Design of the aerosol sampling manifold for the Southern Great Plains site

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

Leifer, R.; Knuth, R.H.; Guggenheim, S.F.

1995-04-01

To meet the needs of the ARM program, the Environmental Measurements Laboratory (EML) has the responsibility to establish a surface aerosol measurements program at the Southern Great Plains (SGP) site in Lamont, OK. At the present time, EML has scheduled installation of five instruments at SGP: a single wavelength nephelometer, an optical particle counter (OPC), a condensation particle counter (CPC), an optical absorption monitor (OAM), and an ozone monitor. ARM`s operating protocol requires that all the observational data be placed online and sent to the main computer facility in real time. EML currently maintains a computer file containing back trajectorymore » (BT) analyses for the SGP site. These trajectories are used to characterize air mass types as they pass over the site. EML is continuing to calculate and store the resulting trajectory analyses for future use by the ARM science team.« less

Application of Microtremor Horizontal-to-Vertical Spectral Ratio (MHVSR) Analysis for Site Characterization: State of the Art

NASA Astrophysics Data System (ADS)

Molnar, S.; Cassidy, J. F.; Castellaro, S.; Cornou, C.; Crow, H.; Hunter, J. A.; Matsushima, S.; Sánchez-Sesma, F. J.; Yong, A.

2018-03-01

Nakamura (Q Rep Railway Tech Res Inst 30:25-33, 1989) popularized the application of the horizontal-to-vertical spectral ratio (HVSR) analysis of microtremor (seismic noise or ambient vibration) recordings to estimate the predominant frequency and amplification factor of earthquake shaking. During the following quarter century, popularity in the microtremor HVSR (MHVSR) method grew; studies have verified the stability of a site's MHVSR response over time and validated the MHVSR response with that of earthquake HVSR response. Today, MHVSR analysis is a popular reconnaissance tool used worldwide for seismic microzonation and earthquake site characterization in numerous regions, specifically, in the mapping of site period or fundamental frequency and inverted for shear-wave velocity depth profiles, respectively. However, the ubiquity of MHVSR analysis is predominantly a consequence of its ease in application rather than our full understanding of its theory. We present the state of the art in MHVSR analyses in terms of the development of its theoretical basis, current state of practice, and we comment on its future for applications in earthquake site characterization.

Application of Microtremor Horizontal-to-Vertical Spectral Ratio (MHVSR) Analysis for Site Characterization: State of the Art

NASA Astrophysics Data System (ADS)

Molnar, S.; Cassidy, J. F.; Castellaro, S.; Cornou, C.; Crow, H.; Hunter, J. A.; Matsushima, S.; Sánchez-Sesma, F. J.; Yong, A.

2018-07-01

Nakamura (Q Rep Railway Tech Res Inst 30:25-33, 1989) popularized the application of the horizontal-to-vertical spectral ratio (HVSR) analysis of microtremor (seismic noise or ambient vibration) recordings to estimate the predominant frequency and amplification factor of earthquake shaking. During the following quarter century, popularity in the microtremor HVSR (MHVSR) method grew; studies have verified the stability of a site's MHVSR response over time and validated the MHVSR response with that of earthquake HVSR response. Today, MHVSR analysis is a popular reconnaissance tool used worldwide for seismic microzonation and earthquake site characterization in numerous regions, specifically, in the mapping of site period or fundamental frequency and inverted for shear-wave velocity depth profiles, respectively. However, the ubiquity of MHVSR analysis is predominantly a consequence of its ease in application rather than our full understanding of its theory. We present the state of the art in MHVSR analyses in terms of the development of its theoretical basis, current state of practice, and we comment on its future for applications in earthquake site characterization.

An HIV/AIDS Knowledge Scale for Adolescents: Item Response Theory Analyses Based on Data from a Study in South Africa and Tanzania

ERIC Educational Resources Information Center

Aaro, Leif E.; Breivik, Kyrre; Klepp, Knut-Inge; Kaaya, Sylvia; Onya, Hans E.; Wubs, Annegreet; Helleve, Arnfinn; Flisher, Alan J.

2011-01-01

A 14-item human immunodeficiency virus/acquired immunodeficiency syndrome knowledge scale was used among school students in 80 schools in 3 sites in Sub-Saharan Africa (Cape Town and Mankweng, South Africa, and Dar es Salaam, Tanzania). For each item, an incorrect or don't know response was coded as 0 and correct response as 1. Exploratory factor…

Evaluating Why and How the Teen Outreach Program Works: Years 3-5 of the Teen Outreach National Replication (1986/87-1988/89).

ERIC Educational Resources Information Center

Allen, Joseph P.; Philliber, Susan

An evaluative study was done of the Teen Outreach Program, a national, multi-site effort to reduce teenage pregnancy, school failure, and dropout. The study sought to identify the critical "active ingredients" of the program responsible for its success. The study was based on analyses of data collected at 114 different sites nationally,…

An assessment of non-volant terrestrial vertebrates response to wind farms--a study of small mammals.

PubMed

Łopucki, Rafał; Mróz, Iwona

2016-02-01

The majority of studies on the effects of wind energy development on wildlife have been focused on birds and bats, whereas knowledge of the response of terrestrial, non-flying vertebrates is very scarce. In this paper, the impact of three functioning wind farms on terrestrial small mammal communities (rodents and shrews) and the population parameters of the most abundant species were studied. The study was carried out in southeastern Poland within the foothills of the Outer Western Carpathians. Small mammals were captured at 12 sites around wind turbines and at 12 control sites. In total, from 1200 trap-days, 885 individuals of 14 studied mammal species were captured. There was no difference in the characteristics of communities of small mammals near wind turbines and within control sites; i.e. these types of sites were inhabited by a similar number of species of similar abundance, similar species composition, species diversity (H' index) and species evenness (J') (Pielou's index). For the two species with the highest proportion in the communities (Apodemus agrarius and Microtus arvalis), the parameters of their populations (mean body mass, sex ratio, the proportion of adult individuals and the proportion of reproductive female) were analysed. In both species, none of the analysed parameters differed significantly between sites in the vicinity of turbines and control sites. For future studies on the impact of wind turbines on small terrestrial mammals in different geographical areas and different species communities, we recommend the method of paired 'turbine-control sites' as appropriate for animal species with pronounced fluctuations in population numbers.

Relations of alpine plant communities across environmental gradients: Multilevel versus multiscale analyses

USGS Publications Warehouse

Malanson, George P.; Zimmerman, Dale L.; Kinney, Mitch; Fagre, Daniel B.

2017-01-01

Alpine plant communities vary, and their environmental covariates could influence their response to climate change. A single multilevel model of how alpine plant community composition is determined by hierarchical relations is compared to a separate examination of those relations at different scales. Nonmetric multidimensional scaling of species cover for plots in four regions across the Rocky Mountains created dependent variables. Climate variables are derived for the four regions from interpolated data. Plot environmental variables are measured directly and the presence of thirty-seven site characteristics is recorded and used to create additional independent variables. Multilevel and best subsets regressions are used to determine the strength of the hypothesized relations. The ordinations indicate structure in the assembly of plant communities. The multilevel analyses, although revealing significant relations, provide little explanation; of the site variables, those related to site microclimate are most important. In multiscale analyses (whole and separate regions), different variables are better explanations within the different regions. This result indicates weak environmental niche control of community composition. The weak relations of the structure in the patterns of species association to the environment indicates that either alpine vegetation represents a case of the neutral theory of biogeography being a valid explanation or that it represents disequilibrium conditions. The implications of neutral theory and disequilibrium explanations are similar: Response to climate change will be difficult to quantify above equilibrium background turnover.

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.

PubMed

Chen, Lin-xing; Hu, Min; Huang, Li-nan; Hua, Zheng-shuang; Kuang, Jia-liang; Li, Sheng-jin; Shu, Wen-sheng

2015-07-01

The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

Soil functional diversity analysis of a bauxite-mined restoration chronosequence.

PubMed

Lewis, Dawn E; White, John R; Wafula, Denis; Athar, Rana; Dickerson, Tamar; Williams, Henry N; Chauhan, Ashvini

2010-05-01

Soil microorganisms are sensitive to environmental perturbations such that changes in microbial community structure and function can provide early signs of anthropogenic disturbances and even predict restoration success. We evaluated the bacterial functional diversity of un-mined and three chronosequence sites at various stages of rehabilitation (0, 10, and 20 years old) located in the Mocho Mountains of Jamaica. Samples were collected during the dry and wet seasons and analyzed for metal concentrations, microbial biomass carbon, bacterial numbers, and functional responses of soil microbiota using community-level physiological profile (CLPP) assays. Regardless of the season, un-mined soils consisted of higher microbial biomass and numbers than any of the rehabilitated sites. Additionally, the number and rate of substrates utilized and substrate evenness (the distribution of color development between the substrates) were significantly greater in the un-mined soils with carbohydrates being preferentially utilized than amino acids, polymers, carboxylic acids, and esters. To some extent, functional responses varied with the seasons but the least physiological activity was shown by the site rehabilitated in 1987 indicating long-term perturbation to this ecosystem. Small subunit ribosomal DNA (SSUrDNA)-denaturing gradient-gel electrophoresis analyses on the microbiota collected from the most preferred CLPP substrates followed by taxonomic analyses showed Proteobacteria, specifically the gamma-proteobacteria, as the most functionally active phyla, indicating a propensity of this phyla to out-compete other groups under the prevailing conditions. Additionally, multivariate statistical analyses, Shannon's diversity, and evenness indices, principal component analysis, biplot and un-weighted-pair-group method with arithmetic averages dendrograms further confirmed that un-mined sites were distinctly different from the rehabilitated soils.

Study of obligations defined in agreements between parties involved in clinical trials of medicinal products in Bulgaria.

PubMed

N Getov, Ilko; Gocheva-Hristova, Tanya; Lebanova, Hristina V; Grigorov, Evgeni E

2012-08-01

To analyse and assess the legislative and contractual obligations of the parties involved in the conduct of clinical trials, with identification of the needs for comprehensive contractual regulation of their rights and responsibilities. This survey has been carried out by means of review, analysis of comprehensiveness, comparative legislative analysis and assessment of compliance with the legislation of sample of investigator and site agreements governing the process of conducting clinical trials. The survey comprises analyses of contractual relations between the sponsor of the study and the investigator, and between the sponsor of the study and the trial site, respectively, relevant to clinical trials which are actually conducted in Bulgaria at the time of and following the survey. Comparative method based on pre-defined structured indices was employed to outline the major variances in the volume of responsibilities and obligations of the said parties to the clinical trial, as regulated by the investigator and site agreements. The analysis of comprehensiveness showed evident omissions in the regulation of relations and interactions between the parties to the agreements. The detailed contractual regulation providing for the statutory obligations and responsibilities of the parties involved in the conduct of clinical trials is a good guarantee for proper understanding of the obligations of each party and for compliance with their relevant responsibilities in view of protecting the rights of the participants in the clinical trials - patients or healthy volunteers.

Evaluating Changes in Distributions of Summer Stream Temperature following Forest Harvest

NASA Astrophysics Data System (ADS)

Johnson, S. L.; Reiter, M.; Jones, J.

2016-12-01

Stream temperature heat budgets are influenced by numerous processes; changes in incoming radiation have been shown to be a major driver of increased stream temperatures. Maximum daily temperature is a commonly used metric for evaluating stream temperature responses to land use. However, single metrics are not able to fully represent the magnitude and duration of temperatures experienced by instream biota. Analyses that make use of all the data: a) more accurately characterize shifts in summer stream temperature regimes, b) quantify potential exposure to critical and non-critical temperatures, and c) help researchers and managers to better understand stream temperature responses to manipulation of streamside and watershed vegetation. Here we examine the distributions of summer stream temperatures before and after forest harvest in the Trask River Watershed Study, in northwestern Oregon. We studied 15 small streams for 10 years; half of the sites had their catchments clearcut harvested in 2012. Four sites had no buffers, with some leave trees, and three sites had 25 ft buffers on both sides. Temperatures were measured during at 30min intervals. Even though these streams are generally cold, we observed high spatial and temporal variation among sites and years, with some sites having normally distributed temperatures, while others showed skewed distributions and long tails. Forest cover, aspect or elevation were not good predictors of temperature distributions pre-harvest. Preliminary analyses using travel time of the stream water suggest that sites with hyporheic flows had narrower distributions of temperatures. After harvest, sites without buffers showed the greatest shift in distributions of temperatures and widest temperature ranges, while sites with narrow buffers showed little change. We are exploring the implications of shifts in temperature distributions before and after harvest against the known thermal tolerances for the dominant resident species (Ascaphus truei; tailed frog tadpoles) in these headwater streams. Rarely in forested mountain landscapes do stream temperatures exceed lethal thresholds for cold water biota; with these analyses, we are quantifying chronic exposure, which could subsequently result in shifts in phenology or community structure.

Identification of site frequencies from building records

USGS Publications Warehouse

Celebi, M.

2003-01-01

A simple procedure to identify site frequencies using earthquake response records from roofs and basements of buildings is presented. For this purpose, data from five different buildings are analyzed using only spectral analyses techniques. Additional data such as free-field records in close proximity to the buildings and site characterization data are also used to estimate site frequencies and thereby to provide convincing evidence and confirmation of the site frequencies inferred from the building records. Furthermore, simple code-formula is used to calculate site frequencies and compare them with the identified site frequencies from records. Results show that the simple procedure is effective in identification of site frequencies and provides relatively reliable estimates of site frequencies when compared with other methods. Therefore the simple procedure for estimating site frequencies using earthquake records can be useful in adding to the database of site frequencies. Such databases can be used to better estimate site frequencies of those sites with similar geological structures.

Integration of Genome-Wide Computation DRE Search, AhR ChIP-chip and Gene Expression Analyses of TCDD-Elicited Responses in the Mouse Liver

PubMed Central

2011-01-01

Background The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor (TF) that mediates responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Integration of TCDD-induced genome-wide AhR enrichment, differential gene expression and computational dioxin response element (DRE) analyses further elucidate the hepatic AhR regulatory network. Results Global ChIP-chip and gene expression analyses were performed on hepatic tissue from immature ovariectomized mice orally gavaged with 30 μg/kg TCDD. ChIP-chip analysis identified 14,446 and 974 AhR enriched regions (1% false discovery rate) at 2 and 24 hrs, respectively. Enrichment density was greatest in the proximal promoter, and more specifically, within ± 1.5 kb of a transcriptional start site (TSS). AhR enrichment also occurred distal to a TSS (e.g. intergenic DNA and 3' UTR), extending the potential gene expression regulatory roles of the AhR. Although TF binding site analyses identified over-represented DRE sequences within enriched regions, approximately 50% of all AhR enriched regions lacked a DRE core (5'-GCGTG-3'). Microarray analysis identified 1,896 number of TCDD-responsive genes (|fold change| ≥ 1.5, P1(t) > 0.999). Integrating this gene expression data with our ChIP-chip and DRE analyses only identified 625 differentially expressed genes that involved an AhR interaction at a DRE. Functional annotation analysis of differentially regulated genes associated with AhR enrichment identified overrepresented processes related to fatty acid and lipid metabolism and transport, and xenobiotic metabolism, which are consistent with TCDD-elicited steatosis in the mouse liver. Conclusions Details of the AhR regulatory network have been expanded to include AhR-DNA interactions within intragenic and intergenic genomic regions. Moreover, the AhR can interact with DNA independent of a DRE core suggesting there are alternative mechanisms of AhR-mediated gene regulation. PMID:21762485

Effects of physical exercise training in DNA damage and repair activity in humans with different genetic polymorphisms of hOGG1 (Ser326Cys).

PubMed

Soares, Jorge Pinto; Silva, Ana Inês; Silva, Amélia M; Almeida, Vanessa; Teixeira, João Paulo; Matos, Manuela; Gaivão, Isabel; Mota, Maria Paula

2015-12-01

The main purpose of this pilot study was to investigate the possible influence of genetic polymorphisms of the hOGG1 (Ser326Cys) gene in DNA damage and repair activity by 8-oxoguanine DNA glycosylase 1 (OGG1 enzyme) in response to 16 weeks of combined physical exercise training. Thirty-two healthy Caucasian men (40-74 years old) were enrolled in this study. All the subjects were submitted to a training of 16 weeks of combined physical exercise. The subjects with Ser/Ser genotype were considered as wild-type group (WTG), and Ser/Cys and Cys/Cys genotype were analysed together as mutant group (MG). We used comet assay in conjunction with formamidopyrimidine DNA glycoslyase (FPG) to analyse both strand breaks and FPG-sensitive sites. DNA repair activity were also analysed with the comet assay technique. Our results showed no differences between DNA damage (both strand breaks and FPG-sensitive sites) and repair activity (OGG1) between genotype groups (in the pre-training condition). Regarding the possible influence of genotype in the response to 16 weeks of physical exercise training, the results revealed a decrease in DNA strand breaks in both groups, a decrease in FPG-sensitive sites and an increase in total antioxidant capacity in the WTG, but no changes were found in MG. No significant changes in DNA repair activity was observed in both genotype groups with physical exercise training. This preliminary study suggests the possibility of different responses in DNA damage to the physical exercise training, considering the hOGG1 Ser326Cys polymorphism. Copyright © 2015 John Wiley & Sons, Ltd.

Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease

PubMed Central

Romero-Garmendia, Irati; Jauregi-Miguel, Amaia; Plaza-Izurieta, Leticia; Cros, Marie-Pierre; Legarda, Maria; Irastorza, Iñaki; Herceg, Zdenko; Fernandez-Jimenez, Nora

2018-01-01

The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD). Differential co-expression modules were identified in the acute and chronic responses to gliadin using expression data from a previous microarray study in duodenal biopsies. Transcription factor binding site (TFBS) and Gene Ontology (GO) annotation enrichment analyses were performed in differentially co-expressed genes (DCGs) and selection of candidate regulators was performed. Expression of candidates was measured in clinical samples and the activation of the TFs was further characterized in C2BBe1 cells upon gliadin challenge. Enrichment analyses of the DCGs identified 10 TFs and five were selected for further investigation. Expression changes related to active CD were detected in four TFs, as well as in several of their in silico predicted targets. The activation of TFs was further characterized in C2BBe1 cells upon gliadin challenge, and an increase in nuclear translocation of CAMP Responsive Element Binding Protein 1 (CREB1) and IFN regulatory factor-1 (IRF1) in response to gliadin was observed. Using transcriptome-wide co-expression analyses we are able to propose novel genes involved in CD pathogenesis that respond upon gliadin stimulation, also in non-celiac models. PMID:29748492

Transcription Factor Binding Site Enrichment Analysis in Co-Expression Modules in Celiac Disease.

PubMed

Romero-Garmendia, Irati; Garcia-Etxebarria, Koldo; Hernandez-Vargas, Hector; Santin, Izortze; Jauregi-Miguel, Amaia; Plaza-Izurieta, Leticia; Cros, Marie-Pierre; Legarda, Maria; Irastorza, Iñaki; Herceg, Zdenko; Fernandez-Jimenez, Nora; Bilbao, Jose Ramon

2018-05-10

The aim of this study was to construct celiac co-expression patterns at a whole genome level and to identify transcription factors (TFs) that could drive the gliadin-related changes in coordination of gene expression observed in celiac disease (CD). Differential co-expression modules were identified in the acute and chronic responses to gliadin using expression data from a previous microarray study in duodenal biopsies. Transcription factor binding site (TFBS) and Gene Ontology (GO) annotation enrichment analyses were performed in differentially co-expressed genes (DCGs) and selection of candidate regulators was performed. Expression of candidates was measured in clinical samples and the activation of the TFs was further characterized in C2BBe1 cells upon gliadin challenge. Enrichment analyses of the DCGs identified 10 TFs and five were selected for further investigation. Expression changes related to active CD were detected in four TFs, as well as in several of their in silico predicted targets. The activation of TFs was further characterized in C2BBe1 cells upon gliadin challenge, and an increase in nuclear translocation of CAMP Responsive Element Binding Protein 1 (CREB1) and IFN regulatory factor-1 (IRF1) in response to gliadin was observed. Using transcriptome-wide co-expression analyses we are able to propose novel genes involved in CD pathogenesis that respond upon gliadin stimulation, also in non-celiac models.

Application of microtremor horizontal-to-vertical spectral ratio (MHVSR) analysis for site characterization: State of the art

USGS Publications Warehouse

Molnar, S.; Cassidy, J. F.; Castellaro, S.; Cornou, C.; Crow, H.; Hunter, J. A.; Matsushima, S.; Sanchez-Sesma, F. J.; Yong, Alan

2018-01-01

Nakamura (Q Rep Railway Tech Res Inst 30:25–33, 1989) popularized the application of the horizontal-to-vertical spectral ratio (HVSR) analysis of microtremor (seismic noise or ambient vibration) recordings to estimate the predominant frequency and amplification factor of earthquake shaking. During the following quarter century, popularity in the microtremor HVSR (MHVSR) method grew; studies have verified the stability of a site’s MHVSR response over time and validated the MHVSR response with that of earthquake HVSR response. Today, MHVSR analysis is a popular reconnaissance tool used worldwide for seismic microzonation and earthquake site characterization in numerous regions, specifically, in the mapping of site period or fundamental frequency and inverted for shear-wave velocity depth profiles, respectively. However, the ubiquity of MHVSR analysis is predominantly a consequence of its ease in application rather than our full understanding of its theory. We present the state of the art in MHVSR analyses in terms of the development of its theoretical basis, current state of practice, and we comment on its future for applications in earthquake site characterization.

Relations between rainfall–runoff-induced erosion and aeolian deposition at archaeological sites in a semi-arid dam-controlled river corridor

USGS Publications Warehouse

Collins, Brian D.; Bedford, David; Corbett, Skye C.; Fairley, Helen C.; Cronkite-Ratcliff, Collin

2016-01-01

Process dynamics in fluvial-based dryland environments are highly complex with fluvial, aeolian, and alluvial processes all contributing to landscape change. When anthropogenic activities such as dam-building affect fluvial processes, the complexity in local response can be further increased by flood- and sediment-limiting flows. Understanding these complexities is key to predicting landscape behavior in drylands and has important scientific and management implications, including for studies related to paleoclimatology, landscape ecology evolution, and archaeological site context and preservation. Here we use multi-temporal LiDAR surveys, local weather data, and geomorphological observations to identify trends in site change throughout the 446-km-long semi-arid Colorado River corridor in Grand Canyon, Arizona, USA, where archaeological site degradation related to the effects of upstream dam operation is a concern. Using several site case studies, we show the range of landscape responses that might be expected from concomitant occurrence of dam-controlled fluvial sand bar deposition, aeolian sand transport, and rainfall-induced erosion. Empirical rainfall-erosion threshold analyses coupled with a numerical rainfall–runoff–soil erosion model indicate that infiltration-excess overland flow and gullying govern large-scale (centimeter- to decimeter-scale) landscape changes, but that aeolian deposition can in some cases mitigate gully erosion. Whereas threshold analyses identify the normalized rainfall intensity (defined as the ratio of rainfall intensity to hydraulic conductivity) as the primary factor governing hydrologic-driven erosion, assessment of false positives and false negatives in the dataset highlight topographic slope as the next most important parameter governing site response. Analysis of 4+ years of high resolution (four-minute) weather data and 75+ years of low resolution (daily) climate records indicates that dryland erosion is dependent on short-term, storm-driven rainfall intensity rather than cumulative rainfall, and that erosion can occur outside of wet seasons and even wet years. These results can apply to other similar semi-arid landscapes where process complexity may not be fully understood.

Histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and alters HagB-induced chemokine responses

NASA Astrophysics Data System (ADS)

Borgwardt, Derek S.; Martin, Aaron D.; van Hemert, Jonathan R.; Yang, Jianyi; Fischer, Carol L.; Recker, Erica N.; Nair, Prashant R.; Vidva, Robinson; Chandrashekaraiah, Shwetha; Progulske-Fox, Ann; Drake, David; Cavanaugh, Joseph E.; Vali, Shireen; Zhang, Yang; Brogden, Kim A.

2014-01-01

Histatins are human salivary gland peptides with anti-microbial and anti-inflammatory activities. In this study, we hypothesized that histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and attenuates HagB-induced chemokine responses in human myeloid dendritic cells. Histatin 5 bound to immobilized HagB in a surface plasmon resonance (SPR) spectroscopy-based biosensor system. SPR spectroscopy kinetic and equilibrium analyses, protein microarray studies, and I-TASSER structural modeling studies all demonstrated two histatin 5 binding sites on HagB. One site had a stronger affinity with a KD1 of 1.9 μM and one site had a weaker affinity with a KD2 of 60.0 μM. Binding has biological implications and predictive modeling studies and exposure of dendritic cells both demonstrated that 20.0 μM histatin 5 attenuated (p < 0.05) 0.02 μM HagB-induced CCL3/MIP-1α, CCL4/MIP-1β, and TNFα responses. Thus histatin 5 is capable of attenuating chemokine responses, which may help control oral inflammation.

Neuroplastic changes in the sensorimotor cortex associated with orthodontic tooth movement in rats.

PubMed

Sood, Mandeep; Lee, Jye-Chang; Avivi-Arber, Limor; Bhatt, Poolak; Sessle, Barry J

2015-07-01

Orthodontic tooth movement (OTM) causes transient pain and changes in the dental occlusion that may lead to altered somatosensory inputs and patterns of mastication. This study used intracortical microstimulation (ICMS) and electromyographic (EMG) recordings to test whether neuroplastic changes occur in the ICMS-defined motor representations of left and right anterior digastric (LAD, RAD), masseter, buccinator, and genioglossus (GG) muscles within the rat's face primary motor cortex (face-M1) and adjacent face primary somatosensory cortex (face-S1) during OTM. Analyses included any changes in the number of ICMS sites representing these muscles and in the onset latencies of ICMS-evoked responses in the muscles. Sprague-Dawley rats were divided into experimental (E), sham (S), and naive (N) groups; OTM was induced in the E group. Statistical analyses involved a mixed model repeated-measures analysis of variance (MMRM ANOVA). OTM resulted in significant neuroplastic changes in the number of positive sites in the E group for LAD, RAD, and GG muscles in face-M1 and face-S1 at days 1, 7, and 28 of continuous orthodontic force application, and in the number of sites in face-M1 from which ICMS could simultaneously evoke EMG responses in different combinations of LAD, RAD, and GG muscles. However, the onset latencies of ICMS-evoked responses were not significantly different between groups or between face-M1 and face-S1. The neuroplastic changes documented in this study may reflect adaptive sensorimotor changes in response to the altered environment in the oral cavity induced by OTM. © 2015 Wiley Periodicals, Inc.

Hyalella azteca Responses to Coldwater River Backwater Sediments in Mississippi, USA

USDA-ARS?s Scientific Manuscript database

Sediment from three Coldwater River, Mississippi backwaters was examined using 28 d Hyalella azteca bioassays and chemical analyses for 33 pesticides, 7 metals and 7 PCBs. Hydrologic connectivity between the main river channel and backwater varied widely among the three sites. Mortality occurred i...

Paleolimnology of Lake Tanganyika, East Africa, over the past 100 k yr

USGS Publications Warehouse

Scholz, C.A.; King, J.W.; Ellis, G.S.; Swart, Peter K.; Stager, J.C.; Colman, Steven M.

2003-01-01

New sediment core data from a unique slow-sedimentation rate site in Lake Tanganyika contain a much longer and continuous record of limnological response to climate change than have been previously observed in equatorial regions of central Africa. The new core site was first located through an extensive seismic reflection survey over the Kavala Island Ridge (KIR), a sedimented basement high that separates the Kigoma and Kalemie Basins in Lake Tanganyika. Proxy analyses of paleoclimate response carried out on core T97-52V include paleomagnetic and index properties, TOC and isotopic analyses of organic carbon, and diatom and biogenic silica analyses. A robust age model based on 11 radiocarbon (AMS) dates indicates a linear, continuous sedimentation rate nearly an order of magnitude slower here compared to other core sites around the lake. This age model indicates continuous sedimentation over the past 79 k yr, and a basal age in excess of 100 k yr. The results of the proxy analyses for the past ??? 20 k yr are comparable to previous studies focused on that interval in Lake Tanganyika, and show that the lake was about 350 m lower than present at the Last Glacial Maximum (LGM). Repetitive peaks in TOC and corresponding drops in ??13C over the past 79 k yr indicate periods of high productivity and mixing above the T97-52V core site, probably due to cooler and perhaps windier conditions. From ??? 80 through ??? 58 k yr the ??13C values are relatively negative (-26 to -28???) suggesting predominance of algal contributions to bottom sediments at this site during this time. Following this interval there is a shift to higher values of ??13C, indicating a possible shift to C-4 pathway-dominated grassland-type vegetation in the catchment, and indicating cooler, dryer conditions from ??? 55 k yr through the LGM. Two seismic sequence boundaries are observed at shallow stratigraphic levels in the seismic reflection data, and the upper boundary correlates to a major discontinuity near the base of T97-52V. We interpret these discontinuities to reflect major, prolonged drops in lake level below the core site (393 m), with the lower boundary correlating to marine oxygen isotope Stage 6. This suggests that the previous glacial period was considerably cooler and more arid in the equatorial tropics than was the last glacial period.

Characterizing grazing disturbance in semiarid ecosystems across broad scales, using diverse indices

USGS Publications Warehouse

Beever, E.A.; Tausch, R.J.; Brussard, P.F.

2003-01-01

Although management and conservation strategies continue to move toward broader spatial scales and consideration of many taxonomic groups simultaneously, researchers have struggled to characterize responses to disturbance at these scales. Most studies of disturbance by feral grazers investigate effects on only one or two ecosystem elements across small spatial scales, limiting their applicability to ecosystem-level management. To address this inadequacy, in 1997 and 1998 we examined disturbance created by feral horses (Equus caballus) in nine mountain ranges of the western Great Basin, USA, using plants, small mammals, ants, and soil compaction as indicators. Nine horse-occupied and 10 horse-removed sites were stratified into high- and low-elevation groups, and all sites at each elevation had similar vegetation type, aspect, slope gradient, and recent (≥15-yr) fire and livestock-grazing histories. Using reciprocal averaging and TWINSPAN analyses, we compared relationships among sites using five data sets: abiotic variables, percent cover by plant species, an index of abundance by plant species, 10 disturbance-sensitive response variables, and grass and shrub species considered “key” indicators by land managers. Although reciprocal averaging and TWINSPAN analyses of percent cover, abiotic variables, and key species suggested relationships between sites influenced largely by biogeography (i.e., mountain range), disturbance-sensitive variables clearly segregated horse-occupied and horse-removed sites. These analyses suggest that the influence of feral horses on many Great Basin ecosystem attributes is not being detected by monitoring only palatable plant species. We recommend development of an expanded monitoring strategy based not only on established vegetation measurements investigating forage consumption, but also including disturbance-sensitive variables (e.g., soil surface hardness, abundance of ant mounds) that more completely reflect the suite of effects that a large-bodied grazer may impose on mountain ecosystems, independent of vegetation differences. By providing a broader-based mechanism for detection of adverse effects, this strategy would provide management agencies with defensible data in a sociopolitical arena that has been embroiled in conflict for several decades.

Characterizing grazing disturbance in semiarid ecosystems across broad spatial scales using multiple indices.

USGS Publications Warehouse

Beever, Erik A.; Tausch, Robin J.; Brussard, Peter F.

2003-01-01

Although management and conservation strategies continue to move toward broader spatial scales and consideration of many taxonomic groups simultaneously, researchers have struggled to characterize responses to disturbance at these scales. Most studies of disturbance by feral grazers investigate effects on only one or two ecosystem elements across small spatial scales, limiting their applicability to ecosystem-level management. To address this inadequacy, in 1997 and 1998 we examined disturbance created by feral horses (Equus caballus) in nine mountain ranges of the western Great Basin, USA, using plants, small mammals, ants, and soil compaction as indicators. Nine horse-occupied and 10 horse-removed sites were stratified into high- and low-elevation groups, and all sites at each elevation had similar vegetation type, aspect, slope gradient, and recent (≥15-yr) fire and livestock-grazing histories. Using reciprocal averaging and TWINSPAN analyses, we compared relationships among sites using five data sets: abiotic variables, percent cover by plant species, an index of abundance by plant species, 10 disturbance-sensitive response variables, and grass and shrub species considered “key” indicators by land managers. Although reciprocal averaging and TWINSPAN analyses of percent cover, abiotic variables, and key species suggested relationships between sites influenced largely by biogeography (i.e., mountain range), disturbance-sensitive variables clearly segregated horse-occupied and horse-removed sites. These analyses suggest that the influence of feral horses on many Great Basin ecosystem attributes is not being detected by monitoring only palatable plant species. We recommend development of an expanded monitoring strategy based not only on established vegetation measurements investigating forage consumption, but also including disturbance-sensitive variables (e.g., soil surface hardness, abundance of ant mounds) that more completely reflect the suite of effects that a large-bodied grazer may impose on mountain ecosystems, independent of vegetation differences. By providing a broader-based mechanism for detection of adverse effects, this strategy would provide management agencies with defensible data in a sociopolitical arena that has been embroiled in conflict for several decades.

Hyalella azteca Responses to Coldwater River Backwater Sediments in Mississippi, USA

USDA-ARS?s Scientific Manuscript database

As part of an environmental quality assessment, sediment from four sites in three Coldwater River, Mississippi backwaters was examined using 28 d Hyalella azteca bioassays and chemical analyses for 33 pesticides, 7 metals and 7 PCBs. Mortality occurred in the DeSoto County backwater while growth imp...

Sensitivity of ground motion parameters to local site effects for areas characterised by a thick buried low-velocity layer.

NASA Astrophysics Data System (ADS)

Farrugia, Daniela; Galea, Pauline; D'Amico, Sebastiano; Paolucci, Enrico

2016-04-01

It is well known that earthquake damage at a particular site depends on the source, the path that the waves travel through and the local geology. The latter is capable of amplifying and changing the frequency content of the incoming seismic waves. In regions of sparse or no strong ground motion records, like Malta (Central Mediterranean), ground motion simulations are used to obtain parameters for purposes of seismic design and analysis. As an input to ground motion simulations, amplification functions related to the shallow subsurface are required. Shear-wave velocity profiles of several sites on the Maltese islands were obtained using the Horizontal-to-Vertical Spectral Ratio (H/V), the Extended Spatial Auto-Correlation (ESAC) technique and the Genetic Algorithm. The sites chosen were all characterised by a layer of Blue Clay, which can be up to 75 m thick, underlying the Upper Coralline Limestone, a fossiliferous coarse grained limestone. This situation gives rise to a velocity inversion. Available borehole data generally extends down till the top of the Blue Clay layer therefore the only way to check the validity of the modelled shear-wave velocity profile is through the thickness of the topmost layer. Surface wave methods are characterised by uncertainties related to the measurements and the model used for interpretation. Moreover the inversion procedure is also highly non-unique. Such uncertainties are not commonly included in site response analysis. Yet, the propagation of uncertainties from the extracted dispersion curves to inversion solutions can lead to significant differences in the simulations (Boaga et al., 2011). In this study, a series of sensitivity analyses will be presented with the aim of better identifying those stratigraphic properties which can perturb the ground motion simulation results. The stochastic one-dimensional site response analysis algorithm, Extended Source Simulation (EXSIM; Motazedian and Atkinson, 2005), was used to perform these analyses. The amplification functions were extracted using the programme SITE_AMP (Boore, 2003), which computes amplifications based on the square root of the effective seismic impedance. Sensitivity indices were obtained by changing two parameters (thickness and shear-wave velocity) of the different layers while keeping the others constant. Additional analyses were carried out by producing various profiles within specified boundaries which are able to fit the experimental data. The analyses also show the important role that the shear-wave velocity profiles play in ground motion simulations. The results obtained highlight the importance of the correct knowledge of both the properties of the Upper Coralline Limestone and the Blue Clay, especially the Blue Clay thickness.

Insulation and wiring specificity of BceR-like response regulators and their target promoters in Bacillus subtilis.

PubMed

Fang, Chong; Nagy-Staroń, Anna; Grafe, Martin; Heermann, Ralf; Jung, Kirsten; Gebhard, Susanne; Mascher, Thorsten

2017-04-01

BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, P bceA or P psdA , resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of P bceA and P psdA that ensure the insulation of these two paralogous pathways at the RR-promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities. © 2016 John Wiley & Sons Ltd.

Influence of Green Tides in Coastal Nursery Grounds on the Habitat Selection and Individual Performance of Juvenile Fish

PubMed Central

Murillo, Laurence; Randon, Marine; Lebot, Clément

2017-01-01

Coastal ecosystems, which provide numerous essential ecological functions for fish, are threatened by the proliferation of green macroalgae that significantly modify habitat conditions in intertidal areas. Understanding the influence of green tides on the nursery function of these ecosystems is essential to determine their potential effects on fish recruitment success. In this study, the influence of green tides on juvenile fish was examined in an intertidal sandy beach area, the Bay of Saint-Brieuc (Northwestern France), during two annual cycles of green tides with varying levels of intensity. The responses of three nursery-dependent fish species, the pelagic Sprattus sprattus (L.), the demersal Dicentrarchus labrax (L.) and the benthic Pleuronectes platessa L., were analysed to determine the effects of green tides according to species-specific habitat niche and behaviour. The responses to this perturbation were investigated based on habitat selection and a comparison of individual performance between a control and an impacted site. Several indices on different integrative scales were examined to evaluate these responses (antioxidant defence capacity, muscle total lipid, morphometric condition and growth). Based on these analyses, green tides affect juvenile fish differently according to macroalgal density and species-specific tolerance, which is linked to their capacity to move and to their distribution in the water column. A decreasing gradient of sensitivity was observed from benthic to demersal and pelagic fish species. At low densities of green macroalgae, the three species stayed at the impacted site and the growth of plaice was reduced. At medium macroalgal densities, plaice disappeared from the impacted site and the growth of sea bass and the muscle total lipid content of sprat were reduced. Finally, when high macroalgal densities were reached, none of the studied species were captured at the impacted site. Hence, sites affected by green tides are less favourable nursery grounds for all the studied species, with species-specific effects related to macroalgal density. PMID:28125605

Influence of Green Tides in Coastal Nursery Grounds on the Habitat Selection and Individual Performance of Juvenile Fish.

PubMed

Le Luherne, Emilie; Le Pape, Olivier; Murillo, Laurence; Randon, Marine; Lebot, Clément; Réveillac, Elodie

2017-01-01

Coastal ecosystems, which provide numerous essential ecological functions for fish, are threatened by the proliferation of green macroalgae that significantly modify habitat conditions in intertidal areas. Understanding the influence of green tides on the nursery function of these ecosystems is essential to determine their potential effects on fish recruitment success. In this study, the influence of green tides on juvenile fish was examined in an intertidal sandy beach area, the Bay of Saint-Brieuc (Northwestern France), during two annual cycles of green tides with varying levels of intensity. The responses of three nursery-dependent fish species, the pelagic Sprattus sprattus (L.), the demersal Dicentrarchus labrax (L.) and the benthic Pleuronectes platessa L., were analysed to determine the effects of green tides according to species-specific habitat niche and behaviour. The responses to this perturbation were investigated based on habitat selection and a comparison of individual performance between a control and an impacted site. Several indices on different integrative scales were examined to evaluate these responses (antioxidant defence capacity, muscle total lipid, morphometric condition and growth). Based on these analyses, green tides affect juvenile fish differently according to macroalgal density and species-specific tolerance, which is linked to their capacity to move and to their distribution in the water column. A decreasing gradient of sensitivity was observed from benthic to demersal and pelagic fish species. At low densities of green macroalgae, the three species stayed at the impacted site and the growth of plaice was reduced. At medium macroalgal densities, plaice disappeared from the impacted site and the growth of sea bass and the muscle total lipid content of sprat were reduced. Finally, when high macroalgal densities were reached, none of the studied species were captured at the impacted site. Hence, sites affected by green tides are less favourable nursery grounds for all the studied species, with species-specific effects related to macroalgal density.

A simple hypothesis of how leaf and canopy-level transpiration and assimilation respond to elevated CO2 reveals distinct response patterns between disturbed and undisturbed vegetation

NASA Astrophysics Data System (ADS)

Donohue, Randall J.; Roderick, Michael L.; McVicar, Tim R.; Yang, Yuting

2017-01-01

Elevated CO2 increases leaf-level water-use efficiency (ω) almost universally. How canopy-level transpiration and assimilation fluxes respond to increased ω is currently unclear. We present a simple, resource-availability-based hypothesis of how equilibrium (or mature) leaf and canopy transpiration and assimilation rates, along with leaf area index (L), respond to elevated CO2. We quantify this hypothesis in the form of a model and test it against observations from eight Free Air CO2 Enrichment sites that span a wide range of resource availabilities. Sites were grouped according to vegetation disturbance status. We find the model adequately accounts for the responses of undisturbed vegetation (R2 = 0.73, 11% error) but cannot account for the responses of disturbed vegetation (R2 = 0.47, 17% error). At undisturbed sites, the responses of L and of leaf and canopy transpiration vary predictably (7% error) with resource availability, whereas the leaf assimilation response is less predictable. In contrast, the L and transpiration flux responses at the disturbed (mostly forested) sites are highly variable and are not strongly related to resource availability. Initial analyses suggest that they are more strongly related to regrowth age than to resource availability. We conclude that (i) our CO2 response hypothesis is valid for capturing the responses of undisturbed vegetation only, (ii) that the responses of disturbed vegetation are distinctly different from undisturbed vegetation, and (iii) that these differences need to be accounted for when predicting the effects of elevated CO2 on land surface processes generally, and on leaf area and water fluxes in particular.

Variation of parasite load and immune parameters in two species of New Zealand shore crabs.

PubMed

Dittmer, Jessica; Koehler, Anson V; Richard, Freddie-Jeanne; Poulin, Robert; Sicard, Mathieu

2011-09-01

While parasites are likely to encounter several potential intermediate hosts in natural communities, a parasite's actual range of compatible hosts is limited by numerous biological factors ranging from behaviour to immunology. In crustaceans, two major components of immunity are haemocytes and the prophenoloxidase system involved in the melanisation of foreign particles. Here, we analysed metazoan parasite prevalence and loads in the two sympatric crab species Hemigrapsus crenulatus and Macrophthalmus hirtipes at two sites. In parallel, we analysed the variation in haemocyte concentration and amount of circulating phenoloxidase (PO) in the haemolymph of the same individuals in an attempt to (a) explain differences in parasite prevalence and loads in the two species at two sites and (b) assess the impact of parasites on these immune parameters. M. hirtipes harboured more parasites but also exhibited higher haemocyte concentrations than H. crenulatus independent of the study site. Thus, higher investment in haemocyte production for M. hirtipes does not seem to result in higher resistance to parasites. Analyses of variation in immune parameters for the two crab species between the two sites that differed in parasite prevalence showed common trends. (a) In general, haemocyte concentrations were higher at the site experiencing higher parasitic pressure while circulating PO activity was lower and (b) haemocyte concentrations were influenced by microphallid trematode metacercariae in individuals from the site with higher parasitic pressure. We suggest that the higher haemocyte concentrations observed in both crab species exposed to higher parasitic pressure may represent an adaptive response to the impact of parasites on this immune parameter.

Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region

PubMed Central

Kasahara, Koji; Ohyama, Yoshifumi; Kokubo, Tetsuro

2011-01-01

Saccharomyces cerevisiae Hmo1 binds to the promoters of ∼70% of ribosomal protein genes (RPGs) at high occupancy, but is observed at lower occupancy on the remaining RPG promoters. In Δhmo1 cells, the transcription start site (TSS) of the Hmo1-enriched RPS5 promoter shifted upstream, while the TSS of the Hmo1-limited RPL10 promoter did not shift. Analyses of chimeric RPS5/RPL10 promoters revealed a region between the RPS5 upstream activating sequence (UAS) and core promoter, termed the intervening region (IVR), responsible for strong Hmo1 binding and an upstream TSS shift in Δhmo1 cells. Chromatin immunoprecipitation analyses showed that the RPS5-IVR resides within a nucleosome-free region and that pre-initiation complex (PIC) assembly occurs at a site between the IVR and a nucleosome overlapping the TSS (+1 nucleosome). The PIC assembly site was shifted upstream in Δhmo1 cells on this promoter, indicating that Hmo1 normally masks the RPS5-IVR to prevent PIC assembly at inappropriate site(s). This novel mechanism ensures accurate transcriptional initiation by delineating the 5′- and 3′-boundaries of the PIC assembly zone. PMID:21288884

Role of environmental pollutants on immune functions, parasitic infections and limb malformations in marine toads and whistling frogs from Bermuda.

PubMed

Linzey, Donald; Burroughs, Joy; Hudson, Lisa; Marini, Michele; Robertson, John; Bacon, Jamie; Nagarkatti, Mitzi; Nagarkatti, Prakash

2003-06-01

Soil, water, and amphibian tissues collected between 1995 and 1999 from 15 study sites in Bermuda were analysed for pesticides and heavy metals. The most abundant pesticide residue in soil was p,p'-dichlorodiphenyldichloroethylene (DDE) which was found at all sites in concentrations ranging from 0.003 to 4.023 p.p.m. No pesticide residues were found in water. DDE was also recovered from the livers and fat bodies of marine toads (Bufo marinus) and whistling frogs (Eleutherodactylus johnstonei). Analyses of food sources consumed by these anuran species revealed residue levels of p, p'-DDE ranging from 0.05 to 0.217 p.p.m. Other soil residues included dichlorodiphenyltrichloroethane (DDT) at eight study sites, Dicofol(kelthane) at eight sites, dieldrin at five sites, and polychlorinated biphenyls (PCBs) as Arochlor 1254 and Arochlor 1260 at seven sites. Analyses of toad livers revealed significant concentrations of cadmium, chromium, copper and zinc. Livers of Bermuda toads exhibited altered hepatocytic morphology and an increased number of melanomacrophages and possible granulomas, while spleens showed a marked decrease in white pulp. Spleen cells from Bufo marinus collected at one site having high levels of cadmium exhibited a decreased B cell response to lipopolysaccharide. The incidence of trematode infection in Bufo marinus increased from 53.8% in 1995 to 90% in 1999. Deformity rates in the limbs of subadult and adult toads ranged between 15 and 25%. Examination of 1,995 newly-metamorphosed toads revealed deformity rates as high as 47%. The current comprehensive study suggests that environmental pollutants may account for immunosuppression, increased susceptibility to infections, limb malformations and possible decline in amphibian populations from Bermuda.

Rapid allergen-induced interleukin-17 and interferon-γ secretion by skin-resident memory CD8+ T cells.

PubMed

Schmidt, Jonas D; Ahlström, Malin G; Johansen, Jeanne D; Dyring-Andersen, Beatrice; Agerbeck, Christina; Nielsen, Morten M; Poulsen, Steen S; Woetmann, Anders; Ødum, Niels; Thomsen, Allan R; Geisler, Carsten; Bonefeld, Charlotte M

2017-04-01

Skin-resident memory T (T RM ) cells are associated with immunological memory in the skin. Whether immunological memory responses to allergens in the skin are solely localized to previously allergen-exposed sites or are present globally in the skin is not clear. Furthermore, the mechanisms whereby T RM cells induce rapid recall responses need further investigation. To study whether contact allergens induce local and/or global memory, and to determine the mechanisms involved in memory responses in the skin. To address these questions, we analysed responses to contact allergens in mice and humans sensitized to 2,4-dinitrofluorobenzene and nickel, respectively. Challenge responses in both mice and humans were dramatically increased at sites previously exposed to allergens as compared with previously unexposed sites. Importantly, the magnitude of the challenge response correlated with the epidermal accumulation of interleukin (IL)-17A-producing and interferon (IFN)-γ-producing T RM cells. Moreover, IL-17A and IFN-γ enhanced allergen-induced IL-1β production in keratinocytes. We show that sensitization with contact allergens induces a strong, long-lasting local memory and a weaker, temporary global immunological memory response to the allergen that is mediated by IL-17A-producing and IFN-γ-producing CD8 + T RM cells. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Transcriptional responses of zebrafish to complex metal mixtures in laboratory studies overestimates the responses observed with environmental water.

PubMed

Pradhan, Ajay; Ivarsson, Per; Ragnvaldsson, Daniel; Berg, Håkan; Jass, Jana; Olsson, Per-Erik

2017-04-15

Metals released into the environment continue to be of concern for human health. However, risk assessment of metal exposure is often based on total metal levels and usually does not take bioavailability data, metal speciation or matrix effects into consideration. The continued development of biological endpoint analyses are therefore of high importance for improved eco-toxicological risk analyses. While there is an on-going debate concerning synergistic or additive effects of low-level mixed exposures there is little environmental data confirming the observations obtained from laboratory experiments. In the present study we utilized qRT-PCR analysis to identify key metal response genes to develop a method for biomonitoring and risk-assessment of metal pollution. The gene expression patterns were determined for juvenile zebrafish exposed to waters from sites down-stream of a closed mining operation. Genes representing different physiological processes including stress response, inflammation, apoptosis, drug metabolism, ion channels and receptors, and genotoxicity were analyzed. The gene expression patterns of zebrafish exposed to laboratory prepared metal mixes were compared to the patterns obtained with fish exposed to the environmental samples with the same metal composition and concentrations. Exposure to environmental samples resulted in fewer alterations in gene expression compared to laboratory mixes. A biotic ligand model (BLM) was used to approximate the bioavailability of the metals in the environmental setting. However, the BLM results were not in agreement with the experimental data, suggesting that the BLM may be overestimating the risk in the environment. The present study therefore supports the inclusion of site-specific biological analyses to complement the present chemical based assays used for environmental risk-assessment. Copyright © 2017 Elsevier B.V. All rights reserved.

Climate-growth relationships along a black spruce toposequence in Interior Alaska

Treesearch

Jane M. Wolken; Daniel H. Mann; Thomas A. Grant; Andrea H. Lloyd; T. Scott Rupp; Teresa N. Hollingsworth

2016-01-01

Despite its wide geographic distribution and important role in boreal forest fire regimes, little is known about the climate-growth relationships of black spruce (Picea mariana [Mill.] B.S.P.). We used site- and tree-level analyses to evaluate the radial growth responses to climate of black spruce growing...

The Economics of Authorship: Online Paper Mills, Student Writers, and First-Year Composition

ERIC Educational Resources Information Center

Ritter, Kelly

2005-01-01

Using sample student analyses of online paper mill Web sites, student survey responses, and existing scholarship on plagiarism, authorship, and intellectual property, this article examines how the consumerist rhetoric of the online paper mills construes academic writing as a commodity for sale, and why such rhetoric appeals to students in…

Seismic Design of a Single Bored Tunnel: Longitudinal Deformations and Seismic Joints

NASA Astrophysics Data System (ADS)

Oh, J.; Moon, T.

2018-03-01

The large diameter bored tunnel passing through rock and alluvial deposits subjected to seismic loading is analyzed for estimating longitudinal deformations and member forces on the segmental tunnel liners. The project site has challenges including high hydrostatic pressure, variable ground profile and high seismic loading. To ensure the safety of segmental tunnel liner from the seismic demands, the performance-based two-level design earthquake approach, Functional Evaluation Earthquake and Safety Evaluation Earthquake, has been adopted. The longitudinal tunnel and ground response seismic analyses are performed using a three-dimensional quasi-static linear elastic and nonlinear elastic discrete beam-spring elements to represent segmental liner and ground spring, respectively. Three components (longitudinal, transverse and vertical) of free-field ground displacement-time histories evaluated from site response analyses considering wave passage effects have been applied at the end support of the strain-compatible ground springs. The result of the longitudinal seismic analyses suggests that seismic joint for the mitigation measure requiring the design deflection capacity of 5-7.5 cm is to be furnished at the transition zone between hard and soft ground condition where the maximum member forces on the segmental liner (i.e., axial, shear forces and bending moments) are induced. The paper illustrates how detailed numerical analyses can be practically applied to evaluate the axial and curvature deformations along the tunnel alignment under difficult ground conditions and to provide the seismic joints at proper locations to effectively reduce the seismic demands below the allowable levels.

Bacterial responses and interactions with plants during rhizoremediation

PubMed Central

Segura, Ana; Rodríguez‐Conde, Sara; Ramos, Cayo; Ramos, Juan L.

2009-01-01

Summary With the increase in quality of life standards and the awareness of environmental issues, the remediation of polluted sites has become a priority for society. Because of the high economic cost of physico‐chemical strategies for remediation, the use of biological tools for cleaning‐up contaminated sites is a very attractive option. Rhizoremediation, the use of rhizospheric microorganisms in the bioremediation of contaminants, is the biotechnological approach that we explore in this minireview. We focus our attention on bacterial interactions with the plant surface, responses towards root exudates, and how plants and microbes communicate. We analyse certain strategies that may improve rhizoremediation, including the utilization of endophytes, and finally we discuss several rhizoremediation strategies that have opened ways to improve biodegradation. PMID:21255277

Multi-biomarker approach using the blue mussel (Mytilus edulis L.) to assess the quality of marine environments: season and habitat-related impacts.

PubMed

Brenner, M; Broeg, K; Frickenhaus, S; Buck, B H; Koehler, A

2014-04-01

Using a comprehensive approach, intertidal, near- and offshore sites in the German Bight were analysed for their environmental quality by assessing the health of blue mussels (Mytilus edulis). During a ten month sampling period mussels were studied with a set of biomarkers comprising lysosomal membrane stability and accumulation of lipofuscin, supplemented by biomarkers indicating nutritional status such as neutral lipids and glycogen in the cells of the digestive gland. Data were analysed in relation to sex, gonadal status, condition index and for the presence of parasites, to determine the overall health status of mussels at the respective sites. Mussels from all sites showed clear signs of stress, indicating an inferior environmental quality throughout the southern German Bight. Further, habitat characteristics such as inundation time and growing on- or off-bottom, as well as seasonal factors, can clearly influence the response of biomarkers in mussels exposed to similar levels of chemical environmental stress. Copyright © 2013 Elsevier Ltd. All rights reserved.

The adsorption of NO, NH3, N2 on carbon surface: a density functional theory study.

PubMed

Wang, Jiayong; Yang, Mo; Deng, Debing; Qiu, Shuxia

2017-08-11

To explore the adsorption mechanism of NO, NH 3 , N 2 on a carbon surface, and the effect of basic and acidic functional groups, density functional theory was employed to investigate the interactions between these molecules and carbon surfaces. Molecular electrostatic potential, Mulliken population analyses, reduced density gradient, and Mayer bond order analyses were used to clarify the adsorption mechanism. The results indicate that van der Waals interactions are responsible for N 2 physisorption, and N 2 is the least likely to adsorb on a carbon surface. Modification of carbon materials to decorate basic or acidic functional groups could enhance the NH 3 physisorption because of hydrogen bonding or electrostatic interactions, however, NO physisorption on a carbon surface is poor. Zig-zag sites are more reactive than armchair sites when these gas molecules absorb on the edge sites of carbon surface. Graphical abstract NH 3 , N 2 , NO adsortion on carbon surface.

Idaho's surface-water-quality monitoring program: results from five sites sampled during water years 1990-93

USGS Publications Warehouse

,

1994-01-01

In 1990, the U.S. Geological Survey (USGS), in cooperation with the Idaho Department of Health and Welfare, Division of Environmental Quality, implemented a statewide water-quality monitoring program in response to Idaho's antidegradation policy as required by the Clean Water Act. The program objective is to provide water-quality managers with a coordinated statewide network to detect trends in surface-water quality. The monitoring program includes the collection and analysis of samples from 56 sites on the Bear, Clearwater, Kootenai, Pend Oreille, Salmon, Snake, and Spokane Rivers and their tributaries (fig. 1). Samples are collected every year at 5 sites (annual sites) in drainage basins where long-term water-quality management is practiced, every other year at 19 sites (biennial sites) in basins where land and water uses change slowly, and every third year at 32 sites (triennial sites) where future development may affect water quality. Each year, 25 of the 56 sites are sampled. This report discusses results of sampling at five annual sites. During water years 1990-93 (October 1, 1989, through September 30, 1993), samples were collected six times per year at the five annual sites (fig. 1). Onsite analyses were made for discharge, specific conductance, pH, temperature, dissolved oxygen, bacteria (fecal coliform and fecal streptococci), and alkalinity. Laboratory analyses were made for major ions, nutrients, trace elements, and suspended sediment. Suspended sediment, nitrate, fecal coliform, trace elements, and specific conductance were used to characterize surface-water quality. Because concentrations of all trace elements except zinc were near detection limits, only zinc is discussed.

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.

Multi-level stressor analysis from the DNA/biochemical level to community levels in an urban stream and integrative health response (IHR) assessments.

PubMed

Lee, Jae Hoon; Kim, Joon Ha; Oh, Hee-Mock; An, Kwang-Guk

2013-01-01

The objectives of this study were to identify multi-level stressors at the DNA/biochemical level to the community level in fish in an urban stream and to develop an integrative health response (IHR) model for ecological health diagnosis. A pristine control site (S (c) ) and an impacted site (S (i) ) were selected from among seven pre-screened sites studied over seven years. Various chemical analyses indicated that nutrient enrichment (Nitrogen, Phosphorus) and organic pollution were significantly greater (t > 8.783, p < 0.01) at the S (i) site compared to the S (c) site. Single-cell gel electrophoresis (comet assays) of DNA-level impairment indicated significantly (t = 5.678, p < 0.01) greater tail intensity, expressed as % tail-DNA, at the S (i) site and genotoxic responses were detected in the downstream reach. Ethoxyresorufin-O-deethylase (EROD) assays, as a physiological bioindicator, were 2.8-fold higher (p < 0.05, NK-test after ANOVA) at the S (i) site. Tissue analysis using a necropsy-based health assessment index (NHAI) showed distinct internal organ disorders in three tissues, i.e., liver, kidney, and gill, at the S (i) site. Population-level analysis using the sentinel species Zacco platypus showed that the regression coefficient (b) was 3.012 for the S (i) site and 2.915 for the S (c) site, indicating population skewness in the downstream reach. Community-level health was impaired at the S (i) site based on an index of biological integrity (IBI), and physical habitat modifications were identified by a qualitative habitat evaluation index (QHEI). Overall, the model values for the integrative health response (IHR), developed using the star plot approach, were 3.22 (80.5%) at the S (c) site and 0.74 (18.5%) at the S (i) site, indicating that, overall, ecological health impairments were evident in the urban reach. Our study was based on multi-level approaches using biological organization and the results suggest that there is a pivotal point of linkage between mechanistic understanding and real ecological consequences of environmental stressors.

Characterisation of slope directional resonance by analysing ambient noise instantaneous polarisation

NASA Astrophysics Data System (ADS)

Del Gaudio, Vincenzo; Wasowski, Janusz

2014-05-01

Several studies have shown that the dynamic response of landslide prone slopes to seismic shaking can play an important role in failure triggering during earthquakes. It was also demonstrated that slope seismic response is often characterised by directional resonance phenomena. Directivity can be revealed by the analysis of ambient noise recordings according to a technique known as HVNR method based on the analysis of azimuthal variation of spectral ratios between the spectral amplitude of horizontal H and vertical V component of noise recording. Directional resonance is then revealed by the presence of a preferential polarisation of H/V ratio peaks, whose frequencies correspond to resonance frequencies and whose amplitudes depend on the impedance contrast between surface material and bedrock. H/V ratio amplitudes can potentially provide information also on amplification factors. However, the relation is not straightforward depending on the nature of the waves contributing to the ambient noise. Thus, it is desirable to distinguish different kinds of noise wave packets, possibly isolating the contribution of Rayleigh waves, which appear to better reflect site response properties. To identify Rayleigh wave packets in noise recording a new approach was tested, based on a technique of analysis of instantaneous polarisation. The results are promising for the investigation of site response directional properties, particularly in the case of complex site conditions, where resonance can be characterised by multiple anisotropic peaks. In our preliminary tests of noise recordings carried out at a site located on a slope affected by landslides, only a small fraction of data samples (in the order of 1 %) were identified as Rayleigh type waves: this was likely due the fact that the noise recording was dominated by an overlapping of signals with different kinds of polarisation. Thus, it was possible to recognise Rayleigh polarisation only when the energy of this kind of wave was prevalent. However, from a relatively short noise recording (in the order of 30-45 minutes) one can obtain a high number (in the order of thousands) of estimates of H/V amplitude and azimuth, providing a robust statistics to recognise ground vibration properties reflecting site response. The tests on sites where directional resonance properties had been verified through the analysis of seismic event recordings, showed that more coherent observations can be obtained for H/V ratios and directivity estimates by selecting Rayleigh type data samples, rather than analysing the entire data set or SH-type wave packets.This offers the possibility of reducing the uncertainties in data interpretation related to the influence of the nature of the noise wavefield.

Are treelines advancing? A global meta-analysis of treeline response to climate warming.

PubMed

Harsch, Melanie A; Hulme, Philip E; McGlone, Matt S; Duncan, Richard P

2009-10-01

Treelines are temperature sensitive transition zones that are expected to respond to climate warming by advancing beyond their current position. Response to climate warming over the last century, however, has been mixed, with some treelines showing evidence of recruitment at higher altitudes and/or latitudes (advance) whereas others reveal no marked change in the upper limit of tree establishment. To explore this variation, we analysed a global dataset of 166 sites for which treeline dynamics had been recorded since 1900 AD. Advance was recorded at 52% of sites with only 1% reporting treeline recession. Treelines that experienced strong winter warming were more likely to have advanced, and treelines with a diffuse form were more likely to have advanced than those with an abrupt or krummholz form. Diffuse treelines may be more responsive to warming because they are more strongly growth limited, whereas other treeline forms may be subject to additional constraints.

US Department of Energy response to standards for remedial actions at inactive uranium processing sites: Proposed rule

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

Not Available

1988-01-29

The Title I groundwater standards for inactive uranium mill tailings sites, which were promulgated on January 5, 1983, by the US Environmental Protection Agency (EPA) for the Uranium Mill Tailings Remedial Action (UMTRA) Project, were remanded to the EPA on September 3, 1985, by the US Tenth Circuit Court of Appeals. The Court instructed the EPA to compile general groundwater standards for all Title I sites. On September 24, 1987, the EPA published proposed standards (52FR36000-36008) in response to the remand. This report includes an evaluation of the potential effects of the proposed EPA groundwater standards on the UMTRA Project,more » as well as a discussion of the DOE's position on the proposed standards. The report also contains and appendix which provides supporting information and cost analyses. In order to assess the impacts of the proposed EPA standards, this report summarizes the proposed EPA standards in Section 2.0. The next three sections assess the impacts of the three parts of the EPA standards: Subpart A considers disposal sites; Subpart B is concerned with restoration at processing sites; and Subpart C addresses supplemental standards. Section 6.0 integrates previous sections into a recommendations section. Section 7.0 contains the DOE response to questions posed by the EPA in the preamble to the proposed standards. 6 refs., 5 figs., 3 tabs.« less

Determination of Shear Wave Velocity in Offshore Terengganu for Ground Response Analysis

NASA Astrophysics Data System (ADS)

Mazlina, M.; Liew, M. S.; Adnan, A.; Harahap, I. S. H.; Hamid, N. A.

2018-04-01

Amount of vibration received in any location can be analysed by conducting ground response analysis. Even though there are three different methods available in this analysis, One Dimensional ground response analysis method has been widely used. Shear wave velocity is one of the key parameters in this analysis. A lot of correlations have been formulated to determine shear wave velocity with cone penetration test. In this study, correlations developed for Quaternary geological age have been selected. Six equations have been adopted comprise of all soil and soil type dependent correlations. Two platforms sites consist of clay and combination of clay and sand have been analysed. Shear velocity to be used in ground response analysis has been obtained. Results have been illustrated in graphs where shear velocity for each case has been plotted. In avoiding under or over predicting of shear wave velocity, the average of all soil and soil type dependent results will be used as final Vs value.

Utilizing time-lapse micro-CT-correlated bisphosphonate binding kinetics and soft tissue-derived input functions to differentiate site-specific changes in bone metabolism in vivo.

PubMed

Tower, R J; Campbell, G M; Müller, M; Glüer, C C; Tiwari, S

2015-05-01

The turnover of bone is a tightly regulated process between bone formation and resorption to ensure skeletal homeostasis. This process differs between bone types, with trabecular bone often associated with higher turnover than cortical bone. Analyses of bone by micro-computed tomography (micro-CT) reveal changes in structure and mineral content, but are limited in the study of metabolic activity at a single time point, while analyses of serum markers can reveal changes in bone metabolism, but cannot delineate the origin of any aberrant findings. To obtain a site-specific assessment of bone metabolic status, bisphosphonate binding kinetics were utilized. Using a fluorescently-labeled bisphosphonate, we show that early binding kinetics monitored in vivo using fluorescent molecular tomography (FMT) can monitor changes in bone metabolism in response to bone loss, stimulated by ovariectomy (OVX), or bone gain, resulting from treatment with the anabolic bone agent parathyroid hormone (PTH), and is capable of distinguishing different, metabolically distinct skeletal sites. Using time-lapse micro-CT, longitudinal bone turnover was quantified. The spine showed a significantly greater percent resorbing volume and surface in response to OVX, while mice treated with PTH showed significantly greater resorbing volume per bone surface in the spine and significantly greater forming surfaces in the knee. Correlation studies between binding kinetics and micro-CT suggest that forming surfaces, as assessed by time-lapse micro-CT, are preferentially reflected in the rate constant values while forming and resorbing bone volumes primarily affect plateau values. Additionally, we developed a blood pool correction method which now allows for quantitative multi-compartment analyses to be conducted using FMT. These results further expand our understanding of bisphosphonate binding and the use of bisphosphonate binding kinetics as a tool to monitor site-specific changes in bone metabolism in vivo. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

78 FR 11124 - EPA Responses to State and Tribal 2010 Sulfur Dioxide Designation Recommendations: Notice of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-15

... supporting technical analyses, can be found on the EPA's Internet Web site at http://www.epa.gov... you for clarification due to technical difficulties, the EPA may not be able to consider your input... possible in supporting your views. Describe any assumptions and provide any technical information and/or...

Growth response of black walnut to interplanted trees

Treesearch

Richard C. Schlesinger; Robert D. Williams

1984-01-01

Analyses of black walnut tree diameters 13 years after planting showed that interplanting autumn-olive, black locust, and European alder increased walnut tree growtb, but only at certain locations. Interplanting autumn-olive resulted in increases of 56 to 351% at four of five locations and all species resulted in doubled walnut growth on an upland site. The interaction...

Seismic site-response characterization of high-velocity sites using advanced geophysical techniques: application to the NAGRA-Net

NASA Astrophysics Data System (ADS)

Poggi, V.; Burjanek, J.; Michel, C.; Fäh, D.

2017-08-01

The Swiss Seismological Service (SED) has recently finalised the installation of ten new seismological broadband stations in northern Switzerland. The project was led in cooperation with the National Cooperative for the Disposal of Radioactive Waste (Nagra) and Swissnuclear to monitor micro seismicity at potential locations of nuclear-waste repositories. To further improve the quality and usability of the seismic recordings, an extensive characterization of the sites surrounding the installation area was performed following a standardised investigation protocol. State-of-the-art geophysical techniques have been used, including advanced active and passive seismic methods. The results of all analyses converged to the definition of a set of best-representative 1-D velocity profiles for each site, which are the input for the computation of engineering soil proxies (traveltime averaged velocity and quarter-wavelength parameters) and numerical amplification models. Computed site response is then validated through comparison with empirical site amplification, which is currently available for any station connected to the Swiss seismic networks. With the goal of a high-sensitivity network, most of the NAGRA stations have been installed on stiff-soil sites of rather high seismic velocity. Seismic characterization of such sites has always been considered challenging, due to lack of relevant velocity contrast and the large wavelengths required to investigate the frequency range of engineering interest. We describe how ambient vibration techniques can successfully be applied in these particular conditions, providing practical recommendations for best practice in seismic site characterization of high-velocity sites.

Potential negative impacts of nuclear activities on local economies: Rethinking the issue

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

Metz, W.C.

1994-10-01

Surveys of public opinion about perceptions of risk associated with the nuclear fuel cycle have shown that the public professes a widespread feeling of dread, a fear of associated stigmas, and a concern about possible catastrophic nuclear accidents. Various interest groups and state governments that oppose congressionally mandated siting of centralized high-level radioactive waste (HLW) storage and disposal facilities are using this negative imagery to create a powerful, emotional obstacle to the siting process. From statistical analyses of images and location preferences, researchers have claimed that possible significant economic losses could potentially accompany the siting of HLW facilities. However, severalmore » paradoxes, or self-contradictory statements, apparently exist between the responses expressed in surveys and the actual economic and demographic behavior evidenced in the marketplace. Federal policymakers need to evaluate whether the request for a change in siting policy is based on subjective fear of a potential negative economic effect or on proven negative effects. Empirically observed behavior does not support predicted negative economic effects based on survey responses. 41 refs.« less

Limitation and applicability of microtremor records for site-response estimation

NASA Astrophysics Data System (ADS)

Song, G.; Kang, T.; Park, S.

2010-12-01

Site effects are the modifications of seismic motions which are traveling through near-surface materials. The impedance contrast between the topmost layer and bedrock may significantly amplify ground motions and augment their durations. Inelastic behavior of the geological media such as highly fractured/weathered rocks and unconsolidated sediments may absorb seismic energy, and thus damp the resulting ground motions. It is inherently most desirable to evaluate the site effects using seismic records from large earthquakes. If there are only small events that will be recorded by several seismograph stations, it becomes difficult to evaluate site effects using earthquake data. Recently a number of studies pay attention to microtremor records to assess site effects. The main reason of such efforts is that measurements are relatively easy regardless of site condition and cost-effective without necessity of waiting for earthquakes or of using active sources. Especially microtremor measurements are exclusively a useful option to assess site effects, and thus seismic microzonation, in the urban area and/or region of low to moderate seismicity. Spectral ratios of horizontal components to vertical component (HVSR) of microtremor records have been popular for estimation of site resonant frequency. Although some studies have shown that the amplitude of spectral ratios is an indicator of site amplification relative to bedrock motion, there are still debates on it. This discrepancy may originate from the deficiency of our understanding on the nature of microtremor. Therefore, it is important to understand the limitation and applicability of microtremor records for site-effect assessments. The focus on this problem is how microtremor responses on the subsurface structures and their physical properties, and how parameters deduced from microtremor analyses are related to site responses during earthquake ground motions. In order to investigate how these issues have a practical meaning in real cases, results obtained using the microtremor method were compared with results from a field test, a spectral inversion method, and the reference station method for sites of strong motion stations in the southern Korean Peninsula.

Gingival abrasion and recession in manual and oscillating-rotating power brush users.

PubMed

Rosema, N A M; Adam, R; Grender, J M; Van der Sluijs, E; Supranoto, S C; Van der Weijden, G A

2014-11-01

To assess gingival recession (GR) in manual and power toothbrush users and evaluate the relationship between GR and gingival abrasion scores (GA). This was an observational (cross-sectional), single-centre, examiner-blind study involving a single-brushing exercise, with 181 young adult participants: 90 manual brush users and 91 oscillating-rotating power brush users. Participants were assessed for GR and GA as primary response variables. Secondary response variables were the level of gingival inflammation, plaque score reduction and brushing duration. Pearson correlation was used to describe the relationship between number of recession sites and number of abrasions. Prebrushing (baseline) and post-brushing GA and plaque scores were assessed and differences analysed using paired tests. Two-sample t-test was used to analyse group differences; ancova was used for analyses of post-brushing changes with baseline as covariate. Overall, 97.8% of the study population had at least one site of ≥1 mm of gingival recession. For the manual group, this percentage was 98.9%, and for the power group, this percentage was 96.7% (P = 0.621). Post-brushing, the power group showed a significantly smaller GA increase than the manual group (P = 0.004); however, there was no significant correlation between number of recession sites and number of abrasions for either group (P ≥ 0.327). Little gingival recession was observed in either toothbrush user group; the observed GR levels were comparable. Lower post-brushing gingival abrasion levels were seen in the power group. There was no correlation between gingival abrasion as a result of brushing and the observed gingival recession following use of either toothbrush. © 2014 The Authors International Journal of Dental Hygiene Published by John Wiley & Sons Ltd.

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.

Gingival abrasion and recession in manual and oscillating–rotating power brush users

PubMed Central

Rosema, NAM; Adam, R; Grender, JM; Van der Sluijs, E; Supranoto, SC; Van der Weijden, GA

2014-01-01

Objective To assess gingival recession (GR) in manual and power toothbrush users and evaluate the relationship between GR and gingival abrasion scores (GA). Methods This was an observational (cross-sectional), single-centre, examiner-blind study involving a single-brushing exercise, with 181 young adult participants: 90 manual brush users and 91 oscillating–rotating power brush users. Participants were assessed for GR and GA as primary response variables. Secondary response variables were the level of gingival inflammation, plaque score reduction and brushing duration. Pearson correlation was used to describe the relationship between number of recession sites and number of abrasions. Prebrushing (baseline) and post-brushing GA and plaque scores were assessed and differences analysed using paired tests. Two-sample t-test was used to analyse group differences; ancova was used for analyses of post-brushing changes with baseline as covariate. Results Overall, 97.8% of the study population had at least one site of ≥1 mm of gingival recession. For the manual group, this percentage was 98.9%, and for the power group, this percentage was 96.7% (P = 0.621). Post-brushing, the power group showed a significantly smaller GA increase than the manual group (P = 0.004); however, there was no significant correlation between number of recession sites and number of abrasions for either group (P ≥ 0.327). Conclusions Little gingival recession was observed in either toothbrush user group; the observed GR levels were comparable. Lower post-brushing gingival abrasion levels were seen in the power group. There was no correlation between gingival abrasion as a result of brushing and the observed gingival recession following use of either toothbrush. PMID:24871587

Overview of topographic effects based on experimental observations: meaning, causes and possible interpretations

NASA Astrophysics Data System (ADS)

Massa, Marco; Barani, Simone; Lovati, Sara

2014-06-01

The paper presents an extensive review of topographic effects in seismology taking into account the knowledge of 40 yr of scientific literature. An overview of topographic effects based on experimental observations and numerical modelling is presented with the aim of highlighting meaning and causes of these phenomena as well as possible correlations between site response (fundamental frequency, amplification level) and geometrical (width and shape ratio of a relief) parameters. After a thorough summary of topographic effects, the paper focuses on five Italian sites whose seismic response is potentially affected by local morphology, as already evidenced by previous studies. In this study, seismic data recorded at these sites are analysed computing directional spectral ratios both in terms of horizontal to vertical spectral ratios (HVSRs) and, wherever possible, in terms of standard spectral ratios (SSRs). The analysis lead to the conclusion that wavefield tends to be polarized along a direction perpendicular to the main axis of a topographic irregularity, direction along which ground motion amplification is maximum. The final section of the article compares and contrasts different spectral ratio techniques in order to examine their effectiveness and reliability in detecting topographic effects. The examples discussed in the paper show that site responses based on HVSRs rather than SSR measurements could lead to misinterpretation of ground response results, both as concerns the definition of the site fundamental frequency and amplification level. Results and findings of this work will be used as starting point to discuss the influence of topographic effects on ground motion prediction equations and regulations for design. These topics will be discussed in the companion article.

A Hierarchical Analysis of Tree Growth and Environmental Drivers Across Eastern US Temperate Forests

NASA Astrophysics Data System (ADS)

Mantooth, J.; Dietze, M.

2014-12-01

Improving predictions of how forests in the eastern United States will respond to future global change requires a better understanding of the drivers of variability in tree growth rates. Current inventory data lack the temporal resolution to characterize interannual variability, while existing growth records lack the extent required to assess spatial scales of variability. Therefore, we established a network of forest inventory plots across ten sites across the eastern US, and measured growth in adult trees using increment cores. Sites were chosen to maximize climate space explored, while within sites, plots were spread across primary environmental gradients to explore landscape-level variability in growth. Using the annual growth record available from tree cores, we explored the responses of trees to multiple environmental covariates over multiple spatial and temporal scales. We hypothesized that within and across sites growth rates vary among species, and that intraspecific growth rates increase with temperature along a species' range. We also hypothesized that trees show synchrony in growth responses to landscape-scale climatic changes. Initial analyses of growth increments indicate that across sites, trees with intermediate shade tolerance, e.g. Red Oak (Quercus rubra), tend to have the highest growth rates. At the site level, there is evidence for synchrony in response to large-scale climatic events (e.g. prolonged drought and above average temperatures). However, growth responses to climate at the landscape scale have yet to be detected. Our current analysis utilizes hierarchical Bayesian state-space modeling to focus on growth responses of adult trees to environmental covariates at multiple spatial and temporal scales. This predictive model of tree growth currently incorporates observed effects at the individual, plot, site, and landscape scale. Current analysis using this model shows a potential slowing of growth in the past decade for two sites in the northeastern US (Harvard Forest and Bartlett Experimental Forest), however more work is required to determine the robustness of this trend. Finally, these observations are being incorporated into ecosystem models using the Brown Dog informatics tools and the Predictive Ecosystem Analyzer (PEcAn) data assimilation workflow.

Maintenance Plan for the Composite Analysis of the Hanford Site, Southeast Washington.

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

Lehman, L. L.; Nichols, W. E.

The U.S. Department of Energy (DOE) manuals for radioactive waste management, DOE M 435.1-1 Chg 21 and DOE-STD-5002-2017, require that the Hanford Site maintain site performance assessments and composite analyses (CAs). This document describes the plan for maintaining the CA that supports waste disposal and remedial actions for the Hanford Site. An initial CA of the site was issued in 1998, conditionally approved in 1999, received further analysis to satisfy conditions in an addendum in 2001, and was approved in 2002. This document meets the maintenance plan requirements described in DOE M 435.1-1 Chg 2 and DOE-STD-5002-2017 and implements themore » requirements of the disposal authorization related to the CA for the U.S. Department of Energy, Richland Operations Office, the responsible field office, and its contractors.« less

Effects of the number of people on efficient capture and sample collection: a lion case study.

PubMed

Ferreira, Sam M; Maruping, Nkabeng T; Schoultz, Darius; Smit, Travis R

2013-05-24

Certain carnivore research projects and approaches depend on successful capture of individuals of interest. The number of people present at a capture site may determine success of a capture. In this study 36 lion capture cases in the Kruger National Park were used to evaluate whether the number of people present at a capture site influenced lion response rates and whether the number of people at a sampling site influenced the time it took to process the collected samples. The analyses suggest that when nine or fewer people were present, lions appeared faster at a call-up locality compared with when there were more than nine people. The number of people, however, did not influence the time it took to process the lions. It is proposed that efficient lion capturing should spatially separate capture and processing sites and minimise the number of people at a capture site.

Genetic and epigenetic differences associated with environmental gradients in replicate populations of two salt marsh perennials.

PubMed

Foust, C M; Preite, V; Schrey, A W; Alvarez, M; Robertson, M H; Verhoeven, K J F; Richards, C L

2016-04-01

While traits and trait plasticity are partly genetically based, investigating epigenetic mechanisms may provide more nuanced understanding of the mechanisms underlying response to environment. Using AFLP and methylation-sensitive AFLP, we tested the hypothesis that differentiation to habitats along natural salt marsh environmental gradients occurs at epigenetic, but not genetic loci in two salt marsh perennials. We detected significant genetic and epigenetic structure among populations and among subpopulations, but we found multilocus patterns of differentiation to habitat type only in epigenetic variation for both species. In addition, more epigenetic than genetic loci were correlated with habitat in both species. When we analysed genetic and epigenetic variation simultaneously with partial Mantel, we found no correlation between genetic variation and habitat and a significant correlation between epigenetic variation and habitat in Spartina alterniflora. In Borrichia frutescens, we found significant correlations between epigenetic and/or genetic variation and habitat in four of five populations when populations were analysed individually, but there was no significant correlation between genetic or epigenetic variation and habitat when analysed jointly across the five populations. These analyses suggest that epigenetic mechanisms are involved in the response to salt marsh habitats, but also that the relationships among genetic and epigenetic variation and habitat vary by species. Site-specific conditions may also cloud our ability to detect response in replicate populations with similar environmental gradients. Future studies analysing sequence data and the correlation between genetic variation and DNA methylation will be powerful to identify the contributions of genetic and epigenetic response to environmental gradients. © 2016 John Wiley & Sons Ltd.

Crystal Structure Analyses of the Fosmidomycin-Target Enzyme from Plasmodium Falciparum

NASA Astrophysics Data System (ADS)

Umeda, Tomonobu; Kusakabe, Yoshio; Tanaka, Nobutada

The human malaria parasite Plasmodium falciparum is responsible for the death of more than a million people each year. Fosmidomycin has proved to be efficient in the treatment of P. falciparum malaria through the inhibition of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), an enzyme of the non-mevalonate pathway of isoprenoid biosynthesis, which is absent in humans. Crystal structure analyses of P. falciparum DXR (PfDXR) revealed that (i) an intrinsic flexibility of the PfDXR molecule accounts for the induced-fit movement to accommodate the bound inhibitor in the active site, and (ii) a cis arrangement of the oxygen atoms of the hydroxamate group of the bound inhibitor is essential for tight binding of the inhibitor to the active site metal. We believe that our study will serve as a useful guide to develop more potent PfDXR inhibitors.

Strength reduction factors for seismic analyses of buildings exposed to near-fault ground motions

NASA Astrophysics Data System (ADS)

Qu, Honglue; Zhang, Jianjing; Zhao, J. X.

2011-06-01

To estimate the near-fault inelastic response spectra, the accuracy of six existing strength reduction factors ( R) proposed by different investigators were evaluated by using a suite of near-fault earthquake records with directivity-induced pulses. In the evaluation, the force-deformation relationship is modelled by elastic-perfectly plastic, bilinear and stiffness degrading models, and two site conditions, rock and soil, are considered. The R-value ratio (ratio of the R value obtained from the existing R-expressions (or the R-µ- T relationships) to that from inelastic analyses) is used as a measurement parameter. Results show that the R-expressions proposed by Ordaz & Perez-Rocha are the most suitable for near-fault ground motions, followed by the Newmark & Hall and the Berrill et al. relationships. Based on an analysis using the near-fault ground motion dataset, new expressions of R that consider the effects of site conditions are presented and verified.

The IceCube realtime alert system

NASA Astrophysics Data System (ADS)

Aartsen, M. G.; Ackermann, M.; Adams, J.; Aguilar, J. A.; Ahlers, M.; Ahrens, M.; Altmann, D.; Andeen, K.; Anderson, T.; Ansseau, I.; Anton, G.; Archinger, M.; Argüelles, C.; Auffenberg, J.; Axani, S.; Bai, X.; Barwick, S. W.; Baum, V.; Bay, R.; Beatty, J. J.; Becker Tjus, J.; Becker, K.-H.; BenZvi, S.; Berley, D.; Bernardini, E.; Bernhard, A.; Besson, D. Z.; Binder, G.; Bindig, D.; Bissok, M.; Blaufuss, E.; Blot, S.; Bohm, C.; Börner, M.; Bos, F.; Bose, D.; Böser, S.; Botner, O.; Braun, J.; Brayeur, L.; Bretz, H.-P.; Bron, S.; Burgman, A.; Carver, T.; Casier, M.; Cheung, E.; Chirkin, D.; Christov, A.; Clark, K.; Classen, L.; Coenders, S.; Collin, G. H.; Conrad, J. M.; Cowen, D. F.; Cross, R.; Day, M.; de André, J. P. A. M.; De Clercq, C.; del Pino Rosendo, E.; Dembinski, H.; De Ridder, S.; Desiati, P.; de Vries, K. D.; de Wasseige, G.; de With, M.; DeYoung, T.; Díaz-Vélez, J. C.; di Lorenzo, V.; Dujmovic, H.; Dumm, J. P.; Dunkman, M.; Eberhardt, B.; Ehrhardt, T.; Eichmann, B.; Eller, P.; Euler, S.; Evenson, P. A.; Fahey, S.; Fazely, A. R.; Feintzeig, J.; Felde, J.; Filimonov, K.; Finley, C.; Flis, S.; Fösig, C.-C.; Franckowiak, A.; Friedman, E.; Fuchs, T.; Gaisser, T. K.; Gallagher, J.; Gerhardt, L.; Ghorbani, K.; Giang, W.; Gladstone, L.; Glauch, T.; Glüsenkamp, T.; Goldschmidt, A.; Gonzalez, J. G.; Grant, D.; Griffith, Z.; Haack, C.; Hallgren, A.; Halzen, F.; Hansen, E.; Hansmann, T.; Hanson, K.; Hebecker, D.; Heereman, D.; Helbing, K.; Hellauer, R.; Hickford, S.; Hignight, J.; Hill, G. C.; Hoffman, K. D.; Hoffmann, R.; Hoshina, K.; Huang, F.; Huber, M.; Hultqvist, K.; In, S.; Ishihara, A.; Jacobi, E.; Japaridze, G. S.; Jeong, M.; Jero, K.; Jones, B. J. P.; Kang, W.; Kappes, A.; Karg, T.; Karle, A.; Katz, U.; Kauer, M.; Keivani, A.; Kelley, J. L.; Kheirandish, A.; Kim, J.; Kim, M.; Kintscher, T.; Kiryluk, J.; Kittler, T.; Klein, S. R.; Kohnen, G.; Koirala, R.; Kolanoski, H.; Konietz, R.; Köpke, L.; Kopper, C.; Kopper, S.; Koskinen, D. J.; Kowalski, M.; Krings, K.; Kroll, M.; Krückl, G.; Krüger, C.; Kunnen, J.; Kunwar, S.; Kurahashi, N.; Kuwabara, T.; Labare, M.; Lanfranchi, J. L.; Larson, M. J.; Lauber, F.; Lennarz, D.; Lesiak-Bzdak, M.; Leuermann, M.; Lu, L.; Lünemann, J.; Madsen, J.; Maggi, G.; Mahn, K. B. M.; Mancina, S.; Mandelartz, M.; Maruyama, R.; Mase, K.; Maunu, R.; McNally, F.; Meagher, K.; Medici, M.; Meier, M.; Meli, A.; Menne, T.; Merino, G.; Meures, T.; Miarecki, S.; Montaruli, T.; Moulai, M.; Nahnhauer, R.; Naumann, U.; Neer, G.; Niederhausen, H.; Nowicki, S. C.; Nygren, D. R.; Obertacke Pollmann, A.; Olivas, A.; O'Murchadha, A.; Palczewski, T.; Pandya, H.; Pankova, D. V.; Peiffer, P.; Penek, Ö.; Pepper, J. A.; Pérez de los Heros, C.; Pieloth, D.; Pinat, E.; Price, P. B.; Przybylski, G. T.; Quinnan, M.; Raab, C.; Rädel, L.; Rameez, M.; Rawlins, K.; Reimann, R.; Relethford, B.; Relich, M.; Resconi, E.; Rhode, W.; Richman, M.; Riedel, B.; Robertson, S.; Rongen, M.; Rott, C.; Ruhe, T.; Ryckbosch, D.; Rysewyk, D.; Sabbatini, L.; Sanchez Herrera, S. E.; Sandrock, A.; Sandroos, J.; Sarkar, S.; Satalecka, K.; Schlunder, P.; Schmidt, T.; Schoenen, S.; Schöneberg, S.; Schumacher, L.; Seckel, D.; Seunarine, S.; Soldin, D.; Song, M.; Spiczak, G. M.; Spiering, C.; Stanev, T.; Stasik, A.; Stettner, J.; Steuer, A.; Stezelberger, T.; Stokstad, R. G.; Stößl, A.; Ström, R.; Strotjohann, N. L.; Sullivan, G. W.; Sutherland, M.; Taavola, H.; Taboada, I.; Tatar, J.; Tenholt, F.; Ter-Antonyan, S.; Terliuk, A.; Tešić, G.; Tilav, S.; Toale, P. A.; Tobin, M. N.; Toscano, S.; Tosi, D.; Tselengidou, M.; Turcati, A.; Unger, E.; Usner, M.; Vandenbroucke, J.; van Eijndhoven, N.; Vanheule, S.; van Rossem, M.; van Santen, J.; Vehring, M.; Voge, M.; Vogel, E.; Vraeghe, M.; Walck, C.; Wallace, A.; Wallraff, M.; Wandkowsky, N.; Weaver, Ch.; Weiss, M. J.; Wendt, C.; Westerhoff, S.; Whelan, B. J.; Wickmann, S.; Wiebe, K.; Wiebusch, C. H.; Wille, L.; Williams, D. R.; Wills, L.; Wolf, M.; Wood, T. R.; Woolsey, E.; Woschnagg, K.; Xu, D. L.; Xu, X. W.; Xu, Y.; Yanez, J. P.; Yodh, G.; Yoshida, S.; Zoll, M.

