WorldWideScience

Sample records for assessing functional annotation

  1. Critical Assessment of Function Annotation Meeting, 2011

    Energy Technology Data Exchange (ETDEWEB)

    Friedberg, Iddo

    2015-01-21

    The Critical Assessment of Function Annotation meeting was held July 14-15, 2011 at the Austria Conference Center in Vienna, Austria. There were 73 registered delegates at the meeting. We thank the DOE for this award. It helped us organize and support a scientific meeting AFP 2011 as a special interest group (SIG) meeting associated with the ISMB 2011 conference. The conference was held in Vienna, Austria, in July 2011. The AFP SIG was held on July 15-16, 2011 (immediately preceding the conference). The meeting consisted of two components, the first being a series of talks (invited and contributed) and discussion sections dedicated to protein function research, with an emphasis on the theory and practice of computational methods utilized in functional annotation. The second component provided a large-scale assessment of computational methods through participation in the Critical Assessment of Functional Annotation (CAFA).

  2. Algal functional annotation tool

    Energy Technology Data Exchange (ETDEWEB)

    2012-07-12

    Abstract BACKGROUND: Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. DESCRIPTION: The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes

  3. Algal functional annotation tool

    Energy Technology Data Exchange (ETDEWEB)

    Lopez, D. [UCLA; Casero, D. [UCLA; Cokus, S. J. [UCLA; Merchant, S. S. [UCLA; Pellegrini, M. [UCLA

    2012-07-01

    The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG pathway maps and batch gene identifier conversion.

  4. Functional annotation and ENU

    OpenAIRE

    Gunn, Teresa M.

    2012-01-01

    Functional annotation of every gene in the mouse genome is a herculean task that requires a multifaceted approach. Many large-scale initiatives are contributing to this undertaking. The International Knockout Mouse Consortium (IKMC) plans to mutate every protein-coding gene, using a combination of gene trapping and gene targeting in embryonic stem cells. Many other groups are performing using the chemical mutagen ethylnitrosourea (ENU) or transpon-based systems to induce mutations, screening ...

  5. Phylogenetic molecular function annotation

    OpenAIRE

    Barbara E Engelhardt; Jordan, Michael I.; Repo, Susanna T; Brenner, Steven E

    2009-01-01

    It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic ...

  6. Harnessing Collaborative Annotations on Online Formative Assessments

    Science.gov (United States)

    Lin, Jian-Wei; Lai, Yuan-Cheng

    2013-01-01

    This paper harnesses collaborative annotations by students as learning feedback on online formative assessments to improve the learning achievements of students. Through the developed Web platform, students can conduct formative assessments, collaboratively annotate, and review historical records in a convenient way, while teachers can generate…

  7. Facilitating functional annotation of chicken microarray data

    Directory of Open Access Journals (Sweden)

    Gresham Cathy R

    2009-10-01

    Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

  8. Facilitating functional annotation of chicken microarray data

    OpenAIRE

    Buza, Teresia J; Kumar, Ranjit; Gresham, Cathy R; Burgess, Shane C.; McCarthy, Fiona M

    2009-01-01

    Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO). However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually...

  9. SURFACE: a database of protein surface regions for functional annotation

    OpenAIRE

    Ferrè, Fabrizio; Ausiello, Gabriele; Zanzoni, Andreas; Helmer-Citterich, Manuela

    2004-01-01

    The SURFACE (SUrface Residues and Functions Annotated, Compared and Evaluated, URL http://cbm.bio.uniroma2.it/surface/) database is a repository of annotated and compared protein surface regions. SURFACE contains the results of a large-scale protein annotation and local structural comparison project. A non-redundant set of protein chains is used to build a database of protein surface patches, defined as putative surface functional sites. Each patch is annotated with sequence and structure-der...

  10. Comparing functional annotation analyses with Catmap

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    Krogh Morten

    2004-12-01

    Full Text Available Abstract Background Ranked gene lists from microarray experiments are usually analysed by assigning significance to predefined gene categories, e.g., based on functional annotations. Tools performing such analyses are often restricted to a category score based on a cutoff in the ranked list and a significance calculation based on random gene permutations as null hypothesis. Results We analysed three publicly available data sets, in each of which samples were divided in two classes and genes ranked according to their correlation to class labels. We developed a program, Catmap (available for download at http://bioinfo.thep.lu.se/Catmap, to compare different scores and null hypotheses in gene category analysis, using Gene Ontology annotations for category definition. When a cutoff-based score was used, results depended strongly on the choice of cutoff, introducing an arbitrariness in the analysis. Comparing results using random gene permutations and random sample permutations, respectively, we found that the assigned significance of a category depended strongly on the choice of null hypothesis. Compared to sample label permutations, gene permutations gave much smaller p-values for large categories with many coexpressed genes. Conclusions In gene category analyses of ranked gene lists, a cutoff independent score is preferable. The choice of null hypothesis is very important; random gene permutations does not work well as an approximation to sample label permutations.

  11. COFECO: composite function annotation enriched by protein complex data

    OpenAIRE

    Sun, Choong-Hyun; Kim, Min-Sung; Han, Youngwoong; Yi, Gwan-Su

    2009-01-01

    COFECO is a web-based tool for a composite annotation of protein complexes, KEGG pathways and Gene Ontology (GO) terms within a class of genes and their orthologs under study. Widely used functional enrichment tools using GO and KEGG pathways create large list of annotations that make it difficult to derive consolidated information and often include over-generalized terms. The interrelationship of annotation terms can be more clearly delineated by integrating the information of physically int...

  12. A clustering method for robust and reliable large scale functional and structural protein sequence annotation

    OpenAIRE

    Piovesan, Damiano

    2013-01-01

    Bioinformatics, in the last few decades, has played a fundamental role to give sense to the huge amount of data produced. Obtained the complete sequence of a genome, the major problem of knowing as much as possible of its coding regions, is crucial. Protein sequence annotation is challenging and, due to the size of the problem, only computational approaches can provide a feasible solution. As it has been recently pointed out by the Critical Assessment of Function Annotations (CAFA), most accu...

  13. Functional identification in correlation networks using gene ontology edge annotation.

    Science.gov (United States)

    Dempsey, Kathryn; Thapa, Ishwor; Bastola, Dhundy; Ali, Hesham

    2012-01-01

    Correlation networks identify mechanisms behind observed change in temporal data sets; however, it is often difficult to discriminate between causative versus coincidental structures in such networks. We propose a method to enhance causative relationships based on annotations derived from the Gene Ontology (GO). Enriching correlation networks with biological relationships is likely to conserve relevant signals while reducing the network size. The obtained results are structures enriched in GO functions, despite reduction in network size. Our proposed method annotates edges according to the shortest path between elements and the position of the deepest common parent in the GO tree. Our results show that such enrichment brings functional relationships to the forefront which allows for the identification of clusters with significant biological relevance. Further, this method impacts the identification of essential genes within a network model. This approach for uncovering true function of relationships provides annotation beyond traditional statistical analysis. PMID:23013651

  14. Gene coexpression network analysis as a source of functional annotation for rice genes.

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    Kevin L Childs

    Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

  15. JAFA: a protein function annotation meta-server

    DEFF Research Database (Denmark)

    Friedberg, Iddo; Harder, Tim; Godzik, Adam

    Function Annotations, or JAFA server. JAFA queries several function prediction servers with a protein sequence and assembles the returned predictions in a legible, non-redundant format. In this manner, JAFA combines the predictions of several servers to provide a comprehensive view of what are the...

