustration in the inactive form, while eliminating locally frustrated sites and restoring structural rigidity of the active form. The energy landsape analysis of protein kinases and the proposed role of locally frustrated sites in activation mechanisms may have useful implications for bioinformatics-based screening and detection of functional sites critical for allosteric regulation in complex biomolecular systems. PMID:21998754
Fish assemblages of the Casiquiare River, a corridor and zoogeographical filter for dispersal between the Orinoco and Amazon basins

USGS Publications Warehouse

Winemiller, K.O.; Lopez-Fernandez, H.; Taphorn, D.C.; Nico, L.G.; Duque, A.B.

2008-01-01

Aim: The aim of this study was to determine whether the Casiquiare River functions as a free dispersal corridor or as a partial barrier (i.e. filter) for the interchange of fish species of the Orinoco and Negro/Amazon basins using species assemblage patterns according to geographical location and environmental features. Location: The Casiquiare, Upper Orinoco and Upper Negro rivers in southern Venezuela, South America. Methods: Our study was based on an analysis of species presence/absence data and environmental information (11 habitat characteristics) collected by the authors and colleagues between the years 1984 and 1999. The data set consisted of 269 sampled sites and 452 fish species (> 50,000 specimens). A wide range of habitat types was included in the samples, and the collection sites were located at various points along the entire length of the Casiquiare main channel, at multiple sites on its tributary streams, as well as at various nearby sites outside the Casiquiare drainage, within the Upper Orinoco and Upper Rio Negro river systems. Most specimens and field data used in this analysis are archived in the Museo de Ciencias Naturales in Guanare, Venezuela. We performed canonical correspondence analysis (CCA) based on species presence/absence using two versions of the data set: one that eliminated sites having < 5 species and species occurring at < 5 sites; and another that eliminated sites having < 10 species and species occurring at < 10 sites. Cluster analysis was performed on sites based on species assemblage similarity, and a separate analysis was performed on species based on CCA loadings. Results: The CCA results for the two versions of the data set were qualitatively the same. The dominant environmental axis contrasted assemblages and sites associated with blackwater vs. clearwater conditions. Longitudinal position on the Casiquiare River was correlated (r2 = 0.33) with CCA axis-1 scores, reflecting clearwater conditions nearer to its origin (bifurcation of the Orinoco) and blackwater conditions nearer to its mouth (junction with the Rio Negro). The second CCA axis was most strongly associated with habitat size and structural complexity. Species associations derived from the unweighted pair-group average clustering method and pair-wise squared Euclidean distances calculated from species loadings on CCA axes 1 and 2 showed seven ecological groupings. Cluster analysis of species assemblages according to watershed revealed a stronger influence of local environmental conditions than of geographical proximity. Main conclusions: Fish assemblage composition is more consistently associated with local environmental conditions than with geographical position within the river drainages. Nonetheless, the results support the hypothesis that the mainstem Casiquiare represents a hydrochemical gradient between clearwaters at its origin and blackwaters at its mouth, and as such appears to function as a semi-permeable barrier (environmental filter) to dispersal and faunal exchanges between the partially vicariant fish faunas of the Upper Orinoco and Upper Negro rivers. ?? 2008 The Authors.
Model-based recursive partitioning to identify risk clusters for metabolic syndrome and its components: findings from the International Mobility in Aging Study

PubMed Central

Pirkle, Catherine M; Wu, Yan Yan; Zunzunegui, Maria-Victoria; Gómez, José Fernando

2018-01-01

Objective Conceptual models underpinning much epidemiological research on ageing acknowledge that environmental, social and biological systems interact to influence health outcomes. Recursive partitioning is a data-driven approach that allows for concurrent exploration of distinct mixtures, or clusters, of individuals that have a particular outcome. Our aim is to use recursive partitioning to examine risk clusters for metabolic syndrome (MetS) and its components, in order to identify vulnerable populations. Study design Cross-sectional analysis of baseline data from a prospective longitudinal cohort called the International Mobility in Aging Study (IMIAS). Setting IMIAS includes sites from three middle-income countries—Tirana (Albania), Natal (Brazil) and Manizales (Colombia)—and two from Canada—Kingston (Ontario) and Saint-Hyacinthe (Quebec). Participants Community-dwelling male and female adults, aged 64–75 years (n=2002). Primary and secondary outcome measures We apply recursive partitioning to investigate social and behavioural risk factors for MetS and its components. Model-based recursive partitioning (MOB) was used to cluster participants into age-adjusted risk groups based on variabilities in: study site, sex, education, living arrangements, childhood adversities, adult occupation, current employment status, income, perceived income sufficiency, smoking status and weekly minutes of physical activity. Results 43% of participants had MetS. Using MOB, the primary partitioning variable was participant sex. Among women from middle-incomes sites, the predicted proportion with MetS ranged from 58% to 68%. Canadian women with limited physical activity had elevated predicted proportions of MetS (49%, 95% CI 39% to 58%). Among men, MetS ranged from 26% to 41% depending on childhood social adversity and education. Clustering for MetS components differed from the syndrome and across components. Study site was a primary partitioning variable for all components except HDL cholesterol. Sex was important for most components. Conclusion MOB is a promising technique for identifying disease risk clusters (eg, vulnerable populations) in modestly sized samples. PMID:29500203
Solid-state NMR/NQR and first-principles study of two niobium halide cluster compounds.

PubMed

Perić, Berislav; Gautier, Régis; Pickard, Chris J; Bosiočić, Marko; Grbić, Mihael S; Požek, Miroslav

2014-01-01

Two hexanuclear niobium halide cluster compounds with a [Nb6X12](2+) (X=Cl, Br) diamagnetic cluster core, have been studied by a combination of experimental solid-state NMR/NQR techniques and PAW/GIPAW calculations. For niobium sites the NMR parameters were determined by using variable Bo field static broadband NMR measurements and additional NQR measurements. It was found that they possess large positive chemical shifts, contrary to majority of niobium compounds studied so far by solid-state NMR, but in accordance with chemical shifts of (95)Mo nuclei in structurally related compounds containing [Mo6Br8](4+) cluster cores. Experimentally determined δiso((93)Nb) values are in the range from 2,400 to 3,000 ppm. A detailed analysis of geometrical relations between computed electric field gradient (EFG) and chemical shift (CS) tensors with respect to structural features of cluster units was carried out. These tensors on niobium sites are almost axially symmetric with parallel orientation of the largest EFG and the smallest CS principal axes (Vzz and δ33) coinciding with the molecular four-fold axis of the [Nb6X12](2+) unit. Bridging halogen sites are characterized by large asymmetry of EFG and CS tensors, the largest EFG principal axis (Vzz) is perpendicular to the X-Nb bonds, while intermediate EFG principal axis (Vyy) and the largest CS principal axis (δ11) are oriented in the radial direction with respect to the center of the cluster unit. For more symmetrical bromide compound the PAW predictions for EFG parameters are in better correspondence with the NMR/NQR measurements than in the less symmetrical chlorine compound. Theoretically predicted NMR parameters of bridging halogen sites were checked by (79/81)Br NQR and (35)Cl solid-state NMR measurements. Copyright © 2014 Elsevier Inc. All rights reserved.
Clustering approaches to identifying gene expression patterns from DNA microarray data.

PubMed

Do, Jin Hwan; Choi, Dong-Kug

2008-04-30

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.
Power Calculations for Moderators in Multi-Site Cluster Randomized Trials

ERIC Educational Resources Information Center

Spybrook, Jessaca; Kelcey, Ben; Dong, Nianbo

2016-01-01

Cluster randomized trials (CRTs), or studies in which intact groups of individuals are randomly assigned to a condition, are becoming more common in evaluation studies of educational programs. A specific type of CRT in which clusters are randomly assigned to treatment within blocks or sites, known as multisite cluster randomized trials (MSCRTs),…
Spatial and Temporal Variation in DeSoto Canyon Macrofaunal Community Structure

NASA Astrophysics Data System (ADS)

Baco-Taylor, A.; Shantharam, A. K.

2016-02-01

Sediment-dwelling macrofauna (polychaetes, bivalves, and assorted crustaceans ≥ 300 µm) have long served as biological indicators of ecosystem stress. As part of evaluating the 2010 impact from the Deepwater Horizon blowout, we sampled 12 sites along and transverse to the DeSoto Canyon axis, Gulf of Mexico, as well as 2 control sites outside the Canyon. Sites ranged in depth from 479-2310 m. Three of the sites (PCB06, S36, and XC4) were sampled annually from 2012-2014. We provide an overview of the macrofauna community structure of canyon and non-canyon sites, as well as trends in community structure and diversity at the time-series sites. Compositionally, polychaetes dominated the communities, followed by tanaid crustaceans and bivalves. The total number of individuals was not significantly correlated with depth while the total number of taxa and species richness were. Rarefaction shows the deepest station, XC4 (2310 m) had the lowest diversity while NT800 (a non-canyon control at 800m) had the highest. Multivariate analysis shows the canyon assemblages fall into eight clusters with the non-canyon stations forming a separate ninth cluster, indicating a detectable difference in canyon and non-canyon communities. Time series stations show an increase in diversity from 2012-2014 with a strong overlap in community structure in 2013 and 2014 samples. Environmental analysis, via BEST, using data from 10 canyon sites and the controls, indicated depth in combination with latitude explain the most variation in macrofaunal community structure.
The effect of sewage effluent on the physico-chemical and biological characteristics of the Sand River, Limpopo, South Africa

NASA Astrophysics Data System (ADS)

Seanego, K. G.; Moyo, N. A. G.

Population growth in urban areas is putting pressure on sewage treatment plants. The improper treatment of sewage entering the aquatic ecosystems causes deterioration of the water quality of the receiving water body. The effect of sewage effluent on the Sand River was assessed. Eight sampling sites were selected, site 1 and 2 were upstream of the sewage treatment plant along the urbanised area of Polokwane, whilst sites 3, 4, 5, 6, 7 and 8 were downstream. The physico-chemical parameters and coliform counts in the water samples were determined. The suitability of the water for irrigation was also determined. Hierarchical average linkage cluster analysis produced two clusters, grouping two sites above the sewage treatment works and six sites downstream of the sewage effluent discharge point. Principal component analysis (PCA) identified total nitrogen, total phosphorus, conductivity and salinity as the major factors contributing to the variability of the Sand River water quality. These factors are strongly associated with the downstream sites. Canonial correspondence analysis (CCA) indicated the macroinvertebrates, Chironomidae, Belastomatidae, Chaoborus and Hirudinea being strongly associated with nitrogen, phosphorus, conductivity and temperature. Escherichia coli levels in the Polokwane wastewater treatment works maturation ponds, could potentially lead to contamination of the Polokwane aquifer. The Sodium Adsorption Ratio was between 1.5 and 3.0 and residual sodium carbonate was below 1.24 Meq/l, indicating that the Sand River water is still suitable for irrigation. The total phosphorus concentrations fluctuated across the different site. Total nitrogen concentrations showed a gradual decrease downstream from the point of discharge. This shows that the river still has a good self-purification capacity.
Environmental Impact Analysis Process, Groom Mountain Range, Lincoln County, Nevada

DTIC Science & Technology

1985-10-01

bases clustered around springs, temporary camps, rock shelters , quarries, lithic scatters, rock art, pinyon caches, pot drops, isolates, and historic...include pinyon caches and rock shelters with associated historic artifacts and many of the spring sites. These sites provide an unusual research...Management. (b) Proposed Action: Renewed Withdrawal of Groom Mountain Range Addition to Nellis Air Force Bombing and Gunnery Range, Lincoln County, Nevada. (c
Application of radioisotope XRF and thermoluminescence (TL) dating in investigation of pottery from Tell AL-Kasra archaeological site, Syria.

PubMed

Abboud, R; Issa, H; Abed-Allah, Y D; Bakraji, E H

2015-11-01

Statistical analysis based on chemical composition, using radioisotope X-ray fluorescence, have been applied on 39 ancient pottery fragments coming from the excavation at Tell Al-Kasra archaeological site, Syria. Three groups were defined by applying Cluster and Factor analysis statistical methods. Thermoluminescence (TL) dating was investigated on three sherds taken from the bathroom (hammam) on the site. Multiple aliquot additive dose (MAAD) was used to estimate the paleodose value, and the gamma spectrometry was used to estimate the dose rate. The average age was found to be 715±36 year. Copyright © 2015 Elsevier Ltd. All rights reserved.
ANALYSIS OF LOTIC MACROINVERTEBRATE ASSEMBLAGES IN CALIFORNIA'S CENTRAL VALLEY

EPA Science Inventory

Using multivariate and cluster analyses, we examined the relaitonships between chemical and physical characteristics and macroinvertebrate assemblages at sites sampled by R-EMAP in California's Central Valley. By contrasting results where community structure was summarized as met...
Cemeteries Are Effective Sites For Monitoring La Crosse Virus (LACv) and these Environments May Play a Role in LACv Infection

PubMed Central

Trout Fryxell, Rebecca T.; Freyman, Kimberly; Ulloa, Armando; Hendricks, Brian; Paulsen, Dave; Odoi, Agricola; Moncayo, Abelardo

2015-01-01

La Crosse encephalitis (LAC) is the leading arboviral disease among children, and was previously limited to the upper Midwest. In 2012 nine pediatric cases of LAC occurred in eastern Tennessee, including one fatal case. In an attempt to identify sites near an active LACv infection and describe the abundance and distribution of potential LACv vectors near a fatal LAC case in the Appalachian region, we initiated an end of season study using a combination of questing and oviposition mosquito traps placed at forty-nine sites consisting of cemeteries and houses within 16 radial kilometers of two pediatric infections. LACv was isolated from three Aedes triseriatus pools collected from cemeteries and spatial clustering analysis identified clusters of Ae. triseriatus and Ae. albopictus populations that overlapped in the same area as the 2012 LACv cases. Results indicate cemeteries are effective sites for monitoring LACv. The role of cemeteries and specific environmental features will be the focus of future investigations. PMID:25860584
Multivariate analysis of water quality and environmental variables in the Great Barrier Reef catchments

NASA Astrophysics Data System (ADS)

Ryu, D.; Liu, S.; Western, A. W.; Webb, J. A.; Lintern, A.; Leahy, P.; Wilson, P.; Watson, M.; Waters, D.; Bende-Michl, U.

2016-12-01

The Great Barrier Reef (GBR) lagoon has been experiencing significant water quality deterioration due in part to agricultural intensification and urban settlement in adjacent catchments. The degradation of water quality in rivers is caused by land-derived pollutants (i.e. sediment, nutrient and pesticide). A better understanding of dynamics of water quality is essential for land management to improve the GBR ecosystem. However, water quality is also greatly influenced by natural hydrological processes. To assess influencing factors and predict the water quality accurately, selection of the most important predictors of water quality is necessary. In this work, multivariate statistical techniques - cluster analysis (CA), principal component analysis (PCA) and factor analysis (FA) - are used to reduce the complexity derived from the multidimensional water quality monitoring data. Seventeen stations are selected across the GBR catchments, and the event-based measurements of 12 variables monitored during 9 years (2006 - 2014) were analysed by means of CA and PCA/FA. The key findings are: (1) 17 stations can be grouped into two clusters according to the hierarchical CA, and the spatial dissimilarity between these sites is characterised by the different climatic and land use in the GBR catchments. (2) PCA results indicate that the first 3 PCs explain 85% of the total variance, and FA on the entire data set shows that the varifactor (VF) loadings can be used to interpret the sources of spatial variation in water quality on the GBR catchments level. The impact of soil erosion and non-point source of pollutants from agriculture contribution to VF1 and the variability in hydrological conditions and biogeochemical processes can explain the loadings in VF2. (3) FA is also performed on two groups of sites identified in CA individually, to evaluate the underlying sources that are responsible for spatial variability in water quality in the two groups. For the Cluster 1 sites, spatial variations in water quality are likely from the agricultural inputs (fertilises) and for the Cluster 2 sites, the differences in hydrological transport is responsible for large spatial variations in water quality. These findings can be applied to water quality assessment along with establish effective water and land management in the future.

Unsupervised classification of remote multispectral sensing data

NASA Technical Reports Server (NTRS)

Su, M. Y.

1972-01-01

The new unsupervised classification technique for classifying multispectral remote sensing data which can be either from the multispectral scanner or digitized color-separation aerial photographs consists of two parts: (a) a sequential statistical clustering which is a one-pass sequential variance analysis and (b) a generalized K-means clustering. In this composite clustering technique, the output of (a) is a set of initial clusters which are input to (b) for further improvement by an iterative scheme. Applications of the technique using an IBM-7094 computer on multispectral data sets over Purdue's Flight Line C-1 and the Yellowstone National Park test site have been accomplished. Comparisons between the classification maps by the unsupervised technique and the supervised maximum liklihood technique indicate that the classification accuracies are in agreement.
Architecture of Eph receptor clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Himanen, Juha P.; Yermekbayeva, Laila; Janes, Peter W.

2010-10-04

Eph receptor tyrosine kinases and their ephrin ligands regulate cell navigation during normal and oncogenic development. Signaling of Ephs is initiated in a multistep process leading to the assembly of higher-order signaling clusters that set off bidirectional signaling in interacting cells. However, the structural and mechanistic details of this assembly remained undefined. Here we present high-resolution structures of the complete EphA2 ectodomain and complexes with ephrin-A1 and A5 as the base unit of an Eph cluster. The structures reveal an elongated architecture with novel Eph/Eph interactions, both within and outside of the Eph ligand-binding domain, that suggest the molecular mechanismmore » underlying Eph/ephrin clustering. Structure-function analysis, by using site-directed mutagenesis and cell-based signaling assays, confirms the importance of the identified oligomerization interfaces for Eph clustering.« less
Pattern Activity Clustering and Evaluation (PACE)

NASA Astrophysics Data System (ADS)

Blasch, Erik; Banas, Christopher; Paul, Michael; Bussjager, Becky; Seetharaman, Guna

2012-06-01

With the vast amount of network information available on activities of people (i.e. motions, transportation routes, and site visits) there is a need to explore the salient properties of data that detect and discriminate the behavior of individuals. Recent machine learning approaches include methods of data mining, statistical analysis, clustering, and estimation that support activity-based intelligence. We seek to explore contemporary methods in activity analysis using machine learning techniques that discover and characterize behaviors that enable grouping, anomaly detection, and adversarial intent prediction. To evaluate these methods, we describe the mathematics and potential information theory metrics to characterize behavior. A scenario is presented to demonstrate the concept and metrics that could be useful for layered sensing behavior pattern learning and analysis. We leverage work on group tracking, learning and clustering approaches; as well as utilize information theoretical metrics for classification, behavioral and event pattern recognition, and activity and entity analysis. The performance evaluation of activity analysis supports high-level information fusion of user alerts, data queries and sensor management for data extraction, relations discovery, and situation analysis of existing data.
Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

PubMed Central

Jusakul, Apinya; Cutcutache, Ioana; Yong, Chern Han; Lim, Jing Quan; Huang, Mi Ni; Padmanabhan, Nisha; Nellore, Vishwa; Kongpetch, Sarinya; Ng, Alvin Wei Tian; Ng, Ley Moy; Choo, Su Pin; Myint, Swe Swe; Thanan, Raynoo; Nagarajan, Sanjanaa; Lim, Weng Khong; Ng, Cedric Chuan Young; Boot, Arnoud; Liu, Mo; Ong, Choon Kiat; Rajasegaran, Vikneswari; Lie, Stefanus; Lim, Alvin Soon Tiong; Lim, Tse Hui; Tan, Jing; Loh, Jia Liang; McPherson, John R.; Khuntikeo, Narong; Bhudhisawasdi, Vajaraphongsa; Yongvanit, Puangrat; Wongkham, Sopit; Totoki, Yasushi; Nakamura, Hiromi; Arai, Yasuhito; Yamasaki, Satoshi; Chow, Pierce Kah-Hoe; Chung, Alexander Yaw Fui; Ooi, London Lucien Peng Jin; Lim, Kiat Hon; Dima, Simona; Duda, Dan G.; Popescu, Irinel; Broet, Philippe; Hsieh, Sen-Yung; Yu, Ming-Chin; Scarpa, Aldo; Lai, Jiaming; Luo, Di-Xian; Carvalho, André Lopes; Vettore, André Luiz; Rhee, Hyungjin; Park, Young Nyun; Alexandrov, Ludmil B.; Gordân, Raluca; Rozen, Steven G.; Shibata, Tatsuhiro; Pairojkul, Chawalit; Teh, Bin Tean; Tan, Patrick

2017-01-01

Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analysed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined four CCA clusters – Fluke-Positive CCAs (Clusters 1/2) are enriched in ERBB2 amplifications and TP53 mutations, conversely Fluke-Negative CCAs (Clusters 3/4) exhibit high copy-number alterations and PD-1/PD-L2 expression, or epigenetic mutations (IDH1/2, BAP1) and FGFR/PRKA-related gene rearrangements. Whole-genome analysis highlighted FGFR2 3′UTR deletion as a mechanism of FGFR2 upregulation. Integration of non-coding promoter mutations with protein-DNA binding profiles demonstrates pervasive modulation of H3K27me3-associated sites in CCA. Clusters 1 and 4 exhibit distinct DNA hypermethylation patterns targeting either CpG islands or shores – mutation signature and subclonality analysis suggests that these reflect different mutational pathways. Our results exemplify how genetics, epigenetics and environmental carcinogens can interplay across different geographies to generate distinct molecular subtypes of cancer. PMID:28667006
DOE Office of Scientific and Technical Information (OSTI.GOV)

Jusakul, Apinya; Cutcutache, Ioana; Yong, Chern Han

Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analysed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined four CCA clusters - Fluke- Positive CCAs (Clusters 1/2) are enriched in ERBB2 amplifications and TP53 mutations, conversely Fluke-Negative CCAs (Clusters 3/4) exhibit high copy-number alterations and PD-1/PD-L2 expression, or epigenetic mutations (IDH1/2, BAP1) and FGFR/PRKA-related gene rearrangements. Whole-genome analysis highlighted FGFR2 3’UTR deletion as a mechanism of FGFR2 upregulation. Integration of non-coding promoter mutations with protein-DNA binding profiles demonstrates pervasive modulation ofmore » H3K27me3-associated sites in CCA. Clusters 1 and 4 exhibit distinct DNA hypermethylation patterns targeting either CpG islands or shores - mutation signature and subclonality analysis suggests that these reflect different mutational pathways. Lastly, our results exemplify how genetics, epigenetics and environmental carcinogens can interplay across different geographies to generate distinct molecular subtypes of cancer.« less
Ecological characteristics of Simulium breeding sites in West Africa.

PubMed

Cheke, Robert A; Young, Stephen; Garms, Rolf

2017-03-01

Twenty-nine taxa of Simulium were identified amongst 527 collections of larvae and pupae from untreated rivers and streams in Liberia (362 collections in 1967-71 & 1989), Togo (125 in 1979-81), Benin (35 in 1979-81) and Ghana (5 in 1980-81). Presence or absence of associations between different taxa were used to group them into six clusters using Ward agglomerative hierarchical cluster analysis. Environmental data associated with the pre-imaginal habitats were then analysed in relation to the six clusters by one way ANOVA. The results revealed significant effects in determining the clusters of maximum river width (all P<0.001 unless stated otherwise), water temperature, dry bulb air temperature, relative humidity, altitude, type of water (on a range from trickle to large river), water level, slope, current, vegetation, light conditions, discharge, length of breeding area, environs, terrain, river bed type (P<0.01), and the supports to which the insects were attached (P<0.01). When four non-significant contributors (wet bulb temperature, river features, height of waterfall and depth) were excluded and the reduced data-set analysed by principal components analysis (PCA), the first two principal components (PCs) accounted for 87% of the variance, with geographical features dominant in PC1 and hydrological characteristics in PC2. The analyses also revealed the ecological characteristics of each taxon's pre-imaginal habitats, which are discussed with particular reference to members of the Simulium damnosum species complex, whose breeding site distributions were further analysed by canonical correspondence analysis (CCA), a method also applied to the data on non-vector species. Copyright © 2016 Elsevier B.V. All rights reserved.
Symptom clusters in women with breast cancer: an analysis of data from social media and a research study

PubMed Central

Marshall, Sarah A.; Yang, Christopher C.; Ping, Qing; Zhao, Mengnan; Avis, Nancy E.

2016-01-01

Purpose User-generated content on social media sites, such as health-related online forums, offers researchers a tantalizing amount of information, but concerns regarding scientific application of such data remain. This paper compares and contrasts symptom cluster patterns derived from messages on a breast cancer forum with those from a symptom checklist completed by breast cancer survivors participating in a research study. Methods Over 50,000 messages generated by 12,991 users of the breast cancer forum on MedHelp.org were transformed into a standard form and examined for the co-occurrence of 25 symptoms. The k-medoid clustering method was used to determine appropriate placement of symptoms within clusters. Findings were compared with a similar analysis of a symptom checklist administered to 653 breast cancer survivors participating in a research study. Results The following clusters were identified using forum data: menopausal/psychological, pain/fatigue, gastrointestinal, and miscellaneous. Study data generated the clusters: menopausal, pain, fatigue/sleep/gastrointestinal, psychological, and increased weight/appetite. Although the clusters are somewhat different, many symptoms that clustered together in the social media analysis remained together in the analysis of the study participants. Density of connections between symptoms, as reflected by rates of co-occurrence and similarity, was higher in the study data. Conclusions The copious amount of data generated by social media outlets can augment findings from traditional data sources. When different sources of information are combined, areas of overlap and discrepancy can be detected, perhaps giving researchers a more accurate picture of reality. However, data derived from social media must be used carefully and with understanding of its limitations. PMID:26476836
Symptom clusters in women with breast cancer: an analysis of data from social media and a research study.

PubMed

Marshall, Sarah A; Yang, Christopher C; Ping, Qing; Zhao, Mengnan; Avis, Nancy E; Ip, Edward H

2016-03-01

User-generated content on social media sites, such as health-related online forums, offers researchers a tantalizing amount of information, but concerns regarding scientific application of such data remain. This paper compares and contrasts symptom cluster patterns derived from messages on a breast cancer forum with those from a symptom checklist completed by breast cancer survivors participating in a research study. Over 50,000 messages generated by 12,991 users of the breast cancer forum on MedHelp.org were transformed into a standard form and examined for the co-occurrence of 25 symptoms. The k-medoid clustering method was used to determine appropriate placement of symptoms within clusters. Findings were compared with a similar analysis of a symptom checklist administered to 653 breast cancer survivors participating in a research study. The following clusters were identified using forum data: menopausal/psychological, pain/fatigue, gastrointestinal, and miscellaneous. Study data generated the clusters: menopausal, pain, fatigue/sleep/gastrointestinal, psychological, and increased weight/appetite. Although the clusters are somewhat different, many symptoms that clustered together in the social media analysis remained together in the analysis of the study participants. Density of connections between symptoms, as reflected by rates of co-occurrence and similarity, was higher in the study data. The copious amount of data generated by social media outlets can augment findings from traditional data sources. When different sources of information are combined, areas of overlap and discrepancy can be detected, perhaps giving researchers a more accurate picture of reality. However, data derived from social media must be used carefully and with understanding of its limitations.
A new clustering algorithm applicable to multispectral and polarimetric SAR images

NASA Technical Reports Server (NTRS)

Wong, Yiu-Fai; Posner, Edward C.

1993-01-01

We describe an application of a scale-space clustering algorithm to the classification of a multispectral and polarimetric SAR image of an agricultural site. After the initial polarimetric and radiometric calibration and noise cancellation, we extracted a 12-dimensional feature vector for each pixel from the scattering matrix. The clustering algorithm was able to partition a set of unlabeled feature vectors from 13 selected sites, each site corresponding to a distinct crop, into 13 clusters without any supervision. The cluster parameters were then used to classify the whole image. The classification map is much less noisy and more accurate than those obtained by hierarchical rules. Starting with every point as a cluster, the algorithm works by melting the system to produce a tree of clusters in the scale space. It can cluster data in any multidimensional space and is insensitive to variability in cluster densities, sizes and ellipsoidal shapes. This algorithm, more powerful than existing ones, may be useful for remote sensing for land use.
Vaccines for preventing anthrax.

PubMed

Donegan, Sarah; Bellamy, Richard; Gamble, Carrol L

2009-04-15

Anthrax is a bacterial zoonosis that occasionally causes human disease and is potentially fatal. Anthrax vaccines include a live-attenuated vaccine, an alum-precipitated cell-free filtrate vaccine, and a recombinant protein vaccine. To evaluate the effectiveness, immunogenicity, and safety of vaccines for preventing anthrax. We searched the following databases (November 2008): Cochrane Infectious Diseases Group Specialized Register; CENTRAL (The Cochrane Library 2008, Issue 4); MEDLINE; EMBASE; LILACS; and mRCT. We also searched reference lists. We included randomized controlled trials (RCTs) of individuals and cluster-RCTs comparing anthrax vaccine with placebo, other (non-anthrax) vaccines, or no intervention; or comparing administration routes or treatment regimens of anthrax vaccine. Two authors independently considered trial eligibility, assessed risk of bias, and extracted data. We presented cases of anthrax and seroconversion rates using risk ratios (RR) and 95% confidence intervals (CI). We summarized immunoglobulin G (IgG) concentrations using geometric means. We carried out a sensitivity analysis to investigate the effect of clustering on the results from one cluster-RCT. No meta-analysis was undertaken. One cluster-RCT (with 157,259 participants) and four RCTs of individuals (1917 participants) met the inclusion criteria. The cluster-RCT from the former USSR showed that, compared with no vaccine, a live-attenuated vaccine (called STI) protected against clinical anthrax whether given by a needleless device (RR 0.16; 102,737 participants, 154 clusters) or the scarification method (RR 0.25; 104,496 participants, 151 clusters). Confidence intervals were statistically significant in unadjusted calculations, but when a small amount of association within clusters was assumed, the differences were not statistically significant. The four RCTs (of individuals) of inactivated vaccines (anthrax vaccine absorbed and recombinant protective antigen) showed a dose response relationship for the anti-protective antigen IgG antibody titre. Intramuscular administration was associated with fewer injection site reactions than subcutaneous injection, and injection site reaction rates were lower when the dosage interval was longer. One cluster-RCT provides limited evidence that a live-attenuated vaccine is effective in preventing cutaneous anthrax. Vaccines based on anthrax antigens are immunogenic in most vaccinees with few adverse events or reactions. Ongoing randomized controlled trials are investigating the immunogenicity and safety of anthrax vaccines.
A Simple Model for the Earthquake Cycle Combining Self-Organized Criticality with Critical Point Behavior

NASA Astrophysics Data System (ADS)

Newman, W. I.; Turcotte, D. L.

2002-12-01

We have studied a hybrid model combining the forest-fire model with the site-percolation model in order to better understand the earthquake cycle. We consider a square array of sites. At each time step, a "tree" is dropped on a randomly chosen site and is planted if the site is unoccupied. When a cluster of "trees" spans the site (a percolating cluster), all the trees in the cluster are removed ("burned") in a "fire." The removal of the cluster is analogous to a characteristic earthquake and planting "trees" is analogous to increasing the regional stress. The clusters are analogous to the metastable regions of a fault over which an earthquake rupture can propagate once triggered. We find that the frequency-area statistics of the metastable regions are power-law with a negative exponent of two (as in the forest-fire model). This is analogous to the Gutenberg-Richter distribution of seismicity. This "self-organized critical behavior" can be explained in terms of an inverse cascade of clusters. Individual trees move from small to larger clusters until they are destroyed. This inverse cascade of clusters is self-similar and the power-law distribution of cluster sizes has been shown to have an exponent of two. We have quantified the forecasting of the spanning fires using error diagrams. The assumption that "fires" (earthquakes) are quasi-periodic has moderate predictability. The density of trees gives an improved degree of predictability, while the size of the largest cluster of trees provides a substantial improvement in forecasting a "fire."
Position-specific binding of FUS to nascent RNA regulates mRNA length

PubMed Central

Masuda, Akio; Takeda, Jun-ichi; Okuno, Tatsuya; Okamoto, Takaaki; Ohkawara, Bisei; Ito, Mikako; Ishigaki, Shinsuke; Sobue, Gen

2015-01-01

More than half of all human genes produce prematurely terminated polyadenylated short mRNAs. However, the underlying mechanisms remain largely elusive. CLIP-seq (cross-linking immunoprecipitation [CLIP] combined with deep sequencing) of FUS (fused in sarcoma) in neuronal cells showed that FUS is frequently clustered around an alternative polyadenylation (APA) site of nascent RNA. ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing) of RNA polymerase II (RNAP II) demonstrated that FUS stalls RNAP II and prematurely terminates transcription. When an APA site is located upstream of an FUS cluster, FUS enhances polyadenylation by recruiting CPSF160 and up-regulates the alternative short transcript. In contrast, when an APA site is located downstream from an FUS cluster, polyadenylation is not activated, and the RNAP II-suppressing effect of FUS leads to down-regulation of the alternative short transcript. CAGE-seq (cap analysis of gene expression [CAGE] combined with deep sequencing) and PolyA-seq (a strand-specific and quantitative method for high-throughput sequencing of 3' ends of polyadenylated transcripts) revealed that position-specific regulation of mRNA lengths by FUS is operational in two-thirds of transcripts in neuronal cells, with enrichment in genes involved in synaptic activities. PMID:25995189
Structural, electronic, and magnetic properties of Y(n)O (n=2-14) clusters: Density functional study.

PubMed

Yang, Zhi; Xiong, Shi-Jie

2008-09-28

The geometries stability, electronic properties, and magnetism of Y(n)O clusters up to n=14 are systematically studied with density functional theory. In the lowest-energy structures of Y(n)O clusters, the equilibrium site of the oxygen atom gradually moves from an outer site of the cluster, via a surface site, and finally, to an interior site as the number of the Y atoms increases from 2 to 14. Starting from n=12, the O atom falls into the center of the cluster with the Y atoms forming the outer frame. The results show that clusters with n=2, 4, 8, and 12 are more stable than their respective neighbors, and that the total magnetic moments of Y(n)O clusters are all quite small except Y(12)O cluster. The lowest-energy structure of Y(12)O cluster is a perfect icosahedron with a large magnetic moment 6mu(B). In addition, we find that the total magnetic moments are quenched for n=2, 6, and 8 due to the closed-shell electronic configuration. The calculated ionization potentials and electron affinities are in good agreement with the experimental results, which imply that the present theoretical treatments are satisfactory.
LCGTO-Xα model cluster study for the chemisorption of CO on twofold sites of Ni surfaces

NASA Astrophysics Data System (ADS)

Jörg, H.; Rösch, N.

The cluster Ni 2CO is studied as a simplified model for the chemisorption of CO on twofold bridging sites of transition metal surfaces. Using the LCGTO-Xα method we have calculated the potential energy surface for the totally symmetric stretching motion keeping the Ni-Ni distance fixed at the bulk value. The minimum energy is found at a Ni-C distance of 1.72 Å and a C-O bond length of 1.19 Å. The vibrational frequency for the CO bond (1850 cm -1) shows reasonable agreement with EELS data (1810, 1870 cm -1), whereas the (Ni 2)-C frequency of 495 cm -1 is remarkably higher than the experimental values (380, 400 cm -1) indicating an overestimation of the chemisorption bond strength in this simple cluster model. The bonding between CO and Ni is analyzed using orbital correlations, ionization energies and Mulliken population analysis. Important bonding contributions from π backdonation are identified while the a 1 orbital manifold exhibits strong antibonding effects.
LCGTO-Xα model cluster study for the chemisorption of CO on twofold sites of Ni surfaces

NASA Astrophysics Data System (ADS)

Jörg, H.; Rösch, N.

1985-11-01

The cluster Ni 2CO is studied as a simplified model for the chemisorption of CO on twofold bridging sites of transition metal surfaces. Using the LCGTO-Xα method we have calculated the potential energy surface for the totally symmetric stretching motion keeping the NiNi distance fixed at the bulk value. The minimum energy is found at a NiC distance of 1.72 Å and a CO bond length of 1.19 Å. The vibrational frequency for the CO bond (1850 cm -1) shows reasonable agreement with EELS data (1810, 1870 cm -1), whereas the (Ni 2)C frequency of 495 cm -1 is remarkably higher than the experimental values (380, 400 cm -1) indicating an overestimation of the chemisorption bond strength in this simple cluster model. The bonding between CO and Ni is analyzed using orbital correlations, ionization energies and Mulliken population analysis. Important bonding contributions from π backdonation are identified while the a 1orbital manifold exhibits strong antibonding effects.
Biomass, community structure and nutritional status attributes of the deep subsurface microbiota---at Idaho and Hanford sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, D.C.; Ringelberg, D.B.

1991-10-28

The signature lipid biomarker technique based on phospholipid ester-linked fatty acid pattern analysis (PLFA) provides data on the total viable or potentially viable communities without the necessity of: (1) Quantitative recovery from the sediments or (2) The ability to culture the organisms. Analysis of PLFA provides evidence for the nutritional status (starvation and/or unbalanced growth) in situ. PLFA analysis of SSP samples from the INEL and PNL sites vadose zones showed higher biomass at the surface with prominent Actinomyces biomarkers with lower biomasses of stressed microbiota at progressively greater depth. The biomass and community diversity increased at the water tablemore » at both sites. Both these Western sites showed lower viable microbial biomasses than the WSRS samples. Cluster analysis of the total patterns from various sedimentary horizons showed three major consortia of microbes, with surface microbiota related at both sites, low viable biomass sites closely related at both sites, with anaerobic desaturase pathway being predominant at INEL and consortia utilizing predominantly branched saturated and the aerobic desaturase pathway at both sites. Preliminary examination of the consortia recovered from NTS show a clear relationship to water level.« less
Multi-scale visual analysis of time-varying electrocorticography data via clustering of brain regions

DOE PAGES

Murugesan, Sugeerth; Bouchard, Kristofer; Chang, Edward; ...

2017-06-06

There exists a need for effective and easy-to-use software tools supporting the analysis of complex Electrocorticography (ECoG) data. Understanding how epileptic seizures develop or identifying diagnostic indicators for neurological diseases require the in-depth analysis of neural activity data from ECoG. Such data is multi-scale and is of high spatio-temporal resolution. Comprehensive analysis of this data should be supported by interactive visual analysis methods that allow a scientist to understand functional patterns at varying levels of granularity and comprehend its time-varying behavior. We introduce a novel multi-scale visual analysis system, ECoG ClusterFlow, for the detailed exploration of ECoG data. Our systemmore » detects and visualizes dynamic high-level structures, such as communities, derived from the time-varying connectivity network. The system supports two major views: 1) an overview summarizing the evolution of clusters over time and 2) an electrode view using hierarchical glyph-based design to visualize the propagation of clusters in their spatial, anatomical context. We present case studies that were performed in collaboration with neuroscientists and neurosurgeons using simulated and recorded epileptic seizure data to demonstrate our system's effectiveness. ECoG ClusterFlow supports the comparison of spatio-temporal patterns for specific time intervals and allows a user to utilize various clustering algorithms. Neuroscientists can identify the site of seizure genesis and its spatial progression during various the stages of a seizure. Our system serves as a fast and powerful means for the generation of preliminary hypotheses that can be used as a basis for subsequent application of rigorous statistical methods, with the ultimate goal being the clinical treatment of epileptogenic zones.« less
Infrared spectroscopy reveals both qualitative and quantitative differences in equine subchondral bone during maturation

NASA Astrophysics Data System (ADS)

Kobrina, Yevgeniya; Isaksson, Hanna; Sinisaari, Miikka; Rieppo, Lassi; Brama, Pieter A.; van Weeren, René; Helminen, Heikki J.; Jurvelin, Jukka S.; Saarakkala, Simo

2010-11-01

The collagen phase in bone is known to undergo major changes during growth and maturation. The objective of this study is to clarify whether Fourier transform infrared (FTIR) microspectroscopy, coupled with cluster analysis, can detect quantitative and qualitative changes in the collagen matrix of subchondral bone in horses during maturation and growth. Equine subchondral bone samples (n = 29) from the proximal joint surface of the first phalanx are prepared from two sites subjected to different loading conditions. Three age groups are studied: newborn (0 days old), immature (5 to 11 months old), and adult (6 to 10 years old) horses. Spatial collagen content and collagen cross-link ratio are quantified from the spectra. Additionally, normalized second derivative spectra of samples are clustered using the k-means clustering algorithm. In quantitative analysis, collagen content in the subchondral bone increases rapidly between the newborn and immature horses. The collagen cross-link ratio increases significantly with age. In qualitative analysis, clustering is able to separate newborn and adult samples into two different groups. The immature samples display some nonhomogeneity. In conclusion, this is the first study showing that FTIR spectral imaging combined with clustering techniques can detect quantitative and qualitative changes in the collagen matrix of subchondral bone during growth and maturation.
IR signature of the photoionization-induced hydrophobic-->hydrophilic site switching in phenol-Arn clusters

NASA Astrophysics Data System (ADS)

Ishiuchi, Shun-ichi; Sakai, Makoto; Tsuchida, Yuji; Takeda, Akihiro; Kawashima, Yasutake; Dopfer, Otto; Müller-Dethlefs, Klaus; Fujii, Masaaki

2007-09-01

IR spectra of phenol-Arn (PhOH-Arn) clusters with n =1 and 2 were measured in the neutral and cationic electronic ground states in order to determine the preferential intermolecular ligand binding motifs, hydrogen bonding (hydrophilic interaction) versus π bonding (hydrophobic interaction). Analysis of the vibrational frequencies of the OH stretching motion, νOH, observed in nanosecond IR spectra demonstrates that neutral PhOH-Ar and PhOH -Ar2 as well as cationic PhOH +-Ar have a π-bound structure, in which the Ar atoms bind to the aromatic ring. In contrast, the PhOH +-Ar2 cluster cation is concluded to have a H-bound structure, in which one Ar atom is hydrogen-bonded to the OH group. This π →H binding site switching induced by ionization was directly monitored in real time by picosecond time-resolved IR spectroscopy. The π-bound νOH band is observed just after the ionization and disappears simultaneously with the appearance of the H-bound νOH band. The analysis of the picosecond IR spectra demonstrates that (i) the π →H site switching is an elementary reaction with a time constant of ˜7ps, which is roughly independent of the available internal vibrational energy, (ii) the barrier for the isomerization reaction is rather low(<100cm-1), (iii) both the position and the width of the H-bound νOH band change with the delay time, and the time evolution of these spectral changes can be rationalized by intracluster vibrational energy redistribution occurring after the site switching. The observation of the ionization-induced switch from π bonding to H bonding in the PhOH +-Ar2 cation corresponds to the first manifestation of an intermolecular isomerization reaction in a charged aggregate.
Analysis of a two-domain binding site for the urokinase-type plasminogen activator-plasminogen activator inhibitor-1 complex in low-density-lipoprotein-receptor-related protein.

PubMed

Andersen, O M; Petersen, H H; Jacobsen, C; Moestrup, S K; Etzerodt, M; Andreasen, P A; Thøgersen, H C

2001-07-01

The low-density-lipoprotein-receptor (LDLR)-related protein (LRP) is composed of several classes of domains, including complement-type repeats (CR), which occur in clusters that contain binding sites for a multitude of different ligands. Each approximately 40-residue CR domain contains three conserved disulphide linkages and an octahedral Ca(2+) cage. LRP is a scavenging receptor for ligands from extracellular fluids, e.g. alpha(2)-macroglobulin (alpha(2)M)-proteinase complexes, lipoprotein-containing particles and serine proteinase-inhibitor complexes, like the complex between urokinase-type plasminogen activator (uPA) and the plasminogen activator inhibitor-1 (PAI-1). In the present study we analysed the interaction of the uPA-PAI-1 complex with an ensemble of fragments representing a complete overlapping set of two-domain fragments accounting for the ligand-binding cluster II (CR3-CR10) of LRP. By ligand blotting, solid-state competition analysis and surface-plasmon-resonance analysis, we demonstrate binding to multiple CR domains, but show a preferential interaction between the uPA-PAI-1 complex and a two-domain fragment comprising CR domains 5 and 6 of LRP. We demonstrate that surface-exposed aspartic acid and tryptophan residues at identical positions in the two homologous domains, CR5 and CR6 (Asp(958,CR5), Asp(999,CR6), Trp(953,CR5) and Trp(994,CR6)), are critical for the binding of the complex as well as for the binding of the receptor-associated protein (RAP) - the folding chaperone/escort protein required for transport of LRP to the cell surface. Accordingly, the present work provides (1) an identification of a preferred binding site within LRP CR cluster II; (2) evidence that the uPA-PAI-1 binding site involves residues from two adjacent protein domains; and (3) direct evidence identifying specific residues as important for the binding of uPA-PAI-1 as well as for the binding of RAP.

Factors influencing epibenthic assemblages in the Minho Estuary (NW Iberian Peninsula).

PubMed

Costa-Dias, Sérgia; Freitas, Vânia; Sousa, Ronaldo; Antunes, Carlos

2010-01-01

The epibenthic community of the Minho Estuary was studied during the summer of 2006. Diversity was generally low and a total of 14 fish and five crustacean taxa were identified. Multivariate analysis revealed two site clusters (A and B). Water conductivity and percentage of fine sand were the abiotic variables that most contributed to the spatial distinction between clusters. The species contributing the most to the average similarity within Cluster A were Crangon crangon and Pomatoschistus microps, while in Cluster B was Atyaephyra desmarestii. Possible factors responsible for the low diversity of the epibenthic community in Minho Estuary were the low macrozoobenthic abundance and diversity, and the high abiotic oscillations between tides (mainly salinity) acting on the ecosystem. Copyright 2010 Elsevier Ltd. All rights reserved.
Conformational Clusters of Phosphorylated Tyrosine.

PubMed

Abdelrasoul, Maha; Ponniah, Komala; Mao, Alice; Warden, Meghan S; Elhefnawy, Wessam; Li, Yaohang; Pascal, Steven M

2017-12-06

Tyrosine phosphorylation plays an important role in many cellular and intercellular processes including signal transduction, subcellular localization, and regulation of enzymatic activity. In 1999, Blom et al., using the limited number of protein data bank (PDB) structures available at that time, reported that the side chain structures of phosphorylated tyrosine (pY) are partitioned into two conserved conformational clusters ( Blom, N.; Gammeltoft, S.; Brunak, S. J. Mol. Biol. 1999 , 294 , 1351 - 1362 ). We have used the spectral clustering algorithm to cluster the increasingly growing number of protein structures with pY sites, and have found that the pY residues cluster into three distinct side chain conformations. Two of these pY conformational clusters associate strongly with a narrow range of tyrosine backbone conformation. The novel cluster also highly correlates with the identity of the n + 1 residue, and is strongly associated with a sequential pYpY conformation which places two adjacent pY side chains in a specific relative orientation. Further analysis shows that the three pY clusters are associated with distinct distributions of cognate protein kinases.
Mapping of terrain by computer clustering techniques using multispectral scanner data and using color aerial film

NASA Technical Reports Server (NTRS)

Smedes, H. W.; Linnerud, H. J.; Woolaver, L. B.; Su, M. Y.; Jayroe, R. R.

1972-01-01

Two clustering techniques were used for terrain mapping by computer of test sites in Yellowstone National Park. One test was made with multispectral scanner data using a composite technique which consists of (1) a strictly sequential statistical clustering which is a sequential variance analysis, and (2) a generalized K-means clustering. In this composite technique, the output of (1) is a first approximation of the cluster centers. This is the input to (2) which consists of steps to improve the determination of cluster centers by iterative procedures. Another test was made using the three emulsion layers of color-infrared aerial film as a three-band spectrometer. Relative film densities were analyzed using a simple clustering technique in three-color space. Important advantages of the clustering technique over conventional supervised computer programs are (1) human intervention, preparation time, and manipulation of data are reduced, (2) the computer map, gives unbiased indication of where best to select the reference ground control data, (3) use of easy to obtain inexpensive film, and (4) the geometric distortions can be easily rectified by simple standard photogrammetric techniques.
Site-Specific Biomolecule Labeling with Gold Clusters

PubMed Central

Ackerson, Christopher J.; Powell, Richard D.; Hainfeld, James F.

2013-01-01

Site-specific labeling of biomolecules in vitro with gold clusters can enhance the information content of electron cryomicroscopy experiments. This chapter provides a practical overview of well-established techniques for forming biomolecule/gold cluster conjugates. Three bioconjugation chemistries are covered: Linker-mediated bioconjugation, direct gold–biomolecule bonding, and coordination-mediated bonding of nickel(II) nitrilotriacetic acid (NTA)-derivatized gold clusters to polyhistidine (His)-tagged proteins. PMID:20887859
Density functional theory and surface reactivity study of bimetallic AgnYm (n+m = 10) clusters

NASA Astrophysics Data System (ADS)

Hussain, Riaz; Hussain, Abdullah Ijaz; Chatha, Shahzad Ali Shahid; Hussain, Riaz; Hanif, Usman; Ayub, Khurshid

2018-06-01

Density functional theory calculations have been performed on pure silver (Agn), yttrium (Ym) and bimetallic silver yttrium clusters AgnYm (n + m = 2-10) for reactivity descriptors in order to realize sites for nucleophilic and electrophilic attack. The reactivity descriptors of the clusters, studied as a function of cluster size and shape, reveal the presence of different type of reactive sites in a cluster. The size and shape of the pure silver, yttrium and bimetallic silver yttrium cluster (n = 2-10) strongly influences the number and position of active sites for an electrophilic and/or nucleophilic attack. The trends of reactivities through reactivity descriptors are confirmed through comparison with experimental data for CO binding with silver clusters. Moreover, the adsorption of CO on bimetallic silver yttrium clusters is also evaluated. The trends of binding energies support the reactivity descriptors values. Doping of pure cluster with the other element also influence the hardness, softness and chemical reactivity of the clusters. The softness increases as we increase the number of silver atoms in the cluster, whereas the hardness decreases. The chemical reactivity increases with silver doping whereas it decreases by increasing yttrium concentration. Silver atoms are nucleophilic in small clusters but changed to electrophilic in large clusters.
The Effects of Cumulative Violence Clusters on Young Mothers' School Participation: Examining Attention and Behavior Problems as Mediators.

PubMed

Kennedy, Angie C; Adams, Adrienne E

2016-04-01

Using a cluster analysis approach with a sample of 205 young mothers recruited from community sites in an urban Midwestern setting, we examined the effects of cumulative violence exposure (community violence exposure, witnessing intimate partner violence, physical abuse by a caregiver, and sexual victimization, all with onset prior to age 13) on school participation, as mediated by attention and behavior problems in school. We identified five clusters of cumulative exposure, and found that the HiAll cluster (high levels of exposure to all four types) consistently fared the worst, with significantly higher attention and behavior problems, and lower school participation, in comparison with the LoAll cluster (low levels of exposure to all types). Behavior problems were a significant mediator of the effects of cumulative violence exposure on school participation, but attention problems were not. © The Author(s) 2014.
Single Molecule Cluster Analysis Identifies Signature Dynamic Conformations along the Splicing Pathway

PubMed Central

Blanco, Mario R.; Martin, Joshua S.; Kahlscheuer, Matthew L.; Krishnan, Ramya; Abelson, John; Laederach, Alain; Walter, Nils G.

2016-01-01

The spliceosome is the dynamic RNA-protein machine responsible for faithfully splicing introns from precursor messenger RNAs (pre-mRNAs). Many of the dynamic processes required for the proper assembly, catalytic activation, and disassembly of the spliceosome as it acts on its pre-mRNA substrate remain poorly understood, a challenge that persists for many biomolecular machines. Here, we developed a fluorescence-based Single Molecule Cluster Analysis (SiMCAn) tool to dissect the manifold conformational dynamics of a pre-mRNA through the splicing cycle. By clustering common dynamic behaviors derived from selectively blocked splicing reactions, SiMCAn was able to identify signature conformations and dynamic behaviors of multiple ATP-dependent intermediates. In addition, it identified a conformation adopted late in splicing by a 3′ splice site mutant, invoking a mechanism for substrate proofreading. SiMCAn presents a novel framework for interpreting complex single molecule behaviors that should prove widely useful for the comprehensive analysis of a plethora of dynamic cellular machines. PMID:26414013
This is like that, only bigger and messier

USDA-ARS?s Scientific Manuscript database

Cluster analysis is a core tool of vegetation science; we have always wanted to divide a complex world into manageable chunks. In vegetation science, we classify both vegetation and sites. Both have clear management applications. Various types of spatial classifications are used to delineate agroec...
Protonation/reduction dynamics at the [4Fe-4S] cluster of the hydrogen-forming cofactor in [FeFe]-hydrogenases.

PubMed

Senger, Moritz; Mebs, Stefan; Duan, Jifu; Shulenina, Olga; Laun, Konstantin; Kertess, Leonie; Wittkamp, Florian; Apfel, Ulf-Peter; Happe, Thomas; Winkler, Martin; Haumann, Michael; Stripp, Sven T

2018-01-31

The [FeFe]-hydrogenases of bacteria and algae are the most efficient hydrogen conversion catalysts in nature. Their active-site cofactor (H-cluster) comprises a [4Fe-4S] cluster linked to a unique diiron site that binds three carbon monoxide (CO) and two cyanide (CN - ) ligands. Understanding microbial hydrogen conversion requires elucidation of the interplay of proton and electron transfer events at the H-cluster. We performed real-time spectroscopy on [FeFe]-hydrogenase protein films under controlled variation of atmospheric gas composition, sample pH, and reductant concentration. Attenuated total reflection Fourier-transform infrared spectroscopy was used to monitor shifts of the CO/CN - vibrational bands in response to redox and protonation changes. Three different [FeFe]-hydrogenases and several protein and cofactor variants were compared, including element and isotopic exchange studies. A protonated equivalent (HoxH) of the oxidized state (Hox) was found, which preferentially accumulated at acidic pH and under reducing conditions. We show that the one-electron reduced state Hred' represents an intrinsically protonated species. Interestingly, the formation of HoxH and Hred' was independent of the established proton pathway to the diiron site. Quantum chemical calculations of the respective CO/CN - infrared band patterns favored a cysteine ligand of the [4Fe-4S] cluster as the protonation site in HoxH and Hred'. We propose that proton-coupled electron transfer facilitates reduction of the [4Fe-4S] cluster and prevents premature formation of a hydride at the catalytic diiron site. Our findings imply that protonation events both at the [4Fe-4S] cluster and at the diiron site of the H-cluster are important in the hydrogen conversion reaction of [FeFe]-hydrogenases.
Elemental Mixing State of Aerosol Particles Collected in Central Amazonia during GoAmazon2014/15

DOE PAGES

Fraund, Matthew; Pham, Don; Bonanno, Daniel; ...

2017-09-15

Two complementary techniques, Scanning Transmission X-ray Microscopy/Near Edge Fine Structure spectroscopy (STXM/NEXAFS) and Scanning Electron Microscopy/Energy Dispersive X-ray spectroscopy (SEM/EDX), have been quantitatively combined to characterize individual atmospheric particles. This pair of techniques was applied to particle samples at three sampling sites (ATTO, ZF2, and T3) in the Amazon basin as part of the Observations and Modeling of the Green Ocean Amazon (GoAmazon2014/5) field campaign during the dry season of 2014. The combined data was subjected to k-means clustering using mass fractions of the following elements: C, N, O, Na, Mg, P, S, Cl, K, Ca, Mn, Fe, Ni, andmore » Zn. Cluster analysis identified 12 particle types, across different sampling sites and particle sizes. Samples from the remote Amazon Tall Tower Observatory (ATTO, also T0a) exhibited less cluster variety and fewer anthropogenic clusters than samples collected at the sites nearer to the Manaus metropolitan region, ZF2 (also T0t) or T3. Samples from the ZF2 site contained aged/anthropogenic clusters not readily explained by transport from ATTO or Manaus, possibly suggesting the effects of long range atmospheric transport or other local aerosol sources present during sampling. In addition, this data set allowed for recently established diversity parameters to be calculated. All sample periods had high mixing state indices (χ) that were >0.8. Two individual particle diversity (D i) populations were observed, with particles <0.5 μm having a D i of ~2.4 and >0.5 μm particles having a D i of ~3.6, which likely correspond to fresh and aged aerosols respectively. The diversity parameters determined by the quantitative method presented here will serve to aid in the accurate representation of aerosol mixing state, source apportionment, and aging in both less polluted and more industrialized environments in the Amazon Basin.« less
Effects of Vegetation Composition and Trophic Structure on Pathways of Mercury Methylation in Alaskan Peatlands

NASA Astrophysics Data System (ADS)

Hines, M. E.; Zhang, L.; Barkay, T.; Krabbenhoft, D. P.; Liu, X.

2016-12-01

Methyl mercury (MeHg) can be produced by diverse microbes including syntrophs, methanogens, and fermenters, besides sulfate (SO42-, SRB) and iron- reducing bacteria. Many freshwater wetlands are deficient in electron acceptors that support the traditional respiratory pathways of methylation, yet high levels of MeHg can accumulate. To investigate methylation pathways in these wetlands and to connect these pathways with surface vegetation and microbial communities, experiments were conducted using peats from 28 sites in Alaska collected during the summer of 2015. The sites were clustered using multiple factor analysis based on pH, temp, CH4 and volatile fatty acids production rates, and surface vegetation composition. Three clusters were generated and corresponded to three trophic levels that were manifested by three pH levels (4.2, 5.3, and 5.8). Hg methylation activity in laboratory incubations was determined using the short-lived radioisotope 197Hg. In the low pH, Sphagnum fuscum dominated cluster, methylation rates were less than 0.1% day-1. Conversely, the high pH trophic cluster dominated by Carex aquatilis, Carex tenuiflora, and active syntrophy, exhibited Hg methylation rates as high as 10% day-1. In intermediate sites, rich in Sphagnum magellanicum with less Carex, a gradient in syntrophy and Hg methylation paths was observed. Amendments with SO42- showed very active sulfate reduction but no stimulation of methylation; another set of amendments with methanogenic inhibitors greatly reduced methylation rates at intermediate and high trophic clusters. These results suggested that SRB, metabolizing either syntrophically with methanogens and/or by fermentation, likely methylated Hg. While metatranscriptomics studies are being conducted to verify the role of syntrophs, fermenters, and methanogens as methylators, these incubation results revealed that Hg methylation pathways change greatly along trophic gradients with a dominance of respiratory pathways in rich fens, syntrophy dominance in intermediate sites, and fermentation dominance in poor bogs.
Elemental Mixing State of Aerosol Particles Collected in Central Amazonia during GoAmazon2014/15

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fraund, Matthew; Pham, Don; Bonanno, Daniel

Two complementary techniques, Scanning Transmission X-ray Microscopy/Near Edge Fine Structure spectroscopy (STXM/NEXAFS) and Scanning Electron Microscopy/Energy Dispersive X-ray spectroscopy (SEM/EDX), have been quantitatively combined to characterize individual atmospheric particles. This pair of techniques was applied to particle samples at three sampling sites (ATTO, ZF2, and T3) in the Amazon basin as part of the Observations and Modeling of the Green Ocean Amazon (GoAmazon2014/5) field campaign during the dry season of 2014. The combined data was subjected to k-means clustering using mass fractions of the following elements: C, N, O, Na, Mg, P, S, Cl, K, Ca, Mn, Fe, Ni, andmore » Zn. Cluster analysis identified 12 particle types, across different sampling sites and particle sizes. Samples from the remote Amazon Tall Tower Observatory (ATTO, also T0a) exhibited less cluster variety and fewer anthropogenic clusters than samples collected at the sites nearer to the Manaus metropolitan region, ZF2 (also T0t) or T3. Samples from the ZF2 site contained aged/anthropogenic clusters not readily explained by transport from ATTO or Manaus, possibly suggesting the effects of long range atmospheric transport or other local aerosol sources present during sampling. In addition, this data set allowed for recently established diversity parameters to be calculated. All sample periods had high mixing state indices (χ) that were >0.8. Two individual particle diversity (D i) populations were observed, with particles <0.5 μm having a D i of ~2.4 and >0.5 μm particles having a D i of ~3.6, which likely correspond to fresh and aged aerosols respectively. The diversity parameters determined by the quantitative method presented here will serve to aid in the accurate representation of aerosol mixing state, source apportionment, and aging in both less polluted and more industrialized environments in the Amazon Basin.« less
Endocytic pathway rapidly delivers internalized molecules to lysosomes: an analysis of vesicle trafficking, clustering and mass transfer.

PubMed

Pangarkar, Chinmay; Dinh, Anh-Tuan; Mitragotri, Samir

2012-08-20

Lysosomes play a critical role in intracellular drug delivery. For enzyme-based therapies, they represent a potential target site whereas for nucleic acid or many protein drugs, they represent the potential degradation site. Either way, understanding the mechanisms and processes involved in routing of materials to lysosomes after cellular entry is of high interest to the field of drug delivery. Most therapeutic cargoes other than small hydrophobic molecules enter the cells through endocytosis. Endocytosed cargoes are routed to lysosomes via microtubule-based transport and are ultimately shared by various lysosomes via tethering and clustering of endocytic vesicles followed by exchange of their contents. Using a combined experimental and numerical approach, here we studied the rates of mass transfer into and among the endocytic vesicles in a model cell line, 3T3 fibroblasts. In order to understand the relationship of mass transfer with microtubular transport and vesicle clustering, we varied both properties through various pharmacological agents. At the same time, microtubular transport and vesicle clustering were modeled through diffusion-advection equations and the Smoluchowski equations, respectively. Our analysis revealed that the rate of mass transfer is optimally related to microtubular transport and clustering properties of vesicles. Further, the rate of mass transfer is highest in the innate state of the cell. Any perturbation to either microtubular transport or vesicle aggregation led to reduced mass transfer to lysosome. These results suggest that in the absence of an external intervention the endocytic pathway appears to maximize molecular delivery to lysosomes. Strategies are discussed to reduce mass transfer to lysosomes so as to extend the residence time of molecules in endosomes or late endosomes, thus potentially increasing the likelihood of their escape before disposition in the lysosomes. Copyright © 2012 Elsevier B.V. All rights reserved.
Bioinformatic analysis of the nucleotide binding site-encoding disease-resistance genes in foxtail millet (Setaria italica (L.) Beauv.).

