High Throughput Computing Impact on Meta Genomics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Gore, Brooklin

2018-02-01

This presentation includes a brief background on High Throughput Computing, correlating gene transcription factors, optical mapping, genotype to phenotype mapping via QTL analysis, and current work on next gen sequencing.

Mapping Common Aphasia Assessments to Underlying Cognitive Processes and Their Neural Substrates.

PubMed

Lacey, Elizabeth H; Skipper-Kallal, Laura M; Xing, Shihui; Fama, Mackenzie E; Turkeltaub, Peter E

2017-05-01

Understanding the relationships between clinical tests, the processes they measure, and the brain networks underlying them, is critical in order for clinicians to move beyond aphasia syndrome classification toward specification of individual language process impairments. To understand the cognitive, language, and neuroanatomical factors underlying scores of commonly used aphasia tests. Twenty-five behavioral tests were administered to a group of 38 chronic left hemisphere stroke survivors and a high-resolution magnetic resonance image was obtained. Test scores were entered into a principal components analysis to extract the latent variables (factors) measured by the tests. Multivariate lesion-symptom mapping was used to localize lesions associated with the factor scores. The principal components analysis yielded 4 dissociable factors, which we labeled Word Finding/Fluency, Comprehension, Phonology/Working Memory Capacity, and Executive Function. While many tests loaded onto the factors in predictable ways, some relied heavily on factors not commonly associated with the tests. Lesion symptom mapping demonstrated discrete brain structures associated with each factor, including frontal, temporal, and parietal areas extending beyond the classical language network. Specific functions mapped onto brain anatomy largely in correspondence with modern neural models of language processing. An extensive clinical aphasia assessment identifies 4 independent language functions, relying on discrete parts of the left middle cerebral artery territory. A better understanding of the processes underlying cognitive tests and the link between lesion and behavior may lead to improved aphasia diagnosis, and may yield treatments better targeted to an individual's specific pattern of deficits and preserved abilities.

Examining the Alignment of Subject Learning Outcomes and Course Curricula through Curriculum Mapping

ERIC Educational Resources Information Center

Lam, Bick-Har; Tsui, Kwok-Tung

2013-01-01

Content analysis has been used to conduct curriculum mapping to map the course objectives, course content, and the assessment tasks of 14 compulsory courses, onto the five Subject Learning Objective (SLO) factors of the Department of Curriculum and Instruction (DC&I) in a teacher education institution in Hong Kong. The results show that the…

Application of Remote Sensing in Geological Mapping, Case Study al Maghrabah Area - Hajjah Region, Yemen

NASA Astrophysics Data System (ADS)

Al-Nahmi, F.; Saddiqi, O.; Hilali, A.; Rhinane, H.; Baidder, L.; El arabi, H.; Khanbari, K.

2017-11-01

Remote sensing technology plays an important role today in the geological survey, mapping, analysis and interpretation, which provides a unique opportunity to investigate the geological characteristics of the remote areas of the earth's surface without the need to gain access to an area on the ground. The aim of this study is achievement a geological map of the study area. The data utilizes is Sentinel-2 imagery, the processes used in this study, the OIF Optimum Index Factor is a statistic value that can be used to select the optimum combination of three bands in a satellite image. It's based on the total variance within bands and correlation coefficient between bands, ICA Independent component analysis (3, 4, 6) is a statistical and computational technique for revealing hidden factors that underlie sets of random variables, measurements, or signals, MNF Minimum Noise Fraction (1, 2, 3) is used to determine the inherent dimensionality of image data to segregate noise in the data and to reduce the computational requirements for subsequent processing, Optimum Index Factor is a good method for choosing the best band for lithological mapping. ICA, MNF, also a practical way to extract the structural geology maps. The results in this paper indicate that, the studied area can be divided into four main geological units: Basement rocks (Meta volcanic, Meta sediments), Sedimentary rocks, Intrusive rocks, volcanic rocks. The method used in this study offers great potential for lithological mapping, by using Sentinel-2 imagery, the results were compared with existing geologic maps and were superior and could be used to update the existing maps.

Electricity Consumption Risk Map - The use of Urban Climate Mapping for smarter analysis: Case study for Birmingham, UK.

NASA Astrophysics Data System (ADS)

Antunes Azevedo, Juliana; Burghardt, René; Chapman, Lee; Katzchner, Lutz; Muller, Catherine L.

2015-04-01

Climate is a key driving factor in energy consumption. However, income, vegetation, building mass structure, topography also impact on the amount of energy consumption. In a changing climate, increased temperatures are likely to lead to increased electricity consumption, affecting demand, distribution and generation. Furthermore, as the world population becomes more urbanized, increasing numbers of people will need to deal with not only increased temperatures from climate change, but also from the unintentional modification of the urban climate in the form of urban heat islands. Hence, climate and climate change needs to be taken into account for future urban planning aspects to increase the climate and energy resilience of the community and decrease the future social and economic costs. Geographical Information Systems provide a means to create urban climate maps as part of the urban planning process. Geostatistical analyses linking these maps with demographic and social data, enables a geo-statistical analysis to identify linkages to high-risk groups of the community and vulnerable areas of town and cities. Presently, the climatope classification is oriented towards thermal aspects and the ventilation quality (roughness) of the urban areas but can also be adapted to take into account other structural "environmental factors". This study aims to use the climatope approach to predict areas of potential high electricity consumption in Birmingham, UK. Several datasets were used to produce an average surface temperature map, vegetation map, land use map, topography map, building height map, built-up area roughness calculations, an average air temperature map and a domestic electricity consumption map. From the correlations obtained between the layers it is possible to average the importance of each factor and create a map for domestic electricity consumption to understand the influence of environmental aspects on spatial energy consumption. Based on these results city planners and local authorities can guide their directives and policies towards electricity consumption, demand, generation and distribution.

Mapping one strong 'Ohana: using network analysis and GIS to enhance the effectiveness of a statewide coalition to prevent child abuse and neglect.

PubMed

Cardazone, Gina; U Sy, Angela; Chik, Ivan; Corlew, Laura Kate

2014-06-01

Network analysis and GIS enable the presentation of meaningful data about organizational relationships and community characteristics, respectively. Together, these tools can provide a concrete representation of the ecological context in which coalitions operate, and may help coalitions identify opportunities for growth and enhanced effectiveness. This study uses network analysis and GIS mapping as part of an evaluation of the One Strong 'Ohana (OSO) campaign. The OSO campaign was launched in 2012 via a partnership between the Hawai'i Children's Trust Fund (HCTF) and the Joyful Heart Foundation. The OSO campaign uses a collaborative approach aimed at increasing public awareness of child maltreatment and protective factors that can prevent maltreatment, as well as enhancing the effectiveness of the HCTF Coalition. This study focuses on three elements of the OSO campaign evaluation: (1) Network analysis exploring the relationships between 24 active Coalition member organizations, (2) GIS mapping of responses to a randomized statewide phone survey (n = 1,450) assessing awareness of factors contributing to child maltreatment, and (3) Combined GIS maps and network data, illustrating opportunities for geographically-targeted coalition building and public awareness activities.

Relationship of students' conceptual representations and problem-solving abilities in acid-base chemistry

NASA Astrophysics Data System (ADS)

Powers, Angela R.

2000-10-01

This study explored the relationship between secondary chemistry students' conceptual representations of acid-base chemistry, as shown in student-constructed concept maps, and their ability to solve acid-base problems, represented by their score on an 18-item paper and pencil test, the Acid-Base Concept Assessment (ABCA). The ABCA, consisting of both multiple-choice and short-answer items, was originally designed using a question-type by subtopic matrix, validated by a panel of experts, and refined through pilot studies and factor analysis to create the final instrument. The concept map task included a short introduction to concept mapping, a prototype concept map, a practice concept-mapping activity, and the instructions for the acid-base concept map task. The instruments were administered to chemistry students at two high schools; 108 subjects completed both instruments for this study. Factor analysis of ABCA results indicated that the test was unifactorial for these students, despite the intention to create an instrument with multiple "question-type" scales. Concept maps were scored both holistically and by counting valid concepts. The two approaches were highly correlated (r = 0.75). The correlation between ABCA score and concept-map score was 0.29 for holistically-scored concept maps and 0.33 for counted-concept maps. Although both correlations were significant, they accounted for only 8.8 and 10.2% of variance in ABCA scores, respectively. However, when the reliability of the instruments used is considered, more than 20% of the variance in ABCA scores may be explained by concept map scores. MANOVAs for ABCA and concept map scores by instructor, student gender, and year in school showed significant differences for both holistic and counted concept-map scores. Discriminant analysis revealed that the source of these differences was the instruction variable. Significant differences between classes receiving different instruction were found in the frequency of concepts listed by students for 9 of 10 concepts evaluated. Mean ABCA scores did not differ significantly between the two instruction groups. The results of this study failed to provide evidence of conceptual distinctions among different "types" of problem-solving items. The results suggested that several factors influence success in chemistry problem solving, including concept knowledge and organization. Further research into the nature of chemistry problems and problem solving is recommended.

Analysis of Factors and Implications Influencing Leadership Ascension of Female Athletic Directors in Intercollegiate Athletics

ERIC Educational Resources Information Center

Burney, Rolanda C.

2010-01-01

This narrative analysis/life story study was designed to understand the factors influencing the career trajectory of female athletic directors in National Collegiate Athletic Association affiliated institutions and to discover how those factors functioned as a road map for future female administrators. Both social role and role congruity theories…

Spatial prediction of ground subsidence susceptibility using an artificial neural network.

PubMed

Lee, Saro; Park, Inhye; Choi, Jong-Kuk

2012-02-01

Ground subsidence in abandoned underground coal mine areas can result in loss of life and property. We analyzed ground subsidence susceptibility (GSS) around abandoned coal mines in Jeong-am, Gangwon-do, South Korea, using artificial neural network (ANN) and geographic information system approaches. Spatial data of subsidence area, topography, and geology, as well as various ground-engineering data, were collected and used to create a raster database of relevant factors for a GSS map. Eight major factors causing ground subsidence were extracted from the existing ground subsidence area: slope, depth of coal mine, distance from pit, groundwater depth, rock-mass rating, distance from fault, geology, and land use. Areas of ground subsidence were randomly divided into a training set to analyze GSS using the ANN and a test set to validate the predicted GSS map. Weights of each factor's relative importance were determined by the back-propagation training algorithms and applied to the input factor. The GSS was then calculated using the weights, and GSS maps were created. The process was repeated ten times to check the stability of analysis model using a different training data set. The map was validated using area-under-the-curve analysis with the ground subsidence areas that had not been used to train the model. The validation showed prediction accuracies between 94.84 and 95.98%, representing overall satisfactory agreement. Among the input factors, "distance from fault" had the highest average weight (i.e., 1.5477), indicating that this factor was most important. The generated maps can be used to estimate hazards to people, property, and existing infrastructure, such as the transportation network, and as part of land-use and infrastructure planning.

CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome.

PubMed

Zhang, Zijun; Xing, Yi

2017-09-19

Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation. CLAM recovered a large number of novel RNA regulatory sites inaccessible by uniquely mapped reads. The functional significance of these sites was demonstrated by consensus motif patterns and association with alternative splicing (splicing factors), transcript abundance (AGO2) and mRNA half-life (m6A). CLAM provides a useful tool to discover novel protein-RNA interactions and RNA modification sites from CLIP-seq and RIP-seq data, and reveals the significant contribution of repetitive elements to the RNA regulatory landscape of the human transcriptome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Application of an adaptive neuro-fuzzy inference system to ground subsidence hazard mapping

NASA Astrophysics Data System (ADS)

Park, Inhye; Choi, Jaewon; Jin Lee, Moung; Lee, Saro

2012-11-01

We constructed hazard maps of ground subsidence around abandoned underground coal mines (AUCMs) in Samcheok City, Korea, using an adaptive neuro-fuzzy inference system (ANFIS) and a geographical information system (GIS). To evaluate the factors related to ground subsidence, a spatial database was constructed from topographic, geologic, mine tunnel, land use, and ground subsidence maps. An attribute database was also constructed from field investigations and reports on existing ground subsidence areas at the study site. Five major factors causing ground subsidence were extracted: (1) depth of drift; (2) distance from drift; (3) slope gradient; (4) geology; and (5) land use. The adaptive ANFIS model with different types of membership functions (MFs) was then applied for ground subsidence hazard mapping in the study area. Two ground subsidence hazard maps were prepared using the different MFs. Finally, the resulting ground subsidence hazard maps were validated using the ground subsidence test data which were not used for training the ANFIS. The validation results showed 95.12% accuracy using the generalized bell-shaped MF model and 94.94% accuracy using the Sigmoidal2 MF model. These accuracy results show that an ANFIS can be an effective tool in ground subsidence hazard mapping. Analysis of ground subsidence with the ANFIS model suggests that quantitative analysis of ground subsidence near AUCMs is possible.

Mapping common aphasia assessments to underlying cognitive processes and their neural substrates

PubMed Central

Lacey, Elizabeth H.; Skipper-Kallal, LM; Xing, S; Fama, ME; Turkeltaub, PE

2017-01-01

Background Understanding the relationships between clinical tests, the processes they measure, and the brain networks underlying them, is critical in order for clinicians to move beyond aphasia syndrome classification toward specification of individual language process impairments. Objective To understand the cognitive, language, and neuroanatomical factors underlying scores of commonly used aphasia tests. Methods 25 behavioral tests were administered to a group of 38 chronic left hemisphere stroke survivors and a high resolution MRI was obtained. Test scores were entered into a principal components analysis to extract the latent variables (factors) measured by the tests. Multivariate lesion-symptom mapping was used to localize lesions associated with the factor scores. Results The principal components analysis yielded four dissociable factors, which we labeled Word Finding/Fluency, Comprehension, Phonology/Working Memory Capacity, and Executive Function. While many tests loaded onto the factors in predictable ways, some relied heavily on factors not commonly associated with the tests. Lesion symptom mapping demonstrated discrete brain structures associated with each factor, including frontal, temporal, and parietal areas extending beyond the classical language network. Specific functions mapped onto brain anatomy largely in correspondence with modern neural models of language processing. Conclusions An extensive clinical aphasia assessment identifies four independent language functions, relying on discrete parts of the left middle cerebral artery territory. A better understanding of the processes underlying cognitive tests and the link between lesion and behavior may lead to improved aphasia diagnosis, and may yield treatments better targeted to an individual’s specific pattern of deficits and preserved abilities. PMID:28135902

c-Jun controls the efficiency of MAP kinase signaling by transcriptional repression of MAP kinase phosphatases

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

Sprowles, Amy; Robinson, Dan; Wu Yimi

2005-08-15

The mammalian JNK signaling pathway regulates the transcriptional response of cells to environmental stress, including UV irradiation. This signaling pathway is composed of a classical MAP kinase cascade; activation results in phosphorylation of the transcription factor substrates c-Jun and ATF2, and leads to changes in gene expression. The defining components of this pathway are conserved in the fission yeast S. pombe, where the genetic studies have shown that the ability of the JNK homolog Spc1 to be activated in response to UV irradiation is dependent on the presence of the transcription factor substrate Atf1. We have used genetic analysis tomore » define the role of c-Jun in activation of the mammalian JNK signaling pathway. Our results show that optimal activation of JNK requires the presence of its transcription factor substrate c-Jun. Mutational analysis shows that the ability of c-Jun to support efficient activation of JNK requires the ability of Jun to bind DNA, suggesting a transcriptional mechanism. Consistent with this, we show that c-Jun represses the expression of several MAP kinase phosphatases. In the absence of c-Jun, the increased expression of MAP kinase phosphatases leads to impaired activation of the ERK, JNK, and p38 MAP kinases after pathway activation. The results show that one function of c-Jun is to regulate the efficiency of signaling by the ERK, p38, and JNK MAP kinases, a function that is likely to affect cellular responses to many different stimuli.« less

Analysis of slope stabillity and controlling factor on residual soil of folded breccia formation

NASA Astrophysics Data System (ADS)

Rachman, S.; Muslim, D.; Sulaksana, N.; Burhannuddinnur, M.; Pramudito, H.

2018-01-01

This research aims to obtain a potential landslide zonation. Theresearch area is located in Depok Village and surroundings, Jatigede District, Sumedang regency, West Java province. Geographically located at the point of coordinates 06°50‧33-06°51‧00″ South Latitude and 108°05‧37 ″- 108°06‧17″ East Longitude. This research is intended to mapping the identification of landslide and soil properties data. The mapping and soil sampling were conducted only in the research area. The methodology used was mapping and finding the safety factor with Bishop Analysis. The morphological condition of the study area indicates moderate conditions undulating hilly area with slopes between 15° - 40°, with a tick soil layer was covering the slope. This condition is greatly affected by rainfall. This research is to know the type of ground movement along with the value of the safety factor of the slope so that can provide suggestions for overcoming instability in the study area.

A factor analysis of landscape pattern and structure metrics

Treesearch

Kurt H. Riitters; R.V. O' Neill; C.T. Hunsaker; James D. Wickham; D.H. Yankee; S.P. Timmins; K.B. Jones; B.L. Jackson

1995-01-01

Fifty-five metrics of landscape pattern and structure were calculated for 85 maps of land use and land cover. A multivariate factor analysis was used to identify the common axes (or dimensions) of pattern and structure which were measured by a reduced set of 26 metrics. The first six factors explained about 87% of the variation in the 26 landscape metrics. These...

Airborne gamma-ray spectrometer and magnetometer survey, Durango A, B, C, and D, Colorado. Volume I. Detail area. Final report

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

Not Available

1983-01-01

An airborne combined radiometric and magnetic survey was performed for the Department of Energy (DOE) over the Durango A, Durango B, Durango C, and Durango D Detail Areas of southwestern Colorado. The Durango A Detail Area is within the coverage of the Needle Mountains and Silverton 15' map sheets, and the Pole Creek Mountain, Rio Grande Pyramid, Emerald Lake, Granite Peak, Vallecito Reservoir, and Lemon Reservoir 7.5' map sheets of the National Topographic Map Series (NTMS). The Durango B Detail Area is within the coverage of the Silverton 15' map sheet and the Wetterhorn Peak, Uncompahgre Peak, Lake City, Redcloudmore » Peak, Lake San Cristobal, Pole Creek Mountain, and Finger Mesa 7.5' map sheets of the NTMS. The Durango C Detail Area is within the coverage of the Platoro and Wolf Creek Pass 15' map sheets of the NTMS. The Durango D Detail Area is within the coverage of the Granite Lake, Cimarrona Peak, Bear Mountain, and Oakbrush Ridge 7.5' map sheets of the NTMS. Radiometric data were corrected for live time, aircraft and equipment background, cosmic background, atmospheric radon, Compton scatter, and altitude dependence. The corrected data were statistically evaluated, gridded, and contoured to produce maps of the radiometric variables, uranium, potassium, and thorium; their ratios; and the residual magnetic field. These maps have been analyzed in order to produce a multi-variant analysis contour map based on the radiometric response of the individual geological units. A geochemical analysis has been performed, using the radiometric and magnetic contour maps, the multi-variant analysis map, and factor analysis techniques, to produce a geochemical analysis map for the area.« less

GIS and statistical analysis for landslide susceptibility mapping in the Daunia area, Italy

NASA Astrophysics Data System (ADS)

Mancini, F.; Ceppi, C.; Ritrovato, G.

2010-09-01

This study focuses on landslide susceptibility mapping in the Daunia area (Apulian Apennines, Italy) and achieves this by using a multivariate statistical method and data processing in a Geographical Information System (GIS). The Logistic Regression (hereafter LR) method was chosen to produce a susceptibility map over an area of 130 000 ha where small settlements are historically threatened by landslide phenomena. By means of LR analysis, the tendency to landslide occurrences was, therefore, assessed by relating a landslide inventory (dependent variable) to a series of causal factors (independent variables) which were managed in the GIS, while the statistical analyses were performed by means of the SPSS (Statistical Package for the Social Sciences) software. The LR analysis produced a reliable susceptibility map of the investigated area and the probability level of landslide occurrence was ranked in four classes. The overall performance achieved by the LR analysis was assessed by local comparison between the expected susceptibility and an independent dataset extrapolated from the landslide inventory. Of the samples classified as susceptible to landslide occurrences, 85% correspond to areas where landslide phenomena have actually occurred. In addition, the consideration of the regression coefficients provided by the analysis demonstrated that a major role is played by the "land cover" and "lithology" causal factors in determining the occurrence and distribution of landslide phenomena in the Apulian Apennines.

Landslide Susceptibility Mapping of Tegucigalpa, Honduras Using Artificial Neural Network, Bayesian Network and Decision Trees

NASA Astrophysics Data System (ADS)

Garcia Urquia, E. L.; Braun, A.; Yamagishi, H.

2016-12-01

Tegucigalpa, the capital city of Honduras, experiences rainfall-induced landslides on a yearly basis. The high precipitation regime and the rugged topography the city has been built in couple with the lack of a proper urban expansion plan to contribute to the occurrence of landslides during the rainy season. Thousands of inhabitants live at risk of losing their belongings due to the construction of precarious shelters in landslide-prone areas on mountainous terrains and next to the riverbanks. Therefore, the city is in the need for landslide susceptibility and hazard maps to aid in the regulation of future development. Major challenges in the context of highly dynamic urbanizing areas are the overlap of natural and anthropogenic slope destabilizing factors, as well as the availability and accuracy of data. Data-driven multivariate techniques have proven to be powerful in discovering interrelations between factors, identifying important factors in large datasets, capturing non-linear problems and coping with noisy and incomplete data. This analysis focuses on the creation of a landslide susceptibility map using different methods from the field of data mining, Artificial Neural Networks (ANN), Bayesian Networks (BN) and Decision Trees (DT). The input dataset of the study contains geomorphological and hydrological factors derived from a digital elevation model with a 10 m resolution, lithological factors derived from a geological map, and anthropogenic factors, such as information on the development stage of the neighborhoods in Tegucigalpa and road density. Moreover, a landslide inventory map that was developed in 2014 through aerial photo interpretation was used as target variable in the analysis. The analysis covers an area of roughly 100 km2, while 8.95 km2 are occupied by landslides. In a first step, the dataset was explored by assessing and improving the data quality, identifying unimportant variables and finding interrelations. Then, based on a training partition of the dataset, the ANN, BN and DT were optimized for the prediction of landslides. The predictive power and ability to generalize of the resulting models were assessed in a test partition and evaluated using success rate curves, skill scores and by ensuring the spatial plausibility of the prediction.

Rates and patterns of deforestation in the Philippines: application of geographic information system analysis

Treesearch

Dawning S. Lui; Louis R. Iverson; Sandra Brown

1993-01-01

Land-use maps for 1934 and 1988, and a 1941 road map of the Philippines were digitized into a geographic information system. These maps were then analyzed to determine the rates of deforestation and their relationship with factors such as the distance of forests to roads and forest fragmentation (measured by perimeter-to-area ratio (P/A ratio) of forest patches) for...

Diagnostic classification of macular ganglion cell and retinal nerve fiber layer analysis: differentiation of false-positives from glaucoma.

PubMed

Kim, Ko Eun; Jeoung, Jin Wook; Park, Ki Ho; Kim, Dong Myung; Kim, Seok Hwan

2015-03-01

To investigate the rate and associated factors of false-positive diagnostic classification of ganglion cell analysis (GCA) and retinal nerve fiber layer (RNFL) maps, and characteristic false-positive patterns on optical coherence tomography (OCT) deviation maps. Prospective, cross-sectional study. A total of 104 healthy eyes of 104 normal participants. All participants underwent peripapillary and macular spectral-domain (Cirrus-HD, Carl Zeiss Meditec Inc, Dublin, CA) OCT scans. False-positive diagnostic classification was defined as yellow or red color-coded areas for GCA and RNFL maps. Univariate and multivariate logistic regression analyses were used to determine associated factors. Eyes with abnormal OCT deviation maps were categorized on the basis of the shape and location of abnormal color-coded area. Differences in clinical characteristics among the subgroups were compared. (1) The rate and associated factors of false-positive OCT maps; (2) patterns of false-positive, color-coded areas on the GCA deviation map and associated clinical characteristics. Of the 104 healthy eyes, 42 (40.4%) and 32 (30.8%) showed abnormal diagnostic classifications on any of the GCA and RNFL maps, respectively. Multivariate analysis revealed that false-positive GCA diagnostic classification was associated with longer axial length and larger fovea-disc angle, whereas longer axial length and smaller disc area were associated with abnormal RNFL maps. Eyes with abnormal GCA deviation map were categorized as group A (donut-shaped round area around the inner annulus), group B (island-like isolated area), and group C (diffuse, circular area with an irregular inner margin in either). The axial length showed a significant increasing trend from group A to C (P=0.001), and likewise, the refractive error was more myopic in group C than in groups A (P=0.015) and B (P=0.014). Group C had thinner average ganglion cell-inner plexiform layer thickness compared with other groups (group A=B>C, P=0.004). Abnormal OCT diagnostic classification should be interpreted with caution, especially in eyes with long axial lengths, large fovea-disc angles, and small optic discs. Our findings suggest that the characteristic patterns of OCT deviation map can provide useful clues to distinguish glaucomatous changes from false-positive findings. Copyright © 2015 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

A comprehensive pathway map of epidermal growth factor receptor signaling

PubMed Central

Oda, Kanae; Matsuoka, Yukiko; Funahashi, Akira; Kitano, Hiroaki

2005-01-01

The epidermal growth factor receptor (EGFR) signaling pathway is one of the most important pathways that regulate growth, survival, proliferation, and differentiation in mammalian cells. Reflecting this importance, it is one of the best-investigated signaling systems, both experimentally and computationally, and several computational models have been developed for dynamic analysis. A map of molecular interactions of the EGFR signaling system is a valuable resource for research in this area. In this paper, we present a comprehensive pathway map of EGFR signaling and other related pathways. The map reveals that the overall architecture of the pathway is a bow-tie (or hourglass) structure with several feedback loops. The map is created using CellDesigner software that enables us to graphically represent interactions using a well-defined and consistent graphical notation, and to store it in Systems Biology Markup Language (SBML). PMID:16729045

Application of LiDAR Date to Assess the Landslide Susceptibility Map Using Weights of Evidence Method - AN Example from Podhale Region (southern Poland)

NASA Astrophysics Data System (ADS)

Kamiński, Mirosław

2016-06-01

Podhale is a region in southern Poland, which is the northernmost part of the Central Carpathian Mountains. It is characterized by the presence of a large number of landslides that threaten the local infrastructure. In an article presents application of LiDAR data and geostatistical methods to assess landslides susceptibility map. Landslide inventory map were performed using LiDAR data and field work. The Weights of Evidence method was applied to assess landslides susceptibility map. Used factors for modeling: slope gradient, slope aspect, elevation, drainage density, faults density, lithology and curvature. All maps were subdivided into different classes. Then were converted to grid format in the ArcGIS 10.0. The conditional independence test was carried out to determine factors that are conditionally independent of each other with landslides. As a result, chi-square test for further GIS analysis used only five factors: slope gradient, slope aspect, elevation, drainage density and lithology. The final prediction results, it is concluded that the susceptibility map gives useful information both on present instability of the area and its possible future evolution in agreement with the morphological evolution of the area.

Direct optical mapping of transcription factor binding sites on field-stretched λ-DNA in nanofluidic devices

PubMed Central

Sriram, K. K.; Yeh, Jia-Wei; Lin, Yii-Lih; Chang, Yi-Ren; Chou, Chia-Fu

2014-01-01

Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage λ-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (∼ 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites. PMID:24753422

The use of process mapping in healthcare quality improvement projects.

PubMed

Antonacci, Grazia; Reed, Julie E; Lennox, Laura; Barlow, James

2018-05-01

Introduction Process mapping provides insight into systems and processes in which improvement interventions are introduced and is seen as useful in healthcare quality improvement projects. There is little empirical evidence on the use of process mapping in healthcare practice. This study advances understanding of the benefits and success factors of process mapping within quality improvement projects. Methods Eight quality improvement projects were purposively selected from different healthcare settings within the UK's National Health Service. Data were gathered from multiple data-sources, including interviews exploring participants' experience of using process mapping in their projects and perceptions of benefits and challenges related to its use. These were analysed using inductive analysis. Results Eight key benefits related to process mapping use were reported by participants (gathering a shared understanding of the reality; identifying improvement opportunities; engaging stakeholders in the project; defining project's objectives; monitoring project progress; learning; increased empathy; simplicity of the method) and five factors related to successful process mapping exercises (simple and appropriate visual representation, information gathered from multiple stakeholders, facilitator's experience and soft skills, basic training, iterative use of process mapping throughout the project). Conclusions Findings highlight benefits and versatility of process mapping and provide practical suggestions to improve its use in practice.

Science in the Sun: How Science is Performed as a Spatial Practice

NASA Astrophysics Data System (ADS)

Kass, Natalie

This study analyzes how spatial organization impacts science communication at the St. Petersburg Science Festival in Florida. Through map analysis, qualitative interviews, and a close reading of evaluation reports, the author determines that sponsorship, logistics, exhibitor ambience, and map usability and design are the factors most affecting the spatial performance of science. To mitigate their effects, technical communicators can identify these factors and provide the necessary revisions when considering how science is communicated to the public.

Bulk tank milk prevalence and production losses, spatial analysis, and predictive risk mapping of Ostertagia ostertagi infections in Mexican cattle herds.

PubMed

Villa-Mancera, Abel; Pastelín-Rojas, César; Olivares-Pérez, Jaime; Córdova-Izquierdo, Alejandro; Reynoso-Palomar, Alejandro

2018-05-01

This study investigated the prevalence, production losses, spatial clustering, and predictive risk mapping in different climate zones in five states of Mexico. The bulk tank milk samples obtained between January and April 2015 were analyzed for antibodies against Ostertagia ostertagi using the Svanovir ELISA. A total of 1204 farm owners or managers answered the questionnaire. The overall herd prevalence and mean optical density ratio (ODR) of parasite were 61.96% and 0.55, respectively. Overall, the production loss was approximately 0.542 kg of milk per parasited cow per day (mean ODR = 0.92, 142 farms, 11.79%). The spatial disease cluster analysis using SatScan software indicated that two high-risk clusters were observed. In the multivariable analysis, three models were tested for potential association with the ELISA results supported by climatic, environmental, and management factors. The final logistic regression model based on both climatic/environmental and management variables included the factors rainfall, elevation, land surface temperature (LST) day, and parasite control program that were significantly associated with an increased risk of infection. Geostatistical kriging was applied to generate a risk map for the presence of parasite in dairy cattle herds in Mexico. The results indicate that climatic and meteorological factors had a higher potential impact on the spatial distribution of O. ostertagi than the management factors.

Mapping and QTL analysis of drought tolerance in a spring wheat population using AFLP and DArt markers

USDA-ARS?s Scientific Manuscript database

Water availability is commonly the most limiting factor to crop production. This study was conducted to map quantitative trait loci (QTL) involved in drought tolerance in wheat (Triticum aestivum L.) to enable their use for marker assisted selection (MAS) in breeding. Using amplified fragment leng...

Susceptibility and triggering scenarios at a regional scale for shallow landslides

NASA Astrophysics Data System (ADS)

Gullà, G.; Antronico, L.; Iaquinta, P.; Terranova, O.

2008-07-01

The work aims at identifying susceptible areas and pluviometric triggering scenarios at a regional scale in Calabria (Italy), with reference to shallow landsliding events. The proposed methodology follows a statistical approach and uses a database linked to a GIS that has been created to support the various steps of spatial data management and manipulation. The shallow landslide predisposing factors taken into account are derived from (i) the 40-m digital terrain model of the region, an ˜ 15,075 km 2 extension; (ii) outcropping lithology; (iii) soils; and (iv) land use. More precisely, a map of the slopes has been drawn from the digital terrain model. Two kinds of covers [prevalently coarse-grained (CG cover) or fine-grained (FG cover)] were identified, referring to the geotechnical characteristics of geomaterial covers and to the lithology map; soilscapes were drawn from soil maps; and finally, the land use map was employed without any prior processing. Subsequently, the inventory maps of some shallow landsliding events, totaling more than 30,000 instabilities of the past and detected by field surveys and photo aerial restitution, were employed to calibrate the relative importance of these predisposing factors. The use of single factors (first level analysis) therefore provides three different susceptibility maps. Second level analysis, however, enables better location of areas susceptible to shallow landsliding events by crossing the single susceptibility maps. On the basis of the susceptibility map obtained by the second level analysis, five different classes of susceptibility to shallow landsliding events have been outlined over the regional territory: 8.9% of the regional territory shows very high susceptibility, 14.3% high susceptibility, 15% moderate susceptibility, 3.6% low susceptibility, and finally, about 58% very low susceptibility. Finally, the maps of two significant shallow landsliding events of the past and their related rainfalls have been utilized to identify the relevant pluviometric triggering scenarios. By using 205 daily rainfall series, different triggering pluviometric scenarios have been identified with reference to CG and FG covers: a value of 365 mm of the total rainfall of the event and/or 170 mm/d of the rainfall maximum intensity and a value of 325 mm of the total rainfall of the event and/or 158 mm/d of the rainfall maximum intensity are able to trigger shallow landsliding events for CG and FG covers, respectively. The results obtained from this study can help administrative authorities to plan future development activities and mitigation measures in shallow landslide-prone areas. In addition, the proposed methodology can be useful in managing emergency situations at a regional scale for shallow landsliding events triggered by intense rainfalls; through this approach, the susceptibility and the pluviometric triggering scenario maps will be improved by means of finer calibration of the involved factors.

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

Deshmukh, Ranjit; Wu, Grace

The MapRE (Multi-criteria Analysis for Planning Renewable Energy) GIS (Geographic Information Systems) Tools are a set of ArcGIS tools to a) conduct site suitability analysis for wind and solar resources using inclusion and exclusion criteria, and create resource maps, b) create project opportunity areas and compute various attributes such as cost, distances to existing and planned infrastructure. and environmental impact factors; and c) calculate and update various attributes for already processed renewable energy zones. In addition, MapRE data sets are geospatial data of renewable energy project opportunity areas and zones with pre-calculated attributes for several countries. These tools and datamore » are available at mapre.lbl.gov.« less

SPSS and SAS programs for determining the number of components using parallel analysis and velicer's MAP test.

PubMed

O'Connor, B P

2000-08-01

Popular statistical software packages do not have the proper procedures for determining the number of components in factor and principal components analyses. Parallel analysis and Velicer's minimum average partial (MAP) test are validated procedures, recommended widely by statisticians. However, many researchers continue to use alternative, simpler, but flawed procedures, such as the eigenvalues-greater-than-one rule. Use of the proper procedures might be increased if these procedures could be conducted within familiar software environments. This paper describes brief and efficient programs for using SPSS and SAS to conduct parallel analyses and the MAP test.

Geospatial Approach on Landslide Hazard Zonation Mapping Using Multicriteria Decision Analysis: A Study on Coonoor and Ooty, Part of Kallar Watershed, The Nilgiris, Tamil Nadu

NASA Astrophysics Data System (ADS)

Rahamana, S. Abdul; Aruchamy, S.; Jegankumar, R.

2014-12-01

Landslides are one of the critical natural phenomena that frequently lead to serious problems in hilly area, resulting to loss of human life and property, as well as causing severe damage to natural resources. The local geology with high degree of slope coupled with high intensity of rainfall along with unplanned human activities of the study area causes many landslides in this region. The present study area is more attracted by tourist throughout the year, so this area must be considered for preventive measures. Geospatial based Multicriteria decision analysis (MCDA) technique is increasingly used for landslide vulnerability and hazard zonation mapping. It enables the integration of different data layers with different levels of uncertainty. In this present study, it is used analytic hierarchy process (AHP) method to prepare landslide hazard zones of the Coonoor and Ooty, part of Kallar watershed, The Nilgiris, Tamil Nadu. The study was carried out using remote sensing data, field surveys and geographic information system (GIS) tools. The ten factors that influence landslide occurrence, such as elevation, slope aspect, slope angle, drainage density, lineament density, soil, precipitation, land use/land cover (LULC), distance from road and NDVI were considered. These factors layers were extracted from the various related spatial data's. These factors were evaluated, and then, the individual factor weight and class weight were assigned to each of the related factors. The Landslide Hazard Zone Index (LHZI) was calculated using Multicriteria decision analysis (MCDA) the technique based on the assigned weight and the rating is given by the Analytical Hierarchy Process (AHP) method. The final cumulative map of the study area was categorized into four hazard zones and classified as zone I to IV. There are 3.56% of the area comes under the hazard zone IV fallowed by 48.19% of the area comes under zone III, 43.63 % of the area in zone II and 4.61% of the area comes hazard zone I. Further resulted hazard zone map and landuse/landcover map are overlaid to check the hazard status, and existing inventory of known landslides within the present study area was compared with the resulting vulnerable and hazard zone maps. The landslide hazard zonation map is useful for landslide hazard prevention, mitigation, and improvement to society, and proper planning for land use and construction in the future.

Comparison of manually produced and automated cross country movement maps using digital image processing techniques

NASA Technical Reports Server (NTRS)

Wynn, L. K.

1985-01-01

The Image-Based Information System (IBIS) was used to automate the cross country movement (CCM) mapping model developed by the Defense Mapping Agency (DMA). Existing terrain factor overlays and a CCM map, produced by DMA for the Fort Lewis, Washington area, were digitized and reformatted into geometrically registered images. Terrain factor data from Slope, Soils, and Vegetation overlays were entered into IBIS, and were then combined utilizing IBIS-programmed equations to implement the DMA CCM model. The resulting IBIS-generated CCM map was then compared with the digitized manually produced map to test similarity. The numbers of pixels comprising each CCM region were compared between the two map images, and percent agreement between each two regional counts was computed. The mean percent agreement equalled 86.21%, with an areally weighted standard deviation of 11.11%. Calculation of Pearson's correlation coefficient yielded +9.997. In some cases, the IBIS-calculated map code differed from the DMA codes: analysis revealed that IBIS had calculated the codes correctly. These highly positive results demonstrate the power and accuracy of IBIS in automating models which synthesize a variety of thematic geographic data.

A combined approach based on MAF analysis and AHP method to fault detection mapping: A case study from a gas field, southwest of Iran

NASA Astrophysics Data System (ADS)

Shakiba, Sima; Asghari, Omid; Khah, Nasser Keshavarz Faraj

2018-01-01

A combined geostatitical methodology based on Min/Max Auto-correlation Factor (MAF) analysis and Analytical Hierarchy Process (AHP) is presented to generate a suitable Fault Detection Map (FDM) through seismic attributes. Five seismic attributes derived from a 2D time slice obtained from data related to a gas field located in southwest of Iran are used including instantaneous amplitude, similarity, energy, frequency, and Fault Enhancement Filter (FEF). The MAF analysis is implemented to reduce dimension of input variables, and then AHP method is applied on three obtained de-correlated MAF factors as evidential layer. Three Decision Makers (DMs) are used to construct PCMs for determining weights of selected evidential layer. Finally, weights obtained by AHP were multiplied in normalized valued of each alternative (MAF layers) and the concluded weighted layers were integrated in order to prepare final FDM. Results proved that applying algorithm proposed in this study generate a map more acceptable than the each individual attribute and sharpen the non-surface discontinuities as well as enhancing continuity of detected faults.

Groundwater productivity potential mapping using evidential belief function.

PubMed

Park, Inhye; Kim, Yongsung; Lee, Saro

2014-09-01

The evidential belief function (EBF) model was applied and validated for analysis of groundwater-productivity potential (GPP) in Boryeong and Pohang cities, agriculture region in Korea using geographic information systems (GIS). Data about related factors, including topography, lineament, geology, forest, soil, and groundwater data were collected and input into a spatial database. Additionally, in the Boryeong area, specific capacity (SPC) data not lower than 4.55 m3 /d/m were collected, corresponding to 300 m3 /d yield from 72 well locations. In the Pohang area, SPC data of ≥ 6.25 m3 /d/m were collected, corresponding to a yield of 500 m3 /d from 44 well locations. By using the constructed spatial database, 19 factors related to groundwater productivity were extracted. The relationships between the well locations and the factors were identified and quantified by using the EBF model. Four relationships were calculated: belief (Bel), disbelief (Dis), uncertainty (Unc), and plausibility (Pls). The relationships were used as factor ratings in the overlay analysis to create GPP indices and maps. The resulting GPP maps showed 83.41% and 77.53% accuracy in Boryeong and Pohang areas, respectively. The EBF model was found to be more effective in terms of prediction accuracy. © 2014, National Ground Water Association.

Assessment of potential soil degradation on agricultural land in the czech republic.

PubMed

Šarapatka, Bořivoj; Bednář, Marek

2015-01-01

Many attempts have been made worldwide to develop methods to identify the areas most threatened by soil degradation. Some soils in afflicted areas may be irreversibly degraded and thus have very little resilience (the ability to restore themselves). For the purpose of assessing the current state of soil degradation in the Czech Republic (CZ) we have developed an overall indicator of land vulnerability to the threat of soil degradation on the basis of individual factors that contribute to soil degradation and are monitored on a long-term basis in various research worksites in the CZ. Individual degradation factors were divided into two groups: chemical and physical degradation. On the basis of principal component analysis, individual degradation factors were assigned a specific weight of influence. With the use of a GIS, the input factors of degradation were combined to create maps of chemical and physical soil degradation, and consequently a map of overall degradation-threatened soils for the CZ, along with a map of areas differentiated according to the prevailing type of degradation. Results showed that, at present, the most important degradation factor in the CZ is water erosion, followed by loss of organic matter. Statistical analysis showed that approximately 51% of agricultural land is moderately threatened in the CZ. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Determination of important topographic factors for landslide mapping analysis using MLP network.

PubMed

Alkhasawneh, Mutasem Sh; Ngah, Umi Kalthum; Tay, Lea Tien; Mat Isa, Nor Ashidi; Al-batah, Mohammad Subhi

2013-01-01

Landslide is one of the natural disasters that occur in Malaysia. Topographic factors such as elevation, slope angle, slope aspect, general curvature, plan curvature, and profile curvature are considered as the main causes of landslides. In order to determine the dominant topographic factors in landslide mapping analysis, a study was conducted and presented in this paper. There are three main stages involved in this study. The first stage is the extraction of extra topographic factors. Previous landslide studies had identified mainly six topographic factors. Seven new additional factors have been proposed in this study. They are longitude curvature, tangential curvature, cross section curvature, surface area, diagonal line length, surface roughness, and rugosity. The second stage is the specification of the weight of each factor using two methods. The methods are multilayer perceptron (MLP) network classification accuracy and Zhou's algorithm. At the third stage, the factors with higher weights were used to improve the MLP performance. Out of the thirteen factors, eight factors were considered as important factors, which are surface area, longitude curvature, diagonal length, slope angle, elevation, slope aspect, rugosity, and profile curvature. The classification accuracy of multilayer perceptron neural network has increased by 3% after the elimination of five less important factors.

Determination of Important Topographic Factors for Landslide Mapping Analysis Using MLP Network

PubMed Central

Alkhasawneh, Mutasem Sh.; Ngah, Umi Kalthum; Mat Isa, Nor Ashidi; Al-batah, Mohammad Subhi

2013-01-01

Landslide is one of the natural disasters that occur in Malaysia. Topographic factors such as elevation, slope angle, slope aspect, general curvature, plan curvature, and profile curvature are considered as the main causes of landslides. In order to determine the dominant topographic factors in landslide mapping analysis, a study was conducted and presented in this paper. There are three main stages involved in this study. The first stage is the extraction of extra topographic factors. Previous landslide studies had identified mainly six topographic factors. Seven new additional factors have been proposed in this study. They are longitude curvature, tangential curvature, cross section curvature, surface area, diagonal line length, surface roughness, and rugosity. The second stage is the specification of the weight of each factor using two methods. The methods are multilayer perceptron (MLP) network classification accuracy and Zhou's algorithm. At the third stage, the factors with higher weights were used to improve the MLP performance. Out of the thirteen factors, eight factors were considered as important factors, which are surface area, longitude curvature, diagonal length, slope angle, elevation, slope aspect, rugosity, and profile curvature. The classification accuracy of multilayer perceptron neural network has increased by 3% after the elimination of five less important factors. PMID:24453846

The poor man's Geographic Information System: plot expansion factors

Treesearch

Paul C. Van Deusen

2007-01-01

Plot expansion factors can serve as a crude Geographic Information System for users of Forest Inventory and Analysis (FIA) data. Each FIA plot has an associated expansion factor that is often interpreted as the number of forested acres that the plot represents. The derivation of expansion factors is discussed and it is shown that the mapped plot design requires a...

Participatory Risk Mapping of Malaria Vector Exposure in Northern South America using Environmental and Population Data

PubMed Central

Fuller, D.O.; Troyo, A.; Alimi, T.O.; Beier, J.C.

2014-01-01

Malaria elimination remains a major public health challenge in many tropical regions, including large areas of northern South America. In this study, we present a new high spatial resolution (90 × 90 m) risk map for Colombia and surrounding areas based on environmental and human population data. The map was created through a participatory multi-criteria decision analysis in which expert opinion was solicited to determine key environmental and population risk factors, different fuzzy functions to standardize risk factor inputs, and variable factor weights to combine risk factors in a geographic information system. The new risk map was compared to a map of malaria cases in which cases were aggregated to the municipio (municipality) level. The relationship between mean municipio risk scores and total cases by muncípio showed a weak correlation. However, the relationship between pixel-level risk scores and vector occurrence points for two dominant vector species, Anopheles albimanus and An. darlingi, was significantly different (p < 0.05) from a random point distribution, as was a pooled point distribution for these two vector species and An. nuneztovari. Thus, we conclude that the new risk map derived based on expert opinion provides an accurate spatial representation of risk of potential vector exposure rather than malaria transmission as shown by the pattern of malaria cases, and therefore it may be used to inform public health authorities as to where vector control measures should be prioritized to limit human-vector contact in future malaria outbreaks. PMID:24976656

A simple landslide susceptibility analysis for hazard and risk assessment in developing countries

NASA Astrophysics Data System (ADS)

Guinau, M.; Vilaplana, J. M.

2003-04-01

In recent years, a number of techniques and methodologies have been developed for mitigating natural disasters. The complexity of these methodologies and the scarcity of material and data series justify the need for simple methodologies to obtain the necessary information for minimising the effects of catastrophic natural phenomena. The work with polygonal maps using a GIS allowed us to develop a simple methodology, which was developed in an area of 473 Km2 in the Departamento de Chinandega (NW Nicaragua). This area was severely affected by a large number of landslides (mainly debris flows), triggered by the Hurricane Mitch rainfalls in October 1998. With the aid of aerial photography interpretation at 1:40.000 scale, amplified to 1:20.000, and detailed field work, a landslide map at 1:10.000 scale was constructed. The failure zones of landslides were digitized in order to obtain a failure zone digital map. A terrain unit digital map, in which a series of physical-environmental terrain factors are represented, was also used. Dividing the studied area into two zones (A and B) with homogeneous physical and environmental characteristics, allows us to develop the proposed methodology and to validate it. In zone A, the failure zone digital map is superimposed onto the terrain unit digital map to establish the relationship between the different terrain factors and the failure zones. The numerical expression of this relationship enables us to classify the terrain by its landslide susceptibility. In zone B, this numerical relationship was employed to obtain a landslide susceptibility map, obviating the need for a failure zone map. The validity of the methodology can be tested in this area by using the degree of superposition of the susceptibility map and the failure zone map. The implementation of the methodology in tropical countries with physical and environmental characteristics similar to those of the study area allows us to carry out a landslide susceptibility analysis in areas where landslide records do not exist. This analysis is essential to landslide hazard and risk assessment, which is necessary to determine the actions for mitigating landslide effects, e.g. land planning, emergency aid actions, etc.

The constellation of dietary factors in adolescent acne: a semantic connectivity map approach.

PubMed

Grossi, E; Cazzaniga, S; Crotti, S; Naldi, L; Di Landro, A; Ingordo, V; Cusano, F; Atzori, L; Tripodi Cutrì, F; Musumeci, M L; Pezzarossa, E; Bettoli, V; Caproni, M; Bonci, A

2016-01-01

Different lifestyle and dietetic factors have been linked with the onset and severity of acne. To assess the complex interconnection between dietetic variables and acne. This was a reanalysis of data from a case-control study by using a semantic connectivity map approach. 563 subjects, aged 10-24 years, involved in a case-control study of acne between March 2009 and February 2010, were considered in this study. The analysis evaluated the link between a moderate to severe acne and anthropometric variables, family history and dietetic factors. Analyses were conducted by relying on an artificial adaptive system, the Auto Semantic Connectivity Map (AutoCM). The AutoCM map showed that moderate-severe acne was closely associated with family history of acne in first degree relatives, obesity (BMI ≥ 30), and high consumption of milk, in particular skim milk, cheese/yogurt, sweets/cakes, chocolate, and a low consumption of fish, and limited intake of fruits/vegetables. Our analyses confirm the link between several dietetic items and acne. When providing care, dermatologists should also be aware of the complex interconnection between dietetic factors and acne. © 2014 European Academy of Dermatology and Venereology.

Occurrence of Mycobacterium avium subspecies paratuberculosis and Neospora caninum in Alberta cow-calf operations.

PubMed

Pruvot, M; Kutz, S; Barkema, H W; De Buck, J; Orsel, K

2014-11-01

Mycobacterium avium subsp. paratuberculosis (MAP) and Neospora caninum (NC) are two pathogens causing important production limiting diseases in the cattle industry. Significant impacts of MAP and NC have been reported on dairy cattle herds, but little is known about the importance, risk factors and transmission patterns in western Canadian cow-calf herds. In this cross-sectional study, the prevalence of MAP and NC infection in southwest Alberta cow-calf herds was estimated, risk factors for NC were identified, and the reproductive impacts of the two pathogens were assessed. Blood and fecal samples were collected from 840 cows on 28 cow-calf operations. Individual cow and herd management information was collected by self-administered questionnaires and one-on-one interviews. Bayesian estimates of the true prevalence of MAP and NC were computed, and bivariable and multivariable statistical analysis were done to assess the association between the NC serological status and ranch management risk factors, and the clinical effects of the two pathogens. Bayesian estimates of true prevalence indicated that 20% (95% probability interval: 8-38%) of herds had at least one MAP-positive cow, with a within-herd prevalence in positive herds of 22% (8-45%). From the Bayesian posterior distributions of NC prevalence, the median herd-level prevalence was 66% (33-95%) with 10% (4-21%) cow-level prevalence in positive herds. Multivariable analysis indicated that introducing purchased animals in the herd might increase the risk of NC. The negative association of NC with proper carcass disposal and presence of horses on ranch (possibly in relation to herd monitoring and guarding activities), may suggest the importance of wild carnivores in the dynamics of this pathogen in the study area. We also observed an association between MAP and NC serological status and the number of abortions. Additional studies should be done to further examine specific risk factors for MAP and NC, assess the consequences on the reproductive performances in cow-calf herds, and evaluate the overall impact of these pathogens on cow-calf operations. Copyright © 2014 Elsevier B.V. All rights reserved.

Malaria Disease Mapping in Malaysia based on Besag-York-Mollie (BYM) Model

NASA Astrophysics Data System (ADS)

Azah Samat, Nor; Mey, Liew Wan

2017-09-01

Disease mapping is the visual representation of the geographical distribution which give an overview info about the incidence of disease within a population through spatial epidemiology data. Based on the result of map, it helps in monitoring and planning resource needs at all levels of health care and designing appropriate interventions, tailored towards areas that deserve closer scrutiny or communities that lead to further investigations to identify important risk factors. Therefore, the choice of statistical model used for relative risk estimation is important because production of disease risk map relies on the model used. This paper proposes Besag-York-Mollie (BYM) model to estimate the relative risk for Malaria in Malaysia. The analysis involved using the number of Malaria cases that obtained from the Ministry of Health Malaysia. The outcomes of analysis are displayed through graph and map, including Malaria disease risk map that constructed according to the estimation of relative risk. The distribution of high and low risk areas of Malaria disease occurrences for all states in Malaysia can be identified in the risk map.

Elastostatic stress analysis of orthotropic rectangular center-cracked plates

NASA Technical Reports Server (NTRS)

Gyekenyesi, G. S.; Mendelson, A.

1972-01-01

A mapping-collocation method was developed for the elastostatic stress analysis of finite, anisotropic plates with centrally located traction-free cracks. The method essentially consists of mapping the crack into the unit circle and satisfying the crack boundary conditions exactly with the help of Muskhelishvili's function extension concept. The conditions on the outer boundary are satisfied approximately by applying the method of least-squares boundary collocation. A parametric study of finite-plate stress intensity factors, employing this mapping-collocation method, is presented. It shows the effects of varying material properties, orientation angle, and crack-length-to-plate-width and plate-height-to-plate-width ratios for rectangular orthotropic plates under constant tensile and shear loads.

Construct Validity and Measurement Invariance of Computerized Adaptive Testing: Application to Measures of Academic Progress (MAP) Using Confirmatory Factor Analysis

ERIC Educational Resources Information Center

Wang, Shudong; McCall, Marty; Jiao, Hong; Harris, Gregg

2012-01-01

The purposes of this study are twofold. First, to investigate the construct or factorial structure of a set of Reading and Mathematics computerized adaptive tests (CAT), "Measures of Academic Progress" (MAP), given in different states at different grades and academic terms. The second purpose is to investigate the invariance of test…

New geospatial approaches for efficiently mapping forest biomass logistics at high resolution over large areas

Treesearch

John Hogland; Nathaniel Anderson; Woodam Chung

2018-01-01

Adequate biomass feedstock supply is an important factor in evaluating the financial feasibility of alternative site locations for bioenergy facilities and for maintaining profitability once a facility is built. We used newly developed spatial analysis and logistics software to model the variables influencing feedstock supply and to estimate and map two components of...

Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

PubMed Central

Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

2015-01-01

Mapping expression quantitative trait loci (eQTLs) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at molecular level. In this paper, we present an integrative analysis approach that leverages eQTL data collected from multiple population groups. In particular, our approach effectively identifies multiple independent cis-eQTL signals that are consistent across populations, accounting for population heterogeneity in allele frequencies and linkage disequilibrium patterns. Furthermore, by integrating genomic annotations, our analysis framework enables high-resolution functional analysis of eQTLs. We applied our statistical approach to analyze the GEUVADIS data consisting of samples from five population groups. From this analysis, we concluded that i) jointly analysis across population groups greatly improves the power of eQTL discovery and the resolution of fine mapping of causal eQTL ii) many genes harbor multiple independent eQTLs in their cis regions iii) genetic variants that disrupt transcription factor binding are significantly enriched in eQTLs (p-value = 4.93 × 10-22). PMID:25906321

Mapping the Factors Affecting Household Food Security of Tuberculosis Patients in Coastal Region of Surabaya

NASA Astrophysics Data System (ADS)

Susilaningrum, D.; Ulama, B. S. S.; Lathifah, R.

2018-04-01

Food security is a condition of a person who has access to adequate, safe, and nutritious food to meet the needs of a healthy life. Affordability of food is determined by the aggregate purchasing power. It is also can be measured by the amount of poverty in Indonesia which reached 28,07 million in 2014. According to data from the health department, the largest TB cases in Indonesia were in East Java Province and Surabaya accounted for the largest number, there are 48379 cases in 2015. This study mapping the factors that affect household food security of TB patients in the coastal areas of Surabaya. This study used secondary data sources from 11 clinics i.e. TB patient's addres and primary data source to survey patients about food security. Variables used in this study are variables related to socioeconomic factors and sanitary factors. Those variables will be analyzed descriptively and mapping using biplot analysis. Biplot generated based on socio-economic factors, sanitary factors, and status of households in 11 districts Surabaya that near the beach geographically. The result shows that 64% of TB patient households are food insecure than the left are food secure. More than 50% of TB patient households have a good house physically. From the result of mapping between sub-districts and factors, formed five groups consisting of: 1) Benowo and Mulyorejo; 2) Asemrowo, Gunung Anyar, Sukolilo and Pabean Cantikan; 3) Semampir, Krembangan and Bulak; 4) Kenjeran; and 5) Rungkut.

Drivers of wetland conversion: a global meta-analysis.

PubMed

van Asselen, Sanneke; Verburg, Peter H; Vermaat, Jan E; Janse, Jan H

2013-01-01

Meta-analysis of case studies has become an important tool for synthesizing case study findings in land change. Meta-analyses of deforestation, urbanization, desertification and change in shifting cultivation systems have been published. This present study adds to this literature, with an analysis of the proximate causes and underlying forces of wetland conversion at a global scale using two complementary approaches of systematic review. Firstly, a meta-analysis of 105 case-study papers describing wetland conversion was performed, showing that different combinations of multiple-factor proximate causes, and underlying forces, drive wetland conversion. Agricultural development has been the main proximate cause of wetland conversion, and economic growth and population density are the most frequently identified underlying forces. Secondly, to add a more quantitative component to the study, a logistic meta-regression analysis was performed to estimate the likelihood of wetland conversion worldwide, using globally-consistent biophysical and socioeconomic location factor maps. Significant factors explaining wetland conversion, in order of importance, are market influence, total wetland area (lower conversion probability), mean annual temperature and cropland or built-up area. The regression analyses results support the outcomes of the meta-analysis of the processes of conversion mentioned in the individual case studies. In other meta-analyses of land change, similar factors (e.g., agricultural development, population growth, market/economic factors) are also identified as important causes of various types of land change (e.g., deforestation, desertification). Meta-analysis helps to identify commonalities across the various local case studies and identify which variables may lead to individual cases to behave differently. The meta-regression provides maps indicating the likelihood of wetland conversion worldwide based on the location factors that have determined historic conversions.

Drivers of Wetland Conversion: a Global Meta-Analysis

PubMed Central

van Asselen, Sanneke; Verburg, Peter H.; Vermaat, Jan E.; Janse, Jan H.

2013-01-01

Meta-analysis of case studies has become an important tool for synthesizing case study findings in land change. Meta-analyses of deforestation, urbanization, desertification and change in shifting cultivation systems have been published. This present study adds to this literature, with an analysis of the proximate causes and underlying forces of wetland conversion at a global scale using two complementary approaches of systematic review. Firstly, a meta-analysis of 105 case-study papers describing wetland conversion was performed, showing that different combinations of multiple-factor proximate causes, and underlying forces, drive wetland conversion. Agricultural development has been the main proximate cause of wetland conversion, and economic growth and population density are the most frequently identified underlying forces. Secondly, to add a more quantitative component to the study, a logistic meta-regression analysis was performed to estimate the likelihood of wetland conversion worldwide, using globally-consistent biophysical and socioeconomic location factor maps. Significant factors explaining wetland conversion, in order of importance, are market influence, total wetland area (lower conversion probability), mean annual temperature and cropland or built-up area. The regression analyses results support the outcomes of the meta-analysis of the processes of conversion mentioned in the individual case studies. In other meta-analyses of land change, similar factors (e.g., agricultural development, population growth, market/economic factors) are also identified as important causes of various types of land change (e.g., deforestation, desertification). Meta-analysis helps to identify commonalities across the various local case studies and identify which variables may lead to individual cases to behave differently. The meta-regression provides maps indicating the likelihood of wetland conversion worldwide based on the location factors that have determined historic conversions. PMID:24282580

Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms

DTIC Science & Technology

2015-03-04

were shown to attenuate disease progression in an aerosol infection animal model using the virulent Burkholderia mallei ATCC 23344 strain. Here, we...performed an extended analysis of primarily nine B. mallei virulence factors and their interactions with human proteins to map out how the bacteria can...virulent Burkholderia mallei ATCC 23344 strain. Here, we performed an extended analysis of primarily nine B. mallei virulence factors and their

Tetlin National Wildlife Refuge land cover mapping project users guide

USGS Publications Warehouse

Markon, Carl J.

1987-01-01

The U. S. Fish & Wildlife Service (USFWS) has the responsibility for collecting the resource information to address the research, management, development and planning requirements identified in Section 304. Because of the brief period provided by the Act for data collection, habitat mapping, and habitat assessment, the USFWS in cooperation with the U.S. Geological Survey's EROS Field Office, used digital Landsat multispectral scanner data (MSS) and digital terrain data to produce land cover and terrain maps. A computer assisted digital analysis of Landsat MSS data was used because coverage by aerial photographs was incomplete for much of the refuge and because the level of detail, obtained from the analysis of Landsat data, is adequate to meet most USFWS research, management and planning needs. Relative cost and time requirements were also factors in the decision to use the digital analysis approach.

A mucus adhesion promoting protein, MapA, mediates the adhesion of Lactobacillus reuteri to Caco-2 human intestinal epithelial cells.

PubMed

Miyoshi, Yukihiro; Okada, Sanae; Uchimura, Tai; Satoh, Eiichi

2006-07-01

Lactobacillus reuteri is one of the dominant lactobacilli found in the gastrointestinal tract of various animals. A surface protein of L. reuteri 104R, mucus adhesion promoting protein (MapA), is considered to be an adhesion factor of this strain. We investigated the relation between MapA and adhesion of L. reuteri to human intestinal (Caco-2) cells. Quantitative analysis of the adhesion of L. reuteri strains to Caco-2 cells showed that various L. reuteri strains bind not only to mucus but also to intestinal epithelial cells. In addition, purified MapA bound to Caco-2 cells, and this binding inhibited the adhesion of L. reuteri in a concentration-dependent manner. Based on these observations, the adhesion of L. reuteri appears due to the binding of MapA to receptor-like molecules on Caco-2 cells. Further, far-western analysis indicated the existence of multiple receptor-like molecules in Caco-2 cells.

Analysis and determination of susceptibility Risk from slope instability at Colima State Mexico due to the accelerators factors of rain and seismicity

NASA Astrophysics Data System (ADS)

Ramirez-Ruiz, J. J.

2016-12-01

Slope instability is presented each year in the mountain region of the Colima State, Mexico. It occurs due to the combination of different factors existing in this area as: Precipitation, topography contrast, type and mechanical properties of deposits that constitute the rocks and soils of the region and the erosion due to the elimination of vegetation deck to develop and grow urban areas. To these geological factors we can extend the tectonic activity of the Western part of Mexico that originate high seismicity by the interaction of Cocos plate and North America plate forming the region of Graben de Colima, were is located our study area. Here we will present a Zonification and determination of the Susceptibility maps of slope instability due to the rain and seismicity accelerators factors. The North part of the State Colima is covered by deposits of the Volcan de Colima with an elevation of 3860 masl. It is the area of major precipitation yearly with more than 1200 mm in comparison to the average precipitation of about 900 mm of the State of Colima. Using a SIG system and the mapping of more than 30 sites we realize a zonification and analysis of the Risk using a methodology developed by CENAPRED. The susceptibility map developed in this area in combination with erosion factors permit us to determine an approximation of the Risk considering some limitations that will be present in this study.

A national scale flood hazard mapping methodology: The case of Greece - Protection and adaptation policy approaches.

PubMed

Kourgialas, Nektarios N; Karatzas, George P

2017-12-01

The present work introduces a national scale flood hazard assessment methodology, using multi-criteria analysis and artificial neural networks (ANNs) techniques in a GIS environment. The proposed methodology was applied in Greece, where flash floods are a relatively frequent phenomenon and it has become more intense over the last decades, causing significant damages in rural and urban sectors. In order the most prone flooding areas to be identified, seven factor-maps (that are directly related to flood generation) were combined in a GIS environment. These factor-maps are: a) the Flow accumulation (F), b) the Land use (L), c) the Altitude (A), b) the Slope (S), e) the soil Erodibility (E), f) the Rainfall intensity (R), and g) the available water Capacity (C). The name to the proposed method is "FLASERC". The flood hazard for each one of these factors is classified into five categories: Very low, low, moderate, high, and very high. The above factors are combined and processed using the appropriate ANN algorithm tool. For the ANN training process spatial distribution of historical flooded points in Greece within the five different flood hazard categories of the aforementioned seven factor-maps were combined. In this way, the overall flood hazard map for Greece was determined. The final results are verified using additional historical flood events that have occurred in Greece over the last 100years. In addition, an overview of flood protection measures and adaptation policy approaches were proposed for agricultural and urban areas located at very high flood hazard areas. Copyright © 2017 Elsevier B.V. All rights reserved.

Expression of a Recombinant Anti-HIV and Anti-Tumor Protein, MAP30, in Nicotiana tobacum Hairy Roots: A pH-Stable and Thermophilic Antimicrobial Protein.

PubMed

Moghadam, Ali; Niazi, Ali; Afsharifar, Alireza; Taghavi, Seyed Mohsen

2016-01-01

In contrast to conventional antibiotics, which microorganisms can readily evade, it is nearly impossible for a microbial strain that is sensitive to antimicrobial proteins to convert to a resistant strain. Therefore, antimicrobial proteins and peptides that are promising alternative candidates for the control of bacterial infections are under investigation. The MAP30 protein of Momordica charantia is a valuable type I ribosome-inactivating protein (RIP) with anti-HIV and anti-tumor activities. Whereas the antimicrobial activity of some type I RIPs has been confirmed, less attention has been paid to the antimicrobial activity of MAP30 produced in a stable, easily handled, and extremely cost-effective protein-expression system. rMAP30-KDEL was expressed in Nicotiana tobacum hairy roots, and its effect on different microorganisms was investigated. Analysis of the extracted total proteins of transgenic hairy roots showed that rMAP30-KDEL was expressed effectively and that this protein exhibited significant antibacterial activity in a dose-dependent manner. rMAP30-KDEL also possessed thermal and pH stability. Bioinformatic analysis of MAP30 and other RIPs regarding their conserved motifs, amino-acid contents, charge, aliphatic index, GRAVY value, and secondary structures demonstrated that these factors accounted for their thermophilicity. Therefore, RIPs such as MAP30 and its derived peptides might have promising applications as food preservatives, and their analysis might provide useful insights into designing clinically applicable antibiotic agents.

Expression of a Recombinant Anti-HIV and Anti-Tumor Protein, MAP30, in Nicotiana tobacum Hairy Roots: A pH-Stable and Thermophilic Antimicrobial Protein

PubMed Central

Moghadam, Ali; Niazi, Ali; Afsharifar, Alireza; Taghavi, Seyed Mohsen

2016-01-01

In contrast to conventional antibiotics, which microorganisms can readily evade, it is nearly impossible for a microbial strain that is sensitive to antimicrobial proteins to convert to a resistant strain. Therefore, antimicrobial proteins and peptides that are promising alternative candidates for the control of bacterial infections are under investigation. The MAP30 protein of Momordica charantia is a valuable type I ribosome-inactivating protein (RIP) with anti-HIV and anti-tumor activities. Whereas the antimicrobial activity of some type I RIPs has been confirmed, less attention has been paid to the antimicrobial activity of MAP30 produced in a stable, easily handled, and extremely cost-effective protein-expression system. rMAP30-KDEL was expressed in Nicotiana tobacum hairy roots, and its effect on different microorganisms was investigated. Analysis of the extracted total proteins of transgenic hairy roots showed that rMAP30-KDEL was expressed effectively and that this protein exhibited significant antibacterial activity in a dose-dependent manner. rMAP30-KDEL also possessed thermal and pH stability. Bioinformatic analysis of MAP30 and other RIPs regarding their conserved motifs, amino-acid contents, charge, aliphatic index, GRAVY value, and secondary structures demonstrated that these factors accounted for their thermophilicity. Therefore, RIPs such as MAP30 and its derived peptides might have promising applications as food preservatives, and their analysis might provide useful insights into designing clinically applicable antibiotic agents. PMID:27459300

A GIS-based extended fuzzy multi-criteria evaluation for landslide susceptibility mapping

NASA Astrophysics Data System (ADS)

Feizizadeh, Bakhtiar; Shadman Roodposhti, Majid; Jankowski, Piotr; Blaschke, Thomas

2014-12-01

Landslide susceptibility mapping (LSM) is making increasing use of GIS-based spatial analysis in combination with multi-criteria evaluation (MCE) methods. We have developed a new multi-criteria decision analysis (MCDA) method for LSM and applied it to the Izeh River basin in south-western Iran. Our method is based on fuzzy membership functions (FMFs) derived from GIS analysis. It makes use of nine causal landslide factors identified by local landslide experts. Fuzzy set theory was first integrated with an analytical hierarchy process (AHP) in order to use pairwise comparisons to compare LSM criteria for ranking purposes. FMFs were then applied in order to determine the criteria weights to be used in the development of a landslide susceptibility map. Finally, a landslide inventory database was used to validate the LSM map by comparing it with known landslides within the study area. Results indicated that the integration of fuzzy set theory with AHP produced significantly improved accuracies and a high level of reliability in the resulting landslide susceptibility map. Approximately 53% of known landslides within our study area fell within zones classified as having "very high susceptibility", with the further 31% falling into zones classified as having "high susceptibility".

A GIS-based extended fuzzy multi-criteria evaluation for landslide susceptibility mapping

PubMed Central

Feizizadeh, Bakhtiar; Shadman Roodposhti, Majid; Jankowski, Piotr; Blaschke, Thomas

2014-01-01

Landslide susceptibility mapping (LSM) is making increasing use of GIS-based spatial analysis in combination with multi-criteria evaluation (MCE) methods. We have developed a new multi-criteria decision analysis (MCDA) method for LSM and applied it to the Izeh River basin in south-western Iran. Our method is based on fuzzy membership functions (FMFs) derived from GIS analysis. It makes use of nine causal landslide factors identified by local landslide experts. Fuzzy set theory was first integrated with an analytical hierarchy process (AHP) in order to use pairwise comparisons to compare LSM criteria for ranking purposes. FMFs were then applied in order to determine the criteria weights to be used in the development of a landslide susceptibility map. Finally, a landslide inventory database was used to validate the LSM map by comparing it with known landslides within the study area. Results indicated that the integration of fuzzy set theory with AHP produced significantly improved accuracies and a high level of reliability in the resulting landslide susceptibility map. Approximately 53% of known landslides within our study area fell within zones classified as having “very high susceptibility”, with the further 31% falling into zones classified as having “high susceptibility”. PMID:26089577

A GIS-based extended fuzzy multi-criteria evaluation for landslide susceptibility mapping.

PubMed

Feizizadeh, Bakhtiar; Shadman Roodposhti, Majid; Jankowski, Piotr; Blaschke, Thomas

2014-12-01

Landslide susceptibility mapping (LSM) is making increasing use of GIS-based spatial analysis in combination with multi-criteria evaluation (MCE) methods. We have developed a new multi-criteria decision analysis (MCDA) method for LSM and applied it to the Izeh River basin in south-western Iran. Our method is based on fuzzy membership functions (FMFs) derived from GIS analysis. It makes use of nine causal landslide factors identified by local landslide experts. Fuzzy set theory was first integrated with an analytical hierarchy process (AHP) in order to use pairwise comparisons to compare LSM criteria for ranking purposes. FMFs were then applied in order to determine the criteria weights to be used in the development of a landslide susceptibility map. Finally, a landslide inventory database was used to validate the LSM map by comparing it with known landslides within the study area. Results indicated that the integration of fuzzy set theory with AHP produced significantly improved accuracies and a high level of reliability in the resulting landslide susceptibility map. Approximately 53% of known landslides within our study area fell within zones classified as having "very high susceptibility", with the further 31% falling into zones classified as having "high susceptibility".

Cardiac Fibroblast-Specific Activating Transcription Factor 3 Protects Against Heart Failure by Suppressing MAP2K3-p38 Signaling.

PubMed

Li, Yulin; Li, Zhenya; Zhang, Congcong; Li, Ping; Wu, Yina; Wang, Chunxiao; Bond Lau, Wayne; Ma, Xin-Liang; Du, Jie

2017-05-23

Hypertensive ventricular remodeling is a common cause of heart failure. However, the molecular mechanisms regulating ventricular remodeling remain poorly understood. We used a discovery-driven/nonbiased approach to identify increased activating transcription factor 3 (ATF3) expression in hypertensive heart. We used loss/gain of function approaches to understand the role of ATF3 in heart failure. We also examined the mechanisms through transcriptome, chromatin immunoprecipitation sequencing analysis, and in vivo and in vitro experiments. ATF3 expression increased in murine hypertensive heart and human hypertrophic heart. Cardiac fibroblast cells are the primary cell type expressing high ATF3 levels in response to hypertensive stimuli. ATF3 knockout (ATF3KO) markedly exaggerated hypertensive ventricular remodeling, a state rescued by lentivirus-mediated/miRNA-aided cardiac fibroblast-selective ATF3 overexpression. Conversely, conditional cardiac fibroblast cell-specific ATF3 transgenic overexpression significantly ameliorated ventricular remodeling and heart failure. We identified Map2K3 as a novel ATF3 target. ATF3 binds with the Map2K3 promoter, recruiting HDAC1, resulting in Map2K3 gene-associated histone deacetylation, thereby inhibiting Map2K3 expression. Genetic Map2K3 knockdown rescued the profibrotic/hypertrophic phenotype in ATF3KO cells. Last, we demonstrated that p38 is the downstream molecule of Map2K3 mediating the profibrotic/hypertrophic effects in ATF3KO animals. Inhibition of p38 signaling reduced transforming growth factor-β signaling-related profibrotic and hypertrophic gene expression, and blocked exaggerated cardiac remodeling in ATF3KO cells. Our study provides the first evidence that ATF3 upregulation in cardiac fibroblasts in response to hypertensive stimuli protects the heart by suppressing Map2K3 expression and subsequent p38-transforming growth factor-β signaling. These results suggest that positive modulation of cardiac fibroblast ATF3 may represent a novel therapeutic approach against hypertensive cardiac remodeling. © 2017 American Heart Association, Inc.

An approach for recreation suitability analysis to recreation planning in Gölcük Nature Park.

PubMed

Gül, Atila; Orücü, M Kamil; Karaca, Oznur

2006-05-01

Gölcük Nature Park (GNP) is an area protected by law in Turkey. It is an important nature park with rich flora, fauna, geomorphologic forms, landscape features, and recreational potential in the region. However, GNP does not have a recreation management plan. The purpose of this study was to determine the actual natural, cultural, and visual resources of GNP, determine the most suitable recreational sites with multiple factors, evaluate the demands and tendencies of visitors, and suggest recreational activities and facilities for the most suitable sites of GNP. However, it was also conceived as leading to a recreational plan and design of GNP in the future and identifying the entire appropriate and current data of GNP with the creation of various maps. This study used multifactor analysis to determine the most suitable recreation sites of GNP. Used recreation factors were established including degree of slope, proximity to water resources, accessibility, elevation, vegetation, soil, climate, aspect, current cultural facilities, visual values, and some limiting factors in accordance with the characteristics of GNP. Weighting and suitability values of factors were determined by 30 local expert surveys. All obtained data were evaluated and integrated in the Geographical Information Systems base. Obtained maps were overlapped. Thus, recreational suitability zones map were created manually. However, the demands and behaviours from visitor surveys in GNP were focused on the most suitable recreation sites of the park. Finally, 10% of GNP was identified as the most suitable sites for recreational use. Various recreational facilities and activities (including picnicking, sports facilities and playgrounds, camping sites, walking paths, food and local outlets, etc.) were recommended for nine of the most suitable areas on the proposed recreational map.

Understanding semantic mapping evolution by observing changes in biomedical ontologies.

PubMed

dos Reis, Julio Cesar; Pruski, Cédric; Da Silveira, Marcos; Reynaud-Delaître, Chantal

2014-02-01

Knowledge Organization Systems (KOSs) are extensively used in the biomedical domain to support information sharing between software applications. KOSs are proposed covering different, but overlapping subjects, and mappings indicate the semantic relation between concepts from two KOSs. Over time, KOSs change as do the mappings between them. This can result from a new discovery or a revision of existing knowledge which includes corrections of concepts or mappings. Indeed, changes affecting KOS entities may force the underline mappings to be updated in order to ensure their reliability over time. To tackle this open research problem, we study how mappings are affected by KOS evolution. This article presents a detailed descriptive analysis of the impact that changes in KOS have on mappings. As a case study, we use the official mappings established between SNOMED CT and ICD-9-CM from 2009 to 2011. Results highlight factors according to which KOS changes in varying degrees influence the evolution of mappings. Copyright © 2013 Elsevier Inc. All rights reserved.

Trajectory analysis of land use and land cover maps to improve spatial-temporal patterns, and impact assessment on groundwater recharge

NASA Astrophysics Data System (ADS)

Zomlot, Z.; Verbeiren, B.; Huysmans, M.; Batelaan, O.

2017-11-01

Land use/land cover (LULC) change is a consequence of human-induced global environmental change. It is also considered one of the major factors affecting groundwater recharge. Uncertainties and inconsistencies in LULC maps are one of the difficulties that LULC timeseries analysis face and which have a significant effect on hydrological impact analysis. Therefore, an accuracy assessment approach of LULC timeseries is needed for a more reliable hydrological analysis and prediction. The objective of this paper is to assess the impact of land use uncertainty and to improve the accuracy of a timeseries of CORINE (coordination of information on the environment) land cover maps by using a new approach of identifying spatial-temporal LULC change trajectories as a pre-processing tool. This ensures consistency of model input when dealing with land-use dynamics and as such improves the accuracy of land use maps and consequently groundwater recharge estimation. As a case study the impact of consistent land use changes from 1990 until 2013 on groundwater recharge for the Flanders-Brussels region is assessed. The change trajectory analysis successfully assigned a rational trajectory to 99% of all pixels. The methodology is shown to be powerful in correcting interpretation inconsistencies and overestimation errors in CORINE land cover maps. The overall kappa (cell-by-cell map comparison) improved from 0.6 to 0.8 and from 0.2 to 0.7 for forest and pasture land use classes respectively. The study shows that the inconsistencies in the land use maps introduce uncertainty in groundwater recharge estimation in a range of 10-30%. The analysis showed that during the period of 1990-2013 the LULC changes were mainly driven by urban expansion. The results show that the resolution at which the spatial analysis is performed is important; the recharge differences using original and corrected CORINE land cover maps increase considerably with increasing spatial resolution. This study indicates that improving consistency of land use map timeseries is of critical importance for assessing land use change and its environmental impact.

Slope Stability Analysis for Shallow Landslides using TRIGRS: A Case Study for Sta. Cruz, Zambales, Philippines

NASA Astrophysics Data System (ADS)

Mendoza, J. P. A.

2016-12-01

The Philippines, being located in the circum-Pacific, bounded by multiple subduction zones, open seas and ocean, is one of the most hazard-prone countries in the world (Benson, 1997). This widespread recurrence of natural hazards in the country requires much attention for disaster management (Aurelio, 2006). On the average, 21 typhoons enter the Philippine area of responsibility annually with 6-9 making a landfall. Several rainfall-induced landslide events are reported annually particularly during and after the inundation of major typhoons which imposes hazards to communities and causes destruction of properties due to the moving mass and possible flash floods it may induce. Shallow landslides are the most commonly observed failure involving soil-mantled slopes and are considered major geohazards, often causing property damage and other economic loss. Hence numerous studies on landslide susceptibility including numerical models based on infinite slope equation are used in order to identify slopes prone to occurrences of shallow landslides. The study aims to determine the relationships between the slope and elevation to the factor of safety for laterite-mantled topography by incorporating precipitation values in the determination of landslide susceptibility. Using a DEM, flow direction map and slope map of the Sta Cruz (Zambales, Philippines), the FORTRAN based program TRIGRS, was used to generate the values for the factors of safety in the study area. Overlays with a generated slope map and elevation map were used to determine relationships of the mentioned factors and the factors of safety. A slope in a topography mantled with lateritic soil will fail at a slope angle higher than 20 degrees. Generally, the factor of safety decreases as the slope angle increases; this increases the probability and risk of slope failure. Elevation has no bearing on the computation for the factor of safety. The factor of safety is heavily dependent on the slope angle. The value of generated factor of safety coincides with the published geohazard map from Mines and Geosciences Bureau(MGB).

Ground Vehicle Condition Based Maintenance

DTIC Science & Technology

2010-10-04

Diagnostic Process Map 32 FMEAs Developed : • Diesel Engine • Transmission • Alternators Analysis : • Identify failure modes • Derive design factors and...S&T Initiatives  TARDEC P&D Process Map  Component Testing  ARL CBM Research  AMSAA SDC & Terrain Modeling UNCLASSIFIED 3 CBM+ Overview...UNCLASSIFIED 4 RCM and CBM are core processes for CBM+ System Development • Army Regulation 750-1, 20 Sep 2007, p. 79 - Reliability Centered Maintenance (RCM

Germplasm-regression-combined (GRC) marker-trait association identification in plant breeding: a challenge for plant biotechnological breeding under soil water deficit conditions.

PubMed

Ruan, Cheng-Jiang; Xu, Xue-Xuan; Shao, Hong-Bo; Jaleel, Cheruth Abdul

2010-09-01

In the past 20 years, the major effort in plant breeding has changed from quantitative to molecular genetics with emphasis on quantitative trait loci (QTL) identification and marker assisted selection (MAS). However, results have been modest. This has been due to several factors including absence of tight linkage QTL, non-availability of mapping populations, and substantial time needed to develop such populations. To overcome these limitations, and as an alternative to planned populations, molecular marker-trait associations have been identified by the combination between germplasm and the regression technique. In the present preview, the authors (1) survey the successful applications of germplasm-regression-combined (GRC) molecular marker-trait association identification in plants; (2) describe how to do the GRC analysis and its differences from mapping QTL based on a linkage map reconstructed from the planned populations; (3) consider the factors that affect the GRC association identification, including selections of optimal germplasm and molecular markers and testing of identification efficiency of markers associated with traits; and (4) finally discuss the future prospects of GRC marker-trait association analysis used in plant MAS/QTL breeding programs, especially in long-juvenile woody plants when no other genetic information such as linkage maps and QTL are available.