2017-06-01

Although high-energy astrophysical neutrinos were discovered in 2013, their origin is still unknown. Aiming for the identification of an electromagnetic counterpart of a rapidly fading source, we have implemented a realtime analysis framework for the IceCube neutrino observatory. Several analyses selecting neutrinos of astrophysical origin are now operating in realtime at the detector site in Antarctica and are producing alerts for the community to enable rapid follow-up observations. The goal of these observations is to locate the astrophysical objects responsible for these neutrino signals. This paper highlights the infrastructure in place both at the South Pole site and at IceCube facilities in the north that have enabled this fast follow-up program to be implemented. Additionally, this paper presents the first realtime analyses to be activated within this framework, highlights their sensitivities to astrophysical neutrinos and background event rates, and presents an outlook for future discoveries.

Tickled to death: analysing public perceptions of 'cute' videos of threatened species (slow lorises - Nycticebus spp.) on Web 2.0 sites.

PubMed

Anne-Isola Nekaris, K; Nekaris, By K Anne-Isola; Campbell, Nicola; Coggins, Tim G; Rode, E Johanna; Nijman, Vincent

2013-01-01

The internet is gaining importance in global wildlife trade and changing perceptions of threatened species. There is little data available to examine the impact that popular Web 2.0 sites play on public perceptions of threatened species. YouTube videos portraying wildlife allow us to quantify these perceptions. Focussing on a group of threatened and globally protected primates, slow lorises, we quantify public attitudes towards wildlife conservation by analysing 12,411 comments and associated data posted on a viral YouTube video 'tickling slow loris' over a 33-months period. In the initial months a quarter of commentators indicated wanting a loris as a pet, but as facts about their conservation and ecology became more prevalent this dropped significantly. Endorsements, where people were directed to the site by celebrities, resulted mostly in numerous neutral responses with few links to conservation or awareness. Two conservation-related events, linked to Wikipedia and the airing of a television documentary, led to an increase in awareness, and ultimately to the removal of the analysed video. Slow loris videos that have gone viral have introduced these primates to a large cross-section of society that would not normally come into contact with them. Analyses of webometric data posted on the internet allow us quickly to gauge societal sentiments. We showed a clear temporal change in some views expressed but without an apparent increase in knowledge about the conservation plight of the species, or the illegal nature of slow loris trade. Celebrity endorsement of videos showing protected wildlife increases visits to such sites, but does not educate about conservation issues. The strong desire of commentators to express their want for one as a pet demonstrates the need for Web 2.0 sites to provide a mechanism via which illegal animal material can be identified and policed.

Tickled to Death: Analysing Public Perceptions of ‘Cute’ Videos of Threatened Species (Slow Lorises – Nycticebus spp.) on Web 2.0 Sites

PubMed Central

Nekaris, By K. Anne-Isola; Campbell, Nicola; Coggins, Tim G.; Rode, E. Johanna; Nijman, Vincent

2013-01-01

Background The internet is gaining importance in global wildlife trade and changing perceptions of threatened species. There is little data available to examine the impact that popular Web 2.0 sites play on public perceptions of threatened species. YouTube videos portraying wildlife allow us to quantify these perceptions. Methodology/Principal Findings Focussing on a group of threatened and globally protected primates, slow lorises, we quantify public attitudes towards wildlife conservation by analysing 12,411 comments and associated data posted on a viral YouTube video ‘tickling slow loris’ over a 33-months period. In the initial months a quarter of commentators indicated wanting a loris as a pet, but as facts about their conservation and ecology became more prevalent this dropped significantly. Endorsements, where people were directed to the site by celebrities, resulted mostly in numerous neutral responses with few links to conservation or awareness. Two conservation-related events, linked to Wikipedia and the airing of a television documentary, led to an increase in awareness, and ultimately to the removal of the analysed video. Conclusions/Significance Slow loris videos that have gone viral have introduced these primates to a large cross-section of society that would not normally come into contact with them. Analyses of webometric data posted on the internet allow us quickly to gauge societal sentiments. We showed a clear temporal change in some views expressed but without an apparent increase in knowledge about the conservation plight of the species, or the illegal nature of slow loris trade. Celebrity endorsement of videos showing protected wildlife increases visits to such sites, but does not educate about conservation issues. The strong desire of commentators to express their want for one as a pet demonstrates the need for Web 2.0 sites to provide a mechanism via which illegal animal material can be identified and policed. PMID:23894432

New dimension analyses with error analysis for quaking aspen and black spruce

NASA Technical Reports Server (NTRS)

Woods, K. D.; Botkin, D. B.; Feiveson, A. H.

1987-01-01

Dimension analysis for black spruce in wetland stands and trembling aspen are reported, including new approaches in error analysis. Biomass estimates for sacrificed trees have standard errors of 1 to 3%; standard errors for leaf areas are 10 to 20%. Bole biomass estimation accounts for most of the error for biomass, while estimation of branch characteristics and area/weight ratios accounts for the leaf area error. Error analysis provides insight for cost effective design of future analyses. Predictive equations for biomass and leaf area, with empirically derived estimators of prediction error, are given. Systematic prediction errors for small aspen trees and for leaf area of spruce from different site-types suggest a need for different predictive models within species. Predictive equations are compared with published equations; significant differences may be due to species responses to regional or site differences. Proportional contributions of component biomass in aspen change in ways related to tree size and stand development. Spruce maintains comparatively constant proportions with size, but shows changes corresponding to site. This suggests greater morphological plasticity of aspen and significance for spruce of nutrient conditions.

Deep aquifer prokaryotic community responses to CO2 geosequestration

NASA Astrophysics Data System (ADS)

Mu, A.; Moreau, J. W.

2015-12-01

Little is known about potential microbial responses to supercritical CO2 (scCO2) injection into deep subsurface aquifers, a currently experimental means for mitigating atmospheric CO2 pollution being trialed at several locations around the world. One such site is the Paaratte Formation of the Otway Basin (~1400 m below surface; 60°C; 2010 psi), Australia. Microbial responses to scCO2 are important to understand as species selection may result in changes to carbon and electron flow. A key aim is to determine if biofilm may form in aquifer pore spaces and reduce aquifer permeability and storage. This study aimed to determine in situ, using 16S rRNA gene, and functional metagenomic analyses, how the microbial community in the Otway Basin geosequestration site responded to experimental injection of 150 tons of scCO2. We demonstrate an in situ sampling approach for detecting deep subsurface microbial community changes associated with geosequestration. First-order level analyses revealed a distinct shift in microbial community structure following the scCO2 injection event, with proliferation of genera Comamonas and Sphingobium. Similarly, functional profiling of the formation revealed a marked increase in biofilm-associated genes (encoding for poly-β-1,6-N-acetyl-D-glucosamine). Global analysis of the functional gene profile highlights that scCO2 injection potentially degraded the metabolism of CH4 and lipids. A significant decline in carboxydotrophic gene abundance (cooS) and an anaerobic carboxydotroph OTU (Carboxydocella), was observed in post-injection samples. The potential impacts on the flow networks of carbon and electrons to heterotrophs are discussed. Our findings yield insights for other subsurface systems, such as hydrocarbon-rich reservoirs and high-CO2 natural analogue sites.

Deficient prepulse inhibition in schizophrenia in a multi-site cohort: Internal replication and extension.

PubMed

Swerdlow, Neal R; Light, Gregory A; Thomas, Michael L; Sprock, Joyce; Calkins, Monica E; Green, Michael F; Greenwood, Tiffany A; Gur, Raquel E; Gur, Ruben C; Lazzeroni, Laura C; Nuechterlein, Keith H; Radant, Allen D; Seidman, Larry J; Siever, Larry J; Silverman, Jeremy M; Stone, William S; Sugar, Catherine A; Tsuang, Debby W; Tsuang, Ming T; Turetsky, Bruce I; Braff, David L

2017-05-23

The Consortium on the Genetics of Schizophrenia (COGS) collected case-control endophenotype and genetic information from 2457 patients and healthy subjects (HS) across 5 test sites over 3.5 years. Analysis of the first "wave" (W1) of 1400 subjects identified prepulse inhibition (PPI) deficits in patients vs. HS. Data from the second COGS "wave" (W2), and the combined W(1+2), were used to assess: 1) the replicability of PPI deficits in this design; 2) the impact of response criteria on PPI deficits; and 3) PPI in a large cohort of antipsychotic-free patients. PPI in W2 HS (n=315) and schizophrenia patients (n=326) was compared to findings from W1; planned analyses assessed the impact of diagnosis, "wave" (1 vs. 2), and startle magnitude criteria. Combining waves allowed us to assess PPI in 120 antipsychotic-free patients, including many in the early course of illness. ANOVA of all W(1+2) subjects revealed robust PPI deficits in patients across "waves" (p<0.0004). Strict response criteria excluded almost 39% of all subjects, disproportionately impacting specific subgroups; ANOVA in this smaller cohort confirmed no significant effect of "wave" or "wave x diagnosis" interaction, and a significant effect of diagnosis (p<0.002). Antipsychotic-free, early-illness patients had particularly robust PPI deficits. Schizophrenia-linked PPI deficits were replicable across two multi-site "waves" of subjects collected over 3.5years. Strict response criteria disproportionately excluded older, male, non-Caucasian patients with low-normal hearing acuity. These findings set the stage for genetic analyses of PPI using the combined COGS wave 1 and 2 cohorts. Copyright © 2017 Elsevier B.V. All rights reserved.

Improving 1D Site Specific Velocity Profiles for the Kik-Net Network

NASA Astrophysics Data System (ADS)

Holt, James; Edwards, Benjamin; Pilz, Marco; Fäh, Donat; Rietbrock, Andreas

2017-04-01

Ground motion predication equations (GMPEs) form the cornerstone of modern seismic hazard assessments. When produced to a high standard they provide reliable estimates of ground motion/spectral acceleration for a given site and earthquake scenario. This information is crucial for engineers to optimise design and for regulators who enforce legal minimum safe design capacities. Classically, GMPEs were built upon the assumption that variability around the median model could be treated as aleatory. As understanding improved, it was noted that the propagation could be segregated into the response of the average path from the source and the response of the site. This is because the heterogeneity of the near-surface lithology is significantly different from that of the bulk path. It was then suggested that the semi-ergodic approach could be taken if the site response could be determined, moving uncertainty away from aleatory to epistemic. The determination of reliable site-specific response models is therefore becoming increasingly critical for ground motion models used in engineering practice. Today it is common practice to include proxies for site response within the scope of a GMPE, such as Vs30 or site classification, in an effort to reduce the overall uncertainty of the predication at a given site. However, these proxies are not always reliable enough to give confident ground motion estimates, due to the complexity of the near-surface. Other approaches of quantifying the response of the site include detailed numerical simulations (1/2/3D - linear, EQL, non-linear etc.). However, in order to be reliable, they require highly detailed and accurate velocity and, for non-linear analyses, material property models. It is possible to obtain this information through invasive methods, but is expensive, and not feasible for most projects. Here we propose an alternative method to derive reliable velocity profiles (and their uncertainty), calibrated using almost 20 years of recorded data from the Kik-Net network. First, using a reliable subset of sites, the empirical surface to borehole (S/B) ratio is calculated in the frequency domain using all events recorded at that site. In a subsequent step, we use numerical simulation to produce 1D SH transfer function curves using a suite of stochastic velocity models. Comparing the resulting amplification with the empirical S/B ratio we find optimal 1D velocity models and their uncertainty. The method will be tested to determine the level of initial information required to obtain a reliable Vs profile (e.g., starting Vs model, only Vs30, site-class, H/V ratio etc.) and then applied and tested against data from other regions using site-to-reference or empirical spectral model amplification.

Modeled ecohydrological responses to climate change at seven small watersheds in the northeastern United States

USGS Publications Warehouse

Pourmokhtarian, Afshin; Driscoll, Charles T.; Campbell, John L.; Hayhoe, Katharine; Stoner, Anne M. K.; Adams, Mary Beth; Burns, Douglas; Fernandez, Ivan; Mitchell, Myron J.; Shanley, James B.

2017-01-01

A cross-site analysis was conducted on seven diverse, forested watersheds in the northeastern United States to evaluate hydrological responses (evapotranspiration, soil moisture, seasonal and annual streamflow, and water stress) to projections of future climate. We used output from four atmosphere–ocean general circulation models (AOGCMs; CCSM4, HadGEM2-CC, MIROC5, and MRI-CGCM3) included in Phase 5 of the Coupled Model Intercomparison Project, coupled with two Representative Concentration Pathways (RCP 8.5 and 4.5). The coarse resolution AOGCMs outputs were statistically downscaled using an asynchronous regional regression model to provide finer resolution future climate projections as inputs to the deterministic dynamic ecosystem model PnET-BGC. Simulation results indicated that projected warmer temperatures and longer growing seasons in the northeastern United States are anticipated to increase evapotranspiration across all sites, although invoking CO2 effects on vegetation (growth enhancement and increases in water use efficiency (WUE)) diminish this response. The model showed enhanced evapotranspiration resulted in drier growing season conditions across all sites and all scenarios in the future. Spruce-fir conifer forests have a lower optimum temperature for photosynthesis, making them more susceptible to temperature stress than more tolerant hardwood species, potentially giving hardwoods a competitive advantage in the future. However, some hardwood forests are projected to experience seasonal water stress, despite anticipated increases in precipitation, due to the higher temperatures, earlier loss of snow packs, longer growing seasons, and associated water deficits. Considering future CO2effects on WUE in the model alleviated water stress across all sites. Modeled streamflow responses were highly variable, with some sites showing significant increases in annual water yield, while others showed decreases. This variability in streamflow responses poses a challenge to water resource management in the northeastern United States. Our analyses suggest that dominant vegetation type and soil type are important attributes in determining future hydrological responses to climate change.

Modeled ecohydrological responses to climate change at seven small watersheds in the northeastern United States.

PubMed

Pourmokhtarian, Afshin; Driscoll, Charles T; Campbell, John L; Hayhoe, Katharine; Stoner, Anne M K; Adams, Mary Beth; Burns, Douglas; Fernandez, Ivan; Mitchell, Myron J; Shanley, James B

2017-02-01

A cross-site analysis was conducted on seven diverse, forested watersheds in the northeastern United States to evaluate hydrological responses (evapotranspiration, soil moisture, seasonal and annual streamflow, and water stress) to projections of future climate. We used output from four atmosphere-ocean general circulation models (AOGCMs; CCSM4, HadGEM2-CC, MIROC5, and MRI-CGCM3) included in Phase 5 of the Coupled Model Intercomparison Project, coupled with two Representative Concentration Pathways (RCP 8.5 and 4.5). The coarse resolution AOGCMs outputs were statistically downscaled using an asynchronous regional regression model to provide finer resolution future climate projections as inputs to the deterministic dynamic ecosystem model PnET-BGC. Simulation results indicated that projected warmer temperatures and longer growing seasons in the northeastern United States are anticipated to increase evapotranspiration across all sites, although invoking CO 2 effects on vegetation (growth enhancement and increases in water use efficiency (WUE)) diminish this response. The model showed enhanced evapotranspiration resulted in drier growing season conditions across all sites and all scenarios in the future. Spruce-fir conifer forests have a lower optimum temperature for photosynthesis, making them more susceptible to temperature stress than more tolerant hardwood species, potentially giving hardwoods a competitive advantage in the future. However, some hardwood forests are projected to experience seasonal water stress, despite anticipated increases in precipitation, due to the higher temperatures, earlier loss of snow packs, longer growing seasons, and associated water deficits. Considering future CO 2 effects on WUE in the model alleviated water stress across all sites. Modeled streamflow responses were highly variable, with some sites showing significant increases in annual water yield, while others showed decreases. This variability in streamflow responses poses a challenge to water resource management in the northeastern United States. Our analyses suggest that dominant vegetation type and soil type are important attributes in determining future hydrological responses to climate change. © 2016 John Wiley & Sons Ltd.

Cytokinin induces genome-wide binding of the type-B response regulator ARR10 to regulate growth and development in Arabidopsis

PubMed Central

Zubo, Yan O.; Blakley, Ivory Clabaugh; Yamburenko, Maria V.; Worthen, Jennifer M.; Street, Ian H.; Franco-Zorrilla, José M.; Zhang, Wenjing; Raines, Tracy; Kieber, Joseph J.; Loraine, Ann E.

2017-01-01

The plant hormone cytokinin affects a diverse array of growth and development processes and responses to the environment. How a signaling molecule mediates such a diverse array of outputs and how these response pathways are integrated with other inputs remain fundamental questions in plant biology. To this end, we characterized the transcriptional network initiated by the type-B ARABIDOPSIS RESPONSE REGULATORs (ARRs) that mediate the cytokinin primary response, making use of chromatin immunoprecipitation sequencing (ChIP-seq), protein-binding microarrays, and transcriptomic approaches. By ectopic overexpression of ARR10, Arabidopsis lines hypersensitive to cytokinin were generated and used to clarify the role of cytokinin in regulation of various physiological responses. ChIP-seq was used to identify the cytokinin-dependent targets for ARR10, thereby defining a crucial link between the cytokinin primary-response pathway and the transcriptional changes that mediate physiological responses to this phytohormone. Binding of ARR10 was induced by cytokinin with binding sites enriched toward the transcriptional start sites for both induced and repressed genes. Three type-B ARR DNA-binding motifs, determined by use of protein-binding microarrays, were enriched at ARR10 binding sites, confirming their physiological relevance. WUSCHEL was identified as a direct target of ARR10, with its cytokinin-enhanced expression resulting in enhanced shooting in tissue culture. Results from our analyses shed light on the physiological role of the type-B ARRs in regulating the cytokinin response, mechanism of type-B ARR activation, and basis by which cytokinin regulates diverse aspects of growth and development as well as responses to biotic and abiotic factors. PMID:28673986

Pressure-specific and multiple pressure response of fish assemblages in European running waters☆

PubMed Central

Schinegger, Rafaela; Trautwein, Clemens; Schmutz, Stefan

2013-01-01

We classified homogenous river types across Europe and searched for fish metrics qualified to show responses to specific pressures (hydromorphological pressures or water quality pressures) vs. multiple pressures in these river types. We analysed fish taxa lists from 3105 sites in 16 ecoregions and 14 countries. Sites were pre-classified for 15 selected pressures to separate unimpacted from impacted sites. Hierarchical cluster analysis was used to split unimpacted sites into four homogenous river types based on species composition and geographical location. Classification trees were employed to predict associated river types for impacted sites with four environmental variables. We defined a set of 129 candidate fish metrics to select the best reacting metrics for each river type. The candidate metrics represented tolerances/intolerances of species associated with six metric types: habitat, migration, water quality sensitivity, reproduction, trophic level and biodiversity. The results showed that 17 uncorrelated metrics reacted to pressures in the four river types. Metrics responded specifically to water quality pressures and hydromorphological pressures in three river types and to multiple pressures in all river types. Four metrics associated with water quality sensitivity showed a significant reaction in up to three river types, whereas 13 metrics were specific to individual river types. Our results contribute to the better understanding of fish assemblage response to human pressures at a pan-European scale. The results are especially important for European river management and restoration, as it is necessary to uncover underlying processes and effects of human pressures on aquatic communities. PMID:24003262

Controls on seasonal patterns of maximum ecosystem carbon uptake and canopy-scale photosynthetic light response: contributions from both temperature and photoperiod.

PubMed

Stoy, Paul C; Trowbridge, Amy M; Bauerle, William L

2014-02-01

Most models of photosynthetic activity assume that temperature is the dominant control over physiological processes. Recent studies have found, however, that photoperiod is a better descriptor than temperature of the seasonal variability of photosynthetic physiology at the leaf scale. Incorporating photoperiodic control into global models consequently improves their representation of the seasonality and magnitude of atmospheric CO2 concentration. The role of photoperiod versus that of temperature in controlling the seasonal variability of photosynthetic function at the canopy scale remains unexplored. We quantified the seasonal variability of ecosystem-level light response curves using nearly 400 site years of eddy covariance data from over eighty Free Fair-Use sites in the FLUXNET database. Model parameters describing maximum canopy CO2 uptake and the initial slope of the light response curve peaked after peak temperature in about 2/3 of site years examined, emphasizing the important role of temperature in controlling seasonal photosynthetic function. Akaike's Information Criterion analyses indicated that photoperiod should be included in models of seasonal parameter variability in over 90% of the site years investigated here, demonstrating that photoperiod also plays an important role in controlling seasonal photosynthetic function. We also performed a Granger causality analysis on both gross ecosystem productivity (GEP) and GEP normalized by photosynthetic photon flux density (GEP n ). While photoperiod Granger-caused GEP and GEP n in 99 and 92% of all site years, respectively, air temperature Granger-caused GEP in a mere 32% of site years but Granger-caused GEP n in 81% of all site years. Results demonstrate that incorporating photoperiod may be a logical step toward improving models of ecosystem carbon uptake, but not at the expense of including enzyme kinetic-based temperature constraints on canopy-scale photosynthesis.

An Early Pleistocene 190 kyr pollen record from the ODP Site 976, Western Mediterranean region

NASA Astrophysics Data System (ADS)

Joannin, Sebastien; Combourieu Nebout, Nathalie

2010-05-01

The Mid-Pleistocene Transition (1.200 to 0.500 Ma) corresponded to a period of increased cooling and the shift from "41 kyr world" to "100 kyr world". Climate cycles were 41 kyr long as a response of the climate system to the obliquity orbital parameter forcing, then the climate system responded to a combination of eccentricity and precession resulting in 100 kyr long cycles. The Mediterranean region offers the opportunity to study climate response to orbital forcing at this particular period. It is usually done on marine proxies that are preserved in continuous sediments with good age attributions but may be affected by calorific inertia of marine environments. We investigate continental palaeoenvironment changes inferred from pollen analyses through time on a short interval of the ODP Site 976 (259.50 to 230.42 mcd). In order to search for short climate oscillations, the chronology has been refined according to the comparison between the pollen ratio "mesothermic vs. Caryophyllaceae, Amaranthaceae-Chenopodiaceae and steppe elements" curve and Mediterranean and LR04 oxygen isotope curves. The time slice runs from ~1.090 Ma (MIS 31) to ~0.900 Ma (MIS 23). Pollen analyses provide a new record of the south western Mediterranean vegetation and climate changes at the beginning of the Mid-Pleistocene Transition. Vegetation successions are evidenced in pollen diagram with replacement of mesothermic elements by mid- and high-altitude trees, ended by strengthening of Caryophyllaceae, Amaranthaceae-Chenopodiaceae, and steppe vegetation. These vegetation successions reveal two overlapping rhythms that may be related to climate responses to both obliquity and precession orbital parameters, while wavelet analyses on pollen ratio only indicate the shift from precession to obliquity dominance. The comparison of these two approaches raised the question of their own limit.

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

PubMed Central

2012-01-01

Background Through next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years. Simultaneously, the risk of incorporating ‘noisy’ data with misleading phylogenetic signal has also increased, and may disproportionately influence the topology of weakly supported nodes and lineages featuring rapid radiations and/or elevated rates of evolution. Results We investigated the influence of phylogenetic noise in large data sets by applying two fundamental strategies, variable site removal and long-branch exclusion, to the phylogenetic analysis of a full plastome alignment of 107 species of Pinus and six Pinaceae outgroups. While high overall phylogenetic resolution resulted from inclusion of all data, three historically recalcitrant nodes remained conflicted with previous analyses. Close investigation of these nodes revealed dramatically different responses to data removal. Whereas topological resolution and bootstrap support for two clades peaked with removal of highly variable sites, the third clade resolved most strongly when all sites were included. Similar trends were observed using long-branch exclusion, but patterns were neither as strong nor as clear. When compared to previous phylogenetic analyses of nuclear loci and morphological data, the most highly supported topologies seen in Pinus plastome analysis are congruent for the two clades gaining support from variable site removal and long-branch exclusion, but in conflict for the clade with highest support from the full data set. Conclusions These results suggest that removal of misleading signal in phylogenomic datasets can result not only in increased resolution for poorly supported nodes, but may serve as a tool for identifying erroneous yet highly supported topologies. For Pinus chloroplast genomes, removal of variable sites appears to be more effective than long-branch exclusion for clarifying phylogenetic hypotheses. PMID:22731878

Modified Vaccinia Virus Ankara Vector Induces Specific Cellular and Humoral Responses in the Female Reproductive Tract, the Main HIV Portal of Entry.

PubMed

Marlin, Romain; Nugeyre, Marie-Thérèse; Tchitchek, Nicolas; Parenti, Matteo; Hocini, Hakim; Benjelloun, Fahd; Cannou, Claude; Dereuddre-Bosquet, Nathalie; Levy, Yves; Barré-Sinoussi, Françoise; Scarlatti, Gabriella; Le Grand, Roger; Menu, Elisabeth

2017-09-01

The female reproductive tract (FRT) is one of the major mucosal invasion sites for HIV-1. This site has been neglected in previous HIV-1 vaccine studies. Immune responses in the FRT after systemic vaccination remain to be characterized. Using a modified vaccinia virus Ankara (MVA) as a vaccine model, we characterized specific immune responses in all compartments of the FRT of nonhuman primates after systemic vaccination. Memory T cells were preferentially found in the lower tract (vagina and cervix), whereas APCs and innate lymphoid cells were mainly located in the upper tract (uterus and fallopian tubes). This compartmentalization of immune cells in the FRT was supported by transcriptomic analyses and a correlation network. Polyfunctional MVA-specific CD8 + T cells were detected in the blood, lymph nodes, vagina, cervix, uterus, and fallopian tubes. Anti-MVA IgG and IgA were detected in cervicovaginal fluid after a second vaccine dose. Thus, systemic vaccination with an MVA vector elicits cellular and Ab responses in the FRT. Copyright © 2017 by The American Association of Immunologists, Inc.

Posttest analysis of the 1:6-scale reinforced concrete containment

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

Pfeiffer, P.A.; Kennedy, J.M.; Marchertas, A.H.

A prediction of the response of the Sandia National Laboratories 1:6- scale reinforced concrete containment model test was made by Argonne National Laboratory. ANL along with nine other organizations performed a detailed nonlinear response analysis of the 1:6-scale model containment subjected to overpressurization in the fall of 1986. The two-dimensional code TEMP-STRESS and the three-dimensional NEPTUNE code were utilized (1) to predict the global response of the structure, (2) to identify global failure sites and the corresponding failure pressures and (3) to identify some local failure sites and pressure levels. A series of axisymmetric models was studied with the two-dimensionalmore » computer program TEMP-STRESS. The comparison of these pretest computations with test data from the containment model has provided a test for the capability of the respective finite element codes to predict global failure modes, and hence serves as a validation of these codes. Only the two-dimensional analyses will be discussed in this paper. 3 refs., 10 figs.« less

HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells

PubMed Central

Zhang, Shaofei; Zhu, Iris; Deng, Tao; Furusawa, Takashi; Rochman, Mark; Vacchio, Melanie S.; Bosselut, Remy; Yamane, Arito; Casellas, Rafael; Landsman, David; Bustin, Michael

2016-01-01

The activation of naïve B lymphocyte involves rapid and major changes in chromatin organization and gene expression; however, the complete repertoire of nuclear factors affecting these genomic changes is not known. We report that HMGN proteins, which bind to nucleosomes and affect chromatin structure and function, co-localize with, and maintain the intensity of DNase I hypersensitive sites genome wide, in resting but not in activated B cells. Transcription analyses of resting and activated B cells from wild-type and Hmgn−/− mice, show that loss of HMGNs dampens the magnitude of the transcriptional response and alters the pattern of gene expression during the course of B-cell activation; defense response genes are most affected at the onset of activation. Our study provides insights into the biological function of the ubiquitous HMGN chromatin binding proteins and into epigenetic processes that affect the fidelity of the transcriptional response during the activation of B cell lymphocytes. PMID:27112571

Seismic responses of two adjacent buildings. I. Data and analyses

USGS Publications Warehouse

Çelebi, Mehmet

1993-01-01

In this two-part paper, responses of two, adjacent, seven-story buildings in Norwalk, California, to the Whittier-Narrows, Calif, earthquake of Oct. 1, 1987 are studied. Building A, instrumented according to code recommendations, and building B, extensively instrumented, are offset by 16.3 m from one another. The data set includes motions from the superstructure of both buildings, from a downhole below the foundation of building B, and from three free-field sites. Part I of the paper includes descriptions of the buildings, site, instrumentation, and analysis of the data of each building. System identification and spectral analysis techniques are employed in part I. Building A has identical first-mode frequencies of 0.65 Hz for both building axes. The strong-motion response characteristics of building A are considerably different than those determined from low-amplitude tests. Building B has fundamental modes at 0.76 Hz and 0.83 Hz in the major and minor axes, respectively. Torsional and diaphragm effects in building B are negligible.

Responses in bird communities to wildland fires in southern California

USGS Publications Warehouse

Mendelsohn, Mark B.; Brehme, Cheryl S.; Rochester, Carlton J.; Stokes, Drew C.; Hathaway, Stacie A.; Fisher, Robert N.

2008-01-01

There is a growing body of literature covering the responses of bird species to wildland fire events. Our study was unique among these because we investigated the effects of large-scale wildland fires on entire bird communities across multiple vegetation types. We conducted avian point counts during the breeding seasons for two years before and two years after the Cedar and Otay Fires in 2003 in southern California. Our balanced sampling effort took place at two sites, one low-elevation and one high-elevation, each containing replicate stations (burned and unburned) within five vegetation types: chaparral, coastal sage scrub, grassland, oak woodland, and riparian. Although fire caused some degree of change in the vegetation structure at all of our impacted survey points, we found that the post-fire shrub and tree cover was significantly lower in only two of the vegetation types within the low-elevation site, coastal sage scrub and chaparral. We found no significant changes in cover at the high-elevation site. Using univariate and multivariate analyses, we tested whether the fires were associated with a change in bird species diversity, community structure, and the relative abundance of individuals within a species. We found that species diversity changed in only one circumstance: it increased in coastal sage scrub at the low-elevation site. Multivariate analyses revealed significant differences in the post-fire bird community structure in the low-elevation chaparral, low-elevation coastal sage scrub, and the high-elevation grassland communities. Vegetation characteristics altered by fire, such as decreases in shrub and tree cover, influenced the changes we observed in the bird communities. The relative abundance of some species (lazuli bunting [Passerina amoena] and horned lark [Eremophila alpestris]) significantly increased after the fires, while other species declined significantly (Anna's hummingbird [Calypte anna], wrentit [Chamaea fasciata], and bushtit [Psaltriparus minimus]). We detected mixed results for the spotted towhee (Pipilo maculatus), which increased in burned chaparral and declined in burned coastal sage scrub within the low-elevation site. We suggest that the observed responses of birds to these fires may be attributed to: (1) the availability of nearby unburned refugia, (2) the continued suitability of post-fire vegetation at the study sites, and (3) the generally high mobility of this taxon.

Response of key stress-related genes of the seagrass Posidonia oceanica in the vicinity of submarine volcanic vents

NASA Astrophysics Data System (ADS)

Lauritano, C.; Ruocco, M.; Dattolo, E.; Buia, M. C.; Silva, J.; Santos, R.; Olivé, I.; Costa, M. M.; Procaccini, G.

2015-03-01

Submarine volcanic vents are being used as natural laboratories to assess the effects of CO2 on marine organisms and communities, as this gas is the main component of emissions. Seagrasses should positively react to increased dissolved carbon, but in vicinity of volcanic vents there may be toxic substances, that can have indirect effects on seagrasses. Here we analysed the expression of 35 stress-related genes in the Mediterranean keystone seagrass species P. oceanica in the vicinity of submerged volcanic vents located in the Islands of Ischia and Panarea, Italy, and compared them with those from control sites away from the influence of vents. Reverse Transcription-Quantitative Polymerase Chain Reaction (RT-qPCR) was used to characterize the expression levels of genes. Fifty one per cent of genes analysed showed significant expression changes. Metal detoxification genes were mostly down-regulated in relation to controls both in Ischia and Panarea locations, indicating that P. oceanica does not increase the synthesis of heavy metal detoxification proteins in response to the environmental conditions present at the two vents. The expression levels of genes involved in free radical detoxification indicate that, in contrast with Ischia, P. oceanica at the Panarea vent face stressors that result in the production of reactive oxygen species triggering antioxidant responses. In addition, heat shock proteins were also activated at Panarea and not at Ischia. Overall, our study reveals that P. oceanica is generally under higher stress in the vicinity of the vents at Panarea than at Ischia, possibly resulting from environmental and evolutionary differences existing between the two volcanic sites. This is the first study analysing gene responses in marine plants living near natural CO2 vents and our results call for a careful consideration of factors, other than CO2 and acidification, that can cause stress to seagrasses and other organisms near volcanic vents.

Tree growth-climate relationships in a forest-plot network on Mediterranean mountains.

PubMed

Fyllas, Nikolaos M; Christopoulou, Anastasia; Galanidis, Alexandros; Michelaki, Chrysanthi Z; Dimitrakopoulos, Panayiotis G; Fulé, Peter Z; Arianoutsou, Margarita

2017-11-15

In this study we analysed a novel tree-growth dataset, inferred from annual ring-width measurements, of 7 forest tree species from 12 mountain regions in Greece, in order to identify tree growth - climate relationships. The tree species of interest were: Abies cephalonica, Abies borisii-regis, Picea abies, Pinus nigra, Pinus sylvestris, Fagus sylvatica and Quercus frainetto growing across a gradient of climate conditions with mean annual temperature ranging from 5.7 to 12.6°C and total annual precipitation from 500 to 950mm. In total, 344 tree cores (one per tree) were analysed across a network of 20 study sites. We found that water availability during the summer period (May-August) was a strong predictor of interannual variation in tree growth for all study species. Across species and sites, annual tree growth was positively related to summer season precipitation (P SP ). The responsiveness of annual growth to P SP was tightly related to species and site specific measurements of instantaneous photosynthetic water use efficiency (WUE), suggesting that the growth of species with efficient water use is more responsive to variations in precipitation during the dry months of the year. Our findings support the importance of water availability for the growth of mountainous Mediterranean tree species and highlight that future reductions in precipitation are likely to lead to reduced tree-growth under climate change conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Biomarker responses and contamination levels in the clam Ruditapes philippinarum for biomonitoring the Lagoon of Venice (Italy).

PubMed

Matozzo, Valerio; Binelli, Andrea; Parolini, Marco; Locatello, Lisa; Marin, Maria Gabriella

2010-03-01

A multibiomarker approach was used to assess effects of environmental contaminants in the clam Ruditapes philippinarum from the Lagoon of Venice. Bivalves were collected in 8 sites of the Lagoon (Campalto, Marghera, Palude del Monte, Valle di Brenta, Cà Roman, San Servolo, Fusina and Canale Dese), differently influenced by both anthropogenic impact and natural conditions. The following biomarkers were chosen: total haemocyte count and lysozyme activity in cell-free haemolymph as immunomarkers, acetylcholinesterase activity in gills as a biomarker of exposure to neurotoxic compounds, vitellogenin-like protein levels in both digestive gland and cell-free haemolymph as a biomarker of exposure to estrogenic compounds, and survival-in-air widely used to evaluate general stress conditions in clams. In addition, polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), 1,1,1-Trichloro-2,2-bis(p-chlorophenyl)ethane (p,p'-DDT) and its breakdown products (DDE, DDD), hexachlorobenzene (HCB) and hexachlorocyclohexane (HCH) were measured in clams. Results demonstrated that the integrated approach between biomarkers and chemical analyses in R. philippinarum is a useful tool in biomonitoring the Lagoon of Venice. The biomarker responses suggested quite similar contamination levels in the entire Lagoon, although the relative impact of differing classes of pollutants changed among sites according to potential sources, as chemical analyses demonstrated. Overall, among the sampling sites investigated, Palude del Monte can represent an environmental risk area, bearing in mind its peculiar use for clam culture.

The wheat homolog of putative nucleotide-binding site-leucine-rich repeat resistance gene TaRGA contributes to resistance against powdery mildew.

PubMed

Wang, Defu; Wang, Xiaobing; Mei, Yu; Dong, Hansong

2016-03-01

Powdery mildew, one of the most destructive wheat diseases worldwide, is caused by Blumeria graminis f. sp. tritici (Bgt), a fungal species with a consistently high mutation rate that makes individual resistance (R) genes ineffective. Therefore, effective resistance-related gene cloning is vital for breeding and studying the resistance mechanisms of the disease. In this study, a putative nucleotide-binding site-leucine-rich repeat (NBS-LRR) R gene (TaRGA) was cloned using a homology-based cloning strategy and analyzed for its effect on powdery mildew disease and wheat defense responses. Real-time reverse transcription-PCR (RT-PCR) analyses revealed that a Bgt isolate 15 and salicylic acid stimulation significantly induced TaRGA in the resistant variety. Furthermore, the silencing of TaRGA in powdery mildew-resistant plants increased susceptibility to Bgt15 and prompted conidia propagation at the infection site. However, the expression of TaRGA in leaf segments after single-cell transient expression assay highly increased the defense responses to Bgt15 by enhancing callose deposition and phenolic autofluorogen accumulation at the pathogen invading sites. Meanwhile, the expression of pathogenesis-related genes decreased in the TaRGA-silenced plants and increased in the TaRGA-transient-overexpressing leaf segments. These results implied that the TaRGA gene positively regulates the defense response to powdery mildew disease in wheat.

Archaeology of fire: Methodological aspects of reconstructing fire history of prehistoric archaeological sites

NASA Astrophysics Data System (ADS)

Alperson-Afil, Nira

2012-07-01

Concepts which are common in the reconstruction of fire histories are employed here for the purpose of interpreting fires identified at archaeological sites. When attempting to evaluate the fire history of ancient occupations we are limited by the amount and quality of the available data. Furthermore, the identification of archaeological burned materials, such as stone, wood, and charcoal, is adequate for the general assumption of a "fire history", but the agent responsible - anthropogenic or natural - cannot be inferred from the mere presence of burned items. The large body of scientific data that has accumulated, primarily through efforts to prevent future fire disasters, enables us to reconstruct scenarios of past natural fires. Adopting this line of thought, this paper attempts to evaluate the circumstances in which a natural fire may have ignited and spread at the 0.79 Ma occupation site of Gesher Benot Ya'aqov (Israel), resulting with burned wood and burned flint within the archaeological layers. At Gesher Benot Ya'aqov, possible remnants of hearths are explored through analyses of the spatial distribution of burned flint-knapping waste products. These occur in dense clusters in each of the archaeological occupations throughout the long stratigraphic sequence. In this study, the combination between the spatial analyses results, paleoenvironmental information, and various factors involved in the complex process of fire ignition, combustion, and behavior, has enabled the firm rejection of recurrent natural fires as the responsible agent for the burned materials. In addition, it suggested that mainly at early sites, where evidence for burning is present yet scarce, data on fire ecology can be particularly useful when it is considered in relation to paleoenvironmental information.

A Comparison of Forest Survey Data with Forest Dynamics Simulators FORCLIM and ZELIG along Climatic Gradients in the Pacific Northwest

USGS Publications Warehouse

Busing, Richard T.; Solomon, Allen M.

2004-01-01

Two forest dynamics simulators are compared along climatic gradients in the Pacific Northwest. The ZELIG and FORCLIM models are tested against forest survey data from western Oregon. Their ability to generate accurate patterns of forest basal area and species composition is evaluated for series of sites with contrasting climate. Projections from both models approximate the basal area and composition patterns for three sites along the elevation gradient at H.J. Andrews Experimental Forest in the western Cascade Range. The ZELIG model is somewhat more accurate than FORCLIM at the two low-elevation sites. Attempts to project forest composition along broader climatic gradients reveal limitations of ZELIG, however. For example, ZELIG is less accurate than FORCLIM at projecting the average composition of a west Cascades ecoregion selected for intensive analysis. Also, along a gradient consisting of several sites on an east to west transect at 44.1oN latitude, both the FORCLIM model and the actual data show strong changes in composition and total basal area, but the ZELIG model shows a limited response. ZELIG does not simulate the declines in forest basal area and the diminished dominance of mesic coniferous species east of the Cascade crest. We conclude that ZELIG is suitable for analyses of certain sites for which it has been calibrated. FORCLIM can be applied in analyses involving a range of climatic conditions without requiring calibration for specific sites.

Ecosystem processes and human influences regulate streamflow response to climate change at long-term ecological research sites

Treesearch

Julia A. Jones; Irena F. Creed; Kendra L. Hatcher; Robert J. Warren; Mary Beth Adams; Melinda H. Benson; Emery Boose; Warren A. Brown; John L. Campbell; Alan Covich; David W. Clow; Clifford N. Dahm; Kelly Elder; Chelcy R. Ford; Nancy B. Grimm; Donald L Henshaw; Kelli L. Larson; Evan S. Miles; Kathleen M. Miles; Stephen D. Sebestyen; Adam T. Spargo; Asa B. Stone; James M. Vose; Mark W. Williams

2012-01-01

Analyses of long-term records at 35 headwater basins in the United States and Canada indicate that climate change effects on streamflow are not as clear as might be expected, perhaps because of ecosystem processes and human influences. Evapotranspiration was higher than was predicted by temperature in water-surplus ecosystems and lower than was predicted in water-...

Assessing pollution in marine protected areas: the role of a multi-biomarker and multi-organ approach.

PubMed

Gusso-Choueri, Paloma Kachel; Choueri, Rodrigo Brasil; de Araújo, Giuliana Seraphim; Cruz, Ana Carolina Feitosa; Stremel, Tatiana; Campos, Sandro; Abessa, Denis Moledo de Sousa; Ribeiro, Ciro Alberto Oliveira

2015-11-01

Marine protected areas (MPAs) are vulnerable to many pressures, including pollution. However, environmental quality monitoring in these areas traditionally relies on only water chemistry and microbiological parameters. The goal of the current study was to investigate the role of a set of biomarkers in different target organs (liver, kidney, and gills) of fish in order to assess the environmental quality of an MPA (MTs, GPx, GST, GSH, DNA damage, LPO, AChE, and condition index). Chemical analyses were also performed on liver and muscle tissues to evaluate metal body burdens, and PAHs were identified in bile. A demersal fish (Cathorops spixii) that is widely consumed by the local population was used as bioindicator species, and the results were integrated using multivariate analysis. The use of the biomarker approach allowed for the identification of both seasonal and spatial variations in pollution sources around the Environmental Protected Area of Cananéia-Iguape-Peruíbe (APA-CIP). Higher metal body burdens associated with biological responses were found in the sites under the influence of urban areas during the dry season, and they were found in the sites under the influence of the Ribeira de Iguape River (RIR) during the rainy season. The liver was found to be more responsive in terms of its antioxidant responses, whereas gills were found to be more responsive to biomarkers of effect. These results show that this set of biomarker analyses in different organs of fish is a useful tool for assessing chemical pollution in an MPA.

Evolutionary Analysis of Structural Protein Gene VP1 of Foot-and-Mouth Disease Virus Serotype Asia 1

PubMed Central

Zhang, Qingxun; Liu, Xinsheng; Fang, Yuzhen; Pan, Li; Lv, Jianliang; Zhang, Zhongwang; Zhou, Peng; Ding, Yaozhong; Chen, Haotai; Shao, Junjun; Zhao, Furong; Lin, Tong; Chang, Huiyun; Zhang, Jie; Wang, Yonglu; Zhang, Yongguang

2015-01-01

Foot-and-mouth disease virus (FMDV) serotype Asia 1 was mostly endemic in Asia and then was responsible for economically important viral disease of cloven-hoofed animals, but the study on its selection and evolutionary process is comparatively rare. In this study, we characterized 377 isolates from Asia collected up until 2012, including four vaccine strains. Maximum likelihood analysis suggested that the strains circulating in Asia were classified into 8 different groups (groups I–VIII) or were unclassified (viruses collected before 2000). On the basis of divergence time analyses, we infer that the TMRCA of Asia 1 virus existed approximately 86.29 years ago. The result suggested that the virus had a high mutation rate (5.745 × 10−3 substitutions/site/year) in comparison to the other serotypes of FMDV VP1 gene. Furthermore, the structural protein VP1 was under lower selection pressure and the positive selection occurred at many sites, and four codons (positions 141, 146, 151, and 169) were located in known critical antigenic residues. The remaining sites were not located in known functional regions and were moderately conserved, and the reason for supporting all sites under positive selection remains to be elucidated because the power of these analyses was largely unknown. PMID:25793223

Functional overload increases beta-MHC promoter activity in rodent fast muscle via the proximal MCAT (betae3) site.

PubMed

Giger, Julia M; Haddad, Fadia; Qin, Anqi X; Baldwin, Kenneth M

2002-03-01

Functional overload (OL) of the rat plantaris muscle by the removal of synergistic muscles induces a shift in the myosin heavy chain (MHC) isoform expression profile from the fast isoforms toward the slow type I, or, beta-MHC isoform. Different length rat beta-MHC promoters were linked to a firefly luciferase reporter gene and injected in control and OL plantaris muscles. Reporter activities of -3,500, -914, -408, and -215 bp promoters increased in response to 1 wk of OL. The smallest -171 bp promoter was not responsive to OL. Mutation analyses of putative regulatory elements within the -171 and -408 bp region were performed. The -408 bp promoters containing mutations of the betae1, distal muscle CAT (MCAT; betae2), CACC, or A/T-rich (GATA), were still responsive to OL. Only the proximal MCAT (betae3) mutation abolished the OL response. Gel mobility shift assays revealed a significantly higher level of complex formation of the betae3 probe with nuclear protein from OL plantaris compared with control plantaris. These results suggest that the betae3 site functions as a putative OL-responsive element in the rat beta-MHC gene promoter.

Lateralisation effect in comprehension of emotional facial expression: a comparison between EEG alpha band power and behavioural inhibition (BIS) and activation (BAS) systems.

PubMed

Balconi, Michela; Mazza, Guido

2010-05-01

Asymmetry in comprehension of facial expression of emotions was explored in the present study by analysing alpha band variation within the right and left cortical sides. Second, the behavioural activation system (BAS) and behavioural inhibition system (BIS) were considered as an explicative factor to verify the effect of a motivational/emotional variable on alpha activity. A total of 19 participants looked at an ample range of facial expressions of emotions (anger, fear, surprise, disgust, happiness, sadness, and neutral) in random order. The results demonstrated that anterior frontal sites were more active than central and parietal sites in response to facial stimuli. Moreover, right and left side responses varied as a function of emotional types, with an increased right frontal activity for negative, aversive emotions vs an increased left response for positive emotion. Finally, whereas higher BIS participants generated more right hemisphere activation for some negative emotions (such as fear, anger, surprise, and disgust), BAS participants were more responsive to positive emotion (happiness) within the left hemisphere. Motivational significance of facial expressions was considered to elucidate cortical differences in participants' responses to emotional types.

Report of the Peer Review Panel on the early site suitability evaluation of the Potential Repository Site at Yucca Mountain, Nevada; Yucca Mountain Site Characterization Project

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

NONE

1992-01-01

The US Department of Energy (DOE) Yucca mountain Site Characterization Project Office (YMPO) assigned Science Applications International Corporation (SAIC), the Technical and Management Support Services (T&MSS) contractor to the YmPo, the task of conducting an Early Site Suitability Evaluation (ESSE) of the Yucca mountain site as a potential site for a high-level radioactive waste repository. First, the assignment called for the development of a method to evaluate a single site against the DOE General Guidelines for Recommendation of Sites for Nuclear Waste Repositories, 10 CFR Part 960. Then, using this method, an evaluation team, the ESSE Core Team, of seniormore » YMP scientists, engineers, and technical experts, evaluated new information obtained about the site since publication of the final Environmental Assessment (DOE, 1986) to determine if new suitability/unsuitability findings could be recommended. Finally, the Core Team identified further information and analyses needed to make final determinations for each of the guidelines. As part of the task, an independent peer review of the ESSE report has been conducted. Expertise was solicited that covered the entire spectrum of siting guidelines in 10 CFR Part 960 in order to provide a complete, in-depth critical review of the data evaluated and cited in the ESSE report, the methods used to evaluate the data, and the conclusions and recommendations offered by the report. Fourteen nationally recognized technical experts (Table 2) served on the Peer Review Panel. The comments from the Panel and the responses prepared by the ESSE Core Team, documented on formal Comment Response Forms, constitute the body of this document.« less

Recovery of perennial vegetation in military target sites in the eastern Mohave Desert, Arizona

USGS Publications Warehouse

Steiger, John W.; Webb, Robert H.

2000-01-01

The effect of the age of geomorphic surfaces on the recovery of desert vegetation in military target sites was studied in the Mohave and Cerbat Mountains of northwestern Arizona. The target sites were cleared of all vegetation during military exercises in 1942-1943 and have not been subsequently disturbed. The degree of recovery was measured by calculating percentage-similarity (PS) and correlation-coefficient indices on the basis of differences in cover, density, and volume of species growing in and out of each target site. PS values, ranging from 22.7 to 95.1 percent (100 percent = identical composition), indicate a wide range of recovery that is partially controlled by the edaphic properties of the geomorphic surfaces. Statistical analyses show a strong pattern that indicates a greater variability in the degree of recovery for sites on older surfaces than on younger surfaces and a weak pattern that indicates an inverse relation between the degree of recovery and geomorphic age. Comparisons of the different effects of target site construction on the edaphic characteristics of each target site provides an explanation for these patterns and suggests the soil properties critical to the recovery process. Statistically significant negative or positive response to disturbance for most species are independent of the age of the geomorphic surfaces; however, there is strong evidence for a shift in response for the common perennial species Acamptopappus sphaerocephalus, and to a lesser extent, Salazaria mexicana, Encelia farinosa, and Coldenia canescens, among different geomorphic surfaces.

Effect of site level environmental variables, spatial autocorrelation and sampling intensity on arthropod communities in an ancient temperate lowland woodland area.

PubMed

Horak, Jakub

2013-01-01

The interaction of arthropods with the environment and the management of their populations is a focus of the ecological agenda. Spatial autocorrelation and under-sampling may generate bias and, when they are ignored, it is hard to determine if results can in any way be trusted. Arthropod communities were studied during two seasons and using two methods: window and panel traps, in an area of ancient temperate lowland woodland of Zebracka (Czech Republic). The composition of arthropod communities was studied focusing on four site level variables (canopy openness, diameter in the breast height and height of tree, and water distance) and finally analysed using two approaches: with and without effects of spatial autocorrelation. I found that the proportion of variance explained by space cannot be ignored (≈20% in both years). Potential bias in analyses of the response of arthropods to site level variables without including spatial co-variables is well illustrated by redundancy analyses. Inclusion of space led to more accurate results, as water distance and tree diameter were significant, showing approximately the same ratio of explained variance and direction in both seasons. Results without spatial co-variables were much more disordered and were difficult to explain. This study showed that neglecting the effects of spatial autocorrelation could lead to wrong conclusions in site level studies and, furthermore, that inclusion of space may lead to more accurate and unambiguous outcomes. Rarefactions showed that lower sampling intensity, when appropriately designed, can produce sufficient results without exploitation of the environment.

Tumour response endpoints in the BA1112 rat sarcoma.

PubMed Central

Martin, D. F.; Moulder, J. E.; Fischer, J. J.

1980-01-01

The rat rhabdomyosarcoma BA1112 has a number of features which make it a useful model for the study of tumour response to radiation therapy. It is a transplantable tumour, isologous to an inbred line of WAG/Rij rats and it elicits no demonstrable host immune response. The tumour grows locally at the implantation site and rarely metastasizes. It is known to contain hypoxic cells which reoxygenate during a prolonged course of fractionated radiation therapy. The growth and radiation response characteristics of the tumour have remained stable for over 15 years. A newly developed in vitro assay for tumour cell clonogenicity greatly facilitates the measurement of radiation dose-response curves and the monitoring of cell response following in vivo treatment. The in vivo response of the tumour to fractionated radiation therapy is analysed in terms of cellular response, reoxygenation and cell proliferation. PMID:6932936

Impacts of wastewater treatment plant effluent on energetics and stress response of rainbow darter (Etheostoma caeruleum) in the Grand River watershed.

PubMed

Mehdi, Hossein; Dickson, Fiona H; Bragg, Leslie M; Servos, Mark R; Craig, Paul M

2017-11-22

The objective of this study was to assess the effects of municipal wastewater treatment plant effluent on the energetics and stress response of rainbow darter (Etheostoma caeruleum). Male and female rainbow darter were collected upstream and downstream of the Waterloo WWTP in the Grand River watershed, ON, Canada. To assess the effects of wastewater treatment plant effluent on whole-body and tissue specific metabolic capacity, closed-chamber respirometry and muscle-enzyme activity analyses were performed. Plasma cortisol was also collected from fish before and after an acute air-exposure stressor to evaluate the cortisol stress response in fish exposed to additional stressors. Male and female rainbow darter collected downstream of the effluent had higher oxygen consumption rates, while differences in enzyme activities were primarily associated with sex rather than collection site. No impairment in the cortisol stress response between downstream and upstream fish was observed, however baseline cortisol levels in female fish from the downstream site were significantly higher compared to other baseline groups. Stress-induced cortisol levels were also higher in female fish from both sites when compared to their male counterparts. Overall, this study demonstrates that chronic exposure to WWTP effluent impacts whole-body metabolic performance. This study was also able to demonstrate that sex-differences are a key determinant of various metabolic changes in response to physiological stress, thereby, providing a novel avenue to be considered and further explored. Copyright © 2017 Elsevier Inc. All rights reserved.

Climate variability slows evolutionary responses of Colias butterflies to recent climate change.

PubMed

Kingsolver, Joel G; Buckley, Lauren B

2015-03-07

How does recent climate warming and climate variability alter fitness, phenotypic selection and evolution in natural populations? We combine biophysical, demographic and evolutionary models with recent climate data to address this question for the subalpine and alpine butterfly, Colias meadii, in the southern Rocky Mountains. We focus on predicting patterns of selection and evolution for a key thermoregulatory trait, melanin (solar absorptivity) on the posterior ventral hindwings, which affects patterns of body temperature, flight activity, adult and egg survival, and reproductive success in Colias. Both mean annual summer temperatures and thermal variability within summers have increased during the past 60 years at subalpine and alpine sites. At the subalpine site, predicted directional selection on wing absorptivity has shifted from generally positive (favouring increased wing melanin) to generally negative during the past 60 years, but there is substantial variation among years in the predicted magnitude and direction of selection and the optimal absorptivity. The predicted magnitude of directional selection at the alpine site declined during the past 60 years and varies substantially among years, but selection has generally been positive at this site. Predicted evolutionary responses to mean climate warming at the subalpine site since 1980 is small, because of the variability in selection and asymmetry of the fitness function. At both sites, the predicted effects of adaptive evolution on mean population fitness are much smaller than the fluctuations in mean fitness due to climate variability among years. Our analyses suggest that variation in climate within and among years may strongly limit evolutionary responses of ectotherms to mean climate warming in these habitats. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

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.

A decade of insights into grassland ecosystem responses to global environmental change

USGS Publications Warehouse

Borer, Elizabeth T.; Grace, James B.; Harpole, W. Stanley; MacDougall, Andrew S.; Seabloom, Eric W.

2017-01-01

Earth’s biodiversity and carbon uptake by plants, or primary productivity, are intricately interlinked, underlie many essential ecosystem processes, and depend on the interplay among environmental factors, many of which are being changed by human activities. While ecological theory generalizes across taxa and environments, most empirical tests of factors controlling diversity and productivity have been observational, single-site experiments, or meta-analyses, limiting our understanding of variation among site-level responses and tests of general mechanisms. A synthesis of results from ten years of a globally distributed, coordinated experiment, the Nutrient Network (NutNet), demonstrates that species diversity promotes ecosystem productivity and stability, and that nutrient supply and herbivory control diversity via changes in composition, including invasions of non-native species and extinction of native species. Distributed experimental networks are a powerful tool for tests and integration of multiple theories and for generating multivariate predictions about the effects of global changes on future ecosystems.

Groundwater biofilm dynamics grown in situ along a nutrient gradient.

PubMed

Williamson, Wendy M; Close, Murray E; Leonard, Margaret M; Webber, Judith B; Lin, Susan

2012-01-01

This paper describes the in situ response of groundwater biofilms in an alluvial gravel aquifer system on the Canterbury Plains, New Zealand. Biofilms were developed on aquifer gravel, encased in fine mesh bags and suspended in protective columns in monitoring wells for at least 20 weeks. Four sites were selected in the same groundwater system where previous analyses indicated a gradient of increasing nitrate down the hydraulic gradient from Sites 1 to 4. Measurements during the current study classified the groundwater as oligotrophic. Biofilm responses to the nutrient gradients were assessed using bioassays, with biomass determined using protein and cellular and nucleic acid staining and biofilm activity using enzyme assays for lipid, carbohydrate, phosphate metabolism, and cell viability. In general, biofilm activity decreased as nitrate levels increased from Sites 1 to 4, with the opposite relationship for carbon and phosphorus concentrations. These results showed that the groundwater system supported biofilm growth and that the upper catchment supported efficient and productive biofilms (high ratio of activity per unit biomass). © 2012, Institute of Environmental Science & Research Ltd (ESR). Ground Water © 2012, National Ground Water Association.

Rapid assessment of postfire plant invasions in coniferous forests of the western United States

USGS Publications Warehouse

Freeman, J.P.; Stohlgren, T.J.; Hunter, M.E.; Omi, Philip N.; Martinson, E.J.; Chong, G.W.; Brown, C.S.

2007-01-01

Fire is a natural part of most forest ecosystems in the western United States, but its effects on nonnative plant invasion have only recently been studied. Also, forest managers are engaging in fuel reduction projects to lessen fire severity, often without considering potential negative ecological consequences such as nonnative plant species introductions. Increased availability of light, nutrients, and bare ground have all been associated with high-severity fires and fuel treatments and are known to aid in the establishment of nonnative plant species. We use vegetation and environmental data collected after wildfires at seven sites in coniferous forests in the western United States to study responses of nonnative plants to wildfire. We compared burned vs. unburned plots and plots treated with mechanical thinning and/or prescribed burning vs. untreated plots for nonnative plant species richness and cover and used correlation analyses to infer the effect of abiotic site conditions on invasibility. Wildfire was responsible for significant increases in nonnative species richness and cover, and a significant decrease in native cover. Mechanical thinning and prescribed fire fuel treatments were associated with significant changes in plant species composition at some sites. Treatment effects across sites were minimal and inconclusive due to significant site and site x treatment interaction effects caused by variation between sites including differences in treatment and fire severities and initial conditions (e.g., nonnative species sources). We used canonical correspondence analysis (CCA) to determine what combinations of environmental variables best explained patterns of nonnative plant species richness and cover. Variables related to fire severity, soil nutrients, and elevation explained most of the variation in species composition. Nonnative species were generally associated with sites with higher fire severity, elevation, percentage of bare ground, and lower soil nutrient levels and lower canopy cover. Early assessments of postfire stand conditions can guide rapid responses to nonnative plant invasions. ?? 2007 by the Ecological Society of America.

Roles and responsibilities in newborn care in four African sites.

PubMed

Iganus, R; Hill, Z; Manzi, F; Bee, M; Amare, Y; Shamba, D; Odebiyi, A; Adejuyigbe, E; Omotara, B; Skordis-Worrall, J

2015-10-01

To explore roles and responsibilities in newborn care in the intra- and postpartum period in Nigeria, Tanzania and Ethiopia. Qualitative data were collected using in-depth interviews with mothers, grandmothers, fathers, health workers and birth attendants and were analysed through content and framework analyses. We found that birth attendants were the main decision-makers and care takers in the intrapartum period. Birth attendants varied across sites and included female relatives (Ethiopia and Nigeria), traditional birth attendants (Tanzania and Nigeria), spiritual birth attendants (Nigeria) and health workers (Tanzania and Nigeria). In the early newborn period, when the mother is deemed to be resting, female family members assumed this role. The mothers themselves only took full responsibility for newborn care after a few days or weeks. The early newborn period was protracted for first-time mothers, who were perceived as needing training on caring for the baby. Clear gender roles were described, with newborn care being considered a woman's domain. Fathers had little physical contact with the newborn, but played an important role in financing newborn care, and were considered the ultimate decision-maker in the family. Interventions should move beyond a focus on the mother-child dyad, to include other carers who perform and decide on newborn care practices. Given this power dynamic, interventions that involve men have the potential to result in behaviour change. © 2015 The Authors. Tropical Medicine & International Health Published by John Wiley & Sons Ltd.

Institutional racism in public health contracting: Findings of a nationwide survey from New Zealand.

PubMed

Came, H; Doole, C; McKenna, B; McCreanor, T

2018-02-01

Public institutions within New Zealand have long been accused of mono-culturalism and institutional racism. This study sought to identify inconsistencies and bias by comparing government funded contracting processes for Māori public health providers (n = 60) with those of generic providers (n = 90). Qualitative and quantitative data were collected (November 2014-May 2015), through a nationwide telephone survey of public health providers, achieving a 75% response rate. Descriptive statistical analyses were applied to quantitative responses and an inductive approach was taken to analyse data from open-ended responses in the survey domains of relationships with portfolio contract managers, contracting and funding. The quantitative data showed four sites of statistically significant variation: length of contracts, intensity of monitoring, compliance costs and frequency of auditing. Non-significant data involved access to discretionary funding and cost of living adjustments, the frequency of monitoring, access to Crown (government) funders and representation on advisory groups. The qualitative material showed disparate provider experiences, dependent on individual portfolio managers, with nuanced differences between generic and Māori providers' experiences. This study showed that monitoring government performance through a nationwide survey was an innovative way to identify sites of institutional racism. In a policy context where health equity is a key directive to the health sector, this study suggests there is scope for New Zealand health funders to improve their contracting practices. Copyright © 2017 Elsevier Ltd. All rights reserved.

76 FR 24831 - Site-Specific Analyses for Demonstrating Compliance With Subpart C Performance Objectives

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-03

... available under ADAMS accession number ML111040419, and the ``Technical Analysis Supporting Definition of... NUCLEAR REGULATORY COMMISSION 10 CFR Part 61 RIN 3150-AI92 [NRC-2011-0012] Site-Specific Analyses...-level radioactive waste disposal facilities to conduct site-specific analyses to demonstrate compliance...

Solar arc method for the analysis of burial places in Eneolithic

NASA Astrophysics Data System (ADS)

Szucs-Csillik, Iharka; Comsa, Alexandra

2017-12-01

In this study is presented the solar arc method used in the NeolithicEneolithic of central Europe to analyse and compare three sites of the Gumelnitţa culture: V\\varǎşti-Grǎdiştea Ulmilor, Dridu and Durankulak. The scope of this paper is to find the possible responses by alignment difference through the same culture to understand better the Eneolithic period.

Differential histone modification and protein expression associated with cell wall removal and regeneration in rice (Oryza sativa).

PubMed

Tan, Feng; Zhang, Kangling; Mujahid, Hana; Verma, Desh Pal S; Peng, Zhaohua

2011-02-04

The cell wall is a critical extracellular structure that provides protection and structural support in plant cells. To study the biological function of the cell wall and the regulation of cell wall resynthesis, we examined cellular responses to enzymatic removal of the cell wall in rice (Oryza sativa) suspension cells using proteomic approaches. We find that removal of cell wall stimulates cell wall synthesis from multiple sites in protoplasts instead of from a single site as in cytokinesis. Nucleus DAPI stain and MNase digestion further show that removal of the cell wall is concomitant with substantial chromatin reorganization. Histone post-translational modification studies using both Western blots and isotope labeling assisted quantitative mass spectrometry analyses reveal that substantial histone modification changes, particularly H3K18(AC) and H3K23(AC), are associated with the removal and regeneration of the cell wall. Label-free quantitative proteome analyses further reveal that chromatin associated proteins undergo dramatic changes upon removal of the cell wall, along with cytoskeleton, cell wall metabolism, and stress-response proteins. This study demonstrates that cell wall removal is associated with substantial chromatin change and may lead to stimulation of cell wall synthesis using a novel mechanism.

A systematic analysis of factors localized to damaged chromatin reveals PARP-dependent recruitment of transcription factors

PubMed Central

Izhar, Lior; Adamson, Britt; Ciccia, Alberto; Lewis, Jedd; Pontano-Vaites, Laura; Leng, Yumei; Liang, Anthony C.; Westbrook, Thomas F.; Harper, J. Wade; Elledge, Stephen J.

2015-01-01

Localization to sites of DNA damage is a hallmark of DNA damage response (DDR) proteins. To identify new DDR factors, we screened epitope-tagged proteins for localization to sites of chromatin damaged by UV laser microirradiation and found >120 proteins that localize to damaged chromatin. These include the BAF tumor suppressor complex and the ALS candidate protein TAF15. TAF15 contains multiple domains that bind damaged chromatin in a PARP-dependent manner, suggesting a possible role as glue that tethers multiple PAR chains together. Many positives were transcription factors and >70% of randomly tested transcription factors localized to sites of DNA damage and approximately 90% were PARP-dependent for localization. Mutational analyses showed that localization to damaged chromatin is DNA-binding domain-dependent. By examining Hoechst staining patterns at damage sites, we see evidence of chromatin decompaction that is PARP-dependent. We propose that PARP-regulated chromatin remodeling at sites of damage allows transient accessibility of DNA-binding proteins. PMID:26004182

Short-term prey field lability constrains individual specialisation in resource selection and foraging site fidelity in a marine predator.

PubMed

Courbin, Nicolas; Besnard, Aurélien; Péron, Clara; Saraux, Claire; Fort, Jérôme; Perret, Samuel; Tornos, Jérémy; Grémillet, David

2018-04-16

Spatio-temporally stable prey distributions coupled with individual foraging site fidelity are predicted to favour individual resource specialisation. Conversely, predators coping with dynamic prey distributions should diversify their individual diet and/or shift foraging areas to increase net intake. We studied individual specialisation in Scopoli's shearwaters (Calonectris diomedea) from the highly dynamic Western Mediterranean, using daily prey distributions together with resource selection, site fidelity and trophic-level analyses. As hypothesised, we found dietary diversification, low foraging site fidelity and almost no individual specialisation in resource selection. Crucially, shearwaters switched daily foraging tactics, selecting areas with contrasting prey of varying trophic levels. Overall, information use and plastic resource selection of individuals with reduced short-term foraging site fidelity allow predators to overcome prey field lability. Our study is an essential step towards a better understanding of individual responses to enhanced environmental stochasticity driven by global changes, and of pathways favouring population persistence. © 2018 John Wiley & Sons Ltd/CNRS.

Hydraulic properties of three types of glacial deposits in Ohio

USGS Publications Warehouse

Strobel, M.L.

1993-01-01

The effects of thickness, grain size, fractures, weathering, and atmosphericconditions on vertical ground-water flow in glacial deposits were studied at three sites that represent ground moraine, end moraine, and lacustrine depositional environments. Vertical hydraulic conductivities computed from pumped-well tests were 3.24 x 10-1 to 6.47 x 10-1 ft/d (feet per day) at the site representing end moraine and 1.17 ft/d at the site representing lacustrine deposits. Analysis of test data for the ground moraine site did not yield estimates of hydraulic conductivities, but did indicate that ground water flows through the total thickness of deposits in response to discharge from a lower gravel unit. Vertical hydraulic conductivities computed from pumped-well tests of nested wells and data from drill-core analyses indicate that fractures affect the migration of ground water downward through the glacial deposits at these sites. Flow through glacial deposits is complex; it is controlled by fractures, gram-size distribution, clay content, thickness, and degree of weathering, and atmospheric conditions.

Neutralization of Diverse Human Cytomegalovirus Strains Conferred by Antibodies Targeting Viral gH/gL/pUL128-131 Pentameric Complex

PubMed Central

Ha, Sha; Li, Fengsheng; Troutman, Matthew C.; Freed, Daniel C.; Tang, Aimin; Loughney, John W.; Wang, I-Ming; Vlasak, Josef; Nickle, David C.; Rustandi, Richard R.; Hamm, Melissa; DePhillips, Pete A.; Zhang, Ningyan; McLellan, Jason S.; Zhu, Hua; Adler, Stuart P.; McVoy, Michael A.; An, Zhiqiang

2017-01-01

ABSTRACT Human cytomegalovirus (HCMV) is the leading cause of congenital viral infection, and developing a prophylactic vaccine is of high priority to public health. We recently reported a replication-defective human cytomegalovirus with restored pentameric complex glycoprotein H (gH)/gL/pUL128-131 for prevention of congenital HCMV infection. While the quantity of vaccine-induced antibody responses can be measured in a viral neutralization assay, assessing the quality of such responses, including the ability of vaccine-induced antibodies to cross-neutralize the field strains of HCMV, remains a challenge. In this study, with a panel of neutralizing antibodies from three healthy human donors with natural HCMV infection or a vaccinated animal, we mapped eight sites on the dominant virus-neutralizing antigen—the pentameric complex of glycoprotein H (gH), gL, and pUL128, pUL130, and pUL131. By evaluating the site-specific antibodies in vaccine immune sera, we demonstrated that vaccination elicited functional antiviral antibodies to multiple neutralizing sites in rhesus macaques, with quality attributes comparable to those of CMV hyperimmune globulin. Furthermore, these immune sera showed antiviral activities against a panel of genetically distinct HCMV clinical isolates. These results highlighted the importance of understanding the quality of vaccine-induced antibody responses, which includes not only the neutralizing potency in key cell types but also the ability to protect against the genetically diverse field strains. IMPORTANCE HCMV is the leading cause of congenital viral infection, and development of a preventive vaccine is a high public health priority. To understand the strain coverage of vaccine-induced immune responses in comparison with natural immunity, we used a panel of broadly neutralizing antibodies to identify the immunogenic sites of a dominant viral antigen—the pentameric complex. We further demonstrated that following vaccination of a replication-defective virus with the restored pentameric complex, rhesus macaques can develop broadly neutralizing antibodies targeting multiple immunogenic sites of the pentameric complex. Such analyses of site-specific antibody responses are imperative to our assessment of the quality of vaccine-induced immunity in clinical studies. PMID:28077654

Untangling the effects of multiple human stressors and their impacts on fish assemblages in European running waters.

PubMed

Schinegger, Rafaela; Palt, Martin; Segurado, Pedro; Schmutz, Stefan

2016-12-15

This work addresses human stressors and their impacts on fish assemblages at pan-European scale by analysing single and multiple stressors and their interactions. Based on an extensive dataset with 3105 fish sampling sites, patterns of stressors, their combination and nature of interactions, i.e. synergistic, antagonistic and additive were investigated. Geographical distribution and patterns of seven human stressor variables, belonging to four stressor groups (hydrological-, morphological-, water quality- and connectivity stressors), were examined, considering both single and multiple stressor combinations. To quantify the stressors' ecological impact, a set of 22 fish metrics for various fish assemblage types (headwaters, medium gradient rivers, lowland rivers and Mediterranean streams) was analysed by comparing their observed and expected response to different stressors, both acting individually and in combination. Overall, investigated fish sampling sites are affected by 15 different stressor combinations, including 4 stressors acting individually and 11 combinations of two or more stressors; up to 4 stressor groups per fish sampling site occur. Stressor-response analysis shows divergent results among different stressor categories, even though a general trend of decreasing ecological integrity with increasing stressor quantity can be observed. Fish metrics based on density of species 'intolerant to water quality degradation' and 'intolerant to oxygen depletion" responded best to single and multiple stressors and their interactions. Interactions of stressors were additive (40%), synergistic (30%) or antagonistic (30%), emphasizing the importance to consider interactions in multi-stressor analyses. While antagonistic effects are only observed in headwaters and medium-gradient rivers, synergistic effects increase from headwaters over medium gradient rivers and Mediterranean streams to large lowland rivers. The knowledge gained in this work provides a basis for advanced investigations in European river basins and helps prioritizing further restoration and management actions. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Phenology and growth adjustments of oil palm (Elaeis guineensis) to photoperiod and climate variability

PubMed Central

Legros, S.; Mialet-Serra, I.; Caliman, J.-P.; Siregar, F. A.; Clément-Vidal, A.; Dingkuhn, M.

2009-01-01

Background and Aims Oil palm flowering and fruit production show seasonal maxima whose causes are unknown. Drought periods confound these rhythms, making it difficult to analyse or predict dynamics of production. The present work aims to analyse phenological and growth responses of adult oil palms to seasonal and inter-annual climatic variability. Methods Two oil palm genotypes planted in a replicated design at two sites in Indonesia underwent monthly observations during 22 months in 2006–2008. Measurements included growth of vegetative and reproductive organs, morphology and phenology. Drought was estimated from climatic water balance (rainfall – potential evapotranspiration) and simulated fraction of transpirable soil water. Production history of the same plants for 2001–2005 was used for inter-annual analyses. Key Results Drought was absent at the equatorial Kandista site (0°55′N) but the Batu Mulia site (3°12′S) had a dry season with variable severity. Vegetative growth and leaf appearance rate fluctuated with drought level. Yield of fruit, a function of the number of female inflorescences produced, was negatively correlated with photoperiod at Kandista. Dual annual maxima were observed supporting a recent theory of circadian control. The photoperiod-sensitive phases were estimated at 9 (or 9 + 12 × n) months before bunch maturity for a given phytomer. The main sensitive phase for drought effects was estimated at 29 months before bunch maturity, presumably associated with inflorescence sex determination. Conclusion It is assumed that seasonal peaks of flowering in oil palm are controlled even near the equator by photoperiod response within a phytomer. These patterns are confounded with drought effects that affect flowering (yield) with long time-lag. Resulting dynamics are complex, but if the present results are confirmed it will be possible to predict them with models. PMID:19748909

Seismic Safety Of Simple Masonry Buildings

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

Guadagnuolo, Mariateresa; Faella, Giuseppe

2008-07-08

Several masonry buildings comply with the rules for simple buildings provided by seismic codes. For these buildings explicit safety verifications are not compulsory if specific code rules are fulfilled. In fact it is assumed that their fulfilment ensures a suitable seismic behaviour of buildings and thus adequate safety under earthquakes. Italian and European seismic codes differ in the requirements for simple masonry buildings, mostly concerning the building typology, the building geometry and the acceleration at site. Obviously, a wide percentage of buildings assumed simple by codes should satisfy the numerical safety verification, so that no confusion and uncertainty have tomore » be given rise to designers who must use the codes. This paper aims at evaluating the seismic response of some simple unreinforced masonry buildings that comply with the provisions of the new Italian seismic code. Two-story buildings, having different geometry, are analysed and results from nonlinear static analyses performed by varying the acceleration at site are presented and discussed. Indications on the congruence between code rules and results of numerical analyses performed according to the code itself are supplied and, in this context, the obtained result can provide a contribution for improving the seismic code requirements.« less

Expression of genes involved in oxidative stress response in colonies of the ascidian Botryllus schlosseri exposed to various environmental conditions

NASA Astrophysics Data System (ADS)

Tasselli, Stefano; Ballin, Francesca; Franchi, Nicola; Fabbri, Elena; Ballarin, Loriano

2017-03-01

Environmental stress conditions are ultimately related to the induction of oxidative stress in organisms, as a consequence of an increased production of reactive oxygen species (ROS). This could be exploited to study sub-lethal effects induced by the environment in the organisms. In the present work, we evaluate the possibility to use the colonial ascidian Botryllus schlosseri as a bioindicator, to assess the environmental quality in the Lagoon of Venice. Three colony batches were immersed, for 22 days, at two sites (1 and 2) with different grades of hydrodynamics and anthropogenic impact and physico-chemical features of seawater; a control batch was kept in a large tank with continuous seawater flow at the Marine Station of the Department of Biology, University of Padova, in Chioggia (site 3). Seawater at site 2 had higher pH and temperature than site 1. Colonies were then retrieved, their mRNA was extracted and the level of transcription of genes involved in oxidative stress response (glutathione synthase, γ-glutamyl-cysteine ligase, modulatory subunit, two isoforms of glutathione peroxidases and Cu/Zn superoxide dismutase) was evaluated. In colonies from sites 1 and 2, most genes showed significantly increased transcriptional levels with respect to control values. Spectrophotometric analyses of colony homogenates revealed that the enzymatic activity of superoxide dismutase and catalase was higher in colonies from site 2 as compared to site 1, allowing us to speculate that colonies in site 2 were under higher stress level than those in site 1. Overall, we can conclude that B. schlosseri seems a good indicator of the ecological status of the Lagoon environment, within a range of pH and temperature in which colonies are used to live.

The Importance of Biotic vs. Abiotic Drivers of Local Plant Community Composition Along Regional Bioclimatic Gradients

PubMed Central

Klanderud, Kari; Vandvik, Vigdis; Goldberg, Deborah

2015-01-01

We assessed if the relative importance of biotic and abiotic factors for plant community composition differs along environmental gradients and between functional groups, and asked which implications this may have in a warmer and wetter future. The study location is a unique grid of sites spanning regional-scale temperature and precipitation gradients in boreal and alpine grasslands in southern Norway. Within each site we sampled vegetation and associated biotic and abiotic factors, and combined broad- and fine-scale ordination analyses to assess the relative explanatory power of these factors for species composition. Although the community responses to biotic and abiotic factors did not consistently change as predicted along the bioclimatic gradients, abiotic variables tended to explain a larger proportion of the variation in species composition towards colder sites, whereas biotic variables explained more towards warmer sites, supporting the stress gradient hypothesis. Significant interactions with precipitation suggest that biotic variables explained more towards wetter climates in the sub alpine and boreal sites, but more towards drier climates in the colder alpine. Thus, we predict that biotic interactions may become more important in alpine and boreal grasslands in a warmer future, although more winter precipitation may counteract this trend in oceanic alpine climates. Our results show that both local and regional scales analyses are needed to disentangle the local vegetation-environment relationships and their regional-scale drivers, and biotic interactions and precipitation must be included when predicting future species assemblages. PMID:26091266

The Importance of Biotic vs. Abiotic Drivers of Local Plant Community Composition Along Regional Bioclimatic Gradients.

PubMed

Klanderud, Kari; Vandvik, Vigdis; Goldberg, Deborah

2015-01-01

We assessed if the relative importance of biotic and abiotic factors for plant community composition differs along environmental gradients and between functional groups, and asked which implications this may have in a warmer and wetter future. The study location is a unique grid of sites spanning regional-scale temperature and precipitation gradients in boreal and alpine grasslands in southern Norway. Within each site we sampled vegetation and associated biotic and abiotic factors, and combined broad- and fine-scale ordination analyses to assess the relative explanatory power of these factors for species composition. Although the community responses to biotic and abiotic factors did not consistently change as predicted along the bioclimatic gradients, abiotic variables tended to explain a larger proportion of the variation in species composition towards colder sites, whereas biotic variables explained more towards warmer sites, supporting the stress gradient hypothesis. Significant interactions with precipitation suggest that biotic variables explained more towards wetter climates in the sub alpine and boreal sites, but more towards drier climates in the colder alpine. Thus, we predict that biotic interactions may become more important in alpine and boreal grasslands in a warmer future, although more winter precipitation may counteract this trend in oceanic alpine climates. Our results show that both local and regional scales analyses are needed to disentangle the local vegetation-environment relationships and their regional-scale drivers, and biotic interactions and precipitation must be included when predicting future species assemblages.

Wind/seismic comparisons for upgrading existing structures

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

Giller, R.A.

1989-10-01

This paper depicts the analysis procedures and methods used to evaluate three existing building structures for extreme wind loads. The three structures involved in this evaluation are located at the US Department of Energy's Hanford Site near Richland, Washington. This site is characterized by open flat grassland with few surrounding obstructions and has extreme winds in lieu of tornados as a design basis accident condition. This group of buildings represents a variety of construction types, including a concrete stack, a concrete load-bearing wall structure, and a rigid steel-frame building. The three structures included in this group have recently been evaluatedmore » for response to the design basis earthquake that included non-linear time history effects. The resulting loads and stresses from the wind analyses were compared to the loads and stresses resulting from seismic analyses. This approach eliminated the need to prepare additional capacity calculations that were already contained in the seismic evaluations. 4 refs., 5 figs., 5 tabs.« less

Theory and Design Tools For Studies of Reactions to Abrupt Changes in Noise Exposure

NASA Technical Reports Server (NTRS)

Fields, James M.; Ehrlich, Gary E.; Zador, Paul; Shepherd, Kevin P. (Technical Monitor)

2000-01-01

Study plans, a pre-tested questionnaire, a sample design evaluation tool, a community publicity monitoring plan, and a theoretical framework have been developed to support combined social/acoustical surveys of residents' reactions to an abrupt change in environmental noise, Secondary analyses of more than 20 previous surveys provide estimates of three parameters of a study simulation model; within individual variability, between study wave variability, and between neighborhood variability in response to community noise. The simulation model predicts the precision of the results from social surveys of reactions to noise, including changes in noise. When the study simulation model analyzed the population distribution, noise exposure environments and feasible noise measurement program at a proposed noise change survey site, it was concluded that the site could not yield sufficient precise estimates of human reaction model to justify conducting a survey. Additional secondary analyses determined that noise reactions are affected by the season of the social survey.

Assessment of Effectiveness of Geologic Isolation Systems: REFERENCE SITE INITIAL ASSESSMENT FOR A SALT DOME REPOSITORY

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

Harwell, M. A.; Brandstetter, A.; Benson, G. L.

1982-06-01

As a methodology demonstration for the Office of Nuclear Waste Isolation (ONWI), the Assessment of Effectiveness of Geologic Isolation Systems (AEGIS) Program conducted an initial reference site analysis of the long-term effectiveness of a salt dome repository. The Hainesville Salt Dome in Texas was chosen to be representative of the Gulf Coast interior salt domes; however, the Hainesville Site has been eliminated as a possible nuclear waste repository site. The data used for this exercise are not adequate for an actual assessment, nor have all the parametric analyses been made that would adequately characterize the response of the geosystem surroundingmore » the repository. Additionally, because this was the first exercise of the complete AEGIS and WASTE Rock Interaction Technology (WRIT) methodology, this report provides the initial opportunity for the methodology, specifically applied to a site, to be reviewed by the community outside the AEGIS. The scenario evaluation, as a part of the methodology demonstration, involved consideration of a large variety of potentially disruptive phenomena, which alone or in concert could lead to a breach in a salt dome repository and to a subsequent transport of the radionuclides to the environment. Without waste- and repository-induced effects, no plausible natural geologic events or processes which would compromise the repository integrity could be envisioned over the one-million-year time frame after closure. Near-field (waste- and repository-induced) effects were excluded from consideration in this analysis, but they can be added in future analyses when that methodology development is more complete. The potential for consequential human intrusion into salt domes within a million-year time frame led to the consideration of a solution mining intrusion scenario. The AEGIS staff developed a specific human intrusion scenario at 100 years and 1000 years post-closure, which is one of a whole suite of possible scenarios. This scenario resulted in the delivery of radionuclidecontaminated brine to the surface, where a portion was diverted to culinary salt for direct ingestion by the existing population. Consequence analyses indicated calculated human doses that would be highly deleterious. Additional analyses indicated that doses well above background would occur from such a scenario t even if it occurred a million years into the future. The way to preclude such an intrusion is for continued control over the repository sitet either through direct institutional control or through the effective passive transfer of information. A secondary aspect of the specific human intrusion scenario involved a breach through the side of the salt dome t through which radionuclides migrated via the ground-water system to the accessible environment. This provided a demonstration of the geotransport methodology that AEGIS can use in actual site evaluations, as well as the WRIT program's capabilities with respect to defining the source term and retardation rates of the radionuclides in the repository. This reference site analysis was initially published as a Working Document in December 1979. That version was distributed for a formal peer review by individuals and organizations not involved in its development. The present report represents a revisiont based in part on the responses received from the external reviewers. Summaries of the comments from the reviewers and responses to these comments by the AEGIS staff are presented. The exercise of the AEGIS methodology was sUGcessful in demonstrating the methodologyt and thus t in providing a basis for substantive peer review, in terms of further development of the AEGIS site-applications capability and in terms of providing insight into the potential for consequential human intrusion into a salt dome repository.« less

Assessment of Effectiveness of Geologic Isolation Systems: REFERENCE SITE INITIAL ASSESSMENT FOR A SALT DOME REPOSITORY

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

Harwell, M. A.; Brandstetter, A.; Benson, G. L.