  16. Biocuration of functional annotation at the European nucleotide archive.

    Science.gov (United States)

    Gibson, Richard; Alako, Blaise; Amid, Clara; Cerdeño-Tárraga, Ana; Cleland, Iain; Goodgame, Neil; Ten Hoopen, Petra; Jayathilaka, Suran; Kay, Simon; Leinonen, Rasko; Liu, Xin; Pallreddy, Swapna; Pakseresht, Nima; Rajan, Jeena; Rosselló, Marc; Silvester, Nicole; Smirnov, Dmitriy; Toribio, Ana Luisa; Vaughan, Daniel; Zalunin, Vadim; Cochrane, Guy

    2016-01-01

    The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the submission, maintenance and presentation of nucleotide sequence data and related sample and experimental information. In this article we report on ENA in 2015 regarding general activity, notable published data sets and major achievements. This is followed by a focus on sustainable biocuration of functional annotation, an area which has particularly felt the pressure of sequencing growth. The importance of functional annotation, how it can be submitted and the shifting role of the biocurator in the context of increasing volumes of data are all discussed. PMID:26615190

  17. Systematic Functional Annotation and Visualization of Biological Networks.

    Science.gov (United States)

    Baryshnikova, Anastasia

    2016-06-22

    Large-scale biological networks represent relationships between genes, but our understanding of how networks are functionally organized is limited. Here, I describe spatial analysis of functional enrichment (SAFE), a systematic method for annotating biological networks and examining their functional organization. SAFE visualizes the network in 2D space and measures the continuous distribution of functional enrichment across local neighborhoods, producing a list of the associated functions and a map of their relative positioning. I applied SAFE to annotate the Saccharomyces cerevisiae genetic interaction similarity network and protein-protein interaction network with gene ontology terms. SAFE annotations of the genetic network matched manually derived annotations, while taking less than 1% of the time, and proved robust to noise and sensitive to biological signal. Integration of genetic interaction and chemical genomics data using SAFE revealed a link between vesicle-mediate transport and resistance to the anti-cancer drug bortezomib. These results demonstrate the utility of SAFE for examining biological networks and understanding their functional organization. PMID:27237738

  18. Certifying and reasoning on cost annotations of functional programs

    CERN Document Server

    Amadio, Roberto M

    2011-01-01

    We present a so-called labelling method to insert cost annotations in a higher-order functional program, to certify their correctness with respect to a standard compilation chain to assembly code, and to reason on them in a higher-order Hoare logic.

  19. Functional annotation of the human retinal pigment epithelium transcriptome

    NARCIS (Netherlands)

    J.C. Booij (Judith); S. van Soest (Simone); S.M.A. Swagemakers (Sigrid); A.H.W. Essing (Anke); J.H.M. Verkerk (Annemieke); P.J. van der Spek (Peter); T.G.M.F. Gorgels (Theo); A.A.B. Bergen (Arthur)

    2009-01-01

    textabstractBackground: To determine level, variability and functional annotation of gene expression of the human retinal pigment epithelium (RPE), the key tissue involved in retinal diseases like age-related macular degeneration and retinitis pigmentosa. Macular RPE cells from six selected healthy

  20. PROSITE, a protein domain database for functional characterization and annotation.

    Science.gov (United States)

    Sigrist, Christian J A; Cerutti, Lorenzo; de Castro, Edouard; Langendijk-Genevaux, Petra S; Bulliard, Virginie; Bairoch, Amos; Hulo, Nicolas

    2010-01-01

    PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE is largely used for the annotation of domain features of UniProtKB/Swiss-Prot entries. Among the 983 (DNA-binding) domains, repeats and zinc fingers present in Swiss-Prot (release 57.8 of 22 September 2009), 696 ( approximately 70%) are annotated with PROSITE descriptors using information from ProRule. In order to allow better functional characterization of domains, PROSITE developments focus on subfamily specific profiles and a new profile building method giving more weight to functionally important residues. Here, we describe AMSA, an annotated multiple sequence alignment format used to build a new generation of generalized profiles, the migration of ScanProsite to Vital-IT, a cluster of 633 CPUs, and the adoption of the Distributed Annotation System (DAS) to facilitate PROSITE data integration and interchange with other sources. The latest version of PROSITE (release 20.54, of 22 September 2009) contains 1308 patterns, 863 profiles and 869 ProRules. PROSITE is accessible at: http://www.expasy.org/prosite/. PMID:19858104

  1. Protein function annotation by homology-based inference

    OpenAIRE

    Loewenstein, Yaniv; Raimondo, Domenico; Redfern, Oliver C.; Watson, James; Frishman, Dmitrij; Linial, Michal; Orengo, Christine; Thornton, Janet; Tramontano, Anna

    2009-01-01

    With many genomes now sequenced, computational annotation methods to characterize genes and proteins from their sequence are increasingly important. The BioSapiens Network has developed tools to address all stages of this process, and here we review progress in the automated prediction of protein function based on protein sequence and structure.

  2. Eliciting the Functional Taxonomy from protein annotations and taxa.

    Science.gov (United States)

    Falda, Marco; Lavezzo, Enrico; Fontana, Paolo; Bianco, Luca; Berselli, Michele; Formentin, Elide; Toppo, Stefano

    2016-01-01

    The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules. PMID:27534507

  3. Functional annotation of human cytomegalovirus gene products: an update

    Directory of Open Access Journals (Sweden)

    Ellen eVan Damme

    2014-05-01

    Full Text Available Human Cytomegalovirus is an opportunistic double-stranded DNA virus with one of the largest viral genomes known. The 235kB genome is divided in a unique long (UL and a unique short (US region which are flanked by terminal and internal repeats. The expression of HCMV genes is highly complex and involves the production of protein coding transcripts, polyadenylated long non-coding RNAs, polyadenylated anti-sense transcripts and a variety of non-polyadenylated RNAs such as microRNAs. Although the function of many of these transcripts is unknown, they are suggested play a direct or regulatory role in the delicately orchestrated processes that ensure HCMV replication and life-long persistence. This review focuses on annotating the complete viral genome based on three sources of information. First, previous reviews were used as a template for the functional keywords to ensure continuity; second, the Uniprot database was used to further enrich the functional database; and finally, the literature was manually curated for novel functions of HCMV gene products. Novel discoveries were discussed in light of the viral life cycle. This functional annotation highlights still poorly understood regions of the genome but most importantly it can give insight in functional clusters and/or may be helpful in the analysis of transcriptomics and proteomics studies.

  4. Automatic annotation of protein motif function with Gene Ontology terms

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2004-09-01

    Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

  5. nGASP - the nematode genome annotation assessment project

    Energy Technology Data Exchange (ETDEWEB)

    Coghlan, A; Fiedler, T J; McKay, S J; Flicek, P; Harris, T W; Blasiar, D; Allen, J; Stein, L D

    2008-12-19

    While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second place. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy as reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs were the most challenging for gene-finders. While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets for 10 Mb of the C

  6. Functional annotation of the human retinal pigment epithelium transcriptome

    Directory of Open Access Journals (Sweden)

    Gorgels Theo GMF

    2009-04-01

    Full Text Available Abstract Background To determine level, variability and functional annotation of gene expression of the human retinal pigment epithelium (RPE, the key tissue involved in retinal diseases like age-related macular degeneration and retinitis pigmentosa. Macular RPE cells from six selected healthy human donor eyes (aged 63–78 years were laser dissected and used for 22k microarray studies (Agilent technologies. Data were analyzed with Rosetta Resolver, the web tool DAVID and Ingenuity software. Results In total, we identified 19,746 array entries with significant expression in the RPE. Gene expression was analyzed according to expression levels, interindividual variability and functionality. A group of highly (n = 2,194 expressed RPE genes showed an overrepresentation of genes of the oxidative phosphorylation, ATP synthesis and ribosome pathways. In the group of moderately expressed genes (n = 8,776 genes of the phosphatidylinositol signaling system and aminosugars metabolism were overrepresented. As expected, the top 10 percent (n = 2,194 of genes with the highest interindividual differences in expression showed functional overrepresentation of the complement cascade, essential in inflammation in age-related macular degeneration, and other signaling pathways. Surprisingly, this same category also includes the genes involved in Bruch's membrane (BM composition. Among the top 10 percent of genes with low interindividual differences, there was an overrepresentation of genes involved in local glycosaminoglycan turnover. Conclusion Our study expands current knowledge of the RPE transcriptome by assigning new genes, and adding data about expression level and interindividual variation. Functional annotation suggests that the RPE has high levels of protein synthesis, strong energy demands, and is exposed to high levels of oxidative stress and a variable degree of inflammation. Our data sheds new light on the molecular composition of BM, adjacent to the

  7. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.