PubMed

Zhu, Y B; Xie, X Q; Li, Z Y; Bai, H; Dong, L; Dong, Z P; Dong, J G

2014-08-28

The nucleotide-binding site (NBS) disease-resistance genes are the largest category of plant disease-resistance gene analogs. The complete set of disease-resistant candidate genes, which encode the NBS sequence, was filtered in the genomes of two varieties of foxtail millet (Yugu1 and 'Zhang gu'). This study investigated a number of characteristics of the putative NBS genes, such as structural diversity and phylogenetic relationships. A total of 269 and 281 NBS-coding sequences were identified in Yugu1 and 'Zhang gu', respectively. When the two databases were compared, 72 genes were found to be identical and 164 genes showed more than 90% similarity. Physical positioning and gene family analysis of the NBS disease-resistance genes in the genome revealed that the number of genes on each chromosome was similar in both varieties. The eighth chromosome contained the largest number of genes and the ninth chromosome contained the lowest number of genes. Exactly 34 gene clusters containing the 161 genes were found in the Yugu1 genome, with each cluster containing 4.7 genes on average. In comparison, the 'Zhang gu' genome possessed 28 gene clusters, which had 151 genes, with an average of 5.4 genes in each cluster. The largest gene cluster, located on the eighth chromosome, contained 12 genes in the Yugu1 database, whereas it contained 16 genes in the 'Zhang gu' database. The classification results showed that the CC-NBS-LRR gene made up the largest part of each chromosome in the two databases. Two TIR-NBS genes were also found in the Yugu1 genome.
High ozone levels in the northeast of Portugal: Analysis and characterization

NASA Astrophysics Data System (ADS)

Carvalho, A.; Monteiro, A.; Ribeiro, I.; Tchepel, O.; Miranda, A. I.; Borrego, C.; Saavedra, S.; Souto, J. A.; Casares, J. J.

2010-03-01

Each summer period extremely high ozone levels are registered at the rural background station of Lamas d'Olo, located in the Northeast of Portugal. In average, 30% of the total alert threshold registered in Portugal is detected at this site. The main purpose of this study is to characterize the atmospheric conditions that lead to the ozone-rich episodes at this site. Synoptic patterns anomalies and back trajectories cluster analysis were performed, for the period between 2004 and 2007, considering 76 days when ozone maximum hourly concentrations were above 200 μg m -3. The obtained atmospheric anomaly fields suggested that a positive temperature anomaly is visible above the Iberian Peninsula. A strong wind flow pattern from NE is observable in the North of Portugal and Galicia, in Spain. These two features may lead to an enhancement of the photochemical production and to the transport of pollutants from Spain to Portugal. In addition, the 3D mean back trajectories associated to the ozone episode days were analysed. A clustering method has been applied to the obtained back trajectories. Four main clusters of ozone-rich episodes were identified, with different frequencies of occurrence: north-westerly flows (11%); north-easterly flows (45%), southern flow (4%) and westerly flows (40%). Both analyses highlight the NE flow as a dominant pattern over the North of Portugal during summer. The analysis of the ozone concentrations for each selected cluster indicates that this northeast circulation pattern, together with the southern flow, are responsible for the highest ozone peak episodes. This also suggests that long-range transport of atmospheric pollutants is the main contributor to the ozone levels registered at Lamas d'Olo. This is also highlighted by the correlation of the ozone time-series with the meteorological parameters analysed in the frequency domain.
Prediction of tautomer ratios by embedded-cluster integral equation theory

NASA Astrophysics Data System (ADS)

Kast, Stefan M.; Heil, Jochen; Güssregen, Stefan; Schmidt, K. Friedemann

2010-04-01

The "embedded cluster reference interaction site model" (EC-RISM) approach combines statistical-mechanical integral equation theory and quantum-chemical calculations for predicting thermodynamic data for chemical reactions in solution. The electronic structure of the solute is determined self-consistently with the structure of the solvent that is described by 3D RISM integral equation theory. The continuous solvent-site distribution is mapped onto a set of discrete background charges ("embedded cluster") that represent an additional contribution to the molecular Hamiltonian. The EC-RISM analysis of the SAMPL2 challenge set of tautomers proceeds in three stages. Firstly, the group of compounds for which quantitative experimental free energy data was provided was taken to determine appropriate levels of quantum-chemical theory for geometry optimization and free energy prediction. Secondly, the resulting workflow was applied to the full set, allowing for chemical interpretations of the results. Thirdly, disclosure of experimental data for parts of the compounds facilitated a detailed analysis of methodical issues and suggestions for future improvements of the model. Without specifically adjusting parameters, the EC-RISM model yields the smallest value of the root mean square error for the first set (0.6 kcal mol-1) as well as for the full set of quantitative reaction data (2.0 kcal mol-1) among the SAMPL2 participants.
Dissolved heavy metal concentrations of the Kralkızı, Dicle and Batman dam reservoirs in the Tigris River basin, Turkey.

PubMed

Varol, Memet

2013-10-01

Water samples were collected at monthly intervals during 1 year of monitoring from Kralkızı, Dicle and Batman dam reservoirs in the Tigris River basin to assess the concentrations of dissolved heavy metals and to determine their spatial and seasonal variations. The results indicated that dissolved heavy metal concentrations in the reservoirs were very low, reflecting the natural background levels. The lowest total metal concentrations in the three dam reservoirs were detected at sampling sites close to the dam wall. However, the highest total concentrations were observed at sites, which are located at the entrance of the streams to the reservoirs. Fe, Cr and Ni were the most abundant elements in the reservoirs, whereas Cd and As were the less abundant. The mean concentrations of dissolved metals in the dam reservoirs never exceeded the maximum permitted concentrations established by EC (European Community), WHO and USEPA drinking water quality guidelines. All heavy metals showed significant seasonal variations. As, Cd, Cr, Cu, Fe, Ni and Pb displayed higher values in the dry season, while higher values for Zn in the wet season. Cluster analysis grouped all ten sampling sites into three clusters. Clusters 1 and 2, and cluster 3 corresponded to relatively low polluted and moderate polluted regions, respectively. PCA/FA demonstrated the dissolved metals in the dam reservoirs controlled by natural sources. Copyright © 2013 Elsevier Ltd. All rights reserved.
Intraclass Correlations for Three-Level Multi-Site Cluster-Randomized Trials of Science Achievement

ERIC Educational Resources Information Center

Westine, Carl D.

2015-01-01

A cluster-randomized trial (CRT) relies on random assignment of intact clusters to treatment conditions, such as classrooms or schools (Raudenbush & Bryk, 2002). One specific type of CRT, a multi-site CRT (MSCRT), is commonly employed in educational research and evaluation studies (Spybrook & Raudenbush, 2009; Spybrook, 2014; Bloom,…
Untangling Magmatic Processes and Hydrothermal Alteration of in situ Superfast Spreading Ocean Crust at ODP/IODP Site 1256 with Fuzzy c-means Cluster Analysis of Rock Magnetic Properties

NASA Astrophysics Data System (ADS)

Dekkers, M. J.; Heslop, D.; Herrero-Bervera, E.; Acton, G.; Krasa, D.

2014-12-01

Ocean Drilling Program (ODP)/Integrated ODP (IODP) Hole 1256D (6.44.1' N, 91.56.1' W) on the Cocos Plate occurs in 15.2 Ma oceanic crust generated by superfast seafloor spreading. Presently, it is the only drill hole that has sampled all three oceanic crust layers in a tectonically undisturbed setting. Here we interpret down-hole trends in several rock-magnetic parameters with fuzzy c-means cluster analysis, a multivariate statistical technique. The parameters include the magnetization ratio, the coercivity ratio, the coercive force, the low-field susceptibility, and the Curie temperature. By their combined, multivariate, analysis the effects of magmatic and hydrothermal processes can be evaluated. The optimal number of clusters - a key point in the analysis because there is no a priori information on this - was determined through a combination of approaches: by calculation of several cluster validity indices, by testing for coherent cluster distributions on non-linear-map plots, and importantly by testing for stability of the cluster solution from all possible starting points. Here, we consider a solution robust if the cluster allocation is independent of the starting configuration. The five-cluster solution appeared to be robust. Three clusters are distinguished in the extrusive segment of the Hole that express increasing hydrothermal alteration of the lavas. The sheeted dike and gabbro portions are characterized by two clusters, both with higher coercivities than in lava samples. Extensive alteration, however, can obliterate magnetic property differences between lavas, dikes, and gabbros. The imprint of thermochemical alteration on the iron-titanium oxides is only partially related to the porosity of the rocks. All clusters display rock magnetic characteristics in line with a stable NRM. This implies that the entire sampled sequence of ocean crust can contribute to marine magnetic anomalies. Determination of the absolute paleointensity with thermal techniques is not straightforward because of the propensity of oxyexsolution during laboratory heating and/or the presence of intergrowths. The upper part of the extrusive sequence, the granoblastic portion of the dikes, and moderately altered gabbros may contain a comparatively uncontaminated thermoremanent magnetization.
The dynamics of methane emissions in Alaskan peatlands at different trophic levels

NASA Astrophysics Data System (ADS)

Zhang, L.; Liu, X.; Langford, L.; Chanton, J.; Hines, M. E.

2016-12-01

One major uncertainty in estimating methane (CH4) emission from wetlands is extrapolating from highly heterogeneous and inadequately studied local sites to larger scales. The heterogeneity of peatlands comes from contrasting surface vegetation compositions within short distances that are usually associated with different nutrient sources and trophic status. Different microbial communities and metabolic pathways occur at different trophic levels. Stable isotope C ratios (δ13C) have been used as a robust tool to distinguish methanogenic pathways, but different sources of parent compounds (acetate and CO2) with unique δ13C signatures, and unresolved fractionation factors associated with different methanogens, add complexity. To better understand the relationships between trophic status, surface vegetation compositions and methanogenic pathways, 28 peatland sites were studied in Fairbanks and Anchorage, Alaska in the summer of 2015. These sites were ordinated using multiple factor analysis into 3 clusters based on pH, temp, CH4 and volatile fatty acids production rates, δ13C values, and surface vegetation composition. In the low-pH trophic cluster (pH 4.2), Sphagnum fuscum was the dominant species with specific sedges (Ledum decumbens), and primary fermentation rates was slow with no CH4 detected. In the intermediate trophic level (pH 5.3), in which Sphagnum magellanicum was largely present, both hydrogenotrophic (HM) and acetoclastic methanogenesis (AM) were very active. Syntrophy was present at certain sites, which may provide CO2 and acetate with unique δ13C for CH4 production. At the highest pH trophic cluster examined in this study (pH 5.8), Carex tenuiflora, Carex aquatilis, and Sphagnum Squarrosum dominated. CH4 production rates were higher than those in the intermediate cluster and the apparent fractionation factor a was lower.

Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jusakul, Apinya; Cutcutache, Ioana; Yong, Chern Han

Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analysed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined four CCA clusters - Fluke- Positive CCAs (Clusters 1/2) are enriched in ERBB2 amplifications and TP53 mutations, conversely Fluke-Negative CCAs (Clusters 3/4) exhibit high copy-number alterations and PD-1/PD-L2 expression, or epigenetic mutations (IDH1/2, BAP1) and FGFR/PRKA-related gene rearrangements. Whole-genome analysis highlighted FGFR2 3’UTR deletion as a mechanism of FGFR2 upregulation. Integration of non-coding promoter mutations with protein-DNA binding profiles demonstrates pervasive modulation ofmore » H3K27me3-associated sites in CCA. Clusters 1 and 4 exhibit distinct DNA hypermethylation patterns targeting either CpG islands or shores - mutation signature and subclonality analysis suggests that these reflect different mutational pathways. Lastly, our results exemplify how genetics, epigenetics and environmental carcinogens can interplay across different geographies to generate distinct molecular subtypes of cancer.« less
Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

DOE PAGES

Jusakul, Apinya; Cutcutache, Ioana; Yong, Chern Han; ...

2017-06-30

Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analysed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined four CCA clusters - Fluke- Positive CCAs (Clusters 1/2) are enriched in ERBB2 amplifications and TP53 mutations, conversely Fluke-Negative CCAs (Clusters 3/4) exhibit high copy-number alterations and PD-1/PD-L2 expression, or epigenetic mutations (IDH1/2, BAP1) and FGFR/PRKA-related gene rearrangements. Whole-genome analysis highlighted FGFR2 3’UTR deletion as a mechanism of FGFR2 upregulation. Integration of non-coding promoter mutations with protein-DNA binding profiles demonstrates pervasive modulation ofmore » H3K27me3-associated sites in CCA. Clusters 1 and 4 exhibit distinct DNA hypermethylation patterns targeting either CpG islands or shores - mutation signature and subclonality analysis suggests that these reflect different mutational pathways. Lastly, our results exemplify how genetics, epigenetics and environmental carcinogens can interplay across different geographies to generate distinct molecular subtypes of cancer.« less
Site-specific biomolecule labeling with gold clusters.

PubMed

Ackerson, Christopher J; Powell, Richard D; Hainfeld, James F

2010-01-01

Site-specific labeling of biomolecules in vitro with gold clusters can enhance the information content of electron cryomicroscopy experiments. This chapter provides a practical overview of well-established techniques for forming biomolecule/gold cluster conjugates. Three bioconjugation chemistries are covered: linker-mediated bioconjugation, direct gold-biomolecule bonding, and coordination-mediated bonding of nickel(II) nitrilotriacetic acid (NTA)-derivatized gold clusters to polyhistidine (His)-tagged proteins. Copyright © 2010 Elsevier Inc. All rights reserved.
Identification and Validation of Novel Hedgehog-Responsive Enhancers Predicted by Computational Analysis of Ci/Gli Binding Site Density

PubMed Central

Richards, Neil; Parker, David S.; Johnson, Lisa A.; Allen, Benjamin L.; Barolo, Scott; Gumucio, Deborah L.

2015-01-01

The Hedgehog (Hh) signaling pathway directs a multitude of cellular responses during embryogenesis and adult tissue homeostasis. Stimulation of the pathway results in activation of Hh target genes by the transcription factor Ci/Gli, which binds to specific motifs in genomic enhancers. In Drosophila, only a few enhancers (patched, decapentaplegic, wingless, stripe, knot, hairy, orthodenticle) have been shown by in vivo functional assays to depend on direct Ci/Gli regulation. All but one (orthodenticle) contain more than one Ci/Gli site, prompting us to directly test whether homotypic clustering of Ci/Gli binding sites is sufficient to define a Hh-regulated enhancer. We therefore developed a computational algorithm to identify Ci/Gli clusters that are enriched over random expectation, within a given region of the genome. Candidate genomic regions containing Ci/Gli clusters were functionally tested in chicken neural tube electroporation assays and in transgenic flies. Of the 22 Ci/Gli clusters tested, seven novel enhancers (and the previously known patched enhancer) were identified as Hh-responsive and Ci/Gli-dependent in one or both of these assays, including: Cuticular protein 100A (Cpr100A); invected (inv), which encodes an engrailed-related transcription factor expressed at the anterior/posterior wing disc boundary; roadkill (rdx), the fly homolog of vertebrate Spop; the segment polarity gene gooseberry (gsb); and two previously untested regions of the Hh receptor-encoding patched (ptc) gene. We conclude that homotypic Ci/Gli clustering is not sufficient information to ensure Hh-responsiveness; however, it can provide a clue for enhancer recognition within putative Hedgehog target gene loci. PMID:26710299
The Strength of an Ig Switch Region is Determined by its Ability to Drive R-loop Formation and its Number of WGCW Sites

PubMed Central

Zhang, Zheng Z.; Pannunzio, Nicholas R.; Han, Li; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R.

2014-01-01

SUMMARY R-loops exist at the murine IgH switch regions and possibly other locations, but their functional importance is unclear. In biochemical systems, R-loop initiation requires DNA sequence regions containing clusters of G nucleotides, but cellular studies have not been done. Here, we vary the G-clustering, total switch region length, and the number of target sites (WGCW sites for the activation-induced deaminase) at synthetic switch regions in a murine B cell line to determine the effect on class switch recombination (CSR). G-clusters increase CSR, regardless of their immediate proximity to the WGCW sites. This increase is accompanied by an increase in R-loop formation. CSR efficiency correlates better with the absolute number of WGCW sites in the switch region rather than the total switch region length or density of WGCW sites. Thus, the overall strength of the switch region depends on G-clusters, which initiate R-loop formation, and on the number of WGCW sites. PMID:25017067
Magnetic properties of Co-doped Nb clusters

NASA Astrophysics Data System (ADS)

Diaz-Bachs, A.; Peters, L.; Logemann, R.; Chernyy, V.; Bakker, J. M.; Katsnelson, M. I.; Kirilyuk, A.

2018-04-01

Magnetic deflection experiments on isolated Co-doped Nb clusters demonstrate a strong size dependence of magnetic properties, with large magnetic moments in certain cluster sizes and fully nonmagnetic behavior of others. There are in principle two explanations for this behavior. Either the local moment at the Co site is absent or it is screened by the delocalized electrons of the cluster, i.e., the Kondo effect. In order to reveal the physical origin, first, we established the ground state geometry of the clusters by experimentally obtaining their vibrational spectra and comparing them with a density functional theory study. Then, we performed an analysis based on the Anderson impurity model. It appears that the nonmagnetic clusters are due to the absence of the local Co moment and not due to the Kondo effect. In addition, the magnetic behavior of the clusters can be understood from an inspection of their electronic structure. Here magnetism is favored when the effective hybridization around the chemical potential is small, while the absence of magnetism is signaled by a large effective hybridization around the chemical potential.
Template growth of Au, Ni and Ni–Au nanoclusters on hexagonal boron nitride/Rh(111): a combined STM, TPD and AES study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Fanglue; Huang, Dali; Yue, Yuan

In this study, the template growth of Au, Ni, and Ni–Au bimetallic nanoclusters on hexagonal boron nitride/Rh(111), i.e. h-BN/Rh(111), was investigated via scanning tunneling microscopy (STM), temperature programmed-desorption (TPD), and Auger electron spectroscopy (AES). STM study shows that template growth of Au clusters on h-BN/Rh(111) forms mainly well-dispersed monolayer clusters. In contrast, Ni forms large multilayer clusters showing a relatively high diffusivity on h-BN/Rh(111) substrate. Ni–Au bimetallic clusters are effectively formed first by Au deposition followed by Ni deposition, with the Au clusters functioning as nucleation sites for the subsequently deposited Ni. Further structural analysis was carried out via TPDmore » and AES. The resulting TPD and AES data show the surface composition and charge transfer between Au and Ni of the bimetallic clusters. These results suggest that the h-BN/Rh(111) substrate represents a unique candidate for supporting Ni–Au bimetallic clusters in further catalytic reactions.« less
Template growth of Au, Ni and Ni–Au nanoclusters on hexagonal boron nitride/Rh(111): a combined STM, TPD and AES study

DOE PAGES

Wu, Fanglue; Huang, Dali; Yue, Yuan; ...

2017-09-12

In this study, the template growth of Au, Ni, and Ni–Au bimetallic nanoclusters on hexagonal boron nitride/Rh(111), i.e. h-BN/Rh(111), was investigated via scanning tunneling microscopy (STM), temperature programmed-desorption (TPD), and Auger electron spectroscopy (AES). STM study shows that template growth of Au clusters on h-BN/Rh(111) forms mainly well-dispersed monolayer clusters. In contrast, Ni forms large multilayer clusters showing a relatively high diffusivity on h-BN/Rh(111) substrate. Ni–Au bimetallic clusters are effectively formed first by Au deposition followed by Ni deposition, with the Au clusters functioning as nucleation sites for the subsequently deposited Ni. Further structural analysis was carried out via TPDmore » and AES. The resulting TPD and AES data show the surface composition and charge transfer between Au and Ni of the bimetallic clusters. These results suggest that the h-BN/Rh(111) substrate represents a unique candidate for supporting Ni–Au bimetallic clusters in further catalytic reactions.« less
Tracing the `ninth sulfur' of the nitrogenase cofactor via a semi-synthetic approach

NASA Astrophysics Data System (ADS)

Tanifuji, Kazuki; Lee, Chi Chung; Sickerman, Nathaniel S.; Tatsumi, Kazuyuki; Ohki, Yasuhiro; Hu, Yilin; Ribbe, Markus W.

2018-05-01

The M-cluster is the [(homocitrate)MoFe7S9C] active site of nitrogenase that is derived from an 8Fe core assembled viacoupling and rearrangement of two [Fe4S4] clusters concomitant with the insertion of an interstitial carbon and a `ninth sulfur'. Combining synthetic [Fe4S4] clusters with an assembly protein template, here we show that sulfite can give rise to the ninth sulfur that is incorporated in the catalytically important belt region of the cofactor after the radical S-adenosyl-l-methionine-dependent carbide insertion and the concurrent 8Fe-core rearrangement have already taken place. Based on the differential reactivity of the formed cluster species, we also propose a new [Fe8S8C] cluster intermediate, the L*-cluster, which is similar to the [Fe8S9C] L-cluster, but lacks the ninth sulfur from sulfite. This work provides a semi-synthetic tool for protein reconstitution that could be widely applicable for the functional analysis of other FeS systems.
Tracing the 'ninth sulfur' of the nitrogenase cofactor via a semi-synthetic approach.

PubMed

Tanifuji, Kazuki; Lee, Chi Chung; Sickerman, Nathaniel S; Tatsumi, Kazuyuki; Ohki, Yasuhiro; Hu, Yilin; Ribbe, Markus W

2018-05-01

The M-cluster is the [(homocitrate)MoFe 7 S 9 C] active site of nitrogenase that is derived from an 8Fe core assembled viacoupling and rearrangement of two [Fe 4 S 4 ] clusters concomitant with the insertion of an interstitial carbon and a 'ninth sulfur'. Combining synthetic [Fe 4 S 4 ] clusters with an assembly protein template, here we show that sulfite can give rise to the ninth sulfur that is incorporated in the catalytically important belt region of the cofactor after the radical S-adenosyl-L-methionine-dependent carbide insertion and the concurrent 8Fe-core rearrangement have already taken place. Based on the differential reactivity of the formed cluster species, we also propose a new [Fe 8 S 8 C] cluster intermediate, the L*-cluster, which is similar to the [Fe 8 S 9 C] L-cluster, but lacks the ninth sulfur from sulfite. This work provides a semi-synthetic tool for protein reconstitution that could be widely applicable for the functional analysis of other FeS systems.
Water Oxidation Catalysis via Size-Selected Iridium Clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halder, Avik; Liu, Cong; LIU, ZHUN

The detailed mechanism and efficacy of four electron electrochemical water oxidation depend critically upon the detailed atomic structure of each catalytic site, which are numerous and diverse in most metal oxides anodes. In order to limit the diversity of sites, arrays of discrete iridium clusters with identical metal atom number (Ir-2, Ir-4, or Ir-8) were deposited in submonolayer coverage on conductive oxide supports, and the electrochemical properties and activity of each was evaluated. Exceptional electroactivity for the oxygen evolving reaction (OER) was observed for all cluster samples in acidic electrolyte. Reproducible cluster-size-dependent trends in redox behavior were also resolved. First-principlesmore » computational models of the individual discrete-size clusters allow correlation of catalytic-site structure and multiplicity with redox behavior.« less
Comparing Chemistry to Outcome: The Development of a Chemical Distance Metric, Coupled with Clustering and Hierarchal Visualization Applied to Macromolecular Crystallography

PubMed Central

Bruno, Andrew E.; Ruby, Amanda M.; Luft, Joseph R.; Grant, Thomas D.; Seetharaman, Jayaraman; Montelione, Gaetano T.; Hunt, John F.; Snell, Edward H.

2014-01-01

Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails) is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be time-consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192) overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and to the insertion and correct placement of sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient, CDcoeff, appears to be robust in this application, and coupled with hierarchical clustering and the overlay of crystallization outcome, reveals information of biological relevance. While tested with a single example the potential applications related to crystallography appear promising and the distance coefficient, clustering, and hierarchal visualization of results undoubtedly have applications in wider fields. PMID:24971458
Characterizing UT/LS O3 from Global Ozonesonde Profiles Using a Clustering Technique and Meteorological Reanalyses

NASA Astrophysics Data System (ADS)

Stauffer, R. M.; Thompson, A. M.

2017-12-01

Previous studies employing the self-organizing map (SOM) clustering technique to US ozonesonde data proved valuable for quantifying UT/LS O3 variability, and linking meteorological and chemical drivers to the shape of the ozone (O3) profile from the troposphere to the lower stratosphere. Focus has thus far been limited to specific geographical regions, but SOM has demonstrated the advantages of clustering over monthly climatological O3 averages, which mask day-to-day variability in the O3 profile and the correspondence between O3 and meteorology. We expand SOM to a global set of ozonesonde profiles, mostly from WOUDC, spanning 1980-present from 30 sites to evaluate global O3 climatologies and quantify links to geophysical processes for various meteorological regimes. Four clusters of O3 mixing ratio profiles are generated for each site, which show dominant profile shapes that correspond to site latitude. Offsets among O3 profile clusters and monthly O3 climatologies are 100s of ppbv in the UT/LS at higher latitude sites with active dynamics. Examination of meteorological reanalyses reveals a clear relationship among SOM clusters and covarying meteorological fields (geopotential height, potential vorticity, and tropopause height) for most sites. Tropical SOM clusters show marked dependence on velocity potential anomalies calculated from reanalysis winds, with low UT/LS O3 amounts corresponding to enhanced upper-level divergence, and vice versa. In addition to creating SOM cluster-based O3 climatologies, these results are meant to inform future approaches to validation of chemical transport models and satellite retrievals, which often struggle in the UT/LS region.
Impact of a cancer clinical trials web site on discussions about trial participation: a cluster randomized trial.

PubMed

Dear, R F; Barratt, A L; Askie, L M; Butow, P N; McGeechan, K; Crossing, S; Currow, D C; Tattersall, M H N

2012-07-01

Cancer patients want access to reliable information about currently recruiting clinical trials. Oncologists and their patients were randomly assigned to access a consumer-friendly cancer clinical trials web site [Australian Cancer Trials (ACT), www.australiancancertrials.gov.au] or to usual care in a cluster randomized controlled trial. The primary outcome, measured from audio recordings of oncologist-patient consultations, was the proportion of patients with whom participation in any clinical trial was discussed. Analysis was by intention-to-treat accounting for clustering and stratification. Thirty medical oncologists and 493 patients were recruited. Overall, 46% of consultations in the intervention group compared with 34% in the control group contained a discussion about clinical trials (P=0.08). The mean consultation length in both groups was 29 min (P=0.69). The proportion consenting to a trial was 10% in both groups (P=0.65). Patients' knowledge about randomized trials was lower in the intervention than the control group (mean score 3.0 versus 3.3, P=0.03) but decisional conflict scores were similar (mean score 42 versus 43, P=0.83). Good communication between patients and physicians is essential. Within this context, a web site such as Australian Cancer Trials may be an important tool to encourage discussion about clinical trial participation.
Identification and analysis of integrons and cassette arrays in bacterial genomes

PubMed Central

Touchon, Marie; Néron, Bertrand; Rocha, Eduardo PC

2016-01-01

Abstract Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program – IntegronFinder – to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome. PMID:27130947
The Design, Synthesis, and Characterization of Open Sites on Metal Clusters

NASA Astrophysics Data System (ADS)

Nigra, Michael Mark

Coordinatively unsaturated corner and edge atoms have been hypothesized to have the highest activity of sites responsible for many catalytic reactions on a metal surface. Recent studies have validated this hypothesis in varied reaction systems. However, quantification of different types of coordinatively unsaturated sites, and elucidation of their individual catalytic rates has remained a largely unresolved challenge when understanding catalysis on metal surfaces. Yet such structure-function knowledge would be invaluable to the design of more active and selective metal-surface catalysts in the future. I investigated the catalytic contributions of undercoordinated sites such as corner and edge atoms are investigated in a model reaction system using organic ligands bound to the gold nanoparticle surface. The catalyst consisted of 4 nm gold nanoparticles on a metal oxide support, using resazurin to resorufin as a model reaction system. My results demonstrate that in this system, corner atom sites are the most undercoordinated sites, and are over an order of magnitude more active when compared to undercoordinated edge atom sites, while terrace sites remain catalytically inactive for the reduction reaction of resazurin to resorufin. Catalytic activity has been also demonstrated for calixarene-bound gold nanoparticles using the reduction of 4-nitrophenol. With the 4-nitrophenol reduction reaction, a comparative study was undertaken to compare calixarene phosphine and calixarene thiol bound 4 nm gold particles. The results of the study suggested that a leached site was responsible for catalysis and not sites on the original gold nanoparticles. Future experiments with calixarene bound gold clusters could investigate ligand effects in reactions where the active site is not a leached or aggregated gold species, possibly in oxidation reactions, where electron-rich gold is hypothesized to be a good catalyst. The results that emphasize the enhanced catalytic activity of undercoordinated sites led me to synthesize small gold clusters consisting of a high fraction of coordinatively unsaturated open sites. This was enabled through an approach that utilized bulky calix[4]arene ligands that are bound to a gold core. Since the size of the calix[4]arene ligand is commensurate with the size of the gold cluster core, the calix[4]arene ligand does not pack closely together on the gold cluster surface. This in turn results in areas of accessible gold atom sites between ligands. Additionally, these calix[4]arene ligands prevent cluster aggregation and electronically tune the gold core in a manner conceptually similar to enzymes affecting reactivity through organic side-chains acting as ligands. I quantified the number of open sites that result from this packing problem on the gold cluster surface, using fluorescence probe chemisorption experiments. The results of these chemisorption measurements support the mechanical model of accessibility whereby accessibility is not dependent on the identity of the functional group, whether it be calixarene phosphines or N-heterocyclic carbenes, bound to the gold surface, but rather to the relative radii of curvature of bound ligands and the gold cluster core. Additional materials characterization was completed with transmission electron microscopy in both bright-field imaging of zeolites, in MCM-22 and delaminated ITQ-2 and UCB-1 materials, and in dark field imaging of glucan coatings on oxide particles. These materials could prove to be interesting materials as to use as supports for the calixarene-bound metal clusters described above or for other metal clusters.
VAAPA: a web platform for visualization and analysis of alternative polyadenylation.

PubMed

Guan, Jinting; Fu, Jingyi; Wu, Mingcheng; Chen, Longteng; Ji, Guoli; Quinn Li, Qingshun; Wu, Xiaohui

2015-02-01

Polyadenylation [poly(A)] is an essential process during the maturation of most mRNAs in eukaryotes. Alternative polyadenylation (APA) as an important layer of gene expression regulation has been increasingly recognized in various species. Here, a web platform for visualization and analysis of alternative polyadenylation (VAAPA) was developed. This platform can visualize the distribution of poly(A) sites and poly(A) clusters of a gene or a section of a chromosome. It can also highlight genes with switched APA sites among different conditions. VAAPA is an easy-to-use web-based tool that provides functions of poly(A) site query, data uploading, downloading, and APA sites visualization. It was designed in a multi-tier architecture and developed based on Smart GWT (Google Web Toolkit) using Java as the development language. VAAPA will be a valuable addition to the community for the comprehensive study of APA, not only by making the high quality poly(A) site data more accessible, but also by providing users with numerous valuable functions for poly(A) site analysis and visualization. Copyright © 2014 Elsevier Ltd. All rights reserved.
A Detailed Study of Chemical Enrichment History of Galaxy Clusters out to Virial Radius

NASA Astrophysics Data System (ADS)

Loewenstein, Michael

The origin of the metal enrichment of the intracluster medium (ICM) represents a fundamental problem in extragalactic astrophysics, with implications for our understanding of how stars and galaxies form, the nature of Type Ia supernova (SNIa) progenitors, and the thermal history of the ICM. These heavy elements are ultimately synthesized by supernova (SN) explosions; however, the details of the sites of metal production and mechanisms that transport metals to the ICM remain unclear. To make progress, accurate abundance profiles for multiple elements extending from the cluster core out to the virial radius (r180) are required for a significant cluster sample. We propose an X-ray spectroscopic study of a carefully-chosen sample of archival Suzaku and XMM-Newton observations of 23 clusters: XMM-Newton data probe the cluster temperature and abundances out to (0.5-1)r500, while Suzaku data probe the cluster outskirts. A method devised by our team to utilize all elements with emission lines in the X-ray bandpass to measure the relative contributions of supernova explosions by direct modeling of their X-ray spectra will be applied in order to constrain the demographics of the enriching supernova population. In addition we will conduct a stacking analysis of our already existing Suzaku and XMM-Newton cluster spectra to search for weak emssion lines that are important SN diagnostics, and to look for trends with cluster mass and redshift. The funding we propose here will also support the data analysis of our recent Suzaku observations of the archetypal cluster A3112 (200 ks each on the core and outskirts). Our data analysis, intepreted using theoretical models we have developed, will enable us to constrain the star formation history, SN demographics, and nature of SNIa progenitors associated with galaxy cluster stellar populations - and, hence, directly addresess NASA s Strategic Objective 2.4.2 in Astrophysics that aims to improve the understanding of how the Universe works, and explore how it began and evolved.
Spatial pattern evolution of Aedes aegypti breeding sites in an Argentinean city without a dengue vector control programme.

PubMed

Espinosa, Manuel O; Polop, Francisco; Rotela, Camilo H; Abril, Marcelo; Scavuzzo, Carlos M

2016-11-21

The main objective of this study was to obtain and analyse the space-time dynamics of Aedes aegypti breeding sites in Clorinda City, Formosa Province, Argentina coupled with landscape analysis using the maximum entropy approach in order to generate a dengue vector niche model. In urban areas, without vector control activities, 12 entomologic (larval) samplings were performed during three years (October 2011 to October 2014). The entomologic surveillance area represented 16,511 houses. Predictive models for Aedes distribution were developed using vector breeding abundance data, density analysis, clustering and geoprocessing techniques coupled with Earth observation satellite data. The spatial analysis showed a vector spatial distribution pattern with clusters of high density in the central region of Clorinda with a well-defined high-risk area in the western part of the city. It also showed a differential temporal behaviour among different areas, which could have implications for risk models and control strategies at the urban scale. The niche model obtained for Ae. aegypti, based on only one year of field data, showed that 85.8% of the distribution of breeding sites is explained by the percentage of water supply (48.2%), urban distribution (33.2%), and the percentage of urban coverage (4.4%). The consequences for the development of control strategies are discussed with reference to the results obtained using distribution maps based on environmental variables.
Functional analysis of ars gene cluster of Pannonibacter indicus strain HT23(T) (DSM 23407(T)) and identification of a proline residue essential for arsenate reductase activity.

PubMed

Bandyopadhyay, Saumya; Das, Subrata K

2016-04-01

Arsenic is a naturally occurring ubiquitous highly toxic metalloid. In this study, we have identified ars gene cluster in Pannonibacter indicus strain HT23(T) (DSM 23407(T)), responsible for reduction of toxic pentavalent arsenate. The ars gene cluster is comprised of four non-overlapping open reading frames (ORFs) encoding a transcriptional regulator (ArsR), a low molecular weight protein tyrosine phosphatases (LMW-PTPase) with hypothetical function, an arsenite efflux pump (Acr3), and an arsenate reductase (ArsC). Heterologous expression of arsenic inducible ars gene cluster conferred arsenic resistance to Escherichia coli ∆ars mutant strain AW3110. The recombinant ArsC was purified and assayed. Site-directed mutagenesis was employed to ascertain the role of specific amino acids in ArsC catalysis. Pro94X (X = Ala, Arg, Cys, and His) amino acid substitutions led to enzyme inactivation. Circular dichroism spectra analysis suggested Pro94 as an essential amino acid for enzyme catalytic activity as it is indispensable for optimum protein folding in P. indicus Grx-coupled ArsC.

Conserved DNA motifs in the type II-A CRISPR leader region.

PubMed

Van Orden, Mason J; Klein, Peter; Babu, Kesavan; Najar, Fares Z; Rajan, Rakhi

2017-01-01

The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3' end of the leader, are indispensable for adaptation. However, a comprehensive analysis of leader ends remains absent. Here, we have analyzed the leader, repeat, and Cas proteins from 167 type II-A CRISPR loci. Our results indicate two distinct conserved DNA motifs at the 3' leader end: ATTTGAG (noted previously in the CRISPR1 locus of Streptococcus thermophilus DGCC7710) and a newly defined CTRCGAG, associated with the CRISPR3 locus of S. thermophilus DGCC7710. A third group with a very short CG DNA conservation at the 3' leader end is observed mostly in lactobacilli. Analysis of the repeats and Cas proteins revealed clustering of these CRISPR components that mirrors the leader motif clustering, in agreement with the coevolution of CRISPR-Cas components. Based on our analysis of the type II-A CRISPR loci, we implicate leader end sequences that could confer site-specificity for the adaptation-machinery in the different subsets of type II-A CRISPR loci.
Conserved DNA motifs in the type II-A CRISPR leader region

PubMed Central

Babu, Kesavan; Najar, Fares Z.

2017-01-01

The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3′ end of the leader, are indispensable for adaptation. However, a comprehensive analysis of leader ends remains absent. Here, we have analyzed the leader, repeat, and Cas proteins from 167 type II-A CRISPR loci. Our results indicate two distinct conserved DNA motifs at the 3′ leader end: ATTTGAG (noted previously in the CRISPR1 locus of Streptococcus thermophilus DGCC7710) and a newly defined CTRCGAG, associated with the CRISPR3 locus of S. thermophilus DGCC7710. A third group with a very short CG DNA conservation at the 3′ leader end is observed mostly in lactobacilli. Analysis of the repeats and Cas proteins revealed clustering of these CRISPR components that mirrors the leader motif clustering, in agreement with the coevolution of CRISPR-Cas components. Based on our analysis of the type II-A CRISPR loci, we implicate leader end sequences that could confer site-specificity for the adaptation-machinery in the different subsets of type II-A CRISPR loci. PMID:28392985
DOE Office of Scientific and Technical Information (OSTI.GOV)

Murugesan, Sugeerth; Bouchard, Kristofer; Chang, Edward

There exists a need for effective and easy-to-use software tools supporting the analysis of complex Electrocorticography (ECoG) data. Understanding how epileptic seizures develop or identifying diagnostic indicators for neurological diseases require the in-depth analysis of neural activity data from ECoG. Such data is multi-scale and is of high spatio-temporal resolution. Comprehensive analysis of this data should be supported by interactive visual analysis methods that allow a scientist to understand functional patterns at varying levels of granularity and comprehend its time-varying behavior. We introduce a novel multi-scale visual analysis system, ECoG ClusterFlow, for the detailed exploration of ECoG data. Our systemmore » detects and visualizes dynamic high-level structures, such as communities, derived from the time-varying connectivity network. The system supports two major views: 1) an overview summarizing the evolution of clusters over time and 2) an electrode view using hierarchical glyph-based design to visualize the propagation of clusters in their spatial, anatomical context. We present case studies that were performed in collaboration with neuroscientists and neurosurgeons using simulated and recorded epileptic seizure data to demonstrate our system's effectiveness. ECoG ClusterFlow supports the comparison of spatio-temporal patterns for specific time intervals and allows a user to utilize various clustering algorithms. Neuroscientists can identify the site of seizure genesis and its spatial progression during various the stages of a seizure. Our system serves as a fast and powerful means for the generation of preliminary hypotheses that can be used as a basis for subsequent application of rigorous statistical methods, with the ultimate goal being the clinical treatment of epileptogenic zones.« less
Groundwater Quality: Analysis of Its Temporal and Spatial Variability in a Karst Aquifer.

PubMed

Pacheco Castro, Roger; Pacheco Ávila, Julia; Ye, Ming; Cabrera Sansores, Armando

2018-01-01

This study develops an approach based on hierarchical cluster analysis for investigating the spatial and temporal variation of water quality governing processes. The water quality data used in this study were collected in the karst aquifer of Yucatan, Mexico, the only source of drinking water for a population of nearly two million people. Hierarchical cluster analysis was applied to the quality data of all the sampling periods lumped together. This was motivated by the observation that, if water quality does not vary significantly in time, two samples from the same sampling site will belong to the same cluster. The resulting distribution maps of clusters and box-plots of the major chemical components reveal the spatial and temporal variability of groundwater quality. Principal component analysis was used to verify the results of cluster analysis and to derive the variables that explained most of the variation of the groundwater quality data. Results of this work increase the knowledge about how precipitation and human contamination impact groundwater quality in Yucatan. Spatial variability of groundwater quality in the study area is caused by: a) seawater intrusion and groundwater rich in sulfates at the west and in the coast, b) water rock interactions and the average annual precipitation at the middle and east zones respectively, and c) human contamination present in two localized zones. Changes in the amount and distribution of precipitation cause temporal variation by diluting groundwater in the aquifer. This approach allows to analyze the variation of groundwater quality controlling processes efficiently and simultaneously. © 2017, National Ground Water Association.
Identification of segregated regions in the functional brain connectome of autistic patients by a combination of fuzzy spectral clustering and entropy analysis

PubMed Central

Sato, João Ricardo; Balardin, Joana; Vidal, Maciel Calebe; Fujita, André

2016-01-01

Background Several neuroimaging studies support the model of abnormal development of brain connectivity in patients with autism-spectrum disorders (ASD). In this study, we aimed to test the hypothesis of reduced functional network segregation in autistic patients compared with controls. Methods Functional MRI data from children acquired under a resting-state protocol (Autism Brain Imaging Data Exchange [ABIDE]) were submitted to both fuzzy spectral clustering (FSC) with entropy analysis and graph modularity analysis. Results We included data from 814 children in our analysis. We identified 5 regions of interest comprising the motor, temporal and occipito-temporal cortices with increased entropy (p < 0.05) in the clustering structure (i.e., more segregation in the controls). Moreover, we noticed a statistically reduced modularity (p < 0.001) in the autistic patients compared with the controls. Significantly reduced eigenvector centrality values (p < 0.05) in the patients were observed in the same regions that were identified in the FSC analysis. Limitations There is considerable heterogeneity in the fMRI acquisition protocols among the sites that contributed to the ABIDE data set (e.g., scanner type, pulse sequence, duration of scan and resting-state protocol). Moreover, the sites differed in many variables related to sample characterization (e.g., age, IQ and ASD diagnostic criteria). Therefore, we cannot rule out the possibility that additional differences in functional network organization would be found in a more homogeneous data sample of individuals with ASD. Conclusion Our results suggest that the organization of the whole-brain functional network in patients with ASD is different from that observed in controls, which implies a reduced modularity of the brain functional networks involved in sensorimotor, social, affective and cognitive processing. PMID:26505141
Differential regulation of transcription through distinct Suppressor of Hairless DNA binding site architectures during Notch signaling in proneural clusters.

PubMed

Cave, John W; Xia, Li; Caudy, Michael

2011-01-01

In Drosophila melanogaster, achaete (ac) and m8 are model basic helix-loop-helix activator (bHLH A) and repressor genes, respectively, that have the opposite cell expression pattern in proneural clusters during Notch signaling. Previous studies have shown that activation of m8 transcription in specific cells within proneural clusters by Notch signaling is programmed by a "combinatorial" and "architectural" DNA transcription code containing binding sites for the Su(H) and proneural bHLH A proteins. Here we show the novel result that the ac promoter contains a similar combinatorial code of Su(H) and bHLH A binding sites but contains a different Su(H) site architectural code that does not mediate activation during Notch signaling, thus programming a cell expression pattern opposite that of m8 in proneural clusters.
A novel exploratory chemometric approach to environmental monitorring by combining block clustering with Partial Least Square (PLS) analysis

PubMed Central

2013-01-01

Background Given the serious threats posed to terrestrial ecosystems by industrial contamination, environmental monitoring is a standard procedure used for assessing the current status of an environment or trends in environmental parameters. Measurement of metal concentrations at different trophic levels followed by their statistical analysis using exploratory multivariate methods can provide meaningful information on the status of environmental quality. In this context, the present paper proposes a novel chemometric approach to standard statistical methods by combining the Block clustering with Partial least square (PLS) analysis to investigate the accumulation patterns of metals in anthropized terrestrial ecosystems. The present study focused on copper, zinc, manganese, iron, cobalt, cadmium, nickel, and lead transfer along a soil-plant-snai food chain, and the hepatopancreas of the Roman snail (Helix pomatia) was used as a biological end-point of metal accumulation. Results Block clustering deliniates between the areas exposed to industrial and vehicular contamination. The toxic metals have similar distributions in the nettle leaves and snail hepatopancreas. PLS analysis showed that (1) zinc and copper concentrations at the lower trophic levels are the most important latent factors that contribute to metal accumulation in land snails; (2) cadmium and lead are the main determinants of pollution pattern in areas exposed to industrial contamination; (3) at the sites located near roads lead is the most threatfull metal for terrestrial ecosystems. Conclusion There were three major benefits by applying block clustering with PLS for processing the obtained data: firstly, it helped in grouping sites depending on the type of contamination. Secondly, it was valuable for identifying the latent factors that contribute the most to metal accumulation in land snails. Finally, it optimized the number and type of data that are best for monitoring the status of metallic contamination in terrestrial ecosystems exposed to different kinds of anthropic polution. PMID:23987502
Molecular and antigenic traits on hemagglutinin gene of avian influenza H9N2 viruses: Evidence of a new escape mutant in Egypt adapted in quails.

PubMed

Adel, Amany; Arafa, Abdelsatar; Hussein, Hussein A; El-Sanousi, Ahmed A

2017-06-01

The LPAI viruses of H9N2 subtype became widely distributed in Middle Eastern countries, causing great economic losses in poultry industry especially when complicated with other pathogens. The H9N2 viruses in Egypt have a wide spread nature since its first occurrence in 2011. In this study, we collected cloacal and tracheal samples from 19 flocks for detection and propagation of H9N2 virus using real-time RT-PCR and egg inoculation. We studied the molecular evolution of the Hemagglutinin gene of H9N2 viruses by full HA gene sequencing, then the antigenic characterization was implemented using the cross HI assay and analyzed using 3D Bioinformatics cartography software. The phylogenetic analysis of the HA gene of Egyptian H9N2 viruses clearly points out the presence of only one group (Egy/G1) of originally introduced viruses in 2011 related to the G1 lineage within group B, with the presence of multiple minor clusters includes viruses from 2011 to 2015. However, a new variant (Egy/G1var) cluster was detected in quails since 2012. Genetically, Egy/G1var viruses characterized by presence of 20 amino acid substitutions within and adjacent to the antigenic sites in comparison to other Egyptian viruses. In addition, two glycosylation sites at amino acid residues 127 and 189 were determined in close to the receptor binding and antigenic sites. The antigenic analysis based on 3D antigenic mapping showed that the Egy/G1var cluster was clearly distinct from the original Egy/G1 viruses. In conclusion, Egy/G1var is shown to be a new escape mutant variant cluster with an adaptive evolution in quails. Copyright © 2017 Elsevier Ltd. All rights reserved.
Acidity in DMSO from the embedded cluster integral equation quantum solvation model.

PubMed

Heil, Jochen; Tomazic, Daniel; Egbers, Simon; Kast, Stefan M

2014-04-01

The embedded cluster reference interaction site model (EC-RISM) is applied to the prediction of acidity constants of organic molecules in dimethyl sulfoxide (DMSO) solution. EC-RISM is based on a self-consistent treatment of the solute's electronic structure and the solvent's structure by coupling quantum-chemical calculations with three-dimensional (3D) RISM integral equation theory. We compare available DMSO force fields with reference calculations obtained using the polarizable continuum model (PCM). The results are evaluated statistically using two different approaches to eliminating the proton contribution: a linear regression model and an analysis of pK(a) shifts for compound pairs. Suitable levels of theory for the integral equation methodology are benchmarked. The results are further analyzed and illustrated by visualizing solvent site distribution functions and comparing them with an aqueous environment.
A machine learning approach for ranking clusters of docked protein‐protein complexes by pairwise cluster comparison

PubMed Central

Pfeiffenberger, Erik; Chaleil, Raphael A.G.; Moal, Iain H.

2017-01-01

ABSTRACT Reliable identification of near‐native poses of docked protein–protein complexes is still an unsolved problem. The intrinsic heterogeneity of protein–protein interactions is challenging for traditional biophysical or knowledge based potentials and the identification of many false positive binding sites is not unusual. Often, ranking protocols are based on initial clustering of docked poses followed by the application of an energy function to rank each cluster according to its lowest energy member. Here, we present an approach of cluster ranking based not only on one molecular descriptor (e.g., an energy function) but also employing a large number of descriptors that are integrated in a machine learning model, whereby, an extremely randomized tree classifier based on 109 molecular descriptors is trained. The protocol is based on first locally enriching clusters with additional poses, the clusters are then characterized using features describing the distribution of molecular descriptors within the cluster, which are combined into a pairwise cluster comparison model to discriminate near‐native from incorrect clusters. The results show that our approach is able to identify clusters containing near‐native protein–protein complexes. In addition, we present an analysis of the descriptors with respect to their power to discriminate near native from incorrect clusters and how data transformations and recursive feature elimination can improve the ranking performance. Proteins 2017; 85:528–543. © 2016 Wiley Periodicals, Inc. PMID:27935158
Vacancy defects and defect clusters in alkali metal ion-doped MgO nanocrystallites studied by positron annihilation and photoluminescence spectroscopy

NASA Astrophysics Data System (ADS)

Sellaiyan, S.; Uedono, A.; Sivaji, K.; Janet Priscilla, S.; Sivasankari, J.; Selvalakshmi, T.

2016-10-01

Pure and alkali metal ion (Li, Na, and K)-doped MgO nanocrystallites synthesized by solution combustion technique have been studied by positron lifetime and Doppler broadening spectroscopy methods. Positron lifetime analysis exhibits four characteristic lifetime components for all the samples. Doping reduces the Mg vacancy after annealing to 800 °C. It was observed that Li ion migrates to the vacancy site to recover Mg vacancy-type defects, reducing cluster vacancies and micropores. For Na- and K-doped MgO, the aforementioned defects are reduced and immobile at 800 °C. Coincidence Doppler broadening studies show the positron trapping sites as vacancy clusters. The decrease in the S parameter is due to the particle growth and reduction in the defect concentration at 800 °C. Photoluminescence study shows an emission peak at 445 nm and 498 nm, associated with F2 2+ and recombination of higher-order vacancy complexes. Further, annealing process is likely to dissociate F2 2+ to F+ and this F+ is converted into F centers at 416 nm.
Epizoic communities of prokaryotes on healthy and diseased scleractinian corals in Lingayen Gulf, Philippines.

PubMed

Arboleda, Mark; Reichardt, Wolfgang

2009-01-01

In search for microbiological indicators of coral health and coral diseases, community profiles of coral-associated epizoic prokaryotes were investigated because of their dual potential as a source of coral pathogens and their antagonists. In pairwise samples of visually healthy and diseased coral specimens from Bolinao Bay (Pangasinan, Philippines), mixed biofilm communities of ectoderm- and mucus-colonizing epizoic prokaryotes were compared using fluorescent in situ hybridization (FISH). Oligonucleotide probes targeted 13 phylotypes representing the main taxonomic groups of marine prokaryotes. Coral taxa tended to show specific community profiles. An attempt to separate the profiles of healthy and diseased specimens by applying principal component analysis (PCA) to a (nonselective) collection of corals (affected by various diseases) proved unsuccessful. On the other hand, separate PCA clusters were obtained from healthy and diseased corals belonging to a single species (Pocillopora damicornis) only. This cluster formation was dominated by principal component 1 with the genus Vibrio accounting for 18%. At the same time, reef-site-specific clusters were formed as well. At a reef site exposed to pollution from intensive fish cage (Chanos chanos) farming, healthy P. damicornis were mainly (93%) colonized by unicellular cyanobacteria. The formal calculation of diversity parameters suggested that evenness in particular was driven by both health status and reef site location. Despite the low resolution of taxonomic levels achieved with FISH probes targeting only large phylotype groups, significant differences between healthy and diseased corals and also between polluted and nonpolluted reef sites were observed.
Space-time clusters for early detection of grizzly bear predation.

PubMed

Kermish-Wells, Joseph; Massolo, Alessandro; Stenhouse, Gordon B; Larsen, Terrence A; Musiani, Marco

2018-01-01

Accurate detection and classification of predation events is important to determine predation and consumption rates by predators. However, obtaining this information for large predators is constrained by the speed at which carcasses disappear and the cost of field data collection. To accurately detect predation events, researchers have used GPS collar technology combined with targeted site visits. However, kill sites are often investigated well after the predation event due to limited data retrieval options on GPS collars (VHF or UHF downloading) and to ensure crew safety when working with large predators. This can lead to missing information from small-prey (including young ungulates) kill sites due to scavenging and general site deterioration (e.g., vegetation growth). We used a space-time permutation scan statistic (STPSS) clustering method (SaTScan) to detect predation events of grizzly bears ( Ursus arctos ) fitted with satellite transmitting GPS collars. We used generalized linear mixed models to verify predation events and the size of carcasses using spatiotemporal characteristics as predictors. STPSS uses a probability model to compare expected cluster size (space and time) with the observed size. We applied this method retrospectively to data from 2006 to 2007 to compare our method to random GPS site selection. In 2013-2014, we applied our detection method to visit sites one week after their occupation. Both datasets were collected in the same study area. Our approach detected 23 of 27 predation sites verified by visiting 464 random grizzly bear locations in 2006-2007, 187 of which were within space-time clusters and 277 outside. Predation site detection increased by 2.75 times (54 predation events of 335 visited clusters) using 2013-2014 data. Our GLMMs showed that cluster size and duration predicted predation events and carcass size with high sensitivity (0.72 and 0.94, respectively). Coupling GPS satellite technology with clusters using a program based on space-time probability models allows for prompt visits to predation sites. This enables accurate identification of the carcass size and increases fieldwork efficiency in predation studies.
Effect of the coordination of the superficial site in the monomer dimer reaction on a disordered substrate

NASA Astrophysics Data System (ADS)

Valencia, Eliana; Cortés, Joaquín.; Puschmann, Heinrich

2000-12-01

Using Monte Carlo simulation experiments, a study is made of the effect of the superficial coordination number in a square lattice of sites for the monomer-dimer surface reaction (Ziff, Gulari and Barshad model) in the case of disordered substrates showing geometric heterogeneity of the sites, such as the percolation clusters. An analysis is made of the change in character of the phase transitions and in the size of the reactive window in the phase diagram, and the results were also compared with mean field theoretical calculations for disordered systems.
Piezometer completion report for borehole cluster sites DC-19, DC-20, and DC-22

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, R.L.; Diediker, L.D.; Ledgerwood, R.K.

1984-07-01

This report describes the design and installation of multi-level piezometers at borehole cluster sites DC-19, DC-20 and DC-22. The network of borehole cluster sites will provide facilities for multi-level water-level monitoring across the RRL for piezometer baseline monitoring and for large-scale hydraulic stress testing. These groundwater-monitoring facilities were installed between August 1983 and March 1984. Three series of piezometer nests (A-, C- and D-series) were installed in nine hydrogeologic units (monitoring horizons) within the Columbia River Basalt Group at each borehole cluster site. In addition to the piezometer facilities, a B-series pumping well was installed at borehole cluster sites DC-20more » and DC-22. The A-series piezometer nest monitors the basal Ringold sediments and the Rattlesnake Ridge interbed. The C-series piezometer nests monitors the six deepest horizons, which are in increasing depth, the Priest Rapids interflow, Sentinel Gap flow top, Ginkgo flow top, Rocky Coulee flow top, Cohassett flow top and Umtanum flow top. The D-series piezometer monitors the Mabton interbed. The B-series pumping well was completed in the Priest Rapids interflow. 21 refs., 6 figs., 6 tabs.« less
Poly(A)-tag deep sequencing data processing to extract poly(A) sites.

PubMed

Wu, Xiaohui; Ji, Guoli; Li, Qingshun Quinn

2015-01-01

Polyadenylation [poly(A)] is an essential posttranscriptional processing step in the maturation of eukaryotic mRNA. The advent of next-generation sequencing (NGS) technology has offered feasible means to generate large-scale data and new opportunities for intensive study of polyadenylation, particularly deep sequencing of the transcriptome targeting the junction of 3'-UTR and the poly(A) tail of the transcript. To take advantage of this unprecedented amount of data, we present an automated workflow to identify polyadenylation sites by integrating NGS data cleaning, processing, mapping, normalizing, and clustering. In this pipeline, a series of Perl scripts are seamlessly integrated to iteratively map the single- or paired-end sequences to the reference genome. After mapping, the poly(A) tags (PATs) at the same genome coordinate are grouped into one cleavage site, and the internal priming artifacts removed. Then the ambiguous region is introduced to parse the genome annotation for cleavage site clustering. Finally, cleavage sites within a close range of 24 nucleotides and from different samples can be clustered into poly(A) clusters. This procedure could be used to identify thousands of reliable poly(A) clusters from millions of NGS sequences in different tissues or treatments.
Identification of Volcanic Landforms and Processes on Earth and Mars using Geospatial Analysis (Invited)

NASA Astrophysics Data System (ADS)

Fagents, S. A.; Hamilton, C. W.

2009-12-01

Nearest neighbor (NN) analysis enables the identification of landforms using non-morphological parameters and can be useful for constraining the geological processes contributing to observed patterns of spatial distribution. Explosive interactions between lava and water can generate volcanic rootless cone (VRC) groups that are well suited to geospatial analyses because they consist of a large number of landforms that share a common formation mechanism. We have applied NN analysis tools to quantitatively compare the spatial distribution of VRCs in the Laki lava flow in Iceland to analogous landforms in the Tartarus Colles Region of eastern Elysium Planitia, Mars. Our results show that rootless eruption sites on both Earth and Mars exhibit systematic variations in spatial organization that are related to variations in the distribution of resources (lava and water) at different scales. Field observations in Iceland reveal that VRC groups are composite structures formed by the emplacement of chronologically and spatially distinct domains. Regionally, rootless cones cluster into groups and domains, but within domains NN distances exhibit random to repelled distributions. This suggests that on regional scales VRCs cluster in locations that contain sufficient resources, whereas on local scales rootless eruption sites tend to self-organize into distributions that maximize the utilization of limited resources (typically groundwater). Within the Laki lava flow, near-surface water is abundant and pre-eruption topography appears to exert the greatest control on both lava inundation regions and clustering of rootless eruption sites. In contrast, lava thickness appears to be the controlling factor in the formation of rootless eruption sites in the Tartarus Colles Region. A critical lava thickness may be required to initiate rootless eruptions on Mars because the lava flows must contain sufficient heat for transferred thermal energy to reach the underlying cryosphere and volatilize buried ground ice. In both environments, the spatial distribution of rootless eruption sites on local scales may either be random, which indicates that rootless eruption sites form independently of one another, or repelled, which implies resource limitation. Where competition for limited groundwater causes rootless eruption sites to develop greater than random NN separation, rootless eruption sites can be modeled as a system of pumping wells that extract water from a shared aquifer, thereby generating repelled distributions due to non-initiation or early cessation of rootless explosive activity at sites with insufficient access to groundwater. Thus statistical NN analyses can be combined with field observations and remote sensing to obtain information about self-organization processes within geological systems and the effects of environmental resource limitation on the spatial distribution of volcanic landforms. NN analyses may also be used to quantitatively compare the spatial distribution of landforms in different planetary environments and for supplying non-morphological evidence to discriminate between feature identities and geological formation mechanisms.
Determinates of clustering across America's national parks: An application of the Gini coefficients

Treesearch

R. Geoffrey Lacher; Matthew T.J. Brownlee

2012-01-01

The changes in the clustering of visitation across National Park Service (NPS) sites have not been well documented or widely studied. This paper investigates the changes in the dispersion of visitation across NPS sites with the Gini coefficient, a popular measure of inequality used primarily in the field of economics. To calculate the degree of clustering nationally,...
Synthesis of MFe3S4 clusters containing a planar M(II) site (M = Ni, Pd, Pt), a structural element in the C-cluster of carbon monoxide dehydrogenase.

PubMed

Panda, Rashmishree; Berlinguette, Curtis P; Zhang, Yugen; Holm, Richard H

2005-08-10

Synthesis of an analogue of the C-cluster of C. hydrogenoformans carbon monoxide dehydrogenase requires formation of a planar Ni(II) site and attachment of an exo iron atom in the core unit NiFe(4)S(5). The first objective has been achieved by two reactions: (i) displacement of Ph(3)P or Bu(t)()NC at tetrahedral Ni(II) sites of cubane-type [NiFe(3)S(4)](+) clusters with chelating diphosphines, and (ii) metal atom incorporation into a cuboidal [Fe(3)S(4)](0) cluster with a M(0) reactant in the presence of bis(1,2-dimethylphosphino)ethane (dmpe). The isolated product clusters [(dmpe)MFe(3)S(4)(LS(3))](2-) (M = Ni(II) (9), Pd(II) (12), Pt(II) (13); LS(3) = 1,3,5-tris((4,6-dimethyl-3-mercaptophenyl)thio)-2,4,6-tris(p-tolylthio)benzene(3-)) contain the cores [MFe(3)(mu(2)-S)(mu(3)-S)(3)](+) having planar M(II)P(2)S(2) sites and variable nonbonding M...S distances of 2.6-3.4 A. Reaction (i) involves a tetrahedral --> planar Ni(II) structural change between isomeric cubane and cubanoid [NiFe(3)S(4)](+) cores. Based on the magnetic properties of 12 and earlier considerations, the S = (5)/(2) ground state of the cubanoid cluster arises from the [Fe(3)S(4)](-) fragment, whereas the S = (3)/(2) ground state of the cubane cluster is a consequence of antiferromagnetic coupling between the spins of Ni(2+) (S = 1) and [Fe(3)S(4)](-). Other substitution reactions of [NiFe(3)S(4)](+) clusters and 1:3 site-differentiated [Fe(4)S(4)](2+) clusters are described, as are the structures of 12, 13, [(Me(3)P)NiFe(3)S(4)(LS(3))](2-), and [Fe(4)S(4)(LS(3))L'](2-) (L' = Me(2)NC(2)H(4)S(-), Ph(2)P(O)C(2)H(4)S(-)). This work significantly expands our initial report of cluster 9 (Panda et al. J. Am. Chem. Soc. 2004, 126, 6448-6459) and further demonstrates that a planar M(II) site can be stabilized within a cubanoid [NiFe(3)S(4)](+) core.
Influence of birth cohort on age of onset cluster analysis in bipolar I disorder.