1982-06-01

As a methodology demonstration for the Office of Nuclear Waste Isolation (ONWI), the Assessment of Effectiveness of Geologic Isolation Systems (AEGIS) Program conducted an initial reference site analysis of the long-term effectiveness of a salt dome repository. The Hainesville Salt Dome in Texas was chosen to be representative of the Gulf Coast interior salt domes; however, the Hainesville Site has been eliminated as a possible nuclear waste repository site. The data used for this exercise are not adequate for an actual assessment, nor have all the parametric analyses been made that would adequately characterize the response of the geosystem surroundingmore » the repository. Additionally, because this was the first exercise of the complete AEGIS and WASTE Rock Interaction Technology (WRIT) methodology, this report provides the initial opportunity for the methodology, specifically applied to a site, to be reviewed by the community outside the AEGIS. The scenario evaluation, as a part of the methodology demonstration, involved consideration of a large variety of potentially disruptive phenomena, which alone or in concert could lead to a breach in a salt dome repository and to a subsequent transport of the radionuclides to the environment. Without waste- and repository-induced effects, no plausible natural geologic events or processes which would compromise the repository integrity could be envisioned over the one-million-year time frame after closure. Near-field (waste- and repository-induced) effects were excluded from consideration in this analysis, but they can be added in future analyses when that methodology development is more complete. The potential for consequential human intrusion into salt domes within a million-year time frame led to the consideration of a solution mining intrusion scenario. The AEGIS staff developed a specific human intrusion scenario at 100 years and 1000 years post-closure, which is one of a whole suite of possible scenarios. This scenario resulted in the delivery of radionuclidecontaminated brine to the surface, where a portion was diverted to culinary salt for direct ingestion by the existing population. Consequence analyses indicated calculated human doses that would be highly deleterious. Additional analyses indicated that doses well above background would occur from such a scenario t even if it occurred a million years into the future. The way to preclude such an intrusion is for continued control over the repository sitet either through direct institutional control or through the effective passive transfer of information. A secondary aspect of the specific human intrusion scenario involved a breach through the side of the salt dome t through which radionuclides migrated via the ground-water system to the accessible environment. This provided a demonstration of the geotransport methodology that AEGIS can use in actual site evaluations, as well as the WRIT program's capabilities with respect to defining the source term and retardation rates of the radionuclides in the repository. This reference site analysis was initially published as a Working Document in December 1979. That version was distributed for a formal peer review by individuals and organizations not involved in its development. The present report represents a revisiont based in part on the responses received from the external reviewers. Summaries of the comments from the reviewers and responses to these comments by the AEGIS staff are presented. The exercise of the AEGIS methodology was successful in demonstrating the methodologyt and thus t in providing a basis for substantive peer review, in terms of further development of the AEGIS site-applications capability and in terms of providing insight into the potential for consequential human intrusion into a salt dome repository.« less

Hypoxia-induced endothelial NO synthase gene transcriptional activation is mediated through the tax-responsive element in endothelial cells.

PubMed

Min, Jiho; Jin, Yoon-Mi; Moon, Je-Sung; Sung, Min-Sun; Jo, Sangmee Ahn; Jo, Inho

2006-06-01

Although hypoxia is known to induce upregulation of endothelial NO synthase (eNOS) gene expression, the underlying mechanism is largely unclear. In this study, we show that hypoxia increases eNOS gene expression through the binding of phosphorylated cAMP-responsive element binding (CREB) protein (pCREB) to the eNOS gene promoter. Hypoxia (1% O2) increased both eNOS expression and NO production, peaking at 24 hours, in bovine aortic endothelial cells, and these increases were accompanied by increases in pCREB. Treatment with the protein kinase A inhibitor H-89 or transfection with dominant-negative inhibitor of CREB reversed the hypoxia-induced increases in eNOS expression and NO production, with concomitant inhibition of the phosphorylation of CREB induced by hypoxia, suggesting an involvement of protein kinase A/pCREB-mediated pathway. To map the regulatory elements of the eNOS gene responsible for pCREB binding under hypoxia, we constructed an eNOS gene promoter (-1600 to +22 nucleotides) fused with a luciferase reporter gene [pGL2-eNOS(-1600)]. Hypoxia (for 24-hour incubation) increased the promoter activity by 2.36+/-0.18-fold in the bovine aortic endothelial cells transfected with pGL2-eNOS(-1600). However, progressive 5'-deletion from -1600 to -873 completely attenuated the hypoxia-induced increase in promoter activity. Electrophoretic mobility shift, anti-pCREB antibody supershift, and site-specific mutation analyses showed that pCREB is bound to the Tax-responsive element (TRE) site, a cAMP-responsive element-like site, located at -924 to -921 of the eNOS promoter. Our data demonstrate that the interaction between pCREB and the Tax-responsive element site within the eNOS promoter may represent a novel mechanism for the mediation of hypoxia-stimulated eNOS gene expression.

Analysis of Host Responses to Mycobacterium tuberculosis Antigens in a Multi-Site Study of Subjects with Different TB and HIV Infection States in Sub-Saharan Africa

PubMed Central

Sutherland, Jayne S.; Lalor, Maeve K.; Black, Gillian F.; Ambrose, Lyn R.; Loxton, Andre G.; Chegou, Novel N.; Kassa, Desta; Mihret, Adane; Howe, Rawleigh; Mayanja-Kizza, Harriet; Gomez, Marie P.; Donkor, Simon; Franken, Kees; Hanekom, Willem; Klein, Michel R.; Parida, Shreemanta K.; Boom, W. Henry; Thiel, Bonnie A.; Crampin, Amelia C.; Ota, Martin; Walzl, Gerhard; Ottenhoff, Tom H. M.; Dockrell, Hazel M.; Kaufmann, Stefan H. E.

2013-01-01

Background Tuberculosis (TB) remains a global health threat with 9 million new cases and 1.4 million deaths per year. In order to develop a protective vaccine, we need to define the antigens expressed by Mycobacterium tuberculosis (Mtb), which are relevant to protective immunity in high-endemic areas. Methods We analysed responses to 23 Mtb antigens in a total of 1247 subjects with different HIV and TB status across 5 geographically diverse sites in Africa (South Africa, The Gambia, Ethiopia, Malawi and Uganda). We used a 7-day whole blood assay followed by IFN-γ ELISA on the supernatants. Antigens included PPD, ESAT-6 and Ag85B (dominant antigens) together with novel resuscitation-promoting factors (rpf), reactivation proteins, latency (Mtb DosR regulon-encoded) antigens, starvation-induced antigens and secreted antigens. Results There was variation between sites in responses to the antigens, presumably due to underlying genetic and environmental differences. When results from all sites were combined, HIV- subjects with active TB showed significantly lower responses compared to both TST- and TST+ contacts to latency antigens (Rv0569, Rv1733, Rv1735, Rv1737) and the rpf Rv0867; whilst responses to ESAT-6/CFP-10 fusion protein (EC), PPD, Rv2029, TB10.3, and TB10.4 were significantly higher in TST+ contacts (LTBI) compared to TB and TST- contacts fewer differences were seen in subjects with HIV co-infection, with responses to the mitogen PHA significantly lower in subjects with active TB compared to those with LTBI and no difference with any antigen. Conclusions Our multi-site study design for testing novel Mtb antigens revealed promising antigens for future vaccine development. The IFN-γ ELISA is a cheap and useful tool for screening potential antigenicity in subjects with different ethnic backgrounds and across a spectrum of TB and HIV infection states. Analysis of cytokines other than IFN-γ is currently on-going to determine correlates of protection, which may be useful for vaccine efficacy trials. PMID:24040170

Analysis of host responses to Mycobacterium tuberculosis antigens in a multi-site study of subjects with different TB and HIV infection states in sub-Saharan Africa.

PubMed

Sutherland, Jayne S; Lalor, Maeve K; Black, Gillian F; Ambrose, Lyn R; Loxton, Andre G; Chegou, Novel N; Kassa, Desta; Mihret, Adane; Howe, Rawleigh; Mayanja-Kizza, Harriet; Gomez, Marie P; Donkor, Simon; Franken, Kees; Hanekom, Willem; Klein, Michel R; Parida, Shreemanta K; Boom, W Henry; Thiel, Bonnie A; Crampin, Amelia C; Ota, Martin; Walzl, Gerhard; Ottenhoff, Tom H M; Dockrell, Hazel M; Kaufmann, Stefan H E

2013-01-01

Tuberculosis (TB) remains a global health threat with 9 million new cases and 1.4 million deaths per year. In order to develop a protective vaccine, we need to define the antigens expressed by Mycobacterium tuberculosis (Mtb), which are relevant to protective immunity in high-endemic areas. We analysed responses to 23 Mtb antigens in a total of 1247 subjects with different HIV and TB status across 5 geographically diverse sites in Africa (South Africa, The Gambia, Ethiopia, Malawi and Uganda). We used a 7-day whole blood assay followed by IFN-γ ELISA on the supernatants. Antigens included PPD, ESAT-6 and Ag85B (dominant antigens) together with novel resuscitation-promoting factors (rpf), reactivation proteins, latency (Mtb DosR regulon-encoded) antigens, starvation-induced antigens and secreted antigens. There was variation between sites in responses to the antigens, presumably due to underlying genetic and environmental differences. When results from all sites were combined, HIV- subjects with active TB showed significantly lower responses compared to both TST(-) and TST(+) contacts to latency antigens (Rv0569, Rv1733, Rv1735, Rv1737) and the rpf Rv0867; whilst responses to ESAT-6/CFP-10 fusion protein (EC), PPD, Rv2029, TB10.3, and TB10.4 were significantly higher in TST(+) contacts (LTBI) compared to TB and TST(-) contacts fewer differences were seen in subjects with HIV co-infection, with responses to the mitogen PHA significantly lower in subjects with active TB compared to those with LTBI and no difference with any antigen. Our multi-site study design for testing novel Mtb antigens revealed promising antigens for future vaccine development. The IFN-γ ELISA is a cheap and useful tool for screening potential antigenicity in subjects with different ethnic backgrounds and across a spectrum of TB and HIV infection states. Analysis of cytokines other than IFN-γ is currently on-going to determine correlates of protection, which may be useful for vaccine efficacy trials.

Study on accumulation ability of two lichen species Hypogymnia physodes and Usnea hirta at iron-steel factory site, Turkey.

PubMed

Cansaran-Duman, Demet

2011-11-01

The use of biological responses to contaminant exposure by lichen species has become a useful tool in environmental quality evaluation and risk assesment. Lichen Hypogymnia physodes and Usnea hirta samples were collected in 2006 from 10 sites around iron-steel factory in Karabük, Turkey. H. physodes and U. hirta samples from Yenice forest were used as a control. The aim of present study was to evaluate the bioaccumulation ability and to determine the environmental impact of an iron-steel factory in Karabük. Seven elements (Zn, Cu, Mn, Fe, Pb, Ni, Cr and Cd) were analysed by atomic absorption spectrometry (AAS). The analytical results were compared statistically by using SPSS. As expected, the study area (Yenice forest, Karabük) chosen as control site (site no 11) showed significantly lower impact in comparison to other site (site no 1-10). Compared with the two lichen species, H. physodes showed highest metal accumulating capacity while U. hirta showed lowest. These criteria attested the best suitability for H. physodes, followed by U. hirta.

Estimating variation in stomatal frequency at intra-individual, intra-site, and inter-taxonomic levels in populations of the Leonardoxa africana (Fabaceae) complex over environmental gradients in Cameroon

NASA Astrophysics Data System (ADS)

Finsinger, Walter; Dos Santos, Thibaut; McKey, Doyle

2013-07-01

Variation of stomatal frequency (stomatal density and stomatal index) includes genetically-based, potentially-adaptive variation, and variation due to phenotypic plasticity, the degree of which may be fundamental to the ability to maintain high water-use efficiency and thus to deal with environmental change. We analysed stomatal frequency and morphology (pore length, pore width) in leaves from several individuals from nine populations of four sub-species of the Leonardoxa africana complex. The dataset represents a hierarchical sampling wherein factors are nested within each level (leaves in individuals, individuals in sites, etc.), allowing estimation of the contribution of different levels to overall variation, using variance-component analysis. SI showed significant variation among sites ("site" is largely confounded with "sub-species"), being highest in the sub-species localized in the highest-elevation site. However, most of the observed variance was accounted for at intra-site and intra-individual levels. This variance could reflect great phenotypic plasticity, presumably in response to highly local variation in micro-environmental conditions.

Classifying Multi-Model Wheat Yield Impact Response Surfaces Showing Sensitivity to Temperature and Precipitation Change

NASA Technical Reports Server (NTRS)

Fronzek, Stefan; Pirttioja, Nina; Carter, Timothy R.; Bindi, Marco; Hoffmann, Holger; Palosuo, Taru; Ruiz-Ramos, Margarita; Tao, Fulu; Trnka, Miroslav; Acutis, Marco;

Probabilistic and Scenario Seismic and Liquefaction Hazard Analysis of the Mississippi Embayment Incorporating Nonlinear Site Effects

NASA Astrophysics Data System (ADS)

Cramer, C. H.; Dhar, M. S.

2017-12-01

The influence of deep sediment deposits of the Mississippi Embayment (ME) on the propagation of seismic waves is poorly understood and remains a major source of uncertainty for site response analysis. Many researchers have studied the effects of these deposits on seismic hazard of the area using available information at the time. In this study, we have used updated and newly available resources for seismic and liquefaction hazard analyses of the ME. We have developed an improved 3D geological model. Additionally, we used surface geological maps from Cupples and Van Arsdale (2013) to prepare liquefaction hazard maps. Both equivalent linear and nonlinear site response codes were used to develop site amplification distributions for use in generating hazard maps. The site amplification distributions are created using the Monte Carlo approach of Cramer et al. (2004, 2006) on a 0.1-degree grid. The 2014 National Seismic Hazard model and attenuation relations (Petersen et al., 2014) are used to prepare seismic hazard maps. Then liquefaction hazard maps are generated using liquefaction probability curves from Holzer (2011) and Cramer et al. (2015). Equivalent linear response (w/ increased precision, restricted nonlinear behavior with depth) shows similar hazard for the ME compared to nonlinear analysis (w/o pore pressure) results. At short periods nonlinear deamplification dominates the hazard, but at long periods resonance amplification dominates. The liquefaction hazard tends to be high in Holocene and late Pleistocene lowland sediments, even with lowered ground water levels, and low in Pleistocene loess of the uplands. Considering pore pressure effects in nonlinear site response analysis at a test site on the lowlands shows amplification of ground motion at short periods. PGA estimates from ME liquefaction and MMI observations are in the 0.25 to 0.4 g range. Our estimated M7.5 PGA hazard within 10 km of the fault can exceed this. Ground motion observations from liquefaction sites in New Zealand and Japan support PGAs below 0.4 g, except at sites within 20 km exhibiting pore-pressure induced acceleration spikes due to cyclic mobility where PGA ranges from 0.5 to 1.5 g. This study is being extended to more detailed seismic and liquefaction hazard studies in five western Tennessee counties under a five year grant from HUD.

Response of an arctic predator guild to collapsing lemming cycles

PubMed Central

Schmidt, Niels M.; Ims, Rolf A.; Høye, Toke T.; Gilg, Olivier; Hansen, Lars H.; Hansen, Jannik; Lund, Magnus; Fuglei, Eva; Forchhammer, Mads C.; Sittler, Benoit

2012-01-01

Alpine and arctic lemming populations appear to be highly sensitive to climate change, and when faced with warmer and shorter winters, their well-known high-amplitude population cycles may collapse. Being keystone species in tundra ecosystems, changed lemming dynamics may convey significant knock-on effects on trophically linked species. Here, we analyse long-term (1988–2010), community-wide monitoring data from two sites in high-arctic Greenland and document how a collapse in collared lemming cyclicity affects the population dynamics of the predator guild. Dramatic changes were observed in two highly specialized lemming predators: snowy owl and stoat. Following the lemming cycle collapse, snowy owl fledgling production declined by 98 per cent, and there was indication of a severe population decline of stoats at one site. The less specialized long-tailed skua and the generalist arctic fox were more loosely coupled to the lemming dynamics. Still, the lemming collapse had noticeable effects on their reproductive performance. Predator responses differed somewhat between sites in all species and could arise from site-specific differences in lemming dynamics, intra-guild interactions or subsidies from other resources. Nevertheless, population extinctions and community restructuring of this arctic endemic predator guild are likely if the lemming dynamics are maintained at the current non-cyclic, low-density state. PMID:22977153

Response of an arctic predator guild to collapsing lemming cycles.

PubMed

Schmidt, Niels M; Ims, Rolf A; Høye, Toke T; Gilg, Olivier; Hansen, Lars H; Hansen, Jannik; Lund, Magnus; Fuglei, Eva; Forchhammer, Mads C; Sittler, Benoit

2012-11-07

Alpine and arctic lemming populations appear to be highly sensitive to climate change, and when faced with warmer and shorter winters, their well-known high-amplitude population cycles may collapse. Being keystone species in tundra ecosystems, changed lemming dynamics may convey significant knock-on effects on trophically linked species. Here, we analyse long-term (1988-2010), community-wide monitoring data from two sites in high-arctic Greenland and document how a collapse in collared lemming cyclicity affects the population dynamics of the predator guild. Dramatic changes were observed in two highly specialized lemming predators: snowy owl and stoat. Following the lemming cycle collapse, snowy owl fledgling production declined by 98 per cent, and there was indication of a severe population decline of stoats at one site. The less specialized long-tailed skua and the generalist arctic fox were more loosely coupled to the lemming dynamics. Still, the lemming collapse had noticeable effects on their reproductive performance. Predator responses differed somewhat between sites in all species and could arise from site-specific differences in lemming dynamics, intra-guild interactions or subsidies from other resources. Nevertheless, population extinctions and community restructuring of this arctic endemic predator guild are likely if the lemming dynamics are maintained at the current non-cyclic, low-density state.

Metal Binding Properties of Escherichia coli YjiA, a Member of the Metal Homeostasis-Associated COG0523 Family of GTPases

PubMed Central

2013-01-01

GTPases are critical molecular switches involved in a wide range of biological functions. Recent phylogenetic and genomic analyses of the large, mostly uncharacterized COG0523 subfamily of GTPases revealed a link between some COG0523 proteins and metal homeostasis pathways. In this report, we detail the bioinorganic characterization of YjiA, a representative member of COG0523 subgroup 9 and the only COG0523 protein to date with high-resolution structural information. We find that YjiA is capable of binding several types of transition metals with dissociation constants in the low micromolar range and that metal binding affects both the oligomeric structure and GTPase activity of the enzyme. Using a combination of X-ray crystallography and site-directed mutagenesis, we identify, among others, a metal-binding site adjacent to the nucleotide-binding site in the GTPase domain that involves a conserved cysteine and several glutamate residues. Mutations of the coordinating residues decrease the impact of metal, suggesting that metal binding to this site is responsible for modulating the GTPase activity of the protein. These findings point toward a regulatory function for these COG0523 GTPases that is responsive to their metal-bound state. PMID:24449932

Geotechnical Site Investigation Using S-waves with Implications for Ground Motion Analysis

NASA Astrophysics Data System (ADS)

Hassan, Bilal; Butt, Stephen D.; Hurich, Charles A.

2017-12-01

Evaluation results of shear wave attenuation-based ground motion restricted by fracture orientation and rheology, from among those of an extended experimental study, are presented herein. The issues of competence of fractured bedrock dynamically disturbed multilaterally are assessed. Disturbance is primarily modelled by Sh and Sv stimulation, given fracture orientation, while subjected to direct fracture stress regime conditions varying in time. Hence, directionalities of polarisation and stress are taken into consideration simultaneously following simple site-specific non-erodetic approach. Comparison of spectral curves and spectral ratio curves of attenuation with respect to variations of direction and stress emphasise the amplification of the `seismic response' in one direction compared to the other, i.e. vertical vs. horizontal, in terms of weighing possibilities of or predicting structural integrity against failure. The composite analyses of multiple spectral curves not only enable determination of the orientation of the fracture set/s in space but also allow inferring the nature of more amplified response perpendicular to the crack surface compared to that of a response parallel to the crack surface.

Deposition measurement of particulate matter in connection with corrosion studies.

PubMed

Ferm, Martin; Watt, John; O'Hanlon, Samantha; De Santis, Franco; Varotsos, Costas

2006-03-01

A new passive particle collector (inert surrogate surface) that collects particles from all directions has been developed. It was used to measure particle deposition at 35 test sites as part of a project that examined corrosion of materials in order that variation in particulate material could be used in development of dose-response functions in a modern multi-pollutant environment. The project, MULTI-ASSESS, was funded by the EU to examine the effects of air pollution on cultural heritage. Passive samplers were mounted rain-protected, and both in wind-protected and wind-exposed positions, to match the exposure of the samples for corrosion studies. The particle mass and its chemical content (nitrate, ammonium, sulfate, calcium, sodium, chloride, magnesium and potassium) were analysed. The loss of light reflectance on the surrogate surface was also measured. Very little ammonium and potassium was found, and one or more anions are missing in the ion balance. There were many strong correlations between the analysed species. The mass of analysed water-soluble ions was fairly constant at 24% of the total mass. The particle mass deposited to the samplers in the wind-protected position was about 25% of the particles deposited to an openly exposed sampler. The Cl-/Na+ ratios indicate a reaction between HNO(3) and NaCl. The deposited nitrate flux corresponds to the missing chloride. The Ca2+ deposition equals the SO4(2-) deposition and the anion deficiency. The SO4(2-) deposition most likely originates from SO2 that has reacted with basic calcium-containing particles either before or after they were deposited. The particle depositions at the urban sites were much higher than in nearby rural sites. The deposited mass correlated surprisingly well with the PM(10) concentration, except at sites very close to traffic.

Hydrologic characteristics of surface-mined land reclaimed by sludge irrigation, Fulton County, Illinois

USGS Publications Warehouse

Patterson, G.L.; Fuentes, R.F.; Toler, L.G.

1982-01-01

Analyses of water samples collected at four stream-monitoring stations, in an area surface mined for coal and being reclaimed by sludge irrigation, show the principal metals are sodium, calcium, and magnesium and principal non-metals are chloride, sulfate, and bicarbonate. Comparing yearly mean chemical concentrations shows no changing trends since reclamation began, nor are there differences between stations upstream and downstream from the site. Yearly suspended-sediment loads and discharge relations upstream and downstream from the site also show no differences. Discharge hydrographs of two streams draining the site show a delayed response to precipitation due to the storage capacity of several upstream strip-mine lakes. The water-table surface generally follows the irregular topography. Monthly water-level fluctuations were dependent on the surface material (mined or unmined) and proximity to surface discharge. The largest fluctuations were in unmined land away from discharge while the smallest were in mined land near discharge. The water table is closer to the surface in unmined land. Analyses of water samples from 70 wells within or adjacent to the reclamation site showed no differences in water quality which could be attributed to sludge or supernatant application. Samples from wells in mined land, however, had higher concentrations of dissolved sulfate, calcium, magnesium, chloride, iron, zinc, and manganese than samples from wells in unmined land. (USGS)

Field measures show methanotroph sensitivity to soil moisture follows precipitation regime of the grassland sites across the US Great Plains

NASA Astrophysics Data System (ADS)

Koyama, A.; Webb, C. T.; Johnson, N. G.; Brewer, P. E.; von Fischer, J. C.

2015-12-01

Methane uptake rates are known to have temporal variation in response to changing soil moisture levels. However, the relative importance of soil diffusivity vs. methanotroph physiology has not been disentangled to date. Testing methanotroph physiology in the laboratory can lead to misleading results due to changes in the fine-scale habitat where methanotrophs reside. To assay the soil moisture sensitivity of methanotrophs under field conditions, we studied 22 field plots scattered across eight Great Plains grassland sites that differed in precipitation regime and soil moisture, making ca. bi-weekly measures during the growing seasons over three years. Quantification of methanotroph activity was achieved from chamber-based measures of methane uptake coincident with SF6-derived soil diffusivity, and interpretation in a reaction-diffusion model. At each plot, we also measured soil water content (SWC), soil temperature and inorganic nitrogen (N) contents. We also assessed methanotroph community composition via 454 sequencing of the pmoA gene. Statistical analyses showed that methanotroph activity had a parabolic response with SWC (concave down), and significant differences in the shape of this response among sites. Moreover, we found that the SWC at peak methanotroph activity was strongly correlated with mean annual precipitation (MAP) of the site. The sequence data revealed distinct composition patterns, with structure that was associated with variation in MAP and soil texture. These results suggest that local precipitation regime shapes methanotroph community composition, which in turn lead to unique sensitivity of methane uptake rates with soil moisture. Our findings suggest that methanotroph activity may be more accurately modeled when the biological and environmental responses are explicitly described.

Combined use of chemical, biochemical and physiological variables in mussels for the assessment of marine pollution along the N-NW Spanish coast.

PubMed

Bellas, Juan; Albentosa, Marina; Vidal-Liñán, Leticia; Besada, Victoria; Franco, M Ángeles; Fumega, José; González-Quijano, Amelia; Viñas, Lucía; Beiras, Ricardo

2014-05-01

This study undertakes an overall assessment of pollution in a large region (over 2500 km of coastline) of the N-NW Spanish coast, by combining the use of biochemical (AChE, GST, GPx) and physiological (SFG) responses to pollution, with chemical analyses in wild mussel populations (Mytilus galloprovincialis). The application of chemical analysis and biological techniques identified polluted sites and quantified the level of toxicity. High levels of pollutants were found in mussel populations located close to major cities and industrialized areas and, in general, average concentrations were higher in the Cantabrian than in the Iberian Atlantic coast. AChE activities ranged between 5.8 and 27.1 nmol/min/mg prot, showing inhibition in 12 sampling sites, according to available ecotoxicological criteria. GST activities ranged between 29.5 and 112.7 nmol/min/mg prot, and extreme variability was observed in GPx, showing activities between 2.6 and 64.5 nmol/min/mg prot. Regarding SFG, only 5 sites showed 'moderate stress' (SFG value below 20 J/g/h), and most sites presented a 'high potential growth' (>35 J/g/h) corresponding to a 'healthy state'. Multivariate statistical techniques applied to the chemical and biological data identified PCBs, organochlorine pesticides and BDEs as the main responsible of the observed toxicity. However, the alteration of biological responses caused by pollutants seems to be, in general, masked by biological variables, namely age and mussel condition, which have an effect on the mussels' response to pollutant exposure. Copyright © 2013 Elsevier Ltd. All rights reserved.

Do the conventional clinicopathologic parameters predict for response and survival in head and neck cancer patients undergoing neoadjuvant chemotherapy?

PubMed

Fonseca, E; Cruz, J J; Dueñas, A; Gómez, A; Sánchez, P; Martín, G; Nieto, A; Soria, P; Muñoz, A; Gómez, J L; Pardal, J L

1996-01-01

Neoadjuvant chemotherapy for head and neck carcinoma is still an important treatment modality. The prognostic value of patient and tumor parameters has been extensively evaluated in several trials, yielding mixed results. We report the prognostic factors emerging from a group of patients undergoing neoadjuvant chemotherapy. From April 1986 to June 1992, 149 consecutive patients received cisplatin-5-fluorouracil-based neoadjuvant chemotherapy. After four courses of chemotherapy, patients underwent local-regional treatment with surgery, radiation or both. A variety of patient and tumor characteristics were evaluated as predictors for response to chemotherapy and survival. The complete response, partial response and no response rates to NAC were 52%, 33% and 15%, respectively. No parameters predicted response to chemotherapy. At a maximum follow-up of 87 months, overall survival was 39% and disease-free survival was 49%. Variables shown to be predictors of survival in univariate analyses were age, performance status, histology, site, T, N, stage, and response to chemotherapy. Using the Cox regression analysis, only complete response to induction chemotherapy (P = 0.0006), performance status (P = 0.03), stage (P = 0.01), age (P = 0.03) and primary tumor site (P = 0.04) emerged as independent prognostic factors for survival. Complete response to chemotherapy was confirmed as the strongest prognostic factor influencing survival. However, conventional clinicopathologic factors did not predict response, hence, potential prognostic biologic and molecular factors for response must be sought. At present, much effort must be made for the improvement of the complete response rate, which seems to be a requisite to prolong survival.

Physical activity and cancer risk: dose-response and cancer, all sites and site-specific.

PubMed

Thune, I; Furberg, A S

2001-06-01

The association between physical activity and overall and site-specific cancer risk is elaborated in relation to whether any observed dose-response association between physical activity and cancer can be interpreted in terms of how much physical activity (type, intensity, duration, frequency) is needed to influence site- and gender-specific cancer risk. Observational studies were reviewed that have examined the independent effect of the volume of occupational physical activity (OPA) and/or leisure time physical activity (LPA) on overall and site-specific cancer risk. The evidence of cohort and case-control studies suggests that both leisure time and occupational physical activity protect against overall cancer risk, with a graded dose-response association suggested in both sexes. Confounding effects such as diet, body weight, and parity are often included as a covariate in the analyses, with little influence on the observed associations. A crude graded inverse dose-response association was observed between physical activity and colon cancer in 48 studies including 40,674 colon/colorectal cancer cases for both sexes. A dose-response effect of physical activity on colon cancer risk was especially observed, when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed as MET-hours per week. An observed inverse association with a dose-response relationship between physical activity and breast cancer was also identified in the majority of the 41 studies including 108,031 breast cancer cases. The dose-response relationship was in particular observed in case-control studies and supported by observations in cohort studies when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed by MET-hours per week. This association between physical activity and breast cancer risk is possibly dependent on age at exposure, age at diagnosis, menopausal status and other effect modifiers, e.g., body mass index. Furthermore, data concerning carcinoma of other cancers (prostate, lung, endometrium, ovary, and testicular cancers) are required. A protective effect of physical activity on site-specific cancer risk with a dose-response association between physical activity and colon and pre- and postmenopausal breast cancer supported by identified biological mechanisms has been observed. The optimal permutation of type, intensity, duration, and frequency of physical activity across the lifespan is unclear, but it is gender, age, and site specific and supports moderate activity (>4.5 MET) more than light activities (<4.5 MET). The complicated nature of the physical activity variable, combined with lack of knowledge regarding possible biological mechanisms operating between physical activity and cancer, warrants further studies including controlled clinical randomized trials.

Plants and climate change: complexities and surprises

PubMed Central

Parmesan, Camille; Hanley, Mick E.

2015-01-01

Background Anthropogenic climate change (ACC) will influence all aspects of plant biology over coming decades. Many changes in wild species have already been well-documented as a result of increased atmospheric CO2 concentrations, warming climate and changing precipitation regimes. A wealth of available data has allowed the use of meta-analyses to examine plant–climate interactions on more sophisticated levels than before. These analyses have revealed major differences in plant response among groups, e.g. with respect to functional traits, taxonomy, life-history and provenance. Interestingly, these meta-analyses have also exposed unexpected mismatches between theory, experimental, and observational studies. Scope We reviewed the literature on species’ responses to ACC, finding ∼42 % of 4000 species studied globally are plants (primarily terrestrial). We review impacts on phenology, distributions, ecophysiology, regeneration biology, plant–plant and plant–herbivore interactions, and the roles of plasticity and evolution. We focused on apparent deviations from expectation, and highlighted cases where more sophisticated analyses revealed that unexpected changes were, in fact, responses to ACC. Conclusions We found that conventionally expected responses are generally well-understood, and that it is the aberrant responses that are now yielding greater insight into current and possible future impacts of ACC. We argue that inconclusive, unexpected, or counter-intuitive results should be embraced in order to understand apparent disconnects between theory, prediction, and observation. We highlight prime examples from the collection of papers in this Special Issue, as well as general literature. We found use of plant functional groupings/traits had mixed success, but that some underutilized approaches, such as Grime's C/S/R strategies, when incorporated, have improved understanding of observed responses. Despite inherent difficulties, we highlight the need for ecologists to conduct community-level experiments in systems that replicate multiple aspects of ACC. Specifically, we call for development of coordinating experiments across networks of field sites, both natural and man-made. PMID:26555281

Perioperative management of external fixation in staged protocols: an international survey.

PubMed

Hodel, Sandro; Link, Björn-Christian; Babst, Reto; Mallee, W H; Posso, Philippe; Beeres, Frank J P

2018-05-01

Despite the frequent use of external fixation, various regimes of antibiotic prophylaxis, surgical technique and postoperative pin care exist and underline the lack of current evidence. The aim of the study was to assess the variability or consensus in perioperative protocols to prevent implant-associated infections for temporary external fixation in closed fractures of the extremities. A 26-question survey was sent to 170 members of the Traumaplatform. The survey included questions concerning demographics, level of training, type of training and perioperative protocols as: antibiotic prophylaxis, intraoperative management, disinfection and postoperative pin site care. All responses were statistically analysed, and intraoperative measures rated on a 5-point Likert scale. The responses of fifty orthopaedic trauma and general surgeons (response rate, 29.4%) were analysed. The level of experience was more than 5 years in 92% (n = 46) with up to 50 closed fractures of the extremities annually treated with external fixation in 80% (n = 40). Highest consensus could be identified in the following perioperative measures: preoperative antibiotic prophylaxis with a second-generation cephalosporin (86%, n = 43), changing gloves if manipulation of the external fixator is necessary during surgery (86%, n = 43; 4.12 points on the Likert scale), avoid overlapping of the pin sites with the definitive implant site (94%, n = 47; 4.12 points on the Likert scale) and soft tissue protection with a drill sleeve (83.6%, n = 41). Our survey could identify some general principles, which were rated as important by a majority of the respondents. Futures studies' focus should elucidate the role of perioperative antibiotics and different disinfection protocols on implant-associated infections after temporary external fixation in staged protocols. This study provides Level IV evidence according to Oxford centre for evidence-based medicine.

Significance of beating observed in earthquake responses of buildings

USGS Publications Warehouse

Çelebi, Mehmet; Ghahari, S. F.; Taciroglu, E.

2016-01-01

The beating phenomenon observed in the recorded responses of a tall building in Japan and another in the U.S. are examined in this paper. Beating is a periodic vibrational behavior caused by distinctive coupling between translational and torsional modes that typically have close frequencies. Beating is prominent in the prolonged resonant responses of lightly damped structures. Resonances caused by site effects also contribute to accentuating the beating effect. Spectral analyses and system identification techniques are used herein to quantify the periods and amplitudes of the beating effects from the strong motion recordings of the two buildings. Quantification of beating effects is a first step towards determining remedial actions to improve resilient building performance to strong earthquake induced shaking.

Organochlorines and metals induce changes in the mitochondria-rich cells of fish gills: an integrative field study involving chemical, biochemical and morphological analyses.

PubMed

Fernandes, M N; Paulino, M G; Sakuragui, M M; Ramos, C A; Pereira, C D S; Sadauskas-Henrique, H

2013-01-15

Through integrating chemical, biochemical and morphological analyses, this study investigated the effects of multiple pollutants on the gill mitochondria-rich cells (MRCs) in two fish species, Astyanax fasciatus and Pimelodus maculatus, collected from five sites (FU10, FU20, FU30, FU40 and FU50) in the Furnas Hydroelectric Power Station reservoir. Water analyses revealed aluminum, iron and zinc as well as organochlorine (aldrin/dieldrin, endosulfan, heptachlor/heptachlor epoxide and metolachlor) contamination at all of the sites, with the exception of FU10. Copper, chrome, iron and zinc were detected in the gills of both species, and aldrin/dieldrin, endosulfan and heptachlor/heptachlor epoxide were detected in the gills of fish from all of the sites, with the exception of FU10. Fish collected at FU20, FU30 and FU50 exhibited numerous alterations in the surface architecture of their pavement cells and MRCs. The surface MRC density and MRC fractional area were lower in fish from FU20, FU30, FU40 and FU50 than in those from the reference site (FU10) in the winter, and some variability between the sites was observed in the summer. The organochlorine contamination at FU20 and FU50 was associated with variable changes in the MRCs and inhibition of Na(+)/K(+)-ATPase (NKA) activity, especially in P. maculatus. At FU30, the alterations in the MRCs were associated with the contaminants present, especially metals. A multivariate analysis demonstrated a positive association between the biological responses of both species and environmental contamination, indicating that under realistic conditions, a mixture of organochlorines and metals affected the MRCs by inhibiting NKA activity and inducing morphological changes, which may cause an ionic imbalance. Copyright © 2012 Elsevier B.V. All rights reserved.

Cross-correlated and oscillatory visual responses of superficial-layer and tecto-reticular neurones in cat superior colliculus.

PubMed

Chabli, A; Guitton, D; Fortin, S; Molotchnikoff, S

2000-03-01

The present study examined, in the superior colliculus (SC) of anaesthetised cats, the functional connectivity between superficial-layer neurones (SLNs) and tectoreticular neurones (TRNs: collicular output cells). TRNs were antidromically identified by electrical stimulation of the predorsal bundle. The auto- and cross-correlation histograms of visual responses of both types of neurones were recorded and analysed. A delayed, sharp peak in cross-correlograms allowed us to verify whether SLN and TRN cells were coupled; in addition, oscillatory activities were compared to verify if rhythmic responses of SLN sites were transmitted to TRN sites. We found that oscillatory activity was rarely observed in spontaneous activity of superficial (1/74) and TRN sites (1/48). Moving light bars induced oscillation in 31% (23/74) of the superficial-layer and in 23% (11/48) of the TRN sites. The strength of the rhythmic responses was determined by specific ranges of stimulus velocity in 83% (19/23) and 64% (7/11) of oscillating SLN and TRN sites, respectively. Frequencies of oscillations ranged between 5 and 125 Hz and were confined, for 53% of the cells, to the 5-20 Hz band. Thus, the band-width of frequencies of the stimulus-related oscillations in the superior colliculus was broader than the gamma range. Analysis of cross-correlation histograms revealed a significant predominant peak with a mean delay of 2.7+/-0.9 ms in 46% (17/37) of SLN-TRN pairs. Most correlated SLN-TRN pairs (88%: 15/17) had superimposed receptive fields, suggesting they were functionally interconnected. However, individual oscillatory frequencies of correlated and oscillatory SLN and TRN cells were never the same (0/8). Together, these results suggest that the neurones in collicular superficial layer contact TRNs and, consequently, support the idea that the superficial layers contribute to collicular outputs producing eye- and head-orienting movements.

Plant responses to environmental stress: regulation and functions of the Arabidopsis TCH genes

NASA Technical Reports Server (NTRS)

Braam, J.; Sistrunk, M. L.; Polisensky, D. H.; Xu, W.; Purugganan, M. M.; Antosiewicz, D. M.; Campbell, P.; Johnson, K. A.; McIntire, L. V. (Principal Investigator)

1997-01-01

Expression of the Arabidopsis TCH genes is markedly upregulated in response to a variety of environmental stimuli including the seemingly innocuous stimulus of touch. Understanding the mechanism(s) and factors that control TCH gene regulation will shed light on the signaling pathways that enable plants to respond to environmental conditions. The TCH proteins include calmodulin, calmodulin-related proteins and a xyloglucan endotransglycosylase. Expression analyses and localization of protein accumulation indicates that the potential sites of TCH protein function include expanding cells and tissues under mechanical strain. We hypothesize that at least a subset of the TCH proteins may collaborate in cell wall biogenesis.

Broad-band simulation of M7.2 earthquake on the North Tehran fault, considering non-linear soil effects

NASA Astrophysics Data System (ADS)

Majidinejad, A.; Zafarani, H.; Vahdani, S.

2018-05-01

The North Tehran fault (NTF) is known to be one of the most drastic sources of seismic hazard on the city of Tehran. In this study, we provide broad-band (0-10 Hz) ground motions for the city as a consequence of probable M7.2 earthquake on the NTF. Low-frequency motions (0-2 Hz) are provided from spectral element dynamic simulation of 17 scenario models. High-frequency (2-10 Hz) motions are calculated with a physics-based method based on S-to-S backscattering theory. Broad-band ground motions at the bedrock level show amplifications, both at low and high frequencies, due to the existence of deep Tehran basin in the vicinity of the NTF. By employing soil profiles obtained from regional studies, effect of shallow soil layers on broad-band ground motions is investigated by both linear and non-linear analyses. While linear soil response overestimate ground motion prediction equations, non-linear response predicts plausible results within one standard deviation of empirical relationships. Average Peak Ground Accelerations (PGAs) at the northern, central and southern parts of the city are estimated about 0.93, 0.59 and 0.4 g, respectively. Increased damping caused by non-linear soil behaviour, reduces the soil linear responses considerably, in particular at frequencies above 3 Hz. Non-linear deamplification reduces linear spectral accelerations up to 63 per cent at stations above soft thick sediments. By performing more general analyses, which exclude source-to-site effects on stations, a correction function is proposed for typical site classes of Tehran. Parameters for the function which reduces linear soil response in order to take into account non-linear soil deamplification are provided for various frequencies in the range of engineering interest. In addition to fully non-linear analyses, equivalent-linear calculations were also conducted which their comparison revealed appropriateness of the method for large peaks and low frequencies, but its shortage for small to medium peaks and motions with higher than 3 Hz frequencies.

Vegetation response to fire and postburn seeding treatments in juniper woodlands of the Grand Staircase-Escalante National Monument, Utah

USGS Publications Warehouse

Evangelista, P.; Stohlgren, T.J.; Guenther, D.; Stewart, S.

2004-01-01

We compared 3 naturally ignited burns with unburned sites in the Grand Staircase-Escalante National Monument. Each burn site was restored with native and nonnative seed mixes, restored with native seeds only, or regenerated naturally. In general, burned sites had significantly lower native species richness (1.8 vs. 2.9 species), native species cover (11% vs. 22.5%), and soil crust cover (4.1% vs. 15%) than unburned sites. Most burned plots, seeded or not, had significantly higher average nonnative species richness and cover and lower average native species richness and cover than unburned sites. Regression tree analyses suggest site variation was equally important to rehabilitation results as seeding treatments. Low native species richness and cover, high soil C, and low cover of biological soil crusts may facilitate increased nonnative species richness and cover. Our study also found that unburned sites in the region had equally high cover of nonnative species compared with the rest of the Monument. Cheatgrass (Bromus tectorum) dominated both burned and unburned sites. Despite the invasion of cheatgrass, unburned sites still maintain higher native species richness; however, the high cover of cheatgrass may increase fire frequency, further reduce native species richness and cover, and ultimately change vegetation composition in juniper woodlands.

CpG island methylation phenotype (CIMP) in oral cancer: associated with a marked inflammatory response and less aggressive tumour biology.

PubMed

Shaw, Richard J; Hall, Gillian L; Lowe, Derek; Bowers, Naomi L; Liloglou, Triantafillos; Field, John K; Woolgar, Julia A; Risk, Janet M

2007-10-01

Studies in several tumour sites highlight the significance of the CpG island methylation phenotype (CIMP), with distinct features of histology, biological aggression and outcome. We utilise pyrosequencing techniques of quantitative methylation analysis to investigate the presence of CIMP in oral squamous cell carcinoma (OSCC) for the first time, and evaluate its correlation with allelic imbalance, pathology and clinical behaviour. Tumour tissue, control tissue and PBLs were obtained from 74 patients with oral squamous cell carcinoma. Pyrosequencing was used to analyse methylation patterns in 75-200 bp regions of the CpG rich gene promoters of 10 genes with a broad range of cellular functions. Allelic imbalance was investigated using a multiplexed panel of 11 microsatellite markers. Corresponding variables, histopathological staging and grading were correlated with these genetic and epigenetic aberrations. A cluster of tumours with a greater degree of promoter methylation than would be predicted by chance alone (P=0.001) were designated CIMP+ve. This group had less aggressive tumour biology in terms of tumour thickness (p=0.015) and nodal metastasis (P=0.012), this being apparently independent of tumour diameter. Further, it seems that these CIMP+ve tumours excited a greater host inflammatory response (P=0.019). The exact mechanisms underlying CIMP remain obscure but the association with a greater inflammatory host response supports existing theories relating these features in other tumour sites. As CIMP has significant associations with other well documented prognostic indicators, it may prove beneficial to include methylation analyses in molecular risk modelling of tumours.

Internal and external spatial attention examined with lateralized EEG power spectra.

PubMed

Van der Lubbe, Rob H J; Bundt, Carsten; Abrahamse, Elger L

2014-10-02

Several authors argued that retrieval of an item from visual short term memory (internal spatial attention) and focusing attention on an externally presented item (external spatial attention) are similar. Part of the neuroimaging support for this view may be due to the employed experimental procedures. Furthermore, as internal spatial attention may have a more induced than evoked nature some effects may not have been visible in event related analyses of the electroencephalogram (EEG), which limits the possibility to demonstrate differences. In the current study, a colored frame cued which stimulus, one out of four presented in separate quadrants, required a response, which depended on the form of the cued stimulus (circle or square). Importantly, the frame occurred either before (precue), simultaneously with (simultaneous cue), or after the stimuli (postcue). The precue and simultaneous cue condition both concern external attention, while the postcue condition implies the involvement of internal spatial attention. Event-related lateralizations (ERLs), reflecting evoked effects, and lateralized power spectra (LPS), reflecting both evoked and induced effects, were determined. ERLs revealed a posterior contralateral negativity (PCN) only in the precue condition. LPS analyses on the raw EEG showed early increased contralateral theta power at posterior sites and later increased ipsilateral alpha power at occipito-temporal sites in all cue conditions. Responses were faster when the internally or externally attended location corresponded with the required response side than when not. These findings provide further support for the view that internal and external spatial attention share their underlying mechanism. Copyright © 2014 Elsevier B.V. All rights reserved.

CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction.

PubMed

Xu, Youjun; Wang, Shiwei; Hu, Qiwan; Gao, Shuaishi; Ma, Xiaomin; Zhang, Weilin; Shen, Yihang; Chen, Fangjin; Lai, Luhua; Pei, Jianfeng

2018-05-10

CavityPlus is a web server that offers protein cavity detection and various functional analyses. Using protein three-dimensional structural information as the input, CavityPlus applies CAVITY to detect potential binding sites on the surface of a given protein structure and rank them based on ligandability and druggability scores. These potential binding sites can be further analysed using three submodules, CavPharmer, CorrSite, and CovCys. CavPharmer uses a receptor-based pharmacophore modelling program, Pocket, to automatically extract pharmacophore features within cavities. CorrSite identifies potential allosteric ligand-binding sites based on motion correlation analyses between cavities. CovCys automatically detects druggable cysteine residues, which is especially useful to identify novel binding sites for designing covalent allosteric ligands. Overall, CavityPlus provides an integrated platform for analysing comprehensive properties of protein binding cavities. Such analyses are useful for many aspects of drug design and discovery, including target selection and identification, virtual screening, de novo drug design, and allosteric and covalent-binding drug design. The CavityPlus web server is freely available at http://repharma.pku.edu.cn/cavityplus or http://www.pkumdl.cn/cavityplus.

Seismic response of Pacific Park Plaza. I. Data and preliminary analysis

USGS Publications Warehouse

Celebi, M.; Safak, E.

1992-01-01

The objective of this paper is to present analyses of a set of acceleration response records obtained during the October 17, 1989 Loma Prieta earthquake (Ms = 7.1) from the 30-story, three-winged, ductile moment-resistant reinforced-concrete-framed Pacific Park Plaza Building, located in Emeryville, east of San Francisco, Calif. The building was constructed in 1983, and instrumented in 1985 with 21 channels of synchronized uniaxial accelerometers deployed throughout the structure, and three channels of accelerometers located at free-field outside on the north side of the building, all connected to a central recording system. In addition, a triaxial strong-motion accelerograph is deployed at free-field on the south side of the building. The predominant response modes of the building and the associated frequencies at approximately 0.4 Hz and 1.0 Hz are identified visually from the unprocessed records, and also from Fourier amplitude spectra of the processed records, which, as expected, reveal significant torsional motion. In addition, the response spectra of the free-field and basement motions are very similar. These spectra show that significant structural resonances at higher modes influence both the ground level and the free-field motions, thus rising the question as to the definition of free-field motion, at least at this site. This part of the paper includes the preliminary analyses of the data acquired from this building. Part 2 of the paper provides detailed analyses of the data using system identification techniques.

Changes to Idaho's statewide surface-water quality monitoring program since 1995

USGS Publications Warehouse

O'Dell, Ivalou; Maret, Terry R.; Moore, Susan E.

1998-01-01

The program design included chemical analyses of water samples collected at 56 sites on the Bear, Clearwater, Kootenai, Pend Oreille, Salmon, Snake, and Spokane Rivers and their tributaries (fig. 1). Samples were collected every year (1990 through 1995) at 5 sites (annual sites), every other year at 19 sites (biennial sites), and every third year at 32 sites (triennial sites). Each year, 25 of the 56 sites were sampled. During water years 1990–95 (October 1, 1989, to September 30, 1995), samples were collected bimonthly. Onsite analyses consisted of discharge, specific conductance, pH, temperature, dissolved oxygen, bacteria (fecal coliform and fecal streptococci), and alkalinity. Laboratory analyses consisted of major ions, nutrients, trace elements, turbidity, and suspended sediment. Analytical results from the five annual sites sampled during water years 1990–93 are presented in a report by O’Dell and Berenbrock (1994).

Effects of petrochemical contamination on caged marine mussels using a multi-biomarker approach: Histological changes, neurotoxicity and hypoxic stress.

PubMed

Maisano, Maria; Cappello, Tiziana; Natalotto, Antonino; Vitale, Valeria; Parrino, Vincenzo; Giannetto, Alessia; Oliva, Sabrina; Mancini, Giuseppe; Cappello, Simone; Mauceri, Angela; Fasulo, Salvatore

2017-07-01

This work was designed to evaluate the biological effects of petrochemical contamination on marine mussels. Mytilus galloprovincialis, widely used as sentinel organisms in biomonitoring studies, were caged at the "Augusta-Melilli-Priolo" industrial site (eastern Sicily, Italy), chosen as one of the largest petrochemical areas in Europe, and Brucoli, chosen as reference site. Chemical analyses of sediments at the polluted site revealed high levels of PAHs and mercury, exceeding the national and international guideline limits. In mussels from the polluted site, severe morphological alterations were observed in gills, mainly involved in nutrient uptake and gas exchange. Changes in serotonergic and cholinergic systems, investigated through immunohistochemical, metabolomics and enzymatic approaches, were highlighted in gills, as well as onset of hypoxic adaptive responses with up-regulation of hypoxia-inducible factor transcript. Overall, the application of a multi-biomarker panel results effective in assessing the biological effects of petrochemical contamination on the health of aquatic organisms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structure of a Clostridium botulinum C143S thiaminase I/thiamin complex reveals active site architecture .

PubMed

Sikowitz, Megan D; Shome, Brateen; Zhang, Yang; Begley, Tadhg P; Ealick, Steven E

2013-11-05

Thiaminases are responsible for the degradation of thiamin and its metabolites. Two classes of thiaminases have been identified based on their three-dimensional structures and their requirements for a nucleophilic second substrate. Although the reactions of several thiaminases have been characterized, the physiological role of thiamin degradation is not fully understood. We have determined the three-dimensional X-ray structure of an inactive C143S mutant of Clostridium botulinum (Cb) thiaminase I with bound thiamin at 2.2 Å resolution. The C143S/thiamin complex provides atomic level details of the orientation of thiamin upon binding to Cb-thiaminase I and the identity of active site residues involved in substrate binding and catalysis. The specific roles of active site residues were probed by using site directed mutagenesis and kinetic analyses, leading to a detailed mechanism for Cb-thiaminase I. The structure of Cb-thiaminase I is also compared to the functionally similar but structurally distinct thiaminase II.

Allosteric Regulation of Mammalian Pantothenate Kinase*

PubMed Central

Subramanian, Chitra; Yun, Mi-Kyung; Yao, Jiangwei; Sharma, Lalit Kumar; Lee, Richard E.; White, Stephen W.; Jackowski, Suzanne; Rock, Charles O.

2016-01-01

Pantothenate kinase is the master regulator of CoA biosynthesis and is feedback-inhibited by acetyl-CoA. Comparison of the human PANK3·acetyl-CoA complex to the structures of PANK3 in four catalytically relevant complexes, 5′-adenylyl-β,γ-imidodiphosphate (AMPPNP)·Mg2+, AMPPNP·Mg2+·pantothenate, ADP·Mg2+·phosphopantothenate, and AMP phosphoramidate (AMPPN)·Mg2+, revealed a large conformational change in the dimeric enzyme. The amino-terminal nucleotide binding domain rotates to close the active site, and this allows the P-loop to engage ATP and facilitates required substrate/product interactions at the active site. Biochemical analyses showed that the transition between the inactive and active conformations, as assessed by the binding of either ATP·Mg2+ or acyl-CoA to PANK3, is highly cooperative indicating that both protomers move in concert. PANK3(G19V) cannot bind ATP, and biochemical analyses of an engineered PANK3/PANK3(G19V) heterodimer confirmed that the two active sites are functionally coupled. The communication between the two protomers is mediated by an α-helix that interacts with the ATP-binding site at its amino terminus and with the substrate/inhibitor-binding site of the opposite protomer at its carboxyl terminus. The two α-helices within the dimer together with the bound ligands create a ring that stabilizes the assembly in either the active closed conformation or the inactive open conformation. Thus, both active sites of the dimeric mammalian pantothenate kinases coordinately switch between the on and off states in response to intracellular concentrations of ATP and its key negative regulators, acetyl(acyl)-CoA. PMID:27555321

Implications of Climate Change for State Bioassessment ...

EPA Pesticide Factsheets

This draft report uses biological data collected by four states in wadeable rivers and streams to examine the components of state and tribal bioassessment and biomonitoring programs that may be vulnerable to climate change. The study investigates the potential to identify biological response signals to climate change within existing bioassessment data sets; analyzes how biological responses can be categorized and interpreted; and assesses how they may influence decision-making processes. The analyses suggest that several biological indicators may be used to detect climate change effects and such indicators can be used by state bioassessment programs to document changes at high-quality reference sites. The study investigates the potential to identify biological response signals to climate change within existing bioassessment data sets; analyzes how biological responses can be categorized and interpreted; and assesses how they may influence decision-making processes.

Silicone Foul Release Coatings: Effect of the Interaction of Oil and Coating Functionalities on the Magnitude of Macrofouling Attachment Strengths

DTIC Science & Technology

2003-01-01

Hawaii) is described. The response of tubeworms (Hydroides elegans, Hydroides dianthus ), oysters (Ostrea sp., Crassostrea sp.) and barnacles (Balanus...8 and Hydroides dianthus ) and oysters (Ostrea sp. and Crassostrea sp.) to the silicone coatings were measured using ASTM D 5618-94 (1994), in which...Oyster (Crassostrea sp.) and tubeworm (H. dianthus ) attachment strengths at the Indian River Lagoon site Linear regression analyses of the adhesion

Plasma Triglyceride Levels May Be Modulated by Gene Expression of IQCJ, NXPH1, PHF17 and MYB in Humans.

PubMed

Vallée Marcotte, Bastien; Guénard, Frédéric; Cormier, Hubert; Lemieux, Simone; Couture, Patrick; Rudkowska, Iwona; Vohl, Marie-Claude

2017-01-26

A genome-wide association study (GWAS) by our group identified loci associated with the plasma triglyceride (TG) response to ω-3 fatty acid (FA) supplementation in IQCJ , NXPH1 , PHF17 and MYB . Our aim is to investigate potential mechanisms underlying the associations between single nucleotide polymorphisms (SNPs) in the four genes and TG levels following ω-3 FA supplementation. 208 subjects received 3 g/day of ω-3 FA (1.9-2.2 g of EPA and 1.1 g of docosahexaenoic acid (DHA)) for six weeks. Plasma TG were measured before and after the intervention. 67 SNPs were selected to increase the density of markers near GWAS hits. Genome-wide expression and methylation analyses were conducted on respectively 30 and 35 participants' blood sample together with in silico analyses. Two SNPs of IQCJ showed different affinities to splice sites depending on alleles. Expression levels were influenced by genotype for one SNP in NXPH1 and one in MYB . Associations between 12 tagged SNPs of IQCJ , 26 of NXPH1 , seven of PHF17 and four of MYB and gene-specific CpG site methylation levels were found. The response of plasma TG to ω-3 FA supplementation may be modulated by the effect of DNA methylation on expression levels of genes revealed by GWAS.

Plasma Triglyceride Levels May Be Modulated by Gene Expression of IQCJ, NXPH1, PHF17 and MYB in Humans

PubMed Central

Vallée Marcotte, Bastien; Guénard, Frédéric; Cormier, Hubert; Lemieux, Simone; Couture, Patrick; Rudkowska, Iwona; Vohl, Marie-Claude

2017-01-01

A genome-wide association study (GWAS) by our group identified loci associated with the plasma triglyceride (TG) response to ω-3 fatty acid (FA) supplementation in IQCJ, NXPH1, PHF17 and MYB. Our aim is to investigate potential mechanisms underlying the associations between single nucleotide polymorphisms (SNPs) in the four genes and TG levels following ω-3 FA supplementation. 208 subjects received 3 g/day of ω-3 FA (1.9–2.2 g of EPA and 1.1 g of docosahexaenoic acid (DHA)) for six weeks. Plasma TG were measured before and after the intervention. 67 SNPs were selected to increase the density of markers near GWAS hits. Genome-wide expression and methylation analyses were conducted on respectively 30 and 35 participants’ blood sample together with in silico analyses. Two SNPs of IQCJ showed different affinities to splice sites depending on alleles. Expression levels were influenced by genotype for one SNP in NXPH1 and one in MYB. Associations between 12 tagged SNPs of IQCJ, 26 of NXPH1, seven of PHF17 and four of MYB and gene-specific CpG site methylation levels were found. The response of plasma TG to ω-3 FA supplementation may be modulated by the effect of DNA methylation on expression levels of genes revealed by GWAS. PMID:28134766

Multiple-methods investigation of recharge at a humid-region fractured rock site, Pennsylvania, USA

USGS Publications Warehouse

Heppner, C.S.; Nimmo, J.R.; Folmar, G.J.; Gburek, W.J.; Risser, D.W.

2007-01-01

Lysimeter-percolate and well-hydrograph analyses were combined to evaluate recharge for the Masser Recharge Site (central Pennsylvania, USA). In humid regions, aquifer recharge through an unconfined low-porosity fractured-rock aquifer can cause large magnitude water-table fluctuations over short time scales. The unsaturated hydraulic characteristics of the subsurface porous media control the magnitude and timing of these fluctuations. Data from multiple sets of lysimeters at the site show a highly seasonal pattern of percolate and exhibit variability due to both installation factors and hydraulic property heterogeneity. Individual event analysis of well hydrograph data reveals the primary influences on water-table response, namely rainfall depth, rainfall intensity, and initial water-table depth. Spatial and seasonal variability in well response is also evident. A new approach for calculating recharge from continuous water-table elevation records using a master recession curve (MRC) is demonstrated. The recharge estimated by the MRC approach when assuming a constant specific yield is seasonal to a lesser degree than the recharge estimate resulting from the lysimeter analysis. Partial reconciliation of the two recharge estimates is achieved by considering a conceptual model of flow processes in the highly-heterogeneous underlying fractured porous medium. ?? Springer-Verlag 2007.

A procedure to select ground-motion time histories for deterministic seismic hazard analysis from the Next Generation Attenuation (NGA) database

NASA Astrophysics Data System (ADS)

Huang, Duruo; Du, Wenqi; Zhu, Hong

2017-10-01

In performance-based seismic design, ground-motion time histories are needed for analyzing dynamic responses of nonlinear structural systems. However, the number of ground-motion data at design level is often limited. In order to analyze seismic performance of structures, ground-motion time histories need to be either selected from recorded strong-motion database or numerically simulated using stochastic approaches. In this paper, a detailed procedure to select proper acceleration time histories from the Next Generation Attenuation (NGA) database for several cities in Taiwan is presented. Target response spectra are initially determined based on a local ground-motion prediction equation under representative deterministic seismic hazard analyses. Then several suites of ground motions are selected for these cities using the Design Ground Motion Library (DGML), a recently proposed interactive ground-motion selection tool. The selected time histories are representatives of the regional seismic hazard and should be beneficial to earthquake studies when comprehensive seismic hazard assessments and site investigations are unavailable. Note that this method is also applicable to site-specific motion selections with the target spectra near the ground surface considering the site effect.

Projected effects of Climate-change-induced flow alterations on stream macroinvertebrate abundances.

PubMed

Kakouei, Karan; Kiesel, Jens; Domisch, Sami; Irving, Katie S; Jähnig, Sonja C; Kail, Jochem

2018-03-01

Global change has the potential to affect river flow conditions which are fundamental determinants of physical habitats. Predictions of the effects of flow alterations on aquatic biota have mostly been assessed based on species ecological traits (e.g., current preferences), which are difficult to link to quantitative discharge data. Alternatively, we used empirically derived predictive relationships for species' response to flow to assess the effect of flow alterations due to climate change in two contrasting central European river catchments. Predictive relationships were set up for 294 individual species based on (1) abundance data from 223 sampling sites in the Kinzig lower-mountainous catchment and 67 sites in the Treene lowland catchment, and (2) flow conditions at these sites described by five flow metrics quantifying the duration, frequency, magnitude, timing and rate of flow events using present-day gauging data. Species' abundances were predicted for three periods: (1) baseline (1998-2017), (2) horizon 2050 (2046-2065) and (3) horizon 2090 (2080-2099) based on these empirical relationships and using high-resolution modeled discharge data for the present and future climate conditions. We compared the differences in predicted abundances among periods for individual species at each site, where the percent change served as a proxy to assess the potential species responses to flow alterations. Climate change was predicted to most strongly affect the low-flow conditions, leading to decreased abundances of species up to -42%. Finally combining the response of all species over all metrics indicated increasing overall species assemblage responses in 98% of the studied river reaches in both projected horizons and were significantly larger in the lower-mountainous Kinzig compared to the lowland Treene catchment. Such quantitative analyses of freshwater taxa responses to flow alterations provide valuable tools for predicting potential climate-change impacts on species abundances and can be applied to any stressor, species, or region.

Evaluation of the Significance of Starch Surface Binding Sites on Human Pancreatic α-Amylase.

PubMed

Zhang, Xiaohua; Caner, Sami; Kwan, Emily; Li, Chunmin; Brayer, Gary D; Withers, Stephen G

2016-11-01

Starch provides the major source of caloric intake in many diets. Cleavage of starch into malto-oligosaccharides in the gut is catalyzed by pancreatic α-amylase. These oligosaccharides are then further cleaved by gut wall α-glucosidases to release glucose, which is absorbed into the bloodstream. Potential surface binding sites for starch on the pancreatic amylase, distinct from the active site of the amylase, have been identified through X-ray crystallographic analyses. The role of these sites in the degradation of both starch granules and soluble starch was probed by the generation of a series of surface variants modified at each site to disrupt binding. Kinetic analysis of the binding and/or cleavage of substrates ranging from simple maltotriosides to soluble starch and insoluble starch granules has allowed evaluation of the potential role of each such surface site. In this way, two key surface binding sites, on the same face as the active site, are identified. One site, containing a pair of aromatic residues, is responsible for attachment to starch granules, while a second site featuring a tryptophan residue around which a malto-oligosaccharide wraps is shown to heavily influence soluble starch binding and hydrolysis. These studies provide insights into the mechanisms by which enzymes tackle the degradation of largely insoluble polymers and also present some new approaches to the interrogation of the binding sites involved.

A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors.

PubMed

Izhar, Lior; Adamson, Britt; Ciccia, Alberto; Lewis, Jedd; Pontano-Vaites, Laura; Leng, Yumei; Liang, Anthony C; Westbrook, Thomas F; Harper, J Wade; Elledge, Stephen J

2015-06-09

Localization to sites of DNA damage is a hallmark of DNA damage response (DDR) proteins. To identify DDR factors, we screened epitope-tagged proteins for localization to sites of chromatin damaged by UV laser microirradiation and found >120 proteins that localize to damaged chromatin. These include the BAF tumor suppressor complex and the amyotrophic lateral sclerosis (ALS) candidate protein TAF15. TAF15 contains multiple domains that bind damaged chromatin in a poly-(ADP-ribose) polymerase (PARP)-dependent manner, suggesting a possible role as glue that tethers multiple PAR chains together. Many positives were transcription factors; > 70% of randomly tested transcription factors localized to sites of DNA damage, and of these, ∼90% were PARP dependent for localization. Mutational analyses showed that localization to damaged chromatin is DNA-binding-domain dependent. By examining Hoechst staining patterns at damage sites, we see evidence of chromatin decompaction that is PARP dependent. We propose that PARP-regulated chromatin remodeling at sites of damage allows transient accessibility of DNA-binding proteins. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

The genomic structure of the human UFO receptor.

PubMed

Schulz, A S; Schleithoff, L; Faust, M; Bartram, C R; Janssen, J W

1993-02-01

Using a DNA transfection-tumorigenicity assay we have recently identified the UFO oncogene. It encodes a tyrosine kinase receptor characterized by the juxtaposition of two immunoglobulin-like and two fibronectin type III repeats in its extracellular domain. Here we describe the genomic organization of the human UFO locus. The UFO receptor is encoded by 20 exons that are distributed over a region of 44 kb. Different isoforms of UFO mRNA are generated by alternative splicing of exon 10 and differential usage of two imperfect polyadenylation sites resulting in the presence or absence of 1.5-kb 3' untranslated sequences. Primer extension and S1 nuclease analyses revealed multiple transcriptional initiation sites including a major site 169 bp upstream of the translation start site. The promoter region is GC rich, lacks TATA and CAAT boxes, but contains potential recognition sites for a variety of trans-acting factors, including Sp1, AP-2 and the cyclic AMP response element-binding protein. Proto-UFO and its oncogenic counterpart exhibit identical cDNA and promoter regions sequences. Possible modes of UFO activation are discussed.

Anabolic Responses of an Adult Cancellous Bone Site to Prostaglandin E2 in the Rat

NASA Technical Reports Server (NTRS)

Ito, Hiroshi; Ke, Hua Zhu; Jee, Webster S. S.; Sakou, Takashi

1993-01-01

The objects of this study were to determine: (1) the response of a non-growing cancellous bone site to daily prostaglandin E2 (PGE2) administration; and (2) the differences in the effects of daily PGE2, administration in growing (proximal tibial metaphysis, PTM) and non-growing cancellous bone sites (distal tibial metaphysis, DTM). Seven-month-old male Sprague-Dawley rats were given daily subcutaneous injections of 0, 1, 3 and 6 mg PGE2/kg per day for 60, 120 and 180 days. The static and dynamic histomorphometric analyses were performed on double-fluorescent labeled undecalcified distal tibial metaphyses (DTM). No age-related changes were found in static and dynamic histomorphometry of DTM cancellous bone between 7 and 13 months of age. The DTM of 7-month-old (basal controls) rats consisted of a 24.5 +/- 7.61%-metaphyseal cancellous bone mass, and a thick trabeculae (92 +/- 12 micro-m). It also had a very low tissue-base bone formation rate (3.0 +/- 7.31%/year). Exogenous PGE2 administration produced the following transient changes in a dose-response manner between zero and 60 days: (1) increased trabecular bone mass and improved architecture (increased trabecular bone area, width and number, and decreased trabecular separation); (2) increased trabecular interconnections: (3) increased bone formation parameters; and (4) decreased eroded perimeter. A new steady state with more cancellous bone mass and higher bone turnover was observed from day 60 onward, The elevated bone mass induced by the first 60 days of PGE2 treatment was maintained by another 60 and 120 days with continuous daily PGE2 treatment. When these findings were compared to those previously reported for the PTM, we found that the DTM was much more responsive to PGE2 treatment than the PTM. Percent trabecular bone area and tissue based bone formation rate increased significantly more in DTM as compared to PTM after the 60 days of 6 mg PGE2 treatment. These observations indicate that a non-growing cancellous bone site is more responsive than growing bone site to long-term daily administration of PGE2.

Coastal Bacterioplankton Community Dynamics in Response to a Natural Disturbance

PubMed Central

Rappé, Michael S.

2013-01-01

In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of Gammaproteobacteria, Betaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition. PMID:23409156

A geographic comparison of the resting site fidelity behaviour in an intertidal limpet: Correlation with biological and physical factors

NASA Astrophysics Data System (ADS)

Nuñez, Jesús D.; Ocampo, Emiliano H.; Cledón, Maximiliano

2014-05-01

Many organisms vary their behaviour in response to environmental change. In stressful habitats motile organisms often exhibit behavioural patterns that are consistent with stress-minimizing strategies. In the present study we analysed the proportions of individuals with strong site fidelity and distances travelled by “unfaithful” individuals from their home scar at different temporal and spatial scales in the intertidal gastropod Siphonaria lessoni. We also assessed the behavioural response of S. lessoni to biological pressures such as conspecific population density and food availability (assessed by measures of chlorophyll a). The experiments were carried out in the arid climate of Patagonia on the rocky intertidal of Las Grutas (LG), and in the humid climate of The Pampas on the rocky intertidal of Mar del Plata (MDP) Argentina. At each site, shells of five hundred animals were marked with epoxy paint. Movement was measured as distance to a reference point after periods of one, five and ten days. Our results showed a positive relationship between food availability, site fidelity and distance to home scar for almost all observation days, but no relationship between population density and behavioural variables. Limpets in LG were more “faithful” than in MDP. Unfaithful limpets had the same mean displacement for all days and seasons except for Spring day-1 where MDP was higher than in LG and in Autumn day-10 where MDP was smaller than LG. The present results thus show differential response behaviour in intertidal limpets probably driven by the environmental conditions in which they live.

Soil Microbial Responses to Increased Moisture and Organic Resources along a Salinity Gradient in a Polar Desert

PubMed Central

Van Horn, David J.; Okie, Jordan G.; Buelow, Heather N.; Gooseff, Michael N.; Barrett, John E.

2014-01-01

Microbial communities in extreme environments often have low diversity and specialized physiologies suggesting a limited resistance to change. The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change-induced disturbances, including the melting of massive buried ice, cutting through of permafrost by streams, and warming events. These processes are increasing moisture across the landscape, altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment. Soil respiration and the activity of carbon-acquiring extracellular enzymes increased significantly (P < 0.05) with the addition of resources at the low- and moderate-salinity sites but not the high-salinity site. The bacterial community composition was altered, with an increase in Proteobacteria and Firmicutes with water and organic matter additions at the low- and moderate-salinity sites and a near dominance of Firmicutes at the high-salinity site. Principal coordinate analyses of all samples using a phylogenetically informed distance matrix (UniFrac) demonstrated discrete clustering among sites (analysis of similarity [ANOSIM], P < 0.05 and R > 0.40) and among most treatments within sites. The results from this experimental work suggest that microbial communities in this environment will undergo rapid change in response to the altered resources resulting from climate change impacts occurring in this region. PMID:24610850

Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert.

PubMed

Van Horn, David J; Okie, Jordan G; Buelow, Heather N; Gooseff, Michael N; Barrett, John E; Takacs-Vesbach, Cristina D

2014-05-01

Microbial communities in extreme environments often have low diversity and specialized physiologies suggesting a limited resistance to change. The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change-induced disturbances, including the melting of massive buried ice, cutting through of permafrost by streams, and warming events. These processes are increasing moisture across the landscape, altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment. Soil respiration and the activity of carbon-acquiring extracellular enzymes increased significantly (P < 0.05) with the addition of resources at the low- and moderate-salinity sites but not the high-salinity site. The bacterial community composition was altered, with an increase in Proteobacteria and Firmicutes with water and organic matter additions at the low- and moderate-salinity sites and a near dominance of Firmicutes at the high-salinity site. Principal coordinate analyses of all samples using a phylogenetically informed distance matrix (UniFrac) demonstrated discrete clustering among sites (analysis of similarity [ANOSIM], P < 0.05 and R > 0.40) and among most treatments within sites. The results from this experimental work suggest that microbial communities in this environment will undergo rapid change in response to the altered resources resulting from climate change impacts occurring in this region.

Life-history, substrate choice and Cytochrome Oxidase I variations in sandy beach peracaridans along the Rio de la Plata estuary

NASA Astrophysics Data System (ADS)

Fanini, L.; Zampicinini, G.; Tsigenopoulos, C. S.; Barboza, F. R.; Lozoya, J. P.; Gómez, J.; Celentano, E.; Lercari, D.; Marchetti, G. M.; Defeo, O.

2017-03-01

Life-history, substrate choice and Cytochrome Oxidase I (COI) sequences were analysed in populations of two peracaridans, the supralittoral talitrid Atlantorchestoidea brasiliensis and the intertidal cirolanid Excirolana armata. Three populations of each species, from beaches with similar grain size and located at different points along the natural gradient generated by the Rio de la Plata estuary were analysed. Abundance of E. armata increased with distance from the estuary, while the opposite trend was observed for A. brasiliensis. The proportion of females decreased towards high salinities for both species, significantly for E. armata. A test on substrate salinity preference revealed the absence of patterns due to active choice in E. armata. By contrast, A. brasiliensis showed no preference for the population closer to the estuary, while individuals from the other two sites significantly preferred high salinity substrates. Mitochondrial COI sequences were obtained from A. brasiliensis specimens tested for behaviour. Sequence analysis showed the population from the intermediate site to differ significantly from the other two. No significant genetic differentiation was instead found between populations from the two most distant sites, nor between individuals that expressed different salinity preference. Results showed that diverse sets of traits at the population level enable sandy beach species to cope with local environmental changes: life-history and behavioural traits appear to change in response to different ecological conditions, and, in the case of A brasiliensis, independently of the population structure inferred from COI sequence variation. Information from multiple traits allowed detection of population profiles, highlighting the relevance of multidisciplinary information and the concurrent analysis of field data and laboratory experiments, to detect responses of resident biota to environmental changes.

Two CGTCA motifs and a GHF1/Pit1 binding site mediate cAMP-dependent protein kinase A regulation of human growth hormone gene expression in rat anterior pituitary GC cells.

PubMed

Shepard, A R; Zhang, W; Eberhardt, N L

1994-01-21

We established the cis-acting elements which mediate cAMP responsiveness of the human growth hormone (hGH) gene in transiently transfected rat anterior pituitary tumor GC cells. Analysis of the intact hGH gene or hGH 5'-flanking DNA (5'-FR) coupled to the hGh cDNA or chloramphenicol acetyltransferase or luciferase genes, indicated that cAMP primarily stimulated hGH promoter activity. Cotransfection of a protein kinase A inhibitory protein cDNA demonstrated that the cAMP response was mediated by protein kinase A. Mutational analysis of the hGH promoter identified two core cAMP response element motifs (CGTCA) located at nucleotides -187/-183 (distal cAMP response element; dCRE) and -99/-95 (proximal cAMP response element; pCRE) and a pituitary-specific transcription factor (GHF1/Pit1) binding site at nucleotides -123/-112 (dGHF1) which were required for cAMP responsiveness. GHF1 was not a limiting factor, since overexpression of GHF1 in cotransfections increased basal but not forskolin induction levels. Gel shift analyses indicated that similar, ubiquitous, thermostable protein(s) specifically bound the pCRE and dCRE motifs. The CGTCA motif-binding factors were cAMP response element binding protein (CREB)/activating transcription factor-1 (ATF-1)-related, since the DNA-protein complex was competed by unlabeled CREB consensus oligonucleotide, specifically supershifted by antisera to CREB and ATF-1 but not ATF-2, and was bound by purified CREB with the same relative binding affinity (pCRE < dCRE < CREB) and mobility as the GC nuclear extract. UV cross-linking and Southwestern blot analyses revealed multiple DNA-protein interactions of which approximately 100- and approximately 45-kDa proteins were predominant; the approximately 45-kDa protein may represent CREB. These results indicate that CREB/ATF-1-related factors act coordinately with the cell-specific factor GHF1 to mediate cAMP-dependent regulation of hGH-1 gene transcription in anterior pituitary somatotrophs.

Which came first, people or pollution? A review of theory and evidence from longitudinal environmental justice studies

NASA Astrophysics Data System (ADS)

Mohai, Paul; Saha, Robin

2015-12-01

A considerable number of quantitative analyses have been conducted in the past several decades that demonstrate the existence of racial and socioeconomic disparities in the distribution of a wide variety of environmental hazards. The vast majority of these have been cross-sectional, snapshot studies employing data on hazardous facilities and population characteristics at only one point in time. Although some limited hypotheses can be tested with cross-sectional data, fully understanding how present-day disparities come about requires longitudinal analyses that examine the demographic characteristics of sites at the time of facility siting and track demographic changes after siting. Relatively few such studies exist and those that do exist have often led to confusing and contradictory findings. In this paper we review the theoretical arguments, methods, findings, and conclusions drawn from existing longitudinal environmental justice studies. Our goal is to make sense of this literature and to identify the direction future research should take in order to resolve confusion and arrive at a clearer understanding of the processes and contributory factors by which present-day racial and socioeconomic disparities in the distribution of environmental hazards have come about. Such understandings also serve as an important step in identifying appropriate and effective societal responses to ameliorate environmental disparities.

Prostaglandin E2 Adds Bone to a Cancellous Bone Site with a Closed Growth Plate and Low Bone Turnover in Ovariectomized Rats

NASA Technical Reports Server (NTRS)

Ma, Y. F.; Ke, H. Z.; Jee, W. S. S.

1994-01-01

The objects of this study were to determine the responses of a cancellous bone site with a closed growth plate, (the distal tibial metaphysis (DTM), to ovariectomy (OVX) and OVX plus a prostaglandin E(2) treatment, and compare the site's response to previous findings reported for another site, the proximal tibial metaphysis (PTM). Thirty five 3-month old female Sprague-Dawley rats were divided into five groups; basal, sham OVX, and OVX+0, +1, or +6 mg PGE(2)/kg/d injected subcutaneously for 3 months and given double fluorescent labels before sacrifice. Cancellous bone histomorphometric analyses were performed on 20 micrometer thick undecalcified DTM sections. Similar to the PTM, the DTM showed age-related decreases in bone formation and increases in bone resorption, but it differed in that at 3 months POST OVX there was neither bone loss nor changes in formation endpoints. Giving 1 mg PGE(2)/kg/d to OVX rats prevented most age-related changes and maintained the bone formation histomorphometry near basal levels. Treating OVX rats with 6 mg PGE(2)/kd/d prevented age-related bone changes, added extra bone, and improved microanatomical structure by stimulating bone formation, without altering bone resportion. Futhermore, After PGE(2) admimnistration, the DTM, a cancellous bone site with a closed growth plate, increased bone formation more than did the cancellous bone in the PTM.

Prostaglandin E2 Adds Bone to a Cancellous Bone Site with a Closed Growth Plate and Low Bone Turnover in Ovariectomized Rats

NASA Technical Reports Server (NTRS)

Ma, Y. F.; Ke, H. Z.; Jee, W. S. S.

1994-01-01

The objects of this study were to determine the responses of a cancellous bone site with a closed growth plate (the distal tibial metaphysis, DTM) to ovariectomy (OVX) and OVX plus a prostaglandin E2 (PGE2) treatment, and compare the site's response to previous findings reported for another site (the proximal tibial metaphysis, PTM). Thirty-five 3-month old female Sprague-Dawley rats were divided into five groups: basal, sham-OVX, and OVX+0, +1, or +6 mg PGE2/kg/d injected subcutaneously for 3 months and given double fluorescent labels before sacrifice. Cancellous bone histomorphometric analyses were performed on 20-micron-thick undecalcified DTM sections. Similar to the PTM, the DTM showed age-related decreases in bone formation and increases in bone resorption, but it differed in that at 3 months post-OVX; there was neither bone loss nor changes in formation endpoints. Giving 1 mg PGE2/kg/d to OVX rats prevented most age-related changes and maintained the bone formation histomorphometry near basal levels. Treating OVX rats with 6 mg PGE2/kg/d prevented age-related bone changes, added extra bone, and improved microanatomical structure by stimulating bone formation without altering bone resorption. Furthermore, after PGE2 administration, the DTM, a cancellous bone site with a closed growth plate, inereased bone formation more than did the cancellous bone in the PTM.

Alternative Endpoints and Approaches Selected for the Remediation of Contaminated Groundwater at Complex Sites

NASA Astrophysics Data System (ADS)

Deeb, R. A.; Hawley, E.

2011-12-01

This presentation will focus on findings, statistics, and case studies from a recently-completed report for the Department of Defense's Environmental Security Technology Certification Program (ESTCP) (Project ER-0832) on alternative endpoints and alternative remedial strategies for groundwater remediation under a variety of Federal and state cleanup programs, including technical impracticability (TI) and other Applicable or Relevant and Appropriate Requirement (ARAR) waivers, state and local designations such as groundwater management zones, Alternate Concentration Limits (ACLs), use of monitored natural attenuation (MNA) over long timeframes, and more. The primary objective of the project was to provide environmental managers and regulators with tools, metrics, and information needed to evaluate alternative endpoints for groundwater remediation at complex sites. A statistical analysis of Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) sites receiving TI waivers will be presented as well as case studies of other types of alternative endpoints and alternative remedial strategies to illustrate the variety of approaches used at complex sites and the technical analyses used to predict and document cost, timeframe, and potential remedial effectiveness. Case studies provide examples of the flexible, site-specific, application of alternative endpoints and alternative remedial strategies that have been used in the past to manage and remediate groundwater contamination at complex sites. For example, at least 13 states consider some designation for groundwater containment in their corrective action policies, such as groundwater management zones, containment zones, and groundwater classification exemption areas. These designations typically indicate that groundwater contamination is present above permissible levels. Soil and groundwater within these zones are managed to protect human health and the environment. Lesson learned for the analyses conducted and the case studies evaluated allow for a more careful consideration of alternative, beneficial, and cost-effective cleanup objectives and metrics that can be achieved over the short-term (while eventually meeting long-term cleanup objectives or demonstrating the applicability of alternative endpoints), thus improving the site cleanup process at complex sites where appropriate.

A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases

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

Bradshaw, Niels; Levdikov, Vladimir M.; Zimanyi, Christina M.

PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an α-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor. Our analysis indicates that this switch is widely conserved among PP2C family members, serving as a platform to control phosphatase activitymore » in response to diverse inputs. Remarkably, the switch is shared with proteasomal proteases, which we identify as evolutionary and structural relatives of PP2C phosphatases. Although these proteases use an unrelated catalytic mechanism, rotation of equivalent helices controls protease activity by movement of the equivalent carbonyl oxygen into the active site.« less

Multiple transcription factor codes activate epidermal wound–response genes in Drosophila

PubMed Central

Pearson, Joseph C.; Juarez, Michelle T.; Kim, Myungjin; Drivenes, Øyvind; McGinnis, William

2009-01-01

Wounds in Drosophila and mouse embryos induce similar genetic pathways to repair epidermal barriers. However, the transcription factors that transduce wound signals to repair epidermal barriers are largely unknown. We characterize the transcriptional regulatory enhancers of 4 genes—Ddc, ple, msn, and kkv—that are rapidly activated in epidermal cells surrounding wounds in late Drosophila embryos and early larvae. These epidermal wound enhancers all contain evolutionarily conserved sequences matching binding sites for JUN/FOS and GRH transcription factors, but vary widely in trans- and cis-requirements for these inputs and their binding sites. We propose that the combination of GRH and FOS is part of an ancient wound–response pathway still used in vertebrates and invertebrates, but that other mechanisms have evolved that result in similar transcriptional output. A common, but largely untested assumption of bioinformatic analyses of gene regulatory networks is that transcription units activated in the same spatial and temporal patterns will require the same cis-regulatory codes. Our results indicate that this is an overly simplistic view. PMID:19168633

Canine scent detection and microbial source tracking of human waste contamination in storm drains.

PubMed

Van De Werfhorst, Laurie C; Murray, Jill L S; Reynolds, Scott; Reynolds, Karen; Holden, Patricia A

2014-06-01

Human fecal contamination of surface waters and drains is difficult to diagnose. DNA-based and chemical analyses of water samples can be used to specifically quantify human waste contamination, but their expense precludes routine use. We evaluated canine scent tracking, using two dogs trained to respond to the scent of municipal wastewater, as a field approach for surveying human fecal contamination. Fecal indicator bacteria, as well as DNA-based and chemical markers of human waste, were analyzed in waters sampled from canine scent-evaluated sites (urban storm drains and creeks). In the field, the dogs responded positively (70% and 100%) at sites for which sampled waters were then confirmed as contaminated with human waste. When both dogs indicated a negative response, human waste markers were absent. Overall, canine scent tracking appears useful for prioritizing sampling sites for which DNA-based and similarly expensive assays can confirm and quantify human waste contamination.

SbnG, a Citrate Synthase in Staphylococcus aureus

PubMed Central

Kobylarz, Marek J.; Grigg, Jason C.; Sheldon, Jessica R.; Heinrichs, David E.; Murphy, Michael E. P.

2014-01-01

In response to iron deprivation, Staphylococcus aureus produces staphyloferrin B, a citrate-containing siderophore that delivers iron back to the cell. This bacterium also possesses a second citrate synthase, SbnG, that is necessary for supplying citrate to the staphyloferrin B biosynthetic pathway. We present the structure of SbnG bound to the inhibitor calcium and an active site variant in complex with oxaloacetate. The overall fold of SbnG is structurally distinct from TCA cycle citrate synthases yet similar to metal-dependent class II aldolases. Phylogenetic analyses revealed that SbnG forms a separate clade with homologs from other siderophore biosynthetic gene clusters and is representative of a metal-independent subgroup in the phosphoenolpyruvate/pyruvate domain superfamily. A structural superposition of the SbnG active site to TCA cycle citrate synthases and site-directed mutagenesis suggests a case for convergent evolution toward a conserved catalytic mechanism for citrate production. PMID:25336653

Final environmental assessment for the U.S. Department of Energy, Oak Ridge Operations receipt and storage of uranium materials from the Fernald Environmental Management Project site

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

NONE

Through a series of material transfers and sales agreements over the past 6 to 8 years, the Fernald Environmental Management Project (FEMP) has reduced its nuclear material inventory from 14,500 to approximately 6,800 metric tons of uranium (MTU). This effort is part of the US Department of energy`s (DOE`s) decision to change the mission of the FEMP site; it is currently shut down and the site is being remediated. This EA focuses on the receipt and storage of uranium materials at various DOE-ORO sites. The packaging and transportation of FEMP uranium material has been evaluated in previous NEPA and othermore » environmental evaluations. A summary of these evaluation efforts is included as Appendix A. The material would be packaged in US Department of Transportation-approved shipping containers and removed from the FEMP site and transported to another site for storage. The Ohio Field Office will assume responsibility for environmental analyses and documentation for packaging and transport of the material as part of the remediation of the site, and ORO is preparing this EA for receipt and storage at one or more sites.« less

Post-Closure Inspection, Sampling, and Maintenance Report for the Salmon, Mississippi, Site Calendar Year 2012

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

None

2013-03-01

This report summarizes the 2012 annual inspection, sampling, measurement, and maintenance activities performed at the Salmon, Mississippi, Site (Salmon site). The draft Long-Term Surveillance and Maintenance Plan for the Salmon Site, Lamar County, Mississippi (DOE 2007) specifies the submittal of an annual report of site activities with the results of sample analyses. A revised plan is in preparation. The Long-Term Surveillance Plan for the Salmon, Mississippi, Site is intended for release in 2013. The Salmon site consists of 1,470 acres. The site is located in Lamar County, Mississippi, approximately 10 miles west of Purvis, Mississippi, and about 21 miles southwestmore » of Hattiesburg, Mississippi The State of Mississippi owns the surface real estate subject to certain restrictions related to subsurface penetration. The State is the surface operator; the Mississippi Forestry Commission is its agent. The federal government owns the subsurface real estate (including minerals and some surface features), shares right-of-entry easements with the State, and retains rights related to subsurface monitoring. The U.S. Department of Energy (DOE) Office of Legacy Management (LM), a successor agency to the U.S. Atomic Energy Commission, is responsible for the long-term surveillance of the subsurface real estate« less

Evaluating the response of biological assemblages as potential indicators for restoration measures in an intermittent Mediterranean river.