    Science.gov (United States)

    Gaudet, Pascale; Livstone, Michael S; Lewis, Suzanna E; Thomas, Paul D

    2011-09-01

    The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods. PMID:21873635

  8. Functional Annotation and Comparative Analysis of a Zygopteran Transcriptome.

    Science.gov (United States)

    Shanku, Alexander G; McPeek, Mark A; Kern, Andrew D

    2013-03-11

    In this paper we present a de novo assembly of the transcriptome of the damselfly, Enallagma hageni, through the use of 454 pyrosequencing. E. hageni is a member of the suborder Zygoptera within the order Odonata, and the Odonata are the basal lineage of the winged insects (Pterygota). To date, sequence data used in phylogenetic analysis of Enallagma species have been derived from either mtDNA or ribosomal nuclear DNA. This transcriptome contained 31,661 contigs that were assembled and translated into 14,813 individual open reading frames. Using these data, we constructed an extensive dataset of 634 orthologous nuclear protein-coding genes across 11 species of Arthropoda, and used Bayesian techniques to elucidate Enallagma's place in the Arthropod phylogenetic tree. Additionally, we demonstrate that the Enallagma transcriptome contains 169 genes that are evolving at rates that differ relative to the rest of the transcriptome (29 accelerated and 140 decreased), and through multiple Gene Ontology searches and clustering methods, we present the first functional-annotation of any palaeopteran's transcriptome in the literature. PMID:23550132

  9. Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome

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    McCarthy Fiona M

    2007-11-01

    Full Text Available Abstract Background The chicken genome was sequenced because of its phylogenetic position as a non-mammalian vertebrate, its use as a biomedical model especially to study embryology and development, its role as a source of human disease organisms and its importance as the major source of animal derived food protein. However, genomic sequence data is, in itself, of limited value; generally it is not equivalent to understanding biological function. The benefit of having a genome sequence is that it provides a basis for functional genomics. However, the sequence data currently available is poorly structurally and functionally annotated and many genes do not have standard nomenclature assigned. Results We analysed eight chicken tissues and improved the chicken genome structural annotation by providing experimental support for the in vivo expression of 7,809 computationally predicted proteins, including 30 chicken proteins that were only electronically predicted or hypothetical translations in human. To improve functional annotation (based on Gene Ontology, we mapped these identified proteins to their human and mouse orthologs and used this orthology to transfer Gene Ontology (GO functional annotations to the chicken proteins. The 8,213 orthology-based GO annotations that we produced represent an 8% increase in currently available chicken GO annotations. Orthologous chicken products were also assigned standardized nomenclature based on current chicken nomenclature guidelines. Conclusion We demonstrate the utility of high-throughput expression proteomics for rapid experimental structural annotation of a newly sequenced eukaryote genome. These experimentally-supported predicted proteins were further annotated by assigning the proteins with standardized nomenclature and functional annotation. This method is widely applicable to a diverse range of species. Moreover, information from one genome can be used to improve the annotation of other genomes and

  10. Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data

    Directory of Open Access Journals (Sweden)

    Merchant Sabeeha S

    2011-07-01

    Full Text Available Abstract Background Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. Description The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of

  11. Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets

    Directory of Open Access Journals (Sweden)

    Burgun Anita

    2006-05-01

    Full Text Available Abstract Background Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology allows a coherent and consistent description of the knowledge about gene functions. The GO terms related to genes come primarily from semi-automatic annotations made by trained biologists (annotation based on evidence or text-mining of the published scientific literature (literature profiling. Results We report an original functional annotation method based on a combination of evidence and literature that overcomes the weaknesses and the limitations of each approach. It relies on the Gene Ontology Annotation database (GOA Human and the PubGene biomedical literature index. We support these annotations with statistically associated GO terms and retrieve associative relations across the three GO hierarchies to emphasise the major pathways involved by a gene cluster. Both annotation methods and associative relations were quantitatively evaluated with a reference set of 7397 genes and a multi-cluster study of 14 clusters. We also validated the biological appropriateness of our hybrid method with the annotation of a single gene (cdc2 and that of a down-regulated cluster of 37 genes identified by a transcriptome study of an in vitro enterocyte differentiation model (CaCo-2 cells. Conclusion The combination of both approaches is more informative than either separate approach: literature mining can enrich an annotation based only on evidence. Text-mining of the literature can also find valuable associated MEDLINE references that confirm the relevance of the annotation. Eventually, GO terms networks can be built with associative relations in order to highlight cooperative and competitive pathways and their connected molecular functions.

  12. Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets.

    OpenAIRE

    Burgun Anita; Galibert Marie-Dominique; de Tayrac Marie; Chicault Celine; Monnier Annabelle; Aubry Marc; Mosser Jean

    2006-01-01

    Abstract Background Large-scale genomic studies based on transcriptome technologies provide clusters of genes that need to be functionally annotated. The Gene Ontology (GO) implements a controlled vocabulary organised into three hierarchies: cellular components, molecular functions and biological processes. This terminology allows a coherent and consistent description of the knowledge about gene functions. The GO terms related to genes come primarily from semi-automatic annotations made by tr...

  13. Assessment of community-submitted ontology annotations from a novel database-journal partnership.

    Science.gov (United States)

    Berardini, Tanya Z; Li, Donghui; Muller, Robert; Chetty, Raymond; Ploetz, Larry; Singh, Shanker; Wensel, April; Huala, Eva

    2012-01-01

    As the scientific literature grows, leading to an increasing volume of published experimental data, so does the need to access and analyze this data using computational tools. The most commonly used method to convert published experimental data on gene function into controlled vocabulary annotations relies on a professional curator, employed by a model organism database or a more general resource such as UniProt, to read published articles and compose annotation statements based on the articles' contents. A more cost-effective and scalable approach capable of capturing gene function data across the whole range of biological research organisms in computable form is urgently needed. We have analyzed a set of ontology annotations generated through collaborations between the Arabidopsis Information Resource and several plant science journals. Analysis of the submissions entered using the online submission tool shows that most community annotations were well supported and the ontology terms chosen were at an appropriate level of specificity. Of the 503 individual annotations that were submitted, 97% were approved and community submissions captured 72% of all possible annotations. This new method for capturing experimental results in a computable form provides a cost-effective way to greatly increase the available body of annotations without sacrificing annotation quality. Database URL: www.arabidopsis.org. PMID:22859749

  14. New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'.

    Science.gov (United States)

    Bromberg, Yana; Yachdav, Guy; Ofran, Yanay; Schneider, Reinhard; Rost, Burkhard

    2009-05-01

    The rapidly increasing quantity of protein sequence data continues to widen the gap between available sequences and annotations. Comparative modeling suggests some aspects of the 3D structures of approximately half of all known proteins; homology- and network-based inferences annotate some aspect of function for a similar fraction of the proteome. For most known protein sequences, however, there is detailed knowledge about neither their function nor their structure. Comprehensive efforts towards the expert curation of sequence annotations have failed to meet the demand of the rapidly increasing number of available sequences. Only the automated prediction of protein function in the absence of homology can close the gap between available sequences and annotations in the foreseeable future. This review focuses on two novel methods for automated annotation, and briefly presents an outlook on how modern web software may revolutionize the field of protein sequence annotation. First, predictions of protein binding sites and functional hotspots, and the evolution of these into the most successful type of prediction of protein function from sequence will be discussed. Second, a new tool, comprehensive in silico mutagenesis, which contributes important novel predictions of function and at the same time prepares for the onset of the next sequencing revolution, will be described. While these two new sub-fields of protein prediction represent the breakthroughs that have been achieved methodologically, it will then be argued that a different development might further change the way biomedical researchers benefit from annotations: modern web software can connect the worldwide web in any browser with the 'Deep Web' (ie, proprietary data resources). The availability of this direct connection, and the resulting access to a wealth of data, may impact drug discovery and development more than any existing method that contributes to protein annotation. PMID:19396742

  15. Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

    OpenAIRE

    Schnoes, Alexandra M.; Ream, David C; Thorman, Alexander W.; Babbitt, Patricia C; Friedberg, Iddo

    2013-01-01

    The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases. Here we investigate just how prevalent is the "few articles -- many proteins" phenomenon. We examine the experimentally val...