PubMed

Bauer, M; Glenn, T; Alda, M; Andreassen, O A; Angelopoulos, E; Ardau, R; Baethge, C; Bauer, R; Bellivier, F; Belmaker, R H; Berk, M; Bjella, T D; Bossini, L; Bersudsky, Y; Cheung, E Y W; Conell, J; Del Zompo, M; Dodd, S; Etain, B; Fagiolini, A; Frye, M A; Fountoulakis, K N; Garneau-Fournier, J; Gonzalez-Pinto, A; Harima, H; Hassel, S; Henry, C; Iacovides, A; Isometsä, E T; Kapczinski, F; Kliwicki, S; König, B; Krogh, R; Kunz, M; Lafer, B; Larsen, E R; Lewitzka, U; Lopez-Jaramillo, C; MacQueen, G; Manchia, M; Marsh, W; Martinez-Cengotitabengoa, M; Melle, I; Monteith, S; Morken, G; Munoz, R; Nery, F G; O'Donovan, C; Osher, Y; Pfennig, A; Quiroz, D; Ramesar, R; Rasgon, N; Reif, A; Ritter, P; Rybakowski, J K; Sagduyu, K; Scippa, A M; Severus, E; Simhandl, C; Stein, D J; Strejilevich, S; Hatim Sulaiman, A; Suominen, K; Tagata, H; Tatebayashi, Y; Torrent, C; Vieta, E; Viswanath, B; Wanchoo, M J; Zetin, M; Whybrow, P C

2015-01-01

Two common approaches to identify subgroups of patients with bipolar disorder are clustering methodology (mixture analysis) based on the age of onset, and a birth cohort analysis. This study investigates if a birth cohort effect will influence the results of clustering on the age of onset, using a large, international database. The database includes 4037 patients with a diagnosis of bipolar I disorder, previously collected at 36 collection sites in 23 countries. Generalized estimating equations (GEE) were used to adjust the data for country median age, and in some models, birth cohort. Model-based clustering (mixture analysis) was then performed on the age of onset data using the residuals. Clinical variables in subgroups were compared. There was a strong birth cohort effect. Without adjusting for the birth cohort, three subgroups were found by clustering. After adjusting for the birth cohort or when considering only those born after 1959, two subgroups were found. With results of either two or three subgroups, the youngest subgroup was more likely to have a family history of mood disorders and a first episode with depressed polarity. However, without adjusting for birth cohort (three subgroups), family history and polarity of the first episode could not be distinguished between the middle and oldest subgroups. These results using international data confirm prior findings using single country data, that there are subgroups of bipolar I disorder based on the age of onset, and that there is a birth cohort effect. Including the birth cohort adjustment altered the number and characteristics of subgroups detected when clustering by age of onset. Further investigation is needed to determine if combining both approaches will identify subgroups that are more useful for research. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Insights into magmatic processes and hydrothermal alteration of in situ superfast spreading ocean crust at ODP/IODP site 1256 from a cluster analysis of rock magnetic properties

NASA Astrophysics Data System (ADS)

Dekkers, Mark J.; Heslop, David; Herrero-Bervera, Emilio; Acton, Gary; Krasa, David

2014-08-01

We analyze magnetic properties from Ocean Drilling Program (ODP)/Integrated ODP (IODP) Hole 1256D (6°44.1' N, 91°56.1' W) on the Cocos Plate in ˜15.2 Ma oceanic crust generated by superfast seafloor spreading, the only drill hole that has sampled all three oceanic crust layers in a tectonically undisturbed setting. Fuzzy c-means cluster analysis and nonlinear mapping are utilized to study down-hole trends in the ratio of the saturation remanent magnetization and the saturation magnetization, the coercive force, the ratio of the remanent coercive force and coercive force, the low-field magnetic susceptibility, and the Curie temperature, to evaluate the effects of magmatic and hydrothermal processes on magnetic properties. A statistically robust five cluster solution separates the data predominantly into three clusters that express increasing hydrothermal alteration of the lavas, which differ from two distinct clusters mainly representing the dikes and gabbros. Extensive alteration can obliterate magnetic property differences between lavas, dikes, and gabbros. The imprint of thermochemical alteration on the iron-titanium oxides is only partially related to the porosity of the rocks. Thus, the analysis complements interpretation based on electrofacies analysis. All clusters display rock magnetic characteristics compatible with an ability to retain a stable natural remanent magnetization suggesting that the entire sampled sequence of ocean crust can contribute to marine magnetic anomalies. Paleointensity determination is difficult because of the propensity of oxyexsolution during laboratory heating and/or the presence of intergrowths. The upper part of the extrusive sequence, the granoblastic dikes, and moderately altered gabbros may contain a comparatively uncontaminated thermoremanent magnetization.
Local resonances in STM manipulation of chlorobenzene on Si(111)-7×7: performance of different cluster models and density functionals

NASA Astrophysics Data System (ADS)

Utecht, Manuel; Klamroth, Tillmann

2018-07-01

Hot localised charge carriers on the Si(111)-7×7 surface are modelled by small charged clusters. Such resonances induce non-local desorption, i.e. more than 10 nm away from the injection site, of chlorobenzene in scanning tunnelling microscope experiments. We used such a cluster model to characterise resonance localisation and vibrational activation for positive and negative resonances recently. In this work, we investigate to which extent the model depends on details of the used cluster or quantum chemistry methods and try to identify the smallest possible cluster suitable for a description of the neutral surface and the ion resonances. Furthermore, a detailed analysis for different chemisorption orientations is performed. While some properties, as estimates of the resonance energy or absolute values for atomic changes, show such a dependency, the main findings are very robust with respect to changes in the model and/or the chemisorption geometry.
Structure function and splice site analysis of the synaptogenic activity of the neurexin-1 beta LNS domain.

PubMed

Graf, Ethan R; Kang, Yunhee; Hauner, Anna M; Craig, Ann Marie

2006-04-19

Recent findings suggest that the neurexin-neuroligin link promotes both GABAergic and glutamatergic synaptogenesis, but the mechanism by which neurexins influence the clustering of appropriate neuroligins and postsynaptic differentiation remains unclear. Previous studies suggested that the presence or absence of alternatively spliced residues at splice site 4 (S4) in the neurexin LNS domain may regulate neurexin function. We demonstrate that addition of the S4 insert selectively reduces the ability of neurexin-1beta to cluster neuroligin-1/3/4 and glutamatergic postsynaptic proteins, although clustering of neuroligin-2 and GABAergic postsynaptic proteins remain strong. Furthermore, addition of the S4 insert decreases the binding affinity of neurexin-1beta to neuroligins-1 and -4 but has little effect on binding to neuroligins-2 and -3. Additional structure-function studies reveal the neurexin binding interface mediating synaptogenic activity to be composed primarily of residues in the beta2beta3, beta6beta7, and beta10beta11 loops on one rim of the LNS domain beta sandwich. Mutation of two predicted Ca(2+)-binding residues disrupts postsynaptic protein clustering and binding to neuroligins, consistent with previous findings that neurexin-neuroligin binding is Ca2+ dependent. Glutamatergic postsynaptic clustering was more readily disrupted by the mutagenesis than GABAergic postsynaptic protein clustering. Perhaps neurexins-neuroligins, or neurexin-1beta at least, is most important for GABA synapse formation or controlling the balance of GABA and glutamate synapses. These results suggest that differential neurexin-neuroligin binding affinities and splice variations may play an instructive role in postsynaptic differentiation.
Characterization of electrically-active defects in ultraviolet light-emitting diodes with laser-based failure analysis techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Mary A.; Tangyunyong, Paiboon; Cole, Edward I.

2016-01-14

Laser-based failure analysis techniques demonstrate the ability to quickly and non-intrusively screen deep ultraviolet light-emitting diodes (LEDs) for electrically-active defects. In particular, two laser-based techniques, light-induced voltage alteration and thermally-induced voltage alteration, generate applied voltage maps (AVMs) that provide information on electrically-active defect behavior including turn-on bias, density, and spatial location. Here, multiple commercial LEDs were examined and found to have dark defect signals in the AVM indicating a site of reduced resistance or leakage through the diode. The existence of the dark defect signals in the AVM correlates strongly with an increased forward-bias leakage current. This increased leakage ismore » not present in devices without AVM signals. Transmission electron microscopy analysis of a dark defect signal site revealed a dislocation cluster through the pn junction. The cluster included an open core dislocation. Even though LEDs with few dark AVM defect signals did not correlate strongly with power loss, direct association between increased open core dislocation densities and reduced LED device performance has been presented elsewhere [M. W. Moseley et al., J. Appl. Phys. 117, 095301 (2015)].« less
Hydrogen storage in metal-organic frameworks: An investigation of structure-property relationships

NASA Astrophysics Data System (ADS)

Rowsell, Jesse

Metal-organic frameworks (MOFs) have been identified as candidate hydrogen storage materials due to their ability to physisorb large quantities of small molecules. Thirteen compounds (IRMOF-1, -2, -3, -6, -8, -9, -11, -13, -18, -20, MOF-74, MOF-177 and HKUST-1) have been prepared and fully characterized for the evaluation of their dihydrogen (H2) adsorption properties. All compounds display approximately type I isotherms with no hysteresis at 77 K up to 1 atm. The amount adsorbed ranges from 0.89 to 2.54 wt%; however, saturation is not achieved under these conditions. The influences of link functionalization, catenation and topology are examined for the eleven MOFs composed of Zn4O(O2C-)6 clusters. Enhanced H2 uptake by catenated compounds is rationalized by increased overlap of the surface potentials within their narrower pores. This is corroborated by the larger isosteric heat of adsorption of IRMOF-11 compared to IRMOF-1. Inelastic neutron scattering spectroscopic analysis of four Zn4O-based materials (IRMOF-1, -8, -11, and MOF-74) under a range of H2 loading suggests the presence of multiple localized adsorption sites on both the inorganic and organic moieties. To determine the structural details of the adsorption sites, variable temperature single crystal X-ray diffraction was used to analyze adsorbed argon and dinitrogen molecules in IRMOF-1. The principle binding site was found to be the same for both adsorbates and is located on faces of the octahedral Zn4O(O2C-)6 clusters with close contacts to three carboxylate groups. A total of eight symmetry-independent adsorption sites were identified for argon at 30 K. Similar sites were observed for dinitrogen, suggesting that they are good model adsorbates for the behaviour of dihydrogen. Two additional materials composed of inorganic clusters with coordinatively unsaturated metal sites (MOF-74, HKUST-1) were examined and their increased capacities and isosteric heats of adsorption provide further evidence that the interaction is strongest at the inorganic clusters. This enhancement becomes less important at high pressure, where large pore volume proves to be the greater contributor to capacity.
Improving ATLAS grid site reliability with functional tests using HammerCloud

NASA Astrophysics Data System (ADS)

Elmsheuser, Johannes; Legger, Federica; Medrano Llamas, Ramon; Sciacca, Gianfranco; van der Ster, Dan

2012-12-01

With the exponential growth of LHC (Large Hadron Collider) data in 2011, and more coming in 2012, distributed computing has become the established way to analyse collider data. The ATLAS grid infrastructure includes almost 100 sites worldwide, ranging from large national computing centers to smaller university clusters. These facilities are used for data reconstruction and simulation, which are centrally managed by the ATLAS production system, and for distributed user analysis. To ensure the smooth operation of such a complex system, regular tests of all sites are necessary to validate the site capability of successfully executing user and production jobs. We report on the development, optimization and results of an automated functional testing suite using the HammerCloud framework. Functional tests are short lightweight applications covering typical user analysis and production schemes, which are periodically submitted to all ATLAS grid sites. Results from those tests are collected and used to evaluate site performances. Sites that fail or are unable to run the tests are automatically excluded from the PanDA brokerage system, therefore avoiding user or production jobs to be sent to problematic sites.
X-ray and EPR Characterization of the Auxiliary Fe-S Clusters in the Radical SAM Enzyme PqqE.

PubMed

Barr, Ian; Stich, Troy A; Gizzi, Anthony S; Grove, Tyler L; Bonanno, Jeffrey B; Latham, John A; Chung, Tyler; Wilmot, Carrie M; Britt, R David; Almo, Steven C; Klinman, Judith P

2018-02-27

The Radical SAM (RS) enzyme PqqE catalyzes the first step in the biosynthesis of the bacterial cofactor pyrroloquinoline quinone, forming a new carbon-carbon bond between two side chains within the ribosomally synthesized peptide substrate PqqA. In addition to the active site RS 4Fe-4S cluster, PqqE is predicted to have two auxiliary Fe-S clusters, like the other members of the SPASM domain family. Here we identify these sites and examine their structure using a combination of X-ray crystallography and Mössbauer and electron paramagnetic resonance (EPR) spectroscopies. X-ray crystallography allows us to identify the ligands to each of the two auxiliary clusters at the C-terminal region of the protein. The auxiliary cluster nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines, an Fe-S center not seen previously in other SPASM domain proteins; this assignment is further supported by Mössbauer and EPR spectroscopies. The second, more remote cluster (AuxII) is a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue. In addition, we examined the roles these ligands play in catalysis by the RS and AuxII clusters using site-directed mutagenesis coupled with EPR spectroscopy. Lastly, we discuss the possible functional consequences that these unique AuxI and AuxII clusters may have in catalysis for PqqE and how these may extend to additional RS enzymes catalyzing the post-translational modification of ribosomally encoded peptides.
Density functional theory study on the metal-support interaction between a Au9 cluster and an anatase TiO2(001) surface.

PubMed

Jiang, Zong-You; Zhao, Zong-Yan

2017-08-23

Noble metals supported on TiO 2 surfaces have shown extraordinary photocatalytic properties in many important processes such as hydrogenation, water splitting, degradation of hazards, and so on. Using density functional theory calculations, this work has systematically investigated the microstructure and electronic structure of three different Au 9 isomers loaded on anatase TiO 2 (001) surface. The calculated results show that the interaction between the Au 9 cluster and the TiO 2 support is closely related to the adsorption site and the stability of the Au 9 cluster in the gas phase. The adsorption energy of the 2D configuration is larger than that of the 3D configuration of the Au 9 cluster, owing to the stronger interactions between more adsorption sites. The stable adsorption site for Au 9 clusters deposited on the anatase TiO 2 (001) surface tends to be the O 2c -O 2c hollow site. The presentation of the MIGS of the Au 9 cluster, the disappearance of surface states of the TiO 2 (001) surface, and the shifting of the Fermi level from the top of the valence band to the bottom of the conduction band suggest strong interactions between the Au 9 clusters and the TiO 2 (001) surface. Importantly, the electron transfer from the Au 9 clusters to the TiO 2 support occurs mainly through Au-O 2c interactions, which are mainly localized at the contact layer of the Au 9 clusters. These conclusions are useful to understand various physical and chemical properties of noble metal clusters loaded onto an oxide surface, and helpful to design novel metal/semiconductor functional composite materials and devices.
Proteomic analysis of protein-protein interactions within the Cysteine Sulfinate Desulfinase Fe-S cluster biogenesis system.

PubMed

Bolstad, Heather M; Botelho, Danielle J; Wood, Matthew J

2010-10-01

Fe-S cluster biogenesis is of interest to many fields, including bioenergetics and gene regulation. The CSD system is one of three Fe-S cluster biogenesis systems in E. coli and is comprised of the cysteine desulfurase CsdA, the sulfur acceptor protein CsdE, and the E1-like protein CsdL. The biological role, biochemical mechanism, and protein targets of the system remain uncharacterized. Here we present that the active site CsdE C61 has a lowered pK(a) value of 6.5, which is nearly identical to that of C51 in the homologous SufE protein and which is likely critical for its function. We observed that CsdE forms disulfide bonds with multiple proteins and identified the proteins that copurify with CsdE. The identification of Fe-S proteins and both putative and established Fe-S cluster assembly (ErpA, glutaredoxin-3, glutaredoxin-4) and sulfur trafficking (CsdL, YchN) proteins supports the two-pathway model, in which the CSD system is hypothesized to synthesize both Fe-S clusters and other sulfur-containing cofactors. We suggest that the identified Fe-S cluster assembly proteins may be the scaffold and/or shuttle proteins for the CSD system. By comparison with previous analysis of SufE, we demonstrate that there is some overlap in the CsdE and SufE interactomes.
Influence of the South-to-North Water Transfer and the Yangtze River Mitigation Projects on the water quality of Han River, China

NASA Astrophysics Data System (ADS)

Liu, W.; Kuo, Y. M.

2016-12-01

The Middle Route of China's South-to-North Water Transfer (MSNW) and Yangtze-Han River Water Diversion (YHWD) Projects have been operated since 2014, which may deteriorate water quality in Han River. The 11 water sampling sites distributed from the middle and down streams of Han River watershed were monitored monthly between July 2014 and December 2015. Factor analysis and cluster analysis were applied to investigate the major pollution types and main variables influencing water quality in Han River. The factor analysis distinguishes three main pollution types (agricultural nonpoint source, organic, and phosphorus point source pollution) affecting water quality of Han River. Cluster analysis classified all sampling sites into four groups and determined their pollution source for both Dry and Wet seasons. The sites located at central city receive point source pollution in both seasons. The water quality in downstream Han River (excluding central city sites) was influenced by nonpoint source pollution from Jianghan Plain. Variations of water qualities are associated with hydrological conditions varied from operations of engineering projects and seasonal variability especially in Dry season. Good water quality as Class III mainly occurred when flow rate is greater than 800 cms in Dry season. The low average flow rate below 583 cms will degrade water quality as Class V at almost all sites. Elevating the flow rate discharged from MSNW and YHWD Projects to Han River can avoid degrading water quality especially in low flow conditions and may decrease the probability of algal bloom occurrence in Han River. Increasing the flow rate from 400 cms to 700 cms in main Han River can obviously improve the water quality of Han River. The investigation of relationships between water quality and flow rate in both projects can provide management strategies of water quality for various flow conditions.
A simple and efficient method for predicting protein-protein interaction sites.

PubMed

Higa, R H; Tozzi, C L

2008-09-23

Computational methods for predicting protein-protein interaction sites based on structural data are characterized by an accuracy between 70 and 80%. Some experimental studies indicate that only a fraction of the residues, forming clusters in the center of the interaction site, are energetically important for binding. In addition, the analysis of amino acid composition has shown that residues located in the center of the interaction site can be better discriminated from the residues in other parts of the protein surface. In the present study, we implement a simple method to predict interaction site residues exploiting this fact and show that it achieves a very competitive performance compared to other methods using the same dataset and criteria for performance evaluation (success rate of 82.1%).
Unusual interaction of human apurinic/apyrimidinic endonuclease 1 (APE1) with abasic sites via the Schiff-base-dependent mechanism.

PubMed

Ilina, Ekaterina S; Khodyreva, Svetlana N; Lavrik, Olga I

2018-05-03

Clustered apurinic/apyrimidinic (AP) sites are more cytotoxic than isolated AP lesions because double strand breaks (DSB) can be formed during repair of closely positioned bistranded AP sites. Formation of DSB due to simultaneous cleavage of bistranded AP sites may be regulated by proteins specifically interacting with this complex lesion. A set of AP DNA duplexes containing AP sites in both strands in different mutual orientation (BS-AP DNAs) was used for search in the extracts of human cells proteins specifically recognizing clustered AP sites. A protein, which formed the Schiff-base-dependent covalent products having an apparent molecular mass of 50 kDa with the subset of BS-AP DNAs, was identified by mass spectrometry as apurinic/apyrimidinic endonuclease 1 (APE1). The identity of trapped protein was confirmed by Western blot analysis with anti-APE1 antibodies. Purified recombinant human APE1 is also capable of forming the 50 kDa-adducts with efficiency of BS-AP DNAs cross-linking to APE1 being dependent on the mutual orientation of AP sites. In spite of formation of the Schiff-base-dependent intermediate, which is prerequisite for the β-elimination mechanism, APE1 is unable to cleave AP sites. APE1 lacking the first 34 amino acids at the N-terminus, unlike wild type enzyme, is unable to form cross-links with BS-AP DNAs that testifies to the involvement of disordered N-terminal extension, which is enriched in lysine residues, in the interaction with AP sites. The yield of APE1-AP DNA cross-links was found to correlate with the enzyme amount in the extracts estimated by the immunochemical approach; therefore the BS-AP DNA-probes can be useful for comparative analysis of APE1 content in cell extracts. Copyright © 2018. Published by Elsevier B.V.
Neurons in cat V1 show significant clustering by degree of tuning

PubMed Central

Ziskind, Avi J.; Emondi, Al A.; Kurgansky, Andrei V.; Rebrik, Sergei P.

2015-01-01

Neighboring neurons in cat primary visual cortex (V1) have similar preferred orientation, direction, and spatial frequency. How diverse is their degree of tuning for these properties? To address this, we used single-tetrode recordings to simultaneously isolate multiple cells at single recording sites and record their responses to flashed and drifting gratings of multiple orientations, spatial frequencies, and, for drifting gratings, directions. Orientation tuning width, spatial frequency tuning width, and direction selectivity index (DSI) all showed significant clustering: pairs of neurons recorded at a single site were significantly more similar in each of these properties than pairs of neurons from different recording sites. The strength of the clustering was generally modest. The percent decrease in the median difference between pairs from the same site, relative to pairs from different sites, was as follows: for different measures of orientation tuning width, 29–35% (drifting gratings) or 15–25% (flashed gratings); for DSI, 24%; and for spatial frequency tuning width measured in octaves, 8% (drifting gratings). The clusterings of all of these measures were much weaker than for preferred orientation (68% decrease) but comparable to that seen for preferred spatial frequency in response to drifting gratings (26%). For the above properties, little difference in clustering was seen between simple and complex cells. In studies of spatial frequency tuning to flashed gratings, strong clustering was seen among simple-cell pairs for tuning width (70% decrease) and preferred frequency (71% decrease), whereas no clustering was seen for simple-complex or complex-complex cell pairs. PMID:25652921
Degradation of Perfluorinated Ether Lubricants on Pure Aluminum Surfaces: Semiempirical Quantum Chemical Modeling

NASA Technical Reports Server (NTRS)

Slaby, Scott M.; Ewing, David W.; Zehe, Michael J.

1997-01-01

The AM1 semiempirical quantum chemical method was used to model the interaction of perfluoroethers with aluminum surfaces. Perfluorodimethoxymethane and perfluorodimethyl ether were studied interacting with aluminum surfaces, which were modeled by a five-atom cluster and a nine-atom cluster. Interactions were studied for edge (high index) sites and top (low index) sites of the clusters. Both dissociative binding and nondissociative binding were found, with dissociative binding being stronger. The two different ethers bound and dissociated on the clusters in different ways: perfluorodimethoxymethane through its oxygen atoms, but perfluorodimethyl ether through its fluorine atoms. The acetal linkage of perfluorodimeth-oxymethane was the key structural feature of this molecule in its binding and dissociation on the aluminum surface models. The high-index sites of the clusters caused the dissociation of both ethers. These results are consistent with the experimental observation that perfluorinated ethers decompose in contact with sputtered aluminum surfaces.
Interaction of size-selected gold nanoclusters with dopamine

NASA Astrophysics Data System (ADS)

Montone, Georgia R.; Hermann, Eric; Kandalam, Anil K.

2016-12-01

We present density functional theory based results on the interaction of size-selected gold nanoclusters, Au10 and Au20, with dopamine molecule. The gold clusters interact strongly with the nitrogen site of dopamine, thereby forming stable gold-dopamine complexes. Our calculations further show that there is no site specificity on the planar Au10 cluster with all the edge gold atoms equally preferred. On the other hand, in the pyramidal Au20 cluster, the vertex metal atom is the most active site. As the size increased from Au10 to Au20, the interaction strength has shown a declining trend. The effect of aqueous environment on the interaction strengths were also studied by solvation model. It is found that the presence of solvent water stabilizes the interaction between the metal cluster and dopamine molecule, even though for Au10 cluster the energy ordering of the isomers changed from that of the gas-phase.
Risk-adapted monitoring is not inferior to extensive on-site monitoring: Results of the ADAMON cluster-randomised study.

PubMed

Brosteanu, Oana; Schwarz, Gabriele; Houben, Peggy; Paulus, Ursula; Strenge-Hesse, Anke; Zettelmeyer, Ulrike; Schneider, Anja; Hasenclever, Dirk

2017-12-01

Background According to Good Clinical Practice, clinical trials must protect rights and safety of patients and make sure that the trial results are valid and interpretable. Monitoring on-site has an important role in achieving these objectives; it controls trial conduct at trial sites and informs the sponsor on systematic problems. In the past, extensive on-site monitoring with a particular focus on formal source data verification often lost sight of systematic problems in study procedures that endanger Good Clinical Practice objectives. ADAMON is a prospective, stratified, cluster-randomised, controlled study comparing extensive on-site monitoring with risk-adapted monitoring according to a previously published approach. Methods In all, 213 sites from 11 academic trials were cluster-randomised between extensive on-site monitoring (104) and risk-adapted monitoring (109). Independent post-trial audits using structured manuals were performed to determine the frequency of major Good Clinical Practice findings at the patient level. The primary outcome measure is the proportion of audited patients with at least one major audit finding. Analysis relies on logistic regression incorporating trial and monitoring arm as fixed effects and site as random effect. The hypothesis was that risk-adapted monitoring is non-inferior to extensive on-site monitoring with a non-inferiority margin of 0.60 (logit scale). Results Average number of monitoring visits and time spent on-site was 2.1 and 2.7 times higher in extensive on-site monitoring than in risk-adapted monitoring, respectively. A total of 156 (extensive on-site monitoring: 76; risk-adapted monitoring: 80) sites were audited. In 996 of 1618 audited patients, a total of 2456 major audit findings were documented. Depending on the trial, findings were identified in 18%-99% of the audited patients, with no marked monitoring effect in any of the trials. The estimated monitoring effect is -0.04 on the logit scale with two-sided 95% confidence interval (-0.40; 0.33), demonstrating that risk-adapted monitoring is non-inferior to extensive on-site monitoring. At most, extensive on-site monitoring could reduce the frequency of major Good Clinical Practice findings by 8.2% compared with risk-adapted monitoring. Conclusion Compared with risk-adapted monitoring, the potential benefit of extensive on-site monitoring is small relative to overall finding rates, although risk-adapted monitoring requires less than 50% of extensive on-site monitoring resources. Clusters of findings within trials suggest that complicated, overly specific or not properly justified protocol requirements contributed to the overall frequency of findings. Risk-adapted monitoring in only a sample of patients appears sufficient to identify systematic problems in the conduct of clinical trials. Risk-adapted monitoring has a part to play in quality control. However, no monitoring strategy can remedy defects in quality of design. Monitoring should be embedded in a comprehensive quality management approach covering the entire trial lifecycle.
Risk-adapted monitoring is not inferior to extensive on-site monitoring: Results of the ADAMON cluster-randomised study

PubMed Central

Brosteanu, Oana; Schwarz, Gabriele; Houben, Peggy; Paulus, Ursula; Strenge-Hesse, Anke; Zettelmeyer, Ulrike; Schneider, Anja; Hasenclever, Dirk

2017-01-01

Background According to Good Clinical Practice, clinical trials must protect rights and safety of patients and make sure that the trial results are valid and interpretable. Monitoring on-site has an important role in achieving these objectives; it controls trial conduct at trial sites and informs the sponsor on systematic problems. In the past, extensive on-site monitoring with a particular focus on formal source data verification often lost sight of systematic problems in study procedures that endanger Good Clinical Practice objectives. ADAMON is a prospective, stratified, cluster-randomised, controlled study comparing extensive on-site monitoring with risk-adapted monitoring according to a previously published approach. Methods In all, 213 sites from 11 academic trials were cluster-randomised between extensive on-site monitoring (104) and risk-adapted monitoring (109). Independent post-trial audits using structured manuals were performed to determine the frequency of major Good Clinical Practice findings at the patient level. The primary outcome measure is the proportion of audited patients with at least one major audit finding. Analysis relies on logistic regression incorporating trial and monitoring arm as fixed effects and site as random effect. The hypothesis was that risk-adapted monitoring is non-inferior to extensive on-site monitoring with a non-inferiority margin of 0.60 (logit scale). Results Average number of monitoring visits and time spent on-site was 2.1 and 2.7 times higher in extensive on-site monitoring than in risk-adapted monitoring, respectively. A total of 156 (extensive on-site monitoring: 76; risk-adapted monitoring: 80) sites were audited. In 996 of 1618 audited patients, a total of 2456 major audit findings were documented. Depending on the trial, findings were identified in 18%–99% of the audited patients, with no marked monitoring effect in any of the trials. The estimated monitoring effect is −0.04 on the logit scale with two-sided 95% confidence interval (−0.40; 0.33), demonstrating that risk-adapted monitoring is non-inferior to extensive on-site monitoring. At most, extensive on-site monitoring could reduce the frequency of major Good Clinical Practice findings by 8.2% compared with risk-adapted monitoring. Conclusion Compared with risk-adapted monitoring, the potential benefit of extensive on-site monitoring is small relative to overall finding rates, although risk-adapted monitoring requires less than 50% of extensive on-site monitoring resources. Clusters of findings within trials suggest that complicated, overly specific or not properly justified protocol requirements contributed to the overall frequency of findings. Risk-adapted monitoring in only a sample of patients appears sufficient to identify systematic problems in the conduct of clinical trials. Risk-adapted monitoring has a part to play in quality control. However, no monitoring strategy can remedy defects in quality of design. Monitoring should be embedded in a comprehensive quality management approach covering the entire trial lifecycle. PMID:28786330
Population-genetic analysis of HvABCG31 promoter sequence in wild barley (Hordeum vulgare ssp. spontaneum)

PubMed Central

2012-01-01

Background The cuticle is an important adaptive structure whose origin played a crucial role in the transition of plants from aqueous to terrestrial conditions. HvABCG31/Eibi1 is an ABCG transporter gene, involved in cuticle formation that was recently identified in wild barley (Hordeum vulgare ssp. spontaneum). To study the genetic variation of HvABCG31 in different habitats, its 2 kb promoter region was sequenced from 112 wild barley accessions collected from five natural populations from southern and northern Israel. The sites included three mesic and two xeric habitats, and differed in annual rainfall, soil type, and soil water capacity. Results Phylogenetic analysis of the aligned HvABCG31 promoter sequences clustered the majority of accessions (69 out of 71) from the three northern mesic populations into one cluster, while all 21 accessions from the Dead Sea area, a xeric southern population, and two isolated accessions (one from a xeric population at Mitzpe Ramon and one from the xeric ‘African Slope’ of “Evolution Canyon”) formed the second cluster. The southern arid populations included six haplotypes, but they differed from the consensus sequence at a large number of positions, while the northern mesic populations included 15 haplotypes that were, on average, more similar to the consensus sequence. Most of the haplotypes (20 of 22) were unique to a population. Interestingly, higher genetic variation occurred within populations (54.2%) than among populations (45.8%). Analysis of the promoter region detected a large number of transcription factor binding sites: 121–128 and 121–134 sites in the two southern arid populations, and 123–128,125–128, and 123–125 sites in the three northern mesic populations. Three types of TFBSs were significantly enriched: those related to GA (gibberellin), Dof (DNA binding with one finger), and light. Conclusions Drought stress and adaptive natural selection may have been important determinants in the observed sequence variation of HvABCG31 promoter. Abiotic stresses may be involved in the HvABCG31 gene transcription regulations, generating more protective cuticles in plants under stresses. PMID:23006777
Meteorology-induced variations in the spatial behavior of summer ozone pollution in Central California

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Ling; Harley, Robert A.; Brown, Nancy J.

Cluster analysis was applied to daily 8 h ozone maxima modeled for a summer season to characterize meteorology-induced variations in the spatial distribution of ozone. Principal component analysis is employed to form a reduced dimension set to describe and interpret ozone spatial patterns. The first three principal components (PCs) capture {approx}85% of total variance, with PC1 describing a general spatial trend, and PC2 and PC3 each describing a spatial contrast. Six clusters were identified for California's San Joaquin Valley (SJV) with two low, three moderate, and one high-ozone cluster. The moderate ozone clusters are distinguished by elevated ozone levels inmore » different parts of the valley: northern, western, and eastern, respectively. The SJV ozone clusters have stronger coupling with the San Francisco Bay area (SFB) than with the Sacramento Valley (SV). Variations in ozone spatial distributions induced by anthropogenic emission changes are small relative to the overall variations in ozone amomalies observed for the whole summer. Ozone regimes identified here are mostly determined by the direct and indirect meteorological effects. Existing measurement sites are sufficiently representative to capture ozone spatial patterns in the SFB and SV, but the western side of the SJV is under-sampled.« less
Chapter 7. Cloning and analysis of natural product pathways.

PubMed

Gust, Bertolt

2009-01-01

The identification of gene clusters of natural products has lead to an enormous wealth of information about their biosynthesis and its regulation, and about self-resistance mechanisms. Well-established routine techniques are now available for the cloning and sequencing of gene clusters. The subsequent functional analysis of the complex biosynthetic machinery requires efficient genetic tools for manipulation. Until recently, techniques for the introduction of defined changes into Streptomyces chromosomes were very time-consuming. In particular, manipulation of large DNA fragments has been challenging due to the absence of suitable restriction sites for restriction- and ligation-based techniques. The homologous recombination approach called recombineering (referred to as Red/ET-mediated recombination in this chapter) has greatly facilitated targeted genetic modifications of complex biosynthetic pathways from actinomycetes by eliminating many of the time-consuming and labor-intensive steps. This chapter describes techniques for the cloning and identification of biosynthetic gene clusters, for the generation of gene replacements within such clusters, for the construction of integrative library clones and their expression in heterologous hosts, and for the assembly of entire biosynthetic gene clusters from the inserts of individual library clones. A systematic approach toward insertional mutation of a complete Streptomyces genome is shown by the use of an in vitro transposon mutagenesis procedure.

ELKS, a Protein Structurally Related to the Active Zone-associated Protein CAST, Is Expressed in Pancreatic β Cells and Functions in Insulin Exocytosis: Interaction of ELKS with Exocytotic Machinery Analyzed by Total Internal Reflection Fluorescence MicroscopyV⃞

PubMed Central

Ohara-Imaizumi, Mica; Ohtsuka, Toshihisa; Matsushima, Satsuki; Akimoto, Yoshihiro; Nishiwaki, Chiyono; Nakamichi, Yoko; Kikuta, Toshiteru; Nagai, Shintaro; Kawakami, Hayato; Watanabe, Takashi; Nagamatsu, Shinya

2005-01-01

The cytomatrix at the active zone (CAZ) has been implicated in defining the site of Ca2+-dependent exocytosis of neurotransmitters. Here, we demonstrate the expression and function of ELKS, a protein structurally related to the CAZ protein CAST, in insulin exocytosis. The results of confocal and immunoelectron microscopic analysis showed that ELKS is present in pancreatic β cells and is localized close to insulin granules docked on the plasma membrane-facing blood vessels. Total internal reflection fluorescence microscopy imaging in insulin-producing clonal cells revealed that the ELKS clusters are less dense and unevenly distributed than syntaxin 1 clusters, which are enriched in the plasma membrane. Most of the ELKS clusters were on the docking sites of insulin granules that were colocalized with syntaxin 1 clusters. Total internal reflection fluorescence images of single-granule motion showed that the fusion events of insulin granules mostly occurred on the ELKS cluster, where repeated fusion was sometimes observed. When the Bassoon-binding region of ELKS was introduced into the cells, the docking and fusion of insulin granules were markedly reduced. Moreover, attenuation of ELKS expression by small interfering RNA reduced the glucose-evoked insulin release. These data suggest that the CAZ-related protein ELKS functions in insulin exocytosis from pancreatic β cells. PMID:15888548
Variation in selection of microhabitats by Merriam's turkey brood hens

Treesearch

Mark A. Rumble; Stanley H. Anderson

1997-01-01

We studied microhabitats of Merriamâs turkey (Meleagris gallopavo merriami) brood hens in a ponderosa pine (Pinus ponderosa) ecosystem in South Dakota from 1986 to 1988. Cluster analysis indicated three groups of microhabitats, open-shrub, open-grasslforb and forest, based on vegetation characteristics at sites selected by brood...
Relationships between diatoms and tidal environments in Oregon and Washington, USA

USGS Publications Warehouse

Sawai, Yuki; Horton, Benjamin P.; Kemp, Andrew C.; Hawkes, Andrea D.; Nagumo, Tamostsu; Nelson, Alan R.

2016-01-01

A new regional dataset comprising 425 intertidal diatom taxa from 175 samples from 11 ecologically diverse Oregon and Washington estuaries illustrates the importance of compiling a large modern dataset from a range of sites. Cluster analyses and detrended correspondence analysis of the diatom assemblages identify distinct vertical zones within supratidal, intertidal and subtidal environments at six of the 11 study sites, but the abundance of some of the most common species varies widely among and within sites. Canonical correspondence analysis of the regional dataset shows relationships between diatom species and tidal exposure, salinity and substratum (grain size and organic content). Correspondence analyses of local datasets show higher values of explained variation than the analysis of the combined regional dataset. Our results emphasize that studies of the autecology of diatom species require many samples from a range of modern environments to adequately characterize species–environment relationships.
Association between maternal health literacy and child vaccination in India: a cross-sectional study

PubMed Central

Johri, Mira; Subramanian, S V; Sylvestre, Marie-Pierre; Dudeja, Sakshi; Chandra, Dinesh; Koné, Georges K; Sharma, Jitendar K; Pahwa, Smriti

2015-01-01

Background Education of mothers may improve child health. We investigated whether maternal health literacy, a rapidly modifiable factor related to mother's education, was associated with children's receipt of vaccines in two underserved Indian communities. Methods Cross-sectional surveys in an urban and a rural site. We assessed health literacy using Indian child health promotion materials. The outcome was receipt of three doses of diphtheria-tetanus-pertussis (DTP3) vaccine. We used multivariate logistic regression to investigate the relationship between maternal health literacy and vaccination status independently in each site. For both sites, adjusted models considered maternal age, maternal and paternal education, child sex, birth order, household religion and wealth quintile. Rural analyses used multilevel models adjusted for service delivery characteristics. Urban analyses represented cluster characteristics through fixed effects. Results The rural analysis included 1170 women from 60 villages. The urban analysis included 670 women from nine slum clusters. In each site, crude and adjusted models revealed a positive association between maternal health literacy and DTP3. In the rural site, the adjusted OR was 1.57 (95% CI 1.11 to 2.21, p=0.010) for those with medium health literacy, and OR=1.30 (95% CI 0.89 to 1.91, p=0.172) for those with high health literacy. In the urban site, the adjusted OR was 1.10 (95% CI 0.65 to 1.88, p=0.705) for those with medium health literacy, and OR=2.06 (95% CI 1.06 to 3.99, p=0.032) for those with high health literacy. Conclusions In these study settings, maternal health literacy is independently associated with child vaccination. Initiatives targeting health literacy could improve vaccination coverage. PMID:25827469
Nationwide inventory of mosquito biodiversity (Diptera: Culicidae) in Belgium, Europe.

PubMed

Versteirt, V; Boyer, S; Damiens, D; De Clercq, E M; Dekoninck, W; Ducheyne, E; Grootaert, P; Garros, C; Hance, T; Hendrickx, G; Coosemans, M; Van Bortel, W

2013-04-01

To advance our restricted knowledge on mosquito biodiversity and distribution in Belgium, a national inventory started in 2007 (MODIRISK) based on a random selection of 936 collection points in three main environmental types: urban, rural and natural areas. Additionally, 64 sites were selected because of the risk of importing a vector or pathogen in these sites. Each site was sampled once between May and October 2007 and once in 2008 using Mosquito Magnet Liberty Plus traps. Diversity in pre-defined habitat types was calculated using three indices. The association between species and environmental types was assessed using a correspondence analysis. Twenty-three mosquito species belonging to traditionally recognized genera were found, including 21 indigenous and two exotic species. Highest species diversity (Simpson 0.765) and species richness (20 species) was observed in natural areas, although urban sites scored also well (Simpson 0.476, 16 species). Four clusters could be distinguished based on the correspondence analysis. The first one is related to human modified landscapes (such as urban, rural and industrial sites). A second is composed of species not associated with a specific habitat type, including the now widely distributed Anopheles plumbeus. A third group includes species commonly found in restored natural or bird migration areas, and a fourth cluster is composed of forest species. Outcomes of this study demonstrate the effectiveness of the designed sampling scheme and support the choice of the trap type. Obtained results of this first country-wide inventory of the Culicidae in Belgium may serve as a basis for risk assessment of emerging mosquito-borne diseases.
Evidence based community mobilization for dengue prevention in Nicaragua and Mexico (Camino Verde, the Green Way): cluster randomized controlled trial

PubMed Central

Nava-Aguilera, Elizabeth; Arosteguí, Jorge; Morales-Perez, Arcadio; Suazo-Laguna, Harold; Legorreta-Soberanis, José; Hernandez-Alvarez, Carlos; Fernandez-Salas, Ildefonso; Paredes-Solís, Sergio; Balmaseda, Angel; Cortés-Guzmán, Antonio Juan; Serrano de los Santos, René; Coloma, Josefina; Ledogar, Robert J; Harris, Eva

2015-01-01

Objective To test whether community mobilization adds effectiveness to conventional dengue control. Design Pragmatic open label parallel group cluster randomized controlled trial. Those assessing the outcomes and analyzing the data were blinded to group assignment. Centralized computerized randomization after the baseline study allocated half the sites to intervention, stratified by country, evidence of recent dengue virus infection in children aged 3-9, and vector indices. Setting Random sample of communities in Managua, capital of Nicaragua, and three coastal regions in Guerrero State in the south of Mexico. Participants Residents in a random sample of census enumeration areas across both countries: 75 intervention and 75 control clusters (about 140 households each) were randomized and analyzed (60 clusters in Nicaragua and 90 in Mexico), including 85 182 residents in 18 838 households. Interventions A community mobilization protocol began with community discussion of baseline results. Each intervention cluster adapted the basic intervention—chemical-free prevention of mosquito reproduction—to its own circumstances. All clusters continued the government run dengue control program. Main outcome measures Primary outcomes per protocol were self reported cases of dengue, serological evidence of recent dengue virus infection, and conventional entomological indices (house index: households with larvae or pupae/households examined; container index: containers with larvae or pupae/containers examined; Breteau index: containers with larvae or pupae/households examined; and pupae per person: pupae found/number of residents). Per protocol secondary analysis examined the effect of Camino Verde in the context of temephos use. Results With cluster as the unit of analysis, serological evidence from intervention sites showed a lower risk of infection with dengue virus in children (relative risk reduction 29.5%, 95% confidence interval 3.8% to 55.3%), fewer reports of dengue illness (24.7%, 1.8% to 51.2%), fewer houses with larvae or pupae among houses visited (house index) (44.1%, 13.6% to 74.7%), fewer containers with larvae or pupae among containers examined (container index) (36.7%, 24.5% to 44.8%), fewer containers with larvae or pupae among houses visited (Breteau index) (35.1%, 16.7% to 55.5%), and fewer pupae per person (51.7%, 36.2% to 76.1%). The numbers needed to treat were 30 (95% confidence interval 20 to 59) for a lower risk of infection in children, 71 (48 to 143) for fewer reports of dengue illness, 17 (14 to 20) for the house index, 37 (35 to 67) for the container index, 10 (6 to 29) for the Breteau index, and 12 (7 to 31) for fewer pupae per person. Secondary per protocol analysis showed no serological evidence of a protective effect of temephos. Conclusions Evidence based community mobilization can add effectiveness to dengue vector control. Each site implementing the intervention in its own way has the advantage of local customization and strong community engagement. Trial registration ISRCTN27581154 PMID:26156323
Evidence based community mobilization for dengue prevention in Nicaragua and Mexico (Camino Verde, the Green Way): cluster randomized controlled trial.

PubMed

Andersson, Neil; Nava-Aguilera, Elizabeth; Arosteguí, Jorge; Morales-Perez, Arcadio; Suazo-Laguna, Harold; Legorreta-Soberanis, José; Hernandez-Alvarez, Carlos; Fernandez-Salas, Ildefonso; Paredes-Solís, Sergio; Balmaseda, Angel; Cortés-Guzmán, Antonio Juan; Serrano de Los Santos, René; Coloma, Josefina; Ledogar, Robert J; Harris, Eva

2015-07-08

To test whether community mobilization adds effectiveness to conventional dengue control. Pragmatic open label parallel group cluster randomized controlled trial. Those assessing the outcomes and analyzing the data were blinded to group assignment. Centralized computerized randomization after the baseline study allocated half the sites to intervention, stratified by country, evidence of recent dengue virus infection in children aged 3-9, and vector indices. Random sample of communities in Managua, capital of Nicaragua, and three coastal regions in Guerrero State in the south of Mexico. Residents in a random sample of census enumeration areas across both countries: 75 intervention and 75 control clusters (about 140 households each) were randomized and analyzed (60 clusters in Nicaragua and 90 in Mexico), including 85,182 residents in 18,838 households. A community mobilization protocol began with community discussion of baseline results. Each intervention cluster adapted the basic intervention-chemical-free prevention of mosquito reproduction-to its own circumstances. All clusters continued the government run dengue control program. Primary outcomes per protocol were self reported cases of dengue, serological evidence of recent dengue virus infection, and conventional entomological indices (house index: households with larvae or pupae/households examined; container index: containers with larvae or pupae/containers examined; Breteau index: containers with larvae or pupae/households examined; and pupae per person: pupae found/number of residents). Per protocol secondary analysis examined the effect of Camino Verde in the context of temephos use. With cluster as the unit of analysis, serological evidence from intervention sites showed a lower risk of infection with dengue virus in children (relative risk reduction 29.5%, 95% confidence interval 3.8% to 55.3%), fewer reports of dengue illness (24.7%, 1.8% to 51.2%), fewer houses with larvae or pupae among houses visited (house index) (44.1%, 13.6% to 74.7%), fewer containers with larvae or pupae among containers examined (container index) (36.7%, 24.5% to 44.8%), fewer containers with larvae or pupae among houses visited (Breteau index) (35.1%, 16.7% to 55.5%), and fewer pupae per person (51.7%, 36.2% to 76.1%). The numbers needed to treat were 30 (95% confidence interval 20 to 59) for a lower risk of infection in children, 71 (48 to 143) for fewer reports of dengue illness, 17 (14 to 20) for the house index, 37 (35 to 67) for the container index, 10 (6 to 29) for the Breteau index, and 12 (7 to 31) for fewer pupae per person. Secondary per protocol analysis showed no serological evidence of a protective effect of temephos. Evidence based community mobilization can add effectiveness to dengue vector control. Each site implementing the intervention in its own way has the advantage of local customization and strong community engagement. ISRCTN27581154. © Andersson et al 2015.
Spiral ganglion cell site of excitation I: comparison of scala tympani and intrameatal electrode responses.

PubMed

Cartee, Lianne A; Miller, Charles A; van den Honert, Chris

2006-05-01

To determine the site of excitation on the spiral ganglion cell in response to electrical stimulation similar to that from a cochlear implant, single-fiber responses to electrical stimuli delivered by an electrode positioned in the scala tympani were compared to responses from stimuli delivered by an electrode placed in the internal auditory meatus. The response to intrameatal stimulation provided a control set of data with a known excitation site, the central axon of the spiral ganglion cell. For both intrameatal and scala tympani stimuli, the responses to single-pulse, summation, and refractory stimulus protocols were recorded. The data demonstrated that summation pulses, as opposed to single pulses, are likely to give the most insightful measures for determination of the site of excitation. Single-fiber summation data for both scala tympani and intrameatally stimulated fibers were analyzed with a clustering algorithm. Combining cluster analysis and additional numerical modeling data, it was hypothesized that the scala tympani responses corresponded to central excitation, peripheral excitation adjacent to the cell body, and peripheral excitation at a site distant from the cell body. Fibers stimulated by an intrameatal electrode demonstrated the greatest range of jitter measurements indicating that greater fiber independence may be achieved with intrameatal stimulation.
Sequential analysis of hydrochemical data for watershed characterization.

PubMed

Thyne, Geoffrey; Güler, Cüneyt; Poeter, Eileen

2004-01-01

A methodology for characterizing the hydrogeology of watersheds using hydrochemical data that combine statistical, geochemical, and spatial techniques is presented. Surface water and ground water base flow and spring runoff samples (180 total) from a single watershed are first classified using hierarchical cluster analysis. The statistical clusters are analyzed for spatial coherence confirming that the clusters have a geological basis corresponding to topographic flowpaths and showing that the fractured rock aquifer behaves as an equivalent porous medium on the watershed scale. Then principal component analysis (PCA) is used to determine the sources of variation between parameters. PCA analysis shows that the variations within the dataset are related to variations in calcium, magnesium, SO4, and HCO3, which are derived from natural weathering reactions, and pH, NO3, and chlorine, which indicate anthropogenic impact. PHREEQC modeling is used to quantitatively describe the natural hydrochemical evolution for the watershed and aid in discrimination of samples that have an anthropogenic component. Finally, the seasonal changes in the water chemistry of individual sites were analyzed to better characterize the spatial variability of vertical hydraulic conductivity. The integrated result provides a method to characterize the hydrogeology of the watershed that fully utilizes traditional data.
Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens

PubMed Central

Rensing, Stefan A; Fritzowsky, Dana; Lang, Daniel; Reski, Ralf

2005-01-01

Background The moss Physcomitrella patens is an emerging plant model system due to its high rate of homologous recombination, haploidy, simple body plan, physiological properties as well as phylogenetic position. Available EST data was clustered and assembled, and provided the basis for a genome-wide analysis of protein encoding genes. Results We have clustered and assembled Physcomitrella patens EST and CDS data in order to represent the transcriptome of this non-seed plant. Clustering of the publicly available data and subsequent prediction resulted in a total of 19,081 non-redundant ORF. Of these putative transcripts, approximately 30% have a homolog in both rice and Arabidopsis transcriptome. More than 130 transcripts are not present in seed plants but can be found in other kingdoms. These potential "retained genes" might have been lost during seed plant evolution. Functional annotation of these genes reveals unequal distribution among taxonomic groups and intriguing putative functions such as cytotoxicity and nucleic acid repair. Whereas introns in the moss are larger on average than in the seed plant Arabidopsis thaliana, position and amount of introns are approximately the same. Contrary to Arabidopsis, where CDS contain on average 44% G/C, in Physcomitrella the average G/C content is 50%. Interestingly, moss orthologs of Arabidopsis genes show a significant drift of codon fraction usage, towards the seed plant. While averaged codon bias is the same in Physcomitrella and Arabidopsis, the distribution pattern is different, with 15% of moss genes being unbiased. Species-specific, sensitive and selective splice site prediction for Physcomitrella has been developed using a dataset of 368 donor and acceptor sites, utilizing a support vector machine. The prediction accuracy is better than those achieved with tools trained on Arabidopsis data. Conclusion Analysis of the moss transcriptome displays differences in gene structure, codon and splice site usage in comparison with the seed plant Arabidopsis. Putative retained genes exhibit possible functions that might explain the peculiar physiological properties of mosses. Both the transcriptome representation (including a BLAST and retrieval service) and splice site prediction have been made available on , setting the basis for assembly and annotation of the Physcomitrella genome, of which draft shotgun sequences will become available in 2005. PMID:15784153
Site-directed mutagenesis of Azotobacter vinelandii ferredoxin I: [Fe-S] cluster-driven protein rearrangement.

PubMed Central

Martín, A E; Burgess, B K; Stout, C D; Cash, V L; Dean, D R; Jensen, G M; Stephens, P J

1990-01-01

Azotobacter vinelandii ferredoxin I is a small protein that contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. Recently the x-ray crystal structure has been redetermined and the fdxA gene, which encodes the protein, has been cloned and sequenced. Here we report the site-directed mutation of Cys-20, which is a ligand of the [4Fe-4S] cluster in the native protein, to alanine and the characterization of the protein product by x-ray crystallographic and spectroscopic methods. The data show that the mutant protein again contains one [4Fe-4S] cluster and one [3Fe-4S] cluster. The new [4Fe-4S] cluster obtains its fourth ligand from Cys-24, a free cysteine in the native structure. The formation of this [4Fe-4S] cluster drives rearrangement of the protein structure. PMID:2153958
Site-specific polarizabilities as descriptors of metallic behavior in atomic clusters

NASA Astrophysics Data System (ADS)

Jackson, Koblar; Jellinek, Julius

The electric dipole polarizability of a cluster is a measure of its response to an applied electric field. The site specific polarizability method decomposes the total cluster polarizability into contributions from individual atoms and also allows it to be partitioned into charge transfer and electric dipole contributions. By systematically examining the trends in these quantities for several types of metal atom clusters over a wide range of cluster sizes, we find common characteristics that uniquely link the behavior of the clusters to that of the corresponding bulk metals for clusters as small as 10 atoms. We discuss these trends and compare and contrast them with results for non-metal clusters. This work was supported by the Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences, U.S. Department of Energy under Grant SC0001330 (KAJ) and Contract No. DE-AC02-06CH11357 (JJ).
A baseline record of trace elements concentration along the beach placer mining areas of Kanyakumari coast, South India.

PubMed

Simon Peter, T; Chandrasekar, N; John Wilson, J S; Selvakumar, S; Krishnakumar, S; Magesh, N S

2017-06-15

Trace element concentration in the beach placer mining areas of Kanyakumari coast, South India was assessed. Sewage and contaminated sediments from mining sites has contaminated the surface sediments. Enrichment factor indicates moderately severe enrichment for Pb, minor enrichment for Mn, Zn, Ni, Fe and no enrichment for Cr and Cu. The Igeo values show higher concentration of Pb ranging in the scale of 3-4, which shows strong contamination due to high anthropogenic activity such as mining and terrestrial influences into the coastal regions. Correlation coefficient shows that most of the elements are associated with each other except Ni and Pb. Factor analysis reveals that Mn, Zn, Fe, Cr, Pb and Cu are having a significant loading and it indicates that these elements are mainly derived from similar origin. The cluster analysis clearly indicated that the mining areas are grouped under cluster 2 and non-mining areas are clustered under group 1. Copyright © 2017 Elsevier Ltd. All rights reserved.
Helium behavior in oxide dispersion strengthened (ODS) steel: Insights from ab initio modeling

NASA Astrophysics Data System (ADS)

Sun, Dan; Li, Ruihuan; Ding, Jianhua; Huang, Shaosong; Zhang, Pengbo; Lu, Zheng; Zhao, Jijun

2018-02-01

Using first-principles calculations, we systemically investigate the energetics and stability behavior of helium (He) atoms and small Hen (n = 2-4) clusters inside oxide dispersion strengthened (ODS) steel, as well as the incorporation of large amount of He atoms inside Y2O3 crystal. From the energetic point of view, He atom inside Y2O3 cluster is most stable, followed by the interstitial sites at the α-Fe/Y2O3 interface, and the tetrahedral interstitial sites inside α-Fe region. We further consider Hen (n = 2-4) clusters at the tetrahedral interstitial site surrounded by four Y atoms, which is the most stable site in the ODS steel model. The incorporation energies of all these Hen clusters are lower than that of single He atom in α-Fe, while the binding energy between two He atoms is relatively small. With insertion of 15 He atoms into 80-atom unit cell of Y2O3 crystal, the incorporation energy of He atoms is still lower than that of He4 cluster in α-Fe crystal. These theoretical results suggest that He atoms tend to aggregate inside Y2O3 clusters or at the α-Fe/Y2O3 interface, which is beneficial to prevent the He embrittlement in ODS steels.
Allopatric integrations selectively change host transcriptomes, leading to varied expression efficiencies of exotic genes in Myxococcus xanthus.

PubMed

Zhu, Li-Ping; Yue, Xin-Jing; Han, Kui; Li, Zhi-Feng; Zheng, Lian-Shuai; Yi, Xiu-Nan; Wang, Hai-Long; Zhang, You-Ming; Li, Yue-Zhong

2015-07-22

Exotic genes, especially clustered multiple-genes for a complex pathway, are normally integrated into chromosome for heterologous expression. The influences of insertion sites on heterologous expression and allotropic expressions of exotic genes on host remain mostly unclear. We compared the integration and expression efficiencies of single and multiple exotic genes that were inserted into Myxococcus xanthus genome by transposition and attB-site-directed recombination. While the site-directed integration had a rather stable chloramphenicol acetyl transferase (CAT) activity, the transposition produced varied CAT enzyme activities. We attempted to integrate the 56-kb gene cluster for the biosynthesis of antitumor polyketides epothilones into M. xanthus genome by site-direction but failed, which was determined to be due to the insertion size limitation at the attB site. The transposition technique produced many recombinants with varied production capabilities of epothilones, which, however, were not paralleled to the transcriptional characteristics of the local sites where the genes were integrated. Comparative transcriptomics analysis demonstrated that the allopatric integrations caused selective changes of host transcriptomes, leading to varied expressions of epothilone genes in different mutants. With the increase of insertion fragment size, transposition is a more practicable integration method for the expression of exotic genes. Allopatric integrations selectively change host transcriptomes, which lead to varied expression efficiencies of exotic genes.
Identification and analysis of integrons and cassette arrays in bacterial genomes.

PubMed

Cury, Jean; Jové, Thomas; Touchon, Marie; Néron, Bertrand; Rocha, Eduardo Pc

2016-06-02

Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program - IntegronFinder - to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
On-demand provisioning of HEP compute resources on cloud sites and shared HPC centers

NASA Astrophysics Data System (ADS)

Erli, G.; Fischer, F.; Fleig, G.; Giffels, M.; Hauth, T.; Quast, G.; Schnepf, M.; Heese, J.; Leppert, K.; Arnaez de Pedro, J.; Sträter, R.

2017-10-01

This contribution reports on solutions, experiences and recent developments with the dynamic, on-demand provisioning of remote computing resources for analysis and simulation workflows. Local resources of a physics institute are extended by private and commercial cloud sites, ranging from the inclusion of desktop clusters over institute clusters to HPC centers. Rather than relying on dedicated HEP computing centers, it is nowadays more reasonable and flexible to utilize remote computing capacity via virtualization techniques or container concepts. We report on recent experience from incorporating a remote HPC center (NEMO Cluster, Freiburg University) and resources dynamically requested from the commercial provider 1&1 Internet SE into our intitute’s computing infrastructure. The Freiburg HPC resources are requested via the standard batch system, allowing HPC and HEP applications to be executed simultaneously, such that regular batch jobs run side by side to virtual machines managed via OpenStack [1]. For the inclusion of the 1&1 commercial resources, a Python API and SDK as well as the possibility to upload images were available. Large scale tests prove the capability to serve the scientific use case in the European 1&1 datacenters. The described environment at the Institute of Experimental Nuclear Physics (IEKP) at KIT serves the needs of researchers participating in the CMS and Belle II experiments. In total, resources exceeding half a million CPU hours have been provided by remote sites.
Combining microseismic and geomechanical observations to interpret storage integrity at the In Salah CCS site

NASA Astrophysics Data System (ADS)

Goertz-Allmann, Bettina P.; Kühn, Daniela; Oye, Volker; Bohloli, Bahman; Aker, Eyvind

2014-07-01

We present results from microseismic monitoring and geomechanical analysis obtained at the industrial-scale CO2 sequestration site at the In Salah gas development project in Algeria. More than 5000 microseismic events have been detected at a pilot monitoring well using a master event cross-correlation method. The microseismic activity occurs in four distinct clusters and thereof three clearly correlate with injection rates and wellhead pressures. These event clusters are consistent with a location within the reservoir interval. However, due to insufficient network geometry there are large uncertainties on event location. We estimate a fracture pressure of 155 bar (at the wellhead) from the comparison of injection pressure and injection rate and conclude that reservoir fracture pressure of the injection horizon has most likely been exceeded occasionally, accompanied by increased microseismic activity. Our analysis of 3-D ray tracing for direct and converted phases suggests that one of the event clusters is located at a shallower depth than the reservoir injection interval. However, this event cluster is most likely unrelated to changes in the injection activity at a single well, as the event times do not correlate with the wellhead pressures. Furthermore, this event cluster shows b-values close to one, indicating re-activated natural or tectonic seismicity on pre-existing weakness zones rather than injection induced seismicity. Analysis of event azimuths and significant shear wave splitting of up to 5 per cent provide further valuable insight into fluid migration and fracture orientation at the reservoir level. Although only one geophone was available during the critical injection period, the microseismic monitoring of CO2 injection at In Salah is capable of addressing some of the most relevant questions about fluid migration and reservoir integrity. An improved monitoring array with larger aperture and higher sensitivity is highly recommended, as it could greatly enhance the value of this technique. As such, real-time microseismic monitoring can be used to guide the injection pressure below fracture pressure, thus providing a tool to mitigate the risk of inducing felt seismicity and compromising seal integrity.
Detection of canonical A-to-G editing events at 3′ UTRs and microRNA target sites in human lungs using next-generation sequencing

PubMed Central

Soundararajan, Ramani; Stearns, Timothy M.; Griswold, Anthony J.; Mehta, Arpit; Czachor, Alexander; Fukumoto, Jutaro; Lockey, Richard F.; King, Benjamin L.; Kolliputi, Narasaiah

2015-01-01

RNA editing is a post-transcriptional modification of RNA. The majority of these changes result from adenosine deaminase acting on RNA (ADARs) catalyzing the conversion of adenosine residues to inosine in double-stranded RNAs (dsRNAs). Massively parallel sequencing has enabled the identification of RNA editing sites in human transcriptomes. In this study, we sequenced DNA and RNA from human lungs and identified RNA editing sites with high confidence via a computational pipeline utilizing stringent analysis thresholds. We identified a total of 3,447 editing sites that overlapped in three human lung samples, and with 50% of these sites having canonical A-to-G base changes. Approximately 27% of the edited sites overlapped with Alu repeats, and showed A-to-G clustering (>3 clusters in 100 bp). The majority of edited sites mapped to either 3′ untranslated regions (UTRs) or introns close to splice sites; whereas, only few sites were in exons resulting in non-synonymous amino acid changes. Interestingly, we identified 652 A-to-G editing events in the 3′ UTR of 205 target genes that mapped to 932 potential miRNA target binding sites. Several of these miRNA edited sites were validated in silico. Additionally, we validated several A-to-G edited sites by Sanger sequencing. Altogether, our study suggests a role for RNA editing in miRNA-mediated gene regulation and splicing in human lungs. In this study, we have generated a RNA editome of human lung tissue that can be compared with other RNA editomes across different lung tissues to delineate a role for RNA editing in normal and diseased states. PMID:26486088
Detection of canonical A-to-G editing events at 3' UTRs and microRNA target sites in human lungs using next-generation sequencing.