PubMed

Hughes, Samantha Jane; Santos, Jose; Ferreira, Teresa; Mendes, Ana

2010-08-01

Bioindicators are essential for detecting environmental degradation and for assessing the success of river restoration initiatives. River restoration projects require the identification of environmental and pressure gradients that affect the river system under study and the selection of suitable indicators to assess habitat quality before, during and after restoration. We assessed the response of benthic macroinvertebrates, fish, bird and macrophyte assemblages to environmental and pressure gradients from sites situated upstream and downstream of a cofferdam on the River Odelouca, an intermittent Mediterranean river in southwest Portugal. The Odelouca will be permanently dammed in 2010. Principal Component Analyses (PCA) of environmental and pressure variables revealed that most variance was explained by environmental factors that clearly separated sites upstream and downstream of the partially built cofferdam. The pressure gradient describing physical impacts to the banks and channel as a result of land use change was less distinct. Redundancy Analysis revealed significant levels of explained variance to species distribution patterns in relation to environmental and pressure variables for all 4 biological assemblages. Partial Redundancy analyses revealed high levels of redundancy for pH between groups and that the avifauna was best associated with pressures acting upon the system. Patterns in invertebrates and fish were associated with descriptors of habitat quality, although fish distribution patterns were affected by reduced connectivity. Procrustean and RELATE (Mantel test) analyses gave broadly similar results and supported these findings. We give suggestions on the suitability of key indicator groups such as benthic macroinvertebrates and endemic fish species to assess in stream habitat quality and appropriate restoration measures, such as the release of peak flow patterns that mimic intermittent Mediterranean systems to combat habitat fragmentation and reduced connectivity.

Evaluating the Response of Biological Assemblages as Potential Indicators for Restoration Measures in an Intermittent Mediterranean River

NASA Astrophysics Data System (ADS)

Hughes, Samantha Jane; Santos, Jose; Ferreira, Teresa; Mendes, Ana

2010-08-01

Bioindicators are essential for detecting environmental degradation and for assessing the success of river restoration initiatives. River restoration projects require the identification of environmental and pressure gradients that affect the river system under study and the selection of suitable indicators to assess habitat quality before, during and after restoration. We assessed the response of benthic macroinvertebrates, fish, bird and macrophyte assemblages to environmental and pressure gradients from sites situated upstream and downstream of a cofferdam on the River Odelouca, an intermittent Mediterranean river in southwest Portugal. The Odelouca will be permanently dammed in 2010. Principal Component Analyses (PCA) of environmental and pressure variables revealed that most variance was explained by environmental factors that clearly separated sites upstream and downstream of the partially built cofferdam. The pressure gradient describing physical impacts to the banks and channel as a result of land use change was less distinct. Redundancy Analysis revealed significant levels of explained variance to species distribution patterns in relation to environmental and pressure variables for all 4 biological assemblages. Partial Redundancy analyses revealed high levels of redundancy for pH between groups and that the avifauna was best associated with pressures acting upon the system. Patterns in invertebrates and fish were associated with descriptors of habitat quality, although fish distribution patterns were affected by reduced connectivity. Procrustean and RELATE (Mantel test) analyses gave broadly similar results and supported these findings. We give suggestions on the suitability of key indicator groups such as benthic macroinvertebrates and endemic fish species to assess in stream habitat quality and appropriate restoration measures, such as the release of peak flow patterns that mimic intermittent Mediterranean systems to combat habitat fragmentation and reduced connectivity.

Cell size and wall dimensions drive distinct variability of earlywood and latewood density in Northern Hemisphere conifers.

PubMed

Björklund, Jesper; Seftigen, Kristina; Schweingruber, Fritz; Fonti, Patrick; von Arx, Georg; Bryukhanova, Marina V; Cuny, Henri E; Carrer, Marco; Castagneri, Daniele; Frank, David C

2017-11-01

Interannual variability of wood density - an important plant functional trait and environmental proxy - in conifers is poorly understood. We therefore explored the anatomical basis of density. We hypothesized that earlywood density is determined by tracheid size and latewood density by wall dimensions, reflecting their different functional tasks. To determine general patterns of variability, density parameters from 27 species and 349 sites across the Northern Hemisphere were correlated to tree-ring width parameters and local climate. We performed the same analyses with density and width derived from anatomical data comprising two species and eight sites. The contributions of tracheid size and wall dimensions to density were disentangled with sensitivity analyses. Notably, correlations between density and width shifted from negative to positive moving from earlywood to latewood. Temperature responses of density varied intraseasonally in strength and sign. The sensitivity analyses revealed tracheid size as the main determinant of earlywood density, while wall dimensions become more influential for latewood density. Our novel approach of integrating detailed anatomical data with large-scale tree-ring data allowed us to contribute to an improved understanding of interannual variations of conifer growth and to illustrate how conifers balance investments in the competing xylem functions of hydraulics and mechanical support. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Assessment of climate change effects on mountain ecosystems through a cross-site analysis in the Alps and Apennines.

PubMed

Rogora, M; Frate, L; Carranza, M L; Freppaz, M; Stanisci, A; Bertani, I; Bottarin, R; Brambilla, A; Canullo, R; Carbognani, M; Cerrato, C; Chelli, S; Cremonese, E; Cutini, M; Di Musciano, M; Erschbamer, B; Godone, D; Iocchi, M; Isabellon, M; Magnani, A; Mazzola, L; Morra di Cella, U; Pauli, H; Petey, M; Petriccione, B; Porro, F; Psenner, R; Rossetti, G; Scotti, A; Sommaruga, R; Tappeiner, U; Theurillat, J-P; Tomaselli, M; Viglietti, D; Viterbi, R; Vittoz, P; Winkler, M; Matteucci, G

2018-05-15

Mountain ecosystems are sensitive and reliable indicators of climate change. Long-term studies may be extremely useful in assessing the responses of high-elevation ecosystems to climate change and other anthropogenic drivers from a broad ecological perspective. Mountain research sites within the LTER (Long-Term Ecological Research) network are representative of various types of ecosystems and span a wide bioclimatic and elevational range. Here, we present a synthesis and a review of the main results from ecological studies in mountain ecosystems at 20 LTER sites in Italy, Switzerland and Austria covering in most cases more than two decades of observations. We analyzed a set of key climate parameters, such as temperature and snow cover duration, in relation to vascular plant species composition, plant traits, abundance patterns, pedoclimate, nutrient dynamics in soils and water, phenology and composition of freshwater biota. The overall results highlight the rapid response of mountain ecosystems to climate change, with site-specific characteristics and rates. As temperatures increased, vegetation cover in alpine and subalpine summits increased as well. Years with limited snow cover duration caused an increase in soil temperature and microbial biomass during the growing season. Effects on freshwater ecosystems were also observed, in terms of increases in solutes, decreases in nitrates and changes in plankton phenology and benthos communities. This work highlights the importance of comparing and integrating long-term ecological data collected in different ecosystems for a more comprehensive overview of the ecological effects of climate change. Nevertheless, there is a need for (i) adopting co-located monitoring site networks to improve our ability to obtain sound results from cross-site analysis, (ii) carrying out further studies, in particular short-term analyses with fine spatial and temporal resolutions to improve our understanding of responses to extreme events, and (iii) increasing comparability and standardizing protocols across networks to distinguish local patterns from global patterns. Copyright © 2017 Elsevier B.V. All rights reserved.

NEW COLUMN SEPARATION METHOD FOR EMERGENCY URINE SAMPLES

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

Maxwell, S; Brian Culligan, B

2007-08-28

The Savannah River Site Environmental Bioassay Lab participated in the 2007 NRIP Emergency Response program administered by the National Institute for Standards and Technology (NIST) in May, 2007. A new rapid column separation method was applied directly to the NRIP 2007 emergency urine samples, with only minimal sample preparation to reduce preparation time. Calcium phosphate precipitation, previously used to pre-concentrate actinides and Sr-90 in NRIP 2006 urine and water samples, was not used for the NRIP 2007 urine samples. Instead, the raw urine was acidified and passed directly through the stacked resin columns (TEVA+TRU+SR Resins) to separate the actinides andmore » strontium from the NRIP urine samples more quickly. This improvement reduced sample preparation time for the NRIP 2007 emergency urine analyses significantly. This approach works well for small volume urine samples expected during an emergency response event. Based on initial feedback from NIST, the SRS Environmental Bioassay Lab had the most rapid analysis times for actinides and strontium-90 analyses for NRIP 2007 urine samples.« less

Lessons from Star Carr on the vulnerability of organic archaeological remains to environmental change

PubMed Central

Milner, Nicky; Panter, Ian; Penkman, Kirsty E. H.

2016-01-01

Examples of wetland deposits can be found across the globe and are known for preserving organic archaeological and environmental remains that are vitally important to our understanding of past human–environment interactions. The Mesolithic site of Star Carr (Yorkshire, United Kingdom) represents one of the most influential archives of human response to the changing climate at the end of the last glacial in Northern Europe. A hallmark of the site since its discovery in 1948 has been the exceptional preservation of its organic remains. Disturbingly, recent excavations have suggested that the geochemistry of the site is no longer conducive to such remarkable survival of organic archaeological and environmental materials. Microcosm (laboratory-based) burial experiments have been undertaken, alongside analysis of artifacts excavated from the site, to assess the effect of these geochemical changes on the remaining archaeological material. By applying a suite of macroscopic and molecular analyses, we demonstrate that the geochemical changes at Star Carr are contributing to the inexorable and rapid loss of valuable archaeological and paleoenvironmental information. Our findings have global implications for other wetland sites, particularly archaeological sites preserved in situ. PMID:27799567

Simulation of the effects of rainfall and groundwater use on historical lake water levels, groundwater levels, and spring flows in central Florida

USGS Publications Warehouse

O'Reilly, Andrew M.; Roehl, Edwin A.; Conrads, Paul; Daamen, Ruby C.; Petkewich, Matthew D.

2014-01-01

The urbanization of central Florida has progressed substantially in recent decades, and the total population in Lake, Orange, Osceola, Polk, and Seminole Counties more than quadrupled from 1960 to 2010. The Floridan aquifer system is the primary source of water for potable, industrial, and agricultural purposes in central Florida. Despite increases in groundwater withdrawals to meet the demand of population growth, recharge derived by infiltration of rainfall in the well-drained karst terrain of central Florida is the largest component of the long-term water balance of the Floridan aquifer system. To complement existing physics-based groundwater flow models, artificial neural networks and other data-mining techniques were used to simulate historical lake water level, groundwater level, and spring flow at sites throughout the area. Historical data were examined using descriptive statistics, cluster analysis, and other exploratory analysis techniques to assess their suitability for more intensive data-mining analysis. Linear trend analyses of meteorological data collected by the National Oceanic and Atmospheric Administration at 21 sites indicate 67 percent of sites exhibited upward trends in air temperature over at least a 45-year period of record, whereas 76 percent exhibited downward trends in rainfall over at least a 95-year period of record. Likewise, linear trend analyses of hydrologic response data, which have varied periods of record ranging in length from 10 to 79 years, indicate that water levels in lakes (307 sites) were about evenly split between upward and downward trends, whereas water levels in 69 percent of wells (out of 455 sites) and flows in 68 percent of springs (out of 19 sites) exhibited downward trends. Total groundwater use in the study area increased from about 250 million gallons per day (Mgal/d) in 1958 to about 590 Mgal/d in 1980 and remained relatively stable from 1981 to 2008, with a minimum of 559 Mgal/d in 1994 and a maximum of 773 Mgal/d in 2000. The change in groundwater-use trend in the early 1980s and the following period of relatively slight trend is attributable to the concomitant effects of increasing public-supply withdrawals and decreasing use of water by the phosphate industry and agriculture. On the basis of available historical data and exploratory analyses, empirical lake water-level, groundwater-level, and spring-flow models were developed for 22 lakes, 23 wells, and 6 springs. Input time series consisting of various frequencies and frequency-band components of daily rainfall (1942 to 2008) and monthly total groundwater use (1957 to 2008) resulted in hybrid signal-decomposition artificial neural network models. The final models explained much of the variability in observed hydrologic data, with 43 of the 51 sites having coefficients of determination exceeding 0.6, and the models matched the magnitude of the observed data reasonably well, such that models for 32 of the 51 sites had root-mean-square errors less than 10 percent of the measured range of the data. The Central Florida Artificial Neural Network Decision Support System was developed to integrate historical databases and the 102 site-specific artificial neural network models, model controls, and model output into a spreadsheet application with a graphical user interface that allows the user to simulate scenarios of interest. Overall, the data-mining analyses indicate that the Floridan aquifer system in central Florida is a highly conductive, dynamic, open system that is strongly influenced by external forcing. The most important external forcing appears to be rainfall, which explains much of the multiyear cyclic variability and long-term downward trends observed in lake water levels, groundwater levels, and spring flows. For most sites, groundwater use explains less of the observed variability in water levels and flows than rainfall. Relative groundwater-use impacts are greater during droughts, however, and long-term trends in water levels and flows were identified that are consistent with historical groundwater-use patterns. The sensitivity of the hydrologic system to rainfall is expected, owing to the well-drained karst terrain and relatively thin confinement of the Floridan aquifer system in much of central Florida. These characteristics facilitate the relatively rapid transmission of infiltrating water from rainfall to the water table and contribute to downward leakage of water to the Floridan aquifer system. The areally distributed nature of rainfall, as opposed to the site-specific nature of groundwater use, and the generally high transmissivity and low storativity properties of the semiconfined Floridan aquifer system contribute to the prevalence of water-level and flow patterns that mimic rainfall patterns. In general, the data-mining analyses demonstrate that the hydrologic system in central Florida is affected by groundwater use differently during wet periods, when little or no system storage is available (high water levels), compared to dry periods, when there is excess system storage (low water levels). Thus, by driving the overall behavior of the system, rainfall indirectly influences the degree to which groundwater use will effect persistent trends in water levels and flows, with groundwater-use impacts more prevalent during periods of low water levels and spring flows caused by low rainfall and less prevalent during periods of high water levels and spring flows caused by high rainfall. Differences in the magnitudes of rainfall and groundwater use during wet and dry periods also are important determinants of hydrologic response. An important implication of the data-mining analyses is that rainfall variability at subannual to multidecadal timescales must be considered in combination with groundwater use to provide robust system-response predictions that enhance sustainable resource management in an open karst aquifer system. The data-driven approach was limited, however, by the confounding effects of correlation between rainfall and groundwater use, the quality and completeness of the historical databases, and the spatial variations in groundwater use. The data-mining analyses indicate that available historical data when used alone do not contain sufficient information to definitively quantify the related individual effects of rainfall and groundwater use on hydrologic response. The knowledge gained from data-driven modeling and the results from physics-based modeling, when compared and used in combination, can yield a more comprehensive assessment and a more robust understanding of the hydrologic system than either of the approaches used separately.

Variation in Responses of Fishes across Multiple Reserves within a Network of Marine Protected Areas in Temperate Waters

PubMed Central

Starr, Richard M.; Wendt, Dean E.; Barnes, Cheryl L.; Marks, Corina I.; Malone, Dan; Waltz, Grant; Schmidt, Katherine T.; Chiu, Jennifer; Launer, Andrea L.; Hall, Nathan C.; Yochum, Noëlle

2015-01-01

Meta-analyses of field studies have shown that biomass, density, species richness, and size of organisms protected by no-take marine reserves generally increase over time. The magnitude and timing of changes in these response variables, however, vary greatly and depend upon the taxonomic groups protected, size and type of reserve, oceanographic regime, and time since the reserve was implemented. We conducted collaborative, fishery-independent surveys of fishes for seven years in and near newly created marine protected areas (MPAs) in central California, USA. Results showed that initially most MPAs contained more and larger fishes than associated reference sites, likely due to differences in habitat quality. The differences between MPAs and reference sites did not greatly change over the seven years of our study, indicating that reserve benefits will be slow to accumulate in California’s temperate eastern boundary current. Fishes in an older reserve that has been closed to fishing since 1973, however, were significantly more abundant and larger than those in associated reference sites. This indicates that reserve benefits are likely to accrue in the California Current ecosystem, but that 20 years or more may be needed to detect significant changes in response variables that are due to MPA implementation. Because of the high spatial and temporal variability of fish recruitment patterns, long-term monitoring is needed to identify positive responses of fishes to protection in the diverse set of habitats in a dynamic eastern boundary current. Qualitative estimates of response variables, such as would be obtained from an expert opinion process, are unlikely to provide an accurate description of MPA performance. Similarly, using one species or one MPA as an indicator is unlikely to provide sufficient resolution to accurately describe the performance of multiple MPAs. PMID:25760856

Detection of environmentally persistent free radicals at a superfund wood treating site.

PubMed

dela Cruz, Albert Leo N; Gehling, William; Lomnicki, Slawomir; Cook, Robert; Dellinger, Barry

2011-08-01

Environmentally persistent free radicals (EPFRs) have previously been observed in association with combustion-generated particles and airborne PM(2.5) (particulate matter, d < 2.5um). The purpose of this study was to determine if similar radicals were present in soils and sediments at Superfund sites. The site was a former wood treating facility containing pentachlorophenol (PCP) as a major contaminant. Both contaminated and noncontaminated (just outside the contaminated area) soil samples were collected. The samples were subjected to the conventional humic substances (HS) extraction procedure. Electron paramagnetic resonance (EPR) spectroscopy was used to measure the EPFR concentrations and determine their structure for each sample fraction. Analyses revealed a ∼30× higher EPFR concentration in the PCP contaminated soils (20.2 × 10(17) spins/g) than in the noncontaminated soil (0.7 × 10(17) spins/g). Almost 90% of the EPFR signal originated from the minerals/clays/humins fraction. GC-MS analyses revealed ∼6500 ppm of PCP in the contaminated soil samples and none detected in the background samples. Inductively coupled plasma-atomic emission spectrophotometry (ICP-AES) analyses revealed ∼7× higher concentrations of redox-active transition metals, in the contaminated soils than the noncontaminated soil. Vapor phase and liquid phase dosing of the clays/minerals/humins fraction of the soil with PCP resulted in an EPR signal identical to that observed in the contaminated soil, strongly suggesting the observed EPFR is pentachlorophenoxyl radical. Chemisorption and electron transfer from PCP to transition metals and other electron sinks in the soil are proposed to be responsible for EPFR formation.

Sampling effort affects multivariate comparisons of stream assemblages

USGS Publications Warehouse

Cao, Y.; Larsen, D.P.; Hughes, R.M.; Angermeier, P.L.; Patton, T.M.

2002-01-01

Multivariate analyses are used widely for determining patterns of assemblage structure, inferring species-environment relationships and assessing human impacts on ecosystems. The estimation of ecological patterns often depends on sampling effort, so the degree to which sampling effort affects the outcome of multivariate analyses is a concern. We examined the effect of sampling effort on site and group separation, which was measured using a mean similarity method. Two similarity measures, the Jaccard Coefficient and Bray-Curtis Index were investigated with 1 benthic macroinvertebrate and 2 fish data sets. Site separation was significantly improved with increased sampling effort because the similarity between replicate samples of a site increased more rapidly than between sites. Similarly, the faster increase in similarity between sites of the same group than between sites of different groups caused clearer separation between groups. The strength of site and group separation completely stabilized only when the mean similarity between replicates reached 1. These results are applicable to commonly used multivariate techniques such as cluster analysis and ordination because these multivariate techniques start with a similarity matrix. Completely stable outcomes of multivariate analyses are not feasible. Instead, we suggest 2 criteria for estimating the stability of multivariate analyses of assemblage data: 1) mean within-site similarity across all sites compared, indicating sample representativeness, and 2) the SD of within-site similarity across sites, measuring sample comparability.

The Ecology of Sustainable Implementation: Reflection on a 10-Year Case History Illustration.

PubMed

Rimehaug, Tormod

2014-01-01

The primary aim of this paper is to illustrate the strategic and ecological nature of implementation. The ultimate aim of implementation is not dissemination but sustainability beyond the implementation effort. A case study is utilized to illustrate these broad and long-term perspectives of sustainable implementation based on qualitative analyses of a 10-year implementation effort. The purveyors aimed to develop selective community prevention services for children in families burdened by parental psychiatric or addictive problems. Services were gradually disseminated to 23 sites serving 40 municipalities by 2013. Up to 2013, only one site terminated services after initial implementation. Although many sites suspended services for shorter periods, services are still offered at 22 sites. This case analysis is based on project reports, user evaluations, practitioner interviews, and service statistics. The paper focuses on the analyses and strategies utilized to cope with quality decay and setbacks as well as progress and success in disseminating and sustaining the services and their quality. Low-cost multilevel strategies to implement services at the community level were organized by a prevention unit in child psychiatry, supervised by a university department (purveyors). The purveyors were also involved in national and international collaboration and development. Multilevel strategies included manualized intervention, in-practice training methods, organizational responsibility, media strategies, service evaluation, staff motivation maintenance, quality assurance, and proposals for new law regulations. These case history aspects will be discussed in relation to the implementation literature, focusing on possible applicability across settings.

Mapping contacts between gRNA and mRNA in trypanosome RNA editing.

PubMed

Leung, S S; Koslowsky, D J

1999-02-01

All guide RNAs (gRNAs) identified to date have defined 5' anchor sequences, guiding sequences and a non-encoded 3' uridylate tail. The 5' anchor is required for in vitro editing and is thought to be responsible for selection and binding to the pre-edited mRNA. Little is known, however, about how the gRNAs are used to direct RNA editing. Utilizing the photo-reactive crosslinking agent, azidophenacyl (APA), attached to the 5'- or 3'-terminus of the gRNA, we have begun to map the structural relationships between the different defined regions of the gRNA with the pre-edited mRNA. Analyses of crosslinked conjugates produced with a 5'-terminal APA group confirm that the anchor of the gRNA is correctly positioning the interacting molecules. 3' Crosslinks (X-linker placed at the 3'-end of a U10tail) have also been mapped for three different gRNA/mRNA pairs. In all cases, analyses indicate that the U-tail can interact with a range of nucleotides located upstream of the first edited site. It appears that the U-tail prefers purine-rich sites, close to the first few editing sites. These results suggest that the U-tail may act in concert with the anchor to melt out secondary structure in the mRNA in the immediate editing domain, possibly increasing the accessibility of the editing complex to the proper editing sites.

Microclimatic variation in UV perception and related disparity in tropane and quinolizidine alkaloid composition of Atropa acuminata, Lupinus polyphyllus and Hyoscyamus niger.

PubMed

Jan, Sumira; Kamili, Azra N; Parray, Javid A; Bedi, Yashbir S; Ahmad, Parvaiz

2016-08-01

The aim of current research was to evaluate the physiological adjustment in three medicinal herbs viz., Atropa acuminata, Lupinus polyphyllus and Hyoscyamus niger to the winter period characterised by intense UV flux in Kashmir valley across the North Western Himalaya. Quinolizidine (QA) and tropane alkaloid (TA) concentrations were analysed in these herbs thriving at two different altitudes via GC-MS and correlated by PCA analysis. This study investigated the hypothesis that UV reflectance and absorbance at low temperatures are directly related to disparity in alkaloid accumulation. Among QAs in L. polyphyllus, ammodendrine and lupanine accumulated at higher concentration and exhibited significant variation of 186.36% and 95.91% in ammodendrine and lupanine respectively in both sites. Tetrahydrohombifoline displayed non-significant variation of about 9.60% irrespective of sites. Among tropane alkaloid (TA), hyoscyamine was recorded as the most abundant constituent irrespective of the plant and site while apotropine accumulated in lesser quantity in A. acuminata than H. niger. However, apotropine demonstrated significant variation of 175% among both sites. The final concentration of quinolizidine (QA) and tropane alkaloid (TA) reflects the interplay between reflectance and absorbance of UV radiation response field. These findings suggest that spectral response of UV light contributes directly to alkaloid biosynthesis. Copyright © 2016 Elsevier B.V. All rights reserved.

Drought impact on water use efficiency and intra-annual density fluctuations in Erica arborea on Elba (Italy).

PubMed

Battipaglia, Giovanna; DE Micco, Veronica; Brand, Willi A; Saurer, Matthias; Aronne, Giovanna; Linke, Petra; Cherubini, Paolo

2014-02-01

Erica arborea (L) is a widespread Mediterranean species, able to cope with water stress and colonize semiarid environments. The eco-physiological plasticity of this species was evaluated by studying plants growing at two sites with different soil moistures on the island of Elba (Italy), through dendrochronological, wood-anatomical analyses and stable isotopes measurements. Intra-annual density fluctuations (IADFs) were abundant in tree rings, and were identified as the key parameter to understand site-specific plant responses to water stress. Our findings showed that the formation of IADFs is mainly related to the high temperature, precipitation patterns and probably to soil water availability, which differs at the selected study sites. The recorded increase in the (13) C-derived intrinsic water use efficiency at the IADFs level was linked to reduced water loss rather than to increasing C assimilation. The variation in vessel size and the different absolute values of δ(18) O among trees growing at the two study sites underlined possible differences in stomatal control of water loss and possible differences in sources of water uptake. This approach not only helped monitor seasonal environmental differences through tree-ring width, but also added valuable information on E. arborea responses to drought and their ecological implications for Mediterranean vegetation dynamics. © 2013 John Wiley & Sons Ltd.

Nematode communities in sediments of the Kermadec Trench, Southwest Pacific Ocean

NASA Astrophysics Data System (ADS)

Leduc, Daniel; Rowden, Ashley A.

2018-04-01

Hadal trenches are characterized by environmental conditions not found in any other deep-sea environment, such as steep topography and periodic disturbance by turbidity flows, which are likely responsible for the distinct nature of benthic communities of hadal trenches relative to those of the abyssal plain. Nematodes are the most abundant metazoans in the deep-sea benthos, but it is not yet clear if different trenches host distinct nematode communities, and no data are yet available on the communities of most trenches, including the Kermadec Trench in the Southwest Pacific. Quantitative core samples from the seafloor of the Kermadec Trench were recently obtained from four sites at 6000-9000 m depth which allowed for analyses of meiofauna, and nematodes in particular, for the first time. Nematode community and trophic structure was also compared with other trenches using published data. There was a bathymetric gradient in meiofauna abundance, biomass, and community structure within the Kermadec Trench, but patterns for species richness were ambiguous depending on which metric was used. There was a change in community structure from shallow to deep sites, as well as a consistent change in community structure from the upper sediment layers to the deeper sediment layers across the four sites. These patterns are most likely explained by variation in food availability within the trench, and related to trench topography. Together, deposit and microbial feeders represented 48-92% of total nematode abundance in the samples, which suggests that fine organic detritus and bacteria are major food sources. The relatively high abundance of epigrowth feeders at the 6000 and 9000 m sites (38% and 31%, respectively) indicates that relatively freshly settled microalgal cells represent another important food source at these sites. We found a significant difference in species community structure between the Kermadec and Tonga trenches, which was due to both the presence/absence of species as well as differences in relative abundances of shared species. The cluster and SIMPROF analyses of nematode genus community data across Pacific and Atlantic trenches identified two statistically significant natural groupings: the first group comprised all three Puerto Rico Trench samples, and the second comprised all remaining trenches (South Sandwich, Atacama, Tonga, and Kermadec). Our analyses show that differences in nematode between the adjacent Kermadec and Tonga trenches are observable when analyses are conducted with species-level identifications, but genera-based and trophic structure analyses revealed only limited heterogeneity among trenches. The present study contributes to the growing amount of information on hadal trench environments, which ultimately will build a greater understanding of these rarely sampled deep-sea habitats.

e-phenology: monitoring leaf phenology and tracking climate changes in the tropics

NASA Astrophysics Data System (ADS)

Morellato, Patrícia; Alberton, Bruna; Almeida, Jurandy; Alex, Jefersson; Mariano, Greice; Torres, Ricardo

2014-05-01

The e-phenology is a multidisciplinary project combining research in Computer Science and Phenology. Its goal is to attack theoretical and practical problems involving the use of new technologies for remote phenological observation aiming to detect local environmental changes. It is geared towards three objectives: (a) the use of new technologies of environmental monitoring based on remote phenology monitoring systems; (b) creation of a protocol for a Brazilian long term phenology monitoring program and for the integration across disciplines, advancing our knowledge of seasonal responses within tropics to climate change; and (c) provide models, methods and algorithms to support management, integration and analysis of data of remote phenology systems. The research team is composed by computer scientists and biology researchers in Phenology. Our first results include: Phenology towers - We set up the first phenology tower in our core cerrado-savanna 1 study site at Itirapina, São Paulo, Brazil. The tower received a complete climatic station and a digital camera. The digital camera is set up to take daily sequence of images (five images per hour, from 6:00 to 18:00 h). We set up similar phenology towers with climatic station and cameras in five more sites: cerrado-savanna 2 (Pé de Gigante, SP), cerrado grassland 3 (Itirapina, SP), rupestrian fields 4 ( Serra do Cipo, MG), seasonal forest 5 (Angatuba, SP) and Atlantic raiforest 6 (Santa Virginia, SP). Phenology database - We finished modeling and validation of a phenology database that stores ground phenology and near-remote phenology, and we are carrying out the implementation with data ingestion. Remote phenology and image processing - We performed the first analyses of the cerrado sites 1 to 4 phenology derived from digital images. Analysis were conducted by extracting color information (RGB Red, Green and Blue color channels) from selected parts of the image named regions of interest (ROI). using the green color channel. We analyzed a daily sequence of images (6:00 to 18:00 h). Our results are innovative and indicate the great variation in color change response for tropical trees. We validate the camera phenology with our on the ground direct observation in the core cerrado site 1. We are developing a Image processing software to authomatic process the digital images and to generate the time series for further analyses. New techniques and image features have been used to extract seasonal features from data and for data processing, such as machine learning and visual rhythms. Machine learning was successful applied to identify similar species within the image. Visual rhythms show up as a new analytic tool for phenological interpretation. Next research steps include the analyses of longer data series, correlation with local climatic data, analyses and comparison of patterns among different vegetation sites, prepare a compressive protocol for digital camera phenology and develop new technologies to access vegetation changes using digital cameras. Support: FAPESP-Micorsoft Research, CNPq, CAPES.

Comparison of different spatial transformations applied to EEG data: A case study of error processing.

PubMed

Cohen, Michael X

2015-09-01

The purpose of this paper is to compare the effects of different spatial transformations applied to the same scalp-recorded EEG data. The spatial transformations applied are two referencing schemes (average and linked earlobes), the surface Laplacian, and beamforming (a distributed source localization procedure). EEG data were collected during a speeded reaction time task that provided a comparison of activity between error vs. correct responses. Analyses focused on time-frequency power, frequency band-specific inter-electrode connectivity, and within-subject cross-trial correlations between EEG activity and reaction time. Time-frequency power analyses showed similar patterns of midfrontal delta-theta power for errors compared to correct responses across all spatial transformations. Beamforming additionally revealed error-related anterior and lateral prefrontal beta-band activity. Within-subject brain-behavior correlations showed similar patterns of results across the spatial transformations, with the correlations being the weakest after beamforming. The most striking difference among the spatial transformations was seen in connectivity analyses: linked earlobe reference produced weak inter-site connectivity that was attributable to volume conduction (zero phase lag), while the average reference and Laplacian produced more interpretable connectivity results. Beamforming did not reveal any significant condition modulations of connectivity. Overall, these analyses show that some findings are robust to spatial transformations, while other findings, particularly those involving cross-trial analyses or connectivity, are more sensitive and may depend on the use of appropriate spatial transformations. Copyright © 2014 Elsevier B.V. All rights reserved.

Examining the response of larch needle carbohydrates to climate using compound-specific δ13C and concentration analyses

NASA Astrophysics Data System (ADS)

Rinne, Katja T.; Saurer, Matthias; Kirdyanov, Alexander V.; Bryukhanova, Marina V.; Prokushkin, Anatoly S.; Churakova Sidorova, Olga V.; Siegwolf, Rolf T. W.

2016-04-01

Little is known about the dynamics of concentrations and carbon isotope ratios of individual carbohydrates in leaves in response to climatic and physiological factors. Improved knowledge of the isotopic ratio in sugars will enhance our understanding of the tree ring isotope ratio and will help to decipher environmental conditions in retrospect more reliably. Carbohydrate samples from larch (Larix gmelinii) needles of two sites in the continuous permafrost zone of Siberia with differing growth conditions were analysed with the Compound-Specific Isotope Analysis (CSIA). We compared concentrations and carbon isotope values (δ13C) of sucrose, fructose, glucose and pinitol combined with phenological data. The results for the variability of the needle carbohydrates show high dynamics with distinct seasonal characteristics between and within the studied years with a clear link to the climatic conditions, particularly vapour pressure deficit. Compound-specific differences in δ13C values as a response to climate were detected. The δ13C of pinitol, which contributes up to 50% of total soluble carbohydrates, was almost invariant during the whole growing season. Our study provides the first in-depth characterization of compound-specific needle carbohydrate isotope variability, identifies involved mechanisms and shows the potential of such results for linking tree physiological responses to different climatic conditions.

Repeated seizures induce long-term increase in hippocampal benzodiazepine receptors.

PubMed Central

McNamara, J O; Peper, A M; Patrone, V

1980-01-01

Repeated seizures, whether induced by kindling or electroshock, caused a long-lasting (at least 24 hr) increase of [3H]diazepam binding in hippocampal membranes of Sprague-Dawley rats. Scatchard analyses demonstrated that increased numbers of binding sites accounted for the increase. Neither repeated hypoxia nor repeated administration of electrical current without inducing seizures caused an increase of [3H]diazepam binding. Regardless of the method used for seizure induction, the response was graded in that large numbers of seizures were required to induce significant increases, whereas fewer seizures induced only slight increases. We suggest that the receptor increases imply a heightened response to benzodiazepines and more powerful hippocampal recurrent inhibition. PMID:6930682

Quercus rubra-associated ectomycorrhizal fungal communities of disturbed urban sites and mature forests.

PubMed

Karpati, Amy S; Handel, Steven N; Dighton, John; Horton, Thomas R

2011-08-01

The presence and quality of the belowground mycorrhizal fungal community could greatly influence plant community structure and host species response. This study tests whether mycorrhizal fungal communities in areas highly impacted by anthropogenic disturbance and urbanization are less species rich or exhibit lower host root colonization rates when compared to those of less disturbed systems. Using a soil bioassay, we sampled the ectomycorrhizal fungal (EMF) communities associating with Quercus rubra (northern red oak) seedlings in soil collected from seven sites: two mature forest reference sites and five urban sites of varying levels of disturbance. Morphological and polymerase chain reaction-restriction fragment length polymorphism analyses of fungi colonizing root tips revealed that colonization rates and fungal species richness were significantly lower on root systems of seedlings grown in disturbed site soils. Analysis of similarity showed that EMF community composition was not significantly different among several urban site soils but did differ significantly between mature forest sites and all but one urban site. We identified a suite of fungal species that occurred across several urban sites. Lack of a diverse community of belowground mutualists could be a constraint on urban plant community development, especially of late-successional woodlands. Analysis of urban EMF communities can add to our understanding of urban plant community structure and should be addressed during ecological assessment before pragmatic decisions to restore habitats are framed.

Taxonomic and Functional Responses to Fire and Post-Fire Management of a Mediterranean Hymenoptera Community

NASA Astrophysics Data System (ADS)

Mateos, Eduardo; Santos, Xavier; Pujade-Villar, Juli

2011-11-01

Fire is one of the commonest disturbances worldwide, transforming habitat structure and affecting ecosystem functioning. Understanding how species respond to such environmental disturbances is a major conservation goal that should be monitored using functionally and taxonomically diverse groups such as Hymenoptera. In this respect, we have analyzed the taxonomic and functional response to fire and post-fire management of a Hymenoptera community from a Mediterranean protected area. Thus, Hymenoptera were sampled at fifteen sites located in three burnt areas submitted to different post-fire practices, as well as at five sites located in peripheral unburnt pine forest. A total of 4882 specimens belonging to 33 families, which were classified into six feeding groups according to their dietary preferences, were collected. ANOVA and Redundancy Analyses showed a taxonomic and functional response to fire as all burnt areas had more Hymenoptera families, different community composition and higher numbers of parasitoids than the unburnt area. Taxonomic differences were also found between burnt areas in terms of the response of Hymenoptera to post-fire management. In general the number of parasitoids was positively correlated to the number of potential host arthropods. Parasitoids are recognized to be sensitive to habitat changes, thus highlighting their value for monitoring the functional responses of organisms to habitat disturbance. The taxonomic and functional responses of Hymenoptera suggest that some pine-forest fires can enhance habitat heterogeneity and arthropod diversity, hence increasing interspecific interactions such as those established by parasitoids and their hosts.

Taxonomic and functional responses to fire and post-fire management of a Mediterranean hymenoptera community.

PubMed

Mateos, Eduardo; Santos, Xavier; Pujade-Villar, Juli

2011-11-01

Fire is one of the commonest disturbances worldwide, transforming habitat structure and affecting ecosystem functioning. Understanding how species respond to such environmental disturbances is a major conservation goal that should be monitored using functionally and taxonomically diverse groups such as Hymenoptera. In this respect, we have analyzed the taxonomic and functional response to fire and post-fire management of a Hymenoptera community from a Mediterranean protected area. Thus, Hymenoptera were sampled at fifteen sites located in three burnt areas submitted to different post-fire practices, as well as at five sites located in peripheral unburnt pine forest. A total of 4882 specimens belonging to 33 families, which were classified into six feeding groups according to their dietary preferences, were collected. ANOVA and Redundancy Analyses showed a taxonomic and functional response to fire as all burnt areas had more Hymenoptera families, different community composition and higher numbers of parasitoids than the unburnt area. Taxonomic differences were also found between burnt areas in terms of the response of Hymenoptera to post-fire management. In general the number of parasitoids was positively correlated to the number of potential host arthropods. Parasitoids are recognized to be sensitive to habitat changes, thus highlighting their value for monitoring the functional responses of organisms to habitat disturbance. The taxonomic and functional responses of Hymenoptera suggest that some pine-forest fires can enhance habitat heterogeneity and arthropod diversity, hence increasing interspecific interactions such as those established by parasitoids and their hosts.

Analyses of water, bank material, bottom material, and elutriate samples collected near Belzoni, Mississippi (upper Yazoo projects)

USGS Publications Warehouse

Brightbill, David B.; Treadway, Joseph B.

1980-01-01

Four core-material-sampling sites and one bottom-material site were chosen by the U.S. Army Corps of Engineers to represent areas of proposed dredging activity along a 24.9-mile reach of the upper Yazoo River. Five receiving-water sites also were selected to represent the water that will contact the proposed dredged material. Chemical and physical analyses were performed upon core or bottom material and native-water (receiving-water) samples from these sites as well as upon elutriate samples of the mixture of sediment and receiving water. The results of these analyses are presented without interpertation. (USGS)

Contrasting dissolved organic carbon dynamics at two forested catchments interpreted from high-frequency optical sensor measurements

NASA Astrophysics Data System (ADS)

Saraceno, J.; Shanley, J. B.

2015-12-01

Stream dissolved organic carbon (DOC) concentrations can change rapidly during high-flow events. The timing and magnitude of these changes relative to the event hydrograph can yield insights about possible DOC sources its flow paths to the stream. In situ fluorescent dissolved organic matter (FDOM) sensors that generate high-frequency observations enable detailed examination of high-flow DOC- discharge hysteresis. In this presentation, we interpret high-flow DOC dynamics at two of the five U.S. Geological Survey (USGS) Water, Energy, and Biogeochemical Budgets (WEBB) sites - Panola Mountain, Georgia and Sleepers River, Vermont. Based on laboratory analyses of weekly and event grab samples, both USGS WEBB sites had a similar DOC ranges: from ~1 milligrams per liter (mg/L) at base flow to ~11-15 mg/L during the largest events. A curvilinear relationship between DOC and FDOM (corrected for temperature and turbidity interferences) was used to model a continuous time series of DOC. At the Sleepers River site, DOC showed a seasonal pattern of increasing DOC response; from fairly subdued during spring snowmelt, to a maximum during autumn leaf-fall. The DOC response to discharge showed a consistent clockwise hysteresis (DOC peak, lagged discharge peak). At the Panola Mountain site, maximum event DOC response was lower during wet conditions in the winter and spring. Hysteresis was less expressed at Panola Mountain relative to Sleepers River and displayed both clockwise and counterclockwise patterns, which were dependent on antecedent moisture conditions. The greater synchrony of DOC and discharge peaks at Panola Mountain suggests that DOC sources are closer to the stream and (or) move to the stream more quickly, than at Sleepers River.

Site Response for Micro-Zonation from Small Earthquakes

NASA Astrophysics Data System (ADS)

Gospe, T. B.; Hutchings, L.; Liou, I. Y. W.; Jarpe, S.

2017-12-01

We have developed a method to obtain absolute geologic site response from small earthquakes using inexpensive instrumentation that enables us to perform micro-zonation inexpensively and in a short amount of time. We record small earthquakes (M<3) at several sites simultaneously and perform inversion to obtain actual absolute site response. The key to the inversion is that recordings at several stations from an earthquake have the same moment, source corner frequency and whole path Q effect on their spectra, but have individual Kappa and spectral amplification as a function of frequency. When these source and path effects are removed and corrections for different propagation distances are performed, we are left with actual site response. We develop site response functions from 0.5 to 25.0 Hz. Cities situated near active and dangerous faults experience small earthquakes on a regular basis. We typically record at least ten small earthquakes over time to stabilize the uncertainly. Of course, dynamic soil modeling is necessary to scale our linear site response to non-linear regime for large earthquakes. Our instrumentation is very inexpensive and virtually disposable, and can be placed throughout a city at a high density. Operation only requires turning on a switch, and data processing is automated to minimize human labor. We have installed a test network and implemented our full methodology in upper Napa Valley, California where there is variable geology and nearby rock outcrop sites, and a supply of small earthquakes from the nearby Geysers development area. We test several methbods of obtaining site response. We found that rock sites have a site response of their own and distort the site response estimate based upon spectral ratios with soil sites. Also, rock sites may not even be available near all sites throughout a city. Further, H/V site response estimates from earthquakes are marginally better, but vertical motion also has a site response of its own. H/V spectral ratios of noise don't provide accurate site response estimates either. Vs30 only provides one amplification number and doesn't account for the variable three-dimensional structure beneath sites. We conclude that absolute site response obtained directly from earthquakes is the best, and possibly, the only way to get accurate site response estimates.

The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation

DOE PAGES

Xiong, Yi; Coradetti, Samuel T.; Li, Xin; ...

2014-05-29

Improving cellulolytic enzyme production by plant biomass degrading fungi holds great potential in reducing costs associated with production of next-generation biofuels generated from lignocellulose. How fungi sense cellulosic materials and respond by secreting enzymes has mainly been examined by assessing function of transcriptional regulators and via transcriptional profiling. Here, we obtained global proteomic and phosphoproteomic profiles of the plant biomass degrading filamentous fungus Neurospora crassa grown on different carbon sources, i.e. sucrose, no carbon, and cellulose, by performing isobaric tags for relative and absolute quantification (iTRAQ) -based LC-MS/MS analyses. A comparison between proteomes and transcriptomes under identical carbon conditions suggestsmore » that extensive post-transcriptional regulation occurs in N. crassa in response to exposure to cellulosic material. Several hundred amino acid residues with differential phosphorylation levels on crystalline cellulose (Avicel) or carbon-free medium versus sucrose medium were identified, including phosphorylation sites in a major transcriptional activator for cellulase genes, CLR1, as well as a cellobionic acid transporter, CBT1. Finally, we found mutation of phosphorylation sites on CLR1 did not have a major effect on transactivation of cellulase production, while mutation of phosphorylation sites in CBT1 increased its transporting capacity. Our data provides rich information at both the protein and phosphorylation levels of the early cellular responses to carbon starvation and cellulosic induction and aids in a greater understanding of the underlying post-transcriptional regulatory mechanisms in filamentous fungi.« less

Antibacterial and antiviral roles of a fish β-defensin expressed both in pituitary and testis.

PubMed

Jin, Jun-Yan; Zhou, Li; Wang, Yang; Li, Zhi; Zhao, Jiu-Gang; Zhang, Qi-Ya; Gui, Jian-Fang

2010-12-20

Defensins are a group of cationic peptides that exhibit broad-spectrum antimicrobial activity. In this study, we cloned and characterized a β-defensin from pituitary cDNA library of a protogynous hermaphroditic orange-spotted grouper (Epinephelus coioides). Interestingly, the β-defensin was shown to be dominantly expressed in pituitary and testis by RT-PCR and Western blot analysis, and its transcript level is significantly upregulated in reproduction organs from intersexual gonad to testis during the natural and artificial sex reversal. Promoter sequence and the responsible activity region analyses revealed the pituitary-specific POU1F1a transcription binding site and testis-specific SRY responsible site, and demonstrated that the pituitary-specific POU1F1a transcription binding site that locates between -180 and -208 bp is the major responsible region of grouper β-defensin promoter activity. Immunofluorescence localization observed its pituicyte expression in pituitary and spermatogonic cell expression in testis. Moreover, both in vitro antibacterial activity assay of the recombinant β-defensin and in vivo embryo microinjection of the β-defensin mRNA were shown to be effective in killing gram-negative bacteria. And, its antiviral role was also demonstrated in EPC cells transfected with the β-defensin construct. Additionally, the antibacterial activity was sensitive to concentrations of Na(+), K(+), Ca(2+) and Mg(2+). The above intriguing findings strongly suggest that the fish β-defensin might play significant roles in both innate immunity defense and reproduction endocrine regulation.

Water-quality and biological data for selected streams, lakes, and wells in the High Point Lake watershed, Guilford County, North Carolina, 1988-89

USGS Publications Warehouse

Davenport, M.S.

1993-01-01

Water and bottom-sediment samples were collected at 26 sites in the 65-square-mile High Point Lake watershed area of Guilford County, North Carolina, from December 1988 through December 1989. Sampling locations included 10 stream sites, 8 lake sites, and 8 ground-water sites. Generally, six steady-flow samples were collected at each stream site and three storm samples were collected at five sites. Four lake samples and eight ground-water samples also were collected. Chemical analyses of stream and lake sediments and particle-size analyses of lake sediments were performed once during the study. Most stream and lake samples were analyzed for field characteristics, nutrients, major ions, trace elements, total organic carbon, and chemical-oxygen demand. Analyses were performed to detect concentrations of 149 selected organic compounds, including acid and base/neutral extractable and volatile constituents and carbamate, chlorophenoxy acid, triazine, organochlorine, and organophosphorus pesticides and herbicides. Selected lake samples were analyzed for all constituents listed in the Safe Drinking Water Act of 1986, including Giardia, Legionella, radiochemicals, asbestos, and viruses. Various chromatograms from organic analyses were submitted to computerized library searches. The results of these and all other analyses presented in this report are in tabular form.

Plants and climate change: complexities and surprises.

PubMed

Parmesan, Camille; Hanley, Mick E

2015-11-01

Anthropogenic climate change (ACC) will influence all aspects of plant biology over coming decades. Many changes in wild species have already been well-documented as a result of increased atmospheric CO2 concentrations, warming climate and changing precipitation regimes. A wealth of available data has allowed the use of meta-analyses to examine plant-climate interactions on more sophisticated levels than before. These analyses have revealed major differences in plant response among groups, e.g. with respect to functional traits, taxonomy, life-history and provenance. Interestingly, these meta-analyses have also exposed unexpected mismatches between theory, experimental, and observational studies. We reviewed the literature on species' responses to ACC, finding ∼42 % of 4000 species studied globally are plants (primarily terrestrial). We review impacts on phenology, distributions, ecophysiology, regeneration biology, plant-plant and plant-herbivore interactions, and the roles of plasticity and evolution. We focused on apparent deviations from expectation, and highlighted cases where more sophisticated analyses revealed that unexpected changes were, in fact, responses to ACC. We found that conventionally expected responses are generally well-understood, and that it is the aberrant responses that are now yielding greater insight into current and possible future impacts of ACC. We argue that inconclusive, unexpected, or counter-intuitive results should be embraced in order to understand apparent disconnects between theory, prediction, and observation. We highlight prime examples from the collection of papers in this Special Issue, as well as general literature. We found use of plant functional groupings/traits had mixed success, but that some underutilized approaches, such as Grime's C/S/R strategies, when incorporated, have improved understanding of observed responses. Despite inherent difficulties, we highlight the need for ecologists to conduct community-level experiments in systems that replicate multiple aspects of ACC. Specifically, we call for development of coordinating experiments across networks of field sites, both natural and man-made. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Effect of bedrock permeability on stream base flow mean transit time scaling relations: 1. A multiscale catchment intercomparison

NASA Astrophysics Data System (ADS)

Hale, V. Cody; McDonnell, Jeffrey J.

2016-02-01

The effect of bedrock permeability and underlying catchment boundaries on stream base flow mean transit time (MTT) and MTT scaling relationships in headwater catchments is poorly understood. Here we examine the effect of bedrock permeability on MTT and MTT scaling relations by comparing 15 nested research catchments in western Oregon; half within the HJ Andrews Experimental Forest and half at the site of the Alsea Watershed Study. The two sites share remarkably similar vegetation, topography, and climate and differ only in bedrock permeability (one poorly permeable volcanic rock and the other more permeable sandstone). We found longer MTTs in the catchments with more permeable fractured and weathered sandstone bedrock than in the catchments with tight, volcanic bedrock (on average, 6.2 versus 1.8 years, respectively). At the permeable bedrock site, 67% of the variance in MTT across catchments scales was explained by drainage area, with no significant correlation to topographic characteristics. The poorly permeable site had opposite scaling relations, where MTT showed no correlation to drainage area but the ratio of median flow path length to median flow path gradient explained 91% of the variance in MTT across seven catchment scales. Despite these differences, hydrometric analyses, including flow duration and recession analysis, and storm response analysis, show that the two sites share relatively indistinguishable hydrodynamic behavior. These results show that similar catchment forms and hydrologic regimes hide different subsurface routing, storage, and scaling behavior—a major issue if only hydrometric data are used to define hydrological similarity for assessing land use or climate change response.

Analysis of Aquifer Response, Groundwater Flow, and PlumeEvolution at Site OU 1, Former Fort Ord, California

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

Jordan, Preston D.; Oldenburg, Curtis M.; Su, Grace W.

2005-02-24

This report presents a continuation from Oldenburg et al. (2002) of analysis of the hydrogeology, In-Situ Permeable Flow Sensor (ISPFS) results, aquifer response, and changes in the trichloroethylene (TCE) groundwater plume at Operational Unit 1 (OU 1) adjacent to the former Fritzsche Army Airfield at the former Fort Ord Army Base, located on Monterey Bay in northern Monterey County. Fuels and solvents were burned on a portion of OU 1 called the Fire Drill Area (FDA) during airport fire suppression training between 1962 and 1985. This activity resulted in soil and groundwater contamination in the unconfined A-aquifer. In the latemore » 1980's, soil excavation and bioremediation were successful in remediating soil contamination at the site. Shortly thereafter, a groundwater pump, treat, and recharge system commenced operation. This system has been largely successful at remediating groundwater contamination at the head of the groundwater plume. However, a trichloroethylene (TCE) groundwater plume extends approximately 3000 ft (900 m) to the northwest away from the FDA. In the analyses presented here, we augment our prior work (Oldenburg et al., 2002) with new information including treatment-system totalizer data, recent water-level and chemistry data, and data collected from new wells to discern trends in contaminant migration and groundwater flow that may be useful for ongoing remediation efforts. Some conclusions from the prior study have been modified based on these new analyses, and these are pointed out clearly in this report.« less

Intraspecific variation in stomatal traits, leaf traits and physiology reflects adaptation along aridity gradients in a South African shrub

PubMed Central

Carlson, Jane E.; Adams, Christopher A.; Holsinger, Kent E.

2016-01-01

Background and Aims Trait–environment relationships are commonly interpreted as evidence for local adaptation in plants. However, even when selection analyses support this interpretation, the mechanisms underlying differential benefits are often unknown. This study addresses this gap in knowledge using the broadly distributed South African shrub Protea repens. Specifically, the study examines whether broad-scale patterns of trait variation are consistent with spatial differences in selection and ecophysiology in the wild. Methods In a common garden study of plants sourced from 19 populations, associations were measured between five morphological traits and three axes describing source climates. Trait–trait and trait–environment associations were analysed in a multi-response model. Within two focal populations in the wild, selection and path analyses were used to test associations between traits, fecundity and physiological performance. Key Results Across 19 populations in a common garden, stomatal density increased with the source population’s mean annual temperature and decreased with its average amount of rainfall in midsummer. Concordantly, selection analysis in two natural populations revealed positive selection on stomatal density at the hotter, drier site, while failing to detect selection at the cooler, moister site. Dry-site plants with high stomatal density also had higher stomatal conductances, cooler leaf temperatures and higher light-saturated photosynthetic rates than those with low stomatal density, but no such relationships were present among wet-site plants. Leaf area, stomatal pore index and specific leaf area in the garden also co-varied with climate, but within-population differences were not associated with fitness in either wild population. Conclusions The parallel patterns of broad-scale variation, differences in selection and differences in trait–ecophysiology relationships suggest a mechanism for adaptive differentiation in stomatal density. Densely packed stomata may improve performance by increasing transpiration and cooling, but predominately in drier, hotter climates. This study uniquely shows context-dependent benefits of stomatal density – a trait rarely linked to local adaptation in plants. PMID:26424782

Estimating Children's Soil/Dust Ingestion Rates through Retrospective Analyses of Blood Lead Biomonitoring from the Bunker Hill Superfund Site in Idaho.

PubMed

von Lindern, Ian; Spalinger, Susan; Stifelman, Marc L; Stanek, Lindsay Wichers; Bartrem, Casey

2016-09-01

Soil/dust ingestion rates are important variables in assessing children's health risks in contaminated environments. Current estimates are based largely on soil tracer methodology, which is limited by analytical uncertainty, small sample size, and short study duration. The objective was to estimate site-specific soil/dust ingestion rates through reevaluation of the lead absorption dose-response relationship using new bioavailability data from the Bunker Hill Mining and Metallurgical Complex Superfund Site (BHSS) in Idaho, USA. The U.S. Environmental Protection Agency (EPA) in vitro bioavailability methodology was applied to archived BHSS soil and dust samples. Using age-specific biokinetic slope factors, we related bioavailable lead from these sources to children's blood lead levels (BLLs) monitored during cleanup from 1988 through 2002. Quantitative regression analyses and exposure assessment guidance were used to develop candidate soil/dust source partition scenarios estimating lead intake, allowing estimation of age-specific soil/dust ingestion rates. These ingestion rate and bioavailability estimates were simultaneously applied to the U.S. EPA Integrated Exposure Uptake Biokinetic Model for Lead in Children to determine those combinations best approximating observed BLLs. Absolute soil and house dust bioavailability averaged 33% (SD ± 4%) and 28% (SD ± 6%), respectively. Estimated BHSS age-specific soil/dust ingestion rates are 86-94 mg/day for 6-month- to 2-year-old children and 51-67 mg/day for 2- to 9-year-old children. Soil/dust ingestion rate estimates for 1- to 9-year-old children at the BHSS are lower than those commonly used in human health risk assessment. A substantial component of children's exposure comes from sources beyond the immediate home environment. von Lindern I, Spalinger S, Stifelman ML, Stanek LW, Bartrem C. 2016. Estimating children's soil/dust ingestion rates through retrospective analyses of blood lead biomonitoring from the Bunker Hill Superfund Site in Idaho. Environ Health Perspect 124:1462-1470; http://dx.doi.org/10.1289/ehp.1510144.

No evidence for consistent long-term growth stimulation of 13 tropical tree species: results from tree-ring analysis.

PubMed

Groenendijk, Peter; van der Sleen, Peter; Vlam, Mart; Bunyavejchewin, Sarayudh; Bongers, Frans; Zuidema, Pieter A

2015-10-01

The important role of tropical forests in the global carbon cycle makes it imperative to assess changes in their carbon dynamics for accurate projections of future climate-vegetation feedbacks. Forest monitoring studies conducted over the past decades have found evidence for both increasing and decreasing growth rates of tropical forest trees. The limited duration of these studies restrained analyses to decadal scales, and it is still unclear whether growth changes occurred over longer time scales, as would be expected if CO2 -fertilization stimulated tree growth. Furthermore, studies have so far dealt with changes in biomass gain at forest-stand level, but insights into species-specific growth changes - that ultimately determine community-level responses - are lacking. Here, we analyse species-specific growth changes on a centennial scale, using growth data from tree-ring analysis for 13 tree species (~1300 trees), from three sites distributed across the tropics. We used an established (regional curve standardization) and a new (size-class isolation) growth-trend detection method and explicitly assessed the influence of biases on the trend detection. In addition, we assessed whether aggregated trends were present within and across study sites. We found evidence for decreasing growth rates over time for 8-10 species, whereas increases were noted for two species and one showed no trend. Additionally, we found evidence for weak aggregated growth decreases at the site in Thailand and when analysing all sites simultaneously. The observed growth reductions suggest deteriorating growth conditions, perhaps due to warming. However, other causes cannot be excluded, such as recovery from large-scale disturbances or changing forest dynamics. Our findings contrast growth patterns that would be expected if elevated CO2 would stimulate tree growth. These results suggest that commonly assumed growth increases of tropical forests may not occur, which could lead to erroneous predictions of carbon dynamics of tropical forest under climate change. © 2015 John Wiley & Sons Ltd.

Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide

PubMed Central

Omura, Hiroki; Oikawa, Daisuke; Nakane, Takanori; Kato, Megumi; Ishii, Ryohei; Ishitani, Ryuichiro; Tokunaga, Fuminori; Nureki, Osamu

2016-01-01

In the innate immune system, pattern recognition receptors (PRRs) specifically recognize ligands derived from bacteria or viruses, to trigger the responsible downstream pathways. DEAD box protein 41 (DDX41) is an intracellular PRR that triggers the downstream pathway involving the adapter STING, the kinase TBK1, and the transcription factor IRF3, to activate the type I interferon response. DDX41 is unique in that it recognizes two different ligands; i.e., double-stranded DNA (dsDNA) and cyclic dinucleotides (CDN), via its DEAD domain. However, the structural basis for the ligand recognition by the DDX41 DEAD domain has remained elusive. Here, we report two crystal structures of the DDX41 DEAD domain in apo forms, at 1.5 and 2.2 Å resolutions. A comparison of the two crystal structures revealed the flexibility in the ATP binding site, suggesting its formation upon ATP binding. Structure-guided functional analyses in vitro and in vivo demonstrated the overlapped binding surface for dsDNA and CDN, which is distinct from the ATP-binding site. We propose that the structural rearrangement of the ATP binding site is crucial for the release of ADP, enabling the fast turnover of DDX41 for the dsDNA/CDN-induced STING activation pathway. PMID:27721487

Differences in laser-Doppler indices between skin-surface measurement sites in subjects with diabetes.

PubMed

Hsiu, Hsin; Hu, Hsiao-Feng; Tsai, Hung-Chi

2018-01-01

This study performed laser-Doppler flowmetry (LDF) measurements with the aim of identifying differences in diabetes-induced microcirculatory-blood-flow (MBF) responses between the following skin surface measurement sites: an acupoint around the wrist, an acupoint around the ankle, and a nearby nonacupoint around the ankle. The 67 study subjects were assigned to diabetic, prediabetic, and healthy groups according to the results of oral glucose tolerance tests. Beat-to-beat and spectral analyses were applied to the LDF waveform to obtain the foot delay time (FDT), the flow rise time (FRT), and the relative energy contributions (RECs) in five frequency bands. FRT and FDT were significantly shorter and the RECs of the endothelial-, neural-, and myogenic-related frequency bands were significantly smaller in the diabetic group than in the control group at the acupoint around the ankle, but there were no such prominent differences at the other sites. The acupoint around the ankle was better than the nearby nonacupoint and the acupoint around the wrist for distinguishing the age-matched diabetic, prediabetic, and healthy subjects. These findings imply that when monitoring diabetes-induced MBF responses, the measurement locations should be chosen carefully in order to minimize interference effects and to improve the ability to distinguish subjects with different conditions. Copyright © 2017 Elsevier Inc. All rights reserved.

The liver but not the skin is the site for conversion of a red carotenoid in a passerine bird

NASA Astrophysics Data System (ADS)

Del Val, Esther; Senar, Juan Carlos; Garrido-Fernández, Juan; Jarén, Manuel; Borràs, Antoni; Cabrera, Josep; Negro, Juan José

2009-07-01

Carotenoids may provide numerous health benefits and are also responsible for the integumentary coloration of many bird species. Despite their importance, many aspects of their metabolism are still poorly known, and even basic issues such as the anatomical sites of conversion remain controversial. Recent studies suggest that the transformation of carotenoid pigments takes place directly in the follicles during feather growth, even though the liver has been previously recognised as a storing organ for these pigments with a certain potential for conversion. In this context, we analysed the carotenoid profile of plasma, liver, skin and feathers of male Common Crossbills ( Loxia curvirostra). Interestingly, the derivative feather pigment 3-hydroxy-echinenone was detected in the liver and in the bloodstream (i.e. the necessary vehicle to transport metabolites to colourful peripheral tissues). Our results demonstrate for the first time with empirical data that the liver may act as the main site for the synthesis of integumentary carotenoids. This finding contradicts previous assumptions and raises the question of possible inter-specific differences in the site of carotenoid conversion in birds.

Impact assessment of a wastewater treatment plant effluent using the fish biomarker ethoxyresorufin-O-deethylase: field and on-site experiments.

PubMed

Kosmala, A; Migeon, B; Flammarion, P; Garric, J

1998-09-01

The impact of a wastewater treatment plant (WWTP) effluent was assessed with the fish biomarker ethoxyresorufin-O-deethylase (EROD) using field and on-site laboratory experiments. EROD activity was measured in chub (Leuciscus cephalus) and stone loach (Noemacheilus barbatulus) caught at three sites of the Chalaronne River (southeast France). Liver somatic index (LSI) and organochloride bioaccumulation in muscle were estimated for chub only. In September, EROD activity and LSI of chub increased significantly between the sites above and below the WWTP effluent discharge. EROD induction detected in chub was confirmed by on-site tank experiments. EROD levels were determined in juvenile rainbow trout (Oncorhynchus mykiss) and mirror carp (Cyprinus carpio) exposed to different concentrations of the WWTP effluent and river water for 16 days. After a 4-day exposure, EROD activities of the carp exposed to the effluent increased significantly compared with the control. The response was linked to the effluent concentration and was stable with exposure time. WWTP effluent induced EROD activity, whereas organic and metal analyses, performed on fish muscle and sediment, did not indicate any difference between upstream and downstream of the discharge. Copyright 1998 Academic Press.

Earthquake Hazard Class Mapping by Parcel in Las Vegas Valley

NASA Astrophysics Data System (ADS)

Pancha, A.; Pullammanappallil, S.; Louie, J. N.; Hellmer, W. K.

2011-12-01

Clark County, Nevada completed the very first effort in the United States to map earthquake hazard class systematically through an entire urban area. The map is used in development and disaster response planning, in addition to its direct use for building code implementation and enforcement. The County contracted with the Nevada System of Higher Education to classify about 500 square miles including urban Las Vegas Valley, and exurban areas considered for future development. The Parcel Map includes over 10,000 surface-wave array measurements accomplished over three years using Optim's SeisOpt° ReMi measurement and processing techniques adapted for large scale data. These array measurements classify individual parcels on the NEHRP hazard scale. Parallel "blind" tests were conducted at 93 randomly selected sites. The rms difference between the Vs30 values yielded by the blind data and analyses and the Parcel Map analyses is 4.92%. Only six of the blind-test sites showed a difference with a magnitude greater than 10%. We describe a "C+" Class for sites with Class B average velocities but soft surface soil. The measured Parcel Map shows a clearly definable C+ to C boundary on the west side of the Valley. The C to D boundary is much more complex. Using the parcel map in computing shaking in the Valley for scenario earthquakes is crucial for obtaining realistic predictions of ground motions.

Investigations in site response from ground motion observations in vertical arrays

NASA Astrophysics Data System (ADS)

Baise, Laurie Gaskins

The aim of the research is to improve the understanding of earthquake site response and to improve the techniques available to investigate issues in this field. Vertical array ground motion data paired with the empirical transfer function (ETF) methodology is shown to accurately characterize site response. This manuscript draws on methods developed in the field of signal processing and statistical time series analysis to parameterize the ETF as an autoregressive moving-average (ARMA) system which is justified theoretically, historically, and by example. Site response is evaluated at six sites in California, Japan, and Taiwan using ETF estimates, correlation analysis, and full waveform modeling. Correlation analysis is proposed as a required data quality evaluation imperative to any subsequent site response analysis. ETF estimates and waveform modeling are used to decipher the site response at sites with simple and complex geologic structure, which provide simple time-invariant and time-variant methods for evaluating both linear site transfer functions and nonlinear site response for sites experiencing liquefaction of the soils. The Treasure and Yerba Buena Island sites, however, require 2-D waveform modeling to accurately evaluate the effects of the shallow sedimentary basin. ETFs are used to characterize the Port Island site and corresponding shake table tests before, during, and after liquefaction. ETFs derived from the shake table tests were demonstrated to consistently predict the linear field ground response below 16 m depth and the liquefied behavior above 15 m depth. The liquefied interval response was demonstrated to gradually return to pre-liquefied conditions within several weeks of the 1995 Hyogo-ken Nanbu earthquake. Both the site's and the shake table test's response were shown to be effectively linear up to 0.5 g in the native materials below 16 m depth. The effective linearity of the site response at GVDA, Chiba, and Lotting up to 0.1 g, 0.33 g, and 0.49 g, respectively, further confirms that site response in the field may be more linear than expected from laboratory tests. Strong motions were predicted at these sites with normalized mean square error less than 0.10 using ETFs generated from weak motions. The Treasure Island site response was shown to be dominated by surface waves propagating in the shallow sediments of the San Francisco Bay. Low correlation of the ground motions recorded on rock at Yerba Buena Island and in rock beneath the Treasure Island site intimates that the Yerba Buena site is an inappropriate reference site for Treasure Island site response studies. Accurate simulation of the Treasure Island site response was achieved using a 2-D velocity structure comprised of a 100 m uniform soil basin (Vs = 400 m/s) over a weathered rock veneer (Vs = 1.5 km/s) to 200 m depth.

Investigation into the response of the auditory and acoustic communications systems in the Beluga whale (Delphinapterus leucas) of the St. Lawrence River Estuary to noise, using vocal classification

NASA Astrophysics Data System (ADS)

Scheifele, Peter Martin

2003-06-01

Noise pollution has only recently become recognized as a potential danger to marine mammals in general, and to the Beluga Whale (Delphinapterus leucas) in particular. These small gregarious Odontocetes make extensive use of sound for social communication and pod cohesion. The St. Lawrence River Estuary is habitat to a small, critically endangered population of about 700 Beluga whales who congregate in four different sites in its upper estuary. The population is believed to be threatened by the stress of high-intensity, low frequency noise. One way to determine whether noise is having an effect on an animal's auditory ability might be to observe a natural and repeatable response of the auditory and vocal systems to varying noise levels. This can be accomplished by observing changes in animal vocalizations in response to auditory feedback. A response such as this observed in humans and some animals is known as the Lombard Vocal Response, which represents a reaction of the auditory system directly manifested by changes in vocalization level. In this research this population of Beluga Whales was tested to determine whether a vocalization-as-a-function-of-noise phenomenon existed by using Hidden Markhov "classified" vocalizations as targets for acoustical analyses. Correlation and regression analyses indicated that the phenomenon does exist and results of a human subjects experiment along with results from other animal species known to exhibit the response strongly implicate the Lombard Vocal Response in the Beluga.

The Dynamics and Evolutionary Potential of Domain Loss and Emergence

PubMed Central

Moore, Andrew D.; Bornberg-Bauer, Erich

2012-01-01

The wealth of available genomic data presents an unrivaled opportunity to study the molecular basis of evolution. Studies on gene family expansions and site-dependent analyses have already helped establish important insights into how proteins facilitate adaptation. However, efforts to conduct full-scale cross-genomic comparisons between species are challenged by both growing amounts of data and the inherent difficulty in accurately inferring homology between deeply rooted species. Proteins, in comparison, evolve by means of domain rearrangements, a process more amenable to study given the strength of profile-based homology inference and the lower rates with which rearrangements occur. However, adapting to a constantly changing environment can require molecular modulations beyond reach of rearrangement alone. Here, we explore rates and functional implications of novel domain emergence in contrast to domain gain and loss in 20 arthropod species of the pancrustacean clade. Emerging domains are more likely disordered in structure and spread more rapidly within their genomes than established domains. Furthermore, although domain turnover occurs at lower rates than gene family turnover, we find strong evidence that the emergence of novel domains is foremost associated with environmental adaptation such as abiotic stress response. The results presented here illustrate the simplicity with which domain-based analyses can unravel key players of nature's adaptational machinery, complementing the classical site-based analyses of adaptation. PMID:22016574

Determining return water levels at ungauged coastal sites: a case study for northern Germany

NASA Astrophysics Data System (ADS)

Arns, Arne; Wahl, Thomas; Haigh, Ivan D.; Jensen, Jürgen

2015-04-01

We estimate return periods and levels of extreme still water levels for the highly vulnerable and historically and culturally important small marsh islands known as the Halligen, located in the Wadden Sea offshore of the coast of northern Germany. This is a challenging task as only few water level records are available for this region, and they are currently too short to apply traditional extreme value analysis methods. Therefore, we use the Regional Frequency Analysis (RFA) approach. This originates from hydrology but has been used before in several coastal studies and is also currently applied by the local federal administration responsible for coastal protection in the study area. The RFA enables us to indirectly estimate return levels by transferring hydrological information from gauged to related ungauged sites. Our analyses highlight that this methodology has some drawbacks and may over- or underestimate return levels compared to direct analyses using station data. To overcome these issues, we present an alternative approach, combining numerical and statistical models. First, we produced a numerical multidecadal model hindcast of water levels for the entire North Sea. Predicted water levels from the hindcast are bias corrected using the information from the available tide gauge records. Hence, the simulated water levels agree well with the measured water levels at gauged sites. The bias correction is then interpolated spatially to obtain correction functions for the simulated water levels at each coastal and island model grid point in the study area. Using a recommended procedure to conduct extreme value analyses from a companion study, return water levels suitable for coastal infrastructure design are estimated continuously along the entire coastline of the study area, including the offshore islands. A similar methodology can be applied in other regions of the world where tide gauge observations are sparse.

Public health concerns for anti-obesity medicines imported for personal use through the internet: a cross-sectional study

PubMed Central

Tanimoto, Tsuyoshi; Nakanishi, Yoko; Yoshida, Naoko; Tsuboi, Hirohito; Kimura, Kazuko

2012-01-01

Objective To explore the circulation of anti-obesity medicines via the internet and their quality. Design Cross-sectional study. Setting Internet pharmacies and pharmaceutical suppliers accessible from Japan. Participants Anti-obesity medicines were purchased using relevant keywords on Japanese Google search engine. Blogs and advertisement-only sites were excluded. Primary and secondary outcome measures The authenticity of the samples was investigated in collaboration with the manufacturers of the samples and medicine regulatory authorities. Quality of the samples was assessed by pharmacopoeial analyses using high-performance liquid chromatography. Results 82 samples were purchased from 36 internet sites. Approximately half of the sites did not mention a physical address, and 45% of the samples did not contain a package insert. A variety of custom declarations were made for the shipments of the samples: personal health items, supplement, medicines, general merchandise, tea and others. Among 82 samples, 52 samples were analysed to check their pharmacopoeial quality. Authenticity responses were received from only five of 20 manufacturing companies. According to the pharmacopoeial analyses and authenticity investigation, three of the samples were identified as counterfeits and did not contain any active ingredients. Two of these samples were confirmed as counterfeits by the manufacturer of the authentic products. The manufacturer of the other sample did not respond to our request for an authenticity check even after several communication attempts. These counterfeit cases have been reported at the rapid alert system of Western Pacific Region of the WHO. Conclusions Many counterfeit and unapproved anti-obesity medicines may be easily bypassing regulatory checks during shipping and are widely circulated through the internet. Regulatory authorities should take measures to prevent these medicines from entering countries to safeguard their citizens. PMID:22581794

In Situ Flow MAS NMR Spectroscopy and Synchrotron PDF Analyses of the Local Response of the Brønsted Acidic Site in SAPO-34 during Hydration at Elevated Temperatures.

PubMed

Kalantzopoulos, Georgios N; Lundvall, Fredrik; Checchia, Stefano; Lind, Anna; Wragg, David S; Fjellvåg, Helmer; Arstad, Bjørnar

2018-02-19

In situ flow magic-angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy and synchrotron-based pair distribution function (PDF) analyses were applied to study water's interactions with the Brønsted acidic site and the surrounding framework in the SAPO-34 catalyst at temperatures up to 300 °C for NMR spectroscopy and 700 °C for PDF. 29 Si enrichment of the sample enabled detailed NMR spectroscopy investigations of the T-atom generating the Brønsted site. By NMR spectroscopy, we observed dehydration above 100 °C and a coalescence of Si peaks due to local framework adjustments. Towards 300 °C, the NMR spectroscopy data indicated highly mobile acidic protons. In situ total X-ray scattering measurements analyzed by PDF showed clear changes in the Al local environment in the 250-300 °C region, as the Al-O bond lengths showed a sudden change. This fell within the same temperature range as the increased Brønsted proton mobility. We suggest that the active site in this catalyst under industrial conditions comprises not only the Brønsted proton but also SiO 4 . To the best of our knowledge, this is the first work proposing a structural model of a SAPO catalyst by atomic PDF analysis. The combination of synchrotron PDF analysis with in situ NMR spectroscopy is promising in revealing the dynamic features of a working catalyst. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

dbPAF: an integrative database of protein phosphorylation in animals and fungi.

PubMed

Ullah, Shahid; Lin, Shaofeng; Xu, Yang; Deng, Wankun; Ma, Lili; Zhang, Ying; Liu, Zexian; Xue, Yu

2016-03-24

Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. Recent progresses in phosphoproteomic identifications have generated a flood of phosphorylation sites, while the integration of these sites is an urgent need. In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. Based on the new data set, we computationally detected significantly over-represented sequence motifs around phosphorylation sites, predicted potential kinases that are responsible for the modification of collected phospho-sites, and evolutionarily analyzed phosphorylation conservation states across different species. Besides to be largely consistent with previous reports, our results also proposed new features of phospho-regulation. Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. The dbPAF database was implemented in PHP + MySQL and freely available at http://dbpaf.biocuckoo.org.

Role of cyclooxygenase in the vascular response to locally delivered acetylcholine in Caucasian and African descent individuals.

PubMed

Maley, Matthew J; House, James R; Tipton, Michael J; Eglin, Clare M

2017-05-01

Individuals of African descent (AFD) are more susceptible to non-freezing cold injury (NFCI) compared with Caucasian individuals (CAU). Vasodilatation to acetylcholine (ACh) is lower in AFD compared with CAU in the non-glabrous foot and finger skin sites; the reason for this is unknown. Prostanoids are responsible, in part, for the vasodilator response to ACh, however it is not known whether the contribution differs between ethnicities. 12 CAU and 12 AFD males received iontophoresis of ACh (1 w/v%) on non-glabrous foot and finger skin sites following placebo and then aspirin (600mg, single blinded). Aspirin was utilised to inhibit prostanoid production by inhibiting the cyclooxygenase (COX) enzyme. Laser Doppler flowmetry was utilised to measure changes in skin blood flow. Not all participants could receive iontophoresis charge due to high skin resistance; these participants were therefore excluded from the analyses. Foot: ACh elicited greater maximal vasodilatation in CAU than AFD following placebo (P=0.003) and COX inhibition (COXib) (P<0.001). COXib did not affect blood flow responses in AFD, but caused a reduction in the area under the curve for CAU (P=0.031). Finger: ACh elicited a greater maximal vasodilatation in CAU than AFD following placebo (P=0.013) and COXib (P=0.001). COXib tended to reduce the area under the curve in AFD (P=0.053), but did not affect CAU. CAU have a greater endothelial reactivity than AFD in both foot and finger skin sites irrespective of COXib. It is concluded that the lower ACh-induced vasodilatation in AFD is not due to a compromised COX pathway. Copyright © 2017 Elsevier Inc. All rights reserved.

Multisite Reliability of Cognitive BOLD Data

PubMed Central

Brown, Gregory G.; Mathalon, Daniel H.; Stern, Hal; Ford, Judith; Mueller, Bryon; Greve, Douglas N.; McCarthy, Gregory; Voyvodic, Jim; Glover, Gary; Diaz, Michele; Yetter, Elizabeth; Burak Ozyurt, I.; Jorgensen, Kasper W.; Wible, Cynthia G.; Turner, Jessica A.; Thompson, Wesley K.; Potkin, Steven G.

2010-01-01

Investigators perform multi-site functional magnetic resonance imaging studies to increase statistical power, to enhance generalizability, and to improve the likelihood of sampling relevant subgroups. Yet undesired site variation in imaging methods could off-set these potential advantages. We used variance components analysis to investigate sources of variation in the blood oxygen level dependent (BOLD) signal across four 3T magnets in voxelwise and region of interest (ROI) analyses. Eighteen participants traveled to four magnet sites to complete eight runs of a working memory task involving emotional or neutral distraction. Person variance was more than 10 times larger than site variance for five of six ROIs studied. Person-by-site interactions, however, contributed sizable unwanted variance to the total. Averaging over runs increased between-site reliability, with many voxels showing good to excellent between-site reliability when eight runs were averaged and regions of interest showing fair to good reliability. Between-site reliability depended on the specific functional contrast analyzed in addition to the number of runs averaged. Although median effect size was correlated with between-site reliability, dissociations were observed for many voxels. Brain regions where the pooled effect size was large but between-site reliability was poor were associated with reduced individual differences. Brain regions where the pooled effect size was small but between-site reliability was excellent were associated with a balance of participants who displayed consistently positive or consistently negative BOLD responses. Although between-site reliability of BOLD data can be good to excellent, acquiring highly reliable data requires robust activation paradigms, ongoing quality assurance, and careful experimental control. PMID:20932915

Adaptive mechanisms and genomic plasticity for drought tolerance identified in European black poplar (Populus nigra L.)

PubMed Central

Viger, Maud; Smith, Hazel K.; Cohen, David; Dewoody, Jennifer; Trewin, Harriet; Steenackers, Marijke; Bastien, Catherine; Taylor, Gail

2016-01-01

Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ∼500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. ‘North eastern’ genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by Δ13C. In contrast, ‘southern’ genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH, ANT, ER, AS1, AS2, PHB, CLV1, ERL1–3 and TMM, were down-regulated in Ita but not in Sp2 in response to drought. PMID:27174702

Can Tree Ring Analyses Predict Resilience of Black Spruce Forests to Fire in Interior Alaska?

NASA Astrophysics Data System (ADS)

Walker, X. J.; Johnstone, J. F.; Mack, M. C.

2015-12-01

Climate change has increased the occurrence, severity, and impact of disturbances on forested ecosystems worldwide. As such there is a growing need to identify factors that contribute to an ecosystem's ability to recover from disturbance, commonly referred to as ecosystem resilience. In trees, drought-induced growth declines may signal decreased ecosystem resilience if mature trees are able to survive in stressful environmental conditions that do not permit successful post-disturbance recruitment and survival. Here we explore links between ecosystem resilience and the growth-climate relationships of pre-fire trees, specifically drought stress signals, across topographic moisture gradients within the boreal forest. We sampled 72 recently (2004) burned black spruce stands within interior Alaska and found the proportion of black spruce relative to deciduous trees decreased post-fire, ranging from almost no change to a 90% decrease. The largest shifts in post-fire species composition occurred in sites where trees showed negative growth responses to warm spring temperatures, and shallow post-fire organic layer depths due to dry site conditions or high fire severity. These sites were generally located at warmer and drier landscape positions, suggesting they are less resilient to disturbance than sites at the wetter end of the gradient. Tree growth-climate responses can provide an estimate of stand environmental stress to ongoing climate change and as such are a valuable tool for predicting landscape variations in forest ecosystem resilience and forecasting future forest composition.

Sex and migratory strategy influence corticosterone levels in winter-grown feathers, with positive breeding effects in a migratory pelagic seabird.

PubMed

Pérez, Cristóbal; Granadeiro, José Pedro; Dias, Maria P; Catry, Paulo

2016-08-01

To overcome unpredictable stressful transitory events, animals trigger an allostatic response involving the hypothalamic-pituitary-adrenal cortex. This hormonal response, which involves the release of glucocorticoids which in turn mediate between the main physiological mechanisms that regulate the energetic demands and resource allocation trade-off with behavioural responses to environmental perturbations and may ultimately lead to variation in fitness. We have used the Cory's shearwater Calonectris borealis, a sexually dimorphic pelagic seabird with a partial migratory strategy, as a model bird species to analyse a number of traits related to the stress response. We investigated whether the activation of a stressful response, mediated by corticosterone, during the wintering period (1) correlated with the previous breeding success, (2) was affected by the migratory behaviour of male birds and (3) had consequences in the fitness of the birds. Corticosterone levels in feathers grown overwinter were analysed in 61 adult birds during three consecutive migratory periods (2009-2012) and in 14 immature birds in the wintering period 2010-2011. Moreover, the levels of corticosterone were analysed in experimental birds which were freed from their reproductive duties and compared with control birds which raised fledglings to the end of the breeding period. The results show that the levels of corticosterone were sex dependent, differed between years and were affected by the migratory strategy performed by the birds. The activation of the stressful response over the wintering period generated residual carry-over effects that positively affected the reproductive output in the subsequent breeding stage, a phenomenon previously undescribed in a long-lived pelagic seabird. Our study provides evidence that the analysis of corticosterone from feathers is a useful tool to evaluate carry-over effects in birds far away from breeding sites, opening new possibilities for future studies in this field.

SAPFLUXNET: towards a global database of sap flow measurements.

PubMed

Poyatos, Rafael; Granda, Víctor; Molowny-Horas, Roberto; Mencuccini, Maurizio; Steppe, Kathy; Martínez-Vilalta, Jordi

2016-12-01

Plant transpiration is the main evaporative flux from terrestrial ecosystems; it controls land surface energy balance, determines catchment hydrological responses and influences regional and global climate. Transpiration regulation by plants is a key (and still not completely understood) process that underlies vegetation drought responses and land evaporative fluxes under global change scenarios. Thermometric methods of sap flow measurement have now been widely used to quantify whole-plant and stand transpiration in forests, shrublands and orchards around the world. A large body of research has applied sap flow methods to analyse seasonal and diurnal patterns of transpiration and to quantify their responses to hydroclimatic variability, but syntheses of sap flow data at regional to global scales are extremely rare. Here we present the SAPFLUXNET initiative, aimed at building the first global database of plant-level sap flow measurements. A preliminary metadata survey launched in December 2015 showed an encouraging response by the sap flow community, with sap flow data sets from field studies representing >160 species and >120 globally distributed sites. The main goal of SAPFLUXNET is to analyse the ecological factors driving plant- and stand-level transpiration. SAPFLUXNET will open promising research avenues at an unprecedented global scope, namely: (i) exploring the spatio-temporal variability of plant transpiration and its relationship with plant and stand attributes, (ii) summarizing physiological regulation of transpiration by means of few water-use traits, usable for land surface models, (iii) improving our understanding of the coordination between gas exchange and plant-level traits (e.g., hydraulics) and (iv) analysing the ecological factors controlling stand transpiration and evapotranspiration partitioning. Finally, SAPFLUXNET can provide a benchmark to test models of physiological controls of transpiration, contributing to improve the accuracy of individual water stress responses, a key element to obtain robust predictions of vegetation responses to climate change. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Selective oviposition by Aedes aegypti (Diptera: culicidae) in response to Mesocyclops longisetus (Copepoda: Cyclopoidea) under laboratory and field conditions.

PubMed

Torres-Estrada, J L; Rodríguez, M H; Cruz-López, L; Arredondo-Jimenez, J I

2001-03-01

The influence of predacious Mesocyclops longisetus Thiebaud on the selection of oviposition sites by prey Aedes aegypti (L.) was studied under laboratory and field conditions. In both cases, gravid Ae. aegypti females were significantly more attracted to ovitraps containing copepods or to ovitraps with water in which copepods were held previously than to distilled water. Monoterpene and sesquiterpene compounds including 3-carene, alpha-terpinene, alpha-copaene, alpha-longipinene, alpha-cedrene, and delta-cadinene were found in hexane extracts of copepods by gas chromatography and mass spectrometry analyses. These compounds may be responsible for attracting gravid Ae. aegypti females and may increase the number of potential prey for the copepod.

Molecular evolution of bovine Toll-like receptor 2 suggests substitutions of functional relevance.

PubMed

Jann, Oliver C; Werling, Dirk; Chang, Jung-Su; Haig, David; Glass, Elizabeth J

2008-10-20

There is accumulating evidence that polymorphism in Toll-like receptor (TLR) genes might be associated with disease resistance or susceptibility traits in livestock. Polymorphic sites affecting TLR function should exhibit signatures of positive selection, identified as a high ratio of non-synonymous to synonymous nucleotide substitutions (omega). Phylogeny based models of codon substitution based on estimates of omega for each amino acid position can therefore offer a valuable tool to predict sites of functional relevance. We have used this approach to identify such polymorphic sites within the bovine TLR2 genes from ten Bos indicus and Bos taurus cattle breeds. By analysing TLR2 gene phylogeny in a set of mammalian species and a subset of ruminant species we have estimated the selective pressure on individual sites and domains and identified polymorphisms at sites of putative functional importance. The omega were highest in the mammalian TLR2 domains thought to be responsible for ligand binding and lowest in regions responsible for heterodimerisation with other TLR-related molecules. Several positively-selected sites were detected in or around ligand-binding domains. However a comparison of the ruminant subset of TLR2 sequences with the whole mammalian set of sequences revealed that there has been less selective pressure among ruminants than in mammals as a whole. This suggests that there have been functional changes during ruminant evolution. Twenty newly-discovered non-synonymous polymorphic sites were identified in cattle. Three of them were localised at positions shaped by positive selection in the ruminant dataset (Leu227Phe, His305Pro, His326Gln) and in domains involved in the recognition of ligands. His326Gln is of particular interest as it consists of an exchange of differentially-charged amino acids at a position which has previously been shown to be crucial for ligand binding in human TLR2. Within bovine TLR2, polymorphisms at amino acid positions 227, 305 and 326 map to functionally important sites of TLR2 and should be considered as candidate SNPs for immune related traits in cattle. A final proof of their functional relevance requires further studies to determine their functional effect on the immune response after stimulation with relevant ligands and/or their association with immune related traits in animals.