Communicating and Evaluating the Causes of Seismicity in Oklahoma Using ArcGIS Online Story Map Web Applications

NASA Astrophysics Data System (ADS)

Justman, D.; Rose, K.; Bauer, J. R.; Miller, R., III; Vasylkivska, V.; Romeo, L.

2016-12-01

ArcGIS Online story maps allows users to communicate complex topics with geospatially enabled stories. This story map web application entitled "Evaluating the Mysteries of Seismicity in Oklahoma" has been employed as part of a broader research effort investigating the relationships between spatiotemporal systems and seismicity to understand the recent increase in seismicity by reviewing literature, exploring, and performing analyses on key datasets. It offers information about the unprecedented increase in seismic events since 2008, earthquake history, the risk to the population, physical mechanisms behind earthquakes, natural and anthropogenic earthquake factors, and individual & cumulative spatial extents of these factors. The cumulative spatial extents for natural, anthropogenic, and all combined earthquake factors were determined using the Cumulative Spatial Impact Layers (CSILs) tool developed at the National Energy Technology Laboratory (NETL). Results show positive correlations between the average number of influences (datasets related to individual factors) and the number of earthquakes for every 100 square mile grid cell in Oklahoma, along with interesting spatial correlations for the individual & cumulative spatial extents of these factors when overlaid with earthquake density and a hotspot analysis for earthquake magnitude from 2010 to 2015.

Concept mapping as a tool to engage a community in health disparity identification.

PubMed

Risisky, Debra; Hogan, Vijaya K; Kane, Mary; Burt, Beneta; Dove, Cassandra; Payton, Marinelle

2008-01-01

To engage a community to critically examine local health disparities. Concept mapping is a tool used to rapidly assess the variations in thinking of large stakeholder groups' about a particular topic. Jackson, Mississippi. Community members. Dialog groups and community meetings were held, and participants were asked to respond to the statement, "A specific thing that causes African Americans to get sicker and die sooner is..." Aggregate responses were rated for importance and feasibility and then sorted into related groups. Aggregate sorts and ratings were then processed by using multidimensional scaling and hierarchical cluster analysis. There were 132 (unduplicated) reported contributors to health disparities. These responses fell into eight general clusters: economic issues, government, contextual factors, cultural factors, HIV, stress, environment, and motivation. Factors respondents felt were the most important contributors to disparities (economic factors, contextual factors, stress) did not correlate with those that they thought were most likely to be changed in society (contextual factors, government, motivation). Concept mapping provided a mechanism for rapidly documenting community thinking about health disparities. This mechanism stimulated community dialog and was used as a first step toward the long-term goal of creating equal community, academic, and medical partnerships for addressing disparities. The concept mapping process stimulated critical thinking about contributors to health inequities and uncovered contextual factors previously unknown to researchers and public health planners. The process allowed for active engagement and exchange of knowledge between the community and researchers and allowed a mechanism for identifying and rectifying disconnects in knowledge within and between stakeholder groups.

A GIS based spatially-explicit sensitivity and uncertainty analysis approach for multi-criteria decision analysis.

PubMed

Feizizadeh, Bakhtiar; Jankowski, Piotr; Blaschke, Thomas

2014-03-01

GIS multicriteria decision analysis (MCDA) techniques are increasingly used in landslide susceptibility mapping for the prediction of future hazards, land use planning, as well as for hazard preparedness. However, the uncertainties associated with MCDA techniques are inevitable and model outcomes are open to multiple types of uncertainty. In this paper, we present a systematic approach to uncertainty and sensitivity analysis. We access the uncertainty of landslide susceptibility maps produced with GIS-MCDA techniques. A new spatially-explicit approach and Dempster-Shafer Theory (DST) are employed to assess the uncertainties associated with two MCDA techniques, namely Analytical Hierarchical Process (AHP) and Ordered Weighted Averaging (OWA) implemented in GIS. The methodology is composed of three different phases. First, weights are computed to express the relative importance of factors (criteria) for landslide susceptibility. Next, the uncertainty and sensitivity of landslide susceptibility is analyzed as a function of weights using Monte Carlo Simulation and Global Sensitivity Analysis. Finally, the results are validated using a landslide inventory database and by applying DST. The comparisons of the obtained landslide susceptibility maps of both MCDA techniques with known landslides show that the AHP outperforms OWA. However, the OWA-generated landslide susceptibility map shows lower uncertainty than the AHP-generated map. The results demonstrate that further improvement in the accuracy of GIS-based MCDA can be achieved by employing an integrated uncertainty-sensitivity analysis approach, in which the uncertainty of landslide susceptibility model is decomposed and attributed to model's criteria weights.

A GIS based spatially-explicit sensitivity and uncertainty analysis approach for multi-criteria decision analysis

NASA Astrophysics Data System (ADS)

Feizizadeh, Bakhtiar; Jankowski, Piotr; Blaschke, Thomas

2014-03-01

GIS multicriteria decision analysis (MCDA) techniques are increasingly used in landslide susceptibility mapping for the prediction of future hazards, land use planning, as well as for hazard preparedness. However, the uncertainties associated with MCDA techniques are inevitable and model outcomes are open to multiple types of uncertainty. In this paper, we present a systematic approach to uncertainty and sensitivity analysis. We access the uncertainty of landslide susceptibility maps produced with GIS-MCDA techniques. A new spatially-explicit approach and Dempster-Shafer Theory (DST) are employed to assess the uncertainties associated with two MCDA techniques, namely Analytical Hierarchical Process (AHP) and Ordered Weighted Averaging (OWA) implemented in GIS. The methodology is composed of three different phases. First, weights are computed to express the relative importance of factors (criteria) for landslide susceptibility. Next, the uncertainty and sensitivity of landslide susceptibility is analyzed as a function of weights using Monte Carlo Simulation and Global Sensitivity Analysis. Finally, the results are validated using a landslide inventory database and by applying DST. The comparisons of the obtained landslide susceptibility maps of both MCDA techniques with known landslides show that the AHP outperforms OWA. However, the OWA-generated landslide susceptibility map shows lower uncertainty than the AHP-generated map. The results demonstrate that further improvement in the accuracy of GIS-based MCDA can be achieved by employing an integrated uncertainty-sensitivity analysis approach, in which the uncertainty of landslide susceptibility model is decomposed and attributed to model's criteria weights.

Anomaly Detection for Beam Loss Maps in the Large Hadron Collider

NASA Astrophysics Data System (ADS)

Valentino, Gianluca; Bruce, Roderik; Redaelli, Stefano; Rossi, Roberto; Theodoropoulos, Panagiotis; Jaster-Merz, Sonja

2017-07-01

In the LHC, beam loss maps are used to validate collimator settings for cleaning and machine protection. This is done by monitoring the loss distribution in the ring during infrequent controlled loss map campaigns, as well as in standard operation. Due to the complexity of the system, consisting of more than 50 collimators per beam, it is difficult to identify small changes in the collimation hierarchy, which may be due to setting errors or beam orbit drifts with such methods. A technique based on Principal Component Analysis and Local Outlier Factor is presented to detect anomalies in the loss maps and therefore provide an automatic check of the collimation hierarchy.

A comparison between univariate probabilistic and multivariate (logistic regression) methods for landslide susceptibility analysis: the example of the Febbraro valley (Northern Alps, Italy)

NASA Astrophysics Data System (ADS)

Rossi, M.; Apuani, T.; Felletti, F.

2009-04-01

The aim of this paper is to compare the results of two statistical methods for landslide susceptibility analysis: 1) univariate probabilistic method based on landslide susceptibility index, 2) multivariate method (logistic regression). The study area is the Febbraro valley, located in the central Italian Alps, where different types of metamorphic rocks croup out. On the eastern part of the studied basin a quaternary cover represented by colluvial and secondarily, by glacial deposits, is dominant. In this study 110 earth flows, mainly located toward NE portion of the catchment, were analyzed. They involve only the colluvial deposits and their extension mainly ranges from 36 to 3173 m2. Both statistical methods require to establish a spatial database, in which each landslide is described by several parameters that can be assigned using a main scarp central point of landslide. The spatial database is constructed using a Geographical Information System (GIS). Each landslide is described by several parameters corresponding to the value of main scarp central point of the landslide. Based on bibliographic review a total of 15 predisposing factors were utilized. The width of the intervals, in which the maps of the predisposing factors have to be reclassified, has been defined assuming constant intervals to: elevation (100 m), slope (5 °), solar radiation (0.1 MJ/cm2/year), profile curvature (1.2 1/m), tangential curvature (2.2 1/m), drainage density (0.5), lineament density (0.00126). For the other parameters have been used the results of the probability-probability plots analysis and the statistical indexes of landslides site. In particular slope length (0 ÷ 2, 2 ÷ 5, 5 ÷ 10, 10 ÷ 20, 20 ÷ 35, 35 ÷ 260), accumulation flow (0 ÷ 1, 1 ÷ 2, 2 ÷ 5, 5 ÷ 12, 12 ÷ 60, 60 ÷27265), Topographic Wetness Index 0 ÷ 0.74, 0.74 ÷ 1.94, 1.94 ÷ 2.62, 2.62 ÷ 3.48, 3.48 ÷ 6,00, 6.00 ÷ 9.44), Stream Power Index (0 ÷ 0.64, 0.64 ÷ 1.28, 1.28 ÷ 1.81, 1.81 ÷ 4.20, 4.20 ÷ 9.40). Geological map and land use map were also used, considering geological and land use properties as categorical variables. Appling the univariate probabilistic method the Landslide Susceptibility Index (LSI) is defined as the sum of the ratio Ra/Rb calculated for each predisposing factor, where Ra is the ratio between number of pixel of class and the total number of pixel of the study area, and Rb is the ratio between number of landslides respect to the pixel number of the interval area. From the analysis of the Ra/Rb ratio the relationship between landslide occurrence and predisposing factors were defined. Then the equation of LSI was used in GIS to trace the landslide susceptibility maps. The multivariate method for landslide susceptibility analysis, based on logistic regression, was performed starting from the density maps of the predisposing factors, calculated with the intervals defined above using the equation Rb/Rbtot, where Rbtot is a sum of all Rb values. Using stepwise forward algorithms the logistic regression was performed in two successive steps: first a univariate logistic regression is used to choose the most significant predisposing factors, then the multivariate logistic regression can be performed. The univariate regression highlighted the importance of the following factors: elevation, accumulation flow, drainage density, lineament density, geology and land use. When the multivariate regression was applied the number of controlling factors was reduced neglecting the geological properties. The resulting final susceptibility equation is: P = 1 / (1 + exp-(6.46-22.34*elevation-5.33*accumulation flow-7.99* drainage density-4.47*lineament density-17.31*land use)) and using this equation the susceptibility maps were obtained. To easy compare the results of the two methodologies, the susceptibility maps were reclassified in five susceptibility intervals (very high, high, moderate, low and very low) using natural breaks. Then the maps were validated using two cumulative distribution curves, one related to the landslides (number of landslides in each susceptibility class) and one to the basin (number of pixel covering each class). Comparing the curves for each method, it results that the two approaches (univariate and multivariate) are appropriate, providing acceptable results. In both maps the distribution of high susceptibility condition is mainly localized on the left slope of the catchment in agreement with the field evidences. The comparison between the methods was obtained by subtraction of the two maps. This operation shows that about 40% of the basin is classified by the same class of susceptibility. In general the univariate probabilistic method tends to overestimate the areal extension of the high susceptibility class with respect to the maps obtained by the logistic regression method.

Aquifer configuration and geostructural links control the groundwater quality in thin-bedded carbonate-siliciclastic alternations of the Hainich CZE, central Germany

NASA Astrophysics Data System (ADS)

Kohlhepp, Bernd; Lehmann, Robert; Seeber, Paul; Küsel, Kirsten; Trumbore, Susan E.; Totsche, Kai U.

2017-12-01

The quality of near-surface groundwater reservoirs is controlled, but also threatened, by manifold surface-subsurface interactions. Vulnerability studies typically evaluate the variable interplay of surface factors (land management, infiltration patterns) and subsurface factors (hydrostratigraphy, flow properties) in a thorough way, but disregard the resulting groundwater quality. Conversely, hydrogeochemical case studies that address the chemical evolution of groundwater often lack a comprehensive analysis of the structural buildup. In this study, we aim to reconstruct the actual spatial groundwater quality pattern from a synoptic analysis of the hydrostratigraphy, lithostratigraphy, pedology and land use in the Hainich Critical Zone Exploratory (Hainich CZE). This CZE represents a widely distributed yet scarcely described setting of thin-bedded mixed carbonate-siliciclastic strata in hillslope terrains. At the eastern Hainich low-mountain hillslope, bedrock is mainly formed by alternated marine sedimentary rocks of the Upper Muschelkalk (Middle Triassic) that partly host productive groundwater resources. Spatial patterns of the groundwater quality of a 5.4 km long well transect are derived by principal component analysis and hierarchical cluster analysis. Aquifer stratigraphy and geostructural links were deduced from lithological drill core analysis, mineralogical analysis, geophysical borehole logs and mapping data. Maps of preferential recharge zones and recharge potential were deduced from digital (soil) mapping, soil survey data and field measurements of soil hydraulic conductivities (Ks). By attributing spatially variable surface and subsurface conditions, we were able to reconstruct groundwater quality clusters that reflect the type of land management in their preferential recharge areas, aquifer hydraulic conditions and cross-formational exchange via caprock sinkholes or ascending flow. Generally, the aquifer configuration (spatial arrangement of strata, valley incision/outcrops) and related geostructural links (enhanced recharge areas, karst phenomena) control the role of surface factors (input quality and locations) vs. subsurface factors (water-rock interaction, cross-formational flow) for groundwater quality in the multi-layered aquifer system. Our investigation reveals general properties of alternating sequences in hillslope terrains that are prone to forming multi-layered aquifer systems. This synoptic analysis is fundamental and indispensable for a mechanistic understanding of ecological functioning, sustainable resource management and protection.

Cloning the promoter for transforming growth factor-beta type III receptor. Basal and conditional expression in fetal rat osteoblasts

NASA Technical Reports Server (NTRS)

Ji, C.; Chen, Y.; McCarthy, T. L.; Centrella, M.

1999-01-01

Transforming growth factor-beta binds to three high affinity cell surface molecules that directly or indirectly regulate its biological effects. The type III receptor (TRIII) is a proteoglycan that lacks significant intracellular signaling or enzymatic motifs but may facilitate transforming growth factor-beta binding to other receptors, stabilize multimeric receptor complexes, or segregate growth factor from activating receptors. Because various agents or events that regulate osteoblast function rapidly modulate TRIII expression, we cloned the 5' region of the rat TRIII gene to assess possible control elements. DNA fragments from this region directed high reporter gene expression in osteoblasts. Sequencing showed no consensus TATA or CCAAT boxes, whereas several nuclear factors binding sequences within the 3' region of the promoter co-mapped with multiple transcription initiation sites, DNase I footprints, gel mobility shift analysis, or loss of activity by deletion or mutation. An upstream enhancer was evident 5' proximal to nucleotide -979, and a silencer region occurred between nucleotides -2014 and -2194. Glucocorticoid sensitivity mapped between nucleotides -687 and -253, whereas bone morphogenetic protein 2 sensitivity co-mapped within the silencer region. Thus, the TRIII promoter contains cooperative basal elements and dispersed growth factor- and hormone-sensitive regulatory regions that can control TRIII expression by osteoblasts.

Mapping of the Rsd Contact Site on the Sigma 70 Subunit of Escherichia coli RNA Polymerase

PubMed Central

Jishage, Miki; Dasgupta, Dipak; Ishihama, Akira

2001-01-01

Rsd (regulator of sigma D) is an anti-sigma factor for the Escherichia coli RNA polymerase ς70 subunit. The contact site of Rsd on ς70 was analyzed after mapping of the contact-dependent cleavage sites by Rsd-tethered iron-p-bromoacetamidobenzyl EDTA and by analysis of the complex formation between Ala-substituted ς70 and Rsd. Results indicate that the Rsd contact site is located downstream of the promoter −35 recognition helix-turn-helix motif within region 4, overlapping with the regions involved in interaction with both core enzyme and ς70 contact transcription factors. PMID:11292818

Mapping of the Rsd contact site on the sigma 70 subunit of Escherichia coli RNA polymerase.

PubMed

Jishage, M; Dasgupta, D; Ishihama, A

2001-05-01

Rsd (regulator of sigma D) is an anti-sigma factor for the Escherichia coli RNA polymerase sigma(70) subunit. The contact site of Rsd on sigma(70) was analyzed after mapping of the contact-dependent cleavage sites by Rsd-tethered iron-p-bromoacetamidobenzyl EDTA and by analysis of the complex formation between Ala-substituted sigma(70) and Rsd. Results indicate that the Rsd contact site is located downstream of the promoter -35 recognition helix-turn-helix motif within region 4, overlapping with the regions involved in interaction with both core enzyme and sigma(70) contact transcription factors.

Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii.

PubMed

Im, Chak Han; Park, Young-Hoon; Hammel, Kenneth E; Park, Bokyung; Kwon, Soon Wook; Ryu, Hojin; Ryu, Jae-San

2016-07-01

Breeding new strains with improved traits is a long-standing goal of mushroom breeders that can be expedited by marker-assisted selection (MAS). We constructed a genetic linkage map of Pleurotus eryngii based on segregation analysis of markers in postmeiotic monokaryons from KNR2312. In total, 256 loci comprising 226 simple sequence-repeat (SSR) markers, 2 mating-type factors, and 28 insertion/deletion (InDel) markers were mapped. The map consisted of 12 linkage groups (LGs) spanning 1047.8cM, with an average interval length of 4.09cM. Four independent populations (Pd3, Pd8, Pd14, and Pd15) derived from crossing between four monokaryons from KNR2532 as a tester strain and 98 monokaryons from KNR2312 were used to characterize quantitative trait loci (QTL) for nine traits such as yield, quality, cap color, and earliness. Using composite interval mapping (CIM), 71 QTLs explaining between 5.82% and 33.17% of the phenotypic variations were identified. Clusters of more than five QTLs for various traits were identified in three genomic regions, on LGs 1, 7 and 9. Regardless of the population, 6 of the 9 traits studied and 18 of the 71 QTLs found in this study were identified in the largest cluster, LG1, in the range from 65.4 to 110.4cM. The candidate genes for yield encoding transcription factor, signal transduction, mycelial growth and hydrolase are suggested by using manual and computational analysis of genome sequence corresponding to QTL region with the highest likelihood odds (LOD) for yield. The genetic map and the QTLs established in this study will help breeders and geneticists to develop selection markers for agronomically important characteristics of mushrooms and to identify the corresponding genes. Copyright © 2016 Elsevier Inc. All rights reserved.

Application of a computerized environmental information system to master and sector planning

NASA Technical Reports Server (NTRS)

Stewart, J. C.

1978-01-01

A computerized composite mapping system developed as an aid in the land use decision making process is described. Emphasis is placed on consideration of the environment in urban planning. The presence of alluvium, shallow bedrock, surface water, and vegetation growth are among the environmental factors considered. An analysis of the Shady Grove Sector planning is presented as an example of the use of computerized composite mapping for long range planning.

Mapa Sociolinguistico. Analisis demolinguistico de la Comunidad Autonoma Vasca derivado del padron de 1986 (Sociolinguistic Map. Demolinguistic analysis of the Autonomous Basque Community derived from the 1986 Census).

ERIC Educational Resources Information Center

Basque Autonomous Community, Vitoria (Spain). General Secretariat of Linguistic Policy.

Sociolinguistic data are presented in the form of sophisticated maps and tables in this pioneering study on the status of the Basque language. Based on information collected from the 1986 census, the major demographic characteristics of Basque are examined in order to ascertain the factors and processes that have contributed to its current status.…

Assessment of the Appalachian Basin Geothermal Field: Combining Risk Factors to Inform Development of Low Temperature Projects

NASA Astrophysics Data System (ADS)

Smith, J. D.; Whealton, C.; Camp, E. R.; Horowitz, F.; Frone, Z. S.; Jordan, T. E.; Stedinger, J. R.

2015-12-01

Exploration methods for deep geothermal energy projects must primarily consider whether or not a location has favorable thermal resources. Even where the thermal field is favorable, other factors may impede project development and success. A combined analysis of these factors and their uncertainty is a strategy for moving geothermal energy proposals forward from the exploration phase at the scale of a basin to the scale of a project, and further to design of geothermal systems. For a Department of Energy Geothermal Play Fairway Analysis we assessed quality metrics, which we call risk factors, in the Appalachian Basin of New York, Pennsylvania, and West Virginia. These included 1) thermal field variability, 2) productivity of natural reservoirs from which to extract heat, 3) potential for induced seismicity, and 4) presence of thermal utilization centers. The thermal field was determined using a 1D heat flow model for 13,400 bottomhole temperatures (BHT) from oil and gas wells. Steps included the development of i) a set of corrections to BHT data and ii) depth models of conductivity stratigraphy at each borehole based on generalized stratigraphy that was verified for a select set of wells. Wells are control points in a spatial statistical analysis that resulted in maps of the predicted mean thermal field properties and of the standard error of the predicted mean. Seismic risk was analyzed by comparing earthquakes and stress orientations in the basin to gravity and magnetic potential field edges at depth. Major edges in the potential fields served as interpolation boundaries for the thermal maps (Figure 1). Natural reservoirs were identified from published studies, and productivity was determined based on the expected permeability and dimensions of each reservoir. Visualizing the natural reservoirs and population centers on a map of the thermal field communicates options for viable pilot sites and project designs (Figure 1). Furthermore, combining the four risk factors at favorable sites enables an evaluation of project feasibility across sites based on tradeoffs in the risk factors. Uncertainties in each risk factor can also be considered to determine if the tradeoffs in risk factors between sites are meaningful.

Mapping Infected Area after a Flash-Flooding Storm Using Multi Criteria Analysis and Spectral Indices

NASA Astrophysics Data System (ADS)

Al-Akad, S.; Akensous, Y.; Hakdaoui, M.

2017-11-01

This research article is summarize the applications of remote sensing and GIS to study the urban floods risk in Al Mukalla. Satellite acquisition of a flood event on October 2015 in Al Mukalla (Yemen) by using flood risk mapping techniques illustrate the potential risk present in this city. Satellite images (The Landsat and DEM images data were atmospherically corrected, radiometric corrected, and geometric and topographic distortions rectified.) are used for flood risk mapping to afford a hazard (vulnerability) map. This map is provided by applying image-processing techniques and using geographic information system (GIS) environment also the application of NDVI, NDWI index, and a method to estimate the flood-hazard areas. Four factors were considered in order to estimate the spatial distribution of the hazardous areas: flow accumulation, slope, land use, geology and elevation. The multi-criteria analysis, allowing to deal with vulnerability to flooding, as well as mapping areas at the risk of flooding of the city Al Mukalla. The main object of this research is to provide a simple and rapid method to reduce and manage the risks caused by flood in Yemen by take as example the city of Al Mukalla.

Forecast and analysis of the ratio of electric energy to terminal energy consumption for global energy internet

NASA Astrophysics Data System (ADS)

Wang, Wei; Zhong, Ming; Cheng, Ling; Jin, Lu; Shen, Si

2018-02-01

In the background of building global energy internet, it has both theoretical and realistic significance for forecasting and analysing the ratio of electric energy to terminal energy consumption. This paper firstly analysed the influencing factors of the ratio of electric energy to terminal energy and then used combination method to forecast and analyse the global proportion of electric energy. And then, construct the cointegration model for the proportion of electric energy by using influence factor such as electricity price index, GDP, economic structure, energy use efficiency and total population level. At last, this paper got prediction map of the proportion of electric energy by using the combination-forecasting model based on multiple linear regression method, trend analysis method, and variance-covariance method. This map describes the development trend of the proportion of electric energy in 2017-2050 and the proportion of electric energy in 2050 was analysed in detail using scenario analysis.

Procedures for adjusting regional regression models of urban-runoff quality using local data

USGS Publications Warehouse

Hoos, A.B.; Sisolak, J.K.

1993-01-01

Statistical operations termed model-adjustment procedures (MAP?s) can be used to incorporate local data into existing regression models to improve the prediction of urban-runoff quality. Each MAP is a form of regression analysis in which the local data base is used as a calibration data set. Regression coefficients are determined from the local data base, and the resulting `adjusted? regression models can then be used to predict storm-runoff quality at unmonitored sites. The response variable in the regression analyses is the observed load or mean concentration of a constituent in storm runoff for a single storm. The set of explanatory variables used in the regression analyses is different for each MAP, but always includes the predicted value of load or mean concentration from a regional regression model. The four MAP?s examined in this study were: single-factor regression against the regional model prediction, P, (termed MAP-lF-P), regression against P,, (termed MAP-R-P), regression against P, and additional local variables (termed MAP-R-P+nV), and a weighted combination of P, and a local-regression prediction (termed MAP-W). The procedures were tested by means of split-sample analysis, using data from three cities included in the Nationwide Urban Runoff Program: Denver, Colorado; Bellevue, Washington; and Knoxville, Tennessee. The MAP that provided the greatest predictive accuracy for the verification data set differed among the three test data bases and among model types (MAP-W for Denver and Knoxville, MAP-lF-P and MAP-R-P for Bellevue load models, and MAP-R-P+nV for Bellevue concentration models) and, in many cases, was not clearly indicated by the values of standard error of estimate for the calibration data set. A scheme to guide MAP selection, based on exploratory data analysis of the calibration data set, is presented and tested. The MAP?s were tested for sensitivity to the size of a calibration data set. As expected, predictive accuracy of all MAP?s for the verification data set decreased as the calibration data-set size decreased, but predictive accuracy was not as sensitive for the MAP?s as it was for the local regression models.

Analysis of the effects of geological and geomorphological factors on earthquake triggered landslides using artificial neural networks (ANN)

NASA Astrophysics Data System (ADS)

Kawabata, D.; Bandibas, J.

2007-12-01

The occurrence of landslide is the result of the interaction of complex and diverse environmental factors. The geomorphic and geologic features, rock types and vegetative cover are important base factors of landslide occurrence. However, determining the relationship between these factors and landslide occurrence is very difficult using conventional mathematical analysis. The use of an advanced computing technique for this kind of analysis is very important. Artificial neural network (ANN) has recently been included in the list of analytical tools for a wide range of applications in the natural sciences research fields. One of the advantages of using ANN for pattern recognition is that it can handle data at any measurement scale ranging from nominal, ordinal to linear and ratio, and any form of data distribution (Wang et al., 1995). In addition, it can easily handle qualitative variables making it widely used in integrated analysis of spatial data from multiple sources for predicting and classification. This study focuses on the definition of the relationship between geological factors and landslide occurrence using artificial neural networks. The study also focuses on the effect of the DTMs (e.g. ASTER DTM, ALSM, digitized from paper map and digital photogrammetric measurement data). The main aim of the study is to generate landslide susceptibility index map using the defined relationship using ANN. Landslide data in the Chuetsu region were used in this research. The 2004 earthquake triggered many landslides in the region. The initial results of the study showed that ANN is more accurate in defining the relationship between geological and geomorphological factors and landslide occurrence. It also determined the best combination of geological and geomorphological factors that is directly related to landslide occurrence.

Monitoring and analysis of the change process in curriculum mapping compared to the National Competency-based Learning Objective Catalogue for Undergraduate Medical Education (NKLM) at four medical faculties. Part II: Key factors for motivating the faculty during the process.

PubMed

Lammerding-Koeppel, Maria; Giesler, Marianne; Gornostayeva, Maryna; Narciss, Elisabeth; Wosnik, Annette; Zipfel, Stephan; Griewatz, Jan; Fritze, Olaf

2017-01-01

Objective: After adoption of the National Competency-based Learning Objectives Catalogue in Medicine [Nationaler Kompetenzbasierter Lernzielkatalog Medizin, NKLM], the German medical faculties are asked to test the learning obejctives recorded in it and evaluate them critically. The faculties require curricular transparency for competence-oriented transition of present curricula, which is best achieved by systematic curriculum mapping in comparison to the NKLM. Based on this inventory, curricula can be further developed target-oriented. Considerable resistance has to be expected when a complex existing curriculum is to be mapped for the first time and a faculty must be convinced of its usefulness. Headed by Tübingen, the faculties of Freiburg, Heidelberg, Mannheim and Tübingen rose to this task. This two-part article analyses and summarises how NKLM curriculum mapping was successful at the locations despite resistance. Part I presented the resources and structures that supported implementation. Part II focuses on factors that motivate individuals and groups of persons to cooperate in the faculties. Method: Both parts used the same method. In short, the joint project was systematically planned following the steps of project and change management and adjusted in the course of the process. From the beginning of the project, a Grounded-Theory approach was used to systematically collect detailed information on measures and developments at the faculties, to continually analyse them and to draw final conclusions. Results: At all sites, faculties, teachers, students and administrative staff were not per se willing to deal with the NKLM and its contents, and even less to map their present curricula. Analysis of the development reflected a number of factors that had either a negative effect on the willingness to cooperate when missing, or a positive one when present. These were: clear top-down and bottom-up management; continuous information of the faculty; user-oriented support in the mapping process by reduction of the mapping categories, portioning and condensation of the NKLM via student pre-mapping (blueprint) and visibility of growing consent. Apart from that, there were a series of frequent questions, objections and concerns that could be countered strategically and by argumentation. They particularly referred to relevance, benefit, feasibility and effort of curriculum mapping. Conclusion: An overview of beneficial framework conditions, strategies and results from different points of view is achieved and interrelations are made visible. Based on literature results, the motivating factors as well as their implementation and effects in the faculties involved are critically reflected on. Recommendations can be derived that can support other faculties in practice.

Monitoring and analysis of the change process in curriculum mapping compared to the National Competency-based Learning Objective Catalogue for Undergraduate Medical Education (NKLM) at four medical faculties. Part II: Key factors for motivating the faculty during the process

PubMed Central

Lammerding-Koeppel, Maria; Giesler, Marianne; Gornostayeva, Maryna; Narciss, Elisabeth; Wosnik, Annette; Zipfel, Stephan; Griewatz, Jan; Fritze, Olaf

2017-01-01

Objective: After adoption of the National Competency-based Learning Objectives Catalogue in Medicine [Nationaler Kompetenzbasierter Lernzielkatalog Medizin, NKLM], the German medical faculties are asked to test the learning obejctives recorded in it and evaluate them critically. The faculties require curricular transparency for competence-oriented transition of present curricula, which is best achieved by systematic curriculum mapping in comparison to the NKLM. Based on this inventory, curricula can be further developed target-oriented. Considerable resistance has to be expected when a complex existing curriculum is to be mapped for the first time and a faculty must be convinced of its usefulness. Headed by Tübingen, the faculties of Freiburg, Heidelberg, Mannheim and Tübingen rose to this task. This two-part article analyses and summarises how NKLM curriculum mapping was successful at the locations despite resistance. Part I presented the resources and structures that supported implementation. Part II focuses on factors that motivate individuals and groups of persons to cooperate in the faculties. Method: Both parts used the same method. In short, the joint project was systematically planned following the steps of project and change management and adjusted in the course of the process. From the beginning of the project, a Grounded-Theory approach was used to systematically collect detailed information on measures and developments at the faculties, to continually analyse them and to draw final conclusions. Results: At all sites, faculties, teachers, students and administrative staff were not per se willing to deal with the NKLM and its contents, and even less to map their present curricula. Analysis of the development reflected a number of factors that had either a negative effect on the willingness to cooperate when missing, or a positive one when present. These were: clear top-down and bottom-up management; continuous information of the faculty; user-oriented support in the mapping process by reduction of the mapping categories, portioning and condensation of the NKLM via student pre-mapping (blueprint) and visibility of growing consent. Apart from that, there were a series of frequent questions, objections and concerns that could be countered strategically and by argumentation. They particularly referred to relevance, benefit, feasibility and effort of curriculum mapping. Conclusion: An overview of beneficial framework conditions, strategies and results from different points of view is achieved and interrelations are made visible. Based on literature results, the motivating factors as well as their implementation and effects in the faculties involved are critically reflected on. Recommendations can be derived that can support other faculties in practice. PMID:28293673

A GIS based spatially-explicit sensitivity and uncertainty analysis approach for multi-criteria decision analysis☆

PubMed Central

Feizizadeh, Bakhtiar; Jankowski, Piotr; Blaschke, Thomas

2014-01-01

GIS multicriteria decision analysis (MCDA) techniques are increasingly used in landslide susceptibility mapping for the prediction of future hazards, land use planning, as well as for hazard preparedness. However, the uncertainties associated with MCDA techniques are inevitable and model outcomes are open to multiple types of uncertainty. In this paper, we present a systematic approach to uncertainty and sensitivity analysis. We access the uncertainty of landslide susceptibility maps produced with GIS-MCDA techniques. A new spatially-explicit approach and Dempster–Shafer Theory (DST) are employed to assess the uncertainties associated with two MCDA techniques, namely Analytical Hierarchical Process (AHP) and Ordered Weighted Averaging (OWA) implemented in GIS. The methodology is composed of three different phases. First, weights are computed to express the relative importance of factors (criteria) for landslide susceptibility. Next, the uncertainty and sensitivity of landslide susceptibility is analyzed as a function of weights using Monte Carlo Simulation and Global Sensitivity Analysis. Finally, the results are validated using a landslide inventory database and by applying DST. The comparisons of the obtained landslide susceptibility maps of both MCDA techniques with known landslides show that the AHP outperforms OWA. However, the OWA-generated landslide susceptibility map shows lower uncertainty than the AHP-generated map. The results demonstrate that further improvement in the accuracy of GIS-based MCDA can be achieved by employing an integrated uncertainty–sensitivity analysis approach, in which the uncertainty of landslide susceptibility model is decomposed and attributed to model's criteria weights. PMID:25843987

Physical mapping of a pollen modifier locus controlling self-incompatibility in apricot and synteny analysis within the Rosaceae.

PubMed

Zuriaga, Elena; Molina, Laura; Badenes, María Luisa; Romero, Carlos

2012-06-01

S-locus products (S-RNase and F-box proteins) are essential for the gametophytic self-incompatibility (GSI) specific recognition in Prunus. However, accumulated genetic evidence suggests that other S-locus unlinked factors are also required for GSI. For instance, GSI breakdown was associated with a pollen-part mutation unlinked to the S-locus in the apricot (Prunus armeniaca L.) cv. 'Canino'. Fine-mapping of this mutated modifier gene (M-locus) and the synteny analysis of the M-locus within the Rosaceae are here reported. A segregation distortion loci mapping strategy, based on a selectively genotyped population, was used to map the M-locus. In addition, a bacterial artificial chromosome (BAC) contig was constructed for this region using overlapping oligonucleotides probes, and BAC-end sequences (BES) were blasted against Rosaceae genomes to perform micro-synteny analysis. The M-locus was mapped to the distal part of chr.3 flanked by two SSR markers within an interval of 1.8 cM corresponding to ~364 Kb in the peach (Prunus persica L. Batsch) genome. In the integrated genetic-physical map of this region, BES were mapped against the peach scaffold_3 and BACs were anchored to the apricot map. Micro-syntenic blocks were detected in apple (Malus × domestica Borkh.) LG17/9 and strawberry (Fragaria vesca L.) FG6 chromosomes. The M-locus fine-scale mapping provides a solid basis for self-compatibility marker-assisted selection and for positional cloning of the underlying gene, a necessary goal to elucidate the pollen rejection mechanism in Prunus. In a wider context, the syntenic regions identified in peach, apple and strawberry might be useful to interpret GSI evolution in Rosaceae.

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

PubMed

Chung, Dongjun; Kuan, Pei Fen; Li, Bo; Sanalkumar, Rajendran; Liang, Kun; Bresnick, Emery H; Dewey, Colin; Keleş, Sündüz

2011-07-01

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

PubMed Central

Chèneby, Jeanne; Gheorghe, Marius; Artufel, Marie

2018-01-01

Abstract With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as transcription factors, transcriptional co-activators and chromatin regulators. In 2015, we introduced the ReMap database to capture the genome regulatory space by integrating public ChIP-seq datasets, covering 237 TRs across 13 million (M) peaks. In this release, we have extended this catalog to constitute a unique collection of regulatory regions. Specifically, we have collected, analyzed and retained after quality control a total of 2829 ChIP-seq datasets available from public sources, covering a total of 485 TRs with a catalog of 80M peaks. Additionally, the updated database includes new search features for TR names as well as aliases, including cell line names and the ability to navigate the data directly within genome browsers via public track hubs. Finally, full access to this catalog is available online together with a TR binding enrichment analysis tool. ReMap 2018 provides a significant update of the ReMap database, providing an in depth view of the complexity of the regulatory landscape in human. PMID:29126285

Using Behavior Sequence Analysis to Map Serial Killers' Life Histories.

PubMed

Keatley, David A; Golightly, Hayley; Shephard, Rebecca; Yaksic, Enzo; Reid, Sasha

2018-03-01

The aim of the current research was to provide a novel method for mapping the developmental sequences of serial killers' life histories. An in-depth biographical account of serial killers' lives, from birth through to conviction, was gained and analyzed using Behavior Sequence Analysis. The analyses highlight similarities in behavioral events across the serial killers' lives, indicating not only which risk factors occur, but the temporal order of these factors. Results focused on early childhood environment, indicating the role of parental abuse; behaviors and events surrounding criminal histories of serial killers, showing that many had previous convictions and were known to police for other crimes; behaviors surrounding their murders, highlighting differences in victim choice and modus operandi; and, finally, trial pleas and convictions. The present research, therefore, provides a novel approach to synthesizing large volumes of data on criminals and presenting results in accessible, understandable outcomes.

Analysis of interstellar fragmentation structure based on IRAS images

NASA Technical Reports Server (NTRS)

Scalo, John M.

1989-01-01

The goal of this project was to develop new tools for the analysis of the structure of densely sampled maps of interstellar star-forming regions. A particular emphasis was on the recognition and characterization of nested hierarchical structure and fractal irregularity, and their relation to the level of star formation activity. The panoramic IRAS images provided data with the required range in spatial scale, greater than a factor of 100, and in column density, greater than a factor of 50. In order to construct a densely sampled column density map of a cloud complex which is both self-gravitating and not (yet?) stirred up much by star formation, a column density image of the Taurus region has been constructed from IRAS data. The primary drawback to using the IRAS data for this purpose is that it contains no velocity information, and the possible importance of projection effects must be kept in mind.

Selawik National Wildlife Refuge land cover mapping project users guide

USGS Publications Warehouse

Markon, Carl J.

1988-01-01

The U.S. Fish & Wildlife Service (USFWS) has the responsibility for collecting the resource information to address the research, management, development and planning requirements identified in Section 304. Because of the brief period provided by the Act for data collection, habitat mapping, and habitat assessment, the USFWS in cooperation with the U.S. Geological Survey's EROS Field Office, used digital Landsat multispectral scanner (MSS) data and digital terrain data to produce land cover and terrain maps. A computer assisted digital analysis of Landsat MSS data was used because coverage by aerial photographs was incomplete for the refuge and because the level of detail obtained from Landsat data was adequate to meet most USFWS research, management and planning needs. Relative cost and time requirements were also factors in the decision to use the digital analysis approach.

Yukon Flats National Wildlife Refuge land cover mapping project users guide

USGS Publications Warehouse

Markon, Carl J.

1987-01-01

The U. S. Fish & Wildlife Service (USFWS) has the responsibility for collecting the resource information to address the research, management, development and planning requirements identified in Section 304. Because of the brief period provided by the Act for data collection, habitat mapping, and habitat assessment, the USFWS in cooperation with the U.S. Geological Survey's EROS Field Office, used digital Landsat multispectral scanner (MSS) data and digital terrain data to produce land cover and terrain maps. A computer assisted digital analysis of Landsat MSS data was used because coverage by aerial photographs was incomplete for much of the refuge and because the level of detail obtained from Landsat data was adequate to meet most USFWS research, management and planning needs. Relative cost and time requirements were also factors in the decision to use the digital analysis approach.

Modeling Chinese ionospheric layer parameters based on EOF analysis

NASA Astrophysics Data System (ADS)

Yu, You; Wan, Weixing; Xiong, Bo; Ren, Zhipeng; Zhao, Biqiang; Zhang, Yun; Ning, Baiqi; Liu, Libo

2015-05-01

Using 24-ionosonde observations in and around China during the 20th solar cycle, an assimilative model is constructed to map the ionospheric layer parameters (foF2, hmF2, M(3000)F2, and foE) over China based on empirical orthogonal function (EOF) analysis. First, we decompose the background maps from the International Reference Ionosphere model 2007 (IRI-07) into different EOF modes. The obtained EOF modes consist of two factors: the EOF patterns and the corresponding EOF amplitudes. These two factors individually reflect the spatial distributions (e.g., the latitudinal dependence such as the equatorial ionization anomaly structure and the longitude structure with east-west difference) and temporal variations on different time scales (e.g., solar cycle, annual, semiannual, and diurnal variations) of the layer parameters. Then, the EOF patterns and long-term observations of ionosondes are assimilated to get the observed EOF amplitudes, which are further used to construct the Chinese Ionospheric Maps (CIMs) of the layer parameters. In contrast with the IRI-07 model, the mapped CIMs successfully capture the inherent temporal and spatial variations of the ionospheric layer parameters. Finally, comparison of the modeled (EOF and IRI-07 model) and observed values reveals that the EOF model reproduces the observation with smaller root-mean-square errors and higher linear correlation coefficients. In addition, IRI discrepancy at the low latitude especially for foF2 is effectively removed by EOF model.

Modeling Chinese ionospheric layer parameters based on EOF analysis

NASA Astrophysics Data System (ADS)

Yu, You; Wan, Weixing

2016-04-01

Using 24-ionosonde observations in and around China during the 20th solar cycle, an assimilative model is constructed to map the ionospheric layer parameters (foF2, hmF2, M(3000)F2, and foE) over China based on empirical orthogonal function (EOF) analysis. First, we decompose the background maps from the International Reference Ionosphere model 2007 (IRI-07) into different EOF modes. The obtained EOF modes consist of two factors: the EOF patterns and the corresponding EOF amplitudes. These two factors individually reflect the spatial distributions (e.g., the latitudinal dependence such as the equatorial ionization anomaly structure and the longitude structure with east-west difference) and temporal variations on different time scales (e.g., solar cycle, annual, semiannual, and diurnal variations) of the layer parameters. Then, the EOF patterns and long-term observations of ionosondes are assimilated to get the observed EOF amplitudes, which are further used to construct the Chinese Ionospheric Maps (CIMs) of the layer parameters. In contrast with the IRI-07 model, the mapped CIMs successfully capture the inherent temporal and spatial variations of the ionospheric layer parameters. Finally, comparison of the modeled (EOF and IRI-07 model) and observed values reveals that the EOF model reproduces the observation with smaller root-mean-square errors and higher linear correlation co- efficients. In addition, IRI discrepancy at the low latitude especially for foF2 is effectively removed by EOF model.

Global Mapping of Transcription Factor Binding Sites by Sequencing Chromatin Surrogates: a Perspective on Experimental Design, Data Analysis, and Open Problems.

PubMed

Wei, Yingying; Wu, George; Ji, Hongkai

2013-05-01

Mapping genome-wide binding sites of all transcription factors (TFs) in all biological contexts is a critical step toward understanding gene regulation. The state-of-the-art technologies for mapping transcription factor binding sites (TFBSs) couple chromatin immunoprecipitation (ChIP) with high-throughput sequencing (ChIP-seq) or tiling array hybridization (ChIP-chip). These technologies have limitations: they are low-throughput with respect to surveying many TFs. Recent advances in genome-wide chromatin profiling, including development of technologies such as DNase-seq, FAIRE-seq and ChIP-seq for histone modifications, make it possible to predict in vivo TFBSs by analyzing chromatin features at computationally determined DNA motif sites. This promising new approach may allow researchers to monitor the genome-wide binding sites of many TFs simultaneously. In this article, we discuss various experimental design and data analysis issues that arise when applying this approach. Through a systematic analysis of the data from the Encyclopedia Of DNA Elements (ENCODE) project, we compare the predictive power of individual and combinations of chromatin marks using supervised and unsupervised learning methods, and evaluate the value of integrating information from public ChIP and gene expression data. We also highlight the challenges and opportunities for developing novel analytical methods, such as resolving the one-motif-multiple-TF ambiguity and distinguishing functional and non-functional TF binding targets from the predicted binding sites. The online version of this article (doi:10.1007/s12561-012-9066-5) contains supplementary material, which is available to authorized users.

Appendix E: Research papers. Use of remote sensing in landscape stratification for environmental impact assessment

NASA Technical Reports Server (NTRS)

Stanturf, J. A.; Heimbuch, D. G.

1980-01-01

A refinement to the matrix approach to environmental impact assessment is to use landscape units in place of separate environmental elements in the analysis. Landscape units can be delineated by integrating remotely sensed data and available single-factor data. A remote sensing approach to landscape stratification is described and the conditions under which it is superior to other approaches that require single-factor maps are indicated. Flowcharts show the steps necessary to develop classification criteria, delineate units and a map legend, and use the landscape units in impact assessment. Application of the approach to assessing impacts of a transmission line in Montana is presented to illustrate the method.

[Medical and ecological assessment of climate effects on urolithiasis morbidity in population of Primorsky territory].

PubMed

Koval'chuk, V K

2004-01-01

The article presents medicoecological estimation of quantitative relations between monsoon climate and urolithiasis primary morbidity in the Primorsky Territory. Quantitative estimation of the climate was performed by V. I. Rusanov (1973) who calculated daily meteorological data for 1 p.m. throughout 1991-1999. Primary urolithiasis morbidity for this period of time was provided by regional health department. The data were processed by methods of medical mapping and paired correlation analysis. In the Territory, mapping revealed the same location of the zones with high frequency of discomfortable weather of class V and VI causing chilblain in positive air temperatures and zones with elevated primary urolithiasis morbidity in children and adults. Correlation analysis confirmed mapping results and determined significant negative correlations between frequency of relatively comfortable moment weather classes II-IV and morbidity of children and adults, positive correlation between frequency of discomfortable class VI and adult morbidity. Thus, high frequency of days per year with discomfortable classes of moment weather in low positive air temperatures may be one of the factors of urolithiasis risk in population of the Primorsky Territory. Climatic factors should be taken into consideration in planning primary prophylaxis of this disease in the Primorsky Territory.

Preliminary investigation of Large Format Camera photography utility in soil mapping and related agricultural applications

NASA Technical Reports Server (NTRS)

Pelletier, R. E.; Hudnall, W. H.

1987-01-01

The use of Space Shuttle Large Format Camera (LFC) color, IR/color, and B&W images in large-scale soil mapping is discussed and illustrated with sample photographs from STS 41-6 (October 1984). Consideration is given to the characteristics of the film types used; the photographic scales available; geometric and stereoscopic factors; and image interpretation and classification for soil-type mapping (detecting both sharp and gradual boundaries), soil parent material topographic and hydrologic assessment, natural-resources inventory, crop-type identification, and stress analysis. It is suggested that LFC photography can play an important role, filling the gap between aerial and satellite remote sensing.

Evaluation of four supervised learning methods for groundwater spring potential mapping in Khalkhal region (Iran) using GIS-based features

NASA Astrophysics Data System (ADS)

Naghibi, Seyed Amir; Moradi Dashtpagerdi, Mostafa

2017-01-01

One important tool for water resources management in arid and semi-arid areas is groundwater potential mapping. In this study, four data-mining models including K-nearest neighbor (KNN), linear discriminant analysis (LDA), multivariate adaptive regression splines (MARS), and quadric discriminant analysis (QDA) were used for groundwater potential mapping to get better and more accurate groundwater potential maps (GPMs). For this purpose, 14 groundwater influence factors were considered, such as altitude, slope angle, slope aspect, plan curvature, profile curvature, slope length, topographic wetness index (TWI), stream power index, distance from rivers, river density, distance from faults, fault density, land use, and lithology. From 842 springs in the study area, in the Khalkhal region of Iran, 70 % (589 springs) were considered for training and 30 % (253 springs) were used as a validation dataset. Then, KNN, LDA, MARS, and QDA models were applied in the R statistical software and the results were mapped as GPMs. Finally, the receiver operating characteristics (ROC) curve was implemented to evaluate the performance of the models. According to the results, the area under the curve of ROCs were calculated as 81.4, 80.5, 79.6, and 79.2 % for MARS, QDA, KNN, and LDA, respectively. So, it can be concluded that the performances of KNN and LDA were acceptable and the performances of MARS and QDA were excellent. Also, the results depicted high contribution of altitude, TWI, slope angle, and fault density, while plan curvature and land use were seen to be the least important factors.

Appalachian Basin Play Fairway Analysis: Thermal Quality Analysis in Low-Temperature Geothermal Play Fairway Analysis (GPFA-AB

DOE Data Explorer

Teresa E. Jordan

2015-11-15

This collection of files are part of a larger dataset uploaded in support of Low Temperature Geothermal Play Fairway Analysis for the Appalachian Basin (GPFA-AB, DOE Project DE-EE0006726). Phase 1 of the GPFA-AB project identified potential Geothermal Play Fairways within the Appalachian basin of Pennsylvania, West Virginia and New York. This was accomplished through analysis of 4 key criteria or ‘risks’: thermal quality, natural reservoir productivity, risk of seismicity, and heat utilization. Each of these analyses represent a distinct project task, with the fifth task encompassing combination of the 4 risks factors. Supporting data for all five tasks has been uploaded into the Geothermal Data Repository node of the National Geothermal Data System (NGDS). This submission comprises the data for Thermal Quality Analysis (project task 1) and includes all of the necessary shapefiles, rasters, datasets, code, and references to code repositories that were used to create the thermal resource and risk factor maps as part of the GPFA-AB project. The identified Geothermal Play Fairways are also provided with the larger dataset. Figures (.png) are provided as examples of the shapefiles and rasters. The regional standardized 1 square km grid used in the project is also provided as points (cell centers), polygons, and as a raster. Two ArcGIS toolboxes are available: 1) RegionalGridModels.tbx for creating resource and risk factor maps on the standardized grid, and 2) ThermalRiskFactorModels.tbx for use in making the thermal resource maps and cross sections. These toolboxes contain “item description” documentation for each model within the toolbox, and for the toolbox itself. This submission also contains three R scripts: 1) AddNewSeisFields.R to add seismic risk data to attribute tables of seismic risk, 2) StratifiedKrigingInterpolation.R for the interpolations used in the thermal resource analysis, and 3) LeaveOneOutCrossValidation.R for the cross validations used in the thermal interpolations. Some file descriptions make reference to various 'memos'. These are contained within the final report submitted October 16, 2015. Each zipped file in the submission contains an 'about' document describing the full Thermal Quality Analysis content available, along with key sources, authors, citation, use guidelines, and assumptions, with the specific file(s) contained within the .zip file highlighted.

Spatial diffusion of influenza outbreak-related climate factors in Chiang Mai Province, Thailand.

PubMed

Nakapan, Supachai; Tripathi, Nitin Kumar; Tipdecho, Taravudh; Souris, Marc

2012-10-24

Influenza is one of the most important leading causes of respiratory illness in the countries located in the tropical areas of South East Asia and Thailand. In this study the climate factors associated with influenza incidence in Chiang Mai Province, Northern Thailand, were investigated. Identification of factors responsible for influenza outbreaks and the mapping of potential risk areas in Chiang Mai are long overdue. This work examines the association between yearly climate patterns between 2001 and 2008 and influenza outbreaks in the Chiang Mai Province. The climatic factors included the amount of rainfall, percent of rainy days, relative humidity, maximum, minimum temperatures and temperature difference. The study develops a statistical analysis to quantitatively assess the relationship between climate and influenza outbreaks and then evaluate its suitability for predicting influenza outbreaks. A multiple linear regression technique was used to fit the statistical model. The Inverse Distance Weighted (IDW) interpolation and Geographic Information System (GIS) techniques were used in mapping the spatial diffusion of influenza risk zones. The results show that there is a significance correlation between influenza outbreaks and climate factors for the majority of the studied area. A statistical analysis was conducted to assess the validity of the model comparing model outputs and actual outbreaks.

Distortions in memory for visual displays

NASA Technical Reports Server (NTRS)

Tversky, Barbara

1989-01-01

Systematic errors in perception and memory present a challenge to theories of perception and memory and to applied psychologists interested in overcoming them as well. A number of systematic errors in memory for maps and graphs are reviewed, and they are accounted for by an analysis of the perceptual processing presumed to occur in comprehension of maps and graphs. Visual stimuli, like verbal stimuli, are organized in comprehension and memory. For visual stimuli, the organization is a consequence of perceptual processing, which is bottom-up or data-driven in its earlier stages, but top-down and affected by conceptual knowledge later on. Segregation of figure from ground is an early process, and figure recognition later; for both, symmetry is a rapidly detected and ecologically valid cue. Once isolated, figures are organized relative to one another and relative to a frame of reference. Both perceptual (e.g., salience) and conceptual factors (e.g., significance) seem likely to affect selection of a reference frame. Consistent with the analysis, subjects perceived and remembered curves in graphs and rivers in maps as more symmetric than they actually were. Symmetry, useful for detecting and recognizing figures, distorts map and graph figures alike. Top-down processes also seem to operate in that calling attention to the symmetry vs. asymmetry of a slightly asymmetric curve yielded memory errors in the direction of the description. Conceptual frame of reference effects were demonstrated in memory for lines embedded in graphs. In earlier work, the orientation of map figures was distorted in memory toward horizontal or vertical. In recent work, graph lines, but not map lines, were remembered as closer to an imaginary 45 deg line than they had been. Reference frames are determined by both perceptual and conceptual factors, leading to selection of the canonical axes as a reference frame in maps, but selection of the imaginary 45 deg as a reference frame in graphs.

Dairy farms testing positive for Mycobacterium avium ssp. paratuberculosis have poorer hygiene practices and are less cautious when purchasing cattle than test-negative herds.

PubMed

Wolf, R; Barkema, H W; De Buck, J; Orsel, K

2016-06-01

Mycobacterium avium ssp. paratuberculosis (MAP), the causative agent of Johne's disease, is present on most dairy farms in Alberta, causing economic losses and presenting a potential public health concern. The objective of this cross-sectional study was to identify risk factors for Alberta dairy herds being MAP-positive based on environmental samples (ES). Risk assessments were conducted and ES were collected on 354 Alberta dairy farms (62% of eligible producers) voluntarily participating in the Alberta Johne's Disease Initiative. In univariate logistic regression, risk factors addressing animal and pen hygiene, as well as the use of feeding equipment to remove manure and manure application on pastures, were all associated with the number of positive ES. Furthermore, based on factor analysis, risk factors were clustered and could be summarized as 4 independent factors: (1) animal, pen, and feeder contamination; (2) shared equipment and pasture contamination; (3) calf diet; and (4) cattle purchase. Using these factor scores as independent variables in multivariate logistic regression models, a 1-unit increase in animal, pen, and feeder contamination resulted in 1.31 times higher odds of having at least 1 positive ES. Furthermore, a 1-unit increase in cattle purchase also resulted in 1.31 times the odds of having at least 1 positive ES. Finally, a 100-cow increase in herd size resulted in an odds ratio of 2.1 for having at least 1 positive ES. In conclusion, cleanliness of animals, pens, and feeders, as well as cattle purchase practices, affected risk of herd infection with MAP. Therefore, improvements in those management practices should be the focus of effective tools to control MAP on dairy farms. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Predicting a roadkill hotspots based on spatial distribution of Korean water deer (Hydropotes inermis argyropus) using Maxent model in South Korea Expressway : In Case of Cheongju-Sangju Expressway

NASA Astrophysics Data System (ADS)

Park, Hyomin; Lee, Sangdon

2016-04-01

Road construction has direct and indirect effects on ecosystems. Especially wildlife-vehicle conflicts (roadkills) caused by roads are a considerable threat for population of many species. This study aims to identify the effects of topographic characteristics and spatial distribution of Korean water deer (Hydropotes inermis). Korean water deer is indigenous and native species in Korea that listed LC (least concern) by IUCN redlist categories. Korean water deer population is growing every year occupying for most of roadkills (>70%) in Korean express highway. In order to predict a distribution of the Korean water deer, we selected factors that most affected water deer's habitat. Major habitats of waterdeer are known as agricultural area, forest area and water. Based on this result, eight factors were selected (land cover map, vegetation map, age class of forest, diameter class of tree, population, slope of study site, elevation of study site, distance of river), and made a thematic map by using GIS program (ESRI, Arc GIS 10.3.1 ver.). To analyze the affected factors of waterdeer distribution, GPS data and thematic map of study area were entered into Maxent model (Maxent 3.3.3.k.). Results of analysis were verified by the AUC (Area Unit Curve) of ROC (Receiver Operating Characteristic). The ROC curve used the sensitivity and specificity as a reference for determining the prediction efficiency of the model and AUC area of ROC curve was higher prediction efficiency closer to '1.' Selecting factors that affected the distribution of waterdeer were land cover map, diameter class of tree and elevation of study site. The value of AUC was 0.623. To predict the water deer's roadkills hot spot on Cheongju-Sangju Expressway, the thematic map was prepared based on GPS data of roadkill spots. As a result, the topographic factors that affected waterdeer roadkill were land cover map, actual vegetation map and age class of forest and the value of AUC was 0.854. Through this study, we could identify the site and hot spots that water deer frequently expected to use based on quantitative data on the spatial and topographic factors. Therefore, we can suggest ways to minimize roadkills by selecting the hot spots and by suggesting construction of eco-corridors. This study will significantly enhance human-wildlife conflicts by identifying key habitat areas for wild mammals.

Sensitivity of thermal inertia calculations to variations in environmental factors. [in mapping of Earth's surface by remote sensing

NASA Technical Reports Server (NTRS)

Kahle, A. B.; Alley, R. E.; Schieldge, J. P.

1984-01-01

The sensitivity of thermal inertia (TI) calculations to errors in the measurement or parameterization of a number of environmental factors is considered here. The factors include effects of radiative transfer in the atmosphere, surface albedo and emissivity, variations in surface turbulent heat flux density, cloud cover, vegetative cover, and topography. The error analysis is based upon data from the Heat Capacity Mapping Mission (HCMM) satellite for July 1978 at three separate test sites in the deserts of the western United States. Results show that typical errors in atmospheric radiative transfer, cloud cover, and vegetative cover can individually cause root-mean-square (RMS) errors of about 10 percent (with atmospheric effects sometimes as large as 30-40 percent) in HCMM-derived thermal inertia images of 20,000-200,000 pixels.

The use of crop rotation for mapping soil organic content in farmland

NASA Astrophysics Data System (ADS)

Yang, Lin; Song, Min; Zhu, A.-Xing; Qin, Chengzhi

2017-04-01

Most of the current digital soil mapping uses natural environmental covariates. However, human activities have significantly impacted the development of soil properties since half a century, and therefore become an important factor affecting soil spatial variability. Many researches have done field experiments to show how soil properties are impacted and changed by human activities, however, spatial variation data of human activities as environmental covariates have been rarely used in digital soil mapping. In this paper, we took crop rotation as an example of agricultural activities, and explored its effectiveness in characterizing and mapping the spatial variability of soil. The cultivated area of Xuanzhou city and Langxi County in Anhui Province was chosen as the study area. Three main crop rotations,including double-rice, wheat-rice,and oilseed rape-cotton were observed through field investigation in 2010. The spatial distribution of the three crop rotations in the study area was obtained by multi-phase remote sensing image interpretation using a supervised classification method. One-way analysis of variance (ANOVA) for topsoil organic content in the three crop rotation groups was performed. Factor importance of seven natural environmental covariates, crop rotation, Land use and NDVI were generated by variable importance criterion of Random Forest. Different combinations of environmental covariates were selected according to the importance rankings of environmental covariates for predicting SOC using Random Forest and Soil Landscape Inference Model (SOLIM). A cross validation was generated to evaluated the mapping accuracies. The results showed that there were siginificant differences of topsoil organic content among the three crop rotation groups. The crop rotation is more important than parent material, land use or NDVI according to the importance ranking calculated by Random Forest. In addition, crop rotation improved the mapping accuracy, especially for the flat clutivated area. This study demonstrates the usefulness of human activities in digital soil mapping and thus indicates the necessity for human activity factors in digital soil mapping studies.

Development of spatial density maps based on geoprocessing web services: application to tuberculosis incidence in Barcelona, Spain.

PubMed

Dominkovics, Pau; Granell, Carlos; Pérez-Navarro, Antoni; Casals, Martí; Orcau, Angels; Caylà, Joan A

2011-11-29

Health professionals and authorities strive to cope with heterogeneous data, services, and statistical models to support decision making on public health. Sophisticated analysis and distributed processing capabilities over geocoded epidemiological data are seen as driving factors to speed up control and decision making in these health risk situations. In this context, recent Web technologies and standards-based web services deployed on geospatial information infrastructures have rapidly become an efficient way to access, share, process, and visualize geocoded health-related information. Data used on this study is based on Tuberculosis (TB) cases registered in Barcelona city during 2009. Residential addresses are geocoded and loaded into a spatial database that acts as a backend database. The web-based application architecture and geoprocessing web services are designed according to the Representational State Transfer (REST) principles. These web processing services produce spatial density maps against the backend database. The results are focused on the use of the proposed web-based application to the analysis of TB cases in Barcelona. The application produces spatial density maps to ease the monitoring and decision making process by health professionals. We also include a discussion of how spatial density maps may be useful for health practitioners in such contexts. In this paper, we developed web-based client application and a set of geoprocessing web services to support specific health-spatial requirements. Spatial density maps of TB incidence were generated to help health professionals in analysis and decision-making tasks. The combined use of geographic information tools, map viewers, and geoprocessing services leads to interesting possibilities in handling health data in a spatial manner. In particular, the use of spatial density maps has been effective to identify the most affected areas and its spatial impact. This study is an attempt to demonstrate how web processing services together with web-based mapping capabilities suit the needs of health practitioners in epidemiological analysis scenarios.

Participatory Development and Analysis of a Fuzzy Cognitive Map of the Establishment of a Bio-Based Economy in the Humber Region

PubMed Central

Penn, Alexandra S.; Knight, Christopher J. K.; Lloyd, David J. B.; Avitabile, Daniele; Kok, Kasper; Schiller, Frank; Woodward, Amy; Druckman, Angela; Basson, Lauren

2013-01-01

Fuzzy Cognitive Mapping (FCM) is a widely used participatory modelling methodology in which stakeholders collaboratively develop a ‘cognitive map’ (a weighted, directed graph), representing the perceived causal structure of their system. This can be directly transformed by a workshop facilitator into simple mathematical models to be interrogated by participants by the end of the session. Such simple models provide thinking tools which can be used for discussion and exploration of complex issues, as well as sense checking the implications of suggested causal links. They increase stakeholder motivation and understanding of whole systems approaches, but cannot be separated from an intersubjective participatory context. Standard FCM methodologies make simplifying assumptions, which may strongly influence results, presenting particular challenges and opportunities. We report on a participatory process, involving local companies and organisations, focussing on the development of a bio-based economy in the Humber region. The initial cognitive map generated consisted of factors considered key for the development of the regional bio-based economy and their directional, weighted, causal interconnections. A verification and scenario generation procedure, to check the structure of the map and suggest modifications, was carried out with a second session. Participants agreed on updates to the original map and described two alternate potential causal structures. In a novel analysis all map structures were tested using two standard methodologies usually used independently: linear and sigmoidal FCMs, demonstrating some significantly different results alongside some broad similarities. We suggest a development of FCM methodology involving a sensitivity analysis with different mappings and discuss the use of this technique in the context of our case study. Using the results and analysis of our process, we discuss the limitations and benefits of the FCM methodology in this case and in general. We conclude by proposing an extended FCM methodology, including multiple functional mappings within one participant-constructed graph. PMID:24244303

Development of spatial density maps based on geoprocessing web services: application to tuberculosis incidence in Barcelona, Spain

PubMed Central

2011-01-01

Background Health professionals and authorities strive to cope with heterogeneous data, services, and statistical models to support decision making on public health. Sophisticated analysis and distributed processing capabilities over geocoded epidemiological data are seen as driving factors to speed up control and decision making in these health risk situations. In this context, recent Web technologies and standards-based web services deployed on geospatial information infrastructures have rapidly become an efficient way to access, share, process, and visualize geocoded health-related information. Methods Data used on this study is based on Tuberculosis (TB) cases registered in Barcelona city during 2009. Residential addresses are geocoded and loaded into a spatial database that acts as a backend database. The web-based application architecture and geoprocessing web services are designed according to the Representational State Transfer (REST) principles. These web processing services produce spatial density maps against the backend database. Results The results are focused on the use of the proposed web-based application to the analysis of TB cases in Barcelona. The application produces spatial density maps to ease the monitoring and decision making process by health professionals. We also include a discussion of how spatial density maps may be useful for health practitioners in such contexts. Conclusions In this paper, we developed web-based client application and a set of geoprocessing web services to support specific health-spatial requirements. Spatial density maps of TB incidence were generated to help health professionals in analysis and decision-making tasks. The combined use of geographic information tools, map viewers, and geoprocessing services leads to interesting possibilities in handling health data in a spatial manner. In particular, the use of spatial density maps has been effective to identify the most affected areas and its spatial impact. This study is an attempt to demonstrate how web processing services together with web-based mapping capabilities suit the needs of health practitioners in epidemiological analysis scenarios. PMID:22126392

Use of Satellite Remote Sensing Data in the Mapping of Global Landslide Susceptibility

NASA Technical Reports Server (NTRS)

Hong, Yang; Adler, Robert F.; Huffman, George J.

2007-01-01

Satellite remote sensing data has significant potential use in analysis of natural hazards such as landslides. Relying on the recent advances in satellite remote sensing and geographic information system (GIS) techniques, this paper aims to map landslide susceptibility over most of the globe using a GIs-based weighted linear combination method. First , six relevant landslide-controlling factors are derived from geospatial remote sensing data and coded into a GIS system. Next, continuous susceptibility values from low to high are assigned to each of the six factors. Second, a continuous scale of a global landslide susceptibility index is derived using GIS weighted linear combination based on each factor's relative significance to the process of landslide occurrence (e.g., slope is the most important factor, soil types and soil texture are also primary-level parameters, while elevation, land cover types, and drainage density are secondary in importance). Finally, the continuous index map is further classified into six susceptibility categories. Results show the hot spots of landslide-prone regions include the Pacific Rim, the Himalayas and South Asia, Rocky Mountains, Appalachian Mountains, Alps, and parts of the Middle East and Africa. India, China, Nepal, Japan, the USA, and Peru are shown to have landslide-prone areas. This first-cut global landslide susceptibility map forms a starting point to provide a global view of landslide risks and may be used in conjunction with satellite-based precipitation information to potentially detect areas with significant landslide potential due to heavy rainfall. 1

Differentiating the Spatiotemporal Distribution of Natural and Anthropogenic Processes on River Water-Quality Variation Using a Self-Organizing Map With Factor Analysis.

PubMed

Wang, Yeuh-Bin; Liu, Chen-Wuing; Lee, Jin-Jing

2015-08-01

To elucidate the historical improvement and advanced measure of river water quality in the Taipei metropolitan area, this study applied the self-organizing map (SOM) technique with factor analysis (FA) to differentiate the spatiotemporal distribution of natural and anthropogenic processes on river water-quality variation spanning two decades. The SOM clustered river water quality into five groups: very low pollution, low pollution, moderate pollution, high pollution, and very high pollution. FA was then used to extract four latent factors that dominated water quality from 1991 to 2011 including three anthropogenic process factors (organic, industrial, and copper pollution) and one natural process factor [suspended solids (SS) pollution]. The SOM revealed that the water quality improved substantially over time. However, the downstream river water quality was still classified as high pollution because of an increase in anthropogenic activity. FA showed the spatiotemporal pattern of each factor score decreasing over time, but the organic pollution factor downstream of the Tamsui River, as well as the SS factor scores in the upstream major tributary (the Dahan Stream), remained within the high pollution level. Therefore, we suggest that public sewage-treatment plants should be upgraded from their current secondary biological processing to advanced treatment processing. The conservation of water and soil must also be reinforced to decrease the SS loading of the Dahan Stream from natural erosion processes in the future.

Mapping ash properties using principal components analysis

NASA Astrophysics Data System (ADS)

Pereira, Paulo; Brevik, Eric; Cerda, Artemi; Ubeda, Xavier; Novara, Agata; Francos, Marcos; Rodrigo-Comino, Jesus; Bogunovic, Igor; Khaledian, Yones

2017-04-01

In post-fire environments ash has important benefits for soils, such as protection and source of nutrients, crucial for vegetation recuperation (Jordan et al., 2016; Pereira et al., 2015a; 2016a,b). The thickness and distribution of ash are fundamental aspects for soil protection (Cerdà and Doerr, 2008; Pereira et al., 2015b) and the severity at which was produced is important for the type and amount of elements that is released in soil solution (Bodi et al., 2014). Ash is very mobile material, and it is important were it will be deposited. Until the first rainfalls are is very mobile. After it, bind in the soil surface and is harder to erode. Mapping ash properties in the immediate period after fire is complex, since it is constantly moving (Pereira et al., 2015b). However, is an important task, since according the amount and type of ash produced we can identify the degree of soil protection and the nutrients that will be dissolved. The objective of this work is to apply to map ash properties (CaCO3, pH, and select extractable elements) using a principal component analysis (PCA) in the immediate period after the fire. Four days after the fire we established a grid in a 9x27 m area and took ash samples every 3 meters for a total of 40 sampling points (Pereira et al., 2017). The PCA identified 5 different factors. Factor 1 identified high loadings in electrical conductivity, calcium, and magnesium and negative with aluminum and iron, while Factor 3 had high positive loadings in total phosphorous and silica. Factor 3 showed high positive loadings in sodium and potassium, factor 4 high negative loadings in CaCO3 and pH, and factor 5 high loadings in sodium and potassium. The experimental variograms of the extracted factors showed that the Gaussian model was the most precise to model factor 1, the linear to model factor 2 and the wave hole effect to model factor 3, 4 and 5. The maps produced confirm the patternd observed in the experimental variograms. Factor 1 and 2 maps showed high values in one area of the plot, while factors 3,4 and 5 had a cycled pattern. Using a PCA we resume the information of all dataset and we identify that ash properties have a different distribution in the studied area, that may be attributed to the different fire severities. References Bodi, M., Martin, D.A., Santin, C., Balfour, V., Doerr, S.H., Pereira, P., Cerda, A., Mataix-Solera, J. (2014) Wildland fire ash: production, composition and eco-hydro-geomorphic effects. Earth-Science Reviews, 130, 103-127. Cerdà A, Doerr SH. (2008) The effect of ash and needle cover on surface runoff and erosion in the immediate post-fire period. Catena 74, 256-263. Jordan, A., Zavala, L., Granjed, A.J., Gordillo-Rivero, A.J., Garcia-Moreno, J., Pereira, P., Barcenas-Moreno, G., Celis, R., Jimenez-Compan, E., Alanis, N. Wettability of ash conditions splash erosion and runoff rates in the postfire. Science of the Total Environment, 572, 1261-1268. Pereira, P. Cerdà, A., Úbeda, X., Mataix-Solera, J. Arcenegui, V., Zavala, L. (2015b) Modelling the impacts of wildfire on ash thickness in a short-term period. Land Degradation and Development, 26, 180-192. Pereira, P., Brevik, E., Cerda, A., Ubeda, X., Novara, A., Francos, M., Comino, R., Bogunovic, I., Khaledian, Y. Mapping ash extractable elements using principal component analysis In: Pereira, P., Brevik, E., Munoz-Rojas, M., Miller, B. (eds) Soil mapping and process modelling for sustainable land use management (Elsevier Publishing House) ISBN: 9780128052006 Pereira, P., Cerdà, A., Jordan, A., Zavala, L., Mataix-Solera, J., Arcenegui, V., Misiune, I., Keesstra, S., Novara, A. (2016) Vegetation recovery after a grassland fire in Lithuania. The effects of fire severity, slope position and aspect. Land Degradation and Development, 27, 1523-1534. Pereira, P., Rein, G., Martin, D. Editorial: Past and Present Post-Fire Environments. Science of the Total Environment, 573, 442-436. Pereira, P., Jordan, A., Cerdà, A., Martin, D. Editorial: The role of ash in fire-affected ecosystems. Catena, 135, 337-379.

Capturing multidimensionality in stroke aphasia: mapping principal behavioural components to neural structures

PubMed Central

Butler, Rebecca A.

2014-01-01

Stroke aphasia is a multidimensional disorder in which patient profiles reflect variation along multiple behavioural continua. We present a novel approach to separating the principal aspects of chronic aphasic performance and isolating their neural bases. Principal components analysis was used to extract core factors underlying performance of 31 participants with chronic stroke aphasia on a large, detailed battery of behavioural assessments. The rotated principle components analysis revealed three key factors, which we labelled as phonology, semantic and executive/cognition on the basis of the common elements in the tests that loaded most strongly on each component. The phonology factor explained the most variance, followed by the semantic factor and then the executive-cognition factor. The use of principle components analysis rendered participants’ scores on these three factors orthogonal and therefore ideal for use as simultaneous continuous predictors in a voxel-based correlational methodology analysis of high resolution structural scans. Phonological processing ability was uniquely related to left posterior perisylvian regions including Heschl’s gyrus, posterior middle and superior temporal gyri and superior temporal sulcus, as well as the white matter underlying the posterior superior temporal gyrus. The semantic factor was uniquely related to left anterior middle temporal gyrus and the underlying temporal stem. The executive-cognition factor was not correlated selectively with the structural integrity of any particular region, as might be expected in light of the widely-distributed and multi-functional nature of the regions that support executive functions. The identified phonological and semantic areas align well with those highlighted by other methodologies such as functional neuroimaging and neurostimulation. The use of principle components analysis allowed us to characterize the neural bases of participants’ behavioural performance more robustly and selectively than the use of raw assessment scores or diagnostic classifications because principle components analysis extracts statistically unique, orthogonal behavioural components of interest. As such, in addition to improving our understanding of lesion–symptom mapping in stroke aphasia, the same approach could be used to clarify brain–behaviour relationships in other neurological disorders. PMID:25348632

Analysis of regolith electromagnetic scattering as constrained by high resolution Earth-based measurements of the lunar microwave emission

NASA Technical Reports Server (NTRS)

Keihm, S. J.

1983-01-01

When high resolution measurements of the phase variation of the lunar disk center brightness temperature revealed that in situ regolith electrical losses were larger than those measured on returned samples by a factor of 1.5 to 2.0 at centimeter wavelengths, the need for a refinement of the regolith model to include realistic treatment of scattering effects was identified. Two distinct scattering regimes are considered: vertial variations in dielectric constant and volume scattering due to subsurface rock fragments. Models of lunar regolith energy transport processes are now at the state for which a maximum scientific return could be realized from a lunar orbiter microwave mapping experiment. A detailed analysis, including the effects of scattering produced a set of nominal brightness temperature spectra for lunar equatorial regions, which can be used for mapping as a calibration reference for mapping variations in mineralogy and heat flow.

US Topo: topographic maps for the nation

USGS Publications Warehouse

Carswell, William J.

2013-01-01

US Topo is the next generation of topographic maps from the U.S. Geological Survey (USGS). Arranged in the familiar 7.5-minute quadrangle format, digital US Topo maps are designed to look and feel (and perform) like the traditional paper topographic maps for which the USGS is so well known. In contrast to paper-based maps, US Topo maps provide modern technical advantages that support faster, wider public distribution and enable basic, on-screen geographic analysis for all users. The US Topo quadrangle map has been redesigned so that map elements are visually distinguishable with the imagery turned on and off, while keeping the file size as small as possible. The US Topo map redesign includes improvements to various display factors, including symbol definitions (color, line thickness, line symbology, area fills), layer order, and annotation fonts. New features for 2013 include the following: a raster shaded relief layer, military boundaries, cemeteries and post offices, and a US Topo cartographic symbols legend as an attachment. US Topo quadrangle maps are available free on the Web. Each map quadrangle is constructed in GeoPDF® format using key layers of geographic data (orthoimagery, roads, geographic names, topographic contours, and hydrographic features) from The National Map databases. US Topo quadrangle maps can be printed from personal computers or plotters as complete, full-sized, maps or in customized sections, in a user-desired specific format. Paper copies of the maps can also be purchased from the USGS Store. Download links and a users guide are featured on the US Topo Web site. US Topo users can turn geographic data layers on and off as needed; they can zoom in and out to highlight specific features or see a broader area. File size for each digital 7.5-minute quadrangle, about 30 megabytes. Associated electronic tools for geographic analysis are available free for download. The US Topo provides the Nation with a topographic product that users can quickly incorporate into decisionmaking, operational or recreational activities.

The relationship between phonological short-term memory, receptive vocabulary, and fast mapping in children with specific language impairment.

PubMed

Jackson, Emily; Leitao, Suze; Claessen, Mary

2016-01-01

Children with specific language impairment (SLI) often experience word-learning difficulties, which are suggested to originate in the early stage of word learning: fast mapping. Some previous research indicates significantly poorer fast mapping capabilities in children with SLI compared with typically developing (TD) counterparts, with a range of methodological factors impacting on the consistency of this finding. Research has explored key issues that might underlie fast mapping difficulties in children with SLI, with strong theoretical support but little empirical evidence for the role of phonological short-term memory (STM). Additionally, further research is required to explore the influence of receptive vocabulary on fast mapping capabilities. Understanding the factors associated with fast mapping difficulties that are experienced by children with SLI may lead to greater theoretically driven word-learning intervention. To investigate whether children with SLI demonstrate significant difficulties with fast mapping, and to explore the related factors. It was hypothesized that children with SLI would score significantly lower on a fast mapping production task compared with TD children, and that phonological STM and receptive vocabulary would significantly predict fast mapping production scores in both groups of children. Twenty-three children with SLI (mean = 64.39 months, SD = 4.10 months) and 26 TD children (mean = 65.92 months, SD = 2.98) were recruited from specialist language and mainstream schools. All participants took part in a unique, interactive fast-mapping task whereby nine novel objects with non-word labels were presented and production accuracy was assessed. A non-word repetition test and the Peabody Picture Vocabulary Test-Fourth Edition (PPVT-IV) were also administered as measures of phonological STM capacity and receptive vocabulary, respectively. Results of the fast-mapping task indicated that children with SLI had significantly poorer fast mapping production scores than TD children. Scores from the non-word repetition task were also significantly lower for the SLI group, revealing reduced phonological STM capacity. Phonological STM capacity and receptive vocabulary emerged as significant predictors of fast mapping performance when the group data were combined in a multiple regression analysis. These results suggest that the word-learning difficulties experienced by children with SLI may originate at the fast mapping stage, and that phonological STM and receptive vocabulary significantly predict fast mapping ability. These findings contribute to the theoretical understanding of word-learning difficulties in children with SLI and may inform lexical learning intervention. © 2015 Royal College of Speech and Language Therapists.

A Model for the Description, Analysis, and Perhaps Evaluation of Bilingual Education. Navajo Reading Study Progress Report No. 23.

ERIC Educational Resources Information Center

Spolsky, Bernard; And Others

The model attempts to map all relevant factors onto a single integrated structure and to suggest some of the interaction lines. Based on a hexagonal figure, each side represents a set of factors which may have a bearing on, or be affected by, the bilingual program's operation in a particular situation--psychological, sociological, economic,…

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.

PubMed

Chèneby, Jeanne; Gheorghe, Marius; Artufel, Marie; Mathelier, Anthony; Ballester, Benoit

2018-01-04

With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as transcription factors, transcriptional co-activators and chromatin regulators. In 2015, we introduced the ReMap database to capture the genome regulatory space by integrating public ChIP-seq datasets, covering 237 TRs across 13 million (M) peaks. In this release, we have extended this catalog to constitute a unique collection of regulatory regions. Specifically, we have collected, analyzed and retained after quality control a total of 2829 ChIP-seq datasets available from public sources, covering a total of 485 TRs with a catalog of 80M peaks. Additionally, the updated database includes new search features for TR names as well as aliases, including cell line names and the ability to navigate the data directly within genome browsers via public track hubs. Finally, full access to this catalog is available online together with a TR binding enrichment analysis tool. ReMap 2018 provides a significant update of the ReMap database, providing an in depth view of the complexity of the regulatory landscape in human. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Analysis of interstellar cloud structure based on IRAS images

NASA Technical Reports Server (NTRS)

Scalo, John M.

1992-01-01

The goal of this project was to develop new tools for the analysis of the structure of densely sampled maps of interstellar star-forming regions. A particular emphasis was on the recognition and characterization of nested hierarchical structure and fractal irregularity, and their relation to the level of star formation activity. The panoramic IRAS images provided data with the required range in spatial scale, greater than a factor of 100, and in column density, greater than a factor of 50. In order to construct densely sampled column density maps of star-forming clouds, column density images of four nearby cloud complexes were constructed from IRAS data. The regions have various degrees of star formation activity, and most of them have probably not been affected much by the disruptive effects of young massive stars. The largest region, the Scorpius-Ophiuchus cloud complex, covers about 1000 square degrees (it was subdivided into a few smaller regions for analysis). Much of the work during the early part of the project focused on an 80 square degree region in the core of the Taurus complex, a well-studied region of low-mass star formation.