  16. Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Dwayne A.; Mukhopadhyay, Aindrila; Joachimiak, Marcin P.; Drury, Elliott C.; Redding, Alyssa M.; Yen, Huei-Che B.; Fields, Matthew W.; Hazen, Terry C.; Arkin, Adam P.; Keasling, Jay D.; Wall, Judy D.

    2008-10-27

    Hypothetical and conserved hypothetical genes account for>30percent of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved hypothetical (9.5percent) along with 887 hypothetical genes (24.4percent). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 hypothetical and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC-MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. 1212 of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes. Except for the latter, monocistronic gene annotation was expanded using the above criteria along with matching Clusters of Orthologous Groups. Polycistronic genes were annotated in the same manner with inferences from their proximity to more confidently annotated genes. Two targeted deletion mutants were used as test cases to determine the relevance of the inferred functional annotations.

  17. Annotation and retrieval system of CAD models based on functional semantics

    Science.gov (United States)

    Wang, Zhansong; Tian, Ling; Duan, Wenrui

    2014-11-01

    CAD model retrieval based on functional semantics is more significant than content-based 3D model retrieval during the mechanical conceptual design phase. However, relevant research is still not fully discussed. Therefore, a functional semantic-based CAD model annotation and retrieval method is proposed to support mechanical conceptual design and design reuse, inspire designer creativity through existing CAD models, shorten design cycle, and reduce costs. Firstly, the CAD model functional semantic ontology is constructed to formally represent the functional semantics of CAD models and describe the mechanical conceptual design space comprehensively and consistently. Secondly, an approach to represent CAD models as attributed adjacency graphs(AAG) is proposed. In this method, the geometry and topology data are extracted from STEP models. On the basis of AAG, the functional semantics of CAD models are annotated semi-automatically by matching CAD models that contain the partial features of which functional semantics have been annotated manually, thereby constructing CAD Model Repository that supports model retrieval based on functional semantics. Thirdly, a CAD model retrieval algorithm that supports multi-function extended retrieval is proposed to explore more potential creative design knowledge in the semantic level. Finally, a prototype system, called Functional Semantic-based CAD Model Annotation and Retrieval System(FSMARS), is implemented. A case demonstrates that FSMARS can successfully botain multiple potential CAD models that conform to the desired function. The proposed research addresses actual needs and presents a new way to acquire CAD models in the mechanical conceptual design phase.

  18. Biases in the experimental annotations of protein function and their effect on our understanding of protein function space.

    Science.gov (United States)

    Schnoes, Alexandra M; Ream, David C; Thorman, Alexander W; Babbitt, Patricia C; Friedberg, Iddo

    2013-01-01

    The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases. Here, we investigate just how prevalent is the "few articles - many proteins" phenomenon. We examine the experimentally validated annotation of proteins provided by several groups in the GO Consortium, and show that the distribution of proteins per published study is exponential, with 0.14% of articles providing the source of annotations for 25% of the proteins in the UniProt-GOA compilation. Since each of the dominant articles describes the use of an assay that can find only one function or a small group of functions, this leads to substantial biases in what we know about the function of many proteins. Mass-spectrometry, microscopy and RNAi experiments dominate high throughput experiments. Consequently, the functional information derived from these experiments is mostly of the subcellular location of proteins, and of the participation of proteins in embryonic developmental pathways. For some organisms, the information provided by different studies overlap by a large amount. We also show that the information provided by high throughput experiments is less specific than those provided by low throughput experiments. Given the experimental techniques available, certain biases in protein function annotation due to high-throughput experiments are unavoidable. Knowing that these biases exist and understanding their characteristics and extent is important for database curators, developers of function annotation programs, and anyone who uses protein function annotation data to plan experiments. PMID:23737737

  19. A Method of Gene-Function Annotation Based on Variable Precision Rough Sets

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotation of new biological sequences is presented by using the variable-precision rough set theory. The proposed method is applied to the real data in GO database to examine its effectiveness. Numerical results show that the proposed method has better precision, recall-rate and harmonic mean value compared with existing methods.

  20. Functional annotation of 2D protein maps: The GelMap portal

    Directory of Open Access Journals (Sweden)

    Hans-Peter eBraun

    2012-05-01

    Full Text Available In classical proteome analyses, final experimental data are (a images of 2D protein separations obtained by gel electrophoresis and (b corresponding lists of proteins which were identified by mass spectrometry (MS. For data annotation, software tools were developed which allow to link protein identity data directly to 2D gels (clickable gels. GelMap is a new online software tool to annotate 2D protein maps. It allows (i functional annotation of all identified proteins according to biological categories defined by the user, e.g. subcellular localization, metabolic pathway, or assignment to a protein complex and (ii annotation of several proteins per analyzed protein spot according to MS primary data. Options to differentially display proteins of functional categories offer new opportunities for data evaluation. For instance, if used for the annotation of 2D Blue native / SDS gels, GelMap allows identifying protein complexes of low abundance. A web portal has been established for presentation and evaluation of protein identity data related to 2D gels and is freely accessible at http://www.gelmap.de/.

  1. Genome-wide functional annotation of Phomopsis longicolla isolate MSPL 10-6.

    Science.gov (United States)

    Darwish, Omar; Li, Shuxian; Matthews, Benjamin; Alkharouf, Nadim

    2016-06-01

    Phomopsis seed decay of soybean is caused primarily by the seed-borne fungal pathogen Phomopsis longicolla (syn. Diaporthe longicolla). This disease severely decreases soybean seed quality, reduces seedling vigor and stand establishment, and suppresses yield. It is one of the most economically important soybean diseases. In this study we annotated the entire genome of P. longicolla isolate MSPL 10-6, which was isolated from field-grown soybean seed in Mississippi, USA. This study represents the first reported genome-wide functional annotation of a seed borne fungal pathogen in the Diaporthe-Phomopsis complex. The P. longicolla genome annotation will enable research into the genetic basis of fungal infection of soybean seed and provide information for the study of soybean-fungal interactions. The genome annotation will also be a valuable resource for the research and agricultural communities. It will aid in the development of new control strategies for this pathogen. The annotations can be found from: http://bioinformatics.towson.edu/phomopsis_longicolla/download.html. NCBI accession number is: AYRD00000000. PMID:27222801

  2. AIGO: Towards a unified framework for the Analysis and the Inter-comparison of GO functional annotations

    Directory of Open Access Journals (Sweden)

    Defoin-Platel Michael

    2011-11-01

    Full Text Available Abstract Background In response to the rapid growth of available genome sequences, efforts have been made to develop automatic inference methods to functionally characterize them. Pipelines that infer functional annotation are now routinely used to produce new annotations at a genome scale and for a broad variety of species. These pipelines differ widely in their inference algorithms, confidence thresholds and data sources for reasoning. This heterogeneity makes a comparison of the relative merits of each approach extremely complex. The evaluation of the quality of the resultant annotations is also challenging given there is often no existing gold-standard against which to evaluate precision and recall. Results In this paper, we present a pragmatic approach to the study of functional annotations. An ensemble of 12 metrics, describing various aspects of functional annotations, is defined and implemented in a unified framework, which facilitates their systematic analysis and inter-comparison. The use of this framework is demonstrated on three illustrative examples: analysing the outputs of state-of-the-art inference pipelines, comparing electronic versus manual annotation methods, and monitoring the evolution of publicly available functional annotations. The framework is part of the AIGO library (http://code.google.com/p/aigo for the Analysis and the Inter-comparison of the products of Gene Ontology (GO annotation pipelines. The AIGO library also provides functionalities to easily load, analyse, manipulate and compare functional annotations and also to plot and export the results of the analysis in various formats. Conclusions This work is a step toward developing a unified framework for the systematic study of GO functional annotations. This framework has been designed so that new metrics on GO functional annotations can be added in a very straightforward way.

  3. Guidelines for the functional annotation of microRNAs using the Gene Ontology

    Science.gov (United States)

    D'Eustachio, Peter; Smith, Jennifer R.; Zampetaki, Anna

    2016-01-01

    MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual). PMID:26917558

  4. Guidelines for the functional annotation of microRNAs using the Gene Ontology.

    Science.gov (United States)

    Huntley, Rachael P; Sitnikov, Dmitry; Orlic-Milacic, Marija; Balakrishnan, Rama; D'Eustachio, Peter; Gillespie, Marc E; Howe, Doug; Kalea, Anastasia Z; Maegdefessel, Lars; Osumi-Sutherland, David; Petri, Victoria; Smith, Jennifer R; Van Auken, Kimberly; Wood, Valerie; Zampetaki, Anna; Mayr, Manuel; Lovering, Ruth C

    2016-05-01

    MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual). PMID:26917558

  5. Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin.