Bipartite functions of the CREB co-activators selectively direct alternative splicing or transcriptional activation

PubMed Central

Amelio, Antonio L; Caputi, Massimo; Conkright, Michael D

2009-01-01

The CREB regulated transcription co-activators (CRTCs) regulate many biological processes by integrating and converting environmental inputs into transcriptional responses. Although the mechanisms by which CRTCs sense cellular signals are characterized, little is known regarding how CRTCs contribute to the regulation of cAMP inducible genes. Here we show that these dynamic regulators, unlike other co-activators, independently direct either pre-mRNA splice-site selection or transcriptional activation depending on the cell type or promoter context. Moreover, in other scenarios, the CRTC co-activators coordinately regulate transcription and splicing. Mutational analyses showed that CRTCs possess distinct functional domains responsible for regulating either pre-mRNA splicing or transcriptional activation. Interestingly, the CRTC1–MAML2 oncoprotein lacks the splicing domain and is incapable of altering splice-site selection despite robustly activating transcription. The differential usage of these distinct domains allows CRTCs to selectively mediate multiple facets of gene regulation, indicating that co-activators are not solely restricted to coordinating alternative splicing with increase in transcriptional activity. PMID:19644446

A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases

PubMed Central

Bradshaw, Niels; Levdikov, Vladimir M; Zimanyi, Christina M; Gaudet, Rachelle; Wilkinson, Anthony J; Losick, Richard

2017-01-01

PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an α-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor. Our analysis indicates that this switch is widely conserved among PP2C family members, serving as a platform to control phosphatase activity in response to diverse inputs. Remarkably, the switch is shared with proteasomal proteases, which we identify as evolutionary and structural relatives of PP2C phosphatases. Although these proteases use an unrelated catalytic mechanism, rotation of equivalent helices controls protease activity by movement of the equivalent carbonyl oxygen into the active site. DOI: http://dx.doi.org/10.7554/eLife.26111.001 PMID:28527238

A -Site Ordered Double Perovskite CaMnTi 2 O 6 as a Multifunctional Piezoelectric and Ferroelectric–Photovoltaic Material

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

Gou, Gaoyang; Charles, Nenian; Shi, Jing

2017-09-11

The double perovskite CaMnTi2O6, is a rare A site ordered perovskite oxide that exhibits a sizable ferroelectric polarization and relatively high Curie temperature. Using first-principles calculations combined with detailed symmetry analyses, we identify the origin of the ferroelectricity in CaMnTi2O6. We further explore the material properties of CaMnTi2O6, including its ferroelectric polarization, dielectric and piezoelectric responses, magnetic order, electronic structure, and optical absorption coefficient. It is found that CaMnTi2O6 exhibits room-temperature-stable ferroelectricity and moderate piezoelectric responses. Moreover, CaMnTi2O6 is predicted to have a semiconducting energy band gap similar to that of BiFeO3, and its band gap can further be tuned-viamore » distortions of the planar Mn-O bond lengths. CaMnTi2O6 exemplifies a new class of single-phase semiconducting ferroelectric perovskites for potential applications in ferroelectric photovoltaic solar cells.« less

Biological integrity in mid-atlantic coastal plains headwater streams.

PubMed

Megan, Mehaffey H; Nash, Maliha S; Neale, Anne C; Pitchford, Ann M

2007-01-01

The objective of this study was to assess the applicability of using landscape variables in conjunction with water quality and benthic data to efficiently estimate stream condition of select headwater streams in the Mid-Atlantic Coastal Plains. Eighty-two streams with riffle sites were selected from eight-two independent watersheds across the region for sampling and analyses. Clustering of the watersheds by landscape resulted in three distinct groups (forest, crop, and urban) which coincided with watersheds dominant land cover or use. We used non-parametric analyses to test differences in benthos and water chemistry between groups, and used regression analyses to evaluate responses of benthic communities to water chemistry within each of the landscape groups. We found that typical water chemistry measures associated with urban runoff such as specific conductance and dissolved chloride were significantly higher in the urban group. In the crop group, we found variables commonly associated with farming such as nutrients and pesticides significantly greater than in the other two groups. Regression analyses demonstrated that the numbers of tolerant and facultative macroinvertebrates increased significantly in forested watersheds with small shifts in pollutants, while in human use dominated watersheds the intolerant macroinvertebrates were more sensitive to shifts in chemicals present at lower concentrations. The results from this study suggest that landscape based clustering can be used to link upstream landscape characteristics, water chemistry and biotic integrity in order to assess stream condition and likely cause of degradation without the use of reference sites. Notice: Although this work was reviewed by EPA and approved for publication, it may not necessarily reflect official Agency policy.

The effects of urbanization on the biological, physical, and chemical characteristics of coastal New England streams

USGS Publications Warehouse

Coles, J.F.; Cuffney, T.F.; McMahon, G.; Beaulieu, K.M.

2004-01-01

During August 2000, responses of biological communities (invertebrates, fish, and algae), physical habitat, and water chemistry to urban intensity were compared among 30 streams within 80 miles of Boston, Massachusetts. Sites chosen for sampling represented a gradient of the intensity of urban development (urban intensity) among drainage basins that had minimal natural variability. In this study, spatial differences were used as surrogates for temporal changes to represent the effects of urbanization over time. The degree of urban intensity for each drainage basin was characterized with a standardized urban index (0?100, lowest to highest) derived from land cover, infrastructure, and socioeconomic variables. Multivariate and multimetric analyses were used to compare urban index values with biological, physical, and chemical data to determine how the data indicated responses to urbanization. Multivariate ordinations were derived for the invertebrate-, fish-, and algaecommunity data by use of correspondence analysis, and ordinations were derived for the chemical and physical data by use of principal-component analysis. Site scores from each of the ordinations were plotted in relation to the urban index to test for a response. In all cases, the primary axis scores showed the strongest response to the urban index, indicating that urbanization was a primary factor affecting the data ordination. For the multimetric analyses, each of the biological data sets was used to calculate a series of community metrics. For the sets of chemical and physical data, the individual variables and various combinations of individual variables were used as measured and derived metrics, respectively. Metrics that were generally most responsive to the urban index for each data set included: EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa for invertebrates; cyprinid taxa for fish; diatom taxa for algae; bicarbonate, conductivity, and nitrogen for chemistry; and water depth and temperature for physical habitat. The slopes of the responses generally were higher between the urban index values of 0 to 35, indicating that the greatest change in aquatic health may occur between low and moderate levels of urban intensity. Additionally, many of the responses showed that at urban index values greater than 35, there was a threshold effect where the response variable no longer changed with respect to urban intensity. Recognizing and understanding this type of response is important in management and monitoring programs that rely on decisive interpretations of variable responses. Any biological, physical, or chemical variable that is used to haracterize stream health over a gradient of disturbance would not be a reliable indicator when a level of disturbance is reached where the variable does not respond in a predictable manner.

Glycosylation Focuses Sequence Variation in the Influenza A Virus H1 Hemagglutinin Globular Domain

PubMed Central

Hensley, Scott E.; Hurt, Darrell E.; Bennink, Jack R.; Yewdell, Jonathan W.

2010-01-01

Antigenic drift in the influenza A virus hemagglutinin (HA) is responsible for seasonal reformulation of influenza vaccines. Here, we address an important and largely overlooked issue in antigenic drift: how does the number and location of glycosylation sites affect HA evolution in man? We analyzed the glycosylation status of all full-length H1 subtype HA sequences available in the NCBI influenza database. We devised the “flow index” (FI), a simple algorithm that calculates the tendency for viruses to gain or lose consensus glycosylation sites. The FI predicts the predominance of glycosylation states among existing strains. Our analyses show that while the number of glycosylation sites in the HA globular domain does not influence the overall magnitude of variation in defined antigenic regions, variation focuses on those regions unshielded by glycosylation. This supports the conclusion that glycosylation generally shields HA from antibody-mediated neutralization, and implies that fitness costs in accommodating oligosaccharides limit virus escape via HA hyperglycosylation. PMID:21124818

Lower Columbia River and Estuary Ecosystem Restoration Program Reference Site Study: 2011 Restoration Analysis - FINAL REPORT

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

Borde, Amy B.; Cullinan, Valerie I.; Diefenderfer, Heida L.

The Reference Site (RS) study is part of the research, monitoring, and evaluation (RME) effort developed by the Action Agencies (Bonneville Power Administration [BPA], U.S. Army Corps of Engineers, Portland District [USACE], and U.S. Bureau of Reclamation) in response to Federal Columbia River Power System (FCRPS) Biological Opinions (BiOp). While the RS study was initiated in 2007, data have been collected at relatively undisturbed reference wetland sites in the LCRE by PNNL and collaborators since 2005. These data on habitat structural metrics were previously summarized to provide baseline characterization of 51 wetlands throughout the estuarine and tidal freshwater portions ofmore » the 235-km LCRE; however, further analysis of these data has been limited. Therefore, in 2011, we conducted additional analyses of existing field data previously collected for the Columbia Estuary Ecosystem Restoration Program (CEERP) - including data collected by PNNL and others - to help inform the multi-agency restoration planning and ecosystem management work underway in the LCRE.« less

Wind/Tornado Guidelines Study

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

Ng, D.S.; Holman, G.S.

1991-10-01

This report documents the strategy employed to develop recommended wind/tornado hazard design guidelines for a New Production Reactor (NRP) currently planned for either the Idaho National Engineering Laboratory (INEL) or the Savannah River (SR) site. The Wind/Tornado Working Group (WTWG), comprising six nationally recognized experts in structural engineering, wind engineering, and meteorology, formulated an independent set of guidelines based on site-specific wind/tornado hazard curves and state-of-the-art tornado missile technology. The basic philosophy was to select realistic wind and missile load specifications, and to meet performance goals by applying conservative structural response evaluation and acceptance criteria. Simplified probabilistic risk analyses (PRAs)more » for wind speeds and missile impact were performed to estimate annual damage risk frequencies for both the INEL and SR sites. These PRAs indicate that the guidelines will lead to facilities that meet the US Department of Energy (DOE) design requirements and that the Nuclear Regulatory Commission guidelines adopted by the DOE for design are adequate to meet the NPR safety goals.« less

Analysing biodiversity and conservation knowledge products to support regional environmental assessments.

PubMed

Brooks, Thomas M; Akçakaya, H Resit; Burgess, Neil D; Butchart, Stuart H M; Hilton-Taylor, Craig; Hoffmann, Michael; Juffe-Bignoli, Diego; Kingston, Naomi; MacSharry, Brian; Parr, Mike; Perianin, Laurence; Regan, Eugenie C; Rodrigues, Ana S L; Rondinini, Carlo; Shennan-Farpon, Yara; Young, Bruce E

2016-02-16

Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird &Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments.

Multiple sup 3 H-oxytocin binding sites in rat myometrial plasma membranes

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

Crankshaw, D.; Gaspar, V.; Pliska, V.

1990-01-01

The affinity spectrum method has been used to analyse binding isotherms for {sup 3}H-oxytocin to rat myometrial plasma membranes. Three populations of binding sites with dissociation constants (Kd) of 0.6-1.5 x 10(-9), 0.4-1.0 x 10(-7) and 7 x 10(-6) mol/l were identified and their existence verified by cluster analysis based on similarities between Kd, binding capacity and Hill coefficient. When experimental values were compared to theoretical curves constructed using the estimated binding parameters, good fits were obtained. Binding parameters obtained by this method were not influenced by the presence of GTP gamma S (guanosine-5'-O-3-thiotriphosphate) in the incubation medium. The bindingmore » parameters agree reasonably well with those found in uterine cells, they support the existence of a medium affinity site and may allow for an explanation of some of the discrepancies between binding and response in this system.« less

SbnG, a citrate synthase in Staphylococcus aureus: A new fold on an old enzyme

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

Kobylarz, Marek J.; Grigg, Jason C.; Sheldon, Jessica R.

In response to iron deprivation, Staphylococcus aureus produces staphyloferrin B, a citrate-containing siderophore that delivers iron back to the cell. This bacterium also possesses a second citrate synthase, SbnG, that is necessary for supplying citrate to the staphyloferrin B biosynthetic pathway. In this paper, we present the structure of SbnG bound to the inhibitor calcium and an active site variant in complex with oxaloacetate. The overall fold of SbnG is structurally distinct from TCA cycle citrate synthases yet similar to metal-dependent class II aldolases. Phylogenetic analyses revealed that SbnG forms a separate clade with homologs from other siderophore biosynthetic genemore » clusters and is representative of a metal-independent subgroup in the phosphoenolpyruvate/pyruvate domain superfamily. Finally, a structural superposition of the SbnG active site to TCA cycle citrate synthases and site-directed mutagenesis suggests a case for convergent evolution toward a conserved catalytic mechanism for citrate production.« less

SbnG, a citrate synthase in Staphylococcus aureus: A new fold on an old enzyme

DOE PAGES

Kobylarz, Marek J.; Grigg, Jason C.; Sheldon, Jessica R.; ...

2014-10-21

In response to iron deprivation, Staphylococcus aureus produces staphyloferrin B, a citrate-containing siderophore that delivers iron back to the cell. This bacterium also possesses a second citrate synthase, SbnG, that is necessary for supplying citrate to the staphyloferrin B biosynthetic pathway. In this paper, we present the structure of SbnG bound to the inhibitor calcium and an active site variant in complex with oxaloacetate. The overall fold of SbnG is structurally distinct from TCA cycle citrate synthases yet similar to metal-dependent class II aldolases. Phylogenetic analyses revealed that SbnG forms a separate clade with homologs from other siderophore biosynthetic genemore » clusters and is representative of a metal-independent subgroup in the phosphoenolpyruvate/pyruvate domain superfamily. Finally, a structural superposition of the SbnG active site to TCA cycle citrate synthases and site-directed mutagenesis suggests a case for convergent evolution toward a conserved catalytic mechanism for citrate production.« less

SbnG, a citrate synthase in Staphylococcus aureus: a new fold on an old enzyme.

PubMed

Kobylarz, Marek J; Grigg, Jason C; Sheldon, Jessica R; Heinrichs, David E; Murphy, Michael E P

2014-12-05

In response to iron deprivation, Staphylococcus aureus produces staphyloferrin B, a citrate-containing siderophore that delivers iron back to the cell. This bacterium also possesses a second citrate synthase, SbnG, that is necessary for supplying citrate to the staphyloferrin B biosynthetic pathway. We present the structure of SbnG bound to the inhibitor calcium and an active site variant in complex with oxaloacetate. The overall fold of SbnG is structurally distinct from TCA cycle citrate synthases yet similar to metal-dependent class II aldolases. Phylogenetic analyses revealed that SbnG forms a separate clade with homologs from other siderophore biosynthetic gene clusters and is representative of a metal-independent subgroup in the phosphoenolpyruvate/pyruvate domain superfamily. A structural superposition of the SbnG active site to TCA cycle citrate synthases and site-directed mutagenesis suggests a case for convergent evolution toward a conserved catalytic mechanism for citrate production. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Hyalella azteca (Saussure) responses to Coldwater River backwater sediments in Mississippi, USA.

PubMed

Knight, Scott S; Lizotte, Richard E; Shields, F Douglas

2009-10-01

Sediment from three Coldwater River, Mississippi backwaters was examined using 28 day Hyalella azteca bioassays and chemical analyses for 33 pesticides, seven metals and seven PCB mixtures. Hydrologic connectivity between the main river channel and backwater varied widely among the three sites. Mortality occurred in the most highly connected backwater while growth impairment occurred in the other two. Precopulatory guarding behavior was not as sensitive as growth. Fourteen contaminants (seven metals, seven pesticides) were detected in sediments. Survival was associated with the organochlorine insecticide heptachlor.

Consistent C3 plant habitat of hominins during 400-300 ka at the Longyadong Cave site (Luonan Basin, central China) revealed by stable carbon isotope analyses of loess deposits

NASA Astrophysics Data System (ADS)

Zhang, Hongyan; Lu, Huayu; Wang, Shejiang

2017-04-01

The proportions of woody and grassland taxa in terrestrial ecosystems played an important role in the origin and evolution of early Palaeolithic hominins. However the influence of ecosystem changes on hominin behavior and adaptations in Asia has not been studied in detail. Hominins have exploited the Luonan Basin in the Eastern Qinling Mountains, central China, since the early Paleolithic. Dated sites, consisting of alternating loess and soil deposits with in situ artefacts, are common in the region, and provide a detailed record of Early to Middle Pleistocene hominin environments. Here, we present the results of measurements of the stable carbon isotopic composition of soil organic matter (δ13C) in the loess-paleosol sequences from the Longyadong Cave site. Our analyses of δ13C show that for at least 400 ka the Longyadong Cave site and its surroundings were dominated by C3 woody plants, whereas the nearby Liuwan site was dominated by C4 and C3 mixed grassland or woody grassland vegetation. These findings demonstrate that between 400 and 300 ka in the Luonan Basin, hominins occupied a habitat consisting of a mosaic of grassland and woodland/forest. Although the vegetation of the region changed in response to the glacial-interglacial climatic cycles, patches of woody vegetation in landscapes such as at Longyadong Cave site persisted continuously. Such environments seem to be have been favored by hominins living in the Luonan Basin, possibly because they provided a diverse range of food resources during both glacial and interglacial intervals of the Middle Pleistocene, when most of northern China was experiencing an increasing trend of drying and cooling and steppe environments were expanding. Thus, the Luonan Basin would have served as a refugium for hominin occupation in China during the Middle Pleistocene.

Constructing a framework for risk analyses of climate change effects on the water budget of differently sloped vineyards with a numeric simulation using the Monte Carlo method coupled to a water balance model

PubMed Central

Hofmann, Marco; Lux, Robert; Schultz, Hans R.

2014-01-01

Grapes for wine production are a highly climate sensitive crop and vineyard water budget is a decisive factor in quality formation. In order to conduct risk assessments for climate change effects in viticulture models are needed which can be applied to complete growing regions. We first modified an existing simplified geometric vineyard model of radiation interception and resulting water use to incorporate numerical Monte Carlo simulations and the physical aspects of radiation interactions between canopy and vineyard slope and azimuth. We then used four regional climate models to assess for possible effects on the water budget of selected vineyard sites up 2100. The model was developed to describe the partitioning of short-wave radiation between grapevine canopy and soil surface, respectively, green cover, necessary to calculate vineyard evapotranspiration. Soil water storage was allocated to two sub reservoirs. The model was adopted for steep slope vineyards based on coordinate transformation and validated against measurements of grapevine sap flow and soil water content determined down to 1.6 m depth at three different sites over 2 years. The results showed good agreement of modeled and observed soil water dynamics of vineyards with large variations in site specific soil water holding capacity (SWC) and viticultural management. Simulated sap flow was in overall good agreement with measured sap flow but site-specific responses of sap flow to potential evapotranspiration were observed. The analyses of climate change impacts on vineyard water budget demonstrated the importance of site-specific assessment due to natural variations in SWC. The improved model was capable of describing seasonal and site-specific dynamics in soil water content and could be used in an amended version to estimate changes in the water budget of entire grape growing areas due to evolving climatic changes. PMID:25540646

Long-term Glacial History of the West Antarctic Ice Sheet from Cosmogenic Nuclides in a Subglacial Bedrock Core

NASA Astrophysics Data System (ADS)

Spector, P. E.; Stone, J.; Hillebrand, T.; Gombiner, J. H.

2017-12-01

To investigate the response of the West Antarctic Ice Sheet (WAIS) to climatic conditions warmer than present, we are analyzing cosmogenic nuclides in a bedrock core from beneath 150 m of ice at a site near the Pirrit Hills. Our aim is to determine whether the WAIS has thinned in the past, exposing bedrock at this site, and if so, when. This will help to determine the vulnerability of the ice sheet to future warming, and identify climatic thresholds capable of inducing WAIS collapse. We selected a site where the ice-sheet surface lies at 1300 m, approximately halfway from the ice-sheet divide to the grounding line. We expect ice thickness at the site to reflect WAIS dynamics, rather than local meteorology or topography. Ice flow speeds are moderate and ice above the core site is thin enough to remain cold-based, limiting the possibility of subglacial erosion which would compromise the cosmogenic nuclide record. We targeted a subglacial ridge adjacent to an exposed granite nunatak. This lithology provides minerals suitable for analysis of multiple cosmogenic nuclides with different half-lives. Although we aimed to collect two cores from different depths to compare exposure histories, hydrofracture of the basal ice prevented us from reaching the bed at the first drill site. The second hole produced 5.5 m of discontinuous ice core above 8 m of bedrock core. Initial analyses of quartz from the bedrock show low levels of Be-10. Further analyses of Be-10, Al-26, Cl-36 and Ne-21 from the full length of the core will be required to determine whether this is because the surface has never been exposed, or because the cosmogenic nuclide profile has been truncated by glacial erosion. We will present comprehensive cosmogenic nuclide data, and discuss implications for WAIS deglaciation history, at the meeting. Supported by US National Science Foundation awards ANT-1142162 and PLR-1341728.

Stone tool function at the paleolithic sites of Starosele and Buran Kaya III, Crimea: Behavioral implications

PubMed Central

Hardy, Bruce L.; Kay, Marvin; Marks, Anthony E.; Monigal, Katherine

2001-01-01

Stone tools are often the most abundant type of cultural remains at Paleolithic sites, yet their function is often poorly understood. Investigations of stone tool function, including microscopic use-wear and residue analyses, were performed on a sample of artifacts from the Paleolithic sites of Starosele (40,000–80,000 years BP) and Buran Kaya III (32,000–37,000 years BP). The Middle Paleolithic levels at Starosele exhibit a typical variant of the local Micoquian Industry. The artifacts from Buran Kaya III most closely resemble an Early Streletskayan Industry associated with the early Upper Paleolithic. The results of the functional analyses suggest that hominids at both sites were exploiting woody and starchy plant material as well as birds and mammals. Both sites show evidence of hafting of a wide variety of tools and the possible use of projectile or thrusting spears. These analyses were performed by using two different techniques conducted by independent researchers. Combined residue and use-wear analyses suggest that both the Upper Paleolithic and Middle Paleolithic hominids at these sites were broad-based foragers capable of exploiting a wide range of resources. PMID:11535837

Assessing the health status of farmed mussels (Mytilus galloprovincialis) through histological, microbiological and biomarker analyses.

PubMed

Matozzo, Valerio; Ercolini, Carlo; Serracca, Laura; Battistini, Roberta; Rossini, Irene; Granato, Giulia; Quaglieri, Elisabetta; Perolo, Alberto; Finos, Livio; Arcangeli, Giuseppe; Bertotto, Daniela; Radaelli, Giuseppe; Chollet, Bruno; Arzul, Isabelle; Quaglio, Francesco

2018-03-01

The Gulf of La Spezia (northern Tyrrhenian Sea, Italy) is a commercially important area both as a shipping port and for mussel farming. Recently, there has been increased concern over environmental disturbances caused by anthropogenic activities such as ship traffic and dredging and the effects they have on the health of farmed mussels. This paper reports the results of microbiological and histological analyses, as well as of measurement of several biomarkers which were performed to assess the health status of mussels (Mytilus galloprovincialis) from four rearing sites in the Gulf of La Spezia. Mussels were collected between October 2015 and September 2016 and histological analyses (including gonadal maturation stage), as well as the presence of pathogenic bacteria (Vibrio splendidus clade, V. aestuarianus and V. harveyi), viruses (Herpes virus and ostreid Herpes virus 1) and protozoa (Marteilia spp., in the summer season only) were carried out on a monthly basis. Conversely, biomarker responses in haemocyte/haemolymph (total haemocyte count, haemocyte diameter and volume, lysozyme and lactate dehydrogenase activities in cell-free haemolymph, and micronuclei frequency) and in gills and digestive gland (cortisol-like steroids and lipid peroxidation levels), were evaluated bimonthly. Microbiological data indicated that mussels contain a reservoir of potentially pathogenic bacteria, viruses and protozoa that in certain environmental conditions may cause a weakening of the immune system of animals leading to mortality episodes. The percentage of parasites detected in the mussels was generally low (9.6% for Steinhausia mytilovum, that is 17 samples out of 177 examined females; 3.4% for Proctoeces maculatus; 0.9% for Mytilicola intestinalis and 2% for ciliated protozoa), while symbiont loads were higher (31% for Eugymnanthea inquilina and Urastoma cyprinae). Interestingly, a previously undescribed haplosporidian was detected in a single mussel sample (0.2%) and was confirmed by in situ hybridization. Cells morphologically similar to Perkinsus sp. trophozoites were observed in 0.7% of the mussels analysed; however, infection with Perkinsus spp. could neither be confirmed by ISH nor by PCR. Different pathological aspects, such as host defence responses and regressive/progressive changes were detected in the gills, digestive glands, gonads and mantle. Only one single case of disseminated neoplasia (0.2%) was observed. As for the biomarker evaluation, the MANOVA analysis revealed the statistically significant effect that the variable "sampling site" had on the biological parameter measured, thus suggesting that the multibiomarker approach was able to differentiate the rearing sites. Copyright © 2018 Elsevier Inc. All rights reserved.

Functional, structural and phylogenetic analysis of domains underlying the Al sensitivity of the aluminum-activated malate/anion transporter, TaALMT1.

PubMed

Ligaba, Ayalew; Dreyer, Ingo; Margaryan, Armine; Schneider, David J; Kochian, Leon; Piñeros, Miguel

2013-12-01

Triticum aestivum aluminum-activated malate transporter (TaALMT1) is the founding member of a unique gene family of anion transporters (ALMTs) that mediate the efflux of organic acids. A small sub-group of root-localized ALMTs, including TaALMT1, is physiologically associated with in planta aluminum (Al) resistance. TaALMT1 exhibits significant enhancement of transport activity in response to extracellular Al. In this study, we integrated structure-function analyses of structurally altered TaALMT1 proteins expressed in Xenopus oocytes with phylogenic analyses of the ALMT family. Our aim is to re-examine the role of protein domains in terms of their potential involvement in the Al-dependent enhancement (i.e. Al-responsiveness) of TaALMT1 transport activity, as well as the roles of all its 43 negatively charged amino acid residues. Our results indicate that the N-domain, which is predicted to form the conductive pathway, mediates ion transport even in the absence of the C-domain. However, segments in both domains are involved in Al(3+) sensing. We identified two regions, one at the N-terminus and a hydrophobic region at the C-terminus, that jointly contribute to the Al-response phenotype. Interestingly, the characteristic motif at the N-terminus appears to be specific for Al-responsive ALMTs. Our study highlights the need to include a comprehensive phylogenetic analysis when drawing inferences from structure-function analyses, as a significant proportion of the functional changes observed for TaALMT1 are most likely the result of alterations in the overall structural integrity of ALMT family proteins rather than modifications of specific sites involved in Al(3+) sensing. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Understory vegetation as an indicator for floodplain forest restoration in the Mississippi River Alluvial Valley, U.S.A.

USGS Publications Warehouse

De Steven, Diane; Faulkner, Stephen; Keeland, Bobby D.; Baldwin, Michael; McCoy, John W.; Hughes, Steven C.

2015-01-01

In the Mississippi River Alluvial Valley (MAV), complete alteration of river-floodplain hydrology allowed for widespreadconversion of forested bottomlands to intensive agriculture, resulting in nearly 80% forest loss. Governmental programs haveattempted to restore forest habitat and functions within this altered landscape by the methods of tree planting (afforestation)and local hydrologic enhancement on reclaimed croplands. Early assessments identified factors that influenced whetherplanting plus tree colonization could establish an overstory community similar to natural bottomland forests. The extentto which afforested sites develop typical understory vegetation has not been evaluated, yet understory composition may beindicative of restored site conditions. As part of a broad study quantifying the ecosystem services gained from restorationefforts, understory vegetation was compared between 37 afforested sites and 26 mature forest sites. Differences in vegetationattributes for species growth forms, wetland indicator classes, and native status were tested with univariate analyses;floristic composition data were analyzed by multivariate techniques. Understory vegetation of restoration sites was generallyhydrophytic, but species composition differed from that of mature bottomland forest because of young successional age anddiffering responses of plant growth forms. Attribute and floristic variation among restoration sites was related to variationin canopy development and local wetness conditions, which in turn reflected both intrinsic site features and outcomes ofrestoration practices. Thus, understory vegetation is a useful indicator of functional progress in floodplain forest restoration.

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

Bevelhimer, Mark S.; Adams, Marshall; Fortner, Allison M.

The effect of coal ash exposure on fish health in freshwater communities is largely unknown. Given the large number of possible pathways of effects (e.g., toxicological effect of exposure to multiple metals, physical effects from ash exposure, and food web effects), measurement of only a few health metrics is not likely to give a complete picture. The authors measured a suite of 20 health metrics from 1100+ fish collected from 5 sites (3 affected and 2 reference) near a coal ash spill in east Tennessee over a 4.5-yr period. The metrics represented a wide range of physiological and energetic responsesmore » and were evaluated simultaneously using 2 multivariate techniques. Results from both hierarchical clustering and canonical discriminant analyses suggested that for most speciesXseason combinations, the suite of fish health indicators varied more among years than between spill and reference sites within a year. In a few cases, spill sites from early years in the investigation stood alone or clustered together separate from reference sites and later year spill sites. Outlier groups of fish with relatively unique health profiles were most often from spill sites, suggesting that some response to the ash exposure may have occurred. Results from the 2 multivariate methods suggest that any change in the health status of fish at the spill sites was small and appears to have diminished since the first 2 to 3 yr after the spill.« less

The human haptoglobin gene promoter: interleukin-6-responsive elements interact with a DNA-binding protein induced by interleukin-6.

PubMed Central

Oliviero, S; Cortese, R

1989-01-01

Transcription of the human haptoglobin (Hp) gene is induced by interleukin-6 (IL-6) in the human hepatoma cell line Hep3B. Cis-acting elements responsible for this response are localized within the first 186 bp of the 5'-flanking region. Site-specific mutants of the Hp promoter fused to the chloramphenicol acetyl transferase (CAT) gene were analysed by transient transfection into uninduced and IL-6-treated Hep3B cells. We identified three regions, A, B and C, defined by mutation, which are important for the IL-6 response. Band shift experiments using nuclear extracts from untreated or IL-6-treated cells revealed the presence of IL-6-inducible DNA binding activities when DNA fragments containing the A or the C sequences were used. Competition experiments showed that both sequences bind to the same nuclear factors. Polymers of oligonucleotides containing either the A or the C regions confer IL-6 responsiveness to a truncated SV40 promoter. The B region forms several complexes with specific DNA-binding proteins different from those which bind to the A and C region. The B region complexes are identical in nuclear extracts from IL-6-treated and untreated cells. While important for IL-6 induction in the context of the haptoglobin promoter, the B site does not confer IL-6 inducibility to the SV40 promoter. Our results indicate that the IL-6 response of the haptoglobin promoter is dependent on the presence of multiple, partly redundant, cis-acting elements. Images PMID:2787245

Characterization of the Kootenai River Algae Community and Primary Productivity Before and After Experimental Nutrient Addition, 2004–2007 [Chapter 2, Kootenai River Algal Community Characterization, 2009 KTOI REPORT].

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

Holderman, Charlie; Bonners Ferry, ID; Anders, Paul

2009-07-01

The Kootenai River ecosystem (spelled Kootenay in Canada) has experienced numerous ecological changes since the early 1900s. Some of the largest impacts to habitat, biological communities, and ecological function resulted from levee construction along the 120 km of river upstream from Kootenay Lake, completed by the 1950s, and the construction and operation of Libby Dam on the river near Libby Montana, completed in 1972. Levee construction isolated tens of thousands of hectares of historic functioning floodplain habitat from the river channel downstream in Idaho and British Columbia (B.C.) severely reducing natural biological productivity and habitat diversity crucial to large river-floodplainmore » ecosystem function. Libby Dam greatly reduces sediment and nutrient transport to downstream river reaches, and dam operations cause large changes in the timing, duration, and magnitude of river flows. These and other changes have contributed to the ecological collapse of the post-development Kootenai River ecosystem and its native biological communities. In response to large scale loss of nutrients, experimental nutrient addition was initiated in the North Arm of Kootenay Lake in 1992, in the South Arm of Kootenay Lake in 2004, and in the Kootenai River at the Idaho-Montana border during 2005. This report characterizes baseline chlorophyll concentration and accrual (primary productivity) rates and diatom and algal community composition and ecological metrics in the Kootenai River for four years, one (2004) before, and three (2005 through 2007) after nutrient addition. The study area encompassed a 325 km river reach from the upper Kootenay River at Wardner, B.C. (river kilometer (rkm) 445) downstream through Montana and Idaho to Kootenay Lake in B.C. (rkm 120). Sampling reaches included an unimpounded reach furthest upstream and four reaches downstream from Libby Dam affected by impoundment: two in the canyon reach (one with and one without nutrient addition), a braided reach, and a meandering reach. The study design included 14 sampling sites: an upstream, unimpounded reference site (KR-14), four control (non-fertilized) canyon sites downstream from Libby Dam, but upstream from nutrient addition (KR-10 through KR-13), two treatment sites referred to collectively as the nutrient addition zone (KR-9 and KR-9.1, located at and 5 km downstream from the nutrient addition site), two braided reach sites (KR-6 and KR-7), and four meander reach sites (KR-1 through KR-4). A series of qualitative evaluations and quantitative analyses were used to assess baseline conditions and effects of experimental nutrient addition treatments on chlorophyll, primary productivity, and taxonomic composition and metric arrays for the diatom and green algae communities. Insufficient density in the samples precluded analyses of bluegreen algae taxa and metrics for pre- and post-nutrient addition periods. Chlorophyll a concentration (mg/m{sup 2}), chlorophyll accrual rate (mg/m{sup 2}/30d), total chlorophyll concentration (chlorophyll a and b) (mg/m{sup 2}), and total chlorophyll accrual rate (mg/m{sup 2}/30d) were calculated. Algal taxa were identified and grouped by taxonomic order as Cyanophyta (blue-greens), Chlorophyta (greens), Bacillariophyta (diatoms), Chrysophyta (goldens), and dominant species from each sample site were identified. Algal densities (number/ml) in periphyton samples were calculated for each sample site and sampling date. Principal Component Analysis (PCA) was performed to reduce the dimension of diatom and algae data and to determine which taxonomic groups and metrics were contributing significantly to the observed variation. PCA analyses were tabulated to indicate eigenvalues, proportion, and cumulative percent variation, as well as eigenvectors (loadings) for each of the components. Biplot graphic displays of PCA axes were also generated to characterize the pattern and structure of the underlying variation. Taxonomic data and a series of biological and ecological metrics were used with PCA for diatoms and algae. Algal metrics included a suite of abundance, diversity, richness, dominance, and other measures, whereas additional trophic status and chemical limnology metrics, Van Dam indices and morphological groupings were employed in diatom PCAs. Analysis of Variance (ANOVA) was carried out using chlorophyll metrics and taxa and metric arrays for the diatom and green algae community data for comparing site differences from 2004 through 2007. Clear, statistically significant, biological responses from chlorophyll metrics, and taxa and metrics of the diatom and algal communities were revealed following experimental nutrient addition in the Kootenai River. Chlorophyll metric responses were more often significant and generally greater in magnitude than diatom and green algae taxa and metric responses.« less

Toxicity evaluation with the microtox® test to assess the impact of in situ oiled shoreline treatment options: natural attenuation and sediment relocation

USGS Publications Warehouse

Lee, Kenneth; Wohlgeschaffen, Gary; Tremblay, Gilles H.; Johnson, B. Thomas; Sergy, Gary A.; Prince, Roger C.; Guenette, Chantal C.; Owens, Edward H.

2003-01-01

Changes in the toxicity levels of beach sediment, nearshore water, and bottom sediment samples were monitored with the Microtox® Test to evaluate the two in situ oil spill treatment options of natural attenuation (natural recovery––no treatment) and sediment relocation (surf washing). During a series of field trials, IF-30 fuel oil was intentionally sprayed onto the surface of three mixed sediment (pebble and sand) beaches on the island of Spitsbergen, Svalbard, Norway (78°56′ N, 16°45′ E). At a low wave-energy site (Site 1 with a 3-km wind fetch), where oil was stranded within the zone of normal wave action, residual oil concentrations and beach sediment toxicity levels were significantly reduced by both options in less than five days. At Site 3, a higher wave-energy site with a 40-km wind fetch, oil was intentionally stranded on the beach face in the upper intertidal/supratidal zones, above the level of normal wave activity. At this site under these experimental conditions, sediment relocation was effective in accelerating the removal of the oil from the sediments and reducing the Microtox® Test toxicity response to background levels. In the untreated (natural attenuation) plot at this site, the fraction of residual oil remaining within the beach sediments after one year (70%) continued to generate a toxic response. Chemical and toxicological analyses of nearshore sediment and sediment-trap samples at both sites confirmed that oil and suspended mineral fines were effectively dispersed into the surrounding environment by the in situ treatments. In terms of secondary potential detrimental effects from the release of stranded oil from the beaches, the toxicity level (Microtox® Test) of adjacent nearshore sediment samples did not exceed the Canadian regulatory limit for dredged spoils destined for ocean disposal.

A portable analyser for the measurement of ammonium in marine waters.

PubMed

Amornthammarong, Natchanon; Zhang, Jia-Zhong; Ortner, Peter B; Stamates, Jack; Shoemaker, Michael; Kindel, Michael W

2013-03-01

A portable ammonium analyser was developed and used to measure in situ ammonium in the marine environment. The analyser incorporates an improved LED photodiode-based fluorescence detector (LPFD). This system is more sensitive and considerably smaller than previous systems and incorporates a pre-filtering subsystem enabling measurements in turbid, sediment-laden waters. Over the typical range for ammonium in marine waters (0–10 mM), the response is linear (r(2) = 0.9930) with a limit of detection (S/N ratio > 3) of 10 nM. The working range for marine waters is 0.05–10 mM. Repeatability is 0.3% (n =10) at an ammonium level of 2 mM. Results from automated operation in 15 min cycles over 16 days had good overall precision (RSD = 3%, n = 660). The system was field tested at three shallow South Florida sites. Diurnal cycles and possibly a tidal influence were expressed in the concentration variability observed.

40 CFR 1400.1 - Purpose.

Code of Federal Regulations, 2012 CFR

2012-07-01

... OFF-SITE CONSEQUENCE ANALYSIS INFORMATION DISTRIBUTION OF OFF-SITE CONSEQUENCE ANALYSIS INFORMATION... chemical accidents and submit the results of their analyses to the U.S. Environmental Protection Agency as... the portions of risk management plans containing the results of those analyses and certain related...

40 CFR 1400.1 - Purpose.

Code of Federal Regulations, 2013 CFR

2013-07-01

... OFF-SITE CONSEQUENCE ANALYSIS INFORMATION DISTRIBUTION OF OFF-SITE CONSEQUENCE ANALYSIS INFORMATION... chemical accidents and submit the results of their analyses to the U.S. Environmental Protection Agency as... the portions of risk management plans containing the results of those analyses and certain related...

40 CFR 1400.1 - Purpose.

Code of Federal Regulations, 2014 CFR

2014-07-01

... OFF-SITE CONSEQUENCE ANALYSIS INFORMATION DISTRIBUTION OF OFF-SITE CONSEQUENCE ANALYSIS INFORMATION... chemical accidents and submit the results of their analyses to the U.S. Environmental Protection Agency as... the portions of risk management plans containing the results of those analyses and certain related...

40 CFR 1400.1 - Purpose.

Code of Federal Regulations, 2011 CFR

2011-07-01

... OFF-SITE CONSEQUENCE ANALYSIS INFORMATION DISTRIBUTION OF OFF-SITE CONSEQUENCE ANALYSIS INFORMATION... chemical accidents and submit the results of their analyses to the U.S. Environmental Protection Agency as... the portions of risk management plans containing the results of those analyses and certain related...

Phospholipid and Respiratory Quinone Analyses From Extreme Environments

NASA Astrophysics Data System (ADS)

Pfiffner, S. M.

2008-12-01

Extreme environments on Earth have been chosen as surrogate sites to test methods and strategies for the deployment of space craft in the search for extraterrestrial life. Surrogate sites for many of the NASA astrobiology institutes include the South African gold mines, Canadian subpermafrost, Atacama Desert, and acid rock drainage. Soils, sediments, rock cores, fracture waters, biofilms, and service and drill waters represent the types of samples collected from these sites. These samples were analyzed by gas chromatography mass spectrometry for phospholipid fatty acid methyl esters and by high performance liquid chromatography atmospheric pressure chemical ionization tandem mass spectrometry for respiratory quinones. Phospholipid analyses provided estimates of biomass, community composition, and compositional changes related to nutritional limitations or exposure to toxic conditions. Similar to phospholipid analyses, respiratory quinone analyses afforded identification of certain types of microorganisms in the community based on respiration and offered clues to in situ redox conditions. Depending on the number of samples analyzed, selected multivariate statistical methods were applied to relate membrane lipid results with site biogeochemical parameters. Successful detection of life signatures and refinement of methodologies at surrogate sites on Earth will be critical for the recognition of extraterrestrial life. At this time, membrane lipid analyses provide useful information not easily obtained by other molecular techniques.

Climate Shocks and Migration: An Agent-Based Modeling Approach.

PubMed

Entwisle, Barbara; Williams, Nathalie E; Verdery, Ashton M; Rindfuss, Ronald R; Walsh, Stephen J; Malanson, George P; Mucha, Peter J; Frizzelle, Brian G; McDaniel, Philip M; Yao, Xiaozheng; Heumann, Benjamin W; Prasartkul, Pramote; Sawangdee, Yothin; Jampaklay, Aree

2016-09-01

This is a study of migration responses to climate shocks. We construct an agent-based model that incorporates dynamic linkages between demographic behaviors, such as migration, marriage, and births, and agriculture and land use, which depend on rainfall patterns. The rules and parameterization of our model are empirically derived from qualitative and quantitative analyses of a well-studied demographic field site, Nang Rong district, Northeast Thailand. With this model, we simulate patterns of migration under four weather regimes in a rice economy: 1) a reference, 'normal' scenario; 2) seven years of unusually wet weather; 3) seven years of unusually dry weather; and 4) seven years of extremely variable weather. Results show relatively small impacts on migration. Experiments with the model show that existing high migration rates and strong selection factors, which are unaffected by climate change, are likely responsible for the weak migration response.

Climate Shocks and Migration: An Agent-Based Modeling Approach

PubMed Central

Entwisle, Barbara; Williams, Nathalie E.; Verdery, Ashton M.; Rindfuss, Ronald R.; Walsh, Stephen J.; Malanson, George P.; Mucha, Peter J.; Frizzelle, Brian G.; McDaniel, Philip M.; Yao, Xiaozheng; Heumann, Benjamin W.; Prasartkul, Pramote; Sawangdee, Yothin; Jampaklay, Aree

2016-01-01

This is a study of migration responses to climate shocks. We construct an agent-based model that incorporates dynamic linkages between demographic behaviors, such as migration, marriage, and births, and agriculture and land use, which depend on rainfall patterns. The rules and parameterization of our model are empirically derived from qualitative and quantitative analyses of a well-studied demographic field site, Nang Rong district, Northeast Thailand. With this model, we simulate patterns of migration under four weather regimes in a rice economy: 1) a reference, ‘normal’ scenario; 2) seven years of unusually wet weather; 3) seven years of unusually dry weather; and 4) seven years of extremely variable weather. Results show relatively small impacts on migration. Experiments with the model show that existing high migration rates and strong selection factors, which are unaffected by climate change, are likely responsible for the weak migration response. PMID:27594725

Integration of genotoxicity and population genetic analyses in kangaroo rats (Dipodomys merriami) exposed to radionuclide contamination at the Nevada Test Site, USA

USGS Publications Warehouse

Theodorakis, Christopher W.; Bickham, John W.; Lamb, Trip; Medica, Philip A.; Lyne, T. Barrett

2001-01-01

We examined effects of radionuclide exposure at two atomic blast sites on kangaroo rats (Dipodomys merriami) at the Nevada Test Site, Nevada, USA, using genotoxicity and population genetic analyses. We assessed chromosome damage by micronucleus and flow cytometric assays and genetic variation by randomly amplified polymorphic DNA (RAPD) and mitochondrial DNA (mtDNA) analyses. The RAPD analysis showed no population structure, but mtDNA exhibited differentiation among and within populations. Genotoxicity effects were not observed when all individuals were analyzed. However, individuals with mtDNA haplotypes unique to the contaminated sites had greater chromosomal damage than contaminated-site individuals with haplotypes shared with reference sites. When interpopulation comparisons used individuals with unique haplotypes, one contaminated site had greater levels of chromosome damage than one or both of the reference sites. We hypothesize that shared-haplotype individuals are potential migrants and that unique-haplotype individuals are potential long-term residents. A parsimony approach was used to estimate the minimum number of migration events necessary to explain the haplotype distributions on a phylogenetic tree. The observed predominance of migration events into the contaminated sites supported our migration hypothesis. We conclude the atomic blast sites are ecological sinks and that immigration masks the genotoxic effects of radiation on the resident populations.

The dimensionality of alcohol use disorders and alcohol consumption in a cross-national perspective

PubMed Central

Borges, Guilherme; Ye, Yu; Bond, Jason; Cherpitel, Cheryl J.; Cremonte, Mariana; Moskalewicz, Jacek; Swiatkiewicz, Grazyna; Rubio-Stipec, Maritza

2009-01-01

Aims To replicate the finding that there is a single dimension trait in alcohol use disorders and to test whether usual 5+ drinks for men and/4+ drinks for women and other measures of alcohol consumption help to improve alcohol use disorder criteria in a series of diverse patients from Emergency Departments (EDs) in four countries. Design Cross-sectional surveys of patient 18 and older that reflected consecutive arrival at the ED. The Composite International Diagnostic Interview Core was used to obtain a diagnosis of DSM-IV alcohol dependence and alcohol abuse. Quantity and frequency of drinking and drunkenness as well as usual number of drinks consumed during the last year. Setting Participants were 5,195 injured and non-injured patients attending 7 EDs in 4 countries, Argentina, Mexico, Poland the U.S., (between 1995-2001). Findings Using exploratory factor analyses alcohol use disorders can be described as a single, unidimensional continuum without any clear cut distinction between the criterions for dependence and abuse in all sites. Results from item response theory analyses showed that the current DSM-IV criterions tap people in the middle-upper end of the alcohol use disorder continuum. Alcohol consumption (amount and frequency of use) can be used in all EDs with the current DSM-IV diagnostic criterions to help tap the middle-lower part of this continuum. Even though some specific diagnostic criterions and some alcohol consumption variables showed differential item function across sites, test response curves were invariant for ED sites and their inclusion would not impact the final (total) performance of the diagnostic system. Conclusions DSM-IV abuse and dependence form a unidimensional continuum in ED patients regardless of country of survey. Alcohol consumption variables, if added, would help to tap patients with more moderate severity. DSM diagnostic system for alcohol use disorders showed invariance and performed extremely well in these samples. PMID:20078482

Short-Term and Long-Term Biological Effects of Chronic Chemical Contamination on Natural Populations of a Marine Bivalve.

PubMed

Breitwieser, Marine; Viricel, Amélia; Graber, Marianne; Murillo, Laurence; Becquet, Vanessa; Churlaud, Carine; Fruitier-Arnaudin, Ingrid; Huet, Valérie; Lacroix, Camille; Pante, Eric; Le Floch, Stéphane; Thomas-Guyon, Hélène

2016-01-01

Understanding the effects of chronic chemical contamination on natural populations of marine organisms is complex due to the combined effects of different types of pollutants and environmental parameters that can modulate the physiological responses to stress. Here, we present the effects of a chronic contamination in a marine bivalve by combining multiple approaches that provide information on individual and population health. We sampled variegated scallops (Mimachlamys varia) at sites characterized by different contaminants and contamination levels to study the short and long-term (intergenerational) responses of this species to physiological stress. We used biomarkers (SOD, MDA, GST, laccase, citrate synthase and phosphatases) as indicators of oxidative stress, immune system alteration, mitochondrial respiration and general metabolism, and measured population genetic diversity at each site. In parallel, concentration of 14 trace metals and 45 organic contaminants (PAHs, PCBs, pesticides) in tissues were measured. Scallops were collected outside and during their reproductive season to investigate temporal variability in contaminant and biomarker levels. Our analyses revealed that the levels of two biomarkers (Laccase-type phenoloxidase and malondialdehyde) were significantly correlated with Cd concentration. Additionally, we observed significant seasonal differences for four of the five biomarkers, which is likely due to the scallop reproductive status at time of sampling. As a source of concern, a location that was identified as a reference site on the basis of inorganic contaminant levels presented the same level of some persistent organic pollutants (DDT and its metabolites) than more impacted sites. Finally, potential long-term effects of heavy metal contamination were observed for variegated scallops as genetic diversity was depressed in the most polluted sites.

Organic pollution and its effects in the marine mussel Mytilus galloprovincialis in Eastern Mediterranean coasts.

PubMed

Kasiotis, Konstantinos M; Emmanouil, Christina; Anastasiadou, Pelagia; Papadi-Psyllou, Asimina; Papadopoulos, Antonis; Okay, Oya; Machera, Kyriaki

2015-01-01

Persistent chemicals and emerging pollutants are continuously detected in marine waters and biota. Out of these, polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCs) are significant contaminants with decades of presence in the marine environment. The Mediterranean Sea is an ecosystem directly affected by a variety of anthropogenic activities including industry, municipal, touristic, commercial and agricultural. The Mediterranean mussel (Mytilus galloprovincialis) is a filter feeder, which presents wide distribution. In this regard, the specific organism was used as a biological indicator for the monitoring and evaluation of pollution in the studied areas with focus on the mentioned chemical groups. Pristine Turkish sites with minimum effect from anthropogenic activities, in contrast with Greek sites which were subjected to heavy industrial and shipping activity, were selected. A gas chromatographic tandem mass spectrometric method (GC-MS/MS) was developed and validated to monitor 34 compounds (16 EPA priority PAHs and 18 OCs). Analyses of mussel samples in 2011 from sites with the limited anthropogenic pollution shores have shown the occurrence of 11 pollutants (6 PAHs, 5 OCs), while in the samples from sites with intensive activity and expected pollution, 12 PAHs and 6 OCs were detected. Biochemical and biological responses studied only in mussels samples from the sites with the highest contamination showed a situation that was under strong seasonal influence. The intensity of the response was also influenced by deployment duration. Noteworthy correlations were detected among biochemical/biological effects and between mussel body burden and these effects. Continuous monitoring of priority pollutants of East Mediterranean Sea is vital both for ecological and human risk assessment purposes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Relationships between lines of evidence of pollution in estuarine areas: Linking contaminant levels with biomarker responses in mussels and with structure of macroinvertebrate benthic communities.

PubMed

De Los Ríos, A; Echavarri-Erasun, B; Lacorte, S; Sánchez-Ávila, J; De Jonge, M; Blust, R; Orbea, A; Juanes, J A; Cajaraville, M P

2016-10-01

Data obtained in a pollution survey performed in estuarine areas were integrated using multivariate statistics. The sites selected for the study were areas affected by treated and untreated urban discharges, harbours or industrial activities as well as reference sites. Mussels were transplanted to each site and after different times of exposure, samples of water, sediments and mussels were collected. Biomarkers were analysed on mussels after 3 and 21 days of transplant whereas concentrations of contaminants were measured in water, sediments and mussels after 21 days of transplant. The structure of macroinvertebrate benthic communities was studied in sediment samples. Studied variables were organised into 5 datasets, each one constituting a line of evidence (LOE): contaminants in water, contaminants in sediments, contaminants accumulated by transplanted mussels, biomarkers in transplanted mussels and changes in the structure of macroinvertebrate benthic communities of each sampling site. Principal Component Analysis (PCA) identified the variables of each LOE best explaining variability among sites. In order to know how LOEs relate to each other, Pearson's correlations were performed. Contaminants in sediments were not correlated with the rest of LOEs. Contaminants in water were significantly correlated with contaminants and biomarkers in mussels and with structure of macroinvertebrate benthic communities. Similarly, significant correlations were found between contaminants and biomarkers in mussels and between biomarkers in mussels and structure of macroinvertebrate benthic communities. In conclusion, biomarker responses give relevant information on pollution in estuarine areas and provide a link between chemical and ecological statuses of water bodies in the context of the Water Framework Directive. Copyright © 2016 Elsevier Ltd. All rights reserved.

Short-Term and Long-Term Biological Effects of Chronic Chemical Contamination on Natural Populations of a Marine Bivalve

PubMed Central

Graber, Marianne; Murillo, Laurence; Becquet, Vanessa; Churlaud, Carine; Fruitier-Arnaudin, Ingrid; Huet, Valérie; Lacroix, Camille; Pante, Eric; Le Floch, Stéphane; Thomas-Guyon, Hélène

2016-01-01

Understanding the effects of chronic chemical contamination on natural populations of marine organisms is complex due to the combined effects of different types of pollutants and environmental parameters that can modulate the physiological responses to stress. Here, we present the effects of a chronic contamination in a marine bivalve by combining multiple approaches that provide information on individual and population health. We sampled variegated scallops (Mimachlamys varia) at sites characterized by different contaminants and contamination levels to study the short and long-term (intergenerational) responses of this species to physiological stress. We used biomarkers (SOD, MDA, GST, laccase, citrate synthase and phosphatases) as indicators of oxidative stress, immune system alteration, mitochondrial respiration and general metabolism, and measured population genetic diversity at each site. In parallel, concentration of 14 trace metals and 45 organic contaminants (PAHs, PCBs, pesticides) in tissues were measured. Scallops were collected outside and during their reproductive season to investigate temporal variability in contaminant and biomarker levels. Our analyses revealed that the levels of two biomarkers (Laccase-type phenoloxidase and malondialdehyde) were significantly correlated with Cd concentration. Additionally, we observed significant seasonal differences for four of the five biomarkers, which is likely due to the scallop reproductive status at time of sampling. As a source of concern, a location that was identified as a reference site on the basis of inorganic contaminant levels presented the same level of some persistent organic pollutants (DDT and its metabolites) than more impacted sites. Finally, potential long-term effects of heavy metal contamination were observed for variegated scallops as genetic diversity was depressed in the most polluted sites. PMID:26938082

Assessment of the implementation of a national patient safety alert to reduce wrong site surgery.

PubMed

Rhodes, P; Giles, S J; Cook, G A; Grange, A; Hayton, R; Maxwell, M J; Sheldon, T A; Wright, J

2008-12-01

In 2005, guidance on how to prevent wrong site surgery in the form of a national safety alert was issued to all NHS hospital trusts in England and Wales by the National Patient Safety Agency. To investigate the response to the alert among clinicians in England and Wales 12-15 months after it had been issued. A before-after study, using telephone/face-to-face interviews with consultant surgeons and senior nurses in ophthalmology, orthopaedics and urology in 11 NHS hospitals in England & Wales in the year prior to the alert and 12-15 months after. The interviews were coded and analysed thematically. The study revealed marked heterogeneity in organisational processes in response to a national alert. There was a significant change in surgeons' self-reported practice, with only 48% of surgeons routinely marking patients prior to the alert and 85% after (p<0.001). However, inter-specialty differences remained and change in practice was not always matched by change in attitude. Compliance with the detailed recommendations about how marking should be carried out was inconsistent. There were unintended consequences in terms of greater bureaucracy and concerns about diffusion of responsibility and hastily performed marking to enable release of patients from wards. The alert was effective in promoting presurgical marking and encouraging awareness of safety issues in relation to correct site surgery. However, care should be taken to monitor unintended consequences and whether change is sustained. Greater flexibility for local adaptation coupled with better design and early testing of safety alerts prior to national dissemination may facilitate more sustainable changes in practice.

Microgrid Selection and Operation for Commercial Buildings in California and New York States

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

Environmental Energy Technologies Division; Lacommare, Kristina S H; Marnay, Chris

The addition of storage technologies such as lead-acid batteries, flow batteries, or heat storage can potentially improve the economic and environmental attractiveness of on-site generation such as PV, fuel cells, reciprocating engines or microturbines (with or without CHP), and can contribute to enhanced demand response. Preliminary analyses for a Californian nursing home indicate that storage technologies respond effectively to time-varying electricity prices, i.e., by charging batteries during periods of low electricity prices and discharging them during peak hours. While economic results do not make a compelling case for storage, they indicate that storage technologies significantly alter the residual load profile,more » which may lower carbon emissions as well as energy costs depending on the test site, its load profile, and DER technology adoption.« less

Distance-responsive genes found in dancing honey bees.

PubMed

Sen Sarma, M; Rodriguez-Zas, S L; Gernat, T; Nguyen, T; Newman, T; Robinson, G E

2010-10-01

We report that regions of the honey bee brain involved in visual processing and learning and memory show a specific genomic response to distance information. These results were obtained with an established method that separates effects of perceived distance from effects of actual distance flown. Individuals forced to shift from a short to perceived long distance to reach a feeding site showed gene expression differences in the optic lobes and mushroom bodies relative to individuals that continued to perceive a short distance, even though they all flew the same distance. Bioinformatic analyses suggest that the genomic response to distance information involves learning and memory systems associated with well-known signaling pathways, synaptic remodeling, transcription factors and protein metabolism. By showing distance-sensitive brain gene expression, our findings also significantly extend the emerging paradigm of the genome as a dynamic regulator of behavior, that is particularly responsive to stimuli important in social life. © 2010 The Authors. Genes, Brain and Behavior © 2010 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.

Saccharomyces cerevisiae gene expression changes during rotating wall vessel suspension culture

NASA Technical Reports Server (NTRS)

Johanson, Kelly; Allen, Patricia L.; Lewis, Fawn; Cubano, Luis A.; Hyman, Linda E.; Hammond, Timothy G.

2002-01-01

This study utilizes Saccharomyces cerevisiae to study genetic responses to suspension culture. The suspension culture system used in this study is the high-aspect-ratio vessel, one type of the rotating wall vessel, that provides a high rate of gas exchange necessary for rapidly dividing cells. Cells were grown in the high-aspect-ratio vessel, and DNA microarray and metabolic analyses were used to determine the resulting changes in yeast gene expression. A significant number of genes were found to be up- or downregulated by at least twofold as a result of rotational growth. By using Gibbs promoter alignment, clusters of genes were examined for promoter elements mediating these genetic changes. Candidate binding motifs similar to the Rap1p binding site and the stress-responsive element were identified in the promoter regions of differentially regulated genes. This study shows that, as in higher order organisms, S. cerevisiae changes gene expression in response to rotational culture and also provides clues for investigations into the signaling pathways involved in gravitational response.

32 CFR Appendix A to Part 179 - Tables of the Munitions Response Site Prioritization Protocol

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 1 2010-07-01 2010-07-01 false Tables of the Munitions Response Site... OF DEFENSE CLOSURES AND REALIGNMENT MUNITIONS RESPONSE SITE PRIORITIZATION PROTOCOL (MRSPP) Pt. 179, App. A Appendix A to Part 179—Tables of the Munitions Response Site Prioritization Protocol The tables...

32 CFR Appendix A to Part 179 - Tables of the Munitions Response Site Prioritization Protocol

Code of Federal Regulations, 2012 CFR

2012-07-01

... 32 National Defense 1 2012-07-01 2012-07-01 false Tables of the Munitions Response Site... OF DEFENSE CLOSURES AND REALIGNMENT MUNITIONS RESPONSE SITE PRIORITIZATION PROTOCOL (MRSPP) Pt. 179, App. A Appendix A to Part 179—Tables of the Munitions Response Site Prioritization Protocol The tables...

32 CFR Appendix A to Part 179 - Tables of the Munitions Response Site Prioritization Protocol

Code of Federal Regulations, 2014 CFR

2014-07-01

... 32 National Defense 1 2014-07-01 2014-07-01 false Tables of the Munitions Response Site... OF DEFENSE CLOSURES AND REALIGNMENT MUNITIONS RESPONSE SITE PRIORITIZATION PROTOCOL (MRSPP) Pt. 179, App. A Appendix A to Part 179—Tables of the Munitions Response Site Prioritization Protocol The tables...

32 CFR Appendix A to Part 179 - Tables of the Munitions Response Site Prioritization Protocol

Code of Federal Regulations, 2011 CFR

2011-07-01

... 32 National Defense 1 2011-07-01 2011-07-01 false Tables of the Munitions Response Site... OF DEFENSE CLOSURES AND REALIGNMENT MUNITIONS RESPONSE SITE PRIORITIZATION PROTOCOL (MRSPP) Pt. 179, App. A Appendix A to Part 179—Tables of the Munitions Response Site Prioritization Protocol The tables...

32 CFR Appendix A to Part 179 - Tables of the Munitions Response Site Prioritization Protocol

Code of Federal Regulations, 2013 CFR

2013-07-01

... 32 National Defense 1 2013-07-01 2013-07-01 false Tables of the Munitions Response Site... OF DEFENSE CLOSURES AND REALIGNMENT MUNITIONS RESPONSE SITE PRIORITIZATION PROTOCOL (MRSPP) Pt. 179, App. A Appendix A to Part 179—Tables of the Munitions Response Site Prioritization Protocol The tables...

Psychometric Analysis of the Revised Memory and Behavior Problems Checklist: Factor Structure of Occurrence and Reaction Ratings

PubMed Central

Roth, David L.; Gitlin, Laura N.; Coon, David W.; Stevens, Alan B.; Burgio, Louis D.; Gallagher-Thompson, Dolores; Belle, Steven H.; Burns, Robert

2008-01-01

A modified version of the Revised Memory and Behavior Problems Checklist (RMBPC; L. Teri et al., 1992) was administered across 6 different sites to 1,229 family caregivers of community-dwelling adults with dementia. The total sample was divided randomly into 2 subsamples. Principal components analyses on occurrence responses and reaction ratings from the first subsample resulted in a 3-factor solution that closely resembled the originally proposed dimensions (memory-related problems, disruptive behaviors, and depression). Confirmatory factor analyses on data from the second subsample indicated adequate fit for the 3-factor model. Correlations with other caregiver and care-recipient measures supported the convergent and discriminant validity of the RMBPC measures. In addition, female caregivers and White caregivers reported more problems, on average, than male caregivers and African American caregivers, respectively. PMID:14692875

High-Explosives Applications Facility (HEAF)

NASA Astrophysics Data System (ADS)

Morse, J. L.; Weingart, R. C.

1989-03-01

This Safety Analysis Report (SAR) reviews the safety and environmental aspects of the High Explosives Applications Facility (HEAF). Topics covered include the site selected for the HEAF, safety design criteria, operations planned within the facility, and the safety and environmental analyses performed on this project to date. Provided in the Summary section is a review of hazards and the analyses, conclusions, and operating limits developed in this SAR. Appendices provide supporting documents relating to this SAR. This SAR is required by the LLNL Health and Safety Manual and DOE Order 5481.1B(2) to document the safety analysis efforts. The SAR was assembled by the Hazards Control Department, B-Division, and HEAF project personnel. This document was reviewed by B Division, the Chemistry Department, the Hazards Control Department, the Laboratory Associate Director for Administration and Operations, and the Associate Directors ultimately responsible for HEAF operations.

Disaggregated seismic hazard and the elastic input energy spectrum: An approach to design earthquake selection

NASA Astrophysics Data System (ADS)

Chapman, Martin Colby

1998-12-01

The design earthquake selection problem is fundamentally probabilistic. Disaggregation of a probabilistic model of the seismic hazard offers a rational and objective approach that can identify the most likely earthquake scenario(s) contributing to hazard. An ensemble of time series can be selected on the basis of the modal earthquakes derived from the disaggregation. This gives a useful time-domain realization of the seismic hazard, to the extent that a single motion parameter captures the important time-domain characteristics. A possible limitation to this approach arises because most currently available motion prediction models for peak ground motion or oscillator response are essentially independent of duration, and modal events derived using the peak motions for the analysis may not represent the optimal characterization of the hazard. The elastic input energy spectrum is an alternative to the elastic response spectrum for these types of analyses. The input energy combines the elements of amplitude and duration into a single parameter description of the ground motion that can be readily incorporated into standard probabilistic seismic hazard analysis methodology. This use of the elastic input energy spectrum is examined. Regression analysis is performed using strong motion data from Western North America and consistent data processing procedures for both the absolute input energy equivalent velocity, (Vsbea), and the elastic pseudo-relative velocity response (PSV) in the frequency range 0.5 to 10 Hz. The results show that the two parameters can be successfully fit with identical functional forms. The dependence of Vsbea and PSV upon (NEHRP) site classification is virtually identical. The variance of Vsbea is uniformly less than that of PSV, indicating that Vsbea can be predicted with slightly less uncertainty as a function of magnitude, distance and site classification. The effects of site class are important at frequencies less than a few Hertz. The regression modeling does not resolve significant effects due to site class at frequencies greater than approximately 5 Hz. Disaggregation of general seismic hazard models using Vsbea indicates that the modal magnitudes for the higher frequency oscillators tend to be larger, and vary less with oscillator frequency, than those derived using PSV. Insofar as the elastic input energy may be a better parameter for quantifying the damage potential of ground motion, its use in probabilistic seismic hazard analysis could provide an improved means for selecting earthquake scenarios and establishing design earthquakes for many types of engineering analyses.

Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay.

PubMed

Jiang, Peng; Singh, Mona; Coller, Hilary A

2013-01-01

Transcript degradation is a widespread and important mechanism for regulating protein abundance. Two major regulators of transcript degradation are RNA Binding Proteins (RBPs) and microRNAs (miRNAs). We computationally explored whether RBPs and miRNAs cooperate to promote transcript decay. We defined five RBP motifs based on the evolutionary conservation of their recognition sites in 3'UTRs as the binding motifs for Pumilio (PUM), U1A, Fox-1, Nova, and UAUUUAU. Recognition sites for some of these RBPs tended to localize at the end of long 3'UTRs. A specific group of miRNA recognition sites were enriched within 50 nts from the RBP recognition sites for PUM and UAUUUAU. The presence of both a PUM recognition site and a recognition site for preferentially co-occurring miRNAs was associated with faster decay of the associated transcripts. For PUM and its co-occurring miRNAs, binding of the RBP to its recognition sites was predicted to release nearby miRNA recognition sites from RNA secondary structures. The mammalian miRNAs that preferentially co-occur with PUM binding sites have recognition seeds that are reverse complements to the PUM recognition motif. Their binding sites have the potential to form hairpin secondary structures with proximal PUM binding sites that would normally limit RISC accessibility, but would be more accessible to miRNAs in response to the binding of PUM. In sum, our computational analyses suggest that a specific set of RBPs and miRNAs work together to affect transcript decay, with the rescue of miRNA recognition sites via RBP binding as one possible mechanism of cooperativity.

Effects of selective logging on bat communities in the southeastern Amazon.

PubMed

Peters, Sandra L; Malcolm, Jay R; Zimmerman, Barbara L

2006-10-01

Although extensive areas of tropical forest are selectively logged each year, the responses of bat communities to this form of disturbance have rarely been examined. Our objectives were to (1) compare bat abundance, species composition, and feeding guild structure between unlogged and low-intensity selectively logged (1-4 logged stems/ha) sampling grids in the southeastern Amazon and (2) examine correlations between logging-induced changes in bat communities and forest structure. We captured bats in understory and canopy mist nets set in five 1-ha study grids in both logged and unlogged forest. We captured 996 individuals, representing 5 families, 32 genera, and 49 species. Abundances of nectarivorous and frugivorous taxa (Glossophaginae, Lonchophyllinae, Stenodermatinae, and Carolliinae) were higher at logged sites, where canopy openness and understory foliage density were greatest. In contrast, insectivorous and omnivorous species (Emballonuridae, Mormoopidae, Phyllostominae, and Vespertilionidae) were more abundant in unlogged sites, where canopy foliage density and variability in the understory stratum were greatest. Multivariate analyses indicated that understory bat species composition differed strongly between logged and unlogged sites but provided little evidence of logging effects for the canopy fauna. Different responses among feeding guilds and taxonomic groups appeared to be related to foraging and echolocation strategies and to changes in canopy cover and understory foliage densities. Our results suggest that even low-intensity logging modifies habitat structure, leading to changes in bat species composition.

Using community-level metrics to monitor the effects of marine protected areas on biodiversity.

PubMed

Soykan, Candan U; Lewison, Rebecca L

2015-06-01

Marine protected areas (MPAs) are used to protect species, communities, and their associated habitats, among other goals. Measuring MPA efficacy can be challenging, however, particularly when considering responses at the community level. We gathered 36 abundance and 14 biomass data sets on fish assemblages and used meta-analysis to evaluate the ability of 22 distinct community diversity metrics to detect differences in community structure between MPAs and nearby control sites. We also considered the effects of 6 covariates-MPA size and age, MPA size and age interaction, latitude, total species richness, and level of protection-on each metric. Some common metrics, such as species richness and Shannon diversity, did not differ consistently between MPA and control sites, whereas other metrics, such as total abundance and biomass, were consistently different across studies. Metric responses derived from the biomass data sets were more consistent than those based on the abundance data sets, suggesting that community-level biomass differs more predictably than abundance between MPA and control sites. Covariate analyses indicated that level of protection, latitude, MPA size, and the interaction between MPA size and age affect metric performance. These results highlight a handful of metrics, several of which are little known, that could be used to meet the increasing demand for community-level indicators of MPA effectiveness. © 2015 Society for Conservation Biology.

CO{sub 2} Sequestration Capacity and Associated Aspects of the Most Promising Geologic Formations in the Rocky Mountain Region: Local-Scale Analyses

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

Laes, Denise; Eisinger, Chris; Morgan, Craig

2013-07-30

The purpose of this report is to provide a summary of individual local-­scale CCS site characterization studies conducted in Colorado, New Mexico and Utah. These site-­ specific characterization analyses were performed as part of the “Characterization of Most Promising Sequestration Formations in the Rocky Mountain Region” (RMCCS) project. The primary objective of these local-­scale analyses is to provide a basis for regional-­scale characterization efforts within each state. Specifically, limits on time and funding will typically inhibit CCS projects from conducting high-­ resolution characterization of a state-­sized region, but smaller (< 10,000 km{sup 2}) site analyses are usually possible, and suchmore » can provide insight regarding limiting factors for the regional-­scale geology. For the RMCCS project, the outcomes of these local-­scale studies provide a starting point for future local-­scale site characterization efforts in the Rocky Mountain region.« less

Discovering biomarkers for antidepressant response: protocol from the Canadian biomarker integration network in depression (CAN-BIND) and clinical characteristics of the first patient cohort.

PubMed

Lam, Raymond W; Milev, Roumen; Rotzinger, Susan; Andreazza, Ana C; Blier, Pierre; Brenner, Colleen; Daskalakis, Zafiris J; Dharsee, Moyez; Downar, Jonathan; Evans, Kenneth R; Farzan, Faranak; Foster, Jane A; Frey, Benicio N; Geraci, Joseph; Giacobbe, Peter; Feilotter, Harriet E; Hall, Geoffrey B; Harkness, Kate L; Hassel, Stefanie; Ismail, Zahinoor; Leri, Francesco; Liotti, Mario; MacQueen, Glenda M; McAndrews, Mary Pat; Minuzzi, Luciano; Müller, Daniel J; Parikh, Sagar V; Placenza, Franca M; Quilty, Lena C; Ravindran, Arun V; Salomons, Tim V; Soares, Claudio N; Strother, Stephen C; Turecki, Gustavo; Vaccarino, Anthony L; Vila-Rodriguez, Fidel; Kennedy, Sidney H

2016-04-16

Major Depressive Disorder (MDD) is among the most prevalent and disabling medical conditions worldwide. Identification of clinical and biological markers ("biomarkers") of treatment response could personalize clinical decisions and lead to better outcomes. This paper describes the aims, design, and methods of a discovery study of biomarkers in antidepressant treatment response, conducted by the Canadian Biomarker Integration Network in Depression (CAN-BIND). The CAN-BIND research program investigates and identifies biomarkers that help to predict outcomes in patients with MDD treated with antidepressant medication. The primary objective of this initial study (known as CAN-BIND-1) is to identify individual and integrated neuroimaging, electrophysiological, molecular, and clinical predictors of response to sequential antidepressant monotherapy and adjunctive therapy in MDD. CAN-BIND-1 is a multisite initiative involving 6 academic health centres working collaboratively with other universities and research centres. In the 16-week protocol, patients with MDD are treated with a first-line antidepressant (escitalopram 10-20 mg/d) that, if clinically warranted after eight weeks, is augmented with an evidence-based, add-on medication (aripiprazole 2-10 mg/d). Comprehensive datasets are obtained using clinical rating scales; behavioural, dimensional, and functioning/quality of life measures; neurocognitive testing; genomic, genetic, and proteomic profiling from blood samples; combined structural and functional magnetic resonance imaging; and electroencephalography. De-identified data from all sites are aggregated within a secure neuroinformatics platform for data integration, management, storage, and analyses. Statistical analyses will include multivariate and machine-learning techniques to identify predictors, moderators, and mediators of treatment response. From June 2013 to February 2015, a cohort of 134 participants (85 outpatients with MDD and 49 healthy participants) has been evaluated at baseline. The clinical characteristics of this cohort are similar to other studies of MDD. Recruitment at all sites is ongoing to a target sample of 290 participants. CAN-BIND will identify biomarkers of treatment response in MDD through extensive clinical, molecular, and imaging assessments, in order to improve treatment practice and clinical outcomes. It will also create an innovative, robust platform and database for future research. ClinicalTrials.gov identifier NCT01655706 . Registered July 27, 2012.

Epigenetic and genetic variation among three separate introductions of the house sparrow (Passer domesticus) into Australia

PubMed Central

Schrey, A.; Ragsdale, A.; Griffith, S. C.

2018-01-01

Invasive populations are often associated with low levels of genetic diversity owing to population bottlenecks at the initial stages of invasion. Despite this, the ability of invasive species to adapt rapidly in response to novel environments is well documented. Epigenetic mechanisms have recently been proposed to facilitate the success of invasive species by compensating for reduced levels of genetic variation. Here, we use methylation sensitive-amplification fragment length polymorphism and microsatellite analyses to compare levels of epigenetic and genetic diversity and differentiation across 15 sites in the introduced Australian house sparrow population. We find patterns of epigenetic and genetic differentiation that are consistent with historical descriptions of three distinct, introductions events. However unlike genetic differentiation, epigenetic differentiation was higher among sample sites than among invasion clusters, suggesting that patterns of epigenetic variation are more strongly influenced by local environmental stimuli or sequential founder events than the initial diversity in the introduction population. Interestingly, we fail to detect correlations between pairwise site comparisons of epigenetic and genetic differentiation, suggesting that some of the observed epigenetic variation has arisen independently of genetic variation. We also fail to detect the potentially compensatory relationship between epigenetic and genetic diversity that has been detected in a more recent house sparrow invasion in Africa. We discuss the potential for this relationship to be obscured by recovered genetic diversity in more established populations, and highlight the importance of incorporating introduction history into population-wide epigenetic analyses. PMID:29765671

Vaccines and Internet: characteristics of the vaccine safety net web sites and suggested improvements.

PubMed

Martínez-Mora, Marta; Alvarez-Pasquín, María José; Rodríguez-Salvanés, Francisco

2008-12-09

The Internet contains a large amount of useful information on many subjects, but also information of doubtful quality. To help identify Web sites on vaccine safety that fulfil good practice, the Global Advisory Committee on Vaccine Safety of the World Health Organization (WHO) has published criteria to which sites should adhere and a listing of Web sites that fulfil them. There are no studies describing the common attributes of these sites. To examine the attributes, design characteristics and resources of Web sites belonging to the Vaccine Safety Net (VSN) of the WHO. A cross-sectional, descriptive observational study using an evaluation questionnaire was carried out applied to the VSN web sites listed in March-April 2007. Twenty-six Web sites accredited by the VSN by April 2007 were analysed. With respect to design and quality, all sites contained information about the site manager. Postal and Email addresses were available for 84.6% of the sites. About privacy and personal data processing, 73.1% of sites specified the data protection procedure used and stated that data were not sold or passed third parties. The most-used language was English (76.9%). 96.3% of sites had links to other pro-vaccination sites and 19.2% provided the addresses of vaccination centres. 63.6% of webs were aimed at general public and health care workers but there was no clear separation of documents or different entry routes. With respect to information on vaccine safety, 84.6% of sites had information on adverse effects. In the general information section, 92.3% of sites had a new developments section. Some sites had multiple sources of financing and in 57% of sites, the financing was public. The most-important plus factors found were the transparency of financing, the lack of links to the pharmaceutical industry, the transparency of site management and responsibility and the proven scientific quality and constant updating of contents.

Molecular and genetic ecotoxicologic approaches to aquatic environmental bioreporting.

PubMed Central

Beaty, B J; Black, W C; Carlson, J O; Clements, W H; DuTeau, N; Harrahy, E; Nuckols, J; Kenneth, E; Olson, K E; Rayms-Keller, A

1998-01-01

Molecular and population genetic ecotoxicologic approaches are being developed for the utilization of arthropods as bioreporters of heavy metal mixtures in the environment. The explosion of knowledge in molecular biology, molecular genetics, and biotechnology provides an unparalleled opportunity to use arthropods as bioreporter organisms. Interspecific differences in aquatic arthropod populations have been previously demonstrated in response to heavy metal insult in the Arkansas River (AR) California Gulch Superfund site (CGSS). Population genetic analyses were conducted on the mayfly Baetis tricaudatus. Genetic polymorphisms were detected in polymerase chain reaction amplified 16S mitochondrial rDNA (a selectively neutral gene) of B tricaudatus using single-strand conformation polymorphism analysis. Genetic differences may have resulted from impediments to gene flow in the population caused by mortality arising from exposure to heavy metal mixture pollution. In laboratory studies a candidate metal-responsive mucinlike gene, which is metal and dose specific, has been identified in Chironomus tentans and other potential AR-CGSS bioreporter species. Population genetic analyses using the mucinlike gene may provide insight into the role of this selectable gene in determining the breeding structure of B. tricaudatus in the AR-CGSS and may provide mechanistic insight into determinants of aquatic arthropod response to heavy metal insult. Metal-responsive (MR) genes and regulatory sequences are being isolated, characterized, and assayed for differential gene expression in response to heavy metal mixture pollution in the AR-CGSS. Identified promoter sequences can then be engineered into previously developed MR constructs to provide sensitive in vitro assays for environmental bioreporting of heavy metal mixtures. The results of the population genetic studies are being entered into an AR geographic information system that contains substantial biological, chemical, and geophysical information. Integrated spatial, structural, and temporal analyses of these parameters will provide invaluable information concerning environmental determinants that restrict or promote gene flow in bioreporter populations. Images Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 PMID:9860898

Plant-Pathogenic Oomycetes, Escherichia coli Strains, and Salmonella spp. Frequently Found in Surface Water Used for Irrigation of Fruit and Vegetable Crops in New York State

PubMed Central

Jones, Lisa A.; Worobo, Randy W.

2014-01-01

In the United States, surface water is commonly used to irrigate a variety of produce crops and can harbor pathogens responsible for food-borne illnesses and plant diseases. Understanding when pathogens infest water sources is valuable information for produce growers to improve the food safety and production of these crops. In this study, prevalence data along with regression tree analyses were used to correlate water quality parameters (pH, temperature, turbidity), irrigation site properties (source, the presence of livestock or fowl nearby), and precipitation data to the presence and concentrations of Escherichia coli, Salmonella spp., and hymexazol-insensitive (HIS) oomycetes (Phytophthora and Pythium spp.) in New York State surface waters. A total of 123 samples from 18 sites across New York State were tested for E. coli and Salmonella spp., of which 33% and 43% were positive, respectively. Additionally, 210 samples from 38 sites were tested for HIS oomycetes, and 88% were found to be positive, with 10 species of Phytophthora and 11 species of Pythium being identified from the samples. Regression analysis found no strong correlations between water quality parameters, site factors, or precipitation to the presence or concentration of E. coli in irrigation sources. For Salmonella, precipitation (≤0.64 cm) 3 days before sampling was correlated to both presence and the highest counts. Analyses for oomycetes found creeks to have higher average counts than ponds, and higher turbidity levels were associated with higher oomycete counts. Overall, information gathered from this study can be used to better understand the food safety and plant pathogen risks of using surface water for irrigation. PMID:24878603

Development and evaluation of human AP endonuclease inhibitors in melanoma and glioma cell lines.

PubMed

Mohammed, M Z; Vyjayanti, V N; Laughton, C A; Dekker, L V; Fischer, P M; Wilson, D M; Abbotts, R; Shah, S; Patel, P M; Hickson, I D; Madhusudan, S

2011-02-15

Modulation of DNA base excision repair (BER) has the potential to enhance response to chemotherapy and improve outcomes in tumours such as melanoma and glioma. APE1, a critical protein in BER that processes potentially cytotoxic abasic sites (AP sites), is a promising new target in cancer. In the current study, we aimed to develop small molecule inhibitors of APE1 for cancer therapy. An industry-standard high throughput virtual screening strategy was adopted. The Sybyl8.0 (Tripos, St Louis, MO, USA) molecular modelling software suite was used to build inhibitor templates. Similarity searching strategies were then applied using ROCS 2.3 (Open Eye Scientific, Santa Fe, NM, USA) to extract pharmacophorically related subsets of compounds from a chemically diverse database of 2.6 million compounds. The compounds in these subsets were subjected to docking against the active site of the APE1 model, using the genetic algorithm-based programme GOLD2.7 (CCDC, Cambridge, UK). Predicted ligand poses were ranked on the basis of several scoring functions. The top virtual hits with promising pharmaceutical properties underwent detailed in vitro analyses using fluorescence-based APE1 cleavage assays and counter screened using endonuclease IV cleavage assays, fluorescence quenching assays and radiolabelled oligonucleotide assays. Biochemical APE1 inhibitors were then subjected to detailed cytotoxicity analyses. Several specific APE1 inhibitors were isolated by this approach. The IC(50) for APE1 inhibition ranged between 30 nM and 50 μM. We demonstrated that APE1 inhibitors lead to accumulation of AP sites in genomic DNA and potentiated the cytotoxicity of alkylating agents in melanoma and glioma cell lines. Our study provides evidence that APE1 is an emerging drug target and could have therapeutic application in patients with melanoma and glioma.

Ash cap influences on site productivity and fertilizer response in forests of the Inland Northwest

Treesearch

Mariann T. Garrison-Johnston; Peter G. Mika; Dan L. Miller; Phil Cannon; Leonard R. Johnson

2007-01-01

Data from 139 research sites throughout the Inland Northwest were analyzed for effects of ash cap on site productivity, nutrient availability and fertilization response. Stand productivity and nitrogen (N) fertilizer response were greater on sites with ash cap than on sites without. Where ash was present, depth of ash had no effect on site productivity or N fertilizer...

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

Tyrrell, Evan; Denny, Angelita

Fifty-two groundwater samples and one surface water sample were collected at the Monument Valley, Arizona, Processing Site to monitor groundwater contaminants for evaluating the effectiveness of the proposed compliance strategy as specified in the 1999 Final Site Observational Work Plan for the UMTRA Project Site at Monument Valley, Arizona. Sampling and analyses were conducted as specified in the Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated, http://energy.gov/lm/downloads/sampling-and-analysis-plan-us-department- energy-office-legacy-management-sites). Samples were collected for metals, anions, nitrate + nitrite as N, and ammonia as N analyses at all locations.

Evolution of nonspectral rhodopsin function at high altitudes.

PubMed

Castiglione, Gianni M; Hauser, Frances E; Liao, Brian S; Lujan, Nathan K; Van Nynatten, Alexander; Morrow, James M; Schott, Ryan K; Bhattacharyya, Nihar; Dungan, Sarah Z; Chang, Belinda S W

2017-07-11

High-altitude environments present a range of biochemical and physiological challenges for organisms through decreases in oxygen, pressure, and temperature relative to lowland habitats. Protein-level adaptations to hypoxic high-altitude conditions have been identified in multiple terrestrial endotherms; however, comparable adaptations in aquatic ectotherms, such as fishes, have not been as extensively characterized. In enzyme proteins, cold adaptation is attained through functional trade-offs between stability and activity, often mediated by substitutions outside the active site. Little is known whether signaling proteins [e.g., G protein-coupled receptors (GPCRs)] exhibit natural variation in response to cold temperatures. Rhodopsin (RH1), the temperature-sensitive visual pigment mediating dim-light vision, offers an opportunity to enhance our understanding of thermal adaptation in a model GPCR. Here, we investigate the evolution of rhodopsin function in an Andean mountain catfish system spanning a range of elevations. Using molecular evolutionary analyses and site-directed mutagenesis experiments, we provide evidence for cold adaptation in RH1. We find that unique amino acid substitutions occur at sites under positive selection in high-altitude catfishes, located at opposite ends of the RH1 intramolecular hydrogen-bonding network. Natural high-altitude variants introduced into these sites via mutagenesis have limited effects on spectral tuning, yet decrease the stability of dark-state and light-activated rhodopsin, accelerating the decay of ligand-bound forms. As found in cold-adapted enzymes, this phenotype likely compensates for a cold-induced decrease in kinetic rates-properties of rhodopsin that mediate rod sensitivity and visual performance. Our results support a role for natural variation in enhancing the performance of GPCRs in response to cold temperatures.

Optimal mapping of site-specific multivariate soil properties.

PubMed

Burrough, P A; Swindell, J

1997-01-01

This paper demonstrates how geostatistics and fuzzy k-means classification can be used together to improve our practical understanding of crop yield-site response. Two aspects of soil are important for precision farming: (a) sensible classes for a given crop, and (b) their spatial variation. Local site classifications are more sensitive than general taxonomies and can be provided by the method of fuzzy k-means to transform a multivariate data set with i attributes measured at n sites into k overlapping classes; each site has a membership value mk for each class in the range 0-1. Soil variation is of interest when conditions vary over patches manageable by agricultural machinery. The spatial variation of each of the k classes can be analysed by computing the variograms of mk over the n sites. Memberships for each of the k classes can be mapped by ordinary kriging. Areas of class dominance and the transition zones between them can be identified by an inter-class confusion index; reducing the zones to boundaries gives crisp maps of dominant soil groups that can be used to guide precision farming equipment. Automation of the procedure is straightforward given sufficient data. Time variations in soil properties can be automatically incorporated in the computation of membership values. The procedures are illustrated with multi-year crop yield data collected from a 5 ha demonstration field at the Royal Agricultural College in Cirencester, UK.

Structural and functional analysis of mouse Msx1 gene promoter: sequence conservation with human MSX1 promoter points at potential regulatory elements.

PubMed

Gonzalez, S M; Ferland, L H; Robert, B; Abdelhay, E

1998-06-01

Vertebrate Msx genes are related to one of the most divergent homeobox genes of Drosophila, the muscle segment homeobox (msh) gene, and are expressed in a well-defined pattern at sites of tissue interactions. This pattern of expression is conserved in vertebrates as diverse as quail, zebrafish, and mouse in a range of sites including neural crest, appendages, and craniofacial structures. In the present work, we performed structural and functional analyses in order to identify potential cis-acting elements that may be regulating Msx1 gene expression. To this end, a 4.9-kb segment of the 5'-flanking region was sequenced and analyzed for transcription-factor binding sites. Four regions showing a high concentration of these sites were identified. Transfection assays with fragments of regulatory sequences driving the expression of the bacterial lacZ reporter gene showed that a region of 4 kb upstream of the transcription start site contains positive and negative elements responsible for controlling gene expression. Interestingly, a fragment of 130 bp seems to contain the minimal elements necessary for gene expression, as its removal completely abolishes gene expression in cultured cells. These results are reinforced by comparison of this region with the human Msx1 gene promoter, which shows extensive conservation, including many consensus binding sites, suggesting a regulatory role for them.