Cross-correlating 2D and 3D galaxy surveys

DOE PAGES

Passaglia, Samuel; Manzotti, Alessandro; Dodelson, Scott

2017-06-08

Galaxy surveys probe both structure formation and the expansion rate, making them promising avenues for understanding the dark universe. Photometric surveys accurately map the 2D distribution of galaxy positions and shapes in a given redshift range, while spectroscopic surveys provide sparser 3D maps of the galaxy distribution. We present a way to analyse overlapping 2D and 3D maps jointly and without loss of information. We represent 3D maps using spherical Fourier-Bessel (sFB) modes, which preserve radial coverage while accounting for the spherical sky geometry, and we decompose 2D maps in a spherical harmonic basis. In these bases, a simple expression exists for the cross-correlation of the two fields. One very powerful application is the ability to simultaneously constrain the redshift distribution of the photometric sample, the sample biases, and cosmological parameters. We use our framework to show that combined analysis of DESI and LSST can improve cosmological constraints by factors ofmore » $${\\sim}1.2$$ to $${\\sim}1.8$$ on the region where they overlap relative to identically sized disjoint regions. We also show that in the overlap of DES and SDSS-III in Stripe 82, cross-correlating improves photo-$z$ parameter constraints by factors of $${\\sim}2$$ to $${\\sim}12$$ over internal photo-$z$ reconstructions.« less

Cross-correlating 2D and 3D galaxy surveys

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

Passaglia, Samuel; Manzotti, Alessandro; Dodelson, Scott

Galaxy surveys probe both structure formation and the expansion rate, making them promising avenues for understanding the dark universe. Photometric surveys accurately map the 2D distribution of galaxy positions and shapes in a given redshift range, while spectroscopic surveys provide sparser 3D maps of the galaxy distribution. We present a way to analyse overlapping 2D and 3D maps jointly and without loss of information. We represent 3D maps using spherical Fourier-Bessel (sFB) modes, which preserve radial coverage while accounting for the spherical sky geometry, and we decompose 2D maps in a spherical harmonic basis. In these bases, a simple expression exists for the cross-correlation of the two fields. One very powerful application is the ability to simultaneously constrain the redshift distribution of the photometric sample, the sample biases, and cosmological parameters. We use our framework to show that combined analysis of DESI and LSST can improve cosmological constraints by factors ofmore » $${\\sim}1.2$$ to $${\\sim}1.8$$ on the region where they overlap relative to identically sized disjoint regions. We also show that in the overlap of DES and SDSS-III in Stripe 82, cross-correlating improves photo-$z$ parameter constraints by factors of $${\\sim}2$$ to $${\\sim}12$$ over internal photo-$z$ reconstructions.« less

Concept mapping as an approach for expert-guided model building: The example of health literacy.

PubMed

Soellner, Renate; Lenartz, Norbert; Rudinger, Georg

2017-02-01

Concept mapping served as the starting point for the aim of capturing the comprehensive structure of the construct of 'health literacy.' Ideas about health literacy were generated by 99 experts and resulted in 105 statements that were subsequently organized by 27 experts in an unstructured card sorting. Multidimensional scaling was applied to the sorting data and a two and three-dimensional solution was computed. The three dimensional solution was used in subsequent cluster analysis and resulted in a concept map of nine "clusters": (1) self-regulation, (2) self-perception, (3) proactive approach to health, (4) basic literacy and numeracy skills, (5) information appraisal, (6) information search, (7) health care system knowledge and acting, (8) communication and cooperation, and (9) beneficial personality traits. Subsequently, this concept map served as a starting point for developing a "qualitative" structural model of health literacy and a questionnaire for the measurement of health literacy. On the basis of questionnaire data, a "quantitative" structural model was created by first applying exploratory factor analyses (EFA) and then cross-validating the model with confirmatory factor analyses (CFA). Concept mapping proved to be a highly valuable tool for the process of model building up to translational research in the "real world". Copyright © 2016 Elsevier Ltd. All rights reserved.

Initial deployment of the cardiogenic gene regulatory network in the basal chordate, Ciona intestinalis.

PubMed

Woznica, Arielle; Haeussler, Maximilian; Starobinska, Ella; Jemmett, Jessica; Li, Younan; Mount, David; Davidson, Brad

2012-08-01

The complex, partially redundant gene regulatory architecture underlying vertebrate heart formation has been difficult to characterize. Here, we dissect the primary cardiac gene regulatory network in the invertebrate chordate, Ciona intestinalis. The Ciona heart progenitor lineage is first specified by Fibroblast Growth Factor/Map Kinase (FGF/MapK) activation of the transcription factor Ets1/2 (Ets). Through microarray analysis of sorted heart progenitor cells, we identified the complete set of primary genes upregulated by FGF/Ets shortly after heart progenitor emergence. Combinatorial sequence analysis of these co-regulated genes generated a hypothetical regulatory code consisting of Ets binding sites associated with a specific co-motif, ATTA. Through extensive reporter analysis, we confirmed the functional importance of the ATTA co-motif in primary heart progenitor gene regulation. We then used the Ets/ATTA combination motif to successfully predict a number of additional heart progenitor gene regulatory elements, including an intronic element driving expression of the core conserved cardiac transcription factor, GATAa. This work significantly advances our understanding of the Ciona heart gene network. Furthermore, this work has begun to elucidate the precise regulatory architecture underlying the conserved, primary role of FGF/Ets in chordate heart lineage specification. Copyright © 2012 Elsevier Inc. All rights reserved.

Application of Dempster-Shafer theory, spatial analysis and remote sensing for groundwater potentiality and nitrate pollution analysis in the semi-arid region of Khuzestan, Iran.

PubMed

Rahmati, Omid; Melesse, Assefa M

2016-10-15

Effective management and sustainable development of groundwater resources of arid and semi-arid environments require monitoring of groundwater quality and quantity. The aim of this paper is to develop a reasonable methodological framework for producing the suitability map for drinking water through the geographic information system, remote sensing and field surveys of the Andimeshk-Dezful, Khozestan province, Iran as a semi-arid region. This study investigated the delineation of groundwater potential zone based on Dempster-Shafer (DS) theory of evidence and evaluate its applicability for groundwater potentiality mapping. The study also analyzed the spatial distribution of groundwater nitrate concentration; and produced the suitability map for drinking water. The study has been carried out with the following steps: i) creation of maps of groundwater conditioning factors; ii) assessment of groundwater occurrence characteristics; iii) creation of groundwater potentiality map (GPM) and model validation; iv) collection and chemical analysis of water samples; v) assessment of groundwater nitrate pollution; and vi) creation of groundwater potentiality and quality map. The performance of the DS was also evaluated using the receiver operating characteristic (ROC) curve method and pumping test data to ensure its generalization ability, which eventually, the GPM showed 87.76% accuracy. The detailed analysis of groundwater potentiality and quality revealed that the 'non acceptable' areas covers an area of about 1479km(2) (60%). The study will provide significant information for groundwater management and exploitation in areas where groundwater is a major source of water and its exploration is critical to support drinking water need. Copyright © 2016 Elsevier B.V. All rights reserved.

Spatial Epidemiology of Plasmodium vivax, Afghanistan

PubMed Central

Leslie, Toby; Kolaczinski, Kate; Mohsen, Engineer; Mehboob, Najeebullah; Saleheen, Sarah; Khudonazarov, Juma; Freeman, Tim; Clements, Archie; Rowland, Mark; Kolaczinski, Jan

2006-01-01

Plasmodium vivax is endemic to many areas of Afghanistan. Geographic analysis helped highlight areas of malaria risk and clarified ecologic risk factors for transmission. Remote sensing enabled development of a risk map, thereby providing a valuable tool to help guide malaria control strategies. PMID:17176583

Prebiotic Low Sugar Chocolate Dairy Desserts: Physical and Optical Characteristics and Performance of PARAFAC and PCA Preference Map.

PubMed

Morais, E C; Esmerino, E A; Monteiro, R A; Pinheiro, C M; Nunes, C A; Cruz, A G; Bolini, Helena M A

2016-01-01

The addition of prebiotic and sweeteners in chocolate dairy desserts opens up new opportunities to develop dairy desserts that besides having a lower calorie intake still has functional properties. In this study, prebiotic low sugar dairy desserts were evaluated by 120 consumers using a 9-point hedonic scale, in relation to the attributes of appearance, aroma, flavor, texture, and overall liking. Internal preference map using parallel factor analysis (PARAFAC) and principal component analysis (PCA) was performed using the consumer data. In addition, physical (texture profile) and optical (instrumental color) analyses were also performed. Prebiotic dairy desserts containing sucrose and sucralose were equally liked by the consumers. These samples were characterized by firmness and gumminess, which can be considered drivers of liking by the consumers. Optimization of the prebiotic low sugar dessert formulation should take in account the choice of ingredients that contribute in a positive manner for these parameters. PARAFAC allowed the extraction of more relevant information in relation to PCA, demonstrating that consumer acceptance analysis can be evaluated by simultaneously considering several attributes. Multiple factor analysis reported Rv value of 0.964, suggesting excellent concordance for both methods. © 2015 Institute of Food Technologists®

High Resolution Mapping of Genetic Factors Affecting Abdominal Bristle Number in Drosophila Melanogaster

PubMed Central

Long, A. D.; Mullaney, S. L.; Reid, L. A.; Fry, J. D.; Langley, C. H.; Mackay, TFC.

1995-01-01

Factors responsible for selection response for abdominal bristle number and correlated responses in sternopleural bristle number were mapped to the X and third chromosome of Drosophila melanogaster. Lines divergent for high and low abdominal bristle number were created by 25 generations of artificial selection from a large base population, with an intensity of 25 individuals of each sex selected from 100 individuals of each sex scored per generation. Isogenic chromosome substitution lines in which the high (H) X or third chromosome were placed in an isogenic low (L) background were derived from the selection lines and from the 93 recombinant isogenic (RI) HL X and 67 RI chromosome 3 lines constructed from them. Highly polymorphic neutral r00 transposable elements were hybridized in situ to the polytene chromosomes of the RI lines to create a set of cytogenetic markers. These techniques yielded a dense map with an average spacing of 4 cM between informative markers. Factors affecting bristle number, and relative viability of the chromosome 3 RI lines, were mapped using a multiple regression interval mapping approach, conditioning on all markers >/=10 cM from the tested interval. Two factors with large effects on abdominal bristle number were mapped on the X chromosome and five factors on the third chromosome. One factor with a large effect on sternopleural bristle number was mapped to the X and two were mapped to the third chromosome; all factors with sternopleural effects corresponded to those with effects on abdominal bristle number. Two of the chromosome 3 factors with large effects on abdominal bristle number were also associated with reduced viability. Significant sex-specific effects and epistatic interactions between mapped factors of the same order of magnitude as the additive effects were observed. All factors mapped to the approximate positions of likely candidate loci (ASC, bb, emc, h, mab, Dl and E(spl)), previously characterized by mutations with large effects on bristle number. PMID:7768438

Cognitive mapping tools: review and risk management needs.

PubMed

Wood, Matthew D; Bostrom, Ann; Bridges, Todd; Linkov, Igor

2012-08-01

Risk managers are increasingly interested in incorporating stakeholder beliefs and other human factors into the planning process. Effective risk assessment and management requires understanding perceptions and beliefs of involved stakeholders, and how these beliefs give rise to actions that influence risk management decisions. Formal analyses of risk manager and stakeholder cognitions represent an important first step. Techniques for diagramming stakeholder mental models provide one tool for risk managers to better understand stakeholder beliefs and perceptions concerning risk, and to leverage this new understanding in developing risk management strategies. This article reviews three methodologies for assessing and diagramming stakeholder mental models--decision-analysis-based mental modeling, concept mapping, and semantic web analysis--and assesses them with regard to their ability to address risk manager needs. © 2012 Society for Risk Analysis.

Application of sensitivity-analysis techniques to the calculation of topological quantities

NASA Astrophysics Data System (ADS)

Gilchrist, Stuart

2017-08-01

Magnetic reconnection in the corona occurs preferentially at sites where the magnetic connectivity is either discontinuous or has a large spatial gradient. Hence there is a general interest in computing quantities (like the squashing factor) that characterize the gradient in the field-line mapping function. Here we present an algorithm for calculating certain (quasi)topological quantities using mathematical techniques from the field of ``sensitivity-analysis''. The method is based on the calculation of a three dimensional field-line mapping Jacobian from which all the present topological quantities of interest can be derived. We will present the algorithm and the details of a publicly available set of libraries that implement the algorithm.

Experimental philosophy leading to a small scale digital data base of the conterminous United States for designing experiments with remotely sensed data

NASA Technical Reports Server (NTRS)

Labovitz, M. L.; Masuoka, E. J.; Broderick, P. W.; Garman, T. R.; Ludwig, R. W.; Beltran, G. N.; Heyman, P. J.; Hooker, L. K.

1983-01-01

Research using satellite remotely sensed data, even within any single scientific discipline, often lacked a unifying principle or strategy with which to plan or integrate studies conducted over an area so large that exhaustive examination is infeasible, e.g., the U.S.A. However, such a series of studies would seem to be at the heart of what makes satellite remote sensing unique, that is the ability to select for study from among remotely sensed data sets distributed widely over the U.S., over time, where the resources do not exist to examine all of them. Using this philosophical underpinning and the concept of a unifying principle, an operational procedure for developing a sampling strategy and formal testable hypotheses was constructed. The procedure is applicable across disciplines, when the investigator restates the research question in symbolic form, i.e., quantifies it. The procedure is set within the statistical framework of general linear models. The dependent variable is any arbitrary function of remotely sensed data and the independent variables are values or levels of factors which represent regional climatic conditions and/or properties of the Earth's surface. These factors are operationally defined as maps from the U.S. National Atlas (U.S.G.S., 1970). Eighty-five maps from the National Atlas, representing climatic and surface attributes, were automated by point counting at an effective resolution of one observation every 17.6 km (11 miles) yielding 22,505 observations per map. The maps were registered to one another in a two step procedure producing a coarse, then fine scale registration. After registration, the maps were iteratively checked for errors using manual and automated procedures. The error free maps were annotated with identification and legend information and then stored as card images, one map to a file. A sampling design will be accomplished through a regionalization analysis of the National Atlas data base (presently being conducted). From this analysis a map of homogeneous regions of the U.S.A. will be created and samples (LANDSAT scenes) assigned by region.

Isotypic analysis of antibodies against activated Factor VII in patients with Factor VII deficiency using the x-MAP technology.

PubMed

Pfeiffer, Caroline; Mathieu-Dupas, Eve; Logghe, Pauline; Lissalde-Lavigne, Géraldine; Balicchi, Julien; Caliskan, Umran; Valentin, Thomas; Laune, Daniel; Molina, Franck; Schved, Jean François; Giansily-Blaizot, Muriel

2016-05-01

While the immune response to hemophilic factors in hemophilia has been widely studied, little is known about the development of anti-Factor VII (FVII) antibodies in FVII deficiency. We developed a robust technique based on the x-MAP technology to detect the presence of antibodies against FVII and characterize their isotype and validated this method using blood samples from 100 patients with FVII deficiency (median FVII clotting activity [FVII:C]: 6%) and 95 healthy controls. Anti-FVII antibodies were detected in patients but also in some controls, although the concentration of total immunoglobulin G (IgGt) and IgG1 and IgG4 subclasses was significantly different between groups. The IgG1 subclass concentrations remained significantly different also when only untreated patients were compared with controls. This difference could partially be related to the F7 genotype, particularly in patients harboring the p.Arg139Gln mutation. This x-MAP-based method might be useful for assessing the immunogenicity of novel FVII compounds and of activated FVII (FVIIa) concentrates. Further prospective studies are needed to better understand the clinical relevance of these antibodies in the management of patients with FVII deficiency. Copyright © 2016 Elsevier Ltd. All rights reserved.

Fracture trace map and single-well aquifer test results in a carbonate aquifer in Berkeley County, West Virginia

USGS Publications Warehouse

McCoy, Kurt J.; Podwysocki, Melvin H.; Crider, E. Allen; Weary, David J.

2005-01-01

These data contain information on the results of single-well aquifer tests, lineament analysis, and a bedrock geologic map compilation for the low-lying carbonate and shale areas of eastern Berkeley County, West Virginia. Efforts have been initiated by management agencies of Berkeley County in cooperation with the U.S. Geological Survey to further the understanding of the spatial distribution of fractures in the carbonate regions and their correlation with aquifer properties. This report presents transmissivity values from about 200 single-well aquifer tests and a map of fracture-traces determined from aerial photos and field investigations. Transmissivity values were compared to geologic factors possibly affecting its magnitude.

The intercrater plains of Mercury and the Moon: Their nature, origin and role in terrestrial planet evolution. Areal measurement of Mercury's first quadrant. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Leake, M. A.

1982-01-01

Various linear and areal measurements of Mercury's first quadrant which were used in geological map preparation, map analysis, and statistical surveys of crater densities are discussed. Accuracy of each method rests on the determination of the scale of the photograph, i.e., the conversion factor between distances on the planet (in km) and distances on the photograph (in cm). Measurement errors arise due to uncertainty in Mercury's radius, poor resolution, poor coverage, high Sun angle illumination in the limb regions, planetary curvature, limited precision in measuring instruments, and inaccuracies in the printed map scales. Estimates are given for these errors.

How large B-factors can be in protein crystal structures.

PubMed

Carugo, Oliviero

2018-02-23

Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the electron density maps, are allowed to reach extremely large B-factors, even above 100 square Angstroms, and their final positions are purely speculative and not based on any experimental evidence. A strategy to define B-factors upper limits is described here, based on the analysis of protein crystal structures deposited in the Protein Data Bank prior 2008, when the tendency to allow B-factor to arbitrary inflate was limited. This B-factor upper limit (B_max) is determined by extrapolating the relationship between crystal structure average B-factor and percentage of crystal volume occupied by solvent (pcVol) to pcVol =100%, when, ab absurdo, the crystal contains only liquid solvent, the structure of which is, by definition, undetectable in electron density maps. It is thus possible to highlight structures with average B-factors larger than B_max, which should be considered with caution by the users of the information deposited in the Protein Data Bank, in order to avoid scientifically deleterious over-interpretations.

Geodiversity and biodiversity assessment of the Słupsk Bank, Baltic Sea

NASA Astrophysics Data System (ADS)

Najwer, Alicja; Zelewska, Izabela; Zwoliński, Zbigniew

2017-04-01

Recognizing the most diversified parts of the territory turns out to be very crucial for management and planning of natural protected areas. There is an increasing number of studies concerning assessing geodiversity and biodiversity of the land areas. However, there is noticeable lack of such publications for submerged zones. The study area consists of 100km2 Słupsk sandy shoal sporadically covered with boulder layers, located in the southern part of the Baltic Sea. It is characterised by landscapes of a significant nature value protected by Natura 2000 and is as well designated as an open sea by Helsinki Commission Baltic Sea Protected Area (HELCOM BSPA). The main aim of the presentation is an attempt to integrate geodiversity and biodiversity assessments of the submerged area using GIS platform. The basis for the diversity assessment is the proper selection of features of the marine environment, its reclassification and integration by the map algebra analysis. The map of geodiversity is based on three factor maps: a relief energy map (classification based on bathymetric model, a landform fragmentation/geomorphological map (expert classification using BPI - Bathymetric Position Index), and a lithological map (classification of the average size of grain fraction). The map of biodiversity is based on the following factor maps: a map of biomass distribution of Ceraminum Diaphanum, a map of biomass distribution of Coccotylus Truncatus, a map of biomass distribution of Polysiphonia Fucoides, a map of biomass distribution of Mytilus Edulis Trossulus, a map of distribution of macroalgae, and finally a map of distribution of macrozoobenthos. It was decided to use four classes of diversity (from low through medium and high, up to very high). The designation of the lowest class was abandoned because it characterizes areas with high anthropopressure. Maps of geodiversity and biodiversity may prove to be helpful in determining the directions for management of the most valuable parts of the areas from the nature point of view, as well as delimitation of the geodiveristy/biodiversity hotspots for purpose of the strict nature protection. This study is the first attempt to use methods of diversity assessment for marine environment.

Non-price competition in the regional high-rise construction market

NASA Astrophysics Data System (ADS)

Ganebnykh, Elena; Burtseva, Tatyana; Gurova, Ekaterina; Polyakova, Irina

2018-03-01

The article analyzes the market of high-rise residential construction in the city of Kirov (Russia). A minimal significance of price factors has been revealed in the process of the market analysis. This suggests that a lower price does not guarantee an increase in consumer demand. Thus, factors of non-price competition are of great importance in the market in question. The expert survey has identified the factors of non-price competition which influence consumer perceptions. A perceptual map has been constructed on the basis of the identified factors by means of the factor analysis to determine the positioning of each high-rise building relative to the consumer requirements. None of the high-rise residential buildings in the market in question meets the consumers' expectations of an "ideal facility".

The effect of Mycobacterium avium ssp. paratuberculosis infection on clinical mastitis occurrence in dairy cows.

PubMed

Rossi, G; Grohn, Y T; Schukken, Y H; Smith, R L

2017-09-01

Endemic diseases can be counted among the most serious sources of losses for livestock production. In dairy farms in particular, one of the most common diseases is Johne's disease, caused by Mycobacterium avium ssp. paratuberculosis (MAP). Infection with MAP causes direct costs because it affects milk production, but it has also been suspected to increase the risk of clinical mastitis (CM) among infected animals. This might contribute to further costs for farmers. We asked whether MAP infection represents a risk factor for CM and, in particular, whether CM occurrences were more common in MAP-infected animals. Our results, obtained by survival analysis, suggest that MAP-infected cows had an increased probability of experiencing CM during lactation. These results highlight the need to account for the interplay of infectious diseases and other health conditions in economic and epidemiological modeling. In this case, accounting for MAP-infected cows having an increased CM occurrence might have nonnegligible effects on the estimated benefit of MAP control. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Mycobacterium paratuberculosis, Mycobacterium smegmatis, and lipopolysaccharide induce different transcriptional and post-transcriptional regulation of the IRG1 gene in murine macrophages.

PubMed

Basler, Tina; Jeckstadt, Sabine; Valentin-Weigand, Peter; Goethe, Ralph

2006-03-01

Mycobacterium avium subspecies paratuberculosis (MAP) causes a chronic enteritis in ruminants. In addition, MAP is presently the most favored pathogen linked to Crohn's disease. In this study, we were interested in dissecting the molecular mechanisms of macrophage activation or deactivation after infection with MAP. By subtractive hybridization of cDNAs, we identified the immune-responsive gene 1 (IRG1), which was expressed substantially higher in lipopolysaccharide (LPS)-stimulated than in MAP-infected murine macrophage cell lines. A nuclear run-on transcription assay revealed that the IRG1 gene was activated transcriptionally in LPS-stimulated and MAP-infected macrophages with higher expression in LPS-stimulated cells. Analysis of post-transcriptional regulation demonstrated that IRG1 mRNA stability was increased in LPS-stimulated but not in MAP-infected macrophages. Furthermore, IRG1 gene expression of macrophages infected with the nonpathogenic Mycobacterium smegmatis differed from those of LPS-stimulated and MAP-infected macrophages. At 2 h postinfection, M. smegmatis-induced IRG1 gene expression was as low as in MAP-infected, and 8 h postinfection, it increased nearly to the level in LPS-stimulated macrophages. Transient transfection experiments revealed similar IRG1 promoter activities in MAP- and M. smegmatis-infected cells. Northern analysis demonstrated increased IRG1 mRNA stability in M. smegmatis-infected macrophages. IRG1 mRNA stabilization was p38 mitogen-activated protein kinase-independent. Inhibition of protein synthesis revealed that constitutively expressed factors seemed to be responsible for IRG1 mRNA destabilization. Thus, our data demonstrate that transcriptional and post-transcriptional mechanisms are responsible for a differential IRG1 gene expression in murine macrophages treated with LPS, MAP, and M. smegmatis.

Stability of radiomic features in CT perfusion maps

NASA Astrophysics Data System (ADS)

Bogowicz, M.; Riesterer, O.; Bundschuh, R. A.; Veit-Haibach, P.; Hüllner, M.; Studer, G.; Stieb, S.; Glatz, S.; Pruschy, M.; Guckenberger, M.; Tanadini-Lang, S.

2016-12-01

This study aimed to identify a set of stable radiomic parameters in CT perfusion (CTP) maps with respect to CTP calculation factors and image discretization, as an input for future prognostic models for local tumor response to chemo-radiotherapy. Pre-treatment CTP images of eleven patients with oropharyngeal carcinoma and eleven patients with non-small cell lung cancer (NSCLC) were analyzed. 315 radiomic parameters were studied per perfusion map (blood volume, blood flow and mean transit time). Radiomics robustness was investigated regarding the potentially standardizable (image discretization method, Hounsfield unit (HU) threshold, voxel size and temporal resolution) and non-standardizable (artery contouring and noise threshold) perfusion calculation factors using the intraclass correlation (ICC). To gain added value for our model radiomic parameters correlated with tumor volume, a well-known predictive factor for local tumor response to chemo-radiotherapy, were excluded from the analysis. The remaining stable radiomic parameters were grouped according to inter-parameter Spearman correlations and for each group the parameter with the highest ICC was included in the final set. The acceptance level was 0.9 and 0.7 for the ICC and correlation, respectively. The image discretization method using fixed number of bins or fixed intervals gave a similar number of stable radiomic parameters (around 40%). The potentially standardizable factors introduced more variability into radiomic parameters than the non-standardizable ones with 56-98% and 43-58% instability rates, respectively. The highest variability was observed for voxel size (instability rate  >97% for both patient cohorts). Without standardization of CTP calculation factors none of the studied radiomic parameters were stable. After standardization with respect to non-standardizable factors ten radiomic parameters were stable for both patient cohorts after correction for inter-parameter correlations. Voxel size, image discretization, HU threshold and temporal resolution have to be standardized to build a reliable predictive model based on CTP radiomics analysis.

Using patient data similarities to predict radiation pneumonitis via a self-organizing map

NASA Astrophysics Data System (ADS)

Chen, Shifeng; Zhou, Sumin; Yin, Fang-Fang; Marks, Lawrence B.; Das, Shiva K.

2008-01-01

This work investigates the use of the self-organizing map (SOM) technique for predicting lung radiation pneumonitis (RP) risk. SOM is an effective method for projecting and visualizing high-dimensional data in a low-dimensional space (map). By projecting patients with similar data (dose and non-dose factors) onto the same region of the map, commonalities in their outcomes can be visualized and categorized. Once built, the SOM may be used to predict pneumonitis risk by identifying the region of the map that is most similar to a patient's characteristics. Two SOM models were developed from a database of 219 lung cancer patients treated with radiation therapy (34 clinically diagnosed with Grade 2+ pneumonitis). The models were: SOMall built from all dose and non-dose factors and, for comparison, SOMdose built from dose factors alone. Both models were tested using ten-fold cross validation and Receiver Operating Characteristics (ROC) analysis. Models SOMall and SOMdose yielded ten-fold cross-validated ROC areas of 0.73 (sensitivity/specificity = 71%/68%) and 0.67 (sensitivity/specificity = 63%/66%), respectively. The significant difference between the cross-validated ROC areas of these two models (p < 0.05) implies that non-dose features add important information toward predicting RP risk. Among the input features selected by model SOMall, the two with highest impact for increasing RP risk were: (a) higher mean lung dose and (b) chemotherapy prior to radiation therapy. The SOM model developed here may not be extrapolated to treatment techniques outside that used in our database, such as several-field lung intensity modulated radiation therapy or gated radiation therapy.

A Study on the Assessment of Multi-Factors Affecting Urban Floods Using Satellite Image: A Case Study in Nakdong Basin, S. Korea

NASA Astrophysics Data System (ADS)

Kwak, Youngjoo; Kondoh, Akihiko

2010-05-01

Floods are also related to the changes in social economic conditions and land use. Recently, floods increased due to rapid urbanization and human activity in the lowland. Therefore, integrated management of total basin system is necessary to get the secure society. Typhoon ‘Rusa’ swept through eastern and southern parts of South Korea in the 2002. This pity experience gave us valuable knowledge that could be used to mitigate the future flood hazards. The purpose of this study is to construct the digital maps of the multi-factors related to urban flood concerning geomorphologic characteristics, land cover, and surface wetness. Parameters particularly consider geomorphologic functional unit, geomorphologic parameters derived from DEM (digital elevation model), and land use. The research area is Nakdong River Basin in S. Korea. As a result of preliminary analysis for Pusan area, the vulnerability map and the flood-prone areas can be extracted by applying spatial analysis on GIS (geographic information system).

Morphometric Analysis to Prioritize Sub-Watershed for Flood Risk Assessment in Central Karakoram National Park Using Gis/rs Approach

NASA Astrophysics Data System (ADS)

Syed, N. H.; Rehman, A. A.; Hussain, D.; Ishaq, S.; Khan, A. A.

2017-11-01

Morphometric analysis is vital for any watershed investigation and it is inevitable for flood risk assessment in sub-watershed basins. Present study undertaken to carry out critical evaluation and assessment of sub watershed morphological parameters for flood risk assessment of Central Karakorum National Park (CKNP), where Geographical information system and remote sensing (GIS & RS) approach used for quantifying the parameter and mapping of sub watershed units. ASTER DEM used as a geo-spatial data for watershed delineation and stream network. Morphometric analysis carried out using spatial analyst tool of ArcGIS 10.2. The parameters included were bifurcation ratio (Rb), Drainage Texture (Rt), Circulatory ratio (Rc), Elongated ratio (Re), Drainage density (Dd), Stream Length (Lu), Stream order (Su), Slope and Basin length (Lb) have calculated separately. The analysis revealed that the stream order varies from order 1 to 6 and the total numbers of stream segments of all orders were 52. Multi criteria analysis process used to calculate the risk factor. As an accomplished result, map of sub watershed prioritization developed using weighted standardized risk factor. These results helped to understand sensitivity of flush floods in different sub watersheds of the study area and leaded to better management of the mountainous regions in prospect of flush floods.

Information-dependent enrichment analysis reveals time-dependent transcriptional regulation of the estrogen pathway of toxicity.

PubMed

Pendse, Salil N; Maertens, Alexandra; Rosenberg, Michael; Roy, Dipanwita; Fasani, Rick A; Vantangoli, Marguerite M; Madnick, Samantha J; Boekelheide, Kim; Fornace, Albert J; Odwin, Shelly-Ann; Yager, James D; Hartung, Thomas; Andersen, Melvin E; McMullen, Patrick D

2017-04-01

The twenty-first century vision for toxicology involves a transition away from high-dose animal studies to in vitro and computational models (NRC in Toxicity testing in the 21st century: a vision and a strategy, The National Academies Press, Washington, DC, 2007). This transition requires mapping pathways of toxicity by understanding how in vitro systems respond to chemical perturbation. Uncovering transcription factors/signaling networks responsible for gene expression patterns is essential for defining pathways of toxicity, and ultimately, for determining the chemical modes of action through which a toxicant acts. Traditionally, transcription factor identification is achieved via chromatin immunoprecipitation studies and summarized by calculating which transcription factors are statistically associated with up- and downregulated genes. These lists are commonly determined via statistical or fold-change cutoffs, a procedure that is sensitive to statistical power and may not be as useful for determining transcription factor associations. To move away from an arbitrary statistical or fold-change-based cutoff, we developed, in the context of the Mapping the Human Toxome project, an enrichment paradigm called information-dependent enrichment analysis (IDEA) to guide identification of the transcription factor network. We used a test case of activation in MCF-7 cells by 17β estradiol (E2). Using this new approach, we established a time course for transcriptional and functional responses to E2. ERα and ERβ were associated with short-term transcriptional changes in response to E2. Sustained exposure led to recruitment of additional transcription factors and alteration of cell cycle machinery. TFAP2C and SOX2 were the transcription factors most highly correlated with dose. E2F7, E2F1, and Foxm1, which are involved in cell proliferation, were enriched only at 24 h. IDEA should be useful for identifying candidate pathways of toxicity. IDEA outperforms gene set enrichment analysis (GSEA) and provides similar results to weighted gene correlation network analysis, a platform that helps to identify genes not annotated to pathways.

Medical Geography: a Promising Field of Application for Geostatistics.

PubMed

Goovaerts, P

2009-01-01

The analysis of health data and putative covariates, such as environmental, socio-economic, behavioral or demographic factors, is a promising application for geostatistics. It presents, however, several methodological challenges that arise from the fact that data are typically aggregated over irregular spatial supports and consist of a numerator and a denominator (i.e. population size). This paper presents an overview of recent developments in the field of health geostatistics, with an emphasis on three main steps in the analysis of areal health data: estimation of the underlying disease risk, detection of areas with significantly higher risk, and analysis of relationships with putative risk factors. The analysis is illustrated using age-adjusted cervix cancer mortality rates recorded over the 1970-1994 period for 118 counties of four states in the Western USA. Poisson kriging allows the filtering of noisy mortality rates computed from small population sizes, enhancing the correlation with two putative explanatory variables: percentage of habitants living below the federally defined poverty line, and percentage of Hispanic females. Area-to-point kriging formulation creates continuous maps of mortality risk, reducing the visual bias associated with the interpretation of choropleth maps. Stochastic simulation is used to generate realizations of cancer mortality maps, which allows one to quantify numerically how the uncertainty about the spatial distribution of health outcomes translates into uncertainty about the location of clusters of high values or the correlation with covariates. Last, geographically-weighted regression highlights the non-stationarity in the explanatory power of covariates: the higher mortality values along the coast are better explained by the two covariates than the lower risk recorded in Utah.

Field protocol and GIS analysis of connectivity in semiarid headwaters: metrics and evidences from Carcavo Basin (SE Spain)

NASA Astrophysics Data System (ADS)

Marchamalo, Miguel; Hooke, Janet; Gonzalez-Rodrigo, Beatriz; Sandercock, Peter

2017-04-01

Soil erosion and land degradation are severe problems in headwaters of ephemeral streams in semiarid Mediterranean regions, particularly in marginal upland areas over erodible parent material. Field-based information is required about the main pathways of sediment movement, the identification of sources and sinks and the influence of relevant factors. The EU-funded project RECONDES approached this reality by monitoring connectivity pathways of water and sediment movement in the landscape with the aim of identifying hotspots that could then be strategically targeted to reduce soil erosion and off-site effects. A protocol including field work and GIS analysis was developed and applied to a set of microcatchments in Carcavo Basin (Spain). The philosophy of the protocol was based on the repeated mapping after rainfall events so that frequency of activity of pathways could be evaluated. Connectivity was evaluated for each site and event using specific metrics: maximum mapped connectivity (corresponding to the largest recorded event), density of connected pathway links (m/ha) and frequency of activity (times active/total). Repeated connectivity mapping allowed identifying hotspots of erosion. The effect of structural and functional factors on connectivity was investigated. Field data is also valuable for validating future connectivity models in semiarid landscapes under highly variable and unpredictable conditions.

Fast neutron background characterization with the Radiological Multi-sensor Analysis Platform (RadMAP)

DOE PAGES

Davis, John R.; Brubaker, Erik; Vetter, Kai

2017-03-29

In an effort to characterize the fast neutron radiation background, 16 EJ-309 liquid scintillator cells were installed in the Radiological Multi-sensor Analysis Platform (RadMAP) to collect data in the San Francisco Bay Area. Each fast neutron event was associated with specific weather metrics (pressure, temperature, absolute humidity) and GPS coordinates. Furthermore, the expected exponential dependence of the fast neutron count rate on atmospheric pressure was demonstrated and event rates were subsequently adjusted given the measured pressure at the time of detection. Pressure adjusted data was also used to investigate the influence of other environmental conditions on the neutron background rate.more » Using National Oceanic and Atmospheric Administration (NOAA) coastal area lidar data, an algorithm was implemented to approximate sky-view factors (the total fraction of visible sky) for points along RadMAPs route. In the three areas we analyzed, San Francisco, Downtown Oakland, and Berkeley, all demonstrated a suppression in the background rate of over 50% for the range of sky-view factors measured. This effect, which is due to the shielding of cosmic-ray produced neutrons by surrounding buildings, was comparable to the pressure influence which yielded a 32% suppression in the count rate over the range of pressures measured.« less

Stream gradient Hotspot and Cluster Analysis (SL-HCA) for improving the longitudinal profiles metrics

NASA Astrophysics Data System (ADS)

Troiani, Francesco; Piacentini, Daniela; Seta Marta, Della

2016-04-01

Many researches successfully focused on stream longitudinal profiles analysis through Stream Length-gradient (SL) index for detecting, at different spatial scales, either tectonic structures or hillslope processes. The analysis and interpretation of spatial variability of SL values, both at a regional and local scale, is often complicated due to the concomitance of different factors generating SL anomalies, including the bedrock composition. The creation of lithologically-filtered SL maps is often problematic in areas where homogeneously surveyed geological maps, with a sufficient resolution are unavailable. Moreover, both the SL map classification and the unbiased anomaly detection are rather difficult. For instance, which is the best threshold to define the anomalous SL values? Further, is there a minimum along-channel extent of anomalous SL values for objectively defining over-steeped segments on long-profiles? This research investigates the relevance and potential of a new approach based on Hotspot and Cluster Analysis of SL values (SL-HCA) for detecting knickzones on long-profiles at a regional scale and for fine-tuning the interpretation of their geological-geomorphological meaning. We developed this procedure within a 2800 km2-wide area located in the mountainous sector of the Northern Apennines of Italy. The Getis-Ord Gi∗ statistic is applied for the SL-HCA approach. The value of SL, calculated starting from a 5x5 m Digital Elevation Model, is used as weighting factor and the Gi∗ index is calculated for each 50 m-long channel segment for the whole fluvial system. The outcomes indicate that high positive Gi∗ values imply the clustering of SL anomalies, thus the occurrence of knickzones on the stream long-profiles. Results show that high and very high Gi* values (i.e. values beyond two standard deviations from the mean) correlate well with the principal knickzones detected with existent lithologically-filtered SL maps. Field checks and remote sensing analysis conducted on 52 clusters of high and very high Gi* values indicate that mass movement of slope material represents the dominant process producing over-steeped long-profiles along connected streams, whereas the litho-structure accounts for the main anomalies along disconnected steams. Tectonic structures generally provide to the largest clusters. Our results demonstrate that SL-HCA maps have the same potential of lithologically-filtered SL maps for detecting knickzones due to hillslope processes and/or tectonic structures. The reduced-complexity model derived from SL-HCA approach highly improve the readability of the morphometric outcomes, thus the interpretation at a regional scale of the geological-geomorphological meaning of over-steeped segments on long-profiles. SL-HCA maps are useful to investigate and better interpret knickzones within regions poorly covered by geological data and where field surveys are difficult to be performed.

Medial meniscal posterior root/horn radial tears correlate with cartilage degeneration detected by T1ρ relaxation mapping.

PubMed

Takahashi, Kenji; Hashimoto, Sanshiro; Nakamura, Hiroshi; Mori, Atsushi; Sato, Akiko; Majima, Tokifumi; Takai, Shinro

2015-06-01

This study aimed to identify factors on routine pulse sequence MRI associated with cartilage degeneration observed on T1ρ relaxation mapping. This study included 137 subjects with knee pain. T1ρ values were measured in the regions of interest on the surface layer of the cartilage on mid-coronal images of the femorotibial joint. Assessment of cartilage, subchondral bone, meniscus and ligaments was performed using routine pulse sequence MRI. Radiographic evaluation for osteoarthritis was also performed. Multiple regression analysis revealed posterior root/horn tears to be independent factors increasing the T1ρ values of the cartilage in the medial compartment of the femorotibial joint. Even when adjusted for radiographically defined early-stage osteoarthritis, medial posterior meniscal radial tears significantly increased the T1ρ values. This study showed that posterior root/horn radial tears in the medial meniscus are particularly important MRI findings associated with cartilage degeneration observed on T1ρ relaxation mapping. Morphological factors of the medial meniscus on MRI provide findings useful for screening early-stage osteoarthritis. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

TFOS DEWS II Epidemiology Report.

PubMed

Stapleton, Fiona; Alves, Monica; Bunya, Vatinee Y; Jalbert, Isabelle; Lekhanont, Kaevalin; Malet, Florence; Na, Kyung-Sun; Schaumberg, Debra; Uchino, Miki; Vehof, Jelle; Viso, Eloy; Vitale, Susan; Jones, Lyndon

2017-07-01

The subcommittee reviewed the prevalence, incidence, risk factors, natural history, morbidity and questionnaires reported in epidemiological studies of dry eye disease (DED). A meta-analysis of published prevalence data estimated the impact of age and sex. Global mapping of prevalence was undertaken. The prevalence of DED ranged from 5 to 50%. The prevalence of signs was higher and more variable than symptoms. There were limited prevalence studies in youth and in populations south of the equator. The meta-analysis confirmed that prevalence increases with age, however signs showed a greater increase per decade than symptoms. Women have a higher prevalence of DED than men, although differences become significant only with age. Risk factors were categorized as modifiable/non-modifiable, and as consistent, probable or inconclusive. Asian ethnicity was a mostly consistent risk factor. The economic burden and impact of DED on vision, quality of life, work productivity, psychological and physical impact of pain, are considerable, particularly costs due to reduced work productivity. Questionnaires used to evaluate DED vary in their utility. Future research should establish the prevalence of disease of varying severity, the incidence in different populations and potential risk factors such as youth and digital device usage. Geospatial mapping might elucidate the impact of climate, environment and socioeconomic factors. Given the limited study of the natural history of treated and untreated DED, this remains an important area for future research. Copyright © 2017 Elsevier Inc. All rights reserved.

Coastal habitat mapping in the Aegean Sea using high resolution orthophoto maps

NASA Astrophysics Data System (ADS)

Topouzelis, Konstantinos; Papakonstantinou, Apostolos; Doukari, Michaela; Stamatis, Panagiotis; Makri, Despina; Katsanevakis, Stelios

2017-09-01

The significance of coastal habitat mapping lies in the need to prevent from anthropogenic interventions and other factors. Until 2015, Landsat-8 (30m) imagery were used as medium spatial resolution satellite imagery. So far, Sentinel-2 satellite imagery is very useful for more detailed regional scale mapping. However, the use of high resolution orthophoto maps, which are determined from UAV data, is expected to improve the mapping accuracy. This is due to small spatial resolution of the orthophoto maps (30 cm). This paper outlines the integration of UAS for data acquisition and Structure from Motion (SfM) pipeline for the visualization of selected coastal areas in the Aegean Sea. Additionally, the produced orthophoto maps analyzed through an object-based image analysis (OBIA) and nearest-neighbor classification for mapping the coastal habitats. Classification classes included the main general habitat types, i.e. seagrass, soft bottom, and hard bottom The developed methodology applied at the Koumbara beach (Ios Island - Greece). Results showed that UAS's data revealed the sub-bottom complexity in large shallow areas since they provide such information in the spatial resolution that permits the mapping of seagrass meadows with extreme detail. The produced habitat vectors are ideal as reference data for studies with satellite data of lower spatial resolution.

Stream network analysis and geomorphic flood plain mapping from orbital and suborbital remote sensing imagery application to flood hazard studies in central Texas

NASA Technical Reports Server (NTRS)

Baker, V. R. (Principal Investigator); Holz, R. K.; Hulke, S. D.; Patton, P. C.; Penteado, M. M.

1975-01-01

The author has identified the following significant results. Development of a quantitative hydrogeomorphic approach to flood hazard evaluation was hindered by (1) problems of resolution and definition of the morphometric parameters which have hydrologic significance, and (2) mechanical difficulties in creating the necessary volume of data for meaningful analysis. Measures of network resolution such as drainage density and basin Shreve magnitude indicated that large scale topographic maps offered greater resolution than small scale suborbital imagery and orbital imagery. The disparity in network resolution capabilities between orbital and suborbital imagery formats depends on factors such as rock type, vegetation, and land use. The problem of morphometric data analysis was approached by developing a computer-assisted method for network analysis. The system allows rapid identification of network properties which can then be related to measures of flood response.

Activated actin-depolymerizing factor/cofilin sequesters phosphorylated microtubule-associated protein during the assembly of alzheimer-like neuritic cytoskeletal striations.

PubMed

Whiteman, Ineka T; Gervasio, Othon L; Cullen, Karen M; Guillemin, Gilles J; Jeong, Erica V; Witting, Paul K; Antao, Shane T; Minamide, Laurie S; Bamburg, James R; Goldsbury, Claire

2009-10-14

In Alzheimer's disease (AD), rod-like cofilin aggregates (cofilin-actin rods) and thread-like inclusions containing phosphorylated microtubule-associated protein (pMAP) tau form in the brain (neuropil threads), and the extent of their presence correlates with cognitive decline and disease progression. The assembly mechanism of these respective pathological lesions and the relationship between them is poorly understood, yet vital to understanding the causes of sporadic AD. We demonstrate that, during mitochondrial inhibition, activated actin-depolymerizing factor (ADF)/cofilin assemble into rods along processes of cultured primary neurons that recruit pMAP/tau and mimic neuropil threads. Fluorescence resonance energy transfer analysis revealed colocalization of cofilin-GFP (green fluorescent protein) and pMAP in rods, suggesting their close proximity within a cytoskeletal inclusion complex. The relationship between pMAP and cofilin-actin rods was further investigated using actin-modifying drugs and small interfering RNA knockdown of ADF/cofilin in primary neurons. The results suggest that activation of ADF/cofilin and generation of cofilin-actin rods is required for the subsequent recruitment of pMAP into the inclusions. Additionally, we were able to induce the formation of pMAP-positive ADF/cofilin rods by exposing cells to exogenous amyloid-beta (Abeta) peptides. These results reveal a common pathway for pMAP and cofilin accumulation in neuronal processes. The requirement of activated ADF/cofilin for the sequestration of pMAP suggests that neuropil thread structures in the AD brain may be initiated by elevated cofilin activation and F-actin bundling that can be caused by oxidative stress, mitochondrial dysfunction, or Abeta peptides, all suspected initiators of synaptic loss and neurodegeneration in AD.

Metabolic Predictors of Change in Vascular Function: Prospective Associations From a Community-Based Cohort.

PubMed

Zachariah, Justin P; Rong, Jian; Larson, Martin G; Hamburg, Naomi M; Benjamin, Emelia J; Vasan, Ramachandran S; Mitchell, Gary F

2018-02-01

Vascular function varies with age because of physiological and pathological factors. We examined relations of longitudinal change in vascular function with change in metabolic traits. Longitudinal changes in vascular function and metabolic traits were examined in 5779 participants (mean age, 49.8±14.5 years; 54% women) who attended sequential examinations of the Framingham Offspring, Third Generation, and Omni-1 and Omni-2 cohorts. Multivariable regression analysis related changes in vascular measures (dependent variables), including carotid-femoral pulse wave velocity (CFPWV), forward pressure wave amplitude, characteristic impedance, central pulse pressure, and mean arterial pressure (MAP), with change in body mass index, fasting total:high-density lipoprotein cholesterol ratio, serum triglycerides, and blood glucose. Analyses accounted for baseline value of each vascular and metabolic measure, MAP change, and multiple comparisons. On follow-up (mean, 5.9±0.6 years), aortic stiffness (CFPWV, 0.2±1.6 m/s), and pressure pulsatility (forward pressure wave, 1.2±12.4 mm Hg; characteristic impedance, 23±73 dyne×sec/cm 5 ; central pulse pressure, 2.6±14.7 mm Hg; all P <0.0001) increased, whereas MAP fell (-3±10 mm Hg; P <0.0001). Worsening of each metabolic trait was associated with increases in CFPWV and MAP ( P <0.0001 for all associations) and an increase in MAP was associated with an increase in CFPWV. Overall, worsening metabolic traits were associated with worsening aortic stiffness and MAP. Opposite net change in aortic stiffness and MAP suggests that factors other than distending pressure contributed to the observed increase in aortic stiffness. Change in metabolic traits explained a greater proportion of the change in CFPWV and MAP than baseline metabolic values. © 2017 American Heart Association, Inc.

Some Comments on Mapping from Disease-Specific to Generic Health-Related Quality-of-Life Scales

PubMed Central

Palta, Mari

2013-01-01

An article by Lu et al. in this issue of Value in Health addresses the mapping of treatment or group differences in disease-specific measures (DSMs) of health-related quality of life onto differences in generic health-related quality-of-life scores, with special emphasis on how the mapping is affected by the reliability of the DSM. In the proposed mapping, a factor analytic model defines a conversion factor between the scores as the ratio of factor loadings. Hence, the mapping applies to convert true underlying scales and has desirable properties facilitating the alignment of instruments and understanding their relationship in a coherent manner. It is important to note, however, that when DSM means or differences in mean DSMs are estimated, their mapping is still of a measurement error–prone predictor, and the correct conversion coefficient is the true mapping multiplied by the reliability of the DSM in the relevant sample. In addition, the proposed strategy for estimating the factor analytic mapping in practice requires assumptions that may not hold. We discuss these assumptions and how they may be the reason we obtain disparate estimates of the mapping factor in an application of the proposed methods to groups of patients. PMID:23337233

Quantitative X-ray mapping, scatter diagrams and the generation of correction maps to obtain more information about your material

NASA Astrophysics Data System (ADS)

Wuhrer, R.; Moran, K.

2014-03-01

Quantitative X-ray mapping with silicon drift detectors and multi-EDS detector systems have become an invaluable analysis technique and one of the most useful methods of X-ray microanalysis today. The time to perform an X-ray map has reduced considerably with the ability to map minor and trace elements very accurately due to the larger detector area and higher count rate detectors. Live X-ray imaging can now be performed with a significant amount of data collected in a matter of minutes. A great deal of information can be obtained from X-ray maps. This includes; elemental relationship or scatter diagram creation, elemental ratio mapping, chemical phase mapping (CPM) and quantitative X-ray maps. In obtaining quantitative x-ray maps, we are able to easily generate atomic number (Z), absorption (A), fluorescence (F), theoretical back scatter coefficient (η), and quantitative total maps from each pixel in the image. This allows us to generate an image corresponding to each factor (for each element present). These images allow the user to predict and verify where they are likely to have problems in our images, and are especially helpful to look at possible interface artefacts. The post-processing techniques to improve the quantitation of X-ray map data and the development of post processing techniques for improved characterisation are covered in this paper.

VLBI Analysis with the Multi-Technique Software GEOSAT

NASA Technical Reports Server (NTRS)

Kierulf, Halfdan Pascal; Andersen, Per-Helge; Boeckmann, Sarah; Kristiansen, Oddgeir

2010-01-01

GEOSAT is a multi-technique geodetic analysis software developed at Forsvarets Forsknings Institutt (Norwegian defense research establishment). The Norwegian Mapping Authority has now installed the software and has, together with Forsvarets Forsknings Institutt, adapted the software to deliver datum-free normal equation systems in SINEX format. The goal is to be accepted as an IVS Associate Analysis Center and to provide contributions to the IVS EOP combination on a routine basis. GEOSAT is based on an upper diagonal factorized Kalman filter which allows estimation of time variable parameters like the troposphere and clocks as stochastic parameters. The tropospheric delays in various directions are mapped to tropospheric zenith delay using ray-tracing. Meteorological data from ECMWF with a resolution of six hours is used to perform the ray-tracing which depends both on elevation and azimuth. Other models are following the IERS and IVS conventions. The Norwegian Mapping Authority has submitted test SINEX files produced with GEOSAT to IVS. The results have been compared with the existing IVS combined products. In this paper the outcome of these comparisons is presented.

Development and Assessment of a Geographic Knowledge-Based Model for Mapping Suitable Areas for Rift Valley Fever Transmission in Eastern Africa

PubMed Central

Tran, Annelise; Trevennec, Carlène; Lutwama, Julius; Sserugga, Joseph; Gély, Marie; Pittiglio, Claudia; Pinto, Julio; Chevalier, Véronique

2016-01-01

Rift Valley fever (RVF), a mosquito-borne disease affecting ruminants and humans, is one of the most important viral zoonoses in Africa. The objective of the present study was to develop a geographic knowledge-based method to map the areas suitable for RVF amplification and RVF spread in four East African countries, namely, Kenya, Tanzania, Uganda and Ethiopia, and to assess the predictive accuracy of the model using livestock outbreak data from Kenya and Tanzania. Risk factors and their relative importance regarding RVF amplification and spread were identified from a literature review. A numerical weight was calculated for each risk factor using an analytical hierarchy process. The corresponding geographic data were collected, standardized and combined based on a weighted linear combination to produce maps of the suitability for RVF transmission. The accuracy of the resulting maps was assessed using RVF outbreak locations in livestock reported in Kenya and Tanzania between 1998 and 2012 and the ROC curve analysis. Our results confirmed the capacity of the geographic information system-based multi-criteria evaluation method to synthesize available scientific knowledge and to accurately map (AUC = 0.786; 95% CI [0.730–0.842]) the spatial heterogeneity of RVF suitability in East Africa. This approach provides users with a straightforward and easy update of the maps according to data availability or the further development of scientific knowledge. PMID:27631374

Utilization Analysis in Low-Temperature Geothermal Play Fairway Analysis for the Appalachian Basin (GPFA-AB)

DOE Data Explorer

Jordan, Teresa E.

2015-09-30

This submission of Utilization Analysis data to the Geothermal Data Repository (GDR) node of the National Geothermal Data System (NGDS) is in support of Phase 1 Low Temperature Geothermal Play Fairway Analysis for the Appalachian Basin (project DE-EE0006726). The submission includes data pertinent to the methods and results of an analysis of the Surface Levelized Cost of Heat (SLCOH) for US Census Bureau Places within the study area. This was calculated using a modification of a program called GEOPHIRES, available at http://koenraadbeckers.net/geophires/index.php. The MATLAB modules used in conjunction with GEOPHIRES, the MATLAB data input file, the GEOPHIRES output data file, and an explanation of the software components have been provided. Results of the SLCOH analysis appear on 4 .png image files as mapped risk of heat utilization. For each of the 4 image (.png) files, there is an accompanying georeferenced TIF (.tif) file by the same name. In addition to calculating SLCOH, this Task 4 also identified many sites that may be prospects for use of a geothermal district heating system, based on their size and industry, rather than on the SLCOH. An industry sorted listing of the sites (.xlsx) and a map of these sites plotted as a layer onto different iterations of maps combining the three geological risk factors (Thermal Quality, Natural Reservoir Quality, and Risk of Seismicity) has been provided. In addition to the 6 image (.png) files of the maps in this series, a shape (.shp) file and 7 associated files are included as well. Finally, supporting files (.pdf) describing the utilization analysis methodology and summarizing the anticipated permitting for a deep district heating system are supplied. UPDATE: Newer version of the Utilization Analysis has been added here: https://gdr.openei.org/submissions/878

Sensitivity Analysis of earth and environmental models: a systematic review to guide scientific advancement

NASA Astrophysics Data System (ADS)

Wagener, Thorsten; Pianosi, Francesca

2016-04-01

Sensitivity Analysis (SA) investigates how the variation in the output of a numerical model can be attributed to variations of its input factors. SA is increasingly being used in earth and environmental modelling for a variety of purposes, including uncertainty assessment, model calibration and diagnostic evaluation, dominant control analysis and robust decision-making. Here we provide some practical advice regarding best practice in SA and discuss important open questions based on a detailed recent review of the existing body of work in SA. Open questions relate to the consideration of input factor interactions, methods for factor mapping and the formal inclusion of discrete factors in SA (for example for model structure comparison). We will analyse these questions using relevant examples and discuss possible ways forward. We aim at stimulating the discussion within the community of SA developers and users regarding the setting of good practices and on defining priorities for future research.

Characterization of the human SDHD gene encoding the small subunit of cytochrome b (cybS) in mitochondrial succinate-ubiquinone oxidoreductase.

PubMed

Hirawake, H; Taniwaki, M; Tamura, A; Amino, H; Tomitsuka, E; Kita, K

1999-08-04

We have mapped large (cybL) and small (cybS) subunits of cytochrome b in the succinate-ubiquinone oxidoreductase (complex II) of human mitochondria to chromosome 1q21 and 11q23, respectively (H. Hirawake et al., Cytogenet. Cell Genet. 79 (1997) 132-138). In the present study, the human SDHD gene encoding cybS was cloned and characterized. The gene comprises four exons and three introns extending over 19 kb. Sequence analysis of the 5' promoter region showed several motifs for the binding of transcription factors including nuclear respiratory factors NRF-1 and NRF-2 at positions -137 and -104, respectively. In addition to this gene, six pseudogenes of cybS were isolated and mapped on the chromosome.

Analysis of the Image Quality of no Ground Controlled Positioning Precision about Surveying and Mapping Satellite

NASA Astrophysics Data System (ADS)

Wang, Y.; Hu, X.; Yang, X.; Xie, G.

2018-04-01

The image quality of the surveying camera will affect the stereoscopic positioning accuracy of the remote sensing satellite. The key factors closely related to the image quality are Modulation Transfer Function(MTF),Signal to Noise Ratio(SNR) and Quantization Bits(QB). In "Mapping Satellite-1" image as the background, research the effect of positioning precision about the image quality in no ground controlled conditions, and evaluate the quantitative relationship with the positioning precision. At last verify the validity of the experimental results by simulating three factors of the degraded data on orbit, and counting the number of matching points, the mismatch rate, and the matching residuals of the degraded data. The reason for the variety of the positioning precision was analyzed.

A Statistical Analysis of Corona Topography: New Insights into Corona Formation and Evolution

NASA Technical Reports Server (NTRS)

Stofan, E. R.; Glaze, L. S.; Smrekar, S. E.; Baloga, S. M.

2003-01-01

Extensive mapping of the surface of Venus and continued analysis of Magellan data have allowed a more comprehensive survey of coronae to be conducted. Our updated corona database contains 514 features, an increase from the 326 coronae of the previous survey. We include a new set of 106 Type 2 or stealth coronae, which have a topographic rather than a fracture annulus. The large increase in the number of coronae over the 1992 survey results from several factors, including the use of the full Magellan data set and the addition of features identified as part of the systematic geologic mapping of Venus. Parameters of the population that we have analyzed to date include size and topography.

Data Mining of Determinants of Intrauterine Growth Retardation Revisited Using Novel Algorithms Generating Semantic Maps and Prototypical Discriminating Variable Profiles

PubMed Central

Buscema, Massimo; Grossi, Enzo; Montanini, Luisa; Street, Maria E.

2015-01-01

Objectives Intra-uterine growth retardation is often of unknown origin, and is of great interest as a “Fetal Origin of Adult Disease” has been now well recognized. We built a benchmark based upon a previously analysed data set related to Intrauterine Growth Retardation with 46 subjects described by 14 variables, related with the insulin-like growth factor system and pro-inflammatory cytokines, namely interleukin -6 and tumor necrosis factor -α. Design and Methods We used new algorithms for optimal information sorting based on the combination of two neural network algorithms: Auto-contractive Map and Activation and Competition System. Auto-Contractive Map spatializes the relationships among variables or records by constructing a suitable embedding space where ‘closeness’ among variables or records reflects accurately their associations. The Activation and Competition System algorithm instead works as a dynamic non linear associative memory on the weight matrices of other algorithms, and is able to produce a prototypical variable profile of a given target. Results Classical statistical analysis, proved to be unable to distinguish intrauterine growth retardation from appropriate-for-gestational age (AGA) subjects due to the high non-linearity of underlying functions. Auto-contractive map succeeded in clustering and differentiating completely the conditions under study, while Activation and Competition System allowed to develop the profile of variables which discriminated the two conditions under study better than any other previous form of attempt. In particular, Activation and Competition System showed that ppropriateness for gestational age was explained by IGF-2 relative gene expression, and by IGFBP-2 and TNF-α placental contents. IUGR instead was explained by IGF-I, IGFBP-1, IGFBP-2 and IL-6 gene expression in placenta. Conclusion This further analysis provided further insight into the placental key-players of fetal growth within the insulin-like growth factor and cytokine systems. Our previous published analysis could identify only which variables were predictive of fetal growth in general, and identified only some relationships. PMID:26158499

An integrated remote sensing approach for identifying ecological range sites. [parker mountain

NASA Technical Reports Server (NTRS)

Jaynes, R. A.

1983-01-01

A model approach for identifying ecological range sites was applied to high elevation sagebrush-dominated rangelands on Parker Mountain, in south-central Utah. The approach utilizes map information derived from both high altitude color infrared photography and LANDSAT digital data, integrated with soils, geological, and precipitation maps. Identification of the ecological range site for a given area requires an evaluation of all relevant environmental factors which combine to give that site the potential to produce characteristic types and amounts of vegetation. A table is presented which allows the user to determine ecological range site based upon an integrated use of the maps which were prepared. The advantages of identifying ecological range sites through an integrated photo interpretation/LANDSAT analysis are discussed.

Mapping "StrengthsQuest" Themes to Holland's Vocational Personality Types

ERIC Educational Resources Information Center

Carson, Andrew D.; Evans, Karen; Gitin, Elena; Eads, Jonathan

2011-01-01

A sample of 1,747 students attending undergraduate classes in legal education at an online university completed the "StrengthsQuest" assessment as part of a larger investigation; of this number, 117 students also completed the "Kuder Career Search". Exploratory factor analysis (principal components followed varimax rotation) of…

Some comments on mapping from disease-specific to generic health-related quality-of-life scales.

PubMed

Palta, Mari

2013-01-01

An article by Lu et al. in this issue of Value in Health addresses the mapping of treatment or group differences in disease-specific measures (DSMs) of health-related quality of life onto differences in generic health-related quality-of-life scores, with special emphasis on how the mapping is affected by the reliability of the DSM. In the proposed mapping, a factor analytic model defines a conversion factor between the scores as the ratio of factor loadings. Hence, the mapping applies to convert true underlying scales and has desirable properties facilitating the alignment of instruments and understanding their relationship in a coherent manner. It is important to note, however, that when DSM means or differences in mean DSMs are estimated, their mapping is still of a measurement error-prone predictor, and the correct conversion coefficient is the true mapping multiplied by the reliability of the DSM in the relevant sample. In addition, the proposed strategy for estimating the factor analytic mapping in practice requires assumptions that may not hold. We discuss these assumptions and how they may be the reason we obtain disparate estimates of the mapping factor in an application of the proposed methods to groups of patients. Copyright © 2013 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

The Dokuchaev hypothesis as a basis for predictive digital soil mapping (on the 125th anniversary of its publication)

NASA Astrophysics Data System (ADS)

Florinsky, I. V.

2012-04-01

Predictive digital soil mapping is widely used in soil science. Its objective is the prediction of the spatial distribution of soil taxonomic units and quantitative soil properties via the analysis of spatially distributed quantitative characteristics of soil-forming factors. Western pedometrists stress the scientific priority and principal importance of Hans Jenny's book (1941) for the emergence and development of predictive soil mapping. In this paper, we demonstrate that Vasily Dokuchaev explicitly defined the central idea and statement of the problem of contemporary predictive soil mapping in the year 1886. Then, we reconstruct the history of the soil formation equation from 1899 to 1941. We argue that Jenny adopted the soil formation equation from Sergey Zakharov, who published it in a well-known fundamental textbook in 1927. It is encouraging that this issue was clarified in 2011, the anniversary year for publications of Dokuchaev and Jenny.

Electron energy-loss spectroscopy of single nanocrystals: mapping of tin allotropes.

PubMed

Roesgaard, Søren; Ramasse, Quentin; Chevallier, Jacques; Fyhn, Mogens; Julsgaard, Brian

2018-05-25

Using monochromated electron energy-loss spectroscopy (EELS), we are able to map different allotropes in Sn-nanocrystals embedded in Si. It is demonstrated that α-Sn and β-Sn, as well as an interface related plasmon, can be distinguished in embedded Sn-nanostructures. The EELS data is interpreted by standard non-negative matrix factorization followed by a manual Lorentzian decomposition. The decomposition allows for a more physical understanding of the EELS mapping without reducing the level of information. Extending the analysis from a reference system to smaller nanocrystals demonstrates that allotrope determination in nanoscale systems down below 5 nm is possible. Such local information proves the use of monochromated EELS mapping as a powerful technique to study nanoscale systems. This possibility enables investigation of small nanostructures that cannot be investigated through other means, allowing for a better understanding and thus leading to realizations that can result in nanomaterials with improved properties.

Electron energy-loss spectroscopy of single nanocrystals: mapping of tin allotropes

NASA Astrophysics Data System (ADS)

Roesgaard, Søren; Ramasse, Quentin; Chevallier, Jacques; Fyhn, Mogens; Julsgaard, Brian

2018-05-01

Using monochromated electron energy-loss spectroscopy (EELS), we are able to map different allotropes in Sn-nanocrystals embedded in Si. It is demonstrated that α-Sn and β-Sn, as well as an interface related plasmon, can be distinguished in embedded Sn-nanostructures. The EELS data is interpreted by standard non-negative matrix factorization followed by a manual Lorentzian decomposition. The decomposition allows for a more physical understanding of the EELS mapping without reducing the level of information. Extending the analysis from a reference system to smaller nanocrystals demonstrates that allotrope determination in nanoscale systems down below 5 nm is possible. Such local information proves the use of monochromated EELS mapping as a powerful technique to study nanoscale systems. This possibility enables investigation of small nanostructures that cannot be investigated through other means, allowing for a better understanding and thus leading to realizations that can result in nanomaterials with improved properties.

Rapid field-based landslide hazard assessment in response to post-earthquake emergency

NASA Astrophysics Data System (ADS)

Frattini, Paolo; Gambini, Stefano; Cancelliere, Giorgio

2016-04-01

On April 25, 2015 a Mw 7.8 earthquake occurred 80 km to the northwest of Kathmandu (Nepal). The largest aftershock, occurred on May 12, 2015, was the Mw 7.3 Nepal earthquake (SE of Zham, China), 80 km to the east of Kathmandu. . The earthquakes killed ~9000 people and severely damaged a 10,000 sqkm region in Nepal and neighboring countries. Several thousands of landslides have been triggered during the event, causing widespread damages to mountain villages and the evacuation of thousands of people. Rasuwa was one of the most damaged districts. This contribution describes landslide hazard analysis of the Saramthali, Yarsa and Bhorle VDCs (122 km2, Rasuwa district). Hazard is expressed in terms of qualitative classes (low, medium, high), through a simple matrix approach that combines frequency classes and magnitude classes. The hazard analysis is based primarily on the experience gained during a field survey conducted in September 2014. During the survey, local knowledge has been systematically exploited through interviews with local people that have experienced the earthquake and the coseismic landslides. People helped us to recognize fractures and active deformations, and allowed to reconstruct a correct chronicle of landslide events, in order to assign the landslide events to the first shock, the second shock, or the post-earthquake 2015 monsoon. The field experience was complemented with a standard analysis of the relationship between potential controlling factors and the distribution of landslides reported in Kargel et al (2016). This analysis allowed recognizing the most important controlling factor. This information was integrated with the field observations to verify the mapped units and to complete the mapping in area not accessible for field activity. Finally, the work was completed with the analysis and the use of a detailed landslide inventory produced by the University of Milano Bicocca that covers most of the area affected by coseismic landslides in Nepal (Valagussa et al, 2016). As a result, a 1:10.000 hazard map was produced. About 47% of the area is classified at high hazard, almost 19 % at medium level and 34% at low risk. In addition, the hazard map reports 262 polygons of active coseismic or postseismic landslides.

Method for removing atomic-model bias in macromolecular crystallography

DOEpatents

Terwilliger, Thomas C [Santa Fe, NM

2006-08-01

Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

Spatial analysis for susceptibility of second-time karst sinkholes: A case study of Jili Village in Guangxi, China

NASA Astrophysics Data System (ADS)

Zhou, Guoqing; Yan, Hongbo; Chen, Kunhua; Zhang, Rongting

2016-04-01

After a big karst sinkhole happened in Jili Village of Guangxi, China, the local government was eager to quantitatively analyze and map susceptible areas of the potential second-time karst sinkholes in order to make timely decisions whether the residents living in the first-time sinkhole areas should move. For this reason, karst sinkholes susceptibility geospatial analysis is investigated using multivariate spatial data, logistic regression model (LRM) and Geographical Information System (GIS). Ten major karst sinkholes related factors, including (1) formation lithology, (2) soil structure, (3) profile curvature, (4) groundwater depth, (5) fluctuation of groundwater level, (6) percolation rate of soil, (7) degree of karst development, (8) distance from fault, (9) distance from the traffic route, and (10) overburden thickness were selected, and then each of factors was classified and quantitated with the three or four levels. The LRM was applied to evaluate which factor makes significant contributions to sinkhole. The results demonstrated that formation lithology, soil structure, profile curvature, groundwater depth, ground water level, percolation rate of soil, and degree of karst development, the distance from fault, and overburden thickness are positive, while one factor, the distance from traffic routes is negative, which is deleted from LRM model. The susceptibility of the potential sinkholes in the study area is estimated and mapped using the solved impact factors. The susceptible degrees of the study area are classified into five levels, very high, high, moderate, low, and ignore susceptibility. It has been found that that both very high and high susceptibility areas are along Datou Hill and the foothills of the study area. This finding is verified by field observations. With the investigations conducted in this paper, it can be concluded that the susceptibility maps produced in this paper are reliable and accurate, and useful as a reference for local governments to make decisions regarding whether or not residents living within sinkhole areas should move.

An innovative tool for landslide susceptibility mapping in Kyrgyzstan, Central Asia

NASA Astrophysics Data System (ADS)

Saponaro, Annamaria; Pilz, Marco; Wieland, Marc; Bindi, Dino; Parolai, Stefano

2013-04-01

Kyrgyzstan is among the most exposed countries in the world to landslide susceptibility. The high seismicity of the area, the presence of high mountain ridges and topographic relieves, the geology of the local materials and the occurrence of heavy precipitations represent the main factors responsible for slope failures. In particular, the large variability of material properties and slope conditions as well as the difficulties in forecasting heavy precipitations locally and in quantifying the level of ground shaking call for harmonized procedures for reducing the negative impact of these factors. Several studies have recently been carried out aiming at preparing landslide susceptibility and hazard maps; however, some of them - qualitative-based - suffer from the application of subjective decision rules from experts in the classification of parameters that influence the occurrence of a landslide. On the other hand, statistical methods provide objectivity over qualitative ones since they allow a numerical evaluation of landslide spatial distribution with landslide potential factors. For this reason, we will make use of a bivariate technique known as Weight-Of-Evidence method to evaluate the influence of landslide predictive factors. The aim of this study is to identify areas in Kyrgyzstan being more prone to earthquake-triggered landslides. An innovative approach which exploits the new advances of GIS technology together with statistical concepts is presented. A range of conditioning factors and their potential impact on landslide activation is quantitatively assessed on the basis of landslide spatial distribution and seismic zonation. Results show areas which are more susceptible to landslides induced by earthquakes. Our approach can be used to fill the gap of subjectivity that typically affects already performed qualitative analysis. The resulting landslide susceptibility map represents a potentially supportive tool for disaster management and planning activities at regional level; furthermore, it can be used as a starting point for further constraining the analysis which might also consider meteorological influences and for carrying out an extension to all Central Asian countries in the framework of cross-border activities.

Development of two socioeconomic indices for Saudi Arabia.

PubMed

AlOmar, Reem S; Parslow, Roger C; Law, Graham R

2018-06-26

Health and socioeconomic status (SES) are linked in studies worldwide. Measures of SES exist for many countries, however not for Saudi Arabia (SA). We describe two indices of area-based SES for SA. Routine census data has been used to construct two indices of SES at the geographically-delimited administrative region of Governorates in SA (n = 118). The data used included indicators of educational status, employment status, car and material ownership. A continuous measure of SES was constructed using exploratory factor analysis (EFA) and a categorical measure of SES using latent class analysis (LCA). Both indices were mapped by Governorates. The EFA identified three factors: The first explained 51.58% of the common variance within the interrelated factors, the second 15.14%, and the third 14.26%. These proportions were used in the formulation of the standard index. The scores were fixed to range from 100 for the affluent Governorate and 0 for the deprived. The LCA found a 4 class model as the best model fit. Class 1 was termed "affluent" and included 11.01% of Governorates, class 2 "upper middle class" (44.91%), class 3 "lower middle class" (33.05%) and class 4 "deprived" (11.01%). The populated urbanised Governorates were found to be the most affluent whereas the smaller rural Governorates were the most deprived. This is the first description of measures of SES in SA at a geographical level. Two measures have been successfully constructed and mapped. The maps show similar patterns suggesting validity. Both indices support the common perception of SES in SA.

Development and Psychometric Validation of the Dementia Attitudes Scale

PubMed Central

O'Connor, Melissa L.; McFadden, Susan H.

2010-01-01

This study employed qualitative construct mapping and factor analysis to construct a scale to measure attitudes toward dementia. Five family caregivers, five professionals, and five college students participated in structured interviews. Qualitative analysis of the interviews led to a 46-item scale, which was reduced to 20 items following principal axis factoring with two different samples: college students (N = 302) and certified nursing assistant students (N = 145). Confirmatory factor analysis was then conducted with another sample of college students (N = 157). The final scale, titled the Dementia Attitudes Scale (DAS), essentially had a two-factor structure; the factors were labeled “dementia knowledge” and “social comfort.” Total-scale Cronbach's alphas ranged 0.83–0.85. Evidence for convergent validity was promising, as the DAS correlated significantly with scales that measured ageism and attitudes toward disabilities (range of correlations = 0.44–0.55; mean correlation = 0.50). These findings demonstrate the reliability and validity of the DAS, supporting its use as a research tool.

Improving FIA trend analysis through model-based estimation using landsat disturbance maps and the forest vegetation simulator

Treesearch

Sean P. Healey; Gretchen G. Moisen; Paul L. Patterson

2012-01-01

The Forest Inventory and Analysis (FIA) Program's panel system, in which 10-20 percent of the sample is measured in any given year, is designed to increase the currency of FIA reporting and its sensitivity to factors operating at relatively fine temporal scales. Now that much of the country has completed at least one measurement cycle over all panels, there is an...

A novel approach combining self-organizing map and parallel factor analysis for monitoring water quality of watersheds under non-point source pollution

PubMed Central

Zhang, Yixiang; Liang, Xinqiang; Wang, Zhibo; Xu, Lixian

2015-01-01

High content of organic matter in the downstream of watersheds underscored the severity of non-point source (NPS) pollution. The major objectives of this study were to characterize and quantify dissolved organic matter (DOM) in watersheds affected by NPS pollution, and to apply self-organizing map (SOM) and parallel factor analysis (PARAFAC) to assess fluorescence properties as proxy indicators for NPS pollution and labor-intensive routine water quality indicators. Water from upstreams and downstreams was sampled to measure dissolved organic carbon (DOC) concentrations and excitation-emission matrix (EEM). Five fluorescence components were modeled with PARAFAC. The regression analysis between PARAFAC intensities (Fmax) and raw EEM measurements indicated that several raw fluorescence measurements at target excitation-emission wavelength region could provide similar DOM information to massive EEM measurements combined with PARAFAC. Regression analysis between DOC concentration and raw EEM measurements suggested that some regions in raw EEM could be used as surrogates for labor-intensive routine indicators. SOM can be used to visualize the occurrence of pollution. Relationship between DOC concentration and PARAFAC components analyzed with SOM suggested that PARAFAC component 2 might be the major part of bulk DOC and could be recognized as a proxy indicator to predict the DOC concentration. PMID:26526140

Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines.

PubMed

Wang, Ju; McClean, Phillip E; Lee, Rian; Goos, R Jay; Helms, Ted

2008-04-01

Association mapping is an alternative to mapping in a biparental population. A key to successful association mapping is to avoid spurious associations by controlling for population structure. Confirming the marker/trait association in an independent population is necessary for the implementation of the marker in other genetic studies. Two independent soybean populations consisting of advanced breeding lines representing the diversity within maturity groups 00, 0, and I were screened in multi-site, replicated field trials to discover molecular markers associated with iron deficiency chlorosis (IDC), a major yield-limiting factor in soybean. Lines with extreme phenotypes were initially screened to identify simple sequence repeat (SSR) markers putatively associated with the IDC. Marker data collected from all lines were used to control for population structure and kinship relationships. Single factor analysis of variance (SFA) and mixed linear model (MLM) analyses were used to discover marker/trait associations. The MLM analyses, which include population structure, kinship or both factors, reduced the number of markers significantly associated with IDC by 50% compared with SFA. With the MLM approach, three markers were found to be associated with IDC in the first population. Two of these markers, Satt114 and Satt239, were also found to be associated with IDC in the second confirmation population. For both populations, those lines with the tolerance allele at both these two marker loci had significantly lower IDC scores than lines with one or no tolerant alleles.

Spatial relationships between above-ground biomass and bird species biodiversity in Palawan, Philippines.

PubMed

Singh, Minerva; Friess, Daniel A; Vilela, Bruno; Alban, Jose Don T De; Monzon, Angelica Kristina V; Veridiano, Rizza Karen A; Tumaneng, Roven D

2017-01-01

This study maps distribution and spatial congruence between Above-Ground Biomass (AGB) and species richness of IUCN listed conservation-dependent and endemic avian fauna in Palawan, Philippines. Grey Level Co-Occurrence Texture Matrices (GLCMs) extracted from Landsat and ALOS-PALSAR were used in conjunction with local field data to model and map local-scale field AGB using the Random Forest algorithm (r = 0.92 and RMSE = 31.33 Mg·ha-1). A support vector regression (SVR) model was used to identify the factors influencing variation in avian species richness at a 1km scale. AGB is one of the most important determinants of avian species richness for the study area. Topographic factors and anthropogenic factors such as distance from the roads were also found to strongly influence avian species richness. Hotspots of high AGB and high species richness concentration were mapped using hotspot analysis and the overlaps between areas of high AGB and avian species richness was calculated. Results show that the overlaps between areas of high AGB with high IUCN red listed avian species richness and endemic avian species richness were fairly limited at 13% and 8% at the 1-km scale. The overlap between 1) low AGB and low IUCN richness, and 2) low AGB and low endemic avian species richness was higher at 36% and 12% respectively. The enhanced capacity to spatially map the correlation between AGB and avian species richness distribution will further assist the conservation and protection of forest areas and threatened avian species.

A comparison of policy and direct practice stakeholder perceptions of factors affecting evidence-based practice implementation using concept mapping

PubMed Central

2011-01-01

Background The goal of this study was to assess potential differences between administrators/policymakers and those involved in direct practice regarding factors believed to be barriers or facilitating factors to evidence-based practice (EBP) implementation in a large public mental health service system in the United States. Methods Participants included mental health system county officials, agency directors, program managers, clinical staff, administrative staff, and consumers. As part of concept mapping procedures, brainstorming groups were conducted with each target group to identify specific factors believed to be barriers or facilitating factors to EBP implementation in a large public mental health system. Statements were sorted by similarity and rated by each participant in regard to their perceived importance and changeability. Multidimensional scaling, cluster analysis, descriptive statistics and t-tests were used to analyze the data. Results A total of 105 statements were distilled into 14 clusters using concept-mapping procedures. Perceptions of importance of factors affecting EBP implementation varied between the two groups, with those involved in direct practice assigning significantly higher ratings to the importance of Clinical Perceptions and the impact of EBP implementation on clinical practice. Consistent with previous studies, financial concerns (costs, funding) were rated among the most important and least likely to change by both groups. Conclusions EBP implementation is a complex process, and different stakeholders may hold different opinions regarding the relative importance of the impact of EBP implementation. Implementation efforts must include input from stakeholders at multiple levels to bring divergent and convergent perspectives to light. PMID:21899754

A comparison of policy and direct practice stakeholder perceptions of factors affecting evidence-based practice implementation using concept mapping.

PubMed

Green, Amy E; Aarons, Gregory A

2011-09-07

The goal of this study was to assess potential differences between administrators/policymakers and those involved in direct practice regarding factors believed to be barriers or facilitating factors to evidence-based practice (EBP) implementation in a large public mental health service system in the United States. Participants included mental health system county officials, agency directors, program managers, clinical staff, administrative staff, and consumers. As part of concept mapping procedures, brainstorming groups were conducted with each target group to identify specific factors believed to be barriers or facilitating factors to EBP implementation in a large public mental health system. Statements were sorted by similarity and rated by each participant in regard to their perceived importance and changeability. Multidimensional scaling, cluster analysis, descriptive statistics and t-tests were used to analyze the data. A total of 105 statements were distilled into 14 clusters using concept-mapping procedures. Perceptions of importance of factors affecting EBP implementation varied between the two groups, with those involved in direct practice assigning significantly higher ratings to the importance of Clinical Perceptions and the impact of EBP implementation on clinical practice. Consistent with previous studies, financial concerns (costs, funding) were rated among the most important and least likely to change by both groups. EBP implementation is a complex process, and different stakeholders may hold different opinions regarding the relative importance of the impact of EBP implementation. Implementation efforts must include input from stakeholders at multiple levels to bring divergent and convergent perspectives to light.

Participatory GIS for Soil Conservation in Phewa Watershed of Nepal

NASA Astrophysics Data System (ADS)

Bhandari, K. P.

2012-07-01

Participatory Geographic Information Systems (PGIS) can integrate participatory methodologies with geo-spatial technologies for the representation of characteristic of particular place. Over the last decade, researchers use this method to integrate the local knowledge of community within a GIS and Society conceptual framework. Participatory GIS are tailored to answer specific geographic questions at the local level and their modes of implementation vary considerably across space, ranging from field-based, qualitative approaches to more complex web-based applications. These broad ranges of techniques, PGIS are becoming an effective methodology for incorporating community local knowledge into complex spatial decision-making processes. The objective of this study is to reduce the soil erosion by formulating the general rule for the soil conservation by participation of the stakeholders. The poster was prepared by satellite image, topographic map and Arc GIS software including the local knowledge. The data were collected from the focus group discussion and the individual questionnaire for incorporate the local knowledge and use it to find the risk map on the basis of economic, social and manageable physical factors for the sensitivity analysis. The soil erosion risk map is prepared by the physical factors Rainfall-runoff erosivity, Soil erodibility, Slope length, Slope steepness, Cover-management, Conservation practice using RUSLE model. After the comparison and discussion among stakeholders, researcher and export group, and the soil erosion risk map showed that socioeconomic, social and manageable physical factors management can reduce the soil erosion. The study showed that the preparation of the poster GIS map and implement this in the watershed area could reduce the soil erosion in the study area compared to the existing national policy.