PubMed

Soundararajan, Ramani; Stearns, Timothy M; Griswold, Anthony L; Mehta, Arpit; Czachor, Alexander; Fukumoto, Jutaro; Lockey, Richard F; King, Benjamin L; Kolliputi, Narasaiah

2015-11-03

RNA editing is a post-transcriptional modification of RNA. The majority of these changes result from adenosine deaminase acting on RNA (ADARs) catalyzing the conversion of adenosine residues to inosine in double-stranded RNAs (dsRNAs). Massively parallel sequencing has enabled the identification of RNA editing sites in human transcriptomes. In this study, we sequenced DNA and RNA from human lungs and identified RNA editing sites with high confidence via a computational pipeline utilizing stringent analysis thresholds. We identified a total of 3,447 editing sites that overlapped in three human lung samples, and with 50% of these sites having canonical A-to-G base changes. Approximately 27% of the edited sites overlapped with Alu repeats, and showed A-to-G clustering (>3 clusters in 100 bp). The majority of edited sites mapped to either 3' untranslated regions (UTRs) or introns close to splice sites; whereas, only few sites were in exons resulting in non-synonymous amino acid changes. Interestingly, we identified 652 A-to-G editing events in the 3' UTR of 205 target genes that mapped to 932 potential miRNA target binding sites. Several of these miRNA edited sites were validated in silico. Additionally, we validated several A-to-G edited sites by Sanger sequencing. Altogether, our study suggests a role for RNA editing in miRNA-mediated gene regulation and splicing in human lungs. In this study, we have generated a RNA editome of human lung tissue that can be compared with other RNA editomes across different lung tissues to delineate a role for RNA editing in normal and diseased states.

Distribution of beach litter along the coastline of Cádiz, Spain.

PubMed

Williams, Allan Thomas; Randerson, Peter; Di Giacomo, Carlo; Anfuso, Giorgio; Macias, Ana; Perales, José Antonio

2016-06-15

A total of 59 categories of litter items were found at 20 beaches (13 mechanically cleaned, 7 non-cleaned) in the Cádiz tourist environment, Spain. Cluster Analysis and Principal Components Analysis were used to highlight similarities and contrasts between sites and/or associations between litter categories. Multivariate analyses separated beaches according to the total numbers of litter items present. Non-cleaned sites showed a variety of litter category abundance with distinct origins and abundant, ubiquitous items (plastic and glass fragments). Of the 7 non-cleaned beaches (49 litter categories) river-mouth sites were distinct due with high numbers of litter items. The sheltered inner part of Cádiz Bay beaches had a wide range of litter type. Many sites were associated with locally deposited recreational litter categories; while industrial/commercial/fishing categories were abundant only at a few sites, indicating items transported onto the shore from the Guadalete river. Copyright © 2016 Elsevier Ltd. All rights reserved.
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

PubMed Central

Blin, Kai; Duddela, Srikanth; Krug, Daniel; Kim, Hyun Uk; Bruccoleri, Robert; Lee, Sang Yup; Fischbach, Michael A; Müller, Rolf; Wohlleben, Wolfgang; Breitling, Rainer; Takano, Eriko

2015-01-01

Abstract Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software. PMID:25948579
Redox Behavior of the S-Adenosylmethionine (SAM)-Binding Fe-S Cluster in Methylthiotransferase RimO, toward Understanding Dual SAM Activity.

PubMed

Molle, Thibaut; Moreau, Yohann; Clemancey, Martin; Forouhar, Farhad; Ravanat, Jean-Luc; Duraffourg, Nicolas; Fourmond, Vincent; Latour, Jean-Marc; Gambarelli, Serge; Mulliez, Etienne; Atta, Mohamed

2016-10-18

RimO, a radical-S-adenosylmethionine (SAM) enzyme, catalyzes the specific C 3 methylthiolation of the D89 residue in the ribosomal S 12 protein. Two intact iron-sulfur clusters and two SAM cofactors both are required for catalysis. By using electron paramagnetic resonance, Mössbauer spectroscopies, and site-directed mutagenesis, we show how two SAM molecules sequentially bind to the unique iron site of the radical-SAM cluster for two distinct chemical reactions in RimO. Our data establish that the two SAM molecules bind the radical-SAM cluster to the unique iron site, and spectroscopic evidence obtained under strongly reducing conditions supports a mechanism in which the first molecule of SAM causes the reoxidation of the reduced radical-SAM cluster, impeding reductive cleavage of SAM to occur and allowing SAM to methylate a HS - ligand bound to the additional cluster. Furthermore, by using density functional theory-based methods, we provide a description of the reaction mechanism that predicts the attack of the carbon radical substrate on the methylthio group attached to the additional [4Fe-4S] cluster.
Reduced repair capacity of a DNA clustered damage site comprised of 8-oxo-7,8-dihydro-2'-deoxyguanosine and 2-deoxyribonolactone results in an increased mutagenic potential of these lesions

DOE PAGES

Cunniffe, Siobhan; O’Neill, Peter; Greenberg, Marc M.; ...

2014-04-01

A signature of ionizing radiation is the induction of DNA clustered damaged sites. Non-double strand break (DSB) clustered damage has been shown to compromise the base excision repair pathway, extending the lifetimes of the lesions within the cluster, compared to isolated lesions. This increases the likelihood the lesions persist to replication and thus increasing the mutagenic potential of the lesions within the cluster. Lesions formed by ionizing radiation include 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) and 2-deoxyribonolactone (dL). dL poses an additional challenge to the cell as it is not repaired by the short-patch base excision repair pathway. Here we show recalcitrant dL repairmore » is reflected in mutations observed when DNA containing it and a proximal 8-oxodGuo is replicated in Escherichia coli. 8-oxodGuo in close proximity to dL on the opposing DNA strand results in an enhanced frequency of mutation of the lesions within the cluster and a 20 base sequence flanking the clustered damage site in an E. coli based plasmid assay. In vitro repair of a dL lesion is reduced when compared to the repair of an abasic (AP) site and a tetrahydrofuran (THF), and this is due mainly to a reduction in the activity of polymerase β, leading to retarded FEN1 and ligase 1 activities. This study has given insights in to the biological effects of clusters containing dL.« less
H 2 Adsorbed Site-to-Site Electronic Delocalization within IRMOF-1: Understanding Non-Negligible Interactions at High Pressure

DOE PAGES

Wu, Jian; Kucukkal, Mustafa U.; Clark, Aurora E.

2016-07-15

Isoreticular metal organic frameworks (IRMOFs) have shown high uptake capabilities for storage of H 2 (11.5 wt % at 77 K and 170 bar). A significant literature has employed fragment models and a single adsorbed H 2 to identify adsorption sites within IRMOFs, as well as the necessary adsorbate–adsorbent interactions needed to reach sufficient adsorption enthalpy for practical usage, however at high pressures it remains to be seen if H 2···H 2 intermolecular interactions may influence the energetics. This study focuses upon IRMOF-1 (also known as MOF-5), and examines the individual H 2 stabilization energies at different sites using Möller–Plessetmore » perturbation theory and density functional theory alongside chemical models that consist of isolated fragment models and a cubic super cell cluster consisting of both the face- and edge-cube’s of IRMOF-1. Optimization of twenty stable configurations of singly adsorbed H 2 in the super-cell cluster is observed to be essential to obtain energy ordering of the five primary sites consistent with experiment and prior benchmark calculations (α >> β > γ > δ ≈ ε). To examine site-to-site interactions that may occur in the high-pressure regime, 64 co-adsorbed H2 within a super-cell cluster have been studied (a theoretical maximum of all adsorption sites, 14 wt %). There, delocalization and/or charge transfer of electrons is observed from the σ orbitals of the H 2 bound at the γ positions into the σ* orbitals of H 2 bound at the α sites leads to stabilization of the interaction of H 2 at the γ, by 1.4 kJ/mol, respectively (using M06-2X/LANL2DZ). Furthermore, this effect has been confirmed to be charge transfer, and not a manifestation of enhanced dispersion at high loading, through natural bond order (NBO) analysis and by comparisons of the square of off-diagonal NBO Fock matrix elements for both density functionals that account for dispersion interactions and Hartree–Fock calculations that ignore dispersion.« less
SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes.

PubMed

Mason, Amanda G; Slieker, Roderick C; Balog, Judit; Lemmers, Richard J L F; Wong, Chao-Jen; Yao, Zizhen; Lim, Jong-Won; Filippova, Galina N; Ne, Enrico; Tawil, Rabi; Heijmans, Bas T; Tapscott, Stephen J; van der Maarel, Silvère M

2017-06-06

Facioscapulohumeral muscular dystrophy (FSHD) is in most cases caused by a contraction of the D4Z4 macrosatellite repeat on chromosome 4 (FSHD1) or by mutations in the SMCHD1 or DNMT3B gene (FSHD2). Both situations result in the incomplete epigenetic repression of the D4Z4-encoded retrogene DUX4 in somatic cells, leading to the aberrant expression of DUX4 in the skeletal muscle. In mice, Smchd1 regulates chromatin repression at different loci, having a role in CpG methylation establishment and/or maintenance. To investigate the global effects of harboring heterozygous SMCHD1 mutations on DNA methylation in humans, we combined 450k methylation analysis on mononuclear monocytes from female heterozygous SMCHD1 mutation carriers and unaffected controls with reduced representation bisulfite sequencing (RRBS) on FSHD2 and control myoblast cell lines. Candidate loci were then evaluated for SMCHD1 binding using ChIP-qPCR and expression was evaluated using RT-qPCR. We identified a limited number of clustered autosomal loci with CpG hypomethylation in SMCHD1 mutation carriers: the protocadherin (PCDH) cluster on chromosome 5, the transfer RNA (tRNA) and 5S rRNA clusters on chromosome 1, the HOXB and HOXD clusters on chromosomes 17 and 2, respectively, and the D4Z4 repeats on chromosomes 4 and 10. Furthermore, minor increases in RNA expression were seen in FSHD2 myoblasts for some of the PCDHβ cluster isoforms, tRNA isoforms, and a HOXB isoform in comparison to controls, in addition to the previously reported effects on DUX4 expression. SMCHD1 was bound at DNAseI hypersensitivity sites known to regulate the PCDHβ cluster and at the chromosome 1 tRNA cluster, with decreased binding in SMCHD1 mutation carriers at the PCDHβ cluster sites. Our study is the first to investigate the global methylation effects in humans resulting from heterozygous mutations in SMCHD1. Our results suggest that SMCHD1 acts as a repressor on a limited set of autosomal gene clusters, as an observed reduction in methylation associates with a loss of SMCHD1 binding and increased expression for some of the loci.
Cluster Analysis of Atmospheric Dynamics and Pollution Transport in a Coastal Area

NASA Astrophysics Data System (ADS)

Sokolov, Anton; Dmitriev, Egor; Maksimovich, Elena; Delbarre, Hervé; Augustin, Patrick; Gengembre, Cyril; Fourmentin, Marc; Locoge, Nadine

2016-11-01

Summertime atmospheric dynamics in the coastal zone of the industrialized Dunkerque agglomeration in northern France was characterized by a cluster analysis of back trajectories in the context of pollution transport. The MESO-NH atmospheric model was used to simulate the local dynamics at multiple scales with horizontal resolution down to 500 m, and for the online calculation of the Lagrangian backward trajectories with 30-min temporal resolution. Airmass transport was performed along six principal pathways obtained by the weighted k-means clustering technique. Four of these centroids corresponded to a range of wind speeds over the English Channel: two for wind directions from the north-east and two from the south-west. Another pathway corresponded to a south-westerly continental transport. The backward trajectories of the largest and most dispersed sixth cluster contained low wind speeds, including sea-breeze circulations. Based on analyses of meteorological data and pollution measurements, the principal atmospheric pathways were related to local air-contamination events. Continuous air quality and meteorological data were collected during the Benzene-Toluene-Ethylbenzene-Xylene 2006 campaign. The sites of the pollution measurements served as the endpoints for the backward trajectories. Pollutant transport pathways corresponding to the highest air contamination were defined.
Relations Between Residential Proximity to EPA-Designated Toxic Release Sites and Diffuse Large B-Cell Lymphoma Incidence.

PubMed

Bulka, Catherine; Nastoupil, Loretta J; Koff, Jean L; Bernal-Mizrachi, Leon; Ward, Kevin C; Williams, Jessica N; Bayakly, A Rana; Switchenko, Jeffrey M; Waller, Lance A; Flowers, Christopher R

2016-10-01

Examining the spatial patterns of diffuse large B-cell lymphoma (DLBCL) incidence and residential proximity to toxic release locations may provide insight regarding environmental and sociodemographic risk factors. We linked and geocoded cancer incidence data for the period 1999-2008 from the Georgia Comprehensive Cancer Registry with population data from the US Census and the Environmental Protection Agency's Toxics Release Inventory. We conducted cluster analyses and constructed Poisson regression models to assess DLBCL incidence as a function of mean distance to the toxic release sites. In total, 3851 incident DLBCL cases occurred among adults residing in Georgia between 1999 and 2008. Significant focal clustering was observed around 57% of ethylene oxide sites, 5% of benzene sites, 9% of tetrachloroethylene sites, 7% of styrene sites, 10% of formaldehyde sites, 5% of trichloroethylene sites, and 10% of all release sites. Mean distance to sites was significantly associated with DLBCL risk for all chemicals. Proximity to Toxics Release Inventory sites can be linked to increased DLBCL risk as assessed through focal clustering and Poisson regression, and confirmatory studies using geospatial mapping can aid in further specifying risk factors for DLBCL.
Allosteric binding sites in Rab11 for potential drug candidates

PubMed Central

2018-01-01

Rab11 is an important protein subfamily in the RabGTPase family. These proteins physiologically function as key regulators of intracellular membrane trafficking processes. Pathologically, Rab11 proteins are implicated in many diseases including cancers, neurodegenerative diseases and type 2 diabetes. Although they are medically important, no previous study has found Rab11 allosteric binding sites where potential drug candidates can bind to. In this study, by employing multiple clustering approaches integrating principal component analysis, independent component analysis and locally linear embedding, we performed structural analyses of Rab11 and identified eight representative structures. Using these representatives to perform binding site mapping and virtual screening, we identified two novel binding sites in Rab11 and small molecules that can preferentially bind to different conformations of these sites with high affinities. After identifying the binding sites and the residue interaction networks in the representatives, we computationally showed that these binding sites may allosterically regulate Rab11, as these sites communicate with switch 2 region that binds to GTP/GDP. These two allosteric binding sites in Rab11 are also similar to two allosteric pockets in Ras that we discovered previously. PMID:29874286
Ab initio study of the Coulomb interaction in NbxCo clusters: Strong on-site versus weak nonlocal screening

NASA Astrophysics Data System (ADS)

Peters, L.; Şaşıoǧlu, E.; Mertig, I.; Katsnelson, M. I.

2018-01-01

By means of ab initio calculations in conjunction with the random-phase approximation (RPA) within the full-potential linearized augmented plane wave method, we study the screening of the Coulomb interaction in NbxCo (1 ≤x ≤9 ) clusters. In addition, these results are compared with pure bcc Nb bulk. We find that for all clusters the on-site Coulomb interaction in RPA is strongly screened, whereas the intersite nonlocal Coulomb interaction is weakly screened and for some clusters it is unscreened or even antiscreened. This is in strong contrast with pure Nb bulk, where the intersite Coulomb interaction is almost completely screened. Furthermore, constrained RPA calculations reveal that the contribution of the Co 3 d → 3 d channel to the total screening of the Co 3 d electrons is small. Moreover, we find that both the on-site and intersite Coulomb interaction parameters decrease in a reasonable approximation linearly with the cluster size and for clusters having more than 20 Nb atoms a transition from 0D to 3D screening is expected to take place.
Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses.

PubMed

Miki, Takafumi; Kaufmann, Walter A; Malagon, Gerardo; Gomez, Laura; Tabuchi, Katsuhiko; Watanabe, Masahiko; Shigemoto, Ryuichi; Marty, Alain

2017-06-27

Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such "simple synapses" indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Ca v 2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Ca v 2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1-10) and 2.03 at 4 wk (range: 1-4), whereas the mean numbers of Ca v 2.1 clusters were 2.84 at 2 wk (range: 1-8) and 2.37 at 4 wk (range: 1-5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm 2 to 0.0234 μm 2 ), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels.
Classification of mechanisms, climatic context, areal scaling, and synchronization of floods: the hydroclimatology of floods in the Upper Paraná River basin, Brazil

NASA Astrophysics Data System (ADS)

Lima, Carlos H. R.; AghaKouchak, Amir; Lall, Upmanu

2017-12-01

Floods are the main natural disaster in Brazil, causing substantial economic damage and loss of life. Studies suggest that some extreme floods result from a causal climate chain. Exceptional rain and floods are determined by large-scale anomalies and persistent patterns in the atmospheric and oceanic circulations, which influence the magnitude, extent, and duration of these extremes. Moreover, floods can result from different generating mechanisms. These factors contradict the assumptions of homogeneity, and often stationarity, in flood frequency analysis. Here we outline a methodological framework based on clustering using self-organizing maps (SOMs) that allows the linkage of large-scale processes to local-scale observations. The methodology is applied to flood data from several sites in the flood-prone Upper Paraná River basin (UPRB) in southern Brazil. The SOM clustering approach is employed to classify the 6-day rainfall field over the UPRB into four categories, which are then used to classify floods into four types based on the spatiotemporal dynamics of the rainfall field prior to the observed flood events. An analysis of the vertically integrated moisture fluxes, vorticity, and high-level atmospheric circulation revealed that these four clusters are related to known tropical and extratropical processes, including the South American low-level jet (SALLJ); extratropical cyclones; and the South Atlantic Convergence Zone (SACZ). Persistent anomalies in the sea surface temperature fields in the Pacific and Atlantic oceans are also found to be associated with these processes. Floods associated with each cluster present different patterns in terms of frequency, magnitude, spatial variability, scaling, and synchronization of events across the sites and subbasins. These insights suggest new directions for flood risk assessment, forecasting, and management.
Putting Humpty-Dumpty Together: Clustering the Functional Dynamics of Single Biomolecular Machines Such as the Spliceosome.

PubMed

Rohlman, C E; Blanco, M R; Walter, N G

2016-01-01

The spliceosome is a biomolecular machine that, in all eukaryotes, accomplishes site-specific splicing of introns from precursor messenger RNAs (pre-mRNAs) with high fidelity. Operating at the nanometer scale, where inertia and friction have lost the dominant role they play in the macroscopic realm, the spliceosome is highly dynamic and assembles its active site around each pre-mRNA anew. To understand the structural dynamics underlying the molecular motors, clocks, and ratchets that achieve functional accuracy in the yeast spliceosome (a long-standing model system), we have developed single-molecule fluorescence resonance energy transfer (smFRET) approaches that report changes in intra- and intermolecular interactions in real time. Building on our work using hidden Markov models (HMMs) to extract kinetic and conformational state information from smFRET time trajectories, we recognized that HMM analysis of individual state transitions as independent stochastic events is insufficient for a biomolecular machine as complex as the spliceosome. In this chapter, we elaborate on the recently developed smFRET-based Single-Molecule Cluster Analysis (SiMCAn) that dissects the intricate conformational dynamics of a pre-mRNA through the splicing cycle in a model-free fashion. By leveraging hierarchical clustering techniques developed for Bioinformatics, SiMCAn efficiently analyzes large datasets to first identify common molecular behaviors. Through a second level of clustering based on the abundance of dynamic behaviors exhibited by defined functional intermediates that have been stalled by biochemical or genetic tools, SiMCAn then efficiently assigns pre-mRNA FRET states and transitions to specific splicing complexes, with the potential to find heretofore undescribed conformations. SiMCAn thus arises as a general tool to analyze dynamic cellular machines more broadly. © 2016 Elsevier Inc. All rights reserved.
[Molecular epidemiologic study on Mycobacterium tuberculosis from drug resistance monitoring sites of Guangdong Province, 2015].

PubMed

Huang, X C; Guo, H X; Wu, Z H; Guo, C X; Wei, W J; Li, H C; Sun, Q; Zhang, C C; Li, Z Y; Chen, T; Zhong, Q; Zhou, L

2017-05-12

Objective: To understand the characteristics of Mycobacterium tuberculosis (MTB) in epidemiology and distribution from Guangdong Province, and to explore the risk factors associated with drug resistance. Methods: A total of 225 clinical strains of MTB collected from 5 drug resistance monitoring sites of Guangdong Province in 2015 were tested by Regions of Difference 105 (RD105) deletion test and 15 loci mycobacterial interspersed repetitive units (MIRU) were used for genotyping. Gene clustering was analyzed using BioNumerics7.6. Drug susceptibility test was tested by proportion method. The statistical analysis used chi-square test and multivariate logistic regression. Results: There were 158 (70.2%) Beijing family strains from the 225 cases. Hunter-gaston index of MIRU loci varied from each other. The MTBs from Guangdong Province were categorized into 2 gene clusters by clustering analysis in which the rate of cluster of complexⅠwas significantly higher than complexⅡ(χ(2) values were 9.331, P values were 0.020). It was found by multivariate logistic regression that Qub11b was associated with resistance to rifampicin and isoniazid ( P values were 0.013, 0.012 respectively.), ETR F with resistance to isoniazid, streptomycin, ethambutol and ofloxacin ( P values were 0.039, 0.040, 0.023 and 0.003 respectively), Mtub21 with resistance to capreomycin ( P values were 0.040), and QUB26 with resistance to ethionamide ( P values were 0.047). Conclusions: The genes of MTB from Guangdong Province were of polymorphisms and the distribution of strains were stable. QUB11b, ETR F, Mtub21 and QUB26 could be related to biomarkers for predicting drug resistance.
Impact of the Atmospheric Transport on the Seasonal Variations and Trends of the Surface Ozone Concentration at Caucasian and Central European Mountain Sites

NASA Astrophysics Data System (ADS)

Tarasova, O. A.; Staehelin, J.; Senik, I. A.; Sosonkin, M. G.; Cui, J.; Prevot, A. S.

2008-12-01

An analysis of the atmospheric transport influence on the seasonal variations and trends of the surface ozone for two mountain sites, namely Kislovodsk High Mountain Station (KHMS) in Caucasus, Russia (43.7°N, 42.7°E, 2070 m asl.) and Jungfraujoch (JFJ) in Switzerland (46.5°N, 7.9°E, 3580 m asl) will be presented. Transport patterns are analyzed using 3D LAGRANTO trajectories. Main transport directions are obtained with the help of k-means trajectories clustering for the period 1990-2006. For each selected cluster average seasonal cycle and trends at two mountain locations are analyzed. Due to non-monotonous behavior of the trend the entire period is divided into two subsets (1991-2001 and 1997- 2006) which are studied separately. For both sites (JFJ and KHMS) the highest spring maximum is observed in May in the cluster, originating in East Asia and traveling to both sites with the longest contact with the upper free troposphere. Moreover, for both locations the excess of the summer maximum above the spring one is observed in the cluster of the local/regional transport due to ozone photochemical production in the polluted continental PBL. Trend of the surface ozone concentration at JFJ in 1991-2001 is connected with increased ozone concentrations in the free troposphere of mid latitude over West Atlantic/USA influenced by stratospheric concentration increase (most positive spring trend in trans-Atlantic clusters). The response to the regional European emission decrease observed in the local/regional advection cluster is less important but it is contributing to the seasonality of the trend. In 1997-2006 the trends at JFJ are more connected with European emissions regulations (the strongest trend are in the cluster of local/regional advection). The strong negative trends of the surface ozone concentrations at KHMS during both considered periods (1991-2001 and 1996-2007) are likely to be associated with different regime of emission (both of the local and regional scale), with abrupt emissions reduction in the beginning of 1990s in Former USSR and economical recovery during more recent period. The mentioned trends are best seen in the cluster with local/regional transport. Other reasons are also discussed in the presentation. The work is financially supported by the Swiss National Science Foundation (JRP IB7320-110831), European Commission (Marie-Curie IIF project N 039905 - FP6-2005-Mobility-7) and Russian Foundation for Basic Research (projects 06-05-64427 and 06-05-65308) and contributes to ACCENT T&TP project.
Cytoskeletal regulation of CD44 membrane organization and interactions with E-selectin.

PubMed

Wang, Ying; Yago, Tadayuki; Zhang, Nan; Abdisalaam, Salim; Alexandrakis, George; Rodgers, William; McEver, Rodger P

2014-12-19

Interactions of CD44 on neutrophils with E-selectin on activated endothelial cells mediate rolling under flow, a prerequisite for neutrophil arrest and migration into perivascular tissues. How CD44 functions as a rolling ligand despite its weak affinity for E-selectin is unknown. We examined the nanometer scale organization of CD44 on intact cells. CD44 on leukocytes and transfected K562 cells was cross-linked within a 1.14-nm spacer. Depolymerizing actin with latrunculin B reduced cross-linking. Fluorescence resonance energy transfer (FRET) revealed tight co-clustering between CD44 fused to yellow fluorescent protein (YFP) and CD44 fused to cyan fluorescent protein on K562 cells. Latrunculin B reduced FRET-reported co-clustering. Number and brightness analysis confirmed actin-dependent CD44-YFP clusters on living cells. CD44 lacking binding sites for ankyrin and for ezrin/radixin/moesin (ERM) proteins on its cytoplasmic domain (ΔANKΔERM) did not cluster. Unexpectedly, CD44 lacking only the ankyrin-binding site (ΔANK) formed larger but looser clusters. Fluorescence recovery after photobleaching demonstrated increased CD44 mobility by latrunculin B treatment or by deleting the cytoplasmic domain. ΔANKΔERM mobility increased only modestly, suggesting that the cytoplasmic domain engages the cytoskeleton by an additional mechanism. Ex vivo differentiated CD44-deficient neutrophils expressing exogenous CD44 rolled on E-selectin and activated Src kinases after binding anti-CD44 antibody. In contrast, differentiated neutrophils expressing ΔANK had impaired rolling and kinase activation. These data demonstrate that spectrin and actin networks regulate CD44 clustering and suggest that ankyrin enhances CD44-mediated neutrophil rolling and signaling. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
Cytoskeletal Regulation of CD44 Membrane Organization and Interactions with E-selectin*

PubMed Central

Wang, Ying; Yago, Tadayuki; Zhang, Nan; Abdisalaam, Salim; Alexandrakis, George; Rodgers, William; McEver, Rodger P.

2014-01-01

Interactions of CD44 on neutrophils with E-selectin on activated endothelial cells mediate rolling under flow, a prerequisite for neutrophil arrest and migration into perivascular tissues. How CD44 functions as a rolling ligand despite its weak affinity for E-selectin is unknown. We examined the nanometer scale organization of CD44 on intact cells. CD44 on leukocytes and transfected K562 cells was cross-linked within a 1.14-nm spacer. Depolymerizing actin with latrunculin B reduced cross-linking. Fluorescence resonance energy transfer (FRET) revealed tight co-clustering between CD44 fused to yellow fluorescent protein (YFP) and CD44 fused to cyan fluorescent protein on K562 cells. Latrunculin B reduced FRET-reported co-clustering. Number and brightness analysis confirmed actin-dependent CD44-YFP clusters on living cells. CD44 lacking binding sites for ankyrin and for ezrin/radixin/moesin (ERM) proteins on its cytoplasmic domain (ΔANKΔERM) did not cluster. Unexpectedly, CD44 lacking only the ankyrin-binding site (ΔANK) formed larger but looser clusters. Fluorescence recovery after photobleaching demonstrated increased CD44 mobility by latrunculin B treatment or by deleting the cytoplasmic domain. ΔANKΔERM mobility increased only modestly, suggesting that the cytoplasmic domain engages the cytoskeleton by an additional mechanism. Ex vivo differentiated CD44-deficient neutrophils expressing exogenous CD44 rolled on E-selectin and activated Src kinases after binding anti-CD44 antibody. In contrast, differentiated neutrophils expressing ΔANK had impaired rolling and kinase activation. These data demonstrate that spectrin and actin networks regulate CD44 clustering and suggest that ankyrin enhances CD44-mediated neutrophil rolling and signaling. PMID:25359776
Development of deformation band clusters in porous quartz sandstones - Contribution from microstructural analysis and numerical modeling

NASA Astrophysics Data System (ADS)

Philit, S.; Soliva, R.; Chemenda, A. I.

2017-12-01

Because sandstones form good reservoirs for hydrocarbon, water or C02 storage, the understanding of the deformation processes in sandstones is major. The deformation band clusters result from the localization of the deformation in porous sandstones under the form of gathered low-permeability cataclastic deformation bands. It has recently been shown that this localization is favored in extensional tectonics. The clusters measure tens to hundreds of meters in extent and propagate vertically as long as the sandstone is clean. Because the clusters can form several kilometers long networks, they are likely to hamper fluid flow during reservoir exploitation. Yet, the processes of band accumulation linked to the evolution of the clusters to a potential faulting are poorly understood. An integrated study coupling a microscopic analysis of the deformed granular material in clusters from 7 sites in the world and distinct element numerical modeling permits to propose a model for cluster growth. Our microscopic analysis reveals that the clusters display varying degree of cataclasis, with the most important degrees in the bands. This cataclasis is accompanied by porosity reduction (more reduced in thrust Andersonian regime), and increased Particle Size Distribution. This testifies of an important packing and implies an increased number of particle coordination. During deformation, the grain shape is both smoothened and roughened; the averaged values of the roundness and circularity indicate a rapid roughening of the clasts at the first stages of deformation followed by a slight smoothening. The roughening of the clasts in densely packed material induces high friction and strengthens the material. High residual porosity at some band edges suggests a local dilatant behavior of sheared material. Our distinct element numerical models and other particle models in the literature confirm this observation. The development of force chains with low particle coordination at these locations would weaken the stress resistance at the contact points. Hence, the cluster growth would be promoted by the successive localization of bands the edges of preexisting bands. Faulting could occur at any stage of the cluster development, probably favored along interfaces of minimized strength with smooth geometry.
Occurrence and distribution of bacteria indicators, chemical tracers and pathogenic vibrios in Singapore coastal waters.

PubMed

Goh, Shin Giek; Bayen, Stéphane; Burger, David; Kelly, Barry C; Han, Ping; Babovic, Vladan; Gin, Karina Yew-Hoong

2017-01-15

Water quality in Singapore's coastal area was evaluated with microbial indicators, pathogenic vibrios, chemical tracers and physico-chemical parameters. Sampling sites were grouped into two clusters (coastal sites at (i) northern and (ii) southern part of Singapore). The coastal sites located at northern part of Singapore along the Johor Straits exhibited greater pollution. Principal component analysis revealed that sampling sites at Johor Straits have greater loading on carbamazepine, while turbidity poses greater influence on sampling sites at Singapore Straits. Detection of pathogenic vibrios was also more prominent at Johor Straits than the Singapore Straits. This study examined the spatial variations in Singapore's coastal water quality and provided the baseline information for health risk assessment and future pollution management. Copyright © 2016 Elsevier Ltd. All rights reserved.
Galaxies Gather at Great Distances

NASA Technical Reports Server (NTRS)

2006-01-01

[figure removed for brevity, see original site] Distant Galaxy Cluster Infrared Survey Poster [figure removed for brevity, see original site] [figure removed for brevity, see original site] Bird's Eye View Mosaic Bird's Eye View Mosaic with Clusters [figure removed for brevity, see original site] [figure removed for brevity, see original site] [figure removed for brevity, see original site] 9.1 Billion Light-Years 8.7 Billion Light-Years 8.6 Billion Light-Years
Astronomers have discovered nearly 300 galaxy clusters and groups, including almost 100 located 8 to 10 billion light-years away, using the space-based Spitzer Space Telescope and the ground-based Mayall 4-meter telescope at Kitt Peak National Observatory in Tucson, Ariz. The new sample represents a six-fold increase in the number of known galaxy clusters and groups at such extreme distances, and will allow astronomers to systematically study massive galaxies two-thirds of the way back to the Big Bang.
A mosaic portraying a bird's eye view of the field in which the distant clusters were found is shown at upper left. It spans a region of sky 40 times larger than that covered by the full moon as seen from Earth. Thousands of individual images from Spitzer's infrared array camera instrument were stitched together to create this mosaic. The distant clusters are marked with orange dots.
Close-up images of three of the distant galaxy clusters are shown in the adjoining panels. The clusters appear as a concentration of red dots near the center of each image. These images reveal the galaxies as they were over 8 billion years ago, since that's how long their light took to reach Earth and Spitzer's infrared eyes.
These pictures are false-color composites, combining ground-based optical images captured by the Mosaic-I camera on the Mayall 4-meter telescope at Kitt Peak, with infrared pictures taken by Spitzer's infrared array camera. Blue and green represent visible light at wavelengths of 0.4 microns and 0.8 microns, respectively, while red indicates infrared light at 4.5 microns.
Kitt Peak National Observatory is part of the National Optical Astronomy Observatory in Tuscon, Ariz.

Coverage and beliefs about temephos application for control of dengue vectors and impact of a community-based prevention intervention: secondary analysis from the Camino Verde trial in Mexico.

PubMed

Legorreta-Soberanis, José; Paredes-Solís, Sergio; Morales-Pérez, Arcadio; Nava-Aguilera, Elizabeth; de Los Santos, Felipé René Serrano; Sánchez-Gervacio, Belén Madeline; Ledogar, Robert J; Cockcroft, Anne; Andersson, Neil

2017-05-30

Temephos in domestic water containers remains a mainstay of Latin American government programmes for control of Aedes aegypti and associated illnesses, including dengue. There is little published evidence about coverage of routine temephos programmes. A cluster randomised controlled trial of community mobilisation in Mexico and Nicaragua reduced vector indices, dengue infection, and clinical dengue cases. Secondary analysis from the Mexican arm of the trial examined temephos coverage and beliefs, and the impact of the trial on these outcomes. The trial impact survey in December 2012, in 10,491 households in 45 intervention and 45 control clusters, asked about visits from the temephos programme, retention of applied temephos, and views about temephos and mosquito control. Fieldworkers noted if temephos was present in water containers. Some 42.4% of rural and 20.7% of urban households reported no temephos programme visits within the last 12 months. Overall, 42.0% reported they had temephos placed in their water containers less than 3 months previously. Fieldworkers observed temephos in at least one container in 21.1% of households. Recent temephos application and observed temephos were both significantly more common in urban households, when other household variables were taken into account; in rural areas, smaller households were more likely to have temephos present. Most households (74.4%) did not think bathing with water containing temephos carried any health risk. Half (51%) believed drinking or cooking with such water could be harmful and 17.6% were unsure. Significantly fewer households in intervention sites (16.5%) than in control sites (26.0%) (Risk Difference - 0.095, 95% confidence interval - 0.182 to -0.009) had temephos observed in their water; more households in intervention clusters (41.8%) than in control clusters (31.6%) removed the applied temephos quickly. Although fewer households in intervention sites (82.7%) compared with control sites (86.7%) (RD -0.04, 95% CI -0.067 to -0.013) agreed temephos and fumigation was the best way to avoid mosquitoes, the proportion believing this remained very high. Coverage with the government temephos programme was low, especially in rural areas. Despite an intervention encouraging non-chemical mosquito control, most households continued to believe that chemicals are the best control method. ISRCTN: 27581154 .
Boron Nitride-supported Sub-nanometer Pd 6 Clusters for Formic Acid Decomposition: A DFT Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schimmenti, Roberto; Cortese, Remedios; Duca, Dario

A periodic, self-consistent planewave DFT study was carried out to explore the potential use of Pd 6 clusters supported on a boron nitride sheet as a catalyst for the selective decomposition of formic acid (HCOOH) to CO 2 and H 2. The competition between formate (HCOO) and carboxyl (COOH) paths on catalytic sites, with different proximities to the support, was studied. Based on energetics alone, the reaction may mainly follow the HCOO route. Slightly lower activation energies were found at the lateral sites of the cluster as compared to top face sites. This is particularly true for the bidentate tomore » monodentate HCOO conversion. Through comparison of results with similar studies on HCOOH decomposition on extended Pd surfaces, it was demonstrated that the existence of undercoordinated sites in the sub-nanometer cluster could play a key role in preferentially stabilizing HCOO over COOH, which is a common CO precursor in this reaction. A hydrogen spillover mechanism was also investigated; migration toward the boron nitride support is not favorable, at least in the early stages of the reaction. However, hydrogen diffusion on the cluster has low barriers compared to those involved in formic acid decomposition.« less
Boron Nitride-supported Sub-nanometer Pd 6 Clusters for Formic Acid Decomposition: A DFT Study

DOE PAGES

Schimmenti, Roberto; Cortese, Remedios; Duca, Dario; ...

2017-04-25

A periodic, self-consistent planewave DFT study was carried out to explore the potential use of Pd 6 clusters supported on a boron nitride sheet as a catalyst for the selective decomposition of formic acid (HCOOH) to CO 2 and H 2. The competition between formate (HCOO) and carboxyl (COOH) paths on catalytic sites, with different proximities to the support, was studied. Based on energetics alone, the reaction may mainly follow the HCOO route. Slightly lower activation energies were found at the lateral sites of the cluster as compared to top face sites. This is particularly true for the bidentate tomore » monodentate HCOO conversion. Through comparison of results with similar studies on HCOOH decomposition on extended Pd surfaces, it was demonstrated that the existence of undercoordinated sites in the sub-nanometer cluster could play a key role in preferentially stabilizing HCOO over COOH, which is a common CO precursor in this reaction. A hydrogen spillover mechanism was also investigated; migration toward the boron nitride support is not favorable, at least in the early stages of the reaction. However, hydrogen diffusion on the cluster has low barriers compared to those involved in formic acid decomposition.« less
The electron affinity of Al13H cluster: high level ab initio study

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2014-11-01

Al13H clusters have been considered candidates for cluster assembled materials. Here we have carried out benchmark calculations for the Al13H cluster, both neutral and anionic, with the aim of verifying the nature of stationary points on the potential energy surface, studying dynamics of H atom and determining an adiabatic electron affinity. A range of correlated methods applied include second-order perturbation theory (MP2), spin-component-scaled MP2, coupled electron pair (CEPA) and coupled cluster singles and doubles with perturbative triple corrections (CCSD(T)). These methods are used in combination with the correlation consistent basis sets through aug-cc-pVTZ including extrapolation to the complete basis set (CBS) limit. Performance of several different flavours of density functional theory (DFT) such as generalised gradient approximation (GGA), hybrid GGA, meta-GGA and hybrid-meta-GGA is assessed with respect to the ab initio correlated reference data. The harmonic force constant analysis is systematically performed with the MP2 and DFT methods. The MP2 results show that for neutral Al13H only the hollow structure is a potential energy minimum, with the bridged structure being a transition state for the H shift from the hollow site to the adjacent hollow site. The CCSD(T)/aug-cc-pVTZ (CCSD(T)/CBS) estimate of the energy barrier to this H shift is 2.6 (2.9) kcal/mol, implying that the H atom movement over the Al13H cluster surface is facile. By contrast, the DFT force constant analysis results suggest additional terminal and bridged minima structures. For the anion Al13H-, exhibiting 'stiffer' potential energy surface compared to the neutral, the existence of the hollow and terminal isomers is consistent with the earlier photoelectron spectroscopy assignment. The adiabatic electron affinity of Al13H is determined to be 2.00 and 1.95 eV (the latter including the ΔZPE correction) based on the CCSD(T) energies extrapolated to the CBS limit, whereas the respective CCSD(T)/CBS thermodynamic EA values are 2.79 and 2.80 eV.
Stellar and Binary Evolution in Star Clusters

NASA Technical Reports Server (NTRS)

McMillan, Stephen L. W.

2001-01-01

This paper presents a final report on research activities covered on Stellar and Binary Evolution in Star Clusters. Substantial progress was made in the development and dissemination of the "Starlab" software environment. Significant improvements were made to "kira," an N-body simulation program tailored to the study of dense stellar systems such as star clusters and galactic nuclei. Key advances include (1) the inclusion of stellar and binary evolution in a self-consistent manner, (2) proper treatment of the anisotropic Galactic tidal field, (3) numerous technical enhancements in the treatment of binary dynamics and interactions, and (4) full support for the special-purpose GRAPE-4 hardware, boosting the program's performance by a factor of 10-100 over the accelerated version. The data-reduction and analysis tools in Starlab were also substantially expanded. A Starlab Web site (http://www.sns.ias.edu/-starlab) was created and developed. The site contains detailed information on the structure and function of the various tools that comprise the package, as well as download information, "how to" tips and examples of common operations, demonstration programs, animations, etc. All versions of the software are freely distributed to all interested users, along with detailed installation instructions.
An AERONET-Based Aerosol Classification Using the Mahalanobis Distance

NASA Technical Reports Server (NTRS)

Hamill, Patrick; Giordano, Marco; Ward, Carolyne; Giles, David; Holben, Brent

2016-01-01

We present an aerosol classification based on AERONET aerosol data from 1993 to 2012. We used the AERONET Level 2.0 almucantar aerosol retrieval products to define several reference aerosol clusters which are characteristic of the following general aerosol types: Urban-Industrial, Biomass Burning, Mixed Aerosol, Dust, and Maritime. The classification of a particular aerosol observation as one of these aerosol types is determined by its five-dimensional Mahalanobis distance to each reference cluster. We have calculated the fractional aerosol type distribution at 190 AERONET sites, as well as the monthly variation in aerosol type at those locations. The results are presented on a global map and individually in the supplementary material. Our aerosol typing is based on recognizing that different geographic regions exhibit characteristic aerosol types. To generate reference clusters we only keep data points that lie within a Mahalanobis distance of 2 from the centroid. Our aerosol characterization is based on the AERONET retrieved quantities, therefore it does not include low optical depth values. The analysis is based on point sources (the AERONET sites) rather than globally distributed values. The classifications obtained will be useful in interpreting aerosol retrievals from satellite borne instruments.
Site-specific tumor grading system in colorectal cancer: multicenter pathologic review of the value of quantifying poorly differentiated clusters.

PubMed

Ueno, Hideki; Hase, Kazuo; Hashiguchi, Yojiro; Shimazaki, Hideyuki; Tanaka, Masafumi; Miyake, Ohki; Masaki, Tadahiko; Shimada, Yoshifumi; Kinugasa, Yusuke; Mori, Yoshiyuki; Kishimoto, Mitsuo; Kameoka, Shingo; Sato, Yu; Matsuda, Keiji; Nakadoi, Koichi; Shinto, Eiji; Nakamura, Takahiro; Sugihara, Kenichi

2014-02-01

The study aimed to determine the value of a novel site-specific grading system based on quantifying poorly differentiated clusters (PDC; Grade(PDC)) in colorectal cancer (CRC). A multicenter pathologic review involving 12 institutions was performed on 3243 CRC cases (stage I, 583; II, 1331; III, 1329). Cancer clusters of ≥5 cancer cells and lacking a gland-like structure (PDCs) were counted under a ×20 objective lens in a field containing the maximum clusters. Tumors with <5, 5 to 9, and ≥10 PDCs were classified as grades G1, G2, and G3, respectively. According to Grade(PDC), 1594, 1005, and 644 tumors were classified as G1, G2, and G3 and had 5-year recurrence-free survival rates of 91.6%, 75.4%, and 59.6%, respectively (P<0.0001). Multivariate analysis showed that Grade exerted an influence on prognostic outcome independently of TNM staging; approximately 20% and 46% of stage I and II patients, respectively, were selected by Grade(PDC) as a population whose survival estimate was comparable to or even worse than that of stage III patients. Grade(PDC) surpassed TNM staging in the ability to stratify patients by recurrence-free survival (Akaike information criterion, 2915.6 vs. 2994.0) and had a higher prognostic value than American Joint Committee on Cancer (AJCC) grading (Grade(AJCC)) at all stages. Regarding judgment reproducibility of grading tumors, weighted κ among the 12 institutions was 0.40 for Grade(AJCC) and 0.52 for Grade(PDC). Grade(PDC) has a robust prognostic power and promises to be of sufficient clinical value to merit implementation as a site-specific grading system in CRC.
Identifying a typology of men who use anabolic androgenic steroids (AAS).

PubMed

Zahnow, Renee; McVeigh, Jim; Bates, Geoff; Hope, Vivian; Kean, Joseph; Campbell, John; Smith, Josie

2018-05-01

Despite recognition that the Anabolic Androgenic Steroid (AAS) using population is diverse, empirical studies to develop theories to conceptualise this variance in use have been limited. In this study, using cluster analysis and multinomial logistic regression, we identify typologies of people who use AAS and examine variations in motivations for AAS use across types in a sample of 611 men who use AAS. The cluster analysis identified four groups in the data with different risk profiles. These groups largely reflect the ideal types of people who use AAS proposed by Christiansen et al. (2016): Cluster 1 (You Only Live Once (YOLO) type, n = 68, 11.1%) were younger and motivated by fat loss; Cluster 2 (Well-being type, n = 236, 38.6%) were concerned with getting fit; Cluster 3 (Athlete type, n = 155, 25.4%) were motivated by muscle and strength gains; Cluster 4 (Expert type, n = 152, 24.9%) were focused on specific goals (i.e. not 'getting fit'). The results of this study demonstrate the need to make information about AAS accessible to the general population and to inform health service providers about variations in motivations and associated risk behaviours. Attention should also be given to ensuring existing harm minimisation services are equipped to disseminate information about safe intra-muscular injecting and ensuring needle disposal sites are accessible to the different types. Copyright © 2018 Elsevier B.V. All rights reserved.
Human avian influenza in Indonesia: are they really clustered?

PubMed

Eyanoer, Putri Chairani; Singhasivanon, Pratap; Kaewkungwal, Jaranit; Apisarnthanarak, Anucha

2011-05-01

Understanding the epidemiology of human H5N1 cases in Indonesia is important. The question of whether cases are clustered or not is unclear. An increase in clustered cases suggests greater transmissibility. In the present study, 107 confirmed and 302 suspected human H5N1 cases in Indonesia during 2005-2007 were analyzed for spatial and temporal distribution. Most confirmed cases (97.2%) occurred on two main islands (Java and Sumatera). There were no patterns of disease occurrence over time. There were also no correlations between occurrence patterns in humans and poultry. Statistical analysis showed confirmed cases were clustered within an area on Java island covered by 8 districts along the border of three neighboring provinces (Jakarta, West Java, and Banten). This study shows human H5N1 cases in Indonesia were clustered at two sites where there was a high rate of infection among poultry. These findings are important since they highlight areas of high risk for possible human H5N1 infection in Indonesia, thus, preventive measures may be taken.
Applying Pose Clustering and MD Simulations To Eliminate False Positives in Molecular Docking.

PubMed

Makeneni, Spandana; Thieker, David F; Woods, Robert J

2018-03-26

In this work, we developed a computational protocol that employs multiple molecular docking experiments, followed by pose clustering, molecular dynamic simulations (10 ns), and energy rescoring to produce reliable 3D models of antibody-carbohydrate complexes. The protocol was applied to 10 antibody-carbohydrate co-complexes and three unliganded (apo) antibodies. Pose clustering significantly reduced the number of potential poses. For each system, 15 or fewer clusters out of 100 initial poses were generated and chosen for further analysis. Molecular dynamics (MD) simulations allowed the docked poses to either converge or disperse, and rescoring increased the likelihood that the best-ranked pose was an acceptable pose. This approach is amenable to automation and can be a valuable aid in determining the structure of antibody-carbohydrate complexes provided there is no major side chain rearrangement or backbone conformational change in the H3 loop of the CDR regions. Further, the basic protocol of docking a small ligand to a known binding site, clustering the results, and performing MD with a suitable force field is applicable to any protein ligand system.
The role of extended Fe4S4 cluster ligands in mediating sulfite reductase hemoprotein activity.

PubMed

Cepeda, Marisa R; McGarry, Lauren; Pennington, Joseph M; Krzystek, J; Elizabeth Stroupe, M

2018-05-28

The siroheme-containing subunit from the multimeric hemoflavoprotein NADPH-dependent sulfite reductase (SiR/SiRHP) catalyzes the six electron-reduction of SO 3 2- to S 2- . Siroheme is an iron-containing isobacteriochlorin that is found in sulfite and homologous siroheme-containing nitrite reductases. Siroheme does not work alone but is covalently coupled to a Fe 4 S 4 cluster through one of the cluster's ligands. One long-standing hypothesis predicted from this observation is that the environment of one iron-containing cofactor influences the properties of the other. We tested this hypothesis by identifying three amino acids (F437, M444, and T477) that interact with the Fe 4 S 4 cluster and probing the effect of altering them to alanine on the function and structure of the resulting enzymes by use of activity assays, X-ray crystallographic analysis, and EPR spectroscopy. We showed that F437 and M444 gate access for electron transfer to the siroheme-cluster assembly and the direct hydrogen bond between T477 and one of the cluster sulfides is important for determining the geometry of the siroheme active site. Copyright © 2018. Published by Elsevier B.V.
Comparative bacterial community analysis in relatively pristine and anthropogenically influenced mangrove ecosystems on the Red Sea.

PubMed

Ullah, Riaz; Yasir, Muhammad; Khan, Imran; Bibi, Fehmida; Sohrab, Sayed Sartaj; Al-Ansari, Ahmed; Al-Abbasi, Fahad; Al-Sofyani, Abdulmohsin A; Daur, Ihsanullah; Lee, Seon-Woo; Azhar, Esam I

2017-08-01

Mangrove habitats are ecologically important ecosystems that are under severe pressure worldwide because of environmental changes and human activities. In this study, 16S rRNA gene amplicon deep-sequencing was used to compare bacterial communities in Red Sea mangrove ecosystems at anthropogenically influenced coastal sites with those at a relatively pristine island site. In total, 32 phyla were identified from the mangrove rhizospheres, with Proteobacteria predominating at each of the studied sites; however, the relative abundance was significantly decreased at the coastal sites (Mastorah, MG-MS; Ar-Rayis, MG-AR) compared with the pristine island site near Dhahban (MG-DBI). The phyla Actinobacteria, Firmicutes, Acidobacteria, Chloroflexi, Spirochetes, and Planctomycetes were present at a relative abundance of >1% at the MG-MS and MG-AR sites, but their concentration was <1% at the MG-DBI site. A total of 1659 operational taxonomic units (OTUs) were identified at the species level, and approximately 945 OTUs were shared across the different sampling sites. Multivariate principal coordinate data analysis separated the MG-DBI site from the MG-AR and MG-MS cluster. Specific bacterial taxa were enriched at each location, and in particular, the genera Pseudoalteromonas and Cobetia were predominantly identified in the MG-DBI site compared with the anthropogenically influenced coastal sites.
Molecular scaffold reorganization at the transmitter release site with vesicle exocytosis or botulinum toxin C1.

PubMed

Stanley, Elise F; Reese, Tom S; Wang, Gary Z

2003-10-01

Neurotransmitter release sites at the freeze-fractured frog neuromuscular junction are composed of inner and outer paired rows of large membrane particles, the putative calcium channels, anchored by the ribs of an underlying protein scaffold. We analysed the locations of the release site particles as a reflection of the scaffold structure, comparing particle distributions in secreting terminals with those where secretion was blocked with botulinum toxin A, which cleaves a small segment off SNAP-25, or botulinum toxin C1, which cleaves the cytoplasmic domain of syntaxin. In the idle terminal the inner and outer paired rows were located approximately 25 and approximately 44 nm, respectively, from the release site midline. However, adjacent to vesicular fusion sites both particle rows were displaced towards the midline by approximately 25%. The intervals between the particles along each row were examined by a nearest-neighbour approach. In control terminals the peak interval along the inner row was approximately 17 nm, consistent with previous reports and the spacing of the scaffold ribs. While the average distance between particles in the outer row was also approximately 17 nm, a detailed analysis revealed short 'linear clusters' with a approximately 14 nm interval. These clusters were enriched at vesicle fusion sites, suggesting an association with the docking sites, and were eliminated by botulinum C1, but not A. Our findings suggest, first, that the release site scaffold ribs undergo a predictable, and possibly active, shortening during exocytosis and, second, that at the vesicle docking site syntaxin plays a role in the cross-linking of the rib tips to form the vesicle docking sites.
Constructing Ozone Profile Climatologies with Self-Organizing Maps: Illustrations with CONUS Ozonesonde Data

NASA Astrophysics Data System (ADS)

Thompson, A. M.; Stauffer, R. M.; Young, G. S.

2015-12-01

Ozone (O3) trends analysis is typically performed with monthly or seasonal averages. Although this approach works well for stratospheric or total O3, uncertainties in tropospheric O3 amounts may be large due to rapid meteorological changes near the tropopause and in the lower free troposphere (LFT) where pollution has a days-weeks lifetime. We use self-organizing maps (SOM), a clustering technique, as an alternative for creating tropospheric climatologies from O3 soundings. In a previous study of 900 tropical ozonesondes, clusters representing >40% of profiles deviated > 1-sigma from mean O3. Here SOM are based on 15 years of data from four sites in the contiguous US (CONUS; Boulder, CO; Huntsville, AL; Trinidad Head, CA; Wallops Island, VA). Ozone profiles from 2 - 12 km are used to evaluate the impact of tropopause variability on climatology; 2 - 6 km O3 profile segments are used for the LFT. Near-tropopause O3 is twice the mean O3 mixing ratio in three clusters of 2 - 12 km O3, representing > 15% of profiles at each site. Large mid and lower-tropospheric O3 deviations from monthly means are found in clusters of both 2 - 12 and 2 - 6 km O3. Positive offsets result from pollution and stratosphere-to-troposphere exchange. In the LFT the lowest tropospheric O3 is associated with subtropical air. Some clusters include profiles with common seasonality but other factors, e.g., tropopause height or LFT column amount, characterize other SOM nodes. Thus, as for tropical profiles, CONUS O3 averages can be a poor choice for a climatology.
Structural characterization of the P1+ intermediate state of the P-cluster of nitrogenase.

PubMed

Keable, Stephen M; Zadvornyy, Oleg A; Johnson, Lewis E; Ginovska, Bojana; Rasmussen, Andrew J; Danyal, Karamatullah; Eilers, Brian J; Prussia, Gregory A; LeVan, Axl X; Raugei, Simone; Seefeldt, Lance C; Peters, John W

2018-05-02

Nitrogenase is the enzyme that reduces atmospheric dinitrogen (N 2 ) to ammonia (NH 3 ) in biological systems. It catalyzes a series of single-electron transfers from the donor iron protein (Fe protein) to the molybdenum-iron protein (MoFe protein) that contains the iron-molybdenum cofactor (FeMo-co) sites where N 2 is reduced to NH 3 The [8Fe-7S] P-cluster in the MoFe protein functions in nitrogenase catalysis as an intermediate electron carrier between the external electron donor, the Fe protein, and the FeMo-co sites of the MoFe protein. Previous work has revealed that the P-cluster undergoes redox dependent structural changes and that the transition from the all-ferrous resting (P N ) state to the two electron oxidized P 2+ state is accompanied by protein serince hydroxyl and backbone amide ligation to Fe. In this work, the MoFe protein was poised at defined potentials with redox mediators in an electrochemical cell, and the three distinct structural states of the P-cluster (P 2+ , P 1+ , and P N ) were characterized by X-ray crystallography and confirmed by computational analysis. These analyses revealed that the three oxidation states differ in coordination implicating that the P 1+ state retains the serine hydroxyl coordination but lacks the backbone amide coordination observed in the P 2+ states. These results provide a complete picture of the redox-dependent ligand rearrangements of the three P-cluster redox states. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.
From clusters to bulk: A relativistic density functional investigation on a series of gold clusters Aun, n=6,…,147

NASA Astrophysics Data System (ADS)

Häberlen, Oliver D.; Chung, Sai-Cheong; Stener, Mauro; Rösch, Notker

1997-03-01

A series of gold clusters spanning the size range from Au6 through Au147 (with diameters from 0.7 to 1.7 nm) in icosahedral, octahedral, and cuboctahedral structure has been theoretically investigated by means of a scalar relativistic all-electron density functional method. One of the main objectives of this work was to analyze the convergence of cluster properties toward the corresponding bulk metal values and to compare the results obtained for the local density approximation (LDA) to those for a generalized gradient approximation (GGA) to the exchange-correlation functional. The average gold-gold distance in the clusters increases with their nuclearity and correlates essentially linearly with the average coordination number in the clusters. An extrapolation to the bulk coordination of 12 yields a gold-gold distance of 289 pm in LDA, very close to the experimental bulk value of 288 pm, while the extrapolated GGA gold-gold distance is 297 pm. The cluster cohesive energy varies linearly with the inverse of the calculated cluster radius, indicating that the surface-to-volume ratio is the primary determinant of the convergence of this quantity toward bulk. The extrapolated LDA binding energy per atom, 4.7 eV, overestimates the experimental bulk value of 3.8 eV, while the GGA value, 3.2 eV, underestimates the experiment by almost the same amount. The calculated ionization potentials and electron affinities of the clusters may be related to the metallic droplet model, although deviations due to the electronic shell structure are noticeable. The GGA extrapolation to bulk values yields 4.8 and 4.9 eV for the ionization potential and the electron affinity, respectively, remarkably close to the experimental polycrystalline work function of bulk gold, 5.1 eV. Gold 4f core level binding energies were calculated for sites with bulk coordination and for different surface sites. The core level shifts for the surface sites are all positive and distinguish among the corner, edge, and face-centered sites; sites in the first subsurface layer show still small positive shifts.
Atmospheric speciated mercury concentrations on an island between China and Korea: sources and transport pathways

NASA Astrophysics Data System (ADS)

Lee, G.-S.; Kim, P.-R.; Han, Y.-J.; Holsen, T. M.; Seo, Y.-S.; Yi, S.-M.

2015-11-01

As a global pollutant, mercury (Hg) is of particular concern in East Asia where anthropogenic emissions are the largest. In this study, speciated Hg concentrations were measured in the western most island in Korea, located between China and the Korean mainland to identify the importance of local, regional and distant Hg sources. Various tools including correlations with other pollutants, conditional probability function, and back-trajectory based analysis consistently indicated that Korean sources were important for gaseous oxidized mercury (GOM) whereas, for total gaseous mercury (TGM) and particulate bound mercury (PBM), long-range and regional transport were also important. A trajectory cluster based approach considering both Hg concentration and the fraction of time each cluster was impacting the site was developed to quantify the effect of Korean sources and out-of-Korean source. This analysis suggests that Korean sources contributed approximately 55 % of the GOM and PBM while there were approximately equal contributions from Korean and out-of-Korean sources for the TGM measured at the site. The ratio of GOM / PBM decreased when the site was impacted by long-range transport, suggesting that this ratio may be a useful tool for identifying the relative significance of local sources vs. long-range transport. The secondary formation of PBM through gas-particle partitioning with GOM was found to be important at low temperatures and high relative humidity.
Diversity and Characterization of Sulfate-Reducing Bacteria in Groundwater at a Uranium Mill Tailings Site

PubMed Central

Chang, Yun-Juan; Peacock, Aaron D.; Long, Philip E.; Stephen, John R.; McKinley, James P.; Macnaughton, Sarah J.; Hussain, A. K. M. Anwar; Saxton, Arnold M.; White, David C.

2001-01-01

Microbially mediated reduction and immobilization of U(VI) to U(IV) plays a role in both natural attenuation and accelerated bioremediation of uranium-contaminated sites. To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites. In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex., was investigated. Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis. A remarkable diversity among the DSR sequences was revealed, including sequences from δ-Proteobacteria, gram-positive organisms, and the Nitrospira division. PLFA analysis detected at least 52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0. Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected. Those belonging to SRB within δ-Proteobacteria were mainly recovered from low-uranium (≤302 ppb) samples. One Desulfotomaculum-like sequence cluster overwhelmingly dominated high-U (>1,500 ppb) sites. Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P = 0.0001). This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium. The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research. PMID:11425735
Population structure of the predatory mite Neoseiulus womersleyi in a tea field based on an analysis of microsatellite DNA markers

PubMed Central

Todokoro, Yasuhiro; Higaki, Tomomi

2010-01-01

The predatory mite Neoseiulus womersleyi (Schicha) (Acari: Phytoseiidae) is an important natural enemy of the Kanzawa spider mite, Tetranychus kanzawaki Kishida (Acari: Tetranychidae), in tea fields. Attraction and preservation of natural enemies by habitat management to reduce the need for acaricide sprays is thought to enhance the activity of N. womersleyi. To better conserve N. womersleyi in the field, however, it is essential to elucidate the population genetic structure of this species. To this end, we developed ten microsatellite DNA markers for N. womersleyi. We then evaluated population structure of N. womersleyi collected from a tea field, where Mexican sunflower, Tithonia rotundifolia (Mill.), was planted to preserve N. womersleyi. Seventy-seven adult females were collected from four sites within 200 m. The fixation indexes FST among subpopulations were not significantly different. The kinship coefficients between individuals did not differ significantly within a site as a function of the sampling dates, but the coefficients gradually decreased with increasing distance. Bayesian clustering analysis revealed that the population consisted of three genetic clusters, and that subpopulations within 100 m, including those collected on T. rotundifolia, were genetically similar to each other. Given the previously observed population dynamics of N. womersleyi, it appears that the area inhabited by a given cluster of the mite did not exceed 100 m. The estimation of population structure using microsatellite markers will provide valuable information in conservation biological control. PMID:20625919
Tissue-specific promoter utilisation of the kallikrein-related peptidase genes, KLK5 and KLK7, and cellular localisation of the encoded proteins suggest roles in exocrine pancreatic function.

