Classification and area estimation of land covers in Kansas using ground-gathered and LANDSAT digital data

Ground-gathered data and LANDSAT multispectral scanner (MSS) digital data from 1981 were analyzed to produce a classification of Kansas land areas into specific types called land covers. The land covers included rangeland, forest, residential, commercial/industrial, and various types of water. The analysis produced two outputs: acreage estimates with measures of precision, and map-type or photo products of the classification which can be overlaid on maps at specific scales. State-level acreage estimates were obtained and substate-level land cover classification overlays and estimates were generated for selected geographical areas. These products were found to be of potential use in managing land and water resources

Annotating the human genome with Disease Ontology

<p>Abstract</p> <p>Background</p> <p>The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases.</p> <p>Results</p> <p>We used the Unified Medical Language System (UMLS) MetaMap Transfer tool (MMTx) to discover gene-disease relationships from the GeneRIF database. We utilized a comprehensive subset of UMLS, which is disease-focused and structured as a directed acyclic graph (the Disease Ontology), to filter and interpret results from MMTx. The results were validated against the Homayouni gene collection using recall and precision measurements. We compared our results with the widely used Online Mendelian Inheritance in Man (OMIM) annotations.</p> <p>Conclusion</p> <p>The validation data set suggests a 91% recall rate and 97% precision rate of disease annotation using GeneRIF, in contrast with a 22% recall and 98% precision using OMIM. Our thesaurus-based approach allows for comparisons to be made between disease containing databases and allows for increased accuracy in disease identification through synonym matching. The much higher recall rate of our approach demonstrates that annotating human genome with Disease Ontology and GeneRIF for diseases dramatically increases the coverage of the disease annotation of human genome.</p

From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations

Subjective methods have been reported to adapt a general-purpose ontology for a specific application. For example, Gene Ontology (GO) Slim was created from GO to generate a highly aggregated report of the human-genome annotation. We propose statistical methods to adapt the general purpose, OBO Foundry Disease Ontology (DO) for the identification of gene-disease associations. Thus, we need a simplified definition of disease categories derived from implicated genes. On the basis of the assumption that the DO terms having similar associated genes are closely related, we group the DO terms based on the similarity of gene-to-DO mapping profiles. Two types of binary distance metrics are defined to measure the overall and subset similarity between DO terms. A compactness-scalable fuzzy clustering method is then applied to group similar DO terms. To reduce false clustering, the semantic similarities between DO terms are also used to constrain clustering results. As such, the DO terms are aggregated and the redundant DO terms are largely removed. Using these methods, we constructed a simplified vocabulary list from the DO called Disease Ontology Lite (DOLite). We demonstrated that DOLite results in more interpretable results than DO for gene-disease association tests. The resultant DOLite has been used in the Functional Disease Ontology (FunDO) Web application at http://www.projects.bioinformatics.northwestern.edu/fundo

Comparison of two methods to assess heterogeneity of water flow in soils

The heterogeneity of water flow and solute transport was assessed during radioactive tracer infiltration experiment in a black clay loam soil using modified methods to estimate the effective cross section (ECS) and the degree of preferential flow (DPF). The results of field and numerical experiments showed that these parameters characterized the heterogeneity of water flow in the soils unequivocally. The ECS decreases non-linearly and the DPF increases linearly with an increase of the bypassing ratio (ratio of macropore flow rate to total flow rate). The ECS decreased and the DPF increased with depth, which suggests an increase in the heterogeneity of water flow with depth. The plot of the DPF against ECS values calculated from the tracer experiment data was consistent with the relationship obtained by the numerical simulation assuming preferential flow in the neighbourhood of three probes

Turismo acessível para todos, um paradigma emergente e um desafio para a oferta turística. O caso dos espaços museológicos e empreendimentos turísticos de Cascais.

Reflexão sobre o turismo acessível para todos, como modelo que se revela cada vez mais essencial para todo o sistema turístico, que se afirma não só pela sua relevância social, cívica e demográfica mas também pelas potencialidades económicas associadas. Todavia, o turismo acessível constitui um desafio de adaptação para a oferta turística instalada há vários anos, em destinos turísticos mais antigos, como é o caso de Cascais.Reflection on accessible tourism for all, as an increasingly essential model for the touristic system, that claims not only for its social, civic and demographic significance, but also for the economic potential associated. However, the accessible tourism is an adaptation challenge for the elderly tourism supply, at long-established tourism destinations, such as Cascais

NCBI GEO: archive for functional genomics data sets—10 years on

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20 000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/

Toward a common methodological framework for the sampling, extraction, and isotopic analysis of water in the Critical Zone to study vegetation water use

The analysis of the stable isotopic composition of hydrogen and oxygen in water samples from soils and plants can help to identify sources of vegetation water uptake. This approach requires that the heterogeneous nature of plant and soil matrices is carefully accounted for during experimental design, sample collection, water extraction and analyses. The comparability and shortcomings of the different methods for extracting water and analyzing isotopic composition have been discussed in specialized literature. Yet, despite insightful comparisons of extraction methods and benchmarking methodologies of laboratories worldwide, the community still lacks a roadmap to guide sample collection, extraction, and isotopic analyses, and many practical issues for potential users remain unresolved: for example, which (soil or plant) water pool(s) does the extracted water represent? These constitute a hurdle for the implementation of the approach by newcomers. Here, we summarize discussions led in the framework of the COST Action WATSON (“WATer isotopeS in the critical zONe: from groundwater recharge to plant transpiration”—CA19120). We provide guidelines for (1) sampling soil and plant material for isotopic analysis, (2) methods for laboratory or in situ water extraction, and (3) measurements of isotopic composition. We highlight the importance of considering the process chain as a whole, from experimental design to isotopic analysis to minimize biased estimates of the relative contribution of different water sources to plant water uptake. We conclude by acknowledging some of the limitations of this methodology and advice on the collection of key environmental parameters prior to sample collection for isotopic analyses.This article is categorized under: Science of Water > Hydrological Processes Science of Water > Water and Environmental Change Science of Water > Water Extreme

Land use change impacts on floods at the catchment scale: Challenges and opportunities for future research

Research gaps in understanding flood changes at the catchment scale caused by changes in forest management, agricultural practices, artificial drainage and terracing are identified. Potential strategies in addressing these gaps are proposed, such as complex systems approaches to link processes across time scales, long-term experiments on physical-chemical-biological process interactions, and a focus on connectivity and patterns across spatial scales. It is suggested that these strategies will stimulate new research that coherently addresses the issues across hydrology, soil and agricultural sciences, forest engineering, forest ecology and geomorphology