Landscape Heterogeneity mapping for Access to Tribal health care in Nilgiris District of Tamil Nadu, India

NASA Astrophysics Data System (ADS)

Brindha, B.; Prashanthi Devi, M.

2014-11-01

The Nilgiris district in Tamilnadu has a rich biodiversity in terms of flora, fauna and ethnic population. The district is basically a mountainous region, situated at an elevation of 2000 to 2,600 meters above MSL and constituting of several hill and Steep Mountain valleys. This region houses six tribes who are mainly forest dwellers and live in close settlements depending on the forest resources for their livelihood. The Tribes of Nilgiris have been diagnosed and monitored for Sickle cell Anemia which is a disease of major concern among these ethnic populations. This genetic disorder developed due to the sickling of Red Blood Cells has increased during the past few decades. The Tribes, as they live in close encounter with the forest regions and have strict social cultural barriers, face difficulty in availing treatment or counseling from the Sickle Cell Research Center (SCRC) and other NGOs like NAWA and AHWINI in the region. It was observed that many factors such as landscape terrain, climatic conditions and improper roads tend to hinder the access to appropriate health care. The SCRC in Gudalur region is a facility established to monitor the disease cases inspite of these influencing factors. On analyzing the year bound age wise classification among male and female patients, certain dropouts in cases were observed which may be due to inaccessible condition or migration of the patient. In our study, Landscape heterogeneity mapping for different climatic seasons was done in ArcGIS 10.1. For this, contour and terrain maps, road networks and villages were prepared and factors that determine Terrain Difficulty were assessed. Vegetation mapping using IRS satellite images for the study region was attempted and associated with the landscape map. A risk analysis was proposed based on terrain difficulty and access to the nearest Health care Center. Based on this, the above factors alternate routes were suggested to access the difficult areas.

Determining Coastal Hazards Risk Perception to Enhance Local Mitigation Planning through a Participatory Mapping Approach

NASA Astrophysics Data System (ADS)

Bethel, M.; Braud, D.; Lambeth, T.; Biber, P.; Wu, W.

2017-12-01

Coastal community leaders, government officials, and natural resource managers must be able to accurately assess and predict a given coastal landscape's sustainability and/or vulnerability as coastal habitat continues to undergo rapid and dramatic changes associated with natural and anthropogenic activities such as accelerated relative sea level rise (SLR). To help address this information need, a multi-disciplinary project team conducted Sea Grant sponsored research in Louisiana and Mississippi with traditional ecosystem users and natural resource managers to determine a method for producing localized vulnerability and sustainability maps for projected SLR and storm surge impacts, and determine how and whether the results of such an approach can provide more useful information to enhance hazard mitigation planning. The goals of the project are to develop and refine SLR visualization tools for local implementation in areas experiencing subsidence and erosion, and discover the different ways stakeholder groups evaluate risk and plan mitigation strategies associated with projected SLR and storm surge. Results from physical information derived from data and modeling of subsidence, erosion, engineered restoration and coastal protection features, historical land loss, and future land projections under SLR are integrated with complimentary traditional ecological knowledge (TEK) offered by the collaborating local ecosystem users for these assessments. The data analysis involves interviewing stakeholders, coding the interviews for themes, and then converting the themes into vulnerability and sustainability factors. Each factor is weighted according to emphasis by the TEK experts and number of experts who mention it to determine which factors are the highest priority. The priority factors are then mapped with emphasis on the perception of contributing to local community vulnerability or sustainability to SLR and storm surge. The maps are used by the collaborators to benefit local hazard mitigation and adaptation planning. The results to date in achieving the project objectives will be presented that include: analyses of scientific field data collected related to marsh vegetation biomass characteristics, analyses of TEK data collected, and mapping products developed.

Assessing Local Knowledge Use in Agroforestry Management with Cognitive Maps

NASA Astrophysics Data System (ADS)

Isaac, Marney E.; Dawoe, Evans; Sieciechowicz, Krystyna

2009-06-01

Small-holder farmers often develop adaptable agroforestry management techniques to improve and diversify crop production. In the cocoa growing region of Ghana, local knowledge on such farm management holds a noteworthy role in the overall farm development. The documentation and analysis of such knowledge use in cocoa agroforests may afford an applicable framework to determine mechanisms driving farmer preference and indicators in farm management. This study employed 12 in-depth farmer interviews regarding variables in farm management as a unit of analysis and utilized cognitive mapping as a qualitative method of analysis. Our objectives were (1) to illustrate and describe agroforestry management variables and associated farm practices, (2) to determine the scope of decision making of individual farmers, and (3) to investigate the suitability of cognitive mapping as a tool for assessing local knowledge use. Results from the cognitive maps revealed an average of 16 ± 3 variables and 19 ± 3 links between management variables in the farmer cognitive maps. Farmer use of advantageous ecological processes was highly central to farm management (48% of all variables), particularly manipulation of organic matter, shade and food crop establishment, and maintenance of a tree stratum as the most common, highly linked variables. Over 85% of variables included bidirectional arrows, interpreted as farm management practices dominated by controllable factors, insofar as farmers indicated an ability to alter most farm characteristics. Local knowledge use on cocoa production revealed detailed indicators for site evaluation, thus affecting farm preparation and management. Our findings suggest that amid multisourced information under conditions of uncertainty, strategies for adaptable agroforestry management should integrate existing and localized management frameworks and that cognitive mapping provides a tool-based approach to advance such a management support system.

Assessing local knowledge use in agroforestry management with cognitive maps.

PubMed

Isaac, Marney E; Dawoe, Evans; Sieciechowicz, Krystyna

2009-06-01

Small-holder farmers often develop adaptable agroforestry management techniques to improve and diversify crop production. In the cocoa growing region of Ghana, local knowledge on such farm management holds a noteworthy role in the overall farm development. The documentation and analysis of such knowledge use in cocoa agroforests may afford an applicable framework to determine mechanisms driving farmer preference and indicators in farm management. This study employed 12 in-depth farmer interviews regarding variables in farm management as a unit of analysis and utilized cognitive mapping as a qualitative method of analysis. Our objectives were (1) to illustrate and describe agroforestry management variables and associated farm practices, (2) to determine the scope of decision making of individual farmers, and (3) to investigate the suitability of cognitive mapping as a tool for assessing local knowledge use. Results from the cognitive maps revealed an average of 16 +/- 3 variables and 19 +/- 3 links between management variables in the farmer cognitive maps. Farmer use of advantageous ecological processes was highly central to farm management (48% of all variables), particularly manipulation of organic matter, shade and food crop establishment, and maintenance of a tree stratum as the most common, highly linked variables. Over 85% of variables included bidirectional arrows, interpreted as farm management practices dominated by controllable factors, insofar as farmers indicated an ability to alter most farm characteristics. Local knowledge use on cocoa production revealed detailed indicators for site evaluation, thus affecting farm preparation and management. Our findings suggest that amid multisourced information under conditions of uncertainty, strategies for adaptable agroforestry management should integrate existing and localized management frameworks and that cognitive mapping provides a tool-based approach to advance such a management support system.

Understanding help-seeking intentions in male military cadets: An application of perceptual mapping.

PubMed

Bass, Sarah Bauerle; Muñiz, Javier; Gordon, Thomas F; Maurer, Laurie; Patterson, Freda

2016-05-17

Research suggests that men are less likely to seek help for depression, substance abuse, and stressful life events due to negative perceptions of asking for and receiving help. This may be exacerbated in male military cadets who exhibit higher levels of gender role conflict because of military culture. This exploratory study examined the perceptions of 78 male military cadets toward help-seeking behaviors. Cadets completed the 31-item Barriers to Help Seeking Scale (BHSS) and a component factor analysis was used to generate five composite variables and compare to validated factors. Perceptual mapping and vector modeling, which produce 3-dimensional models of a group's perceptions, were then used to model how they conceptualize help-seeking. Factor analysis showed slightly different groupings than the BHSS, perhaps attributed to different characteristics of respondents, who are situated in a military school compared to general university males. Perceptual maps show that cadets perceive trust of doctors closest to them and help-seeking farthest, supporting the concept that these males have rigid beliefs about having control and its relationship to health seeking. Differences were seen when comparing maps of White and non-White cadets. White cadets positioned themselves far away from all variables, while non-White cadets were closest to "emotional control". To move these cadets toward help-seeking, vector modeling suggests that interventions should focus on their general trust of doctors, accepting lack of control, and decreasing feelings of weakness when asking for help. For non-White cadets a focus on self-reliance may also need to be emphasized. Use of these unique methods resulted in articulation of specific barriers that if addressed early, may have lasting effects on help-seeking behavior as these young men become adults. Future studies are needed to develop and test specific interventions to promote help-seeking among military cadets.

Spatial analysis of the relationship between mortality from cardiovascular and cerebrovascular disease and drinking water hardness.

PubMed

Ferrandiz, Juan; Abellan, Juan J; Gomez-Rubio, Virgilio; Lopez-Quilez, Antonio; Sanmartin, Pilar; Abellan, Carlos; Martinez-Beneito, Miguel A; Melchor, Inmaculada; Vanaclocha, Hermelinda; Zurriaga, Oscar; Ballester, Ferran; Gil, Jose M; Perez-Hoyos, Santiago; Ocana, Ricardo

2004-06-01

Previously published scientific papers have reported a negative correlation between drinking water hardness and cardiovascular mortality. Some ecologic and case-control studies suggest the protective effect of calcium and magnesium concentration in drinking water. In this article we present an analysis of this protective relationship in 538 municipalities of Comunidad Valenciana (Spain) from 1991-1998. We used the Spanish version of the Rapid Inquiry Facility (RIF) developed under the European Environment and Health Information System (EUROHEIS) research project. The strategy of analysis used in our study conforms to the exploratory nature of the RIF that is used as a tool to obtain quick and flexible insight into epidemiologic surveillance problems. This article describes the use of the RIF to explore possible associations between disease indicators and environmental factors. We used exposure analysis to assess the effect of both protective factors--calcium and magnesium--on mortality from cerebrovascular (ICD-9 430-438) and ischemic heart (ICD-9 410-414) diseases. This study provides statistical evidence of the relationship between mortality from cardiovascular diseases and hardness of drinking water. This relationship is stronger in cerebrovascular disease than in ischemic heart disease, is more pronounced for women than for men, and is more apparent with magnesium than with calcium concentration levels. Nevertheless, the protective nature of these two factors is not clearly established. Our results suggest the possibility of protectiveness but cannot be claimed as conclusive. The weak effects of these covariates make it difficult to separate them from the influence of socioeconomic and environmental factors. We have also performed disease mapping of standardized mortality ratios to detect clusters of municipalities with high risk. Further standardization by levels of calcium and magnesium in drinking water shows changes in the maps when we remove the effect of these covariates.

GIS-aided low flow mapping

NASA Astrophysics Data System (ADS)

Saghafian, B.; Mohammadi, A.

2003-04-01

Most studies involving water resources allocation, water quality, hydropower generation, and allowable water withdrawal and transfer require estimation of low flows. Normally, frequency analysis on at-station D-day low flow data is performed to derive various T-yr return period values. However, this analysis is restricted to the location of hydrometric stations where the flow discharge is measured. Regional analysis is therefore conducted to relate the at-station low flow quantiles to watershed characteristics. This enables the transposition of low flow quantiles to ungauged sites. Nevertheless, a procedure to map the regional regression relations for the entire stream network, within the bounds of the relations, is particularly helpful when one studies and weighs alternative sites for certain water resources project. In this study, we used a GIS-aided procedure for low flow mapping in Gilan province, part of northern region in Iran. Gilan enjoys a humid climate with an average of 1100 mm annual precipitation. Although rich in water resources, the highly populated area is quite dependent on minimum amount of water to sustain the vast rice farming and to maintain required flow discharge for quality purposes. To carry out the low flow analysis, a total of 36 hydrometric stations with sufficient and reliable discharge data were identified in the region. The average area of the watersheds was 250 sq. km. Log Pearson type 3 was found the best distribution for flow durations over 60 days, while log normal fitted well the shorter duration series. Low flows with return periods of 2, 5, 10, 25, 50, and 100 year were then computed. Cluster analysis identified two homogeneous areas. Although various watershed parameters were examined in factor analysis, the results showed watershed area, length of the main stream, and annual precipitation were the most effective low flow parameters. The regression equations were then mapped with the aid of GIS based on flow accumulation maps and the corresponding spatially averaged values of other parameters over the upslope area of all stream pixels exceeding a certain threshold area. Such map clearly shows the spatial variation of low flow quantiles along the stream network and enables the study of low flow profiles along any stream.

Flood Hazard Mapping by Applying Fuzzy TOPSIS Method

NASA Astrophysics Data System (ADS)

Han, K. Y.; Lee, J. Y.; Keum, H.; Kim, B. J.; Kim, T. H.

2017-12-01

There are lots of technical methods to integrate various factors for flood hazard mapping. The purpose of this study is to suggest the methodology of integrated flood hazard mapping using MCDM(Multi Criteria Decision Making). MCDM problems involve a set of alternatives that are evaluated on the basis of conflicting and incommensurate criteria. In this study, to apply MCDM to assessing flood risk, maximum flood depth, maximum velocity, and maximum travel time are considered as criterion, and each applied elements are considered as alternatives. The scheme to find the efficient alternative closest to a ideal value is appropriate way to assess flood risk of a lot of element units(alternatives) based on various flood indices. Therefore, TOPSIS which is most commonly used MCDM scheme is adopted to create flood hazard map. The indices for flood hazard mapping(maximum flood depth, maximum velocity, and maximum travel time) have uncertainty concerning simulation results due to various values according to flood scenario and topographical condition. These kind of ambiguity of indices can cause uncertainty of flood hazard map. To consider ambiguity and uncertainty of criterion, fuzzy logic is introduced which is able to handle ambiguous expression. In this paper, we made Flood Hazard Map according to levee breach overflow using the Fuzzy TOPSIS Technique. We confirmed the areas where the highest grade of hazard was recorded through the drawn-up integrated flood hazard map, and then produced flood hazard map can be compared them with those indicated in the existing flood risk maps. Also, we expect that if we can apply the flood hazard map methodology suggested in this paper even to manufacturing the current flood risk maps, we will be able to make a new flood hazard map to even consider the priorities for hazard areas, including more varied and important information than ever before. Keywords : Flood hazard map; levee break analysis; 2D analysis; MCDM; Fuzzy TOPSIS Acknowlegement This research was supported by a grant (17AWMP-B079625-04) from Water Management Research Program funded by Ministry of Land, Infrastructure and Transport of Korean government.

Medical Geography: a Promising Field of Application for Geostatistics

PubMed Central

Goovaerts, P.

2008-01-01

The analysis of health data and putative covariates, such as environmental, socio-economic, behavioral or demographic factors, is a promising application for geostatistics. It presents, however, several methodological challenges that arise from the fact that data are typically aggregated over irregular spatial supports and consist of a numerator and a denominator (i.e. population size). This paper presents an overview of recent developments in the field of health geostatistics, with an emphasis on three main steps in the analysis of areal health data: estimation of the underlying disease risk, detection of areas with significantly higher risk, and analysis of relationships with putative risk factors. The analysis is illustrated using age-adjusted cervix cancer mortality rates recorded over the 1970–1994 period for 118 counties of four states in the Western USA. Poisson kriging allows the filtering of noisy mortality rates computed from small population sizes, enhancing the correlation with two putative explanatory variables: percentage of habitants living below the federally defined poverty line, and percentage of Hispanic females. Area-to-point kriging formulation creates continuous maps of mortality risk, reducing the visual bias associated with the interpretation of choropleth maps. Stochastic simulation is used to generate realizations of cancer mortality maps, which allows one to quantify numerically how the uncertainty about the spatial distribution of health outcomes translates into uncertainty about the location of clusters of high values or the correlation with covariates. Last, geographically-weighted regression highlights the non-stationarity in the explanatory power of covariates: the higher mortality values along the coast are better explained by the two covariates than the lower risk recorded in Utah. PMID:19412347

Interferon regulatory factor 5 is a potential target of autoimmune response triggered by Epstein-barr virus and Mycobacterium avium subsp. paratuberculosis in rheumatoid arthritis: investigating a mechanism of molecular mimicry.

PubMed

Bo, Marco; Erre, Gian Luca; Niegowska, Magdalena; Piras, Marco; Taras, Loredana; Longu, Maria Giovanna; Passiu, Giuseppe; Sechi, Leonardo A

2018-01-01

Rheumatoid arthritis (RA) is a chronic disease characterised by a pro-inflammatory cytokines linked erosive joint damage and by humoral and cellular response against a broad range of self-peptides. Molecular mimicry between Epstein-Barr virus (EBV), Mycobacterium avium subsp. paratuberculosis (MAP) and host peptides has long been regarded as an RA pathogenetic mechanism. Using bioinformatic analysis we identified high sequence homology among interferon regulatory factor 5 (IRF5), EBV antigen BOLF1 and MAP antigen MAP_4027. Our objective was to evaluate the presence in sera of RA patients of antibodies (Abs) directed against human homologous IRF5 cross-reacting with BOLF1 and MAP_4027. Frequency of reactivity against IRF5424-434, BOLF1305-320 and MAP_402718-32 was tested by indirect ELISA in sera from 71 RA patients and 60 healthy controls (HCs). RA sera show a remarkable high frequency of reactivity against IRF5424-434 in comparison to HCs (69% vs. 8%; p<0.0001). Similarly, seroreactivity against BOLF1305-320 was more frequently detected in RA sera than in HCs counterpart (58% vs. 8%; p<0.0001). Frequency of Abs against MAP_402718-32 was 17% in RA sera vs. 5% in HCs with a p-value at the threshold level (p<0.051). Prevalence of Abs against at least one of the assessed epitopes reached 72% in RA patients and 15% among HCs. Levels of Abs in RA patients were significantly related to systemic inflammation. IRF5 is a potential autoimmune target of RA. Our results support the hypothesis that EBV and MAP infections may be involved in the pathogenesis of RA, igniting a secondary immune response that cross-reacts against RA self-peptides.

Where do students struggle in the field? Computer-aided evaluation of mapping errors from an undergraduate Field Geology summer course

NASA Astrophysics Data System (ADS)

Lang, K. A.; Petrie, G.

2014-12-01

Extended field-based summer courses provide an invaluable field experience for undergraduate majors in the geosciences. These courses often utilize the construction of geological maps and structural cross sections as the primary pedagogical tool to teach basic map orientation, rock identification and structural interpretation. However, advances in the usability and ubiquity of Geographic Information Systems in these courses presents new opportunities to evaluate student work. In particular, computer-based quantification of systematic mapping errors elucidates the factors influencing student success in the field. We present a case example from a mapping exercise conducted in a summer Field Geology course at a popular field location near Dillon, Montana. We use a computer algorithm to automatically compare the placement and attribution of unit contacts with spatial variables including topographic slope, aspect, bedding attitude, ground cover and distance from starting location. We compliment analyses with anecdotal and survey data that suggest both physical factors (e.g. steep topographic slope) as well as structural nuance (e.g. low angle bedding) may dominate student frustration, particularly in courses with a high student to instructor ratio. We propose mechanisms to improve student experience by allowing students to practice skills with orientation games and broadening student background with tangential lessons (e.g. on colluvial transport processes). As well, we suggest low-cost ways to decrease the student to instructor ratio by supporting returning undergraduates from previous years or staging mapping over smaller areas. Future applications of this analysis might include a rapid and objective system for evaluation of student maps (including point-data, such as attitude measurements) and quantification of temporal trends in student work as class sizes, pedagogical approaches or environmental variables change. Long-term goals include understanding and characterizing stochasticity in geological mapping beyond the undergraduate classroom, and better quantifying uncertainty in published map products.

Applying process mapping and analysis as a quality improvement strategy to increase the adoption of fruit, vegetable, and water breaks in Australian primary schools.

PubMed

Biggs, Janice S; Farrell, Louise; Lawrence, Glenda; Johnson, Julie K

2014-03-01

Over the past decade, public health policy in Australia has prioritized the prevention and control of obesity and invested in programs that promote healthy eating-related behaviors, which includes increasing fruit and vegetable consumption in children. This article reports on a study that used process mapping and analysis as a quality improvement strategy to improve the delivery of a nutrition primary prevention program delivered in primary schools in New South Wales, Australia. Crunch&Sip® has been delivered since 2008. To date, adoption is low with only 25% of schools implementing the program. We investigated the cause of low adoption and propose actions to increase school participation. We conducted semistructured interviews with key stakeholders and analyzed the process of delivering Crunch&Sip to schools. Interviews and process mapping and analysis identified a number of barriers to schools adopting the program. The analyses identified the need to simplify and streamline the process of delivering the program to schools and introduce monitoring and feedback loops to track ongoing participation. The combination of stakeholder interviews and process mapping and analysis provided important practical solutions to improving program delivery and also contributed to building an understanding of factors that help and hinder program adoption. The insight provided by this analysis helped identify usable routine measures of adoption, which were an improvement over those used in the existing program plan. This study contributed toward improving the quality and efficiency of delivering a health promoting program to work toward achieving healthy eating behaviors in children.

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome.

PubMed

Ribeiro, Antonio; Golicz, Agnieszka; Hackett, Christine Anne; Milne, Iain; Stephen, Gordon; Marshall, David; Flavell, Andrew J; Bayer, Micha

2015-11-11

Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling - quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth. This resulted in 576 possible factor level combinations. We used error- and variant-free simulated reads to ensure that every SNP found was indeed a false positive. The variation in the number of FP SNPs generated ranged from 0 to 36,621 for the 120 million base pairs (Mbp) genome. All of the experimental factors tested had statistically significant effects on the number of FP SNPs generated and there was a considerable amount of interaction between the different factors. Using a fragmented reference sequence led to a dramatic increase in the number of FP SNPs generated, as did relaxed read mapping and a lack of SNP filtering. The choice of reference assembler, mapper and variant caller also significantly affected the outcome. The effect of read length was more complex and suggests a possible interaction between mapping specificity and the potential for contributing more false positives as read length increases. The choice of tools and parameters involved in variant calling can have a dramatic effect on the number of FP SNPs produced, with particularly poor combinations of software and/or parameter settings yielding tens of thousands in this experiment. Between-factor interactions make simple recommendations difficult for a SNP discovery pipeline but the quality of the reference sequence is clearly of paramount importance. Our findings are also a stark reminder that it can be unwise to use the relaxed mismatch settings provided as defaults by some read mappers when reads are being mapped to a relatively unfinished reference sequence from e.g. a non-model organism in its early stages of genomic exploration.

Relationship of nutrition and physical activity behaviors and fitness measures to academic performance for sixth graders in a midwest city school district.

PubMed

Edwards, Jane U; Mauch, Lois; Winkelman, Mark R

2011-02-01

To support curriculum and policy, a midwest city school district assessed the association of selected categories of nutrition and physical activity (NUTR/PA) behaviors, fitness measures, and body mass index (BMI) with academic performance (AP) for 800 sixth graders. Students completed an adapted Youth Risk Behavior Surveillance Survey (NUTR/PA behaviors), fitness assessments (mile run, curl-ups, push-ups, height, and weight) with results matched to standardized scores (Measures of Academic Progress [MAP]), meal price status, and gender. Differences in mean MAP scores (math and reading) were compared by selected categories of each variable utilizing 1-way analysis of variance. Associations were determined by stepwise multiple regression utilizing mean MAP scores (for math and for reading) as the dependent variable and NUTR/PA behaviors, fitness, and BMI categories as independent variables. Significance was set at α = 0.05. Higher MAP math scores were associated with NUTR (more milk and breakfast; less 100% fruit juice and sweetened beverages [SB]) and PA (increased vigorous PA and sports teams; reduced television), and fitness (higher mile run performance). Higher MAP reading scores were associated with NUTR (fewer SB) and PA (increased vigorous PA, reduced television). Regression analysis indicated about 11.1% of the variation in the mean MAP math scores and 6.7% of the mean MAP reading scores could be accounted for by selected NUTR/PA behaviors, fitness, meal price status, and gender. Many positive NUTR/PA behaviors and fitness measures were associated with higher MAP scores supporting the school district focus on healthy lifestyles. Additional factors, including meal price status and gender, contribute to AP. © 2011, Fargo Public School.

Mapping seabed sediments: Comparison of manual, geostatistical, object-based image analysis and machine learning approaches

NASA Astrophysics Data System (ADS)

Diesing, Markus; Green, Sophie L.; Stephens, David; Lark, R. Murray; Stewart, Heather A.; Dove, Dayton

2014-08-01

Marine spatial planning and conservation need underpinning with sufficiently detailed and accurate seabed substrate and habitat maps. Although multibeam echosounders enable us to map the seabed with high resolution and spatial accuracy, there is still a lack of fit-for-purpose seabed maps. This is due to the high costs involved in carrying out systematic seabed mapping programmes and the fact that the development of validated, repeatable, quantitative and objective methods of swath acoustic data interpretation is still in its infancy. We compared a wide spectrum of approaches including manual interpretation, geostatistics, object-based image analysis and machine-learning to gain further insights into the accuracy and comparability of acoustic data interpretation approaches based on multibeam echosounder data (bathymetry, backscatter and derivatives) and seabed samples with the aim to derive seabed substrate maps. Sample data were split into a training and validation data set to allow us to carry out an accuracy assessment. Overall thematic classification accuracy ranged from 67% to 76% and Cohen's kappa varied between 0.34 and 0.52. However, these differences were not statistically significant at the 5% level. Misclassifications were mainly associated with uncommon classes, which were rarely sampled. Map outputs were between 68% and 87% identical. To improve classification accuracy in seabed mapping, we suggest that more studies on the effects of factors affecting the classification performance as well as comparative studies testing the performance of different approaches need to be carried out with a view to developing guidelines for selecting an appropriate method for a given dataset. In the meantime, classification accuracy might be improved by combining different techniques to hybrid approaches and multi-method ensembles.

An offline-online Web-GIS Android application for fast data acquisition of landslide hazard and risk

NASA Astrophysics Data System (ADS)

Olyazadeh, Roya; Sudmeier-Rieux, Karen; Jaboyedoff, Michel; Derron, Marc-Henri; Devkota, Sanjaya

2017-04-01

Regional landslide assessments and mapping have been effectively pursued by research institutions, national and local governments, non-governmental organizations (NGOs), and different stakeholders for some time, and a wide range of methodologies and technologies have consequently been proposed. Land-use mapping and hazard event inventories are mostly created by remote-sensing data, subject to difficulties, such as accessibility and terrain, which need to be overcome. Likewise, landslide data acquisition for the field navigation can magnify the accuracy of databases and analysis. Open-source Web and mobile GIS tools can be used for improved ground-truthing of critical areas to improve the analysis of hazard patterns and triggering factors. This paper reviews the implementation and selected results of a secure mobile-map application called ROOMA (Rapid Offline-Online Mapping Application) for the rapid data collection of landslide hazard and risk. This prototype assists the quick creation of landslide inventory maps (LIMs) by collecting information on the type, feature, volume, date, and patterns of landslides using open-source Web-GIS technologies such as Leaflet maps, Cordova, GeoServer, PostgreSQL as the real DBMS (database management system), and PostGIS as its plug-in for spatial database management. This application comprises Leaflet maps coupled with satellite images as a base layer, drawing tools, geolocation (using GPS and the Internet), photo mapping, and event clustering. All the features and information are recorded into a GeoJSON text file in an offline version (Android) and subsequently uploaded to the online mode (using all browsers) with the availability of Internet. Finally, the events can be accessed and edited after approval by an administrator and then be visualized by the general public.

Cross-Cultural Adaptation of the Profile Fitness Mapping Neck Questionnaire to Brazilian Portuguese: Internal Consistency, Reliability, and Construct and Structural Validity.

PubMed

Ferreira, Mariana Cândido; Björklund, Martin; Dach, Fabiola; Chaves, Thais Cristina

The purpose of this study was to adapt and evaluate the psychometric properties of the ProFitMap-neck to Brazilian Portuguese. The cross-cultural adaptation consisted of 5 stages, and 180 female patients with chronic neck pain participated in the study. A subsample (n = 30) answered the pretest, and another subsample (n = 100) answered the questionnaire a second time. Internal consistency, test-retest reliability, and construct validity (hypothesis testing and structural validity) were estimated. For construct validity, the scores of the questionnaire were correlated with the Neck Disability Index (NDI), and the Hospital Anxiety and Depression Scale (HADS), the Tampa Scale of Kinesiophobia (TSK), and the 36-item Short-Form Health Survey (SF-36). Internal consistency was determined by adequate Cronbach's α values (α > 0.70). Strong reliability was identified by high intraclass correlation coefficients (ICC > 0.75). Construct validity was identified by moderate and strong correlations of the Br-ProFitMap-neck with total NDI score (-0.56 50%, Kaiser-Meyer-Olkin index > 0.50, eigenvalue > 1, and factor loadings > 0.2. Br-ProFitMap-neck had adequate psychometric properties and can be used in clinical settings, as well as research, in patients with chronic neck pain. Copyright © 2017. Published by Elsevier Inc.

[Relationship between reference values of fibrinogen and geographical factors based on neural network analysis].

PubMed

Li, Meng-Jiao; Ge, Miao; Wang, Cong-Xia; Cen, Min-Yi; Jiang, Ji-Lin; He, Jin-Wei; Lin, Qian-Yi; Liu, Xin

2016-08-20

To analyze the relationship between the reference values of fibrinogen (FIB) in healthy Chinese adults and geographical factors to provide scientific evidences for establishing the uniform standard. The reference values of FIB of 10701 Chinese healthy adults from 103 cities were collected to investigate their relationship with 18 geographical factors including spatial index, terrain index, climate index, and soil index. Geographical factors that significantly correlated with the reference values were selected for constructing the BP neural network model. The spatial distribution map of the reference value of FIB of healthy Chinese adults was fitted by disjunctive kriging interpolation. We used the 5-layer neural network and selected 2000 times of training covering 11 hidden layers to build the simulation rule for simulating the relationship between FIB and geographical environmental factors using the MATLAB software. s The reference value of FIB in healthy Chinese adults was significantly correlated with the latitude, sunshine duration, annual average temperature, annual average relative humidity, annual precipitation, annual range of air temperature, average annual soil gravel content, and soil cation exchange capacity (silt). The artificial neural networks were created to analyze the simulation of the selected indicators of geographical factors. The spatial distribution map of the reference values of FIB in healthy Chinese adults showed a distribution pattern that FIB levels were higher in the South and lower in the North, and higher in the East and lower in the West. When the geographical factors of a certain area are known, the reference values of FIB in healthy Chinese adults can be obtained by establishing the neural network mode or plotting the spatial distribution map.

Information theory applications for biological sequence analysis.

PubMed

Vinga, Susana

2014-05-01

Information theory (IT) addresses the analysis of communication systems and has been widely applied in molecular biology. In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy and mutual information. This review covers several aspects of IT applications, ranging from genome global analysis and comparison, including block-entropy estimation and resolution-free metrics based on iterative maps, to local analysis, comprising the classification of motifs, prediction of transcription factor binding sites and sequence characterization based on linguistic complexity and entropic profiles. IT has also been applied to high-level correlations that combine DNA, RNA or protein features with sequence-independent properties, such as gene mapping and phenotype analysis, and has also provided models based on communication systems theory to describe information transmission channels at the cell level and also during evolutionary processes. While not exhaustive, this review attempts to categorize existing methods and to indicate their relation with broader transversal topics such as genomic signatures, data compression and complexity, time series analysis and phylogenetic classification, providing a resource for future developments in this promising area.

A new technique for ordering asymmetrical three-dimensional data sets in ecology.

PubMed

Pavoine, Sandrine; Blondel, Jacques; Baguette, Michel; Chessel, Daniel

2007-02-01

The aim of this paper is to tackle the problem that arises from asymmetrical data cubes formed by two crossed factors fixed by the experimenter (factor A and factor B, e.g., sites and dates) and a factor which is not controlled for (the species). The entries of this cube are densities in species. We approach this kind of data by the comparison of patterns, that is to say by analyzing first the effect of factor B on the species-factor A pattern, and second the effect of factor A on the species-factor B pattern. The analysis of patterns instead of individual responses requires a correspondence analysis. We use a method we call Foucart's correspondence analysis to coordinate the correspondence analyses of several independent matrices of species x factor A (respectively B) type, corresponding to each modality of factor B (respectively A). Such coordination makes it possible to evaluate the effect of factor B (respectively A) on the species-factor A (respectively B) pattern. The results obtained by such a procedure are much more insightful than those resulting from a classical single correspondence analysis applied to the global matrix that is obtained by simply unrolling the data cube, juxtaposing for example the individual species x factor A matrices through modalities of factor B. This is because a single global correspondence analysis combines three effects of factors in a way that cannot be determined from factorial maps (factor A, factor B, and factor A x factor B interaction) whereas the applications of Foucart's correspondence analysis clearly discriminate two different issues. Using two data sets, we illustrate that this technique proves to be particularly powerful in the analyses of ecological convergence which include several distinct data sets and in the analyses of spatiotemporal variations of species distributions.

Likelihood-based modification of experimental crystal structure electron density maps

DOEpatents

Terwilliger, Thomas C [Sante Fe, NM

2005-04-16

A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

Family-based linkage and association mapping reveals novel genes affecting Plum pox virus infection in Arabidopsis thaliana.

PubMed

Pagny, Gaëlle; Paulstephenraj, Pauline S; Poque, Sylvain; Sicard, Ophélie; Cosson, Patrick; Eyquard, Jean-Philippe; Caballero, Mélodie; Chague, Aurélie; Gourdon, Germain; Negrel, Lise; Candresse, Thierry; Mariette, Stéphanie; Decroocq, Véronique

2012-11-01

Sharka is a devastating viral disease caused by the Plum pox virus (PPV) in stone fruit trees and few sources of resistance are known in its natural hosts. Since any knowledge gained from Arabidopsis on plant virus susceptibility factors is likely to be transferable to crop species, Arabidopsis's natural variation was searched for host factors essential for PPV infection. To locate regions of the genome associated with susceptibility to PPV, linkage analysis was performed on six biparental populations as well as on multiparental lines. To refine quantitative trait locus (QTL) mapping, a genome-wide association analysis was carried out using 147 Arabidopsis accessions. Evidence was found for linkage on chromosomes 1, 3 and 5 with restriction of PPV long-distance movement. The most relevant signals occurred within a region at the bottom of chromosome 3, which comprises seven RTM3-like TRAF domain-containing genes. Since the resistance mechanism analyzed here is recessive and the rtm3 knockout mutant is susceptible to PPV infection, it suggests that other gene(s) present in the small identified region encompassing RTM3 are necessary for PPV long-distance movement. In consequence, we report here the occurrence of host factor(s) that are indispensable for virus long-distance movement. © 2012 INRA. New Phytologist © 2012 New Phytologist Trust.

Molecular-biological analysis of the effect of methamphetamine on the heart in restrained mice.

PubMed

Shinone, Kotaro; Tomita, Masafumi; Inoue, Hiromasa; Nakagawa, Yasuhisa; Ikemura, Mayumi; Nata, Masayuki

2010-03-01

In order to investigate the interaction in the heart between the administration of methamphetamine (MAP) and restraint of the body following it, we administrated MAP intraperitoneally to mice and restrained them, and then determined the level of mRNA expression of 22 genes in the heart using quantitative RT-PCR method. The mRNA expressions of Nfkbiz, Nr4a1 and Dusp1 changed significantly after the administration of MAP, suggesting the induction of an inflammatory condition such as damage to the myocardium. Moreover, the serum concentrations of inflammatory cytokines such as tumor necrosis factor-alpha, interleukin (IL)-1 beta and IL-6 were significantly increased by the administration of MAP. On the other hand, the mRNA expressions of Rgs2 and Rasd1 were changed by both the administration of MAP and body restraint without interaction, which indicated that these insults affected the circulatory system additively or synergistically. From these results, it is likely that the administration of MAP, followed by body restraint, might cause acute myocardial damage due to the direct myocardial toxic effect of MAP, myocardial hypoxia and/or severe hypertension, which is one of the mechanisms for sudden death in MAP abusers who were restrained due to their excited state. (c) 2010. Published by Elsevier Ireland Ltd.

Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors

NASA Astrophysics Data System (ADS)

Murumkar, Prashant Revan; Zambre, Vishal Prakash; Yadav, Mange Ram

2010-02-01

A chemical feature-based pharmacophore model was developed for Tumor Necrosis Factor-α converting enzyme (TACE) inhibitors. A five point pharmacophore model having two hydrogen bond acceptors (A), one hydrogen bond donor (D) and two aromatic rings (R) with discrete geometries as pharmacophoric features was developed. The pharmacophore model so generated was then utilized for in silico screening of a database. The pharmacophore model so developed was validated by using four compounds having proven TACE inhibitory activity which were grafted into the database. These compounds mapped well onto the five listed pharmacophoric features. This validated pharmacophore model was also used for alignment of molecules in CoMFA and CoMSIA analysis. The contour maps of the CoMFA/CoMSIA models were utilized to provide structural insight for activity improvement of potential novel TACE inhibitors. The pharmacophore model so developed could be used for in silico screening of any commercial/in house database for identification of TACE inhibiting lead compounds, and the leads so identified could be optimized using the developed CoMSIA model. The present work highlights the tremendous potential of the two mutually complementary ligand-based drug designing techniques (i.e. pharmacophore mapping and 3D-QSAR analysis) using TACE inhibitors as prototype biologically active molecules.

Quantitative characterization of material surface — Application to Ni + Mo electrolytic composite coatings

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

Kubisztal, J., E-mail: julian.kubisztal@us.edu.pl

A new approach to numerical analysis of maps of material surface has been proposed and discussed in detail. It was concluded that the roughness factor RF and the root mean square roughness S{sub q} show a saturation effect with increasing size of the analysed maps what allows determining the optimal map dimension representative of the examined material. A quantitative method of determining predominant direction of the surface texture based on the power spectral density function is also proposed and discussed. The elaborated method was applied in surface analysis of Ni + Mo composite coatings. It was shown that co-deposition ofmore » molybdenum particles in nickel matrix leads to an increase in surface roughness. In addition, a decrease in size of the embedded Mo particles in Ni matrix causes an increase of both the surface roughness and the surface texture. It was also stated that the relation between the roughness factor and the double layer capacitance C{sub dl} of the studied coatings is linear and allows determining the double layer capacitance of the smooth nickel electrode. - Highlights: •Optimization of the procedure for the scanning of the material surface •Quantitative determination of the surface roughness and texture intensity •Proposition of the parameter describing privileged direction of the surface texture •Determination of the double layer capacitance of the smooth electrode.« less

Landslide and flood hazard assessment in urban areas of Levoča region (Eastern Slovakia)

NASA Astrophysics Data System (ADS)

Magulova, Barbora; Caporali, Enrica; Bednarik, Martin

2010-05-01

The case study presents the use of statistical methods and analysis tools, for hazard assessment of "urbanization units", implemented in a Geographic Information Systems (GIS) environment. As a case study, the Levoča region (Slovakia) is selected. The region, with a total area of about 351 km2, is widely affected by landslides and floods. The problem, for small urbanization areas, is nowadays particularly significant from the socio-economic point of view. It is considered, presently, also an increasing problem, mainly because of climate change and more frequent extreme rainfall events. The geo-hazards are evaluated using a multivariate analysis. The landslide hazard assessment is based on the comparison and subsequent statistical elaboration of territorial dependence among different input factors influencing the instability of the slopes. Particularly, five factors influencing slope stability are evaluated, i.e. lithology, slope aspect, slope angle, hypsographic level and present land use. As a result a new landslide susceptibility map is compiled and different zones of stable, dormant and non-stable areas are defined. For flood hazard map a detailed digital elevation model is created. A compose index of flood hazard is derived from topography, land cover and pedology related data. To estimate flood discharge, time series of stream flow and precipitation measurements are used. The assessment results are prognostic maps of landslide hazard and flood hazard, which presents the optimal base for urbanization planning.

Box-Cox transformation for QTL mapping.

PubMed

Yang, Runqing; Yi, Nengjun; Xu, Shizhong

2006-01-01

The maximum likelihood method of QTL mapping assumes that the phenotypic values of a quantitative trait follow a normal distribution. If the assumption is violated, some forms of transformation should be taken to make the assumption approximately true. The Box-Cox transformation is a general transformation method which can be applied to many different types of data. The flexibility of the Box-Cox transformation is due to a variable, called transformation factor, appearing in the Box-Cox formula. We developed a maximum likelihood method that treats the transformation factor as an unknown parameter, which is estimated from the data simultaneously along with the QTL parameters. The method makes an objective choice of data transformation and thus can be applied to QTL analysis for many different types of data. Simulation studies show that (1) Box-Cox transformation can substantially increase the power of QTL detection; (2) Box-Cox transformation can replace some specialized transformation methods that are commonly used in QTL mapping; and (3) applying the Box-Cox transformation to data already normally distributed does not harm the result.

Space-time patterns of Campylobacter spp. colonization in broiler flocks, 2002-2006.

PubMed

Jonsson, M E; Norström, M; Sandberg, M; Ersbøll, A K; Hofshagen, M

2010-09-01

This study was performed to investigate space-time patterns of Campylobacter spp. colonization in broiler flocks in Norway. Data on the Campylobacter spp. status at the time of slaughter of 16 054 broiler flocks from 580 farms between 2002 and 2006 was included in the study. Spatial relative risk maps together with maps of space-time clustering were generated, the latter by using spatial scan statistics. These maps identified the same areas almost every year where there was a higher risk for a broiler flock to test positive for Campylobacter spp. during the summer months. A modified K-function analysis showed significant clustering at distances between 2.5 and 4 km within different years. The identification of geographical areas with higher risk for Campylobacter spp. colonization in broilers indicates that there are risk factors associated with Campylobacter spp. colonization in broiler flocks varying with region and time, e.g. climate, landscape or geography. These need to be further explored. The results also showed clustering at shorter distances indicating that there are risk factors for Campylobacter spp. acting in a more narrow scale as well.

Qualitative Analysis of Attitudes Toward Adult-Child Sexual Activity Among Minor-Attracted Persons.

PubMed

Spriggs, Sharron A; Cohen, Lisa J; Valencia, Ashley; S Zimri, Yaseen; Galynker, Igor I

2018-05-09

This study uses qualitative methodology to explore narrative responses to a question regarding the harmful versus beneficial effects of adult-child sex on children. Data were gathered from a survey of self-identified minor-attracted persons (MAPs). Two hundred and sixty-seven survey participants provided narrative responses. Results indicated a significant amount of variability in perceptions of harm and of mitigating or aggravating factors. Understanding the subjective perspectives of MAPs, the range of their attitudes, and the issues that they identify as pertinent is critically important for clinical efficacy in the treatment of pedophilia.

Self-organizing map analysis using multivariate data from theophylline powders predicted by a thin-plate spline interpolation.

PubMed

Yasuda, Akihito; Onuki, Yoshinori; Kikuchi, Shingo; Takayama, Kozo

2010-11-01

The quality by design concept in pharmaceutical formulation development requires establishment of a science-based rationale and a design space. We integrated thin-plate spline (TPS) interpolation and Kohonen's self-organizing map (SOM) to visualize the latent structure underlying causal factors and pharmaceutical responses. As a model pharmaceutical product, theophylline powders were prepared based on the standard formulation. The angle of repose, compressibility, cohesion, and dispersibility were measured as the response variables. These responses were predicted quantitatively on the basis of a nonlinear TPS. A large amount of data on these powders was generated and classified into several clusters using an SOM. The experimental values of the responses were predicted with high accuracy, and the data generated for the powders could be classified into several distinctive clusters. The SOM feature map allowed us to analyze the global and local correlations between causal factors and powder characteristics. For instance, the quantities of microcrystalline cellulose (MCC) and magnesium stearate (Mg-St) were classified distinctly into each cluster, indicating that the quantities of MCC and Mg-St were crucial for determining the powder characteristics. This technique provides a better understanding of the relationships between causal factors and pharmaceutical responses in theophylline powder formulations. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association

Prediction of soil water erosion risk within GIS-case study of Beni Amrane Dam catchment (North of Algeria)

NASA Astrophysics Data System (ADS)

Touahir, S.; Khenter, K.; Remini, B.; Saad, H.

2017-08-01

Isser River is one of North Algeria’s major resources. It is vulnerable to water soil erosion because of favourable conjunctions of different geomorphological, hydro-climatic and lithologic factors. This case study has been carried out on the Beni Amrane dam Catchment, which is located in the bottom of Isser River, in North Algeria. The study involves a mapping of main factors of water erosion: rainfall erosivity, soil erodibility, slope and land use. Essentially a data mapping specification analysis shows, on each factor, how to identify the areas that are prone to water erosion. 04 classes of multifactorial vulnerability to water erosion have been identified: areas with low vulnerability (10 per cent); area with middle vulnerability (49 per cent); areas with high and very high vulnerability (38 per cent and 3 per cent). This could be a first guidance document for a rational use of land in the region and better secure the Beni Amrane dam against reservoir siltation.

A Two-Factor Model Better Explains Heterogeneity in Negative Symptoms: Evidence from the Positive and Negative Syndrome Scale.

PubMed

Jang, Seon-Kyeong; Choi, Hye-Im; Park, Soohyun; Jaekal, Eunju; Lee, Ga-Young; Cho, Young Il; Choi, Kee-Hong

2016-01-01

Acknowledging separable factors underlying negative symptoms may lead to better understanding and treatment of negative symptoms in individuals with schizophrenia. The current study aimed to test whether the negative symptoms factor (NSF) of the Positive and Negative Syndrome Scale (PANSS) would be better represented by expressive and experiential deficit factors, rather than by a single factor model, using confirmatory factor analysis (CFA). Two hundred and twenty individuals with schizophrenia spectrum disorders completed the PANSS; subsamples additionally completed the Brief Negative Symptom Scale (BNSS) and the Motivation and Pleasure Scale-Self-Report (MAP-SR). CFA results indicated that the two-factor model fit the data better than the one-factor model; however, latent variables were closely correlated. The two-factor model's fit was significantly improved by accounting for correlated residuals between N2 (emotional withdrawal) and N6 (lack of spontaneity and flow of conversation), and between N4 (passive social withdrawal) and G16 (active social avoidance), possibly reflecting common method variance. The two NSF factors exhibited differential patterns of correlation with subdomains of the BNSS and MAP-SR. These results suggest that the PANSS NSF would be better represented by a two-factor model than by a single-factor one, and support the two-factor model's adequate criterion-related validity. Common method variance among several items may be a potential source of measurement error under a two-factor model of the PANSS NSF.

Prediction of Rainfall-Induced Landslides in Tegucigalpa, Honduras, Using a Hydro-Geotechnical Model

NASA Astrophysics Data System (ADS)

Garcia Urquia, Elias; Axelsson, K.

2010-05-01

Central America is constantly being affected by natural hazards. Among these events are hurricanes and earthquakes, capable of triggering landslides that can alter the natural landscape, destroy infrastructure and cause the death of people in the most important settlements of the region. Hurricane Mitch in October of 1998 was of particular interest for the region, since it provoked hundreds of rainfall-induced landslides, mainly in 4 different countries. Studies carried out after Hurricane Mitch have allowed researchers to identify the factors that contribute to slope instability in many vulnerable areas. As Tegucigalpa, Honduras was partially destroyed due to the various landslide and flooding events triggered by this devastating hurricane, various research teams have deepened in their investigations and have proposed measures to mitigate the effects of similar future incidents. A model coupling an infinite-slope analysis and a simple groundwater flow approach can serve as a basis to predict the occurrence of landslides in Tegucigalpa, Honduras as a function of topographic, hydrological and soil variables. A safety map showing the rainfall-triggered landslide risk zones for Tegucigalpa, Honduras is to be created. As opposed to previous safety maps in which only steady-state conditions are studied, this analysis is extended and different steady-state and quasi-dynamic scenarios are considered for comparison. For the purpose of the latter settings, a hydrological analysis that determines the rainfall extreme values and their return periods in Tegucigalpa will account for the influence of rainfall on the groundwater flow and strength of soils. It is known that the spatial distribution of various factors that contribute to the risk of landslides (i.e. soil thickness, conductivity and strength properties; rainfall intensity and duration; root strength; subsurface flow orientation) is hard to determine. However, an effort is done to derive correlations for these parameters based on the existing information (i.e. rainfall data, soil testing data, land-use data). In addition, the spatial data management and manipulation is done by means of a Geographic Information System (GIS). For such purpose, maps of land-use, topography and geology provided by JICA have bee manually digitized and converted into GIS raster maps. The resulting safety map is then validated by comparing it with existing slope-failure-maps that have been created to show the affected areas during Hurricane Mitch. This safety map represents a useful tool in the prevention of landslide-related disasters, as it would be able to point out which segments of the population are at risk as a consequence of the rainfall-slope interaction in Tegucigalpa.

Method for the Preparation of Hazard Map in Urban Area Using Soil Depth and Groundwater Level

NASA Astrophysics Data System (ADS)

Kim, Sung-Wook; Choi, Eun-Kyeong; Cho, Jin Woo; Lee, Ju-Hyoung

2017-04-01

The hazard maps for predicting collapse on natural slopes consists of a combination of topographic, hydrological, and geological factors. Topographic factors are extracted from DEM, including aspect, slope, curvature, and topographic index. Hydrological factors, such as distance to drainage, drainage density, stream-power index, and wetness index are most important factors for slope instability. However, most of the urban areas are located on the plains and it is difficult to apply the hazard map using the topography and hydrological factors. In order to evaluate the risk of collapse of flat and low slope areas, soil depth and groundwater level data were collected and used as a factor for interpretation. In addition, the reliability of the hazard map was compared with the disaster history of the study area (Gangnam-gu and Yeouido district). In the disaster map of the disaster prevention agency, the urban area was mostly classified as the stable area and did not reflect the collapse history. Soil depth, drainage conditions and groundwater level obtained from boreholes were added as input data of hazard map, and disaster vulnerability increased at the location where the actual collapse points. In the study area where damage occurred, the moderate and low grades of the vulnerability of previous hazard map were 12% and 88%, respectively. While, the improved map showed 2% high grade, moderate grade 29%, low grade 66% and very low grade 2%. These results were similar to actual damage. Keywords: hazard map, urban area, soil depth, ground water level Acknowledgement This research was supported by a Grant from a Strategic Research Project (Horizontal Drilling and Stabilization Technologies for Urban Search and Rescue (US&R) Operation) funded by the Korea Institute of Civil Engineering and Building Technology.

QTL mapping and candidate gene analysis of telomere length control factors in maize (Zea mays L.)

USDA-ARS?s Scientific Manuscript database

Telomere length is under genetic control and important for essential telomere functions. Failure to regulate telomere length homeostasis contributes to cancers and aging-related diseases in animals, but the effects of telomere length defects in plants remains poorly understood. To learn more about t...

Human Hrs, a tyrosine kinase substrate in growth factor-stimulated cells: cDNA cloning and mapping of the gene to chromosome 17.

PubMed

Lu, L; Komada, M; Kitamura, N

1998-06-15

Hrs is a 115kDa zinc finger protein which is rapidly tyrosine phosphorylated in cells stimulated with various growth factors. We previously purified the protein from a mouse cell line and cloned its cDNA. In the present study, we cloned a human Hrs cDNA from a human placenta cDNA library by cross-hybridization, using the mouse cDNA as a probe, and determined its nucleotide sequence. The human Hrs cDNA encoded a 777-amino-acid protein whose sequence was 93% identical to that of mouse Hrs. Northern blot analysis showed that the Hrs mRNA was about 3.0kb long and was expressed in all the human adult and fetal tissues tested. In addition, we showed by genomic Southern blot analysis that the human Hrs gene was a single-copy gene with a size of about 20kb. Furthermore, the human Hrs gene was mapped to chromosome 17 by Southern blotting of genomic DNAs from human/rodent somatic cell hybrids. Copyright 1998 Elsevier Science B.V. All rights reserved.

Landslide susceptibility mapping using a neuro-fuzzy

NASA Astrophysics Data System (ADS)

Lee, S.; Choi, J.; Oh, H.

2009-12-01

This paper develops and applied an adaptive neuro-fuzzy inference system (ANFIS) based on a geographic information system (GIS) environment using landslide-related factors and location for landslide susceptibility mapping. A neuro-fuzzy system is based on a fuzzy system that is trained by a learning algorithm derived from the neural network theory. The learning procedure operates on local information, and causes only local modifications in the underlying fuzzy system. The study area, Boun, suffered much damage following heavy rain in 1998 and was selected as a suitable site for the evaluation of the frequency and distribution of landslides. Boun is located in the central part of Korea. Landslide-related factors such as slope, soil texture, wood type, lithology, and density of lineament were extracted from topographic, soil, forest, and lineament maps. Landslide locations were identified from interpretation of aerial photographs and field surveys. Landslide-susceptible areas were analyzed by the ANFIS method and mapped using occurrence factors. In particular, we applied various membership functions (MFs) and analysis results were verified using the landslide location data. The predictive maps using triangular, trapezoidal, and polynomial MFs were the best individual MFs for modeling landslide susceptibility maps (84.96% accuracy), proving that ANFIS could be very effective in modeling landslide susceptibility mapping. Various MFs were used in this study, and after verification, the difference in accuracy according to the MFs was small, between 84.81% and 84.96%. The difference was just 0.15% and therefore the choice of MFs was not important in the study. Also, compared with the likelihood ratio model, which showed 84.94%, the accuracy was similar. Thus, the ANFIS could be applied to other study areas with different data and other study methods such as cross-validation. The developed ANFIS learns the if-then rules between landslide-related factors and landslide location for generalization and prediction. It is easy to understand and interpret, therefore it is a good choice for modeling landslide susceptibility mapping, which are also of great help for planners and engineers in selecting highly susceptible areas for further detail surveys and suitable locations to implement development. Although they may be less useful at the site-specific scale, where local geological and geographic heterogeneities may prevail, the results herein may be used as basic data to assist slope management and land use planning. For the method to be more generally applied, more landslide data are needed and more case studies should be conducted.

A study of the breast cancer dynamics in North Carolina.

PubMed

Christakos, G; Lai, J J

1997-11-01

This work is concerned with the study of breast cancer incidence in the State of North Carolina. Methodologically, the current analysis illustrates the importance of spatiotemporal random field modelling and introduces a mode of reasoning that is based on a combination of inductive and deductive processes. The composite space/time analysis utilizes the variability characteristics of incidence and the mathematical features of the random field model to fit it to the data. The analysis is significantly general and can efficiently represent non-homogeneous and non-stationary characteristics of breast cancer variation. Incidence predictions are produced using data at the same time period as well as data from other time periods and disease registries. The random field provides a rigorous and systematic method for generating detailed maps, which offer a quantitative description of the incidence variation from place to place and from time to time, together with a measure of the accuracy of the incidence maps. Spatiotemporal mapping accounts for the geographical locations and the time instants of the incidence observations, which is not usually the case with most empirical Bayes methods. It is also more accurate than purely spatial statistics methods, and can offer valuable information about the breast cancer risk and dynamics in North Carolina. Field studies could be initialized in high-rate areas identified by the maps in an effort to uncover environmental or life-style factors that might be responsible for the high risk rates. Also, the incidence maps can help elucidate causal mechanisms, explain disease occurrences at a certain scale, and offer guidance in health management and administration.

An overview of animal science research 1945-2011 through science mapping analysis.

PubMed

Rodriguez-Ledesma, A; Cobo, M J; Lopez-Pujalte, C; Herrera-Viedma, E

2015-12-01

The conceptual structure of the field of Animal Science (AS) research is examined by means of a longitudinal science mapping analysis. The whole of the AS research field is analysed, revealing its conceptual evolution. To this end, an automatic approach to detecting and visualizing hidden themes or topics and their evolution across a consecutive span of years was applied to AS publications of the JCR category 'Agriculture, Dairy & Animal Science' during the period 1945-2011. This automatic approach was based on a coword analysis and combines performance analysis and science mapping. To observe the conceptual evolution of AS, six consecutive periods were defined: 1945-1969, 1970-1979, 1980-1989, 1990-1999, 2000-2005 and 2006-2011. Research in AS was identified as having focused on ten main thematic areas: ANIMAL-FEEDING, SMALL-RUMINANTS, ANIMAL-REPRODUCTION, DAIRY-PRODUCTION, MEAT-QUALITY, SWINE-PRODUCTION, GENETICS-AND-ANIMAL-BREEDING, POULTRY, ANIMAL-WELFARE and GROWTH-FACTORS-AND-FATTY-ACIDS. The results show how genomic studies gain in weight and integrate with other thematic areas. The whole of AS research has become oriented towards an overall framework in which animal welfare, sustainable management and human health play a major role. All this would affect the future structure and management of livestock farming. © 2014 Blackwell Verlag GmbH.

Modeling of natural risks in GIS, decision support in the Civil Protection and Emergency Planning

NASA Astrophysics Data System (ADS)

Santos, M.; Martins, L.; Moreira, S.; Costa, A.; Matos, F.; Teixeira, M.; Bateira, C.

2012-04-01

The assessment of natural hazards in Civil Protection is essential in the prevention and mitigation of emergency situations. This paper presents the results of the development of mapping susceptibility to landslides, floods, forest fires and soil erosion, using GIS (Geographic Information System) tools in two municipalities - Santo Tirso and Trofa - in the district of Oporto, in the northwest of Portugal. The mapping of natural hazards fits in the legislative plan of the Municipal Civil Protection (Law No. 65/2007 of 12 November) and it provides the key elements to planning and preparing an appropriate response in case some of the processes / phenomena occur, thus optimizing the procedures for protection and relief provided by the Municipal Civil Protection Service. Susceptibility mapping to landslides, floods, forest fires and soil erosion was performed with GIS tools resources. The methodology used to compile the mapping of landslides, forest fires and soil erosion was based on the modeling of different conditioning factors and validated with field work and event log. The mapping of susceptibility to floods and flooding was developed through mathematical parameters (statistical, hydrologic and hydraulic), supported by field work and the recognition of individual characteristics of each sector analysis and subsequently analyzed in a GIS environment The mapping proposal was made in 1:5000 scale which allows not only the identification of large sets affected by the spatial dynamics of the processes / phenomena, but also a more detailed analysis, especially when combined with geographic information systems (GIS) thus allowing to study more specific situations that require a quick response. The maps developed in this study are fundamental to the understanding, prediction and prevention of susceptibility and risks present in the municipalities, being a valuable tool in the process of Emergency Planning, since it identifies priority areas of intervention for farther detail analysis, promote and safeguard mechanisms to prevent injury and it anticipates the possibility of potential interventions that can minimize the risk.

Construction of a yeast artificial chromosome contig encompassing the chromosome 14 Alzheimer`s disease locus

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

Sharma, V.; Bonnycastle, L.; Poorkai, P.

1994-09-01

We have constructed a yeast artificial chromosome (YAC) contig of chromosome 14q24.3 which encompasses the chromosome 14 Alzheimer`s disease locus (AD3). Determined by linkage analysis of early-onset Alzheimer`s disease kindreds, this interval is bounded by the genetic markers D14S61-D14S63 and spans approximately 15 centimorgans. The contig consists of 29 markers and 74 YACs of which 57 are defined by one or more sequence tagged sites (STSs). The STS markers comprise 5 genes, 16 short tandem repeat polymorphisms and 8 cDNA clones. An additional number of genes, expressed sequence tags and cDNA fragments have been identified and localized to the contigmore » by hybridization and sequence analysis of anonymous clones isolated by cDNA direct selection techniques. A minimal contig of about 15 YACs averaging 0.5-1.5 megabase in length will span this interval and is, at first approximation, in rough agreement with the genetic map. For two regions of the contig, our coverage has relied on L1/THE fingerprint and Alu-PCR hybridization data of YACs provided by CEPH/Genethon. We are currently developing sequence tagged sites from these to confirm the overlaps revealed by the fingerprint data. Among the genes which map to the contig are transforming growth factor beta 3, c-fos, and heat shock protein 2A (HSPA2). C-fos is not a candidate gene for AD3 based on the sequence analysis of affected and unaffected individuals. HSPA2 maps to the proximal edge of the contig and Calmodulin 1, a candidate gene from 4q24.3, maps outside of the region. The YAC contig is a framework physical map from which cosmid or P1 clone contigs can be constructed. As more genes and cDNAs are mapped, a highly resolved transcription map will emerge, a necessary step towards positionally cloning the AD3 gene.« less

Soil erosion assessment and its correlation with landslide events using remote sensing data and GIS: a case study at Penang Island, Malaysia.

PubMed

Pradhan, Biswajeet; Chaudhari, Amruta; Adinarayana, J; Buchroithner, Manfred F

2012-01-01

In this paper, an attempt has been made to assess, prognosis and observe dynamism of soil erosion by universal soil loss equation (USLE) method at Penang Island, Malaysia. Multi-source (map-, space- and ground-based) datasets were used to obtain both static and dynamic factors of USLE, and an integrated analysis was carried out in raster format of GIS. A landslide location map was generated on the basis of image elements interpretation from aerial photos, satellite data and field observations and was used to validate soil erosion intensity in the study area. Further, a statistical-based frequency ratio analysis was carried out in the study area for correlation purposes. The results of the statistical correlation showed a satisfactory agreement between the prepared USLE-based soil erosion map and landslide events/locations, and are directly proportional to each other. Prognosis analysis on soil erosion helps the user agencies/decision makers to design proper conservation planning program to reduce soil erosion. Temporal statistics on soil erosion in these dynamic and rapid developments in Penang Island indicate the co-existence and balance of ecosystem.

[Multivariate geostatistics and GIS-based approach to study the spatial distribution and sources of heavy metals in agricultural soil in the Pearl River Delta, China].

PubMed

Cai, Li-mei; Ma, Jin; Zhou, Yong-zhang; Huang, Lan-chun; Dou, Lei; Zhang, Cheng-bo; Fu, Shan-ming

2008-12-01

One hundred and eighteen surface soil samples were collected from the Dongguan City, and analyzed for concentration of Cu, Zn, Ni, Cr, Pb, Cd, As, Hg, pH and OM. The spatial distribution and sources of soil heavy metals were studied using multivariate geostatistical methods and GIS technique. The results indicated concentrations of Cu, Zn, Ni, Pb, Cd and Hg were beyond the soil background content in Guangdong province, and especially concentrations of Pb, Cd and Hg were greatly beyond the content. The results of factor analysis group Cu, Zn, Ni, Cr and As in Factor 1, Pb and Hg in Factor 2 and Cd in Factor 3. The spatial maps based on geostatistical analysis show definite association of Factor 1 with the soil parent material, Factor 2 was mainly affected by industries. The spatial distribution of Factor 3 was attributed to anthropogenic influence.

Geostatistics for spatial genetic structures: study of wild populations of perennial ryegrass.

PubMed

Monestiez, P; Goulard, M; Charmet, G

1994-04-01

Methods based on geostatistics were applied to quantitative traits of agricultural interest measured on a collection of 547 wild populations of perennial ryegrass in France. The mathematical background of these methods, which resembles spatial autocorrelation analysis, is briefly described. When a single variable is studied, the spatial structure analysis is similar to spatial autocorrelation analysis, and a spatial prediction method, called "kriging", gives a filtered map of the spatial pattern over all the sampled area. When complex interactions of agronomic traits with different evaluation sites define a multivariate structure for the spatial analysis, geostatistical methods allow the spatial variations to be broken down into two main spatial structures with ranges of 120 km and 300 km, respectively. The predicted maps that corresponded to each range were interpreted as a result of the isolation-by-distance model and as a consequence of selection by environmental factors. Practical collecting methodology for breeders may be derived from such spatial structures.

Satellite Image Analysis along the Kuala Selangor to Sabak Bernam Rural Tourism Routes

NASA Astrophysics Data System (ADS)

Ibrahim, I.; Zakariya, K.; Wahab, N. A.

2018-02-01

This research focuses on the analysis of land cover map using satellite imagery along the rural routes. The aim of this research is to study the landscape features that can be seen by the tourists around the rural routes. The objectives of the study are twofold: (i) to analyse the land cover types along the rural routes and (ii) to create a tourist map along the rural routes. The method adopted was to use Supervised Classification by creating multiple polygons to ensure that each information is sufficient to create appropriate spectral signatures. The finding shows that 80% of the landscape features along the Point of Interest (POI) are paddy field. According to the analysis using the indicators criteria for choosing the rural routes, this research shows that this area has the potential to be part of a tourism area because it has many historical and cultural elements that can be exposed to tourists. Future research will be a factor analysis on the significance of the criteria to rural tourism attraction.

An integrated GIS application system for soil moisture data assimilation

NASA Astrophysics Data System (ADS)

Wang, Di; Shen, Runping; Huang, Xiaolong; Shi, Chunxiang

2014-11-01

The gaps in knowledge and existing challenges in precisely describing the land surface process make it critical to represent the massive soil moisture data visually and mine the data for further research.This article introduces a comprehensive soil moisture assimilation data analysis system, which is instructed by tools of C#, IDL, ArcSDE, Visual Studio 2008 and SQL Server 2005. The system provides integrated service, management of efficient graphics visualization and analysis of land surface data assimilation. The system is not only able to improve the efficiency of data assimilation management, but also comprehensively integrate the data processing and analysis tools into GIS development environment. So analyzing the soil moisture assimilation data and accomplishing GIS spatial analysis can be realized in the same system. This system provides basic GIS map functions, massive data process and soil moisture products analysis etc. Besides,it takes full advantage of a spatial data engine called ArcSDE to effeciently manage, retrieve and store all kinds of data. In the system, characteristics of temporal and spatial pattern of soil moiture will be plotted. By analyzing the soil moisture impact factors, it is possible to acquire the correlation coefficients between soil moisture value and its every single impact factor. Daily and monthly comparative analysis of soil moisture products among observations, simulation results and assimilations can be made in this system to display the different trends of these products. Furthermore, soil moisture map production function is realized for business application.

Combine bivariate statistics analysis and multivariate statistics analysis to assess landslide susceptibility in Chen-Yu-Lan watershed, Nantou, Taiwan.

NASA Astrophysics Data System (ADS)

Ngan Nguyen, Thi To; Liu, Cheng-Chien

2013-04-01

How landslides occurred and which factors triggered and sped up landslide occurrences were usually asked by researchers in the past decades. Many investigations carried out in many places in the world to finding out methods that predict and prevent damages from landslides phenomena. Chen-Yu-Lan River watershed is reputed as a 'hot pot' of landslide researches in Taiwan by its complicated geological structures with the significant tectonic fault systems and steeply mountainous terrain. Beside annual high precipitation concentration and the abrupt slopes, some natural disaster, as typhoons (Sinlaku-2008, Kalmaegi-2008, and Marakot-2009) and earthquake (Chi-Chi earthquake-1999) are also the triggered factors cause landslides with serious damages in this place. This research expresses the quantitative approaches to generate landslide susceptible map for Chen-Yu-Lan watershed, a mountainous area in the central Taiwan. Landslide inventories data, which were detected from the Formosat-2 imageries for eight years from 2004 to 2011, were applied to carry out landslide susceptibility mapping. Bivariate statistics analysis and multivariate statistics analysis would be applied to calculate susceptible index of landslides. The weights of parameters were computed based on landslide data for eight years from 2004 to 2011. To validate effective levels of factors to landslide occurrences, this method built some multivariate algorithms and compared these results with real landslide occurrences. Besides this method, the historical data of landslides were also used to assess and classify landslide susceptibility levels. From long-term landslide data, relation between landslide susceptibility levels and landslide repetition was assigned. The results demonstrated differently effective levels of potential factors, such as, slope gradient, drainage density, lithology and land use to landslide phenomena. The results also showed logical relationship between weights and characteristics of factors' classes. Depending on these results be able to help planning managers localize the high risk areas of landslide or safely areas by building and human activities.

An improved bias correction method of daily rainfall data using a sliding window technique for climate change impact assessment

NASA Astrophysics Data System (ADS)

Smitha, P. S.; Narasimhan, B.; Sudheer, K. P.; Annamalai, H.

2018-01-01

Regional climate models (RCMs) are used to downscale the coarse resolution General Circulation Model (GCM) outputs to a finer resolution for hydrological impact studies. However, RCM outputs often deviate from the observed climatological data, and therefore need bias correction before they are used for hydrological simulations. While there are a number of methods for bias correction, most of them use monthly statistics to derive correction factors, which may cause errors in the rainfall magnitude when applied on a daily scale. This study proposes a sliding window based daily correction factor derivations that help build reliable daily rainfall data from climate models. The procedure is applied to five existing bias correction methods, and is tested on six watersheds in different climatic zones of India for assessing the effectiveness of the corrected rainfall and the consequent hydrological simulations. The bias correction was performed on rainfall data downscaled using Conformal Cubic Atmospheric Model (CCAM) to 0.5° × 0.5° from two different CMIP5 models (CNRM-CM5.0, GFDL-CM3.0). The India Meteorological Department (IMD) gridded (0.25° × 0.25°) observed rainfall data was considered to test the effectiveness of the proposed bias correction method. The quantile-quantile (Q-Q) plots and Nash Sutcliffe efficiency (NSE) were employed for evaluation of different methods of bias correction. The analysis suggested that the proposed method effectively corrects the daily bias in rainfall as compared to using monthly factors. The methods such as local intensity scaling, modified power transformation and distribution mapping, which adjusted the wet day frequencies, performed superior compared to the other methods, which did not consider adjustment of wet day frequencies. The distribution mapping method with daily correction factors was able to replicate the daily rainfall pattern of observed data with NSE value above 0.81 over most parts of India. Hydrological simulations forced using the bias corrected rainfall (distribution mapping and modified power transformation methods that used the proposed daily correction factors) was similar to those simulated by the IMD rainfall. The results demonstrate that the methods and the time scales used for bias correction of RCM rainfall data have a larger impact on the accuracy of the daily rainfall and consequently the simulated streamflow. The analysis suggests that the distribution mapping with daily correction factors can be preferred for adjusting RCM rainfall data irrespective of seasons or climate zones for realistic simulation of streamflow.

Human factors considerations in the design and evaluation of moving map displays of ownership on the airport surface

DOT National Transportation Integrated Search

2004-09-01

The Federal Aviation Administration (FAA) has requested human factors guidance to support the new moving map Technical Standard Order (TSO)-C165, Electronic Map Display Equipment for Graphical Depiction of Aircraft Position. This document was develop...

Spatial Assessment of Forest Ecosystem Functions and Services using Human Relating Factors for SDG

NASA Astrophysics Data System (ADS)

Song, C.; Lee, W. K.; Jeon, S. W.; Kim, T.; Lim, C. H.

2015-12-01

Application of ecosystem service concept in environmental related decision making could be numerical and objective standard for policy maker between preserving and developing perspective of environment. However, pursuing maximum benefit from natural capital through ecosystem services caused failure by losing ecosystem functions through its trade-offs. Therefore, difference between ecosystem functions and services were demonstrated and would apply human relating perspectives. Assessment results of ecosystem functions and services can be divided 3 parts. Tree growth per year set as the ecosystem function factor and indicated through so called pure function map. After that, relating functions can be driven such as water conservation, air pollutant purification, climate change regulation, and timber production. Overall process and amount are numerically quantified. These functional results can be transferred to ecosystem services by multiplying economic unit value, so function reflecting service maps can be generated. On the other hand, above services, to implement more reliable human demand, human reflecting service maps are also be developed. As the validation, quantified ecosystem functions are compared with former results through pixel based analysis. Three maps are compared, and through comparing difference between ecosystem function and services and inversed trends in function based and human based service are analysed. In this study, we could find differences in PF, FRS, and HRS in relation to based ecosystem conditions. This study suggests that the differences in PF, FRS, and HRS should be understood in the decision making process for sustainable management of ecosystem services. Although the analysis is based on in sort existing process separation, it is important to consider the possibility of different usage of ecosystem function assessment results and ecosystem service assessment results in SDG policy making. Furthermore, process based functional approach can suggest environmental information which is reflected the other kinds of perspective.

The hunt for origins of DNA replication in multicellular eukaryotes

PubMed Central

Urban, John M.; Foulk, Michael S.; Casella, Cinzia

2015-01-01

Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope that features for ORI specification might emerge. These methods are reviewed here with analysis of their advantages and shortcomings. The various factors that may influence ORI selection for initiation of DNA replication are discussed. PMID:25926981

Satellite SAR interferometric techniques applied to emergency mapping

NASA Astrophysics Data System (ADS)

Stefanova Vassileva, Magdalena; Riccardi, Paolo; Lecci, Daniele; Giulio Tonolo, Fabio; Boccardo Boccardo, Piero; Chiesa, Giuliana; Angeluccetti, Irene

2017-04-01

This paper aim to investigate the capabilities of the currently available SAR interferometric algorithms in the field of emergency mapping. Several tests have been performed exploiting the Copernicus Sentinel-1 data using the COTS software ENVI/SARscape 5.3. Emergency Mapping can be defined as "creation of maps, geo-information products and spatial analyses dedicated to providing situational awareness emergency management and immediate crisis information for response by means of extraction of reference (pre-event) and crisis (post-event) geographic information/data from satellite or aerial imagery". The conventional differential SAR interferometric technique (DInSAR) and the two currently available multi-temporal SAR interferometric approaches, i.e. Permanent Scatterer Interferometry (PSI) and Small BAseline Subset (SBAS), have been applied to provide crisis information useful for the emergency management activities. Depending on the considered Emergency Management phase, it may be distinguished between rapid mapping, i.e. fast provision of geospatial data regarding the area affected for the immediate emergency response, and monitoring mapping, i.e. detection of phenomena for risk prevention and mitigation activities. In order to evaluate the potential and limitations of the aforementioned SAR interferometric approaches for the specific rapid and monitoring mapping application, five main factors have been taken into account: crisis information extracted, input data required, processing time and expected accuracy. The results highlight that DInSAR has the capacity to delineate areas affected by large and sudden deformations and fulfills most of the immediate response requirements. The main limiting factor of interferometry is the availability of suitable SAR acquisition immediately after the event (e.g. Sentinel-1 mission characterized by 6-day revisiting time may not always satisfy the immediate emergency request). PSI and SBAS techniques are suitable to produce monitoring maps for risk prevention and mitigation purposes. Nevertheless, multi-temporal techniques require large SAR temporal datasets, i.e. 20 and more images. Being the Sentinel-1 missions operational only since April 2014, multi-mission SAR datasets should be therefore exploited to carry out historical analysis.

Predisposing factors and susceptibility assessment for deep-seated gravitational slope deformations (DSGSDs): a case study (NW Alps, Italy)

NASA Astrophysics Data System (ADS)

Lo Russo, S.; Forno, M. G.; Taddia, G.; Gnavi, L.

2012-04-01

KEY WORDS: Deep-seated gravitational slope deformation (DSGSD); Risk; Hazard; Susceptibility; Piemonte; Italy Deep-seated gravitational slope deformations (DSGSDs) and "sackung" deformations are complex processes of gravitational movement that involve large volumes of rock, often several tens of meters thick and several kilometers long. The development and characteristics of deep-seated gravitational slope deformations (DSGSDs) have not yet been fully explained. If unrecognized, these deformations can cause serious damage to rigid infrastructures such as dams, tunnels, and water conduits. Early identification of these phenomena and their predisposing factors through detailed geological and geomorphological surveys is therefore necessary for the correct location, construction, and expansion of fixed infrastructures. The hazard evaluation component of landslide risk assessment combines measures of susceptibility and triggering variables. This approach may not be applicable to DSGSDs, given the difficulty of quantifying the probability of occurrence within a specified period of time without well-defined DSGSD triggering factors. Evaluation of DSGSDs should thus be restricted to the assessment of susceptibility. Zones of DSGSD susceptibility can be identified through geological and geomorphological analysis, by overlapping maps of the four main predisposing factors (lithology, neotectonic activity, relief energy, morphological deglaciation evidence). The attribution of a susceptibility level to a certain zone cannot replace a hazard evaluation, but it can be a good index of the potential presence of a DSGSD. A DSGSD is most likely in a territory characterized by the worst combination of predisposing factors (high susceptibility): poor rock mechanics, intense neotectonic activity (high seismicity, active faults), high energy relief, and evidence of past glacialism. The probability of a DSGSD correspondingly decreases if one or more of the predisposing factors are absent (low susceptibility). A case study of two DSGSDs located in the Rodoretto Valley (northwestern Alps, Italy) has been examined. After detailed field survey provided morphological identification of these features, the authors conducted a back-analysis to assess the susceptibility of the entire valley. Each main predisposing factor has been independently mapped, and the level of susceptibility to DSGSD has been identified through geographic information system (GIS) overlapping of the four maps. The results confirm the combined presence of four main predisposing factors for the examined DGSDs, indicating high susceptibility.

Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression

PubMed Central

Sun, Xiaoji; Wang, Xuya; Tang, Zuojian; Grivainis, Mark; Kahler, David; Yun, Chi; Mita, Paolo; Fenyö, David

2018-01-01

Transposable elements (TEs) represent a substantial fraction of many eukaryotic genomes, and transcriptional regulation of these factors is important to determine TE activities in human cells. However, due to the repetitive nature of TEs, identifying transcription factor (TF)-binding sites from ChIP-sequencing (ChIP-seq) datasets is challenging. Current algorithms are focused on subtle differences between TE copies and thus bias the analysis to relatively old and inactive TEs. Here we describe an approach termed “MapRRCon” (mapping repeat reads to a consensus) which allows us to identify proteins binding to TE DNA sequences by mapping ChIP-seq reads to the TE consensus sequence after whole-genome alignment. Although this method does not assign binding sites to individual insertions in the genome, it provides a landscape of interacting TFs by capturing factors that bind to TEs under various conditions. We applied this method to screen TFs’ interaction with L1 in human cells/tissues using ENCODE ChIP-seq datasets and identified 178 of the 512 TFs tested as bound to L1 in at least one biological condition with most of them (138) localized to the promoter. Among these L1-binding factors, we focused on Myc and CTCF, as they play important roles in cancer progression and 3D chromatin structure formation. Furthermore, we explored the transcriptomes of The Cancer Genome Atlas breast and ovarian tumor samples in which a consistent anti-/correlation between L1 and Myc/CTCF expression was observed, suggesting that these two factors may play roles in regulating L1 transcription during the development of such tumors. PMID:29802231

Global trends in research related to social media in psychology: mapping and bibliometric analysis.

PubMed

Zyoud, Sa'ed H; Sweileh, Waleed M; Awang, Rahmat; Al-Jabi, Samah W

2018-01-01

Social media, defined as interactive Web applications, have been on the rise globally, particularly among adults. The objective of this study was to investigate the trend of the literature related to the most used social network worldwide (i.e. Facebook, Twitter, LinkedIn, Snapchat, and Instagram) in the field of psychology. Specifically, this study will assess the growth in publications, citation analysis, international collaboration, author productivity, emerging topics and the mapping of frequent terms in publications pertaining to social media in the field of psychology. Publications related to social media in the field of psychology published between 2004 and 2014 were obtained from the Web of Science. The records extracted were analysed for bibliometric characteristics such as the growth in publications, citation analysis, international collaboration, emerging topics and the mapping of frequent terms in publications pertaining to social media in the field of psychology. VOSviewer v.1.6.5 was used to construct scientific maps. Overall, 959 publications were retrieved during the period between 2004 and 2015. The number of research publications in social media in the field of psychology showed a steady upward growth. Publications from the USA accounted for 57.14% of the total publications and the highest h -index (48).The most common document type was research articles (873; 91.03%). Over 99.06% of the publications were published in English. Computers in Human Behavior was the most prolific journal. The University of Wisconsin - Madison ranked first in terms of the total publications (n = 39). A visualisation analysis showed that personality psychology, experimental psychology, psychological risk factors, and developmental psychology were continual concerns of the research. This is the first study reporting the global trends in the research related to social media in the psychology field. Based on the raw data from the Web of Science, publication characteristics such as quality and quantity were assessed using bibliometric techniques over 12 years. The USA and its institutions play a dominant role in this topic. The most preferred topics related to social media in psychology are personality psychology, experimental psychology, psychological risk factors, and developmental psychology.

Genetic mapping and QTL analysis of agronomic traits in Indian Mucuna pruriens using an intraspecific F₂population.

PubMed

Mahesh, S; Leelambika, M; Jaheer, Md; Anithakumari, A M; Sathyanarayana, N

2016-03-01

Mucuna pruriens is a well-recognized agricultural and horticultural crop with important medicinal use. However, antinutritional factors in seed and adverse morphological characters have negatively affected its cultivation. To elucidate the genetic control of agronomic traits, an intraspecific genetic linkage map of Indian M. pruriens has been developed based on amplified fragment length polymorphism (AFLP) markers using 200 F₂ progenies derived from a cross between wild and cultivated genotypes. The resulting linkage map comprised 129 AFLP markers dispersed over 13 linkage groups spanning a total distance of 618.88 cM with an average marker interval of 4.79 cM. For the first time, three QTLs explaining about 6.05-14.77% of the corresponding total phenotypic variation for three quantitative (seed) traits and, eight QTLs explaining about 25.96% of the corresponding total phenotypic variation for three qualitative traits have been detected on four linkage groups. The map presented here will pave a way for mapping of genes/QTLs for the important agronomic and horticultural traits contrasting between the parents used in this study.

Spatial relationships between above-ground biomass and bird species biodiversity in Palawan, Philippines

PubMed Central

Singh, Minerva; Friess, Daniel A.; Vilela, Bruno; Alban, Jose Don T. De; Monzon, Angelica Kristina V.; Veridiano, Rizza Karen A.; Tumaneng, Roven D.