    Science.gov (United States)

    Liu, Ching-Ti; Raghavan, Sridharan; Maruthur, Nisa; Kabagambe, Edmond Kato; Hong, Jaeyoung; Ng, Maggie C Y; Hivert, Marie-France; Lu, Yingchang; An, Ping; Bentley, Amy R; Drolet, Anne M; Gaulton, Kyle J; Guo, Xiuqing; Armstrong, Loren L; Irvin, Marguerite R; Li, Man; Lipovich, Leonard; Rybin, Denis V; Taylor, Kent D; Agyemang, Charles; Palmer, Nicholette D; Cade, Brian E; Chen, Wei-Min; Dauriz, Marco; Delaney, Joseph A C; Edwards, Todd L; Evans, Daniel S; Evans, Michele K; Lange, Leslie A; Leong, Aaron; Liu, Jingmin; Liu, Yongmei; Nayak, Uma; Patel, Sanjay R; Porneala, Bianca C; Rasmussen-Torvik, Laura J; Snijder, Marieke B; Stallings, Sarah C; Tanaka, Toshiko; Yanek, Lisa R; Zhao, Wei; Becker, Diane M; Bielak, Lawrence F; Biggs, Mary L; Bottinger, Erwin P; Bowden, Donald W; Chen, Guanjie; Correa, Adolfo; Couper, David J; Crawford, Dana C; Cushman, Mary; Eicher, John D; Fornage, Myriam; Franceschini, Nora; Fu, Yi-Ping; Goodarzi, Mark O; Gottesman, Omri; Hara, Kazuo; Harris, Tamara B; Jensen, Richard A; Johnson, Andrew D; Jhun, Min A; Karter, Andrew J; Keller, Margaux F; Kho, Abel N; Kizer, Jorge R; Krauss, Ronald M; Langefeld, Carl D; Li, Xiaohui; Liang, Jingling; Liu, Simin; Lowe, William L; Mosley, Thomas H; North, Kari E; Pacheco, Jennifer A; Peyser, Patricia A; Patrick, Alan L; Rice, Kenneth M; Selvin, Elizabeth; Sims, Mario; Smith, Jennifer A; Tajuddin, Salman M; Vaidya, Dhananjay; Wren, Mary P; Yao, Jie; Zhu, Xiaofeng; Ziegler, Julie T; Zmuda, Joseph M; Zonderman, Alan B; Zwinderman, Aeilko H; Adeyemo, Adebowale; Boerwinkle, Eric; Ferrucci, Luigi; Hayes, M Geoffrey; Kardia, Sharon L R; Miljkovic, Iva; Pankow, James S; Rotimi, Charles N; Sale, Michele M; Wagenknecht, Lynne E; Arnett, Donna K; Chen, Yii-Der Ida; Nalls, Michael A; Province, Michael A; Kao, W H Linda; Siscovick, David S; Psaty, Bruce M; Wilson, James G; Loos, Ruth J F; Dupuis, Josée; Rich, Stephen S; Florez, Jose C; Rotter, Jerome I; Morris, Andrew P; Meigs, James B

    2016-07-01

    Knowledge of the genetic basis of the type 2 diabetes (T2D)-related quantitative traits fasting glucose (FG) and insulin (FI) in African ancestry (AA) individuals has been limited. In non-diabetic subjects of AA (n = 20,209) and European ancestry (EA; n = 57,292), we performed trans-ethnic (AA+EA) fine-mapping of 54 established EA FG or FI loci with detailed functional annotation, assessed their relevance in AA individuals, and sought previously undescribed loci through trans-ethnic (AA+EA) meta-analysis. We narrowed credible sets of variants driving association signals for 22/54 EA-associated loci; 18/22 credible sets overlapped with active islet-specific enhancers or transcription factor (TF) binding sites, and 21/22 contained at least one TF motif. Of the 54 EA-associated loci, 23 were shared between EA and AA. Replication with an additional 10,096 AA individuals identified two previously undescribed FI loci, chrX FAM133A (rs213676) and chr5 PELO (rs6450057). Trans-ethnic analyses with regulatory annotation illuminate the genetic architecture of glycemic traits and suggest gene regulation as a target to advance precision medicine for T2D. Our approach to utilize state-of-the-art functional annotation and implement trans-ethnic association analysis for discovery and fine-mapping offers a framework for further follow-up and characterization of GWAS signals of complex trait loci. PMID:27321945

  6. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation.

    Science.gov (United States)

    Engel, Krysta L; Mackiewicz, Mark; Hardigan, Andrew A; Myers, Richard M; Savic, Daniel

    2016-09-01

    Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research. PMID:27224938

  7. A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs proteins family example

    Directory of Open Access Journals (Sweden)

    Blanc M

    2005-11-01

    Full Text Available Abstract Background large scale and reliable proteins' functional annotation is a major challenge in modern biology. Phylogenetic analyses have been shown to be important for such tasks. However, up to now, phylogenetic annotation did not take into account expression data (i.e. ESTs, Microarrays, SAGE, .... Therefore, integrating such data, like ESTs in phylogenetic annotation could be a major advance in post genomic analyses. We developed an approach enabling the combination of expression data and phylogenetic analysis. To illustrate our method, we used an example protein family, the peptidyl arginine deiminases (PADs, probably implied in Rheumatoid Arthritis. Results the analysis was performed as follows: we built a phylogeny of PAD proteins from the NCBI's NR protein database. We completed the phylogenetic reconstruction of PADs using an enlarged sequence database containing translations of ESTs contigs. We then extracted all corresponding expression data contained in EST database This analysis allowed us 1/To extend the spectrum of homologs-containing species and to improve the reconstruction of genes' evolutionary history. 2/To deduce an accurate gene expression pattern for each member of this protein family. 3/To show a correlation between paralogous sequences' evolution rate and pattern of tissular expression. Conclusion coupling phylogenetic reconstruction and expression data is a promising way of analysis that could be applied to all multigenic families to investigate the relationship between molecular and transcriptional evolution and to improve functional annotation.

  8. An Approach to Function Annotation for Proteins of Unknown Function (PUFs in the Transcriptome of Indian Mulberry.

    Directory of Open Access Journals (Sweden)

    K H Dhanyalakshmi

    Full Text Available The modern sequencing technologies are generating large volumes of information at the transcriptome and genome level. Translation of this information into a biological meaning is far behind the race due to which a significant portion of proteins discovered remain as proteins of unknown function (PUFs. Attempts to uncover the functional significance of PUFs are limited due to lack of easy and high throughput functional annotation tools. Here, we report an approach to assign putative functions to PUFs, identified in the transcriptome of mulberry, a perennial tree commonly cultivated as host of silkworm. We utilized the mulberry PUFs generated from leaf tissues exposed to drought stress at whole plant level. A sequence and structure based computational analysis predicted the probable function of the PUFs. For rapid and easy annotation of PUFs, we developed an automated pipeline by integrating diverse bioinformatics tools, designated as PUFs Annotation Server (PUFAS, which also provides a web service API (Application Programming Interface for a large-scale analysis up to a genome. The expression analysis of three selected PUFs annotated by the pipeline revealed abiotic stress responsiveness of the genes, and hence their potential role in stress acclimation pathways. The automated pipeline developed here could be extended to assign functions to PUFs from any organism in general. PUFAS web server is available at http://caps.ncbs.res.in/pufas/ and the web service is accessible at http://capservices.ncbs.res.in/help/pufas.

  9. Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data

    OpenAIRE

    Cunningham Pádraig; Bryan Kenneth

    2008-01-01

    Abstract Background Microarrays have the capacity to measure the expressions of thousands of genes in parallel over many experimental samples. The unsupervised classification technique of bicluster analysis has been employed previously to uncover gene expression correlations over subsets of samples with the aim of providing a more accurate model of the natural gene functional classes. This approach also has the potential to aid functional annotation of unclassified open reading frames (ORFs)....