PubMed

Dong, Ying; Matigian, Nick; Harvey, Tracey J; Samaratunga, Hemamali; Hooper, John D; Clements, Judith A

2008-02-01

Abstract Tissue kallikrein (kallikrein 1) was first identified in pancreas and is the namesake of the kallikrein-related peptidase (KLK) family. KLK1 and the other 14 members of the human KLK family are encoded by 15 serine protease genes clustered at chromosome 19q13.4. Our Northern blot analysis of 19 normal human tissues for expression of KLK4 to KLK15 identified pancreas as a common expression site for the gene cluster spanning KLK5 to KLK13, as well as for KLK15 which is located adjacent to KLK1. Consistent with previous reports detailing the ability of KLK genes to generate organ- and disease-specific transcripts, detailed molecular and in silico analyses indicated that KLK5 and KLK7 generate transcripts in pancreas variant from those in skin or ovary. Consistently, we identified in the promoters of these KLK genes motifs which conform with consensus binding sites for transcription factors conferring pancreatic expression. In addition, immunohistochemical analysis revealed predominant localisation of KLK5 and KLK7 in acinar cells of the exocrine pancreas, suggesting roles for these enzymes in digestion. Our data also support expression patterns derived from gene duplication events in the human KLK cluster. These findings suggest that, in addition to KLK1, other related KLK enzymes will function in the exocrine pancreas.

Constructing simple yet accurate potentials for describing the solvation of HCl/water clusters in bulk helium and nanodroplets.

PubMed

Boese, A Daniel; Forbert, Harald; Masia, Marco; Tekin, Adem; Marx, Dominik; Jansen, Georg

2011-08-28

The infrared spectroscopy of molecules, complexes, and molecular aggregates dissolved in superfluid helium clusters, commonly called HElium NanoDroplet Isolation (HENDI) spectroscopy, is an established, powerful experimental technique for extracting high resolution ro-vibrational spectra at ultra-low temperatures. Realistic quantum simulations of such systems, in particular in cases where the solute is undergoing a chemical reaction, require accurate solute-helium potentials which are also simple enough to be efficiently evaluated over the vast number of steps required in typical Monte Carlo or molecular dynamics sampling. This precludes using global potential energy surfaces as often parameterized for small complexes in the realm of high-resolution spectroscopic investigations that, in view of the computational effort imposed, are focused on the intermolecular interaction of rigid molecules with helium. Simple Lennard-Jones-like pair potentials, on the other hand, fall short in providing the required flexibility and accuracy in order to account for chemical reactions of the solute molecule. Here, a general scheme of constructing sufficiently accurate site-site potentials for use in typical quantum simulations is presented. This scheme employs atom-based grids, accounts for local and global minima, and is applied to the special case of a HCl(H(2)O)(4) cluster solvated by helium. As a first step, accurate interaction energies of a helium atom with a set of representative configurations sampled from a trajectory following the dissociation of the HCl(H(2)O)(4) cluster were computed using an efficient combination of density functional theory and symmetry-adapted perturbation theory, i.e. the DFT-SAPT approach. For each of the sampled cluster configurations, a helium atom was placed at several hundred positions distributed in space, leading to an overall number of about 400,000 such quantum chemical calculations. The resulting total interaction energies, decomposed into several energetic contributions, served to fit a site-site potential, where the sites are located at the atomic positions and, additionally, pseudo-sites are distributed along the lines joining pairs of atom sites within the molecular cluster. This approach ensures that this solute-helium potential is able to describe both undissociated molecular and dissociated (zwitter-) ionic configurations, as well as the interconnecting reaction pathway without re-adjusting partial charges or other parameters depending on the particular configuration. Test calculations of the larger HCl(H(2)O)(5) cluster interacting with helium demonstrate the transferability of the derived site-site potential. This specific potential can be readily used in quantum simulations of such HCl/water clusters in bulk helium or helium nanodroplets, whereas the underlying construction procedure can be generalized to other molecular solutes in other atomic solvents such as those encountered in rare gas matrix isolation spectroscopy.
Characterization of limes (Citrus aurantifolia) grown in Bhutan and Indonesia using high-throughput sequencing

PubMed Central

Penjor, Tshering; Mimura, Takashi; Matsumoto, Ryoji; Yamamoto, Masashi; Nagano, Yukio

2014-01-01

Lime [Citrus aurantifolia (Cristm.) Swingle] is a Citrus species that is a popular ingredient in many cuisines. Some citrus plants are known to originate in the area ranging from northeastern India to southwestern China. In the current study, we characterized and compared limes grown in Bhutan (n = 5 accessions) and Indonesia (n = 3 accessions). The limes were separated into two groups based on their morphology. Restriction site-associated DNA sequencing (RAD-seq) separated the eight accessions into two clusters. One cluster contained four accessions from Bhutan, whereas the other cluster contained one accession from Bhutan and the three accessions from Indonesia. This genetic classification supported the morphological classification of limes. The analysis suggests that the properties associated with asexual reproduction, and somatic homologous recombination, have contributed to the genetic diversification of limes. PMID:24781859
Progress on the Cluster Mission

NASA Technical Reports Server (NTRS)

Kivelson, Margaret; Khurana, Krishan; Acuna, Mario (Technical Monitor)

2002-01-01

Prof M. G. Kivelson and Dr. K. K. Khurana (UCLA (University of California, Los Angeles)) are co-investigators on the Cluster Magnetometer Consortium (CMC) that provided the fluxgate magnetometers and associated mission support for the Cluster Mission. The CMC designated UCLA as the site with primary responsibility for the inter-calibration of data from the four spacecraft and the production of fully corrected data critical to achieving the mission objectives. UCLA will also participate in the analysis and interpretation of the data. The UCLA group here reports its excellent progress in developing fully intra-calibrated data for large portions of the mission and an excellent start in developing inter-calibrated data for selected time intervals, especially extended intervals in August, 2001 on which a workshop held at ESTEC in March, 2002 focused. In addition, some scientific investigations were initiated and results were reported at meetings.
Dynamic Evolution Model Based on Social Network Services

NASA Astrophysics Data System (ADS)

Xiong, Xi; Gou, Zhi-Jian; Zhang, Shi-Bin; Zhao, Wen

2013-11-01

Based on the analysis of evolutionary characteristics of public opinion in social networking services (SNS), in the paper we propose a dynamic evolution model, in which opinions are coupled with topology. This model shows the clustering phenomenon of opinions in dynamic network evolution. The simulation results show that the model can fit the data from a social network site. The dynamic evolution of networks accelerates the opinion, separation and aggregation. The scale and the number of clusters are influenced by confidence limit and rewiring probability. Dynamic changes of the topology reduce the number of isolated nodes, while the increased confidence limit allows nodes to communicate more sufficiently. The two effects make the distribution of opinion more neutral. The dynamic evolution of networks generates central clusters with high connectivity and high betweenness, which make it difficult to control public opinions in SNS.
The INfrared Survey of Young Nebulous Clusters (IN-SYNC): Surveying the Dynamics and Star Formation Histories of Young Clusters with APOGEE

NASA Astrophysics Data System (ADS)

Covey, Kevin R.; Cottaar, Michiel; Foster, Jonathan B.; Da Rio, Nicola; Tan, Jonathan; Meyer, Michael; Nidever, David L.; Flaherty, Kevin M.; Arce, Hector G.; Rebull, Luisa M.; Chojnowski, S. Drew; Frinchaboy, Peter M.; Hearty, Fred R.; Majewski, Steven R.; Skrutskie, Michael F.; Stassun, Keivan; Wilson, John C.; Zasowski, Gail

2015-01-01

Young clusters are the most prolific sites of star formation in the Milky Way, but demographic studies indicate that relatively few of the Milky Way's stellar clusters persist as bound structures for 100 Myrs or longer. Uniform & precise measurements of the stellar populations and internal dynamics of these regions are difficult to obtain, however, particularly for extremely young clusters whose optical visibility is greatly hampered by their parental molecular cloud. The INfrared Survey of Young Nebulous Clusters (IN-SYNC), an SDSS-III ancillary science program, leverages the stability and multiplex capability of the APOGEE spectrograph to obtain high resolution spectra at near-infrared wavelengths, where photospheric emission is better able to penetrate the dusty shrouds that surround sites of active star formation. We summarize our recent measurements of the kinematics and stellar populations of IC 348 and NGC 1333, two young clusters in the Perseus Molecular Cloud, and of the members of the Orion Nebula Cluster (ONC) and L1641 filament in the Orion molecular complex. These measurements highlight the dynamically 'warm' environment within these young clusters, and suggest a range of stellar radii within these quasi-single-age populations. We close with a preview of plans for continuing this work as part of the APOGEE-2 science portfolio: self-consistent measurements of the kinematics and star formation histories for clusters spanning a range of initial conditions and ages will provide a opportunity to disentangle the mechanisms that drive the formation and dissolution of sites of active star formation.
[3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis.

PubMed

Rousset, M; Montet, Y; Guigliarelli, B; Forget, N; Asso, M; Bertrand, P; Fontecilla-Camps, J C; Hatchikian, E C

1998-09-29

The role of the high potential [3Fe-4S]1+,0 cluster of [NiFe] hydrogenase from Desulfovibrio species located halfway between the proximal and distal low potential [4Fe-4S]2+,1+ clusters has been investigated by using site-directed mutagenesis. Proline 238 of Desulfovibrio fructosovorans [NiFe] hydrogenase, which occupies the position of a potential ligand of the lacking fourth Fe-site of the [3Fe-4S] cluster, was replaced by a cysteine residue. The properties of the mutant enzyme were investigated in terms of enzymatic activity, EPR, and redox properties of the iron-sulfur centers and crystallographic structure. We have shown on the basis of both spectroscopic and x-ray crystallographic studies that the [3Fe-4S] cluster of D. fructosovorans hydrogenase was converted into a [4Fe-4S] center in the P238 mutant. The [3Fe-4S] to [4Fe-4S] cluster conversion resulted in a lowering of approximately 300 mV of the midpoint potential of the modified cluster, whereas no significant alteration of the spectroscopic and redox properties of the two native [4Fe-4S] clusters and the NiFe center occurred. The significant decrease of the midpoint potential of the intermediate Fe-S cluster had only a slight effect on the catalytic activity of the P238C mutant as compared with the wild-type enzyme. The implications of the results for the role of the high-potential [3Fe-4S] cluster in the intramolecular electron transfer pathway are discussed.
The effect of heavy metal contamination on the bacterial community structure at Jiaozhou Bay, China.

PubMed

Yao, Xie-Feng; Zhang, Jiu-Ming; Tian, Li; Guo, Jian-Hua

In this study, determination of heavy metal parameters and microbiological characterization of marine sediments obtained from two heavily polluted sites and one low-grade contaminated reference station at Jiaozhou Bay in China were carried out. The microbial communities found in the sampled marine sediments were studied using PCR-DGGE (denaturing gradient gel electrophoresis) fingerprinting profiles in combination with multivariate analysis. Clustering analysis of DGGE and matrix of heavy metals displayed similar occurrence patterns. On this basis, 17 samples were classified into two clusters depending on the presence or absence of the high level contamination. Moreover, the cluster of highly contaminated samples was further classified into two sub-groups based on the stations of their origin. These results showed that the composition of the bacterial community is strongly influenced by heavy metal variables present in the sediments found in the Jiaozhou Bay. This study also suggested that metagenomic techniques such as PCR-DGGE fingerprinting in combination with multivariate analysis is an efficient method to examine the effect of metal contamination on the bacterial community structure. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.
Pattern variation of fish fingerling abundance in the Na Thap Tidal river of Southern Thailand: 2005-2015

NASA Astrophysics Data System (ADS)

Donroman, T.; Chesoh, S.; Lim, A.

2018-04-01

This study aimed to investigate the variation patterns of fish fingerling abundance based on month, year and sampling site. Monthly collecting data set of the Na Thap tidal river of southern Thailand, were obtained from June 2005 to October 2015. The square root transformation was employed for maintaining the fingerling data normality. Factor analysis was applied for clustering number of fingerling species and multiple linear regression was used to examine the association between fingerling density and year, month and site. Results from factor analysis classified fingerling into 3 factors based on saline preference; saline water, freshwater and ubiquitous species. The results showed a statistically high significant relation between fingerling density, month, year and site. Abundance of saline water and ubiquitous fingerling density showed similar pattern. Downstream site presented highest fingerling density whereas almost of freshwater fingerling occurred in upstream. This finding confirmed that factor analysis and the general linear regression method can be used as an effective tool for predicting and monitoring wild fingerling density in order to sustain fish stock management.
Including foreshocks and aftershocks in time-independent probabilistic seismic hazard analyses

USGS Publications Warehouse

Boyd, Oliver S.

2012-01-01

Time‐independent probabilistic seismic‐hazard analysis treats each source as being temporally and spatially independent; hence foreshocks and aftershocks, which are both spatially and temporally dependent on the mainshock, are removed from earthquake catalogs. Yet, intuitively, these earthquakes should be considered part of the seismic hazard, capable of producing damaging ground motions. In this study, I consider the mainshock and its dependents as a time‐independent cluster, each cluster being temporally and spatially independent from any other. The cluster has a recurrence time of the mainshock; and, by considering the earthquakes in the cluster as a union of events, dependent events have an opportunity to contribute to seismic ground motions and hazard. Based on the methods of the U.S. Geological Survey for a high‐hazard site, the inclusion of dependent events causes ground motions that are exceeded at probability levels of engineering interest to increase by about 10% but could be as high as 20% if variations in aftershock productivity can be accounted for reliably.
Interdomain communication revealed in the diabetes drug target mitoNEET

PubMed Central

Jennings, Patricia A.

2011-01-01

MitoNEET is a recently identified drug target for a commonly prescribed diabetes drug, Pioglitazone. It belongs to a previously uncharacterized ancient family of proteins for which the hallmark is the presence of a unique 39 amino acid CDGSH domain. In order to characterize the folding landscape of this novel fold, we performed thermodynamic simulations on MitoNEET using a structure-based model. Additionally, we implement a method of contact map clustering to partition out alternate pathways in folding. This cluster analysis reveals a detour late in folding and enables us to carefully examine the folding mechanism of each pathway rather than the macroscopic average. We observe that tightness in a region distal to the iron–sulfur cluster creates a constraint in folding and additionally appears to mediate communication in folding between the two domains of the protein. We demonstrate that by making changes at this site we are able to tweak the order of folding events in the cluster binding domain as well as decrease the barrier to folding. PMID:21402934
Small clusters of fast-growing trees enhance forest structure on restored bottomland sites

USGS Publications Warehouse

Twedt, D.J.

2006-01-01

Despite the diversity of trees in bottomland forests, restoration on bottomland sites is often initiated by planting only a few species of slow-growing, hard mast?producing trees. Although successful at establishing trees, these young forests are slow to develop vertical structure, which is a key predictor of forest bird colonization. Furthermore, when natural seed sources are few, restored sites may be depauperate in woody species. To increase richness of woody species, maximum tree height, and total stem density, I supplemented traditional plantings on each of 40 bottomland restoration sites by planting 96 Eastern cottonwood (Populus deltoides) and American sycamore (Platanus occidentalis) in eight clusters of 12 trees. First year survival of cottonwood stem cuttings (25%) and sycamore seedlings (47%) was poor, but survival increased when afforded protection from competition with weeds. After five growing seasons, 165 of these 320 supplemental tree clusters had at least one surviving tree. Vegetation surrounding surviving clusters of supplemental trees harbored a greater number of woody species, increased stem density, and greater maximum tree height than was found on paired restoration sites without supplemental trees. These increases were primarily accounted for by the supplemental trees.
Selection of Atmospheric Environmental Monitoring Sites based on Geographic Parameters Extraction of GIS and Fuzzy Matter-Element Analysis.

PubMed

Wu, Jianfa; Peng, Dahao; Ma, Jianhao; Zhao, Li; Sun, Ce; Ling, Huanzhang

2015-01-01

To effectively monitor the atmospheric quality of small-scale areas, it is necessary to optimize the locations of the monitoring sites. This study combined geographic parameters extraction by GIS with fuzzy matter-element analysis. Geographic coordinates were extracted by GIS and transformed into rectangular coordinates. These coordinates were input into the Gaussian plume model to calculate the pollutant concentration at each site. Fuzzy matter-element analysis, which is used to solve incompatible problems, was used to select the locations of sites. The matter element matrices were established according to the concentration parameters. The comprehensive correlation functions KA (xj) and KB (xj), which reflect the degree of correlation among monitoring indices, were solved for each site, and a scatter diagram of the sites was drawn to determine the final positions of the sites based on the functions. The sites could be classified and ultimately selected by the scatter diagram. An actual case was tested, and the results showed that 5 positions can be used for monitoring, and the locations conformed to the technical standard. In the results of this paper, the hierarchical clustering method was used to improve the methods. The sites were classified into 5 types, and 7 locations were selected. Five of the 7 locations were completely identical to the sites determined by fuzzy matter-element analysis. The selections according to these two methods are similar, and these methods can be used in combination. In contrast to traditional methods, this study monitors the isolated point pollutant source within a small range, which can reduce the cost of monitoring.
Modeling Classical Swine Fever Outbreak-Related Outcomes

PubMed Central

Yadav, Shankar; Olynk Widmar, Nicole J.; Weng, Hsin-Yi

2016-01-01

The study was carried out to estimate classical swine fever (CSF) outbreak-related outcomes, such as epidemic duration and number of infected, vaccinated, and depopulated premises, using defined most likely CSF outbreak scenarios. Risk metrics were established using empirical data to select the most likely CSF outbreak scenarios in Indiana. These scenarios were simulated using a stochastic between-premises disease spread model to estimate outbreak-related outcomes. A total of 19 single-site (i.e., with one index premises at the onset of an outbreak) and 15 multiple-site (i.e., with more than one index premises at the onset of an outbreak) outbreak scenarios of CSF were selected using the risk metrics. The number of index premises in the multiple-site outbreak scenarios ranged from 4 to 32. The multiple-site outbreak scenarios were further classified into clustered (N = 6) and non-clustered (N = 9) groups. The estimated median (5th, 95th percentiles) epidemic duration (days) was 224 (24, 343) in the single-site and was 190 (157, 251) and 210 (167, 302) in the clustered and non-clustered multiple-site outbreak scenarios, respectively. The median (5th, 95th percentiles) number of infected premises was 323 (0, 488) in the single-site outbreak scenarios and was 529 (395, 662) and 465 (295, 640) in the clustered and non-clustered multiple-site outbreak scenarios, respectively. Both the number and spatial distributions of the index premises affected the outcome estimates. The results also showed the importance of implementing vaccinations to accommodate depopulation in the CSF outbreak controls. The use of routinely collected surveillance data in the risk metrics and disease spread model allows end users to generate timely outbreak-related information based on the initial outbreak’s characteristics. Swine producers can use this information to make an informed decision on the management of swine operations and continuity of business, so that potential losses could be minimized during a CSF outbreak. Government authorities might use the information to make emergency preparedness plans for CSF outbreak control. PMID:26870741
Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms.

PubMed

Halligan, Brian D; Geiger, Joey F; Vallejos, Andrew K; Greene, Andrew S; Twigger, Simon N

2009-06-01

One of the major difficulties for many laboratories setting up proteomics programs has been obtaining and maintaining the computational infrastructure required for the analysis of the large flow of proteomics data. We describe a system that combines distributed cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without the investment in computational hardware or software licensing fees. Additionally, the pricing structure of distributed computing providers, such as Amazon Web Services, allows laboratories or even individuals to have large-scale computational resources at their disposal at a very low cost per run. We provide detailed step-by-step instructions on how to implement the virtual proteomics analysis clusters as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases on the Medical College of Wisconsin Proteomics Center Web site ( http://proteomics.mcw.edu/vipdac ).
Medicaid-funded home care for the frail elderly and disabled: evaluating the cost savings and outcomes of a service delivery reform.

PubMed Central

Feldman, P H; Latimer, E; Davidson, H

1996-01-01

OBJECTIVES: In response to rising demand and increased costs for home care services for frail elderly and disabled Medicaid clients, New York City implemented cluster care, a shared-aide model of home care. Our objective: to evaluate the effects of cluster care on home care hours and costs, client functioning, depressive symptoms, and satisfaction. DATA SOURCES: Client interviews, conducted prior to implementation and again 16 months later; Medicaid claims records; home attendant payroll files; and vendor agency records. STUDY DESIGN: The study employed a pretest/posttest design, comparing 229 clients at the first seven demonstration sites to 175 clients at four comparison sites before and after cluster care implementation. Regression methods were used to analyze pre and post-intervention data. PRINCIPAL FINDINGS: Cluster care reduced costs by about 10 percent. Most savings occurred among the more vulnerable clients (those with five or more ADL/IADL limitations). Clients at cluster care sites who started out with fewer than five limitations appeared to decline somewhat more slowly than similarly impaired clients at comparison sites, while those with more than five ADL/IADLs tended to decline more rapidly. This difference was small-less than one limitation per year. Cluster care is associated with a significant decline in satisfaction but appears unrelated to depressive symptoms. CONCLUSIONS: Cluster care appears benign for home care clients with fewer limitations. For the more vulnerable, we recommend experimentation with low-cost interventions that might augment service and improve outcomes without reverting to traditional one-on-one care. PMID:8885860
Spatial distribution and cluster analysis of retail drug shop characteristics and antimalarial behaviors as reported by private medicine retailers in western Kenya: informing future interventions.

PubMed

Rusk, Andria; Highfield, Linda; Wilkerson, J Michael; Harrell, Melissa; Obala, Andrew; Amick, Benjamin

2016-02-19

Efforts to improve malaria case management in sub-Saharan Africa have shifted focus to private antimalarial retailers to increase access to appropriate treatment. Demands to decrease intervention cost while increasing efficacy requires interventions tailored to geographic regions with demonstrated need. Cluster analysis presents an opportunity to meet this demand, but has not been applied to the retail sector or antimalarial retailer behaviors. This research conducted cluster analysis on medicine retailer behaviors in Kenya, to improve malaria case management and inform future interventions. Ninety-seven surveys were collected from medicine retailers working in the Webuye Health and Demographic Surveillance Site. Survey items included retailer training, education, antimalarial drug knowledge, recommending behavior, sales, and shop characteristics, and were analyzed using Kulldorff's spatial scan statistic. The Bernoulli purely spatial model for binomial data was used, comparing cases to controls. Statistical significance of found clusters was tested with a likelihood ratio test, using the null hypothesis of no clustering, and a p value based on 999 Monte Carlo simulations. The null hypothesis was rejected with p values of 0.05 or less. A statistically significant cluster of fewer than expected pharmacy-trained retailers was found (RR = .09, p = .001) when compared to the expected random distribution. Drug recommending behavior also yielded a statistically significant cluster, with fewer than expected retailers recommending the correct antimalarial medication to adults (RR = .018, p = .01), and fewer than expected shops selling that medication more often than outdated antimalarials when compared to random distribution (RR = 0.23, p = .007). All three of these clusters were co-located, overlapping in the northwest of the study area. Spatial clustering was found in the data. A concerning amount of correlation was found in one specific region in the study area where multiple behaviors converged in space, highlighting a prime target for interventions. These results also demonstrate the utility of applying geospatial methods in the study of medicine retailer behaviors, making the case for expanding this approach to other regions.
Object-Oriented Image Clustering Method Using UAS Photogrammetric Imagery

NASA Astrophysics Data System (ADS)

Lin, Y.; Larson, A.; Schultz-Fellenz, E. S.; Sussman, A. J.; Swanson, E.; Coppersmith, R.

2016-12-01

Unmanned Aerial Systems (UAS) have been used widely as an imaging modality to obtain remotely sensed multi-band surface imagery, and are growing in popularity due to their efficiency, ease of use, and affordability. Los Alamos National Laboratory (LANL) has employed the use of UAS for geologic site characterization and change detection studies at a variety of field sites. The deployed UAS equipped with a standard visible band camera to collect imagery datasets. Based on the imagery collected, we use deep sparse algorithmic processing to detect and discriminate subtle topographic features created or impacted by subsurface activities. In this work, we develop an object-oriented remote sensing imagery clustering method for land cover classification. To improve the clustering and segmentation accuracy, instead of using conventional pixel-based clustering methods, we integrate the spatial information from neighboring regions to create super-pixels to avoid salt-and-pepper noise and subsequent over-segmentation. To further improve robustness of our clustering method, we also incorporate a custom digital elevation model (DEM) dataset generated using a structure-from-motion (SfM) algorithm together with the red, green, and blue (RGB) band data for clustering. In particular, we first employ an agglomerative clustering to create an initial segmentation map, from where every object is treated as a single (new) pixel. Based on the new pixels obtained, we generate new features to implement another level of clustering. We employ our clustering method to the RGB+DEM datasets collected at the field site. Through binary clustering and multi-object clustering tests, we verify that our method can accurately separate vegetation from non-vegetation regions, and are also able to differentiate object features on the surface.
Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.

PubMed

Jusakul, Apinya; Cutcutache, Ioana; Yong, Chern Han; Lim, Jing Quan; Huang, Mi Ni; Padmanabhan, Nisha; Nellore, Vishwa; Kongpetch, Sarinya; Ng, Alvin Wei Tian; Ng, Ley Moy; Choo, Su Pin; Myint, Swe Swe; Thanan, Raynoo; Nagarajan, Sanjanaa; Lim, Weng Khong; Ng, Cedric Chuan Young; Boot, Arnoud; Liu, Mo; Ong, Choon Kiat; Rajasegaran, Vikneswari; Lie, Stefanus; Lim, Alvin Soon Tiong; Lim, Tse Hui; Tan, Jing; Loh, Jia Liang; McPherson, John R; Khuntikeo, Narong; Bhudhisawasdi, Vajaraphongsa; Yongvanit, Puangrat; Wongkham, Sopit; Totoki, Yasushi; Nakamura, Hiromi; Arai, Yasuhito; Yamasaki, Satoshi; Chow, Pierce Kah-Hoe; Chung, Alexander Yaw Fui; Ooi, London Lucien Peng Jin; Lim, Kiat Hon; Dima, Simona; Duda, Dan G; Popescu, Irinel; Broet, Philippe; Hsieh, Sen-Yung; Yu, Ming-Chin; Scarpa, Aldo; Lai, Jiaming; Luo, Di-Xian; Carvalho, André Lopes; Vettore, André Luiz; Rhee, Hyungjin; Park, Young Nyun; Alexandrov, Ludmil B; Gordân, Raluca; Rozen, Steven G; Shibata, Tatsuhiro; Pairojkul, Chawalit; Teh, Bin Tean; Tan, Patrick

2017-10-01

Cholangiocarcinoma (CCA) is a hepatobiliary malignancy exhibiting high incidence in countries with endemic liver-fluke infection. We analyzed 489 CCAs from 10 countries, combining whole-genome (71 cases), targeted/exome, copy-number, gene expression, and DNA methylation information. Integrative clustering defined 4 CCA clusters-fluke-positive CCAs (clusters 1/2) are enriched in ERBB2 amplifications and TP53 mutations; conversely, fluke-negative CCAs (clusters 3/4) exhibit high copy-number alterations and PD-1 / PD-L2 expression, or epigenetic mutations ( IDH1/2, BAP1 ) and FGFR / PRKA -related gene rearrangements. Whole-genome analysis highlighted FGFR2 3' untranslated region deletion as a mechanism of FGFR2 upregulation. Integration of noncoding promoter mutations with protein-DNA binding profiles demonstrates pervasive modulation of H3K27me3-associated sites in CCA. Clusters 1 and 4 exhibit distinct DNA hypermethylation patterns targeting either CpG islands or shores-mutation signature and subclonality analysis suggests that these reflect different mutational pathways. Our results exemplify how genetics, epigenetics, and environmental carcinogens can interplay across different geographies to generate distinct molecular subtypes of cancer. Significance: Integrated whole-genome and epigenomic analysis of CCA on an international scale identifies new CCA driver genes, noncoding promoter mutations, and structural variants. CCA molecular landscapes differ radically by etiology, underscoring how distinct cancer subtypes in the same organ may arise through different extrinsic and intrinsic carcinogenic processes. Cancer Discov; 7(10); 1116-35. ©2017 AACR. This article is highlighted in the In This Issue feature, p. 1047 . ©2017 American Association for Cancer Research.
Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies.

PubMed

Fetterman, Christina D; Rannala, Bruce; Walter, Michael A

2008-09-24

Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and refinement of domain boundaries. Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species. Overall we found that after gene duplication of forkhead family members, rapid differentiation and subsequent fixation of amino acid changes through negative selection has occurred.
Multiple receptor conformation docking, dock pose clustering and 3D QSAR studies on human poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors.

PubMed

Fatima, Sabiha; Jatavath, Mohan Babu; Bathini, Raju; Sivan, Sree Kanth; Manga, Vijjulatha

2014-10-01

Poly(ADP-ribose) polymerase-1 (PARP-1) functions as a DNA damage sensor and signaling molecule. It plays a vital role in the repair of DNA strand breaks induced by radiation and chemotherapeutic drugs; inhibitors of this enzyme have the potential to improve cancer chemotherapy or radiotherapy. Three-dimensional quantitative structure activity relationship (3D QSAR) models were developed using comparative molecular field analysis, comparative molecular similarity indices analysis and docking studies. A set of 88 molecules were docked into the active site of six X-ray crystal structures of poly(ADP-ribose)polymerase-1 (PARP-1), by a procedure called multiple receptor conformation docking (MRCD), in order to improve the 3D QSAR models through the analysis of binding conformations. The docked poses were clustered to obtain the best receptor binding conformation. These dock poses from clustering were used for 3D QSAR analysis. Based on MRCD and QSAR information, some key features have been identified that explain the observed variance in the activity. Two receptor-based QSAR models were generated; these models showed good internal and external statistical reliability that is evident from the [Formula: see text], [Formula: see text] and [Formula: see text]. The identified key features enabled us to design new PARP-1 inhibitors.

Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis.

PubMed

Venkataramanan, Natarajan Sathiyamoorthy; Suvitha, Ambigapathy

2018-05-01

This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters. Copyright © 2018 Elsevier Inc. All rights reserved.
Statistical mechanics of high-density bond percolation

NASA Astrophysics Data System (ADS)

Timonin, P. N.

2018-05-01

High-density (HD) percolation describes the percolation of specific κ -clusters, which are the compact sets of sites each connected to κ nearest filled sites at least. It takes place in the classical patterns of independently distributed sites or bonds in which the ordinary percolation transition also exists. Hence, the study of series of κ -type HD percolations amounts to the description of classical clusters' structure for which κ -clusters constitute κ -cores nested one into another. Such data are needed for description of a number of physical, biological, and information properties of complex systems on random lattices, graphs, and networks. They range from magnetic properties of semiconductor alloys to anomalies in supercooled water and clustering in biological and social networks. Here we present the statistical mechanics approach to study HD bond percolation on an arbitrary graph. It is shown that the generating function for κ -clusters' size distribution can be obtained from the partition function of the specific q -state Potts-Ising model in the q →1 limit. Using this approach we find exact κ -clusters' size distributions for the Bethe lattice and Erdos-Renyi graph. The application of the method to Euclidean lattices is also discussed.
Rapid broad area search and detection of Chinese surface-to-air missile sites using deep convolutional neural networks

NASA Astrophysics Data System (ADS)

Marcum, Richard A.; Davis, Curt H.; Scott, Grant J.; Nivin, Tyler W.

2017-10-01

We evaluated how deep convolutional neural networks (DCNN) could assist in the labor-intensive process of human visual searches for objects of interest in high-resolution imagery over large areas of the Earth's surface. Various DCNN were trained and tested using fewer than 100 positive training examples (China only) from a worldwide surface-to-air-missile (SAM) site dataset. A ResNet-101 DCNN achieved a 98.2% average accuracy for the China SAM site data. The ResNet-101 DCNN was used to process ˜19.6 M image chips over a large study area in southeastern China. DCNN chip detections (˜9300) were postprocessed with a spatial clustering algorithm to produce a ranked list of ˜2100 candidate SAM site locations. The combination of DCNN processing and spatial clustering effectively reduced the search area by ˜660X (0.15% of the DCNN-processed land area). An efficient web interface was used to facilitate a rapid serial human review of the candidate SAM sites in the China study area. Four novice imagery analysts with no prior imagery analysis experience were able to complete a DCNN-assisted SAM site search in an average time of ˜42 min. This search was ˜81X faster than a traditional visual search over an equivalent land area of ˜88,640 km2 while achieving nearly identical statistical accuracy (˜90% F1).
antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters.

PubMed

Weber, Tilmann; Blin, Kai; Duddela, Srikanth; Krug, Daniel; Kim, Hyun Uk; Bruccoleri, Robert; Lee, Sang Yup; Fischbach, Michael A; Müller, Rolf; Wohlleben, Wolfgang; Breitling, Rainer; Takano, Eriko; Medema, Marnix H

2015-07-01

Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Assignment of sockeye salmon (Oncorhynchus nerka) to spawning sites using DNA markers.

PubMed

Corley-Smith, Graham E; Wennerberg, Liv; Schembri, Joy A; Lim, Chinten J; Cooper, Karen L; Brandhorst, Bruce P

2005-01-01

Randomly amplified polymorphic DNA (RAPD) markers were used to assign individual adult sockeye salmon to their spawning sites using a genotype assignment test. Six primers were selected for use by screening bulked DNA samples for markers missing in fish from one or more of 5 sites in British Columbia or Alaska. Of 73 markers scored, 54 showed variation between or within sites among the sampled fish. Thirty-seven of the variable markers were not detected in any fish from one or more sites; 18 variable markers were detected in all fish from one or more other sites. Thus 25% of markers scored were found in all fish of some sites and in no fish of some other sites. An assignment test placed all 70 fish tested into their correct populations. Principal coordinate analysis of genetic variation produced clusters of fish corresponding to each sampling site. No sex-specific RAPD markers were detected among more than 1300 screened.
Controlled Expansion of a Strong-Field Iron Nitride Cluster: Multi-Site Ligand Substitution as a Strategy for Activating Interstitial Nitride Nucleophilicity.

PubMed

Drance, Myles J; Mokhtarzadeh, Charles C; Melaimi, Mohand; Agnew, Douglas W; Moore, Curtis E; Rheingold, Arnold L; Figueroa, Joshua S

2018-05-02

Multimetallic clusters have long been investigated as molecular surrogates for reactive sites on metal surfaces. In the case of the μ 4 -nitrido cluster [Fe 4 (μ 4 -N)(CO) 12 ] - , this analogy is limited owing to the electron-withdrawing effect of carbonyl ligands on the iron nitride core. Described here is the synthesis and reactivity of [Fe 4 (μ 4 -N)(CO) 8 (CNAr Mes2 ) 4 ] - , an electron-rich analogue of [Fe 4 (μ 4 -N)(CO) 12 ] - , where the interstitial nitride displays significant nucleophilicity. This characteristic enables rational expansion with main-group and transition-metal centers to yield unsaturated sites. The resulting clusters display surface-like reactivity through coordination-sphere-dependent atom rearrangement and metal-metal cooperativity. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Random whole metagenomic sequencing for forensic discrimination of soils.

PubMed

Khodakova, Anastasia S; Smith, Renee J; Burgoyne, Leigh; Abarno, Damien; Linacre, Adrian

2014-01-01

Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification) and SEED Subsystems (metabolic classification) databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER); similarity profile analysis (SIMPROF); non-metric multidimensional scaling (NMDS); and canonical analysis of principal coordinates (CAP) at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations.
Characterization of electrically-active defects in ultraviolet light-emitting diodes with laser-based failure analysis techniques

DOE PAGES

Miller, Mary A.; Tangyunyong, Paiboon; Edward I. Cole, Jr.

2016-01-12

In this study, laser-based failure analysis techniques demonstrate the ability to quickly and non-intrusively screen deep ultraviolet light-emitting diodes(LEDs) for electrically-active defects. In particular, two laser-based techniques, light-induced voltage alteration and thermally-induced voltage alteration, generate applied voltage maps (AVMs) that provide information on electrically-active defect behavior including turn-on bias, density, and spatial location. Here, multiple commercial LEDs were examined and found to have dark defect signals in the AVM indicating a site of reduced resistance or leakage through the diode. The existence of the dark defect signals in the AVM correlates strongly with an increased forward-bias leakage current. This increasedmore » leakage is not present in devices without AVM signals. Transmission electron microscopyanalysis of a dark defect signal site revealed a dislocation cluster through the pn junction. The cluster included an open core dislocation. Even though LEDs with few dark AVM defect signals did not correlate strongly with power loss, direct association between increased open core dislocation densities and reduced LED device performance has been presented elsewhere [M. W. Moseley et al., J. Appl. Phys. 117, 095301 (2015)].« less
Spatial analyses identify the geographic source of patients at a National Cancer Institute Comprehensive Cancer Center.

PubMed

Su, Shu-Chih; Kanarek, Norma; Fox, Michael G; Guseynova, Alla; Crow, Shirley; Piantadosi, Steven

2010-02-01

We examined the geographic distribution of patients to better understand the service area of the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, a designated National Cancer Institute (NCI) comprehensive cancer center located in an urban center. Like most NCI cancer centers, the Sidney Kimmel Comprehensive Cancer Center serves a population beyond city limits. Urban cancer centers are expected to serve their immediate neighborhoods and to address disparities in access to specialty care. Our purpose was to learn the extent and nature of the cancer center service area. Statistical clustering of patient residence in the continental United States was assessed for all patients and by gender, cancer site, and race using SaTScan. Primary clusters detected for all cases and demographically and tumor-defined subpopulations were centered at Baltimore City and consisted of adjacent counties in Delaware, Pennsylvania, Virginia, West Virginia, New Jersey and New York, and the District of Columbia. Primary clusters varied in size by race, gender, and cancer site. Spatial analysis can provide insights into the populations served by urban cancer centers, assess centers' performance relative to their communities, and aid in developing a cancer center business plan that recognizes strengths, regional utility, and referral patterns. Today, 62 NCI cancer centers serve a quarter of the U.S. population in their immediate communities. From the Baltimore experience, we might project that the population served by these centers is actually more extensive and varies by patient characteristics, cancer site, and probably cancer center services offered.
An Evolutionary Landscape of A-to-I RNA Editome across Metazoan Species

PubMed Central

Hung, Li-Yuan; Chen, Yen-Ju; Mai, Te-Lun; Chen, Chia-Ying; Yang, Min-Yu; Chiang, Tai-Wei; Wang, Yi-Da

2018-01-01

Abstract Adenosine-to-inosine (A-to-I) editing is widespread across the kingdom Metazoa. However, for the lack of comprehensive analysis in nonmodel animals, the evolutionary history of A-to-I editing remains largely unexplored. Here, we detect high-confidence editing sites using clustering and conservation strategies based on RNA sequencing data alone, without using single-nucleotide polymorphism information or genome sequencing data from the same sample. We thereby unveil the first evolutionary landscape of A-to-I editing maps across 20 metazoan species (from worm to human), providing unprecedented evidence on how the editing mechanism gradually expands its territory and increases its influence along the history of evolution. Our result revealed that highly clustered and conserved editing sites tended to have a higher editing level and a higher magnitude of the ADAR motif. The ratio of the frequencies of nonsynonymous editing to that of synonymous editing remarkably increased with increasing the conservation level of A-to-I editing. These results thus suggest potentially functional benefit of highly clustered and conserved editing sites. In addition, spatiotemporal dynamics analyses reveal a conserved enrichment of editing and ADAR expression in the central nervous system throughout more than 300 Myr of divergent evolution in complex animals and the comparability of editing patterns between invertebrates and between vertebrates during development. This study provides evolutionary and dynamic aspects of A-to-I editome across metazoan species, expanding this important but understudied class of nongenomically encoded events for comprehensive characterization. PMID:29294013
MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets.

PubMed

Naegle, Kristen M; Welsch, Roy E; Yaffe, Michael B; White, Forest M; Lauffenburger, Douglas A

2011-07-01

Advances in proteomic technologies continue to substantially accelerate capability for generating experimental data on protein levels, states, and activities in biological samples. For example, studies on receptor tyrosine kinase signaling networks can now capture the phosphorylation state of hundreds to thousands of proteins across multiple conditions. However, little is known about the function of many of these protein modifications, or the enzymes responsible for modifying them. To address this challenge, we have developed an approach that enhances the power of clustering techniques to infer functional and regulatory meaning of protein states in cell signaling networks. We have created a new computational framework for applying clustering to biological data in order to overcome the typical dependence on specific a priori assumptions and expert knowledge concerning the technical aspects of clustering. Multiple clustering analysis methodology ('MCAM') employs an array of diverse data transformations, distance metrics, set sizes, and clustering algorithms, in a combinatorial fashion, to create a suite of clustering sets. These sets are then evaluated based on their ability to produce biological insights through statistical enrichment of metadata relating to knowledge concerning protein functions, kinase substrates, and sequence motifs. We applied MCAM to a set of dynamic phosphorylation measurements of the ERRB network to explore the relationships between algorithmic parameters and the biological meaning that could be inferred and report on interesting biological predictions. Further, we applied MCAM to multiple phosphoproteomic datasets for the ERBB network, which allowed us to compare independent and incomplete overlapping measurements of phosphorylation sites in the network. We report specific and global differences of the ERBB network stimulated with different ligands and with changes in HER2 expression. Overall, we offer MCAM as a broadly-applicable approach for analysis of proteomic data which may help increase the current understanding of molecular networks in a variety of biological problems. © 2011 Naegle et al.
Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion

PubMed Central

Bignon, Emmanuelle; Gattuso, Hugo; Morell, Christophe; Dehez, François; Georgakilas, Alexandros G.; Monari, Antonio; Dumont, Elise

2016-01-01

Clustered apurinic/apyrimidinic (AP; abasic) DNA lesions produced by ionizing radiation are by far more cytotoxic than isolated AP lesion entities. The structure and dynamics of a series of seven 23-bp oligonucleotides featuring simple bistranded clustered damage sites, comprising of two AP sites, zero, one, three or five bases 3′ or 5′ apart from each other, were investigated through 400 ns explicit solvent molecular dynamics simulations. They provide representative structures of synthetically engineered multiply damage sites-containing oligonucleotides whose repair was investigated experimentally (Nucl. Acids Res. 2004, 32:5609-5620; Nucl. Acids Res. 2002, 30: 2800–2808). The inspection of extrahelical positioning of the AP sites, bulge and non Watson–Crick hydrogen bonding corroborates the experimental measurements of repair efficiencies by bacterial or human AP endonucleases Nfo and APE1, respectively. This study provides unprecedented knowledge into the structure and dynamics of clustered abasic DNA lesions, notably rationalizing the non-symmetry with respect to 3′ to 5′ position. In addition, it provides strong mechanistic insights and basis for future studies on the effects of clustered DNA damage on the recognition and processing of these lesions by bacterial or human DNA repair enzymes specialized in the processing of such lesions. PMID:27587587
Molecular Control of Polyene Macrolide Biosynthesis

PubMed Central

Santos-Aberturas, Javier; Vicente, Cláudia M.; Guerra, Susana M.; Payero, Tamara D.; Martín, Juan F.; Aparicio, Jesús F.

2011-01-01

Control of polyene macrolide production in Streptomyces natalensis is mediated by the transcriptional activator PimM. This regulator, which combines an N-terminal PAS domain with a C-terminal helix-turn-helix motif, is highly conserved among polyene biosynthetic gene clusters. PimM, truncated forms of the protein without the PAS domain (PimMΔPAS), and forms containing just the DNA-binding domain (DBD) (PimMDBD) were overexpressed in Escherichia coli as GST-fused proteins. GST-PimM binds directly to eight promoters of the pimaricin cluster, as demonstrated by electrophoretic mobility shift assays. Assays with truncated forms of the protein revealed that the PAS domain does not mediate specificity or the distinct recognition of target genes, which rely on the DBD domain, but significantly reduces binding affinity up to 500-fold. Transcription start points were identified by 5′-rapid amplification of cDNA ends, and the binding regions of PimMDBD were investigated by DNase I protection studies. In all cases, binding took place covering the −35 hexamer box of each promoter, suggesting an interaction of PimM and RNA polymerase to cause transcription activation. Information content analysis of the 16 sequences protected in target promoters was used to deduce the structure of the PimM-binding site. This site displays dyad symmetry, spans 14 nucleotides, and adjusts to the consensus TVGGGAWWTCCCBA. Experimental validation of this binding site was performed by using synthetic DNA duplexes. Binding of PimM to the promoter region of one of the polyketide synthase genes from the Streptomyces nodosus amphotericin cluster containing the consensus binding site was also observed, thus proving the applicability of the findings reported here to other antifungal polyketides. PMID:21187288
Reduction Potentials of [FeFe]-Hydrogenase Accessory Iron-Sulfur Clusters Provide Insights into the Energetics of Proton Reduction Catalysis.

PubMed

Artz, Jacob H; Mulder, David W; Ratzloff, Michael W; Lubner, Carolyn E; Zadvornyy, Oleg A; LeVan, Axl X; Williams, S Garrett; Adams, Michael W W; Jones, Anne K; King, Paul W; Peters, John W

2017-07-19

An [FeFe]-hydrogenase from Clostridium pasteurianum, CpI, is a model system for biological H 2 activation. In addition to the catalytic H-cluster, CpI contains four accessory iron-sulfur [FeS] clusters in a branched series that transfer electrons to and from the active site. In this work, potentiometric titrations have been employed in combination with electron paramagnetic resonance (EPR) spectroscopy at defined electrochemical potentials to gain insights into the role of the accessory clusters in catalysis. EPR spectra collected over a range of potentials were deconvoluted into individual components attributable to the accessory [FeS] clusters and the active site H-cluster, and reduction potentials for each cluster were determined. The data suggest a large degree of magnetic coupling between the clusters. The distal [4Fe-4S] cluster is shown to have a lower reduction potential (∼ < -450 mV) than the other clusters, and molecular docking experiments indicate that the physiological electron donor, ferredoxin (Fd), most favorably interacts with this cluster. The low reduction potential of the distal [4Fe-4S] cluster thermodynamically restricts the Fd ox /Fd red ratio at which CpI can operate, consistent with the role of CpI in recycling Fd red that accumulates during fermentation. Subsequent electron transfer through the additional accessory [FeS] clusters to the H-cluster is thermodynamically favorable.
Two Suspected Worksite or Occupational Cancer Clusters Investigated Using the Cancer Data Registry and Multiple Primary Standardized Incidence Ratios in SEER *Stat-Idaho, 2013-2014.

PubMed

Rosenthal, Mariana; Johnson, Christopher J; Scoppa, Steve; Carter, Kris

2016-01-01

Investigations of suspected cancer clusters are resource intensive and rarely identify true clusters: among 428 publicly reported US investigations during 1990-2011, only 1 etiologic cluster was identified. In 2013, the Cancer Data Registry of Idaho (CDRI) was contacted regarding a suspected cancer cluster at a worksite (Cluster A) and among an occupational cohort (Cluster B). We investigated to determine whether these were true clusters. We derived investigation cohorts for Cluster A from facility-provided employee records and for Cluster B from professional licensing records. We used Registry PlusTM Link Plus to conduct probabilistic linkage of cohort members to the CDRI registry and completed matching through manual review by using LexisNexis®, Accurint®, and the Social Security Death Index. We calculated standardized incidence ratios (SIR) using the MP-SIR session type in SEER*Stat and Idaho and US referent populations. For Cluster A, we identified 34 cancer cases during 9,689 person-years; compared with Idaho and US rates, 95 percent CIs for SIRs included 1.0 for 24 of 24 primary site categories. For Cluster B, we identified 78 cancer cases during 15,154 person-years; compared with Idaho rates, 95 percent CI for SIRs included 1.0 for 23 of 24 primary site categories and was less than 1.0 for lung and bronchus cancers, and compared with US rates, 95 percent CI for SIRs included 1.0 for 22 of 24 primary site categories and was less than 1.0 for lung and bronchus and colorectal cancers. We identified no statistically significant excess in cancer incidence in either cohort. SEER*Stat's MP-SIR is an efficient tool for performing SIR assessments, a Centers for Disease Control and Prevention/Council of State and Territorial Epidemiologists-recommended step when investigating suspected cancer clusters.
Cluster analysis of Pinus taiwanensis for its ex situ conservation in China.

PubMed

Gao, X; Shi, L; Wu, Z

2015-06-01

Pinus taiwanensis Hayata is one of the most famous sights in the Huangshan Scenic Resort, China, because of its strong adaptability and ability to survive; however, this endemic species is currently under threat in China. Relationships between different P. taiwanensis populations have been well-documented; however, few studies have been conducted on how to protect this rare pine. In the present study, we propose the ex situ conservation of this species using geographical information system (GIS) cluster and genetic diversity analyses. The GIS cluster method was conducted as a preliminary analysis for establishing a sampling site category based on climatic factors. Genetic diversity was analyzed using morphological and genetic traits. By combining geographical information with genetic data, we demonstrate that growing conditions, morphological traits, and the genetic make-up of the population in the Huangshan Scenic Resort were most similar to conditions on Tianmu Mountain. Therefore, we suggest that Tianmu Mountain is the best choice for the ex situ conservation of P. taiwanensis. Our results provide a molecular basis for the sustainable management, utilization, and conservation of this species in Huangshan Scenic Resort.
Energetics of halogen impurities in thorium dioxide

NASA Astrophysics Data System (ADS)

Kuganathan, Navaratnarajah; Ghosh, Partha S.; Arya, Ashok K.; Dey, Gautam K.; Grimes, Robin W.

2017-11-01

Defect energies for halogen impurity atoms (Cl, Br and I) in thoria are calculated using the generalized gradient approximation and projector augmented plane wave potentials under the framework of density functional theory. The energy to place a halogen atom at a pre-existing lattice site is the incorporation energy. Seven sites are considered: octahedral interstitial, O vacancy, Th vacancy, Th-O di-vacancy cluster (DV) and the three O-Th-O tri-vacancy cluster (NTV) configurations. For point defects and vacancy clusters, neutral and all possible defect charge states up to full formal charge are considered. The most favourable incorporation site for Cl is the singly charged positive oxygen vacancy while for Br and I it is the NTV1 cluster. By considering the energy to form the defect sites, solution energies are generated. These show that in both ThO2-x and ThO2 the most favourable solution equilibrium site for halides is the single positively charged oxygen vacancy (although in ThO2, I demonstrates the same solubility in the NTV1 and DV clusters). Solution energies are much lower in ThO2-x than in ThO2 indicating that stoichiometry is a significant factor in determining solubility. In ThO2, all three halogens are highly insoluble and in ThO2-x Br and I remain insoluble. Although ½Cl2 is soluble in ThO2-x alternative phases such as ZrCl4 exist which are of lower energy.
Application of Inter-Simple Sequence Repeat Markers in the Analysis of Populations of the Chagas Disease Vector Triatoma infestans (Hemiptera, Reduviidae)

PubMed Central

Pérez de Rosas, Alicia R.; Restelli, María F.; Fernández, Cintia J.; Blariza, María J.; García, Beatriz A.

2017-01-01

Here we apply inter-simple sequence repeat (ISSR) markers to explore the fine-scale genetic structure and dispersal in populations of Triatoma infestans. Five selected primers from 30 primers were used to amplify ISSRs by polymerase chain reaction. A total of 90 polymorphic bands were detected across 134 individuals captured from 11 peridomestic sites from the locality of San Martín (Capayán Department, Catamarca Province, Argentina). Significant levels of genetic differentiation suggest limited gene flow among sampling sites. Spatial autocorrelation analysis confirms that dispersal occurs on the scale of ∼469 m, suggesting that insecticide spraying should be extended at least within a radius of ∼500 m around the infested area. Moreover, Bayesian clustering algorithms indicated genetic exchange among different sites analyzed, supporting the hypothesis of an important role of peridomestic structures in the process of reinfestation. PMID:28115670
Characterizing the spatial distribution of brown marmorated stink bug, Halyomorpha halys Stål (Hemiptera: Pentatomidae), populations in peach orchards

PubMed Central

Hahn, Noel G.

2017-01-01

Geospatial analyses were used to investigate the spatial distribution of populations of Halyomorpha halys, an important invasive agricultural pest in mid-Atlantic peach orchards. This spatial analysis will improve efficiency by allowing growers and farm managers to predict insect arrangement and target management strategies. Data on the presence of H. halys were collected from five peach orchards at four farms in New Jersey from 2012–2014 located in different land-use contexts. A point pattern analysis, using Ripley’s K function, was used to describe clustering of H. halys. In addition, the clustering of damage indicative of H. halys feeding was described. With low populations early in the growing season, H. halys did not exhibit signs of clustering in the orchards at most distances. At sites with low populations throughout the season, clustering was not apparent. However, later in the season, high infestation levels led to more evident clustering of H. halys. Damage, although present throughout the entire orchard, was found at low levels. When looking at trees with greater than 10% fruit damage, damage was shown to cluster in orchards. The Moran’s I statistic showed that spatial autocorrelation of H. halys was present within the orchards on the August sample dates, in relation to both populations density and levels of damage. Kriging the abundance of H. halys and the severity of damage to peaches revealed that the estimations of these are generally found in the same region of the orchards. This information on the clustering of H. halys populations will be useful to help predict presence of insects for use in management or scouting programs. PMID:28362797
Using multivariate techniques to assess the effects of urbanization on surface water quality: a case study in the Liangjiang New Area, China.

PubMed

Luo, Kun; Hu, Xuebin; He, Qiang; Wu, Zhengsong; Cheng, Hao; Hu, Zhenlong; Mazumder, Asit

2017-04-01

Rapid urbanization in China has been causing dramatic deterioration in the water quality of rivers and threatening aquatic ecosystem health. In this paper, multivariate techniques, such as factor analysis (FA) and cluster analysis (CA), were applied to analyze the water quality datasets for 19 rivers in Liangjiang New Area (LJNA), China, collected in April (dry season) and September (wet season) of 2014 and 2015. In most sampling rivers, total phosphorus, total nitrogen, and fecal coliform exceeded the Class V guideline (GB3838-2002), which could thereby threaten the water quality in Yangtze and Jialing Rivers. FA clearly identified the five groups of water quality variables, which explain majority of the experimental data. Nutritious pollution, seasonal changes, and construction activities were three key factors influencing rivers' water quality in LJNA. CA grouped 19 sampling sites into two clusters, which located at sub-catchments with high- and low-level urbanization, respectively. One-way ANOVA showed the nutrients (total phosphorus, soluble reactive phosphorus, total nitrogen, ammonium nitrogen, and nitrite), fecal coliform, and conductivity in cluster 1 were significantly greater than in cluster 2. Thus, catchment urbanization degraded rivers' water quality in Liangjiang New Area. Identifying effective buffer zones at riparian scale to weaken the negative impacts of catchment urbanization was recommended.

Climatology of atmospheric PM10 concentration in the Po Valley

NASA Astrophysics Data System (ADS)

Bigi, A.; Ghermandi, G.

2014-01-01

The limits to atmospheric pollutant concentration set by the European Commission provide a challenging target for the municipalities in the Po Valley, because of the characteristic climatic conditions and high population density of this region. In order to assess climatology and trends in the concentration of atmospheric particles in the Po Valley, a dataset of PM10 data from 41 sites across the Po Valley have been analysed, including both traffic and background sites (either urban, suburban or rural). Of these 41 sites, 18 with 10 yr or longer record have been analysed for long term trend in de-seasonalized monthly means, in annual quantiles and in monthly frequency distribution. A widespread significant decreasing trend has been observed at most sites, up to few percent per year, by Generalised Least Square and Theil-Sen method. All 41 sites have been tested for significant weekly periodicity by Kruskal-Wallis test for mean anomalies and by Wilcoxon test for weekend effect magnitude. A significant weekly periodicity has been observed for most PM10 series, particularly in summer and ascribed mainly to anthropic particulate emissions. A cluster analysis has been applied in order to highlight stations sharing similar pollution conditions over the reference period. Five clusters have been found, two gathering the metropolitan areas of Torino and Milano and their respective nearby sites and the other three clusters gathering north-east, north-west and central Po Valley sites respectively. Finally the observed trends in atmospheric PM10 have been compared to trends in provincial emissions of particulates and PM precursors, and analysed along with data on vehicular fleet age, composition and fuel sales. Significant basin-wide drop in emissions occurred for gaseous pollutants, contrarily to emissions of PM10 and PM2.5, whose drop resulted low and restricted to few provinces. It is not clear whether the decrease for only gaseous emissions is sufficient to explain the observed drop in atmospheric PM10, or if the low drop in particulate emissions is indeed due to the uncertainty in the emission inventory data for this species.
Long-term trend and variability of atmospheric PM10 concentration in the Po Valley

NASA Astrophysics Data System (ADS)

Bigi, A.; Ghermandi, G.

2014-05-01

The limits to atmospheric pollutant concentration set by the European Commission provide a challenging target for the municipalities in the Po Valley, because of the characteristic climatic conditions and high population density of this region. In order to assess climatology and trends in the concentration of atmospheric particles in the Po Valley, a data set of PM10 data from 41 sites across the Po Valley have been analysed, including both traffic and background sites (either urban, suburban or rural). Of these 41 sites, 18 with 10 yr or longer record have been analysed for long-term trend in deseasonalized monthly means, in annual quantiles and in monthly frequency distribution. A widespread significant decreasing trend has been observed at most sites, up to a few percent per year, by a generalized least squares and Theil-Sen method. All 41 sites have been tested for significant weekly periodicity by Kruskal-Wallis test for mean anomalies and by Wilcoxon test for weekend effect magnitude. A significant weekly periodicity has been observed for most PM10 series, particularly in summer and ascribed mainly to anthropic particulate emissions. A cluster analysis has been applied in order to highlight stations sharing similar pollution conditions over the reference period. Five clusters have been found, two encompassing the metropolitan areas of Turin and Milan and their respective nearby sites and the other three clusters gathering northeast, northwest and central Po Valley sites respectively. Finally, the observed trends in atmospheric PM10 have been compared to trends in provincial emissions of particulates and PM precursors, and analysed along with data on vehicular fleet age, composition and fuel sales. A significant basin-wide drop in emissions occurred for gaseous pollutants, contrarily to emissions of PM10 and PM2.5, whose drop was low and restricted to a few provinces. It is not clear whether the decrease for only gaseous emissions is sufficient to explain the observed drop in atmospheric PM10, or if the low drop in particulate emissions is indeed due to the uncertainty in the emission inventory data for this species.
Geotemporal Analysis of Neisseria meningitidis Clones in the United States: 2000–2005

PubMed Central

Wiringa, Ann E.; Shutt, Kathleen A.; Marsh, Jane W.; Cohn, Amanda C.; Messonnier, Nancy E.; Zansky, Shelley M.; Petit, Susan; Farley, Monica M.; Gershman, Ken; Lynfield, Ruth; Reingold, Arthur; Schaffner, William; Thompson, Jamie; Brown, Shawn T.; Lee, Bruce Y.; Harrison, Lee H.

2013-01-01

Background The detection of meningococcal outbreaks relies on serogrouping and epidemiologic definitions. Advances in molecular epidemiology have improved the ability to distinguish unique Neisseria meningitidis strains, enabling the classification of isolates into clones. Around 98% of meningococcal cases in the United States are believed to be sporadic. Methods Meningococcal isolates from 9 Active Bacterial Core surveillance sites throughout the United States from 2000 through 2005 were classified according to serogroup, multilocus sequence typing, and outer membrane protein (porA, porB, and fetA) genotyping. Clones were defined as isolates that were indistinguishable according to this characterization. Case data were aggregated to the census tract level and all non-singleton clones were assessed for non-random spatial and temporal clustering using retrospective space-time analyses with a discrete Poisson probability model. Results Among 1,062 geocoded cases with available isolates, 438 unique clones were identified, 78 of which had ≥2 isolates. 702 cases were attributable to non-singleton clones, accounting for 66.0% of all geocoded cases. 32 statistically significant clusters comprised of 107 cases (10.1% of all geocoded cases) were identified. Clusters had the following attributes: included 2 to 11 cases; 1 day to 33 months duration; radius of 0 to 61.7 km; and attack rate of 0.7 to 57.8 cases per 100,000 population. Serogroups represented among the clusters were: B (n = 12 clusters, 45 cases), C (n = 11 clusters, 27 cases), and Y (n = 9 clusters, 35 cases); 20 clusters (62.5%) were caused by serogroups represented in meningococcal vaccines that are commercially available in the United States. Conclusions Around 10% of meningococcal disease cases in the U.S. could be assigned to a geotemporal cluster. Molecular characterization of isolates, combined with geotemporal analysis, is a useful tool for understanding the spread of virulent meningococcal clones and patterns of transmission in populations. PMID:24349182
Task shifting of frontline community health workers for cardiovascular risk reduction: design and rationale of a cluster randomised controlled trial (DISHA study) in India.