2017-01-01

This study maps distribution and spatial congruence between Above-Ground Biomass (AGB) and species richness of IUCN listed conservation-dependent and endemic avian fauna in Palawan, Philippines. Grey Level Co-Occurrence Texture Matrices (GLCMs) extracted from Landsat and ALOS-PALSAR were used in conjunction with local field data to model and map local-scale field AGB using the Random Forest algorithm (r = 0.92 and RMSE = 31.33 Mg·ha-1). A support vector regression (SVR) model was used to identify the factors influencing variation in avian species richness at a 1km scale. AGB is one of the most important determinants of avian species richness for the study area. Topographic factors and anthropogenic factors such as distance from the roads were also found to strongly influence avian species richness. Hotspots of high AGB and high species richness concentration were mapped using hotspot analysis and the overlaps between areas of high AGB and avian species richness was calculated. Results show that the overlaps between areas of high AGB with high IUCN red listed avian species richness and endemic avian species richness were fairly limited at 13% and 8% at the 1-km scale. The overlap between 1) low AGB and low IUCN richness, and 2) low AGB and low endemic avian species richness was higher at 36% and 12% respectively. The enhanced capacity to spatially map the correlation between AGB and avian species richness distribution will further assist the conservation and protection of forest areas and threatened avian species. PMID:29206228

Predicting radiocaesium sorption characteristics with soil chemical properties for Japanese soils.

PubMed

Uematsu, Shinichiro; Smolders, Erik; Sweeck, Lieve; Wannijn, Jean; Van Hees, May; Vandenhove, Hildegarde

2015-08-15

The high variability of the soil-to-plant transfer factor of radiocaesium (RCs) compels a detailed analysis of the radiocaesium interception potential (RIP) of soil, which is one of the specific factors ruling the RCs transfer. The range of the RIP values for agricultural soils in the Fukushima accident affected area has not yet been fully surveyed. Here, the RIP and other major soil chemical properties were characterised for 51 representative topsoils collected in the vicinity of the Fukushima contaminated area. The RIP ranged a factor of 50 among the soils and RIP values were lower for Andosols compared to other soils, suggesting a role of soil mineralogy. Correlation analysis revealed that the RIP was most strongly and negatively correlated to soil organic matter content and oxalate extractable aluminium. The RIP correlated weakly but positively to soil clay content. The slope of the correlation between RIP and clay content showed that the RIP per unit clay was only 4.8 mmol g(-1) clay, about threefold lower than that for clays of European soils, suggesting more amorphous minerals and less micaceous minerals in the clay fraction of Japanese soils. The negative correlation between RIP and soil organic matter may indicate that organic matter can mask highly selective sorption sites to RCs. Multiple regression analysis with soil organic matter and cation exchange capacity explained the soil RIP (R(2)=0.64), allowing us to map soil RIP based on existing soil map information. Copyright © 2015 Elsevier B.V. All rights reserved.

Optimization of Causative Factors for Landslide Susceptibility Evaluation Using Remote Sensing and GIS Data in Parts of Niigata, Japan.

PubMed

Dou, Jie; Tien Bui, Dieu; Yunus, Ali P; Jia, Kun; Song, Xuan; Revhaug, Inge; Xia, Huan; Zhu, Zhongfan

2015-01-01

This paper assesses the potentiality of certainty factor models (CF) for the best suitable causative factors extraction for landslide susceptibility mapping in the Sado Island, Niigata Prefecture, Japan. To test the applicability of CF, a landslide inventory map provided by National Research Institute for Earth Science and Disaster Prevention (NIED) was split into two subsets: (i) 70% of the landslides in the inventory to be used for building the CF based model; (ii) 30% of the landslides to be used for the validation purpose. A spatial database with fifteen landslide causative factors was then constructed by processing ALOS satellite images, aerial photos, topographical and geological maps. CF model was then applied to select the best subset from the fifteen factors. Using all fifteen factors and the best subset factors, landslide susceptibility maps were produced using statistical index (SI) and logistic regression (LR) models. The susceptibility maps were validated and compared using landslide locations in the validation data. The prediction performance of two susceptibility maps was estimated using the Receiver Operating Characteristics (ROC). The result shows that the area under the ROC curve (AUC) for the LR model (AUC = 0.817) is slightly higher than those obtained from the SI model (AUC = 0.801). Further, it is noted that the SI and LR models using the best subset outperform the models using the fifteen original factors. Therefore, we conclude that the optimized factor model using CF is more accurate in predicting landslide susceptibility and obtaining a more homogeneous classification map. Our findings acknowledge that in the mountainous regions suffering from data scarcity, it is possible to select key factors related to landslide occurrence based on the CF models in a GIS platform. Hence, the development of a scenario for future planning of risk mitigation is achieved in an efficient manner.

Optimization of Causative Factors for Landslide Susceptibility Evaluation Using Remote Sensing and GIS Data in Parts of Niigata, Japan

PubMed Central

Dou, Jie; Tien Bui, Dieu; P. Yunus, Ali; Jia, Kun; Song, Xuan; Revhaug, Inge; Xia, Huan; Zhu, Zhongfan

2015-01-01

This paper assesses the potentiality of certainty factor models (CF) for the best suitable causative factors extraction for landslide susceptibility mapping in the Sado Island, Niigata Prefecture, Japan. To test the applicability of CF, a landslide inventory map provided by National Research Institute for Earth Science and Disaster Prevention (NIED) was split into two subsets: (i) 70% of the landslides in the inventory to be used for building the CF based model; (ii) 30% of the landslides to be used for the validation purpose. A spatial database with fifteen landslide causative factors was then constructed by processing ALOS satellite images, aerial photos, topographical and geological maps. CF model was then applied to select the best subset from the fifteen factors. Using all fifteen factors and the best subset factors, landslide susceptibility maps were produced using statistical index (SI) and logistic regression (LR) models. The susceptibility maps were validated and compared using landslide locations in the validation data. The prediction performance of two susceptibility maps was estimated using the Receiver Operating Characteristics (ROC). The result shows that the area under the ROC curve (AUC) for the LR model (AUC = 0.817) is slightly higher than those obtained from the SI model (AUC = 0.801). Further, it is noted that the SI and LR models using the best subset outperform the models using the fifteen original factors. Therefore, we conclude that the optimized factor model using CF is more accurate in predicting landslide susceptibility and obtaining a more homogeneous classification map. Our findings acknowledge that in the mountainous regions suffering from data scarcity, it is possible to select key factors related to landslide occurrence based on the CF models in a GIS platform. Hence, the development of a scenario for future planning of risk mitigation is achieved in an efficient manner. PMID:26214691

Determination of Actual Friction Factors in Metal Forming under Heavy Loaded Regimes Combining Experimental and Numerical Analysis.

PubMed

Camacho, Ana María; Veganzones, Mariano; Claver, Juan; Martín, Francisco; Sevilla, Lorenzo; Sebastián, Miguel Ángel

2016-09-01

Tribological conditions can change drastically during heavy loaded regimes as experienced in metal forming; this is especially critical when lubrication can only be applied at the early stage of the process because the homogeneous lubricant layer can break along the die-workpiece interface. In these cases, adopting a constant friction factor for the lubricant-surface pair may not be a valid assumption. This paper presents a procedure based on the use of dual friction factor maps to determine friction factors employed in heavy loaded regimes. A finite element (FE) simulation is used to obtain the friction factor map for the alloy UNS A96082. Experiments were conducted using four lubricants (aluminum anti-size, MoS₂ grease, silicone oil, and copper paste) to determine the actual friction curves. The experimental procedure is based on the application of lubricant only at the beginning of the first stage of ring compression, and not at intermediate stages as is usual in typical ring compression tests (RCTs). The results show that for small reductions ( r h < 20%), the conventional RCT can be applied because the tribological conditions remain similar. For large reductions ( r h > 20%), it is recommended to obtain an average value of the friction factor for every lubricant-surface pair in the range of deformation considered.

Determination of Actual Friction Factors in Metal Forming under Heavy Loaded Regimes Combining Experimental and Numerical Analysis

PubMed Central

Camacho, Ana María; Veganzones, Mariano; Claver, Juan; Martín, Francisco; Sevilla, Lorenzo; Sebastián, Miguel Ángel

2016-01-01

Tribological conditions can change drastically during heavy loaded regimes as experienced in metal forming; this is especially critical when lubrication can only be applied at the early stage of the process because the homogeneous lubricant layer can break along the die-workpiece interface. In these cases, adopting a constant friction factor for the lubricant-surface pair may not be a valid assumption. This paper presents a procedure based on the use of dual friction factor maps to determine friction factors employed in heavy loaded regimes. A finite element (FE) simulation is used to obtain the friction factor map for the alloy UNS A96082. Experiments were conducted using four lubricants (aluminum anti-size, MoS2 grease, silicone oil, and copper paste) to determine the actual friction curves. The experimental procedure is based on the application of lubricant only at the beginning of the first stage of ring compression, and not at intermediate stages as is usual in typical ring compression tests (RCTs). The results show that for small reductions (rh < 20%), the conventional RCT can be applied because the tribological conditions remain similar. For large reductions (rh > 20%), it is recommended to obtain an average value of the friction factor for every lubricant-surface pair in the range of deformation considered. PMID:28773868

A Scoping Review and Prevalence Analysis of Soil-Transmitted Helminth Infections in Honduras

PubMed Central

Sanchez, Ana Lourdes; Gabrie, José Antonio; Rueda, María Mercedes; Mejia, Rosa Elena; Bottazzi, Maria Elena; Canales, Maritza

2014-01-01

Background Honduras is endemic for soil-transmitted helminth (STH) infections, but critical information gaps still remain on the prevalence and intensity of these infections as well as on their spatial distribution at subnational levels. Objectives Firstly, to review the research activity on STH infections in Honduras and secondly, to carry out a national prevalence analysis and map the geographical distribution of these infections in children. Methods A systematic search was conducted of the published and grey literature to identify scientific work on the impact and prevalence of STH infections done between May 1930 and June 30, 2012. International databases and Honduran journals were searched. Grey literature was gleaned from local libraries and key informants. Select studies conducted between 2001 and 2012 were used to produce prevalence maps and to investigate association between STH prevalence and socio-economic and environmental factors. Results Of 257 identified studies, 211 (21.4% peer-reviewed) were retained for analysis and categorized as clinical research (10.9%), treatment efficacy studies (8.1%) or epidemiological studies (81%). Prevalence analysis and geographical mapping included 36 epidemiological studies from Honduras's 18 departments and 23% of its municipalities. Overall STH prevalence was >50% in 40.6% of municipalities. Prevalences above 20% for each trichuriasis, ascariasis, and hookworm infection were found in 68%, 47.8%, and 7.2% of studied municipalities, respectively. Municipalities with lower human development index, less access to of potable water, and with higher annual precipitation showed higher STH prevalences. Conclusions This is the first study to provide a comprehensive historic review of STH research activity and prevalence in Honduras, revealing important knowledge gaps related to infection risk factors, disease burden, and anti-parasitic drug efficacy, among others. Our decade-long prevalence analysis reveals geographical differences in STH prevalence and these findings suggest that differential intervention strategies might be necessary in Honduras for the control of these infections. PMID:24466359

A scoping review and prevalence analysis of soil-transmitted helminth infections in Honduras.

PubMed

Sanchez, Ana Lourdes; Gabrie, José Antonio; Rueda, María Mercedes; Mejia, Rosa Elena; Bottazzi, Maria Elena; Canales, Maritza

2014-01-01

Honduras is endemic for soil-transmitted helminth (STH) infections, but critical information gaps still remain on the prevalence and intensity of these infections as well as on their spatial distribution at subnational levels. Firstly, to review the research activity on STH infections in Honduras and secondly, to carry out a national prevalence analysis and map the geographical distribution of these infections in children. A systematic search was conducted of the published and grey literature to identify scientific work on the impact and prevalence of STH infections done between May 1930 and June 30, 2012. International databases and Honduran journals were searched. Grey literature was gleaned from local libraries and key informants. Select studies conducted between 2001 and 2012 were used to produce prevalence maps and to investigate association between STH prevalence and socio-economic and environmental factors. Of 257 identified studies, 211 (21.4% peer-reviewed) were retained for analysis and categorized as clinical research (10.9%), treatment efficacy studies (8.1%) or epidemiological studies (81%). Prevalence analysis and geographical mapping included 36 epidemiological studies from Honduras's 18 departments and 23% of its municipalities. Overall STH prevalence was >50% in 40.6% of municipalities. Prevalences above 20% for each trichuriasis, ascariasis, and hookworm infection were found in 68%, 47.8%, and 7.2% of studied municipalities, respectively. Municipalities with lower human development index, less access to of potable water, and with higher annual precipitation showed higher STH prevalences. This is the first study to provide a comprehensive historic review of STH research activity and prevalence in Honduras, revealing important knowledge gaps related to infection risk factors, disease burden, and anti-parasitic drug efficacy, among others. Our decade-long prevalence analysis reveals geographical differences in STH prevalence and these findings suggest that differential intervention strategies might be necessary in Honduras for the control of these infections.

Prioritising coastal zone management issues through fuzzy cognitive mapping approach.

PubMed

Meliadou, Aleka; Santoro, Francesca; Nader, Manal R; Dagher, Manale Abou; Al Indary, Shadi; Salloum, Bachir Abi

2012-04-30

Effective public participation is an essential component of Integrated Coastal Zone Management implementation. To promote such participation, a shared understanding of stakeholders' objectives has to be built to ultimately result in common coastal management strategies. The application of quantitative and semi-quantitative methods involving tools such as Fuzzy Cognitive Mapping is presently proposed for reaching such understanding. In this paper we apply the Fuzzy Cognitive Mapping tool to elucidate the objectives and priorities of North Lebanon's coastal productive sectors, and to formalize their coastal zone perceptions and knowledge. Then, we investigate the potential of Fuzzy Cognitive Mapping as tool for support coastal zone management. Five round table discussions were organized; one for the municipalities of the area and one for each of the main coastal productive sectors (tourism, industry, fisheries, agriculture), where the participants drew cognitive maps depicting their views. The analysis of the cognitive maps showed a large number of factors perceived as affecting the current situation of the North Lebanon coastal zone that were classified into five major categories: governance, infrastructure, environment, intersectoral interactions and sectoral initiatives. Furthermore, common problems, expectations and management objectives for all sectors were exposed. Within this context, Fuzzy Cognitive Mapping proved to be an essential tool for revealing stakeholder knowledge and perception and understanding complex relationships. Copyright © 2011 Elsevier Ltd. All rights reserved.

Assessing the methods needed for improved dengue mapping: a SWOT analysis

PubMed Central

Attaway, David Frost; Jacobsen, Kathryn H; Falconer, Allan; Manca, Germana; Waters, Nigel M

2014-01-01

Introduction Dengue fever, a mosquito-borne viral infection, is a growing threat to human health in tropical and subtropical areas worldwide. There is a demand from public officials for maps that capture the current distribution of dengue and maps that analyze risk factors to predict the future burden of disease. Methods To identify relevant articles, we searched Google Scholar, PubMed, BioMed Central, and WHOLIS (World Health Organization Library Database) for published articles with a specific set of dengue criteria between January 2002 and July 2013. Results After evaluating the currently available dengue models, we identified four key barriers to the creation of high-quality dengue maps: (1) data limitations related to the expense of diagnosing and reporting dengue cases in places where health information systems are underdeveloped; (2) issues related to the use of socioeconomic proxies in places with limited dengue incidence data; (3) mosquito ranges which may be changing as a result of climate changes; and (4) the challenges of mapping dengue events at a variety of scales. Conclusion An ideal dengue map will present endemic and epidemic dengue information from both rural and urban areas. Overcoming the current barriers requires expanded collaboration and data sharing by geographers, epidemiologists, and entomologists. Enhanced mapping techniques would allow for improved visualizations of dengue rates and risks. PMID:25328585

Assessing the methods needed for improved dengue mapping: a SWOT analysis.

PubMed

Attaway, David Frost; Jacobsen, Kathryn H; Falconer, Allan; Manca, Germana; Waters, Nigel M

2014-01-01

Dengue fever, a mosquito-borne viral infection, is a growing threat to human health in tropical and subtropical areas worldwide. There is a demand from public officials for maps that capture the current distribution of dengue and maps that analyze risk factors to predict the future burden of disease. To identify relevant articles, we searched Google Scholar, PubMed, BioMed Central, and WHOLIS (World Health Organization Library Database) for published articles with a specific set of dengue criteria between January 2002 and July 2013. After evaluating the currently available dengue models, we identified four key barriers to the creation of high-quality dengue maps: (1) data limitations related to the expense of diagnosing and reporting dengue cases in places where health information systems are underdeveloped; (2) issues related to the use of socioeconomic proxies in places with limited dengue incidence data; (3) mosquito ranges which may be changing as a result of climate changes; and (4) the challenges of mapping dengue events at a variety of scales. An ideal dengue map will present endemic and epidemic dengue information from both rural and urban areas. Overcoming the current barriers requires expanded collaboration and data sharing by geographers, epidemiologists, and entomologists. Enhanced mapping techniques would allow for improved visualizations of dengue rates and risks.

Seismic hazard assessment of Syria using seismicity, DEM, slope, active tectonic and GIS

NASA Astrophysics Data System (ADS)

Ahmad, Raed; Adris, Ahmad; Singh, Ramesh

2016-07-01

In the present work, we discuss the use of an integrated remote sensing and Geographical Information System (GIS) techniques for evaluation of seismic hazard areas in Syria. The present study is the first time effort to create seismic hazard map with the help of GIS. In the proposed approach, we have used Aster satellite data, digital elevation data (30 m resolution), earthquake data, and active tectonic maps. Many important factors for evaluation of seismic hazard were identified and corresponding thematic data layers (past earthquake epicenters, active faults, digital elevation model, and slope) were generated. A numerical rating scheme has been developed for spatial data analysis using GIS to identify ranking of parameters to be included in the evaluation of seismic hazard. The resulting earthquake potential map delineates the area into different relative susceptibility classes: high, moderate, low and very low. The potential earthquake map was validated by correlating the obtained different classes with the local probability that produced using conventional analysis of observed earthquakes. Using earthquake data of Syria and the peak ground acceleration (PGA) data is introduced to the model to develop final seismic hazard map based on Gutenberg-Richter (a and b values) parameters and using the concepts of local probability and recurrence time. The application of the proposed technique in Syrian region indicates that this method provides good estimate of seismic hazard map compared to those developed from traditional techniques (Deterministic (DSHA) and probabilistic seismic hazard (PSHA). For the first time we have used numerous parameters using remote sensing and GIS in preparation of seismic hazard map which is found to be very realistic.

GPFA-AB_Phase1UtilizationTask4DataUpload

DOE Data Explorer

Teresa E. Jordan

2015-09-30

This submission of Utilization Analysis data to the Geothermal Data Repository (GDR) node of the National Geothermal Data System (NGDS) is in support of Phase 1 Low Temperature Geothermal Play Fairway Analysis for the Appalachian Basin (project DE-EE0006726). The submission includes data pertinent to the methods and results of an analysis of the Surface Levelized Cost of Heat (SLCOH) for US Census Bureau ‘Places’ within the study area. This was calculated using a modification of a program called GEOPHIRES, available at http://koenraadbeckers.net/geophires/index.php. The MATLAB modules used in conjunction with GEOPHIRES, the MATLAB data input file, the GEOPHIRES output data file, and an explanation of the software components have been provided. Results of the SLCOH analysis appear on 4 .png image files as mapped ‘risk’ of heat utilization. For each of the 4 image (.png) files, there is an accompanying georeferenced TIF (.tif) file by the same name. In addition to calculating SLCOH, this Task 4 also identified many sites that may be prospects for use of a geothermal district heating system, based on their size and industry, rather than on the SLCOH. An industry sorted listing of the sites (.xlsx) and a map of these sites plotted as a layer onto different iterations of maps combining the three geological risk factors (Thermal Quality, Natural Reservoir Quality, and Risk of Seismicity) has been provided. In addition to the 6 image (.png) files of the maps in this series, a shape (.shp) file and 7 associated files are included as well. Finally, supporting files (.pdf) describing the utilization analysis methodology and summarizing the anticipated permitting for a deep district heating system are supplied.

Locally advanced rectal cancer: post-chemoradiotherapy ADC histogram analysis for predicting a complete response.

PubMed

Cho, Seung Hyun; Kim, Gab Chul; Jang, Yun-Jin; Ryeom, Hunkyu; Kim, Hye Jung; Shin, Kyung-Min; Park, Jun Seok; Choi, Gyu-Seog; Kim, See Hyung

2015-09-01

The value of diffusion-weighted imaging (DWI) for reliable differentiation between pathologic complete response (pCR) and residual tumor is still unclear. Recently, a few studies reported that histogram analysis can be helpful to monitor the therapeutic response in various cancer research. To investigate whether post-chemoradiotherapy (CRT) apparent diffusion coefficient (ADC) histogram analysis can be helpful to predict a pCR in locally advanced rectal cancer (LARC). Fifty patients who underwent preoperative CRT followed by surgery were enrolled in this retrospective study, non-pCR (n = 41) and pCR (n = 9), respectively. ADC histogram analysis encompassing the whole tumor was performed on two post-CRT ADC600 and ADC1000 (b factors 0, 600 vs. 0, 1000 s/mm(2)) maps. Mean, minimum, maximum, SD, mode, 10th, 25th, 50th, 75th, 90th percentile ADCs, skewness, and kurtosis were derived. Diagnostic performance for predicting pCR was evaluated and compared. On both maps, 10th and 25th ADCs showed better diagnostic performance than that using mean ADC. Tenth percentile ADCs revealed the best diagnostic performance on both ADC600 (AZ 0.841, sensitivity 100%, specificity 70.7%) and ADC1000 (AZ 0.821, sensitivity 77.8%, specificity 87.8%) maps. In comparison between 10th percentile and mean ADC, the specificity was significantly improved on both ADC600 (70.7% vs. 53.7%; P = 0.031) and ADC1000 (87.8% vs. 73.2%; P = 0.039) maps. Post-CRT ADC histogram analysis is helpful for predicting pCR in LARC, especially, in improving the specificity, compared with mean ADC. © The Foundation Acta Radiologica 2014.

Analyzing spatial clustering and the spatiotemporal nature and trends of HIV/AIDS prevalence using GIS: the case of Malawi, 1994-2010.

PubMed

Zulu, Leo C; Kalipeni, Ezekiel; Johannes, Eliza

2014-05-23

Although local spatiotemporal analysis can improve understanding of geographic variation of the HIV epidemic, its drivers, and the search for targeted interventions, it is limited in sub-Saharan Africa. Despite recent declines, Malawi's estimated 10.0% HIV prevalence (2011) remained among the highest globally. Using data on pregnant women in Malawi, this study 1) examines spatiotemporal trends in HIV prevalence 1994-2010, and 2) for 2010, identifies and maps the spatial variation/clustering of factors associated with HIV prevalence at district level. Inverse distance weighting was used within ArcGIS Geographic Information Systems (GIS) software to generate continuous surfaces of HIV prevalence from point data (1994, 1996, 1999, 2001, 2003, 2005, 2007, and 2010) obtained from surveillance antenatal clinics. From the surfaces prevalence estimates were extracted at district level and the results mapped nationally. Spatial dependency (autocorrelation) and clustering of HIV prevalence were also analyzed. Correlation and multiple regression analyses were used to identify factors associated with HIV prevalence for 2010 and their spatial variation/clustering mapped and compared to HIV clustering. Analysis revealed wide spatial variation in HIV prevalence at regional, urban/rural, district and sub-district levels. However, prevalence was spatially leveling out within and across 'sub-epidemics' while declining significantly after 1999. Prevalence exhibited statistically significant spatial dependence nationally following initial (1995-1999) localized, patchy low/high patterns as the epidemic spread rapidly. Locally, HIV "hotspots" clustered among eleven southern districts/cities while a "coldspot" captured configurations of six central region districts. Preliminary multiple regression of 2010 HIV prevalence produced a model with four significant explanatory factors (adjusted R2 = 0.688): mean distance to main roads, mean travel time to nearest transport, percentage that had taken an HIV test ever, and percentage attaining a senior primary education. Spatial clustering linked some factors to particular subsets of high HIV-prevalence districts. Spatial analysis enhanced understanding of local spatiotemporal variation in HIV prevalence, possible underlying factors, and potential for differentiated spatial targeting of interventions. Findings suggest that intervention strategies should also emphasize improved access to health/HIV services, basic education, and syphilis management, particularly in rural hotspot districts, as further research is done on drivers at finer scale.

Analyzing spatial clustering and the spatiotemporal nature and trends of HIV/AIDS prevalence using GIS: the case of Malawi, 1994-2010

PubMed Central

2014-01-01

Background Although local spatiotemporal analysis can improve understanding of geographic variation of the HIV epidemic, its drivers, and the search for targeted interventions, it is limited in sub-Saharan Africa. Despite recent declines, Malawi’s estimated 10.0% HIV prevalence (2011) remained among the highest globally. Using data on pregnant women in Malawi, this study 1) examines spatiotemporal trends in HIV prevalence 1994-2010, and 2) for 2010, identifies and maps the spatial variation/clustering of factors associated with HIV prevalence at district level. Methods Inverse distance weighting was used within ArcGIS Geographic Information Systems (GIS) software to generate continuous surfaces of HIV prevalence from point data (1994, 1996, 1999, 2001, 2003, 2005, 2007, and 2010) obtained from surveillance antenatal clinics. From the surfaces prevalence estimates were extracted at district level and the results mapped nationally. Spatial dependency (autocorrelation) and clustering of HIV prevalence were also analyzed. Correlation and multiple regression analyses were used to identify factors associated with HIV prevalence for 2010 and their spatial variation/clustering mapped and compared to HIV clustering. Results Analysis revealed wide spatial variation in HIV prevalence at regional, urban/rural, district and sub-district levels. However, prevalence was spatially leveling out within and across ‘sub-epidemics’ while declining significantly after 1999. Prevalence exhibited statistically significant spatial dependence nationally following initial (1995-1999) localized, patchy low/high patterns as the epidemic spread rapidly. Locally, HIV “hotspots” clustered among eleven southern districts/cities while a “coldspot” captured configurations of six central region districts. Preliminary multiple regression of 2010 HIV prevalence produced a model with four significant explanatory factors (adjusted R2 = 0.688): mean distance to main roads, mean travel time to nearest transport, percentage that had taken an HIV test ever, and percentage attaining a senior primary education. Spatial clustering linked some factors to particular subsets of high HIV-prevalence districts. Conclusions Spatial analysis enhanced understanding of local spatiotemporal variation in HIV prevalence, possible underlying factors, and potential for differentiated spatial targeting of interventions. Findings suggest that intervention strategies should also emphasize improved access to health/HIV services, basic education, and syphilis management, particularly in rural hotspot districts, as further research is done on drivers at finer scale. PMID:24886573

Mapping Soil Erosion Factors and Potential Erosion Risk for the National Park "Central Balkan"

NASA Astrophysics Data System (ADS)

Ilieva, Diliana; Malinov, Ilia

2014-05-01

Soil erosion is widely recognised environmental problem. The report aims at presenting the main results from assessment and mapping of the factors of sheet water erosion and the potential erosion risk on the territory of National Park "Central Balkan". For this purpose, the Universal Soil Loss Equation (USLE) was used for predicting soil loss from erosion. The influence of topography (LS-factor) and soil erodibility (K-factor) was assessed using small-scale topographic and soil maps. Rainfall erosivity (R-factor) was calculated from data of rainfalls with amounts exceeding 9.5 mm from 14 hydro-meteorological stations. The values of the erosion factors (R, K and LS) were presented for the areas of forest, sub-alpine and alpine zones. Using the methods of GIS, maps were plotted presenting the area distribution among the classes of the soil erosion factors and the potential risk in the respective zones. The results can be used for making accurate decisions for soil conservation and sustainable land management in the park.

Characterization and genetic mapping of a Photoperiod-sensitive dwarf 1 locus in rice (Oryza sativa L.).

PubMed

Li, Riqing; Xia, Jixing; Xu, Yiwei; Zhao, Xiucai; Liu, Yao-Guang; Chen, Yuanling

2014-01-01

Plant height is an important agronomic trait for crop architecture and yield. Most known factors determining plant height function in gibberellin or brassinosteroid biosynthesis or signal transduction. Here, we report a japonica rice (Oryza sativa ssp. japonica) dominant dwarf mutant, Photoperiod-sensitive dwarf 1 (Psd1). The Psd1 mutant showed impaired cell division and elongation, and a severe dwarf phenotype under long-day conditions, but nearly normal growth in short-day. The plant height of Psd1 mutant could not be rescued by gibberellin or brassinosteroid treatment. Genetic analysis with R1 and F2 populations determined that Psd1 phenotype was controlled by a single dominant locus. Linkage analysis with 101 tall F2 plants grown in a long-day season, which were derived from a cross between Psd1 and an indica cultivar, located Psd1 locus on chromosome 1. Further fine-mapping with 1017 tall F2 plants determined this locus on an 11.5-kb region. Sequencing analysis of this region detected a mutation site in a gene encoding a putative lipid transfer protein; the mutation produces a truncated C-terminus of the protein. This study establishes the genetic foundation for understanding the molecular mechanisms regulating plant cell division and elongation mediated by interaction between genetic and environmental factors.

Alterations in the nuclear proteome of HIV-1 infected T-cells

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

DeBoer, Jason; Jagadish, Teena; Haverland, Nicole A.

Virus infection of a cell involves the appropriation of host factors and the innate defensive response of the cell. The identification of proteins critical for virus replication may lead to the development of novel, cell-based inhibitors. In this study we mapped the changes in T-cell nuclei during human immunodeficiency virus type 1 (HIV-1) at 20 hpi. Using a stringent data threshold, a total of 13 and 38 unique proteins were identified in infected and uninfected cells, respectively, across all biological replicates. An additional 15 proteins were found to be differentially regulated between infected and control nuclei. STRING analysis identified fourmore » clusters of protein–protein interactions in the data set related to nuclear architecture, RNA regulation, cell division, and cell homeostasis. Immunoblot analysis confirmed the differential expression of several proteins in both C8166-45 and Jurkat E6-1 T-cells. These data provide a map of the response in host cell nuclei upon HIV-1 infection. - Highlights: • We identify changes in the expression of nuclear proteins during HIV-1 infection. • 163 nuclear proteins were found differentially regulated during HIV-1 infection. • Bioinformatic analysis identified several nuclear pathways altered by HIV infection. • Candidate factors were validated in two independent cell lines.« less

Bibliography of In-House and Contract Reports. Supplement 9.

DTIC Science & Technology

1981-02-01

11;il CasCil roads andl ril roads would significantlN rcduLcc tlic ~anIual labor IMnOls d III V, i 1111111 d il.1 . graphic data bascs. ile effort...GUIDE FOR CLIMA TE (Rpt. No. 5 in the ETL Series on Guides for Army Terrain Analysts) September 1980 Keywords: Climatic Analysis, Factor Mapping

Uncertainty in natural hazards, modeling and decision support: An introduction to this volume [Chapter 1

Treesearch

Karin Riley; Matthew Thompson; Peter Webley; Kevin D. Hyde

2017-01-01

Modeling has been used to characterize and map natural hazards and hazard susceptibility for decades. Uncertainties are pervasive in natural hazards analysis, including a limited ability to predict where and when extreme events will occur, with what consequences, and driven by what contributing factors. Modeling efforts are challenged by the intrinsic...

Correlations between ground motion and building damage. Engineering intensity scale applied to the San Fernando earthquake of February 1971

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

Hafen, D.; Kintzer, F.C.

1977-11-01

The correlation between ground motion and building damage was investigated for the San Fernando earthquake of 1971. A series of iso-intensity maps was compiled to summarize the ground motion in terms of the Blume Engineering Intensity Scale (EIS). This involved the analysis of ground motion records from 62 stations in the Los Angeles area. Damage information for low-rise buildings was obtained in the form of records of loans granted by the Small Business Administration to repair earthquake damage. High-rise damage evaluations were based on direct inquiry and building inspection. Damage factors (ratio of damage repair cost to building value) weremore » calculated and summarized on contour maps. A statistical study was then undertaken to determine relationships between ground motion and damage factor. Several parameters for ground motion were considered and evaluated by means of correlation coefficients.« less

Spatial analysis of geologic and hydrologic features relating to sinkhole occurrence in Jefferson County, West Virginia

USGS Publications Warehouse

Doctor, Daniel H.; Doctor, Katarina Z.

2012-01-01

In this study the influence of geologic features related to sinkhole susceptibility was analyzed and the results were mapped for the region of Jefferson County, West Virginia. A model of sinkhole density was constructed using Geographically Weighted Regression (GWR) that estimated the relations among discrete geologic or hydrologic features and sinkhole density at each sinkhole location. Nine conditioning factors on sinkhole occurrence were considered as independent variables: distance to faults, fold axes, fracture traces oriented along bedrock strike, fracture traces oriented across bedrock strike, ponds, streams, springs, quarries, and interpolated depth to groundwater. GWR model parameter estimates for each variable were evaluated for significance, and the results were mapped. The results provide visual insight into the influence of these variables on localized sinkhole density, and can be used to provide an objective means of weighting conditioning factors in models of sinkhole susceptibility or hazard risk.

Seroprevalence and risk factors of Mycobacterium avium subspecies paratuberculosis infection in domestic sika deer in China.

PubMed

Meng, Qing-Feng; Li, Ying; Yang, Fan; Yao, Gui-Zhi; Qian, Ai-Dong; Wang, Wei-Li; Cong, Wei

2015-06-01

Paratuberculosis or Johne's disease (JD), caused by Mycobacterium avium subspecies paratuberculosis (MAP), is a chronic infectious granulomatous enteritis of ruminants and other animals, which has a worldwide occurrence, but little is known of MAP infection in domestic sika deer in Jilin Province, China. The objective of the present investigation was to examine seroprevalence and risk factors of MAP infection in Jilin Province. Serum samples collected from 1400 sika deer from 16 sika deer herds were collected in the 4 districts of the province between May 2013 and August 2014 and were tested independently for the presence of antibodies against MAP. A total of 247 (17.64 %) sika deer tested positive for MAP antibodies using a commercially available enzyme immunoassay kit. The management level of farm and collecting region of sika deer was the main risk factor associated with MAP infection. The present study revealed the seroprevalence of MAP infection in sika deer in Jilin Province, China, which provided the baseline data for taking comprehensive countermeasures and measures in effectively preventing and controlling MAP infection in sika deer.

Climate change induced lanslide hazard mapping over Greece- A case study in Pelion Mountain (SE Thessaly, Central Greece)

NASA Astrophysics Data System (ADS)

Angelitsa, Varvara; Loupasakis, Constantinos; Anagnwstopoulou, Christina

2015-04-01

Landslides, as a major type of geological hazard, represent one of the natural events that occur most frequently worldwide after hydro-meteorological events. Landslides occur when the stability of a slope changes due to a number of factors, such as the steep terrain and prolonged precipitation. Identification of landslides and compilation of landslide susceptibility, hazard and risk maps are very important issues for the public authorities providing substantial information regarding, the strategic planning and management of the land-use. Although landslides cannot be predicted accurately, many attempts have been made to compile these maps. Important factors for the the compilation of reliable maps are the quality and the amount of available data and the selection of the best method for the analysis. Numerous studies and publications providing landslide susceptibility,hazard and risk maps, for different regions of Greece, have completed up to now. Their common characteristic is that they are static, taking into account parameters like geology, mean annual precipitaion, slope, aspect, distance from roads, faults and drainage network, soil capability, land use etc., without introducing the dimension of time. The current study focuses on the Pelion Mountain, which is located at the southeastern part of Thessaly in Central Greece; aiming to compile "dynamic" susceptibility and hazard maps depending on climate changes. For this purpose, past and future precipipation data from regional climate models (RCMs) datasets are introduced as input parameters for the compilation of "dynamic" landslide hazard maps. Moreover, land motion mapping data produced by Persistent Scatterer Interferometry (PSI) are used for the validation of the landslide occurrence during the period from June 1992 to December 2003 and as a result for the calibration of the mapping procedure. The PSI data can be applied at a regional scale as support for land motion mapping and at local scale for the monitoring of single well-known ground motion event. The PSI data were produced within the framework of the Terrafirma project. Terrafirma is a pan- European ground motion information service focused on seismic risk, flood defense and costal lowland subsidence,inactive mines and hydrogeological risks. The produced maps provided substantial information for the land use planning and the civil protection of an area presenting excelent natural beauty and numerous preservable trtaditional villages. Keywords: landslide, psi technique, regional climate models, lanslide susceptibility maps, Greece

Mapping hard magnetic recording disks by TOF-SIMS

NASA Astrophysics Data System (ADS)

Spool, A.; Forrest, J.

2008-12-01

Mapping of hard magnetic recording disks by TOF-SIMS was performed both to produce significant analytical results for the understanding of the disk surface and the head disk interface in hard disk drives, and as an example of a macroscopic non-rectangular mapping problem for the technique. In this study, maps were obtained by taking discrete samples of the disk surface at set intervals in R and Θ. Because both in manufacturing, and in the disk drive, processes that may affect the disk surface are typically circumferential in nature, changes in the surface are likely to be blurred in the Θ direction. An algorithm was developed to determine the optimum relative sampling ratio in R and Θ. The results confirm what the experience of the analysts suggested, that changes occur more rapidly on disks in the radial direction, and that more sampling in the radial direction is desired. The subsequent use of statistical methods principle component analysis (PCA), maximum auto-correlation factors (MAF), and the algorithm inverse distance weighting (IDW) are explored.

Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants.

PubMed

Dadaev, Tokhir; Saunders, Edward J; Newcombe, Paul J; Anokian, Ezequiel; Leongamornlert, Daniel A; Brook, Mark N; Cieza-Borrella, Clara; Mijuskovic, Martina; Wakerell, Sarah; Olama, Ali Amin Al; Schumacher, Fredrick R; Berndt, Sonja I; Benlloch, Sara; Ahmed, Mahbubl; Goh, Chee; Sheng, Xin; Zhang, Zhuo; Muir, Kenneth; Govindasami, Koveela; Lophatananon, Artitaya; Stevens, Victoria L; Gapstur, Susan M; Carter, Brian D; Tangen, Catherine M; Goodman, Phyllis; Thompson, Ian M; Batra, Jyotsna; Chambers, Suzanne; Moya, Leire; Clements, Judith; Horvath, Lisa; Tilley, Wayne; Risbridger, Gail; Gronberg, Henrik; Aly, Markus; Nordström, Tobias; Pharoah, Paul; Pashayan, Nora; Schleutker, Johanna; Tammela, Teuvo L J; Sipeky, Csilla; Auvinen, Anssi; Albanes, Demetrius; Weinstein, Stephanie; Wolk, Alicja; Hakansson, Niclas; West, Catharine; Dunning, Alison M; Burnet, Neil; Mucci, Lorelei; Giovannucci, Edward; Andriole, Gerald; Cussenot, Olivier; Cancel-Tassin, Géraldine; Koutros, Stella; Freeman, Laura E Beane; Sorensen, Karina Dalsgaard; Orntoft, Torben Falck; Borre, Michael; Maehle, Lovise; Grindedal, Eli Marie; Neal, David E; Donovan, Jenny L; Hamdy, Freddie C; Martin, Richard M; Travis, Ruth C; Key, Tim J; Hamilton, Robert J; Fleshner, Neil E; Finelli, Antonio; Ingles, Sue Ann; Stern, Mariana C; Rosenstein, Barry; Kerns, Sarah; Ostrer, Harry; Lu, Yong-Jie; Zhang, Hong-Wei; Feng, Ninghan; Mao, Xueying; Guo, Xin; Wang, Guomin; Sun, Zan; Giles, Graham G; Southey, Melissa C; MacInnis, Robert J; FitzGerald, Liesel M; Kibel, Adam S; Drake, Bettina F; Vega, Ana; Gómez-Caamaño, Antonio; Fachal, Laura; Szulkin, Robert; Eklund, Martin; Kogevinas, Manolis; Llorca, Javier; Castaño-Vinyals, Gemma; Penney, Kathryn L; Stampfer, Meir; Park, Jong Y; Sellers, Thomas A; Lin, Hui-Yi; Stanford, Janet L; Cybulski, Cezary; Wokolorczyk, Dominika; Lubinski, Jan; Ostrander, Elaine A; Geybels, Milan S; Nordestgaard, Børge G; Nielsen, Sune F; Weisher, Maren; Bisbjerg, Rasmus; Røder, Martin Andreas; Iversen, Peter; Brenner, Hermann; Cuk, Katarina; Holleczek, Bernd; Maier, Christiane; Luedeke, Manuel; Schnoeller, Thomas; Kim, Jeri; Logothetis, Christopher J; John, Esther M; Teixeira, Manuel R; Paulo, Paula; Cardoso, Marta; Neuhausen, Susan L; Steele, Linda; Ding, Yuan Chun; De Ruyck, Kim; De Meerleer, Gert; Ost, Piet; Razack, Azad; Lim, Jasmine; Teo, Soo-Hwang; Lin, Daniel W; Newcomb, Lisa F; Lessel, Davor; Gamulin, Marija; Kulis, Tomislav; Kaneva, Radka; Usmani, Nawaid; Slavov, Chavdar; Mitev, Vanio; Parliament, Matthew; Singhal, Sandeep; Claessens, Frank; Joniau, Steven; Van den Broeck, Thomas; Larkin, Samantha; Townsend, Paul A; Aukim-Hastie, Claire; Gago-Dominguez, Manuela; Castelao, Jose Esteban; Martinez, Maria Elena; Roobol, Monique J; Jenster, Guido; van Schaik, Ron H N; Menegaux, Florence; Truong, Thérèse; Koudou, Yves Akoli; Xu, Jianfeng; Khaw, Kay-Tee; Cannon-Albright, Lisa; Pandha, Hardev; Michael, Agnieszka; Kierzek, Andrzej; Thibodeau, Stephen N; McDonnell, Shannon K; Schaid, Daniel J; Lindstrom, Sara; Turman, Constance; Ma, Jing; Hunter, David J; Riboli, Elio; Siddiq, Afshan; Canzian, Federico; Kolonel, Laurence N; Le Marchand, Loic; Hoover, Robert N; Machiela, Mitchell J; Kraft, Peter; Freedman, Matthew; Wiklund, Fredrik; Chanock, Stephen; Henderson, Brian E; Easton, Douglas F; Haiman, Christopher A; Eeles, Rosalind A; Conti, David V; Kote-Jarai, Zsofia

2018-06-11

Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling.

Adjusting stream-sediment geochemical maps in the Austrian Bohemian Massif by analysis of variance

USGS Publications Warehouse

Davis, J.C.; Hausberger, G.; Schermann, O.; Bohling, G.

1995-01-01

The Austrian portion of the Bohemian Massif is a Precambrian terrane composed mostly of highly metamorphosed rocks intruded by a series of granitoids that are petrographically similar. Rocks are exposed poorly and the subtle variations in rock type are difficult to map in the field. A detailed geochemical survey of stream sediments in this region has been conducted and included as part of the Geochemischer Atlas der Republik O??sterreich, and the variations in stream sediment composition may help refine the geological interpretation. In an earlier study, multivariate analysis of variance (MANOVA) was applied to the stream-sediment data in order to minimize unwanted sampling variation and emphasize relationships between stream sediments and rock types in sample catchment areas. The estimated coefficients were used successfully to correct for the sampling effects throughout most of the region, but also introduced an overcorrection in some areas that seems to result from consistent but subtle differences in composition of specific rock types. By expanding the model to include an additional factor reflecting the presence of a major tectonic unit, the Rohrbach block, the overcorrection is removed. This iterative process simultaneously refines both the geochemical map by removing extraneous variation and the geological map by suggesting a more detailed classification of rock types. ?? 1995 International Association for Mathematical Geology.

Radon potential, geologic formations, and lung cancer risk

PubMed Central

Hahn, Ellen J.; Gokun, Yevgeniya; Andrews, William M.; Overfield, Bethany L.; Robertson, Heather; Wiggins, Amanda; Rayens, Mary Kay

2015-01-01

Objective Exposure to radon is associated with approximately 10% of U.S. lung cancer cases. Geologic rock units have varying concentrations of uranium, producing fluctuating amounts of radon. This exploratory study examined the spatial and statistical associations between radon values and geological formations to illustrate potential population-level lung cancer risk from radon exposure. Method This was a secondary data analysis of observed radon values collected in 1987 from homes (N = 309) in Kentucky and geologic rock formation data from the Kentucky Geological Survey. Radon value locations were plotted on digital geologic maps using ArcGIS and linked to specific geologic map units. Each map unit represented a package of different types of rock (e.g., limestone and/or shale). Log-transformed radon values and geologic formation categories were compared using one-way analysis of variance. Results Observed radon levels varied significantly by geologic formation category. Of the 14 geologic formation categories in north central Kentucky, four were associated with median radon levels, ranging from 8.10 to 2.75 pCi/L. Conclusion Radon potential maps that account for geologic factors and observed radon values may be superior to using observed radon values only. Knowing radon-prone areas could help target population-based lung cancer prevention interventions given the inequities that exist related to radon. PMID:26844090

Multiple Statistical Models Based Analysis of Causative Factors and Loess Landslides in Tianshui City, China

NASA Astrophysics Data System (ADS)

Su, Xing; Meng, Xingmin; Ye, Weilin; Wu, Weijiang; Liu, Xingrong; Wei, Wanhong

2018-03-01

Tianshui City is one of the mountainous cities that are threatened by severe geo-hazards in Gansu Province, China. Statistical probability models have been widely used in analyzing and evaluating geo-hazards such as landslide. In this research, three approaches (Certainty Factor Method, Weight of Evidence Method and Information Quantity Method) were adopted to quantitively analyze the relationship between the causative factors and the landslides, respectively. The source data used in this study are including the SRTM DEM and local geological maps in the scale of 1:200,000. 12 causative factors (i.e., altitude, slope, aspect, curvature, plan curvature, profile curvature, roughness, relief amplitude, and distance to rivers, distance to faults, distance to roads, and the stratum lithology) were selected to do correlation analysis after thorough investigation of geological conditions and historical landslides. The results indicate that the outcomes of the three models are fairly consistent.

Selective corneal optical aberration (SCOA) for customized ablation

NASA Astrophysics Data System (ADS)

Jean, Benedikt J.; Bende, Thomas

2001-06-01

Wavefront analysis still have some technical problems which may be solved within the next years. There are some limitations to use wavefront as a diagnostic tool for customized ablation alone. An ideal combination would be wavefront and topography. Meanwhile Selective Corneal Aberration is a method to visualize the optical quality of a measured corneal surface. It is based on a true measured 3D elevation information of a video topometer. Thus values can be interpreted either using Zernike polynomials or visualized as a so called color coded surface quality map. This map gives a quality factor (corneal aberration) for each measured point of the cornea.

Designing a risk-based surveillance program for Mycobacterium avium ssp. paratuberculosis in Norwegian dairy herds using multivariate statistical process control analysis.

PubMed

Whist, A C; Liland, K H; Jonsson, M E; Sæbø, S; Sviland, S; Østerås, O; Norström, M; Hopp, P

2014-11-01

Surveillance programs for animal diseases are critical to early disease detection and risk estimation and to documenting a population's disease status at a given time. The aim of this study was to describe a risk-based surveillance program for detecting Mycobacterium avium ssp. paratuberculosis (MAP) infection in Norwegian dairy cattle. The included risk factors for detecting MAP were purchase of cattle, combined cattle and goat farming, and location of the cattle farm in counties containing goats with MAP. The risk indicators included production data [culling of animals >3 yr of age, carcass conformation of animals >3 yr of age, milk production decrease in older lactating cows (lactations 3, 4, and 5)], and clinical data (diarrhea, enteritis, or both, in animals >3 yr of age). Except for combined cattle and goat farming and cattle farm location, all data were collected at the cow level and summarized at the herd level. Predefined risk factors and risk indicators were extracted from different national databases and combined in a multivariate statistical process control to obtain a risk assessment for each herd. The ordinary Hotelling's T(2) statistic was applied as a multivariate, standardized measure of difference between the current observed state and the average state of the risk factors for a given herd. To make the analysis more robust and adapt it to the slowly developing nature of MAP, monthly risk calculations were based on data accumulated during a 24-mo period. Monitoring of these variables was performed to identify outliers that may indicate deviance in one or more of the underlying processes. The highest-ranked herds were scattered all over Norway and clustered in high-density dairy cattle farm areas. The resulting rankings of herds are being used in the national surveillance program for MAP in 2014 to increase the sensitivity of the ongoing surveillance program in which 5 fecal samples for bacteriological examination are collected from 25 dairy herds. The use of multivariate statistical process control for selection of herds will be beneficial when a diagnostic test suitable for mass screening is available and validated on the Norwegian cattle population, thus making it possible to increase the number of sampled herds. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Assessing and monitoring the risk of land degradation in Baragan Plain, Romania, using spectral mixture analysis and Landsat imagery.

PubMed

Vorovencii, Iosif

2016-07-01

The fall of the communist regime in Romania at the end of 1989 and the ensuing transition to the market economy brought about many changes in the use of agricultural land. These changes combined with the action of climatic factors led, in most cases, to negative effects increasing the risk of degradation of agricultural land. This study aims to assess and monitor the risk of land degradation in Baragan Plain, Romania, for the period 1988-2011 using Landsat Thematic Mapper (TM) and Spectral Mixture Analysis (SMA). Each satellite image was classified through the Decision Tree Classifier (DTC) method; then, on the basis of certain threshold values, we obtained maps of land degradation and maps showing the passage from various classes of land use/land cover (LULC) to land degradation. The results indicate that during the intermediary periods there was an ascending and descending trend in the risk of land degradation determined by the interaction of climatic factors with the social-economic ones. For the entire period, the overall trend was ascending, the risk of land degradation increasing by around 4.60 % of the studied surface. Out of the climatic factors, high temperatures and, implicitly, drought were the most significant. The social-economic factors are the result of the changes which occurred after the fall of the communist regime, the most important being the fragmentation of agricultural land and the destruction of the irrigation system.

A Geomorphological Approach To Landslide Susceptibility Assessment and Its Application To The Virginio River Basin

NASA Astrophysics Data System (ADS)

Casagli, N.; Catani, F.; Delmonaco, G.; Ermini, L.; Margottini, C.; Puglisi, C.

The present note presents the results of a research project aimed at developing a ge- omorphology based method for the assessment of landslide susceptibility. The work has been carried out in the Virginio River basin, a tributary of the Arno river with confluence located 20 km downstream from Florence (Italy). Starting from a detailed landslide inventory, essentially carried out by aerial-photograph survey, the first phase of the research was directed to geomorphic field investigations, aimed at determining those hillslope factors influencing landslide triggering. This analysis was carried out for a significant sub-sample of the inventoried landslides, allowing the distinction of the most relevant hillslope factors affecting each type of mass movement. Selected factors are a) the past slope gradient in which landslide originated, b) litology and 3) land use. Once defined as thematic vector data, these factors have been handled by GIS overlay mapping, allowing to single out, for the entire Virginio River basin, homogeneous domains (Unique Condition Units) that contain, for each landslide ty- pology, unique combinations of the selected hillslope factors. Those domains are the basic Terrain Units for the following phase of landslide susceptibility assessment and mapping. The hillslope factors not selected in the first phase, however playing an im- portant role in contributing to the activation of the mass movements, have been taken into account for the definition of a landslide susceptibility function. This function is es- sentially a logic function based on the presence/absence of preparatory factors within the previous selected Unique Condition Terrain Units. The final mapping of the ar- eas characterized by different landslide susceptibility levels was performed by vector and raster based GIS techniques on the basis of the number and rank of predisposing factors. These landslide susceptibility classes, defined by a logic and easily replicable function, can be useful in the decision making procedures connected with territorial planning.

CosmoQuest Year 2: Citizen Science Progress, Motivations, and Education

NASA Astrophysics Data System (ADS)

Gugliucci, Nicole E.; Gay, P. L.; Antonenko, I.; Bracey, G.; Costello, K.; Lehan, C.; Moore, J.; Reilly, E.; Robbins, S. J.; Schmidt, B. E.; CosmoQuest Collaboration

2014-01-01

The CosmoQuest citizen science virtual research facility has wrapped up its second year of operations. With projects mapping the surfaces of the Moon, Mercury, and asteroid Vesta, citizen scientists have marked over 2 million craters as well as other surface features. Analysis of the mapping results show that citizen scientists map high resolution features as well as expert crater markers within a small margin of error. We’ve undertaken a study of citizen science motivations with our users, and find that an interest in astronomy and a desire to contribute new knowledge as primary motivating factors. Ten percent of users surveyed list learning or teaching science as the primary motivating factor. A full analysis of this survey will be presented. Along those lines, the CosmoQuest education team has developed a second middle school educational unit to align with its citizen science projects. In-Vesta-Gate explores asteroid science and is in the trial stage, while we report on several teacher professional development opportunities with Terraluna, a Moon-focused educational unit developed last year. We’ve also taken the CosmoQuest citizen science on the road and outside the website, having a booth and activities at several public events. We present visitor survey results from a recent exhibition at Dragon*Con, a sci-fi/fantasy convention with over 50,000 attendees. We discuss future plans for the project, including the release of several mobile apps to be previewed here.

Identification and molecular characterization of MYB Transcription Factor Superfamily in C4 model plant foxtail millet (Setaria italica L.).

PubMed

Muthamilarasan, Mehanathan; Khandelwal, Rohit; Yadav, Chandra Bhan; Bonthala, Venkata Suresh; Khan, Yusuf; Prasad, Manoj

2014-01-01

MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I-X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli.

Visualizing Mobility of Public Transportation System.

PubMed

Zeng, Wei; Fu, Chi-Wing; Arisona, Stefan Müller; Erath, Alexander; Qu, Huamin

2014-12-01

Public transportation systems (PTSs) play an important role in modern cities, providing shared/massive transportation services that are essential for the general public. However, due to their increasing complexity, designing effective methods to visualize and explore PTS is highly challenging. Most existing techniques employ network visualization methods and focus on showing the network topology across stops while ignoring various mobility-related factors such as riding time, transfer time, waiting time, and round-the-clock patterns. This work aims to visualize and explore passenger mobility in a PTS with a family of analytical tasks based on inputs from transportation researchers. After exploring different design alternatives, we come up with an integrated solution with three visualization modules: isochrone map view for geographical information, isotime flow map view for effective temporal information comparison and manipulation, and OD-pair journey view for detailed visual analysis of mobility factors along routes between specific origin-destination pairs. The isotime flow map linearizes a flow map into a parallel isoline representation, maximizing the visualization of mobility information along the horizontal time axis while presenting clear and smooth pathways from origin to destinations. Moreover, we devise several interactive visual query methods for users to easily explore the dynamics of PTS mobility over space and time. Lastly, we also construct a PTS mobility model from millions of real passenger trajectories, and evaluate our visualization techniques with assorted case studies with the transportation researchers.

Groundwater vulnerability to pollution mapping of Ranchi district using GIS

NASA Astrophysics Data System (ADS)

Krishna, R.; Iqbal, J.; Gorai, A. K.; Pathak, G.; Tuluri, F.; Tchounwou, P. B.

2015-12-01

Groundwater pollution due to anthropogenic activities is one of the major environmental problems in urban and industrial areas. The present study demonstrates the integrated approach with GIS and DRASTIC model to derive a groundwater vulnerability to pollution map. The model considers the seven hydrogeological factors [Depth to water table ( D), net recharge ( R), aquifer media ( A), soil media ( S), topography or slope ( T), impact of vadose zone ( I) and hydraulic Conductivity( C)] for generating the groundwater vulnerability to pollution map. The model was applied for assessing the groundwater vulnerability to pollution in Ranchi district, Jharkhand, India. The model was validated by comparing the model output (vulnerability indices) with the observed nitrate concentrations in groundwater in the study area. The reason behind the selection of nitrate is that the major sources of nitrate in groundwater are anthropogenic in nature. Groundwater samples were collected from 30 wells/tube wells distributed in the study area. The samples were analyzed in the laboratory for measuring the nitrate concentrations in groundwater. A sensitivity analysis of the integrated model was performed to evaluate the influence of single parameters on groundwater vulnerability index. New weights were computed for each input parameters to understand the influence of individual hydrogeological factors in vulnerability indices in the study area. Aquifer vulnerability maps generated in this study can be used for environmental planning and groundwater management.

Groundwater vulnerability to pollution mapping of Ranchi district using GIS.

PubMed

Krishna, R; Iqbal, J; Gorai, A K; Pathak, G; Tuluri, F; Tchounwou, P B

2015-12-01

Groundwater pollution due to anthropogenic activities is one of the major environmental problems in urban and industrial areas. The present study demonstrates the integrated approach with GIS and DRASTIC model to derive a groundwater vulnerability to pollution map. The model considers the seven hydrogeological factors [Depth to water table ( D ), net recharge ( R ), aquifer media ( A ), soil media ( S ), topography or slope ( T ), impact of vadose zone ( I ) and hydraulic Conductivity( C )] for generating the groundwater vulnerability to pollution map. The model was applied for assessing the groundwater vulnerability to pollution in Ranchi district, Jharkhand, India. The model was validated by comparing the model output (vulnerability indices) with the observed nitrate concentrations in groundwater in the study area. The reason behind the selection of nitrate is that the major sources of nitrate in groundwater are anthropogenic in nature. Groundwater samples were collected from 30 wells/tube wells distributed in the study area. The samples were analyzed in the laboratory for measuring the nitrate concentrations in groundwater. A sensitivity analysis of the integrated model was performed to evaluate the influence of single parameters on groundwater vulnerability index. New weights were computed for each input parameters to understand the influence of individual hydrogeological factors in vulnerability indices in the study area. Aquifer vulnerability maps generated in this study can be used for environmental planning and groundwater management.

Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation.

PubMed

Horikoshi, Momoko; Mӓgi, Reedik; van de Bunt, Martijn; Surakka, Ida; Sarin, Antti-Pekka; Mahajan, Anubha; Marullo, Letizia; Thorleifsson, Gudmar; Hӓgg, Sara; Hottenga, Jouke-Jan; Ladenvall, Claes; Ried, Janina S; Winkler, Thomas W; Willems, Sara M; Pervjakova, Natalia; Esko, Tõnu; Beekman, Marian; Nelson, Christopher P; Willenborg, Christina; Wiltshire, Steven; Ferreira, Teresa; Fernandez, Juan; Gaulton, Kyle J; Steinthorsdottir, Valgerdur; Hamsten, Anders; Magnusson, Patrik K E; Willemsen, Gonneke; Milaneschi, Yuri; Robertson, Neil R; Groves, Christopher J; Bennett, Amanda J; Lehtimӓki, Terho; Viikari, Jorma S; Rung, Johan; Lyssenko, Valeriya; Perola, Markus; Heid, Iris M; Herder, Christian; Grallert, Harald; Müller-Nurasyid, Martina; Roden, Michael; Hypponen, Elina; Isaacs, Aaron; van Leeuwen, Elisabeth M; Karssen, Lennart C; Mihailov, Evelin; Houwing-Duistermaat, Jeanine J; de Craen, Anton J M; Deelen, Joris; Havulinna, Aki S; Blades, Matthew; Hengstenberg, Christian; Erdmann, Jeanette; Schunkert, Heribert; Kaprio, Jaakko; Tobin, Martin D; Samani, Nilesh J; Lind, Lars; Salomaa, Veikko; Lindgren, Cecilia M; Slagboom, P Eline; Metspalu, Andres; van Duijn, Cornelia M; Eriksson, Johan G; Peters, Annette; Gieger, Christian; Jula, Antti; Groop, Leif; Raitakari, Olli T; Power, Chris; Penninx, Brenda W J H; de Geus, Eco; Smit, Johannes H; Boomsma, Dorret I; Pedersen, Nancy L; Ingelsson, Erik; Thorsteinsdottir, Unnur; Stefansson, Kari; Ripatti, Samuli; Prokopenko, Inga; McCarthy, Mark I; Morris, Andrew P

2015-07-01

Reference panels from the 1000 Genomes (1000G) Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE) Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS), supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI) at genome-wide significance, and two for fasting glucose (FG), none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3) and FG (GCK and G6PC2). The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated.

Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation

PubMed Central

van de Bunt, Martijn; Surakka, Ida; Sarin, Antti-Pekka; Mahajan, Anubha; Marullo, Letizia; Thorleifsson, Gudmar; Hӓgg, Sara; Hottenga, Jouke-Jan; Ladenvall, Claes; Ried, Janina S.; Winkler, Thomas W.; Willems, Sara M.; Pervjakova, Natalia; Esko, Tõnu; Beekman, Marian; Nelson, Christopher P.; Willenborg, Christina; Ferreira, Teresa; Fernandez, Juan; Gaulton, Kyle J.; Steinthorsdottir, Valgerdur; Hamsten, Anders; Magnusson, Patrik K. E.; Willemsen, Gonneke; Milaneschi, Yuri; Robertson, Neil R.; Groves, Christopher J.; Bennett, Amanda J.; Lehtimӓki, Terho; Viikari, Jorma S.; Rung, Johan; Lyssenko, Valeriya; Perola, Markus; Heid, Iris M.; Herder, Christian; Grallert, Harald; Müller-Nurasyid, Martina; Roden, Michael; Hypponen, Elina; Isaacs, Aaron; van Leeuwen, Elisabeth M.; Karssen, Lennart C.; Mihailov, Evelin; Houwing-Duistermaat, Jeanine J.; de Craen, Anton J. M.; Deelen, Joris; Havulinna, Aki S.; Blades, Matthew; Hengstenberg, Christian; Erdmann, Jeanette; Schunkert, Heribert; Kaprio, Jaakko; Tobin, Martin D.; Samani, Nilesh J.; Lind, Lars; Salomaa, Veikko; Lindgren, Cecilia M.; Slagboom, P. Eline; Metspalu, Andres; van Duijn, Cornelia M.; Eriksson, Johan G.; Peters, Annette; Gieger, Christian; Jula, Antti; Groop, Leif; Raitakari, Olli T.; Power, Chris; Penninx, Brenda W. J. H.; de Geus, Eco; Smit, Johannes H.; Boomsma, Dorret I.; Pedersen, Nancy L.; Ingelsson, Erik; Thorsteinsdottir, Unnur; Stefansson, Kari; Ripatti, Samuli; Prokopenko, Inga; McCarthy, Mark I.; Morris, Andrew P.

2015-01-01

Reference panels from the 1000 Genomes (1000G) Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE) Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS), supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI) at genome-wide significance, and two for fasting glucose (FG), none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3) and FG (GCK and G6PC2). The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated. PMID:26132169

A systemic analysis of South Korea Sewol ferry accident - Striking a balance between learning and accountability.

PubMed

Kee, Dohyung; Jun, Gyuchan Thomas; Waterson, Patrick; Haslam, Roger

2017-03-01

The South Korea Sewol ferry accident in April 2014 claimed the lives of over 300 passengers and led to criminal charges of 399 personnel concerned including imprisonment of 154 of them as of Oct 2014. Blame and punishment culture can be prevalent in a more hierarchical society like South Korea as shown in the aftermath of this disaster. This study aims to analyse the South Korea ferry accident using Rasmussen's risk management framework and the associated AcciMap technique and to propose recommendations drawn from an AcciMap-based focus group with systems safety experts. The data for the accident analysis were collected mainly from an interim investigation report by the Board of Audit and Inspection of Korea and major South Korean and foreign newspapers. The analysis showed that the accident was attributed to many contributing factors arising from front-line operators, management, regulators and government. It also showed how the multiple factors including economic, social and political pressures and individual workload contributed to the accident and how they affected each other. This AcciMap was presented to 27 safety researchers and experts at 'the legacy of Jens Rasmussen' symposium adjunct to ODAM2014. Their recommendations were captured through a focus group. The four main recommendations include forgive (no blame and punishment on individuals), analyse (socio-technical system-based), learn (from why things do not go wrong) and change (bottom-up safety culture and safety system management). The findings offer important insights into how this type of accident should be understood, analysed and the subsequent response. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genetic Analysis of Strawberry Fruit Aroma and Identification of O-Methyltransferase FaOMT as the Locus Controlling Natural Variation in Mesifurane Content1[C][W][OA

PubMed Central

Zorrilla-Fontanesi, Yasmín; Rambla, José-Luis; Cabeza, Amalia; Medina, Juan J.; Sánchez-Sevilla, José F.; Valpuesta, Victoriano; Botella, Miguel A.; Granell, Antonio; Amaya, Iraida

2012-01-01

Improvement of strawberry (Fragaria × ananassa) fruit flavor is an important goal in breeding programs. To investigate genetic factors controlling this complex trait, a strawberry mapping population derived from genotype ‘1392’, selected for its superior flavor, and ‘232’ was profiled for volatile compounds over 4 years by headspace solid phase microextraction coupled to gas chromatography and mass spectrometry. More than 300 volatile compounds were detected, of which 87 were identified by comparison of mass spectrum and retention time to those of pure standards. Parental line ‘1392’ displayed higher volatile levels than ‘232’, and these and many other compounds with similar levels in both parents segregated in the progeny. Cluster analysis grouped the volatiles into distinct chemically related families and revealed a complex metabolic network underlying volatile production in strawberry fruit. Quantitative trait loci (QTL) detection was carried out over 3 years based on a double pseudo-testcross strategy. Seventy QTLs covering 48 different volatiles were detected, with several of them being stable over time and mapped as major QTLs. Loci controlling γ-decalactone and mesifurane content were mapped as qualitative traits. Using a candidate gene approach we have assigned genes that are likely responsible for several of the QTLs. As a proof of concept we show that one homoeolog of the O-methyltransferase gene (FaOMT) is the locus responsible for the natural variation of mesifurane content. Sequence analysis identified 30 bp in the promoter of this FaOMT homoeolog containing putative binding sites for basic/helix-loop-helix, MYB, and BZIP transcription factors. This polymorphism fully cosegregates with both the presence of mesifurane and the high expression of FaOMT during ripening. PMID:22474217

Applying the AcciMap methodology to investigate the tragic Sewol Ferry accident in South Korea.

PubMed

Lee, Samuel; Moh, Young Bo; Tabibzadeh, Maryam; Meshkati, Najmedin

2017-03-01

This study applies the AcciMap methodology, which was originally proposed by Professor Jens Rasmussen (1997), to the analysis of the tragic Sewol Ferry accident in South Korea on April 16, 2014, which killed 304 mostly young people and is considered as a national disaster in that country. This graphical representation, by incorporating associated socio-technical factors into an integrated framework, provides a big-picture to illustrate the context in which an accident occurred as well as the interactions between different levels of the studied system that resulted in that event. In general, analysis of past accidents within the stated framework can define the patterns of hazards within an industrial sector. Such analysis can lead to the definition of preconditions for safe operations, which is a main focus of proactive risk management systems. In the case of the Sewol Ferry accident, a lot of the blame has been placed on the Sewol's captain and its crewmembers. However, according to this study, which relied on analyzing all available sources published in English and Korean, the disaster is the result of a series of lapses and disregards for safety across different levels of government and regulatory bodies, Chonghaejin Company, and the Sewol's crewmembers. The primary layers of the AcciMap framework, which include the political environment and non-proactive governmental body; inadequate regulations and their lax oversight and enforcement; poor safety culture; inconsideration of human factors issues; and lack of and/or outdated standard operating and emergency procedures were not only limited to the maritime industry in South Korea, and the Sewol Ferry accident, but they could also subject any safety-sensitive industry anywhere in the world. Copyright © 2016 Elsevier Ltd. All rights reserved.

Sensory factors affecting female consumers' acceptability of nail polish.

PubMed

Sun, C; Koppel, K; Adhikari, K

2015-12-01

The objectives of this study were to determine what sensory factors impact consumers' acceptability of nail polishes, to explore how these sensory factors impact consumers' acceptability of nail polishes, to investigate whether there are any consumer segments according to their overall acceptability on different nail polishes and to scrutinize how the consumer segments are related to the sensory factors. Ninety-eight females participated in a nail polish consumer study at Kansas State University. Eight commercial products belonging to four categories - regular (REG), gel (GEL), flake (FLK) and water-based (WAT) - were evaluated. Each nail polish sample was evaluated twice by each participant in two different tasks - a task devoted to applying and evaluating the product and a task devoted to observing the appearance and evaluating the product. Pearson's correlation analysis, analysis of variance (ANOVA), external preference mapping, cluster analysis and internal preference mapping were applied for data analysis. Participants' scores of overall liking of the nail polishes were similar in the application task and in the observation task. In general, participants liked the REG and GEL product samples more than the FLK and WAT samples. Among all the sensory attributes, appearance attributes were the major factors that affected participants' overall liking. Aroma seemed to be a minor factor to participants' overall liking. Some sensory attributes, such as runny, shininess, opacity, spreadability, smoothness, coverage and wet appearance, were found to drive participants' overall acceptability positively, whereas others such as pinhole, fatty-edges, blister, brushlines, pearl-like, flake-protrusion, glittery and initial-drag impacted participants' overall acceptability negatively. Four clusters of participants were identified according to their overall liking scores from both the application task and the observation task. Participants' acceptability, based on different sensory attributes, could help a nail polish manufacturer modify or improve their nail polish formulas. Nail polish manufacturers could use the consumer cluster information to improve their marketing strategies for specific categories of their products and to target their advertising on particular consumer groups. © 2015 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Dynamic maps of UV damage formation and repair for the human genome

PubMed Central

Hu, Jinchuan; Adebali, Ogun; Adar, Sheera; Sancar, Aziz

2017-01-01

Formation and repair of UV-induced DNA damage in human cells are affected by cellular context. To study factors influencing damage formation and repair genome-wide, we developed a highly sensitive single-nucleotide resolution damage mapping method [high-sensitivity damage sequencing (HS–Damage-seq)]. Damage maps of both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] from UV-irradiated cellular and naked DNA revealed that the effect of transcription factor binding on bulky adducts formation varies, depending on the specific transcription factor, damage type, and strand. We also generated time-resolved UV damage maps of both CPDs and (6-4)PPs by HS–Damage-seq and compared them to the complementary repair maps of the human genome obtained by excision repair sequencing to gain insight into factors that affect UV-induced DNA damage and repair and ultimately UV carcinogenesis. The combination of the two methods revealed that, whereas UV-induced damage is virtually uniform throughout the genome, repair is affected by chromatin states, transcription, and transcription factor binding, in a manner that depends on the type of DNA damage. PMID:28607063

Dynamic maps of UV damage formation and repair for the human genome.

PubMed

Hu, Jinchuan; Adebali, Ogun; Adar, Sheera; Sancar, Aziz

2017-06-27

Formation and repair of UV-induced DNA damage in human cells are affected by cellular context. To study factors influencing damage formation and repair genome-wide, we developed a highly sensitive single-nucleotide resolution damage mapping method [high-sensitivity damage sequencing (HS-Damage-seq)]. Damage maps of both cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] from UV-irradiated cellular and naked DNA revealed that the effect of transcription factor binding on bulky adducts formation varies, depending on the specific transcription factor, damage type, and strand. We also generated time-resolved UV damage maps of both CPDs and (6-4)PPs by HS-Damage-seq and compared them to the complementary repair maps of the human genome obtained by excision repair sequencing to gain insight into factors that affect UV-induced DNA damage and repair and ultimately UV carcinogenesis. The combination of the two methods revealed that, whereas UV-induced damage is virtually uniform throughout the genome, repair is affected by chromatin states, transcription, and transcription factor binding, in a manner that depends on the type of DNA damage.

The gene for human U2 snRNP auxiliary factor small 35-kDa subunit (U2AF1) maps to the progressive myoclonus epilepsy (EPM1) critical region on chromosome 21q22.3

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

Lalioti, M.D.; Rossier, C.; Antonarakis, S.E.

1996-04-15

We used targeted exon trapping to clone portions of genes from human chromosome 21q22.3. One trapped sequence showed complete homology with the cDNA of human U2AF{sup 35} (M96982; HGM-approved nomenclature U2AF1), which encodes for the small 35-kDa subunit of the U2 snRNP auxiliary factor. Using the U2AF1 cDNA as a probe, we mapped this gene to cosmid Q15D2, a P1, and YAC 350F7 of the Chumakov et al. contig, close to the cystathionine-{beta}-synthase gene (CBS) on 21q22.3. This localization was confirmed by PCR using oligonucleotides from the 3{prime} UTR and by FISH. As U2AF1 associated with a number of differentmore » factors during mRNA splicing, overexpression in trisomy 21 individuals could contribute to some Down syndrome phenotypes by interfering with the splicing process. Furthermore, because this gene maps in the critical region for the progressive myoclonus epilepsy I locus (EPM1), mutation analysis will be carried out in patients to evaluate the potential role of U2AF1 as a candidate for EPM1. 24 refs., 1 fig.« less

Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping

PubMed Central

Kujur, Alice; Bajaj, Deepak; Saxena, Maneesha S.; Tripathi, Shailesh; Upadhyaya, Hari D.; Gowda, C.L.L.; Singh, Sube; Jain, Mukesh; Tyagi, Akhilesh K.; Parida, Swarup K.

2013-01-01

We developed 1108 transcription factor gene-derived microsatellite (TFGMS) and 161 transcription factor functional domain-associated microsatellite (TFFDMS) markers from 707 TFs of chickpea. The robust amplification efficiency (96.5%) and high intra-specific polymorphic potential (34%) detected by markers suggest their immense utilities in efficient large-scale genotyping applications, including construction of both physical and functional transcript maps and understanding population structure. Candidate gene-based association analysis revealed strong genetic association of TFFDMS markers with three major seed and pod traits. Further, TFGMS markers in the 5′ untranslated regions of TF genes showing differential expression during seed development had higher trait association potential. The significance of TFFDMS markers was demonstrated by correlating their allelic variation with amino acid sequence expansion/contraction in the functional domain and alteration of secondary protein structure encoded by genes. The seed weight-associated markers were validated through traditional bi-parental genetic mapping. The determination of gene-specific linkage disequilibrium (LD) patterns in desi and kabuli based on single nucleotide polymorphism-microsatellite marker haplotypes revealed extended LD decay, enhanced LD resolution and trait association potential of genes. The evolutionary history of a strong seed-size/weight-associated TF based on natural variation and haplotype sharing among desi, kabuli and wild unravelled useful information having implication for seed-size trait evolution during chickpea domestication. PMID:23633531

Self-organizing map analysis using multivariate data from theophylline tablets predicted by a thin-plate spline interpolation.

PubMed

Yasuda, Akihito; Onuki, Yoshinori; Obata, Yasuko; Yamamoto, Rie; Takayama, Kozo

2013-01-01

The "quality by design" concept in pharmaceutical formulation development requires the establishment of a science-based rationale and a design space. We integrated thin-plate spline (TPS) interpolation and Kohonen's self-organizing map (SOM) to visualize the latent structure underlying causal factors and pharmaceutical responses. As a model pharmaceutical product, theophylline tablets were prepared based on a standard formulation. The tensile strength, disintegration time, and stability of these variables were measured as response variables. These responses were predicted quantitatively based on nonlinear TPS. A large amount of data on these tablets was generated and classified into several clusters using an SOM. The experimental values of the responses were predicted with high accuracy, and the data generated for the tablets were classified into several distinct clusters. The SOM feature map allowed us to analyze the global and local correlations between causal factors and tablet characteristics. The results of this study suggest that increasing the proportion of microcrystalline cellulose (MCC) improved the tensile strength and the stability of tensile strength of these theophylline tablets. In addition, the proportion of MCC has an optimum value for disintegration time and stability of disintegration. Increasing the proportion of magnesium stearate extended disintegration time. Increasing the compression force improved tensile strength, but degraded the stability of disintegration. This technique provides a better understanding of the relationships between causal factors and pharmaceutical responses in theophylline tablet formulations.

Implementing Dementia Care Mapping to develop person-centred care: results of a process evaluation within the Leben-QD II trial.

PubMed

Quasdorf, Tina; Riesner, Christine; Dichter, Martin Nikolaus; Dortmann, Olga; Bartholomeyczik, Sabine; Halek, Margareta

2017-03-01

To evaluate Dementia Care Mapping implementation in nursing homes. Dementia Care Mapping, an internationally applied method for supporting and enhancing person-centred care for people with dementia, must be successfully implemented into care practice for its effective use. Various factors influence the implementation of complex interventions such as Dementia Care Mapping; few studies have examined the specific factors influencing Dementia Care Mapping implementation. A convergent parallel mixed-methods design embedded in a quasi-experimental trial was used to assess Dementia Care Mapping implementation success and influential factors. From 2011-2013, nine nursing units in nine different nursing homes implemented either Dementia Care Mapping (n = 6) or a periodic quality of life measurement using the dementia-specific instrument QUALIDEM (n = 3). Diverse data (interviews, n = 27; questionnaires, n = 112; resident records, n = 81; and process documents) were collected. Each data set was separately analysed and then merged to comprehensively portray the implementation process. Four nursing units implemented the particular intervention without deviating from the preplanned intervention. Translating Dementia Care Mapping results into practice was challenging. Necessary organisational preconditions for Dementia Care Mapping implementation included well-functioning networks, a dementia-friendly culture and flexible organisational structures. Involved individuals' positive attitudes towards Dementia Care Mapping also facilitated implementation. Precisely planning the intervention and its implementation, recruiting champions who supported Dementia Care Mapping implementation and having well-qualified, experienced project coordinators were essential to the implementation process. For successful Dementia Care Mapping implementation, it must be embedded in a systematic implementation strategy considering the specific setting. Organisational preconditions may need to be developed before Dementia Care Mapping implementation. Necessary steps may include team building, developing and realising a person-centred care-based mission statement or educating staff regarding general dementia care. The implementation strategy may include attracting and involving individuals on different hierarchical levels in Dementia Care Mapping implementation and supporting staff to translate Dementia Care Mapping results into practice. The identified facilitating factors can guide Dementia Care Mapping implementation strategy development. © 2016 John Wiley & Sons Ltd.

Multiplex analysis of cytokines as biomarkers that differentiate benign and malignant thyroid diseases

PubMed Central

Linkov, Faina; Ferris, Robert L.; Yurkovetsky, Zoya; Marrangoni, Adele; Velikokhatnaya, Lyudmila; Gooding, William; Nolan, Brian; Winans, Matthew; Siegel, Eric R.; Lokshin, Anna; Stack, Brendan C.

2008-01-01

Thyroid cancer incidence is increasing, and its diagnosis can be challenging. Fine needle biopsy, the principal clinical tool to make a tissue diagnosis, leads to inconclusive diagnoses in up to 30% of the cases, leading to surgery. Advances in proteomics are improving abilities to diagnose malignant conditions using small samples of tissue or body fluids. We hypothesized that analysis of serum growth factors would uncover diagnostically informative differences between benign and malignant thyroid conditions. Using xMAP profiling, we evaluated concentrations of 19 cytokines, chemokines, and growth factors. We used sera from 23 patients with cancer (Malignant group), 24 patients with benign nodular thyroid disease (Benign group), and 23 healthy subjects (Normal group). In univariate analysis, five factors (epithelial growth factor, hepatocyte growth factor, Interleukins-5 and -8, and regulated upon activation, normally T-expressed and presumably secreted (RANTES) distinguished subjects with thyroid disease from the Normal group. In multivariate analysis, the set {Interleukin-8, hepatocyte growth factor, monocyte-induced γ interferon, interleukin-12 p40} achieved noteworthy discrimination between Benign and Malignant groups (area under the receiver operating characteristics curve was 0.81 (95% confidence interval: 0.65–0.90)). Multiplex panels of serum biomarkers may be promising tools to diagnose cancer in patients presenting with evidence of nodular thyroid disease. PMID:19234619

76 FR 78015 - Revised Analysis and Mapping Procedures for Non-Accredited Levees

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-15

...] Revised Analysis and Mapping Procedures for Non-Accredited Levees AGENCY: Federal Emergency Management... comments on the proposed solution for Revised Analysis and Mapping Procedures for Non-Accredited Levees. This document proposes a revised procedure for the analysis and mapping of non-accredited levees on...

Proposed method for hazard mapping of landslide propagation zone

NASA Astrophysics Data System (ADS)

Serbulea, Manole-Stelian; Gogu, Radu; Manoli, Daniel-Marcel; Gaitanaru, Dragos Stefan; Priceputu, Adrian; Andronic, Adrian; Anghel, Alexandra; Liviu Bugea, Adrian; Ungureanu, Constantin; Niculescu, Alexandru

2013-04-01

Sustainable development of communities situated in areas with landslide potential requires a fully understanding of the mechanisms that govern the triggering of the phenomenon as well as the propagation of the sliding mass, with catastrophic consequences on the nearby inhabitants and environment. Modern analysis methods for areas affected by the movement of the soil bodies are presented in this work, as well as a new procedure to assess the landslide hazard. Classical soil mechanics offer sufficient numeric models to assess the landslide triggering zone, such as Limit Equilibrium Methods (Fellenius, Janbu, Morgenstern-Price, Bishop, Spencer etc.), blocks model or progressive mobilization models, Lagrange-based finite element method etc. The computation methods for assessing the propagation zones are quite recent and have high computational requirements, thus not being sufficiently used in practice to confirm their feasibility. The proposed procedure aims to assess not only the landslide hazard factor, but also the affected areas, by means of simple mathematical operations. The method can easily be employed in GIS software, without requiring engineering training. The result is obtained by computing the first and second derivative of the digital terrain model (slope and curvature maps). Using the curvature maps, it is shown that one can assess the areas most likely to be affected by the propagation of the sliding masses. The procedure is first applied on a simple theoretical model and then used on a representative section of a high exposure area in Romania. The method is described by comparison with Romanian legislation for risk and vulnerability assessment, which specifies that the landslide hazard is to be assessed, using an average hazard factor Km, obtained from various other factors. Following the employed example, it is observed that using the Km factor there is an inconsistent distribution of the polygonal surfaces corresponding to different landslide potential. For small values of Km (0.00..0.10) the polygonal surfaces have reduced dimensions along the slopes belonging to main rivers. This can be corrected by including in the analysis the potential areas to be affected by soil instability. Finally, it is shown that the proposed procedure can be used to better assess these areas and to produce more reliable landslide hazard maps. This work was supported by a grant of the Romanian National Authority for Scientific Research, Program for research - Space Technology and Advanced Research - STAR, project number 30/2012.