  10. Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function.

    Science.gov (United States)

    Valli, Minoska; Tatto, Nadine E; Peymann, Armin; Gruber, Clemens; Landes, Nils; Ekker, Heinz; Thallinger, Gerhard G; Mattanovich, Diethard; Gasser, Brigitte; Graf, Alexandra B

    2016-09-01

    As manually curated and non-automated BLAST analysis of the published Pichia pastoris genome sequences revealed many differences between the gene annotations of the strains GS115 and CBS7435, RNA-Seq analysis, supported by proteomics, was performed to improve the genome annotation. Detailed analysis of sequence alignment and protein domain predictions were made to extend the functional genome annotation to all P. pastoris sequences. This allowed the identification of 492 new ORFs, 4916 hypothetical UTRs and the correction of 341 incorrect ORF predictions, which were mainly due to the presence of upstream ATG or erroneous intron predictions. Moreover, 175 previously erroneously annotated ORFs need to be removed from the annotation. In total, we have annotated 5325 ORFs. Regarding the functionality of those genes, we improved all gene and protein descriptions. Thereby, the percentage of ORFs with functional annotation was increased from 48% to 73%. Furthermore, we defined functional groups, covering 25 biological cellular processes of interest, by grouping all genes that are part of the defined process. All data are presented in the newly launched genome browser and database available at www.pichiagenome.org In summary, we present a wide spectrum of curation of the P. pastoris genome annotation from gene level to protein function. PMID:27388471

  11. Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Fan Changyu

    2011-06-01

    Full Text Available Abstract Background Recent advances in the field of metabolic engineering have been expedited by the availability of genome sequences and metabolic modelling approaches. The complete sequencing of the C. reinhardtii genome has made this unicellular alga a good candidate for metabolic engineering studies; however, the annotation of the relevant genes has not been validated and the much-needed metabolic ORFeome is currently unavailable. We describe our efforts on the functional annotation of the ORF models released by the Joint Genome Institute (JGI, prediction of their subcellular localizations, and experimental verification of their structural annotation at the genome scale. Results We assigned enzymatic functions to the translated JGI ORF models of C. reinhardtii by reciprocal BLAST searches of the putative proteome against the UniProt and AraCyc enzyme databases. The best match for each translated ORF was identified and the EC numbers were transferred onto the ORF models. Enzymatic functional assignment was extended to the paralogs of the ORFs by clustering ORFs using BLASTCLUST. In total, we assigned 911 enzymatic functions, including 886 EC numbers, to 1,427 transcripts. We further annotated the enzymatic ORFs by prediction of their subcellular localization. The majority of the ORFs are predicted to be compartmentalized in the cytosol and chloroplast. We verified the structure of the metabolism-related ORF models by reverse transcription-PCR of the functionally annotated ORFs. Following amplification and cloning, we carried out 454FLX and Sanger sequencing of the ORFs. Based on alignment of the 454FLX reads to the ORF predicted sequences, we obtained more than 90% coverage for more than 80% of the ORFs. In total, 1,087 ORF models were verified by 454 and Sanger sequencing methods. We obtained expression evidence for 98% of the metabolic ORFs in the algal cells grown under constant light in the presence of acetate. Conclusions We functionally

  12. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project : open letter

    NARCIS (Netherlands)

    Archibald, A.L.; Bottema, C.D.; Brauning, R.; Burgess, S.C.; Burt, D.W.; Casas, E.; Cheng, H.H.; Clarke, L.; Couldrey, C.; Dalrymple, B.P.; Elsik, C.G.; Foissac, S.; Giuffra, E.; Groenen, M.A.M.; Hayes, B.J.; Huang, L.S.; Khatib, H.; Kijas, J.W.; Kim, H.; Lunney, J.K.; McCarthy, F.M.; McEwan, J.; Moore, S.; Nanduri, B.; Notredame, C.; Palti, Y.; Plastow, G.S.; Reecy, J.M.; Rohrer, G.; Sarropoulou, E.; Schmidt, C.J.; Silverstein, J.; Tellam, R.L.; Tixier-Boichard, M.; Tosser-klopp, G.; Tuggle, C.K.; Vilkki, J.; White, S.N.; Zhao, S.; Zhou, H.

    2015-01-01

    We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

  13. Analysis and comparison of very large metagenomes with fast clustering and functional annotation

    Directory of Open Access Journals (Sweden)

    Li Weizhong

    2009-10-01

    Full Text Available Abstract Background The remarkable advance of metagenomics presents significant new challenges in data analysis. Metagenomic datasets (metagenomes are large collections of sequencing reads from anonymous species within particular environments. Computational analyses for very large metagenomes are extremely time-consuming, and there are often many novel sequences in these metagenomes that are not fully utilized. The number of available metagenomes is rapidly increasing, so fast and efficient metagenome comparison methods are in great demand. Results The new metagenomic data analysis method Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline (RAMMCAP was developed using an ultra-fast sequence clustering algorithm, fast protein family annotation tools, and a novel statistical metagenome comparison method that employs a unique graphic interface. RAMMCAP processes extremely large datasets with only moderate computational effort. It identifies raw read clusters and protein clusters that may include novel gene families, and compares metagenomes using clusters or functional annotations calculated by RAMMCAP. In this study, RAMMCAP was applied to the two largest available metagenomic collections, the "Global Ocean Sampling" and the "Metagenomic Profiling of Nine Biomes". Conclusion RAMMCAP is a very fast method that can cluster and annotate one million metagenomic reads in only hundreds of CPU hours. It is available from http://tools.camera.calit2.net/camera/rammcap/.

  14. Transcriptomal Changes and Functional Annotation of the Developing Nonhuman Primate Choroid Plexus

    Directory of Open Access Journals (Sweden)

    Joakim eEk

    2015-03-01

    Full Text Available The choroid plexuses are small organs that protrude into each brain ventricle producing cerebrospinal fluid that constantly bathes the brain. These organs differentiate early in development just after neural closure at a stage when the brain is little vascularized. In recent years the plexus has been shown to have a much more active role in brain development than previously appreciated thereby it can influence both neurogenesis and neural migration by secreting factors into the CSF. However, much of choroid plexus developmental function is still unclear. Most previous studies on this organ have been undertaken in rodents but translation into humans is not straightforward since they have a different timing of brain maturation processes. We have collected choroid plexus from three fetal gestational ages of a nonhuman primate, the baboon, which has much closer brain development to humans. The transcriptome of the plexuses was determined by next generation sequencing and Ingenuity Pathway Analysis software was used to annotate functions and enrichment of pathways of changes in the transcriptome. The number of unique transcripts decreased with development and the majority of differentially expressed transcripts were down-regulated through development suggesting a more complex and active plexus earlier in fetal development. The functional annotation indicated changes across widespread biological functions in plexus development. In particular we find age-dependent regulation of genes associated with annotation categories: Gene Expression, Development of Cardiovascular System, Nervous System Development and Molecular Transport. Our observations support the idea that the choroid plexus has roles in shaping brain development.