PubMed

Jeemon, Panniyammakal; Narayanan, Gitanjali; Kondal, Dimple; Kahol, Kashvi; Bharadwaj, Ashok; Purty, Anil; Negi, Prakash; Ladhani, Sulaiman; Sanghvi, Jyoti; Singh, Kuldeep; Kapoor, Deksha; Sobti, Nidhi; Lall, Dorothy; Manimunda, Sathyaprakash; Dwivedi, Supriya; Toteja, Gurudyal; Prabhakaran, Dorairaj

2016-03-15

Effective task-shifting interventions targeted at reducing the global cardiovascular disease (CVD) epidemic in low and middle-income countries (LMICs) are urgently needed. DISHA is a cluster randomised controlled trial conducted across 10 sites (5 in phase 1 and 5 in phase 2) in India in 120 clusters. At each site, 12 clusters were randomly selected from a district. A cluster is defined as a small village with 250-300 households and well defined geographical boundaries. They were then randomly allocated to intervention and control clusters in a 1:1 allocation sequence. If any of the intervention and control clusters were <10 km apart, one was dropped and replaced with another randomly selected cluster from the same district. The study included a representative baseline cross-sectional survey, development of a structured intervention model, delivery of intervention for a minimum period of 18 months by trained frontline health workers (mainly Anganwadi workers and ASHA workers) and a post intervention survey in a representative sample. The study staff had no information on intervention allocation until the completion of the baseline survey. In order to ensure comparability of data across sites, the DISHA study follows a common protocol and manual of operation with standardized measurement techniques. Our study is the largest community based cluster randomised trial in low and middle-income country settings designed to test the effectiveness of 'task shifting' interventions involving frontline health workers for cardiovascular risk reduction. CTRI/2013/10/004049 . Registered 7 October 2013.
Clustered DNA damages induced in isolated DNA and in human cells by low doses of ionizing radiation

NASA Technical Reports Server (NTRS)

Sutherland, B. M.; Bennett, P. V.; Sidorkina, O.; Laval, J.; Lowenstein, D. I. (Principal Investigator)

2000-01-01

Clustered DNA damages-two or more closely spaced damages (strand breaks, abasic sites, or oxidized bases) on opposing strands-are suspects as critical lesions producing lethal and mutagenic effects of ionizing radiation. However, as a result of the lack of methods for measuring damage clusters induced by ionizing radiation in genomic DNA, neither the frequencies of their production by physiological doses of radiation, nor their repairability, nor their biological effects are known. On the basis of methods that we developed for quantitating damages in large DNAs, we have devised and validated a way of measuring ionizing radiation-induced clustered lesions in genomic DNA, including DNA from human cells. DNA is treated with an endonuclease that induces a single-strand cleavage at an oxidized base or abasic site. If there are two closely spaced damages on opposing strands, such cleavage will reduce the size of the DNA on a nondenaturing gel. We show that ionizing radiation does induce clustered DNA damages containing abasic sites, oxidized purines, or oxidized pyrimidines. Further, the frequency of each of these cluster classes is comparable to that of frank double-strand breaks; among all complex damages induced by ionizing radiation, double-strand breaks are only about 20%, with other clustered damage constituting some 80%. We also show that even low doses (0.1-1 Gy) of high linear energy transfer ionizing radiation induce clustered damages in human cells.
[3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis

PubMed Central

Rousset, Marc; Montet, Yael; Guigliarelli, Bruno; Forget, Nicole; Asso, Marcel; Bertrand, Patrick; Fontecilla-Camps, Juan C.; Hatchikian, E. Claude

1998-01-01

The role of the high potential [3Fe-4S]1+,0 cluster of [NiFe] hydrogenase from Desulfovibrio species located halfway between the proximal and distal low potential [4Fe-4S]2+,1+ clusters has been investigated by using site-directed mutagenesis. Proline 238 of Desulfovibrio fructosovorans [NiFe] hydrogenase, which occupies the position of a potential ligand of the lacking fourth Fe-site of the [3Fe-4S] cluster, was replaced by a cysteine residue. The properties of the mutant enzyme were investigated in terms of enzymatic activity, EPR, and redox properties of the iron-sulfur centers and crystallographic structure. We have shown on the basis of both spectroscopic and x-ray crystallographic studies that the [3Fe-4S] cluster of D. fructosovorans hydrogenase was converted into a [4Fe-4S] center in the P238 mutant. The [3Fe-4S] to [4Fe-4S] cluster conversion resulted in a lowering of approximately 300 mV of the midpoint potential of the modified cluster, whereas no significant alteration of the spectroscopic and redox properties of the two native [4Fe-4S] clusters and the NiFe center occurred. The significant decrease of the midpoint potential of the intermediate Fe-S cluster had only a slight effect on the catalytic activity of the P238C mutant as compared with the wild-type enzyme. The implications of the results for the role of the high-potential [3Fe-4S] cluster in the intramolecular electron transfer pathway are discussed. PMID:9751716
Antibodies to H2a and H2b histones from the sera of HIV-infected patients catalyze site-specific degradation of these histones.

PubMed

Baranova, Svetlana V; Dmitrienok, Pavel S; Ivanisenko, Nikita V; Buneva, Valentina N; Nevinsky, Georgy A

2017-06-01

Histones and their post-translational modifications have key roles in chromatin remodeling and gene transcription. Besides intranuclear functions, histones act as damage-associated molecules when they are released into the extracellular space. Administration of histones to animals leads to systemic inflammatory and toxic responses. Autoantibodies with enzymatic activities (abzymes) are distinctive features of some autoimmune and viral diseases. Electrophoretically homogeneous IgGs containing no canonical enzymes were isolated from the sera of HIV-infected patients by chromatography on several affinity sorbents including anti-histone Sepharose. In contrast to canonical proteases (trypsin, chymotrypsin, proteinase K), IgGs from HIV-infected patients specifically hydrolyzed only histones but not many other tested globular proteins. Using MALDI mass spectrometry the sites of H2a and H2b histone cleavage by anti-histone IgGs were determined for the first time. One cluster of H2a hydrolysis contains two major (↕) and four moderate (↓) cleavage sites: 31-H↓R↓L↓L↓R↕K G↕N-38. One major and two moderate sites of cleavage were revealed in the second cluster: 14-A↕KSRS↓SRA↓G-22. The third cluster corresponding to the H2a C-terminal part contains only five minor (†) sites of cleavage: 82-H†LQLAIRNDEELN†KLLG†RV†T†I-102. It was shown that two major and four moderate sites of cleavage were present in the main cluster of H2b hydrolysis: 46-K↕QvhpD↓TgiS↓SkA↓M↕GiM↓N-63. Two moderate sites of cleavage correspond to a relatively short 6-mer cluster: 12-K↓GskK↓A-17. The third relatively long 9-mer cluster contains one major and two minor sites of H2b cleavage: 80-L↕AHYN†KRS†T-88. In the nucleosome core particle, most of the major and moderate cleavage sites are located at the H2a/H2b interaction interface. Minor cleavage sites of H2a are involved in binding with H3 in the nucleosome core. Two moderate cleavage sites of H2b and one major cleavage site of H2a are located in the disordered N-terminal region interacting with DNA. According to the crystal structure of the nucleosome core particle, all identified cleavage sites are expected to affect H2a and H2b folding, nucleosome assembly, and binding of H2a and H2b with DNA. The existence of H2a and H2b hydrolyzing abzymes may be very important for the further understanding of unknown possibilities of immune systems and biological functions of antibodies.
Application of trajectory clustering and source attribution methods for investigating regional CO2 and CH4 concentrations at Germany's highest mountain site

NASA Astrophysics Data System (ADS)

Giemsa, Esther; Jacobeit, Jucundus; Ries, Ludwig; Frank, Gabriele; Hachinger, Stephan; Meyer-Arnek, Julian

2017-04-01

Carbon dioxide (CO2) and methane (CH4) represent the most important contributors to increased radiative forcing enhancing it together by contemporary 2.65 W/m2 on the global average (IPCC 2013). The unbroken increase of atmospheric greenhouse gases (GHG) has been unequivocally attributed to human emissions mainly coming from fossil fuel burning and land-use changes, while the oceans and terrestrial ecosystems slightly attenuate this rise with seasonally varying strength. Short-term fluctuations in the GHG concentrations that superimpose the seasonal cycle and the climate change driven trend reflect the presence of regional sources and sinks. A perfect place for investigating the comprehensive influence of these regional emissions is provided by the Environmental Research Station Schneefernerhaus (47.42°N, 10.98°E, 2.650m a.s.l.) situated in the eastern Alps at the southern side of Zugspitze mountain. Located just 300m below the highest peak of the German Alps, the exposed site is one of the currently 30 global core sites of the World Meteorological Organisation (WMO) Global Atmosphere Watch (GAW) programme and thus provides ideal conditions to study source-receptor relationships for greenhouse gases. We propose a stepwise statistical methodology for examining the relationship between synoptic-scale atmospheric transport patterns and climate gas mole fractions to finally receive a characterization of the sampling site with regard to the key processes driving CO2 and CH4 concentration levels. The first step entails a reliable radon-based filtering approach to subdivide the detected air masses according to their regional or 'background' origin. Simultaneously, a large number of ten-day back-trajectories from Schneefernerhaus every two hours over the entire study period 2011 - 2015 is calculated with the Lagrangian transport and dispersion model FLEXPART (Stohl et al. 2005) and subjected to cluster analysis. The weather- and emission strength-related (short-term) components of the regional CO2 and CH4 concentration time-series are assigned to the back-trajectory clusters. The significant differences in the greenhouse gases' distributions associated with each cluster are confirmed by the non-parametric Kruskal-Wallis test thereby delivering the prerequisites for further investigations, in particular by Potential Source Contribution Functions for the detection of probable locations of within-cluster emission sources. The advantages of this comprehensive approach are site-specificity (by considering trajectories arriving at Schneefernerhaus as well as a site-appropriate filter method) and concentration-specificity (each greenhouse gas has its own source regions) combined with granting the space and time scales related to the synoptic flow patterns in source attribution studies. This research received funding from the Bavarian State Ministry of the Environment and Consumer Protection.
Assessment of semi-volatile organic compounds in drinking water sources in Jiangsu, China.

PubMed

Wu, Yifeng; Jia, Yongzhi; Lu, Xiwu

2013-08-01

Many xenobiotic compounds, especially organic pollutants in drinking water, can cause threats to human health and natural ecosystems. The ability to predict the level of pollutants and identify their source is crucial for the design of pollutant risk reduction plans. In this study, 25 semi-volatile organic compounds (SVOCs) were assessed at 16 monitoring sites of drinking water sources in Jiangsu, east China, to evaluate water quality conditions and source of pollutants. Four multivariate statistical techniques were used for this analysis. The correlation test indicated that 25 SVOCs parameters variables had a significant spatial variability (P<0.05). The results of correlation analysis, principal component analysis (PCA) and cluster analysis (CA) suggested that at least four sources, i.e., agricultural residual pesticides, industrial sewage, water transportation vehicles and miscellaneous sources, were responsible for the presence of SVOCs in the drinking water sites examined, accounting for 89.6% of the total variance in the dataset. The analysis of site similarity showed that 16 sites could be divided into high, moderate, and low pollutant level groups at (D(link)/D(max))×25<10, and each group had primary typical SVOCs. These results provide useful information for developing appropriate strategies for contaminants control in drinking water sources. Copyright © 2013 Elsevier Inc. All rights reserved.
Two distinct Photobacterium populations thrive in ancient Mediterranean sapropels.

PubMed

Süss, Jacqueline; Herrmann, Kerstin; Seidel, Michael; Cypionka, Heribert; Engelen, Bert; Sass, Henrik

2008-04-01

Eastern Mediterranean sediments are characterized by the periodic occurrence of conspicuous, organic matter-rich sapropel layers. Phylogenetic analysis of a large culture collection isolated from these sediments revealed that about one third of the isolates belonged to the genus Photobacterium. In the present study, 22 of these strains were examined with respect to their phylogenetic and metabolic diversity. The strains belonged to two distinct Photobacterium populations (Mediterranean cluster I and II). Strains of cluster I were isolated almost exclusively from organic-rich sapropel layers and were closely affiliated with P. aplysiae (based on their 16S rRNA gene sequences). They possessed almost identical Enterobacterial Repetitive Intergenic Consensus (ERIC) and substrate utilization patterns, even among strains from different sampling sites or from layers differing up to 100,000 years in age. Strains of cluster II originated from sapropels and from the surface and carbon-lean intermediate layers. They were related to Photobacterium frigidiphilum but differed significantly in their fingerprint patterns and substrate spectra, even when these strains were obtained from the same sampling site and layer. Temperature range for growth (4 to 33 degrees C), salinity tolerance (5 to 100 per thousand), pH requirements (5.5-9.3), and the composition of polar membrane lipids were similar for both clusters. All strains grew by fermentation (glucose, organic acids) and all but five by anaerobic respiration (nitrate, dimethyl sulfoxide, anthraquinone disulfonate, or humic acids). These results indicate that the genus Photobacterium forms subsurface populations well adapted to life in the deep biosphere.
Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3).

PubMed

Mulepati, Sabin; Bailey, Scott

2011-09-09

RNA transcribed from clustered regularly interspaced short palindromic repeats (CRISPRs) protects many prokaryotes from invasion by foreign DNA such as viruses, conjugative plasmids, and transposable elements. Cas3 (CRISPR-associated protein 3) is essential for this CRISPR protection and is thought to mediate cleavage of the foreign DNA through its N-terminal histidine-aspartate (HD) domain. We report here the 1.8 Å crystal structure of the HD domain of Cas3 from Thermus thermophilus HB8. Structural and biochemical studies predict that this enzyme binds two metal ions at its active site. We also demonstrate that the single-stranded DNA endonuclease activity of this T. thermophilus domain is activated not by magnesium but by transition metal ions such as manganese and nickel. Structure-guided mutagenesis confirms the importance of the metal-binding residues for the nuclease activity and identifies other active site residues. Overall, these results provide a framework for understanding the role of Cas3 in the CRISPR system.
Variable number of tandem repeats and pulsed-field gel electrophoresis cluster analysis of enterohemorrhagic Escherichia coli serovar O157 strains.

PubMed

Yokoyama, Eiji; Uchimura, Masako

2007-11-01

Ninety-five enterohemorrhagic Escherichia coli serovar O157 strains, including 30 strains isolated from 13 intrafamily outbreaks and 14 strains isolated from 3 mass outbreaks, were studied by pulsed-field gel electrophoresis (PFGE) and variable number of tandem repeats (VNTR) typing, and the resulting data were subjected to cluster analysis. Cluster analysis of the VNTR typing data revealed that 57 (60.0%) of 95 strains, including all epidemiologically linked strains, formed clusters with at least 95% similarity. Cluster analysis of the PFGE patterns revealed that 67 (70.5%) of 95 strains, including all but 1 of the epidemiologically linked strains, formed clusters with 90% similarity. The number of epidemiologically unlinked strains forming clusters was significantly less by VNTR cluster analysis than by PFGE cluster analysis. The congruence value between PFGE and VNTR cluster analysis was low and did not show an obvious correlation. With two-step cluster analysis, the number of clustered epidemiologically unlinked strains by PFGE cluster analysis that were divided by subsequent VNTR cluster analysis was significantly higher than the number by VNTR cluster analysis that were divided by subsequent PFGE cluster analysis. These results indicate that VNTR cluster analysis is more efficient than PFGE cluster analysis as an epidemiological tool to trace the transmission of enterohemorrhagic E. coli O157.
Refractory black carbon at the Whistler Peak High Elevation Research Site - Measurements and simulations

NASA Astrophysics Data System (ADS)

Hanna, Sarah J.; Xu, Jun-Wei; Schroder, Jason C.; Wang, Qiaoqiao; McMeeking, Gavin R.; Hayden, Katherine; Leaitch, W. Richard; Macdonald, AnneMarie; von Salzen, Knut; Martin, Randall V.; Bertram, Allan K.

2018-05-01

Measurements of black carbon at remote and high altitude locations provide an important constraint for models. Here we present six months of refractory black carbon (rBC) data collected in July-August of 2009, June-July of 2010, and April-May of 2012 using a single particle soot photometer (SP2) at the remote Whistler High Elevation Research Site in the Coast Mountains of British Columbia (50.06°N, 122.96°W, 2182 m a.m.s.l). In order to reduce regional boundary layer influences, only measurements collected during the night (2000-0800 PST) were considered. Times impacted by local biomass burning were removed from the data set, as were periods of in-cloud sampling. Back trajectories and back trajectory cluster analysis were used to classify the sampled air masses as Southern Pacific, Northern Pacific, Western Pacific/Asian, or Northern Canadian in origin. The largest rBC mass median diameter (182 nm) was seen for air masses in the Southern Pacific cluster, and the smallest (156 nm) was seen for air masses in the Western Pacific/Asian cluster. Considering all the clusters, the median mass concentration of rBC was 25.0 ± 7.6 ng/m3-STP. The Northern Pacific, Southern Pacific, Western Pacific/Asian, and Northern Canada clusters had median mass concentrations of 25.0 ± 7.6, 21.3 ± 6.9, 25.0 ± 7.9, and 40.6 ± 12.9 ng/m3-STP, respectively. We compared these measurements with simulations from the global chemical transport model GEOS-Chem. The default GEOS-Chem simulations overestimated the median rBC mass concentrations for the different clusters by a factor of 1.2-2.2. The largest difference was observed for the Northern Pacific cluster (factor of 2.2) and the smallest difference was observed for the Northern Canada cluster (factor of 1.2). A sensitivity simulation that excluded Vancouver emissions still overestimated the median rBC mass concentrations for the different clusters by a factor of 1.1-2.0. After implementation of a revised wet scavenging scheme, the simulations overestimated the median rBC mass concentrations for the different clusters by a factor of 1.0-2.0.
Patterns of Community Change among Ammonia Oxidizers in Meadow Soils upon Long-Term Incubation at Different Temperatures

PubMed Central

Avrahami, Sharon; Conrad, Ralf

2003-01-01

The effect of temperature on the community structure of ammonia-oxidizing bacteria was investigated in three different meadow soils. Two of the soils (OMS and GMS) were acidic (pH 5.0 to 5.8) and from sites in Germany with low annual mean temperature (about 10°C), while KMS soil was slightly alkaline (pH 7.9) and from a site in Israel with a high annual mean temperature (about 22°C). The soils were fertilized and incubated for up to 20 weeks in a moist state and as a buffered (pH 7) slurry amended with urea at different incubation temperatures (4 to 37°C). OMS soil was also incubated with less fertilizer than the other soils. The community structure of ammonia oxidizers was analyzed before and after incubation by denaturing gradient gel electrophoresis (DGGE) of the amoA gene, which codes for the α subunit of ammonia monooxygenase. All amoA gene sequences found belonged to the genus Nitrosospira. The analysis showed community change due to temperature both in moist soil and in the soil slurry. Two patterns of community change were observed. One pattern was a change between the different Nitrosospira clusters, which was observed in moist soil and slurry incubations of GMS and OMS. Nitrosospira AmoA cluster 1 was mainly detected below 30°C, while Nitrosospira cluster 4 was predominant at 25°C. Nitrosospira clusters 3a, 3b, and 9 dominated at 30°C. The second pattern, observed in KMS, showed a community shift predominantly within a single Nitrosospira cluster. The sequences of the individual DGGE bands that exhibited different trends with temperature belonged almost exclusively to Nitrosospira cluster 3a. We conclude that ammonia oxidizer populations are influenced by temperature. In addition, we confirmed previous observations that N fertilizer also influences the community structure of ammonia oxidizers. Thus, Nitrosospira cluster 1 was absent in OMS soil treated with less fertilizer, while Nitrosospira cluster 9 was only found in the sample given less fertilizer. PMID:14532075
Association between maternal health literacy and child vaccination in India: a cross-sectional study.

PubMed

Johri, Mira; Subramanian, S V; Sylvestre, Marie-Pierre; Dudeja, Sakshi; Chandra, Dinesh; Koné, Georges K; Sharma, Jitendar K; Pahwa, Smriti

2015-09-01

Education of mothers may improve child health. We investigated whether maternal health literacy, a rapidly modifiable factor related to mother's education, was associated with children's receipt of vaccines in two underserved Indian communities. Cross-sectional surveys in an urban and a rural site. We assessed health literacy using Indian child health promotion materials. The outcome was receipt of three doses of diphtheria-tetanus-pertussis (DTP3) vaccine. We used multivariate logistic regression to investigate the relationship between maternal health literacy and vaccination status independently in each site. For both sites, adjusted models considered maternal age, maternal and paternal education, child sex, birth order, household religion and wealth quintile. Rural analyses used multilevel models adjusted for service delivery characteristics. Urban analyses represented cluster characteristics through fixed effects. The rural analysis included 1170 women from 60 villages. The urban analysis included 670 women from nine slum clusters. In each site, crude and adjusted models revealed a positive association between maternal health literacy and DTP3. In the rural site, the adjusted OR was 1.57 (95% CI 1.11 to 2.21, p=0.010) for those with medium health literacy, and OR=1.30 (95% CI 0.89 to 1.91, p=0.172) for those with high health literacy. In the urban site, the adjusted OR was 1.10 (95% CI 0.65 to 1.88, p=0.705) for those with medium health literacy, and OR=2.06 (95% CI 1.06 to 3.99, p=0.032) for those with high health literacy. In these study settings, maternal health literacy is independently associated with child vaccination. Initiatives targeting health literacy could improve vaccination coverage. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
Doubly stochastic Poisson process models for precipitation at fine time-scales

NASA Astrophysics Data System (ADS)

Ramesh, Nadarajah I.; Onof, Christian; Xie, Dichao

2012-09-01

This paper considers a class of stochastic point process models, based on doubly stochastic Poisson processes, in the modelling of rainfall. We examine the application of this class of models, a neglected alternative to the widely-known Poisson cluster models, in the analysis of fine time-scale rainfall intensity. These models are mainly used to analyse tipping-bucket raingauge data from a single site but an extension to multiple sites is illustrated which reveals the potential of this class of models to study the temporal and spatial variability of precipitation at fine time-scales.
Microevolution of symbiotic Bradyrhizobium populations associated with soybeans in east North America

PubMed Central

Tang, Jie; Bromfield, E S P; Rodrigue, N; Cloutier, S; Tambong, J T

2012-01-01

Microevolution and origins of Bradyrhizobium populations associated with soybeans at two field sites (A and B, 280 km apart in Canada) with contrasting histories of inoculation was investigated using probabilistic analyses of six core (housekeeping) gene sequences. These analyses supported division of 220 isolates in five lineages corresponding either to B. japonicum groups 1 and 1a or to one of three novel lineages within the genus Bradyrhizobium. None of the isolates from site A and about 20% from site B (the only site with a recent inoculation history) were attributed to inoculation sources. The data suggest that most isolates were of indigenous origin based on sequence analysis of 148 isolates of soybean-nodulating bacteria from native legumes (Amphicarpaea bracteata and Desmodium canadense). Isolates from D. canadense clustered with B. japonicum group 1, whereas those from A. bracteata were placed in two novel lineages encountered at soybean field sites. One of these novel lineages predominated at soybean sites and exhibited a significant clonal expansion likely reflecting selection by the plant host. Homologous recombination events detected in the 35 sequence types from soybean sites had an effect on genetic diversification that was approximately equal to mutation. Interlineage transfer of core genes was infrequent and mostly attributable to gyrB that had a history of frequent recombination. Symbiotic gene sequences (nodC and nifH) of isolates from soybean sites and native legumes clustered in two lineages corresponding to B. japonicum and B. elkani with the inheritance of these genes appearing predominantly by vertical transmission. The data suggest that soybean-nodulating bacteria associated with native legumes represent a novel source of ecologically adapted bacteria for soybean inoculation. PMID:23301163
Naturally Occurring Structural Isomers in Serum IgA1 O-Glycosylation

PubMed Central

Takahashi, Kazuo; Smith, Archer D.; Poulsen, Knud; Kilian, Mogens; Julian, Bruce A.; Mestecky, Jiri; Novak, Jan; Renfrow, Matthew B.

2013-01-01

IgA is the most abundantly produced antibody and plays an important role in the mucosal immune system. Human IgA is represented by two isotypes, IgA1 and IgA2. The major structural difference between these two subclasses is the presence of nine potential sites of O-glycosylation in the hinge region between the first and second constant region domains of the heavy chain. Thr225, Thr228, Ser230, Ser232 and Thr236 have been identified as the predominant sites of O-glycan attachment. The range and distribution of O-glycan chains at each site within the context of adjacent sites in this clustered region create a complex heterogeneity of surface epitopes that is incompletely defined. We previously described the analysis of IgA1 O-glycan heterogeneity by use of high resolution LC/MS and electron capture dissociation tandem MS to unambiguously localize all amino acid attachment sites in IgA1 (Ale) myeloma protein. Here, we report the identification and elucidation of IgA1 O-glycopeptide structural isomers that occur based on amino acid position of the attached glycans (positional isomers) and the structure of the O-glycan chains at individual sites (glycan isomers). These isomers are present in a model IgA1 (Mce1) myeloma protein and occur naturally in normal human serum IgA1. Variable O-glycan chains attached to Ser230, Thr233 or Thr236 produce the predominant positional isomers, including O-glycans composed of a single GalNAc residue. These findings represent the first definitive identification of structural isomeric IgA1 O-glycoforms, define the single-site heterogeneity for all O-glycan sites in a single sample, and have implications for defining epitopes based on clustered O-glycan variability. PMID:22067045
Correlation study of sodium-atom chemisorption on the GaAs(110) surface

NASA Astrophysics Data System (ADS)

Song, K. M.; Khan, D. C.; Ray, A. K.

1994-01-01

Different possible adsorption sites of sodium atoms on a gallium arsenide surface have been investigated using ab initio self-consistent unrestricted Hartree-Fock total-energy cluster calculations with Hay-Wadt effective core potentials. The effects of electron correlation have been included by invoking the concepts of many-body perturbation theory and are found to be highly significant. We find that the Na-atom adsorption at a site modeled with an NaGa5As4H12 cluster is most favored energetically followed by Na adsorption at the site modeled with the NaGa4As5H12 cluster. The effects of charge transfer from Na to the GaAs surface as also possibilities of metallization are also analyzed and discussed.
Hotspots of Malaria Transmission in the Peruvian Amazon: Rapid Assessment through a Parasitological and Serological Survey

PubMed Central

Rosas-Aguirre, Angel; Speybroeck, Niko; Llanos-Cuentas, Alejandro; Rosanas-Urgell, Anna; Carrasco-Escobar, Gabriel; Rodriguez, Hugo; Gamboa, Dionicia; Contreras-Mancilla, Juan; Alava, Freddy; Soares, Irene S.; Remarque, Edmond; D´Alessandro, Umberto; Erhart, Annette

2015-01-01

Background With low and markedly seasonal malaria transmission, increasingly sensitive tools for better stratifying the risk of infection and targeting control interventions are needed. A cross-sectional survey to characterize the current malaria transmission patterns, identify hotspots, and detect recent changes using parasitological and serological measures was conducted in three sites of the Peruvian Amazon. Material and Methods After full census of the study population, 651 participants were interviewed, clinically examined and had a blood sample taken for the detection of malaria parasites (microscopy and PCR) and antibodies against P. vivax (PvMSP119, PvAMA1) and P. falciparum (PfGLURP, PfAMA1) antigens by ELISA. Risk factors for malaria infection (positive PCR) and malaria exposure (seropositivity) were assessed by multivariate survey logistic regression models. Age-specific seroprevalence was analyzed using a reversible catalytic conversion model based on maximum likelihood for generating seroconversion rates (SCR, λ). SaTScan was used to detect spatial clusters of serology-positive individuals within each site. Results The overall parasite prevalence by PCR was low, i.e. 3.9% for P. vivax and 6.7% for P. falciparum, while the seroprevalence was substantially higher, 33.6% for P. vivax and 22.0% for P. falciparum, with major differences between study sites. Age and location (site) were significantly associated with P. vivax exposure; while location, age and outdoor occupation were associated with P. falciparum exposure. P. falciparum seroprevalence curves showed a stable transmission throughout time, while for P. vivax transmission was better described by a model with two SCRs. The spatial analysis identified well-defined clusters of P. falciparum seropositive individuals in two sites, while it detected only a very small cluster of P. vivax exposure. Conclusion The use of a single parasitological and serological malaria survey has proven to be an efficient and accurate method to characterize the species specific heterogeneity in malaria transmission at micro-geographical level as well as to identify recent changes in transmission. PMID:26356311

Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.

PubMed

Fenwick, Michael K; Mehta, Angad P; Zhang, Yang; Abdelwahed, Sameh H; Begley, Tadhg P; Ealick, Steven E

2015-03-27

Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.
Construction and engineering of large biochemical pathways via DNA assembler

PubMed Central

Shao, Zengyi; Zhao, Huimin

2015-01-01

Summary DNA assembler enables rapid construction and engineering of biochemical pathways in a one-step fashion by exploitation of the in vivo homologous recombination mechanism in Saccharomyces cerevisiae. It has many applications in pathway engineering, metabolic engineering, combinatorial biology, and synthetic biology. Here we use two examples including the zeaxanthin biosynthetic pathway and the aureothin biosynthetic gene cluster to describe the key steps in the construction of pathways containing multiple genes using the DNA assembler approach. Methods for construct design, pathway assembly, pathway confirmation, and functional analysis are shown. The protocol for fine genetic modifications such as site-directed mutagenesis for engineering the aureothin gene cluster is also illustrated. PMID:23996442
Rates of proton transfer to Fe-S-based clusters: comparison of clusters containing {MFe(mu(2)-S)(2)}n+ and {MFe(3)(mu(3)-S)(4)}n+ (M = Fe, Mo, or W) cores.

PubMed

Bates, Katie; Garrett, Brendan; Henderson, Richard A

2007-12-24

The rates of proton transfer from [pyrH]+ (pyr = pyrrolidine) to the binuclear complexes [Fe2S2Cl4]2- and [S2MS2FeCl2]2- (M = Mo or W) are reported. The reactions were studied using stopped-flow spectrophotometry, and the rate constants for proton transfer were determined from analysis of the kinetics of the substitution reactions of these clusters with the nucleophiles Br- or PhS- in the presence of [pyrH]+. In general, Br- is a poor nucleophile for these clusters, and proton transfer occurs before Br- binds, allowing direct measure of the rate of proton transfer from [pyrH]+ to the cluster. In contrast, PhS- is a better nucleophile, and a pathway in which PhS- binds preferentially to the cluster prior to proton transfer from [pyrH]+ usually operates. For the reaction of [Fe2S2Cl4]2- with PhS- in the presence of [pyrH]+ both pathways are observed. Comparison of the results presented in this paper with analogous studies reported earlier on cuboidal Fe-S-based clusters allows discussion of the factors which affect the rates of proton transfer in synthetic clusters including the nuclearity of the cluster core, the metal composition, and the nature of the terminal ligands. The possible relevance of these findings to the protonation sites of natural Fe-S-based clusters, including FeMo-cofactor from nitrogenase, are presented.
White Matter Tract Integrity in Alzheimer's Disease vs. Late Onset Bipolar Disorder and Its Correlation with Systemic Inflammation and Oxidative Stress Biomarkers.

PubMed

Besga, Ariadna; Chyzhyk, Darya; Gonzalez-Ortega, Itxaso; Echeveste, Jon; Graña-Lecuona, Marina; Graña, Manuel; Gonzalez-Pinto, Ana

2017-01-01

Background: Late Onset Bipolar Disorder (LOBD) is the development of Bipolar Disorder (BD) at an age above 50 years old. It is often difficult to differentiate from other aging dementias, such as Alzheimer's Disease (AD), because they share cognitive and behavioral impairment symptoms. Objectives: We look for WM tract voxel clusters showing significant differences when comparing of AD vs. LOBD, and its correlations with systemic blood plasma biomarkers (inflammatory, neurotrophic factors, and oxidative stress). Materials: A sample of healthy controls (HC) ( n = 19), AD patients ( n = 35), and LOBD patients ( n = 24) was recruited at the Alava University Hospital. Blood plasma samples were obtained at recruitment time and analyzed to extract the inflammatory, oxidative stress, and neurotrophic factors. Several modalities of MRI were acquired for each subject, Methods: Fractional anisotropy (FA) coefficients are obtained from diffusion weighted imaging (DWI). Tract based spatial statistics (TBSS) finds FA skeleton clusters of WM tract voxels showing significant differences for all possible contrasts between HC, AD, and LOBD. An ANOVA F -test over all contrasts is carried out. Results of F -test are used to mask TBSS detected clusters for the AD > LOBD and LOBD > AD contrast to select the image clusters used for correlation analysis. Finally, Pearson's correlation coefficients between FA values at cluster sites and systemic blood plasma biomarker values are computed. Results: The TBSS contrasts with by ANOVA F -test has identified strongly significant clusters in the forceps minor, inferior longitudinal fasciculus, inferior fronto-occipital fasciculus, and cingulum gyrus. The correlation analysis of these tract clusters found strong negative correlation of AD with the nerve growth factor (NGF) and brain derived neurotrophic factor (BDNF) blood biomarkers. Negative correlation of AD and positive correlation of LOBD with inflammation biomarker IL6 was also found. Conclusion: TBSS voxel clusters tract atlas localizations are consistent with greater behavioral impairment and mood disorders in LOBD than in AD. Correlation analysis confirms that neurotrophic factors (i.e., NGF, BDNF) play a great role in AD while are absent in LOBD pathophysiology. Also, correlation results of IL1 and IL6 suggest stronger inflammatory effects in LOBD than in AD.
Association with AflR in Endosomes Reveals New Functions for AflJ in Aflatoxin Biosynthesis

PubMed Central

Ehrlich, Kenneth C.; Mack, Brian M.; Wei, Qijian; Li, Ping; Roze, Ludmila V.; Dazzo, Frank; Cary, Jeffrey W.; Bhatnagar, Deepak; Linz, John E.

2012-01-01

Aflatoxins are the most potent naturally occurring carcinogens of fungal origin. Biosynthesis of aflatoxin involves the coordinated expression of more than 25 genes. The function of one gene in the aflatoxin gene cluster, aflJ, is not entirely understood but, because previous studies demonstrated a physical interaction between the Zn2Cys6 transcription factor AflR and AflJ, AflJ was proposed to act as a transcriptional co-activator. Image analysis revealed that, in the absence of aflJ in A. parasiticus, endosomes cluster within cells and near septa. AflJ fused to yellow fluorescent protein complemented the mutation in A. parasiticus ΔaflJ and localized mainly in endosomes. We found that AflJ co-localizes with AflR both in endosomes and in nuclei. Chromatin immunoprecipitation did not detect AflJ binding at known AflR DNA recognition sites suggesting that AflJ either does not bind to these sites or binds to them transiently. Based on these data, we hypothesize that AflJ assists in AflR transport to or from the nucleus, thus controlling the availability of AflR for transcriptional activation of aflatoxin biosynthesis cluster genes. AflJ may also assist in directing endosomes to the cytoplasmic membrane for aflatoxin export. PMID:23342682
The application of automatic recognition techniques in the Apollo 9 SO-65 experiment

NASA Technical Reports Server (NTRS)

Macdonald, R. B.

1970-01-01

A synoptic feature analysis is reported on Apollo 9 remote earth surface photographs that uses the methods of statistical pattern recognition to classify density points and clusterings in digital conversion of optical data. A computer derived geological map of a geological test site indicates that geological features of the range are separable, but that specific rock types are not identifiable.
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets.

PubMed

Koren, Omry; Knights, Dan; Gonzalez, Antonio; Waldron, Levi; Segata, Nicola; Knight, Rob; Huttenhower, Curtis; Ley, Ruth E

2013-01-01

Recent analyses of human-associated bacterial diversity have categorized individuals into 'enterotypes' or clusters based on the abundances of key bacterial genera in the gut microbiota. There is a lack of consensus, however, on the analytical basis for enterotypes and on the interpretation of these results. We tested how the following factors influenced the detection of enterotypes: clustering methodology, distance metrics, OTU-picking approaches, sequencing depth, data type (whole genome shotgun (WGS) vs.16S rRNA gene sequence data), and 16S rRNA region. We included 16S rRNA gene sequences from the Human Microbiome Project (HMP) and from 16 additional studies and WGS sequences from the HMP and MetaHIT. In most body sites, we observed smooth abundance gradients of key genera without discrete clustering of samples. Some body habitats displayed bimodal (e.g., gut) or multimodal (e.g., vagina) distributions of sample abundances, but not all clustering methods and workflows accurately highlight such clusters. Because identifying enterotypes in datasets depends not only on the structure of the data but is also sensitive to the methods applied to identifying clustering strength, we recommend that multiple approaches be used and compared when testing for enterotypes.
A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

PubMed Central

Waldron, Levi; Segata, Nicola; Knight, Rob; Huttenhower, Curtis; Ley, Ruth E.

2013-01-01

Recent analyses of human-associated bacterial diversity have categorized individuals into ‘enterotypes’ or clusters based on the abundances of key bacterial genera in the gut microbiota. There is a lack of consensus, however, on the analytical basis for enterotypes and on the interpretation of these results. We tested how the following factors influenced the detection of enterotypes: clustering methodology, distance metrics, OTU-picking approaches, sequencing depth, data type (whole genome shotgun (WGS) vs.16S rRNA gene sequence data), and 16S rRNA region. We included 16S rRNA gene sequences from the Human Microbiome Project (HMP) and from 16 additional studies and WGS sequences from the HMP and MetaHIT. In most body sites, we observed smooth abundance gradients of key genera without discrete clustering of samples. Some body habitats displayed bimodal (e.g., gut) or multimodal (e.g., vagina) distributions of sample abundances, but not all clustering methods and workflows accurately highlight such clusters. Because identifying enterotypes in datasets depends not only on the structure of the data but is also sensitive to the methods applied to identifying clustering strength, we recommend that multiple approaches be used and compared when testing for enterotypes. PMID:23326225
Correlation between cation conduction and ionic morphology in a PEO-based single ion conductor

NASA Astrophysics Data System (ADS)

Lin, Kan-Ju; Maranas, Janna

2011-03-01

We use molecular dynamics simulation to study ion transport and backbone mobility of a PEO-based single ion conductor. Ion mobility depends on the chemical structure and the local environment of the ions, which consequently impact ionic conductivity. We characterize the aggregation state of the ions, and assess the role of ion complexes in ionomer dynamics. In addition to solvated cations and pairs, higher order ion clusters are found. Most of the ion clusters are in string-like structure and cross-link two or more different ionomer chains through ionic binding. Ionic crosslinks decrease mobility at the ionic co-monomer; hence the mobility of the adjacent PEO segment is influenced. Na ions show slow mobility when they are inside large clusters. The hopping timescale for Na varies from 20 ns to 200. A correlation is found between Na mobility and the number of hops from one coordination site to another. Besides ether oxygens, Na ions in the ionomer also use the anion and the edge of the cluster as hopping sites. The string-like structure of clusters provide less stable sites at the two ends thus ions are more mobile in those regions. We observed Grotthus like mechanism in our ionomer, in which the positive charge migrates within the string-like cluster without the cations actually moving.
Statistical analyses and characteristics of volcanic tremor on Stromboli Volcano (Italy)

NASA Astrophysics Data System (ADS)

Falsaperla, S.; Langer, H.; Spampinato, S.

A study of volcanic tremor on Stromboli is carried out on the basis of data recorded daily between 1993 and 1995 by a permanent seismic station (STR) located 1.8km away from the active craters. We also consider the signal of a second station (TF1), which operated for a shorter time span. Changes in the spectral tremor characteristics can be related to modifications in volcanic activity, particularly to lava effusions and explosive sequences. Statistical analyses were carried out on a set of spectra calculated daily from seismic signals where explosion quakes were present or excluded. Principal component analysis and cluster analysis were applied to identify different classes of spectra. Three clusters of spectra are associated with two different states of volcanic activity. One cluster corresponds to a state of low to moderate activity, whereas the two other clusters are present during phases with a high magma column as inferred from the occurrence of lava fountains or effusions. We therefore conclude that variations in volcanic activity at Stromboli are usually linked to changes in the spectral characteristics of volcanic tremor. Site effects are evident when comparing the spectra calculated from signals synchronously recorded at STR and TF1. However, some major spectral peaks at both stations may reflect source properties. Statistical considerations and polarization analysis are in favor of a prevailing presence of P-waves in the tremor signal along with a position of the source northwest of the craters and at shallow depth.
Assessment of possible airborne impact from nuclear risk sites - Part II: probabilistic analysis of atmospheric transport patterns in Euro-Arctic region

NASA Astrophysics Data System (ADS)

Mahura, A. G.; Baklanov, A. A.

2003-10-01

The probabilistic analysis of atmospheric transport patterns from most important nuclear risk sites in the Euro-Arctic region is performed employing the methodology developed within the "Arctic Risk" Project of the NARP Programme (Baklanov and Mahura, 2003). The risk sites are the nuclear power plants in the Northwest Russia, Finland, Sweden, Lithuania, United Kingdom, and Germany as well as the Novaya Zemlya test site of Russia. The geographical regions of interest are the Northern and Central European countries and Northwest Russia. In this study, the employed research tools are the trajectory model to calculate a multiyear dataset of forward trajectories that originated over the risk site locations, and a set of statistical methods (including exploratory, cluster, and probability fields analyses) for analysis of trajectory modelling results. The probabilistic analyses of trajectory modelling results for eleven sites are presented as a set of various indicators of the risk sites possible impact on geographical regions and countries of interest. The nuclear risk site possible impact (on a particular geographical region, territory, country, site, etc.) due to atmospheric transport from the site after hypothetical accidental release of radioactivity can be properly estimated based on a combined interpretation of the indicators (simple characteristics, atmospheric transport pathways, airflow and fast transport probability fields, maximum reaching distance and maximum possible impact zone, typical transport time and precipitation factor fields) for different time periods (annual, seasonal, and monthly) for any selected site (both separately for each site or grouped for several sites) in the Euro-Arctic region. Such estimation could be the useful input information for the decision-making process, risk assessment, and planning of emergency response systems for sites of nuclear, chemical, and biological danger.
Reduction Potentials of [FeFe]-Hydrogenase Accessory Iron–Sulfur Clusters Provide Insights into the Energetics of Proton Reduction Catalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Artz, Jacob H.; Mulder, David W.; Ratzloff, Michael W.

An [FeFe]-hydrogenase from Clostridium pasteurianum, CpI, is a model system for biological H 2 activation. In addition to the catalytic H-cluster, CpI contains four accessory iron-sulfur [FeS] clusters in a branched series that transfer electrons to and from the active site. In this work, potentiometric titrations have been employed in combination with electron paramagnetic resonance (EPR) spectroscopy at defined electrochemical potentials to gain insights into the role of the accessory clusters in catalysis. EPR spectra collected over a range of potentials were deconvoluted into individual components attributable to the accessory [FeS] clusters and the active site H-cluster, and reduction potentialsmore » for each cluster were determined. The data suggest a large degree of magnetic coupling between the clusters. The distal [4Fe-4S] cluster is shown to have a lower reduction potential (~ < -450 mV) than the other clusters, and molecular docking experiments indicate that the physiological electron donor, ferredoxin (Fd), most favorably interacts with this cluster. The low reduction potential of the distal [4Fe-4S] cluster thermodynamically restricts the Fd ox/Fd red ratio at which CpI can operate, consistent with the role of CpI in recycling Fd redthat accumulates during fermentation. In conclusion, subsequent electron transfer through the additional accessory [FeS] clusters to the H-cluster is thermodynamically favorable.« less
Reduction Potentials of [FeFe]-Hydrogenase Accessory Iron–Sulfur Clusters Provide Insights into the Energetics of Proton Reduction Catalysis

DOE PAGES

Artz, Jacob H.; Mulder, David W.; Ratzloff, Michael W.; ...

2017-06-21

An [FeFe]-hydrogenase from Clostridium pasteurianum, CpI, is a model system for biological H 2 activation. In addition to the catalytic H-cluster, CpI contains four accessory iron-sulfur [FeS] clusters in a branched series that transfer electrons to and from the active site. In this work, potentiometric titrations have been employed in combination with electron paramagnetic resonance (EPR) spectroscopy at defined electrochemical potentials to gain insights into the role of the accessory clusters in catalysis. EPR spectra collected over a range of potentials were deconvoluted into individual components attributable to the accessory [FeS] clusters and the active site H-cluster, and reduction potentialsmore » for each cluster were determined. The data suggest a large degree of magnetic coupling between the clusters. The distal [4Fe-4S] cluster is shown to have a lower reduction potential (~ < -450 mV) than the other clusters, and molecular docking experiments indicate that the physiological electron donor, ferredoxin (Fd), most favorably interacts with this cluster. The low reduction potential of the distal [4Fe-4S] cluster thermodynamically restricts the Fd ox/Fd red ratio at which CpI can operate, consistent with the role of CpI in recycling Fd redthat accumulates during fermentation. In conclusion, subsequent electron transfer through the additional accessory [FeS] clusters to the H-cluster is thermodynamically favorable.« less
Identification of a Pantoea Biosynthetic Cluster That Directs the Synthesis of an Antimicrobial Natural Product

PubMed Central

Walterson, Alyssa M.; Smith, Derek D. N.; Stavrinides, John

2014-01-01

Fire Blight is a destructive disease of apple and pear caused by the enteric bacterial pathogen, Erwinia amylovora. E. amylovora initiates infection by colonizing the stigmata of apple and pear trees, and entering the plants through natural openings. Epiphytic populations of the related enteric bacterium, Pantoea, reduce the incidence of disease through competition and antibiotic production. In this study, we identify an antibiotic from Pantoea ananatis BRT175, which is effective against E. amylovora and select species of Pantoea. We used transposon mutagenesis to create a mutant library, screened approximately 5,000 mutants for loss of antibiotic production, and recovered 29 mutants. Sequencing of the transposon insertion sites of these mutants revealed multiple independent disruptions of an 8.2 kb cluster consisting of seven genes, which appear to be coregulated. An analysis of the distribution of this cluster revealed that it was not present in any other of our 115 Pantoea isolates, or in any of the fully sequenced Pantoea genomes, and is most closely related to antibiotic biosynthetic clusters found in three different species of Pseudomonas. This identification of this biosynthetic cluster highlights the diversity of natural products produced by Pantoea. PMID:24796857
A Study on Regional Frequency Analysis using Artificial Neural Network - the Sumjin River Basin

NASA Astrophysics Data System (ADS)

Jeong, C.; Ahn, J.; Ahn, H.; Heo, J. H.

2017-12-01

Regional frequency analysis means to make up for shortcomings in the at-site frequency analysis which is about a lack of sample size through the regional concept. Regional rainfall quantile depends on the identification of hydrologically homogeneous regions, hence the regional classification based on hydrological homogeneous assumption is very important. For regional clustering about rainfall, multidimensional variables and factors related geographical features and meteorological figure are considered such as mean annual precipitation, number of days with precipitation in a year and average maximum daily precipitation in a month. Self-Organizing Feature Map method which is one of the artificial neural network algorithm in the unsupervised learning techniques solves N-dimensional and nonlinear problems and be shown results simply as a data visualization technique. In this study, for the Sumjin river basin in South Korea, cluster analysis was performed based on SOM method using high-dimensional geographical features and meteorological factor as input data. then, for the results, in order to evaluate the homogeneity of regions, the L-moment based discordancy and heterogeneity measures were used. Rainfall quantiles were estimated as the index flood method which is one of regional rainfall frequency analysis. Clustering analysis using SOM method and the consequential variation in rainfall quantile were analyzed. This research was supported by a grant(2017-MPSS31-001) from Supporting Technology Development Program for Disaster Management funded by Ministry of Public Safety and Security(MPSS) of the Korean government.
Ligand-protected gold clusters: the structure, synthesis and applications

NASA Astrophysics Data System (ADS)

Pichugina, D. A.; Kuz'menko, N. E.; Shestakov, A. F.

2015-11-01

Modern concepts of the structure and properties of atomic gold clusters protected by thiolate, selenolate, phosphine and phenylacetylene ligands are analyzed. Within the framework of the superatom theory, the 'divide and protect' approach and the structure rule, the stability and composition of a cluster are determined by the structure of the cluster core, the type of ligands and the total number of valence electrons. Methods of selective synthesis of gold clusters in solution and on the surface of inorganic composites based, in particular, on the reaction of Aun with RS, RSe, PhC≡C, Hal ligands or functional groups of proteins, on stabilization of clusters in cavities of the α-, β and γ-cyclodextrin molecules (Au15 and Au25) and on anchorage to a support surface (Au25/SiO2, Au20/C, Au10/FeOx) are reviewed. Problems in this field are also discussed. Among the methods for cluster structure prediction, particular attention is given to the theoretical approaches based on the density functional theory (DFT). The structures of a number of synthesized clusters are described using the results obtained by X-ray diffraction analysis and DFT calculations. A possible mechanism of formation of the SR(AuSR)n 'staple' units in the cluster shell is proposed. The structure and properties of bimetallic clusters MxAunLm (M=Pd, Pt, Ag, Cu) are discussed. The Pd or Pt atom is located at the centre of the cluster, whereas Ag and Cu atoms form bimetallic compounds in which the heteroatom is located on the surface of the cluster core or in the 'staple' units. The optical properties, fluorescence and luminescence of ligand-protected gold clusters originate from the quantum effects of the Au atoms in the cluster core and in the oligomeric SR(AuSR)x units in the cluster shell. Homogeneous and heterogeneous reactions catalyzed by atomic gold clusters are discussed in the context of the reaction mechanism and the nature of the active sites. The bibliography includes 345 references.
Characteristics of size-segregated carbonaceous aerosols in the Beijing-Tianjin-Hebei region.

PubMed

Guo, Yuhong

2016-07-01

Mass concentrations of organic carbon (OC) and elemental carbon (EC) in size-resolved aerosols were investigated at four sites (three cities and one country) in the Beijing-Tianjin-Hebei region from September 2009 to August 2011. The size distributions of OC and EC presented large evolutions among rural and urban sites, and among four seasons, with highest peaks of OC and EC in fine mode in urban areas during winter. Geometric mean diameters (GMDs) of OC and EC in fine particles at urban sites during winter were lower than those at rural site mainly due to effects of fine particle coagulation and organic compound repartitioning. Fossil fuel emissions were a dominant source of OC and EC in urban areas, while biomass burning was a major source of OC and EC at rural site. Trajectory clustering and CWT analysis showed that regional transport was an important contributor to OC and EC in Beijing.
Documentation of archaeological sites in northern iraq using remote sensing methods

NASA Astrophysics Data System (ADS)

Matoušková, E.; Pavelka, K.; Nováček, K.; Starková, L.

2015-08-01

The MULINEM (The Medieval Urban Landscape in Northeastern Mesopotamia) project is aiming to investigate a Late Sasanian and Islamic urban network in the land of Erbil, historic province of Hidyab (Adiabene) that is located in the northern Iraq. The research of the hierarchical urban network in a defined area belongs to approaches rarely used in the study of the Islamic urbanism. The project focuses on the cluster of urban sites of the 6th-17th centuries A.D. This paper focuses on remote sensing analysis of historical sites with special interest of FORMOSAT-2 data that have been gained through a research announcement: Free FORMOSAT-2 satellite Imagery. Documentation of two archaeological sites (Makhmúr al-Qadima and Kushaf) are introduced. FORMOSAT-2 data results have been compared to historic CORONA satellite data of mentioned historical sites purchased earlier by the University of West Bohemia. Remote sensing methods were completed using in-situ measurements.
Observations of fluorescent aerosol-cloud interactions in the free troposphere at the Sphinx high Alpine research station, Jungfraujoch

NASA Astrophysics Data System (ADS)

Crawford, I.; Lloyd, G.; Bower, K. N.; Connolly, P. J.; Flynn, M. J.; Kaye, P. H.; Choularton, T. W.; Gallagher, M. W.

2015-09-01

The fluorescent nature of aerosol at a high Alpine site was studied using a wide-band integrated bioaerosol (WIBS-4) single particle multi-channel ultra violet-light induced fluorescence (UV-LIF) spectrometer. This was supported by comprehensive cloud microphysics and meteorological measurements with the aims of cataloguing concentrations of bio-fluorescent aerosols at this high altitude site and also investigating possible influences of UV-fluorescent particle types on cloud-aerosol processes. Analysis of background free tropospheric air masses, using a total aerosol inlet, showed there to be a minor but statistically insignificant increase in the fluorescent aerosol fraction during in-cloud cases compared to out of cloud cases. The size dependence of the fluorescent aerosol fraction showed the larger aerosol to be more likely to be fluorescent with 80 % of 10 μm particles being fluorescent. Whilst the fluorescent particles were in the minority (NFl/NAll = 0.27±0.19), a new hierarchical agglomerative cluster analysis approach, Crawford et al. (2015) revealed the majority of the fluorescent aerosol were likely to be representative of fluorescent mineral dust. A minor episodic contribution from a cluster likely to be representative of primary biological aerosol particles (PBAP) was also observed with a wintertime baseline concentration of 0.1±0.4 L-1. Given the low concentration of this cluster and the typically low ice active fraction of studied PBAP (e.g. pseudomonas syringae) we suggest that the contribution to the observed ice crystal concentration at this location is not significant during the wintertime.
Identifying models of HIV care and treatment service delivery in Tanzania, Uganda, and Zambia using cluster analysis and Delphi survey.

PubMed

Tsui, Sharon; Denison, Julie A; Kennedy, Caitlin E; Chang, Larry W; Koole, Olivier; Torpey, Kwasi; Van Praag, Eric; Farley, Jason; Ford, Nathan; Stuart, Leine; Wabwire-Mangen, Fred

2017-12-06

Organization of HIV care and treatment services, including clinic staffing and services, may shape clinical and financial outcomes, yet there has been little attempt to describe different models of HIV care in sub-Saharan Africa (SSA). Information about the relative benefits and drawbacks of different models could inform the scale-up of antiretroviral therapy (ART) and associated services in resource-limited settings (RLS), especially in light of expanded client populations with country adoption of WHO's test and treat recommendation. We characterized task-shifting/task-sharing practices in 19 diverse ART clinics in Tanzania, Uganda, and Zambia and used cluster analysis to identify unique models of service provision. We ran descriptive statistics to explore how the clusters varied by environmental factors and programmatic characteristics. Finally, we employed the Delphi Method to make systematic use of expert opinions to ensure that the cluster variables were meaningful in the context of actual task-shifting of ART services in SSA. The cluster analysis identified three task-shifting/task-sharing models. The main differences across models were the availability of medical doctors, the scope of clinical responsibility assigned to nurses, and the use of lay health care workers. Patterns of healthcare staffing in HIV service delivery were associated with different environmental factors (e.g., health facility levels, urban vs. rural settings) and programme characteristics (e.g., community ART distribution or integrated tuberculosis treatment on-site). Understanding the relative advantages and disadvantages of different models of care can help national programmes adapt to increased client load, select optimal adherence strategies within decentralized models of care, and identify differentiated models of care for clients to meet the growing needs of long-term ART patients who require more complicated treatment management.

PtdIns(4,5)P2 is not required for secretory granule docking.

PubMed

Omar-Hmeadi, Muhmmad; Gandasi, Nikhil R; Barg, Sebastian

2018-06-01

Phosphoinositides (PtdIns) play important roles in exocytosis and are thought to regulate secretory granule docking by co-clustering with the SNARE protein syntaxin to form a docking receptor in the plasma membrane. Here we tested this idea by high-resolution total internal reflection imaging of EGFP-labeled PtdIns markers or syntaxin-1 at secretory granule release sites in live insulin-secreting cells. In intact cells, PtdIns markers distributed evenly across the plasma membrane with no preference for granule docking sites. In contrast, syntaxin-1 was found clustered in the plasma membrane, mostly beneath docked granules. We also observed rapid accumulation of syntaxin-1 at sites where granules arrived to dock. Acute depletion of plasma membrane phosphatidylinositol (4,5) bisphosphate (PtdIns(4,5)P 2 ) by recruitment of a 5'-phosphatase strongly inhibited Ca 2+ -dependent exocytosis, but had no effect on docked granules or the distribution and clustering of syntaxin-1. Cell permeabilization by α-toxin or formaldehyde-fixation caused PtdIns marker to slowly cluster, in part near docked granules. In summary, our data indicate that PtdIns(4,5)P 2 accelerates granule priming, but challenge a role of PtdIns in secretory granule docking or clustering of syntaxin-1 at the release site. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Efficient and Flexible Climate Analysis with Python in a Cloud-Based Distributed Computing Framework

NASA Astrophysics Data System (ADS)

Gannon, C.

2017-12-01

As climate models become progressively more advanced, and spatial resolution further improved through various downscaling projects, climate projections at a local level are increasingly insightful and valuable. However, the raw size of climate datasets presents numerous hurdles for analysts wishing to develop customized climate risk metrics or perform site-specific statistical analysis. Four Twenty Seven, a climate risk consultancy, has implemented a Python-based distributed framework to analyze large climate datasets in the cloud. With the freedom afforded by efficiently processing these datasets, we are able to customize and continually develop new climate risk metrics using the most up-to-date data. Here we outline our process for using Python packages such as XArray and Dask to evaluate netCDF files in a distributed framework, StarCluster to operate in a cluster-computing environment, cloud computing services to access publicly hosted datasets, and how this setup is particularly valuable for generating climate change indicators and performing localized statistical analysis.
Bagging Voronoi classifiers for clustering spatial functional data

NASA Astrophysics Data System (ADS)

Secchi, Piercesare; Vantini, Simone; Vitelli, Valeria

2013-06-01

We propose a bagging strategy based on random Voronoi tessellations for the exploration of geo-referenced functional data, suitable for different purposes (e.g., classification, regression, dimensional reduction, …). Urged by an application to environmental data contained in the Surface Solar Energy database, we focus in particular on the problem of clustering functional data indexed by the sites of a spatial finite lattice. We thus illustrate our strategy by implementing a specific algorithm whose rationale is to (i) replace the original data set with a reduced one, composed by local representatives of neighborhoods covering the entire investigated area; (ii) analyze the local representatives; (iii) repeat the previous analysis many times for different reduced data sets associated to randomly generated different sets of neighborhoods, thus obtaining many different weak formulations of the analysis; (iv) finally, bag together the weak analyses to obtain a conclusive strong analysis. Through an extensive simulation study, we show that this new procedure - which does not require an explicit model for spatial dependence - is statistically and computationally efficient.
Inferring sources of polycyclic aromatic hydrocarbons (PAHs) in sediments from the western Taiwan Strait through end-member mixing analysis.

PubMed

Li, Tao; Sun, Guihua; Ma, Shengzhong; Liang, Kai; Yang, Chupeng; Li, Bo; Luo, Weidong

2016-11-15

Concentration, spatial distribution, composition and sources of polycyclic aromatic hydrocarbons (PAHs) were investigated based on measurements of 16 PAH compounds in surface sediments of the western Taiwan Strait. Total PAH concentrations ranged from 2.41 to 218.54ngg -1 . Cluster analysis identified three site clusters representing the northern, central and southern regions. Sedimentary PAHs mainly originated from a mixture of pyrolytic and petrogenic in the north, from pyrolytic in the central, and from petrogenic in the south. An end-member mixing model was performed using PAH compound data to estimate mixing proportions for unknown end-members (i.e., extreme-value sample points) proposed by principal component analysis (PCA). The results showed that the analyzed samples can be expressed as mixtures of three end-members, and the mixing of different end-members was strongly related to the transport pathway controlled by two currents, which alternately prevail in the Taiwan Strait during different seasons. Copyright © 2016. Published by Elsevier Ltd.
Characterizing pharmaceutical, personal care product, and hormone contamination in a karst aquifer of southwestern Illinois, USA, using water quality and stream flow parameters.

PubMed

Dodgen, L K; Kelly, W R; Panno, S V; Taylor, S J; Armstrong, D L; Wiles, K N; Zhang, Y; Zheng, W

2017-02-01

Karst aquifers are drinking water sources for 25% of the global population. However, the unique geology of karst areas facilitates rapid transfer of surficial chemicals to groundwater, potentially contaminating drinking water. Contamination of karst aquifers by nitrate, chloride, and bacteria have been previously observed, but little knowledge is available on the presence of contaminants of emerging concern (CECs), such as pharmaceuticals. Over a 17-month period, 58 water samples were collected from 13 sites in the Salem Plateau, a karst region in southwestern Illinois, United States. Water was analyzed for 12 pharmaceutical and personal care products (PPCPs), 7 natural and synthetic hormones, and 49 typical water quality parameters (e.g., nutrients and bacteria). Hormones were detected in only 23% of samples, with concentrations of 2.2-9.1ng/L. In contrast, PPCPs were quantified in 89% of groundwater samples. The two most commonly detected PPCPs were the antimicrobial triclocarban, in 81% of samples, and the cardiovascular drug gemfibrozil, in 57%. Analytical results were combined with data of local stream flow, weather, and land use to 1) characterize the extent of aquifer contamination by CECs, 2) cluster sites with similar PPCP contamination profiles, and 3) develop models to describe PPCP contamination. Median detection in karst groundwater was 3 PPCPs at a summed concentration of 4.6ng/L. Sites clustered into 3 subsets with unique contamination models. PPCP contamination in Cluster I sites was related to stream height, manganese, boron, and heterotrophic bacteria. Cluster II sites were characterized by groundwater temperature, specific conductivity, sodium, and calcium. Cluster III sites were characterized by dissolved oxygen and barium. Across all sites, no single or small set of water quality factors was significantly predictive of PPCP contamination, although gemfibrozil concentrations were strongly related to the sum of PPCPs in karst groundwater. Copyright © 2016 Elsevier B.V. All rights reserved.
Source Evaluation and Trace Metal Contamination in Benthic Sediments from Equatorial Ecosystems Using Multivariate Statistical Techniques

PubMed Central

Benson, Nsikak U.; Asuquo, Francis E.; Williams, Akan B.; Essien, Joseph P.; Ekong, Cyril I.; Akpabio, Otobong; Olajire, Abaas A.

2016-01-01

Trace metals (Cd, Cr, Cu, Ni and Pb) concentrations in benthic sediments were analyzed through multi-step fractionation scheme to assess the levels and sources of contamination in estuarine, riverine and freshwater ecosystems in Niger Delta (Nigeria). The degree of contamination was assessed using the individual contamination factors (ICF) and global contamination factor (GCF). Multivariate statistical approaches including principal component analysis (PCA), cluster analysis and correlation test were employed to evaluate the interrelationships and associated sources of contamination. The spatial distribution of metal concentrations followed the pattern Pb>Cu>Cr>Cd>Ni. Ecological risk index by ICF showed significant potential mobility and bioavailability for Cu, Cu and Ni. The ICF contamination trend in the benthic sediments at all studied sites was Cu>Cr>Ni>Cd>Pb. The principal component and agglomerative clustering analyses indicate that trace metals contamination in the ecosystems was influenced by multiple pollution sources. PMID:27257934
Analysis of Facultative Lithotroph Distribution and Diversity on Volcanic Deposits by Use of the Large Subunit of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase†

PubMed Central

Nanba, K.; King, G. M.; Dunfield, K.

2004-01-01

A 492- to 495-bp fragment of the gene coding for the large subunit of the form I ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) (rbcL) was amplified by PCR from facultatively lithotrophic aerobic CO-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic DNA extracts from tephra and ash deposits from Kilauea volcano, for which atmospheric CO and hydrogen have been previously documented as important substrates. PCR products from the mats and volcanic sites were used to construct rbcL clone libraries. Phylogenetic analyses showed that the rbcL sequences from all isolates clustered with form IC rbcL sequences derived from facultative lithotrophs. In contrast, the microbial mat clone sequences clustered with sequences from obligate lithotrophs representative of form IA rbcL. Clone sequences from volcanic sites fell within the form IC clade, suggesting that these sites were dominated by facultative lithotrophs, an observation consistent with biogeochemical patterns at the sites. Based on phylogenetic and statistical analyses, clone libraries differed significantly among volcanic sites, indicating that they support distinct lithotrophic assemblages. Although some of the clone sequences were similar to known rbcL sequences, most were novel. Based on nucleotide diversity and average pairwise difference, a forested site and an 1894 lava flow were found to support the most diverse and least diverse lithotrophic populations, respectively. These indices of diversity were not correlated with rates of atmospheric CO and hydrogen uptake but were correlated with estimates of respiration and microbial biomass. PMID:15066819
Analysis of facultative lithotroph distribution and diversity on volcanic deposits by use of the large subunit of ribulose 1,5-bisphosphate carboxylase/oxygenase.