Human HST1 (HSTF1) gene maps to chromosome band 11q13 and coamplifies with the INT2 gene in human cancer

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

Yoshida, Michihiro C.; Wada, Makio; Satoh, Hitoshi

1988-07-01

The human HST1 gene, previously designated the hst gene, and now assigned the name HSTF1 for heparin-binding secretory transforming factor in human gene nomenclature, was originally identified as a transforming gene in DNAs from human stomach cancers by transfection assay with mouse NIH 3T3 cells. The amino acid sequence of the product deduced from DNA sequences of the HST1 cDNA and genomic clones had approximately 40% homology to human basic and acidic fibroblast growth factors and mouse Int-2-encoded protein. The authors have mapped the human HST1 gene to chromosome 11 at band q13.3 by Southern blot hybridization analysis of amore » panel of human and mouse somatic cell hybrids and in situ hybridization with an HST1 cDNA probe. The HST1 gene was found to be amplified in DNAs obtained from a stomach cancer and a vulvar carcinoma cell line, A431. In all of these samples of DNA, the INT2 gene, previously mapped to human chromosome 11q13, was also amplified to the same degree as the HST1 gene.« less

Probabilistic landslide susceptibility mapping in the Lai Chau province of Vietnam: focus on the relationship between tectonic fractures and landslides

NASA Astrophysics Data System (ADS)

Lee, Saro; Dan, Nguyen Tu

2005-09-01

This study evaluates the susceptibility of landslides in the Lai Chau province of Vietnam using Geographic Information System (GIS) and remote sensing data to focus on the relationship between tectonic fractures and landslides. Landslide locations were identified from aerial photographs and field surveys. Topographic, geological data and satellite images were collected, processed, and constructed into a spatial database using GIS data and image-processing techniques. A scheme of the tectonic fracturing of crust in the Lai Chau region was established. Lai Chau was identified as a region with many crustal fractures, where the grade of tectonic fracture is closely related to landslide occurrence. The influencing factors of landslide occurrence were: distance from a tectonic fracture, slope, aspect, curvature, soil, and vegetative land cover. Landslide prone areas were analyzed and mapped using the landslide occurrence factors employing the probability-frequency ratio model. The results of the analysis were verified using landslide location data and showed 83.47% prediction accuracy. That emphasized a strong relationship between the susceptibility map and the existing landslide location data. The results of this study can form a basis stable development and land use planning for the region.

Landslides susceptibility change over time according to terrain conditions in a mountain area of the tropic region.

PubMed

Pineda, M C; Viloria, J; Martínez-Casasnovas, J A

2016-04-01

Susceptibility to landslides in mountain areas results from the interaction of various factors related to relief formation and soil development. The assessment of landslide susceptibility has generally taken into account individual events, or it has been aimed at establishing relationships between landslide-inventory maps and maps of environmental factors, without considering that such relationships can change in space and time. In this work, temporal and space changes in landslides were analysed in six different combinations of date and geomorphological conditions, including two different geological units, in a mountainous area in the north-centre of Venezuela, in northern South America. Landslide inventories from different years were compared with a number of environmental factors by means of logistic regression analysis. The resulting equations predicted landslide susceptibility from a range of geomorphometric parameters and a vegetation index, with diverse accuracy, in the study area. The variation of the obtained models and their prediction accuracy between geological units and dates suggests that the complexity of the landslide processes and their explanatory factors changed over space and time in the studied area. This calls into question the use of a single model to evaluate landslide susceptibility over large regions.

Application of decision tree model for the ground subsidence hazard mapping near abandoned underground coal mines.

PubMed

Lee, Saro; Park, Inhye

2013-09-30

Subsidence of ground caused by underground mines poses hazards to human life and property. This study analyzed the hazard to ground subsidence using factors that can affect ground subsidence and a decision tree approach in a geographic information system (GIS). The study area was Taebaek, Gangwon-do, Korea, where many abandoned underground coal mines exist. Spatial data, topography, geology, and various ground-engineering data for the subsidence area were collected and compiled in a database for mapping ground-subsidence hazard (GSH). The subsidence area was randomly split 50/50 for training and validation of the models. A data-mining classification technique was applied to the GSH mapping, and decision trees were constructed using the chi-squared automatic interaction detector (CHAID) and the quick, unbiased, and efficient statistical tree (QUEST) algorithms. The frequency ratio model was also applied to the GSH mapping for comparing with probabilistic model. The resulting GSH maps were validated using area-under-the-curve (AUC) analysis with the subsidence area data that had not been used for training the model. The highest accuracy was achieved by the decision tree model using CHAID algorithm (94.01%) comparing with QUEST algorithms (90.37%) and frequency ratio model (86.70%). These accuracies are higher than previously reported results for decision tree. Decision tree methods can therefore be used efficiently for GSH analysis and might be widely used for prediction of various spatial events. Copyright © 2013. Published by Elsevier Ltd.

Flood Vulnerability Analysis of the part of Karad Region, Satara District, Maharashtra using Remote Sensing and Geographic Information System technique

NASA Astrophysics Data System (ADS)

Warghat, Sumedh R.; Das, Sandipan; Doad, Atul; Mali, Sagar; Moon, Vishal S.

2012-07-01

Karad City is situated on the bank of confluence of river Krishna & Koyana, which is severely flood prone area. The floodwaters enter the city through the roads and disrupt the infrastructure in the whole city. Furthermore, due to negligence of the authorities and unplanned growth of the city, the people living in the city have harnessed the natural flow of water by constructing unnecessary embankments in the river Koyna. Due to this reason now river koyna is flowing in the form of a narrow channel, which very easily over-flows during very minor flooding.Flood Vulnerabilty Analysis has been done for the karad region of satara district, maharashtra using remote sensing and geographic information system technique. The aim of this study is to identify flood vulnerability zone by using GIS and RS technique and an attempt has been to demonstrat the application of remote sensing and GIS in order to map flood vulnerabilty area by utilizing ArcMap, and Erdas software. Flood vulnerabilty analysis of part the Karad Regian of Satara District, Maharashtra has been carried out with the objectives - Identify the Flood Prone area in the Koyana and Krishna river basin, Calculate surface runoff and Delineate flood sensitive areas. Delineate classified hazard Map, Evaluate the Flood affected area, Prepare the Flood Vulnerability Map by utilizing Remote Sensing and GIS technique. (C.J. Kumanan;S.M. Ramasamy)The study is based on GIS and spatial technique is used for analysis and understanding of flood problem in Karad Tahsil. The flood affected areas of the different magnitude has been identified and mapped using Arc GIS software. The analysis is useful for local planning authority for identification of risk areas and taking proper decision in right moment. In the analysis causative factors for flooding in watershed are taken into account as annual rainfall, size of watershed, basin slope, drainage density of natural channels and land use. (Dinand Alkema; Farah Aziz.)This study of flood vulnerable area determination in a part of Karad Tahsil is employed to illustrate the different approaches.

Identification of occult tumors by whole-specimen mapping in solitary papillary thyroid carcinoma.

PubMed

Park, Seog Yun; Jung, Yuh-S; Ryu, Chang Hwan; Lee, Chang Yoon; Lee, You Jin; Lee, Eun Kyung; Kim, Seok-Ki; Kim, Tae Sung; Kim, Tae Hyun; Jang, Jeyun; Park, Daeyoon; Dong, Seung Myung; Kang, Jae-Goo; Lee, Jin Soo; Ryu, Junsun

2015-08-01

We undertook this study to estimate an accurate incidence and spread patterns of occult papillary thyroid carcinoma (PTC) in patients with a preoperative diagnosis of solitary PTC by using whole-specimen mapping of all specimens after a total thyroidectomy. Enrolled prospectively in this whole-thyroid mapping study are 82 consecutive patients who underwent a total thyroidectomy under a preoperative diagnosis of solitary PTC. All thyroidectomy specimens were serially sectioned in 2 mm thickness and whole-thyroid mapping was carried out for additional foci of occult PTC. The frequencies of occult lesions detected in the whole and contralateral lobe were determined, and clinicopathologic factors associated with multifocality were assessed. Whole-thyroid mapping revealed 66 occult PTC lesions missed by preoperative ultrasound in 37 (45.1%) of the 82 patients. The great majority (92.5%) of the occult PTC was smaller than 3 mm in size and 25 patients (30.5%) had contralateral lesions. We found that the male sex was an independent predictor of multifocality (odds ratio (OR), 3.00; 95% CI, 1.11-8.14), adjusting for preoperative findings. Analysis with pathologic parameters showed that the male sex (OR, 5.03; 95% CI, 1.68-15.08) and extrathyroidal extensions (OR, 3.03; 95% CI, 1.03-8.95) were associated with multifocal PTC. However, none of the clinicopathologic factors evaluated predicted contralateral PTC. Our study demonstrates the diagnostic limitations of ultrasound for the detection of multifocal PTC and the need to consider the possibility of occult lesions in the management of solitary PTC, especially in male patients. © 2015 Society for Endocrinology.

Pharmaceutical strategic purchasing requirements in Iran: Price interventions and the related effective factors.

PubMed

Bastani, Peivand; Dinarvand, Rasoul; SamadBeik, Mahnaz; Pourmohammadi, Kimia

2016-01-01

Pharmaceutical access for the poor is an essential factor in developing countries that can be improved through strategic purchasing. This study was conducted to identify the elements affecting price in order to enable insurance organizations to put strategic purchasing into practice. This was a qualitative study conducted through content analysis with an inductive approach applying a five-stage framework analysis (familiarization, identifying a thematic framework, indexing, mapping, and interpretation). Data analysis was started right after transcribing each interview applying ATLAS.ti. Data were saturated after 32 semi-structured interviews by experts. These key informants were selected purposefully and through snowball sampling. Findings showed that there are four main themes as Pharmaceutical Strategic Purchasing Requirements in Iran as follows essential and structural factors, international factors, economical factors, and legal factors. Moreover, totally 14 related sub-themes were extracted in this area as the main effective variables. It seems that paying adequate attention to the four present themes and 14 sub-themes affecting price can enable health system policy-makers of developing countries like Iran to make the best decisions through strategic purchasing of drugs by the main insurers in order to improve access and health in the country.

Global Mapping of Oceanic and Continental Shelf Crustal Thickness and Ocean-Continent Transition Structure

NASA Astrophysics Data System (ADS)

Kusznir, Nick; Alvey, Andy; Roberts, Alan

2017-04-01

The 3D mapping of crustal thickness for continental shelves and oceanic crust, and the determination of ocean-continent transition (OCT) structure and continent-ocean boundary (COB) location, represents a substantial challenge. Geophysical inversion of satellite derived free-air gravity anomaly data incorporating a lithosphere thermal anomaly correction (Chappell & Kusznir, 2008) now provides a useful and reliable methodology for mapping crustal thickness in the marine domain. Using this we have produced the first comprehensive maps of global crustal thickness for oceanic and continental shelf regions. Maps of crustal thickness and continental lithosphere thinning factor from gravity inversion may be used to determine the distribution of oceanic lithosphere, micro-continents and oceanic plateaux including for the inaccessible polar regions (e.g. Arctic Ocean, Alvey et al.,2008). The gravity inversion method provides a prediction of continent-ocean boundary location which is independent of ocean magnetic anomaly and isochron interpretation. Using crustal thickness and continental lithosphere thinning factor maps with superimposed shaded-relief free-air gravity anomaly, we can improve the determination of pre-breakup rifted margin conjugacy and sea-floor spreading trajectory during ocean basin formation. By restoring crustal thickness & continental lithosphere thinning to their initial post-breakup configuration we show the geometry and segmentation of the rifted continental margins at their time of breakup, together with the location of highly-stretched failed breakup basins and rifted micro-continents. For detailed analysis to constrain OCT structure, margin type (i.e. magma poor, "normal" or magma rich) and COB location, a suite of quantitative analytical methods may be used which include: (i) Crustal cross-sections showing Moho depth and crustal basement thickness from gravity inversion. (ii) Residual depth anomaly (RDA) analysis which is used to investigate OCT bathymetric anomalies with respect to expected oceanic values. This includes flexural backstripping to produce bathymetry corrected for sediment loading. (iii) Subsidence analysis which is used to determine the distribution of continental lithosphere thinning. (iv) Joint inversion of time-domain deep seismic reflection and gravity anomaly data which is used to determine lateral variations in crustal basement density and velocity across the OCT, and to validate deep seismic reflection interpretations of Moho depth. The combined interpretation of these independent quantitative measurements is used to determine crustal thickness and composition across the ocean-continent-transition. This integrated approach has been validated on the Iberian margin where ODP drilling provides ground-truth of ocean-continent-transition crustal structure, continent-ocean-boundary location and magmatic type.

Genome-wide association study with the risk of schizophrenia in a Korean population.

PubMed

Kim, Lyoung Hyo; Park, Byung Lae; Cheong, Hyun Sub; Namgoong, Suhg; Kim, Ji On; Kim, Jeong-Hyun; Shin, Joong-Gon; Park, Chul Soo; Kim, Bong-Jo; Kim, Jae Won; Choi, Ihn-Geun; Hwang, Jaeuk; Shin, Hyoung Doo; Woo, Sung-Il

2016-03-01

Schizophrenia is regarded as a multifactorial and polygenic brain disorder that is attributed to different combinations of genetic and environmental risk factors. Recently, several genome-wide association studies (GWASs) of schizophrenia have identified numerous risk factors, but the replication results remain controversial and ambiguous. To identify schizophrenia susceptibility loci in the Korean population, we performed a GWAS using the Illumina HumanOmni1-Quad V1.0 Microarray. We genotyped 1,140,419 single nucleotide polymorphisms (SNPs) in 350 Korea schizophrenia patients and 700 control subjects, and approximately 620,001 autosomal SNPs were passed our quality control. In the case-control analysis, the rs9607195 A>G on intergenic area 250 kb away from the ISX gene and the rs12738007 A>G on the intron of the MECR gene were the most strongly associated SNPs with the risk of schizophrenia (P = 6.2 × 10(-8) , OR = 0.50 and P = 3.7 × 10(-7) , OR = 2.39, respectively). In subsequent fine-mapping analysis, 6 SNPs of MECR were genotyped with 310 schizophrenia patients and 604 control subjects. The association of the MECR rs12738007, a top ranked-SNP in GWAS, was replicated (P = 1.5 × 10(-2) , OR = 1.53 in fine mapping analysis, P = 1.5 × 10(-6) , OR = 1.90 in combined analysis). The identification of putative schizophrenia susceptibility loci could provide new insights into genetic factors related with schizophrenia and clues for the development of diagnosis strategies. © 2015 Wiley Periodicals, Inc.

Spatial Resolution Effects of Digital Terrain Models on Landslide Susceptibility Analysis

NASA Astrophysics Data System (ADS)

Chang, K. T.; Dou, J.; Chang, Y.; Kuo, C. P.; Xu, K. M.; Liu, J. K.

2016-06-01

The purposes of this study are to identify the maximum number of correlated factors for landslide susceptibility mapping and to evaluate landslide susceptibility at Sihjhong river catchment in the southern Taiwan, integrating two techniques, namely certainty factor (CF) and artificial neural network (ANN). The landslide inventory data of the Central Geological Survey (CGS, MOEA) in 2004-2014 and two digital elevation model (DEM) datasets including a 5-meter LiDAR DEM and a 30-meter Aster DEM were prepared. We collected thirteen possible landslide-conditioning factors. Considering the multi-collinearity and factor redundancy, we applied the CF approach to optimize these thirteen conditioning factors. We hypothesize that if the CF values of the thematic factor layers are positive, it implies that these conditioning factors have a positive relationship with the landslide occurrence. Therefore, based on this assumption and positive CF values, seven conditioning factors including slope angle, slope aspect, elevation, terrain roughness index (TRI), terrain position index (TPI), total curvature, and lithology have been selected for further analysis. The results showed that the optimized-factors model provides a better accuracy for predicting landslide susceptibility in the study area. In conclusion, the optimized-factors model is suggested for selecting relative factors of landslide occurrence.

The X-Factor: an evaluation of common methods used to analyse major inter-segment kinematics during the golf swing.

PubMed

Brown, Susan J; Selbie, W Scott; Wallace, Eric S

2013-01-01

A common biomechanical feature of a golf swing, described in various ways in the literature, is the interaction between the thorax and pelvis, often termed the X-Factor. There is no consistent method used within golf biomechanics literature however to calculate these segment interactions. The purpose of this study was to examine X-factor data calculated using three reported methods in order to determine the similarity or otherwise of the data calculated using each method. A twelve-camera three-dimensional motion capture system was used to capture the driver swings of 19 participants and a subject specific three-dimensional biomechanical model was created with the position and orientation of each model estimated using a global optimisation algorithm. Comparison of the X-Factor methods showed significant differences for events during the swing (P < 0.05). Data for each kinematic measure were derived as a times series for all three methods and regression analysis of these data showed that whilst one method could be successfully mapped to another, the mappings between methods are subject dependent (P <0.05). Findings suggest that a consistent methodology considering the X-Factor from a joint angle approach is most insightful in describing a golf swing.

Using concept mapping in the development of the EU-PAD framework (EUropean-Physical Activity Determinants across the life course): a DEDIPAC-study.

PubMed

Condello, Giancarlo; Ling, Fiona Chun Man; Bianco, Antonino; Chastin, Sebastien; Cardon, Greet; Ciarapica, Donatella; Conte, Daniele; Cortis, Cristina; De Craemer, Marieke; Di Blasio, Andrea; Gjaka, Masar; Hansen, Sylvia; Holdsworth, Michelle; Iacoviello, Licia; Izzicupo, Pascal; Jaeschke, Lina; Leone, Liliana; Manoni, Livia; Menescardi, Cristina; Migliaccio, Silvia; Nazare, Julie-Anne; Perchoux, Camille; Pesce, Caterina; Pierik, Frank; Pischon, Tobias; Polito, Angela; Puggina, Anna; Sannella, Alessandra; Schlicht, Wolfgang; Schulz, Holger; Simon, Chantal; Steinbrecher, Astrid; MacDonncha, Ciaran; Capranica, Laura

2016-11-09

A large proportion of European children, adults and older adults do not engage in sufficient physical activity (PA). Understanding individual and contextual factors associated with PA behaviours is essential for the identification and implementation of effective preventative environments, policies, and programmes that can promote an active lifestyle across life course and can potentially improve health. The current paper intends to provide 1) a multi-disciplinary, Pan-European and life course view of key determinants of PA behaviours and 2) a proposal of how these factors may cluster. After gathering a list of 183 potential PA behaviours-associated factors and a consensus meeting to unify/consolidate terminology, a concept mapping software was used to collate European experts' views of 106 identified factors for youth (<19 years), adults (19-64 years), and older adults (≥65 years). The analysis evaluated common trends in the clustering of factors and the ratings of the distinct factors' expected modifiability and population-level impact on PA behaviours across the life course. Priority for research was also assessed for each cluster. The concept mapping resulted in six distinct clusters, broadly merged in two themes: 1) the 'Person', which included clusters 'Intra-Personal Context and Wellbeing' and 'Family and Social Economic Status' (42 % of all factors) and 2) the 'Society', which included the remaining four clusters 'Policy and Provision', 'Cultural Context and Media', 'Social Support and Modelling', and 'Supportive Environment' (58 % of all factors). Overall, 25 factors were rated as the most impactful on PA behaviours across the life course and being the most modifiable. They were mostly situated in the 'Intra-Personal Context and Wellbeing' cluster. Furthermore, 16 of them were rated as top priority for research. The current framework provides a preliminary overview of factors which may account for PA behaviour across the life course and are most relevant to the European community. These insights could potentially be a foundation for future Pan-European research on how these factors might interact with each other, and assist policy makers to identify appropriate interventions to maximize PA behaviours and thus the health of European citizens.

Mapping landslide susceptibility using data-driven methods.

PubMed

Zêzere, J L; Pereira, S; Melo, R; Oliveira, S C; Garcia, R A C

2017-07-01

Most epistemic uncertainty within data-driven landslide susceptibility assessment results from errors in landslide inventories, difficulty in identifying and mapping landslide causes and decisions related with the modelling procedure. In this work we evaluate and discuss differences observed on landslide susceptibility maps resulting from: (i) the selection of the statistical method; (ii) the selection of the terrain mapping unit; and (iii) the selection of the feature type to represent landslides in the model (polygon versus point). The work is performed in a single study area (Silveira Basin - 18.2km 2 - Lisbon Region, Portugal) using a unique database of geo-environmental landslide predisposing factors and an inventory of 82 shallow translational slides. The logistic regression, the discriminant analysis and two versions of the information value were used and we conclude that multivariate statistical methods perform better when computed over heterogeneous terrain units and should be selected to assess landslide susceptibility based on slope terrain units, geo-hydrological terrain units or census terrain units. However, evidence was found that the chosen terrain mapping unit can produce greater differences on final susceptibility results than those resulting from the chosen statistical method for modelling. The landslide susceptibility should be assessed over grid cell terrain units whenever the spatial accuracy of landslide inventory is good. In addition, a single point per landslide proved to be efficient to generate accurate landslide susceptibility maps, providing the landslides are of small size, thus minimizing the possible existence of heterogeneities of predisposing factors within the landslide boundary. Although during last years the ROC curves have been preferred to evaluate the susceptibility model's performance, evidence was found that the model with the highest AUC ROC is not necessarily the best landslide susceptibility model, namely when terrain mapping units are heterogeneous in size and reduced in number. Copyright © 2017 Elsevier B.V. All rights reserved.

Sinkhole Susceptibility Analysis for Karapinar/konya via Multi Criteria Decision

NASA Astrophysics Data System (ADS)

Sarı, F.

2017-11-01

Sinkholes are being a natural hazard which threads economic and human life. Sudden occurrence characteristic of sinkholes make it unable to escape. There are a lot of factor that activate sinkholes such as geology, irrigation, land use and human related factors. In Karapınar, Konya, there are over 200 sinkholes and this count is getting increased in recent years. Especially active agricultural lands, decreasing ground water level, extreme irrigation by 55267 water wells increase the risk factor of Karapınar. Nowadays, considering the economic contribution of Karapınar to Turkey economy in the field of agriculture, solar energy fields and thermal reactor which will be planned in next few years, prediction of sinkholes and searching for preventation ways are being more important issue. In this study, sinkhole susceptibility map via AHP was carried out for Karapınar in Konya. Slope, land use, elevation, geology, water wells, distance to roads and settlements criteria are included to determine susceptibility. The weights are calculated with AHP for each criterion and generated susceptibility map is overlapped with existing sinkholes. Suggestions and results are shared for this study.

Mapping monthly rainfall erosivity in Europe.

PubMed

Ballabio, Cristiano; Borrelli, Pasquale; Spinoni, Jonathan; Meusburger, Katrin; Michaelides, Silas; Beguería, Santiago; Klik, Andreas; Petan, Sašo; Janeček, Miloslav; Olsen, Preben; Aalto, Juha; Lakatos, Mónika; Rymszewicz, Anna; Dumitrescu, Alexandru; Tadić, Melita Perčec; Diodato, Nazzareno; Kostalova, Julia; Rousseva, Svetla; Banasik, Kazimierz; Alewell, Christine; Panagos, Panos

2017-02-01

Rainfall erosivity as a dynamic factor of soil loss by water erosion is modelled intra-annually for the first time at European scale. The development of Rainfall Erosivity Database at European Scale (REDES) and its 2015 update with the extension to monthly component allowed to develop monthly and seasonal R-factor maps and assess rainfall erosivity both spatially and temporally. During winter months, significant rainfall erosivity is present only in part of the Mediterranean countries. A sudden increase of erosivity occurs in major part of European Union (except Mediterranean basin, western part of Britain and Ireland) in May and the highest values are registered during summer months. Starting from September, R-factor has a decreasing trend. The mean rainfall erosivity in summer is almost 4 times higher (315MJmmha -1 h -1 ) compared to winter (87MJmmha -1 h -1 ). The Cubist model has been selected among various statistical models to perform the spatial interpolation due to its excellent performance, ability to model non-linearity and interpretability. The monthly prediction is an order more difficult than the annual one as it is limited by the number of covariates and, for consistency, the sum of all months has to be close to annual erosivity. The performance of the Cubist models proved to be generally high, resulting in R 2 values between 0.40 and 0.64 in cross-validation. The obtained months show an increasing trend of erosivity occurring from winter to summer starting from western to Eastern Europe. The maps also show a clear delineation of areas with different erosivity seasonal patterns, whose spatial outline was evidenced by cluster analysis. The monthly erosivity maps can be used to develop composite indicators that map both intra-annual variability and concentration of erosive events. Consequently, spatio-temporal mapping of rainfall erosivity permits to identify the months and the areas with highest risk of soil loss where conservation measures should be applied in different seasons of the year. Copyright © 2016 British Geological Survey, NERC. Published by Elsevier B.V. All rights reserved.

Proceedings of the international conference on cybernetics and societ

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

Not Available

1985-01-01

This book presents the papers given at a conference on artificial intelligence, expert systems and knowledge bases. Topics considered at the conference included automating expert system development, modeling expert systems, causal maps, data covariances, robot vision, image processing, multiprocessors, parallel processing, VLSI structures, man-machine systems, human factors engineering, cognitive decision analysis, natural language, computerized control systems, and cybernetics.

Leading Schools in Circumstances of Multiple Deprivation in South Africa: Mapping Some Conceptual, Contextual and Research Dimensions

ERIC Educational Resources Information Center

Maringe, Felix; Moletsane, Relebohile

2015-01-01

The paper suggests that multiple deprivation is a concept as yet lacking in substantial theoretical analysis and that its application as a research framing tool in education is relatively recent. As a concept, multiple deprivation suggests a confluence of factors which depress learning and place unique challenges on leadership and which act in…

Determining organisation-specific factors for developing health interventions in companies by a Delphi procedure: Organisational Mapping.

PubMed

van Scheppingen, Arjella R; ten Have, Kristin C J M; Zwetsloot, Gerard J I M; Kok, Gerjo; van Mechelen, Willem

2015-12-01

Companies, seen as social communities, are major health promotion contexts. However, health promotion in the work setting is often less successful than intended. An optimal adjustment to the organisational context is required. Knowledge of which organisation-specific factors are relevant to health promotion is scarce. A Delphi procedure is used to identify these factors. The aim is to contribute to more effective workplace health promotion. The identified factors are described and embedded into a practical methodology (Intervention Mapping). A systematic use of these factors (called 'Organisational Mapping') is likely to contribute to more effective health promotion in the work setting. © The Author(s) 2014.

Association of intraoperative tissue oxygenation with suspected risk factors for tissue hypoxia.

PubMed

Spruit, R J; Schwarte, L A; Hakenberg, O W; Scheeren, T W L

2013-10-01

Tissue hypoxia may cause organ dysfunction, but not much is known about tissue oxygenation in the intraoperative setting. We studied microcirculatory tissue oxygen saturation (StO₂) to determine representative values for anesthetized patients undergoing urological surgery and to test the hypothesis that StO₂ is associated with known perioperative risk factors for morbidity and mortality, conventionally monitored variables, and hypotension requiring norepinephrine. Using near-infrared spectroscopy, we measured StO₂ on the thenar eminence in 160 patients undergoing open urological surgery under general anesthesia (FiO2 0.35-0.4), and calculated its correlations with age, risk level for general perioperative complications and mortality (high if age ≥70 and procedure is radical cystectomy), mean arterial pressure (MAP), hemoglobin concentration (Hb), central venous oxygen saturation (ScvO₂), and norepinephrine use. The time averaged StO₂ was 86 ± 6 % (mean ± SD). In the multivariate analysis, Hb [standardized coefficient (SC) 0.21, p = 0.003], ScvO₂ (SC 0.53, p < 0.001) and high risk level (SC 0.06, p = 0.03) were significant independent variables correlated with StO₂. SStO₂ was partly dependent on MAP only when this was below 65 mmHg (lowest MAP SC 0.20, p = 0.006, MAP area under the curve <65 mmHg SC 0.03, p = 0.02). Finally, StO₂ was slightly lower in patients requiring norepinephrine (85 ± 6 vs. 89 ± 6 %, p = 0.001). Intraoperative StO₂ in urological patients was comparable to that of healthy volunteers breathing room air as reported in the literature and correlated with known perioperative risk factors. Further research should investigate its association with outcome and the effect of interventions aimed at optimizing StO₂.

Slope Instability Risk Analysys of the Municipality of Comala, Colima , Mexico

NASA Astrophysics Data System (ADS)

Ramirez-Ruiz, J. J.

2017-12-01

Every year during the rainy season occur the problem of mass landslide in some areas of the community of Comala, Colima Mexico. Slope instability is studied in this volcanic region which is located in the southern part of the Volcan de Fuego de Colima. It occurs due to the combination of different factors existing in this area as: Precipitation, topography contrast, type and mechanical properties of deposits that constitute the rocks and soils of the region and the erosion due to the elimination of vegetation deck to develop and grow urban areas. To these geological factors we can extend the tectonic activity of the Western part of Mexico that originate high seismicity by the interaction of Cocos plate and North America plate forming the region of Graben de Colima, were is located this area. Here we will present a Zonification and determination of Slope Instability Risk Maps due to the rain and seismicity accelerators factors. This Study is parto of a proyect to reduce the risk of this phenomenon, it was carried out as part of the National Risk Map of Mexico analized using the CENAPRED methodology to zonificate the risk areas. The instability of slopes is determined both in its origin and in its development, by different mechanisms. In such a way that this process of instability can be grouped into four main categories: Falls or landslides, Flows, Slips and expansions or lateral landslides. Here it is presented the Risk analisis to this volcanic area that cover the municipality of Comala in the State of Colima, Mexico using the Susceptibility map, Risk Map and Risk analisis of the Municipality.

Earth observation in support of malaria control and epidemiology: MALAREO monitoring approaches.

PubMed

Franke, Jonas; Gebreslasie, Michael; Bauwens, Ides; Deleu, Julie; Siegert, Florian

2015-06-03

Malaria affects about half of the world's population, with the vast majority of cases occuring in Africa. National malaria control programmes aim to reduce the burden of malaria and its negative, socioeconomic effects by using various control strategies (e.g. vector control, environmental management and case tracking). Vector control is the most effective transmission prevention strategy, while environmental factors are the key parameters affecting transmission. Geographic information systems (GIS), earth observation (EO) and spatial modelling are increasingly being recognised as valuable tools for effective management and malaria vector control. Issues previously inhibiting the use of EO in epidemiology and malaria control such as poor satellite sensor performance, high costs and long turnaround times, have since been resolved through modern technology. The core goal of this study was to develop and implement the capabilities of EO data for national malaria control programmes in South Africa, Swaziland and Mozambique. High- and very high resolution (HR and VHR) land cover and wetland maps were generated for the identification of potential vector habitats and human activities, as well as geoinformation on distance to wetlands for malaria risk modelling, population density maps, habitat foci maps and VHR household maps. These products were further used for modelling malaria incidence and the analysis of environmental factors that favour vector breeding. Geoproducts were also transferred to the staff of national malaria control programmes in seven African countries to demonstrate how EO data and GIS can support vector control strategy planning and monitoring. The transferred EO products support better epidemiological understanding of environmental factors related to malaria transmission, and allow for spatio-temporal targeting of malaria control interventions, thereby improving the cost-effectiveness of interventions.

Intraoperative mapping of language functions: a longitudinal neurolinguistic analysis.

PubMed

Ilmberger, Josef; Ruge, Maximilian; Kreth, Friedrich-Wilhelm; Briegel, Josef; Reulen, Hans-Juergen; Tonn, Joerg-Christian

2008-10-01

This prospective longitudinally designed study was conducted to evaluate language functions pre- and postoperatively in patients who underwent microsurgical treatment of tumors in close proximity to or within language areas and to detect those patients at risk for a postoperative aphasic disturbance. Between 1991 and 2005, 153 awake craniotomies with subsequent cortical mapping of language functions were performed in 149 patients. Language functions were assessed using a standardized test battery. Risk factors were obtained from multivariate logistic regression models. Language mapping was able to be performed in all patients, and complete tumor resection was achieved in 48.4%. Within 21 days after surgery a new language deficit (aphasic disturbance) was observed in 41 (32%) of the 128 cases without preoperative deficits. There were a total of 60 cases involving postoperative aphasic disturbances, including cases both with and without preoperative disturbances. Risk factors for postoperative aphasic disturbance were preoperative aphasia (p<0.0002), intraoperative complications (p<0.02), language-positive sites within the tumor (p<0.001), and nonfrontal lesion location (p<0.001). In patients without a preoperative deficit, a normal (yet submaximal) naming performance was a powerful predictor for an early postoperative aphasic disturbance (p<0.0003). Seven months after treatment 10.9% of the 128 cases without preoperative aphasic disturbances continued to demonstrate new postoperative language disturbances. A total of 17.6% of all cases demonstrated new postoperative language disturbances after 7 months. Risk factors for persistent aphasic disturbance were increased age (>40 years, p<0.02) and preoperative aphasia (p<0.001). Every attempt should be undertaken to preserve language-relevant areas intraoperatively, even when they are located within the tumor. New postoperative deficits resolve in the majority of patients, which may be a result of cortical mapping as well as functional reorganization.

Genetic analysis of QTL for eye cross and eye diameter in common carp (Cyprinus carpio L.) using microsatellites and SNPs.

PubMed

Jin, S B; Zhang, X F; Lu, J G; Fu, H T; Jia, Z Y; Sun, X W

2015-04-17

A group of 107 F1 hybrid common carp was used to construct a linkage map using JoinMap 4.0. A total of 4877 microsatellite and single nucleotide polymorphism (SNP) markers isolated from a genomic library (978 microsatellite and 3899 SNP markers) were assigned to construct the genetic map, which comprised 50 linkage groups. The total length of the linkage map for the common carp was 4775.90 cM with an average distance between markers of 0.98 cM. Ten quantitative trait loci (QTL) were associated with eye diameter, corresponding to 10.5-57.2% of the total phenotypic variation. Twenty QTL were related to eye cross, contributing to 10.8-36.9% of the total phenotypic variation. Two QTL for eye diameter and four QTL for eye cross each accounted for more than 20% of the total phenotypic variation and were considered to be major QTL. One growth factor related to eye diameter was observed on LG10 of the common carp genome, and three growth factors related to eye cross were observed on LG10, LG35, and LG44 of the common carp genome. The significant positive relationship of eye cross and eye diameter with other commercial traits suggests that eye diameter and eye cross can be used to assist in indirect selection for many commercial traits, particularly body weight. Thus, the growth factor for eye cross may also contribute to the growth of body weight, implying that aggregate breeding could have multiple effects. These findings provide information for future genetic studies and breeding of common carp.

Assessment of the behavior of potentially toxic elements (PTEs) in soil from the Sarno River Basin through a compositional data analysis

NASA Astrophysics Data System (ADS)

Matar, Thiombane; Vivo Benedetto, De; Albanese, Stefano; Martín-Fernández, Josep-Antoni; Lima, Annamaria; Doherty, Angela

2017-04-01

The Sarno River Basin (south-west Italy), nestled between the Somma-Vesuvius volcanic complex and the limestone formations of the Campania-Apennine Chain, is one of the most polluted river basins in Europe due to a high rate of industrialization and intensive agriculture. Water from the Sarno River, which is heavily contaminated by the discharge of human and industrial waste, is partially used for irrigation on the agricultural fields surrounding it. We apply compositional data analysis on 319 samples collected during two field campaigns along the river course, and throughout the basin, to determine the level and potential origin (anthropogenic and/or geogenic) of the potentially toxic elements (PTEs). The concentrations of 53 elements determined by ICP-MS, and were subsequently log-transformed. Using a clr-biplot and principal factor analysis, the variability and the correlations between a subset of extracted variables (26 elements) were identified. Using both normalized raw data and clr-transformed coordinates, factor association interpolated maps were generated to better visualize the distribution and potential sources of the PTEs in the Sarno Basin. The underlying geology substrata appear to be associated with raised of levels of Na, K, P, Rb, Ba, V, Co, B, Zr, and Li, due to the presence of pyroclastic rocks from Mt. Somma-Vesuvius. Similarly, elevated Pb, Zn, Cd, and Hg concentrations are most likely related to both geological and anthropogenic sources, the underlying volcanic rocks and contamination from fossil fuel combustion associated with urban centers. Interpolated factors score maps and clr-biplot indicate a clear correlation between Ni and Cr in samples taken along the Sarno River, and Ca and Mg near the Solofra district. After considering nearby anthropogenic sources, the Ni and Cr are PTEs from the Solofra tannery industry, while Ca and Mg correlate to the underlying limestone-rich soils of the area. This study shows the applicability of the compositional data analysis transformations, which relates perfectly relationships and dependencies between elements which can be lost when univariate and classical multivariate analyses are employed on normal data. Keywords: Sarno basin, PTEs, compositional data analysis, centered-log Transformation (clr), Biplot, Factor analysis, ArcGIS

Hydrogen Production Cost Analysis Map (Text Version) | Hyrdrogen and Fuel

Science.gov Websites

Cells | Hydrogen and Fuel Cells | NREL Analysis Map (Text Version) Hydrogen Production Cost Analysis Map (Text Version) Below is a text version of the U.S. map that provides the results of NREL's

Toward Probabilistic Risk Analyses - Development of a Probabilistic Tsunami Hazard Assessment of Crescent City, CA

NASA Astrophysics Data System (ADS)

González, F. I.; Leveque, R. J.; Hatheway, D.; Metzger, N.

2011-12-01

Risk is defined in many ways, but most are consistent with Crichton's [1999] definition based on the ''risk triangle'' concept and the explicit identification of three risk elements: ''Risk is the probability of a loss, and this depends on three elements: hazard, vulnerability, and exposure. If any of these three elements in risk increases or decreases, then the risk increases or decreases respectively." The World Meteorological Organization, for example, cites Crichton [1999] and then defines risk as [WMO, 2008] Risk = function (Hazard x Vulnerability x Exposure) while the Asian Disaster Reduction Center adopts the more general expression [ADRC, 2005] Risk = function (Hazard, Vulnerability, Exposure) In practice, probabilistic concepts are invariably invoked, and at least one of the three factors are specified as probabilistic in nature. The Vulnerability and Exposure factors are defined in multiple ways in the relevant literature; but the Hazard factor, which is the focus of our presentation, is generally understood to deal only with the physical aspects of the phenomena and, in particular, the ability of the phenomena to inflict harm [Thywissen, 2006]. A Hazard factor can be estimated by a methodology known as Probabilistic Tsunami Hazard Assessment (PTHA) [González, et al., 2009]. We will describe the PTHA methodology and provide an example -- the results of a previous application to Seaside, OR. We will also present preliminary results for a PTHA of Crescent City, CA -- a pilot project and coastal modeling/mapping effort funded by the Federal Emergency Management Agency (FEMA) Region IX office as part of the new California Coastal Analysis and Mapping Project (CCAMP). CCAMP and the PTHA in Crescent City are being conducted under the nationwide FEMA Risk Mapping, Assessment, and Planning (Risk MAP) Program which focuses on providing communities with flood information and tools they can use to enhance their mitigation plans and better protect their citizens.

Assessment of Three Flood Hazard Mapping Methods: A Case Study of Perlis

NASA Astrophysics Data System (ADS)

Azizat, Nazirah; Omar, Wan Mohd Sabki Wan

2018-03-01

Flood is a common natural disaster and also affect the all state in Malaysia. Regarding to Drainage and Irrigation Department (DID) in 2007, about 29, 270 km2 or 9 percent of region of the country is prone to flooding. Flood can be such devastating catastrophic which can effected to people, economy and environment. Flood hazard mapping can be used is an important part in flood assessment to define those high risk area prone to flooding. The purposes of this study are to prepare a flood hazard mapping in Perlis and to evaluate flood hazard using frequency ratio, statistical index and Poisson method. The six factors affecting the occurrence of flood including elevation, distance from the drainage network, rainfall, soil texture, geology and erosion were created using ArcGIS 10.1 software. Flood location map in this study has been generated based on flooded area in year 2010 from DID. These parameters and flood location map were analysed to prepare flood hazard mapping in representing the probability of flood area. The results of the analysis were verified using flood location data in year 2013, 2014, 2015. The comparison result showed statistical index method is better in prediction of flood area rather than frequency ratio and Poisson method.

Optimal design method to minimize users' thinking mapping load in human-machine interactions.

PubMed

Huang, Yanqun; Li, Xu; Zhang, Jie

2015-01-01

The discrepancy between human cognition and machine requirements/behaviors usually results in serious mental thinking mapping loads or even disasters in product operating. It is important to help people avoid human-machine interaction confusions and difficulties in today's mental work mastered society. Improving the usability of a product and minimizing user's thinking mapping and interpreting load in human-machine interactions. An optimal human-machine interface design method is introduced, which is based on the purpose of minimizing the mental load in thinking mapping process between users' intentions and affordance of product interface states. By analyzing the users' thinking mapping problem, an operating action model is constructed. According to human natural instincts and acquired knowledge, an expected ideal design with minimized thinking loads is uniquely determined at first. Then, creative alternatives, in terms of the way human obtains operational information, are provided as digital interface states datasets. In the last, using the cluster analysis method, an optimum solution is picked out from alternatives, by calculating the distances between two datasets. Considering multiple factors to minimize users' thinking mapping loads, a solution nearest to the ideal value is found in the human-car interaction design case. The clustering results show its effectiveness in finding an optimum solution to the mental load minimizing problems in human-machine interaction design.

Host gene expression for Mycobacterium avium subsp. paratuberculosis infection in human THP-1 macrophages.

PubMed

Shin, Min-Kyoung; Shin, Seung Won; Jung, Myunghwan; Park, Hongtae; Park, Hyun-Eui; Yoo, Han Sang

2015-07-01

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease, which causes considerable economic loss in the dairy industry and has a possible relationship to Crohn's disease (CD) in humans. As MAP has been detected in retail pasteurized milk samples, its transmission via milk is of concern. Despite its possible role in the etiology of CD, there have been few studies examining the interactions between MAP and human cells. In the current study, we applied Ingenuity Pathway Analysis to the transcription profiles generated from a murine model with MAP infection as part of a previously conducted study. Twenty-one genes were selected as potential host immune responses, compared with the transcriptional profiles in naturally MAP-infected cattle, and validated in MAP-infected human monocyte-derived macrophage THP-1 cells. Of these, the potential host responses included up-regulation of genes related to immune response (CD14, S100A8, S100A9, LTF, HP and CHCIL3), up-regulation of Th1-polarizing factor (CCL4, CCL5, CXCL9 and CXCL10), down-regulation of genes related to metabolism (ELANE, IGF1, TCF7L2 and MPO) and no significant response of other genes (GADD45a, GPNMB, HMOX1, IFNG and NQO1) in THP-1 cells infected with MAP. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Kilometer-Scale Topographic Roughness of Mercury: Correlation with Geologic Features and Units

NASA Technical Reports Server (NTRS)

Kreslavsky, Mikhail A.; Head, James W.; Neumann, Gregory A.; Zuber, Maria T.; Smith, David E.

2014-01-01

We present maps of the topographic roughness of the northern circumpolar area of Mercury at kilometer scales. The maps are derived from range profiles obtained by the Mercury Laser Altimeter (MLA) instrument onboard the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) mission. As measures of roughness, we used the interquartile range of profile curvature at three baselines: 0.7 kilometers, 2.8 kilometers, and 11 kilometers. The maps provide a synoptic overview of variations of typical topographic textures. They show a dichotomy between the smooth northern plains and rougher, more heavily cratered terrains. Analysis of the scale dependence of roughness indicates that the regolith on Mercury is thicker than on the Moon by approximately a factor of three. Roughness contrasts within northern volcanic plains of Mercury indicate a younger unit inside Goethe basin and inside another unnamed stealth basin. These new data permit interplanetary comparisons of topographic roughness.

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

NASA Astrophysics Data System (ADS)

Licatalosi, Donny D.; Mele, Aldo; Fak, John J.; Ule, Jernej; Kayikci, Melis; Chi, Sung Wook; Clark, Tyson A.; Schweitzer, Anthony C.; Blume, John E.; Wang, Xuning; Darnell, Jennifer C.; Darnell, Robert B.

2008-11-01

Protein-RNA interactions have critical roles in all aspects of gene expression. However, applying biochemical methods to understand such interactions in living tissues has been challenging. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova revealed extremely reproducible RNA-binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova-RNA interactions in 3' untranslated regions, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo.

Characterization of a subwavelength-scale 3D void structure using the FDTD-based confocal laser scanning microscopic image mapping technique.

PubMed

Choi, Kyongsik; Chon, James W; Gu, Min; Lee, Byoungho

2007-08-20

In this paper, a simple confocal laser scanning microscopic (CLSM) image mapping technique based on the finite-difference time domain (FDTD) calculation has been proposed and evaluated for characterization of a subwavelength-scale three-dimensional (3D) void structure fabricated inside polymer matrix. The FDTD simulation method adopts a focused Gaussian beam incident wave, Berenger's perfectly matched layer absorbing boundary condition, and the angular spectrum analysis method. Through the well matched simulation and experimental results of the xz-scanned 3D void structure, we first characterize the exact position and the topological shape factor of the subwavelength-scale void structure, which was fabricated by a tightly focused ultrashort pulse laser. The proposed CLSM image mapping technique based on the FDTD can be widely applied from the 3D near-field microscopic imaging, optical trapping, and evanescent wave phenomenon to the state-of-the-art bio- and nanophotonics.

Mapping of a locus for a familial autosomal recessive idiopathic myoclonic epilepsy of infancy to chromosome 16p13.

PubMed Central

Zara, F; Gennaro, E; Stabile, M; Carbone, I; Malacarne, M; Majello, L; Santangelo, R; de Falco, F A; Bricarelli, F D

2000-01-01

Myoclonic epilepsies with onset in infancy and childhood are clinically and etiologically heterogeneous. Although genetic factors are thought to play an important role, to date very little is known about the etiology of these disorders. We ascertained a large Italian pedigree segregating a recessive idiopathic myoclonic epilepsy that starts in early infancy as myoclonic seizures, febrile convulsions, and tonic-clonic seizures. We typed 304 microsatellite markers spanning the 22 autosomes and mapped the locus on chromosome 16p13 by linkage analysis. A maximum LOD score of 4.48 was obtained for marker D16S3027 at recombination fraction 0. Haplotype analysis placed the critical region within a 3.4-cM interval between D16S3024 and D16S423. The present report constitutes the first example of an idiopathic epilepsy that is inherited as an autosomal recessive trait. PMID:10741954

Holographic maps of quasiparticle interference

NASA Astrophysics Data System (ADS)

Dalla Torre, Emanuele G.; He, Yang; Demler, Eugene

2016-11-01

The analysis of Fourier-transformed scanning tunnelling microscopy images with subatomic resolution is a common tool for studying the properties of quasiparticle excitations in strongly correlated materials. Although Fourier amplitudes are generally complex valued, earlier analysis primarily focused on their absolute values. Their complex phases were often deemed random, and thus irrelevant, due to the unknown positions of the impurities in the sample. Here we show how to factor out these random phases by analysing overlaps between Fourier amplitudes that differ by reciprocal lattice vectors. The resulting holographic maps provide important and previously unknown information about the electronic structures. When applied to superconducting cuprates, our method solves a long-standing puzzle of the dichotomy between equivalent wavevectors. We show that d-wave Wannier functions of the conduction band provide a natural explanation for experimental results that were interpreted as evidence for competing unconventional charge modulations. Our work opens a new pathway to identify the nature of electronic states in scanning tunnelling microscopy.

Visualising inter-subject variability in fMRI using threshold-weighted overlap maps

NASA Astrophysics Data System (ADS)

Seghier, Mohamed L.; Price, Cathy J.

2016-02-01

Functional neuroimaging studies are revealing the neural systems sustaining many sensory, motor and cognitive abilities. A proper understanding of these systems requires an appreciation of the degree to which they vary across subjects. Some sources of inter-subject variability might be easy to measure (demographics, behavioural scores, or experimental factors), while others are more difficult (cognitive strategies, learning effects, and other hidden sources). Here, we introduce a simple way of visualising whole-brain consistency and variability in brain responses across subjects using threshold-weighted voxel-based overlap maps. The output quantifies the proportion of subjects activating a particular voxel or region over a wide range of statistical thresholds. The sensitivity of our approach was assessed in 30 healthy adults performing a matching task with their dominant hand. We show how overlap maps revealed many effects that were only present in a subsample of our group; we discuss how overlap maps can provide information that may be missed or misrepresented by standard group analysis, and how this information can help users to understand their data. In particular, we emphasize that functional overlap maps can be particularly useful when it comes to explaining typical (or atypical) compensatory mechanisms used by patients following brain damage.

Evaluation of iconic versus F-map microburst displays

NASA Technical Reports Server (NTRS)

Salzberger, Mark; Hansman, R. John; Wanke, Craig

1994-01-01

Previous studies have shown graphical presentation methods of hazardous wind shear to be superior to textual or audible warnings alone. Positional information and the strength of the hazard were observed to be and were cited by pilots as the most important factors in a display. In this experiment the use of the three different graphical presentations of hazardous wind shear are examined. Airborne predictive detectors of wind shear enable the dissemination of varying levels of information. The effectiveness of iconic and mapping display modes of different complexities are addressed through simulation and analysis. Different positional and time-varying situations are presented in a 'part-task' Boeing 767 simulator using data from actual microburst events. Experienced airline pilots fly approach profiles using both iconic and F-map wind shear alerting displays. Microburst accompanied each event is also shown to the pilot. Mapping display types are expected to be found exceptionally efficient at conveying location comparison information while iconic displays simplify the threat recognition process. Preliminary results from the simulator study are presented. Recommendations concerning the suitability of multilevel iconic and mapping displays are made. Situational problems with current display prototypes are also addressed.

Mapping of non-numerical domains on space: a systematic review and meta-analysis.

PubMed

Macnamara, Anne; Keage, Hannah A D; Loetscher, Tobias

2018-02-01

The spatial numerical association of response code (SNARC) effect is characterized by low numbers mapped to the left side of space and high numbers mapped to the right side of space. In addition to numbers, SNARC-like effects have been found in non-numerical magnitude domains such as time, size, letters, luminance, and more, whereby the smaller/earlier and larger/later magnitudes are typically mapped to the left and right of space, respectively. The purpose of this systematic and meta-analytic review was to identify and summarise all empirical papers that have investigated horizontal (left-right) SNARC-like mappings using non-numerical stimuli. A systematic search was conducted using EMBASE, Medline, and PsycINFO, where 2216 publications were identified, with 57 papers meeting the inclusion criteria (representing 112 experiments). Ninety-five of these experiments were included in a meta-analysis, resulting in an overall effect size of d = .488 for a SNARC-like effect. Additional analyses revealed a significant effect size advantage for explicit instruction tasks compared with implicit instructions, yet yielded no difference for the role of expertise on SNARC-like effects. There was clear evidence for a publication bias in the field, but the impact of this bias is likely to be modest, and it is unlikely that the SNARC-like effect is a pure artefact of this bias. The similarities in the response properties for the spatial mappings of numerical and non-numerical domains support the concept of a general higher order magnitude system. Yet, further research will need to be conducted to identify all the factors modulating the strength of the spatial associations.

Landslide susceptibility mapping for a part of North Anatolian Fault Zone (Northeast Turkey) using logistic regression model

NASA Astrophysics Data System (ADS)

Demir, Gökhan; aytekin, mustafa; banu ikizler, sabriye; angın, zekai

2013-04-01

The North Anatolian Fault is know as one of the most active and destructive fault zone which produced many earthquakes with high magnitudes. Along this fault zone, the morphology and the lithological features are prone to landsliding. However, many earthquake induced landslides were recorded by several studies along this fault zone, and these landslides caused both injuiries and live losts. Therefore, a detailed landslide susceptibility assessment for this area is indispancable. In this context, a landslide susceptibility assessment for the 1445 km2 area in the Kelkit River valley a part of North Anatolian Fault zone (Eastern Black Sea region of Turkey) was intended with this study, and the results of this study are summarized here. For this purpose, geographical information system (GIS) and a bivariate statistical model were used. Initially, Landslide inventory maps are prepared by using landslide data determined by field surveys and landslide data taken from General Directorate of Mineral Research and Exploration. The landslide conditioning factors are considered to be lithology, slope gradient, slope aspect, topographical elevation, distance to streams, distance to roads and distance to faults, drainage density and fault density. ArcGIS package was used to manipulate and analyze all the collected data Logistic regression method was applied to create a landslide susceptibility map. Landslide susceptibility maps were divided into five susceptibility regions such as very low, low, moderate, high and very high. The result of the analysis was verified using the inventoried landslide locations and compared with the produced probability model. For this purpose, Area Under Curvature (AUC) approach was applied, and a AUC value was obtained. Based on this AUC value, the obtained landslide susceptibility map was concluded as satisfactory. Keywords: North Anatolian Fault Zone, Landslide susceptibility map, Geographical Information Systems, Logistic Regression Analysis.

Estimation of regional differences in wind erosion sensitivity in Hungary

NASA Astrophysics Data System (ADS)

Mezősi, G.; Blanka, V.; Bata, T.; Kovács, F.; Meyer, B.

2015-01-01

In Hungary, wind erosion is one of the most serious natural hazards. Spatial and temporal variation in the factors that determine the location and intensity of wind erosion damage are not well known, nor are the regional and local sensitivities to erosion. Because of methodological challenges, no multi-factor, regional wind erosion sensitivity map is available for Hungary. The aim of this study was to develop a method to estimate the regional differences in wind erosion sensitivity and exposure in Hungary. Wind erosion sensitivity was modelled using the key factors of soil sensitivity, vegetation cover and wind erodibility as proxies. These factors were first estimated separately by factor sensitivity maps and later combined by fuzzy logic into a regional-scale wind erosion sensitivity map. Large areas were evaluated by using publicly available data sets of remotely sensed vegetation information, soil maps and meteorological data on wind speed. The resulting estimates were verified by field studies and examining the economic losses from wind erosion as compensated by the state insurance company. The spatial resolution of the resulting sensitivity map is suitable for regional applications, as identifying sensitive areas is the foundation for diverse land development control measures and implementing management activities.

Establishing partnership with traditional birth attendants for improved maternal and newborn health: a review of factors influencing implementation.

PubMed

Miller, Tina; Smith, Helen

2017-10-19

Recent World Health Organization recommendations recognize the important role Traditional Birth Attendants (TBAs) can play in supporting the health of women and newborns. This paper provides an analysis of key factors that affect the implementation of interventions to develop partnerships with TBAs to promote improved access to skilled care at birth. We conducted a secondary analysis of 20 papers identified through two systematic reviews that examined the effectiveness of interventions to find new roles for TBAs on maternal and newborn health outcomes, as well as papers identified through a systematic mapping of the maternal health literature. The Supporting the Use of Research Evidence framework (SURE) guided the thematic analysis to explore the perceptions of various stakeholders and implementation barriers and facilitators, as well as other contextual issues. This analysis identified countries that have implemented interventions to support the transition from birth with a TBA to birth with a skilled birth attendant. Drawing on the experiences of these countries, the analysis highlights factors that are important to consider when designing and implementing such interventions. Barriers to implementation included resistance to change in more traditional communities, negative attitudes between TBAs and skilled attendants and TBAs concerns about the financial implications of assuming new roles. Facilitating factors included stakeholder involvement in devising and implementing interventions, knowledge sharing between TBAs and skilled birth attendants, and formalised roles and responsibilities and remuneration for TBAs. The implementation barriers identified in this analysis could, if not addressed, prevent or discourage TBAs from carrying out newly defined roles supporting women in pregnancy and childbirth and linking them to the formal health system. This paper also identifies the factors that seem critical to success, which new programmes could consider adopting from the outset. In most cases a multi-faceted approach is needed to prepare TBAs and others for new roles, including the training of TBAs to strengthen their knowledge and skills to enable them to be able to assume new roles, alongside the sensitization of healthcare providers, communities, women and their families. Further research is required to map the transition process and stakeholder experiences in more detailed ways and to provide longer-term monitoring of existing interventions.

A Subject-Independent Method for Automatically Grading Electromyographic Features During a Fatiguing Contraction

PubMed Central

Jesunathadas, Mark; Poston, Brach; Santello, Marco; Ye, Jieping; Panchanathan, Sethuraman

2014-01-01

Many studies have attempted to monitor fatigue from electromyogram (EMG) signals. However, fatigue affects EMG in a subject-specific manner. We present here a subject-independent framework for monitoring the changes in EMG features that accompany muscle fatigue based on principal component analysis and factor analysis. The proposed framework is based on several time- and frequency-domain features, unlike most of the existing work, which is based on two to three features. Results show that latent factors obtained from factor analysis on these features provide a robust and unified framework. This framework learns a model from EMG signals of multiple subjects, that form a reference group, and monitors the changes in EMG features during a sustained submaximal contraction on a test subject on a scale from zero to one. The framework was tested on EMG signals collected from 12 muscles of eight healthy subjects. The distribution of factor scores of the test subject, when mapped onto the framework was similar for both the subject-specific and subject-independent cases. PMID:22498666

Psychometric Properties of the Serbian Version of the Maslach Burnout Inventory-Human Services Survey: A Validation Study among Anesthesiologists from Belgrade Teaching Hospitals

PubMed Central

Matejić, Bojana; Milenović, Miodrag; Kisić Tepavčević, Darija; Simić, Dušica; Pekmezović, Tatjana; Worley, Jody A.

2015-01-01

We report findings from a validation study of the translated and culturally adapted Serbian version of Maslach Burnout Inventory-Human Services Survey (MBI-HSS), for a sample of anesthesiologists working in the tertiary healthcare. The results showed the sufficient overall reliability (Cronbach's α = 0.72) of the scores (items 1–22). The results of Bartlett's test of sphericity (χ 2 = 1983.75, df = 231, p < 0.001) and Kaiser-Meyer-Olkin measure of sampling adequacy (0.866) provided solid justification for factor analysis. In order to increase sensitivity of this questionnaire, we performed unfitted factor analysis model (eigenvalue greater than 1) which enabled us to extract the most suitable factor structure for our study instrument. The exploratory factor analysis model revealed five factors with eigenvalues greater than 1.0, explaining 62.0% of cumulative variance. Velicer's MAP test has supported five-factor model with the smallest average squared correlation of 0,184. This study indicated that Serbian version of the MBI-HSS is a reliable and valid instrument to measure burnout among a population of anesthesiologists. Results confirmed strong psychometric characteristics of the study instrument, with recommendations for interpretation of two new factors that may be unique to the Serbian version of the MBI-HSS. PMID:26090517

Psychometric Properties of the Serbian Version of the Maslach Burnout Inventory-Human Services Survey: A Validation Study among Anesthesiologists from Belgrade Teaching Hospitals.

PubMed

Matejić, Bojana; Milenović, Miodrag; Kisić Tepavčević, Darija; Simić, Dušica; Pekmezović, Tatjana; Worley, Jody A

2015-01-01

We report findings from a validation study of the translated and culturally adapted Serbian version of Maslach Burnout Inventory-Human Services Survey (MBI-HSS), for a sample of anesthesiologists working in the tertiary healthcare. The results showed the sufficient overall reliability (Cronbach's α = 0.72) of the scores (items 1-22). The results of Bartlett's test of sphericity (χ(2) = 1983.75, df = 231, p < 0.001) and Kaiser-Meyer-Olkin measure of sampling adequacy (0.866) provided solid justification for factor analysis. In order to increase sensitivity of this questionnaire, we performed unfitted factor analysis model (eigenvalue greater than 1) which enabled us to extract the most suitable factor structure for our study instrument. The exploratory factor analysis model revealed five factors with eigenvalues greater than 1.0, explaining 62.0% of cumulative variance. Velicer's MAP test has supported five-factor model with the smallest average squared correlation of 0,184. This study indicated that Serbian version of the MBI-HSS is a reliable and valid instrument to measure burnout among a population of anesthesiologists. Results confirmed strong psychometric characteristics of the study instrument, with recommendations for interpretation of two new factors that may be unique to the Serbian version of the MBI-HSS.

Genetic analysis of Bacillus stearothermophilus by protoplast fusion

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

Chen, Z.; Wojcik, S.F.; Welker, N.E.

1986-03-01

Efficient and reliable protoplasting, regeneration, and fusion techniques were established for the prototrophic strain Bacillus stearothermophilus NUB36. Auxotrophic mutants were isolated, and protoplast fusion was used to construct isogenic mutant strains and for chromosomal mapping. Markers were mapped using two-, three-, and four-factor crosses. The order of the markers was hom-1-thr-1-his-1-(gly-1 or gly-2)-pur-1-pur-2. These markers may be analogous to hom, thrA, hisA, glyC, and purA markers on the Bacillus subtilis chromosome. No analogous pur-1 marker has been reported in B. subtilis. The relative order of three of the markers (hom-1-thr-1-gly-1) was independently confirmed by transduction.

Numerical solution of Euler's equation by perturbed functionals

NASA Technical Reports Server (NTRS)

Dey, S. K.

1985-01-01

A perturbed functional iteration has been developed to solve nonlinear systems. It adds at each iteration level, unique perturbation parameters to nonlinear Gauss-Seidel iterates which enhances its convergence properties. As convergence is approached these parameters are damped out. Local linearization along the diagonal has been used to compute these parameters. The method requires no computation of Jacobian or factorization of matrices. Analysis of convergence depends on properties of certain contraction-type mappings, known as D-mappings. In this article, application of this method to solve an implicit finite difference approximation of Euler's equation is studied. Some representative results for the well known shock tube problem and compressible flows in a nozzle are given.

Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors.

PubMed

Pfab, Alexander; Antosz, Wojciech; Holzinger, Philipp; Bruckmann, Astrid; Griesenbeck, Joachim; Grasser, Klaus D

2017-01-01

A central step to elucidate the function of proteins commonly comprises the analysis of their molecular interactions in vivo. For nuclear regulatory proteins this involves determining protein-protein interactions as well as mapping of chromatin binding sites. Here, we present two protocols to identify protein-protein and chromatin interactions of transcript elongation factors (TEFs) in Arabidopsis. The first protocol (Subheading 3.1) describes protein affinity-purification coupled to mass spectrometry (AP-MS) that utilizes suspension cultured cells as experimental system. This approach provides an unbiased view of proteins interacting with epitope-tagged TEFs. The second protocol (Subheading 3.2) depicts details about a chromatin immunoprecipitation (ChIP) procedure to characterize genomic binding sites of TEFs. These methods should be valuable tools for the analysis of a broad variety of nuclear proteins.

Sampling intensity and normalizations: Exploring cost-driving factors in nationwide mapping of tree canopy cover

Treesearch

John Tipton; Gretchen Moisen; Paul Patterson; Thomas A. Jackson; John Coulston

2012-01-01

There are many factors that will determine the final cost of modeling and mapping tree canopy cover nationwide. For example, applying a normalization process to Landsat data used in the models is important in standardizing reflectance values among scenes and eliminating visual seams in the final map product. However, normalization at the national scale is expensive and...

Systematic data ingratiation of clinical trial recruitment locations for geographic-based query and visualization

PubMed Central

Luo, Jake; Chen, Weiheng; Wu, Min; Weng, Chunhua

2018-01-01

Background Prior studies of clinical trial planning indicate that it is crucial to search and screen recruitment sites before starting to enroll participants. However, currently there is no systematic method developed to support clinical investigators to search candidate recruitment sites according to their interested clinical trial factors. Objective In this study, we aim at developing a new approach to integrating the location data of over one million heterogeneous recruitment sites that are stored in clinical trial documents. The integrated recruitment location data can be searched and visualized using a map-based information retrieval method. The method enables systematic search and analysis of recruitment sites across a large amount of clinical trials. Methods The location data of more than 1.4 million recruitment sites of over 183,000 clinical trials was normalized and integrated using a geocoding method. The integrated data can be used to support geographic information retrieval of recruitment sites. Additionally, the information of over 6000 clinical trial target disease conditions and close to 4000 interventions was also integrated into the system and linked to the recruitment locations. Such data integration enabled the construction of a novel map-based query system. The system will allow clinical investigators to search and visualize candidate recruitment sites for clinical trials based on target conditions and interventions. Results The evaluation results showed that the coverage of the geographic location mapping for the 1.4 million recruitment sites was 99.8%. The evaluation of 200 randomly retrieved recruitment sites showed that the correctness of geographic information mapping was 96.5%. The recruitment intensities of the top 30 countries were also retrieved and analyzed. The data analysis results indicated that the recruitment intensity varied significantly across different countries and geographic areas. Conclusion This study contributed a new data processing framework to extract and integrate the location data of heterogeneous recruitment sites from clinical trial documents. The developed system can support effective retrieval and analysis of potential recruitment sites using target clinical trial factors. PMID:29132636

Accelerated Brain DCE-MRI Using Iterative Reconstruction With Total Generalized Variation Penalty for Quantitative Pharmacokinetic Analysis: A Feasibility Study.

PubMed

Wang, Chunhao; Yin, Fang-Fang; Kirkpatrick, John P; Chang, Zheng

2017-08-01

To investigate the feasibility of using undersampled k-space data and an iterative image reconstruction method with total generalized variation penalty in the quantitative pharmacokinetic analysis for clinical brain dynamic contrast-enhanced magnetic resonance imaging. Eight brain dynamic contrast-enhanced magnetic resonance imaging scans were retrospectively studied. Two k-space sparse sampling strategies were designed to achieve a simulated image acquisition acceleration factor of 4. They are (1) a golden ratio-optimized 32-ray radial sampling profile and (2) a Cartesian-based random sampling profile with spatiotemporal-regularized sampling density constraints. The undersampled data were reconstructed to yield images using the investigated reconstruction technique. In quantitative pharmacokinetic analysis on a voxel-by-voxel basis, the rate constant K trans in the extended Tofts model and blood flow F B and blood volume V B from the 2-compartment exchange model were analyzed. Finally, the quantitative pharmacokinetic parameters calculated from the undersampled data were compared with the corresponding calculated values from the fully sampled data. To quantify each parameter's accuracy calculated using the undersampled data, error in volume mean, total relative error, and cross-correlation were calculated. The pharmacokinetic parameter maps generated from the undersampled data appeared comparable to the ones generated from the original full sampling data. Within the region of interest, most derived error in volume mean values in the region of interest was about 5% or lower, and the average error in volume mean of all parameter maps generated through either sampling strategy was about 3.54%. The average total relative error value of all parameter maps in region of interest was about 0.115, and the average cross-correlation of all parameter maps in region of interest was about 0.962. All investigated pharmacokinetic parameters had no significant differences between the result from original data and the reduced sampling data. With sparsely sampled k-space data in simulation of accelerated acquisition by a factor of 4, the investigated dynamic contrast-enhanced magnetic resonance imaging pharmacokinetic parameters can accurately estimate the total generalized variation-based iterative image reconstruction method for reliable clinical application.

Systematic data ingratiation of clinical trial recruitment locations for geographic-based query and visualization.

PubMed

Luo, Jake; Chen, Weiheng; Wu, Min; Weng, Chunhua

2017-12-01

Prior studies of clinical trial planning indicate that it is crucial to search and screen recruitment sites before starting to enroll participants. However, currently there is no systematic method developed to support clinical investigators to search candidate recruitment sites according to their interested clinical trial factors. In this study, we aim at developing a new approach to integrating the location data of over one million heterogeneous recruitment sites that are stored in clinical trial documents. The integrated recruitment location data can be searched and visualized using a map-based information retrieval method. The method enables systematic search and analysis of recruitment sites across a large amount of clinical trials. The location data of more than 1.4 million recruitment sites of over 183,000 clinical trials was normalized and integrated using a geocoding method. The integrated data can be used to support geographic information retrieval of recruitment sites. Additionally, the information of over 6000 clinical trial target disease conditions and close to 4000 interventions was also integrated into the system and linked to the recruitment locations. Such data integration enabled the construction of a novel map-based query system. The system will allow clinical investigators to search and visualize candidate recruitment sites for clinical trials based on target conditions and interventions. The evaluation results showed that the coverage of the geographic location mapping for the 1.4 million recruitment sites was 99.8%. The evaluation of 200 randomly retrieved recruitment sites showed that the correctness of geographic information mapping was 96.5%. The recruitment intensities of the top 30 countries were also retrieved and analyzed. The data analysis results indicated that the recruitment intensity varied significantly across different countries and geographic areas. This study contributed a new data processing framework to extract and integrate the location data of heterogeneous recruitment sites from clinical trial documents. The developed system can support effective retrieval and analysis of potential recruitment sites using target clinical trial factors. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of spatial distribution of land cover maps accuracy

NASA Astrophysics Data System (ADS)

Khatami, R.; Mountrakis, G.; Stehman, S. V.

2017-12-01

Land cover maps have become one of the most important products of remote sensing science. However, classification errors will exist in any classified map and affect the reliability of subsequent map usage. Moreover, classification accuracy often varies over different regions of a classified map. These variations of accuracy will affect the reliability of subsequent analyses of different regions based on the classified maps. The traditional approach of map accuracy assessment based on an error matrix does not capture the spatial variation in classification accuracy. Here, per-pixel accuracy prediction methods are proposed based on interpolating accuracy values from a test sample to produce wall-to-wall accuracy maps. Different accuracy prediction methods were developed based on four factors: predictive domain (spatial versus spectral), interpolation function (constant, linear, Gaussian, and logistic), incorporation of class information (interpolating each class separately versus grouping them together), and sample size. Incorporation of spectral domain as explanatory feature spaces of classification accuracy interpolation was done for the first time in this research. Performance of the prediction methods was evaluated using 26 test blocks, with 10 km × 10 km dimensions, dispersed throughout the United States. The performance of the predictions was evaluated using the area under the curve (AUC) of the receiver operating characteristic. Relative to existing accuracy prediction methods, our proposed methods resulted in improvements of AUC of 0.15 or greater. Evaluation of the four factors comprising the accuracy prediction methods demonstrated that: i) interpolations should be done separately for each class instead of grouping all classes together; ii) if an all-classes approach is used, the spectral domain will result in substantially greater AUC than the spatial domain; iii) for the smaller sample size and per-class predictions, the spectral and spatial domain yielded similar AUC; iv) for the larger sample size (i.e., very dense spatial sample) and per-class predictions, the spatial domain yielded larger AUC; v) increasing the sample size improved accuracy predictions with a greater benefit accruing to the spatial domain; and vi) the function used for interpolation had the smallest effect on AUC.

Spatial interpolation methods and geostatistics for mapping groundwater contamination in a coastal area.

PubMed

Elumalai, Vetrimurugan; Brindha, K; Sithole, Bongani; Lakshmanan, Elango

2017-04-01

Mapping groundwater contaminants and identifying the sources are the initial steps in pollution control and mitigation. Due to the availability of different mapping methods and the large number of emerging pollutants, these methods need to be used together in decision making. The present study aims to map the contaminated areas in Richards Bay, South Africa and compare the results of ordinary kriging (OK) and inverse distance weighted (IDW) interpolation techniques. Statistical methods were also used for identifying contamination sources. Na-Cl groundwater type was dominant followed by Ca-Mg-Cl. Data analysis indicate that silicate weathering, ion exchange and fresh water-seawater mixing are the major geochemical processes controlling the presence of major ions in groundwater. Factor analysis also helped to confirm the results. Overlay analysis by OK and IDW gave different results. Areas where groundwater was unsuitable as a drinking source were 419 and 116 km 2 for OK and IDW, respectively. Such diverse results make decision making difficult, if only one method was to be used. Three highly contaminated zones within the study area were more accurately identified by OK. If large areas are identified as being contaminated such as by IDW in this study, the mitigation measures will be expensive. If these areas were underestimated, then even though management measures are taken, it will not be effective for a longer time. Use of multiple techniques like this study will help to avoid taking harsh decisions. Overall, the groundwater quality in this area was poor, and it is essential to identify alternate drinking water source or treat the groundwater before ingestion.

Risk analysis for dengue suitability in Africa using the ArcGIS predictive analysis tools (PA tools).

PubMed

Attaway, David F; Jacobsen, Kathryn H; Falconer, Allan; Manca, Germana; Waters, Nigel M

2016-06-01

Risk maps identifying suitable locations for infection transmission are important for public health planning. Data on dengue infection rates are not readily available in most places where the disease is known to occur. A newly available add-in to Esri's ArcGIS software package, the ArcGIS Predictive Analysis Toolset (PA Tools), was used to identify locations within Africa with environmental characteristics likely to be suitable for transmission of dengue virus. A more accurate, robust, and localized (1 km × 1 km) dengue risk map for Africa was created based on bioclimatic layers, elevation data, high-resolution population data, and other environmental factors that a search of the peer-reviewed literature showed to be associated with dengue risk. Variables related to temperature, precipitation, elevation, and population density were identified as good predictors of dengue suitability. Areas of high dengue suitability occur primarily within West Africa and parts of Central Africa and East Africa, but even in these regions the suitability is not homogenous. This risk mapping technique for an infection transmitted by Aedes mosquitoes draws on entomological, epidemiological, and geographic data. The method could be applied to other infectious diseases (such as Zika) in order to provide new insights for public health officials and others making decisions about where to increase disease surveillance activities and implement infection prevention and control efforts. The ability to map threats to human and animal health is important for tracking vectorborne and other emerging infectious diseases and modeling the likely impacts of climate change. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessment of sand encroachment in Kuwait using GIS

NASA Astrophysics Data System (ADS)

Al-Helal, Anwar B.; Al-Awadhi, Jasem M.

2006-04-01

Assessment of sand encroachment in Kuwait using Geographical Information System (GIS) technology has been formulated as a Multi-Criteria Decision Making problem. The Delphi method and Analytical Hierarchy Process were adopted as evaluating techniques, in which experts’ judgments were analyzed for objectively estimating and weighting control factors. Seven triggering factors, depicted in the form of maps, were identified and ordered according to their priority. These factors are (1) wind energy; (2) surface sediment; (3) vegetation density; (4) land use; (5) drainage density; (6) topographic change and (7) vegetation type. The factor maps were digitized, converted to raster data and overlaid to determine their possible spatial relationships. Applying a susceptibility model, a map of sand encroachment susceptibility in Kuwait was developed. The map showed that the areas of very high and high sand encroachment susceptibility are located within the main corridor of sand pathway that coincides with the northwesterly dominant wind direction.

Spatial point analysis based on dengue surveys at household level in central Brazil

PubMed Central

Siqueira-Junior, João B; Maciel, Ivan J; Barcellos, Christovam; Souza, Wayner V; Carvalho, Marilia S; Nascimento, Nazareth E; Oliveira, Renato M; Morais-Neto, Otaliba; Martelli, Celina MT

2008-01-01

Background Dengue virus (DENV) affects nonimunne human populations in tropical and subtropical regions. In the Americas, dengue has drastically increased in the last two decades and Brazil is considered one of the most affected countries. The high frequency of asymptomatic infection makes difficult to estimate prevalence of infection using registered cases and to locate high risk intra-urban area at population level. The goal of this spatial point analysis was to identify potential high-risk intra-urban areas of dengue, using data collected at household level from surveys. Methods Two household surveys took place in the city of Goiania (~1.1 million population), Central Brazil in the year 2001 and 2002. First survey screened 1,586 asymptomatic individuals older than 5 years of age. Second survey 2,906 asymptomatic volunteers, same age-groups, were selected by multistage sampling (census tracts; blocks; households) using available digital maps. Sera from participants were tested by dengue virus-specific IgM/IgG by EIA. A Generalized Additive Model (GAM) was used to detect the spatial varying risk over the region. Initially without any fixed covariates, to depict the overall risk map, followed by a model including the main covariates and the year, where the resulting maps show the risk associated with living place, controlled for the individual risk factors. This method has the advantage to generate smoothed risk factors maps, adjusted by socio-demographic covariates. Results The prevalence of antibody against dengue infection was 37.3% (95%CI [35.5–39.1]) in the year 2002; 7.8% increase in one-year interval. The spatial variation in risk of dengue infection significantly changed when comparing 2001 with 2002, (ORadjusted = 1.35; p < 0.001), while controlling for potential confounders using GAM model. Also increasing age and low education levels were associated with dengue infection. Conclusion This study showed spatial heterogeneity in the risk areas of dengue when using a spatial multivariate approach in a short time interval. Data from household surveys pointed out that low prevalence areas in 2001 surveys shifted to high-risk area in consecutive year. This mapping of dengue risks should give insights for control interventions in urban areas. PMID:18937868

Plenary: Progress in Regional Landslide Hazard Assessment—Examples from the USA

USGS Publications Warehouse

Baum, Rex L.; Schulz, William; Brien, Dianne L.; Burns, William J.; Reid, Mark E.; Godt, Jonathan W.

2014-01-01

Landslide hazard assessment at local and regional scales contributes to mitigation of landslides in developing and densely populated areas by providing information for (1) land development and redevelopment plans and regulations, (2) emergency preparedness plans, and (3) economic analysis to (a) set priorities for engineered mitigation projects and (b) define areas of similar levels of hazard for insurance purposes. US Geological Survey (USGS) research on landslide hazard assessment has explored a range of methods that can be used to estimate temporal and spatial landslide potential and probability for various scales and purposes. Cases taken primarily from our work in the U.S. Pacific Northwest illustrate and compare a sampling of methods, approaches, and progress. For example, landform mapping using high-resolution topographic data resulted in identification of about four times more landslides in Seattle, Washington, than previous efforts using aerial photography. Susceptibility classes based on the landforms captured 93 % of all historical landslides (all types) throughout the city. A deterministic model for rainfall infiltration and shallow landslide initiation, TRIGRS, was able to identify locations of 92 % of historical shallow landslides in southwest Seattle. The potentially unstable areas identified by TRIGRS occupied only 26 % of the slope areas steeper than 20°. Addition of an unsaturated infiltration model to TRIGRS expands the applicability of the model to areas of highly permeable soils. Replacement of the single cell, 1D factor of safety with a simple 3D method of columns improves accuracy of factor of safety predictions for both saturated and unsaturated infiltration models. A 3D deterministic model for large, deep landslides, SCOOPS, combined with a three-dimensional model for groundwater flow, successfully predicted instability in steep areas of permeable outwash sand and topographic reentrants. These locations are consistent with locations of large, deep, historically active landslides. For an area in Seattle, a composite of the three maps illustrates how maps produced by different approaches might be combined to assess overall landslide potential. Examples from Oregon, USA, illustrate how landform mapping and deterministic analysis for shallow landslide potential have been adapted into standardized methods for efficiently producing detailed landslide inventory and shallow landslide susceptibility maps that have consistent content and format statewide.

Deciphering a removed text on a 16th c. centrepiece: The benefits of using AGLAEMap and AXSIA to process PIXE maps.

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

Lemasson, Quentin; Kotula, Paul; Pichon, Laurent

2015-09-01

In the field of archaeometry, it is not uncommon to be presented with art objects that contain inscriptions, signatures and other writings that are nearly impossible to read. Scanned microbeam PIXE offers an attractive approach to attack this problem, but even then the distribution of characteristic X-rays of the element(s) used in these writings can remain illegible. We show in this paper that two methods were used to reveal the inscription: first the use of a GUPIXWin, TRAUPIXE and AGLAEMap software suite enables to make quantitative analysis of each pixel, to visualize the results and to select X-ray peaks thatmore » could enable to distinguish letters. Then, the Automated eXpert Spectral Image Analysis (AXSIA) program developed at Sandia, which analyzes the x-ray intensity vs. Energy and (X, Y) position “datacubes”, was used to factor the datacube into 1) principle component spectral shapes and 2) the weighting images of these components. The specimen selected for this study was a silver plaque representing a scroll from the so-called “MerkelscheTafelaufsatz,” a centrepiece made by the Nuremberg goldsmith Wenzel Jamnitzer in 1549. X-ray radiography of the plaque shows lines of different silver thicknesses, meaning that a text has been removed. The PIXE analysis used a 3-MeV proton beam focused to 50μm and scanned across the sample on different areas of interest of several cm². This analysis showed major elements of Cu and Ag, and minor elements such as Pb, Au, Hg. X-ray intensity maps were then made by setting windows on the various x-ray peaks but the writing on the centrepiece was not revealed even if the map of Cu after data treatment at AGLAE enabled to distinguish some letters. The AXSIA program enabled to factor two main spectral shapes from the datacube that were quite similar and involved virtually all of the X-rays being generated. Nevertheless, small differences between these factors were observed for the Cu K X-rays, Pb, Bi and Au L X-rays. The plot of the factor with the highest Au signal gave also information on the shape of some letters. The comparison of the results obtained by the two methods shows that they both drastically improve the resolution and contrast of such writings and that each of the method can also bring different information on the composition and thus the techniques used for the writing.« less

When tractography meets tracer injections: a systematic study of trends and variation sources of diffusion-based connectivity.

PubMed

Aydogan, Dogu Baran; Jacobs, Russell; Dulawa, Stephanie; Thompson, Summer L; Francois, Maite Christi; Toga, Arthur W; Dong, Hongwei; Knowles, James A; Shi, Yonggang

2018-04-16

Tractography is a powerful technique capable of non-invasively reconstructing the structural connections in the brain using diffusion MRI images, but the validation of tractograms is challenging due to lack of ground truth. Owing to recent developments in mapping the mouse brain connectome, high-resolution tracer injection-based axonal projection maps have been created and quickly adopted for the validation of tractography. Previous studies using tracer injections mainly focused on investigating the match in projections and optimal tractography protocols. Being a complicated technique, however, tractography relies on multiple stages of operations and parameters. These factors introduce large variabilities in tractograms, hindering the optimization of protocols and making the interpretation of results difficult. Based on this observation, in contrast to previous studies, in this work we focused on quantifying and ranking the amount of performance variation introduced by these factors. For this purpose, we performed over a million tractography experiments and studied the variability across different subjects, injections, anatomical constraints and tractography parameters. By using N-way ANOVA analysis, we show that all tractography parameters are significant and importantly performance variations with respect to the differences in subjects are comparable to the variations due to tractography parameters, which strongly underlines the importance of fully documenting the tractography protocols in scientific experiments. We also quantitatively show that inclusion of anatomical constraints is the most significant factor for improving tractography performance. Although this critical factor helps reduce false positives, our analysis indicates that anatomy-informed tractography still fails to capture a large portion of axonal projections.