  15. Transcriptomal changes and functional annotation of the developing non-human primate choroid plexus.

    Science.gov (United States)

    Ek, C Joakim; Nathanielsz, Peter; Li, Cun; Mallard, Carina

    2015-01-01

    The choroid plexuses are small organs that protrude into each brain ventricle producing cerebrospinal fluid that constantly bathes the brain. These organs differentiate early in development just after neural closure at a stage when the brain is little vascularized. In recent years the plexus has been shown to have a much more active role in brain development than previously appreciated thereby it can influence both neurogenesis and neural migration by secreting factors into the CSF. However, much of choroid plexus developmental function is still unclear. Most previous studies on this organ have been undertaken in rodents but translation into humans is not straightforward since they have a different timing of brain maturation processes. We have collected choroid plexus from three fetal gestational ages of a non-human primate, the baboon, which has much closer brain development to humans. The transcriptome of the plexuses was determined by next generation sequencing and Ingenuity Pathway Analysis software was used to annotate functions and enrichment of pathways of changes in the transcriptome. The number of unique transcripts decreased with development and the majority of differentially expressed transcripts were down-regulated through development suggesting a more complex and active plexus earlier in fetal development. The functional annotation indicated changes across widespread biological functions in plexus development. In particular we find age-dependent regulation of genes associated with annotation categories: Gene Expression, Development of Cardiovascular System, Nervous System Development and Molecular Transport. Our observations support the idea that the choroid plexus has roles in shaping brain development. PMID:25814924

  16. Emerging applications of read profiles towards the functional annotation of the genome

    DEFF Research Database (Denmark)

    Pundhir, Sachin; Poirazi, Panayiota; Gorodkin, Jan

    2015-01-01

    Functional annotation of the genome is important to understand the phenotypic complexity of various species. The road toward functional annotation involves several challenges ranging from experiments on individual molecules to large-scale analysis of high-throughput sequencing (HTS) data. HTS data...... is typically a result of the protocol designed to address specific research questions. The sequencing results in reads, which when mapped to a reference genome often leads to the formation of distinct patterns (read profiles). Interpretation of these read profiles is essential for their analysis in relation...... to the research question addressed. Several strategies have been employed at varying levels of abstraction ranging from a somewhat ad hoc to a more systematic analysis of read profiles. These include methods which can compare read profiles, e.g., from direct (non-sequence based) alignments to classification...

  17. Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation

    OpenAIRE

    Celaj, Albi; Markle, Janet; Danska, Jayne; Parkinson, John

    2014-01-01

    Background Microbiome-wide gene expression profiling through high-throughput RNA sequencing (‘metatranscriptomics’) offers a powerful means to functionally interrogate complex microbial communities. Key to successful exploitation of these datasets is the ability to confidently match relatively short sequence reads to known bacterial transcripts. In the absence of reference genomes, such annotation efforts may be enhanced by assembling reads into longer contiguous sequences (‘contigs’), prior ...

  18. MassNet: a functional annotation service for protein mass spectrometry data

    OpenAIRE

    Park, Daeui; Kim, Byoung-Chul; Cho, Seong-Woong; Park, Seong-Jin; Choi, Jong-Soon; Kim, Seung Il; Bhak, Jong; Lee, Sunghoon

    2008-01-01

    Although mass spectrometry has been frequently used to identify proteins, there are no web servers that provide comprehensive functional annotation of those identified proteins. It is necessary to provide such web service due to a rapid increase in the data. We, therefore, introduce MassNet, which provides (i) physico-chemical analysis information, (ii) KEGG pathway assignment (iii) Gene Ontology mapping and (iv) protein–protein interaction (PPI) prediction for the data from MASCOT, Prospecto...

  19. GenoQuery: a new querying module for functional annotation in a genomic warehouse

    OpenAIRE

    Lemoine, Frédéric; Labedan, Bernard; Froidevaux, Christine

    2008-01-01

    Motivation: We have to cope with both a deluge of new genome sequences and a huge amount of data produced by high-throughput approaches used to exploit these genomic features. Crossing and comparing such heterogeneous and disparate data will help improving functional annotation of genomes. This requires designing elaborate integration systems such as warehouses for storing and querying these data. Results: We have designed a relational genomic warehouse with an original multi-layer architectu...

  20. Emerging applications of read profiles towards the functional annotation of the genome

    Directory of Open Access Journals (Sweden)

    Sachin Pundhir

    2015-05-01

    Full Text Available Functional annotation of the genome in various species is important to understand their phenotypic complexity. The road towards functional annotation involves several challenges ranging from experiments on individual molecules to large-scale analysis of high-throughput sequencing (HTS data. HTS data is typically a result of the protocol designed to address specific research questions. The sequencing results in reads, which when mapped to a reference genome often leads to the formation of distinct patterns (read profiles. Interpretation of these read profiles are essential for the analysis in relation to the research question addressed. Several strategies have been employed at varying levels of abstraction ranging from a somewhat ad hoc to a more systematic analysis of read profiles. These include methods which can compare read profiles, e.g. from direct (non-sequence based alignments to classification of patterns into functional groups. In this review, we highlight the emerging applications of read profiles for the annotation of non-coding RNA and cis-regulatory regions such as enhancers and promoters. We also discuss the biological rationale behind their formation.

  1. CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data.

    Science.gov (United States)

    Wang, Jiawei; Qi, Meifang; Liu, Jian; Zhang, Yijing

    2015-07-01

    High-throughput technology is gradually becoming a powerful tool for routine research in rice. Interpretation of biological significance from the huge amount of data is a critical but non-trivial task, especially for rice, for which gene annotations rely heavily on sequence similarity rather than direct experimental evidence. Here we describe the annotation platform for comprehensive annotation of rice multi-omics data (CARMO), which provides multiple web-based analysis tools for in-depth data mining and visualization. The central idea involves systematic integration of 1819 samples from omics studies and diverse sources of functional evidence (15 401 terms), which are further organized into gene sets and higher-level gene modules. In this way, the high-throughput data may easily be compared across studies and platforms, and integration of multiple types of evidence allows biological interpretation from the level of gene functional modules with high confidence. In addition, the functions and pathways for thousands of genes lacking description or validation may be deduced based on concerted expression of genes within the constructed co-expression networks or gene modules. Overall, CARMO provides comprehensive annotations for transcriptomic datasets, epi-genomic modification sites, single nucleotide polymorphisms identified from genome re-sequencing, and the large gene lists derived from these omics studies. Well-organized results, as well as multiple tools for interactive visualization, are available through a user-friendly web interface. Finally, we illustrate how CARMO enables biological insights using four examples, demonstrating that CARMO is a highly useful resource for intensive data mining and hypothesis generation based on rice multi-omics data. CARMO is freely available online (http://bioinfo.sibs.ac.cn/carmo). PMID:26040787

  2. The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component.

    Science.gov (United States)

    Cherry, J Michael

    2015-12-01

    An ontology is a highly structured form of controlled vocabulary. Each entry in the ontology is commonly called a term. These terms are used when talking about an annotation. However, each term has a definition that, like the definition of a word found within a dictionary, provides the complete usage and detailed explanation of the term. It is critical to consult a term's definition because the distinction between terms can be subtle. The use of ontologies in biology started as a way of unifying communication between scientific communities and to provide a standard dictionary for different topics, including molecular functions, biological processes, mutant phenotypes, chemical properties and structures. The creation of ontology terms and their definitions often requires debate to reach agreement but the result has been a unified descriptive language used to communicate knowledge. In addition to terms and definitions, ontologies require a relationship used to define the type of connection between terms. In an ontology, a term can have more than one parent term, the term above it in an ontology, as well as more than one child, the term below it in the ontology. Many ontologies are used to construct annotations in the Saccharomyces Genome Database (SGD), as in all modern biological databases; however, Gene Ontology (GO), a descriptive system used to categorize gene function, is the most extensively used ontology in SGD annotations. Examples included in this protocol illustrate the structure and features of this ontology. PMID:26631125

  3. Genome-Wide Functional Annotation of Human Protein-Coding Splice Variants Using Multiple Instance Learning.

    Science.gov (United States)

    Panwar, Bharat; Menon, Rajasree; Eksi, Ridvan; Li, Hong-Dong; Omenn, Gilbert S; Guan, Yuanfang

    2016-06-01

    The vast majority of human multiexon genes undergo alternative splicing and produce a variety of splice variant transcripts and proteins, which can perform different functions. These protein-coding splice variants (PCSVs) greatly increase the functional diversity of proteins. Most functional annotation algorithms have been developed at the gene level; the lack of isoform-level gold standards is an important intellectual limitation for currently available machine learning algorithms. The accumulation of a large amount of RNA-seq data in the public domain greatly increases our ability to examine the functional annotation of genes at isoform level. In the present study, we used a multiple instance learning (MIL)-based approach for predicting the function of PCSVs. We used transcript-level expression values and gene-level functional associations from the Gene Ontology database. A support vector machine (SVM)-based 5-fold cross-validation technique was applied. Comparatively, genes with multiple PCSVs performed better than single PCSV genes, and performance also improved when more examples were available to train the models. We demonstrated our predictions using literature evidence of ADAM15, LMNA/C, and DMXL2 genes. All predictions have been implemented in a web resource called "IsoFunc", which is freely available for the global scientific community through http://guanlab.ccmb.med.umich.edu/isofunc . PMID:27142340