In vitro transcription in the presence of DNA oligonucleotides can generate strong anomalous initiation sites.

PubMed

Chow, C W; Clark, M P; Rinaldo, J E; Chalkley, R

1996-03-01

In the present study, we have explored an unexpected observation in transcription initiation that is mediated by single-stranded oligonucleotides. Initially, our goal was to understand the function of different upstream regulatory elements/initiation sites in the rat xanthine dehydrogenase/oxidase (XDH/XO) promoter. We performed in vitro transcription with HeLa nuclear extracts in the presence of different double-stranded oligonucleotides against upstream elements as competitors. A new and unusual transcription initiation site was detected by primer extension. This new initiation site maps to the downstream region of the corresponding competitor. Subsequent analyses have indicated that the induction of a new transcription initiation site is anomalous which is due to the presence of a small amount of single-stranded oligonucleotide in the competitor. We found that this anomalous initiation site is insensitive to the orientation of the promoter and requires only a small amount of single-stranded oligonucleotide (< 2-fold molar excess relative to template). We surmise that a complementary interaction between the single-stranded oligonucleotide and transiently denatured promoter template may be responsible for this sequence-specific transcription initiation artifact. To study the regulation of transcription initiation by in vitro transcription approaches, we propose that one should probe the effect of removing transacting factors by adding an excess of a cognate oligonucleotide which does not bear exact sequence identity to the template.

Investigation of Nonlinear Site Response and Seismic Compression from Case History Analysis and Laboratory Testing

NASA Astrophysics Data System (ADS)

Yee, Eric

In this thesis I address a series of issues related to ground failure and ground motions during earthquakes. A major component is the evaluation of cyclic volumetric strain behavior of unsaturated soils, more commonly known as seismic compression, from advanced laboratory testing. Another major component is the application of nonlinear and equivalent linear ground response analyses to large-strain problems involving highly nonlinear dynamic soil behavior. These two components are merged in the analysis of a truly unique and crucial field case history of nonlinear site response and seismic compression. My first topic concerns dynamic soil testing for relatively small strain dynamic soil properties such as threshold strains, gammatv. Such testing is often conducted using specialized devices such as dual-specimen simple-shear, as devices configured for large strain testing produce noisy signals in the small strain range. Working with a simple shear device originally developed for large-strain testing, I extend its low-strain capabilities by characterizing noisy signals and utilizing several statistical methods to extract meaningful responses in the small strain range. I utilize linear regression of a transformed variable to estimate the cyclic shear strain from a noisy signal and the confidence interval on its amplitude. I utilize Kernel regression with the Nadaraya-Watson estimator and a Gaussian kernel to evaluate vertical strain response. A practical utilization of these techniques is illustrated by evaluating threshold shear strains for volume change with a procedure that takes into account uncertainties in the measured shear and vertical strains. My second topic concerns the seismic compression characteristics of non-plastic and low-plasticity silty sands with varying fines content (10 ≤ FC ≤ 60%). Simple shear testing was performed on various sand-fines mixtures at a range of modified Proctor relative compaction levels ( RC) and degrees-of-saturation (S). Aside from the expected strong influence of RC, increasing fines content is found to generally decrease volume change for fines fractions consisting of silts and clayey silts with moderate to low plasticity. With truly non-plastic fines (rock flour), cyclic volume change increases with FC. Some materials also exhibit an effect of as-compacted saturation in which moderate saturation levels associated with high matric suction cause volume change to decrease. A preliminary empirical model to capture these effects is presented. The balance of the dissertation is related to a case history of strongly nonlinear site response and seismic compression associated with a free-field downhole array installed near the Service Hall at the Kashiwazaki-Kariwa nuclear power plant, which recorded strong ground motions from the Mw 6.6 2007 Niigata-ken Chuetsu-oki earthquake. Site conditions at the array consist of about 70 m of medium-dense sands overlying clayey bedrock, with ground water located at 45 m. Ground shaking at the bedrock level had geometric mean peak accelerations of 0.55 g which is reduced to 0.4 g at the ground surface, indicating nonlinear site response. Ground settlements of approximately 15+/-5 cm occurred at the site. A site investigation was performed to develop relevant soil properties for ground response and seismic compression analysis, including shear wave velocities, shear strength, relative density, and modulus reduction and damping curves. (Abstract shortened by UMI.)

Changes in Nannoplankton Assemblages during the recovery of the Paleocene Eocene Thermal Maximum (PETM)

NASA Astrophysics Data System (ADS)

Grey, J. A.; Bralower, T. J.; Self-Trail, J. M.

2016-12-01

The recovery interval of the Paleocene Eocene Thermal Maximum (PETM) presents an opportunity to examine how organisms adapt to environmental change after a rapid global warming event. Calcareous nannoplankton survived the PETM, but we lack an understanding of how long it took for assemblages to adapt to a changing climate and the millennial-scale changes in their ecology. Here, we present the first high-resolution record of nannoplankton community change during the PETM recovery using a global data set (United States Geological Survey (USGS) Wilson Lake core, USGS Cam-Dor core, Ocean Drilling Program (ODP) Sites 690, 1265, and 1209) to assess millennial-scale assemblage change across space and time. Preliminary multivariate analyses on assemblage changes at Wilson Lake demonstrate that within 20,000 years after the onset, the structure of nannoplankton communities shifts from an assemblage dominated by warm eutrophic specialists to one dominated by eutrophic low salinity specialists. In the late recovery, ubiquitous taxa dominate assemblages, suggesting that the shelf environment became favorable for generalists. The latest part of the recovery is marked by a slight increase in oligotrophic specialists, indicating that the shelf became less eutrophic into the early Eocene. Overall, these analyses suggest that assemblages changed rapidly in response to cooling and changing ocean circulation during the early recovery of the PETM. Future analyses will build on these data by comparing assemblage change from other PETM coastal and open ocean sites. These analyses will help us better understand the spatial and temporal changes of nannoplankton communities on a global scale, lessons that can inform how nannoplankton will respond to future climate change.

Serum autoantibodies directed against transglutaminase-2 have a low avidity compared with alloantibodies against gliadin in coeliac disease.

PubMed

Gelderman, K A; Drop, A C A D; Trouw, L A; Bontkes, H J; Bouma, G; van Hoogstraten, I M W; von Blomberg, B M E

2014-07-01

Coeliac disease is characterized by intolerance to gliadin and related gluten components present in wheat, barley and rye. Coeliac disease patients harbour antibodies directed against alloantigens such as gliadin, but also against the autoantigen transglutaminase-2 (TG2). The type and quality of antibody responses provides insight into the underlying immune activation processes. Therefore, in this study we have analysed the avidity of the antibody response directed against the autoantigen TG2 and compared this with antibody responses against the alloantigens gliadin and Escherichia coli. We observed that the immunoglobulin (Ig)A autoantibody response directed against TG2 is of low avidity compared with the IgA response against the alloantigens gliadin and E. coli in the same patients; the same was true for IgG, both in IgA-deficient and in -sufficient coeliac patients. The observed avidities appear not to be related to disease stage, antibody levels, age or duration of exposure to gluten. In conclusion, in coeliac disease there is a clear difference in avidity of the antibody responses directed against the auto- and alloantigens, indicating different regulation or site of initiation of these responses. © 2014 British Society for Immunology.

Characterizing phosphorus speciation of Chesapeake Bay sediments using chemical extraction, 31P NMR, and X-ray absorption fine structure spectroscopy.

PubMed

Li, Wei; Joshi, Sunendra R; Hou, Guangjin; Burdige, David J; Sparks, Donald L; Jaisi, Deb P

2015-01-06

Nutrient contamination has been one of the lingering issues in the Chesapeake Bay because the bay restoration is complicated by temporally and seasonally variable nutrient sources and complex interaction between imported and regenerated nutrients. Differential reactivity of sedimentary phosphorus (P) pools in response to imposed biogeochemical conditions can record past sediment history and therefore a detailed sediment P speciation may provide information on P cycling particularly the stability of a P pool and the formation of one pool at the expense of another. This study examined sediment P speciation from three sites in the Chesapeake Bay: (i) a North site in the upstream bay, (ii) a middle site in the central bay dominated by seasonally hypoxic bottom water, and (iii) a South site at the bay-ocean boundary using a combination of sequential P extraction (SEDEX) and spectroscopic techniques, including (31)P NMR, P X-ray absorption near edge structure spectroscopy (XANES), and Fe extended X-ray absorption fine structure (EXAFS). Results from sequential P extraction reveal that sediment P is composed predominantly of ferric Fe-bound P and authigenic P, which was further confirmed by solid-state (31)P NMR, XANES, and EXAFS analyses. Additionally, solution (31)P NMR results show that the sediments from the middle site contain high amounts of organic P such as monoesters and diesters, compared to the other two sites, but that these compounds rapidly decrease with sediment depth indicating remineralized P could have precipitated as authigenic P. Fe EXAFS enabled to identify the changes in Fe mineral composition and P sinks in response to imposed redox condition in the middle site sediments. The presence of lepidocrocite, vermiculite, and Fe smectite in the middle site sediments indicates that some ferric Fe minerals can still be present along with pyrite and vivianite, and that ferric Fe-bound P pool can be a major P sink in anoxic sediments. These results provide improved insights into sediment P dynamics, particularly the rapid remineralization of organic P and the stability of Fe minerals and the ferric Fe-bound P pool in anoxic sediments in the Chesapeake Bay.

An introduction to the Australian and New Zealand flux tower network - OzFlux

NASA Astrophysics Data System (ADS)

Beringer, Jason; Hutley, Lindsay B.; McHugh, Ian; Arndt, Stefan K.; Campbell, David; Cleugh, Helen A.; Cleverly, James; Resco de Dios, Víctor; Eamus, Derek; Evans, Bradley; Ewenz, Cacilia; Grace, Peter; Griebel, Anne; Haverd, Vanessa; Hinko-Najera, Nina; Huete, Alfredo; Isaac, Peter; Kanniah, Kasturi; Leuning, Ray; Liddell, Michael J.; Macfarlane, Craig; Meyer, Wayne; Moore, Caitlin; Pendall, Elise; Phillips, Alison; Phillips, Rebecca L.; Prober, Suzanne M.; Restrepo-Coupe, Natalia; Rutledge, Susanna; Schroder, Ivan; Silberstein, Richard; Southall, Patricia; Yee, Mei Sun; Tapper, Nigel J.; van Gorsel, Eva; Vote, Camilla; Walker, Jeff; Wardlaw, Tim

2016-10-01

OzFlux is the regional Australian and New Zealand flux tower network that aims to provide a continental-scale national research facility to monitor and assess trends, and improve predictions, of Australia's terrestrial biosphere and climate. This paper describes the evolution, design, and current status of OzFlux as well as provides an overview of data processing. We analyse measurements from all sites within the Australian portion of the OzFlux network and two sites from New Zealand. The response of the Australian biomes to climate was largely consistent with global studies except that Australian systems had a lower ecosystem water-use efficiency. Australian semi-arid/arid ecosystems are important because of their huge extent (70 %) and they have evolved with common moisture limitations. We also found that Australian ecosystems had a similar radiation-use efficiency per unit leaf area compared to global values that indicates a convergence toward a similar biochemical efficiency. The two New Zealand sites represented extremes in productivity for a moist temperate climate zone, with the grazed dairy farm site having the highest GPP of any OzFlux site (2620 gC m-2 yr-1) and the natural raised peat bog site having a very low GPP (820 gC m-2 yr-1). The paper discusses the utility of the flux data and the synergies between flux, remote sensing, and modelling. Lastly, the paper looks ahead at the future direction of the network and concludes that there has been a substantial contribution by OzFlux, and considerable opportunities remain to further advance our understanding of ecosystem response to disturbances, including drought, fire, land-use and land-cover change, land management, and climate change, which are relevant both nationally and internationally. It is suggested that a synergistic approach is required to address all of the spatial, ecological, human, and cultural challenges of managing the delicately balanced ecosystems in Australasia.

Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of Fundulus heteroclitus

PubMed Central

Biancani, Leann M.; Flight, Patrick A.; Nacci, Diane E.; Rand, David M.; Crawford, Douglas L.; Oleksiak, Marjorie F.

2018-01-01

Populations of the non-migratory estuarine fish Fundulus heteroclitus inhabiting the heavily polluted New Bedford Harbour (NBH) estuary have shown inherited tolerance to local pollutants introduced to their habitats in the past 100 years. Here we examine two questions: (i) Is there pollution-driven selection on the mitochondrial genome across a fine geographical scale? and (ii) What is the pattern of migration among sites spanning a strong pollution gradient? Whole mitochondrial genomes were analysed for 133 F. heteroclitus from seven nearby collection sites: four sites along the NBH pollution cline (approx. 5 km distance), which had pollution-adapted fish, as well as one site adjacent to the pollution cline and two relatively unpolluted sites about 30 km away, which had pollution-sensitive fish. Additionally, we used microsatellite analyses to quantify genetic variation over three F. heteroclitus generations in both pollution-adapted and sensitive individuals collected from two sites at two different time points (1999/2000 and 2007/2008). Our results show no evidence for a selective sweep of mtDNA in the polluted sites. Moreover, mtDNA analyses revealed that both pollution-adapted and sensitive populations harbour similar levels of genetic diversity. We observed a high level of non-synonymous mutations in the most polluted site. This is probably associated with a reduction in Ne and concomitant weakening of purifying selection, a demographic expansion following a pollution-related bottleneck or increased mutation rates. Our demographic analyses suggest that isolation by distance influences the distribution of mtDNA genetic variation between the pollution cline and the clean populations at broad spatial scales. At finer scales, population structure is patchy, and neither spatial distance, pollution concentration or pollution tolerance is a good predictor of mtDNA variation. Lastly, microsatellite analyses revealed stable population structure over the last decade. PMID:29892357

Hydrologic data from urban watersheds in the Tampa Bay area, Florida

USGS Publications Warehouse

Lopez, Miguel A.; Michaelis, D.M.

1979-01-01

Hydrologic data are being collected in 10 urbanized watersheds located in the Tampa Bay area, Florida. The gaged watersheds have impervious areas that range from 19 percent for a residential watershed in north Tampa to nearly 100 percent for a downtown Tampa watershed. Land-use types, including roads, residential, commercial, industrial, institutional, recreational , and open space, have been determined for each watershed. Rainfall and storm runoff data collected since 1971 for one site and since 1975 for six other sites through September 1976, have been processed. These data are recorded at 5-minute intervals and are stored in the U. S. Geological Survey WATSTORE unit values file. Daily rainfall at 12 sites and daily pan evaporation at one site have been stored in the WATSTORE daily values file. Chemical and biological analyses of storm runoff for six sites, base flow for seven sites, and analyses of bottom material for seven sites are also stored in the WATSTORE water-quality files. Rainfall and storm runoff for selected storms, daily rainfall, and daily pan-evaporation data are summarized in this report. Water-quality analyses of all water-quality samples also are listed. (Woodard-USGS).

Seismic isolation of nuclear power plants using sliding isolation bearings

NASA Astrophysics Data System (ADS)

Kumar, Manish

Nuclear power plants (NPP) are designed for earthquake shaking with very long return periods. Seismic isolation is a viable strategy to protect NPPs from extreme earthquake shaking because it filters a significant fraction of earthquake input energy. This study addresses the seismic isolation of NPPs using sliding bearings, with a focus on the single concave Friction Pendulum(TM) (FP) bearing. Friction at the sliding surface of an FP bearing changes continuously during an earthquake as a function of sliding velocity, axial pressure and temperature at the sliding surface. The temperature at the sliding surface, in turn, is a function of the histories of coefficient of friction, sliding velocity and axial pressure, and the travel path of the slider. A simple model to describe the complex interdependence of the coefficient of friction, axial pressure, sliding velocity and temperature at the sliding surface is proposed, and then verified and validated. Seismic hazard for a seismically isolated nuclear power plant is defined in the United States using a uniform hazard response spectrum (UHRS) at mean annual frequencies of exceedance (MAFE) of 10-4 and 10 -5. A key design parameter is the clearance to the hard stop (CHS), which is influenced substantially by the definition of the seismic hazard. Four alternate representations of seismic hazard are studied, which incorporate different variabilities and uncertainties. Response-history analyses performed on single FP-bearing isolation systems using ground motions consistent with the four representations at the two shaking levels indicate that the CHS is influenced primarily by whether the observed difference between the two horizontal components of ground motions in a given set is accounted for. The UHRS at the MAFE of 10-4 is increased by a design factor (≥ 1) for conventional (fixed base) nuclear structure to achieve a target annual frequency of unacceptable performance. Risk oriented calculations are performed for eight sites across the United States to show that the factor is equal to 1.0 for seismically isolated NPPs, if the risk is dominated by horizontal earthquake shaking. Response-history analyses using different models of seismically isolated NPPs are performed to understand the importance of the choice of friction model, model complexity and vertical ground motion for calculating horizontal displacement response across a wide range of sites and shaking intensities. A friction model for the single concave FP bearing should address heating. The pressure- and velocity-dependencies were not important for the models and sites studied. Isolation-system displacements can be computed using a macro model comprising a single FP bearing.

Prenatal arsenic exposure and the epigenome: identifying sites of 5-methylcytosine alterations that predict functional changes in gene expression in newborn cord blood and subsequent birth outcomes.

PubMed

Rojas, Daniel; Rager, Julia E; Smeester, Lisa; Bailey, Kathryn A; Drobná, Zuzana; Rubio-Andrade, Marisela; Stýblo, Miroslav; García-Vargas, Gonzalo; Fry, Rebecca C

2015-01-01

Prenatal exposure to inorganic arsenic (iAs) is detrimental to the health of newborns and increases the risk of disease development later in life. Here we examined a subset of newborn cord blood leukocyte samples collected from subjects enrolled in the Biomarkers of Exposure to ARsenic (BEAR) pregnancy cohort in Gómez Palacio, Mexico, who were exposed to a range of drinking water arsenic concentrations (0.456-236 µg/l). Changes in iAs-associated DNA 5-methylcytosine methylation were assessed across 424,935 CpG sites representing 18,761 genes and compared with corresponding mRNA expression levels and birth outcomes. In the context of arsenic exposure, a total of 2919 genes were identified with iAs-associated differences in DNA methylation. Site-specific analyses identified DNA methylation changes that were most predictive of gene expression levels where CpG methylation within CpG islands positioned within the first exon, the 5' untranslated region and 200 bp upstream of the transcription start site yielded the most significant association with gene expression levels. A set of 16 genes was identified with correlated iAs-associated changes in DNA methylation and mRNA expression and all were highly enriched for binding sites of the early growth response (EGR) and CCCTC-binding factor (CTCF) transcription factors. Furthermore, DNA methylation levels of 7 of these genes were associated with differences in birth outcomes including gestational age and head circumference.These data highlight the complex interplay between DNA methylation, functional changes in gene expression and health outcomes and underscore the need for functional analyses coupled to epigenetic assessments. © The Author 2014. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The Impact of Rainfall on Soil Moisture Dynamics in a Foggy Desert.

PubMed

Li, Bonan; Wang, Lixin; Kaseke, Kudzai F; Li, Lin; Seely, Mary K

2016-01-01

Soil moisture is a key variable in dryland ecosystems since it determines the occurrence and duration of vegetation water stress and affects the development of weather patterns including rainfall. However, the lack of ground observations of soil moisture and rainfall dynamics in many drylands has long been a major obstacle in understanding ecohydrological processes in these ecosystems. It is also uncertain to what extent rainfall controls soil moisture dynamics in fog dominated dryland systems. To this end, in this study, twelve to nineteen months' continuous daily records of rainfall and soil moisture (from January 2014 to August 2015) obtained from three sites (one sand dune site and two gravel plain sites) in the Namib Desert are reported. A process-based model simulating the stochastic soil moisture dynamics in water-limited systems was used to study the relationships between soil moisture and rainfall dynamics. Model sensitivity in response to different soil and vegetation parameters under diverse soil textures was also investigated. Our field observations showed that surface soil moisture dynamics generally follow rainfall patterns at the two gravel plain sites, whereas soil moisture dynamics in the sand dune site did not show a significant relationship with rainfall pattern. The modeling results suggested that most of the soil moisture dynamics can be simulated except the daily fluctuations, which may require a modification of the model structure to include non-rainfall components. Sensitivity analyses suggested that soil hygroscopic point (sh) and field capacity (sfc) were two main parameters controlling soil moisture output, though permanent wilting point (sw) was also very sensitive under the parameter setting of sand dune (Gobabeb) and gravel plain (Kleinberg). Overall, the modeling results were not sensitive to the parameters in non-bounded group (e.g., soil hydraulic conductivity (Ks) and soil porosity (n)). Field observations, stochastic modeling results as well as sensitivity analyses provide soil moisture baseline information for future monitoring and the prediction of soil moisture patterns in the Namib Desert.

The Impact of Rainfall on Soil Moisture Dynamics in a Foggy Desert

PubMed Central

Li, Bonan; Wang, Lixin; Kaseke, Kudzai F.; Li, Lin; Seely, Mary K.

2016-01-01

Soil moisture is a key variable in dryland ecosystems since it determines the occurrence and duration of vegetation water stress and affects the development of weather patterns including rainfall. However, the lack of ground observations of soil moisture and rainfall dynamics in many drylands has long been a major obstacle in understanding ecohydrological processes in these ecosystems. It is also uncertain to what extent rainfall controls soil moisture dynamics in fog dominated dryland systems. To this end, in this study, twelve to nineteen months’ continuous daily records of rainfall and soil moisture (from January 2014 to August 2015) obtained from three sites (one sand dune site and two gravel plain sites) in the Namib Desert are reported. A process-based model simulating the stochastic soil moisture dynamics in water-limited systems was used to study the relationships between soil moisture and rainfall dynamics. Model sensitivity in response to different soil and vegetation parameters under diverse soil textures was also investigated. Our field observations showed that surface soil moisture dynamics generally follow rainfall patterns at the two gravel plain sites, whereas soil moisture dynamics in the sand dune site did not show a significant relationship with rainfall pattern. The modeling results suggested that most of the soil moisture dynamics can be simulated except the daily fluctuations, which may require a modification of the model structure to include non-rainfall components. Sensitivity analyses suggested that soil hygroscopic point (sh) and field capacity (sfc) were two main parameters controlling soil moisture output, though permanent wilting point (sw) was also very sensitive under the parameter setting of sand dune (Gobabeb) and gravel plain (Kleinberg). Overall, the modeling results were not sensitive to the parameters in non-bounded group (e.g., soil hydraulic conductivity (Ks) and soil porosity (n)). Field observations, stochastic modeling results as well as sensitivity analyses provide soil moisture baseline information for future monitoring and the prediction of soil moisture patterns in the Namib Desert. PMID:27764203

Regeneration of Pinus pinaster Aiton after prescribed fires: Response to burn timing and biogeographical seed provenance across a climatic gradient.

PubMed

Sagra, J; Ferrandis, P; Plaza-Álvarez, P A; Lucas-Borja, M E; González-Romero, J; Alfaro-Sánchez, R; De Las Heras, J; Moya, D

2018-05-17

Prescribed fires are used as a fuel reduction tool, but heat alter microsite conditions affecting the natural regeneration of Mediterranean pine forests. Our study tested the hypothesis that implementing prescription before or after pine seed release may influence the composition of tree communities by changing the regeneration patterns of Pinus pinaster Aiton across a climatic gradient in the eastern Iberian Peninsula. We ran a seed-sowing experiment to analyse the recruitment patterns of this pine species in prescribed-burned stands, in two different biogeographical seed provenances from wetter and drier areas than the local seeding site. Survival of seedlings was through one year, until the end of the first drought and winter period, respectively. >5400 seeds were sown during the study distributed in sixty plots (30 burned, 30 unburned) per site and treatment, with 10 seeding units per plot. General linear models (GLMs) and ANOVA analyses indicated higher performance for the Drier seed provenance in burned areas, whereas a similar performance was recorded in the control area. Control areas showed higher germination and success rates for plant establishment throughout the study period. Total germination and survival after one year were slightly higher, respectively, at northern sites due to massive mortality during summer in the southern stands. At the burned sites, the mean germination time was significantly longer in those seeds sown before fire passage than those sown after fire. Total germination and successful establishment were significantly higher in the individuals sown before the passage of the fire than in those sown after fire. Most of the mortality occurred in summer for the southern stand, while winter was the most constraining period at the northern sites. The understanding of the dynamics in this species' establishment can help managers to perform a better management planning according to the species' ecology. Copyright © 2018 Elsevier B.V. All rights reserved.

Site-Specific Analyses for Demonstrating Compliance with 10 CFR 61 Performance Objectives - 12179

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

Grossman, C.J.; Esh, D.W.; Yadav, P.

2012-07-01

The U.S. Nuclear Regulatory Commission (NRC) is proposing to amend its regulations at 10 CFR Part 61 to require low-level radioactive waste disposal facilities to conduct site-specific analyses to demonstrate compliance with the performance objectives in Subpart C. The amendments would require licensees to conduct site-specific analyses for protection of the public and inadvertent intruders as well as analyses for long-lived waste. The amendments would ensure protection of public health and safety, while providing flexibility to demonstrate compliance with the performance objectives, for current and potential future waste streams. NRC staff intends to submit proposed rule language and associated regulatorymore » basis to the Commission for its approval in early 2012. The NRC staff also intends to develop associated guidance to accompany any proposed amendments. The guidance is intended to supplement existing low-level radioactive waste guidance on issues pertinent to conducting site-specific analyses to demonstrate compliance with the performance objectives. The guidance will facilitate implementation of the proposed amendments by licensees and assist competent regulatory authorities in reviewing the site-specific analyses. Specifically, the guidance provides staff recommendations on general considerations for the site-specific analyses, modeling issues for assessments to demonstrate compliance with the performance objectives including the performance assessment, intruder assessment, stability assessment, and analyses for long-lived waste. This paper describes the technical basis for changes to the rule language and the proposed guidance associated with implementation of the rule language. The NRC staff, per Commission direction, intends to propose amendments to 10 CFR Part 61 to require licensees to conduct site-specific analyses to demonstrate compliance with performance objectives for the protection of public health and the environment. The amendments would require a performance assessment to demonstrate protection of the general population from releases of radioactivity, an assessment to demonstrate protection of a potential inadvertent intruder, and a long-term analysis to assess how the design of the facility considers the potential radiological impacts associated with disposal of long-lived waste streams. Concurrently, the NRC staff intends to propose associated guidance to facilitate the implementation of the requirements to conduct site-specific analyses. In proposing these amendments to the regulation and associated guidance, the NRC staff has conducted extensive public outreach since 2009 including three public meetings and four briefings of the NRC's Advisory Committee on Reactor Safeguards. The NRC staff plans to submit the proposed amendments to the regulations to the Commission in early 2012. Subsequently, the proposed amendments and associated guidance would be published in the Federal Register for public comment pending approval of the proposed amendments to the regulations by the Commission. Following the public comment period, NRC staff plans to address public comments and revise, as necessary, the regulations and associated guidance before publishing a final rule, which is anticipated in 2013. (authors)« less

Estimating Children’s Soil/Dust Ingestion Rates through Retrospective Analyses of Blood Lead Biomonitoring from the Bunker Hill Superfund Site in Idaho

PubMed Central

von Lindern, Ian; Spalinger, Susan; Stifelman, Marc L.; Stanek, Lindsay Wichers; Bartrem, Casey

2016-01-01

Background: Soil/dust ingestion rates are important variables in assessing children’s health risks in contaminated environments. Current estimates are based largely on soil tracer methodology, which is limited by analytical uncertainty, small sample size, and short study duration. Objectives: The objective was to estimate site-specific soil/dust ingestion rates through reevaluation of the lead absorption dose–response relationship using new bioavailability data from the Bunker Hill Mining and Metallurgical Complex Superfund Site (BHSS) in Idaho, USA. Methods: The U.S. Environmental Protection Agency (EPA) in vitro bioavailability methodology was applied to archived BHSS soil and dust samples. Using age-specific biokinetic slope factors, we related bioavailable lead from these sources to children’s blood lead levels (BLLs) monitored during cleanup from 1988 through 2002. Quantitative regression analyses and exposure assessment guidance were used to develop candidate soil/dust source partition scenarios estimating lead intake, allowing estimation of age-specific soil/dust ingestion rates. These ingestion rate and bioavailability estimates were simultaneously applied to the U.S. EPA Integrated Exposure Uptake Biokinetic Model for Lead in Children to determine those combinations best approximating observed BLLs. Results: Absolute soil and house dust bioavailability averaged 33% (SD ± 4%) and 28% (SD ± 6%), respectively. Estimated BHSS age-specific soil/dust ingestion rates are 86–94 mg/day for 6-month- to 2-year-old children and 51–67 mg/day for 2- to 9-year-old children. Conclusions: Soil/dust ingestion rate estimates for 1- to 9-year-old children at the BHSS are lower than those commonly used in human health risk assessment. A substantial component of children’s exposure comes from sources beyond the immediate home environment. Citation: von Lindern I, Spalinger S, Stifelman ML, Stanek LW, Bartrem C. 2016. Estimating children’s soil/dust ingestion rates through retrospective analyses of blood lead biomonitoring from the Bunker Hill Superfund Site in Idaho. Environ Health Perspect 124:1462–1470; http://dx.doi.org/10.1289/ehp.1510144 PMID:26745545

Intraspecific variation in stomatal traits, leaf traits and physiology reflects adaptation along aridity gradients in a South African shrub.

PubMed

Carlson, Jane E; Adams, Christopher A; Holsinger, Kent E

2016-01-01

Trait-environment relationships are commonly interpreted as evidence for local adaptation in plants. However, even when selection analyses support this interpretation, the mechanisms underlying differential benefits are often unknown. This study addresses this gap in knowledge using the broadly distributed South African shrub Protea repens. Specifically, the study examines whether broad-scale patterns of trait variation are consistent with spatial differences in selection and ecophysiology in the wild. In a common garden study of plants sourced from 19 populations, associations were measured between five morphological traits and three axes describing source climates. Trait-trait and trait-environment associations were analysed in a multi-response model. Within two focal populations in the wild, selection and path analyses were used to test associations between traits, fecundity and physiological performance. Across 19 populations in a common garden, stomatal density increased with the source population's mean annual temperature and decreased with its average amount of rainfall in midsummer. Concordantly, selection analysis in two natural populations revealed positive selection on stomatal density at the hotter, drier site, while failing to detect selection at the cooler, moister site. Dry-site plants with high stomatal density also had higher stomatal conductances, cooler leaf temperatures and higher light-saturated photosynthetic rates than those with low stomatal density, but no such relationships were present among wet-site plants. Leaf area, stomatal pore index and specific leaf area in the garden also co-varied with climate, but within-population differences were not associated with fitness in either wild population. The parallel patterns of broad-scale variation, differences in selection and differences in trait-ecophysiology relationships suggest a mechanism for adaptive differentiation in stomatal density. Densely packed stomata may improve performance by increasing transpiration and cooling, but predominately in drier, hotter climates. This study uniquely shows context-dependent benefits of stomatal density--a trait rarely linked to local adaptation in plants. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

An Investigation of the Information Sought by Caregivers of Alzheimer's Patients on Online Peer Support Groups.

PubMed

Scharett, Emma; Madathil, Kapil Chalil; Lopes, Snehal; Rogers, Hunter; Agnisarman, Sruthy; Narasimha, Shraddhaa; Ashok, Aparna; Dye, Cheryl

2017-10-01

Caregivers of Alzheimer's patients find respite in online communities for solutions and emotional support. This study aims to understand the characteristics of information caregivers of Alzheimer's patients are searching for and the kind of support they receive through Internet-based peer support communities. Using a Web crawler written in Python Web programming language, we retrieved publicly available 2,500 random posts and their respective solutions from April 2012 to October 2016 on the solutions category of the Caregiver's Forum on ALZConnected.org . A content analysis was conducted on these randomly selected posts and 4,219 responses to those posts based on a classification system were derived from initial analyses of 750 posts and related responses. The results showed most posts (26%) related to queries about Alzheimer's symptoms, and the highest percentage of responses (45.56%) pertained to caregiver well-being. The LIWC analyses generated an average tone rating of 27.27 for the posts, implying a negative tone and 65.17 for their responses, implying a slightly positive tone. The ALZConnected.org Web site has the potential of being an emotionally supportive tool for caregivers; however, a more user-friendly interface is required to accommodate the needs of most caregivers and their technological skills. Solutions offered on the peer support groups are often subjective opinions of other caregivers and should not be considered professional or comprehensive; further research on educating caregivers using online forums is necessary.

Supplemental oxygen therapy does not affect the systemic inflammatory response to acute myocardial infarction.

PubMed

Hofmann, R; Tornvall, P; Witt, N; Alfredsson, J; Svensson, L; Jonasson, L; Nilsson, L

2018-04-01

Oxygen therapy has been used routinely in normoxemic patients with suspected acute myocardial infarction (AMI) despite limited evidence supporting a beneficial effect. AMI is associated with a systemic inflammation. Here, we hypothesized that the inflammatory response to AMI is potentiated by oxygen therapy. The DETermination of the role of Oxygen in suspected Acute Myocardial Infarction (DETO2X-AMI) multicentre trial randomized patients with suspected AMI to receive oxygen at 6 L min -1 for 6-12 h or ambient air. For this prespecified subgroup analysis, we recruited patients with confirmed AMI from two sites for evaluation of inflammatory biomarkers at randomization and 5-7 h later. Ninety-two inflammatory biomarkers were analysed using proximity extension assay technology, to evaluate the effect of oxygen on the systemic inflammatory response to AMI. Plasma from 144 AMI patients was analysed whereof 76 (53%) were randomized to oxygen and 68 (47%) to air. Eight biomarkers showed a significant increase, whereas 13 were decreased 5-7 h after randomization. The inflammatory response did not differ between the two treatment groups neither did plasma troponin T levels. After adjustment for increase in troponin T over time, age and sex, the release of inflammation-related biomarkers was still similar in the groups. In a randomized controlled setting of normoxemic patients with AMI, the use of supplemental oxygen did not have any significant impact on the early release of systemic inflammatory markers. © 2017 The Association for the Publication of the Journal of Internal Medicine.

Neoadjuvant chemotherapy response influences outcomes in non-colorectal, non-neuroendocrine liver metastases.

PubMed

Lucchese, A M; Kalil, A N; Ruiz, A; Karam, V; Ciacio, O; Pittau, G; Castaing, D; Cherqui, D; Sa Cunha, A; Vibert, E; Adam, R

2018-06-12

Indications for surgical resection of non-colorectal, non-neuroendocrine (NCNNE) liver metastases are unclear. This study analysed the influence of response to neoadjuvant chemotherapy and the presence of extrahepatic disease (EHD) on outcomes. Patients who underwent hepatic resection for NCNNE liver metastases and who received neoadjuvant chemotherapy at a single centre between 1982 and 2016 were analysed retrospectively. Patients were classified as having no EHD, controlled EHD or non-controlled EHD. Hepatic resection was performed in 199 patients (81·2 per cent) after partial or complete response to chemotherapy or disease stabilization, and 46 patients (18·8 per cent) after tumour progression. Patients with progressive disease after chemotherapy had worse overall survival than those without (23 versus 50·4 per cent at 5 years; P = 0·004). Median survival was 63·6 (range 31·1-94·8) months for patients without EHD, 34·8 (19·2-49·2) months for those with controlled EHD and 7·2 (1·2-13·2) months for patients with non-controlled EHD (P = 0·004). In multivariable analysis, EHD (P = 0·004), response to chemotherapy (P = 0·004) and resection margins (P = 0·002) were all independent predictors of overall survival, regardless of primary tumour site. The prognosis of patients with NCNNE liver metastases is influenced by preoperative chemotherapy and resectability. © 2018 BJS Society Ltd Published by John Wiley & Sons Ltd.

High-resolution topography and geomorphology of select archeological sites in Glen Canyon National Recreation Area, Arizona

USGS Publications Warehouse

Collins, Brian D.; Corbett, Skye C.; Sankey, Joel B.; Fairley, Helen C.

2014-01-01

Along the Colorado River corridor between Glen Canyon Dam and Lees Ferry, Arizona, located some 25 km downstream from the dam, archaeological sites dating from 8,000 years before present through the modern era are located within and on top of fluvial and alluvial terraces of the prehistorically undammed river. These terraces are known to have undergone significant erosion and retreat since emplacement of Glen Canyon Dam in 1963. Land managers and policy makers associated with managing the flow of the Colorado River are interested in understanding how the operations of Glen Canyon Dam have affected the archeological sites associated with these terraces and how dam-controlled flows currently interact with other landscape-shaping processes. In 2012, the U.S. Geological Survey initiated a research project in Glen Canyon to study the types and causes of erosion of the terraces. This report provides the first step towards this understanding by presenting comparative analyses on several types of high-resolution topographic data (airborne lidar, terrestrial lidar, and airborne photogrammetry) that can be used in the future to document and analyze changes to terrace-based archaeological sites. Herein, we present topographic and geomorphologic data of four archaeological sites within a 14 km segment of Glen Canyon using each of the three data sources. In addition to comparing each method’s suitability for adequately representing the topography of the sites, we also analyze the data within each site’s context and describe the geomorphological processes responsible for erosion. Our results show that each method has its own strengths and weaknesses, and that terrestrial and airborne lidar are essentially interchangeable for many important topographic characterization and monitoring purposes. However, whereas terrestrial lidar provides enhanced capacity for feature recognition and gully morphology delineation, airborne methods (whether by way of laser or optical sensors) are better suited for reach- and regional-scale mapping. Our site-specific geomorphic analyses of the four archeological sites indicate that their current topographical conditions are a result of different and sometimes competing erosional agents, including bedrock- and terrace-based overland flow, fluvial-induced terrace bank collapse, and alluvial-fan-generated debris flows. Although the influences of anthropogenic-induced erosion from dam operations are not specifically analyzed in this report, we do identify geomorphic settings where dam operations are either more or less likely to affect archeological site stability. This information can be used to assist with future monitoring efforts of these sites and identification of similar conditions for other archeological sites along the Colorado River corridor in Glen Canyon.

Ecological Patterns Among Bacteria and Microbial Eukaryotes Derived from Network Analyses in a Low-Salinity Lake.

PubMed

Jones, Adriane Clark; Hambright, K David; Caron, David A

2018-05-01

Microbial communities are comprised of complex assemblages of highly interactive taxa. We employed network analyses to identify and describe microbial interactions and co-occurrence patterns between microbial eukaryotes and bacteria at two locations within a low salinity (0.5-3.5 ppt) lake over an annual cycle. We previously documented that the microbial diversity and community composition within Lake Texoma, southwest USA, were significantly affected by both seasonal forces and a site-specific bloom of the harmful alga, Prymnesium parvum. We used network analyses to answer ecological questions involving both the bacterial and microbial eukaryotic datasets and to infer ecological relationships within the microbial communities. Patterns of connectivity at both locations reflected the seasonality of the lake including a large rain disturbance in May, while a comparison of the communities between locations revealed a localized response to the algal bloom. A network built from shared nodes (microbial operational taxonomic units and environmental variables) and correlations identified conserved associations at both locations within the lake. Using network analyses, we were able to detect disturbance events, characterize the ecological extent of a harmful algal bloom, and infer ecological relationships not apparent from diversity statistics alone.

Radiation-Related New Primary Solid Cancers in the Childhood Cancer Survivor Study: Comparative Radiation Dose Response and Modification of Treatment Effects

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

Inskip, Peter D., E-mail: inskippeter@gmail.com; Sigurdson, Alice J.; Veiga, Lene

Objectives: The majority of childhood cancer patients now achieve long-term survival, but the treatments that cured their malignancy often put them at risk of adverse health outcomes years later. New cancers are among the most serious of these late effects. The aims of this review are to compare and contrast radiation dose–response relationships for new solid cancers in a large cohort of childhood cancer survivors and to discuss interactions among treatment and host factors. Methods: This review is based on previously published site-specific analyses for subsequent primary cancers of the brain, breast, thyroid gland, bone and soft tissue, salivary glands,more » and skin among 12,268 5-year childhood cancer survivors in the Childhood Cancer Survivor Study. Analyses included tumor site–specific, individual radiation dose reconstruction based on radiation therapy records. Radiation-related second cancer risks were estimated using conditional logistic or Poisson regression models for excess relative risk (ERR). Results: Linear dose–response relationships over a wide range of radiation dose (0-50 Gy) were seen for all cancer sites except the thyroid gland. The steepest slopes occurred for sarcoma, meningioma, and nonmelanoma skin cancer (ERR/Gy > 1.00), with glioma and cancers of the breast and salivary glands forming a second group (ERR/Gy = 0.27-0.36). The relative risk for thyroid cancer increased up to 15-20 Gy and then decreased with increasing dose. The risk of thyroid cancer also was positively associated with chemotherapy, but the chemotherapy effect was not seen among those who also received very high doses of radiation to the thyroid. The excess risk of radiation-related breast cancer was sharply reduced among women who received 5 Gy or more to the ovaries. Conclusions: The results suggest that the effect of high-dose irradiation is consistent with a linear dose–response for most organs, but they also reveal important organ-specific and host-specific differences in susceptibility and interactions between different aspects of treatment.« less

Intramuscular Therapeutic Vaccination Targeting HPV16 Induces T Cell Responses That Localize in Mucosal Lesions

PubMed Central

Jotova, Iveta; Wu, T. C.; Wang, Chenguang; Desmarais, Cindy; Boyer, Jean D.; Tycko, Benjamin; Robins, Harlan S.; Clark, Rachael A.; Trimble, Cornelia L.

2014-01-01

About 25% of high-grade cervical intraepithelial neoplasias (CIN2/3) caused by human papillomavirus serotype 16 (HPV16) undergo complete spontaneous regression. However, to date, therapeutic vaccination strategies for HPV disease have yielded limited success when measured by their ability to induce robust peripheral blood T cell responses to vaccine antigen. We report marked immunologic changes in the target lesion microenvironment after intramuscular therapeutic vaccination targeting HPV16 E6/E7 antigens, in subjects with CIN2/3 who had modest detectable responses in circulating T lymphocytes. Histologic and molecular changes, including markedly (average threefold) increased intensity of CD8+ T cell infiltrates in both the stromal and epithelial compartments, suggest an effector response to vaccination. Postvaccination cervical tissue immune infiltrates included organized tertiary lymphoid-like structures in the stroma subjacent to residual intraepithelial lesions and, unlike infiltrates in unvaccinated lesions, showed evidence of proliferation induced by recognition of cognate antigen. At a molecular level, these histologic changes in the stroma were characterized by increased expression of genes associated with immune activation (CXCR3) and effector function (Tbet and IFNβ), and were also associated with an immunologic signature in the overlying dysplastic epithelium. High-throughput T cell receptor sequencing of unmanipulated specimens identified clonal expansions in the tissue that were not readily detectable in peripheral blood. Together, these findings indicate that peripheral therapeutic vaccination to HPV antigens can induce a robust tissue-localized effector immune response, and that analyses of immune responses at sites of antigen are likely to be much more informative than analyses of cells that remain in the circulation. PMID:24477000

Hand-held analyser based on microchip electrophoresis with contactless conductivity detection for measurement of chemical warfare agent degradation products

NASA Astrophysics Data System (ADS)

Duran, Karolina-Petkovic; Zhu, Yonggang; Chen, Chuanpin; Swallow, Anthony; Stewart, Robert; Hoobin, Pam; Leech, Patrick; Ovenden, Simon

2008-12-01

This paper reports on the development of a hand-held device for on-site detection of organophosphonate nerve agent degradation products. This field-deployable analyzer relies on efficient microchip electrophoresis separation of alkyl methylphosphonic acids and their sensitive contactless conductivity detection. Miniaturized, low-powered design is coupled with promising analytical performance for separating the breakdown products of chemical warfare agents such as Soman, Sarin and VX . The detector has a detection limit of about 10 μg/mL and has a good linear response in the range 10-300 μg/mL concentration range. Applicability to environmental samples is demonstrated .The new hand-held analyzer offers great promise for converting conventional ion chromatography or capillary electrophoresis sophisticated systems into a portable forensic laboratory for faster, simpler and more reliable on-site screening.

Regulation of Drosophila hematopoietic sites by Activin-β from active sensory neurons

PubMed Central

Makhijani, Kalpana; Alexander, Brandy; Rao, Deepti; Petraki, Sophia; Herboso, Leire; Kukar, Katelyn; Batool, Itrat; Wachner, Stephanie; Gold, Katrina S.; Wong, Corinna; O’Connor, Michael B.; Brückner, Katja

2017-01-01

An outstanding question in animal development, tissue homeostasis and disease is how cell populations adapt to sensory inputs. During Drosophila larval development, hematopoietic sites are in direct contact with sensory neuron clusters of the peripheral nervous system (PNS), and blood cells (hemocytes) require the PNS for their survival and recruitment to these microenvironments, known as Hematopoietic Pockets. Here we report that Activin-β, a TGF-β family ligand, is expressed by sensory neurons of the PNS and regulates the proliferation and adhesion of hemocytes. These hemocyte responses depend on PNS activity, as shown by agonist treatment and transient silencing of sensory neurons. Activin-β has a key role in this regulation, which is apparent from reporter expression and mutant analyses. This mechanism of local sensory neurons controlling blood cell adaptation invites evolutionary parallels with vertebrate hematopoietic progenitors and the independent myeloid system of tissue macrophages, whose regulation by local microenvironments remain undefined. PMID:28748922

Don't fight the site: three geomorphic considerations in catchment-scale river rehabilitation planning.

PubMed

Brierley, Gary; Fryirs, Kirstie

2009-06-01

Three geomorphic considerations that underpin the design and implementation of realistic and strategic river conservation and rehabilitation programs that work with the nature are outlined. First, the importance of appreciating the inherent diversity of river forms and processes is discussed. Second, river dynamics are appraised, framing the contemporary behavioral regime of a reach in relation to system evolution to explain changes to river character and behavior over time. Third, the trajectory of a reach is framed in relation to downstream patterns of river types, analyzing landscape connectivity at the catchment scale to interpret geomorphic river recovery potential. The application of these principles is demonstrated using extensive catchment-scale analyses of geomorphic river responses to human disturbance in the Bega and Upper Hunter catchments in southeastern Australia. Differing implications for reach- and catchment-scale rehabilitation planning prompt the imperative that management practices work with nature rather than strive to 'fight the site.'

Effects of Holocene climate change on the historical demography of migrating sharp-shinned hawks (Accipiter striatus velox) in North America.

PubMed

Hull, Joshua M; Girman, Derek J

2005-01-01

DNA sequences of the mitochondrial control region were analysed from 298 individual sharp-shinned hawks (Accipiter striatus velox) sampled at 12 different migration study sites across North America. The control region proved to be an appropriate genetic marker for identification of continental-scale population genetic structure and for determining the historical demography of population units. These data suggest that sharp-shinned hawks sampled at migration sites in North America are divided into distinct eastern and western groups. The eastern group appears to have recently expanded in response to the retreat of glacial ice at the end of the last glacial maximum. The western group appears to have been strongly effected by the Holocene Hypsithermal dry period, with molecular evidence indicating the most recent expansion following this mid-Holocene climatic event 7000-5000 years before present.

The effects of urbanization on the biological, physical, and chemical characteristics of coastal New England streams

USGS Publications Warehouse

Coles, James F.; Cuffney, Thomas F.; McMahon, Gerard; Beaulieu, Karen M.

2004-01-01

During August 2000, responses of biological communities (invertebrates, fish, and algae), physical habitat, and water chemistry to urban intensity were compared among 30 streams within 80 miles of Boston, Massachusetts. Sites chosen for sampling represented a gradient of the intensity of urban development (urban intensity) among drainage basins that had minimal natural variability. In this study, spatial differences were used as surrogates for temporal changes to represent the effects of urbanization over time. The degree of urban intensity for each drainage basin was characterized with a standardized urban index (0-100, lowest to highest) derived from land cover, infrastructure, and socioeconomic variables. Multivariate and multimetric analyses were used to compare urban index values with biological, physical, and chemical data to determine how the data indicated responses to urbanization. Multivariate ordinations were derived for the invertebrate-, fish-, and algae-community data by use of correspondence analysis, and ordinations were derived for the chemical and physical data by use of principal-component analysis. Site scores from each of the ordinations were plotted in relation to the urban index to test for a response. In all cases, the primary axis scores showed the strongest response to the urban index, indicating that urbanization was a primary factor affecting the data ordination. For the multimetric analyses, each of the biological data sets was used to calculate a series of community metrics. For the sets of chemical and physical data, the individual variables and various combinations of individual variables were used as measured and derived metrics, respectively. Metrics that were generally most responsive to the urban index for each data set included: EPT (Ephemeroptera, Plecoptera, Trichoptera) taxa for invertebrates; cyprinid taxa for fish; diatom taxa for algae; bicarbonate, conductivity, and nitrogen for chemistry; and water depth and temperature for physical habitat. The slopes of the responses generally were higher between the urban index values of 0 to 35, indicating that the greatest change in aquatic health may occur between low and moderate levels of urban intensity. Additionally, many of the responses showed that at urban index values greater than 35, there was a threshold effect where the response variable no longer changed with respect to urban intensity. Recognizing and understanding this type of response is important in management and monitoring programs that rely on decisive interpretations of variable responses. Any biological, physical, or chemical variable that is used to characterize stream health over a gradient of disturbance would not be a reliable indicator when a level of disturbance is reached where the variable does not respond in a predictable manner.

How the Scientific Community Reacts to Newly Submitted Preprints: Article Downloads, Twitter Mentions, and Citations

PubMed Central

Shuai, Xin; Pepe, Alberto; Bollen, Johan

2012-01-01

We analyze the online response to the preprint publication of a cohort of 4,606 scientific articles submitted to the preprint database arXiv.org between October 2010 and May 2011. We study three forms of responses to these preprints: downloads on the arXiv.org site, mentions on the social media site Twitter, and early citations in the scholarly record. We perform two analyses. First, we analyze the delay and time span of article downloads and Twitter mentions following submission, to understand the temporal configuration of these reactions and whether one precedes or follows the other. Second, we run regression and correlation tests to investigate the relationship between Twitter mentions, arXiv downloads, and article citations. We find that Twitter mentions and arXiv downloads of scholarly articles follow two distinct temporal patterns of activity, with Twitter mentions having shorter delays and narrower time spans than arXiv downloads. We also find that the volume of Twitter mentions is statistically correlated with arXiv downloads and early citations just months after the publication of a preprint, with a possible bias that favors highly mentioned articles. PMID:23133597

Imaging of Scleral Collagen Deformation Using Combined Confocal Raman Microspectroscopy and Polarized Light Microscopy Techniques.

PubMed

Chakraborty, Nilay; Wang, Mian; Solocinski, Jason; Kim, Wonsuk; Argento, Alan

2016-01-01

This work presents an optospectroscopic characterization technique for soft tissue microstructure using site-matched confocal Raman microspectroscopy and polarized light microscopy. Using the technique, the microstructure of soft tissue samples is directly observed by polarized light microscopy during loading while spatially correlated spectroscopic information is extracted from the same plane, verifying the orientation and arrangement of the collagen fibers. Results show the response and orientation of the collagen fiber arrangement in its native state as well as during tensile and compressive loadings in a porcine sclera model. An example is also given showing how the data can be used with a finite element program to estimate the strain in individual collagen fibers. The measurements demonstrate features that indicate microstructural reorganization and damage of the sclera's collagen fiber arrangement under loading. The site-matched confocal Raman microspectroscopic characterization of the tissue provides a qualitative measure to relate the change in fibrillar arrangement with possible chemical damage to the collagen microstructure. Tests and analyses presented here can potentially be used to determine the stress-strain behavior, and fiber reorganization of the collagen microstructure in soft tissue during viscoelastic response.

The Innate Immune Database (IIDB)

PubMed Central

Korb, Martin; Rust, Aistair G; Thorsson, Vesteinn; Battail, Christophe; Li, Bin; Hwang, Daehee; Kennedy, Kathleen A; Roach, Jared C; Rosenberger, Carrie M; Gilchrist, Mark; Zak, Daniel; Johnson, Carrie; Marzolf, Bruz; Aderem, Alan; Shmulevich, Ilya; Bolouri, Hamid

2008-01-01

Background As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site . Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the internet. It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens. Description We constructed a database indexed on genes and annotations of the immediate surrounding genomic regions. To facilitate both gene-specific and systems biology oriented research, our database provides the means to analyze individual genes or an entire genomic locus. Although our focus to-date has been on mammalian toll-like receptor signaling pathways, our database structure is not limited to this subject, and is intended to be broadly applicable to immunology. By focusing on selected immune-active genes, we were able to perform computationally intensive expression and sequence analyses that would currently be prohibitive if applied to the entire genome. Using six complementary computational algorithms and methodologies, we identified transcription factor binding sites based on the Position Weight Matrices available in TRANSFAC. For one example transcription factor (ATF3) for which experimental data is available, over 50% of our predicted binding sites coincide with genome-wide chromatin immnuopreciptation (ChIP-chip) results. Our database can be interrogated via a web interface. Genomic annotations and binding site predictions can be automatically viewed with a customized version of the Argo genome browser. Conclusion We present the Innate Immune Database (IIDB) as a community resource for immunologists interested in gene regulatory systems underlying innate responses to pathogens. The database website can be freely accessed at . PMID:18321385

The effects of marine sand and gravel extraction on the sediment composition and macrofaunal community of a commercial dredging site (15 years post-dredging).

PubMed

Waye-Barker, Georgia A; McIlwaine, Paul; Lozach, Sophie; Cooper, Keith M

2015-10-15

A prediction that faunal recovery of a marine aggregate extraction site subjected to high dredging intensity was likely to take 15-20 years was investigated. Samples were collected at the high dredging intensity site and two reference sites in 2011 (15 years post-dredging). Results indicated that the high site had similar sediment characteristics to the reference sites by 2011. Macrofaunal data analyses showed no difference between the values of all calculated univariate measures (abundance, number of taxa, biomass and evenness) between the high and reference sites. Multivariate analyses found that the macrofaunal community at the high site was comparable to those of the reference sites by 2011. Overall, the results supported the predicted recovery time. The findings of the study suggest that persistent physical impacts prolonged the biological recovery of the high site. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Antagonism of ligand-gated ion channel receptors: two domains of the glycine receptor alpha subunit form the strychnine-binding site.

PubMed Central

Vandenberg, R J; French, C R; Barry, P H; Shine, J; Schofield, P R

1992-01-01

The inhibitory glycine receptor (GlyR) is a member of the ligand-gated ion channel receptor superfamily. Glycine activation of the receptor is antagonized by the convulsant alkaloid strychnine. Using in vitro mutagenesis and functional analysis of the cDNA encoding the alpha 1 subunit of the human GlyR, we have identified several amino acid residues that form the strychnine-binding site. These residues were identified by transient expression of mutated cDNAs in mammalian (293) cells and examination of resultant [3H]strychnine binding, glycine displacement of [3H]strychnine, and electrophysiological responses to the application of glycine and strychnine. This mutational analysis revealed that residues from two separate domains within the alpha 1 subunit form the binding site for the antagonist strychnine. The first domain includes the amino acid residues Gly-160 and Tyr-161, and the second domain includes the residues Lys-200 and Tyr-202. These results, combined with analyses of other ligand-gated ion channel receptors, suggest a conserved tertiary structure and a common mechanism for antagonism in this receptor superfamily. PMID:1311851

Analysing biodiversity and conservation knowledge products to support regional environmental assessments

PubMed Central

Brooks, Thomas M.; Akçakaya, H. Resit; Burgess, Neil D.; Butchart, Stuart H.M.; Hilton-Taylor, Craig; Hoffmann, Michael; Juffe-Bignoli, Diego; Kingston, Naomi; MacSharry, Brian; Parr, Mike; Perianin, Laurence; Regan, Eugenie C.; Rodrigues, Ana S.L.; Rondinini, Carlo; Shennan-Farpon, Yara; Young, Bruce E.

2016-01-01

Two processes for regional environmental assessment are currently underway: the Global Environment Outlook (GEO) and Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES). Both face constraints of data, time, capacity, and resources. To support these assessments, we disaggregate three global knowledge products according to their regions and subregions. These products are: The IUCN Red List of Threatened Species, Key Biodiversity Areas (specifically Important Bird & Biodiversity Areas [IBAs], and Alliance for Zero Extinction [AZE] sites), and Protected Planet. We present fourteen Data citations: numbers of species occurring and percentages threatened; numbers of endemics and percentages threatened; downscaled Red List Indices for mammals, birds, and amphibians; numbers, mean sizes, and percentage coverages of IBAs and AZE sites; percentage coverage of land and sea by protected areas; and trends in percentages of IBAs and AZE sites wholly covered by protected areas. These data will inform the regional/subregional assessment chapters on the status of biodiversity, drivers of its decline, and institutional responses, and greatly facilitate comparability and consistency between the different regional/subregional assessments. PMID:26881749

Space rescue system definition (system performance analysis and trades)

NASA Astrophysics Data System (ADS)

Housten, Sam; Elsner, Tim; Redler, Ken; Svendsen, Hal; Wenzel, Sheri

This paper addresses key technical issues involved in the system definition of the Assured Crew Return Vehicle (ACRV). The perspective on these issues is that of a prospective ACRV contractor, performing system analysis and trade studies. The objective of these analyses and trade studies is to develop the recovery vehicle system concept and top level requirements. The starting point for this work is the definition of the set of design missions for the ACRV. This set of missions encompasses three classes of contingency/emergency (crew illness/injury, space station catastrophe/failure, transportation element catastrophe/failure). The need is to provide a system to return Space Station crew to Earth quickly (less than 24 hours) in response to randomly occurring contingency events over an extended period of time (30 years of planned Space Station life). The main topics addressed and characterized in this paper include the following: Key Recovery (Rescue) Site Access Considerations; Rescue Site Locations and Distribution; Vehicle Cross Range vs Site Access; On-orbit Loiter Capability and Vehicle Design; and Water vs. Land Recovery.

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

NONE

The Quarterly Environmental Data Summary (QEDS) for the fourth quarter of 1997 is prepared in support of the Weldon Spring Site Remedial Action Project Federal Facilities Agreement. The data presented constitute the QEDS. The data were received from the contract laboratories, verified by the Weldon Spring Site verification group and, except for air monitoring data and site KPA generated data (uranium analyses), merged into the data base during the fourth quarter of 1997. Air monitoring data presented are the most recent complete sets of quarterly data. Air data are not stored in the data base and KPA data are notmore » merged into the regular data base. Significant data, defined as data values that have exceeded defined ``above normal`` level 2 values, are discussed in this letter for Environmental Monitoring Plan (EMP) generated data only. Above normal level 2 values are based, in ES and H procedures, on historical high values, DOE Derived Concentration Guides (DCGs), NPDES limits and other guidelines. The procedures also establish actions to be taken in response to such data. Data received and verified during the fourth quarter were within a permissible range of variability except for those which are detailed.« less

Mortality from all cancers of asbestos factory workers in east London 1933-80

PubMed Central

Berry, G; Newhouse, M; Wagner, J

2000-01-01

OBJECTIVE—To give the observed and expected deaths due to cancer at all separate sites in asbestos workers in east London, and to analyse these for overall effect and exposure-response trend.
METHODS—The mortality experience of a cohort of over 5000 men and women followed up for over 30 years since first exposure to asbestos has been extracted.
RESULTS—There was a large excess of deaths due to cancer (537 observed, 222 expected). Most of these were due to cancer of the lung (232 observed, 77 expected) and pleural (52) and peritoneal (48) mesothelioma. The exposure-response trend for all these three causes was highly significant. There was also an excess of cancer of the colon (27 observed, 15 expected) which was significantly related to exposure. There were significant excesses of cancer of the ovary, of the liver, and of the oesophagus but with no consistent relation to exposure.
CONCLUSIONS—The excess risk of cancer after exposure to asbestos was mainly due to cancer of the lung and mesothelioma. An exposure related excess of cancer of the colon was also detected but the possibility that some of these deaths may have been peritoneal mesotheliomas could not be excluded. There was no consistent evidence of exposure related excesses at any other site.


Keywords: asbestos; cancer; exposure-response PMID:11024203

Protein disulfide isomerase acts as an injury response signal that enhances fibrin generation via tissue factor activation

PubMed Central

Reinhardt, Christoph; von Brühl, Marie-Luise; Manukyan, Davit; Grahl, Lenka; Lorenz, Michael; Altmann, Berid; Dlugai, Silke; Hess, Sonja; Konrad, Ildiko; Orschiedt, Lena; Mackman, Nigel; Ruddock, Lloyd; Massberg, Steffen; Engelmann, Bernd

2008-01-01

The activation of initiator protein tissue factor (TF) is likely to be a crucial step in the blood coagulation process, which leads to fibrin formation. The stimuli responsible for inducing TF activation are largely undefined. Here we show that the oxidoreductase protein disulfide isomerase (PDI) directly promotes TF-dependent fibrin production during thrombus formation in vivo. After endothelial denudation of mouse carotid arteries, PDI was released at the injury site from adherent platelets and disrupted vessel wall cells. Inhibition of PDI decreased TF-triggered fibrin formation in different in vivo murine models of thrombus formation, as determined by intravital fluorescence microscopy. PDI infusion increased — and, under conditions of decreased platelet adhesion, PDI inhibition reduced — fibrin generation at the injury site, indicating that PDI can directly initiate blood coagulation. In vitro, human platelet–secreted PDI contributed to the activation of cryptic TF on microvesicles (microparticles). Mass spectrometry analyses indicated that part of the extracellular cysteine 209 of TF was constitutively glutathionylated. Mixed disulfide formation contributed to maintaining TF in a state of low functionality. We propose that reduced PDI activates TF by isomerization of a mixed disulfide and a free thiol to an intramolecular disulfide. Our findings suggest that disulfide isomerases can act as injury response signals that trigger the activation of fibrin formation following vessel injury. PMID:18274674

Protein disulfide isomerase acts as an injury response signal that enhances fibrin generation via tissue factor activation.

PubMed

Reinhardt, Christoph; von Brühl, Marie-Luise; Manukyan, Davit; Grahl, Lenka; Lorenz, Michael; Altmann, Berid; Dlugai, Silke; Hess, Sonja; Konrad, Ildiko; Orschiedt, Lena; Mackman, Nigel; Ruddock, Lloyd; Massberg, Steffen; Engelmann, Bernd

2008-03-01

The activation of initiator protein tissue factor (TF) is likely to be a crucial step in the blood coagulation process, which leads to fibrin formation. The stimuli responsible for inducing TF activation are largely undefined. Here we show that the oxidoreductase protein disulfide isomerase (PDI) directly promotes TF-dependent fibrin production during thrombus formation in vivo. After endothelial denudation of mouse carotid arteries, PDI was released at the injury site from adherent platelets and disrupted vessel wall cells. Inhibition of PDI decreased TF-triggered fibrin formation in different in vivo murine models of thrombus formation, as determined by intravital fluorescence microscopy. PDI infusion increased - and, under conditions of decreased platelet adhesion, PDI inhibition reduced - fibrin generation at the injury site, indicating that PDI can directly initiate blood coagulation. In vitro, human platelet-secreted PDI contributed to the activation of cryptic TF on microvesicles (microparticles). Mass spectrometry analyses indicated that part of the extracellular cysteine 209 of TF was constitutively glutathionylated. Mixed disulfide formation contributed to maintaining TF in a state of low functionality. We propose that reduced PDI activates TF by isomerization of a mixed disulfide and a free thiol to an intramolecular disulfide. Our findings suggest that disulfide isomerases can act as injury response signals that trigger the activation of fibrin formation following vessel injury.

Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress

PubMed Central

McDade, Simon S.; Patel, Daksha; Moran, Michael; Campbell, James; Fenwick, Kerry; Kozarewa, Iwanka; Orr, Nicholas J.; Lord, Christopher J.; Ashworth, Alan A.; McCance, Dennis J.

2014-01-01

In response to genotoxic stress the TP53 tumour suppressor activates target gene expression to induce cell cycle arrest or apoptosis depending on the extent of DNA damage. These canonical activities can be repressed by TP63 in normal stratifying epithelia to maintain proliferative capacity or drive proliferation of squamous cell carcinomas, where TP63 is frequently overexpressed/amplified. Here we use ChIP-sequencing, integrated with microarray analysis, to define the genome-wide interplay between TP53 and TP63 in response to genotoxic stress in normal cells. We reveal that TP53 and TP63 bind to overlapping, but distinct cistromes of sites through utilization of distinctive consensus motifs and that TP53 is constitutively bound to a number of sites. We demonstrate that cisplatin and adriamycin elicit distinct effects on TP53 and TP63 binding events, through which TP53 can induce or repress transcription of an extensive network of genes by direct binding and/or modulation of TP63 activity. Collectively, this results in a global TP53-dependent repression of cell cycle progression, mitosis and DNA damage repair concomitant with activation of anti-proliferative and pro-apoptotic canonical target genes. Further analyses reveal that in the absence of genotoxic stress TP63 plays an important role in maintaining expression of DNA repair genes, loss of which results in defective repair. PMID:24823795

Fish communities and their associations with environmental variables, lower San Joaquin River drainage, California

USGS Publications Warehouse

Brown, L.R.

2000-01-01

Twenty sites in the lower San Joaquin River drainage, California, were sampled from 1993 to 1995 to characterize fish communities and their associations with measures of water quality and habitat quality. The feasibility of developing an Index of Biotic Integrity was assessed by evaluating four fish community metrics, including percentages of native fish, omnivorous fish, fish intolerant of environmental degradation, and fish with external anomalies. Of the thirty-one taxa of fish captured during the study, only 10 taxa were native to the drainage. Multivariate analyses of percentage data identified four site groups characterized by different groups of species. The distributions of fish species were related to specific conductance, gradient, and mean depth; however, specific conductance acted as a surrogate variable for a large group of correlated variables. Two of the fish community metrics - percentage of introduced fish and percentage of intolerant fish - appeared to be responsive to environmental quality but the responses of the other two metrics - percentage of omnivorous fish and percentage of fish with anomalies - were less direct. The conclusion of the study is that fish communities are responsive to environmental conditions, including conditions associated with human-caused disturbances, particularly agriculture and water development. The results suggest that changes in water management and water quality could result in changes in species distributions. Balancing the costs and benefits of such changes poses a considerable challenge to resource managers.

Assemblages of fishes and their associations with environmental variables, lower San Joaquin River drainage, California

USGS Publications Warehouse

Brown, Larry R.

1998-01-01

Twenty sites in the lower San Joaquin River drainage, California, were sampled from 1993 to 1995 to characterize fish assemblages and their associations with measures of water quality and habitat quality. In addition, four fish community metrics were assessed, including percentages of native fish, omnivorous fish, fish intolerant of environmental degradation, and fish with external anomalies. Of the 31 taxa of fish captured during the study, only 10 taxa were native to the drainage. Multivariate analyses of percentage data identified four site groups characterized by characterized by different groups of species. The distributions of fish species were related to specific conductance, gradient, and mean depth; however, specific conductance acted as a surrogate variable for a large group of correlated variables. Two of the fish community metrics--percentage of introduced fish and percentage of intolerant fish--appeared to be responsive to environmental quality but the responses of the other two metrics--percentage of omnivorous fish and percentage of fish with anomalies--were less direct. The conclusion of the study is that fish assemblages are responsive to environmental conditions, including conditions associated with human-caused disturbances, particularly agriculture and water development. The results suggest that changes in water management and water quality could result in changes in species distributions. Balancing the costs and benefits of such changes poses a considerable challenge to resource managers. different groups of species.

Radiation dose and subsequent risk for stomach cancer in long-term survivors of cervical cancer

PubMed Central

Kleinerman, Ruth A.; Smith, Susan A.; Holowaty, Eric; Hall, Per; Pukkala, Eero; Vaalavirta, Leila; Stovall, Marilyn; Weathers, Rita; Gilbert, Ethel; Aleman, Berthe M.P.; Kaijser, Magnus; Andersson, Michael; Storm, Hans; Joensuu, Heikki; Lynch, Charles F.; Dores, Graça M.; Travis, Lois B.; Morton, Lindsay M.; Curtis, Rochelle E.

2013-01-01

Purpose To assess the dose-response relationship for stomach cancer following radiotherapy for cervical cancer. Methods and Materials We conducted a nested, matched case-control study of 201 cases and 378 controls among 53,547 5-year survivors of cervical cancer diagnosed from 1943–1995, from five international, population-based cancer registries. We estimated individual radiation doses to the site of the stomach cancer for all cases and to corresponding sites for the matched controls (overall mean stomach tumor dose, 2.56 gray [Gy], range 0.03–46.1 and following parallel opposed pelvic fields, 1.63 Gy, range 0.12–6.3). Results Over 90% of women received radiotherapy, mostly with external beam therapy in combination with brachytherapy. Stomach cancer risk was non-significantly increased (odds ratios [ORs] 1.27–2.28) for women receiving between 0.5–4.9 Gy to the stomach cancer site and significantly increased at doses ≥5 Gy (OR=4.20, 95% confidence interval, 1.41–13.4, Ptrend=0.047) compared to non-irradiated women. A highly significant radiation dose-response relationship was evident when analyses were restricted to the 131 cases (251 controls) whose stomach cancer was located in the middle and lower portions of the stomach (Ptrend=0.003), whereas there was no indication of increasing risk with increasing dose for 30 cases (57 controls) whose cancer was located in the upper stomach (Ptrend=0.23). Conclusions Our findings showed for the first time a significant linear dose-response relationship for risk of stomach cancer in long-term survivors of cervical cancer. PMID:23707149

Radiation Dose and Subsequent Risk for Stomach Cancer in Long-term Survivors of Cervical Cancer

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

Kleinerman, Ruth A., E-mail: kleinerr@mail.nih.gov; Smith, Susan A.; Holowaty, Eric

2013-08-01

Purpose: To assess the dose–response relationship for stomach cancer after radiation therapy for cervical cancer. Methods and Materials: We conducted a nested, matched case–control study of 201 cases and 378 controls among 53,547 5-year survivors of cervical cancer diagnosed from 1943 to 1995, from 5 international, population-based cancer registries. We estimated individual radiation doses to the site of the stomach cancer for all cases and to corresponding sites for the matched controls (overall mean stomach tumor dose, 2.56 Gy, range 0.03-46.1 and after parallel opposed pelvic fields, 1.63 Gy, range 0.12-6.3). Results: More than 90% of women received radiation therapy,more » mostly with external beam therapy in combination with brachytherapy. Stomach cancer risk was nonsignificantly increased (odds ratio 1.27-2.28) for women receiving between 0.5 and 4.9 Gy to the stomach cancer site and significantly increased at doses ≥5 Gy (odds ratio 4.20, 95% confidence interval 1.41-13.4, P{sub trend}=.047) compared with nonirradiated women. A highly significant radiation dose–response relationship was evident when analyses were restricted to the 131 cases (251 controls) whose stomach cancer was located in the middle and lower portions of the stomach (P{sub trend}=.003), whereas there was no indication of increasing risk with increasing dose for 30 cases (57 controls) whose cancer was located in the upper stomach (P{sub trend}=.23). Conclusions: Our findings show for the first time a significant linear dose–response relationship for risk of stomach cancer in long-term survivors of cervical cancer.« less

Improved Tumor-Specific Drug Accumulation by Polymer Therapeutics with pH-Sensitive Drug Release Overcomes Chemotherapy Resistance.

PubMed

Heinrich, Anne-Kathrin; Lucas, Henrike; Schindler, Lucie; Chytil, Petr; Etrych, Tomáš; Mäder, Karsten; Mueller, Thomas

2016-05-01

The success of chemotherapy is limited by poor selectivity of active drugs combined with occurrence of tumor resistance. New star-like structured N-(2-hydroxypropyl) methacrylamide (HPMA) copolymer-based drug delivery systems containing doxorubicin attached via a pH-sensitive hydrazone bond were designed and investigated for their ability to overcome chemotherapy resistance. These conjugates combine two strategies to achieve a high drug concentration selectively at the tumor site: (I) high accumulation by passive tumor targeting based on enhanced permeability and retention effect and (II) pH-sensitive site-specific drug release due to an acidic tumor microenvironment. Mice bearing doxorubicin-resistant xenograft tumors were treated with doxorubicin, PBS, poly HPMA (pHPMA) precursor or pHPMA-doxorubicin conjugate at different equivalent doses of 5 mg/kg bodyweight doxorubicin up to a 7-fold total dose using different treatment schedules. Intratumoral drug accumulation was analyzed by fluorescence imaging utilizing intrinsic fluorescence of doxorubicin. Free doxorubicin induced significant toxicity but hardly any tumor-inhibiting effects. Administering at least a 3-fold dose of pHPMA-doxorubicin conjugate was necessary to induce a transient response, whereas doses of about 5- to 6-fold induced strong regressions. Tumors completely disappeared in some cases. The onset of response was differential delayed depending on the tumor model, which could be ascribed to distinct characteristics of the microenvironment. Further fluorescence imaging-based analyses regarding underlying mechanisms of the delayed response revealed a related switch to a more supporting intratumoral microenvironment for effective drug release. In conclusion, the current study demonstrates that the concept of tumor site-restricted high-dose chemotherapy is able to overcome therapy resistance. Mol Cancer Ther; 15(5); 998-1007. ©2016 AACR. ©2016 American Association for Cancer Research.

Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses

PubMed Central

Sakaki, Mizuho; Ebihara, Yukiko; Okamura, Kohji; Nakabayashi, Kazuhiko; Igarashi, Arisa; Matsumoto, Kenji; Hata, Kenichiro; Kobayashi, Yoshiro

2017-01-01

Cellular senescence is classified into two groups: replicative and premature senescence. Gene expression and epigenetic changes are reported to differ between these two groups and cell types. Normal human diploid fibroblast TIG-3 cells have often been used in cellular senescence research; however, their epigenetic profiles are still not fully understood. To elucidate how cellular senescence is epigenetically regulated in TIG-3 cells, we analyzed the gene expression and DNA methylation profiles of three types of senescent cells, namely, replicatively senescent, ras-induced senescent (RIS), and non-permissive temperature-induced senescent SVts8 cells, using gene expression and DNA methylation microarrays. The expression of genes involved in the cell cycle and immune response was commonly either down- or up-regulated in the three types of senescent cells, respectively. The altered DNA methylation patterns were observed in replicatively senescent cells, but not in prematurely senescent cells. Interestingly, hypomethylated CpG sites detected on non-CpG island regions (“open sea”) were enriched in immune response-related genes that had non-CpG island promoters. The integrated analysis of gene expression and methylation in replicatively senescent cells demonstrated that differentially expressed 867 genes, including cell cycle- and immune response-related genes, were associated with DNA methylation changes in CpG sites close to the transcription start sites (TSSs). Furthermore, several miRNAs regulated in part through DNA methylation were found to affect the expression of their targeted genes. Taken together, these results indicate that the epigenetic changes of DNA methylation regulate the expression of a certain portion of genes and partly contribute to the introduction and establishment of replicative senescence. PMID:28158250

Drainage effects on the transient, near-surface hydrologic response of a steep hillslope to rainfall: Implications for slope stability, Edmonds, Washington, USA

USGS Publications Warehouse

Biavati, G.; Godt, J.W.; McKenna, J.P.

2006-01-01

Shallow landslides on steep (>25??) hillsides along Puget Sound have resulted in occasional loss of life and costly damage to property during intense or prolonged rainfall. As part of a larger project to assess landslide hazards in the Seattle area, the U.S. Geological Survey instrumented two coastal bluff sites in 2001 to observe the subsurface hydrologic response to rainfall. The instrumentation at one of these sites, near Edmonds, Washington, consists of two rain gauges, two water-content probes that measure volumetric water content at eight depths between 0.2 and 2.0 m, and two tensiometer nests that measure soil-water suction at six depths ranging from 0.2 to 1.5m. Measurements from these instruments are used to test one- and two-dimensional numerical models of infiltration and groundwater flow. Capillary-rise tests, performed in the laboratory on soil sample from the Edmonds site, are used to define the soil hydraulic properties for the wetting process. The field observations of water content and suction show an apparent effect of porosity variation with depth on the hydraulic response to rainfall. Using a range of physical properties consistent with our laboratory and field measurements, we perform sensitivity analyses to investigate the effects of variation in physical and hydraulic properties of the soil on rainfall infiltration, pore-pressure response, and, hence, slope stability. For a two-layer-system in which the hydraulic conductivity of the upper layer is at least 10 times greater than the conductivity of the lower layer, and the infiltration rate is greater than the conductivity of the lower layer, a perched water table forms above the layer boundary potentially destabilizing the upper layer of soil. Two-dimensional modeling results indicate that the addition of a simple trench drain to the same two-layer slope has differing effects on the hydraulic response depending on the initial pressure head conditions. For slope-parallel flow conditions, pressure head is significantly reduced near the drain; however, for transient, vertical infiltration in a partially saturated soil, conditions consistent with those observed during monitoring at the Edmonds site, the drain decreases the thickness of a perched water table by a small amount.

Shedding light on ovothiol biosynthesis in marine metazoans

PubMed Central

Castellano, Immacolata; Migliaccio, Oriana; D’Aniello, Salvatore; Merlino, Antonello; Napolitano, Alessandra; Palumbo, Anna

2016-01-01

Ovothiol, isolated from marine invertebrate eggs, is considered one of the most powerful antioxidant with potential for drug development. However, its biological functions in marine organisms still represent a matter of debate. In sea urchins, the most accepted view is that ovothiol protects the eggs by the high oxidative burst at fertilization. In this work we address the role of ovothiol during sea urchin development to give new insights on ovothiol biosynthesis in metazoans. The gene involved in ovothiol biosynthesis OvoA was identified in Paracentrotus lividus genome (PlOvoA). PlOvoA embryo expression significantly increased at the pluteus stage and was up-regulated by metals at concentrations mimicking polluted sea-water and by cyclic toxic algal blooms, leading to ovothiol biosynthesis. In silico analyses of the PlOvoA upstream region revealed metal and stress responsive elements. Structural protein models highlighted conserved active site residues likely responsible for ovothiol biosynthesis. Phylogenetic analyses indicated that OvoA evolved in most marine metazoans and was lost in bony vertebrates during the transition from the aquatic to terrestrial environment. These results highlight the crucial role of OvoA in protecting embryos released in seawater from environmental cues, thus allowing the survival under different conditions. PMID:26916575

Application of an integrated biomarker response index to assess ground water contamination in the vicinity of a rare earth mine tailings site.

PubMed

Si, Wantong; He, Xiaoying; Li, Ailing; Liu, Li; Li, Jisheng; Gong, Donghui; Liu, Juan; Liu, Jumei; Shen, Weishou; Zhang, Xuefeng

2016-09-01

We utilized a multi-biomarker approach (Integrated Biomarker Response version 2, IBRv2) to investigate the scope and dispersion of groundwater contamination surrounding a rare earth mine tailings impoundment. Parameters of SD rat included in our IBRv2 analyses were glutathione levels, superoxide dismutase, catalase, and glutathione peroxidase activities, total anti-oxidative capacity, chromosome aberration, and micronucleus formation. The concentration of 20 pollutants including Cl(-), SO4 (2-), Na(+), K(+), Mg(2+), Ca(2+), TH, CODMn, As, Se, TDS, Be, Mn, Co, Ni, Cu, Zn, Mo, Cd, and Pb in the groundwater were also analyzed. The results of this study indicated that groundwater polluted by tailings impoundment leakage exhibited significant ecotoxicological effects. The selected biomarkers responded sensitively to groundwater pollution. Analyses showed a significant relationship between IBRv2 values and the Nemerow composite index. IBRv2 could serve as a sensitive ecotoxicological diagnosis method for assessing groundwater contamination in the vicinity of rare earth mine tailings. According to the trend of IBRv2 value and Nemerow composite index, the maximum diffusion distance of groundwater pollutants from rare earth mine tailings was approximately 5.7 km.

Shedding light on ovothiol biosynthesis in marine metazoans

NASA Astrophysics Data System (ADS)

Castellano, Immacolata; Migliaccio, Oriana; D'Aniello, Salvatore; Merlino, Antonello; Napolitano, Alessandra; Palumbo, Anna

2016-02-01

Ovothiol, isolated from marine invertebrate eggs, is considered one of the most powerful antioxidant with potential for drug development. However, its biological functions in marine organisms still represent a matter of debate. In sea urchins, the most accepted view is that ovothiol protects the eggs by the high oxidative burst at fertilization. In this work we address the role of ovothiol during sea urchin development to give new insights on ovothiol biosynthesis in metazoans. The gene involved in ovothiol biosynthesis OvoA was identified in Paracentrotus lividus genome (PlOvoA). PlOvoA embryo expression significantly increased at the pluteus stage and was up-regulated by metals at concentrations mimicking polluted sea-water and by cyclic toxic algal blooms, leading to ovothiol biosynthesis. In silico analyses of the PlOvoA upstream region revealed metal and stress responsive elements. Structural protein models highlighted conserved active site residues likely responsible for ovothiol biosynthesis. Phylogenetic analyses indicated that OvoA evolved in most marine metazoans and was lost in bony vertebrates during the transition from the aquatic to terrestrial environment. These results highlight the crucial role of OvoA in protecting embryos released in seawater from environmental cues, thus allowing the survival under different conditions.

Origination of asexual plantlets in three species of Crassulaceae.

PubMed

Guo, Jiansheng; Liu, Hailiang; He, Yangyang; Cui, Xianghuan; Du, Xiling; Zhu, Jian

2015-03-01

During asexual plant reproduction, cells from different organs can be reprogrammed to produce new individuals, a process that requires the coordination of cell cycle reactivation with the acquisition of other cellular morphological characteristics. However, the factors that influence the variety of asexual reproduction have not yet been determined. Here, we report on plantlet formation in Kalanchoe daigremontiana, Graptopetalum paraguayense, and Crassula portulacea (Crassulaceae) and analyse the effect of initiating cells on asexual reproduction in these three species. Additionally, the roles of WUSCHEL (WUS) and CUP-SHAPED COTYLEDON 1 (CUC1) in the asexual reproduction of these species were analysed through qRT-PCR. Our results indicated that pre-existing stem cell-like cells at the sites of asexual reproduction were responsible for the formation of plantlets. These cells were arrested in different phases of the cell cycle and showed different cell morphological characteristics and cell counts. The accumulation of auxin and cytokinin at the sites of asexual plantlet formation indicated their important functions, particularly for cell cycle reactivation. These differences may influence the pattern and complexity of asexual reproduction in these Crassulaceae species. Additionally, the dynamic expression levels of CUC1 and WUS may indicate that CUC1 functions in the formation of callus and shoot meristems; whereas, WUS was only associated with shoot induction.

32 CFR 179.3 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... remedial action is required. Munitions response area (MRA) means any area on a defense site that is known... MRA comprises one or more munitions response sites. Munitions response site (MRS) means a discrete location within an MRA that is known to require a munitions response. Operational range means a range that...

32 CFR 179.3 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... remedial action is required. Munitions response area (MRA) means any area on a defense site that is known... MRA comprises one or more munitions response sites. Munitions response site (MRS) means a discrete location within an MRA that is known to require a munitions response. Operational range means a range that...

32 CFR 179.3 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... remedial action is required. Munitions response area (MRA) means any area on a defense site that is known... MRA comprises one or more munitions response sites. Munitions response site (MRS) means a discrete location within an MRA that is known to require a munitions response. Operational range means a range that...

On meta- and mega-analyses for gene–environment interactions

PubMed Central

Huang, Jing; Liu, Yulun; Vitale, Steve; Penning, Trevor M.; Whitehead, Alexander S.; Blair, Ian A.; Vachani, Anil; Clapper, Margie L.; Muscat, Joshua E.; Lazarus, Philip; Scheet, Paul; Moore, Jason H.; Chen, Yong

2017-01-01

Gene-by-environment (G × E) interactions are important in explaining the missing heritability and understanding the causation of complex diseases, but a single, moderately sized study often has limited statistical power to detect such interactions. With the increasing need for integrating data and reporting results from multiple collaborative studies or sites, debate over choice between mega- versus meta-analysis continues. In principle, data from different sites can be integrated at the individual level into a “mega” data set, which can be fit by a joint “mega-analysis.” Alternatively, analyses can be done at each site, and results across sites can be combined through a “meta-analysis” procedure without integrating individual level data across sites. Although mega-analysis has been advocated in several recent initiatives, meta-analysis has the advantages of simplicity and feasibility, and has recently led to several important findings in identifying main genetic effects. In this paper, we conducted empirical and simulation studies, using data from a G × E study of lung cancer, to compare the mega- and meta-analyses in four commonly used G × E analyses under the scenario that the number of studies is small and sample sizes of individual studies are relatively large. We compared the two data integration approaches in the context of fixed effect models and random effects models separately. Our investigations provide valuable insights in understanding the differences between mega- and meta-analyses in practice of combining small number of studies in identifying G × E interactions. PMID:29110346

On meta- and mega-analyses for gene-environment interactions.

PubMed

Huang, Jing; Liu, Yulun; Vitale, Steve; Penning, Trevor M; Whitehead, Alexander S; Blair, Ian A; Vachani, Anil; Clapper, Margie L; Muscat, Joshua E; Lazarus, Philip; Scheet, Paul; Moore, Jason H; Chen, Yong

2017-12-01

Gene-by-environment (G × E) interactions are important in explaining the missing heritability and understanding the causation of complex diseases, but a single, moderately sized study often has limited statistical power to detect such interactions. With the increasing need for integrating data and reporting results from multiple collaborative studies or sites, debate over choice between mega- versus meta-analysis continues. In principle, data from different sites can be integrated at the individual level into a "mega" data set, which can be fit by a joint "mega-analysis." Alternatively, analyses can be done at each site, and results across sites can be combined through a "meta-analysis" procedure without integrating individual level data across sites. Although mega-analysis has been advocated in several recent initiatives, meta-analysis has the advantages of simplicity and feasibility, and has recently led to several important findings in identifying main genetic effects. In this paper, we conducted empirical and simulation studies, using data from a G × E study of lung cancer, to compare the mega- and meta-analyses in four commonly used G × E analyses under the scenario that the number of studies is small and sample sizes of individual studies are relatively large. We compared the two data integration approaches in the context of fixed effect models and random effects models separately. Our investigations provide valuable insights in understanding the differences between mega- and meta-analyses in practice of combining small number of studies in identifying G × E interactions. © 2017 WILEY PERIODICALS, INC.