Mapping Change Management: A Co-citation Analysis

DTIC Science & Technology

2007-03-01

found that both had the recurring theme of corporate management and change; while factor four focused on investments, acquisitions and finances and...L. (2004). Corporate governance of Japanese banks. Journal of Corporate Finance , 10(3), 327-354. Angle, H. L., Manz, C. C., & Vandeven, A. H. (1985...Science Quarterly, Annual Review of Psychology, Industrial and Corporate Change, The Journal of Applied Behavioral Science, Journal of Applied Psychology

Calibration of HEC-Ras hydrodynamic model using gauged discharge data and flood inundation maps

NASA Astrophysics Data System (ADS)

Tong, Rui; Komma, Jürgen

2017-04-01

The estimation of flood is essential for disaster alleviation. Hydrodynamic models are implemented to predict the occurrence and variance of flood in different scales. In practice, the calibration of hydrodynamic models aims to search the best possible parameters for the representation the natural flow resistance. Recent years have seen the calibration of hydrodynamic models being more actual and faster following the advance of earth observation products and computer based optimization techniques. In this study, the Hydrologic Engineering River Analysis System (HEC-Ras) model was set up with high-resolution digital elevation model from Laser scanner for the river Inn in Tyrol, Austria. 10 largest flood events from 19 hourly discharge gauges and flood inundation maps were selected to calibrate the HEC-Ras model. Manning roughness values and lateral inflow factors as parameters were automatically optimized with the Shuffled complex with Principal component analysis (SP-UCI) algorithm developed from the Shuffled Complex Evolution (SCE-UA). Different objective functions (Nash-Sutcliffe model efficiency coefficient, the timing of peak, peak value and Root-mean-square deviation) were used in single or multiple way. It was found that the lateral inflow factor was the most sensitive parameter. SP-UCI algorithm could avoid the local optimal and achieve efficient and effective parameters in the calibration of HEC-Ras model using flood extension images. As results showed, calibration by means of gauged discharge data and flood inundation maps, together with objective function of Nash-Sutcliffe model efficiency coefficient, was very robust to obtain more reliable flood simulation, and also to catch up with the peak value and the timing of peak.

Identification and Molecular Characterization of MYB Transcription Factor Superfamily in C4 Model Plant Foxtail Millet (Setaria italica L.)

PubMed Central

Muthamilarasan, Mehanathan; Khandelwal, Rohit; Yadav, Chandra Bhan; Bonthala, Venkata Suresh; Khan, Yusuf; Prasad, Manoj

2014-01-01

MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I - X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli. PMID:25279462

"Land-Cover Conversion in Amazonia, The Role of ENV" Ironment and Substrate composition in Modifying SOI

NASA Technical Reports Server (NTRS)

Roberts, Dar A.; Chadwick, Oliver A.; Batista, Getulio T.

2003-01-01

LBA research from the first phase of LBA focused on three broad categories: 1) mapping land cover and quantifying rates of change, persistence of pasture, and area of recovering forest; 2) evaluating the role of environmental factors and land-use history on soil biogeochemistry; and 3) quantifying the natural and human controls on stream nutrient concentrations. The focus of the research was regional, concentrating primarily in the state of RondBnia, but also included land-cover mapping in the vicinity of Maraba, Para, and Manaus, Amazonas. Remote sensing analysis utilized Landsat Thematic Mapper (TM) and Multispectral Scanner (MS S) data to map historical patterns of land-cover change. Specific questions addressed by the remote sensing component of the research included: 1) what is the areal extent of dominant land-cover classes? 2) what are the rates of change of dominant land cover through processes of deforestation, disturbance and regeneration? and 3) what are the dynamic properties of each class that characterize temporal variability, duration, and frequency of repeat disturbance? Biogeochemical analysis focused on natural variability and impacts of land-use/land-cover changes on soil and stream biogeochemical properties at the regional scale. An emphasis was given to specific soil properties considered to be primary limiting factors regionally, including phosphorus, nitrogen, base cations and cation-exchange properties. Stream sampling emphasized the relative effects of the rates and timing of land-cover change on stream nutrients, demonstrating that vegetation conversion alone does not impact nutrients as much as subsequent land use and urbanization.

Peculiarities of changes in the soil cover of landscapes adjacent to a megalopolis

NASA Astrophysics Data System (ADS)

Lazareva, Margarita; Aparin, Boris; Sukhacheva, Elena

2017-04-01

The progressive growth of cities has a significant impact on the soil cover of territories adjacent to the same. Megalopolises are centers of anthropogenic impact on the soils. Generally, forms and intensity of the urban impact on the soil cover weaken with increasing distance from the city's boundaries. In this respect, ample opportunities for the analysis of urban impact on the adjacent territories are provided by the study of the soil cover in the Leningrad Region (the LR). Saint Petersburg is a major European megalopolis, which is the administrative center of the LR. The time period of Saint Petersburg's impact on the environment does not exceed 300 years, which allows us to identify very clearly the character and areas of its impact on the soil cover. Over the past decades, there have been significant changes in the soils and the soil cover of the LR. In a large territory, there appeared new anthropogenic soils and soil cover organization forms, having no natural analogues, with a dramatic increase in the surface area of degraded soils. To access the current state of soil cover, to identify the role of anthropogenic factors of changes in this state; to carry out land reclamation, remediation and rehabilitation measures; to perform land cadastral valuation etc., we need an information resource containing data on the current state of soils and soil cover in the LR, the key element of which should be a map. We carried out mapping and created a 1:200 000 digital soil map (DSM) for the LR's territories. Diagnostics of soil contours were performed using traditionally drawn-up (paper) maps of soils and soil-formation factors; satellite images (Google, Yandex); data of remote sensing (Spot 5, Landsat 7,8); digital maps of main soil-formation factors (topographical ones, etc.). The digital soil map of the LR has been created in the geographic information system - QGIS. The map clarifies the contours of natural soils and soil combinations, and shows, for the first time, the contours of: - non-soil formations; - soils of the initial soil formation; - soils of agricultural lands within their existing boundaries; - soils and soil combinations that are specific for human settlements and horticultural land plots; - fallow lands; - anthropogenically disturbed soils. During the analysis of the created digital medium-scale soil map, we identified some changes in the soil cover of the territories adjacent to Saint Petersburg. Virtually in all the landscapes, we found a large number of soil cover structures, the components of which, along with natural soils, are anthropogenically disturbed soils, anthropogenic soils and non-soil formations. We revealed that the human impact on the soil cover is manifested within the range that varies from insignificant changes in soil parameters to radical transformations of the soil profile, complete destruction of soil and "creation" of new soil forms and soil cover organization forms. We have developed a typology of anthropogenically changed and anthropogenically created soil cover structures, taking into consideration the types of the economic impact on and the quality of environmental functions performed by the soils.

[Analysis of the geographical distribution of cases of leprosy. Rio de Janeiro, 2001-2012].

PubMed

Gracie, Renata; Peixoto, Julia Novaes de Barros; Soares, Fabiane Bertoni Dos Reis; Hacker, Mariana de Andrea Vilas-Boas

2017-05-01

Studies have demonstrated that the geographical distribution of leprosy is related to different socioeconomic factors. This article aims to study the geographical distribution of leprosy in the state of Rio de Janeiro. The cases of leprosy reported in the 2001-2012 period were mapped according to municipality. Epidemiological and socioeconomic indicators were calculated. The ArcMap program was used for the construction of maps and Earth View to calculate the Bayesian rate. It was observed that leprosy is presented in hyper-endemic levels especially in the metropolitan area. However, there is also a reduction of the detection rate in the most recent study period. In municipalities in the metropolitan region and the north western region detection in children under 15 is high, indicating an active transmission situation. In municipalities in the south-central region and especially in the coastal region, there was a high proportion of cases diagnosed with level II disability, reflecting late diagnosis. There was no linear correlation between socioeconomic indicators and leprosy rate. These results contribute to the analysis of the geographical distribution of leprosy, important for the identification of areas for resource allocation, aiming to control and eliminate the disease.

The Challenge of Human Spermatozoa Proteome: A Systematic Review.

PubMed

Gilany, Kambiz; Minai-Tehrani, Arash; Amini, Mehdi; Agharezaee, Niloofar; Arjmand, Babak

2017-01-01

Currently, there are 20,197 human protein-coding genes in the most expertly curated database (UniProtKB/Swiss-Pro). Big efforts have been made by the international consortium, the Chromosome-Centric Human Proteome Project (C-HPP) and independent researchers, to map human proteome. In brief, anno 2017 the human proteome was outlined. The male factor contributes to 50% of infertility in couples. However, there are limited human spermatozoa proteomic studies. Firstly, the development of the mapping of the human spermatozoa was analyzed. The human spermatozoa have been used as a model for missing proteins. It has been shown that human spermatozoa are excellent sources for finding missing proteins. Y chromosome proteome mapping is led by Iran. However, it seems that it is extremely challenging to map the human spermatozoa Y chromosome proteins based on current mass spectrometry-based proteomics technology. Post-translation modifications (PTMs) of human spermatozoa proteome are the most unexplored area and currently the exact role of PTMs in male infertility is unknown. Additionally, the clinical human spermatozoa proteomic analysis, anno 2017 was done in this study.

The intellectual core of enterprise information systems: a co-citation analysis

NASA Astrophysics Data System (ADS)

Shiau, Wen-Lung

2016-10-01

Enterprise information systems (EISs) have evolved in the past 20 years, attracting the attention of international practitioners and scholars. Although literature reviews and analyses have been conducted to examine the multiple dimensions of EISs, no co-citation analysis has been conducted to examine the knowledge structures involved in EIS studies; thus, the current study fills this research gap. This study investigated the intellectual structures of EISs. All data source documents (1083 articles and 24,090 citations) were obtained from the Institute for Scientific Information Web of Knowledge database. A co-citation analysis was used to analyse EIS data. By using factor analysis, we identified eight critical factors: (a) factors affecting the implementation and success of information systems (ISs); (b) the successful implementation of enterprise resource planning (ERP); (c) IS evaluation and success, (d) system science studies; (e) factors influencing ERP success; (f) case research and theoretical models; (g) user acceptance of information technology; and (h) IS frameworks. Multidimensional scaling and cluster analysis were used to visually map the resultant EIS knowledge. It is difficult to implement an EIS in an enterprise and each organisation exhibits specific considerations. The current findings indicate that managers must focus on ameliorating inferior project performance levels, enabling a transition from 'vicious' to 'virtuous' projects. Successful EIS implementation yields substantial organisational advantages.

Molecular mapping and genomics of soybean seed protein: a review and perspective for the future.

PubMed

Patil, Gunvant; Mian, Rouf; Vuong, Tri; Pantalone, Vince; Song, Qijian; Chen, Pengyin; Shannon, Grover J; Carter, Tommy C; Nguyen, Henry T

2017-10-01

Genetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches. Meal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr.) 20 (LG-I), and 15 (LG-E). However, practical breeding progress is challenging because of seed protein content's negative genetic correlation with seed yield, other seed components such as oil and sucrose, and interaction with environmental effects such as temperature during seed development. In this review, we discuss rate-limiting factors related to soybean protein content and nutritional quality, and potential control factors regulating seed storage protein. In addition, we describe advances in next-generation sequencing technologies for precise detection of natural variants and their integration with conventional and high-throughput genotyping technologies. A syntenic analysis of QTL on Chr. 15 and 20 was performed. Finally, we discuss comprehensive approaches for integrating protein and amino acid QTL, genome-wide association studies, whole-genome resequencing, and transcriptome data to accelerate identification of genomic hot spots for allele introgression and soybean meal protein improvement.

The Rock Engineering System (RES) applied to landslide susceptibility zonation of the northeastern flank of Etna: methodological approach and results

NASA Astrophysics Data System (ADS)

Apuani, Tiziana; Corazzato, Claudia

2015-04-01

Ground deformations in the northeastern flank of Etna are well known. Despite only a few landslide events have been documented, these have significantly involved and damaged lifelines and buildings. These events are mainly related to the activity of the volcano-tectonic structures and associated seismicity, as in the case of the 2002 reactivation of the Presa landslide during an increased activity of the Pernicana fault system. In order to highlight the areal distribution of potentially unstable slopes based on a detailed, site-specific study of the factors responsible for landslide, and to ultimately contribute to risk management, a landslide susceptibility analysis of the northeastern flank of Etna in the Pernicana area was carried out, and a susceptibility map at 1:10.000 scale was produced, extending over an area of 168 km2. Different methods are proposed in the literature to obtain the regional distribution of potentially unstable slopes, depending on the problem scale, the slope dynamic evolution in the geological context, and the availability of data. Among semi-quantitative approaches, the present research combines the Rock Engineering System (RES) methodology with parameter zonation mapping in a GIS environment. The RES method represents a structured approach to manage a high number of interacting factors involved in the instability problem. A numerically coded, site-specific interaction matrix (IM) analyzes the cause-effect relationship in these factors, and calculates the degree of interactivity of each parameter, normalized by the overall interactivity of the system (weight factor). In the specific Etna case, the considered parameters are: slope attitude, lithotechnical properties (lithology, structural complexity, soil and rock mass quality), land use, tectonic structures, seismic activity (horizontal acceleration) and hydrogeological conditions (groundwater and drainage). Thematic maps are prepared at 1:10.000 scale for each of these parameters, and instability-related numerical ratings are assigned to classes. An instability index map is then produced by assigning, to each areal elementary cell (in our case a 10 m pixel), the sum of the products of each weight factor to the normalized parameter rating coming from each input zonation map. This map is then opportunely classified in landslide susceptibility classes (expressed as a percentage), enabling to discriminate areas prone to instability. Overall, the study area is characterized by a low propensity to slope instability. Few areas have an instability index of more than 45% of the theoretical maximum imposed by the matrix. These are located in the few steep slopes associated with active faults, and strongly depending on the seismic activity. Some other areas correspond to limited outcrops characterized by significantly reduced lithotechnical properties (low shear strength). The produced susceptibility map combines the application of the RES with the parameter zonation, following methodology which had never been applied up to now in in active volcanic environments. The comparison of the results with the ground deformation evidence coming from monitoring networks suggests the validity of the approach.

Analyzing the Scientific Evolution of Social Work Using Science Mapping

ERIC Educational Resources Information Center

Martínez, Ma Angeles; Cobo, Manuel Jesús; Herrera, Manuel; Herrera-Viedma, Enrique

2015-01-01

Objectives: This article reports the first science mapping analysis of the social work field, which shows its conceptual structure and scientific evolution. Methods: Science Mapping Analysis Software Tool, a bibliometric science mapping tool based on co-word analysis and h-index, is applied using a sample of 18,794 research articles published from…

High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus.

PubMed

Chapman, Natalie H; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G; Poole, Mervin; Causse, Mathilde; King, Graham J; Baxter, Charles; Seymour, Graham B

2012-08-01

Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.

New Colors for Histology: Optimized Bivariate Color Maps Increase Perceptual Contrast in Histological Images

PubMed Central

Kather, Jakob Nikolas; Weis, Cleo-Aron; Marx, Alexander; Schuster, Alexander K.; Schad, Lothar R.; Zöllner, Frank Gerrit

2015-01-01

Background Accurate evaluation of immunostained histological images is required for reproducible research in many different areas and forms the basis of many clinical decisions. The quality and efficiency of histopathological evaluation is limited by the information content of a histological image, which is primarily encoded as perceivable contrast differences between objects in the image. However, the colors of chromogen and counterstain used for histological samples are not always optimally distinguishable, even under optimal conditions. Methods and Results In this study, we present a method to extract the bivariate color map inherent in a given histological image and to retrospectively optimize this color map. We use a novel, unsupervised approach based on color deconvolution and principal component analysis to show that the commonly used blue and brown color hues in Hematoxylin—3,3’-Diaminobenzidine (DAB) images are poorly suited for human observers. We then demonstrate that it is possible to construct improved color maps according to objective criteria and that these color maps can be used to digitally re-stain histological images. Validation To validate whether this procedure improves distinguishability of objects and background in histological images, we re-stain phantom images and N = 596 large histological images of immunostained samples of human solid tumors. We show that perceptual contrast is improved by a factor of 2.56 in phantom images and up to a factor of 2.17 in sets of histological tumor images. Context Thus, we provide an objective and reliable approach to measure object distinguishability in a given histological image and to maximize visual information available to a human observer. This method could easily be incorporated in digital pathology image viewing systems to improve accuracy and efficiency in research and diagnostics. PMID:26717571

New Colors for Histology: Optimized Bivariate Color Maps Increase Perceptual Contrast in Histological Images.

PubMed

Kather, Jakob Nikolas; Weis, Cleo-Aron; Marx, Alexander; Schuster, Alexander K; Schad, Lothar R; Zöllner, Frank Gerrit

2015-01-01

Accurate evaluation of immunostained histological images is required for reproducible research in many different areas and forms the basis of many clinical decisions. The quality and efficiency of histopathological evaluation is limited by the information content of a histological image, which is primarily encoded as perceivable contrast differences between objects in the image. However, the colors of chromogen and counterstain used for histological samples are not always optimally distinguishable, even under optimal conditions. In this study, we present a method to extract the bivariate color map inherent in a given histological image and to retrospectively optimize this color map. We use a novel, unsupervised approach based on color deconvolution and principal component analysis to show that the commonly used blue and brown color hues in Hematoxylin-3,3'-Diaminobenzidine (DAB) images are poorly suited for human observers. We then demonstrate that it is possible to construct improved color maps according to objective criteria and that these color maps can be used to digitally re-stain histological images. To validate whether this procedure improves distinguishability of objects and background in histological images, we re-stain phantom images and N = 596 large histological images of immunostained samples of human solid tumors. We show that perceptual contrast is improved by a factor of 2.56 in phantom images and up to a factor of 2.17 in sets of histological tumor images. Thus, we provide an objective and reliable approach to measure object distinguishability in a given histological image and to maximize visual information available to a human observer. This method could easily be incorporated in digital pathology image viewing systems to improve accuracy and efficiency in research and diagnostics.

Pathway-based factor analysis of gene expression data produces highly heritable phenotypes that associate with age.

PubMed

Anand Brown, Andrew; Ding, Zhihao; Viñuela, Ana; Glass, Dan; Parts, Leopold; Spector, Tim; Winn, John; Durbin, Richard

2015-03-09

Statistical factor analysis methods have previously been used to remove noise components from high-dimensional data prior to genetic association mapping and, in a guided fashion, to summarize biologically relevant sources of variation. Here, we show how the derived factors summarizing pathway expression can be used to analyze the relationships between expression, heritability, and aging. We used skin gene expression data from 647 twins from the MuTHER Consortium and applied factor analysis to concisely summarize patterns of gene expression to remove broad confounding influences and to produce concise pathway-level phenotypes. We derived 930 "pathway phenotypes" that summarized patterns of variation across 186 KEGG pathways (five phenotypes per pathway). We identified 69 significant associations of age with phenotype from 57 distinct KEGG pathways at a stringent Bonferroni threshold ([Formula: see text]). These phenotypes are more heritable ([Formula: see text]) than gene expression levels. On average, expression levels of 16% of genes within these pathways are associated with age. Several significant pathways relate to metabolizing sugars and fatty acids; others relate to insulin signaling. We have demonstrated that factor analysis methods combined with biological knowledge can produce more reliable phenotypes with less stochastic noise than the individual gene expression levels, which increases our power to discover biologically relevant associations. These phenotypes could also be applied to discover associations with other environmental factors. Copyright © 2015 Brown et al.

Pathway-Based Factor Analysis of Gene Expression Data Produces Highly Heritable Phenotypes That Associate with Age

PubMed Central

Anand Brown, Andrew; Ding, Zhihao; Viñuela, Ana; Glass, Dan; Parts, Leopold; Spector, Tim; Winn, John; Durbin, Richard

2015-01-01

Statistical factor analysis methods have previously been used to remove noise components from high-dimensional data prior to genetic association mapping and, in a guided fashion, to summarize biologically relevant sources of variation. Here, we show how the derived factors summarizing pathway expression can be used to analyze the relationships between expression, heritability, and aging. We used skin gene expression data from 647 twins from the MuTHER Consortium and applied factor analysis to concisely summarize patterns of gene expression to remove broad confounding influences and to produce concise pathway-level phenotypes. We derived 930 “pathway phenotypes” that summarized patterns of variation across 186 KEGG pathways (five phenotypes per pathway). We identified 69 significant associations of age with phenotype from 57 distinct KEGG pathways at a stringent Bonferroni threshold (P<5.38×10−5). These phenotypes are more heritable (h2=0.32) than gene expression levels. On average, expression levels of 16% of genes within these pathways are associated with age. Several significant pathways relate to metabolizing sugars and fatty acids; others relate to insulin signaling. We have demonstrated that factor analysis methods combined with biological knowledge can produce more reliable phenotypes with less stochastic noise than the individual gene expression levels, which increases our power to discover biologically relevant associations. These phenotypes could also be applied to discover associations with other environmental factors. PMID:25758824

Quantitative water content mapping at clinically relevant field strengths: a comparative study at 1.5 T and 3 T.

PubMed

Abbas, Zaheer; Gras, Vincent; Möllenhoff, Klaus; Oros-Peusquens, Ana-Maria; Shah, Nadim Joni

2015-02-01

Quantitative water content mapping in vivo using MRI is a very valuable technique to detect, monitor and understand diseases of the brain. At 1.5 T, this technology has already been successfully used, but it has only recently been applied at 3T because of significantly increased RF field inhomogeneity at the higher field strength. To validate the technology at 3T, we estimate and compare in vivo quantitative water content maps at 1.5 T and 3T obtained with a protocol proposed recently for 3T MRI. The proposed MRI protocol was applied on twenty healthy subjects at 1.5 T and 3T; the same post-processing algorithms were used to estimate the water content maps. The 1.5 T and 3T maps were subsequently aligned and compared on a voxel-by-voxel basis. Statistical analysis was performed to detect possible differences between the estimated 1.5 T and 3T water maps. Our analysis indicates that the water content values obtained at 1.5 T and 3T did not show significant systematic differences. On average the difference did not exceed the standard deviation of the water content at 1.5 T. Furthermore, the contrast-to-noise ratio (CNR) of the estimated water content map was increased at 3T by a factor of at least 1.5. Vulnerability to RF inhomogeneity increases dramatically with the increasing static magnetic field strength. However, using advanced corrections for the sensitivity profile of the MR coils, it is possible to preserve quantitative accuracy while benefiting from the increased CNR at the higher field strength. Indeed, there was no significant difference in the water content values obtained in the brain at 1.5 T and 3T. Copyright © 2014 Elsevier Inc. All rights reserved.

Remote sensing and GIS-based landslide hazard analysis and cross-validation using multivariate logistic regression model on three test areas in Malaysia

NASA Astrophysics Data System (ADS)

Pradhan, Biswajeet

2010-05-01

This paper presents the results of the cross-validation of a multivariate logistic regression model using remote sensing data and GIS for landslide hazard analysis on the Penang, Cameron, and Selangor areas in Malaysia. Landslide locations in the study areas were identified by interpreting aerial photographs and satellite images, supported by field surveys. SPOT 5 and Landsat TM satellite imagery were used to map landcover and vegetation index, respectively. Maps of topography, soil type, lineaments and land cover were constructed from the spatial datasets. Ten factors which influence landslide occurrence, i.e., slope, aspect, curvature, distance from drainage, lithology, distance from lineaments, soil type, landcover, rainfall precipitation, and normalized difference vegetation index (ndvi), were extracted from the spatial database and the logistic regression coefficient of each factor was computed. Then the landslide hazard was analysed using the multivariate logistic regression coefficients derived not only from the data for the respective area but also using the logistic regression coefficients calculated from each of the other two areas (nine hazard maps in all) as a cross-validation of the model. For verification of the model, the results of the analyses were then compared with the field-verified landslide locations. Among the three cases of the application of logistic regression coefficient in the same study area, the case of Selangor based on the Selangor logistic regression coefficients showed the highest accuracy (94%), where as Penang based on the Penang coefficients showed the lowest accuracy (86%). Similarly, among the six cases from the cross application of logistic regression coefficient in other two areas, the case of Selangor based on logistic coefficient of Cameron showed highest (90%) prediction accuracy where as the case of Penang based on the Selangor logistic regression coefficients showed the lowest accuracy (79%). Qualitatively, the cross application model yields reasonable results which can be used for preliminary landslide hazard mapping.

Contribution of physical modelling to climate-driven landslide hazard mapping: an alpine test site

NASA Astrophysics Data System (ADS)

Vandromme, R.; Desramaut, N.; Baills, A.; Hohmann, A.; Grandjean, G.; Sedan, O.; Mallet, J. P.

2012-04-01

The aim of this work is to develop a methodology for integrating climate change scenarios into quantitative hazard assessment and especially their precipitation component. The effects of climate change will be different depending on both the location of the site and the type of landslide considered. Indeed, mass movements can be triggered by different factors. This paper describes a methodology to address this issue and shows an application on an alpine test site. Mechanical approaches represent a solution for quantitative landslide susceptibility and hazard modeling. However, as the quantity and the quality of data are generally very heterogeneous at a regional scale, it is necessary to take into account the uncertainty in the analysis. In this perspective, a new hazard modeling method is developed and integrated in a program named ALICE. This program integrates mechanical stability analysis through a GIS software taking into account data uncertainty. This method proposes a quantitative classification of landslide hazard and offers a useful tool to gain time and efficiency in hazard mapping. However, an expertise approach is still necessary to finalize the maps. Indeed it is the only way to take into account some influent factors in slope stability such as heterogeneity of the geological formations or effects of anthropic interventions. To go further, the alpine test site (Barcelonnette area, France) is being used to integrate climate change scenarios into ALICE program, and especially their precipitation component with the help of a hydrological model (GARDENIA) and the regional climate model REMO (Jacob, 2001). From a DEM, land-cover map, geology, geotechnical data and so forth the program classifies hazard zones depending on geotechnics and different hydrological contexts varying in time. This communication, realized within the framework of Safeland project, is supported by the European Commission under the 7th Framework Programme for Research and Technological Development, Area "Environment", Activity 1.3.3.1 "Prediction of triggering and risk assessment for landslides".

Analysis of Geothermal Pathway in the Metamorphic Area, Northeastern Taiwan

NASA Astrophysics Data System (ADS)

Wang, C.; Wu, M. Y.; Song, S. R.; Lo, W.

2016-12-01

A quantitative measure by play fairway analysis in geothermal energy development is an important tool that can present the probability map of potential resources through the uncertainty studies in geology for early phase decision making purpose in the related industries. While source, pathway, and fluid are the three main geologic factors in traditional geothermal systems, identifying the heat paths is critical to reduce drilling cost. Taiwan is in East Asia and the western edge of Pacific Ocean, locating on the convergent boundary of Eurasian Plate and Philippine Sea Plate with many earthquake activities. This study chooses a metamorphic area in the western corner of Yi-Lan plain in northeastern Taiwan with high geothermal potential and several existing exploration sites. Having high subsurface temperature gradient from the mountain belts, and plenty hydrologic systems through thousands of millimeters annual precipitation that would bring up heats closer to the surface, current geothermal conceptual model indicates the importance of pathway distribution which affects the possible concentration of extractable heat location. The study conducts surface lineation analysis using analytic hierarchy process to determine weights among various fracture types for their roles in geothermal pathways, based on the information of remote sensing data, published geologic maps and field work measurements, to produce regional fracture distribution probability map. The results display how the spatial distribution of pathways through various fractures could affect geothermal systems, identify the geothermal plays using statistical data analysis, and compare against the existing drilling data.

Perpetual factors involved in performance of air traffic controllers using a microwave landing system

NASA Technical Reports Server (NTRS)

Gershzohn, G.

1978-01-01

The task involved the control of two simulated aircraft targets per trial, in a 37.0 -km radius terminal area, by means of conventional radar vectoring and/or speed control. The goal was to insure that the two targets crossed the Missed Approach Point (MAP) at the runway threshold exactly 60 sec apart. The effects on controller performance of the MLS configuration under wind and no-wind conditions were examined. The data for mean separation time between targets at the MAP and the range about that mean were analyzed by appropriate analyses of variance. Significant effects were found for mean separation times as a result of the configuration of the MLS and for interaction between the configuration and wind conditions. The analysis of variance for range indicated significantly poorer performance under the wind condition. These findings are believed to be a result of certain perceptual factors involved in radar air traffic control (ATC) using the MLS with separation of targets in time.

Identifying transcription factor functions and targets by phenotypic activation

PubMed Central

Chua, Gordon; Morris, Quaid D.; Sopko, Richelle; Robinson, Mark D.; Ryan, Owen; Chan, Esther T.; Frey, Brendan J.; Andrews, Brenda J.; Boone, Charles; Hughes, Timothy R.

2006-01-01

Mapping transcriptional regulatory networks is difficult because many transcription factors (TFs) are activated only under specific conditions. We describe a generic strategy for identifying genes and pathways induced by individual TFs that does not require knowledge of their normal activation cues. Microarray analysis of 55 yeast TFs that caused a growth phenotype when overexpressed showed that the majority caused increased transcript levels of genes in specific physiological categories, suggesting a mechanism for growth inhibition. Induced genes typically included established targets and genes with consensus promoter motifs, if known, indicating that these data are useful for identifying potential new target genes and binding sites. We identified the sequence 5′-TCACGCAA as a binding sequence for Hms1p, a TF that positively regulates pseudohyphal growth and previously had no known motif. The general strategy outlined here presents a straightforward approach to discovery of TF activities and mapping targets that could be adapted to any organism with transgenic technology. PMID:16880382

Satellite imaging coral reef resilience at regional scale. A case-study from Saudi Arabia.

PubMed

Rowlands, Gwilym; Purkis, Sam; Riegl, Bernhard; Metsamaa, Liisa; Bruckner, Andrew; Renaud, Philip

2012-06-01

We propose a framework for spatially estimating a proxy for coral reef resilience using remote sensing. Data spanning large areas of coral reef habitat were obtained using the commercial QuickBird satellite, and freely available imagery (NASA, Google Earth). Principles of coral reef ecology, field observation, and remote observations, were combined to devise mapped indices. These capture important and accessible components of coral reef resilience. Indices are divided between factors known to stress corals, and factors incorporating properties of the reef landscape that resist stress or promote coral growth. The first-basis for a remote sensed resilience index (RSRI), an estimate of expected reef resilience, is proposed. Developed for the Red Sea, the framework of our analysis is flexible and with minimal adaptation, could be extended to other reef regions. We aim to stimulate discussion as to use of remote sensing to do more than simply deliver habitat maps of coral reefs. Copyright © 2012 Elsevier Ltd. All rights reserved.

Design of an image encryption scheme based on a multiple chaotic map

NASA Astrophysics Data System (ADS)

Tong, Xiao-Jun

2013-07-01

In order to solve the problem that chaos is degenerated in limited computer precision and Cat map is the small key space, this paper presents a chaotic map based on topological conjugacy and the chaotic characteristics are proved by Devaney definition. In order to produce a large key space, a Cat map named block Cat map is also designed for permutation process based on multiple-dimensional chaotic maps. The image encryption algorithm is based on permutation-substitution, and each key is controlled by different chaotic maps. The entropy analysis, differential analysis, weak-keys analysis, statistical analysis, cipher random analysis, and cipher sensibility analysis depending on key and plaintext are introduced to test the security of the new image encryption scheme. Through the comparison to the proposed scheme with AES, DES and Logistic encryption methods, we come to the conclusion that the image encryption method solves the problem of low precision of one dimensional chaotic function and has higher speed and higher security.

Identifying environmental features for land management decisions

NASA Technical Reports Server (NTRS)

1981-01-01

The benefits of changes in management organization and facilities for the Center for Remote Sensing and Cartography in Utah are reported as well as interactions with and outreach to state and local agencies. Completed projects are described which studied (1) Unita Basin wetland/land use; (2) Davis County foothill development; (3) Farmington Bay shoreline fluctuation; (4) irrigation detection; and (5) satellite investigation of snow cover/mule deer relationships. Techniques developed for composite computer mapping, contrast enhancement, U-2 CIR/LANDSAT digital interface; factor analysis, and multivariate statistical analysis are described.

Pharmaceutical strategic purchasing requirements in Iran: Price interventions and the related effective factors

PubMed Central

Bastani, Peivand; Dinarvand, Rasoul; SamadBeik, Mahnaz; Pourmohammadi, Kimia

2016-01-01

Objective: Pharmaceutical access for the poor is an essential factor in developing countries that can be improved through strategic purchasing. This study was conducted to identify the elements affecting price in order to enable insurance organizations to put strategic purchasing into practice. Methods: This was a qualitative study conducted through content analysis with an inductive approach applying a five-stage framework analysis (familiarization, identifying a thematic framework, indexing, mapping, and interpretation). Data analysis was started right after transcribing each interview applying ATLAS.ti. Data were saturated after 32 semi-structured interviews by experts. These key informants were selected purposefully and through snowball sampling. Findings: Findings showed that there are four main themes as Pharmaceutical Strategic Purchasing Requirements in Iran as follows essential and structural factors, international factors, economical factors, and legal factors. Moreover, totally 14 related sub-themes were extracted in this area as the main effective variables. Conclusion: It seems that paying adequate attention to the four present themes and 14 sub-themes affecting price can enable health system policy-makers of developing countries like Iran to make the best decisions through strategic purchasing of drugs by the main insurers in order to improve access and health in the country. PMID:26985434

Children's perceptions of their home and neighborhood environments, and their association with objectively measured physical activity: a qualitative and quantitative study.

PubMed

Hume, C; Salmon, J; Ball, K

2005-02-01

Environmental factors may have an important influence on children's physical activity, yet children's perspectives of their home and neighborhood environments have not been widely assessed. The aim of this study was to investigate children's perceptions of their environments, and to examine associations between these perceptions and objectively measured physical activity. The sample consisted of 147, 10-year-old Australian children, who drew maps of their home and neighborhood environments. A subsample of children photographed places and things in these environments that were important to them. The maps were analyzed for themes, and for the frequency with which particular objects and locations appeared. Physical activity was objectively measured using accelerometers. Six themes emerged from the qualitative analysis of the maps and photographs: the family home; opportunities for physical activity and sedentary pursuits; food items and locations; green space and outside areas; the school and opportunities for social interaction. Of the 11 variables established from these themes, one home and two neighborhood factors were associated with children's physical activity. These findings contribute to a broader understanding of children's perceptions of their environment, and highlight the potential importance of the home and neighborhood environments for promoting physical activity behavior.

Urban and regional land use analysis: CARETS and Census Cities experiment package. [mapping land use climatology from MSS imagery

NASA Technical Reports Server (NTRS)

Alexander, R. H. (Principal Investigator)

1973-01-01

The author has identified the following significant results. The arrival of the so-called energy crisis makes the portion of this experiment dealing with land use climatology of more immediate significance than before, since in addition to helping to understand the processes of climatic change associated with urbanization, the knowledge obtained may be useful in assigning an energy balance impact factor to proposed changes in land use in and around cities. Thermal maps derived from S-192 data are to be used as a measure of the energy being radiated into space from the mosaic of different surfaces in and around the city. While presenting excellent spatial sampling potential for a metropolitan area tests site, the Skylab data permit a very poor temporal sampling opportunity, owing to the large number of factors beyond the investigator's control that determine when data will be taken over a given test site. The strategy is to augment the thermal maps derived from S-192 with a modeling technique which enables the simulation of a number of components of the surface energy balance, calculated at regular time intervals throughout the day or year. Preliminary tests on the performance of the model are still underway, using airborne MSS data from NASA aircraft flights. Results look extremely promising.

Human factors considerations for integrating traffic information on airport moving maps.

DOT National Transportation Integrated Search

2011-05-01

The purpose of this research effort was to identify human factors considerations in the integration of traffic information and surface indications and alerts for runway status on airport moving maps for flight deck displays. The information is primar...

Mapping Forest Fire Susceptibility in Temperate Mountain Areas with Expert Knowledge. A Case Study from Iezer Mountains, Romanian Carpathians

NASA Astrophysics Data System (ADS)

Mihai, Bogdan; Savulescu, Ionut

2014-05-01

Forest fires in Romanian Carpathians became a frequent phenomenon during the last decade, although local climate and other environmental features did not create typical conditions. From 2004, forest fires affect in Romania more than 100 hectares/year of different forest types (deciduous and coniferous). Their magnitude and frequency are not known, since a historical forest fire inventory does not exist (only press papers and local witness for some selected events). Forest fires features the summer dry periods but there are dry autumns and early winter periods with events of different magnitudes. The application we propose is based on an empirical modeling of forest fire susceptibility in a typical mountain area from the Southern Carpathians, the Iezer Mountains (2462 m). The study area features almost all the altitudinal vegetation zones of the European temperate mountains, from the beech zone, to the coniferous zone, the subalpine and the alpine zones (Mihai et al., 2007). The analysis combines GIS and remote sensing models (Chuvieco et al., 2012), starting from the ideas that forest fires are featured by the ignition zones and then by the fire propagation zones. The first data layer (ignition zones) is the result of the crossing between the ignition factors: lightning - points of multitemporal occurence and anthropogenic activities (grazing, tourism and traffic) and the ignition zones (forest fuel zonation - forest stands, soil cover and topoclimatic factor zonation). This data is modelled from different sources: the MODIS imagery fire product (Hantson et al., 2012), detailed topographic maps, multitemporal orthophotos at 0.5 m resolution, Landsat multispectral imagery, forestry cadastre maps, detailed soil maps, meteorological data (the WorldClim digital database) as well as the field survey (mapping using GPS and local observation). The second data layer (fire propagation zones) is the result of the crossing between the forest fuel zonation, obtained with the help of forestry data, the wind regime data and the topographic features of the mountain area (elevation, slope declivity, slope aspect). The analysis also consider the insolation degree of mountain slopes, that creates favourable conditions for fire propagation between different canopies. These data layers are integrated within a simple GIS analysis in order to intersect the ignition zones with the fire propagation zones in order to obtain the potential areas to be affected by fire. The digital map show three levels of forest fire susceptibility, differenced on the basis of expert knowledge. The map can be validated from the statistical point of view with the polygons of the forest fire affected areas mapped from Landsat TM, ETM+ and OLI satellite imagery. The mapping results could be integrated within the forest management strategies and especially within the forest cadastre and development maps (updated every ten years). The result can confirm that the data gap in terms of forest fire events can be filled with expert knowledge. References Chuvieco, E, Aguado, I., Jurdao, S., Pettinari, M., Yebra, M., Salas, J., Hantson, S., de la Riva, J., Ibarra, P., Rodrigues, M., Echeverria, M., Azqueta, D., Roman, M., Bastarrika, A., Martinez, S., Recondo, C., Zapico, E., Martinez-Vega F.J. (2012) Integrating geospatial information into fire risk assessment, International Journal of Wildland Fire, 2,2, 69-86. Hantson, S., Padilla, M., Corti., D, Chuvieco, E. (2013) Strenghts and weaknesses of MODIS hotspots to characterize Global fire occurence, Remote Sensing of Environment, 131, 1, 152-159. Mihai, B., Savulescu, I.,Sandric, I. (2007) Change detection analysis (1986/2002) for the alpine, subalpine and forest landscape in Iezer Mountains (Southern Carpathians, Romania), Mountain Research and Development, 27, 250-258.

Processing and analysis of cardiac optical mapping data obtained with potentiometric dyes

PubMed Central

Laughner, Jacob I.; Ng, Fu Siong; Sulkin, Matthew S.; Arthur, R. Martin

2012-01-01

Optical mapping has become an increasingly important tool to study cardiac electrophysiology in the past 20 years. Multiple methods are used to process and analyze cardiac optical mapping data, and no consensus currently exists regarding the optimum methods. The specific methods chosen to process optical mapping data are important because inappropriate data processing can affect the content of the data and thus alter the conclusions of the studies. Details of the different steps in processing optical imaging data, including image segmentation, spatial filtering, temporal filtering, and baseline drift removal, are provided in this review. We also provide descriptions of the common analyses performed on data obtained from cardiac optical imaging, including activation mapping, action potential duration mapping, repolarization mapping, conduction velocity measurements, and optical action potential upstroke analysis. Optical mapping is often used to study complex arrhythmias, and we also discuss dominant frequency analysis and phase mapping techniques used for the analysis of cardiac fibrillation. PMID:22821993

Hematopoietic transcriptional mechanisms: from locus-specific to genome-wide vantage points.

PubMed

DeVilbiss, Andrew W; Sanalkumar, Rajendran; Johnson, Kirby D; Keles, Sunduz; Bresnick, Emery H

2014-08-01

Hematopoiesis is an exquisitely regulated process in which stem cells in the developing embryo and the adult generate progenitor cells that give rise to all blood lineages. Master regulatory transcription factors control hematopoiesis by integrating signals from the microenvironment and dynamically establishing and maintaining genetic networks. One of the most rudimentary aspects of cell type-specific transcription factor function, how they occupy a highly restricted cohort of cis-elements in chromatin, remains poorly understood. Transformative technologic advances involving the coupling of next-generation DNA sequencing technology with the chromatin immunoprecipitation assay (ChIP-seq) have enabled genome-wide mapping of factor occupancy patterns. However, formidable problems remain; notably, ChIP-seq analysis yields hundreds to thousands of chromatin sites occupied by a given transcription factor, and only a fraction of the sites appear to be endowed with critical, non-redundant function. It has become en vogue to map transcription factor occupancy patterns genome-wide, while using powerful statistical tools to establish correlations to inform biology and mechanisms. With the advent of revolutionary genome editing technologies, one can now reach beyond correlations to conduct definitive hypothesis testing. This review focuses on key discoveries that have emerged during the path from single loci to genome-wide analyses, specifically in the context of hematopoietic transcriptional mechanisms. Copyright © 2014 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.

Spatial analysis of land use and shallow groundwater vulnerability in the watershed adjacent to Assateague Island National Seashore, Maryland and Virginia, USA

USGS Publications Warehouse

LaMotte, A.E.; Greene, E.A.

2007-01-01

Spatial relations between land use and groundwater quality in the watershed adjacent to Assateague Island National Seashore, Maryland and Virginia, USA were analyzed by the use of two spatial models. One model used a logit analysis and the other was based on geostatistics. The models were developed and compared on the basis of existing concentrations of nitrate as nitrogen in samples from 529 domestic wells. The models were applied to produce spatial probability maps that show areas in the watershed where concentrations of nitrate in groundwater are likely to exceed a predetermined management threshold value. Maps of the watershed generated by logistic regression and probability kriging analysis showing where the probability of nitrate concentrations would exceed 3 mg/L (>0.50) compared favorably. Logistic regression was less dependent on the spatial distribution of sampled wells, and identified an additional high probability area within the watershed that was missed by probability kriging. The spatial probability maps could be used to determine the natural or anthropogenic factors that best explain the occurrence and distribution of elevated concentrations of nitrate (or other constituents) in shallow groundwater. This information can be used by local land-use planners, ecologists, and managers to protect water supplies and identify land-use planning solutions and monitoring programs in vulnerable areas. ?? 2006 Springer-Verlag.

A map of terminal regulators of neuronal identity in Caenorhabditis elegans

PubMed Central

2016-01-01

Our present day understanding of nervous system development is an amalgam of insights gained from studying different aspects and stages of nervous system development in a variety of invertebrate and vertebrate model systems, with each model system making its own distinctive set of contributions. One aspect of nervous system development that has been among the most extensively studied in the nematode Caenorhabditis elegans is the nature of the gene regulatory programs that specify hardwired, terminal cellular identities. I first summarize a number of maps (anatomical, functional, and molecular) that describe the terminal identity of individual neurons in the C. elegans nervous system. I then provide a comprehensive summary of regulatory factors that specify terminal identities in the nervous system, synthesizing these past studies into a regulatory map of cellular identities in the C. elegans nervous system. This map shows that for three quarters of all neurons in the C. elegans nervous system, regulatory factors that control terminal identity features are known. In‐depth studies of specific neuron types have revealed that regulatory factors rarely act alone, but rather act cooperatively in neuron‐type specific combinations. In most cases examined so far, distinct, biochemically unlinked terminal identity features are coregulated via cooperatively acting transcription factors, termed terminal selectors, but there are also cases in which distinct identity features are controlled in a piecemeal fashion by independent regulatory inputs. The regulatory map also illustrates that identity‐defining transcription factors are reemployed in distinct combinations in different neuron types. However, the same transcription factor can drive terminal differentiation in neurons that are unrelated by lineage, unrelated by function, connectivity and neurotransmitter deployment. Lastly, the regulatory map illustrates the preponderance of homeodomain transcription factors in the control of terminal identities, suggesting that these factors have ancient, phylogenetically conserved roles in controlling terminal neuronal differentiation in the nervous system. WIREs Dev Biol 2016, 5:474–498. doi: 10.1002/wdev.233 For further resources related to this article, please visit the WIREs website. PMID:27136279

Constructing a strategy map for banking institutions with key performance indicators of the balanced scorecard.

PubMed

Wu, Hung-Yi

2012-08-01

This study presents a structural evaluation methodology to link key performance indicators (KPIs) into a strategy map of the balanced scorecard (BSC) for banking institutions. Corresponding with the four BSC perspectives (finance, customer, internal business process, and learning and growth), the most important evaluation indicators of banking performance are synthesized from the relevant literature and screened by a committee of experts. The Decision Making Trial and Evaluation Laboratory (DEMATEL) method, a multiple criteria analysis tool, is then employed to determine the causal relationships between the KPIs, to identify the critical central and influential factors, and to establish a visualized strategy map with logical links to improve banking performance. An empirical application is provided as an example. According to the expert evaluations, the three most essential KPIs for banking performance are customer satisfaction, sales performance, and customer retention rate. The DEMATEL results demonstrate a clear road map to assist management in prioritizing the performance indicators and in focusing attention on the strategy-related activities of the crucial indicators. According to the constructed strategy map, management could better invest limited resources in the areas that need improvement most. Although these strategy maps of the BSC are not universal, the research results show that the presented approach is an objective and feasible way to construct strategy maps more justifiably. The proposed framework can be applicable to institutions in other industries as well. Copyright © 2011 Elsevier Ltd. All rights reserved.

QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis.

PubMed

Appelt, J-U; Giordano, F A; Ecker, M; Roeder, I; Grund, N; Hotz-Wagenblatt, A; Opelz, G; Zeller, W J; Allgayer, H; Fruehauf, S; Laufs, S

2009-07-01

Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set'). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with 'safe' insertion profiles.

Visualizing disease associations: graphic analysis of frequency distributions as a function of age using moving average plots (MAP) with application to Alzheimer's and Parkinson's disease.

PubMed

Payami, Haydeh; Kay, Denise M; Zabetian, Cyrus P; Schellenberg, Gerard D; Factor, Stewart A; McCulloch, Colin C

2010-01-01

Age-related variation in marker frequency can be a confounder in association studies, leading to both false-positive and false-negative findings and subsequently to inconsistent reproducibility. We have developed a simple method, based on a novel extension of moving average plots (MAP), which allows investigators to inspect the frequency data for hidden age-related variations. MAP uses the standard case-control association data and generates a birds-eye view of the frequency distributions across the age spectrum; a picture in which one can see if, how, and when the marker frequencies in cases differ from that in controls. The marker can be specified as an allele, genotype, haplotype, or environmental factor; and age can be age-at-onset, age when subject was last known to be unaffected, or duration of exposure. Signature patterns that emerge can help distinguish true disease associations from spurious associations due to age effects, age-varying associations from associations that are uniform across all ages, and associations with risk from associations with age-at-onset. Utility of MAP is illustrated by application to genetic and epidemiological association data for Alzheimer's and Parkinson's disease. MAP is intended as a descriptive method, to complement standard statistical techniques. Although originally developed for age patterns, MAP is equally useful for visualizing any quantitative trait.

Stability-driven nonnegative matrix factorization to interpret spatial gene expression and build local gene networks.

PubMed

Wu, Siqi; Joseph, Antony; Hammonds, Ann S; Celniker, Susan E; Yu, Bin; Frise, Erwin

2016-04-19

Spatial gene expression patterns enable the detection of local covariability and are extremely useful for identifying local gene interactions during normal development. The abundance of spatial expression data in recent years has led to the modeling and analysis of regulatory networks. The inherent complexity of such data makes it a challenge to extract biological information. We developed staNMF, a method that combines a scalable implementation of nonnegative matrix factorization (NMF) with a new stability-driven model selection criterion. When applied to a set ofDrosophilaearly embryonic spatial gene expression images, one of the largest datasets of its kind, staNMF identified 21 principal patterns (PP). Providing a compact yet biologically interpretable representation ofDrosophilaexpression patterns, PP are comparable to a fate map generated experimentally by laser ablation and show exceptional promise as a data-driven alternative to manual annotations. Our analysis mapped genes to cell-fate programs and assigned putative biological roles to uncharacterized genes. Finally, we used the PP to generate local transcription factor regulatory networks. Spatially local correlation networks were constructed for six PP that span along the embryonic anterior-posterior axis. Using a two-tail 5% cutoff on correlation, we reproduced 10 of the 11 links in the well-studied gap gene network. The performance of PP with theDrosophiladata suggests that staNMF provides informative decompositions and constitutes a useful computational lens through which to extract biological insight from complex and often noisy gene expression data.

Capstone 3 electronic flight bag (EFB) - airport moving map operational evaluation : human factors report

DOT National Transportation Integrated Search

2013-05-30

This report documents the human factors activities conducted as part of the Capstone 3 Electronic Flight Bag (EFB) Airport Moving Map operational evaluation. The purpose of that operational evaluation was to understand the safety implications of ...

Geomorphometry-based method of landform assessment for geodiversity

NASA Astrophysics Data System (ADS)

Najwer, Alicja; Zwoliński, Zbigniew

2015-04-01

Climate variability primarily induces the variations in the intensity and frequency of surface processes and consequently, principal changes in the landscape. As a result, abiotic heterogeneity may be threatened and the key elements of the natural diversity even decay. The concept of geodiversity was created recently and has rapidly gained the approval of scientists around the world. However, the problem recognition is still at an early stage. Moreover, little progress has been made concerning its assessment and geovisualisation. Geographical Information System (GIS) tools currently provide wide possibilities for the Earth's surface studies. Very often, the main limitation in that analysis is acquisition of geodata in appropriate resolution. The main objective of this study was to develop a proceeding algorithm for the landform geodiversity assessment using geomorphometric parameters. Furthermore, final maps were compared to those resulting from thematic layers method. The study area consists of two peculiar valleys, characterized by diverse landscape units and complex geological setting: Sucha Woda in Polish part of Tatra Mts. and Wrzosowka in Sudetes Mts. Both valleys are located in the National Park areas. The basis for the assessment is a proper selection of geomorphometric parameters with reference to the definition of geodiversity. Seven factor maps were prepared for each valley: General Curvature, Topographic Openness, Potential Incoming Solar Radiation, Topographic Position Index, Topographic Wetness Index, Convergence Index and Relative Heights. After the data integration and performing the necessary geoinformation analysis, the next step with a certain degree of subjectivity is score classification of the input maps using an expert system and geostatistical analysis. The crucial point to generate the final maps of geodiversity by multi-criteria evaluation (MCE) with GIS-based Weighted Sum technique is to assign appropriate weights for each factor map by determining the incoherence of the pairwise comparison matrices. The widely accepted rule of inconsistency is according to Saaty's ratio. The accuracy of the obtained final maps is strongly influenced by: the quality of the raw data and the cell size of the basic assessment. Furthermore, it can be stated that selected parameters: Topographic Position Index, Topographic Wetness Index and Total Incoming Solar Radiation could be a relevant choice for geodiversity assessment. The remaining ones are characterized by certain linear correlation and therefore their validity in the weighting process was lower. Geodiversity assessment method based on the geomorphometric parameters provides results at a level similar to the method using thematic layers. What is more significant, it is much less labor-intensive and does not require a whole set of geodata. Recognizing parts of the territory that are the most vulnerable to changes turns out to be very crucial for management and planning of natural protected areas. The proposed methodology meets these proposals well.

Organization, chromosomal localization and promoter analysis of the gene encoding human acidic fibroblast growth factor intracellular binding protein.

PubMed Central

Kolpakova, E; Frengen, E; Stokke, T; Olsnes, S

2000-01-01

Acidic fibroblast growth factor (aFGF) intracellular binding protein (FIBP) is a protein found mainly in the nucleus that might be involved in the intracellular function of aFGF. Here we present a comparative analysis of the deduced amino acid sequences of human, murine and Drosophila FIBP analogues and demonstrate that FIBP is an evolutionarily conserved protein. The human gene spans more than 5 kb, comprising ten exons and nine introns, and maps to chromosome 11q13.1. Two slightly different splice variants found in different tissues were isolated and characterized. Sequence analysis of the region surrounding the translation start revealed a CpG island, a classical feature of widely expressed genes. Functional studies of the promoter region with a luciferase reporter system suggested a strong transcriptional activity residing within 600 bp of the 5' flanking region. PMID:11104667

Analysis of yield and oil from a series of canola breeding trials. Part II. Exploring variety by environment interaction using factor analysis.

PubMed

Cullis, B R; Smith, A B; Beeck, C P; Cowling, W A

2010-11-01

Exploring and exploiting variety by environment (V × E) interaction is one of the major challenges facing plant breeders. In paper I of this series, we presented an approach to modelling V × E interaction in the analysis of complex multi-environment trials using factor analytic models. In this paper, we develop a range of statistical tools which explore V × E interaction in this context. These tools include graphical displays such as heat-maps of genetic correlation matrices as well as so-called E-scaled uniplots that are a more informative alternative to the classical biplot for large plant breeding multi-environment trials. We also present a new approach to prediction for multi-environment trials that include pedigree information. This approach allows meaningful selection indices to be formed either for potential new varieties or potential parents.

A Bibliometric History of the Journal of Psychology Between 1936 and 2015.

PubMed

Tur-Porcar, Ana; Mas-Tur, Alicia; Merigó, José M; Roig-Tierno, Norat; Watt, John

2018-05-19

The Journal of Psychology: Interdisciplinary and Applied is a leading international journal in psychology dating back to 1935. This study examines its publications since its creation utilizing a bibliometric analysis. The primary objective is to provide a complete overview of the key factors affecting the journal. This analysis includes such key issues as the publication and citation structure of the journal, its most cited articles, and the leading authors, institutions, and countries referenced in the journal. The work uses the Scopus database to classify the bibliographic material. Additionally, the analysis provides a graphical mapping of the bibliographic data by using visualization of similarities viewer software. This software uses several bibliometric techniques including co-citation, bibliographic coupling and co-occurrence of keywords. The Journal of Psychology is strongly connected to most of the current leading journals in psychology, and currently has a 5-year impact factor of 1.77 (Thomson Reuters, 2015 Journal Citation Reports).

Application of GIS-based Procedure on Slopeland Use Classification and Identification

NASA Astrophysics Data System (ADS)

KU, L. C.; LI, M. C.

2016-12-01

In Taiwan, the "Slopeland Conservation and Utilization Act" regulates the management of the slopelands. It categorizes the slopeland into land suitable for agricultural or animal husbandry, land suitable for forestry and land for enhanced conservation, according to the environmental factors of average slope, effective soil depth, soil erosion and parental rock. Traditionally, investigations of environmental factors require cost-effective field works. It has been confronted with many practical issues such as non-evaluated cadastral parcels, evaluation results depending on expert's opinion, difficulties in field measurement and judgment, and time consuming. This study aimed to develop a GIS-based procedure involved in the acceleration of slopeland use classification and quality improvement. First, the environmental factors of slopelands were analyzed by GIS and SPSS software. The analysis involved with the digital elevation model (DEM), soil depth map, land use map and satellite images. Second, 5% of the analyzed slopelands were selected to perform the site investigations and correct the results of classification. Finally, a 2nd examination was involved by randomly selected 2% of the analyzed slopelands to perform the accuracy evaluation. It was showed the developed procedure is effective in slopeland use classification and identification. Keywords: Slopeland Use Classification, GIS, Management

Applying Factor Analysis Combined with Kriging and Information Entropy Theory for Mapping and Evaluating the Stability of Groundwater Quality Variation in Taiwan

PubMed Central

Shyu, Guey-Shin; Cheng, Bai-You; Chiang, Chi-Ting; Yao, Pei-Hsuan; Chang, Tsun-Kuo

2011-01-01

In Taiwan many factors, whether geological parent materials, human activities, and climate change, can affect the groundwater quality and its stability. This work combines factor analysis and kriging with information entropy theory to interpret the stability of groundwater quality variation in Taiwan between 2005 and 2007. Groundwater quality demonstrated apparent differences between the northern and southern areas of Taiwan when divided by the Wu River. Approximately 52% of the monitoring wells in southern Taiwan suffered from progressing seawater intrusion, causing unstable groundwater quality. Industrial and livestock wastewaters also polluted 59.6% of the monitoring wells, resulting in elevated EC and TOC concentrations in the groundwater. In northern Taiwan, domestic wastewaters polluted city groundwater, resulting in higher NH3-N concentration and groundwater quality instability was apparent among 10.3% of the monitoring wells. The method proposed in this study for analyzing groundwater quality inspects common stability factors, identifies potential areas influenced by common factors, and assists in elevating and reinforcing information in support of an overall groundwater management strategy. PMID:21695030

A LiDAR-based analysis of the effects of slope, vegetation density, and ground surface roughness on travel rates for wildland firefighter escape route mapping

Treesearch

Michael J. Campbell; Philip E. Dennison; Bret W. Butler

2017-01-01

Escape routes are essential components of wildland firefighter safety, providing pre-defined pathways to a safety zone. Among the many factors that affect travel rates along an escape route, landscape conditions such as slope, lowlying vegetation density, and ground surface roughness are particularly influential, and can be measured using airborne light detection and...

The Model Analyst’s Toolkit: Scientific Model Development, Analysis, and Validation

DTIC Science & Technology

2013-11-20

Granger causality F-test validation 3.1.2. Dynamic time warping for uneven temporal relationships Many causal relationships are imperfectly...mapping for dynamic feedback models Granger causality and DTW can identify causal relationships and consider complex temporal factors. However, many ...variant of the tf-idf algorithm (Manning, Raghavan, Schutze et al., 2008), typically used in search engines, to “score” features. The (-log tf) in

Mapping protease substrates using a biotinylated phage substrate library.

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

Scholle, M. D.; Kriplani, U.; Pabon, A.

We describe a bacteriophage M13 substrate library encoding the AviTag (BirA substrate) and combinatorial heptamer peptides displayed at the N terminus of the mature form of capsid protein III. Phages are biotinylated efficiently (> or = 50%) when grown in E. coli cells coexpressing BirA, and such viral particles can be immobilized on a streptavidin-coated support and released by protease cleavage within the combinatorial peptide. We have used this library to map the specificity of human Factor Xa and a neuropeptidase, neurolysin (EC3.4.24.16). Validation by analysis of isolated peptide substrates has revealed that neurolysin recognizes the motif hydrophobic-X-Pro-Arg-hydrophobic, where Arg-hydrophobicmore » is the scissile bond.« less

Exploring the Specifications of Spatial Adjacencies and Weights in Bayesian Spatial Modeling with Intrinsic Conditional Autoregressive Priors in a Small-area Study of Fall Injuries

PubMed Central

Law, Jane

2016-01-01

Intrinsic conditional autoregressive modeling in a Bayeisan hierarchical framework has been increasingly applied in small-area ecological studies. This study explores the specifications of spatial structure in this Bayesian framework in two aspects: adjacency, i.e., the set of neighbor(s) for each area; and (spatial) weight for each pair of neighbors. Our analysis was based on a small-area study of falling injuries among people age 65 and older in Ontario, Canada, that was aimed to estimate risks and identify risk factors of such falls. In the case study, we observed incorrect adjacencies information caused by deficiencies in the digital map itself. Further, when equal weights was replaced by weights based on a variable of expected count, the range of estimated risks increased, the number of areas with probability of estimated risk greater than one at different probability thresholds increased, and model fit improved. More importantly, significance of a risk factor diminished. Further research to thoroughly investigate different methods of variable weights; quantify the influence of specifications of spatial weights; and develop strategies for better defining spatial structure of a map in small-area analysis in Bayesian hierarchical spatial modeling is recommended. PMID:29546147

Validation of a social vulnerability index in context to river-floods in Germany

NASA Astrophysics Data System (ADS)

Fekete, A.

2009-03-01

Social vulnerability indices are a means for generating information about people potentially affected by disasters that are e.g. triggered by river-floods. The purpose behind such an index is in this study the development and the validation of a social vulnerability map of population characteristics towards river-floods covering all counties in Germany. This map is based on a composite index of three main indicators for social vulnerability in Germany - fragility, socio-economic conditions and region. These indicators have been identified by a factor analysis of selected demographic variables obtained from federal statistical offices. Therefore, these indicators can be updated annually based on a reliable data source. The vulnerability patterns detected by the factor analysis are verified by using an independent second data set. The interpretation of the second data set shows that vulnerability is revealed by a real extreme flood event and demonstrates that the patterns of the presumed vulnerability match the observations of a real event. It comprises a survey of flood-affected households in three federal states. By using logistic regression, it is demonstrated that the theoretically presumed indications of vulnerability are correct and that the indicators are valid. It is shown that indeed certain social groups like the elderly, the financially weak or the urban residents are higher risk groups.

Protein interactome analysis of 12 mitogen-activated protein kinase kinase kinase in rice using a yeast two-hybrid system.

PubMed

Singh, Raksha; Lee, Jae-Eun; Dangol, Sarmina; Choi, Jihyun; Yoo, Ran Hee; Moon, Jae Sun; Shim, Jae-Kyung; Rakwal, Randeep; Agrawal, Ganesh Kumar; Jwa, Nam-Soo

2014-01-01

The mitogen-activated protein kinase (MAPK) cascade is composed at least of MAP3K (for MAPK kinase kinase), MAP2K, and MAPK family modules. These components together play a central role in mediating extracellular signals to the cell and vice versa by interacting with their partner proteins. However, the MAP3K-interacting proteins remain poorly investigated in plants. Here, we utilized a yeast two-hybrid system and bimolecular fluorescence complementation in the model crop rice (Oryza sativa) to map MAP3K-interacting proteins. We identified 12 novel nonredundant interacting protein pairs (IPPs) representing 11 nonredundant interactors using 12 rice MAP3Ks (available as full-length cDNA in the rice KOME (http://cdna01.dna.affrc.go.jp/cDNA/) at the time of experimental design and execution) as bait and a rice seedling cDNA library as prey. Of the 12 MAP3Ks, only six had interacting protein partners. The established MAP3K interactome consisted of two kinases, three proteases, two forkhead-associated domain-containing proteins, two expressed proteins, one E3 ligase, one regulatory protein, and one retrotransposon protein. Notably, no MAP3K showed physical interaction with either MAP2K or MAPK. Seven IPPs (58.3%) were confirmed in vivo by bimolecular fluorescence complementation. Subcellular localization of 14 interactors, together involved in nine IPPs (75%) further provide prerequisite for biological significance of the IPPs. Furthermore, GO of identified interactors predicted their involvement in diverse physiological responses, which were supported by a literature survey. These findings increase our knowledge of the MAP3K-interacting proteins, help in proposing a model of MAPK modules, provide a valuable resource for developing a complete map of the rice MAPK interactome, and allow discussion for translating the interactome knowledge to rice crop improvement against environmental factors. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Properties of anodic oxides grown on a hafnium–tantalum–titanium thin film library

PubMed Central

Mardare, Andrei Ionut; Ludwig, Alfred; Savan, Alan; Hassel, Achim Walter

2014-01-01

A ternary thin film combinatorial materials library of the valve metal system Hf–Ta–Ti obtained by co-sputtering was studied. The microstructural and crystallographic analysis of the obtained compositions revealed a crystalline and textured surface, with the exception of compositions with Ta concentration above 48 at.% which are amorphous and show a flat surface. Electrochemical anodization of the composition spread thin films was used for analysing the growth of the mixed surface oxides. Oxide formation factors, obtained from the potentiodynamic anodization curves, as well as the dielectric constants and electrical resistances, obtained from electrochemical impedance spectroscopy, were mapped along two dimensions of the library using a scanning droplet cell microscope. The semiconducting properties of the anodic oxides were mapped using Mott–Schottky analysis. The degree of oxide mixing was analysed qualitatively using x-ray photoelectron spectroscopy depth profiling. A quantitative analysis of the surface oxides was performed and correlated to the as-deposited metal thin film compositions. In the concurrent transport of the three metal cations during oxide growth a clear speed order of Ti > Hf > Ta was proven. PMID:27877648

In-situ microscale through-silicon via strain measurements by synchrotron x-ray microdiffraction exploring the physics behind data interpretation

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

Liu, Xi; School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332; Thadesar, Paragkumar A.

2014-09-15

In-situ microscale thermomechanical strain measurements have been performed in combination with synchrotron x-ray microdiffraction to understand the fundamental cause of failures in microelectronics devices with through-silicon vias. The physics behind the raster scan and data analysis of the measured strain distribution maps is explored utilizing the energies of indexed reflections from the measured data and applying them for beam intensity analysis and effective penetration depth determination. Moreover, a statistical analysis is performed for the beam intensity and strain distributions along the beam penetration path to account for the factors affecting peak search and strain refinement procedure.

Children's Understanding of Large-Scale Mapping Tasks: An Analysis of Talk, Drawings, and Gesture

ERIC Educational Resources Information Center

Kotsopoulos, Donna; Cordy, Michelle; Langemeyer, Melanie

2015-01-01

This research examined how children represent motion in large-scale mapping tasks that we referred to as "motion maps". The underlying mathematical content was transformational geometry. In total, 19 children, 8- to 10-year-old, created motion maps and captured their motion maps with accompanying verbal description digitally. Analysis of…

Description of a user-oriented geographic information system - The resource analysis program

NASA Technical Reports Server (NTRS)

Tilmann, S. E.; Mokma, D. L.

1980-01-01

This paper describes the Resource Analysis Program, an applied geographic information system. Several applications are presented which utilized soil, and other natural resource data, to develop integrated maps and data analyses. These applications demonstrate the methods of analysis and the philosophy of approach used in the mapping system. The applications are evaluated in reference to four major needs of a functional mapping system: data capture, data libraries, data analysis, and mapping and data display. These four criteria are then used to describe an effort to develop the next generation of applied mapping systems. This approach uses inexpensive microcomputers for field applications and should prove to be a viable entry point for users heretofore unable or unwilling to venture into applied computer mapping.

On the Impact of Anomalous Noise Events on Road Traffic Noise Mapping in Urban and Suburban Environments.

PubMed

Orga, Ferran; Alías, Francesc; Alsina-Pagès, Rosa Ma

2017-12-23

Noise pollution is a critical factor affecting public health, the relationship between road traffic noise (RTN) and several diseases in urban areas being especially disturbing. The Environmental Noise Directive 2002/49/EC and the CNOSSOS-EU framework are the main instruments of the European Union to identify and combat noise pollution, requiring Member States to compose and publish noise maps and noise management action plans every five years. Nowadays, the noise maps are starting to be tailored by means of Wireless Acoustic Sensor Networks (WASN). In order to exclusively monitor the impact of RTN on the well-being of citizens through WASN-based approaches, those noise sources unrelated to RTN denoted as Anomalous Noise Events (ANEs) should be removed from the noise map generation. This paper introduces an analysis methodology considering both Signal-to-Noise Ratio (SNR) and duration of ANEs to evaluate their impact on the A-weighted equivalent RTN level calculation for different integration times. The experiments conducted on 9 h of real-life data from the WASN-based DYNAMAP project show that both individual high-impact events and aggregated medium-impact events bias significantly the equivalent noise levels of the RTN map, making any derived study about public health impact inaccurate.

Rational Variety Mapping for Contrast-Enhanced Nonlinear Unsupervised Segmentation of Multispectral Images of Unstained Specimen

PubMed Central

Kopriva, Ivica; Hadžija, Mirko; Popović Hadžija, Marijana; Korolija, Marina; Cichocki, Andrzej

2011-01-01

A methodology is proposed for nonlinear contrast-enhanced unsupervised segmentation of multispectral (color) microscopy images of principally unstained specimens. The methodology exploits spectral diversity and spatial sparseness to find anatomical differences between materials (cells, nuclei, and background) present in the image. It consists of rth-order rational variety mapping (RVM) followed by matrix/tensor factorization. Sparseness constraint implies duality between nonlinear unsupervised segmentation and multiclass pattern assignment problems. Classes not linearly separable in the original input space become separable with high probability in the higher-dimensional mapped space. Hence, RVM mapping has two advantages: it takes implicitly into account nonlinearities present in the image (ie, they are not required to be known) and it increases spectral diversity (ie, contrast) between materials, due to increased dimensionality of the mapped space. This is expected to improve performance of systems for automated classification and analysis of microscopic histopathological images. The methodology was validated using RVM of the second and third orders of the experimental multispectral microscopy images of unstained sciatic nerve fibers (nervus ischiadicus) and of unstained white pulp in the spleen tissue, compared with a manually defined ground truth labeled by two trained pathophysiologists. The methodology can also be useful for additional contrast enhancement of images of stained specimens. PMID:21708116

A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.

PubMed

Chatake, Toshiyuki; Fujiwara, Satoru

2016-01-01

A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.

On the Impact of Anomalous Noise Events on Road Traffic Noise Mapping in Urban and Suburban Environments

PubMed Central

2017-01-01

Noise pollution is a critical factor affecting public health, the relationship between road traffic noise (RTN) and several diseases in urban areas being especially disturbing. The Environmental Noise Directive 2002/49/EC and the CNOSSOS-EU framework are the main instruments of the European Union to identify and combat noise pollution, requiring Member States to compose and publish noise maps and noise management action plans every five years. Nowadays, the noise maps are starting to be tailored by means of Wireless Acoustic Sensor Networks (WASN). In order to exclusively monitor the impact of RTN on the well-being of citizens through WASN-based approaches, those noise sources unrelated to RTN denoted as Anomalous Noise Events (ANEs) should be removed from the noise map generation. This paper introduces an analysis methodology considering both Signal-to-Noise Ratio (SNR) and duration of ANEs to evaluate their impact on the A-weighted equivalent RTN level calculation for different integration times. The experiments conducted on 9 h of real-life data from the WASN-based DYNAMAP project show that both individual high-impact events and aggregated medium-impact events bias significantly the equivalent noise levels of the RTN map, making any derived study about public health impact inaccurate. PMID:29295492

MAPPING SPATIAL ACCURACY AND ESTIMATING LANDSCAPE INDICATORS FROM THEMATIC LAND COVER MAPS USING FUZZY SET THEORY

EPA Science Inventory

This paper presents a fuzzy set-based method of mapping spatial accuracy of thematic map and computing several ecological indicators while taking into account spatial variation of accuracy associated with different land cover types and other factors (e.g., slope, soil type, etc.)...

Geologic and mineral and water resources investigations in western Colorado using ERTS-1 data

NASA Technical Reports Server (NTRS)

Knepper, D. H., Jr. (Principal Investigator); Hutchinson, R. M.; Sawatzky, D. L.; Trexler, D. W.; Bruns, D. L.; Nicolais, S. M.

1973-01-01

The author has identified the following significant results. Topography was found to be the most important factor defining folds on ERTS-1 imagery of northwestern Colorado; tonal variations caused by rock reflectance and vegetation type and density are the next most important factors. Photo-linears mapped on ERTS-1 imagery of central Colorado correlate well with ground-measured joint and fracture trends. In addition, photo-linears have been successfully used to determine the location and distribution of metallic mineral deposits in the Colorado Mineral Belt. True color composites are best for general geologic analysis and false color composites prepared with positive/negative masks are useful for enhancing local geologic phenomena. During geologic analysis of any given area, ERTS-1 imagery from several different dates should be studied.

Methods of analysis and resources available for genetic trait mapping.

PubMed

Ott, J

1999-01-01

Methods of genetic linkage analysis are reviewed and put in context with other mapping techniques. Sources of information are outlined (books, web sites, computer programs). Special consideration is given to statistical problems in canine genetic mapping (heterozygosity, inbreeding, marker maps).

A Quantitative Chemotherapy Genetic Interaction Map Reveals Factors Associated with PARP Inhibitor Resistance.

PubMed

Hu, Hsien-Ming; Zhao, Xin; Kaushik, Swati; Robillard, Lilliane; Barthelet, Antoine; Lin, Kevin K; Shah, Khyati N; Simmons, Andy D; Raponi, Mitch; Harding, Thomas C; Bandyopadhyay, Sourav

2018-04-17

Chemotherapy is used to treat most cancer patients, yet our understanding of factors that dictate response and resistance to such drugs remains limited. We report the generation of a quantitative chemical-genetic interaction map in human mammary epithelial cells charting the impact of the knockdown of 625 genes related to cancer and DNA repair on sensitivity to 29 drugs, covering all classes of chemotherapy. This quantitative map is predictive of interactions maintained in other cell lines, identifies DNA-repair factors, predicts cancer cell line responses to therapy, and prioritizes synergistic drug combinations. We identify that ARID1A loss confers resistance to PARP inhibitors in cells and ovarian cancer patients and that loss of GPBP1 causes resistance to cisplatin and PARP inhibitors through the regulation of genes involved in homologous recombination. This map helps navigate patient genomic data and optimize chemotherapeutic regimens by delineating factors involved in the response to specific types of DNA damage. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Application of the Risk-Based Early Warning Method in a Fracture-Karst Water Source, North China.

PubMed

Guo, Yongli; Wu, Qing; Li, Changsuo; Zhao, Zhenhua; Sun, Bin; He, Shiyi; Jiang, Guanghui; Zhai, Yuanzheng; Guo, Fang

2018-03-01

  The paper proposes a risk-based early warning considering characteristics of fracture-karst aquifer in North China and applied it in a super-large fracture-karst water source. Groundwater vulnerability, types of land use, water abundance, transmissivity and spatial temporal variation of groundwater quality were chosen as indexes of the method. Weights of factors were obtained by using AHP method based on relative importance of factors, maps of factors were zoned by GIS, early warning map was conducted based on extension theory with the help of GIS, ENVI+IDL. The early warning map fused five factors very well, serious and tremendous warning areas are mainly located in northwest and east with high or relatively high transmissivity and groundwater pollutant loading, and obviously deteriorated or deteriorated trend of petroleum. The early warning map warns people where more attention should be paid, and the paper guides decision making to take appropriate protection actions in different warning levels areas.

A MAP4 kinase related to Ste20 is a nutrient-sensitive regulator of mTOR signalling

PubMed Central

Findlay, Greg M.; Yan, Lijun; Procter, Julia; Mieulet, Virginie; Lamb, Richard F.

2007-01-01

The mTOR (mammalian target of rapamycin) signalling pathway is a key regulator of cell growth and is controlled by growth factors and nutrients such as amino acids. Although signalling pathways from growth factor receptors to mTOR have been elucidated, the pathways mediating signalling by nutrients are poorly characterized. Through a screen for protein kinases active in the mTOR signalling pathway in Drosophila we have identified a Ste20 family member (MAP4K3) that is required for maximal S6K (S6 kinase)/4E-BP1 [eIF4E (eukaryotic initiation factor 4E)-binding protein 1] phosphorylation and regulates cell growth. Importantly, MAP4K3 activity is regulated by amino acids, but not the growth factor insulin and is not regulated by the mTORC1 inhibitor rapamycin. Our results therefore suggest a model whereby nutrients signal to mTORC1 via activation of MAP4K3. PMID:17253963

Length and area equivalents for interpreting wildland resource maps

Treesearch

Elliot L. Amidon; Marilyn S. Whitfield

1969-01-01

Map users must refer to an appropriate scale in interpreting wildland resource maps. Length and area equivalents for nine map scales commonly used have been computed. For each scale a 1-page table consists of map-to-ground equivalents, buffer strip or road widths, and cell dimensions required for a specified acreage. The conversion factors are stored in a Fortran...

Resting-state functional magnetic resonance imaging for surgical planning in pediatric patients: a preliminary experience.

PubMed

Roland, Jarod L; Griffin, Natalie; Hacker, Carl D; Vellimana, Ananth K; Akbari, S Hassan; Shimony, Joshua S; Smyth, Matthew D; Leuthardt, Eric C; Limbrick, David D

2017-12-01

OBJECTIVE Cerebral mapping for surgical planning and operative guidance is a challenging task in neurosurgery. Pediatric patients are often poor candidates for many modern mapping techniques because of inability to cooperate due to their immature age, cognitive deficits, or other factors. Resting-state functional MRI (rs-fMRI) is uniquely suited to benefit pediatric patients because it is inherently noninvasive and does not require task performance or significant cooperation. Recent advances in the field have made mapping cerebral networks possible on an individual basis for use in clinical decision making. The authors present their initial experience translating rs-fMRI into clinical practice for surgical planning in pediatric patients. METHODS The authors retrospectively reviewed cases in which the rs-fMRI analysis technique was used prior to craniotomy in pediatric patients undergoing surgery in their institution. Resting-state analysis was performed using a previously trained machine-learning algorithm for identification of resting-state networks on an individual basis. Network maps were uploaded to the clinical imaging and surgical navigation systems. Patient demographic and clinical characteristics, including need for sedation during imaging and use of task-based fMRI, were also recorded. RESULTS Twenty patients underwent rs-fMRI prior to craniotomy between December 2013 and June 2016. Their ages ranged from 1.9 to 18.4 years, and 12 were male. Five of the 20 patients also underwent task-based fMRI and one underwent awake craniotomy. Six patients required sedation to tolerate MRI acquisition, including resting-state sequences. Exemplar cases are presented including anatomical and resting-state functional imaging. CONCLUSIONS Resting-state fMRI is a rapidly advancing field of study allowing for whole brain analysis by a noninvasive modality. It is applicable to a wide range of patients and effective even under general anesthesia. The nature of resting-state analysis precludes any need for task cooperation. These features make rs-fMRI an ideal technology for cerebral mapping in pediatric neurosurgical patients. This review of the use of rs-fMRI mapping in an initial pediatric case series demonstrates the feasibility of utilizing this technique in pediatric neurosurgical patients. The preliminary experience presented here is a first step in translating this technique to a broader clinical practice.

Evaluation of groundwater potential using geospatial techniques

NASA Astrophysics Data System (ADS)

Hussein, Abdul-Aziz; Govindu, Vanum; Nigusse, Amare Gebre Medhin

2017-09-01

The issue of unsustainable groundwater utilization is becoming increasingly an evident problem and the key concern for many developing countries. One of the problems is the absence of updated spatial information on the quantity and distribution of groundwater resource. Like the other developing countries, groundwater evaluation in Ethiopia has been usually conducted using field survey which is not feasible in terms of time and resource. This study was conducted in Northern Ethiopia, Wollo Zone, in Gerardo River Catchment district to spatially delineate the groundwater potential areas using geospatial and MCDA tools. To do so, eight major biophysical and environmental factors like geomorphology, lithology, slope, rainfall, land use land cover (LULC), soil, lineament density and drainage density were considered. The sources of these data were satellite image, digital elevation model (DEM), existing thematic maps and metrological station data. Landsat image was used in ERDAS Imagine to drive the LULC of the area, while the geomorphology, soil, and lithology of the area were identified and classified through field survey and digitized from existing maps using the ArcGIS software. The slope, lineament and drainage density of the area were derived from DEM using spatial analysis tools. The rainfall surface map was generated using the thissen polygon interpolation. Finally, after all these thematic maps were organized, weighted value determination for each factor and its field value was computed using IDRSI software. At last, all the factors were integrated together and computed the model using the weighted overlay so that potential groundwater areas were mapped. The findings depicted that the most potential groundwater areas are found in the central and eastern parts of the study area, while the northern and western parts of the Gerado River Catchment have poor potential of groundwater availability. This is mainly due to the cumulative effect of steep topographic and high drainage density. At last, once the potential groundwater areas were identified, cross validation of the resultant model was carefully carried out using existing data of dung wells and bore holes. The point data of dung wells and bore holes were overlaid on groundwater potential suitability map and coincide with the expected values. Generally, from this study, it can be concluded that RS and GIS with the help of MCDA are important tools in monitoring and evaluation of groundwater resource potential areas.