PubMed

Nanba, K; King, G M; Dunfield, K

2004-04-01

A 492- to 495-bp fragment of the gene coding for the large subunit of the form I ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) (rbcL) was amplified by PCR from facultatively lithotrophic aerobic CO-oxidizing bacteria, colorless and purple sulfide-oxidizing microbial mats, and genomic DNA extracts from tephra and ash deposits from Kilauea volcano, for which atmospheric CO and hydrogen have been previously documented as important substrates. PCR products from the mats and volcanic sites were used to construct rbcL clone libraries. Phylogenetic analyses showed that the rbcL sequences from all isolates clustered with form IC rbcL sequences derived from facultative lithotrophs. In contrast, the microbial mat clone sequences clustered with sequences from obligate lithotrophs representative of form IA rbcL. Clone sequences from volcanic sites fell within the form IC clade, suggesting that these sites were dominated by facultative lithotrophs, an observation consistent with biogeochemical patterns at the sites. Based on phylogenetic and statistical analyses, clone libraries differed significantly among volcanic sites, indicating that they support distinct lithotrophic assemblages. Although some of the clone sequences were similar to known rbcL sequences, most were novel. Based on nucleotide diversity and average pairwise difference, a forested site and an 1894 lava flow were found to support the most diverse and least diverse lithotrophic populations, respectively. These indices of diversity were not correlated with rates of atmospheric CO and hydrogen uptake but were correlated with estimates of respiration and microbial biomass.
Functional adjustments of xylem anatomy to climatic variability: insights from long-term Ilex aquifolium tree-ring series.

PubMed

Rita, Angelo; Cherubini, Paolo; Leonardi, Stefano; Todaro, Luigi; Borghetti, Marco

2015-08-01

The present study assessed the effects of climatic conditions on radial growth and functional anatomical traits, including ring width, vessel size, vessel frequency and derived variables, i.e., potential hydraulic conductivity and xylem vulnerability to cavitation in Ilex aquifolium L. trees using long-term tree-ring time series obtained at two climatically contrasting sites, one mesic site in Switzerland (CH) and one drought-prone site in Italy (ITA). Relationships were explored by examining different xylem traits, and point pattern analysis was applied to investigate vessel clustering. We also used generalized additive models and bootstrap correlation functions to describe temperature and precipitation effects. Results indicated modified radial growth and xylem anatomy in trees over the last century; in particular, vessel frequency increased markedly at both sites in recent years, and all xylem traits examined, with the exception of xylem cavitation vulnerability, were higher at the CH mesic compared with the ITA drought site. A significant vessel clustering was observed at the ITA site, which could contribute to an enhanced tolerance to drought-induced embolism. Flat and negative relationships between vessel size and ring width were observed, suggesting carbon was not allocated to radial growth under conditions which favored stem water conduction. Finally, in most cases results indicated that climatic conditions influenced functional anatomical traits more substantially than tree radial growth, suggesting a crucial role of functional xylem anatomy in plant acclimation to future climatic conditions. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Genetic characterization of the hemagglutinin genes of wild-type measles virus circulating in china, 1993-2009.

PubMed

Xu, Songtao; Zhang, Yan; Zhu, Zhen; Liu, Chunyu; Mao, Naiying; Ji, Yixin; Wang, Huiling; Jiang, Xiaohong; Li, Chongshan; Tang, Wei; Feng, Daxing; Wang, Changyin; Zheng, Lei; Lei, Yue; Ling, Hua; Zhao, Chunfang; Ma, Yan; He, Jilan; Wang, Yan; Li, Ping; Guan, Ronghui; Zhou, Shujie; Zhou, Jianhui; Wang, Shuang; Zhang, Hong; Zheng, Huanying; Liu, Leng; Ma, Hemuti; Guan, Jing; Lu, Peishan; Feng, Yan; Zhang, Yanjun; Zhou, Shunde; Xiong, Ying; Ba, Zhuoma; Chen, Hui; Yang, Xiuhui; Bo, Fang; Ma, Yujie; Liang, Yong; Lei, Yake; Gu, Suyi; Liu, Wei; Chen, Meng; Featherstone, David; Jee, Youngmee; Bellini, William J; Rota, Paul A; Xu, Wenbo

2013-01-01

China experienced several large measles outbreaks in the past two decades, and a series of enhanced control measures were implemented to achieve the goal of measles elimination. Molecular epidemiologic surveillance of wild-type measles viruses (MeV) provides valuable information about the viral transmission patterns. Since 1993, virologic surveillnace has confirmed that a single endemic genotype H1 viruses have been predominantly circulating in China. A component of molecular surveillance is to monitor the genetic characteristics of the hemagglutinin (H) gene of MeV, the major target for virus neutralizing antibodies. Analysis of the sequences of the complete H gene from 56 representative wild-type MeV strains circulating in China during 1993-2009 showed that the H gene sequences were clustered into 2 groups, cluster 1 and cluster 2. Cluster1 strains were the most frequently detected cluster and had a widespread distribution in China after 2000. The predicted amino acid sequences of the H protein were relatively conserved at most of the functionally significant amino acid positions. However, most of the genotype H1 cluster1 viruses had an amino acid substitution (Ser240Asn), which removed a predicted N-linked glycosylation site. In addition, the substitution of Pro397Leu in the hemagglutinin noose epitope (HNE) was identified in 23 of 56 strains. The evolutionary rate of the H gene of the genotype H1 viruses was estimated to be approximately 0.76×10(-3) substitutions per site per year, and the ratio of dN to dS (dN/dS) was <1 indicating the absence of selective pressure. Although H genes of the genotype H1 strains were conserved and not subjected to selective pressure, several amino acid substitutions were observed in functionally important positions. Therefore the antigenic and genetic properties of H genes of wild-type MeVs should be monitored as part of routine molecular surveillance for measles in China.
Role of protein-glutathione contacts in defining glutaredoxin-3 [2Fe-2S] cluster chirality, ligand exchange and transfer chemistry.

PubMed

Sen, Sambuddha; Cowan, J A

2017-10-01

Monothiol glutaredoxins (Grx) serve as intermediate cluster carriers in iron-sulfur cluster trafficking. The [2Fe-2S]-bound holo forms of Grx proteins display cysteinyl coordination from exogenous glutathione (GSH), in addition to contact from protein-derived Cys. Herein, we report mechanistic studies that investigate the role of exogenous glutathione in defining cluster chirality, ligand exchange, and the cluster transfer chemistry of Saccharomyces cerevisiae Grx3. Systematic perturbations were introduced to the glutathione-binding site by substitution of conserved charged amino acids that form crucial electrostatic contacts with the glutathione molecule. Native Grx3 could also be reconstituted in the absence of glutathione, with either DTT, BME or free L-cysteine as the source of the exogenous Fe-S ligand contact, while retaining full functional reactivity. The delivery of the [2Fe-2S] cluster to Grx3 from cluster donor proteins such as Isa, Nfu, and a [2Fe-2S](GS) 4 complex, revealed that electrostatic contacts are of key importance for positioning the exogenous glutathione that in turn influences the chiral environment of the cluster. All Grx3 derivatives were reconstituted by standard chemical reconstitution protocols and found to transfer cluster to apo ferredoxin 1 (Fdx1) at rates comparable to native protein, even when using DTT, BME or free L-cysteine as a thiol source in place of GSH during reconstitution. Kinetic analysis of cluster transfer from holo derivatives to apo Fdx1 has led to a mechanistic model for cluster transfer chemistry of native holo Grx3, and identification of the likely rate-limiting step for the reaction.
Dialing in single-site reactivity of a supported calixarene-protected tetrairidium cluster catalyst

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palermo, Andrew; Solovyov, Andrew; Ertler, Daniel

2017-05-04

A closed Ir 4carbonyl cluster,1, comprising a tetrahedral metal frame and threetert-butyl-calix[4]arene(OPr) 3(OCH 2PPh 2) (Ph = phenyl; Pr = propyl) ligands at the basal plane, was silica supported and consists of “*” and “S” sites, which could be dialed in selectively for controlling ethylene hydrogenation catalysis.
Electron interactions, spin-orbit coupling, intersite correlations in pyrochlore iridates: a comparison of single-site and cluster calculations

NASA Astrophysics Data System (ADS)

Wang, Runzhi; Go, Ara; Millis, Andrew

Pyrochlore iridates (R2 Ir2O7) are studied using density functional theory plus single-site and cluster dynamical mean-field theory (DFT+DMFT). The calculations include spin-orbit coupling. Significant differences between the single-site and cluster calculations are found. The single-site approximation fails to account for the properties of the paramagnetic insulator phase, in particular predicting a larger gap than found in experiments, while cluster calculations yield gaps consistent with transport data. A ground-state phase diagram is computed. Paramagnetic metal, metallic all-in/all-out (AIAO) and insulating AIAO phases are found. Tilted Weyl cones are observed in the AIAO metallic phase for a relatively wide range of interaction strength. Our paramagnetic calculations predict almost identical behaviors for the Y and Eu compound, conflicting with the strong material dependence reported in experiments. Inclusion of magnetic order restores the material difference. The physical origin of the difference is discussed. The results indicate that intersite effects, most likely of antiferromagnetic origin, play an important role in studying the physics of pyrochlore iridates. This work is supported by DOE-ER046169.
Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks.

PubMed

Cazade, Pierre-André; Berezovska, Ganna; Meuwly, Markus

2015-05-01

The nature of ligand motion in proteins is difficult to characterize directly using experiment. Specifically, it is unclear to what degree these motions are coupled. All-atom simulations are used to sample ligand motion in truncated Hemoglobin N. A transition network analysis including ligand- and protein-degrees of freedom is used to analyze the microscopic dynamics. Clustering of two different subsets of MD trajectories highlights the importance of a diverse and exhaustive description to define the macrostates for a ligand-migration network. Monte Carlo simulations on the transition matrices from one particular clustering are able to faithfully capture the atomistic simulations. Contrary to clustering by ligand positions only, including a protein degree of freedom yields considerably improved coarse grained dynamics. Analysis with and without imposing detailed balance agree closely which suggests that the underlying atomistic simulations are converged with respect to sampling transitions between neighboring sites. Protein and ligand dynamics are not independent from each other and ligand migration through globular proteins is not passive diffusion. Transition network analysis is a powerful tool to analyze and characterize the microscopic dynamics in complex systems. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.
A land classification protocol for pollinator ecology research: An urbanization case study.

PubMed

Samuelson, Ash E; Leadbeater, Ellouise

2018-06-01

Land-use change is one of the most important drivers of widespread declines in pollinator populations. Comprehensive quantitative methods for land classification are critical to understanding these effects, but co-option of existing human-focussed land classifications is often inappropriate for pollinator research. Here, we present a flexible GIS-based land classification protocol for pollinator research using a bottom-up approach driven by reference to pollinator ecology, with urbanization as a case study. Our multistep method involves manually generating land cover maps at multiple biologically relevant radii surrounding study sites using GIS, with a focus on identifying land cover types that have a specific relevance to pollinators. This is followed by a three-step refinement process using statistical tools: (i) definition of land-use categories, (ii) principal components analysis on the categories, and (iii) cluster analysis to generate a categorical land-use variable for use in subsequent analysis. Model selection is then used to determine the appropriate spatial scale for analysis. We demonstrate an application of our protocol using a case study of 38 sites across a gradient of urbanization in South-East England. In our case study, the land classification generated a categorical land-use variable at each of four radii based on the clustering of sites with different degrees of urbanization, open land, and flower-rich habitat. Studies of land-use effects on pollinators have historically employed a wide array of land classification techniques from descriptive and qualitative to complex and quantitative. We suggest that land-use studies in pollinator ecology should broadly adopt GIS-based multistep land classification techniques to enable robust analysis and aid comparative research. Our protocol offers a customizable approach that combines specific relevance to pollinator research with the potential for application to a wide range of ecological questions, including agroecological studies of pest control.
Large-Scale Variations in Lumber Value Recovery of Yellow Birch and Sugar Maple in Quebec, Canada

PubMed Central

Hassegawa, Mariana; Havreljuk, Filip; Ouimet, Rock; Auty, David; Pothier, David; Achim, Alexis

2015-01-01

Silvicultural restoration measures have been implemented in the northern hardwoods forests of southern Quebec, Canada, but their financial applicability is often hampered by the depleted state of the resource. To help identify sites most suited for the production of high quality timber, where the potential return on silvicultural investments should be the highest, this study assessed the impact of stand and site characteristics on timber quality in sugar maple (Acer saccharum Marsh.) and yellow birch (Betula alleghaniensis Britt.). For this purpose, lumber value recovery (LVR), an estimate of the summed value of boards contained in a unit volume of round wood, was used as an indicator of timber quality. Predictions of LVR were made for yellow birch and sugar maple trees contained in a network of more than 22000 temporary sample plots across the Province. Next, stand-level variables were selected and models to predict LVR were built using the boosted regression trees method. Finally, the occurrence of spatial clusters was verified by a hotspot analysis. Results showed that in both species LVR was positively correlated with the stand age and structural diversity index, and negatively correlated with the number of merchantable stems. Yellow birch had higher LVR in areas with shallower soils, whereas sugar maple had higher LVR in regions with deeper soils. The hotspot analysis indicated that clusters of high and low LVR exist across the province for both species. Although it remains uncertain to what extent the variability of LVR may result from variations in past management practices or in inherent site quality, we argue that efforts to produce high quality timber should be prioritized in sites where LVR is predicted to be the highest. PMID:26313689
Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d.

PubMed

Doxey, Andrew C; Cheng, Zhenyu; Moffatt, Barbara A; McConkey, Brendan J

2010-08-03

Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB) for coplanar aromatic motifs similar to those found in known glycan-binding proteins. The proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO) enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192) in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry. Based on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure.
Large-Scale Variations in Lumber Value Recovery of Yellow Birch and Sugar Maple in Quebec, Canada.

PubMed

Hassegawa, Mariana; Havreljuk, Filip; Ouimet, Rock; Auty, David; Pothier, David; Achim, Alexis

2015-01-01

Silvicultural restoration measures have been implemented in the northern hardwoods forests of southern Quebec, Canada, but their financial applicability is often hampered by the depleted state of the resource. To help identify sites most suited for the production of high quality timber, where the potential return on silvicultural investments should be the highest, this study assessed the impact of stand and site characteristics on timber quality in sugar maple (Acer saccharum Marsh.) and yellow birch (Betula alleghaniensis Britt.). For this purpose, lumber value recovery (LVR), an estimate of the summed value of boards contained in a unit volume of round wood, was used as an indicator of timber quality. Predictions of LVR were made for yellow birch and sugar maple trees contained in a network of more than 22000 temporary sample plots across the Province. Next, stand-level variables were selected and models to predict LVR were built using the boosted regression trees method. Finally, the occurrence of spatial clusters was verified by a hotspot analysis. Results showed that in both species LVR was positively correlated with the stand age and structural diversity index, and negatively correlated with the number of merchantable stems. Yellow birch had higher LVR in areas with shallower soils, whereas sugar maple had higher LVR in regions with deeper soils. The hotspot analysis indicated that clusters of high and low LVR exist across the province for both species. Although it remains uncertain to what extent the variability of LVR may result from variations in past management practices or in inherent site quality, we argue that efforts to produce high quality timber should be prioritized in sites where LVR is predicted to be the highest.
Zr 2Ir 6B with an eightfold superstructure of the cubic perovskite-like boride ZrIr 3B 0.5: Synthesis, crystal structure and bonding analysis

NASA Astrophysics Data System (ADS)

Hermus, Martin; Fokwa, Boniface P. T.

2010-04-01

Single phase powder samples and single crystals of Zr 2Ir 6B were successfully synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere. Superstructure reflections were observed both on powder and on single crystal diffraction data, leading to an eightfold superstructure of ZrIr 3B x phase. The new phase, which has a metallic luster, crystallizes in space group Fm3¯m (no. 225) with the lattice parameters a=7.9903(4) Å, V=510.14(4) Å 3. Its crystal structure was refined on the basis of powder as well as single crystal data. The single crystal refinement converged to R1=0.0239 and w R2=0.0624 for all 88 unique reflections and 6 parameters. Zr 2Ir 6B is isotypic to Ti 2Rh 6B and its structure can be described as a defect double perovskite, A2BB' O6, where the A site is occupied by zirconium, the B site by boron, the O site by iridium but the B' site is vacant, leading to the formation of empty and boron-filled octahedral Ir 6 clusters. According to the result of tight-binding electronic structure calculations, Ir-B and Ir-Zr interactions are mainly responsible for the structural stability of the phase. According to COHP bonding analysis, the strongest bonding occurs for the Ir-B contacts, and the Ir-Ir bonding within the empty clusters is two times stronger than that in the BIr 6 octahedra.
Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes

PubMed Central

Kuang, Zheng; Ji, Zhicheng

2018-01-01

Abstract Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. However, most methods are designed to predict TF binding sites only. We present a computational method, dynamic motif occupancy analysis (DynaMO), to infer important TFs and their spatiotemporal binding activities in dynamic biological processes using chromatin profiling data from multiple biological conditions such as time-course histone modification ChIP-seq data. In the first step, DynaMO predicts TF binding sites with a random forests approach. Next and uniquely, DynaMO infers dynamic TF binding activities at predicted binding sites using their local chromatin profiles from multiple biological conditions. Another landmark of DynaMO is to identify key TFs in a dynamic process using a clustering and enrichment analysis of dynamic TF binding patterns. Application of DynaMO to the yeast ultradian cycle, mouse circadian clock and human neural differentiation exhibits its accuracy and versatility. We anticipate DynaMO will be generally useful for elucidating transcriptional programs in dynamic processes. PMID:29325176

The effect of the morphology of supported subnanometer Pt clusters on the first and key step of CO 2 photoreduction [Morphology effect of supported subnanometer Pt clusters on first and key step of CO 2 photoreduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Chi -Ta; Wood, Brandon C.; Bhethanabotla, Venkat R.

2015-09-04

In this study, using density functional theory calculations, we investigate the influence of size-dependent cluster morphology on the synergistic catalytic properties of anatase TiO 2(101) surfaces decorated with subnanometer Pt clusters. Focusing on the formation of the key precursor in the CO 2 photoreduction reaction (bent CO 2 –), we find that flatter (2D-like) Pt clusters that “wet” the TiO 2 surface offer significantly less benefit than 3D-like Pt clusters. We attribute the differences to three factors. First, the 3D clusters provide a greater number of accessible Pt–TiO 2 interfacial sites with geometries that can aid CO 2 bond bendingmore » and charge transfer processes. Second, binding competition among each Pt–CO 2 bonding interaction mitigates maximum orbital overlaps, leading to insufficient CO 2 binding. Third and also most interestingly, the 3D clusters tend to possess higher structural fluxionality than the flatter clusters, which is shown to correlate positively with CO2 binding strength. The preferred morphology adopted by the clusters depends on several factors, including the cluster size and the presence of oxygen vacancies on the TiO 2 surface; this suggests a strategy for optimizing the synergistic effect between Pt clusters and TiO 2 surfaces for CO 2 photocatalysis. Clusters of ~6–8 atoms should provide the largest benefit, since they retain the desired 3D morphology, yet are small enough to exhibit high structural fluxionality. Electronic structure analysis provides additional insight into the electronic motivations for the enhanced binding of CO 2 on TiO 2-supported 3D Pt clusters, as well as suppressed binding on flattened, 2D-like clusters.« less
Assessment and application of clustering techniques to atmospheric particle number size distribution for the purpose of source apportionment

NASA Astrophysics Data System (ADS)

Salimi, F.; Ristovski, Z.; Mazaheri, M.; Laiman, R.; Crilley, L. R.; He, C.; Clifford, S.; Morawska, L.

2014-06-01

Long-term measurements of particle number size distribution (PNSD) produce a very large number of observations and their analysis requires an efficient approach in order to produce results in the least possible time and with maximum accuracy. Clustering techniques are a family of sophisticated methods which have been recently employed to analyse PNSD data, however, very little information is available comparing the performance of different clustering techniques on PNSD data. This study aims to apply several clustering techniques (i.e. K-means, PAM, CLARA and SOM) to PNSD data, in order to identify and apply the optimum technique to PNSD data measured at 25 sites across Brisbane, Australia. A new method, based on the Generalised Additive Model (GAM) with a basis of penalised B-splines, was proposed to parameterise the PNSD data and the temporal weight of each cluster was also estimated using the GAM. In addition, each cluster was associated with its possible source based on the results of this parameterisation, together with the characteristics of each cluster. The performances of four clustering techniques were compared using the Dunn index and silhouette width validation values and the K-means technique was found to have the highest performance, with five clusters being the optimum. Therefore, five clusters were found within the data using the K-means technique. The diurnal occurrence of each cluster was used together with other air quality parameters, temporal trends and the physical properties of each cluster, in order to attribute each cluster to its source and origin. The five clusters were attributed to three major sources and origins, including regional background particles, photochemically induced nucleated particles and vehicle generated particles. Overall, clustering was found to be an effective technique for attributing each particle size spectra to its source and the GAM was suitable to parameterise the PNSD data. These two techniques can help researchers immensely in analysing PNSD data for characterisation and source apportionment purposes.
Assessment and application of clustering techniques to atmospheric particle number size distribution for the purpose of source apportionment

NASA Astrophysics Data System (ADS)

Salimi, F.; Ristovski, Z.; Mazaheri, M.; Laiman, R.; Crilley, L. R.; He, C.; Clifford, S.; Morawska, L.

2014-11-01

Long-term measurements of particle number size distribution (PNSD) produce a very large number of observations and their analysis requires an efficient approach in order to produce results in the least possible time and with maximum accuracy. Clustering techniques are a family of sophisticated methods that have been recently employed to analyse PNSD data; however, very little information is available comparing the performance of different clustering techniques on PNSD data. This study aims to apply several clustering techniques (i.e. K means, PAM, CLARA and SOM) to PNSD data, in order to identify and apply the optimum technique to PNSD data measured at 25 sites across Brisbane, Australia. A new method, based on the Generalised Additive Model (GAM) with a basis of penalised B-splines, was proposed to parameterise the PNSD data and the temporal weight of each cluster was also estimated using the GAM. In addition, each cluster was associated with its possible source based on the results of this parameterisation, together with the characteristics of each cluster. The performances of four clustering techniques were compared using the Dunn index and Silhouette width validation values and the K means technique was found to have the highest performance, with five clusters being the optimum. Therefore, five clusters were found within the data using the K means technique. The diurnal occurrence of each cluster was used together with other air quality parameters, temporal trends and the physical properties of each cluster, in order to attribute each cluster to its source and origin. The five clusters were attributed to three major sources and origins, including regional background particles, photochemically induced nucleated particles and vehicle generated particles. Overall, clustering was found to be an effective technique for attributing each particle size spectrum to its source and the GAM was suitable to parameterise the PNSD data. These two techniques can help researchers immensely in analysing PNSD data for characterisation and source apportionment purposes.
Similarities among receptor pockets and among compounds: analysis and application to in silico ligand screening.

PubMed

Fukunishi, Yoshifumi; Mikami, Yoshiaki; Nakamura, Haruki

2005-09-01

We developed a new method to evaluate the distances and similarities between receptor pockets or chemical compounds based on a multi-receptor versus multi-ligand docking affinity matrix. The receptors were classified by a cluster analysis based on calculations of the distance between receptor pockets. A set of low homologous receptors that bind a similar compound could be classified into one cluster. Based on this line of reasoning, we proposed a new in silico screening method. According to this method, compounds in a database were docked to multiple targets. The new docking score was a slightly modified version of the multiple active site correction (MASC) score. Receptors that were at a set distance from the target receptor were not included in the analysis, and the modified MASC scores were calculated for the selected receptors. The choice of the receptors is important to achieve a good screening result, and our clustering of receptors is useful to this purpose. This method was applied to the analysis of a set of 132 receptors and 132 compounds, and the results demonstrated that this method achieves a high hit ratio, as compared to that of a uniform sampling, using a receptor-ligand docking program, Sievgene, which was newly developed with a good docking performance yielding 50.8% of the reconstructed complexes at a distance of less than 2 A RMSD.
Identification of hydrologically homogeneous regions in Ganga-Brahmaputra river basin using Self Organising Maps

NASA Astrophysics Data System (ADS)

Ojha, C. S. P.; Sharma, C.

2017-12-01

Identification of hydrologically homogeneous regions is crucial for topographically complex regions such as Himalayan river basins. Ganga-Brahmaputra river basin extends through three countries, i.e., India Nepal and China. High elevations and rugged topography impose challenge for in-situ gauges. So, it is always recommended to use data from hydrological similar site in absence of site records. We have tried to find out hydrologically homogeneous regions using Self-Organising-Map (SOM) in Ganga-Brahmaputra river basin. The station characteristics used for identification of homogeneous regions are annual precipitation, total wet season (July to September) precipitation, total dry season (January to March) precipitation, Latitude, Longitude and elevation. Precipitation data was obtained from Climate Research Unit (CRU). Number of cluster are find out using hierarchical k-means clustering. We found that the basin can be divided in 9 clusters. Mere division of regions in clusters does not clarify that identified cluster are homogeneous. The homogeneity of the clusters is found out using Hosking and Wallis heterogeneity test. All the clusters were found to be acceptably homogeneous with the value of Hosking-Wallis test static H<1.
A Potential Biofilm Metabolite Signature for Caries Activity - A Pilot Clinical Study

PubMed Central

Zandona, F; Soini, HA; Novotny, MV; Santiago, E; Eckert, GJ; Preisser, JS; Benecha, HK; Arthur, RA; Zero, DT

2016-01-01

Background This study's aim was to compare the dental biofilm metabolite-profile of caries-active (N=11) or caries-free (N=4) children by gas chromatography-mass spectrometry (GC/MS) analyses. Methods Samples collected after overnight fasting, with or without a previous glucose rinse, were combined for each child based on the caries status of the site, re-suspended in ethanol and analyzed by GC/MS. Results Biofilm from caries-active sites exhibited a different chromatographic profile compared to caries-free sites. Qualitative and quantitative analysis suggested a special cluster of branched alcohols and esters present at substantially higher intensity in biofilms of caries-active sites. Conclusions This pilot study indicates that there are metabolites present in the biofilm which have the potential to provide a characteristic metabolomics signature for caries activity. PMID:27885354
DNA methylation polymorphism in flue-cured tobacco and candidate markers for tobacco mosaic virus resistance.

PubMed

Zhao, Jie-hong; Zhang, Ji-shun; Wang, Yi; Wang, Ren-gang; Wu, Chun; Fan, Long-jiang; Ren, Xue-liang

2011-11-01

DNA methylation plays an important role in the epigenetic regulation of gene expression during plant growth, development, and polyploidization. However, there is still no distinct evidence in tobacco regarding the distribution of the methylation pattern and whether it contributes to qualitative characteristics. We studied the levels and patterns of methylation polymorphism at CCGG sites in 48 accessions of allotetraploid flue-cured tobacco, Nicotiana tabacum, using a methylation-sensitive amplified polymorphism (MSAP) technique. The results showed that methylation existed at a high level among tobacco accessions, among which 49.3% sites were methylated and 69.9% allelic sites were polymorphic. A cluster analysis revealed distinct patterns of geography-specific groups. In addition, three polymorphic sites significantly related to tobacco mosaic virus (TMV) resistance were explored. This suggests that tobacco breeders should pay more attention to epigenetic traits.
WOx supported on γ-Al2O3 with different morphologies as model catalysts for alkanol dehydration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Dachuan; Wang, Huamin; Kovarik, Libor

2018-04-21

The distinctive morphological and surface characteristics of platelet-like γ-Al2O3 were compared to a regular, commercial γ-Al2O3. γ-Al2O3 platelets display dominant (110) surface facets and higher densities of coordinative unsaturated penta-coordinate Al3+ (Al3+penta) sites than regular γ-Al2O3, as measured by solid-state magic-angle spinning nuclear magnetic resonance spectroscopy (MAS NMR). Such Al3+penta sites are also the preferred surface anchoring sites for tungsten oxide (WOx) species consistent with NMR analysis indicating that these sites are consumed upon WOx adsorption. The higher Al3+penta density on γ-Al2O3 platelets leads to greater WOx dispersion (or smaller WOx clusters), as demonstrated by scanning transmission electron microscopy andmore » ultraviolet–visible spectroscopy, and WOx species at intermediate WOx surface concentration are the most active for the probe reaction of 2-butanol dehydration. WOx on γ-Al2O3 platelets approaches the highest turnover rates at higher surface densities than WOx on regular γ-Al2O3, yet with similar highest rate values for both series of catalysts. This indicates that different Al2O3 supports mainly affect the dispersion of supported WOx rather than the intrinsic reactivity of individual WOx clusters with similar size.« less
WO x supported on γ-Al 2 O 3 with different morphologies as model catalysts for alkanol dehydration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Dachuan; Wang, Huamin; Kovarik, Libor

The distinctive morphological and surface characteristics of platelet-like γ-Al2O3 were compared to a regular, commercial γ-Al2O3. γ-Al2O3 platelets display dominant (110) surface facets and higher densities of coordinative unsaturated penta-coordinate Al3+ (Al3+penta) sites than regular γ-Al2O3, as measured by solid-state magic-angle spinning nuclear magnetic resonance spectroscopy (MAS NMR). Such Al3+penta sites are also the preferred surface anchoring sites for tungsten oxide (WOx) species consistent with NMR analysis indicating that these sites are consumed upon WOx adsorption. The higher Al3+penta density on γ-Al2O3 platelets leads to greater WOx dispersion (or smaller WOx clusters), as demonstrated by scanning transmission electron microscopy andmore » ultraviolet–visible spectroscopy, and WOx species at intermediate WOx surface concentration are the most active for the probe reaction of 2-butanol dehydration. WOx on γ-Al2O3 platelets approaches the highest turnover rates at higher surface densities than WOx on regular γ-Al2O3, yet with similar highest rate values for both series of catalysts. This indicates that different Al2O3 supports mainly affect the dispersion of supported WOx rather than the intrinsic reactivity of individual WOx clusters with similar size.« less
Improving the sampling strategy of the Joint Danube Survey 3 (2013) by means of multivariate statistical techniques applied on selected physico-chemical and biological data.

PubMed

Hamchevici, Carmen; Udrea, Ion

2013-11-01

The concept of basin-wide Joint Danube Survey (JDS) was launched by the International Commission for the Protection of the Danube River (ICPDR) as a tool for investigative monitoring under the Water Framework Directive (WFD), with a frequency of 6 years. The first JDS was carried out in 2001 and its success in providing key information for characterisation of the Danube River Basin District as required by WFD lead to the organisation of the second JDS in 2007, which was the world's biggest river research expedition in that year. The present paper presents an approach for improving the survey strategy for the next planned survey JDS3 (2013) by means of several multivariate statistical techniques. In order to design the optimum structure in terms of parameters and sampling sites, principal component analysis (PCA), factor analysis (FA) and cluster analysis were applied on JDS2 data for 13 selected physico-chemical and one biological element measured in 78 sampling sites located on the main course of the Danube. Results from PCA/FA showed that most of the dataset variance (above 75%) was explained by five varifactors loaded with 8 out of 14 variables: physical (transparency and total suspended solids), relevant nutrients (N-nitrates and P-orthophosphates), feedback effects of primary production (pH, alkalinity and dissolved oxygen) and algal biomass. Taking into account the representation of the factor scores given by FA versus sampling sites and the major groups generated by the clustering procedure, the spatial network of the next survey could be carefully tailored, leading to a decreasing of sampling sites by more than 30%. The approach of target oriented sampling strategy based on the selected multivariate statistics can provide a strong reduction in dimensionality of the original data and corresponding costs as well, without any loss of information.
Pairwise additivity in the nuclear magnetic resonance interactions of atomic xenon.

PubMed

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2009-04-14

Nuclear magnetic resonance (NMR) of atomic (129/131)Xe is used as a versatile probe of the structure and dynamics of various host materials, due to the sensitivity of the Xe NMR parameters to intermolecular interactions. The principles governing this sensitivity can be investigated using the prototypic system of interacting Xe atoms. In the pairwise additive approximation (PAA), the binary NMR chemical shift, nuclear quadrupole coupling (NQC), and spin-rotation (SR) curves for the xenon dimer are utilized for fast and efficient evaluation of the corresponding NMR tensors in small xenon clusters Xe(n) (n = 2-12). If accurate, the preparametrized PAA enables the analysis of the NMR properties of xenon clusters, condensed xenon phases, and xenon gas without having to resort to electronic structure calculations of instantaneous configurations for n > 2. The binary parameters for Xe(2) at different internuclear distances were obtained at the nonrelativistic Hartree-Fock level of theory. Quantum-chemical (QC) calculations at the corresponding level were used to obtain the NMR parameters of the Xe(n) (n = 2-12) clusters at the equilibrium geometries. Comparison of PAA and QC data indicates that the direct use of the binary property curves of Xe(2) can be expected to be well-suited for the analysis of Xe NMR in the gaseous phase dominated by binary collisions. For use in condensed phases where many-body effects should be considered, effective binary property functions were fitted using the principal components of QC tensors from Xe(n) clusters. Particularly, the chemical shift in Xe(n) is strikingly well-described by the effective PAA. The coordination number Z of the Xe site is found to be the most important factor determining the chemical shift, with the largest shifts being found for high-symmetry sites with the largest Z. This is rationalized in terms of the density of virtual electronic states available for response to magnetic perturbations.
Urogenital Chlamydia trachomatis infections among ethnic groups in Paramaribo, Suriname; determinants and ethnic sexual mixing patterns.

PubMed

van der Helm, Jannie J; Bom, Reinier J M; Grünberg, Antoon W; Bruisten, Sylvia M; Schim van der Loeff, Maarten F; Sabajo, Leslie O A; de Vries, Henry J C

2013-01-01

Little is known about the epidemiology of urogenital Chlamydia trachomatis infection (chlamydia) in Suriname. Suriname is a society composed of many ethnic groups, such as Creoles, Maroons, Hindustani, Javanese, Chinese, Caucasians, and indigenous Amerindians. We estimated determinants for chlamydia, including the role of ethnicity, and identified transmission patterns and ethnic sexual networks among clients of two clinics in Paramaribo, Suriname. Participants were recruited at two sites a sexually transmitted infections (STI) clinic and a family planning (FP) clinic in Paramaribo. Urine samples from men and nurse-collected vaginal swabs were obtained for nucleic acid amplification testing. Logistic regression analysis was used to identify determinants of chlamydia. Multilocus sequence typing (MLST) was performed to genotype C. trachomatis. To identify transmission patterns and sexual networks, a minimum spanning tree was created, using full MLST profiles. Clusters in the minimum spanning tree were compared for ethnic composition. Between March 2008 and July 2010, 415 men and 274 women were included at the STI clinic and 819 women at the FP clinic. Overall chlamydia prevalence was 15% (224/1508). Age, ethnicity, and recruitment site were significantly associated with chlamydia in multivariable analysis. Participants of Creole and Javanese ethnicity were more frequently infected with urogenital chlamydia. Although sexual mixing with other ethnic groups did differ significantly per ethnicity, this mixing was not independently significantly associated with chlamydia. We typed 170 C. trachomatis-positive samples (76%) and identified three large C. trachomatis clusters. Although the proportion from various ethnic groups differed significantly between the clusters (P = 0.003), all five major ethnic groups were represented in all three clusters. Chlamydia prevalence in Suriname is high and targeted prevention measures are required. Although ethnic sexual mixing differed between ethnic groups, differences in prevalence between ethnic groups could not be explained by sexual mixing.
Urogenital Chlamydia trachomatis Infections among Ethnic Groups in Paramaribo, Suriname; Determinants and Ethnic Sexual Mixing Patterns

PubMed Central

van der Helm, Jannie J.; Bom, Reinier J. M.; Grünberg, Antoon W.; Bruisten, Sylvia M.; Schim van der Loeff, Maarten F.; Sabajo, Leslie O. A.; de Vries, Henry J. C.

2013-01-01

Background Little is known about the epidemiology of urogenital Chlamydia trachomatis infection (chlamydia) in Suriname. Suriname is a society composed of many ethnic groups, such as Creoles, Maroons, Hindustani, Javanese, Chinese, Caucasians, and indigenous Amerindians. We estimated determinants for chlamydia, including the role of ethnicity, and identified transmission patterns and ethnic sexual networks among clients of two clinics in Paramaribo, Suriname. Methods Participants were recruited at two sites a sexually transmitted infections (STI) clinic and a family planning (FP) clinic in Paramaribo. Urine samples from men and nurse-collected vaginal swabs were obtained for nucleic acid amplification testing. Logistic regression analysis was used to identify determinants of chlamydia. Multilocus sequence typing (MLST) was performed to genotype C. trachomatis. To identify transmission patterns and sexual networks, a minimum spanning tree was created, using full MLST profiles. Clusters in the minimum spanning tree were compared for ethnic composition. Results Between March 2008 and July 2010, 415 men and 274 women were included at the STI clinic and 819 women at the FP clinic. Overall chlamydia prevalence was 15% (224/1508). Age, ethnicity, and recruitment site were significantly associated with chlamydia in multivariable analysis. Participants of Creole and Javanese ethnicity were more frequently infected with urogenital chlamydia. Although sexual mixing with other ethnic groups did differ significantly per ethnicity, this mixing was not independently significantly associated with chlamydia. We typed 170 C. trachomatis-positive samples (76%) and identified three large C. trachomatis clusters. Although the proportion from various ethnic groups differed significantly between the clusters (P = 0.003), all five major ethnic groups were represented in all three clusters. Conclusion Chlamydia prevalence in Suriname is high and targeted prevention measures are required. Although ethnic sexual mixing differed between ethnic groups, differences in prevalence between ethnic groups could not be explained by sexual mixing. PMID:23874730
Microstructural and electrical properties of Al/n-type Si Schottky diodes with Au-CuPc nanocomposite films as interlayer

NASA Astrophysics Data System (ADS)

Reddy, P. R. Sekhar; Janardhanam, V.; Jyothi, I.; Chang, Han-Soo; Lee, Sung-Nam; Lee, Myung Sun; Reddy, V. Rajagopal; Choi, Chel-Jong

2017-11-01

Au-CuPc nanocomposite films were prepared by simultaneous evaporation of Au and CuPc with various Au and CuPc concentrations. Microstructural analysis of Au-CuPc films revealed elongated Au cluster formation from isolated Au nanoclusters with increasing Au concentration associated with coalescence of Au clusters. Au-CuPc films with different compositions were employed as interlayer in Al/n-Si Schottky diode. Barrier height and series resistance of the Al/n-Si Schottky diode with Au-CuPc interlayer decreased with increasing Au concentration. This could be associated with the enhancement of electron tunneling between neighboring clusters due to decrease in spacing of Au clusters and formation of conducting paths through the composite material. Interface state density of the Al/n-Si Schottky diode with Au-CuPc interlayer increased with increasing Au concentration. This might be because the inclusion of metal decreases the crystallinity and crystal size of the polymer matrix accompanied by the formation of local defect sites at the places of metal nucleation.
New Insights on co-seismic landslide clustering

NASA Astrophysics Data System (ADS)

Meunier, Patrick; Marc, Odin; Hovius, Niels

2015-04-01

Earthquake-triggered landslides tend to cluster along topographic crests while rainfall-induced landslides should occur downslope preferentially, where pore pressure induced by groundwater flows is the highest [1]. Past studies on landslide clustering are all based on the analysis of complete dataset or subdataset of landslides associated with a given event (seismic or climatic) as a whole. In this work, we document the spatial and temporal variations of the landslide position (on hillslopes) within the epicentral area of the 1994 Northridge, the 1999 Chichi, the 2004 Niigata, the 2008 Iwate and the 2008 Wenchuan earthquakes. We show that crest clustering is not systematic, non uniform in space and exhibit patterns that vary a lot from one case to another. These patterns are not easy to interpret as they don't seem to be controlled by a single governing parameter but result from a complex interaction between local (hillslope length and gradient, lithology) and seismic (distance to source, slope aspect, radiation pattern, coseismic uplift) parameters. [1] Meunier, P., Hovius, N., & Haines, J. A. (2008). Topographic site effects and the location of earthquake induced landslides. Earth and Planetary Science Letters, 275(3), 221-232
Diffuse γ-ray emission in the vicinity of young star cluster Westerlund 2

NASA Astrophysics Data System (ADS)

Yang, Rui-zhi; de Oña Wilhelmi, Emma; Aharonian, Felix

2018-04-01

We report the results of our analysis of the publicly available data obtained by the Large Area Telescope (LAT) on board the Fermi satellite towards the direction of the young massive star cluster Westerlund 2. We found significant extended γ-ray emission in the vicinity of Westerlund 2 with a hard power-law energy spectrum extending from 1 to 250 GeV with a photon index of 2.0 ± 0.1. We argue that amongst several alternatives, the luminous stars in Westerlund 2 are likely sites of acceleration of particles responsible for the diffuse γ-ray emission of the surrounding interstellar medium. In particular, the young star cluster Westerlund 2 can provide sufficient non-thermal energy to account for the γ-ray emission. In this scenario, since the γ-ray production region is significantly larger than the area occupied by the star cluster, we conclude that the γ-ray production is caused by hadronic interactions of accelerated protons and nuclei with the ambient gas. In that case, the total energy budget in relativistic particles is estimated of the order of 1050 erg.
Microbial characterization of nitrification in a shallow, nitrogen-contaminated aquifer, Cape Cod, Massachusetts and detection of a novel cluster associated with nitrifying Betaproteobacteria

USGS Publications Warehouse

Miller, D.N.; Smith, R.L.

2009-01-01

Groundwater nitrification is a poorly characterized process affecting the speciation and transport of nitrogen. Cores from two sites in a plume of contamination were examined using culture-based and molecular techniques targeting nitrification processes. The first site, located beneath a sewage effluent infiltration bed, received treated effluent containing O2 (> 300????M) and NH4+ (51-800????M). The second site was 2.5??km down-gradient near the leading edge of the ammonium zone within the contaminant plume and featured vertical gradients of O2, NH4+, and NO3- (0-300, 0-500, and 100-200????M with depth, respectively). Ammonia- and nitrite-oxidizers enumerated by the culture-based MPN method were low in abundance at both sites (1.8 to 350??g- 1 and 33 to 35,000??g- 1, respectively). Potential nitrifying activity measured in core material in the laboratory was also very low, requiring several weeks for products to accumulate. Molecular analysis of aquifer DNA (nested PCR followed by cloning and 16S rDNA sequencing) detected primarily sequences associated with the Nitrosospira genus throughout the cores at the down-gradient site and a smaller proportion from the Nitrosomonas genus in the deeper anoxic, NH4+ zone at the down-gradient site. Only a single Nitrosospira sequence was detected beneath the infiltration bed. Furthermore, the majority of Nitrosospira-associated sequences represent an unrecognized cluster. We conclude that an uncharacterized group associated with Nitrosospira dominate at the geochemically stable, down-gradient site, but found little evidence for Betaproteobacteria nitrifiers beneath the infiltration beds where geochemical conditions were more variable.
Salton Sea 1/sup 0/ x 2/sup 0/ NTMS area California and Arizona: data report (abbreviated)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heffner, J.D.

1980-09-01

Surface sediment samples were collected at 997 sites. Ground water samples were collected at 76 sites. Neutron activation analysis results are given for uranium and 16 other elements in sediments, and for uranium and 9 other elements in ground water. Mass spectrometry results are given for helium in ground water. Data from ground water sites include (1) water chemistry measurements (pH, conductivity, and alkalinity) (2) physical measurements (water temperature, well description where applicable, and scintillometer reading) and (3) elemental analyses (U, Al, Br, Cl, Dy, F, He, Mg, Mn, Na and V). Data from sediment sites include (1) stream watermore » chemistry measurements from sites where water was available and (2) elemental analyses (U, Th, Hf, Al, Ce, Dy, Eu, Fe, La, Lu, Mn, Sc, Sm, Na, Ti, V, and Yb). Sample site descriptors are given. Areal distribution maps, histograms, and cumulative frequency plots for the elements listed above; U/Th and U/Hf ratios; and scintillometer readings at sediment sample sites are included. Analyses of the sediment fraction finer than 149..mu..m show high uranium values clustered in the Eagle and Chuckwalla Mountains. High uranium values in the 420 ..mu..m to 1000 ..mu..m fraction are clustered in the McCoy Mountains. Both fractions show groups of high values in the Chocolate Mountains at the Southeastern edge of the Chocolate Mountains Aerial Gunnery Range. Aerial distribution of analytical values shows that high values of many elements in both size fractions are grouped around the Eagle Mountains and the Chuckwalla Mountains. Fe, Mn, Ti, V, Sc, Hf, and the rare earth elements, all of which typically occur in high-density minerals, have higher average (log mean) concentrations in the finer fraction than in the coarser fraction.« less
Microbial characterization of nitrification in a shallow, nitrogen-contaminated aquifer, Cape Cod, Massachusetts and detection of a novel cluster associated with nitrifying Betaproteobacteria

NASA Astrophysics Data System (ADS)

Miller, Daniel N.; Smith, Richard L.

2009-01-01

Groundwater nitrification is a poorly characterized process affecting the speciation and transport of nitrogen. Cores from two sites in a plume of contamination were examined using culture-based and molecular techniques targeting nitrification processes. The first site, located beneath a sewage effluent infiltration bed, received treated effluent containing O 2 (> 300 µM) and NH 4+ (51-800 µM). The second site was 2.5 km down-gradient near the leading edge of the ammonium zone within the contaminant plume and featured vertical gradients of O 2, NH 4+, and NO 3- (0-300, 0-500, and 100-200 µM with depth, respectively). Ammonia- and nitrite-oxidizers enumerated by the culture-based MPN method were low in abundance at both sites (1.8 to 350 g - 1 and 33 to 35,000 g - 1 , respectively). Potential nitrifying activity measured in core material in the laboratory was also very low, requiring several weeks for products to accumulate. Molecular analysis of aquifer DNA (nested PCR followed by cloning and 16S rDNA sequencing) detected primarily sequences associated with the Nitrosospira genus throughout the cores at the down-gradient site and a smaller proportion from the Nitrosomonas genus in the deeper anoxic, NH 4+ zone at the down-gradient site. Only a single Nitrosospira sequence was detected beneath the infiltration bed. Furthermore, the majority of Nitrosospira-associated sequences represent an unrecognized cluster. We conclude that an uncharacterized group associated with Nitrosospira dominate at the geochemically stable, down-gradient site, but found little evidence for Betaproteobacteria nitrifiers beneath the infiltration beds where geochemical conditions were more variable.
The Human Skin Microbiome Associates with the Outcome of and Is Influenced by Bacterial Infection

PubMed Central

van Rensburg, Julia J.; Lin, Huaiying; Gao, Xiang; Toh, Evelyn; Fortney, Kate R.; Ellinger, Sheila; Zwickl, Beth; Janowicz, Diane M.; Katz, Barry P.; Nelson, David E.; Dong, Qunfeng

2015-01-01

ABSTRACT The influence of the skin microbiota on host susceptibility to infectious agents is largely unexplored. The skin harbors diverse bacterial species that may promote or antagonize the growth of an invading pathogen. We developed a human infection model for Haemophilus ducreyi in which human volunteers are inoculated on the upper arm. After inoculation, papules form and either spontaneously resolve or progress to pustules. To examine the role of the skin microbiota in the outcome of H. ducreyi infection, we analyzed the microbiomes of four dose-matched pairs of “resolvers” and “pustule formers” whose inoculation sites were swabbed at multiple time points. Bacteria present on the skin were identified by amplification and pyrosequencing of 16S rRNA genes. Nonmetric multidimensional scaling (NMDS) using Bray-Curtis dissimilarity between the preinfection microbiomes of infected sites showed that sites from the same volunteer clustered together and that pustule formers segregated from resolvers (P = 0.001, permutational multivariate analysis of variance [PERMANOVA]), suggesting that the preinfection microbiomes were associated with outcome. NMDS using Bray-Curtis dissimilarity of the endpoint samples showed that the pustule sites clustered together and were significantly different than the resolved sites (P = 0.001, PERMANOVA), suggesting that the microbiomes at the endpoint differed between the two groups. In addition to H. ducreyi, pustule-forming sites had a greater abundance of Proteobacteria, Bacteroidetes, Micrococcus, Corynebacterium, Paracoccus, and Staphylococcus species, whereas resolved sites had higher levels of Actinobacteria and Propionibacterium species. These results suggest that at baseline, resolvers and pustule formers have distinct skin bacterial communities which change in response to infection and the resultant immune response. PMID:26374122

Spectroscopic characterization and O2 reactivity of the trinuclear Cu cluster of mutants of the multicopper oxidase Fet3p.

PubMed

Palmer, Amy E; Quintanar, Liliana; Severance, Scott; Wang, Tzu-Pin; Kosman, Daniel J; Solomon, Edward I

2002-05-21

Fet3p is a multicopper oxidase that uses four copper ions (one type 1, one type 2, and one type 3 binuclear site) to couple substrate oxidation to the reduction of O(2) to H(2)O. The type 1 Cu site shuttles electrons between the substrate and the type 2/type 3 Cu sites which form a trinuclear Cu cluster that is the active site for O(2) reduction. This study extends the spectroscopic and reactivity studies that have been conducted with type 1-substituted Hg (T1Hg) laccase to Fet3p and a mutant of Fet3p in which the trinuclear Cu cluster is perturbed. To examine the reaction between the trinuclear Cu cluster and O(2), the type 1 Cu Cys(484) was mutated to Ser, resulting in a type 1-depleted (T1D) form of the enzyme. Additional His to Gln mutations were made at the trinuclear cluster to further probe specific contributions to reactivity. One of these mutants (His(126)Gln) produces the first stable but perturbed trinuclear Cu cluster (T1DT3' Fet3p). Spectroscopic characterization (absorption, circular dichroism, magnetic circular dichroism, and electron paramagnetic resonance) of the resting trinuclear sites in T1D and T1DT3' Fet3p reveal that the His(126)Gln mutation changes the electronic structure of both the type 3 and type 2 Cu sites. The trinuclear clusters in T1D and T1DT3' Fet3p react with O(2) to produce peroxide intermediates analogous to that observed in T1Hg laccase. Spectroscopic data on the peroxide intermediates in the three forms provide further insight into the structure of this intermediate. In T1D Fet3p, the decay of this peroxide intermediate is pH-dependent, and the rate of decay is 10-fold higher at low pH. In T1DT3' Fet3p, the decay of the peroxide intermediate is pH-independent and is slow at all pH's. This change in the pH dependence provides new insight into the mechanism of intermediate decay involving reductive cleavage of the O-O bond.
Isotopic structure of Lake Whitefish in Lake Huron: Evidence for regional and local populations based on resource use

USGS Publications Warehouse

Eberts, Rebecca L.; Wissel, Bjorn; Simpson, Gavin L.; Crawford, Stephen S.; Stott, Wendylee; Hanner, Robert H.; Manzon, Richard G.; Wilson, Joanna Y.; Boreham, Douglas R.; Somers, Christopher M.

2017-01-01

Lake Whitefish Coregonus clupeaformis is the most commercially valuable species in Lake Huron. The fishery for this species has historically been managed based on 25 management units (17 in Canada, 8 in the USA). However, congruence between the contemporary population structure of Lake Whitefish and management units is poorly understood. We used stable isotopes of carbon (δ13C) and nitrogen (δ15N), food web markers that reflect patterns in resource use (i.e., prey, location, habitat), to assess the population structure of spawning-phase Lake Whitefish collected from 32 sites (1,474 fish) across Lake Huron. We found large isotopic variation among fish from different sites (ranges: δ13C = 10.2‰, δ15N = 5.5‰) and variable niche size and levels of overlap (standard ellipse area = 1.0–4.3‰2). Lake Huron contained spawning-phase fish from four major isotopic clusters largely defined by extensive variation in δ13C, and the isotopic composition of fish sampled was spatially structured both within and between lake basins. Based on cluster compositions, we identified six putative regional groups, some of which represented sites of high diversity (three to four clusters) and others with less (one to two clusters). Analysis of isotopic values from Lake Whitefish collected from summer feeding locations and baseline prey items showed similar isotopic variation and established spatial linkage between spawning-phase and summer fish. Our results show that summer feeding location contributes strongly to the isotopic structure we observed in spawning-phase fish. One of the regional groups we identified in northern Georgian Bay is highly distinct based on isotopic composition and possibly ecologically unique within Lake Huron. Our findings are congruent with several previous studies using different markers (genetics, mark–recapture), and we conclude that current management units are generally too small and numerous to reflect the population structure of Lake Whitefish in Lake Huron.
Assessment of sediment quality in the Mediterranean Sea-Boughrara lagoon exchange areas (southeastern Tunisia): GIS approach-based chemometric methods.

PubMed

Kharroubi, Adel; Gargouri, Dorra; Baati, Houda; Azri, Chafai

2012-06-01

Concentrations of selected heavy metals (Cd, Pb, Zn, Cu, Mn, and Fe) in surface sediments from 66 sites in both northern and eastern Mediterranean Sea-Boughrara lagoon exchange areas (southeastern Tunisia) were studied in order to understand current metal contamination due to the urbanization and economic development of nearby several coastal regions of the Gulf of Gabès. Multiple approaches were applied for the sediment quality assessment. These approaches were based on GIS coupled with chemometric methods (enrichment factors, geoaccumulation index, principal component analysis, and cluster analysis). Enrichment factors and principal component analysis revealed two distinct groups of metals. The first group corresponded to Fe and Mn derived from natural sources, and the second group contained Cd, Pb, Zn, and Cu originated from man-made sources. For these latter metals, cluster analysis showed two distinct distributions in the selected areas. They were attributed to temporal and spatial variations of contaminant sources input. The geoaccumulation index (I (geo)) values explained that only Cd, Pb, and Cu can be considered as moderate to extreme pollutants in the studied sediments.
A web server for analysis, comparison and prediction of protein ligand binding sites.

PubMed

Singh, Harinder; Srivastava, Hemant Kumar; Raghava, Gajendra P S

2016-03-25

One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. In order to address this problem, we developed a web server named 'LPIcom' to facilitate users in understanding protein-ligand interaction. Analysis, comparison and prediction modules are available in the "LPIcom' server to predict protein-ligand interacting residues for 824 ligands. Each ligand must have at least 30 protein binding sites in PDB. Analysis module of the server can identify residues preferred in interaction and binding motif for a given ligand; for example residues glycine, lysine and arginine are preferred in ATP binding sites. Comparison module of the server allows comparing protein-binding sites of multiple ligands to understand the similarity between ligands based on their binding site. This module indicates that ATP, ADP and GTP ligands are in the same cluster and thus their binding sites or interacting residues exhibit a high level of similarity. Propensity-based prediction module has been developed for predicting ligand-interacting residues in a protein for more than 800 ligands. In addition, a number of web-based tools have been integrated to facilitate users in creating web logo and two-sample between ligand interacting and non-interacting residues. In summary, this manuscript presents a web-server for analysis of ligand interacting residue. This server is available for public use from URL http://crdd.osdd.net/raghava/lpicom .
Phylogenetic and Pathotypic Characterization of Newcastle Disease Viruses Circulating in West Africa and Efficacy of a Current Vaccine

PubMed Central

Samuel, Arthur; Nayak, Baibaswata; Paldurai, Anandan; Xiao, Sa; Aplogan, Gilbert L.; Awoume, Kodzo A.; Webby, Richard J.; Ducatez, Mariette F.; Collins, Peter L.

2013-01-01

Newcastle disease (ND) is a deadly avian disease worldwide. In Africa, ND is enzootic and causes large economic losses, but little is known about the Newcastle disease virus (NDV) strains circulating in African countries. In this study, 27 NDV isolates collected from apparently healthy chickens in live-bird markets of the West African countries Benin and Togo in 2009 were characterized. All isolates had polybasic fusion (F)-protein cleavage sites and were shown to be highly virulent in standard pathogenicity assays. Infection of 2-week-old chickens with two of the isolates resulted in 100% mortality within 4 days. Phylogenetic analysis of the 27 isolates based on a partial F-protein gene sequence identified three clusters: one containing all the isolates from Togo and one from Benin (cluster 2), one containing most isolates from Benin (cluster 3), and an outlier isolate from Benin (cluster 1). All the three clusters are related to genotype VII strains of NDV. In addition, the cluster of viruses from Togo contained a recently identified 6-nucleotide insert between the hemagglutinin-neuraminidase (HN) and large polymerase (L) genes in a complete genome of an NDV isolate from this geographical region. Multiple strains that include this novel element suggest local emergence of a new genome length class. These results reveal genetic diversity within and among local NDV populations in Africa. Sequence analysis showed that the F and HN proteins of six West African isolates share 83.2 to 86.6% and 86.5 to 87.9% identities, respectively, with vaccine strain LaSota, indicative of considerable diversity. A vaccine efficacy study showed that the LaSota vaccine protected birds from morbidity and mortality but did not prevent shedding of West African challenge viruses. PMID:23254128
Theoretical insight into Cobalt subnano-clusters adsorption on α-Al{sub 2}O{sub 3} (0001)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Fen-e; Ren, Jun, E-mail: jun.ren@nuc.edu.cn; Wang, Qiang

The investigation on the structural stability, nucleation, growth and interaction of cobalt cluster Con(n=2–7) on the α-Al{sub 2}O{sub 3}(0001) surface by using density functional theory methods has been reported. Energetically, the most favorable adsorption sites were identified and the strongest adsorption energy cluster is the tetrahedral Co{sub 4} cluster. On the other hand, the nucleation of Con(n=2–7) clusters on the surface is exothermic and thermodynamically favorable. Moreover, even-odd alternation was found with respect to clusters nucleation as a function of the number of cobalt atoms (for n=1–7). Meanwhile, the Co{sub n} clusters can be adsorbed on the surface stably owingmore » to the charge transfer from Co atoms to Al and O atoms of the Al{sub 2}O{sub 3} substrate. In addition, we establish the crucial importance of monomer, dimer and trimer diffusion on the surface. The diffusion of the monomer cobalt from Al{sup (3)} to O{sup (5)} or O{sup (5)} to Al{sup (4)} site is quite easy on the Al{sub 2}O{sub 3}(0001) surface, whereas the diffusion of the Co{sub 2} dimer is thermodynamically unfavorable by compared with that of the Co adatom and Co{sub 3} trimer. - Graphical abstract: Diffusion process of Co adatom on the α-Al{sub 2}O{sub 3} (0001) surface, Al{sup (3)} site→O{sup (5)} site→Al{sup (4)} site. Potential energy surface for diffusion of a single Co atom from Al{sup (3)} to O{sup (5)} site, and from O{sup (5)} to Al{sup (4)} site on the surface. The activation energy of the two migration processes from Al{sup (3)} to O{sup (5)} and O{sup (5)} to Al{sup (4)} are 0.06 and 0.09 eV, respectively. This implies the monomer is quite mobile on the surface under typical growth conditions.« less
Estimating carnivoran diets using a combination of carcass observations and scats from GPS clusters

PubMed Central

Tambling, C.J.; Laurence, S.D.; Bellan, S.E.; Cameron, E.Z.; du Toit, J.T.; Getz, W.M.

2011-01-01

Scat analysis is one of the most frequently used methods to assess carnivoran diets and Global Positioning System (GPS) cluster methods are increasingly being used to locate feeding sites for large carnivorans. However, both methods have inherent biases that limit their use. GPS methods to locate kill sites are biased towards large carcasses, while scat analysis over-estimates the biomass consumed from smaller prey. We combined carcass observations and scats collected along known movement routes, assessed using GPS data from four African lion (Panthera leo) prides in the Kruger National Park, South Africa, to determine how a combination of these two datasets change diet estimates. As expected, using carcasses alone under-estimated the number of feeding events on small species, primarily impala (Aepyceros melampus) and warthog (Phacochoerus africanus), in our case by more than 50% and thus significantly under-estimated the biomass consumed per pride per day in comparison to when the diet was assessed using carcass observations alone. We show that an approach that supplements carcass observations with scats that enables the identification of potentially missed feeding events increases the estimates of food intake rates for large carnivorans, with possible ramifications for predator-prey interaction studies dealing with biomass intake rate. PMID:22408290
In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae

PubMed Central

Kurotani, Atsushi; Sakurai, Tetsuya

2015-01-01

Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups. PMID:26307970
In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae.

PubMed

Kurotani, Atsushi; Sakurai, Tetsuya

2015-08-20

Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.
In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

PubMed Central

2016-01-01

Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons. PMID:27698666
Comparative analysis of bones, mites, soil chemistry, nematodes and soil micro-eukaryotes from a suspected homicide to estimate the post-mortem interval.

PubMed

Szelecz, Ildikó; Lösch, Sandra; Seppey, Christophe V W; Lara, Enrique; Singer, David; Sorge, Franziska; Tschui, Joelle; Perotti, M Alejandra; Mitchell, Edward A D

2018-01-08

Criminal investigations of suspected murder cases require estimating the post-mortem interval (PMI, or time after death) which is challenging for long PMIs. Here we present the case of human remains found in a Swiss forest. We have used a multidisciplinary approach involving the analysis of bones and soil samples collected beneath the remains of the head, upper and lower body and "control" samples taken a few meters away. We analysed soil chemical characteristics, mites and nematodes (by microscopy) and micro-eukaryotes (by Illumina high throughput sequencing). The PMI estimate on hair 14 C-data via bomb peak radiocarbon dating gave a time range of 1 to 3 years before the discovery of the remains. Cluster analyses for soil chemical constituents, nematodes, mites and micro-eukaryotes revealed two clusters 1) head and upper body and 2) lower body and controls. From mite evidence, we conclude that the body was probably brought to the site after death. However, chemical analyses, nematode community analyses and the analyses of micro-eukaryotes indicate that decomposition took place at least partly on site. This study illustrates the usefulness of combining several lines of evidence for the study of homicide cases to better calibrate PMI inference tools.
Spatial patterns and origins of heavy metals in Sheyang River catchment in Jiangsu, China based on geographically weighted regression.