Site quality in Appalachian hardwoods: the biological and economic response under selection silviculture

Treesearch

Orris D. McCauley; George R., Jr. Trimble

1975-01-01

The relative or percentage value response after 12 years of selective cutting practices on low- and high-quality sites in Appalachian hardwoods amounted to a 119-percent increase on the low-quality site and 145 percent on the high-quality site. The absolute value or actual dollar response, on the other hand, showed that the low-quality site increased in value only $76/...

Chk1 phosphorylation at Ser286 and Ser301 occurs with both stalled DNA replication and damage checkpoint stimulation.

PubMed

Ikegami, Yosuke; Goto, Hidemasa; Kiyono, Tohru; Enomoto, Masato; Kasahara, Kousuke; Tomono, Yasuko; Tozawa, Keiichi; Morita, Akimichi; Kohri, Kenjiro; Inagaki, Masaki

2008-12-26

We previously reported Chk1 to be phosphorylated at Ser286 and Ser301 by cyclin-dependent kinase (Cdk) 1 during mitosis [T. Shiromizu et al., Genes Cells 11 (2006) 477-485]. Here, we demonstrated that Chk1-Ser286 and -Ser301 phosphorylation also occurs in hydroxyurea (HU)-treated or ultraviolet (UV)-irradiated cells. Unlike the mitosis case, however, Chk1 was phosphorylated not only at Ser286 and Ser301 but also at Ser317 and Ser345 in the checkpoint response. Treatment with Cdk inhibitors diminished Chk1 phosphorylation at Ser286 and Ser301 but not at Ser317 and Ser345 with the latter. In vitro analyses revealed Ser286 and Ser301 on Chk1 to serve as two major phosphorylation sites for Cdk2. Immunoprecipitation analyses further demonstrated that Ser286/Ser301 and Ser317/Ser345 phosphorylation occur in the same Chk1 molecule during the checkpoint response. In addition, Ser286/Ser301 phosphorylation by Cdk2 was observed in Chk1 mutated to Ala at Ser317 and Ser345 (S317A/S345A), as well as Ser317/Ser345 phosphorylation by ATR was in S286A/S301A. Therefore, Chk1 phosphorylation in the checkpoint response is regulated not only by ATR but also by Cdk2.

Monitoring of dioxin-like, estrogenic and anti-androgenic activities in sediments of the Bizerta lagoon (Tunisia) by means of in vitro cell-based bioassays: contribution of low concentrations of polynuclear aromatic hydrocarbons (PAHs).

PubMed

Louiz, I; Kinani, S; Gouze, M-E; Ben-Attia, M; Menif, D; Bouchonnet, S; Porcher, J M; Ben-Hassine, O K; Aït-Aïssa, S

2008-09-01

We used an array of in vitro cell-based bioassays to assess dioxin-like, estrogenic and (anti-)androgenic activities in organic extracts of sediments from the Bizerta lagoon, one of the largest Tunisian lagoons subjected to various anthropogenic and industrial pressures. The sediments were sampled both in winter and summer 2006 in 6 stations differently impacted and in one reference station located in the seawards entrance of Ghar el Melh lagoon. Chemical analyses of the 16 priority PAHs showed that the sediments were low to moderately contaminated (2-537 ng/g dry weight). By using the estrogen- (MELN) and androgen-responsive (MDA-kb2) reporter cell lines, significant estrogenic and anti-androgenic activities were detected only in the Menzel Bourguiba (MB) site, the most contaminated site, both in winter and summer. By using 7-ethoxyresorufin-O-deethylase (EROD) induction in the fish PLHC-1 cell line after both 4 and 24 h of cell exposure, dioxin-like activities were detected in all analysed samples. Dioxin-like activities were higher after 4 h exposure, and varied according to the sites and the sampling season. While highly significant correlation was observed between bioassay- and chemical analyses-derived toxic equivalents (TEQs), PAHs accounted for only a small part (up to 4%) of the detected biological activities, suggesting that other readily metabolised EROD-inducing compounds were present. This study argues for the use of short time exposure to assess biological TEQs in low contaminated samples and provides new induction equivalent factors (IEF(4h)) for 16 PAHs in the PLHC-1 cell line. Finally, our results stress the need to further characterise the nature of organic chemical contamination as well as its long-term impacts on aquatic wildlife in the Bizerta lagoon.

Inter and intrasite analyses of cultural materials from U20aw, Nye County, Nevada. Technical report No. 66

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

Hicks, P.A.; Pippin, L.C.; Henton, G.H.

1991-12-01

In the Spring of 1986 Desert Research Institute (DRI) conducted a Class III archaeological survey of Drill Hole U20aw on the Nevada Test Site, Nye County, Nevada. Seven archaeological sites were located during the course of this survey including two temporary camps, four lithic scatters, and a possible pinyon cache. This report presents the results of the analyses of the data derived from all sites investigated during the data recovery operations on Drill Hole U20aw. Detailed analyses were focused on the spatial distribution of artifacts and features within and between sites in the southern portion of the study area (26Ny4867,more » 26Ny4869, and 26Ny4871). These analyses indicate that 26Ny4871 served principally as a temporary camp, while the area around the canyonhead to the east (which includes 26Ny4867 and 26Ny4869) seems to have been used as a site for both temporary camps and special activity loci. Projectile point styles suggest that the area was occupied from the Early Archaic into the early Historic period. Analyses of the artifacts that were recovered indicate that obsidian was the preferred material for all classes of flaked stone tools. All stages of lithic reduction are represented on the sites, but core reduction and thinning of bifaces appear to have been the primary activities. Processing of floral foods is indicated by the presence of several ground stone artifacts. Pinyon nuts and other items appear to have been stored in the area of 26Ny4869 and to the north of the drill hole as evidenced by the presence of several rock features that may have served as caches.« less

Inter and intrasite analyses of cultural materials from U20aw, Nye County, Nevada

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

Hicks, P.A.; Pippin, L.C.; Henton, G.H.

1991-12-01

In the Spring of 1986 Desert Research Institute (DRI) conducted a Class III archaeological survey of Drill Hole U20aw on the Nevada Test Site, Nye County, Nevada. Seven archaeological sites were located during the course of this survey including two temporary camps, four lithic scatters, and a possible pinyon cache. This report presents the results of the analyses of the data derived from all sites investigated during the data recovery operations on Drill Hole U20aw. Detailed analyses were focused on the spatial distribution of artifacts and features within and between sites in the southern portion of the study area (26Ny4867,more » 26Ny4869, and 26Ny4871). These analyses indicate that 26Ny4871 served principally as a temporary camp, while the area around the canyonhead to the east (which includes 26Ny4867 and 26Ny4869) seems to have been used as a site for both temporary camps and special activity loci. Projectile point styles suggest that the area was occupied from the Early Archaic into the early Historic period. Analyses of the artifacts that were recovered indicate that obsidian was the preferred material for all classes of flaked stone tools. All stages of lithic reduction are represented on the sites, but core reduction and thinning of bifaces appear to have been the primary activities. Processing of floral foods is indicated by the presence of several ground stone artifacts. Pinyon nuts and other items appear to have been stored in the area of 26Ny4869 and to the north of the drill hole as evidenced by the presence of several rock features that may have served as caches.« less

Antigenic Fingerprinting following Primary RSV Infection in Young Children Identifies Novel Antigenic Sites and Reveals Unlinked Evolution of Human Antibody Repertoires to Fusion and Attachment Glycoproteins

PubMed Central

Fuentes, Sandra; Coyle, Elizabeth M.; Beeler, Judy; Golding, Hana; Khurana, Surender

2016-01-01

Respiratory Syncytial Virus (RSV) is the major cause of pneumonia among infants. Here we elucidated the antibody repertoire following primary RSV infection and traced its evolution through adolescence and adulthood. Whole genome-fragment phage display libraries (GFPDL) expressing linear and conformational epitopes in the RSV fusion protein (F) and attachment protein (G) were used for unbiased epitope profiling of infant sera prior to and following RSV infection. F-GFPDL analyses demonstrated modest changes in the anti-F epitope repertoires post-RSV infection, while G-GFPDL analyses revealed 100-fold increase in number of bound phages. The G-reactive epitopes spanned the N- and C-terminus of the G ectodomain, along with increased reactivity to the central conserved domain (CCD). Panels of F and G antigenic sites were synthesized to evaluate sera from young children (<2 yr), adolescents (14–18 yr) and adults (30–45 yr) in SPR real-time kinetics assays. A steady increase in RSV-F epitope repertoires from young children to adults was observed using peptides and F proteins. Importantly, several novel epitopes were identified in pre-fusion F and an immunodominant epitope in the F-p27. In all age groups, antibody binding to pre-fusion F was 2–3 folds higher than to post-fusion form. For RSV-G, antibody responses were high following early RSV infection in children, but declined significantly in adults, using either G proteins or peptides. This study identified unlinked evolution of anti-F and anti G responses and supportive evidence for immune pressure driven evolution of RSV-G. These findings could help development of effective countermeasures including vaccines. PMID:27100289

Phenological behaviour of early spring flowering trees in Spain in response to recent climate changes

NASA Astrophysics Data System (ADS)

Hidalgo-Galvez, M. D.; García-Mozo, H.; Oteros, J.; Mestre, A.; Botey, R.; Galán, C.

2018-04-01

This research reports the phenological trends of four early spring and late winter flowering trees in Spain (south Europe) from a recent period (1986-2012). The studied species were deciduous trees growing in different climatic areas: hazel ( Corylus avellana L.), willow ( Salix alba L.), ash ( Fraxinus angustifolia Vahl.) and white mulberry ( Morus alba L.). We analysed the response to climate and the trends of the following phenophases observed at the field: budburst, leaf unfolding, flowering, fruit ripening, fruit harvesting, leaf colour change and leaf-fall. The study was carried out in 17 sampling sites in the country with the aim of detecting the recent phenological response to the climate of these species, and the possible effect of climate change. We have observed differences in the phenological response to climate depending on each species. Sixty-one percent of studied sites suffered an advance of early spring phenophases, especially budburst on average by -0.67 days and flowering on average by -0.15 days during the studied period, and also in the subsequent fruit ripening and harvesting phases on average by -1.06 days. By contrast, it has been detected that 63% of sampling sites showed a delay in autumn vegetative phases, especially leaf-fall events on average by +1.15 days. The statistic correlation analysis shows in the 55% of the studied localities that phenological advances are the consequence of the increasing trend detected for temperature—being minimum temperature the most influential factor—and in the 52% of them, phenological advances occurred by rainfall variations. In general, leaf unfolding and flowering from these species showed negative correlations in relation to temperature and rainfall, whereas that leaf colour change and leaf-fall presented positive correlations. The results obtained have a great relevance due to the fact that they can be considered as reliable bio-indicators of the impact of the recent climate changes in southern Europe.

Rich fen development in SE Poland and its response to climate changes and human impacts in the late Holocene

NASA Astrophysics Data System (ADS)

Gałka, Mariusz; Apolinarska, Karina; Aunina, Liene; Feurdean, Angelica; Hutchinson, Simon; Kołaczek, Piotr

2016-04-01

Rich fens are one of the most important wetland ecosystems due to their high species-richness and unique species composition. They are occupied by endangered, vulnerable and protected plants, such as Cladium mariscus and Schoenus ferrugineus. For this reason knowledge of the history of rich fens is important for the development of effective management strategies to protect or restore these widely threatened habitats. Our palaeoecological study reconstructs the development of Bagno Serebryskie rich fen (ca. 376 ha), a site with the largest population of Cladium mariscus in CE Europe, and its response to climate changes and human impacts during the last 3500 years. For this we analyse two peat profiles at this site, at a high resolution (1 and 2 cm) using multi-aspect palaeoecological analyses (plant macrofossils, pollen, molluscs, geochemistry, charcoal and AMS 14C radiocarbon) to assess the impact of climate changes, human activity, and fires on local vegetation. Local plant succession in our two coring points followed parallel trajectories; after a lake stage, ca. 1800 cal yr BP (core I) and 3300 cal yr BP (core II), fen species e.g. Menyanthes trifoliata, Mentha aquatic, Carex lasiocarpa appeared, followed at ca. 500 cal. yr BP by Cladium mariscus, which is currently the dominant plant species in the Bagno Serebryskie peatland. In one peat profile (core II) we found abundant macrocharcoal particles at 1050, 700, 400 cal yr BP and the present, but fires had no significant impact on the development of the mire. In the other peat profile (core I) we noted four stages (at 2300, 1350, 400, 100 cal yr BP) with an increasing diversity of mollusc species typical of overgrown, but permanent water bodies. Their increased abundance and diversity can be linked to a rise in mire water table at these times. Our studies indicate that rich fens can provide reliable sites for palaeoecological reconstruction of the late Holocene providing valuable information that can be applied to enhance such sites and maintain their important biodiversity in addition to ecosystem services such as C storage. Research funded by the National Science Centre, grant no UMO-2013/09/B/ST10/01589 (2014-2016).

A Preliminary Analysis on Empirical Attenuation of Absolute Velocity Response Spectra (1 to 10s) in Japan

NASA Astrophysics Data System (ADS)

Dhakal, Y. P.; Kunugi, T.; Suzuki, W.; Aoi, S.

2013-12-01

The Mw 9.1 Tohoku-oki earthquake caused strong shakings of super high rise and high rise buildings constructed on deep sedimentary basins in Japan. Many people felt difficulty in moving inside the high rise buildings even on the Osaka basin located at distances as far as 800 km from the epicentral area. Several empirical equations are proposed to estimate the peak ground motions and absolute acceleration response spectra applicable mainly within 300 to 500km from the source area. On the other hand, Japan Meteorological Agency has recently proposed four classes of absolute velocity response spectra as suitable indices to qualitatively describe the intensity of long-period ground motions based on the observed earthquake records, human experiences, and actual damages that occurred in the high rise and super high rise buildings. The empirical prediction equations have been used in disaster mitigation planning as well as earthquake early warning. In this study, we discuss the results of our preliminary analysis on attenuation relation of absolute velocity response spectra calculated from the observed strong motion records including those from the Mw 9.1 Tohoku-oki earthquake using simple regression models with various model parameters. We used earthquakes, having Mw 6.5 or greater, and focal depths shallower than 50km, which occurred in and around Japanese archipelago. We selected those earthquakes for which the good quality records are available over 50 observation sites combined from K-NET and KiK-net. After a visual inspection on approximately 21,000 three component records from 36 earthquakes, we used about 15,000 good quality records in the period range of 1 to 10s within the hypocentral distance (R) of 800km. We performed regression analyses assuming the following five regression models. (1) log10Y (T) = c+ aMw - log10R - bR (2) log10Y (T) = c+ aMw - log10R - bR +gS (3) log10Y (T) = c+ aMw - log10R - bR + hD (4) log10Y (T) = c+ aMw - log10R - bR +gS +hD (5) log10Y (T) = c+ aMw - log10R - bR +∑gS +hD where Y (T) is the 5% damped peak vector response in cm/s derived from two horizontal component records for a natural period T in second; in (2) S is a dummy variable which is one if a site is located inside a sedimentary basin, otherwise zero. In (3), D is depth to the top of layer having a particular S-wave velocity. We used the deep underground S-wave velocity model available from Japan Seismic Hazard Information Station (J-SHIS). In (5), sites are classified to various sedimentary basins. Analyses show that the standard deviations decrease in the order of the models listed and the all coefficients are significant. Interestingly, coefficients g are found to be different from basin to basin at most periods, and the depth to the top of layer having S-wave velocity of 1.7km/s gives the smallest standard deviation of 0.31 at T=4.4s in (5). This study shows the possibility of describing the observed peak absolute velocity response values by using simple model parameters like site location and sedimentary depth soon after the location and magnitude of an earthquake are known.

Site-dependent proxy response to climate change during the last 140 years observed in varved lake sediments in Northern Poland

NASA Astrophysics Data System (ADS)

Ott, Florian; Kramkowski, Mateusz; Wulf, Sabine; Plessen, Birgit; Serb, Johanna; Tjallingii, Rik; Schwab, Markus; Słowiński, Michał; Brykała, Dariusz; Tyszkowski, Sebastian; Putyrskaya, Victoria; Appelt, Oona; Błaszkiewicz, Mirosław; Brauer, Achim

2017-04-01

This accurate dating and chronological correlation using crypto-tephras provide a powerful way to compare the varved sediment records of the lakes Głęboczek (JG), Czechowskie (JC) and Jelonek (JEL) (north-central Poland). For the last 140 years, high-resolution varve micro-facies analyses (seasonal layer composition and thickness) and µ-XRF element scanning as well as bulk geochemical analyses (TOC, CaCO3) at sub-decadal to decadal resolution were conducted for all three records. Varve chronologies have been independently established by means of annual layer counting. 137Cs activity concentration measurements confirmed the varve chronology from JC. The Askja AD1875 tephra has been used to synchronize the records. A comparison of sediment data with monthly temperature data from Koszalin since 1870 and daily temperature data from Chojnice since 1951 revealed different responses of lake deposition to recent temperature change. Varves are well-preserved over the entire 140 years only in the sediments of JG, while in the JC record two faintly varved intervals are intercalated and in JEL two non-varved intervals occur at the base and top of the profile. These differences likely are due to variations in lake characteristics. Climate changes at the demise of the Little Ice Age and the recent warming since the 1980s are expressed in varve micro-facies, CaCO3 and TOC contents in the three lakes with different response times and amplitudes. This allows us to discuss the role of local parameters like lake size, bathymetry and water depth in transferring climate change signals into lake sediment records. This study is a contribution to the Virtual Institute of Integrated Climate and Landscape Evolution Analyses - ICLEA - of the Helmholtz Association, grant number VH-VI-415.

75 FR 8701 - Settlement Agreement for Recovery of Past Response Costs Colorado Bumper Exchange Site, Pueblo...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-25

... Response Costs incurred at the Site. In exchange, the Settling Party will be granted a covenant not to sue... Costs Colorado Bumper Exchange Site, Pueblo, Pueblo County, CO AGENCY: Environmental Protection Agency... proposes to compromise a claim the United States has at this Site for Past Response Costs, as those terms...

Three-year growth response of young Douglas-fir to nitrogen, calcium, phosphorus, and blended fertilizers in Oregon and Washington

USGS Publications Warehouse

Mainwaring, Douglas B.; Maguire, Douglas A.; Perakis, Steven S.

2014-01-01

Studies of nutrient limitation in Douglas-fir forests of the Pacific Northwest focus predominantly on nitrogen, yet many stands demonstrate negligible or even negative growth response to nitrogen fertilization. To understand what nutrients other than nitrogen may limit forest productivity in this region, we tested six fertilizer treatments for their ability to increase stem volume growth response of dominant and co-dominant trees in young Douglas-fir plantations across a range of foliar and soil chemistry in western Oregon and Washington. We evaluated responses to single applications of urea, lime, calcium chloride, or monosodium phosphate at 16 sites, and to two site-specific nutrients blends at 12 of these sites. Across sites, the average stem volume growth increased marginally with urea, lime, and phosphorus fertilization. Fertilization responses generally aligned with plant and soil indicators of nutrient limitation. Response to nitrogen addition was greatest on soils with low total nitrogen and high exchangeable calcium concentrations. Responses to lime and calcium chloride additions were greatest at sites with low foliar calcium and low soil pH. Response to phosphorus addition was greatest on sites with low foliar phosphorus and high soil pH. Blended fertilizers yielded only marginal growth increases at one site, with no consistent effect across sites. Overall, our results highlight that calcium and phosphorus can be important growth limiting nutrients on specific sites in nitrogen-rich Douglas-fir forests of the Pacific Northwest.

Benefits and Sustainability of a Learning Collaborative for Implementation of Treat to Target in Rheumatoid Arthritis: Results of the TRACTION Trial Phase II.

PubMed

Solomon, Daniel H; Lu, Bing; Yu, Zhi; Corrigan, Cassandra; Harrold, Leslie R; Smolen, Josef S; Fraenkel, Liana; Katz, Jeffrey N; Losina, Elena

2018-01-05

We conducted a two-phase randomized controlled trial of a Learning Collaborative (LC) to facilitate implementation of treat to target (TTT) to manage rheumatoid arthritis (RA). We found substantial improvement in implementation of TTT in Phase I. Herein, we report on a second 9 months (Phase II) where we examined maintenance of response in Phase I and predictors of greater improvement in TTT adherence. We recruited 11 rheumatology sites and randomized them to either receive the LC during Phase I or to a wait-list control group that received the LC intervention during Phase II. The outcome was change in TTT implementation score (0 to 100, 100 is best) from pre- to post-intervention. TTT implementation score is defined as a percent of components documented in visit notes. Analyses examined: 1) the extent that the Phase I intervention teams sustained improvement in TTT; and, 2) predictors of TTT improvement. The analysis included 636 RA patients. At baseline, mean TTT implementation score was 11% in Phase I intervention sites and 13% in Phase II sites. After the intervention, TTT implementation score improved to 57% in the Phase I intervention sites and to 58% in the Phase II sites. Intervention sites from Phase I sustained the improvement during the Phase II (52%). Predictors of greater TTT improvement included only having rheumatologist providers at the site, academic affiliation of the site, fewer providers per site, and the rheumatologist provider being a trainee. Improvement in TTT remained relatively stable over a post-intervention period. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Modeling of site occupancy dynamics for northern spotted owls, with emphasis on the effects of barred owls

USGS Publications Warehouse

Olson, Gail S.; Anthony, Robert G.; Forsman, Eric D.; Ackers, Steven H.; Loschl, Peter J.; Reid, Janice A.; Dugger, Katie M.; Glenn, Elizabeth M.; Ripple, William J.

2005-01-01

Northern spotted owls (Strix occidentalis caurina) have been studied intensively since their listing as a threatened species by the U.S. Fish and Wildlife Service in 1990. Studies of spotted owl site occupancy have used various binary response measures, but most of these studies have made the assumption that detectability is perfect, or at least high and not variable. Further, previous studies did not consider temporal variation in site occupancy. We used relatively new methods for open population modeling of site occupancy that incorporated imperfect and variable detectability of spotted owls and allowed modeling of temporal variation in site occupancy, extinction, and colonization probabilities. We also examined the effects of barred owl (S. varia) presence on these parameters. We used spotted owl survey data from 1990 to 2002 for 3 study areas in Oregon, USA, and we used program MARK to develop and analyze site occupancy models. We found per visit detection probabilities averaged <0.70 and were highly variable among study years and study areas. Site occupancy probabilities for owl pairs declined greatly on 1 study area and slightly on the other 2 areas. For all owls, including singles and pairs, site occupancy was mostly stable through time. Barred owl presence had a negative effect on spotted owl detection probabilities, and it had either a positive effect on local-extinction probabilities or a negative effect on colonization probabilities. We conclude that further analyses of spotted owls must account for imperfect and variable detectability and barred owl presence to properly interpret results. Further, because barred owl presence is increasing within the range of northern spotted owls, we expect to see further declines in the proportion of sites occupied by spotted owls.

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.

Quarterly environmental data summary for first quarter 1999

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

NONE

In support of the Weldon Spring Site Remedial Action Project Federal Facilities Agreement, a copy of the Quarterly Environmental Data Summary (QEDS) for the first quarter of 1999 is enclosed. The data presented in this constitute the QEDS. The data, except for air monitoring data and site KPA generated data (uranium analyses), were received from the contract laboratories, verified by the Weldon Spring Site verification group and merged into the database during the first quarter of 1999. KPA results for on-site total uranium analyses performed during first quarter 1999 are included. Air monitoring data presented are the most recent completemore » sets of quarterly data.« less

Quantitative characterization of the regressive ecological succession by fractal analysis of plant spatial patterns

USGS Publications Warehouse

Alados, C.L.; Pueyo, Y.; Giner, M.L.; Navarro, T.; Escos, J.; Barroso, F.; Cabezudo, B.; Emlen, J.M.

2003-01-01

We studied the effect of grazing on the degree of regression of successional vegetation dynamic in a semi-arid Mediterranean matorral. We quantified the spatial distribution patterns of the vegetation by fractal analyses, using the fractal information dimension and spatial autocorrelation measured by detrended fluctuation analyses (DFA). It is the first time that fractal analysis of plant spatial patterns has been used to characterize the regressive ecological succession. Plant spatial patterns were compared over a long-term grazing gradient (low, medium and heavy grazing pressure) and on ungrazed sites for two different plant communities: A middle dense matorral of Chamaerops and Periploca at Sabinar-Romeral and a middle dense matorral of Chamaerops, Rhamnus and Ulex at Requena-Montano. The two communities differed also in the microclimatic characteristics (sea oriented at the Sabinar-Romeral site and inland oriented at the Requena-Montano site). The information fractal dimension increased as we moved from a middle dense matorral to discontinuous and scattered matorral and, finally to the late regressive succession, at Stipa steppe stage. At this stage a drastic change in the fractal dimension revealed a change in the vegetation structure, accurately indicating end successional vegetation stages. Long-term correlation analysis (DFA) revealed that an increase in grazing pressure leads to unpredictability (randomness) in species distributions, a reduction in diversity, and an increase in cover of the regressive successional species, e.g. Stipa tenacissima L. These comparisons provide a quantitative characterization of the successional dynamic of plant spatial patterns in response to grazing perturbation gradient. ?? 2002 Elsevier Science B.V. All rights reserved.

Biotic mortality factors affecting emerald ash borer (Agrilus planipennis) are highly dependent on life stage and host tree crown condition.

PubMed

Jennings, D E; Duan, J J; Shrewsbury, P M

2015-10-01

Emerald ash borer (EAB), Agrilus planipennis, is a serious invasive forest pest in North America responsible for killing tens to hundreds of millions of ash trees since it was accidentally introduced in the 1990 s. Although host-plant resistance and natural enemies are known to be important sources of mortality for EAB in Asia, less is known about the importance of different sources of mortality at recently colonized sites in the invaded range of EAB, and how these relate to host tree crown condition. To further our understanding of EAB population dynamics, we used a large-scale field experiment and life-table analyses to quantify the fates of EAB larvae and the relative importance of different biotic mortality factors at 12 recently colonized sites in Maryland. We found that the fates of larvae were highly dependent on EAB life stage and host tree crown condition. In relatively healthy trees (i.e., with a low EAB infestation) and for early instars, host tree resistance was the most important mortality factor. Conversely, in more unhealthy trees (i.e., with a moderate to high EAB infestation) and for later instars, parasitism and predation were the major sources of mortality. Life-table analyses also indicated how the lack of sufficient levels of host tree resistance and natural enemies contribute to rapid population growth of EAB at recently colonized sites. Our findings provide further evidence of the mechanisms by which EAB has been able to successfully establish and spread in North America.

An integrated approach for identifying priority contaminant in ...

EPA Pesticide Factsheets

Environmental assessment of complex mixtures typically requires integration of chemical and biological measurements. This study demonstrates the use of a combination of instrumental chemical analyses, effects-based monitoring, and bio-effects prediction approaches to help identify potential hazards and priority contaminants in two Great Lakes Areas of Concern (AOCs), the Lower Green Bay/Fox River located near Green Bay, WI, USA and the Milwaukee River Estuary, located near Milwaukee, WI, USA. Fathead minnows were caged at four sites within each AOC (eight sites total). Following 4 d of in situ exposure, tissues and biofluids were sampled and used for targeted biological effects analyses. Additionally, 4 d composite water samples were collected concurrently at each caged fish site and analyzed for 134 analytes as well as evaluated for total estrogenic and androgenic activity using cell-based bioassays. Of the analytes examined, 75 were detected in composite samples from at least one site. Based on multiple analyses, one site in the East River and another site near a paper mill discharge from lower Green Bay/Fox River AOC, were prioritized due to their estrogenic and androgenic acitvity, respectively. The water samples from other sites generally did not exhibit significant estrogenic or androgenic activity, nor was there evidence for endocrine disruption in the fish exposed at these sites as indicated the the lack of alterations in ex vivo steroid production, c

Quantifying Forest Soil Physical Variables Potentially Important for Site Growth Analyses

Treesearch

John S. Kush; Douglas G. Pitt; Phillip J. Craul; William D. Boyer

2004-01-01

Accurate mean plot values of forest soil factors are required for use as independent variables in site-growth analyses. Adequate accuracy is often difficult to attain because soils are inherently widely variable. Estimates of the variability of appropriate soil factors influencing growth can be used to determine the sampling intensity required to secure accurate mean...

Can ecological history influence immunomarker responses and antioxidant enzyme activities in bivalves that have been experimentally exposed to contaminants? A new subject for discussion in "eco-immunology" studies.

PubMed

Matozzo, Valerio; Giacomazzo, Matteo; Finos, Livio; Marin, Maria Gabriella; Bargelloni, Luca; Milan, Massimo

2013-07-01

Numerous studies have demonstrated that environmental parameters affect bivalve immunomarkers. In the present study, we tested the hypothesis that clams (Venerupis philippinarum) collected in sites with different environmental conditions respond differently to experimental contaminant exposure. Clams were collected at two sites within the Lagoon of Venice that are influenced differently by both anthropogenic impact and natural conditions: Marghera, which is characterised by relatively high contamination levels and restricted clam fishing, and Chioggia, which is inside a licensed clam culture area that is characterised by lower contamination levels. Total haemocyte count, haemocyte diameter and volume, lysozyme activity in both haemocyte lysate and cell-free haemolymph, superoxide dismutase and catalase activities in gills and digestive glands were measured at time 0 (clam sampling time), after 7 days of acclimation in the laboratory and after 1, 3 and 7 days of copper exposure. Interestingly, statistical analyses (three-way ANOVA and Canonical Correlation Analysis) revealed persistent differences in the biological responses of clams from the two sampling sites before and after copper exposure. Conversely, the influence of copper on cellular and biochemical parameters was negligible. Overall, the results obtained indicated that animals with a different ecological history respond differently to experimental contaminant exposure. In addition, this study suggested that immunomarkers and other biomarkers might be used to determine the origin of fishing products. Copyright © 2013 Elsevier Ltd. All rights reserved.

Multiscale site-response mapping: A case study of Parkfield, California

USGS Publications Warehouse

Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Morgan, E.C.; Kaklamanos, J.

2011-01-01

The scale of previously proposed methods for mapping site-response ranges from global coverage down to individual urban regions. Typically, spatial coverage and accuracy are inversely related.We use the densely spaced strong-motion stations in Parkfield, California, to estimate the accuracy of different site-response mapping methods and demonstrate a method for integrating multiple site-response estimates from the site to the global scale. This method is simply a weighted mean of a suite of different estimates, where the weights are the inverse of the variance of the individual estimates. Thus, the dominant site-response model varies in space as a function of the accuracy of the different models. For mapping applications, site-response models should be judged in terms of both spatial coverage and the degree of correlation with observed amplifications. Performance varies with period, but in general the Parkfield data show that: (1) where a velocity profile is available, the square-rootof- impedance (SRI) method outperforms the measured VS30 (30 m divided by the S-wave travel time to 30 m depth) and (2) where velocity profiles are unavailable, the topographic slope method outperforms surficial geology for short periods, but geology outperforms slope at longer periods. We develop new equations to estimate site response from topographic slope, derived from the Next Generation Attenuation (NGA) database.

Understanding variation in ecosystem pulse responses to wetting: Benefits of data-model coupling

NASA Astrophysics Data System (ADS)

Jenerette, D.

2011-12-01

Metabolic pulses of activity are a common ecological response to intermittently available resources and in water-limited ecosystems these pulses often occur in response to wetting. Net ecosystem CO2 exchange (NEE) in response to episodic wetting events is hypothesized to have a complex trajectory reflecting the distinct responses, or "pulses", of respiration and photosynthesis. To help direct research activities a physiological-based model of whole ecosystem metabolic activity up- and down-regulation was developed to investigate ecosystem energy balance and gas exchange pulse responses following precipitation events. This model was to investigate pulse dynamics from a local network of sites in southern Arizona, a global network of eddy-covariance ecosystem monitoring sites, laboratory incubation studies, and field manipulations. Pulse responses were found to be ubiquitous across ecosystem types. These pulses had a highly variable influence on NEE following wetting, ranging from large net sinks to sources of CO2 to the atmosphere. Much of the variability in pulse responses of NEE could be described through a coupled up- and down-regulation pulse response model. Respiration pulses were hypothesized to occur through a reduction in whole ecosystem activation energy; this model was both useful and corroborated through laboratory incubation studies of soil respiration. Using the Fluxnet eddy-covariance measurement database event specific responses were combined with the pulse model into an event specific twenty-five day net flux calculation. Across all events observed a general net accumulation of CO2 following a precipitation event, with the largest net uptake within deciduous broadleaf forests and smallest within grasslands. NEE pulses favored greater uptake when pre-event ecosystem respiration rates and total precipitation were higher. While the latter was expected, the former adds to previous theory by suggesting a larger net uptake of CO2 when pre-event metabolic activity is higher. Scenario analyses of precipitation regimes suggested increased uptake with increasing total precipitation while more complex NEE responses to increasing number of events and interval between events. Pulse dynamics provides a general framework for understanding ecosystem responses to intermittent wetting projected to occur more frequently in future climates. Pulse dynamics also provides an opportunity to evaluate processes spanning cellular upregulation to global change.

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

PubMed Central

Fedrigo, Olivier; Babbitt, Courtney C.; Wortham, Matthew; Tewari, Alok K.; London, Darin; Song, Lingyun; Lee, Bum-Kyu; Iyer, Vishwanath R.; Parker, Stephen C. J.; Margulies, Elliott H.; Wray, Gregory A.; Furey, Terrence S.; Crawford, Gregory E.

2012-01-01

Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge. Mutations in non-coding regulatory DNA that alter gene expression have been hypothesized as a key driver of these phenotypic differences. This has been supported by differential gene expression analyses in general, but not by the identification of specific regulatory elements responsible for changes in transcription and phenotype. To identify the genetic source of regulatory differences, we mapped DNaseI hypersensitive (DHS) sites, which mark all types of active gene regulatory elements, genome-wide in the same cell type isolated from human, chimpanzee, and macaque. Most DHS sites were conserved among all three species, as expected based on their central role in regulating transcription. However, we found evidence that several hundred DHS sites were gained or lost on the lineages leading to modern human and chimpanzee. Species-specific DHS site gains are enriched near differentially expressed genes, are positively correlated with increased transcription, show evidence of branch-specific positive selection, and overlap with active chromatin marks. Species-specific sequence differences in transcription factor motifs found within these DHS sites are linked with species-specific changes in chromatin accessibility. Together, these indicate that the regulatory elements identified here are genetic contributors to transcriptional and phenotypic differences among primate species. PMID:22761590

Structure investigation of codeine drug using mass spectrometry, thermal analyses and semi-emperical molecular orbital (MO) calculations

NASA Astrophysics Data System (ADS)

Zayed, M. A.; Hawash, M. F.; Fahmey, M. A.

2006-05-01

Codeine is an analgesic with uses similar to morphine, but it has a mild sedative effect. It is preferable used as phosphate form and it is often administrated by mouth with aspirin or paracetamol. Therefore, it is important to investigate its structure to know the active groups and weak bonds responsible for its medical activity. Consequently in the present work, codeine was investigated by mass spectrometry and thermal analyses (TG, DTG and DTA) and confirming by semi-empirical MO-calculation (PM3 method) in the neutral and positively charged forms of the drug. Some results of studying the d-block element complexes of codeine were used to declare the relationship between drug structure and its chemical reactivity in vitro system. The mass spectra and thermal analyses fragmentation pathways were proposed and compared to each other to select the most suitable scheme representing the correct fragmentation of this drug. From EI mass spectra, the main primary cleavage site of the charged drug molecule is that due to β-cleavage to nitrogen atom in its skeleton. It occurs in two parallel mechanisms with the same possibility, i.e. no difference in appearance activation energy between them. In the neutral drug form the primary site cleavage is that occurs in the ether ring. Thermal analyses of the neutral form of the drug revealed the high response of the drug to the temperature variation with very fast rate. It decomposed in several sequential steps in the temperature range 200-600 °C. The initial thermal fragments are very similar to that obtained by mass spectrometric fragmentation. Therefore, comparison between mass and thermal helps in selection of the proper pathway representing the fragmentation of this drug. This comparison successfully confirmed by MOC. These calculations give the bond order, charge distribution, heat of formation and possible hybridization of some atoms in different position of the drug skeleton. This helps the successful choice of the weakest bond at which both mass and thermal fragmentation occurs. Therefore, the best fragmentation pathway of this drug is correctly selected. The effect of such fragmentation on the drug behavior in the human body can be expected as a result of comparing these data with that obtained on studying codeine metal complexes using mass and thermal fragmentation techniques.

High cytokinin levels induce a hypersensitive-like response in tobacco.

PubMed

Novák, Jan; Pavlů, Jaroslav; Novák, Ondřej; Nožková-Hlaváčková, Vladimíra; Špundová, Martina; Hlavinka, Jan; Koukalová, Šárka; Skalák, Jan; Černý, Martin; Brzobohatý, Břetislav

2013-07-01

Cytokinins are positive regulators of shoot development. However, it has previously been demonstrated that efficient activation of the cytokinin biosynthesis gene ipt can cause necrotic lesions and wilting in tobacco leaves. Some plant pathogens reportedly use their ability to produce cytokinins in disease development. In response to pathogen attacks, plants can trigger a hypersensitive response that rapidly kills cells near the infection site, depriving the pathogen of nutrients and preventing its spread. In this study, a diverse set of processes that link ipt activation to necrotic lesion formation were investigated in order to evaluate the potential of cytokinins as signals and/or mediators in plant defence against pathogens. The binary pOp-ipt/LhGR system for dexamethasone-inducible ipt expression was used to increase endogenous cytokinin levels in transgenic tobacco. Changes in the levels of cytokinins and the stress hormones salicylic, jasmonic and abscisic acid following ipt activation were determined by ultra-performance liquid chromatography-electrospray tandem mass spectrometry (UPLC-MS/MS). Trends in hydrogen peroxide content and lipid peroxidation were monitored using the potassium iodide and malondialdehyde assays. The subcellular distribution of hydrogen peroxide was investigated using 3,3'-diaminobenzidine staining. The dynamics of transcripts related to photosynthesis and pathogen response were analysed by reverse transcription followed by quantitative PCR. The effects of cytokinins on photosynthesis were deciphered by analysing changes in chlorophyll fluorescence and leaf gas exchange. Plants can produce sufficiently high levels of cytokinins to trigger fast cell death without any intervening chlorosis - a hallmark of the hypersensitive response. The results suggest that chloroplastic hydrogen peroxide orchestrates the molecular responses underpinning the hypersensitive-like response, including the inhibition of photosynthesis, elevated levels of stress hormones, oxidative membrane damage and stomatal closure. Necrotic lesion formation triggered by ipt activation closely resembles the hypersensitive response. Cytokinins may thus act as signals and/or mediators in plant defence against pathogen attack.

Salt Marsh Ecosystem Responses to Restored Tidal Connectivity across a 14y Chronosequence

NASA Astrophysics Data System (ADS)

Capooci, M.; Spivak, A. C.; Gosselin, K.

2016-02-01

Salt marshes support valuable ecosystem services. Yet, human activities negatively impact salt marsh function and contribute to their loss at a global scale. On Cape Cod, MA, culverts and impoundments under roads and railways restricted tidal exchange and resulted in salt marsh conversion to freshwater wetlands. Over the past 14 y, these structures have been removed or replaced, restoring tidal connectivity between marshes and a saltwater bay. We evaluated differences in plant community composition, sediment properties, and pore water chemistry in marshes where tidal connectivity was restored using a space-for-time, or chronosequence approach. Each restored marsh was paired with a nearby, natural salt marsh to control for variability between marshes. In each restored and natural salt marsh we evaluated the plant community by measuring species-specific percent cover and biomass and collected sediment cores for bulk density and pore water analyses. Plant communities responded rapidly: salt-tolerant species, such as Spartina alterniflora, became established while freshwater species, including Phragmites australis, were less abundant within 3 y of restoration. The number of plant species was generally greater in marshes restored within 10 y, compared to older and natural marshes. Sediment bulk density varied with depth and across sites. This likely reflects differences in site history and local conditions. Deeper horizons (24-30cm) generally had higher values in restored sites while surface values (0-3cm) were similar in restored and natural marshes. Porewater pH and sulfide were similar in restored and natural marshes, suggesting rapid microbial responses to seawater reintroduction. Overall, marsh properties and processes reflecting biological communities responded rapidly to tidal restoration. However, variability between study locations underscores the potential importance of site history, local hydrology, and geomorphology in shaping marsh biogeochemistry.

Utilization of protein expression profiles as indicators of environmental impairment of smallmouth bass (Micropterus dolomieu) from the Shenandoah River, Virginia, USA.

PubMed

Ripley, Jennifer; Iwanowicz, Luke; Blazer, Vicki; Foran, Christy

2008-08-01

The Shenandoah River (VA, USA), the largest tributary of the Potomac River (MD, USA) and an important source of drinking water, has been the site of extensive fish kills since 2004. Previous investigations indicate environmental stressors may be adversely modulating the immune system of smallmouth bass (Micropterus dolomieu) and other species. Anterior kidney (AK) tissue, the major site of blood cell production in fish, was collected from smallmouth bass at three sites along the Shenandoah River. The tissue was divided for immune function and proteomics analyses. Bactericidal activity and respiratory burst were significantly different between North Fork and mainstem Shenandoah River smallmouth bass, whereas South Fork AK tissue did not significantly differ in either of these measures compared with the other sites. Cytotoxic cell activity was highest among South Fork and lowest among North Fork AK leukocytes. The composite two-dimension gels of the North Fork and mainstem smallmouth bass AK tissues contained 584 and 591 spots, respectively. South Fork smallmouth bass AK expressed only 335 proteins. Nineteen of 50 proteins analyzed by matrix-assisted laser desorption ionization-time of flight were successfully identified. Three of the four identified proteins with increased expression in South Fork AK tissue were involved in metabolism. Seven proteins exclusive to mainstem and North Fork smallmouth bass AK and expressed at comparable abundances serve immune and stress response functions. The proteomics data indicate these fish differ in metabolic capacity of AK tissue and in the ability to produce functional leukocytes. The variable responses of the immune function assays further indicate disruption to the immune system. Our results allow us to hypothesize underlying physiological changes that may relate to fish kills and suggest relevant contaminants known to produce similar physiological disruption.

Utilization of protein expression profiles as indicators of environmental impairment of smallmouth bass (Micropterus dolomieu) from the Shenandoah River, Virginia, USA

USGS Publications Warehouse

Ripley, J.; Iwanowicz, L.; Blazer, V.; Foran, C.

2008-01-01

The Shenandoah River (VA, USA), the largest tributary of the Potomac River (MD, USA) and an important source of drinking water, has been the site of extensive fish kills since 2004. Previous investigations indicate environmental stressors may be adversely modulating the immune system of smallmouth bass (Micropterus dolomieu) and other species. Anterior kidney (AK) tissue, the major site of blood cell production in fish, was collected from smallmouth bass at three sites along the Shenandoah River. The tissue was divided for immune function and proteomics analyses. Bactericidal activity and respiratory burst were significantly different between North Fork and mainstem Shenandoah River smallmouth bass, whereas South Fork AK tissue did not significantly differ in either of these measures compared with the other sites. Cytotoxic cell activity was highest among South Fork and lowest among North Fork AK leukocytes. The composite two-dimension gels of the North Fork and mainstem smallmouth bass AK tissues contained 584 and 591 spots, respectively. South Fork smallmouth bass AK expressed only 335 proteins. Nineteen of 50 proteins analyzed by matrix-assisted laser desorption ionization-time of flight were successfully identified. Three of the four identified proteins with increased expression in South Fork AK tissue were involved in metabolism. Seven proteins exclusive to mainstem and North Fork smallmouth bass AK and expressed at comparable abundances serve immune and stress response functions. The proteomics data indicate these fish differ in metabolic capacity of AK tissue and in the ability to produce functional leukocytes. The variable responses of the immune function assays further indicate disruption to the immune system. Our results allow us to hypothesize underlying physiological changes that may relate to fish kills and suggest relevant contaminants known to produce similar physiological disruption. ?? 2008 SETAC.

The Effects of Urbanization and Other Environmental Gradients on Algal Assemblages in Nine Metropolitan Areas across the United States

USGS Publications Warehouse

Coles, James F.; Bell, Amanda H.; Scudder, Barbara C.; Carpenter, Kurt D.

2009-01-01

The U.S. Geological Survey conducted studies from 2000 to 2004 to determine the effects of urbanization on stream ecosystems in nine major metropolitan study areas across the United States. Biological, chemical, and physical components of streams were assessed at 28 to 30 sites in each study area. Benthic algae were sampled to compare the degree to which algal assemblages correlated to urbanization, as characterized by an urban intensity index (UII), relative to other environmental gradients that function at either the watershed or reach scales. Ordination site scores were derived from principal components analyses of the environmental data to define environmental gradients at two spatial scales: (1) watershed-scale gradients that summarized (a) landscape modifications and (b) socioeconomic factors, and (2) reach-scale gradients that characterized (a) physical habitat and (b) water chemistry. Algal response was initially quantified by site scores derived from nonmetric multi-dimensional scaling ordinations of the algal assemblage data. The site scores were then correlated with a set of algal metrics of structure and function to help select specific indicators that would best represent changes in the algal assemblages and would infer ecological condition. The selected metrics were correlated to the UII and other environmental gradients. The results indicated that diatom-taxa in the assemblages were distinctly different across the nine study areas, likely due to physiographic differences across the country, but nevertheless, some algal metrics were applicable to all areas. Overall, the study results indicated that although the UII represented various landscape changes associated with urbanization across the country, the algal response was more strongly related to more specific factors generally associated with water quality measured within the stream reach.

Molecular analysis of the differential hepatic expression of rat kininogen family genes.

PubMed Central

Chen, H M; Liao, W S

1993-01-01

Serum concentration of rat T1 kininogen increases 20- to 30-fold in response to acute inflammation, an induced hepatic synthesis regulated primarily at the transcriptional level. We have demonstrated by transient transfection analyses that rat T1 kininogen gene/chloramphenicol acetyltransferase (T1K/CAT) constructs are highly responsive to interleukin-6 and dexamethasone. In these studies we examined the regulation of a highly homologous K kininogen gene promoter and showed that it is minimally induced under identical conditions. The basal expression of the KK/CAT construct was, however, five- to sevenfold higher than that of the analogous T1K/CAT construct. Promoter-swapping experiments to examine the molecular basis of this differentially regulated basal expression showed that at least two K kininogen promoter regions are important for conferring its high basal expression: a distal 19-bp region (C box) constituted a binding site for C/EBP family proteins, and a proximal 66-bp region contained two adjacent binding sites for hepatocyte nuclear factor 3 (HNF-3). While the C box in the K kininogen promoter was able to interact with C/EBP transcription factors, the T1 kininogen promoter C box could not. In addition, HNF-3 binding sites of the K kininogen promoter demonstrated stronger affinities than those of the T1 kininogen promoter. Since C/EBP and HNF-3 are highly enriched in the liver and are known to enhance transcription of liver-specific genes, these differences in their binding activities thus accounted for the K kininogen gene's higher basal expression. Our studies demonstrated that evolutionary divergence of a few critical nucleotides may lead to subtle changes in the binding affinities of a transcription factor to its recognition site, profoundly altering expression of the downstream gene. Images PMID:8413271

Post-fire geomorphic response in steep, forested landscapes: Oregon Coast Range, USA

NASA Astrophysics Data System (ADS)

Jackson, Molly; Roering, Joshua J.

2009-06-01

The role of fire in shaping steep, forested landscapes depends on a suite of hydrologic, biologic, and geological characteristics, including the propensity for hydrophobic soil layers to promote runoff erosion during subsequent rainfall events. In the Oregon Coast Range, several studies postulate that fire primarily modulates sediment production via root reinforcement and shallow landslide susceptibility, although few studies have documented post-fire geomorphic response. Here, we describe field observations and topographic analyses for three sites in the central Oregon Coast Range that burned in 1999, 2002, and 2003. The fires generated strongly hydrophobic soil layers that did not promote runoff erosion because the continuity of the layers was interrupted by pervasive discontinuities that facilitated rapid infiltration. At each of our sites, fire generated significant colluvial transport via dry ravel, consistent with other field-based studies in the western United States. Fire-driven dry ravel accumulation in low-order valleys of our Sulphur Creek site equated to a slope-averaged landscape lowering of 2.5 mm. Given Holocene estimates of fire frequency, these results suggest that fire may contribute 10-20% of total denudation across steep, dissected portions of the Oregon Coast Range. In addition, we documented more rapid decline of root strength at our sites than has been observed after timber harvest, suggesting that root strength was compromised prior to fire or that intense heat damaged roots in the shallow subsurface. Given that fire frequencies in the Pacific Northwest are predicted to increase with continued climate change, our findings highlight the importance of fire-induced dry ravel and post-fire debris flow activity in controlling sediment delivery to channels.

Tracking lags in historical plant species' shifts in relation to regional climate change.

PubMed

Ash, Jeremy D; Givnish, Thomas J; Waller, Donald M

2017-03-01

Can species shift their distributions fast enough to track changes in climate? We used abundance data from the 1950s and the 2000s in Wisconsin to measure shifts in the distribution and abundance of 78 forest-understory plant species over the last half-century and compare these shifts to changes in climate. We estimated temporal shifts in the geographic distribution of each species using vectors to connect abundance-weighted centroids from the 1950s and 2000s. These shifts in distribution reflect colonization, extirpation, and changes in abundance within sites, separately quantified here. We then applied climate analog analyses to compute vectors representing the climate change that each species experienced. Species shifted mostly to the northwest (mean: 49 ± 29 km) primarily reflecting processes of colonization and changes in local abundance. Analog climates for these species shifted even further to the northwest, however, exceeding species' shifts by an average of 90 ± 40 km. Most species thus failed to match recent rates of climate change. These lags decline in species that have colonized more sites and those with broader site occupancy, larger seed mass, and higher habitat fidelity. Thus, species' traits appear to affect their responses to climate change, but relationships are weak. As climate change accelerates, these lags will likely increase, potentially threatening the persistence of species lacking the capacity to disperse to new sites or locally adapt. However, species with greater lags have not yet declined more in abundance. The extent of these threats will likely depend on how other drivers of ecological change and interactions among species affect their responses to climate change. © 2016 John Wiley & Sons Ltd.

An Application of the SSHAC Level 3 Process to the Probabilistic Seismic Hazard Analysis for Nuclear Facilities at the Hanford Site, Eastern Washington, USA

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

Coppersmith , Kevin J.; Bommer, Julian J.; Bryce, Robert W.

Under the sponsorship of the US Department of Energy (DOE) and the electric utility Energy Northwest, the Pacific Northwest National Laboratory (PNNL) is conducting a probabilistic seismic hazard analysis (PSHA) within the framework of a SSHAC Level 3 procedure (Senior Seismic Hazard Analysis Committee; Budnitz et al., 1997). Specifically, the project is being conducted following the guidelines and requirements specified in NUREG-2117 (USNRC, 2012b) and consistent with approach given in the American Nuclear Standard ANSI/ANS-2.29-2008 Probabilistic Seismic Hazard Analysis. The collaboration between DOE and Energy Northwest is spawned by the needs of both organizations for an accepted PSHA with highmore » levels of regulatory assurance that can be used for the design and safety evaluation of nuclear facilities. DOE committed to this study after performing a ten-year review of the existing PSHA, as required by DOE Order 420.1C. The study will also be used by Energy Northwest as a basis for fulfilling the NRC’s 10CFR50.54(f) requirement that the western US nuclear power plants conduct PSHAs in conformance with SSHAC Level 3 procedures. The study was planned and is being carried out in conjunction with a project Work Plan, which identifies the purpose of the study, the roles and responsibilities of all participants, tasks and their associated schedules, Quality Assurance (QA) requirements, and project deliverables. New data collection and analysis activities are being conducted as a means of reducing the uncertainties in key inputs to the PSHA. It is anticipated that the results of the study will provide inputs to the site response analyses at multiple nuclear facility sites within the Hanford Site and at the Columbia Generating Station.« less

Simulating 2,368 temperate lakes reveals weak coherence in stratification phenology

USGS Publications Warehouse

Read, Jordan S.; Winslow, Luke A.; Hansen, Gretchen J. A.; Van Den Hoek, Jamon; Hanson, Paul C.; Bruce, Louise C; Markfort, Corey D.

2014-01-01

Changes in water temperatures resulting from climate warming can alter the structure and function of aquatic ecosystems. Lake-specific physical characteristics may play a role in mediating individual lake responses to climate. Past mechanistic studies of lake-climate interactions have simulated generic lake classes at large spatial scales or performed detailed analyses of small numbers of real lakes. Understanding the diversity of lake responses to climate change across landscapes requires a hybrid approach that couples site-specific lake characteristics with broad-scale environmental drivers. This study provides a substantial advancement in lake ecosystem modeling by combining open-source tools with freely available continental-scale data to mechanistically model daily temperatures for 2,368 Wisconsin lakes over three decades (1979-2011). The model accurately predicted observed surface layer temperatures (RMSE: 1.74°C) and the presence/absence of stratification (81.1% agreement). Among-lake coherence was strong for surface temperatures and weak for the timing of stratification, suggesting individual lake characteristics mediate some - but not all - ecologically relevant lake responses to climate.

Site response for seattle and source parameters of earthquakes in the puget sound region

USGS Publications Warehouse

Frankel, A.; Carver, D.; Cranswick, E.; Meremonte, M.; Bice, T.; Overturf, D.

1999-01-01

We analyzed seismograms from 21 earthquakes (M(L) 2.0-4.9) recorded by digital seismographs we deployed in urban Seatte to determine site response and earthquake stress drops. The seismometers were situated on a wide variety of geologic units, including artificial fill (e.g., Kingdome, Harbor Island), Pleistocene age soils (glacial till and outwash deposits of Seattle's hills), modified land (downtown Seattle, Space Needle), and Tertiary sedimentary rock. Two mainshock-aftershock sequences were recorded: the June 1997 Bremerton sequence (mainshock M(L) 4.9) and the February 1997 South Seattle sequence (mainshock M(L) 3.5), along with other events in the Puget Sound region. We developed a new inversion procedure to estimate site response, source corner frequencies, and seismic moments from the S-wave spectra. This inversion uses corner frequencies determined from spectral ratios of mainshock-aftershock pairs as constraints. The site responses found from the inversion are not relative to the rock site but are relative to an idealized site with a flat frequency response. The response of the rock site is also found from the inversion. The inversion results show high response for the sites on artificial fill, more moderate amplication for most sites on stiff Pleistocene soils or modified land, and low response for the rock site. Some sites display resonances, such as a strong 2-Hz resonance at our site near the Kingdome, which is caused by the surficial layers of fill and younger alluvium. The sites in West Seattle exhibit high amplification, even though they are on relatively stiff soils of glacial outwash. This may be partly caused by basin surface waves produced by conversion of incident S waves. This high response in West Seattle is consistent with damage reports from the 1949 (m(b) 7.1) and 1965 (m(b) 6.5) earthquakes. Stress-drop estimates for the events we recorded were generally low, between 0.4 and 25 bars, although some of the events may have had higher stress drops that could not be resolved because of the limited passband. We calculated a stress drop of 24 bars for the Bremerton mainshock and 10 bars for the South Seattle mainshock.

Characterization of the Kootenai River Aquatic Macroinvertebrate Community before and after Experimental Nutrient Addition, 2003-2006. [Chapter 3

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

Holderman, Charlie

2009-02-19

The Kootenai River ecosystem has experienced numerous ecological changes since the early 1900s. Some of the largest impacts to habitat, biological communities, and ecological function resulted from levee construction along the 120 km of river upstream from Kootenay Lake, completed by the 1950s, and the construction and operation of Libby Dam, completed in 1972 on the river near Libby Montana. Levee construction isolated tens of thousands of hectares of historic functioning floodplain habitat from the river channel, eliminating nutrient production and habitat diversity crucial to the functioning of a large river-floodplain ecosystem. Libby Dam continues to create large changes inmore » the timing, duration, and magnitude of river flows, and greatly reduces sediment and nutrient transport to downstream river reaches. These changes have contributed to the ecological collapse of the post-development Kootenai River ecosystem and its native biological communities. In response to this artificial loss of nutrients, experimental nutrient addition was initiated in the Kootenay Lake's North Arm in 1992, the South Arm in 2004, and in the Kootenai River at the Idaho-Montana border during 2005. This report characterizes the macroinvertebrate community in the Kootenai River and its response to experimental nutrient addition during 2005 and 2006. This report also provides an initial evaluation of cascading trophic interactions in response to nutrient addition. Macroinvertebrates were sampled at 12 sites along a 325 km section of the Kootenai River, representing an upriver unimpounded reference reach, treatment and control canyon reach sites, and braided and meandering reach sites, all downstream from Libby Dam. Principle component analysis revealed that richness explained the greatest amount of variability in response to nutrient addition as did taxa from Acari, Coleoptera, Ephemeroptera, Plecoptera, and Trichoptera. Analysis of variance revealed that nutrient addition had a significant effect (p<0.0001) on invertebrate abundance, biomass, and richness at sites KR-9 and KR-9.1 combined (the zone of maximum biological response). Richness, a valuable ecological metric, increased more than abundance and biomass, which were subject to greater sampling bias. Cascading trophic interactions were observed as increased algal accrual, increased in-river invertebrate abundance, and increased invertebrate counts in mountain whitefish (Prosopium williamsonii) guts samples, but were not quantitatively tested. Sampling and analyses across trophic levels are currently ongoing and are expected to better characterize ecological responses to experimental nutrient addition in the Kootenai River.« less

Analysis of Evolutionary Processes of Species Jump in Waterfowl Parvovirus

PubMed Central

Fan, Wentao; Sun, Zhaoyu; Shen, Tongtong; Xu, Danning; Huang, Kehe; Zhou, Jiyong; Song, Suquan; Yan, Liping

2017-01-01

Waterfowl parvoviruses are classified into goose parvovirus (GPV) and Muscovy duck parvovirus (MDPV) according to their antigenic features and host preferences. A novel duck parvovirus (NDPV), identified as a new variant of GPV, is currently infecting ducks, thus causing considerable economic loss. This study analyzed the molecular evolution and population dynamics of the emerging parvovirus capsid gene to investigate the evolutionary processes concerning the host shift of NDPV. Two important amino acids changes (Asn-489 and Asn-650) were identified in NDPV, which may be responsible for host shift of NDPV. Phylogenetic analysis indicated that the currently circulating NDPV originated from the GPV lineage. The Bayesian Markov chain Monte Carlo tree indicated that the NDPV diverged from GPV approximately 20 years ago. Evolutionary rate analyses demonstrated that GPV evolved with 7.674 × 10-4 substitutions/site/year, and the data for MDPV was 5.237 × 10-4 substitutions/site/year, whereas the substitution rate in NDPV branch was 2.25 × 10-3 substitutions/site/year. Meanwhile, viral population dynamics analysis revealed that the GPV major clade, including NDPV, grew exponentially at a rate of 1.717 year-1. Selection pressure analysis showed that most sites are subject to strong purifying selection and no positively selected sites were found in NDPV. The unique immune-epitopes in waterfowl parvovirus were also estimated, which may be helpful for the prediction of antibody binding sites against NDPV in ducks. PMID:28352261

CO2 fluxes and ecosystem dynamics at five European treeless peatlands - merging data and process oriented modelling

NASA Astrophysics Data System (ADS)

Metzger, C.; Jansson, P.-E.; Lohila, A.; Aurela, M.; Eickenscheidt, T.; Belelli-Marchesini, L.; Dinsmore, K. J.; Drewer, J.; van Huissteden, J.; Drösler, M.

2014-06-01

The carbon dioxide (CO2) exchange of five different peatland systems across Europe with a wide gradient in landuse intensity, water table depth, soil fertility and climate was simulated with the process oriented CoupModel. The aim of the study was to find out to what extent CO2 fluxes measured at different sites, can be explained by common processes and parameters implemented in the model. The CoupModel was calibrated to fit measured CO2 fluxes, soil temperature, snow depth and leaf area index (LAI) and resulting differences in model parameters were analysed. Finding site independent model parameters would mean that differences in the measured fluxes could be explained solely by model input data: water table, meteorological data, management and soil inventory data. The model, utilizing a site independent configuration for most of the parameters, captured seasonal variability in the major fluxes well. Parameters that differed between sites included the rate of soil organic decomposition, photosynthetic efficiency, and regulation of the mobile carbon (C) pool from senescence to shooting in the next year. The largest difference between sites was the rate coefficient for heterotrophic respiration. Setting it to a common value would lead to underestimation of mean total respiration by a factor of 2.8 up to an overestimation by a factor of 4. Despite testing a wide range of different responses to soil water and temperature, heterotrophic respiration rates were consistently lowest on formerly drained sites and highest on the managed sites. Substrate decomposability, pH and vegetation characteristics are possible explanations for the differences in decomposition rates. Applying common parameter values for the timing of plant shooting and senescence, and a minimum temperature for photosynthesis, had only a minor effect on model performance, even though the gradient in site latitude ranged from 48° N (South-Germany) to 68° N (northern Finland). This was also true for common parameters defining the moisture and temperature response for decomposition. CoupModel is able to describe measured fluxes at different sites or under different conditions, providing that the rate of soil organic decomposition, photosynthetic efficiency, and the regulation of the mobile carbon (C) pool are estimated from available information on specific soil conditions, vegetation and management of the ecosystems.

Treatment patterns and outcomes in BRAF V600E-mutant melanoma patients with brain metastases receiving vemurafenib in the real-world setting.

PubMed

Gibney, Geoffrey T; Gauthier, Geneviève; Ayas, Charles; Galebach, Philip; Wu, Eric Q; Abhyankar, Sarang; Reyes, Carolina; Guérin, Annie; Yim, Yeun Mi

2015-08-01

Brain metastases are a common and serious complication among patients with metastatic melanoma. The selective BRAF inhibitor vemurafenib has demonstrated clinical efficacy in patients with BRAF V600E-mutant melanoma brain metastases (MBM). We examined the real-world application and clinical outcomes of vemurafenib in this patient population. Demographic, treatment patterns, response, and survival data were collected from medical charts. Clinical data on 283 patients with active BRAF V600E-mutant MBM treated with vemurafenib were provided by 70 US oncologists. Mean age was 57.2 years, 60.8% were male, 67.5% had ECOG performance status of 0-1, and 43.1% used corticosteroids at vemurafenib initiation. Median follow-up was 5.7 months. Following vemurafenib initiation, 48.1% of patients experienced intracranial response and 45.6% experienced extracranial response. The Kaplan-Meier estimate for overall survival was 59% at 12 months. Multivariate analyses showed associations between intracranial response and both corticosteroid use and vemurafenib as initial therapy after MBM diagnosis. Larger size (5-10 mm vs. < 5 mm) and number of brain metastases (≥ 5 vs. < 2) and progressive extracranial disease at treatment initiation were associated with decreased intracranial response and increased risk of disease progression. Multiple extracranial sites (2 vs. < 2) and the absence of local treatments were also associated with increased risk of progression. Increased risk of death was associated with ≥ 2 extracranial disease sites, progressive extracranial disease, and ≥ 5 brain metastases. Subgroups of MBM patients may derive more benefit with vemurafenib, warranting prospective investigation. © 2015 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Reflex responses of lip muscles in young and older women.

PubMed

Wohlert, A B

1996-06-01

The perioral reflex in response to innocuous mechanical stimulation of the lip vermilion was studied in 20 young and 20 older women. Responses to stimuli at the right and left sides of both the upper and lower lips were recorded. Results show significant specificity of response, especially for upper lip sites. Reflex response at the site of stimulation was greatest in amplitude and shortest in latency, followed by response at sites ipsilateral to the site of stimulation. Younger subjects showed greater localizing tendency than older subjects. Stimulation was significantly less likely to produce a reflex response in the older group. When reflex responses did occur, they were significantly lower in amplitude and longer in latency than the responses of the younger group. Nonetheless, reflex responses were common in both groups, with responses at the site of stimulation occurring 78% of the time in older women and 90% of the time in younger women. Every participant showed at least one reflex response to lip stimulation. Results suggest decreasing complexity of synaptic drive to the perioral system in old age but also show that reflexive response does not deteriorate completely, remaining an available element for motor control in normal older women.

SMARTE'S SITE CHARACTERIZATION TOOL

EPA Science Inventory

Site Characterization involves collecting environmental data to evaluate the nature and extent of contamination. Environmental data could consist of chemical analyses of soil, sediment, water or air samples. Typically site characterization data are statistically evaluated for thr...

Chapter B. Physical, Chemical, and Biological Responses of Streams to Increasing Watershed Urbanization in the Piedmont Ecoregion of Georgia and Alabama, 2003

USGS Publications Warehouse

Gregory, M. Brian; Calhoun, Daniel L.

2007-01-01

As part of the U.S. Geological Survey National Water-Quality Assessment Program?s effort to assess the physical, chemical, and biological responses of streams to urbanization, 30 wadable streams were sampled near Atlanta, Ga., during 2002?2003. Watersheds were selected to minimize natural factors such as geology, altitude, and climate while representing a range of urban development. A multimetric urban intensity index was calculated using watershed land use, land cover, infrastructure, and socioeconomic variables that are highly correlated with population density. The index was used to select sites along a gradient from low to high urban intensity. Response variables measured include stream hydrology and water temperature, instream habitat, field properties (pH, conductivity, dissolved oxygen, turbidity), nutrients, pesticides, suspended sediment, sulfate, chloride, Escherichia coli (E. coli) concentrations, and characterization of algal, invertebrate and fish communities. In addition, semipermeablemembrane devices (SPMDs)?passive samplers that concentrate hydrophobic organic contaminants such as polycyclicaromatic hydrocarbons (PAHs)?were used to evaluate water-quality conditions during the 4 weeks prior to biological sampling. Changes in physical, chemical, and biological conditions were evaluated using both nonparametric correlation analysis and nonmetric multidimensional scaling (MDS) ordinations and associated comparisons of dataset similarity matrices. Many of the commonly reported effects of watershed urbanization on streams were observed in this study, such as altered hydrology and increases in some chemical constituent levels. Analysis of water-chemistry data showed that specific conductance, chloride, sulfate, and pesticides increased as urbanization increased. Nutrient concentrations were not directly correlated to increases in development, but were inversely correlated to percent forest in the watershed. Analyses of SPMD-derived data showed that bioassays and certain chemical constituents such as pyrene and benzophenanthrene, both PAHs found in coal tar, were strongly correlated with measures of watershed urbanization. Hydrologic variability metrics indicated that as urban development increased, streams became flashier, with characteristic high flows having shorter duration. The hydrologic effects associated with urbanization were greatest during the fall and least apparent during the winter. No correlations were observed between increasing urbanization and stream temperature or changes in stream habitat. Algal, invertebrate, and fish communities exhibited statistically significant changes as watersheds became increasingly urban, with the strongest responses observed in the invertebrate community followed by fishes, then algal diatom communities. Invertebrate communities were the most responsive to increasing urbanization with Ephemeroptera, Plecoptera, and Tricoptera taxa, especially Plecoptera (stoneflies) responding negatively and most strongly to increasing urbanization. Invertebrate communities were influenced more significantly by water quality, although significant responses to altered hydrology also were noted. In terms of the fish community, the percentage of cyprinids present in the stream was the only Index of Biotic Integrity metric that responded negatively to increases in watershed urbanization. Fish community response to urbanization was intermediate relative to algae and invertebrates with respect to significant metric responses as well as the overall community response to increasing urbanization. Measures of hydrologic variability were the most influential environmental variables affecting the algal community. Although sites were originally chosen to represent a gradient of increasing urbanization, a cluster analysis performed on the component metrics of the urban index categorized sites into four distinct groups. Multivariate analysis based on nonmetric MDS and related analyses of data ma

Short-term stress experienced at time of immunization induces a long-lasting increase in immunologic memory.

PubMed

Dhabhar, Firdaus S; Viswanathan, Kavitha

2005-09-01

It would be extremely beneficial if one could harness natural, endogenous, health-promoting defense mechanisms to fight disease and restore health. The psychophysiological stress response is the most underappreciated of nature's survival mechanisms. We show that acute stress experienced before primary immunization induces a long-lasting increase in immunity. Compared with controls, mice restrained for 2.5 h before primary immunization with keyhole limpet hemocyanin (KLH) show a significantly enhanced immune response when reexposed to KLH 9 mo later. This immunoenhancement is mediated by an increase in numbers of memory and effector helper T cells in sentinel lymph nodes at the time of primary immunization. Further analyses show that the early stress-induced increase in T cell memory may stimulate the robust increase in infiltrating lymphocyte and macrophage numbers observed months later at a novel site of antigen reexposure. Enhanced leukocyte infiltration may be driven by increased levels of the type 1 cytokines, IL-2 and IFN-gamma, and TNF-alpha, observed at the site of antigen reexposure in animals that had been stressed at the time of primary immunization. In contrast, no differences were observed in type 2 cytokines, IL-4 or IL-5. Given the importance of inducing long-lasting increases in immunologic memory during vaccination, we suggest that the neuroendocrine stress response is nature's adjuvant that could be psychologically and/or pharmacologically manipulated to safely increase vaccine efficacy. These studies introduce the novel concept that a psychophysiological stress response is nature's fundamental survival mechanism that could be therapeutically harnessed to augment immune function during vaccination, wound healing, or infection.

Endotoxin molecule lipopolysaccharide-induced zebrafish inflammation model: a novel screening method for anti-inflammatory drugs.

PubMed

Yang, Li-Ling; Wang, Guo-Quan; Yang, Li-Mei; Huang, Zhi-Bing; Zhang, Wen-Qing; Yu, Lin-Zhong

2014-02-21

Lipopolysaccharide (LPS), an endotoxin molecule, has been used to induce inflammatory responses. In this study, LPS was used to establish an in vivo inflammation model in zebrafish for drug screening. We present an experimental method that conveniently and rapidly assesses the anti-inflammatory properties of drugs. The yolks of 3-day post-fertilization (dpf) larvae were injected with 0.5 mg/mL LPS to induce fatal inflammation. After LPS stimulation, macrophages were tracked by NR and SB staining and neutrophil migration was observed using the MPO:GFP line. Larval mortality was used as the primary end-point. Expression levels of key cytokines involved in the inflammatory response including IL-1β, IL-6, and TNF-α, were measured using quantitative reverse transcription polymerase chain reaction (RT-PCR). Macrophages and neutrophils were both recruited to the LPS-injected site during the inflammatory response. Mortality was increased by LPS in a dose-dependent manner within 48 h. Analyses of IL-1β, IL-6, and TNF-α expression levels revealed the upregulation of the inflammatory response in the LPS-injected larvae. Further, the anti-inflammatory activity of chlorogenic acid (CA) was evaluated in this zebrafish model to screen for anti-inflammatory drugs. A preliminary result showed that CA revealed a similar effect as the corticosteroid dexamethasone (DEX), which was used as a positive control, by inhibiting macrophage and neutrophil recruitment to the LPS site and improving survival. Our results suggest that this zebrafish screening model could be applied to study inflammation-mediated diseases. Moreover, the Traditional Chinese Medicine CA displays potential anti-inflammatory activity.

Effects of wildfire and permafrost on soil organic matter and soil climate in interior Alaska

USGS Publications Warehouse

Harden, J.W.; Manies, K.L.; Turetsky, M.R.; Neff, J.C.

2006-01-01

The influence of discontinuous permafrost on ground-fuel storage, combustion losses, and postfire soil climates was examined after a wildfire near Delta Junction, AK in July 1999. At this site, we sampled soils from a four-way site comparison of burning (burned and unburned) and permafrost (permafrost and nonpermafrost). Soil organic layers (which comprise ground-fuel storage) were thicker in permafrost than nonpermafrost soils both in burned and unburned sites. While we expected fire severity to be greater in the drier site (without permafrost), combustion losses were not significantly different between the two burned sites. Overall, permafrost and burning had significant effects on physical soil variables. Most notably, unburned permafrost sites with the thickest organic mats consistently had the coldest temperatures and wettest mineral soil, while soils in the burned nonpermafrost sites were warmer and drier than the other soils. For every centimeter of organic mat thickness, temperature at 5cm depth was about 0.5??C cooler during summer months. We propose that organic soil layers determine to a large extent the physical and thermal setting for variations in vegetation, decomposition, and carbon balance across these landscapes. In particular, the deep organic layers maintain the legacies of thermal and nutrient cycling governed by fire and revegetation. We further propose that the thermal influence of deep organic soil layers may be an underlying mechanism responsible for large regional patterns of burning and regrowth, detected in fractal analyses of burn frequency and area. Thus, fractal geometry can potentially be used to analyze changes in state of these fire prone systems. ?? 2006 Blackwell Publishing Ltd.

Using propensity scores to estimate the effects of insecticides on stream invertebrates from observational data

USGS Publications Warehouse

Lester L. Yuan,; Amina I. Pollard,; Carlisle, Daren M.

2009-01-01

Analyses of observational data can provide insights into relationships between environmental conditions and biological responses across a broader range of natural conditions than experimental studies, potentially complementing insights gained from experiments. However, observational data must be analyzed carefully to minimize the likelihood that confounding variables bias observed relationships. Propensity scores provide a robust approach for controlling for the effects of measured confounding variables when analyzing observational data. Here, we use propensity scores to estimate changes in mean invertebrate taxon richness in streams that have experienced insecticide concentrations that exceed aquatic life use benchmark concentrations. A simple comparison of richness in sites exposed to elevated insecticides with those that were not exposed suggests that exposed sites had on average 6.8 fewer taxa compared to unexposed sites. The presence of potential confounding variables makes it difficult to assert a causal relationship from this simple comparison. After controlling for confounding factors using propensity scores, the difference in richness between exposed and unexposed sites was reduced to 4.1 taxa, a difference that was still statistically significant. Because the propensity score analysis controlled for the effects of a wide variety of possible confounding variables, we infer that the change in richness observed in the propensity score analysis was likely caused by insecticide exposure.

Using propensity scores to estimate the effects of insecticides on stream invertebrates from observational data

USGS Publications Warehouse

Yuan, L.L.; Pollard, A.I.; Carlisle, D.M.

2009-01-01

Analyses of observational data can provide insights into relationships between environmental conditions and biological responses across a broader range of natural conditions than experimental studies, potentially complementing insights gained from experiments. However, observational data must be analyzed carefully to minimize the likelihood that confounding variables bias observed relationships. Propensity scores provide a robust approach for controlling for the effects of measured confounding variables when analyzing observational data. Here, we use propensity scores to estimate changes in mean invertebrate taxon richness in streams that have experienced insecticide concentrations that exceed aquatic life use benchmark concentrations. A simple comparison of richness in sites exposed to elevated insecticides with those that were not exposed suggests that exposed sites had on average 6.8 fewer taxa compared to unexposed sites. The presence of potential confounding variables makes it difficult to assert a causal relationship from this simple comparison. After controlling for confounding factors using propensity scores, the difference in richness between exposed and unexposed sites was reduced to 4.1 taxa, a difference that was still statistically significant. Because the propensity score analysis controlled for the effects of a wide variety of possible confounding variables, we infer that the change in richness observed in the propensity score analysis was likely caused by insecticide exposure. ?? 2009 SETAC.

Coping with shifting nest predation refuges by European reed Warblers Acrocephalus scirpaceus.

PubMed

Halupka, Lucyna; Halupka, Konrad; Klimczuk, Ewelina; Sztwiertnia, Hanna

2014-01-01

Predation, the most important source of nest mortality in altricial birds, has been a subject of numerous studies during past decades. However, the temporal dynamics between changing predation pressures and parental responses remain poorly understood. We analysed characteristics of 524 nests of European reed warblers monitored during six consecutive breeding seasons in the same area, and found some support for the shifting nest predation refuge hypothesis. Nest site characteristics were correlated with nest fate, but a nest with the same nest-site attributes could be relatively safe in one season and vulnerable to predation in another. Thus nest predation refuges were ephemeral and there was no between-season consistency in nest predation patterns. Reed warblers that lost their first nests in a given season did not disperse farther for the subsequent reproductive attempt, compared to successful individuals, but they introduced more changes to their second nest sites. In subsequent nests, predation risk remained constant for birds that changed nest-site characteristics, but increased for those that did not. At the between-season temporal scale, individual birds did not perform better with age in terms of reducing nest predation risk. We conclude that the experience acquired in previous years may not be useful, given that nest predation refuges are not stable.

Coping with Shifting Nest Predation Refuges by European Reed Warblers Acrocephalus scirpaceus

PubMed Central

Halupka, Lucyna; Halupka, Konrad; Klimczuk, Ewelina; Sztwiertnia, Hanna

2014-01-01

Predation, the most important source of nest mortality in altricial birds, has been a subject of numerous studies during past decades. However, the temporal dynamics between changing predation pressures and parental responses remain poorly understood. We analysed characteristics of 524 nests of European reed warblers monitored during six consecutive breeding seasons in the same area, and found some support for the shifting nest predation refuge hypothesis. Nest site characteristics were correlated with nest fate, but a nest with the same nest-site attributes could be relatively safe in one season and vulnerable to predation in another. Thus nest predation refuges were ephemeral and there was no between-season consistency in nest predation patterns. Reed warblers that lost their first nests in a given season did not disperse farther for the subsequent reproductive attempt, compared to successful individuals, but they introduced more changes to their second nest sites. In subsequent nests, predation risk remained constant for birds that changed nest-site characteristics, but increased for those that did not. At the between-season temporal scale, individual birds did not perform better with age in terms of reducing nest predation risk. We conclude that the experience acquired in previous years may not be useful, given that nest predation refuges are not stable. PMID:25522327

Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation.

PubMed

Yang, Feng; Waters, Katrina M; Miller, John H; Gritsenko, Marina A; Zhao, Rui; Du, Xiuxia; Livesay, Eric A; Purvine, Samuel O; Monroe, Matthew E; Wang, Yingchun; Camp, David G; Smith, Richard D; Stenoien, David L

2010-11-30

High doses of ionizing radiation result in biological damage; however, the precise relationships between long-term health effects, including cancer, and low-dose exposures remain poorly understood and are currently extrapolated using high-dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose-dependent responses to radiation. We have identified 7117 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts 1 h post-exposure. Semi-quantitative label-free analyses were performed to identify phosphopeptides that are apparently altered by radiation exposure. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation-responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatic analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role for MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provide a basis for the systems-level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at different radiation doses and elucidate the impact of low-dose radiation exposure on human health.

Phosphoproteomics Profiling of Human Skin Fibroblast Cells Reveals Pathways and Proteins Affected by Low Doses of Ionizing Radiation

PubMed Central

Yang, Feng; Waters, Katrina M.; Miller, John H.; Gritsenko, Marina A.; Zhao, Rui; Du, Xiuxia; Livesay, Eric A.; Purvine, Samuel O.; Monroe, Matthew E.; Wang, Yingchun; Camp, David G.; Smith, Richard D.; Stenoien, David L.

2010-01-01

Background High doses of ionizing radiation result in biological damage; however, the precise relationships between long-term health effects, including cancer, and low-dose exposures remain poorly understood and are currently extrapolated using high-dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose-dependent responses to radiation. Principal Findings We have identified 7117 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts 1 h post-exposure. Semi-quantitative label-free analyses were performed to identify phosphopeptides that are apparently altered by radiation exposure. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation-responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatic analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role for MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Conclusions Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provide a basis for the systems-level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at different radiation doses and elucidate the impact of low-dose radiation exposure on human health. PMID:21152398

An ABA-responsive element in the AtSUC1 promoter is involved in the regulation of AtSUC1 expression.

PubMed

Hoth, Stefan; Niedermeier, Matthias; Feuerstein, Andrea; Hornig, Julia; Sauer, Norbert

2010-09-01

Abscisic acid (ABA) and sugars regulate many aspects of plant growth and development, and we are only just beginning to understand the complex interactions between ABA and sugar signaling networks. Here, we show that ABA-dependent transcription factors bind to the promoter of the Arabidopsis thaliana AtSUC1 (At1g71880) sucrose transporter gene in vitro. We present the characterization of a cis-regulatory element by truncation of the AtSUC1 promoter and by electrophoretic mobility shift assays that is identical to a previously characterized ABA-responsive element (ABRE). In yeast 1-hybrid analyses we identified ABI5 (AtbZIP39; At2g36270) and AREB3 (AtbZIP66; At3g56850) as potential interactors. Analyses of plants expressing the beta-glucuronidase reporter gene under the control of ABI5 or AREB3 promoter sequences demonstrated that both transcription factor genes are co-expressed with AtSUC1 in pollen and seedlings, the primary sites of AtSUC1 action. Mutational analyses of the identified cis-regulatory element verified its importance for AtSUC1 expression in young seedlings. In abi5-4 seedlings, we observed an increase of sucrose-dependent anthocyanin accumulation and AtSUC1 mRNA levels. This suggests that ABI5 prevents an overshoot of sucrose-induced AtSUC1 expression and confirmed a novel cross-link between sugar and ABA signaling.

Earthquake site response in Santa Cruz, California

USGS Publications Warehouse

Carver, D.; Hartzell, S.H.

1996-01-01

Aftershocks of the 1989 Loma Prieta, California, earthquake are used to estimate site response in a 12-km2 area centered on downtown Santa Cruz. A total of 258 S-wave records from 36 aftershocks recorded at 33 sites are used in a linear inversion for site-response spectra. The inversion scheme takes advantage of the redundancy of the large data set for which several aftershocks are recorded at each site. The scheme decomposes the observed spectra into source, path, and site terms. The path term is specified before the inversion. The undetermined degree of freedom in the decomposition into source and site spectra is removed by specifying the site-response factor to be approximately 1.0 at two sites on crystalline bedrock. The S-wave site responses correlate well with the surficial geology and observed damage pattern of the mainshock. The site-response spectra of the floodplain sites, which include the heavily damaged downtown area, exhibit significant peaks. The largest peaks are between 1 and 4 Hz. Five floodplain sites have amplification factors of 10 or greater. Most of the floodplain site-response spectra also have a smaller secondary peak between 6 and 8 Hz. Residential areas built on marine terraces above the flood-plain experienced much less severe damage. Site-response spectra for these areas also have their largest peaks between 1 and 4 Hz, but the amplification is generally below 6. Several of these sites also have a secondary peak between 6 and 8 Hz. The response peaks seen at nearly all sites between 1 and 4 Hz are probably caused by the natural resonance of the sedimentary rock column. The higher amplifications at floodplain sites may be caused by surface waves generated at the basin margins. The secondary peak between 6 and 8 Hz at many sites may be a harmonic of the 1- to 4-Hz peaks. We used waveforms from a seven-station approximately linear array located on the floodplain to calculate the apparent velocity and azimuth of propagation of coherent arrivals within moving windows of the S-wave codas. The initial windows give results that are consistent with direct S-wave arrivals. The apparent velocities are high (greater than 4.0 km/sec), and azimuths are from the source. Waves arriving later than 2 sec after the direct S waves have apparent velocities of less than 1 km/ sec, indicating that they are surface waves, and arrive from divergent azimuths. This analysis indicates that after the direct S-wave arrival, long-duration shaking comes from surface waves that are generated at the basin margin and reverberate in the floodplain sediments.

Raman Spectroscopy of Rdx Single Crystals Under Static Compression

NASA Astrophysics Data System (ADS)

Dreger, Zbigniew A.; Gupta, Yogendra M.

2007-12-01

To gain insight into the high pressure response of energetic crystal of RDX, Raman measurements were performed under hydrostatic compression up to 15 GPa. Several distinct changes in the spectra were found at 4.0±0.3 GPa, confirming the α-γ phase transition previously observed in polycrystalline samples. Symmetry correlation analyses indicate that the γ-polymorph may assume a space group isomorphous with a point group D2h with eight molecules occupying the C1 symmetry sites, similar to the α-phase. It is proposed that factor group coupling can account for the observed increase in the number of modes in the γ-phase.

An aerial-photographic assessment of reenacted handcart treks on a section of the Mormon Pioneer National Historic Trail, Fremont County, Wyoming

USGS Publications Warehouse

McDougal, Robert R.; Waltermire, Robert G.; Aldridge, Cameron L.; Germaine, Stephen S.; Nielsen, Scott E.; Nielsen, Charlene C.; Hanson, Leanne; Bowen, Zachary H.

2008-01-01

Based on these results, there are identifiable management considerations. Toilet and rest sites need to be carefully located relative to where sensitive vegetation or soils occur. The analyses presented here indicate that limiting motorized vehicle use needs to be a priority over that of adjusting the number of trekkers. Additionally, monitoring of the Trail from Sixth Crossing to Rock Creek Hollow segment needs to consider explicit management targets, such as minimum acceptable levels of bare ground or trail width, and the establishment of permanent monitoring plots to evaluate targets and measure responses to altered management activities.

Hydrogeological Investigations in Deep Wells at the Meuse/Haute Marne Underground Research Laboratory

NASA Astrophysics Data System (ADS)

Delay, Jacques; Distinguin, Marc

ANDRA (Agence Nationale pour la Gestion de Déchets Radioactifs) has developed an integrated approach to characterizing the hydrogeology of the carbonate strata that encase the Callovo-Oxfordian argillite at the Meuse/Haute-Marne Laboratory site. The argillites are difficult to characterize due to their low permeability. The barrier properties of the argillites can be inferred from the flow and chemistry properties of the encasing Oxfordian and Dogger carbonates. Andras deep hole approach uses reverse air circulation drilling, geophysical logging, flow meter logging, geochemical sampling, and analyses of the pumping responses during sampling. The data support numerical simulations that evaluate the argillites hydraulic behaviour.

Site response and attenuation in the Puget Lowland, Washington State

USGS Publications Warehouse

Pratt, T.L.; Brocher, T.M.

2006-01-01

Simple spectral ratio (SSR) and horizontal-to-vertical (HN) site-response estimates at 47 sites in the Puget Lowland of Washington State document significant attenuation of 1.5- to 20-Hz shear waves within sedimentary basins there. Amplitudes of the horizontal components of shear-wave arrivals from three local earthquakes were used to compute SSRs with respect to the average of two bedrock sites and H/V spectral ratios with respect to the vertical component of the shear-wave arrivals at each site. SSR site-response curves at thick basin sites show peak amplifications of 2 to 6 at frequencies of 3 to 6 Hz, and decreasing spectra amplification with increasing frequency above 6 Hz. SSRs at nonbasin sites show a variety of shapes and larger resonance peaks. We attribute the spectral decay at frequencies above the amplification peak at basin sites to attenuation within the basin strata. Computing the frequency-independent, depth-dependent attenuation factor (Qs,int) from the SSR spectral decay between 2 and 20 Hz gives values of 5 to 40 for shallow sedimentary deposits and about 250 for the deepest sedimentary strata (7 km depth). H/V site responses show less spectral decay than the SSR responses but contain many of the same resonance peaks. We hypothesize that the H/V method yields a flatter response across the frequency spectrum than SSRs because the H/V reference signal (vertical component of the shear-wave arrivals) has undergone a degree of attenuation similar to the horizontal component recordings. Correcting the SSR site responses for attenuation within the basins by removing the spectral decay improves agreement between SSR and H/V estimates.