Modelling soil properties in a crop field located in Croatia

NASA Astrophysics Data System (ADS)

Bogunovic, Igor; Pereira, Paulo; Millan, Mesic; Percin, Aleksandra; Zgorelec, Zeljka

2016-04-01

Development of tillage activities had negative effects on soil quality as destruction of soil horizons, compacting and aggregates destruction, increasing soil erosion and loss of organic matter. For a better management in order to mitigate the effects of intensive soil management in land degradation it is fundamental to map the spatial distribution of soil properties (Brevik et al., 2016). The understanding the distribution of the variables in space is very important for a sustainable management, in order to identify areas that need a potential intervention and decrease the economic losses (Galiati et al., 2016). The objective of this work is study the spatial distribution of some topsoil properties as clay, fine silt, coarse silt, fine sand, coarse sand, penetration resistance, moisture and organic matter in a crop field located in Croatia. A grid with 275x25 (625 m2) was designed and a total of 48 samples were collected. Previous to data modelling, data normality was checked using the Shapiro wilk-test. As in previous cases (Pereira et al., 2015), data did not followed the normal distribution, even after a logarithmic (Log), square-root, and box cox transformation. Thus, for modeling proposes, we used the log transformed data, since was the closest to the normality. In order to identify groups among the variables we applied a principal component analysis (PCA), based on the correlation matrix. On average clay content was 15.47% (±3.23), fine silt 24.24% (±4.08), coarse silt 35.34% (±3.12), fine sand 20.93% (±4.68), coarse sand 4.02% (±1.69), penetration resistance 0.66 MPa (±0.28), organic matter 1.51% (±0.25) and soil moisture 32.04% (±3.27). The results showed that the PCA identified three factors explained at least one of the variables. The first factor had high positive loadings in soil clay, fine silt and organic matter and a high negative loading in fine sand. The second factor had high positive loadings in coarse sand and moisture and a high negative loading in coarse silt. Finally, the factor 3 had a positive loading in penetration resistance. The loadings of these three factors were mapped using ordinary kriging method. The analysis of incremental spatial correlation identified that the highest spatial correlation in the factor 1 was identified at 41.87 m, in factor 2 at 75.61 m and factor 3 at 143.9 m. In the case of factor 2, the maximum peak of spatial autocorrelation was significant at a p<0.05. This showed that the variable has a random distribution, as confirmed with the Moran's I spatial correlation analysis. In relation to the other factors the maximum peaks were significantly clustered at a p<0.001. These results suggested that the each factor has a different spatial pattern and the studied soil properties explained by each factor had a different spatial distribution. References Breivik, E., Baumgarten, A., Calzolari, C., Miller, B., Pereira, P., Kabala, C., Jordán, A. Soil mapping, classification, and modelling: history and future directions. Geoderma, 264, Part B, 256-274. Galiati, A., Gristina, L., Crescimanno, Barone, E., Novara, A. (2016) Towards more efficient incentives for agri-environment measures in degraded and eroded vineyards. Land Degradation and Development, DOI: 10.1002/ldr.2389 Pereira, P., Cerdà, A., Úbeda, X., Mataix-Solera, J. Arcenegui, V., Zavala, L. (2015) Modelling the impacts of wildfire on ash thickness in a short-term period, Land Degradation and Development, 26, 180-192.

Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways

PubMed Central

Jo, Kyuri; Jung, Inuk; Moon, Ji Hwan; Kim, Sun

2016-01-01

Motivation: To understand the dynamic nature of the biological process, it is crucial to identify perturbed pathways in an altered environment and also to infer regulators that trigger the response. Current time-series analysis methods, however, are not powerful enough to identify perturbed pathways and regulators simultaneously. Widely used methods include methods to determine gene sets such as differentially expressed genes or gene clusters and these genes sets need to be further interpreted in terms of biological pathways using other tools. Most pathway analysis methods are not designed for time series data and they do not consider gene-gene influence on the time dimension. Results: In this article, we propose a novel time-series analysis method TimeTP for determining transcription factors (TFs) regulating pathway perturbation, which narrows the focus to perturbed sub-pathways and utilizes the gene regulatory network and protein–protein interaction network to locate TFs triggering the perturbation. TimeTP first identifies perturbed sub-pathways that propagate the expression changes along the time. Starting points of the perturbed sub-pathways are mapped into the network and the most influential TFs are determined by influence maximization technique. The analysis result is visually summarized in TF-Pathway map in time clock. TimeTP was applied to PIK3CA knock-in dataset and found significant sub-pathways and their regulators relevant to the PIP3 signaling pathway. Availability and Implementation: TimeTP is implemented in Python and available at http://biohealth.snu.ac.kr/software/TimeTP/. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: sunkim.bioinfo@snu.ac.kr PMID:27307609

Determining areas that require indoor insecticide spraying using Multi Criteria Evaluation, a decision-support tool for malaria vector control programmes in the Central Highlands of Madagascar

PubMed Central

Rakotomanana, Fanjasoa; Randremanana, Rindra V; Rabarijaona, Léon P; Duchemin, Jean Bernard; Ratovonjato, Jocelyn; Ariey, Frédéric; Rudant, Jean Paul; Jeanne, Isabelle

2007-01-01

Background The highlands of Madagascar present an unstable transmission pattern of malaria. The population has no immunity, and the central highlands have been the sites of epidemics with particularly high fatality. The most recent epidemic occurred in the 1980s, and caused about 30,000 deaths. The fight against malaria epidemics in the highlands has been based on indoor insecticide spraying to control malaria vectors. Any preventive programme involving generalised cover in the highlands will require very substantial logistical support. We used multicriteria evaluation, by the method of weighted linear combination, as basis for improved targeting of actions by determining priority zones for intervention. Results Image analysis and field validation showed the accuracy of mapping rice fields to be between 82.3% and 100%, and the Kappa coefficient was 0.86 to 0.99. A significant positive correlation was observed between the abundance of the vector Anopheles funestus and temperature; the correlation coefficient was 0.599 (p < 0.001). A significant negative correlation was observed between vector abundance and human population density: the correlation coefficient was -0.551 (p < 0.003). Factor weights were determined by pair-wise comparison and the consistency ratio was 0.04. Risk maps of the six study zones were obtained according to a gradient of risk. Nine of thirteen results of alert confirmed by the Epidemiological Surveillance Post were in concordance with the risk map. Conclusion This study is particularly valuable for the management of vector control programmes, and particularly the reduction of the vector population with a view to preventing disease. The risk map obtained can be used to identify priority zones for the management of resources, and also help avoid systematic and generalised spraying throughout the highlands: such spraying is particularly difficult and expensive. The accuracy of the mapping, both as concerns time and space, is dependent on the availability of data. Continuous monitoring of malaria transmission factors must be undertaken to detect any changes. A regular case notification allows risk map to be verified. These actions should therefore be implemented so that risk maps can be satisfactorily assessed. PMID:17261177

Assessing Approaches to Teaching Systems Thinking: Reading Article vs. Game Play

NASA Astrophysics Data System (ADS)

Pfirman, S. L.; O'Garra, T.; Lee, J.; Bachrach, E.; Bachman, G.; Orlove, B. S.

2016-12-01

Problem-solving in the complex domain of climate change requires consideration of the dynamics of systems as wholes. The long time frame, coupled with multiple interacting elements is challenging to teach through traditionally linear approaches, such as lectures or reading. On the other hand some have claimed that games are potentially useful in teaching system skills, due to their iterative, interacting, and problem solving character. In this experiment, we evaluated the impact of the EcoChains: Arctic Crisis card game on participants' mental models using a `fuzzy cognitive mapping' approach. The study population included 41 participants randomly assigned to the treatment/game play n=21 and the control/reading illustrated article: n=20. To obtain cognitive maps from participants, the first step was explaining how to draw a map, using an unrelated map as an example. Following the explanation, participants were handed large sheets of paper and asked to write down all the concepts they could think of related to: Arctic marine & sea-ice ecosystems, including the species & inhabitants of these ecosystems, all the different factors that negatively affect the health of Arctic marine & sea-ice ecosystems, its species & inhabitants, all the different factors that positively affect the health of Arctic marine & sea-ice ecosystems, its species & inhabitants. Once participants had drafted their list of concepts, they were asked to construct maps with the concepts in the center followed by arrows drawn between them to represent the direction of relationships between concepts. After the intervention - either playing the EcoChains card game or reading the illustrated article - participants were handed back their maps, together with a different colored pencil from the one they used previously, and asked to adjust the maps based on what they had learned from playing Ecochains/reading the article. Results indicate that both playing EcoChains and reading an illustrated article with similar information, increased systems thinking. Assessment indicates that the text-based approach had greater quantitative gains as evaluated through the number of nodes and types of connections. Additional analysis is ongoing to examine potential differences in the quality of learning gains.

Wingless-type MMTV integration site family member 2 (WNT2) gene is associated with resistance to MAP in faecal culture and antibody response in Holstein cattle.

PubMed

Pauciullo, A; Küpper, J; Brandt, H; Donat, K; Iannuzzi, L; Erhardt, G

2015-04-01

Mycobacterium avium subspecies paratuberculosis (MAP) is a pathogenic bacterium responsible for the lethal Johne's disease in cattle. So far, several genome-wide association studies (GWAS) have been carried out to identify chromosomal regions highly associated with Johne's disease. The aim of this study was to investigate the genetic variability within a pool of seven genes (LAMB1, DLD, WNT2, PRDM1, SOCS5, PTGER4 and IL10) indicated by former GWAS/RNA-Seq studies as putatively associated with MAP infections and to achieve a confirmation study of association with paratuberculosis susceptibility in a population of 324 German Holstein cattle (162 cases MAP positive and 162 controls MAP negative) using ELISA and fecal cultural tests. SNP validation and genotyping information are provided, quick methods for allelic discrimination were set up and transcription factor binding analyses were performed. The rs43390642:G>TSNP in the WNT2 promoter region is associated with paratuberculosis susceptibility (P = 0.013), suggesting a protective role of the T allele (P = 0.043; odds ratio 0.50 [0.25-0.97]). The linkage disequilibrium with the DLD rs134692583:A>T might suggest a combined mechanism of action of these neighboring genes in resistance to MAP infection, which is also supported by a significant effect shown by the haplotype DLD(T) /WNT2(T) (P = 0.047). In silico analysis predicted rs43390642:G>T and rs134692583:A>T as essential parts of binding sites for the transcription factors GR, C/EBPβ and GATA-1, hence suggesting a potential influence on WNT2 and DLD gene expression. This study confirmed the region on BTA 4 (UMD 3.1: 50639460-51397892) as involved in tolerance/resistance to Johne's disease. In addition, this study clarifies the involvement of the investigated genes in MAP infection and contributes to the understanding of genetic variability involved in Johne's disease susceptibility. © 2015 Stichting International Foundation for Animal Genetics.

Fine mapping analysis confirms and strengthens linkage of four chromosomal regions in familial hypospadias

PubMed Central

Söderhäll, Cilla; Körberg, Izabella Baranowska; Thai, Hanh T T; Cao, Jia; Chen, Yougen; Zhang, Xufeng; Shulu, Zu; van der Zanden, Loes F M; van Rooij, Iris A L M; Frisén, Louise; Roeleveld, Nel; Markljung, Ellen; Kockum, Ingrid; Nordenskjöld, Agneta

2015-01-01

Hypospadias is a common male genital malformation and is regarded as a complex disease affected by multiple genetic as well as environmental factors. In a previous genome-wide scan for familial hypospadias, we reported suggestive linkage in nine chromosomal regions. We have extended this analysis by including new families and additional markers using non-parametric linkage. The fine mapping analysis displayed an increased LOD score on chromosome 8q24.1 and 10p15 in altogether 82 families. On chromosome 10p15, with the highest LOD score, we further studied AKR1C2, AKR1C3 and AKR1C4 involved in steroid metabolism, as well as KLF6 expressed in preputial tissue from hypospadias patients. Mutation analysis of the AKR1C3 gene showed a new mutation, c.643G>A (p.(Ala215Thr)), in a boy with penile hypospadias. This mutation is predicted to have an impact on protein function and structure and was not found in controls. Altogether, we homed in on four chromosomal regions likely to harbor genes for hypospadias. Future studies will aim for studying regulatory sequence variants in these regions. PMID:24986825

Research on the Multiple Factors Influencing Human Identification Based on Pyroelectric Infrared Sensors

PubMed Central

Lou, Ping; Hu, Jianmin

2018-01-01

Analysis of the multiple factors affecting human identification ability based on pyroelectric infrared technology is a complex problem. First, we examine various sensed pyroelectric waveforms of the human body thermal infrared signal and reveal a mechanism for affecting human identification. Then, we find that the mechanism is decided by the distance, human target, pyroelectric infrared (PIR) sensor, the body type, human moving velocity, signal modulation mask, and Fresnel lens. The mapping relationship between the sensed waveform and multiple influencing factors is established, and a group of mathematical models are deduced which fuse the macro factors and micro factors. Finally, the experimental results show the macro-factors indirectly affect the recognition ability of human based on the pyroelectric technology. At the same time, the correctness and effectiveness of the mathematical models is also verified, which make it easier to obtain more pyroelectric infrared information about the human body for discriminating human targets. PMID:29462908

Improving the Accuracy of Mapping Urban Vegetation Carbon Density by Combining Shadow Remove, Spectral Unmixing Analysis and Spatial Modeling

NASA Astrophysics Data System (ADS)

Qie, G.; Wang, G.; Wang, M.

2016-12-01

Mixed pixels and shadows due to buildings in urban areas impede accurate estimation and mapping of city vegetation carbon density. In most of previous studies, these factors are often ignored, which thus result in underestimation of city vegetation carbon density. In this study we presented an integrated methodology to improve the accuracy of mapping city vegetation carbon density. Firstly, we applied a linear shadow remove analysis (LSRA) on remotely sensed Landsat 8 images to reduce the shadow effects on carbon estimation. Secondly, we integrated a linear spectral unmixing analysis (LSUA) with a linear stepwise regression (LSR), a logistic model-based stepwise regression (LMSR) and k-Nearest Neighbors (kNN), and utilized and compared the integrated models on shadow-removed images to map vegetation carbon density. This methodology was examined in Shenzhen City of Southeast China. A data set from a total of 175 sample plots measured in 2013 and 2014 was used to train the models. The independent variables statistically significantly contributing to improving the fit of the models to the data and reducing the sum of squared errors were selected from a total of 608 variables derived from different image band combinations and transformations. The vegetation fraction from LSUA was then added into the models as an important independent variable. The estimates obtained were evaluated using a cross-validation method. Our results showed that higher accuracies were obtained from the integrated models compared with the ones using traditional methods which ignore the effects of mixed pixels and shadows. This study indicates that the integrated method has great potential on improving the accuracy of urban vegetation carbon density estimation. Key words: Urban vegetation carbon, shadow, spectral unmixing, spatial modeling, Landsat 8 images

Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant.

PubMed

Almeida, Rodrigo; Ricaño-Ponce, Isis; Kumar, Vinod; Deelen, Patrick; Szperl, Agata; Trynka, Gosia; Gutierrez-Achury, Javier; Kanterakis, Alexandros; Westra, Harm-Jan; Franke, Lude; Swertz, Morris A; Platteel, Mathieu; Bilbao, Jose Ramon; Barisani, Donatella; Greco, Luigi; Mearin, Luisa; Wolters, Victorien M; Mulder, Chris; Mazzilli, Maria Cristina; Sood, Ajit; Cukrowska, Bozena; Núñez, Concepción; Pratesi, Riccardo; Withoff, Sebo; Wijmenga, Cisca

2014-05-01

Using the Immunochip for genotyping, we identified 39 non-human leukocyte antigen (non-HLA) loci associated to celiac disease (CeD), an immune-mediated disease with a worldwide frequency of ∼1%. The most significant non-HLA signal mapped to the intronic region of 70 kb in the LPP gene. Our aim was to fine map and identify possible functional variants in the LPP locus. We performed a meta-analysis in a cohort of 25 169 individuals from six different populations previously genotyped using Immunochip. Imputation using data from the Genome of the Netherlands and 1000 Genomes projects, followed by meta-analysis, confirmed the strong association signal on the LPP locus (rs2030519, P = 1.79 × 10(-49)), without any novel associations. The conditional analysis on this top SNP-indicated association to a single common haplotype. By performing haplotype analyses in each population separately, as well as in a combined group of the four populations that reach the significant threshold after correction (P < 0.008), we narrowed down the CeD-associated region from 70 to 2.8 kb (P = 1.35 × 10(-44)). By intersecting regulatory data from the ENCODE project, we found a functional SNP, rs4686484 (P = 3.12 × 10(-49)), that maps to several B-cell enhancer elements and a highly conserved region. This SNP was also predicted to change the binding motif of the transcription factors IRF4, IRF11, Nkx2.7 and Nkx2.9, suggesting its role in transcriptional regulation. We later found significantly low levels of LPP mRNA in CeD biopsies compared with controls, thus our results suggest that rs4686484 is the functional variant in this locus, while LPP expression is decreased in CeD.

ANFIS modeling for the assessment of landslide susceptibility for the Cameron Highland (Malaysia)

NASA Astrophysics Data System (ADS)

Pradhan, Biswajeet; Sezer, Ebru; Gokceoglu, Candan; Buchroithner, Manfred F.

2010-05-01

Landslides are one of the recurrent natural hazard problems throughout most of Malaysia. In landslide literature, there are several approaches such as probabilistic, bivariate and multivariate statistical models, fuzzy and artificial neural network models etc. However, a neuro-fuzzy application on the landslide susceptibility assessment has not been encountered in the literature. For this reason, this study presents the results of an adaptive neuro-fuzzy inference system (ANFIS) using remote sensing data and GIS for landslide susceptibility analysis in a part of the Cameron Highland areas in Malaysia. Landslide locations in the study area were identified by interpreting aerial photographs and satellite images, supported by extensive field surveys. Landsat TM satellite imagery was used to map vegetation index. Maps of topography, lineaments, NDVI and land cover were constructed from the spatial datasets. Seven landslide conditioning factors such as altitude, slope angle, curvature, distance from drainage, lithology, distance from faults and NDVI were extracted from the spatial database. These factors were analyzed using an ANFIS to produce the landslide susceptibility maps. During the model development works, total 5 landslide susceptibility models were constructed. For verification, the results of the analyses were then compared with the field-verified landslide locations. Additionally, the ROC curves for all landslide susceptibility models were drawn and the area under curve values were calculated. Landslide locations were used to validate results of the landslide susceptibility map and the verification results showed 97% accuracy for the model 5 employing all parameters produced in the present study as the landslide conditioning factors. The validation results showed sufficient agreement between the obtained susceptibility map and the existing data on landslide areas. Qualitatively, the model yields reasonable results which can be used for preliminary land-use planning purposes. As a final conclusion, the results revealed that the ANFIS modeling is a very useful and powerful tool for the regional landslide susceptibility assessments. However, the results to be obtained from the ANFIS modeling should be assessed carefully because the overlearning may cause misleading results. To prevent overlerning, the numbers of membership functions of inputs and the number of training epochs should be selected optimally and carefully.

Use of multiple cluster analysis methods to explore the validity of a community outcomes concept map.

PubMed

Orsi, Rebecca

2017-02-01

Concept mapping is now a commonly-used technique for articulating and evaluating programmatic outcomes. However, research regarding validity of knowledge and outcomes produced with concept mapping is sparse. The current study describes quantitative validity analyses using a concept mapping dataset. We sought to increase the validity of concept mapping evaluation results by running multiple cluster analysis methods and then using several metrics to choose from among solutions. We present four different clustering methods based on analyses using the R statistical software package: partitioning around medoids (PAM), fuzzy analysis (FANNY), agglomerative nesting (AGNES) and divisive analysis (DIANA). We then used the Dunn and Davies-Bouldin indices to assist in choosing a valid cluster solution for a concept mapping outcomes evaluation. We conclude that the validity of the outcomes map is high, based on the analyses described. Finally, we discuss areas for further concept mapping methods research. Copyright © 2016 Elsevier Ltd. All rights reserved.

Using parallel factor analysis modeling (PARAFAC) and self-organizing maps to track senescence-induced patterns in leaf litter leachate

NASA Astrophysics Data System (ADS)

Wheeler, K. I.; Levia, D. F., Jr.; Hudson, J. E.

2017-12-01

As trees undergo autumnal processes such as resorption, senescence, and leaf abscission, the dissolved organic matter (DOM) contribution of leaf litter leachate to streams changes. However, little research has investigated how the fluorescent DOM (FDOM) changes throughout the autumn and how this differs inter- and intraspecifically. Two of the major impacts of global climate change on forested ecosystems include altering phenology and causing forest community species and subspecies composition restructuring. We examined changes in FDOM in leachate from American beech (Fagus grandifolia Ehrh.) leaves in Maryland, Rhode Island, Vermont, and North Carolina and yellow poplar (Liriodendron tulipifera L.) leaves from Maryland throughout three different phenophases: green, senescing, and freshly abscissed. Beech leaves from Maryland and Rhode Island have previously been identified as belonging to the same distinct genetic cluster and beech trees from Vermont and the study site in North Carolina from the other. FDOM in samples was characterized using excitation-emission matrices (EEMs) and a six-component parallel factor analysis (PARAFAC) model was created to identify components. Self-organizing maps (SOMs) were used to visualize variation and patterns in the PARAFAC component proportions of the leachate samples. Phenophase and species had the greatest influence on determining where a sample mapped on the SOM when compared to genetic clusters and geographic origin. Throughout senescence, FDOM from all the trees transitioned from more protein-like components to more humic-like ones. Percent greenness of the sampled leaves and the proportion of the tyrosine-like component 1 were found to significantly differ between the two genetic beech clusters. This suggests possible differences in photosynthesis and resorption between the two genetic clusters of beech. The use of SOMs to visualize differences in patterns of senescence between the different species and genetic populations proved to be useful in ways that other multivariate analysis techniques lack.

StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.

PubMed

Sanchez Sorzano, Carlos Oscar; Alvarez-Cabrera, Ana Lucia; Kazemi, Mohsen; Carazo, Jose María; Jonić, Slavica

2016-04-26

Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Quantitative and Qualitative Assessment of Soil Erosion Risk in Małopolska (Poland), Supported by an Object-Based Analysis of High-Resolution Satellite Images

NASA Astrophysics Data System (ADS)

Drzewiecki, Wojciech; Wężyk, Piotr; Pierzchalski, Marcin; Szafrańska, Beata

2014-06-01

In 2011 the Marshal Office of Małopolska Voivodeship decided to evaluate the vulnerability of soils to water erosion for the entire region. The quantitative and qualitative assessment of the erosion risk for the soils of the Małopolska region was done based on the USLE approach. The special work-flow of geoinformation technologies was used to fulfil this goal. A high-resolution soil map, together with rainfall data, a detailed digital elevation model and statistical information about areas sown with particular crops created the input information for erosion modelling in GIS environment. The satellite remote sensing technology and the object-based image analysis (OBIA) approach gave valuable support to this study. RapidEye satellite images were used to obtain the essential up-to-date data about land use and vegetation cover for the entire region (15,000 km2). The application of OBIA also led to defining the direction of field cultivation and the mapping of contour tillage areas. As a result, the spatially differentiated values of erosion control practice factor were used. Both, the potential and the actual soil erosion risk were assessed quantificatively and qualitatively. The results of the erosion assessment in the Małopolska Voivodeship reveal the fact that a majority of its agricultural lands is characterized by moderate or low erosion risk levels. However, high-resolution erosion risk maps show its substantial spatial diversity. According to our study, average or higher actual erosion intensity levels occur for 10.6 % of agricultural land, i.e. 3.6 % of the entire voivodeship area. In 20 % of the municipalities there is a very urgent demand for erosion control. In the next 23 % an urgent erosion control is needed. Our study showed that even a slight improvement of P-factor estimation may have an influence on modeling results. In our case, despite a marginal change of erosion assessment figures on a regional scale, the influence on the final prioritization of areas (municipalities) according to erosion control needs is visible. The study shows that, high-resolution satellite imagery and OBIA may be efficiently used for P-factor mapping and thus contribute to a refined soil erosion risk assessment.

Human factors analysis for a 2D enroute moving map application

NASA Astrophysics Data System (ADS)

Pschierer, Christian; Wipplinger, Patrick; Schiefele, Jens; Cromer, Scot; Laurin, John; Haffner, Skip

2005-05-01

The paper describes flight trials performed in Centennial, CO with a Piper Cheyenne from Marinvent. Six pilots flew the Cheyenne in twelve enroute segments between Denver Centennial and Colorado Springs. Two different settings (paper chart, enroute moving map) were evaluated with randomized settings. The flight trial goal was to evaluate the objective performance of pilots compared among the different settings. As dependent variables, positional accuracy and situational awareness probe (SAP) were measured. Analysis was conducted by an ANOVA test. In parallel, all pilots answered subjective Cooper-Harper, NASA TLX, situation awareness rating technique (SART), Display Readability Rating and debriefing questionnaires. The tested enroute moving map application has Jeppesen chart compliant symbologies for high-enroute and low-enroute. It has a briefing mode were all information found on today"s enroute paper chart together with a loaded flight plan are displayed in a north-up orientation. The execution mode displays a loaded flight plan routing together with only pertinent flight route relevant information in either a track up or north up orientation. Depiction of an own ship symbol is possible in both modes. All text and symbols are deconflicted. Additional information can be obtained by clicking on symbols. Terrain and obstacle data can be displayed for enhanced situation awareness. The result shows that pilots flying the 2D enroute moving map display perform no worse than pilots with conventional systems. Flight technical error and workload are equivalent or lower, situational awareness is higher than on conventional paper charts.

Use of localized performance-based functions for the specification and correction of hybrid imaging systems

NASA Astrophysics Data System (ADS)

Lisson, Jerold B.; Mounts, Darryl I.; Fehniger, Michael J.

1992-08-01

Localized wavefront performance analysis (LWPA) is a system that allows the full utilization of the system optical transfer function (OTF) for the specification and acceptance of hybrid imaging systems. We show that LWPA dictates the correction of wavefront errors with the greatest impact on critical imaging spatial frequencies. This is accomplished by the generation of an imaging performance map-analogous to a map of the optic pupil error-using a local OTF. The resulting performance map a function of transfer function spatial frequency is directly relatable to the primary viewing condition of the end-user. In addition to optimizing quality for the viewer it will be seen that the system has the potential for an improved matching of the optical and electronic bandpass of the imager and for the development of more realistic acceptance specifications. 1. LOCAL WAVEFRONT PERFORMANCE ANALYSIS The LWPA system generates a local optical quality factor (LOQF) in the form of a map analogous to that used for the presentation and evaluation of wavefront errors. In conjunction with the local phase transfer function (LPTF) it can be used for maximally efficient specification and correction of imaging system pupil errors. The LOQF and LPTF are respectively equivalent to the global modulation transfer function (MTF) and phase transfer function (PTF) parts of the OTF. The LPTF is related to difference of the average of the errors in separated regions of the pupil. Figure

The Topic Analysis of Hospice Care Research Using Co-word Analysis and GHSOM

NASA Astrophysics Data System (ADS)

Yang, Yu-Hsiang; Bhikshu, Huimin; Tsaih, Rua-Huan

The purpose of this study was to propose a multi-layer topic map analysis of palliative care research using co-word analysis of informetrics with Growing Hierarchical Self-Organizing Map (GHSOM). The topic map illustrated the delicate intertwining of subject areas and provided a more explicit illustration of the concepts within each subject area. We applied GHSOM, a text-mining Neural Networks tool, to obtain a hierarchical topic map. The result of the topic map may indicate that the subject area of health care science and service played an importance role in multidiscipline within the research related to palliative care.

Concept mapping and network analysis: an analytic approach to measure ties among constructs.

PubMed

Goldman, Alyssa W; Kane, Mary

2014-12-01

Group concept mapping is a mixed-methods approach that helps a group visually represent its ideas on a topic of interest through a series of related maps. The maps and additional graphics are useful for planning, evaluation and theory development. Group concept maps are typically described, interpreted and utilized through points, clusters and distances, and the implications of these features in understanding how constructs relate to one another. This paper focuses on the application of network analysis to group concept mapping to quantify the strength and directionality of relationships among clusters. The authors outline the steps of this analysis, and illustrate its practical use through an organizational strategic planning example. Additional benefits of this analysis to evaluation projects are also discussed, supporting the overall utility of this supplemental technique to the standard concept mapping methodology. Copyright © 2014 Elsevier Ltd. All rights reserved.

On the derivation of the areal reduction factor of storms

NASA Astrophysics Data System (ADS)

Bacchi, Baldassare; Ranzi, Roberto

A stochastic derivation of the areal reduction factor (ARF) of the storm intensity is presented: it is based on the analysis of the crossing properties of the rainfall process aggregated in space and time. As a working hypothesis, the number of crossings of high rainfall intensity levels is assumed to be Poisson-distributed and a hyperbolic tail of the probability of exceedances of rainfall intensity has been adopted. These hypotheses are supported by the analysis of radar maps during an intense storm event which occurred in Northern Italy. The reduction factor derived from this analysis shows a power-law decay with respect to the area of integration and the duration of the storm. The areal reduction results as a function of the storm duration and of its frequency. A weak, but significant decrease of the areal reduction factor with respect to the return period is shown by the functions derived, and this result is consistent with that of some recent studies on this topic. The results derived, although preliminary, may find useful applications for the definition of the design storm in urban catchments of a size greater than some square kilometres and with duration of some hours.

oPOSSUM: integrated tools for analysis of regulatory motif over-representation

PubMed Central

Ho Sui, Shannan J.; Fulton, Debra L.; Arenillas, David J.; Kwon, Andrew T.; Wasserman, Wyeth W.

2007-01-01

The identification of over-represented transcription factor binding sites from sets of co-expressed genes provides insights into the mechanisms of regulation for diverse biological contexts. oPOSSUM, an internet-based system for such studies of regulation, has been improved and expanded in this new release. New features include a worm-specific version for investigating binding sites conserved between Caenorhabditis elegans and C. briggsae, as well as a yeast-specific version for the analysis of co-expressed sets of Saccharomyces cerevisiae genes. The human and mouse applications feature improvements in ortholog mapping, sequence alignments and the delineation of multiple alternative promoters. oPOSSUM2, introduced for the analysis of over-represented combinations of motifs in human and mouse genes, has been integrated with the original oPOSSUM system. Analysis using user-defined background gene sets is now supported. The transcription factor binding site models have been updated to include new profiles from the JASPAR database. oPOSSUM is available at http://www.cisreg.ca/oPOSSUM/ PMID:17576675

Manifestation of a neuro-fuzzy model to produce landslide susceptibility map using remote sensing data derived parameters

NASA Astrophysics Data System (ADS)

Pradhan, Biswajeet; Lee, Saro; Buchroithner, Manfred

Landslides are the most common natural hazards in Malaysia. Preparation of landslide suscep-tibility maps is important for engineering geologists and geomorphologists. However, due to complex nature of landslides, producing a reliable susceptibility map is not easy. In this study, a new attempt is tried to produce landslide susceptibility map of a part of Cameron Valley of Malaysia. This paper develops an adaptive neuro-fuzzy inference system (ANFIS) based on a geographic information system (GIS) environment for landslide susceptibility mapping. To ob-tain the neuro-fuzzy relations for producing the landslide susceptibility map, landslide locations were identified from interpretation of aerial photographs and high resolution satellite images, field surveys and historical inventory reports. Landslide conditioning factors such as slope, plan curvature, distance to drainage lines, soil texture, lithology, and distance to lineament were extracted from topographic, soil, and lineament maps. Landslide susceptible areas were analyzed by the ANFIS model and mapped using the conditioning factors. Furthermore, we applied various membership functions (MFs) and fuzzy relations to produce landslide suscep-tibility maps. The prediction performance of the susceptibility map is checked by considering actual landslides in the study area. Results show that, triangular, trapezoidal, and polynomial MFs were the best individual MFs for modelling landslide susceptibility maps (86

Prevalence and determinants of albuminuria in a cohort of diabetic patients in Lebanon.

PubMed

Taleb, Nadine; Salti, Haytham; Al-Mokaddam, Mona; Merheb, Marie; Salti, Ibrahim; Nasrallah, Mona

2008-01-01

Few data are available on the extent of albuminuria in diabetic populations in the Middle East generally and in Lebanon specifically. We conducted this study to determine the prevalence of albuminuria and its major risk factors in a cohort of diabetic patients in Lebanon. Diabetic patients followed in the outpatient department at the American University of Beirut Medical Center (AUBMC) were included in a prospective observational study. AUBMC is a tertiary referral center and the outpatient department typically handles patients of low socioeconomic status with advanced disease. Patients were classified according to their urinary albumin-to-creatinine ratio (ACR) as having normoalbuminuria (ACR<30 mg/g creatinine), microalbuminuria (ACR=30 to <300 mg/g creatinine), or macroalbuminuria (ACR > or =300 mg/g creatinine). The three groups were compared to analyze the association between albuminuria and its risk factors. In addition, independent predictors of albuminuria were determined using multivariate logistic regression and presented as an odds ratio. Microalbuminuria and macroalbuminuria were present in 33.3% and 12.7% of 222 patients (mean age 56.4 years, mean deviation of diabetes 8.6 years, 58.7% women, 43.8% obese), respectively. Factors significantly associated with microalbuminuria included glycemic control, insulin use, and total and LDL cholesterol. Those associated with macroalbuminuria included in addition to glycemic control and insulin use, duration of diabetes, hypertension, elevated mean arterial pressure (MAP), and presence of neuropathy, retinopathy and peripheral vascular disease by bivariate analysis. Only glycemic control was an independent risk factor for both in addition to MAP and retinopathy for macroalbuminuria by multivariate analysis. Albuminuria is highly prevalent among this cohort of diabetic patients in Lebanon. Both glycemic control and blood pressure need to be better targeted in its management.

Factors associated with Anaplasma spp. seroprevalence among dogs in the United States.

PubMed

McMahan, Christopher S; Wang, Dongmei; Beall, Melissa J; Bowman, Dwight D; Little, Susan E; Pithua, Patrick O; Sharp, Julia L; Stich, Roger W; Yabsley, Michael J; Lund, Robert B

2016-03-22

Dogs in the United States are hosts to a diverse range of ticks and tick-borne pathogens, including A. phagocytophilum, an important emerging canine and human pathogen. Previously, a Companion Animal Parasite Council (CAPC)-sponsored workshop proposed factors purported to be associated with the infection risk for tick-transmitted pathogens in dogs in the United States, including climate conditions, socioeconomic characteristics, local topography, and vector distribution. Approximately four million test results from routine veterinary diagnostic tests from 2011-2013, which were collected on a county level across the contiguous United States, are statistically analyzed with the proposed factors via logistic regression and generalized estimating equations. Spatial prevalence maps of baseline Anaplasma spp. prevalence are constructed from Kriging and head-banging smoothing methods. All of the examined factors, with the exception of surface water coverage, were significantly associated with Anaplasma spp. prevalence. Overall, Anaplasma spp. prevalence increases with increasing precipitation and forestation coverage and decreases with increasing temperature, population density, relative humidity, and elevation. Interestingly, socioeconomic status and deer/vehicle collisions were positively and negatively correlated with canine Anaplasma seroprevalence, respectively. A spatial map of the canine Anaplasma hazard is an auxiliary product of the analysis. Anaplasma spp. prevalence is highest in New England and the Upper Midwest. The results from the two posited statistical models (one that contains an endemic areas assumption and one that does not) are in general agreement, with the major difference being that the endemic areas model estimates a larger prevalence in Western Texas, New Mexico, and Colorado. As A. phagocytophilum is zoonotic, the results of this analysis could also help predict areas of high risk for human exposure to this pathogen.

Deprivation Indices, Population Health and Geography: An Evaluation of the Spatial Effectiveness of Indices at Multiple Scales

PubMed Central

Bell, Nathaniel; Dunn, James R.; Oliver, Lisa

2007-01-01

Area-based deprivation indices (ABDIs) have become a common tool with which to investigate the patterns and magnitude of socioeconomic inequalities in health. ABDIs are also used as a proxy for individual socioeconomic status. Despite their widespread use, comparably less attention has been focused on their geographic variability and practical concerns surrounding the Modifiable Area Unit Problem (MAUP) than on the individual attributes that make up the indices. Although scale is increasingly recognized as an important factor in interpreting mapped results among population health researchers, less attention has been paid specifically to ABDI and scale. In this paper, we highlight the effect of scale on indices by mapping ABDIs at multiple census scales in an urban area. In addition, we compare self-rated health data from the Canadian Community Health Survey with ABDIs at two census scales. The results of our analysis confirm the influence of spatial extent and scale on mapping population health—with potential implications for health policy implementation and resource distribution. PMID:17447145

Analysis of Ricefield Land Damage in Denpasar City, Bali, Indonesia

NASA Astrophysics Data System (ADS)

Suyarto, R.; Wiyanti; Dibia, I. N.

2018-02-01

Soil as a natural resource, living area, environmental media, and factors of production including biomass production that supports human life and other living beings must be preserved, on the other hand, uncontrolled biomass production activities can cause soil damage, ultimately can threaten the survival of humans and other living things. Therefore, in order to control soil damage, first must inventories the soil condition data and its damage which then visualised in soil damage potential and soil damage status. The activities of the study are the preparation of a map of the initial soil conditions and the delineation of potentially land degradation distribution. Mapping results are used as work maps for verification on the field to take soil samples and create soil damage status. In general, Denpasar City have soil damage potential at very low, low until medium rate. Soil damage status in Denpasar City generally is low damage of bulk volume, total porosity, soil permeability and electrolyte conductivity which beyond limitation thresholds.

Usage of multivariate geostatistics in interpolation processes for meteorological precipitation maps

NASA Astrophysics Data System (ADS)

Gundogdu, Ismail Bulent

2017-01-01

Long-term meteorological data are very important both for the evaluation of meteorological events and for the analysis of their effects on the environment. Prediction maps which are constructed by different interpolation techniques often provide explanatory information. Conventional techniques, such as surface spline fitting, global and local polynomial models, and inverse distance weighting may not be adequate. Multivariate geostatistical methods can be more significant, especially when studying secondary variables, because secondary variables might directly affect the precision of prediction. In this study, the mean annual and mean monthly precipitations from 1984 to 2014 for 268 meteorological stations in Turkey have been used to construct country-wide maps. Besides linear regression, the inverse square distance and ordinary co-Kriging (OCK) have been used and compared to each other. Also elevation, slope, and aspect data for each station have been taken into account as secondary variables, whose use has reduced errors by up to a factor of three. OCK gave the smallest errors (1.002 cm) when aspect was included.

Kilometer-scale topographic roughness of Mercury: Correlation with geologic features and units

NASA Astrophysics Data System (ADS)

Kreslavsky, Mikhail A.; Head, James W.; Neumann, Gregory A.; Zuber, Maria T.; Smith, David E.

2014-12-01

We present maps of the topographic roughness of the northern circumpolar area of 30 Mercury at kilometer scales. The maps are derived from range profiles obtained by the 31 Mercury Laser Altimeter (MLA) instrument onboard the MErcury Surface, Space 32 ENvironment, Geochemistry, and Ranging (MESSENGER) mission. As measures of 33 roughness, we used the interquartile range of profile curvature at three baselines: 0.7 km, 34 2.8 km, and 11 km. The maps provide a synoptic overview of variations of typical 35 topographic textures. They show a dichotomy between the smooth northern plains and 36 rougher, more heavily cratered terrains. Analysis of the scale dependence of roughness 37 indicates that the regolith on Mercury is thicker than on the Moon by approximately a 38 factor of three. Roughness contrasts within northern volcanic plains of Mercury indicate a 39 younger unit inside Goethe basin and inside another unnamed stealth basin. These new 40 data permit interplanetary comparisons of topographic roughness.

Flood inundation extent mapping based on block compressed tracing

NASA Astrophysics Data System (ADS)

Shen, Dingtao; Rui, Yikang; Wang, Jiechen; Zhang, Yu; Cheng, Liang

2015-07-01

Flood inundation extent, depth, and duration are important factors affecting flood hazard evaluation. At present, flood inundation analysis is based mainly on a seeded region-growing algorithm, which is an inefficient process because it requires excessive recursive computations and it is incapable of processing massive datasets. To address this problem, we propose a block compressed tracing algorithm for mapping the flood inundation extent, which reads the DEM data in blocks before transferring them to raster compression storage. This allows a smaller computer memory to process a larger amount of data, which solves the problem of the regular seeded region-growing algorithm. In addition, the use of a raster boundary tracing technique allows the algorithm to avoid the time-consuming computations required by the seeded region-growing. Finally, we conduct a comparative evaluation in the Chin-sha River basin, results show that the proposed method solves the problem of flood inundation extent mapping based on massive DEM datasets with higher computational efficiency than the original method, which makes it suitable for practical applications.

Spatial Analysis in Determining Physical Factors of Pedestrian Space Livability, Case Study: Pedestrian Space on Jalan Kemasan, Yogyakarta

NASA Astrophysics Data System (ADS)

Fauzi, A. F.; Aditianata, A.

2018-02-01

The existence of street as a place to perform various human activities becomes an important issue nowadays. In the last few decades, cars and motorcycles dominate streets in various cities in the world. On the other hand, human activity on the street is the determinant of the city livability. Previous research has pointed out that if there is lots of human activity in the street, then the city will be interesting. Otherwise, if the street has no activity, then the city will be boring. Learning from that statement, now various cities in the world are developing the concept of livable streets. Livable streets shown by diversity of human activities conducted in the streets’ pedestrian space. In Yogyakarta, one of the streets shown diversity of human activities is Jalan Kemasan. This study attempts to determine the physical factors of pedestrian space affecting the livability in Jalan Kemasan Yogyakarta through spatial analysis. Spatial analysis was performed by overlay technique between liveable point (activity diversity) distribution map and variable distribution map. Those physical pedestrian space research variable included element of shading, street vendors, building setback, seat location, divider between street and pedestrian way, and mixed use building function. More diverse the activity of one variable, then those variable are more affected then others. Overlay result then strengthened by field observation to qualitatively ensure the deduction. In the end, this research will provide valuable input for street and pedestrian space planning that is comfortable for human activities.

Replace-approximation method for ambiguous solutions in factor analysis of ultrasonic hepatic perfusion

NASA Astrophysics Data System (ADS)

Zhang, Ji; Ding, Mingyue; Yuchi, Ming; Hou, Wenguang; Ye, Huashan; Qiu, Wu

2010-03-01

Factor analysis is an efficient technique to the analysis of dynamic structures in medical image sequences and recently has been used in contrast-enhanced ultrasound (CEUS) of hepatic perfusion. Time-intensity curves (TICs) extracted by factor analysis can provide much more diagnostic information for radiologists and improve the diagnostic rate of focal liver lesions (FLLs). However, one of the major drawbacks of factor analysis of dynamic structures (FADS) is nonuniqueness of the result when only the non-negativity criterion is used. In this paper, we propose a new method of replace-approximation based on apex-seeking for ambiguous FADS solutions. Due to a partial overlap of different structures, factor curves are assumed to be approximately replaced by the curves existing in medical image sequences. Therefore, how to find optimal curves is the key point of the technique. No matter how many structures are assumed, our method always starts to seek apexes from one-dimensional space where the original high-dimensional data is mapped. By finding two stable apexes from one dimensional space, the method can ascertain the third one. The process can be continued until all structures are found. This technique were tested on two phantoms of blood perfusion and compared to the two variants of apex-seeking method. The results showed that the technique outperformed two variants in comparison of region of interest measurements from phantom data. It can be applied to the estimation of TICs derived from CEUS images and separation of different physiological regions in hepatic perfusion.

Modelling the habitat suitability of cetaceans: Example of the sperm whale in the northwestern Mediterranean Sea

NASA Astrophysics Data System (ADS)

Praca, Emilie; Gannier, Alexandre; Das, Krishna; Laran, Sophie

2009-04-01

Cetaceans are mobile and spend long periods underwater. Because of this, modelling their habitat could be subject to a serious problem of false absence. Furthermore, extensive surveys at sea are time and money consuming, and presence-absence data are difficult to apply. This study compares the ability of two presence-absence and two presence-only habitat modelling methods and uses the example of the sperm whale ( Physeter macrocephalus) in the northwestern Mediterranean Sea. The data consist of summer visual and acoustical detections of sperm whales, compiled between 1998 and 2005. Habitat maps were computed using topographical and hydrological eco-geographical variables. Four methods were compared: principal component analysis (PCA), ecological niche factor analysis (ENFA), generalized linear model (GLM) and multivariate adaptive regression splines (MARS). The evaluation of the models was achieved by calculating the receiver operating characteristic (ROC) of the models and their respective area under the curve (AUC). Presence-absence methods (GLM, AUC=0.70, and MARS, AUC=0.79) presented better AUC than presence-only methods (PCA, AUC=0.58, and ENFA, AUC=0.66), but this difference was not statistically significant, except between the MARS and the PCA models. The four models showed an influence of both topographical and hydrological factors, but the resulting habitat suitability maps differed. The core habitat on the continental slope was well highlighted by the four models, while GLM and MARS maps also showed a suitable habitat in the offshore waters. Presence-absence methods are therefore recommended for modelling the habitat suitability of cetaceans, as they seem more accurate to highlight complex habitat. However, the use of presence-only techniques, in particular ENFA, could be very useful for a first model of the habitat range or when important surveys at sea are not possible.

Towards a standardized nutrition and dietetics terminology for clinical practice: An Austrian multicenter clinical documentation analysis based on the International Classification of Functioning, Disability and Health (ICF)-Dietetics.

PubMed

Gäbler, Gabriele; Coenen, Michaela; Lycett, Deborah; Stamm, Tanja

2018-03-03

High quality, continuity and safe interdisciplinary healthcare is essential. Nutrition and dietetics plays an important part within the interdisciplinary team in many health conditions. In order to work more effectively as an interdisciplinary team, a common terminology is needed. This study investigates which categories of the ICF-Dietetics are used in clinical dietetic care records in Austria and which are most relevant to shared language in different medical areas. A national multicenter retrospective study was conducted to collect clinical dietetic care documentation reports. The analysis included the "best fit" framework synthesis, and a mapping exercise using the ICF Linking Rules. Medical diagnosis and intervention concepts were excluded from the mapping, since they are not supposed to be classified by the ICF. From 100 dietetic records, 307 concepts from 1807 quotations were extracted. Of these, 241 assessment, dietetics diagnosis, goal setting and evaluation concepts were linked to 153 ICF-Dietetics categories. The majority (91.3%) could be mapped to a precise ICF-Dietetics category. The highest number of ICF-Dietetics categories was found in the medical area of diabetes and metabolism and belonged to the ICF component Body Function, while very few categories were used from the component Participation and Environmental Factors. The integration of the ICF-Dietetics in nutrition and dietetic care process is possible. Moreover, it could be considered as a conceptual framework for interdisciplinary nutrition and dietetics care. However, a successful implementation of the ICF-Dietetics in clinical practice requires a paradigm shift from medical diagnosis-focused health care to a holistic perspective of functioning with more attention on Participation and Environmental Factors. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms.

PubMed

N'Diaye, Amidou; Haile, Jemanesh K; Fowler, D Brian; Ammar, Karim; Pozniak, Curtis J

2017-01-01

Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called 'large p, small n' problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly.

Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms

PubMed Central

N’Diaye, Amidou; Haile, Jemanesh K.; Fowler, D. Brian; Ammar, Karim; Pozniak, Curtis J.

2017-01-01

Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called ‘large p, small n’ problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly. PMID:28878789

Nasa's Planetary Geologic Mapping Program: Overview

NASA Astrophysics Data System (ADS)

Williams, D. A.

2016-06-01

NASA's Planetary Science Division supports the geologic mapping of planetary surfaces through a distinct organizational structure and a series of research and analysis (R&A) funding programs. Cartography and geologic mapping issues for NASA's planetary science programs are overseen by the Mapping and Planetary Spatial Infrastructure Team (MAPSIT), which is an assessment group for cartography similar to the Mars Exploration Program Assessment Group (MEPAG) for Mars exploration. MAPSIT's Steering Committee includes specialists in geological mapping, who make up the Geologic Mapping Subcommittee (GEMS). I am the GEMS Chair, and with a group of 3-4 community mappers we advise the U.S. Geological Survey Planetary Geologic Mapping Coordinator (Dr. James Skinner) and develop policy and procedures to aid the planetary geologic mapping community. GEMS meets twice a year, at the Annual Lunar and Planetary Science Conference in March, and at the Annual Planetary Mappers' Meeting in June (attendance is required by all NASA-funded geologic mappers). Funding programs under NASA's current R&A structure to propose geological mapping projects include Mars Data Analysis (Mars), Lunar Data Analysis (Moon), Discovery Data Analysis (Mercury, Vesta, Ceres), Cassini Data Analysis (Saturn moons), Solar System Workings (Venus or Jupiter moons), and the Planetary Data Archiving, Restoration, and Tools (PDART) program. Current NASA policy requires all funded geologic mapping projects to be done digitally using Geographic Information Systems (GIS) software. In this presentation we will discuss details on how geologic mapping is done consistent with current NASA policy and USGS guidelines.

High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut.

PubMed

Agarwal, Gaurav; Clevenger, Josh; Pandey, Manish K; Wang, Hui; Shasidhar, Yaduru; Chu, Ye; Fountain, Jake C; Choudhary, Divya; Culbreath, Albert K; Liu, Xin; Huang, Guodong; Wang, Xingjun; Deshmukh, Rupesh; Holbrook, C Corley; Bertioli, David J; Ozias-Akins, Peggy; Jackson, Scott A; Varshney, Rajeev K; Guo, Baozhu

2018-04-10

Whole-genome resequencing (WGRS) of mapping populations has facilitated development of high-density genetic maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases in peanut causing significant yield loss. We generated WGRS data on a recombinant inbred line population, developed a SNP-based high-density genetic map, and conducted fine mapping, candidate gene discovery and marker validation for ELS, LLS and TSWV. The first sequence-based high-density map was constructed with 8869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the 'T' population (Tifrunner × GT-C20) with a map length of 3120 cM and an average distance of 1.45 cM. The quantitative trait locus (QTL) analysis using high-density genetic map and multiple season phenotyping data identified 35 main-effect QTLs with phenotypic variation explained (PVE) from 6.32% to 47.63%. Among major-effect QTLs mapped, there were two QTLs for ELS on B05 with 47.42% PVE and B03 with 47.38% PVE, two QTLs for LLS on A05 with 47.63% and B03 with 34.03% PVE and one QTL for TSWV on B09 with 40.71% PVE. The epistasis and environment interaction analyses identified significant environmental effects on these traits. The identified QTL regions had disease resistance genes including R-genes and transcription factors. KASP markers were developed for major QTLs and validated in the population and are ready for further deployment in genomics-assisted breeding in peanut. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

GIS and the Analytic Hierarchy Process for Regional Landfill Site Selection in Transitional Countries: A Case Study From Serbia

NASA Astrophysics Data System (ADS)

Zelenović Vasiljević, Tamara; Srdjević, Zorica; Bajčetić, Ratko; Vojinović Miloradov, Mirjana

2012-02-01

The Serbian National Waste Management Strategy for the Period 2010-2019, harmonized with the European Union Directives, mandates new and very strict requirements for landfill sites. To enable analysis of a number of required qualitative and quantitative factors for landfill site selection, the traditional method of site selection must be replaced with a new approach. The combination of GIS and the Analytic Hierarchy Process (AHP) was selected to solve this complex problem. The Srem region in northern Serbia, being one of the most environmentally sensitive areas, was chosen as a case study. Seventeen factors selected as criteria/sub-criteria were recognized as most important, divided into geo-natural, environmental, social and techno-economic factors, and were evaluated by experts from different fields using an AHP extension in Arc GIS. Weighted spatial layers were combined into a landfill suitability map which was then overlapped with four restriction maps, resulting in a final suitability map. According to the results, 82.65% of the territory of Srem is unsuitable for regional landfill siting. The most suitable areas cover 9.14%, suitable areas 5.24%, while areas with low and very low suitability cover 2.21 and 0.76% of the territory, respectively. Based on these findings, five sites close to two large urban agglomerations were suggested as possible locations for a regional landfill site in Srem. However, the final decision will require further field investigation, a public acceptance survey, and consideration of ownership status and price of the land.

Mapping Regional Drought Vulnerability: a Case Study

NASA Astrophysics Data System (ADS)

Karamouz, M.; Zeynolabedin, A.; Olyaei, M. A.

2015-12-01

Drought is among the natural disaster that causes damages and affects many people's life in many part of the world including in Iran. Recently, some factors such as climate variability and the impact of climate change have influenced drought frequency and intensity in many parts of the world. Drought can be divided into four categories of meteorological, hydrological, agricultural and social-economic. In meteorological the important feature is lack of rainfall. In hydrological drought river flows and dam storage are considered. Lack of soil moisture is the key factor in agricultural droughts while in social-economic type of drought the relation between supply and demand and social-economic damages due to water deficiency is studied. While the first three types relates to the lack of some hydrological characteristics, social-economic type of drought is actually the consequence of other types expressed in monetary values. Many indices are used in assessing drought; each has its own advantages and disadvantages and can be used for specific types of drought. Therefore knowing the types of drought can provide a better understanding of shortages and their characteristics. Drought vulnerability is a concept which shows the likelihood of damages from hazard in a particular place by focusing on the system status prior to the disaster. Drought vulnerability has been viewed as a potential for losses in the region due to water deficiency at the time of drought. In this study the application of vulnerability concept in drought management in East Azarbaijan province in Iran is investigated by providing vulnerability maps which demonstrates spatial characteristics of drought vulnerability. In the first step, certain governing parameters in drought analysis such as precipitation, temperature, land use, topography, solar radiation and ground water elevation have been investigated in the region. They are described in details and calculated in suitable time series. Vulnerabilities are ranked in 5 intervals and for each parameter vulnerability maps are prepared in GIS environment. Selection of theses parameters are based on factors such as regional features and availability of data. Considering the fact that the aforementioned parameters have different level of importance in vulnerability maps, different weights are assigned to the parameters considering how critical each parameter is in the overall drought analysis. Expert's opinion is selected in assigning weights. A multi-criteria decision making (MCDM) framework is used to check the consistency of the provided information. Then the weighted maps are overlaid to find the overall vulnerability map. The map shows very low, low, medium, intense and very intense regional vulnerabilities. According to the results, the west part of East Azarbaijan province is the most vulnerable region to drought which is expected due to the vicinity of this part to Urumia Lake that has been lost most of its water during the last decades. The least vulnerable part seems to be the Eastern part of the province with longer lasting resources. Taking into consideration that Caspian Sea is near this part with high precipitation record, the outcome of this study is in line with the general expectations. The result of this study can be used for preparedness planning and for allocating resources for facing droughts in this region.

FACETS: using open data to measure community social determinants of health.

PubMed

Cantor, Michael N; Chandras, Rajan; Pulgarin, Claudia

2018-04-01

To develop a dataset based on open data sources reflective of community-level social determinants of health (SDH). We created FACETS (Factors Affecting Communities and Enabling Targeted Services), an architecture that incorporates open data related to SDH into a single dataset mapped at the census-tract level for New York City. FACETS (https://github.com/mcantor2/FACETS) can be easily used to map individual addresses to their census-tract-level SDH. This dataset facilitates analysis across different determinants that are often not easily accessible. Wider access to open data from government agencies at the local, state, and national level would facilitate the aggregation and analysis of community-level determinants. Timeliness of updates to federal non-census data sources may limit their usefulness. FACETS is an important first step in standardizing and compiling SDH-related data in an open architecture that can give context to a patient's condition and enable better decision-making when developing a plan of care.

On the Usage of GPUs for Efficient Motion Estimation in Medical Image Sequences

PubMed Central

Thiyagalingam, Jeyarajan; Goodman, Daniel; Schnabel, Julia A.; Trefethen, Anne; Grau, Vicente

2011-01-01

Images are ubiquitous in biomedical applications from basic research to clinical practice. With the rapid increase in resolution, dimensionality of the images and the need for real-time performance in many applications, computational requirements demand proper exploitation of multicore architectures. Towards this, GPU-specific implementations of image analysis algorithms are particularly promising. In this paper, we investigate the mapping of an enhanced motion estimation algorithm to novel GPU-specific architectures, the resulting challenges and benefits therein. Using a database of three-dimensional image sequences, we show that the mapping leads to substantial performance gains, up to a factor of 60, and can provide near-real-time experience. We also show how architectural peculiarities of these devices can be best exploited in the benefit of algorithms, most specifically for addressing the challenges related to their access patterns and different memory configurations. Finally, we evaluate the performance of the algorithm on three different GPU architectures and perform a comprehensive analysis of the results. PMID:21869880

A comparative interregional analysis of selected data from LANDSAT-1 and EREP for the inventory and monitoring of natural ecosystems

NASA Technical Reports Server (NTRS)

Poulton, C. E.

1975-01-01

Comparative statistics were presented on the capability of LANDSAT-1 and three of the Skylab remote sensing systems (S-190A, S-190B, S-192) for the recognition and inventory of analogous natural vegetations and landscape features important in resource allocation and management. Two analogous regions presenting vegetational zonation from salt desert to alpine conditions above the timberline were observed, emphasizing the visual interpretation mode in the investigation. An hierarchical legend system was used as the basic classification of all land surface features. Comparative tests were run on image identifiability with the different sensor systems, and mapping and interpretation tests were made both in monocular and stereo interpretation with all systems except the S-192. Significant advantage was found in the use of stereo from space when image analysis is by visual or visual-machine-aided interactive systems. Some cost factors in mapping from space are identified. The various image types are compared and an operational system is postulated.

Decoding the Regulatory Network for Blood Development from Single-Cell Gene Expression Measurements

PubMed Central

Haghverdi, Laleh; Lilly, Andrew J.; Tanaka, Yosuke; Wilkinson, Adam C.; Buettner, Florian; Macaulay, Iain C.; Jawaid, Wajid; Diamanti, Evangelia; Nishikawa, Shin-Ichi; Piterman, Nir; Kouskoff, Valerie; Theis, Fabian J.; Fisher, Jasmin; Göttgens, Berthold

2015-01-01

Here we report the use of diffusion maps and network synthesis from state transition graphs to better understand developmental pathways from single cell gene expression profiling. We map the progression of mesoderm towards blood in the mouse by single-cell expression analysis of 3,934 cells, capturing cells with blood-forming potential at four sequential developmental stages. By adapting the diffusion plot methodology for dimensionality reduction to single-cell data, we reconstruct the developmental journey to blood at single-cell resolution. Using transitions between individual cellular states as input, we develop a single-cell network synthesis toolkit to generate a computationally executable transcriptional regulatory network model that recapitulates blood development. Model predictions were validated by showing that Sox7 inhibits primitive erythropoiesis, and that Sox and Hox factors control early expression of Erg. We therefore demonstrate that single-cell analysis of a developing organ coupled with computational approaches can reveal the transcriptional programs that control organogenesis. PMID:25664528

Asset Mapping: A Course Assignment and Community Assessment

ERIC Educational Resources Information Center

Crozier, Mary; Melchior, Florence

2013-01-01

Asset mapping is a relatively new data collection strategy to identify services, staff capacity, programs, resources, values, and other protective factors in a geographic area that can be juxtaposed to risk factors when initiating community planning. A substance abuse prevention course for undergraduates added an assignment of assessing community…

Human factors considerations for the integration of traffic information and alerts on an airport surface map

DOT National Transportation Integrated Search

2010-12-01

The purpose of this document is to provide human factors considerations in the integration of traffic information and indications and alerts for runway status on an airport surface moving map. The US DOT Volpe Center, in support of the Federal Aviati...

Alzheimer's disease master regulators analysis: search for potential molecular targets and drug repositioning candidates.

PubMed

Vargas, D M; De Bastiani, M A; Zimmer, E R; Klamt, F

2018-06-23

Alzheimer's disease (AD) is a multifactorial and complex neuropathology that involves impairment of many intricate molecular mechanisms. Despite recent advances, AD pathophysiological characterization remains incomplete, which hampers the development of effective treatments. In fact, currently, there are no effective pharmacological treatments for AD. Integrative strategies such as transcription regulatory network and master regulator analyses exemplify promising new approaches to study complex diseases and may help in the identification of potential pharmacological targets. In this study, we used transcription regulatory network and master regulator analyses on transcriptomic data of human hippocampus to identify transcription factors (TFs) that can potentially act as master regulators in AD. All expression profiles were obtained from the Gene Expression Omnibus database using the GEOquery package. A normal hippocampus transcription factor-centered regulatory network was reconstructed using the ARACNe algorithm. Master regulator analysis and two-tail gene set enrichment analysis were employed to evaluate the inferred regulatory units in AD case-control studies. Finally, we used a connectivity map adaptation to prospect new potential therapeutic interventions by drug repurposing. We identified TFs with already reported involvement in AD, such as ATF2 and PARK2, as well as possible new targets for future investigations, such as CNOT7, CSRNP2, SLC30A9, and TSC22D1. Furthermore, Connectivity Map Analysis adaptation suggested the repositioning of six FDA-approved drugs that can potentially modulate master regulator candidate regulatory units (Cefuroxime, Cyproterone, Dydrogesterone, Metrizamide, Trimethadione, and Vorinostat). Using a transcription factor-centered regulatory network reconstruction we were able to identify several potential molecular targets and six drug candidates for repositioning in AD. Our study provides further support for the use of bioinformatics tools as exploratory strategies in neurodegenerative diseases research, and also provides new perspectives on molecular targets and drug therapies for future investigation and validation in AD.

Dynamic Proteomic Analysis of Pancreatic Mesenchyme Reveals Novel Factors That Enhance Human Embryonic Stem Cell to Pancreatic Cell Differentiation.

PubMed

Russ, Holger A; Landsman, Limor; Moss, Christopher L; Higdon, Roger; Greer, Renee L; Kaihara, Kelly; Salamon, Randy; Kolker, Eugene; Hebrok, Matthias

2016-01-01

Current approaches in human embryonic stem cell (hESC) to pancreatic beta cell differentiation have largely been based on knowledge gained from developmental studies of the epithelial pancreas, while the potential roles of other supporting tissue compartments have not been fully explored. One such tissue is the pancreatic mesenchyme that supports epithelial organogenesis throughout embryogenesis. We hypothesized that detailed characterization of the pancreatic mesenchyme might result in the identification of novel factors not used in current differentiation protocols. Supplementing existing hESC differentiation conditions with such factors might create a more comprehensive simulation of normal development in cell culture. To validate our hypothesis, we took advantage of a novel transgenic mouse model to isolate the pancreatic mesenchyme at distinct embryonic and postnatal stages for subsequent proteomic analysis. Refined sample preparation and analysis conditions across four embryonic and prenatal time points resulted in the identification of 21,498 peptides with high-confidence mapping to 1,502 proteins. Expression analysis of pancreata confirmed the presence of three potentially important factors in cell differentiation: Galectin-1 (LGALS1), Neuroplastin (NPTN), and the Laminin α-2 subunit (LAMA2). Two of the three factors (LGALS1 and LAMA2) increased expression of pancreatic progenitor transcript levels in a published hESC to beta cell differentiation protocol. In addition, LAMA2 partially blocks cell culture induced beta cell dedifferentiation. Summarily, we provide evidence that proteomic analysis of supporting tissues such as the pancreatic mesenchyme allows for the identification of potentially important factors guiding hESC to pancreas differentiation.

Dynamic Proteomic Analysis of Pancreatic Mesenchyme Reveals Novel Factors That Enhance Human Embryonic Stem Cell to Pancreatic Cell Differentiation

PubMed Central

Russ, Holger A.; Landsman, Limor; Moss, Christopher L.; Higdon, Roger; Greer, Renee L.; Kaihara, Kelly; Salamon, Randy; Kolker, Eugene; Hebrok, Matthias

2016-01-01

Current approaches in human embryonic stem cell (hESC) to pancreatic beta cell differentiation have largely been based on knowledge gained from developmental studies of the epithelial pancreas, while the potential roles of other supporting tissue compartments have not been fully explored. One such tissue is the pancreatic mesenchyme that supports epithelial organogenesis throughout embryogenesis. We hypothesized that detailed characterization of the pancreatic mesenchyme might result in the identification of novel factors not used in current differentiation protocols. Supplementing existing hESC differentiation conditions with such factors might create a more comprehensive simulation of normal development in cell culture. To validate our hypothesis, we took advantage of a novel transgenic mouse model to isolate the pancreatic mesenchyme at distinct embryonic and postnatal stages for subsequent proteomic analysis. Refined sample preparation and analysis conditions across four embryonic and prenatal time points resulted in the identification of 21,498 peptides with high-confidence mapping to 1,502 proteins. Expression analysis of pancreata confirmed the presence of three potentially important factors in cell differentiation: Galectin-1 (LGALS1), Neuroplastin (NPTN), and the Laminin α-2 subunit (LAMA2). Two of the three factors (LGALS1 and LAMA2) increased expression of pancreatic progenitor transcript levels in a published hESC to beta cell differentiation protocol. In addition, LAMA2 partially blocks cell culture induced beta cell dedifferentiation. Summarily, we provide evidence that proteomic analysis of supporting tissues such as the pancreatic mesenchyme allows for the identification of potentially important factors guiding hESC to pancreas differentiation. PMID:26681951

Sparse multivariate factor analysis regression models and its applications to integrative genomics analysis.

PubMed

Zhou, Yan; Wang, Pei; Wang, Xianlong; Zhu, Ji; Song, Peter X-K

2017-01-01

The multivariate regression model is a useful tool to explore complex associations between two kinds of molecular markers, which enables the understanding of the biological pathways underlying disease etiology. For a set of correlated response variables, accounting for such dependency can increase statistical power. Motivated by integrative genomic data analyses, we propose a new methodology-sparse multivariate factor analysis regression model (smFARM), in which correlations of response variables are assumed to follow a factor analysis model with latent factors. This proposed method not only allows us to address the challenge that the number of association parameters is larger than the sample size, but also to adjust for unobserved genetic and/or nongenetic factors that potentially conceal the underlying response-predictor associations. The proposed smFARM is implemented by the EM algorithm and the blockwise coordinate descent algorithm. The proposed methodology is evaluated and compared to the existing methods through extensive simulation studies. Our results show that accounting for latent factors through the proposed smFARM can improve sensitivity of signal detection and accuracy of sparse association map estimation. We illustrate smFARM by two integrative genomics analysis examples, a breast cancer dataset, and an ovarian cancer dataset, to assess the relationship between DNA copy numbers and gene expression arrays to understand genetic regulatory patterns relevant to the disease. We identify two trans-hub regions: one in cytoband 17q12 whose amplification influences the RNA expression levels of important breast cancer genes, and the other in cytoband 9q21.32-33, which is associated with chemoresistance in ovarian cancer. © 2016 WILEY PERIODICALS, INC.

CrowdMapping: A Crowdsourcing-Based Terminology Mapping Method for Medical Data Standardization.

PubMed

Mao, Huajian; Chi, Chenyang; Huang, Boyu; Meng, Haibin; Yu, Jinghui; Zhao, Dongsheng

2017-01-01

Standardized terminology is the prerequisite of data exchange in analysis of clinical processes. However, data from different electronic health record systems are based on idiosyncratic terminology systems, especially when the data is from different hospitals and healthcare organizations. Terminology standardization is necessary for the medical data analysis. We propose a crowdsourcing-based terminology mapping method, CrowdMapping, to standardize the terminology in medical data. CrowdMapping uses a confidential model to determine how terminologies are mapped to a standard system, like ICD-10. The model uses mappings from different health care organizations and evaluates the diversity of the mapping to determine a more sophisticated mapping rule. Further, the CrowdMapping model enables users to rate the mapping result and interact with the model evaluation. CrowdMapping is a work-in-progress system, we present initial results mapping terminologies.

Placental growth factor (PlGF) is a surrogate marker in preeclamptic hypertension.

PubMed

Teixeira, Patrícia Gonçalves; Cabral, Antônio Carlos Vieira; Andrade, Silvia Passos; Reis, Zilma Silveira Nogueira; da Cruz, Lívia Pieroni Barroso; Pereira, Jacqueline Braga; Martins, Breno Oliveira de Barcelos; Rezende, Cezar Alencar de Lima

2008-01-01

To evaluate plasma levels of angiogenic factors and their association with preeclampsia. Twenty-three women with preeclampsia and nine normotensive pregnant women from the Maternity of Hospital das Clínicas of Belo Horizonte/MG-Brazil were assessed by National High Blood Pressure Education Program Working Group Creteria (NHBPEPWG). The plasma levels of vascular endothelial growth factor (VEGF) and Placental growth factor (PlGF) were determined by ELISA assay. Plasma concentration of PlGF was 12-fold lower in preeclampsia versus non preeclampsia pregnancies. An inverse correlation was observed between PlGF plasma levels and mean arterial pressure (MAP); a decrease in 1pg/mL of PlGF resulted in 6.18 mm Hg increase in MAP. These results indicate that PlGF is related to MAP in pregnant women.

Genome-Wide Investigation and Expression Profiling of AP2/ERF Transcription Factor Superfamily in Foxtail Millet (Setaria italica L.)

PubMed Central

Lata, Charu; Mishra, Awdhesh Kumar; Muthamilarasan, Mehanathan; Bonthala, Venkata Suresh; Khan, Yusuf; Prasad, Manoj

2014-01-01

The APETALA2/ethylene-responsive element binding factor (AP2/ERF) family is one of the largest transcription factor (TF) families in plants that includes four major sub-families, namely AP2, DREB (dehydration responsive element binding), ERF (ethylene responsive factors) and RAV (Related to ABI3/VP). AP2/ERFs are known to play significant roles in various plant processes including growth and development and biotic and abiotic stress responses. Considering this, a comprehensive genome-wide study was conducted in foxtail millet (Setaria italica L.). A total of 171 AP2/ERF genes were identified by systematic sequence analysis and were physically mapped onto nine chromosomes. Phylogenetic analysis grouped AP2/ERF genes into six classes (I to VI). Duplication analysis revealed that 12 (∼7%) SiAP2/ERF genes were tandem repeated and 22 (∼13%) were segmentally duplicated. Comparative physical mapping between foxtail millet AP2/ERF genes and its orthologs of sorghum (18 genes), maize (14 genes), rice (9 genes) and Brachypodium (6 genes) showed the evolutionary insights of AP2/ERF gene family and also the decrease in orthology with increase in phylogenetic distance. The evolutionary significance in terms of gene-duplication and divergence was analyzed by estimating synonymous and non-synonymous substitution rates. Expression profiling of candidate AP2/ERF genes against drought, salt and phytohormones revealed insights into their precise and/or overlapping expression patterns which could be responsible for their functional divergence in foxtail millet. The study showed that the genes SiAP2/ERF-069, SiAP2/ERF-103 and SiAP2/ERF-120 may be considered as potential candidate genes for further functional validation as well for utilization in crop improvement programs for stress resistance since these genes were up-regulated under drought and salinity stresses in ABA dependent manner. Altogether the present study provides new insights into evolution, divergence and systematic functional analysis of AP2/ERF gene family at genome level in foxtail millet which may be utilized for improving stress adaptation and tolerance in millets, cereals and bioenergy grasses. PMID:25409524

Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.).

PubMed

Lata, Charu; Mishra, Awdhesh Kumar; Muthamilarasan, Mehanathan; Bonthala, Venkata Suresh; Khan, Yusuf; Prasad, Manoj

2014-01-01

The APETALA2/ethylene-responsive element binding factor (AP2/ERF) family is one of the largest transcription factor (TF) families in plants that includes four major sub-families, namely AP2, DREB (dehydration responsive element binding), ERF (ethylene responsive factors) and RAV (Related to ABI3/VP). AP2/ERFs are known to play significant roles in various plant processes including growth and development and biotic and abiotic stress responses. Considering this, a comprehensive genome-wide study was conducted in foxtail millet (Setaria italica L.). A total of 171 AP2/ERF genes were identified by systematic sequence analysis and were physically mapped onto nine chromosomes. Phylogenetic analysis grouped AP2/ERF genes into six classes (I to VI). Duplication analysis revealed that 12 (∼7%) SiAP2/ERF genes were tandem repeated and 22 (∼13%) were segmentally duplicated. Comparative physical mapping between foxtail millet AP2/ERF genes and its orthologs of sorghum (18 genes), maize (14 genes), rice (9 genes) and Brachypodium (6 genes) showed the evolutionary insights of AP2/ERF gene family and also the decrease in orthology with increase in phylogenetic distance. The evolutionary significance in terms of gene-duplication and divergence was analyzed by estimating synonymous and non-synonymous substitution rates. Expression profiling of candidate AP2/ERF genes against drought, salt and phytohormones revealed insights into their precise and/or overlapping expression patterns which could be responsible for their functional divergence in foxtail millet. The study showed that the genes SiAP2/ERF-069, SiAP2/ERF-103 and SiAP2/ERF-120 may be considered as potential candidate genes for further functional validation as well for utilization in crop improvement programs for stress resistance since these genes were up-regulated under drought and salinity stresses in ABA dependent manner. Altogether the present study provides new insights into evolution, divergence and systematic functional analysis of AP2/ERF gene family at genome level in foxtail millet which may be utilized for improving stress adaptation and tolerance in millets, cereals and bioenergy grasses.

Large-scale De Novo Prediction of Physical Protein-Protein Association*

PubMed Central

Elefsinioti, Antigoni; Saraç, Ömer Sinan; Hegele, Anna; Plake, Conrad; Hubner, Nina C.; Poser, Ina; Sarov, Mihail; Hyman, Anthony; Mann, Matthias; Schroeder, Michael; Stelzl, Ulrich; Beyer, Andreas

2011-01-01

Information about the physical association of proteins is extensively used for studying cellular processes and disease mechanisms. However, complete experimental mapping of the human interactome will remain prohibitively difficult in the near future. Here we present a map of predicted human protein interactions that distinguishes functional association from physical binding. Our network classifies more than 5 million protein pairs predicting 94,009 new interactions with high confidence. We experimentally tested a subset of these predictions using yeast two-hybrid analysis and affinity purification followed by quantitative mass spectrometry. Thus we identified 462 new protein-protein interactions and confirmed the predictive power of the network. These independent experiments address potential issues of circular reasoning and are a distinctive feature of this work. Analysis of the physical interactome unravels subnetworks mediating between different functional and physical subunits of the cell. Finally, we demonstrate the utility of the network for the analysis of molecular mechanisms of complex diseases by applying it to genome-wide association studies of neurodegenerative diseases. This analysis provides new evidence implying TOMM40 as a factor involved in Alzheimer's disease. The network provides a high-quality resource for the analysis of genomic data sets and genetic association studies in particular. Our interactome is available via the hPRINT web server at: www.print-db.org. PMID:21836163

Assessment of the Eutrophication-Related Environmental Parameters in Two Mediterranean Lakes by Integrating Statistical Techniques and Self-Organizing Maps.

PubMed

Hadjisolomou, Ekaterini; Stefanidis, Konstantinos; Papatheodorou, George; Papastergiadou, Evanthia

2018-03-19

During the last decades, Mediterranean freshwater ecosystems, especially lakes, have been under severe pressure due to increasing eutrophication and water quality deterioration. In this article, we compared the effectiveness of different data analysis methods by assessing the contribution of environmental parameters to eutrophication processes. For this purpose, principal components analysis (PCA), cluster analysis, and a self-organizing map (SOM) were applied, using water quality data from two transboundary lakes of North Greece. SOM is considered as an advanced and powerful data analysis tool because of its ability to represent complex and nonlinear relationships among multivariate data sets. The results of PCA and cluster analysis agreed with the SOM results, although the latter provided more information because of the visualization abilities regarding the parameters' relationships. Besides nutrients that were found to be a key factor for controlling chlorophyll-a (Chl - a), water temperature was related positively with algal production, while the Secchi disk depth parameter was found to be highly important and negatively related toeutrophic conditions. In general, the SOM results were more specific and allowed direct associations between the water quality variables. Our work showed that SOMs can be used effectively in limnological studies to produce robust and interpretable results, aiding scientists and managers to cope with environmental problems such as eutrophication.

Competing Effects Between Screen Media Time and Physical Activity in Adolescent Girls: Clustering a Self-Organizing Maps Analysis.

PubMed

Valencia-Peris, Alexandra; Devís-Devís, José; García-Massó, Xavier; Lizandra, Jorge; Pérez-Gimeno, Esther; Peiró-Velert, Carmen

2016-06-01

Previous research shows contradictory findings on potential competing effects between sedentary screen media usage (SMU) and physical activity (PA). This study examined these effects on adolescent girls via self-organizing maps analysis focusing on 3 target profiles. A sample of 1,516 girls aged 12 to 18 years self-reported daily time engagement in PA (moderate and vigorous intensity) and in screen media activities (TV/video/DVD, computer, and videogames), separately and combined. Topological interrelationships from the 13 emerging maps indicated a moderate competing effect between physically active and sedentary SMU patterns. Higher SES and overweight status were linked to either active or inactive behaviors. Three target clusters were explored in more detail. Cluster 1, named temperate-media actives, showed capabilities of being active while engaging in a moderate level of SMU (TV/video/DVD mainly). In Cluster 2, named prudent-media inactives, and Cluster 3, compulsive-media inactives, a competing effect between SMU and PA emerged, being sedentary SMU behaviors responsible for a low involvement in active pursuits. SMU and PA emerge as both related and independent behaviors in girls, resulting in a moderate competing effect. Findings support the case for recommending the timing of PA and SMU for recreational purposes considering different profiles, sociodemographic factors and types of SMU.

Mapping the Structure-Function Relationship in Glaucoma and Healthy Patients Measured with Spectralis OCT and Humphrey Perimetry

PubMed Central

Muñoz–Negrete, Francisco J.; Oblanca, Noelia; Rebolleda, Gema

2018-01-01

Purpose To study the structure-function relationship in glaucoma and healthy patients assessed with Spectralis OCT and Humphrey perimetry using new statistical approaches. Materials and Methods Eighty-five eyes were prospectively selected and divided into 2 groups: glaucoma (44) and healthy patients (41). Three different statistical approaches were carried out: (1) factor analysis of the threshold sensitivities (dB) (automated perimetry) and the macular thickness (μm) (Spectralis OCT), subsequently applying Pearson's correlation to the obtained regions, (2) nonparametric regression analysis relating the values in each pair of regions that showed significant correlation, and (3) nonparametric spatial regressions using three models designed for the purpose of this study. Results In the glaucoma group, a map that relates structural and functional damage was drawn. The strongest correlation with visual fields was observed in the peripheral nasal region of both superior and inferior hemigrids (r = 0.602 and r = 0.458, resp.). The estimated functions obtained with the nonparametric regressions provided the mean sensitivity that corresponds to each given macular thickness. These functions allowed for accurate characterization of the structure-function relationship. Conclusions Both maps and point-to-point functions obtained linking structure and function damage contribute to a better understanding of this relationship and may help in the future to improve glaucoma diagnosis. PMID:29850196

Heat Wave Vulnerability Mapping for India.

PubMed

Azhar, Gulrez; Saha, Shubhayu; Ganguly, Partha; Mavalankar, Dileep; Madrigano, Jaime

2017-03-30

Assessing geographic variability in heat wave vulnerability forms the basis for planning appropriate targeted adaptation strategies. Given several recent deadly heatwaves in India, heat is increasingly being recognized as a public health problem. However, to date there has not been a country-wide assessment of heat vulnerability in India. We evaluated demographic, socioeconomic, and environmental vulnerability factors and combined district level data from several sources including the most recent census, health reports, and satellite remote sensing data. We then applied principal component analysis (PCA) on 17 normalized variables for each of the 640 districts to create a composite Heat Vulnerability Index (HVI) for India. Of the total 640 districts, our analysis identified 10 and 97 districts in the very high and high risk categories (> 2SD and 2-1SD HVI) respectively. Mapping showed that the districts with higher heat vulnerability are located in the central parts of the country. On examination, these are less urbanized and have low rates of literacy, access to water and sanitation, and presence of household amenities. Therefore, we concluded that creating and mapping a heat vulnerability index is a useful first step in protecting the public from the health burden of heat. Future work should incorporate heat exposure and health outcome data to validate the index, as well as examine sub-district levels of vulnerability.

A Bayesian framework based on a Gaussian mixture model and radial-basis-function Fisher discriminant analysis (BayGmmKda V1.1) for spatial prediction of floods

NASA Astrophysics Data System (ADS)

Tien Bui, Dieu; Hoang, Nhat-Duc

2017-09-01

In this study, a probabilistic model, named as BayGmmKda, is proposed for flood susceptibility assessment in a study area in central Vietnam. The new model is a Bayesian framework constructed by a combination of a Gaussian mixture model (GMM), radial-basis-function Fisher discriminant analysis (RBFDA), and a geographic information system (GIS) database. In the Bayesian framework, GMM is used for modeling the data distribution of flood-influencing factors in the GIS database, whereas RBFDA is utilized to construct a latent variable that aims at enhancing the model performance. As a result, the posterior probabilistic output of the BayGmmKda model is used as flood susceptibility index. Experiment results showed that the proposed hybrid framework is superior to other benchmark models, including the adaptive neuro-fuzzy inference system and the support vector machine. To facilitate the model implementation, a software program of BayGmmKda has been developed in MATLAB. The BayGmmKda program can accurately establish a flood susceptibility map for the study region. Accordingly, local authorities can overlay this susceptibility map onto various land-use maps for the purpose of land-use planning or management.

Spectral transformation of ASTER and Landsat TM bands for lithological mapping of Soghan ophiolite complex, south Iran

NASA Astrophysics Data System (ADS)

Pournamdari, Mohsen; Hashim, Mazlan; Pour, Amin Beiranvand

2014-08-01

Spectral transformation methods, including correlation coefficient (CC) and Optimum Index Factor (OIF), band ratio (BR) and principal component analysis (PCA) were applied to ASTER and Landsat TM bands for lithological mapping of Soghan ophiolitic complex in south of Iran. The results indicated that the methods used evidently showed superior outputs for detecting lithological units in ophiolitic complexes. CC and OIF methods were used to establish enhanced Red-Green-Blue (RGB) color combination bands for discriminating lithological units. A specialized band ratio (4/1, 4/5, 4/7 in RGB) was developed using ASTER bands to differentiate lithological units in ophiolitic complexes. The band ratio effectively detected serpentinite dunite as host rock of chromite ore deposits from surrounding lithological units in the study area. Principal component images derived from first three bands of ASTER and Landsat TM produced well results for lithological mapping applications. ASTER bands contain improved spectral characteristics and higher spatial resolution for detecting serpentinite dunite in ophiolitic complexes. The developed approach used in this study offers great potential for lithological mapping using ASTER and Landsat TM bands, which contributes in economic geology for prospecting chromite ore deposits associated with ophiolitic complexes.