PubMed

Wu, Shan-Shan; Yang, Hao; Guo, Fei; Han, Rui-Ming

2017-02-15

Multivariate statistical analyses combined with geographically weighted regression (GWR) were used to identify spatial variations of heavy metals in sediments and to examine relationships between metal pollution and land use practices in watersheds, including urban land, agriculture land, forest and water bodies. Seven metals (Cu, Zn, Pb, Cr, Ni, Mn and Fe) of sediments were measured at 31 sampling sites in Sheyang River. Most metals were under a certain degree enrichment based on the enrichment factors. Cluster analysis grouped all sites into four statistically significant cluster, severely contaminated areas were concentrated in areas with intensive human activities. Correlation analysis and PCA indicated Cu, Zn and Pb were derived from anthropogenic activities, while the sources of Cr and Ni were complicated. However, Fe and Mn originated from natural sources. According to results of GWR, there are stronger association between metal pollution with urban land than agricultural land and forest. Moreover, the relationships between land use and metal concentration were affected by the urbanization level of watersheds. Agricultural land had a weak associated with heavy metal pollution and the relationships might be stronger in less-urbanized. This study provided useful information for the assessment and management of heavy metal hazards in studied area. Copyright © 2016 Elsevier B.V. All rights reserved.
In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites.

PubMed

Irizarry, Kristopher J L; Bryden, Randall L

2016-01-01

Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus . Our results provide insight into pigment phenotypes in pythons.
Techniques for spatio-temporal analysis of vegetation fires in the topical belt of Africa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brivio, P.A.; Ober, G.; Koffi, B.

1995-12-31

Biomass burning of forests and savannas is a phenomenon of continental or even global proportions, capable of causing large scale environmental changes. Satellite space observations, in particular from NOAA-AVHRR GAC data, are the only source of information allowing one to document burning patterns at regional and continental scale and over long periods of time. This paper presents some techniques, such as clustering and rose-diagram, useful in the spatial-temporal analysis of satellite derived fires maps to characterize the evolution of spatial patterns of vegetation fires at regional scale. An automatic clustering approach is presented which enables one to describe and parameterizemore » spatial distribution of fire patterns at different scales. The problem of geographical distribution of vegetation fires with respect to some location of interest, point or line, is also considered and presented. In particular rose-diagrams are used to relate fires patterns to some reference point, as experimental sites of tropospheric chemistry measurements. Different temporal data-sets in the tropical belt of Africa, covering both Northern and Southern Hemisphere dry seasons, using these techniques were analyzed and showed very promising results when compared with data from rain chemistry studies at different sampling sites in the equatorial forest.« less
Cancer-Related Analysis of Variants Toolkit (CRAVAT) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

CRAVAT is an easy to use web-based tool for analysis of cancer variants (missense, nonsense, in-frame indel, frameshift indel, splice site). CRAVAT provides scores and a variety of annotations that assist in identification of important variants. Results are provided in an interactive, highly graphical webpage and include annotated 3D structure visualization. CRAVAT is also available for local or cloud-based installation as a Docker container. MuPIT provides 3D visualization of mutation clusters and functional annotation and is now integrated with CRAVAT.
Analysis of Alternative (Low Impact) Development on a Theoretical Residential Development in North Central Florida

NASA Astrophysics Data System (ADS)

Wise, W. R.

2001-05-01

Research currently in progress will evaluate land development options on a 161 +/- HA site in North Central Florida lying within a 292+/- HA watershed that contributes to Bullfrog Creek in the Camp Blanding Wildlife Management Area. The research analyzes aspects of an emerging storm-water management philosophy, called low-impact development (LID) by Prince Georges County, Maryland. LID seeks to preserve site hydrology by reducing the area of disturbance on the site, preserving natural drainage features on the site and by utilizing BMPs that promote infiltration and slower transport of runoff. This research investigates the benefits and problems associated with this design philosophy, particularly in Florida. Two scenarios will be investigated: Low density residential and Medium density residential. Within each scenario the hydrologic response of the site under conventional and LID will be explored. Furthermore, the impact of using cluster developments in LIDs will be investigated. Parameters to be measured include: peak flow, runoff volume, pollutant load generated/removed by BMPs, peak-flow timing and base flow. HEC-HMS will be used for hydrologic modeling (soil moisture accounting module). Pollutant loads generated and removed will be based on published data for land use and BMPs. An economic analysis, based on the estimated construction costs of conventional and LID, will also be done. Further sensitivity analyses will be conducted on the effect that various watershed conditions have on the hydrologic response of the site developed as a LID. This research will provide insight to several questions. In the most general sense it will indicate whether this emerging design philosophy, much of which was developed in other regions of the country, is beneficial to Florida watersheds "as it is" and what, if any, alterations should be considered. Secondly, this research will show the impact of development with different site-planning options, for example cluster development versus deed restrictions on lots. Thirdly, the research will give insight to the applicability of this land-development approach under different allowable residential densities. Lastly, the effect of different physical characteristics on the watershed can be explored.
On the bonding mechanism of CO to Pt(111) and its effect on the vibrational frequency of chemisorbed CO

NASA Astrophysics Data System (ADS)

Illas, F.; Zurita, S.; Márquez, A. M.; Rubio, J.

1997-04-01

The chemisorption of CO on the atop site of Pt(111) has been simulated by a Pt4 cluster model. Ab initio self consistent field (SCF) and complete active space self consistent field (CASSCF) cluster model wave functions have been obtained for the electronic ground state. Likewise, ab initio SCF wavefunctions have been obtained for two other electronic states. The optimum geometry and vibrational frequencies of chemisorbed CO are reported for the three states. The interaction energy and vibrational shift of chemisorbed CO, with respect to free gas phase CO, have been analyzed for the three electronic states. This analysis is carried out by means of the constrained space orbital variation (CSOV) method. In all cases the bond is found to be dominated by σ donation and π back-donation, known as Blyholder's mechanism. This mechanism is further supported by SCF calculations on a larger, Pt13, cluster model. For both clusters, the CSOV analysis of the vibrational frequency definitely shows that, contrary to previous recent studies, a major contribution to the experimentally observed vibrational shift comes from the π back-donation mechanism. However, we found that, contrary to common belief, σ donation also acts to lower the CO frequency and not to increase it. Physical reasons for such unexpected behaviour are given.
Symptom clusters in advanced cancer.

PubMed

Jiménez, Ana; Madero, Rosario; Alonso, Alberto; Martínez-Marín, Virginia; Vilches, Yolanda; Martínez, Beatriz; Feliu, Marta; Díaz, Leyre; Espinosa, Enrique; Feliu, Jaime

2011-07-01

Patients with advanced cancer often experience multiple concurrent symptoms. Few studies have explored symptom clusters (SCs) in this population. The aim of the present study was to explore SCs in advanced cancer, evaluate the characteristics associated with various clusters, and determine their relationship to survival. This study included patients in the palliative care program of the Hospital Universitario La Paz from 2003 to 2005. The Edmonton Symptom Assessment System and a supplement including 13 other symptoms were used to detect symptoms. Principal component analysis was performed to determine symptom relationships and compare SCs with associated parameters. In total, 406 patients were included, 61% men and 39% women. The median age was 66.4 (range 18-95). The most common primaries were gastrointestinal (35%), lung (25%), genitourinary (8%), breast (5%), and head and neck (5%) carcinomas. The following clusters were identified: confusion (cognitive impairment, agitation, urinary incontinence), neuropsychological (anxiety, depression, and insomnia), anorexia-cachexia (anorexia, weight loss, and tiredness), and gastrointestinal (nausea and vomiting). The presence of these SCs was influenced by primary cancer site, gender, age, and performance status. Survival was related to the number of SCs present in a given patient: zero SC, 52 days; one SC, 38 days; two SCs, 23 days; and three to four SCs, 19 days; P < 0.001. Different SCs can be identified in patients with advanced cancer. These SCs are influenced by primary cancer site, gender, age, and Eastern Cooperative Oncology Group performance status, and they can have prognostic value. Copyright © 2011 U.S. Cancer Pain Relief Committee. Published by Elsevier Inc. All rights reserved.
Site specific atomic polarizabilities in endohedral fullerenes and carbon onions

NASA Astrophysics Data System (ADS)

Zope, Rajendra R.; Bhusal, Shusil; Basurto, Luis; Baruah, Tunna; Jackson, Koblar

2015-08-01

We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C60@C240 and C60@C180 onions shows that, compared to the polarizability of isolated C60 fullerene, the encapsulation of the C60 in C240 and C180 fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C60 in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.
Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis.

PubMed

Bai, Fang; Morcos, Faruck; Cheng, Ryan R; Jiang, Hualiang; Onuchic, José N

2016-12-13

Protein-protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein-protein interfaces. (i) This method explores the binding of fragment-sized molecular probes on the protein surface using a molecular docking-based screen. (ii) The energetically favorable binding sites of the probes, called hot spots, are spatially clustered to map out candidate binding sites on the protein surface. (iii) A coevolution-based interface interaction score is used to discriminate between different candidate binding sites, yielding potential interfacial targets for therapeutic drug design. This approach is validated for important, well-studied disease-related proteins with known pharmaceutical targets, and also identifies targets that have yet to be studied. Moreover, therapeutic agents are proposed by chemically connecting the fragments that are strongly bound to the hot spots.

Site specific atomic polarizabilities in endohedral fullerenes and carbon onions.

PubMed

Zope, Rajendra R; Bhusal, Shusil; Basurto, Luis; Baruah, Tunna; Jackson, Koblar

2015-08-28

We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C60@C240 and C60@C180 onions shows that, compared to the polarizability of isolated C60 fullerene, the encapsulation of the C60 in C240 and C180 fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C60 in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.
Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures.

PubMed

Kirillova, Svetlana; Carugo, Oliviero

2011-10-19

Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed. The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs.
Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures

PubMed Central

2011-01-01

Background Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. Results A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed. Conclusions The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs. PMID:22011380
Site specific atomic polarizabilities in endohedral fullerenes and carbon onions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zope, Rajendra R., E-mail: rzope@utep.edu; Baruah, Tunna; Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79958

2015-08-28

We investigate the polarizability of trimetallic nitride endohedral fullerenes by partitioning the total polarizability into site specific components. This analysis indicates that the polarizability of the endohedral fullerene is essentially due to the outer fullerene cage and has insignificant contribution from the encapsulated unit. Thus, the outer fullerene cages effectively shield the encapsulated clusters and behave like Faraday cages. The polarizability of endohedral fullerenes is slightly smaller than the polarizability of the corresponding bare carbon fullerenes. The application of the site specific polarizabilities to C{sub 60}@C{sub 240} and C{sub 60}@C{sub 180} onions shows that, compared to the polarizability of isolatedmore » C{sub 60} fullerene, the encapsulation of the C{sub 60} in C{sub 240} and C{sub 180} fullerenes reduces its polarizability by 75% and 83%, respectively. The differences in the polarizability of C{sub 60} in the two onions is a result of differences in the bonding (intershell electron transfer), fullerene shell relaxations, and intershell separations. The site specific analysis further shows that the outer atoms in a fullerene shell contribute most to the fullerene polarizability.« less
Submonolayer Ag films on Fe(100): A first-principles analysis of energetics controlling adlayer thermodynamics and kinetics

DOE PAGES

Li, Wei; Huang, Li; Evans, James W.; ...

2016-04-11

Epitaxial growth of Ag on Fe(100) and postdeposition relaxation have been studied in several experiments. We provide a first-principles density functional theory analysis of key adatom interaction energies and diffusion barriers controlling growth and relaxation kinetics for the submonolayer regime, as these have not been assessed previously. A cluster expansion approach is used to obtain an extensive set of conventional lateral interactions between adatoms on fourfold hollow adsorption sites. We find robust oscillatory decay of pair interactions with increasing separation, and of trio interactions with increasing perimeter length. First- and second-nearest-neighbor pair interactions, as well as compact linear and bentmore » trio interactions, dominate. The adatom terrace diffusion barrier is estimated to be E d ≈ 0.39 eV. We also provide a limited analysis of unconventional interactions for which one adatom is at the bridge-site transition state for hopping and one or more others are at fourfold hollow sites. Furthermore, energy barriers for diffusion along island edges can be determined with the aid of both conventional and unconventional interactions.« less
Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

PubMed

Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

2012-01-01

Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.
ANALYSIS AND CHARACTERIZATION OF OZONE-RICH EPISODES IN NORTHEAST PORTUGAL

NASA Astrophysics Data System (ADS)

Carvalho, A.; Monteiro, A.; Ribeiro, I.; Tchepel, O.; Miranda, A.; Borrego, C.; Saavedra, S.; Souto, J. A.; Casares, J. J.

2009-12-01

Each summer period extremely high ozone levels are registered at the rural background station of Lamas d’Olo, located in the Northeast of Portugal. In average, 30% of the total alert threshold registered in Portugal is detected at this site. The main purpose of this study is to characterize the atmospheric conditions that lead to the ozone-rich episodes. Synoptic patterns anomalies and back trajectories cluster analysis were performed for a period of 76 days where ozone maximum concentrations were above 200 µg.m-3. This analysis was performed for the period between 2004 and 2007. The obtained anomaly fields suggested that a positive temperature anomaly is visible above the Iberian Peninsula. In addition, a strong wind flow pattern from NE is visible in the North of Portugal and Galicia, in Spain. These two features may lead to an enhancement of the photochemical production and to the transport of pollutants from Spain to Portugal. In addition, the 3D mean back trajectories associated to the ozone episode days were analysed. A clustering method has been applied to the obtained back trajectories. Four main clusters of ozone-rich episodes were identified, with different frequencies of occurrence: north-westerly flows (11%); north-easterly flows (45%), southern flow (4%) and westerly flows (40%). Both analyses highlight the NE flow as a dominant pattern over the North of Portugal. The analysis of the ozone concentrations for each selected cluster indicates that this northeast circulation pattern, together with the southern flow, is responsible for the highest ozone peak episodes. This also suggests that long-range transport of atmospheric pollutants may be the main contributor to the ozone levels registered at Lamas d’Olo. This is also highlighted by the correlation of the ozone time series with the meteorological parameters analysed in the frequency domain.
Regional L-Moment-Based Flood Frequency Analysis in the Upper Vistula River Basin, Poland

NASA Astrophysics Data System (ADS)

Rutkowska, A.; Żelazny, M.; Kohnová, S.; Łyp, M.; Banasik, K.

2017-02-01

The Upper Vistula River basin was divided into pooling groups with similar dimensionless frequency distributions of annual maximum river discharge. The cluster analysis and the Hosking and Wallis (HW) L-moment-based method were used to divide the set of 52 mid-sized catchments into disjoint clusters with similar morphometric, land use, and rainfall variables, and to test the homogeneity within clusters. Finally, three and four pooling groups were obtained alternatively. Two methods for identification of the regional distribution function were used, the HW method and the method of Kjeldsen and Prosdocimi based on a bivariate extension of the HW measure. Subsequently, the flood quantile estimates were calculated using the index flood method. The ordinary least squares (OLS) and the generalised least squares (GLS) regression techniques were used to relate the index flood to catchment characteristics. Predictive performance of the regression scheme for the southern part of the Upper Vistula River basin was improved by using GLS instead of OLS. The results of the study can be recommended for the estimation of flood quantiles at ungauged sites, in flood risk mapping applications, and in engineering hydrology to help design flood protection structures.
Explosive site percolation with a product rule.

PubMed

Choi, Woosik; Yook, Soon-Hyung; Kim, Yup

2011-08-01

We study the site percolation under Achlioptas process with a product rule in a two-dimensional square lattice. From the measurement of the cluster size distribution P(s), we find that P(s) has a very robust power-law regime followed by a stable hump near the transition threshold. Based on the careful analysis on the PP(s) distribution, we show that the transition should be discontinuous. The existence of the hysteresis loop in order parameter also verifies that the transition is discontinuous in two dimensions. Moreover, we also show that the transition nature from the product rule is not the same as that from a sum rule in two dimensions.
Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants

PubMed Central

Demir, Özlem; Baronio, Roberta; Salehi, Faezeh; Wassman, Christopher D.; Hall, Linda; Hatfield, G. Wesley; Chamberlin, Richard; Kaiser, Peter; Lathrop, Richard H.; Amaro, Rommie E.

2011-01-01

The tumor suppressor protein p53 can lose its function upon single-point missense mutations in the core DNA-binding domain (“cancer mutants”). Activity can be restored by second-site suppressor mutations (“rescue mutants”). This paper relates the functional activity of p53 cancer and rescue mutants to their overall molecular dynamics (MD), without focusing on local structural details. A novel global measure of protein flexibility for the p53 core DNA-binding domain, the number of clusters at a certain RMSD cutoff, was computed by clustering over 0.7 µs of explicitly solvated all-atom MD simulations. For wild-type p53 and a sample of p53 cancer or rescue mutants, the number of clusters was a good predictor of in vivo p53 functional activity in cell-based assays. This number-of-clusters (NOC) metric was strongly correlated (r2 = 0.77) with reported values of experimentally measured ΔΔG protein thermodynamic stability. Interpreting the number of clusters as a measure of protein flexibility: (i) p53 cancer mutants were more flexible than wild-type protein, (ii) second-site rescue mutations decreased the flexibility of cancer mutants, and (iii) negative controls of non-rescue second-site mutants did not. This new method reflects the overall stability of the p53 core domain and can discriminate which second-site mutations restore activity to p53 cancer mutants. PMID:22028641
Peer-to-peer Cooperative Scheduling Architecture for National Grid Infrastructure

NASA Astrophysics Data System (ADS)

Matyska, Ludek; Ruda, Miroslav; Toth, Simon

For some ten years, the Czech National Grid Infrastructure MetaCentrum uses a single central PBSPro installation to schedule jobs across the country. This centralized approach keeps a full track about all the clusters, providing support for jobs spanning several sites, implementation for the fair-share policy and better overall control of the grid environment. Despite a steady progress in the increased stability and resilience to intermittent very short network failures, growing number of sites and processors makes this architecture, with a single point of failure and scalability limits, obsolete. As a result, a new scheduling architecture is proposed, which relies on higher autonomy of clusters. It is based on a peer to peer network of semi-independent schedulers for each site or even cluster. Each scheduler accepts jobs for the whole infrastructure, cooperating with other schedulers on implementation of global policies like central job accounting, fair-share, or submission of jobs across several sites. The scheduling system is integrated with the Magrathea system to support scheduling of virtual clusters, including the setup of their internal network, again eventually spanning several sites. On the other hand, each scheduler is local to one of several clusters and is able to directly control and submit jobs to them even if the connection of other scheduling peers is lost. In parallel to the change of the overall architecture, the scheduling system itself is being replaced. Instead of PBSPro, chosen originally for its declared support of large scale distributed environment, the new scheduling architecture is based on the open-source Torque system. The implementation and support for the most desired properties in PBSPro and Torque are discussed and the necessary modifications to Torque to support the MetaCentrum scheduling architecture are presented, too.
Gene targeting technologies in rats: zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats.

PubMed

Mashimo, Tomoji

2014-01-01

The laboratory rat has been widely used as an animal model in biomedical science for more than 150 years. Applying zinc-finger nucleases or transcription activator-like effector nucleases to rat embryos via microinjection is an efficient genome editing tool for generating targeted knockout rats. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated endonucleases have been used as an effective tool for precise and multiplex genome editing in mice and rats. In this review, the advantages and disadvantages of these site-specific nuclease technologies for genetic analysis and manipulation in rats are discussed. © 2013 The Author Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.
Differential regulation by ATP versus ADP further links CaMKII aggregation to ischemic conditions

PubMed Central

Vest, Rebekah S.; O’Leary, Heather; Bayer, K. Ulrich

2009-01-01

CaMKII, a major mediator of synaptic plasticity, forms extra-synaptic clusters under ischemic conditions. This study further supports self-aggregation of CaMKII holoenzymes as the underlying mechanism. Aggregation in vitro was promoted by mimicking ischemic conditions: low pH (6.8 or less), Ca2+ (and calmodulin), and low ATP and/or high ADP concentration. Mutational analysis showed that high ATP prevented aggregation by a mechanism involving T286 auto-phosphorylation, and indicated requirement for nucleotide binding but not auto-phosphorylation also for extra-synaptic clustering within neurons. These results clarify a previously apparent paradox in the nucleotide and phosphorylation requirement of aggregation, and support a mechanism that involves inter-holoenzyme T286-region/T-site interaction. PMID:19840793
Integrated self-organization of transitional ER and early Golgi compartments.

PubMed

Glick, Benjamin S

2014-02-01

COPII coated vesicles bud from an ER domain termed the transitional ER (tER), but the mechanism that clusters COPII vesicles at tER sites is unknown. tER sites are closely associated with early Golgi or pre-Golgi structures, suggesting that the clustering of nascent COPII vesicles could be achieved by tethering to adjacent membranes. This model challenges the prevailing view that COPII vesicles are clustered by a scaffolding protein at the ER surface. Although Sec16 was proposed to serve as such a scaffolding protein, recent data suggest that rather than organizing COPII into higher-order structures, Sec16 acts at the level of individual COPII vesicles to regulate COPII turnover. A plausible synthesis is that tER sites are created by tethering to Golgi membranes and are regulated by Sec16. Meanwhile, the COPII vesicles that bud from tER sites are thought to nucleate new Golgi cisternae. Thus, an integrated self-organization process may generate tER-Golgi units. © 2014 WILEY Periodicals, Inc.
On basis set superposition error corrected stabilization energies for large n-body clusters.

PubMed

Walczak, Katarzyna; Friedrich, Joachim; Dolg, Michael

2011-10-07

In this contribution, we propose an approximate basis set superposition error (BSSE) correction scheme for the site-site function counterpoise and for the Valiron-Mayer function counterpoise correction of second order to account for the basis set superposition error in clusters with a large number of subunits. The accuracy of the proposed scheme has been investigated for a water cluster series at the CCSD(T), CCSD, MP2, and self-consistent field levels of theory using Dunning's correlation consistent basis sets. The BSSE corrected stabilization energies for a series of water clusters are presented. A study regarding the possible savings with respect to computational resources has been carried out as well as a monitoring of the basis set dependence of the approximate BSSE corrections. © 2011 American Institute of Physics
Long non-coding RNA H19 suppresses retinoblastoma progression via counteracting miR-17-92 cluster.

PubMed

Zhang, Aihui; Shang, Weiwei; Nie, Qiaoli; Li, Ting; Li, Suhui

2018-04-01

Long non-coding RNAs (lncRNAs) are frequently dysregulated and play important roles in many cancers. lncRNA H19 is one of the earliest discovered lncRNAs which has diverse roles in different cancers. However, the expression, roles, and action mechanisms of H19 in retinoblastoma are still largely unknown. In this study, we found that H19 is downregulated in retinoblastoma tissues and cell lines. Gain-of-function and loss-of-function assays showed that H19 inhibits retinoblastoma cell proliferation, induces retinoblastoma cell cycle arrest and cell apoptosis. Mechanistically, we identified seven miR-17-92 cluster binding sites on H19, and found that H19 directly bound to miR-17-92 cluster via these seven binding sites. Through binding to miR-17-92 cluster, H19 relieves the suppressing roles of miR-17-92 cluster on p21. Furthermore, H19 represses STAT3 activation induced by miR-17-92 cluster. Hence, our results revealed that H19 upregulates p21 expression, inhibits STAT3 phosphorylation, and downregulates the expression of STAT3 target genes BCL2, BCL2L1, and BIRC5. In addition, functional assays demonstrated that the mutation of miR-17-92 cluster binding sites on H19 abolished the proliferation inhibiting, cell cycle arrest and cell apoptosis inducing roles of H19 in retinoblastoma. In conclusion, our data suggested that H19 inhibits retinoblastoma progression via counteracting the roles of miR-17-92 cluster, and implied that enhancing the action of H19 may be a promising therapeutic strategy for retinoblastoma. © 2017 Wiley Periodicals, Inc.
Analysis of β-Subgroup Proteobacterial Ammonia Oxidizer Populations in Soil by Denaturing Gradient Gel Electrophoresis Analysis and Hierarchical Phylogenetic Probing

PubMed Central

Stephen, John R.; Kowalchuk, George A.; Bruns, Mary-Ann V.; McCaig, Allison E.; Phillips, Carol J.; Embley, T. Martin; Prosser, James I.

1998-01-01

A combination of denaturing gradient gel electrophoresis (DGGE) and oligonucleotide probing was used to investigate the influence of soil pH on the compositions of natural populations of autotrophic β-subgroup proteobacterial ammonia oxidizers. PCR primers specific to this group were used to amplify 16S ribosomal DNA (rDNA) from soils maintained for 36 years at a range of pH values, and PCR products were analyzed by DGGE. Genus- and cluster-specific probes were designed to bind to sequences within the region amplified by these primers. A sequence specific to all β-subgroup ammonia oxidizers could not be identified, but probes specific for Nitrosospira clusters 1 to 4 and Nitrosomonas clusters 6 and 7 (J. R. Stephen, A. E. McCaig, Z. Smith, J. I. Prosser, and T. M. Embley, Appl. Environ. Microbiol. 62:4147–4154, 1996) were designed. Elution profiles of probes against target sequences and closely related nontarget sequences indicated a requirement for high-stringency hybridization conditions to distinguish between different clusters. DGGE banding patterns suggested the presence of Nitrosomonas cluster 6a and Nitrosospira clusters 2, 3, and 4 in all soil plots, but results were ambiguous because of overlapping banding patterns. Unambiguous band identification of the same clusters was achieved by combined DGGE and probing of blots with the cluster-specific radiolabelled probes. The relative intensities of hybridization signals provided information on the apparent selection of different Nitrosospira genotypes in samples of soil of different pHs. The signal from the Nitrosospira cluster 3 probe decreased significantly, relative to an internal control probe, with decreasing soil pH in the range of 6.6 to 3.9, while Nitrosospira cluster 2 hybridization signals increased with increasing soil acidity. Signals from Nitrosospira cluster 4 were greatest at pH 5.5, decreasing at lower and higher values, while Nitrosomonas cluster 6a signals did not vary significantly with pH. These findings are in agreement with a previous molecular study (J. R. Stephen, A. E. McCaig, Z. Smith, J. I. Prosser, and T. M. Embley, Appl. Environ. Microbiol 62:4147–4154, 1996) of the same sites, which demonstrated the presence of the same four clusters of ammonia oxidizers and indicated that selection might be occurring for clusters 2 and 3 at acid and neutral pHs, respectively. The two studies used different sets of PCR primers for amplification of 16S rDNA sequences from soil, and the similar findings suggest that PCR bias was unlikely to be a significant factor. The present study demonstrates the value of DGGE and probing for rapid analysis of natural soil communities of β-subgroup proteobacterial ammonia oxidizers, indicates significant pH-associated differences in Nitrosospira populations, and suggests that Nitrosospira cluster 2 may be of significance for ammonia-oxidizing activity in acid soils. PMID:9687457
Passive colloids work together to become Active

NASA Astrophysics Data System (ADS)

Kandula, Hima Nagamanasa; Wang, Wei; Zhang, Jie; Wu, Huanxin; Han, Ming; Luijten, Erik; Granick, Steve

In recent years there is growing body of research to design self-propelled colloids to gain insights into non-equilibrium systems including living matter. While most active colloids developed hitherto entail prefabrication of Janus colloids and possess single fixed active site, we present one simple system where active colloids are formed in-situ naturally with multiple active sites and are reversible as well as reconfigurable. A binary mixture of Brownian colloids which have opposite polarizations when subjected to an AC electric field spontaneously assemble into clusters which are propelled by asymmetric induced charge electro osmosis. We find that tuning the relative sizes of the two species allows for the control over the number of active sites. More interestingly, the patches are dynamic enabling reconfiguration of the active cluster. Consequently, the clusters are active not only in motion but also in their structure.
Heterologous expression of pikromycin biosynthetic gene cluster using Streptomyces artificial chromosome system.

PubMed

Pyeon, Hye-Rim; Nah, Hee-Ju; Kang, Seung-Hoon; Choi, Si-Sun; Kim, Eung-Soo

2017-05-31

Heterologous expression of biosynthetic gene clusters of natural microbial products has become an essential strategy for titer improvement and pathway engineering of various potentially-valuable natural products. A Streptomyces artificial chromosomal conjugation vector, pSBAC, was previously successfully applied for precise cloning and tandem integration of a large polyketide tautomycetin (TMC) biosynthetic gene cluster (Nah et al. in Microb Cell Fact 14(1):1, 2015), implying that this strategy could be employed to develop a custom overexpression scheme of natural product pathway clusters present in actinomycetes. To validate the pSBAC system as a generally-applicable heterologous overexpression system for a large-sized polyketide biosynthetic gene cluster in Streptomyces, another model polyketide compound, the pikromycin biosynthetic gene cluster, was preciously cloned and heterologously expressed using the pSBAC system. A unique HindIII restriction site was precisely inserted at one of the border regions of the pikromycin biosynthetic gene cluster within the chromosome of Streptomyces venezuelae, followed by site-specific recombination of pSBAC into the flanking region of the pikromycin gene cluster. Unlike the previous cloning process, one HindIII site integration step was skipped through pSBAC modification. pPik001, a pSBAC containing the pikromycin biosynthetic gene cluster, was directly introduced into two heterologous hosts, Streptomyces lividans and Streptomyces coelicolor, resulting in the production of 10-deoxymethynolide, a major pikromycin derivative. When two entire pikromycin biosynthetic gene clusters were tandemly introduced into the S. lividans chromosome, overproduction of 10-deoxymethynolide and the presence of pikromycin, which was previously not detected, were both confirmed. Moreover, comparative qRT-PCR results confirmed that the transcription of pikromycin biosynthetic genes was significantly upregulated in S. lividans containing tandem clusters of pikromycin biosynthetic gene clusters. The 60 kb pikromycin biosynthetic gene cluster was isolated in a single integration pSBAC vector. Introduction of the pikromycin biosynthetic gene cluster into the pikromycin non-producing strains resulted in higher pikromycin production. The utility of the pSBAC system as a precise cloning tool for large-sized biosynthetic gene clusters was verified through heterologous expression of the pikromycin biosynthetic gene cluster. Moreover, this pSBAC-driven heterologous expression strategy was confirmed to be an ideal approach for production of low and inconsistent natural products such as pikromycin in S. venezuelae, implying that this strategy could be employed for development of a custom overexpression scheme of natural product biosynthetic gene clusters in actinomycetes.
Structural characterization of metal binding to a cold-adapted frataxin.

PubMed

Noguera, Martín E; Roman, Ernesto A; Rigal, Juan B; Cousido-Siah, Alexandra; Mitschler, André; Podjarny, Alberto; Santos, Javier

2015-06-01

Frataxin is an evolutionary conserved protein that participates in iron metabolism. Deficiency of this small protein in humans causes a severe neurodegenerative disease known as Friedreich's ataxia. A number of studies indicate that frataxin binds iron and regulates Fe-S cluster biosynthesis. Previous structural studies showed that metal binding occurs mainly in a region of high density of negative charge. However, a comprehensive characterization of the binding sites is required to gain further insights into the mechanistic details of frataxin function. In this work, we have solved the X-ray crystal structures of a cold-adapted frataxin from a psychrophilic bacterium in the presence of cobalt or europium ions. We have identified a number of metal-binding sites, mainly solvent exposed, several of which had not been observed in previous studies on mesophilic homologues. No major structural changes were detected upon metal binding, although the structures exhibit significant changes in crystallographic B-factors. The analysis of these B-factors, in combination with crystal packing and RMSD among structures, suggests the existence of localized changes in the internal motions. Based on these results, we propose that bacterial frataxins possess binding sites of moderate affinity for a quick capture and transfer of iron to other proteins and for the regulation of Fe-S cluster biosynthesis, modulating interactions with partner proteins.

Psychological Factors Predict Local and Referred Experimental Muscle Pain: A Cluster Analysis in Healthy Adults

PubMed Central

Lee, Jennifer E.; Watson, David; Frey-Law, Laura A.

2012-01-01

Background Recent studies suggest an underlying three- or four-factor structure explains the conceptual overlap and distinctiveness of several negative emotionality and pain-related constructs. However, the validity of these latent factors for predicting pain has not been examined. Methods A cohort of 189 (99F; 90M) healthy volunteers completed eight self-report negative emotionality and pain-related measures (Eysenck Personality Questionnaire-Revised; Positive and Negative Affect Schedule; State-Trait Anxiety Inventory; Pain Catastrophizing Scale; Fear of Pain Questionnaire; Somatosensory Amplification Scale; Anxiety Sensitivity Index; Whiteley Index). Using principal axis factoring, three primary latent factors were extracted: General Distress; Catastrophic Thinking; and Pain-Related Fear. Using these factors, individuals clustered into three subgroups of high, moderate, and low negative emotionality responses. Experimental pain was induced via intramuscular acidic infusion into the anterior tibialis muscle, producing local (infusion site) and/or referred (anterior ankle) pain and hyperalgesia. Results Pain outcomes differed between clusters (multivariate analysis of variance and multinomial regression), with individuals in the highest negative emotionality cluster reporting the greatest local pain (p = 0.05), mechanical hyperalgesia (pressure pain thresholds; p = 0.009) and greater odds (2.21 OR) of experiencing referred pain compared to the lowest negative emotionality cluster. Conclusion Our results provide support for three latent psychological factors explaining the majority of the variance between several pain-related psychological measures, and that individuals in the high negative emotionality subgroup are at increased risk for (1) acute local muscle pain; (2) local hyperalgesia; and (3) referred pain using a standardized nociceptive input. PMID:23165778
Inferred vs Realized Patterns of Gene Flow: An Analysis of Population Structure in the Andros Island Rock Iguana

PubMed Central

Colosimo, Giuliano; Knapp, Charles R.; Wallace, Lisa E.; Welch, Mark E.

2014-01-01

Ecological data, the primary source of information on patterns and rates of migration, can be integrated with genetic data to more accurately describe the realized connectivity between geographically isolated demes. In this paper we implement this approach and discuss its implications for managing populations of the endangered Andros Island Rock Iguana, Cyclura cychlura cychlura. This iguana is endemic to Andros, a highly fragmented landmass of large islands and smaller cays. Field observations suggest that geographically isolated demes were panmictic due to high, inferred rates of gene flow. We expand on these observations using 16 polymorphic microsatellites to investigate the genetic structure and rates of gene flow from 188 Andros Iguanas collected across 23 island sites. Bayesian clustering of specimens assigned individuals to three distinct genotypic clusters. An analysis of molecular variance (AMOVA) indicates that allele frequency differences are responsible for a significant portion of the genetic variance across the three defined clusters (Fst = 0.117, p0.01). These clusters are associated with larger islands and satellite cays isolated by broad water channels with strong currents. These findings imply that broad water channels present greater obstacles to gene flow than was inferred from field observation alone. Additionally, rates of gene flow were indirectly estimated using BAYESASS 3.0. The proportion of individuals originating from within each identified cluster varied from 94.5 to 98.7%, providing further support for local isolation. Our assessment reveals a major disparity between inferred and realized gene flow. We discuss our results in a conservation perspective for species inhabiting highly fragmented landscapes. PMID:25229344
Prevention of EP Migratory Contamination in a Cluster Randomized Trial to Increase tPA Use in Stroke (The INSTINCT Trial)

PubMed Central

Weston, Victoria C.; Meurer, William J.; Frederiksen, Shirley M.; Fox, Allison K.; Scott, Phillip A.

2016-01-01

Objectives Cluster randomized trials (CRTs) are increasingly utilized to evaluate quality improvement interventions aimed at healthcare providers. In trials testing emergency department interventions, migration of emergency physicians (EPs) between hospitals is an important concern, as contamination may affect both internal and external validity. We hypothesized that geographically isolating emergency departments would prevent migratory contamination in a CRT designed to increase ED delivery of tPA in stroke (The INSTINCT Trial). Methods INSTINCT was a prospective, cluster randomized, controlled trial. 24 Michigan community hospitals were randomly selected in matched pairs for study. Contamination was defined at the cluster level, with substantial contamination defined a priori as >10% of EPs affected. Non-adherence, total crossover (contamination + non-adherence), migration distance and characteristics were determined. Results 307 emergency physicians were identified at all sites. Overall, 7 (2.3%) changed study sites. 1 moved between control sites, leaving 6 (2.0%) total crossovers. Of these, 2 (0.7%) moved from intervention to control (contamination) and 4 (1.3%) moved from control to intervention (non-adherence). Contamination was observed in 2 of 12 control sites, with 17% and 9% contamination of the total site EP workforce at follow-up, respectively. Average migration distance was 42 miles for all EPs moving in the study and 35 miles for EPs moving from intervention to control sites. Conclusion The mobile nature of emergency physicians should be considered in the design of quality improvement CRTs. Increased reporting of contamination in CRTs is encouraged to clarify thresholds and facilitate CRT design. PMID:25440230
Fragile sites, dysfunctional telomere and chromosome fusions: What is 5S rDNA role?

PubMed

Barros, Alain Victor; Wolski, Michele Andressa Vier; Nogaroto, Viviane; Almeida, Mara Cristina; Moreira-Filho, Orlando; Vicari, Marcelo Ricardo

2017-04-15

Repetitive DNA regions are known as fragile chromosomal sites which present a high flexibility and low stability. Our focus was characterize fragile sites in 5S rDNA regions. The Ancistrus sp. species shows a diploid number of 50 and an indicative Robertsonian fusion at chromosomal pair 1. Two sequences of 5S rDNA were identified: 5S.1 rDNA and 5S.2 rDNA. The first sequence gathers the necessary structures to gene expression and shows a functional secondary structure prediction. Otherwise, the 5S.2 rDNA sequence does not contain the upstream sequences that are required to expression, furthermore its structure prediction reveals a nonfunctional ribosomal RNA. The chromosomal mapping revealed several 5S.1 and 5S.2 rDNA clusters. In addition, the 5S.2 rDNA clusters were found in acrocentric and metacentric chromosomes proximal regions. The pair 1 5S.2 rDNA cluster is co-located with interstitial telomeric sites (ITS). Our results indicate that its clusters are hotspots to chromosomal breaks. During the meiotic prophase bouquet arrangement, double strand breaks (DSBs) at proximal 5S.2 rDNA of acrocentric chromosomes could lead to homologous and non-homologous repair mechanisms as Robertsonian fusions. Still, ITS sites provides chromosomal instability, resulting in telomeric recombination via TRF2 shelterin protein and a series of breakage-fusion-bridge cycles. Our proposal is that 5S rDNA derived sequences, act as chromosomal fragile sites in association with some chromosomal rearrangements of Loricariidae. Copyright © 2017 Elsevier B.V. All rights reserved.
Quantitative distribution and functional groups of intertidal macrofaunal assemblages in Fildes Peninsula, King George Island, South Shetland Islands, Southern Ocean.

PubMed

Liu, Xiaoshou; Wang, Lu; Li, Shuai; Huo, Yuanzi; He, Peimin; Zhang, Zhinan

2015-10-15

To evaluate spatial distribution pattern of intertidal macrofauna, quantitative investigation was performed in January to February, 2013 around Fildes Peninsula, King George Island, South Shetland Islands. A total of 34 species were identified, which were dominated by Mollusca, Annelida and Arthropoda. CLUSTER analysis showed that macrofaunal assemblages at sand-bottom sites belonged to one group, which was dominated by Lumbricillus sp. and Kidderia subquadrata. Macrofaunal assemblages at gravel-bottom sites were divided into three groups while Nacella concinna was the dominant species at most sites. The highest values of biomass and Shannon-Wiener diversity index were found in gravel sediment and the highest value of abundance was in sand sediment of eastern coast. In terms of functional group, detritivorous and planktophagous groups had the highest values of abundance and biomass, respectively. Correlation analysis showed that macrofaunal abundance and biomass had significant positive correlations with contents of sediment chlorophyll a, phaeophorbide and organic matter. Copyright © 2015 Elsevier Ltd. All rights reserved.
Epicardial mapping of ventricular fibrillation over the posterior descending artery and left posterior papillary muscle of the swine heart.

PubMed

Nielsen, Thomas D; Huang, Jian; Rogers, Jack M; Killingsworth, Cheryl R; Ideker, Raymond E

2009-01-01

Recent studies suggest that during ventricular fibrillation (VF) epicardial vessels may be a site of conduction block and the posterior papillary muscle (PPM) in the left ventricle (LV) may be the location of a "mother rotor." The goal of this study was to obtain evidence to support or refute these possibilities. Epicardial activation over the posterior LV and right ventricle (RV) was mapped during the first 20 s of electrically induced VF in six open-chest pigs with a 504 electrode plaque covering a 20 cm(2) area centered over the posterior descending artery (PDA). The locations of epicardial breakthrough as well as reentry clustered in time and space during VF. Spatially, reentry occurred significantly more frequently over the LV than the RV in all 48 episodes, and breakthrough clustered near the PPM (p < 0.001). Significant temporal clustering occurred in 79% of breakthrough episodes and 100% of reentry episodes. These temporal clusters occurred at different times so that there was significantly less breakthrough when reentry was present (p < 0.0001). Conduction block occurred significantly more frequently near the PDA than elsewhere. The PDA is a site of epicardial block which may contribute to VF maintenance. Epicardial breakthrough clusters near the PPM. Reentry also clusters in space but at a separate site. The fact that breakthrough and reentry cluster at different locations and at different times supports the possibility of a drifting filament at the PPM so that at times reentry is present on the surface but at other times the reentrant wavefront breaks through to the epicardium.
A Cysteine-Rich CCG Domain Contains a Novel [4Fe-4S] Cluster Binding Motif As Deduced From Studies With Subunit B of Heterodisulfide Reductase From Methanothermobacter Marburgensis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamann, N.; Mander, G.J.; Shokes, J.E.

Heterodisulfide reductase (HDR) of methanogenic archaea with its active-site [4Fe-4S] cluster catalyzes the reversible reduction of the heterodisulfide (CoM-S-S-CoB) of the methanogenic coenzyme M (CoM-SH) and coenzyme B (CoB-SH). CoM-HDR, a mechanistic-based paramagnetic intermediate generated upon half-reaction of the oxidized enzyme with CoM-SH, is a novel type of [4Fe-4S]{sup 3+} cluster with CoM-SH as a ligand. Subunit HdrB of the Methanothermobacter marburgensis HdrABC holoenzyme contains two cysteine-rich sequence motifs (CX{sub 31-39}CCX{sub 35-36}CXXC), designated as CCG domain in the Pfam database and conserved in many proteins. Here we present experimental evidence that the C-terminal CCG domain of HdrB binds this unusualmore » [4Fe-4S] cluster. HdrB was produced in Escherichia coli, and an iron-sulfur cluster was subsequently inserted by in vitro reconstitution. In the oxidized state the cluster without the substrate exhibited a rhombic EPR signal (g{sub zyx} = 2.015, 1.995, and 1.950) reminiscent of the CoM-HDR signal. {sup 57}Fe ENDOR spectroscopy revealed that this paramagnetic species is a [4Fe-4S] cluster with {sup 57}Fe hyperfine couplings very similar to that of CoM-HDR. CoM-{sup 33}SH resulted in a broadening of the EPR signal, and upon addition of CoM-SH the midpoint potential of the cluster was shifted to values observed for CoM-HDR, both indicating binding of CoM-SH to the cluster. Site-directed mutagenesis of all 12 cysteine residues in HdrB identified four cysteines of the C-terminal CCG domain as cluster ligands. Combined with the previous detection of CoM-HDR-like EPR signals in other CCG domain-containing proteins our data indicate a general role of the C-terminal CCG domain in coordination of this novel [4Fe-4S] cluster. In addition, Zn K-edge X-ray absorption spectroscopy identified an isolated Zn site with an S{sub 3}(O/N){sub 1} geometry in HdrB and the HDR holoenzyme. The N-terminal CCG domain is suggested to provide ligands to the Zn site.« less
Statistical analysis of short-term water stress conditions at Riggs Creek OzFlux tower site

NASA Astrophysics Data System (ADS)

Azmi, Mohammad; Rüdiger, Christoph; Walker, Jeffrey P.

2017-10-01

A large range of indices and proxies are available to describe the water stress conditions of an area subject to different applications, which have varying capabilities and limitations depending on the prevailing local climatic conditions and land cover. The present study uses a range of spatio-temporally high-resolution (daily and within daily) data sources to evaluate a number of drought indices (DIs) for the Riggs Creek OzFlux tower site in southeastern Australia. Therefore, the main aim of this study is to evaluate the statistical characteristics of individual DIs subject to short-term water stress conditions. In order to derive a more general and therefore representative DI, a new criterion is required to specify the statistical similarity between each pair of indices to allow determining the dominant drought types along with their representative DIs. The results show that the monitoring of water stress at this case study area can be achieved by evaluating the individual behaviour of three clusters of (i) vegetation conditions, (ii) water availability and (iii) water consumptions. This indicates that it is not necessary to assess all individual DIs one by one to derive a comprehensive and informative data set about the water stress of an area; instead, this can be achieved by analysing one of the DIs from each cluster or deriving a new combinatory index for each cluster, based on established combination methods.
DNA methylation polymorphism in flue-cured tobacco and candidate markers for tobacco mosaic virus resistance*

PubMed Central

Zhao, Jie-hong; Zhang, Ji-shun; Wang, Yi; Wang, Ren-gang; Wu, Chun; Fan, Long-jiang; Ren, Xue-liang

2011-01-01

DNA methylation plays an important role in the epigenetic regulation of gene expression during plant growth, development, and polyploidization. However, there is still no distinct evidence in tobacco regarding the distribution of the methylation pattern and whether it contributes to qualitative characteristics. We studied the levels and patterns of methylation polymorphism at CCGG sites in 48 accessions of allotetraploid flue-cured tobacco, Nicotiana tabacum, using a methylation-sensitive amplified polymorphism (MSAP) technique. The results showed that methylation existed at a high level among tobacco accessions, among which 49.3% sites were methylated and 69.9% allelic sites were polymorphic. A cluster analysis revealed distinct patterns of geography-specific groups. In addition, three polymorphic sites significantly related to tobacco mosaic virus (TMV) resistance were explored. This suggests that tobacco breeders should pay more attention to epigenetic traits. PMID:22042659
Localized Hotspots Drive Continental Geography of Abnormal Amphibians on U.S. Wildlife Refuges

PubMed Central

Reeves, Mari K.; Medley, Kimberly A.; Pinkney, Alfred E.; Holyoak, Marcel; Johnson, Pieter T. J.; Lannoo, Michael J.

2013-01-01

Amphibians with missing, misshapen, and extra limbs have garnered public and scientific attention for two decades, yet the extent of the phenomenon remains poorly understood. Despite progress in identifying the causes of abnormalities in some regions, a lack of knowledge about their broader spatial distribution and temporal dynamics has hindered efforts to understand their implications for amphibian population declines and environmental quality. To address this data gap, we conducted a nationwide, 10-year assessment of 62,947 amphibians on U.S. National Wildlife Refuges. Analysis of a core dataset of 48,081 individuals revealed that consistent with expected background frequencies, an average of 2% were abnormal, but abnormalities exhibited marked spatial variation with a maximum prevalence of 40%. Variance partitioning analysis demonstrated that factors associated with space (rather than species or year sampled) captured 97% of the variation in abnormalities, and the amount of partitioned variance decreased with increasing spatial scale (from site to refuge to region). Consistent with this, abnormalities occurred in local to regional hotspots, clustering at scales of tens to hundreds of kilometers. We detected such hotspot clusters of high-abnormality sites in the Mississippi River Valley, California, and Alaska. Abnormality frequency was more variable within than outside of hotspot clusters. This is consistent with dynamic phenomena such as disturbance or natural enemies (pathogens or predators), whereas similarity of abnormality frequencies at scales of tens to hundreds of kilometers suggests involvement of factors that are spatially consistent at a regional scale. Our characterization of the spatial and temporal variation inherent in continent-wide amphibian abnormalities demonstrates the disproportionate contribution of local factors in predicting hotspots, and the episodic nature of their occurrence. PMID:24260103
Environmetric data interpretation to assess the water quality of Maritsa River catchment.

PubMed

Papazova, Petia; Simeonova, Pavlina

2013-01-01

Maritsa River is one of the largest rivers flowing on Bulgarian territory. The quality of its waters is of substantial importance for irrigation, industrial, recreation and domestic use. Besides, part of the river is flowing on Turkish territory and the control and management of the Maritsa catchment is of mutual interst for the neighboring countires. Thus, performing interpretation and modeling of the river water quality is a major environmetric problem. Two multivariate statstical methods (Cluster analysis/CA/and Principal components analysis/PCA/) were applied for model assessment of the water quality of Maritsa River on Bulgarian territory. The study used long-term monitoring data from 21 sampling sites characterized by 8 surface water quality indicators. The application of CA to the indicators results in 3 significant clusters showing the impact of biological, anthropogenic and eutrophication sources. For further assessment of the monitoring data, PCA was implemented, which identified, again,three latent factors confirming, in principle, the clustering output. The latent factors were conditionally named "biologic", "anthropogenic" and "eutrophication" source. Their identification coinside correctly to the location of real pollution sources along the Maritsa River catchment. The linkage of the sampling sites along the river flow by CA identified four special patterns separated by specific tracers levels: biological and anthropogenic major impact for pattern 1, euthrophication major impact for pattern 2, background levels for pattern 3 and eutrophication and agricultural major impact for pattern 4. The apportionment models of the pollution determined the contribution of each one of identified pollution factors to the total concentration of each one of the water quality parameters. Thus, a better risk management of the surface water quality is achieved both on local and national level.
Evaluation of SNP Data from the Malus Infinium Array Identifies Challenges for Genetic Analysis of Complex Genomes of Polyploid Origin.

PubMed

Troggio, Michela; Surbanovski, Nada; Bianco, Luca; Moretto, Marco; Giongo, Lara; Banchi, Elisa; Viola, Roberto; Fernández, Felicdad Fernández; Costa, Fabrizio; Velasco, Riccardo; Cestaro, Alessandro; Sargent, Daniel James

2013-01-01

High throughput arrays for the simultaneous genotyping of thousands of single-nucleotide polymorphisms (SNPs) have made the rapid genetic characterisation of plant genomes and the development of saturated linkage maps a realistic prospect for many plant species of agronomic importance. However, the correct calling of SNP genotypes in divergent polyploid genomes using array technology can be problematic due to paralogy, and to divergence in probe sequences causing changes in probe binding efficiencies. An Illumina Infinium II whole-genome genotyping array was recently developed for the cultivated apple and used to develop a molecular linkage map for an apple rootstock progeny (M432), but a large proportion of segregating SNPs were not mapped in the progeny, due to unexpected genotype clustering patterns. To investigate the causes of this unexpected clustering we performed BLAST analysis of all probe sequences against the 'Golden Delicious' genome sequence and discovered evidence for paralogous annealing sites and probe sequence divergence for a high proportion of probes contained on the array. Following visual re-evaluation of the genotyping data generated for 8,788 SNPs for the M432 progeny using the array, we manually re-scored genotypes at 818 loci and mapped a further 797 markers to the M432 linkage map. The newly mapped markers included the majority of those that could not be mapped previously, as well as loci that were previously scored as monomorphic, but which segregated due to divergence leading to heterozygosity in probe annealing sites. An evaluation of the 8,788 probes in a diverse collection of Malus germplasm showed that more than half the probes returned genotype clustering patterns that were difficult or impossible to interpret reliably, highlighting implications for the use of the array in genome-wide association studies.
Testing the Prey-Trap Hypothesis at Two Wildlife Conservancies in Kenya.

PubMed

Dupuis-Desormeaux, Marc; Davidson, Zeke; Mwololo, Mary; Kisio, Edwin; Taylor, Sam; MacDonald, Suzanne E

2015-01-01

Protecting an endangered and highly poached species can conflict with providing an open and ecologically connected landscape for coexisting species. In Kenya, about half of the black rhino (Diceros bicornis) live in electrically fenced private conservancies. Purpose-built fence-gaps permit some landscape connectivity for elephant while restricting rhino from escaping. We monitored the usage patterns at these gaps by motion-triggered cameras and found high traffic volumes and predictable patterns of prey movement. The prey-trap hypothesis (PTH) proposes that predators exploit this predictable prey movement. We tested the PTH at two semi-porous reserves using two different methods: a spatial analysis and a temporal analysis. Using spatial analysis, we mapped the location of predation events with GPS and looked for concentration of kill sites near the gaps as well as conducting clustering and hot spot analysis to determine areas of statistically significant predation clustering. Using temporal analysis, we examined the time lapse between the passage of prey and predator and searched for evidence of active prey seeking and/or predator avoidance. We found no support for the PTH and conclude that the design of the fence-gaps is well suited to promoting connectivity in these types of conservancies.
Advanced multivariate analysis to assess remediation of hydrocarbons in soils.

PubMed

Lin, Deborah S; Taylor, Peter; Tibbett, Mark

2014-10-01

Accurate monitoring of degradation levels in soils is essential in order to understand and achieve complete degradation of petroleum hydrocarbons in contaminated soils. We aimed to develop the use of multivariate methods for the monitoring of biodegradation of diesel in soils and to determine if diesel contaminated soils could be remediated to a chemical composition similar to that of an uncontaminated soil. An incubation experiment was set up with three contrasting soil types. Each soil was exposed to diesel at varying stages of degradation and then analysed for key hydrocarbons throughout 161 days of incubation. Hydrocarbon distributions were analysed by Principal Coordinate Analysis and similar samples grouped by cluster analysis. Variation and differences between samples were determined using permutational multivariate analysis of variance. It was found that all soils followed trajectories approaching the chemical composition of the unpolluted soil. Some contaminated soils were no longer significantly different to that of uncontaminated soil after 161 days of incubation. The use of cluster analysis allows the assignment of a percentage chemical similarity of a diesel contaminated soil to an uncontaminated soil sample. This will aid in the monitoring of hydrocarbon contaminated sites and the establishment of potential endpoints for successful remediation.
Widespread Micropollutant Monitoring in the Hudson River Estuary Reveals Spatiotemporal Micropollutant Clusters and Their Sources.

PubMed

Carpenter, Corey M G; Helbling, Damian E

2018-06-05

The objective of this study was to identify sources of micropollutants in the Hudson River Estuary (HRE). We collected 127 grab samples at 17 sites along the HRE over 2 years and screened for up to 200 micropollutants. We quantified 168 of the micropollutants in at least one of the samples. Atrazine, gabapentin, metolachlor, and sucralose were measured in every sample. We used data-driven unsupervised methods to cluster the micropollutants on the basis of their spatiotemporal occurrence and normalized-concentration patterns. Three major clusters of micropollutants were identified: ubiquitous and mixed-use (core micropollutants), sourced from sewage treatment plant outfalls (STP micropollutants), and derived from diffuse upstream sources (diffuse micropollutants). Each of these clusters was further refined into subclusters that were linked to specific sources on the basis of relationships identified through geospatial analysis of watershed features. Evaluation of cumulative loadings of each subcluster revealed that the Mohawk River and Rondout Creek are major contributors of most core micropollutants and STP micropollutants and the upper HRE is a major contributor of diffuse micropollutants. These data provide the first comprehensive evaluation of micropollutants in the HRE and define distinct spatiotemporal micropollutant clusters that are linked to sources and conserved across surface water systems around the world.
An intermetallic Au24Ag20 superatom nanocluster stabilized by labile ligands.

PubMed

Wang, Yu; Su, Haifeng; Xu, Chaofa; Li, Gang; Gell, Lars; Lin, Shuichao; Tang, Zichao; Häkkinen, Hannu; Zheng, Nanfeng

2015-04-08

An intermetallic nanocluster containing 44 metal atoms, Au24Ag20(2-SPy)4(PhC≡C)20Cl2, was successfully synthesized and structurally characterized by single-crystal analysis and density funtional theory computations. The 44 metal atoms in the cluster are arranged as a concentric three-shell Au12@Ag20@Au12 Keplerate structure having a high symmetry. For the first time, the co-presence of three different types of anionic ligands (i.e., phenylalkynyl, 2-pyridylthiolate, and chloride) was revealed on the surface of metal nanoclusters. Similar to thiolates, alkynyls bind linearly to surface Au atoms using their σ-bonds, leading to the formation of two types of surface staple units (PhC≡C-Au-L, L = PhC≡C(-) or 2-pyridylthiolate) on the cluster. The co-presence of three different surface ligands allows the site-specific surface and functional modification of the cluster. The lability of PhC≡C(-) ligands on the cluster was demonstrated, making it possible to keep the metal core intact while removing partial surface capping. Moreover, it was found that ligand exchange on the cluster occurs easily to offer various derivatives with the same metal core but different surface functionality and thus different solubility.
Dependence of Cumulus Anvil Radiative Properties on Environmental Conditions in the Tropical West Pacific

NASA Technical Reports Server (NTRS)

Ye, B.; DelGenio, A. D.

1999-01-01

Areally extensive, optically thick anvil clouds associated with mesoscale convective clusters dominate the shortwave cloud forcing in the tropics and provide longwave forcing comparable to that of thin cirrus. Changes in the cover and optical thickness of tropical anvils as climate warms can regulate the sign of cloud feedback. As a prelude to the study of MMCR data from the ARM TWP sites, we analyze ISCCP-derived radiative characteristics of anvils observed in the tropical west Pacific during the TOGA-COARE IOP. Anvils with radius greater than 100 km were identified and tracked from inception to decay using the Machado-Rossow algorithm. Corresponding environmental conditions just prior to the start of the convectove event were diagnosed using the Lin-Johnson objective analysis product. Small clusters (100-200 km radius) are observed to have a broad range of optical thicknesses (10-50), while intermediate optical thickness clusters are observed to range in size from 100 km to almost 1000 km. Large-size clusters appear to be favored by strong pre-storm large scale upward motion throughout the troposphere, moist low-to-midlevel relative humidities, environments with slightly higher CAPE than those for smaller clusters, and strong front-to-rear flow. Optically thick anvils are favored in situations of strong low-level moisture convergence and strong upper-level shear.
Anthropogenic influence on surface water quality of the Nhue and Day sub-river systems in Vietnam.

PubMed

Hanh, Pham Thi Minh; Sthiannopkao, Suthipong; Kim, Kyoung-Woong; Ba, Dang The; Hung, Nguyen Quang

2010-06-01

In order to investigate the temporal and spatial variations of 14 physical and chemical surface water parameters in the Nhue and Day sub-river systems of Vietnam, surface water samples were taken from 43 sampling sites during the dry and rainy seasons in 2007. The results were statistically examined by Mann-Whitney U-test and hierarchical cluster analysis. The results show that water quality of the Day River was significantly improved during the rainy season while this was not the case of the Nhue River. However, the river water did not meet the Vietnamese surface water quality standards for dissolved oxygen (DO), biological oxygen demand (BOD(5)), chemical oxygen demand (COD), nutrients, total coliform, and fecal coliform. This implies that the health of local communities using untreated river water for drinking purposes as well as irrigation of vegetables may be at risk. Forty-three sampling sites were grouped into four main clusters on the basis of water quality characteristics with particular reference to geographic location and land use and revealed the contamination levels from anthropogenic sources.
Characterization of Archaeal Community in Contaminated and Uncontaminated Surface Stream Sediments

PubMed Central

Porat, Iris; Vishnivetskaya, Tatiana A.; Mosher, Jennifer J.; Brandt, Craig C.; Yang, Zamin K.; Brooks, Scott C.; Liang, Liyuan; Drake, Meghan M.; Podar, Mircea; Brown, Steven D.

2010-01-01

Archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of Oak Ridge, TN, USA. The distribution of the Archaea was determined by pyrosequencing analysis of the V4 region of 16S rRNA amplified from 12 streambed surface sediments. Crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from Euryarchaeota. Phylogenetic analysis further classified the Crenarchaeota as a Freshwater Group, Miscellaneous Crenarchaeota group, Group I3, Rice Cluster VI and IV, Marine Group I and Marine Benthic Group B; and the Euryarchaeota into Methanomicrobiales, Methanosarcinales, Methanobacteriales, Rice Cluster III, Marine Benthic Group D, Deep Sea Hydrothermal Vent Euryarchaeota 1 and Eury 5. All groups were previously described. Both hydrogen- and acetate-dependent methanogens were found in all samples. Most of the groups (with 60% of the sequences) described in this study were not similar to any cultivated isolates, making it difficult to discern their function in the freshwater microbial community. A significant decrease in the number of sequences, as well as in the diversity of archaeal communities was found in the contaminated sites. The Marine Group I, including the ammonia oxidizer Nitrosopumilus maritimus, was the dominant group in both mercury and uranium/nitrate-contaminated sites. The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle. Electronic supplementary material The online version of this article (doi:10.1007/s00248-010-9734-2) contains supplementary material, which is available to authorized users. PMID:20725722
[Use of macroalgae for the evaluation of organic pollution in the Preto river, northwest of São Paulo State].

PubMed

Necchi Júnior, O; Branco, H Z; Dip, M R

1994-01-01

The Preto River, located in the northwest of São Paulo State, receives a total wastewater load of 15.150 kg DBO day-1, from which 13.685 kg DBO day-1 (90.5%) corresponds to domestic sewage, and the city of São José do Rio Preto contributes with 12.400 kg DBO day-1 (90% of domestic sewage). During the period from August 1990 through January 1991, monthly sampling was carried out to evaluate the use of macroalgae as bioindicator of organic pollution. Five sampling sites were established along the main river and the following variables were analised: temperature, conductance, turbidity, dissolved oxygen, BOD, COD, total and fecal coliforms, and composition and abundance of macroalgal communities. Data were submitted to analysis of variance, correlation coefficient, cluster analysis (four different approaches) and converted to biological indices (species deficit, relative pollution, saprobity, diversity and uniformity indices). A wide range in water quality was found (particularly for conductance, oxygen, BOD and COD) among the sampling sites, which were classified into three groups (polluted, moderately polluted and unpolluted/weakly polluted). As regards the occurrence and abundance of macroalgae the Rhodophyta were found only in unpolluted or weakly polluted sites, whereas Cyanophyta occurred mostly under high pollution load; the Chlorophyta species were observed under a wide range of conditions. Among the biological indices, saprobity was the most sensitive and correlated to all water variables and the other indices. Cluster analyses showed that the composition of macroalgal communities was consistent with the levels of organic pollution in the Preto River.

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