Predicting DNAPL Source Zone and Plume Response Using Site-Measured Characteristics

DTIC Science & Technology

2017-05-19

FINAL REPORT Predicting DNAPL Source Zone and Plume Response Using Site- Measured Characteristics SERDP Project ER-1613 MAY 2017...Final Report 3. DATES COVERED (From - To) 2007 - 2017 4. TITLE AND SUBTITLE PREDICTING DNAPL SOURCE ZONE AND PLUME RESPONSE USING SITE- MEASURED ...historical record of concentration and head measurements , particularly in the near-source region. For each site considered, currently available data

Deficient prepulse inhibition in schizophrenia detected by the multi-site COGS.

PubMed

Swerdlow, Neal R; Light, Gregory A; Sprock, Joyce; Calkins, Monica E; Green, Michael F; Greenwood, Tiffany A; Gur, Raquel E; Gur, Ruben C; Lazzeroni, Laura C; Nuechterlein, Keith H; Radant, Allen D; Ray, Amrita; Seidman, Larry J; Siever, Larry J; Silverman, Jeremy M; Stone, William S; Sugar, Catherine A; Tsuang, Debby W; Tsuang, Ming T; Turetsky, Bruce I; Braff, David L

2014-02-01

Startle inhibition by weak prepulses (PPI) is studied to understand the biology of information processing in schizophrenia patients and healthy comparison subjects (HCS). The Consortium on the Genetics of Schizophrenia (COGS) identified associations between PPI and single nucleotide polymorphisms in schizophrenia probands and unaffected relatives, and linkage analyses extended evidence for the genetics of PPI deficits in schizophrenia in the COGS-1 family study. These findings are being extended in a 5-site "COGS-2" study of 1800 patients and 1200 unrelated HCS to facilitate genetic analyses. We describe a planned interim analysis of COGS-2 PPI data. Eyeblink startle was measured in carefully screened HCS and schizophrenia patients (n=1402). Planned analyses of PPI (60 ms intervals) assessed effects of diagnosis, sex and test site, PPI-modifying effects of medications and smoking, and relationships between PPI and neurocognitive measures. 884 subjects met strict inclusion criteria. ANOVA of PPI revealed significant effects of diagnosis (p=0.0005) and sex (p<0.002), and a significant diagnosis×test site interaction. HCS>schizophrenia PPI differences were greatest among patients not taking 2nd generation antipsychotics, and were independent of smoking status. Modest but significant relationships were detected between PPI and performance in specific neurocognitive measures. The COGS-2 multi-site study detects schizophrenia-related PPI deficits reported in single-site studies, including patterns related to diagnosis, prepulse interval, sex, medication and other neurocognitive measures. Site differences were detected and explored. The target COGS-2 schizophrenia "endophenotype" of reduced PPI should prove valuable for identifying and confirming schizophrenia risk genes in future analyses. Copyright © 2013 Elsevier B.V. All rights reserved.

Deficient prepulse inhibition in schizophrenia detected by the multi-site COGS

PubMed Central

Swerdlow, Neal R.; Light, Gregory A.; Sprock, Joyce; Calkins, Monica E.; Green, Michael F.; Greenwood, Tiffany A.; Gur, Raquel E.; Gur, Ruben C.; Lazzeroni, Laura C.; Nuechterlein, Keith H.; Radant, Allen D.; Ray, Amrita; Seidman, Larry J.; Siever, Larry J.; Silverman, Jeremy M.; Stone, William S.; Sugar, Catherine A.; Tsuang, Debby W.; Tsuang, Ming T.; Turetsky, Bruce I.; Braff, David L.

2014-01-01

Background Startle inhibition by weak prepulses (PPI) is studied to understand the biology of information processing in schizophrenia patients and healthy comparison subjects (HCS). The Consortium on the Genetics of Schizophrenia (COGS) identified associations between PPI and single nucleotide polymorphisms in schizophrenia probands and unaffected relatives, and linkage analyses extended evidence for the genetics of PPI deficits in schizophrenia in the COGS-1 family study. These findings are being extended in a 5-site “COGS-2” study of 1800 patients and 1200 unrelated HCS to facilitate genetic analyses. We describe a planned interim analysis of COGS-2 PPI data. Methods Eyeblink startle was measured in carefully screened HCS and schizophrenia patients (n=1402). Planned analyses of PPI (60 ms intervals) assessed effects of diagnosis, sex and test site, PPI-modifying effects of medications and smoking, and relationships between PPI and neurocognitive measures. Results 884 subjects met strict inclusion criteria. ANOVA of PPI revealed significant effects of diagnosis (p=0.0005) and sex (p<0.002), and a significant diagnosis × test site interaction. HCS > schizophrenia PPI differences were greatest among patients not taking 2nd generation antipsychotics, and were independent of smoking status. Modest but significant relationships were detected between PPI and performance in specific neurocognitive measures. Discussion The COGS-2 multi-site study detects schizophrenia-related PPI deficits reported in single-site studies, including patterns related to diagnosis, prepulse interval, sex, medication and other neurocognitive measures. Site differences were detected and explored. The target COGS-2 schizophrenia “endophenotype” of reduced PPI should prove valuable for identifying and confirming schizophrenia risk genes in future analyses. PMID:24405980

Conformational Sampling and Binding Site Assessment of Suppression of Tumorigenicity 2 Ectodomain

PubMed Central

Yang, Chao-Yie; Delproposto, James; Chinnaswamy, Krishnapriya; Brown, William Clay; Wang, Shuying; Stuckey, Jeanne A.; Wang, Xinquan

2016-01-01

Suppression of Tumorigenicity 2 (ST2), a member of the interleukin-1 receptor (IL-1R) family, activates type 2 immune responses to pathogens and tissue damage via binding to IL-33. Dysregulated responses contribute to asthma, graft-versus-host and autoinflammatory diseases and disorders. To study ST2 structure for inhibitor development, we performed the principal component (PC) analysis on the crystal structures of IL1-1R1, IL1-1R2, ST2 and the refined ST2 ectodomain (ST2ECD) models, constructed from previously reported small-angle X-ray scattering data. The analysis facilitates mapping of the ST2ECD conformations to PC subspace for characterizing structural changes. Extensive coverage of ST2ECD conformations was then obtained using the accelerated molecular dynamics simulations started with the IL-33 bound ST2ECD structure as instructed by their projected locations on the PC subspace. Cluster analysis of all conformations further determined representative conformations of ST2ECD ensemble in solution. Alignment of the representative conformations with the ST2/IL-33 structure showed that the D3 domain of ST2ECD (containing D1-D3 domains) in most conformations exhibits no clashes with IL-33 in the crystal structure. Our experimental binding data informed that the D1-D2 domain of ST2ECD contributes predominantly to the interaction between ST2ECD and IL-33 underscoring the importance of the D1-D2 domain in binding. Computational binding site assessment revealed one third of the total detected binding sites in the representative conformations may be suitable for binding to potent small molecules. Locations of these sites include the D1-D2 domain ST2ECD and modulation sites conformed to ST2ECD conformations. Our study provides structural models and analyses of ST2ECD that could be useful for inhibitor discovery. PMID:26735493

Site index curves for black, white, scarlet, and chestnut oaks in the Central States.

Treesearch

Willard H. Carmean

1971-01-01

Stem analyses showed polymorphic patterns of height growth for each species and for different levels of site quality. New site index curves are presented that show better height growth in later years than predicted by older harmonized site index curves.

Integration of CO2 flux and remotely-sensed data for primary production and ecosystem respiration analyses in the Northern Great Plains: potential for quantitative spatial extrapolation

USGS Publications Warehouse

Gilmanov, Tagir G.; Tieszen, Larry L.; Wylie, Bruce K.; Flanagan, Larry B.; Frank, Albert B.; Haferkamp, Marshall R.; Meyers, Tilden P.; Morgan, Jack A.

2005-01-01

Aim  Extrapolation of tower CO2 fluxes will be greatly facilitated if robust relationships between flux components and remotely sensed factors are established. Long-term measurements at five Northern Great Plains locations were used to obtain relationships between CO2fluxes and photosynthetically active radiation (Q), other on-site factors, and Normalized Difference Vegetation Index (NDVI) from the SPOT VEGETATION data set. Location  CO2 flux data from the following stations and years were analysed: Lethbridge, Alberta 1998–2001; Fort Peck, MT 2000, 2002; Miles City, MT 2000–01; Mandan, ND 1999–2001; and Cheyenne, WY 1997–98. Results  Analyses based on light-response functions allowed partitioning net CO2 flux (F) into gross primary productivity (Pg) and ecosystem respiration (Re). Weekly averages of daytime respiration, γday, estimated from light responses were closely correlated with weekly averages of measured night-time respiration, γnight (R2 0.64 to 0.95). Daytime respiration tended to be higher than night-time respiration, and regressions of γday on γnight for all sites were different from 1 : 1 relationships. Over 13 site-years, gross primary production varied from 459 to 2491 g CO2 m−2 year−1, ecosystem respiration from 996 to 1881 g CO2 m−2 year−1, and net ecosystem exchange from −537 (source) to +610 g CO2 m−2 year−1 (sink). Maximum daily ecological light-use efficiencies, ɛd,max = Pg/Q, were in the range 0.014 to 0.032 mol CO2 (mol incident quanta)−1. Main conclusions  Ten-day average Pg was significantly more highly correlated with NDVI than 10-day average daytime flux, Pd (R2 = 0.46 to 0.77 for Pg-NDVI and 0.05 to 0.58 for Pd-NDVI relationships). Ten-day average Re was also positively correlated with NDVI, with R2values from 0.57 to 0.77. Patterns of the relationships of Pg and Re with NDVI and other factors indicate possibilities for establishing multivariate functions allowing scaling-up local fluxes to larger areas using GIS data, temporal NDVI, and other factors.

The utility of P300 as a schizophrenia endophenotype and predictive biomarker: clinical and socio-demographic modulators in COGS-2.

PubMed

Turetsky, Bruce I; Dress, Erich M; Braff, David L; Calkins, Monica E; Green, Michael F; Greenwood, Tiffany A; Gur, Raquel E; Gur, Ruben C; Lazzeroni, Laura C; Nuechterlein, Keith H; Radant, Allen D; Seidman, Larry J; Siever, Larry J; Silverman, Jeremy M; Sprock, Joyce; Stone, William S; Sugar, Catherine A; Swerdlow, Neal R; Tsuang, Debby W; Tsuang, Ming T; Light, Gregory

2015-04-01

Reduced auditory P300 amplitude is a robust schizophrenia deficit exhibiting the qualities of a viable genetic endophenotype. These include heritability, test-retest reliability, and trait-like stability. Recent evidence suggests that P300 may also serve as a predictive biomarker for transition to psychosis during the schizophrenia prodrome. Historically, the utility of the P300 has been limited by its clinical nonspecificity, cross-site measurement variability, and required EEG expertise. The Consortium on the Genetics of Schizophrenia (COGS-2) study provided an opportunity to examine the consistency of the measure across multiple sites with varying degrees of EEG experience, and to identify important modulating factors that contribute to measurement variability. Auditory P300 was acquired from 649 controls and 587 patients at 5 sites. An overall patient deficit was observed with effect size 0.62. Each site independently observed a significant patient deficit, but site differences also existed. In patients, site differences reflected clinical differences in positive symptomatology and functional capacity. In controls, site differences reflected differences in racial stratification, smoking and substance use history. These factors differentially suppressed the P300 response, but only in control subjects. This led to an attenuated patient-control difference among smokers and among African Americans with history of substance use. These findings indicate that the P300 can be adequately assessed quantitatively, across sites, without substantial EEG expertise. Measurements are suitable for both genetic endophenotype analyses and studies of psychosis risk and conversion. However, careful attention must be given to selection of appropriate comparison samples to avoid misleading false negative results. Copyright © 2014 Elsevier B.V. All rights reserved.

The Utility of P300 as a Schizophrenia Endophenotype and Predictive Biomarker: Clinical and Socio-Demographic Modulators in COGS-2

PubMed Central

Turetsky, Bruce I.; Dress, Erich M.; Braff, David L.; Calkins, Monica E.; Green, Michael F.; Greenwood, Tiffany A.; Gur, Raquel E.; Gur, Ruben C.; Lazzeroni, Laura C.; Nuechterlein, Keith H.; Radant, Allen D.; Seidman, Larry J.; Siever, Larry J.; Silverman, Jeremy M.; Sprock, Joyce; Stone, William S.; Sugar, Catherine A.; Swerdlow, Neal R.; Tsuang, Debby W.; Tsuang, Ming T.; Light, Gregory

2014-01-01

Reduced auditory P300 amplitude is a robust schizophrenia deficit exhibiting the qualities of a viable genetic endophenotype. These include heritability, test-retest reliability, and trait-like stability. Recent evidence suggests that P300 may also serve as a predictive biomarker for transition to psychosis during the schizophrenia prodrome. Historically, the utility of the P300 has been limited by its clinical nonspecificity, cross-site measurement variability, and required EEG expertise. The Consortium on the Genetics of Schizophrenia (COGS-2) study provided an opportunity to examine the consistency of the measure across multiple sites with varying degrees of EEG experience, and to identify important modulating factors that contribute to measurement variability. Auditory P300 was acquired from 649 control and 587 patients at 5 sites. An overall patient deficit was observed with effect size 0.62. Each site independently observed a significant patient deficit, but site differences also existed. In patients, site differences reflected clinical differences in positive symptomatology and functional capacity. In controls, site differences reflected differences in racial stratification, smoking and substance use history. These factors differentially suppressed the P300 response, but only in control subjects. This led to an attenuated patient-control difference among smokers and among African Americans with history of substance use. These findings indicate that the P300 can be adequately assessed quantitatively, across sites, without substantial EEG expertise. Measurements are suitable for both genetic endophenotype analyses and studies of psychosis risk and conversion. However, careful attention must be given to selection of appropriate comparison samples to avoid misleading false negative results. PMID:25306203

Current Antimicrobial Usage for the Management of Neutropenic Fever in Korea: A Nationwide Survey

PubMed Central

Choi, Su-Mi; Park, Sun Hee; Lee, Dong-Gun; Choi, Jung-Hyun; Yoo, Jin-Hong

2008-01-01

A nationwide questionnaire-based survey was performed to evaluate the current clinical practices for the management of neutropenic fever in hematology units and hematopoietic stem cell transplantation (HSCT) centers throughout Korea. A 86.9% response rate was obtained from a total of 46 doctors and practical policies of the 33 sites were analysed. Approximately 42.4% and 84.8% of the sites responded that they used oral fluoroquinolone as prophylaxis for neutropenic patients receiving chemotherapy and HSCT, respectively. Additionally, 42.4% of the sites responded that they used antifungal prophylaxis in the chemotherapy groups whereas 90.9% of the sites responded that they used antifungal prophylaxis in HSCT recipients. Approximately half of the responding sites prescribed combination regimen with 3rd or 4th cephalosporin plus aminoglycoside as a first-line therapy. Most of the sites considered persistent fever for 2-4 days or aggravated clinical symptoms for 1-2 days as failure of the first-line regimen, and they changed antibiotics to second-line regimens that varied widely among the sites. Twenty-seven sites (84.4%) responded that they considered adding an antifungal agent when fever persisted for 5-7 days despite antibacterial therapy. Amphotericin B deoxycholate was preferred as a first-line antifungal, which was probably due to the limitations of the national health insurance system. The role of oral antibiotics in the management of neutropenic fever still accounted for a small portion. To the best of our knowledge, this survey is the first report to examine the practical policies currently in place for the management of neutropenic fever in Korea and the results of this survey may help to establish a Korean guideline in the future. PMID:19119433

Seismic site coefficients and acceleration design response spectra based on conditions in South Carolina : final report.

DOT National Transportation Integrated Search

2014-11-15

The simplified procedure in design codes for determining earthquake response spectra involves : estimating site coefficients to adjust available rock accelerations to site accelerations. Several : investigators have noted concerns with the site coeff...

Airway symptoms and lung function in the local population after the oil tank explosion in Gulen, Norway.

PubMed

Granslo, Jens-Tore; Bråtveit, Magne; Hollund, Bjørg Eli; Irgens, Ågot; Svanes, Cecilie; Magerøy, Nils; Moen, Bente Elisabeth

2012-12-12

Oil tanks containing a mixture of hydrocarbons, including sulphuric compounds, exploded and caught fire in an industrial harbour. This study assesses airway symptoms and lung function in the nearby population 1½ years after the explosion. A cross-sectional study included individuals ≥18 years old. Individuals living <6 km (sub-groups <3km and 3-6 km) from the accident site formed the exposed group, individuals living >20 km away formed a control group. A questionnaire and spirometry tests were completed by 223 exposed individuals (response rate men 70%, women 75%) and 179 control individuals (response rate men 51%, women 65%). Regression analyses included adjustment for smoking, occupational exposure, atopy, infection in the preceding month and age. Analyses of symptoms were also adjusted for stress reactions related to the accident. Exposed individuals experienced significantly more blocked nose (odds ratio 1.7 [95% confidence interval 1.0, 2.8]), rhinorrhoea (1.6 [1.1, 3.3]), nose irritation (3.4 [2.0, 5.9]), sore throat (3.1 [1.8, 5.5]), morning cough (3.5 [2.0, 5.5]), daily cough (2.2 [1.4, 3.7]), cough >3 months a year (2.9 [1.5, 5.3]) and cough with phlegm (1.9 [1.2, 3.1]) than control individuals. A significantly increasing trend was found for nose symptoms and cough, depending on the proximity of home address to explosion site (daily cough, 3-6km 1.8 [1.0, 3.1], <3km 3.0 [1.7, 6.4]). Lung function measurements were significantly lower in the exposed group than in the control group, FEV1 adjusted mean difference -123 mL [95% confidence interval -232, -14]), FEV1% predicted -2.5 [-5.5, 0.5], FVC -173 mL [- 297, -50], FVC% predicted -3.1 [- 5.9, -0.4], and airway obstruction (GOLD II/III). Based on cross sectional analyses, individuals living in an area with air pollution from an oil tank explosion had more airway symptoms and lower lung function than a control group 1½ years after the incident.

Engineering analysis of LANDSAT 1 data for Southeast Asian agriculture

NASA Technical Reports Server (NTRS)

Mcnair, A. J.; Heydt, H. L.; Liang, T.; Levine, G. (Principal Investigator)

1976-01-01

The author has identified the following significant results. LANDSAT spatial resolution was estimated to be adequate, but barely so, for the purpose of detailed assessment of rice or site status. This was due to the spatially fine grain, heterogenous nature of most rice areas. Use of two spectral bands of digital data (MSS 5 and MSS 6 or 7) appeared to be adequate for site recognition and gross site status assessment. Spectral/temporal signatures were found to be more powerful than spectra signatures alone and virtually essential for most analyses of rice growth and rice sites in the Philippine environment. Two band, two date signatures were estimated to be adequate for most purposes, although good results were achieved using one band two- or four-date signatures. A radiometric resolution of 64 levels in each band was found adequate for the analyses of LANDSAT digital data for site recognition and gross site or rice growth assessment.

Abnormal B cell memory subsets dominate HIV-specific responses in infected individuals

PubMed Central

Kardava, Lela; Moir, Susan; Shah, Naisha; Wang, Wei; Wilson, Richard; Buckner, Clarisa M.; Santich, Brian H.; Kim, Leo J.Y.; Spurlin, Emily E.; Nelson, Amy K.; Wheatley, Adam K.; Harvey, Christopher J.; McDermott, Adrian B.; Wucherpfennig, Kai W.; Chun, Tae-Wook; Tsang, John S.; Li, Yuxing; Fauci, Anthony S.

2014-01-01

Recently, several neutralizing anti-HIV antibodies have been isolated from memory B cells of HIV-infected individuals. Despite extensive evidence of B cell dysfunction in HIV disease, little is known about the cells from which these rare HIV-specific antibodies originate. Accordingly, we used HIV envelope gp140 and CD4 or coreceptor (CoR) binding site (bs) mutant probes to evaluate HIV-specific responses in peripheral blood B cells of HIV-infected individuals at various stages of infection. In contrast to non-HIV responses, HIV-specific responses against gp140 were enriched within abnormal B cells, namely activated and exhausted memory subsets, which are largely absent in the blood of uninfected individuals. Responses against the CoRbs, which is a poorly neutralizing epitope, arose early, whereas those against the well-characterized neutralizing epitope CD4bs were delayed and infrequent. Enrichment of the HIV-specific response within resting memory B cells, the predominant subset in uninfected individuals, did occur in certain infected individuals who maintained low levels of plasma viremia and immune activation with or without antiretroviral therapy. The distribution of HIV-specific responses among memory B cell subsets was corroborated by transcriptional analyses. Taken together, our findings provide valuable insight into virus-specific B cell responses in HIV infection and demonstrate that memory B cell abnormalities may contribute to the ineffectiveness of the antibody response in infected individuals. PMID:24892810

Evaluation of fault-normal/fault-parallel directions rotated ground motions for response history analysis of an instrumented six-story building

USGS Publications Warehouse

Kalkan, Erol; Kwong, Neal S.

2012-01-01

According to regulatory building codes in United States (for example, 2010 California Building Code), at least two horizontal ground-motion components are required for three-dimensional (3D) response history analysis (RHA) of buildings. For sites within 5 km of an active fault, these records should be rotated to fault-normal/fault-parallel (FN/FP) directions, and two RHA analyses should be performed separately (when FN and then FP are aligned with the transverse direction of the structural axes). It is assumed that this approach will lead to two sets of responses that envelope the range of possible responses over all nonredundant rotation angles. This assumption is examined here using a 3D computer model of a six-story reinforced-concrete instrumented building subjected to an ensemble of bidirectional near-fault ground motions. Peak responses of engineering demand parameters (EDPs) were obtained for rotation angles ranging from 0° through 180° for evaluating the FN/FP directions. It is demonstrated that rotating ground motions to FN/FP directions (1) does not always lead to the maximum responses over all angles, (2) does not always envelope the range of possible responses, and (3) does not provide maximum responses for all EDPs simultaneously even if it provides a maximum response for a specific EDP.

Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment.

PubMed

Störmer, Rebecca; Wichels, Antje; Gerdts, Gunnar

2013-12-15

The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring. Copyright © 2013 Elsevier Ltd. All rights reserved.

1997 Savannah River Site annual epidemiologic surveillance report

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

None

This report provides a summary of epidemiologic surveillance data collected from Savannah River Site from January 1, 1997 through December 31, 1997. The data were collected by a coordinator at Savannah River Site and submitted to the Epidemiologic Surveillance Data Center located at Oak Ridge Institute for Science and Education, where quality control procedures and preliminary data analyses were carried out. The analyses were interpreted and the final report prepared by the DOE Office of Epidemiologic Studies. The information in this report provides highlights of the data analyses conducted on the 1997 data collected from Savannah River Site. The mainmore » sections of the report include: work force characteristics; absences due to injury or illness lasting 5 or more consecutive workdays; workplace illnesses, injuries, and deaths that were reportable to the Occupational Safety and Health Administration (''OSHA-recordable'' events); and disabilities and deaths among current workers. The 199 7 report includes a section on time trends that provides comparative information on the health of the work force from 1994 through 1997.« less

1996 Savannah River Site annual epidemiologic surveillance report

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

None

This report provides a summary of epidemiologic surveillance data collected from Savannah River Site from January 1, 1996 through December 31, 1996. The data were collected by a coordinator at Savannah River Site and submitted to the Epidemiologic Surveillance Data Center located at Oak Ridge Institute for Science and Education, where quality control procedures and preliminary data analyses were carried out. The analyses were interpreted and the final report prepared by the DOE Office of Epidemiologic Studies. The information in this report provides highlights of the data analyses conducted on the 1996 data collected from Savannah River Site. The mainmore » sections of the report include: work force characteristics; absences due to injury or illness lasting 5 or more consecutive workdays; workplace illnesses, injuries, and deaths that were reportable to the Occupational Safety and Health Administration (''OSHA-recordable'' events); and disabilities and deaths among current workers. The 1996 report includes a new section on time trends that provides comparative information on the health of the work force from 1994 through 1996.« less

The Sensitivity of Genetic Connectivity Measures to Unsampled and Under-Sampled Sites

PubMed Central

Koen, Erin L.; Bowman, Jeff; Garroway, Colin J.; Wilson, Paul J.

2013-01-01

Landscape genetic analyses assess the influence of landscape structure on genetic differentiation. It is rarely possible to collect genetic samples from all individuals on the landscape and thus it is important to assess the sensitivity of landscape genetic analyses to the effects of unsampled and under-sampled sites. Network-based measures of genetic distance, such as conditional genetic distance (cGD), might be particularly sensitive to sampling intensity because pairwise estimates are relative to the entire network. We addressed this question by subsampling microsatellite data from two empirical datasets. We found that pairwise estimates of cGD were sensitive to both unsampled and under-sampled sites, and FST, Dest, and deucl were more sensitive to under-sampled than unsampled sites. We found that the rank order of cGD was also sensitive to unsampled and under-sampled sites, but not enough to affect the outcome of Mantel tests for isolation by distance. We simulated isolation by resistance and found that although cGD estimates were sensitive to unsampled sites, by increasing the number of sites sampled the accuracy of conclusions drawn from landscape genetic analyses increased, a feature that is not possible with pairwise estimates of genetic differentiation such as FST, Dest, and deucl. We suggest that users of cGD assess the sensitivity of this measure by subsampling within their own network and use caution when making extrapolations beyond their sampled network. PMID:23409155

Geomorphic responses of Duluth-area streams to the June 2012 flood, Minnesota

USGS Publications Warehouse

Fitzpatrick, Faith A.; Ellison, Christopher A.; Czuba, Christiana R.; Young, Benjamin M.; McCool, Molly M.; Groten, Joel T.

2016-09-01

In 2013, the U.S. Geological Survey, in cooperation with the Minnesota Pollution Control Agency, completed a geomorphic assessment of 51 Duluth-area stream sites in 20 basins to describe and document the stream geomorphic changes associated with the June 2012 flood. Heavy rainfall caused flood peaks with annual exceedance probabilities of less than 0.002 (flood recurrence interval of greater than 500 years) on large and small streams in and surrounding the Duluth area. A geomorphic segment-scale classification previously developed in 2003–4 by the U.S. Geological Survey for Duluth-area streams was used as a framework to characterize the observed flood-related responses along a longitudinal continuum from headwaters to rivermouths at Lake Superior related to drainage network position, slope, geologic setting, and valley type. Field assessments in 2013 followed and expanded on techniques used in 2003–4 at intensive and rapid sites. A third level of assessment was added in 2013 to increase the amount of quantitative data at a subset of 2003–4 rapid sites. Characteristics of channel morphology, channel bed substrate, exposed bars and soft sediment deposition, large wood, pools, and bank erosion were measured; and repeat photographs were taken. Additional measurements in 2013 included identification of Rosgen Level II stream types. The comparative analyses of field data collected in 2003–4 and again in 2013 indicated notable geomorphic changes, some of them expected and others not. As expected, in headwaters with gently sloping wetland segments, geomorphic changes were negligible (little measured or observed change). Downstream, middle main stems generally had bank and bluff erosion and bar formation as expected. Steep bedrock sites along middle and lower main stems had localized bank and bluff erosion in short sections with intermittent bedrock. Lower main stem and alluvial sites had bank erosion, widening, gravel bar deposition, and aggradation. Bar formation and accumulation of gravel was more widespread than expected among all main stems, especially for sites upstream and downstream from channel constrictions from road crossings, or even steep sites with localized, more gently sloping sections. Decreases in large wood and pools also were observed throughout the longitudinal continuum of main-stem sites, with immediate implications for fish and benthic invertebrate aquatic habitat. Whether or not the geomorphic conditions will return to their preflood condition depends on the location along the longitudinal continuum. The amount of large wood and pools may return after more moderate floods, whereas bars with coarse material may remain in place, locally altering flow direction and causing continued bank erosion. Results from this study can be used by local managers in postflood reconstruction efforts and provide baseline information for continued monitoring of geomorphic responses to the June 2012 flood.

Test and Analysis of a Buckling-Critical Large-Scale Sandwich Composite Cylinder

NASA Technical Reports Server (NTRS)

Schultz, Marc R.; Sleight, David W.; Gardner, Nathaniel W.; Rudd, Michelle T.; Hilburger, Mark W.; Palm, Tod E.; Oldfield, Nathan J.

2018-01-01

Structural stability is an important design consideration for launch-vehicle shell structures and it is well known that the buckling response of such shell structures can be very sensitive to small geometric imperfections. As part of an effort to develop new buckling design guidelines for sandwich composite cylindrical shells, an 8-ft-diameter honeycomb-core sandwich composite cylinder was tested under pure axial compression to failure. The results from this test are compared with finite-element-analysis predictions and overall agreement was very good. In particular, the predicted buckling load was within 1% of the test and the character of the response matched well. However, it was found that the agreement could be improved by including composite material nonlinearity in the analysis, and that the predicted buckling initiation site was sensitive to the addition of small bending loads to the primary axial load in analyses.

Molecular and chemical dialogues in bacteria-protozoa interactions.

PubMed

Song, Chunxu; Mazzola, Mark; Cheng, Xu; Oetjen, Janina; Alexandrov, Theodore; Dorrestein, Pieter; Watrous, Jeramie; van der Voort, Menno; Raaijmakers, Jos M

2015-08-06

Protozoan predation of bacteria can significantly affect soil microbial community composition and ecosystem functioning. Bacteria possess diverse defense strategies to resist or evade protozoan predation. For soil-dwelling Pseudomonas species, several secondary metabolites were proposed to provide protection against different protozoan genera. By combining whole-genome transcriptome analyses with (live) imaging mass spectrometry (IMS), we observed multiple changes in the molecular and chemical dialogues between Pseudomonas fluorescens and the protist Naegleria americana. Lipopeptide (LP) biosynthesis was induced in Pseudomonas upon protozoan grazing and LP accumulation transitioned from homogeneous distributions across bacterial colonies to site-specific accumulation at the bacteria-protist interface. Also putrescine biosynthesis was upregulated in P. fluorescens upon predation. We demonstrated that putrescine induces protozoan trophozoite encystment and adversely affects cyst viability. This multifaceted study provides new insights in common and strain-specific responses in bacteria-protozoa interactions, including responses that contribute to bacterial survival in highly competitive soil and rhizosphere environments.

Evolutionary genomics and HIV restriction factors.

PubMed

Pyndiah, Nitisha; Telenti, Amalio; Rausell, Antonio

2015-03-01

To provide updated insights into innate antiviral immunity and highlight prototypical evolutionary features of well characterized HIV restriction factors. Recently, a new HIV restriction factor, Myxovirus resistance 2, has been discovered and the region/residue responsible for its activity identified using an evolutionary approach. Furthermore, IFI16, an innate immunity protein known to sense several viruses, has been shown to contribute to the defense to HIV-1 by causing cell death upon sensing HIV-1 DNA. Restriction factors against HIV show characteristic signatures of positive selection. Different patterns of accelerated sequence evolution can distinguish antiviral strategies--offense or defence--as well as the level of specificity of the antiviral properties. Sequence analysis of primate orthologs of restriction factors serves to localize functional domains and sites responsible for antiviral action. We use recent discoveries to illustrate how evolutionary genomic analyses help identify new antiviral genes and their mechanisms of action.

A computational prediction of structure and function of novel homologue of Arabidopsis thaliana Vps51/Vps67 subunit in Corchorus olitorius.

PubMed

Zaman, Aubhishek; Fancy, Nurun Nahar

2012-12-01

Vps mediated vesicular transport is important for transferring macromolecules trapped inside a vesicle. Although highly abundant, Vps shows tremendous sequence variation among diverse array of species. However, this difference in sequence, which seems to also translate into substantial functional variation, is hardly characterized in Corchorus spp. Here, our computational study investigates structural and functional features of one of the Vps subunit namely Vps51/Vps67 in C. olitorius. Broad scale structural characterization revealed novel information about the overall Vps structure and binding sites. Moreover, functional analyses indicate interaction partners which were unexplored to date. Since membrane trafficking is essentially associated with nutrient uptake and chemical de-toxification, characterization of the Vps subunit can well provide us with better insight into important agronomic traits such as stress response, immune response and phytoremediation capacity.

Modelling the distribution of hard seabed using calibrated multibeam acoustic backscatter data in a tropical, macrotidal embayment: Darwin Harbour, Australia

NASA Astrophysics Data System (ADS)

Siwabessy, P. Justy W.; Tran, Maggie; Picard, Kim; Brooke, Brendan P.; Huang, Zhi; Smit, Neil; Williams, David K.; Nicholas, William A.; Nichol, Scott L.; Atkinson, Ian

2018-06-01

Spatial information on the distribution of seabed substrate types in high use coastal areas is essential to support their effective management and environmental monitoring. For Darwin Harbour, a rapidly developing port in northern Australia, the distribution of hard substrate is poorly documented but known to influence the location and composition of important benthic biological communities (corals, sponges). In this study, we use angular backscatter response curves to model the distribution of hard seabed in the subtidal areas of Darwin Harbour. The angular backscatter response curve data were extracted from multibeam sonar data and analysed against backscatter intensity for sites observed from seabed video to be representative of "hard" seabed. Data from these sites were consolidated into an "average curve", which became a reference curve that was in turn compared to all other angular backscatter response curves using the Kolmogorov-Smirnov goodness-of-fit. The output was used to generate interpolated spatial predictions of the probability of hard seabed ( p-hard) and derived hard seabed parameters for the mapped area of Darwin Harbour. The results agree well with the ground truth data with an overall classification accuracy of 75% and an area under curve measure of 0.79, and with modelled bed shear stress for the Harbour. Limitations of this technique are discussed with attention to discrepancies between the video and acoustic results, such as in areas where sediment forms a veneer over hard substrate.

An Experimental Test of Competition among Mice, Chipmunks, and Squirrels in Deciduous Forest Fragments

PubMed Central

Brunner, Jesse L.; Duerr, Shannon; Keesing, Felicia; Killilea, Mary; Vuong, Holly; Ostfeld, Richard S.

2013-01-01

Mixed hardwood forests of the northeast United States support a guild of granivorous/omnivorous rodents including gray squirrels (Sciurus carolinensis), eastern chipmunks (Tamias striatus), and white-footed mice (Peromyscus leucopus). These species coincide geographically, co-occur locally, and consume similar food resources. Despite their idiosyncratic responses to landscape and patch variables, patch occupancy models suggest that competition may influence their respective distributions and abundances, and accordingly their influence on the rest of the forest community. Experimental studies, however, are wanting. We present the result of a large-scale experiment in which we removed white-footed mice or gray squirrels from small, isolated forest fragments in Dutchess County, New York, and added these mammals to other fragments in order to alter the abundance of these two species. We then used mark–recapture analyses to quantify the population-level and individual-level effects on resident mice, squirrels, and chipmunks. Overall, we found little evidence of competition. There were essentially no within-season numerical responses to changes in the abundance of putative competitors. Moreover, while individual-level responses (apparent survival and capture probability) did vary with competitor densities in some models, these effects were often better explained by site-specific parameters and were restricted to few of the 19 sites we studied. With only weak or nonexistent competition among these three common rodent species, we expect their patterns of habitat occupancy and population dynamics to be largely independent of one another. PMID:23824654

An assessment of pharmacists’ readiness for paperless labeling: a national survey

PubMed Central

Ho, Yun-Xian; Chen, Qingxia; Nian, Hui; Johnson, Kevin B

2014-01-01

Objective To assess the state of readiness for the adoption of paperless labeling among a nationally representative sample of pharmacies, including chain pharmacies, independent retail pharmacies, hospitals, and other rural or urban dispensing sites. Methods Both quantitative and qualitative analyses were used to analyze responses to a cross-sectional survey disseminated to American Pharmacists Association pharmacists nationwide. The survey assessed factors related to pharmacists’ attitudinal readiness (ie, perceptions of impact) and pharmacies’ structural readiness (eg, availability of electronic resources, internet access) for the paperless labeling initiative. Results We received a total of 436 survey responses (6% response rate) from pharmacists representing 44 US states and territories. Across the spectrum of settings we studied, pharmacists had work access to computers, printers, fax machines and access to the internet or intranet. Approximately 79% of respondents believed that the initiative would improve the adequacy of drug information available in their work site and 95% believed it would either not change (33%) or would improve (62%) communication to patients. Overall, respondents’ comments supported advancing the initiative; however, some comments revealed reservations regarding corporate or pharmacy buy-in, success of implementation, and ease of adoption. Conclusions This is the first nationwide study to report about pharmacists’ perspectives on paperless labeling. In general, pharmacists believe they are ready and that their pharmacies are well equipped for the transition to paperless labeling. Further exploration of perspectives from product label manufacturers and corporate pharmacy offices is needed to understand fully what will be necessary to complete this transition. PMID:23523874

An assessment of pharmacists' readiness for paperless labeling: a national survey.

PubMed

Ho, Yun-Xian; Chen, Qingxia; Nian, Hui; Johnson, Kevin B

2014-01-01

To assess the state of readiness for the adoption of paperless labeling among a nationally representative sample of pharmacies, including chain pharmacies, independent retail pharmacies, hospitals, and other rural or urban dispensing sites. Both quantitative and qualitative analyses were used to analyze responses to a cross-sectional survey disseminated to American Pharmacists Association pharmacists nationwide. The survey assessed factors related to pharmacists' attitudinal readiness (ie, perceptions of impact) and pharmacies' structural readiness (eg, availability of electronic resources, internet access) for the paperless labeling initiative. We received a total of 436 survey responses (6% response rate) from pharmacists representing 44 US states and territories. Across the spectrum of settings we studied, pharmacists had work access to computers, printers, fax machines and access to the internet or intranet. Approximately 79% of respondents believed that the initiative would improve the adequacy of drug information available in their work site and 95% believed it would either not change (33%) or would improve (62%) communication to patients. Overall, respondents' comments supported advancing the initiative; however, some comments revealed reservations regarding corporate or pharmacy buy-in, success of implementation, and ease of adoption. This is the first nationwide study to report about pharmacists' perspectives on paperless labeling. In general, pharmacists believe they are ready and that their pharmacies are well equipped for the transition to paperless labeling. Further exploration of perspectives from product label manufacturers and corporate pharmacy offices is needed to understand fully what will be necessary to complete this transition.

SAS Code for Calculating Intraclass Correlation Coefficients and Effect Size Benchmarks for Site-Randomized Education Experiments

ERIC Educational Resources Information Center

Brandon, Paul R.; Harrison, George M.; Lawton, Brian E.

2013-01-01

When evaluators plan site-randomized experiments, they must conduct the appropriate statistical power analyses. These analyses are most likely to be valid when they are based on data from the jurisdictions in which the studies are to be conducted. In this method note, we provide software code, in the form of a SAS macro, for producing statistical…

Variations in protein/flavin hydrogen bonding in a LOV domain produce non-Arrhenius kinetics of adduct decay†

PubMed Central

Zoltowski, Brian D.; Nash, Abigail I.; Gardner, Kevin H.

2011-01-01

Light Oxygen Voltage (LOV) domains utilize a conserved blue light-dependent mechanism to control a diverse array of effector domains in biological and engineered proteins. Variations in the kinetics and efficiency of LOV photochemistry fine tune various aspects of the photic response. Characterization of the kinetics of a key aspect of this photochemical mechanism in EL222, a blue-light responsive DNA binding protein from Erythrobacter litoralis HTCC2594, reveals unique non-Arrhenius behavior in the rate of dark state cleavage of the photochemically-generated adduct. Sequence analysis and mutagenesis studies establish that this effect stems from a Gln to Ala mutation unique to EL222 and homologous proteins from marine bacteria. Kinetic and spectroscopic analyses reveal that hydrogen bonding interactions between the FMN N1, O2 and ribityl hydroxyls with the surrounding protein regulate photocycle kinetics and stabilize the LOV active site from temperature-induced alteration in local structure. Substitution of residues interacting with the N1-O2 locus modulates adduct stability, structural flexibility and sequestration of the active site from bulk solvent without perturbation of light-activated DNA binding. Together, these variants link non-Arrhenius behavior to specific alteration of an H-bonding network, while affording tunability of photocycle kinetics. PMID:21923139

An Australian hospital's training program and referral pathway within a multi-disciplinary health-justice partnership addressing family violence.

PubMed

Forsdike, Kirsty; Humphreys, Cathy; Diemer, Kristin; Ross, Stuart; Gyorki, Linda; Maher, Helena; Vye, Penelope; Llewelyn, Fleur; Hegarty, Kelsey

2018-06-01

An innovative health-justice partnership was established to deliver legal assistance to women experiencing family violence who attended an Australian hospital. This paper reports on a multifaceted response to build capacity and willingness of health professionals to identify signs of family violence and engage with referral pathways to on-site legal assistance. A Realistic Evaluation analysed health professionals' knowledge and attitudes towards identification, response and referral for family violence before and after training; and use of referral pathways. Of 123 health professionals participating in training, 67 completed baseline and follow-up surveys. Training improved health professionals' self-reported knowledge of, and confidence in, responding to family violence and understanding of lawyers' roles in hospitals. Belief that patients should be referred to on-site legal services increased. Training did not correspond to actual increased referrals to legal assistance. The program built capacity and willingness of health professionals to identify signs of, and respond to, family violence. Increase in referral rates to legal assistance was not shown. Potential improvements include better data capture and greater availability of legal services. Implications for public health: Strong hospital system supports and reliable recording of family violence referrals need to be in place before introducing such partnerships to other hospitals. © 2017 The Authors.

Fish community-based measures of estuarine ecological quality and pressure-impact relationships

NASA Astrophysics Data System (ADS)

Fonseca, Vanessa F.; Vasconcelos, Rita P.; Gamito, Rita; Pasquaud, Stéphanie; Gonçalves, Catarina I.; Costa, José L.; Costa, Maria J.; Cabral, Henrique N.

2013-12-01

Community-based responses of fish fauna to anthropogenic pressures have been extensively used to assess the ecological quality of estuarine ecosystems. Several methodologies have been developed recently combining metrics reflecting community structure and function. A fish community facing significant environmental disturbances will be characterized by a simplified structure, with lower diversity and complexity. However, estuaries are naturally dynamic ecosystems exposed to numerous human pressures, making it difficult to distinguish between natural and anthropogenic-induced changes to the biological community. In the present work, the variability of several fish metrics was assessed in relation to different pressures in estuarine sites. The response of a multimetric index (Estuarine Fish Assessment Index) was also analysed. Overall, fish metrics and the multimetric index signalled anthropogenic stress, particularly environmental chemical pollution. The fish assemblage associated with this type of pressure was characterized by lower species diversity, lower number of functional guilds, lower abundance of marine migrants and of piscivorous individuals, and higher abundance of estuarine resident species. A decreased ecological quality status, based on the EFAI, was also determined for sites associated with this pressure group. Ultimately, the definition of each pressure groups favoured a stressor-specific analysis, evidencing pressure patterns and accounting for multiple factors in a highly dynamic environment.

Variations in protein-flavin hydrogen bonding in a light, oxygen, voltage domain produce non-Arrhenius kinetics of adduct decay.

PubMed

Zoltowski, Brian D; Nash, Abigail I; Gardner, Kevin H

2011-10-18

Light, oxygen, voltage (LOV) domains utilize a conserved blue light-dependent mechanism to control a diverse array of effector domains in biological and engineered proteins. Variations in the kinetics and efficiency of LOV photochemistry fine-tune various aspects of the photic response. Characterization of the kinetics of a key aspect of this photochemical mechanism in EL222, a blue light responsive DNA binding protein from Erythrobacter litoralis HTCC2594, reveals unique non-Arrhenius behavior in the rate of dark-state cleavage of the photochemically generated adduct. Sequence analysis and mutagenesis studies establish that this effect stems from a Gln to Ala mutation unique to EL222 and homologous proteins from marine bacteria. Kinetic and spectroscopic analyses reveal that hydrogen bonding interactions between the FMN N1, O2, and ribityl hydroxyls and the surrounding protein regulate photocycle kinetics and stabilize the LOV active site from temperature-induced alteration in local structure. Substitution of residues interacting with the N1-O2 locus modulates adduct stability, structural flexibility, and sequestration of the active site from bulk solvent without perturbation of light-activated DNA binding. Together, these variants link non-Arrhenius behavior to specific alteration of an H-bonding network, while affording tunability of photocycle kinetics. © 2011 American Chemical Society

Assessing PAHs pollution in Shandong coastal area (China) by combination of chemical analysis and responses of reproductive toxicity in crab Portunus trituberculatus.

PubMed

Pan, Luqing; Xu, Ruiyi; Wen, Jianmin; Guo, Ruiming

2017-06-01

The concentrations of PAHs in seawater and sediments were measured at three selected sites (S1, S2, and S3) along the coastal area of Shandong (China) in April, May, and June, 2015, which ranged from 29.72 to 123.88 ng/L and 82.62 to 232.63 ng/g, respectively. Meanwhile, the reproductive toxicity responses in crab Portunus trituberculatus were also evaluated to assess the pollution of PAHs during the sampling period. Chemical analysis showed that S3 was the most PAH-contaminated area while S1 was the least, and the biochemical parameters concerned with reproduction were efficiently responded to the three sites, especially in S3 (p < 0.05). Moreover, the principal component analyses (PCA) showed that parameters for DNA alkaline unwinding, protein carbonyl content, and lipid peroxidation levels in two genders, 17β-estradiol in female, testosterone and TESK2 gene expression in male crabs, were closely correlated with the concentrations of PAHs (2 + 3 rings, 4 rings, and 5 + 6 rings), which were considered to be good candidate indicators to assess the environmental pollutions resulting from PAHs in the coastal area of Shandong, China.

Histopathology and stress biomarkers in the clam Venerupis philippinarum from the Venice Lagoon (Italy).

PubMed

Boscolo Papo, Michele; Bertotto, Daniela; Quaglio, Francesco; Vascellari, Marta; Pascoli, Francesco; Negrato, Elena; Binato, Giovanni; Radaelli, Giuseppe

2014-07-01

The aim of this study was to evaluate the histomorphology and the stress response in the bivalve Venerupis philippinarum sampled in four differently polluted sites of the Venice Lagoon (Palude del Monte, Marghera, Ca' Roman and Val di Brenta). This species is often used as bioindicator of environmental pollution since it can bioaccumulate a large variety of pollutants because of its filter feeding. Chemical analyses for heavy metals (Cd, Cu, Hg and Pb) and polycyclic aromatic hydrocarbons (PAHs) were performed on whole soft tissues of V. philippinarum. The histological evaluation of clams revealed the presence of Perkinsus sp. infection in animals from all sites, although a very high prevalence of parasites was evidenced in clams from Ca' Roman. Perkinsus sp. were systemically distributed in the mantle, in the intestine and digestive gland, in gonads and gills. The trophozoites of Perkinsus sp. were found isolated or in cluster surrounded by a heavy hemocitical response. Haemocytes always exhibited an immunopositivity to cytochrome P4501A (CYP1A), heat shock protein 70 (HSP70), 4-hydroxy-2-nonenal (HNE) and nitrotyrosine (NT) antibodies. The digestive gland of animals from Palude del Monte showed the highest malondialdehyde (MDA) concentration, whereas clams from Ca' Roman exhibited the highest quantity of metallothioneins. Copyright © 2014 Elsevier Ltd. All rights reserved.

Corticosterone stress response in tree swallows nesting near polychlorinated biphenyl- and dioxin-contaminated rivers

USGS Publications Warehouse

Franceschini, M.D.; Custer, Christine M.; Custer, T.W.; Reed, J.M.; Romero, L.M.

2008-01-01

We assayed baseline and stress-induced corticosterone concentrations from adult female and nestling tree swallows, Tachycineta bicolor, from New England, USA, sites with different levels of contamination with polychlorinated biphenyls (PCBs) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Corticosterone was compared over 2 years from a highly contaminated PCB site along the Housatonic River (Berkshire County, MA, USA), a midrange contaminated site upstream, and a reference site. Adult females (n = 29), sampled only in 2003, showed an inverted-U association with PCBs, with higher stress-induced corticosterone with midrange contamination than at the high-contamination site. In nestlings, stress-induced corticosterone was highest for the highly contaminated site compared with the other sites in 2003 (n = 53, 29 nests), with no difference among sites in 2004 (n = 93, 27 nests). In 2004, we began testing mechanisms underlying these changes in nestlings at the high- and low-PCB sites. Corticosterone response to dexamethasone injection (used to test negative feedback) was not different between sites, but stress-induced corticosterone was reduced at the contaminated site after adrenocorticotropin hormone injection (used to test adrenal responsiveness), suggesting an inhibited ability to mount a stress response. We also compared nestlings from a stretch of the Woonasquatucket River, Rhode Island, USA, heavily contaminated with TCDD (n = 80, 43 nests) with nestlings from an upstream site that had lower levels of TCDD and the Berkshire County reference site. Although there were no stress-induced differences, baseline corticosterone was lower at the higher TCDD site than at the reference site. Altogether these findings suggest that tree swallows chronically exposed to high PCB and TCDD levels exhibit altered baseline and stress-induced corticosterone responses, but the patterns of alteration might not be predictable. ?? 2008 SETAC.

Multi-contamination (heavy metals, polychlorinated biphenyls and polycyclic aromatic hydrocarbons) of littoral sediments and the associated ecological risk assessment in a large lake in France (Lake Bourget).

PubMed

Lécrivain, Nathalie; Aurenche, Vincent; Cottin, Nathalie; Frossard, Victor; Clément, Bernard

2018-04-01

The lake littoral sediment is exposed to a large array of contaminants that can exhibit significant spatial variability and challenge our ability to assess contamination at lake scale. In this study, littoral sediment contamination was characterized among ten different sites in a large peri-alpine lake (Lake Bourget) regarding three groups of contaminants: 6 heavy metals, 15 polycyclic aromatic hydrocarbons and 7 polychlorinated biphenyls. The contamination profiles significantly varied among sites and differed from those previously reported for the deepest zone of the lake. An integrative approach including chemical and biological analyses was conducted to relate site contamination to ecological risk. The chemical approach consisted in mean PEC quotient calculation (average of the ratios of the contaminants concentration to their corresponding Probable Effect Concentration values) and revealed a low and heterogeneous toxicity of the contaminant mixture along the littoral. Biological analysis including both laboratory (microcosm assays) and in situ (Acetylcholine Esterase (AChE) and Glutathione S-Transferase (GST) activity measurements) experiments highlighted significant differences among sites both in the field and in laboratory assays suggesting a spatial variation of the biota response to contamination. Linear regressions were performed between mean PEC quotients and biological results to assess whether littoral ecological risk was explained by the contamination profiles. The results highly depended on the study benthic or pelagic compartment. Regarding autochthonous Corbicula fluminea, no significant relationship between mean PEC quotients and biomarker activity was found while a significant increase in AChE was observed on autochthonous chironomids, suggesting different stress among benthic organisms. Both AChE and GST in caged pelagic Daphnia magna showed a significant positive relationship with mean PEC quotients. This study underlines the importance of accounting for spatial variations in lake littoral sediment contamination and the need for performing an integrative approach coupling chemical, field and laboratory analyses to assess the ecological risk. Copyright © 2017 Elsevier B.V. All rights reserved.

Uncertainties in Earthquake Loss Analysis: A Case Study From Southern California

NASA Astrophysics Data System (ADS)

Mahdyiar, M.; Guin, J.

2005-12-01

Probabilistic earthquake hazard and loss analyses play important roles in many areas of risk management, including earthquake related public policy and insurance ratemaking. Rigorous loss estimation for portfolios of properties is difficult since there are various types of uncertainties in all aspects of modeling and analysis. It is the objective of this study to investigate the sensitivity of earthquake loss estimation to uncertainties in regional seismicity, earthquake source parameters, ground motions, and sites' spatial correlation on typical property portfolios in Southern California. Southern California is an attractive region for such a study because it has a large population concentration exposed to significant levels of seismic hazard. During the last decade, there have been several comprehensive studies of most regional faults and seismogenic sources. There have also been detailed studies on regional ground motion attenuations and regional and local site responses to ground motions. This information has been used by engineering seismologists to conduct regional seismic hazard and risk analysis on a routine basis. However, one of the more difficult tasks in such studies is the proper incorporation of uncertainties in the analysis. From the hazard side, there are uncertainties in the magnitudes, rates and mechanisms of the seismic sources and local site conditions and ground motion site amplifications. From the vulnerability side, there are considerable uncertainties in estimating the state of damage of buildings under different earthquake ground motions. From an analytical side, there are challenges in capturing the spatial correlation of ground motions and building damage, and integrating thousands of loss distribution curves with different degrees of correlation. In this paper we propose to address some of these issues by conducting loss analyses of a typical small portfolio in southern California, taking into consideration various source and ground motion uncertainties. The approach is designed to integrate loss distribution functions with different degrees of correlation for portfolio analysis. The analysis is based on USGS 2002 regional seismicity model.

Evaluation of Site Effects Using Numerical and Experimental Analyses In Cittas Di Castello (italy)

NASA Astrophysics Data System (ADS)

Pergalani, F.; de Franco, R.; Compagnoni, M.; Caielli, G.

In the paper the results of the numerical and experimental analyses, in a site of the Umbria Region (Città di Castello - PG), finalized to the evaluations of site effects are shown. The aim of the work was to compare the two type of analyses, to give some methodologies that may be used at the level of urban planning, to consider these as- pects. Therefore a series of geologic, geomorphologic (1:5.000 scale), geotechnic and seismic analyses have been carried out, to identify the areas affected to local effects and to characterize the lithotechnic units. The expected seismic inputs are been indi- viduated and 2D (Quad4M, Hudson et al., 1993) numerical analyses have been done. An experimental analysis, using the registrations of small events, has been done. The results, for the two approaches, were performed in terms of elastic pseudo-acceleration spectra and amplification factors, as a ratio between spectral intensity (Housner, 1952), calculated using the pseudo-velocity spectra, in the periods of 0.1-0.5 s and 0.1-2.5 s of output and input. The results have been analyzed and compared, to give a method- ology that may be exhaustive and precise. The conclusions can be summarized in the following points: u° the results of the two approaches are coherent; u° the differences between the two approaches are: the use of the numerical analysis is easy and quick but, in this case, the use of 2D analysis produces a simplification of real geometry; the use of experimental analysis allows to consider the 3D conditions, but, in this case, the registrations of events characterized by low energy, do not allow to consider the non linear behavior of materials, moreover it is necessary to perform the registrations for a period depending from the seismicity of the region (1 month - two years); u° the possi- bility of integration of the two methodologies allows to perform a complete analysis, using the advantages of the two methods. Housner G.W., Spectrum Intensities of strong motion earthquakes. Proc. of the Symp. on Earth. and Blast Effects on Structures. Earth. Eng. Res. Inst., 1952. Hudson M.B., Idriss I.M., Beikae M. QUAD4M, A computer program for evaluating the seismic response of soil structure by variable damping finite element procedures. Report of Dip. of Civil & Env. Eng., University of California, Davis, 1993.

A Preliminary Examination of the Relationship Between Social Networking Interactions, Internet Use, and Thwarted Belongingness.

PubMed

Moberg, Fallon B; Anestis, Michael D

2015-01-01

Joiner's (2005) interpersonal-psychological theory of suicide hypothesizes that suicidal desire develops in response to the joint presence of thwarted belongingness and perceived burdensomeness. To consider the potential influence of online interactions and behaviors on these outcomes. To address this, we administered an online protocol assessing suicidal desire and online interactions in a sample of 305 undergraduates (83.6% female). We hypothesized negative interactions on social networking sites and a preference for online social interactions would be associated with thwarted belongingness. We also conducted an exploratory analysis examining the associations between Internet usage and perceived burdensomeness. Higher levels of negative interactions on social networking sites, but no other variables, significantly predicted thwarted belongingness. Our exploratory analysis showed that none of our predictors were associated with perceived burdensomeness after accounting for demographics, depression, and thwarted belongingness. Our findings indicate that a general tendency to have negative interactions on social networking sites could possibly impact suicidal desire and that these effects are significant above and beyond depression symptoms. Furthermore, no other aspect of problematic Internet use significantly predicted our outcomes in multivariate analyses, indicating that social networking in particular may have a robust effect on thwarted belongingness.

SOARCA Peach Bottom Atomic Power Station Long-Term Station Blackout Uncertainty Analysis: Knowledge Advancement.

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

Gauntt, Randall O.; Mattie, Patrick D.; Bixler, Nathan E.

2014-02-01

This paper describes the knowledge advancements from the uncertainty analysis for the State-of- the-Art Reactor Consequence Analyses (SOARCA) unmitigated long-term station blackout accident scenario at the Peach Bottom Atomic Power Station. This work assessed key MELCOR and MELCOR Accident Consequence Code System, Version 2 (MACCS2) modeling uncertainties in an integrated fashion to quantify the relative importance of each uncertain input on potential accident progression, radiological releases, and off-site consequences. This quantitative uncertainty analysis provides measures of the effects on consequences, of each of the selected uncertain parameters both individually and in interaction with other parameters. The results measure the modelmore » response (e.g., variance in the output) to uncertainty in the selected input. Investigation into the important uncertain parameters in turn yields insights into important phenomena for accident progression and off-site consequences. This uncertainty analysis confirmed the known importance of some parameters, such as failure rate of the Safety Relief Valve in accident progression modeling and the dry deposition velocity in off-site consequence modeling. The analysis also revealed some new insights, such as dependent effect of cesium chemical form for different accident progressions. (auth)« less

77 FR 31357 - Proposed Agreement Pursuant to the Comprehensive Environmental Response, Compensation, and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-25

... Environmental Response, Compensation, and Liability Act for the Wabash Environmental Technologies Site AGENCY...)(1) agreement with 21 parties for the Wabash Environmental Technologies Superfund Site. SUMMARY: In... concerning the Wabash Environmental Technologies hazardous waste site in Terre Haute, Indiana (the ``Site...

Molecular Analysis of Endocrine Disruption in Hornyhead Turbot at Wastewater Outfalls in Southern California Using a Second Generation Multi-Species Microarray

PubMed Central

Baker, Michael E.; Vidal-Dorsch, Doris E.; Ribecco, Cataldo; Sprague, L. James; Angert, Mila; Lekmine, Narimene; Ludka, Colleen; Martella, Andrea; Ricciardelli, Eugenia; Bay, Steven M.; Gully, Joseph R.; Kelley, Kevin M.; Schlenk, Daniel; Carnevali, Oliana; Šášik, Roman; Hardiman, Gary

2013-01-01

Sentinel fish hornyhead turbot ( Pleuronichthys verticalis ) captured near wastewater outfalls are used for monitoring exposure to industrial and agricultural chemicals of ~ 20 million people living in coastal Southern California. Although analyses of hormones in blood and organ morphology and histology are useful for assessing contaminant exposure, there is a need for quantitative and sensitive molecular measurements, since contaminants of emerging concern are known to produce subtle effects. We developed a second generation multi-species microarray with expanded content and sensitivity to investigate endocrine disruption in turbot captured near wastewater outfalls in San Diego, Orange County and Los Angeles California. Analysis of expression of genes involved in hormone [e.g., estrogen, androgen, thyroid] responses and xenobiotic metabolism in turbot livers was correlated with a series of phenotypic end points. Molecular analyses of turbot livers uncovered altered expression of vitellogenin and zona pellucida protein, indicating exposure to one or more estrogenic chemicals, as well as, alterations in cytochrome P450 (CYP) 1A, CYP3A and glutathione S-transferase-α indicating induction of the detoxification response. Molecular responses indicative of exposure to endocrine disruptors were observed in field-caught hornyhead turbot captured in Southern California demonstrating the utility of molecular methods for monitoring environmental chemicals in wastewater outfalls. Moreover, this approach can be adapted to monitor other sites for contaminants of emerging concern in other fish species for which there are few available gene sequences. PMID:24086568

Development of Preliminary Remediation Goals for Indoor Dust at the Colonie FUSRAP Site - 12273

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

Watters, David J.; Opdyke, Clifford P.; Moore, James T.

2012-07-01

The Colonie FUSRAP Site is located in the Town of Colonie, Albany County, New York. The U.S. Army Corps of Engineers is currently addressing environmental contamination associated with the Site under the Comprehensive Environmental Response, Compensation and Liability Act (CERCLA) process as part of the Formerly Utilized Sites Remedial Action Program (FUSRAP). Soil remediation activities have been substantially completed at the Colonie FUSRAP Site and its vicinity properties under the FUSRAP. A study unrelated to FUSRAP was recently performed by an independent party to establish the distribution of DU contamination in various media in the environs of the Site. Asmore » part of this study, dust samples were collected in residencies and businesses in the immediate vicinity of the Site. These samples were collected in non-living areas such as basement window sills and garages. Many of these samples tested positive for DU. An assessment was performed to establish preliminary remediation goals (PRGs) for indoor dust in non-living areas of residential homes and businesses in the vicinity of the Site. The results of this assessment provide estimates of dose-based, carcinogenic risk-based, and noncarcinogenic-based PRGs derived from a hypothetical exposure scenario with reasonable levels of conservatism. Ultimately, the PRGs will be compared to results of dust sampling and analyses in residences and businesses in proximity of the Site to determine whether a response action is appropriate. This assessment estimates PRGs for DU contaminated dust in non-living areas of residences in the vicinity of the Colonie FUSRAP site based on a reasonably conservative exposure scenario. Estimated PRGs based on residential receptors are considered to be conservatively representative of workers in nearby businesses based on the considerably longer exposure duration of residents relative to workers. This assessment provides reasonably conservative estimates of PRGs for DU contaminated dust in non-living areas within residences in the vicinity of the Site. It should be noted that the PRGs include hypothetical exposures resulting from activities in both the living areas and non-living areas of a residence. The PRGs are derived and presented in terms of DU dust concentration in non-living areas to facilitate comparison to results of a planned Site Investigation that will characterize concentrations of DU in dust in non-living areas. It is important to recognize that the exposure assumptions used to derive these PRGs are based on average dust DU concentrations in non-living areas. It is inappropriate to compare these PRGs to the dust DU concentration in an isolated small area. The ongoing Site Investigation addresses this consideration and is designed to provide reasonable estimates of average dust DU concentrations in non-living areas of vicinity properties. In order to accomplish this, sampling is conducted in accordance with EPA Guidance for the Sampling and Analysis of Lead in Indoor Residential Dust for Use in the Integrated Exposure Uptake Biokinetic (IEUBK) Model, (EPA 2008), which specifically addresses estimating average contaminant concentrations in dust. Four (4) large-area samples are collected from each VP in accordance with this guidance. It is anticipated that the results of the Site Investigation will be used in conjunction with the results of this assessment, and/or subsequent assessments, to establish whether or not a response action is appropriate. (authors)« less

Suitability Analyses of Wind Power Generation Complex in South Korea by Using Environmental & Social Criterias

NASA Astrophysics Data System (ADS)

Zhu, Y.; Jeon, S. W.; Seong, M.

2017-12-01

In case of wind-power, one of the most economical renewable energy resources, it is highly emerged owing to the strategic aspect of the response of environmental restriction and strong energy security as well as the upcoming motivation for huge industrial growth in the future. According to the fourth Fundamental Renewable Energy Plan, declared in Sep. 2014, the government instituted the scheme to minimize the proportion of previous RDF(Refused Derived Fuel) till 2035, promoting the solar power and wind power as the core energy for the next generation. Especially in South Korea, it is somewhat desperate to suggest the standard for environmentally optimal locations of wind power setup accompanied with the prevention of disasters from the climate changes. This is because that in case of South Korea, most of suitable places for Wind power complex are in the ridge of the mountains, where is highly invaluable sites as the pool of bio-resources and ecosystem conservations. In this research, we are to focus on the analysis of suitable locations for wind farm site which is relevant to the meteorological and geological factors, by utilizing GIS techniques through the whole South Korea. Ultimately, this analyses are to minimize the adverse effect derived from the current development of wind power in mountain ridges and the time for negotiation for wind power advance.

Ecological response to collapse of the biological pump following the mass extinction at the Cretaceous-Paleogene boundary

NASA Astrophysics Data System (ADS)

Vellekoop, Johan; Woelders, Lineke; Açikalin, Sanem; Smit, Jan; van de Schootbrugge, Bas; Yilmaz, Ismail Ö.; Brinkhuis, Henk; Speijer, Robert P.

2017-02-01

It is commonly accepted that the mass extinction associated with the Cretaceous-Paleogene (K-Pg) boundary (˜ 66 Ma) is related to the environmental effects of a large extraterrestrial impact. The biological and oceanographic consequences of the mass extinction are, however, still poorly understood. According to the Living Ocean model, the biological crisis at the K-Pg boundary resulted in a long-term reduction of export productivity in the early Paleocene. Here, we combine organic-walled dinoflagellate cyst (dinocyst) and benthic foraminiferal analyses to provide new insights into changes in the coupling of pelagic and benthic ecosystems. To this end, we perform dinocyst and benthic foraminiferal analyses on the recently discovered Tethyan K-Pg boundary section at Okçular, Turkey, and compare the results with other K-Pg boundary sites in the Tethys. The post-impact dominance of epibenthic morphotypes and an increase of inferred heterotrophic dinocysts in the early Paleocene at Okçular are consistent with published records from other western Tethyan sites. Together, these records indicate that during the early Paleocene more nutrients remained available for the Tethyan planktonic community, whereas benthic communities were deprived of food. Hence, in the post-impact phase the reduction of export productivity likely resulted in enhanced recycling of nutrients in the upper part of the water column, all along the western Tethyan margins.

Assessment of conformational, spectral, antimicrobial activity, chemical reactivity and NLO application of Pyrrole-2,5-dicarboxaldehyde bis(oxaloyldihydrazone).

PubMed

Rawat, Poonam; Singh, R N

2015-04-05

An orange colored pyrrole dihydrazone: Pyrrole-2,5-dicarboxaldehyde bis(oxaloyldihydrazone) (PDBO) has been synthesized by reaction of oxalic acid dihydrazide with 2,5 diformyl-1H-pyrrole and has been characterized by spectroscopic analysis (1H, 13C NMR, UV-visible, FT-IR and DART Mass). The properties of the compound has been evaluated using B3LYP functional and 6-31G(d,p)/6-311+G(d,p) basis set. The symmetric (3319, 3320 cm(-1)) and asymmetric (3389, 3382 cm(-1)) stretching wave number confirm free NH2 groups in PDBO. NBO analysis shows, inter/intra molecular interactions within the molecule. Topological parameters have been analyzed by QTAIM theory and provide the existence of intramolecular hydrogen bonding (N-H⋯O). The local reactivity descriptors analyses determine the reactive sites within molecule. The calculated first hyperpolarizability value (β0=23.83×10(-30) esu) of pyrrole dihydrazone shows its suitability for non-linear optical (NLO) response. The preliminary bioassay suggested that the PDBO exhibits relatively good antibacterial and fungicidal activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Candida albicans, Aspergillus niger. The local reactivity descriptors--Fukui functions (fk+, fk-), local softnesses (sk+, sk-) and electrophilicity indices (ωk+, ωk-) analyses have been used to determine the reactive sites within molecule. Copyright © 2014 Elsevier B.V. All rights reserved.

Assessment of conformational, spectral, antimicrobial activity, chemical reactivity and NLO application of Pyrrole-2,5-dicarboxaldehyde bis(oxaloyldihydrazone)

NASA Astrophysics Data System (ADS)

Rawat, Poonam; Singh, R. N.

2015-04-01

An orange colored pyrrole dihydrazone: Pyrrole-2,5-dicarboxaldehyde bis(oxaloyldihydrazone) (PDBO) has been synthesized by reaction of oxalic acid dihydrazide with 2,5 diformyl-1H-pyrrole and has been characterized by spectroscopic analysis (1H, 13C NMR, UV-visible, FT-IR and DART Mass). The properties of the compound has been evaluated using B3LYP functional and 6-31G(d,p)/6-311+G(d,p) basis set. The symmetric (3319, 3320 cm-1) and asymmetric (3389, 3382 cm-1) stretching wave number confirm free NH2 groups in PDBO. NBO analysis shows, inter/intra molecular interactions within the molecule. Topological parameters have been analyzed by QTAIM theory and provide the existence of intramolecular hydrogen bonding (N-H⋯O). The local reactivity descriptors analyses determine the reactive sites within molecule. The calculated first hyperpolarizability value (β0 = 23.83 × 10-30 esu) of pyrrole dihydrazone shows its suitability for non-linear optical (NLO) response. The preliminary bioassay suggested that the PDBO exhibits relatively good antibacterial and fungicidal activity against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Candida albicans, Aspergillus niger. The local reactivity descriptors - Fukui functions (fk+, fk-), local softnesses (sk+, sk-) and electrophilicity indices (ωk+, ωk-) analyses have been used to determine the reactive sites within molecule.

cDNA microarray analyses reveal candidate marker genes for the detection of ascidian disease in Korea.

PubMed

Azumi, Kaoru; Usami, Takeshi; Kamimura, Akiko; Sabau, Sorin V; Miki, Yasufumi; Fujie, Manabu; Jung, Sung-Ju; Kitamura, Shin-Ichi; Suzuki, Satoru; Yokosawa, Hideyoshi

2007-12-01

A serious disease of the ascidian Halocynthia roretzi has been spread extensively among Korean aquaculture sites. To reveal the cause of the disease and establish a monitoring system for it, we constructed a cDNA microarray spotted with 2,688 cDNAs derived from H. roretzi hemocyte cDNA libraries to detect genes differentially expressed in hemocytes between diseased and non-diseased ascidians. We detected 21 genes showing increased expression and 16 genes showing decreased expression in hemocytes from diseased ascidians compared with those from non-diseased ascidians. RT-PCR analyses confirmed that the expression levels of genes encoding astacin, lysozyme, ribosomal protein PO, and ubiquitin-ribosomal protein L40e fusion protein were increased in hemocytes from diseased ascidians, while those of genes encoding HSP40, HSP70, fibronectin, carboxypeptidase and lactate dehydrogenase were decreased. These genes were expressed not only in hemocytes but also in various other tissues in ascidians. Furthermore, the expression of glutathione-S transferase omega, which is known to be up-regulated in H. roretzi hemocytes during inflammatory responses, was strongly increased in hemocytes from diseased ascidians. These gene expression profiles suggest that immune and inflammatory reactions occur in the hemocytes of diseased ascidians. These genes will be good markers for detecting and monitoring this disease of ascidians in Korean aquaculture sites.

Insights into molecular mechanisms of drug metabolism dysfunction of human CYP2C9*30

PubMed Central

Louet, Maxime; Labbé, Céline M.; Aono, Cassiano M.; Homem-de-Mello, Paula; Villoutreix, Bruno O.

2018-01-01

Cytochrome P450 2C9 (CYP2C9) metabolizes about 15% of clinically administrated drugs. The allelic variant CYP2C9*30 (A477T) is associated to diminished response to the antihypertensive effects of the prodrug losartan and affected metabolism of other drugs. Here, we investigated molecular mechanisms involved in the functional consequences of this amino-acid substitution. Molecular dynamics (MD) simulations performed for the active species of the enzyme (heme in the Compound I state), in the apo or substrate-bound state, and binding energy analyses gave insights into altered protein structure and dynamics involved in the defective drug metabolism of human CYP2C9.30. Our data revealed an increased rigidity of the key Substrate Recognition Sites SRS1 and SRS5 and shifting of the β turn 4 of SRS6 toward the helix F in CYP2C9.30. Channel and binding substrate dynamics analyses showed altered substrate channel access and active site accommodation. These conformational and dynamic changes are believed to be involved in the governing mechanism of the reduced catalytic activity. An ensemble of representative conformations of the WT and A477T mutant properly accommodating drug substrates were identified, those structures can be used for prediction of new CYP2C9 and CYP2C9.30 substrates and drug-drug interactions. PMID:29746595

Pollen and palynofacies analyses of Paleocene-Eocene Thermal Maximum sediments from the North American continental shelf

NASA Astrophysics Data System (ADS)

Willard, D. A.; Robinson, M. M.; Self-Trail, J. M.; Wandless, G. A.; Sluijs, A.

2014-12-01

Analyses of pollen and palynofacies from Paleocene-Eocene Thermal Maximum (PETM) sediments from three cores collected on the Atlantic Coastal Plain provide insights into the timing of vegetation and hydrologic changes associated with the PETM in eastern North America. The Mattawoman Creek-Billingsley Road (MCBR2), South Dover Bridge (SDB), and Bass River (ODP Site 1074AX) cores were collected at progressively greater distances from the paleoshoreline in continental shelf deposits in Maryland and New Jersey, USA. The PETM carbon isotope excursion (CIE) at each site is accompanied by sharp increases in pollen and spore concentrations, as well as changes in terrestrial palynomorph assemblage composition. In the two sites proximal to the paleoshoreline in Maryland, CIE fern spore abundance was two- to three times greater than in pre-CIE assemblages. At the distal site at Bass River, fern spores are present in CIE sediments and absent in pre-CIE sediments. Angiosperm pollen is most common in CIE sediments at all three sites. Palynofacies analyses, which quantify contributions of organic material from marine and non-marine sources, indicate that terrestrial influx increased sharply at the CIE onset. This observation is consistent with seasonally increased runoff from the continent.

Long-term CO2 rise has increased photosynthetic efficiency and water use efficiency but did not stimulate diameter growth of tropical trees

NASA Astrophysics Data System (ADS)

Groenendijk, P.; Zuidema, P.; Sleen, P. V. D.; Vlam, M.; Ehlers, I.; Schleucher, J.

2014-12-01

Tropical forests are a crucial component of the global carbon cycle, and their responses to atmospheric changes may shift carbon cycling and climate systems. Dynamic Global Vegetation Models (DGVMs) are the major tools to simulate tropical forest responses to climate change. One of the main determinants of these simulated responses is the effect of CO2 on tropical tree physiology and growth, the 'CO2 fertilization effect'. The paucity of CO2 enrichment experiments in the tropics importantly limits insights into the CO2 fertilization effect as well as the validation of DGVMs. However, use can be made of the 40% rise in atmospheric CO2 concentration since the onset of the Industrial Revolution. The effects of the historical CO2 rise on tree physiology and growth can be obtained from stable isotopes, isotopomers and tree diameter increments obtained in tree-ring studies. We studied the physiological and growth responses of 12 tree species in Bolivia, Cameroon and Thailand to 150 years of CO2 enrichment. Analyses of 13C of wood cellulose revealed strong, long-term increases in leaf intercellular CO2 concentrations for all study species and a marked improvement of intrinsic water use efficiency (iWUE). For a subset of one species per site, we studied the Deuterium isotopomers (isomers with isotopic atoms) of glucose in wood to obtain a direct estimate of the photorespiration-to-photosynthesis ratio. We found that this ratio consistently and strongly decreased over the past century, thus increasing the effeciency and rate of photosynthesis. In spite of these strong physiological responses to increased CO2levels, we did not find evidence for increased tree diameter growth for any of the sites, or for sites combined. Possible reasons for the lack of a growth stimulation include increased (leaf) temperature, insufficient availability of nutrients or a shift in biomass investment in trees. Our results suggest that the strong CO2 fertilization of tropical tree growth often assumed in DGVMs does not hold and that these models may overestimate future biomass production in tropical forests. Empirical information on responses of tropical trees to historical CO2rise as presented here can be used to validate and possibly adapt (components of) DGVMs and improve the projections of tropical forest structure under climate change.

Round-robin analysis of the behavior of a 1:6-scale reinforced concrete containment model pressurized to failure: Posttest evaluations

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

Clauss, D.B.

A 1:6-scale model of a reinforced concrete containment building was pressurized incrementally to failure at a remote site at Sandia National Laboratories. The response of the model was recorded with more than 1000 channels of data (primarily strain and displacement measurements) at 37 discrete pressure levels. The primary objective of this test was to generate data that could be used to validate methods for predicting the performance of containment buildings subject to loads beyond their design basis. Extensive analyses were conducted before the test to predict the behavior of the model. Ten organizations in Europe and the US conducted independentmore » analyses of the model and contributed to a report on the pretest predictions. Predictions included structural response at certain predetermined locations in the model as well as capacity and failure mode. This report discusses comparisons between the pretest predictions and the experimental results. Posttest evaluations that were conducted to provide additional insight into the model behavior are also described. The significance of the analysis and testing of the 1:6-scale model to performance evaluations of actual containments subject to beyond design basis loads is also discussed. 70 refs., 428 figs., 24 tabs.« less

Naturally Occurring Canine Invasive Urinary Bladder Cancer: A Complementary Animal Model to Improve the Success Rate in Human Clinical Trials of New Cancer Drugs.

PubMed

Fulkerson, Christopher M; Dhawan, Deepika; Ratliff, Timothy L; Hahn, Noah M; Knapp, Deborah W

2017-01-01

Genomic analyses are defining numerous new targets for cancer therapy. Therapies aimed at specific genetic and epigenetic targets in cancer cells as well as expanded development of immunotherapies are placing increased demands on animal models. Traditional experimental models do not possess the collective features (cancer heterogeneity, molecular complexity, invasion, metastasis, and immune cell response) critical to predict success or failure of emerging therapies in humans. There is growing evidence, however, that dogs with specific forms of naturally occurring cancer can serve as highly relevant animal models to complement traditional models. Invasive urinary bladder cancer (invasive urothelial carcinoma (InvUC)) in dogs, for example, closely mimics the cancer in humans in pathology, molecular features, biological behavior including sites and frequency of distant metastasis, and response to chemotherapy. Genomic analyses are defining further intriguing similarities between InvUC in dogs and that in humans. Multiple canine clinical trials have been completed, and others are in progress with the aim of translating important findings into humans to increase the success rate of human trials, as well as helping pet dogs. Examples of successful targeted therapy studies and the challenges to be met to fully utilize naturally occurring dog models of cancer will be reviewed.

Induction of cyclooxygenase-2 by ginsenoside Rd via activation of CCAAT-enhancer binding proteins and cyclic AMP response binding protein

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

Jeong, Hye Gwang; Pokharel, Yuba Raj; Han, Eun Hee

2007-07-20

Panax ginseng is a widely used herbal medicine in East Asia and is reported to have a variety of pharmacological effects against cardiovascular diseases and cancers. Here we show a unique effect of ginsenoside Rd (Rd) on cyclooxygenase-2 (COX-2) expression in RAW264.7 macrophages. Rd (100 {mu}g/ml), but not other ginsenosides induced COX-2 and increased prostaglandin E{sub 2} production. Gel shift and Western blot analyses using nuclear fractions revealed that Rd increased both the DNA binding of and the nuclear levels of CCAAT/enhancer binding protein (C/EBP){alpha}/{beta} and cyclic AMP response element binding protein (CREB), but not of p65, in RAW264.7 cells.more » Moreover, Rd increased the luciferase reporter gene activity in cells transfected with a 574-bp mouse COX-2 promoter construct. Site-specific mutation analyses confirmed that Rd-mediated transcriptional activation of COX-2 gene was regulated by C/EBP and CREB. These results provide evidence that Rd activated C/EBP and CREB, and that the activation of C/EBP and CREB appears to be essential for induction of COX-2 in RAW264.7 cells.« less

Naturally Occurring Canine Invasive Urinary Bladder Cancer: A Complementary Animal Model to Improve the Success Rate in Human Clinical Trials of New Cancer Drugs

PubMed Central

Fulkerson, Christopher M.; Ratliff, Timothy L.; Hahn, Noah M.

2017-01-01

Genomic analyses are defining numerous new targets for cancer therapy. Therapies aimed at specific genetic and epigenetic targets in cancer cells as well as expanded development of immunotherapies are placing increased demands on animal models. Traditional experimental models do not possess the collective features (cancer heterogeneity, molecular complexity, invasion, metastasis, and immune cell response) critical to predict success or failure of emerging therapies in humans. There is growing evidence, however, that dogs with specific forms of naturally occurring cancer can serve as highly relevant animal models to complement traditional models. Invasive urinary bladder cancer (invasive urothelial carcinoma (InvUC)) in dogs, for example, closely mimics the cancer in humans in pathology, molecular features, biological behavior including sites and frequency of distant metastasis, and response to chemotherapy. Genomic analyses are defining further intriguing similarities between InvUC in dogs and that in humans. Multiple canine clinical trials have been completed, and others are in progress with the aim of translating important findings into humans to increase the success rate of human trials, as well as helping pet dogs. Examples of successful targeted therapy studies and the challenges to be met to fully utilize naturally occurring dog models of cancer will be reviewed. PMID:28487862

Library Web Sites in Pakistan: An Analysis of Content

ERIC Educational Resources Information Center

Qutab, Saima; Mahmood, Khalid

2009-01-01

Purpose: The purpose of this paper is to investigate library web sites in Pakistan, to analyse their content and navigational strengths and weaknesses and to give recommendations for developing better web sites and quality assessment studies. Design/methodology/approach: Survey of web sites of 52 academic, special, public and national libraries in…

Hydrologic data for aquifers in Philadelphia, Pennsylvania

USGS Publications Warehouse

Paulachok, G.N.; Wood, C.R.; Norton, L.J.

1984-01-01

Selected data on the ground-water resources of Philadelphia, Pennsylvania, are presented in this report. Information including water levels and data on aquifers is tabulated for 828 wells and 3 sumps. Chemical analyses are given for 1,467 water samples obtained from 205 sites and include 103 analyses for trace elements and 68 analyses for volatile organic compounds. An index of geophysical logs including gamma ray, neutron, caliper, fluid conductivity, fluid velocity, single-point resistance, spontaneous potential, and temperature determinations made in 51 wells is also presented. Data-collection sites are shown on a 1:50,000 scale location map.

Measuring Air Quality in a Construction Site Biotope Using the AQM-65 Analyser

NASA Astrophysics Data System (ADS)

Ioana-Alina, Creţan; Nicoleta, Nemeș

2017-10-01

Activities related to the execution of construction works often exert pressure on the quality of environmental factors in adjacent habitat. In various stages of realization of the works if is the opening of the building site and access roads, borrow pits and the storage, or the construction itself, all the related activities will cause harm in various degrees of vegetation on the construction site and its surroundings. Large areas are rendered non-productive and, although they should be restored for use in the same place or elsewhere, sometimes they can lose their natural habitat baseline. The paper is presenting a case study of air quality monitoring using the AQM 65 analyser for a construction site located near Timisoara locality, Timis County, Romania.

40 CFR 300.410 - Removal site evaluation.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 27 2010-07-01 2010-07-01 false Removal site evaluation. 300.410... PLAN Hazardous Substance Response § 300.410 Removal site evaluation. (a) A removal site evaluation... evaluation of a release identified for possible CERCLA response pursuant to § 300.415 shall, as appropriate...

To Stroop or Not to Stroop: Sex-Related Differences in Brain-Behavior Associations During Early Childhood

PubMed Central

Cuevas, Kimberly; Calkins, Susan D.; Bell, Martha Ann

2015-01-01

Executive functions (EFs) are linked with optimal cognitive and social-emotional development. Despite behavioral evidence of sex differences in early childhood EF, little is known about potential sex differences in corresponding brain-behavior associations. The present study examined changes in 4-year-olds’ 6–9 Hz EEG power in response to increased executive processing demands (i.e., “Stroop-like” vs. “non-Stroop” day-night tasks). Although there were no sex differences in task performance, an examination of multiple scalp electrode sites revealed that boys exhibited more widespread changes in EEG power as compared to girls. Further, multiple regression analyses controlling for maternal education and non-EF performance indicated that individual differences in boys’ and girls’ EF performance were associated with different frontal neural correlates (i.e., different frontal scalp sites and different measures of EEG power). These data reveal valuable information concerning sex differences in the neural systems underlying executive processing during early childhood. PMID:26681615

Spatial and vertical distribution of bacterial community in the northern South China Sea.

PubMed

Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Sun, Cui-Ci; Cheng, Hao

2015-10-01

Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments. Learning about this will help us understand the ecology of microbial populations in marine ecosystems. This study aimed to assess the spatial and vertical distributions of the bacterial community in the northern South China Sea. Multi-dimensional scaling analyses revealed structural differences of the bacterial community among sampling sites and vertical depth. Result also indicated that bacterial community in most sites had higher diversity in 0-75 m depths than those in 100-200 m depths. Bacterial community of samples was positively correlation with salinity and depth, whereas was negatively correlation with temperature. Proteobacteria and Cyanobacteria were the dominant groups, which accounted for the majority of sequences. The α-Proteobacteria was highly diverse, and sequences belonged to Rhodobacterales bacteria were dominant in all characterized sequences. The current data indicate that the Rhodobacterales bacteria, especially Roseobacter clade are the diverse group in the tropical waters.

Distinct Ecological Niche of Anal, Oral, and Cervical Mucosal Microbiomes in Adolescent Women.

PubMed

Smith, Benjamin C; Zolnik, Christine P; Usyk, Mykhaylo; Chen, Zigui; Kaiser, Katherine; Nucci-Sack, Anne; Peake, Ken; Diaz, Angela; Viswanathan, Shankar; Strickler, Howard D; Schlecht, Nicolas F; Burk, Robert D

2016-09-01

Human body sites represent ecological niches for microorganisms, each providing variations in microbial exposure, nutrient availability, microbial competition, and host immunological responses. In this study, we investigated the oral, anal, and cervical microbiomes from the same 20 sexually active adolescent females, using culture-independent, next-generation sequencing. DNA from each sample was amplified for the bacterial 16S rRNA gene and sequenced on an Illumina platform using paired-end reads. Across the three anatomical niches, we found significant differences in bacterial community composition and diversity. Overall anal samples were dominated with Prevotella and Bacteriodes , oral samples with Streptococcus and Prevotella , and cervical samples with Lactobacillus . The microbiomes of a few cervical samples clustered with anal samples in weighted principal coordinate analyses, due in part to a higher proportion of Prevotella in those samples. Additionally, cervical samples had the lowest alpha diversity. Our results demonstrate the occurrence of distinct microbial communities across body sites within the same individual.

Implementing a Measurement Feedback System: A Tale of Two Sites

PubMed Central

Douglas, Susan R.; Vides De Andrade, Ana Regina; Tomlinson, Michele; Gleacher, Alissa; Olin, Serene; Hoagwood, Kimberly

2015-01-01

A randomized experiment was conducted in two outpatient clinics evaluating a measurement feedback system called contextualized feedback systems. The clinicians of 257 Youth 11–18 received feedback on progress in mental health symptoms and functioning either every 6 months or as soon as the youth’s, clinician’s or caregiver’s data were entered into the system. The ITT analysis showed that only one of the two participating clinics (Clinic R) had an enhanced outcome because of feedback, and only for the clinicians’ ratings of youth symptom severity on the SFSS. A dose–response effect was found only for Clinic R for both the client and clinician ratings. Implementation analyses showed that Clinic R had better implementation of the feedback intervention. Clinicians’ questionnaire completion rate and feedback viewing at Clinic R were 50 % higher than clinicians at Clinic U. The discussion focused on the differences in implementation at each site and how these differences may have contributed to the different outcomes of the experiment. PMID:25876736