  4. Synergistic use of plant-prokaryote comparative genomics for functional annotations

    Directory of Open Access Journals (Sweden)

    Waller Jeffrey C

    2011-06-01

    Full Text Available Abstract Background Identifying functions for all gene products in all sequenced organisms is a central challenge of the post-genomic era. However, at least 30-50% of the proteins encoded by any given genome are of unknown or vaguely known function, and a large number are wrongly annotated. Many of these ‘unknown’ proteins are common to prokaryotes and plants. We set out to predict and experimentally test the functions of such proteins. Our approach to functional prediction integrates comparative genomics based mainly on microbial genomes with functional genomic data from model microorganisms and post-genomic data from plants. This approach bridges the gap between automated homology-based annotations and the classical gene discovery efforts of experimentalists, and is more powerful than purely computational approaches to identifying gene-function associations. Results Among Arabidopsis genes, we focused on those (2,325 in total that (i are unique or belong to families with no more than three members, (ii occur in prokaryotes, and (iii have unknown or poorly known functions. Computer-assisted selection of promising targets for deeper analysis was based on homology-independent characteristics associated in the SEED database with the prokaryotic members of each family. In-depth comparative genomic analysis was performed for 360 top candidate families. From this pool, 78 families were connected to general areas of metabolism and, of these families, specific functional predictions were made for 41. Twenty-one predicted functions have been experimentally tested or are currently under investigation by our group in at least one prokaryotic organism (nine of them have been validated, four invalidated, and eight are in progress. Ten additional predictions have been independently validated by other groups. Discovering the function of very widespread but hitherto enigmatic proteins such as the YrdC or YgfZ families illustrates the power of our approach

  5. Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779.

    Directory of Open Access Journals (Sweden)

    Astrid Vieler

    Full Text Available Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the assembly of the 28.7 Mb genome of N. oceanica CCMP1779. RNA sequencing data from nitrogen-replete and nitrogen-depleted growth conditions support a total of 11,973 genes, of which in addition to automatic annotation some were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors, and 109 transcriptional regulators were annotated. Comparison of the N. oceanica CCMP1779 gene repertoire with the recently published N. gaditana genome identified 2,649 genes likely specific to N. oceanica CCMP1779. Many of these N. oceanica-specific genes have putative orthologs in other species or are supported by transcriptional evidence. However, because similarity-based annotations are limited, functions of most of these species-specific genes remain unknown. Aside from the genome sequence and its analysis, protocols for the transformation of N. oceanica CCMP1779 are provided. The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols, provides a blueprint for future detailed gene functional analysis and genetic engineering of Nannochloropsis

  6. Integrating biological knowledge based on functional annotations for biclustering of gene expression data.

    Science.gov (United States)

    Nepomuceno, Juan A; Troncoso, Alicia; Nepomuceno-Chamorro, Isabel A; Aguilar-Ruiz, Jesús S

    2015-05-01

    Gene expression data analysis is based on the assumption that co-expressed genes imply co-regulated genes. This assumption is being reformulated because the co-expression of a group of genes may be the result of an independent activation with respect to the same experimental condition and not due to the same regulatory regime. For this reason, traditional techniques are recently being improved with the use of prior biological knowledge from open-access repositories together with gene expression data. Biclustering is an unsupervised machine learning technique that searches patterns in gene expression data matrices. A scatter search-based biclustering algorithm that integrates biological information is proposed in this paper. In addition to the gene expression data matrix, the input of the algorithm is only a direct annotation file that relates each gene to a set of terms from a biological repository where genes are annotated. Two different biological measures, FracGO and SimNTO, are proposed to integrate this information by means of its addition to-be-optimized fitness function in the scatter search scheme. The measure FracGO is based on the biological enrichment and SimNTO is based on the overlapping among GO annotations of pairs of genes. Experimental results evaluate the proposed algorithm for two datasets and show the algorithm performs better when biological knowledge is integrated. Moreover, the analysis and comparison between the two different biological measures is presented and it is concluded that the differences depend on both the data source and how the annotation file has been built in the case GO is used. It is also shown that the proposed algorithm obtains a greater number of enriched biclusters than other classical biclustering algorithms typically used as benchmark and an analysis of the overlapping among biclusters reveals that the biclusters obtained present a low overlapping. The proposed methodology is a general-purpose algorithm which allows

  7. Diversity Indices as Measures of Functional Annotation Methods in Metagenomics Studies

    KAUST Repository

    Jankovic, Boris

    2016-01-26

    Applications of high-throughput techniques in metagenomics studies produce massive amounts of data. Fragments of genomic, transcriptomic and proteomic molecules are all found in metagenomics samples. Laborious and meticulous effort in sequencing and functional annotation are then required to, amongst other objectives, reconstruct a taxonomic map of the environment that metagenomics samples were taken from. In addition to computational challenges faced by metagenomics studies, the analysis is further complicated by the presence of contaminants in the samples, potentially resulting in skewed taxonomic analysis. The functional annotation in metagenomics can utilize all available omics data and therefore different methods that are associated with a particular type of data. For example, protein-coding DNA, non-coding RNA or ribosomal RNA data can be used in such an analysis. These methods would have their advantages and disadvantages and the question of comparison among them naturally arises. There are several criteria that can be used when performing such a comparison. Loosely speaking, methods can be evaluated in terms of computational complexity or in terms of the expected biological accuracy. We propose that the concept of diversity that is used in the ecosystems and species diversity studies can be successfully used in evaluating certain aspects of the methods employed in metagenomics studies. We show that when applying the concept of Hill’s diversity, the analysis of variations in the diversity order provides valuable clues into the robustness of methods used in the taxonomical analysis.

  8. Protein variety and functional diversity: Swiss-Prot annotation in its biological context.

    Science.gov (United States)

    Boeckmann, Brigitte; Blatter, Marie-Claude; Famiglietti, Livia; Hinz, Ursula; Lane, Lydie; Roechert, Bernd; Bairoch, Amos

    2005-01-01

    We all know that the dogma 'one gene, one protein' is obsolete. A functional protein and, likewise, a protein's ultimate function depend not only on the underlying genetic information but also on the ongoing conditions of the cellular system. Frequently the transcript, like the polypeptide, is processed in multiple ways, but only one or a few out of a multitude of possible variants are produced at a time. An overview on processes that can lead to sequence variety and structural diversity in eukaryotes is given. The UniProtKB/Swiss-Prot protein knowledgebase provides a wealth of information regarding protein variety, function and associated disorders. Examples for such annotation are shown and further ones are available at http://www.expasy.org/sprot/tutorial/examples_CRB. PMID:16286078

  9. Is functional behavioral assessment functional?

    OpenAIRE

    2006-01-01

    Abstract Traditional methods of discipline, like punishment, suspension, and expulsion have in the past seemed beneficial, on a short-term basis, against problem behavior in schools. Four schools in Norway have recently implemented Functional Behavior Assessment (FBA) as part of a pilot project, to test the School-Wide Positive Behavioral Support (SW-PBS). A completed FBA procedure reveals the setting events, the antecedents and the consequences around the problem behavior, which provides ...

  10. Gene Ontology annotation quality analysis in model eukaryotes

    OpenAIRE

    Buza, Teresia J; McCarthy, Fiona M; Wang, Nan; Bridges, Susan M.; Burgess, Shane C.

    2008-01-01

    Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different sets of gene products. In many cases the source of the GO annotations and the date the GO annotations were last updated is not apparent, further complicating a researchers’ ability to assess the quality of the GO data provided. Moreover, GO biocurators need to ensure that the GO quality is maintai...

  11. Relating gene expression data on two-component systems to functional annotations in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Sule Preeti

    2008-06-01

    Full Text Available Abstract Background Obtaining physiological insights from microarray experiments requires computational techniques that relate gene expression data to functional information. Traditionally, this has been done in two consecutive steps. The first step identifies important genes through clustering or statistical techniques, while the second step assigns biological functions to the identified groups. Recently, techniques have been developed that identify such relationships in a single step. Results We have developed an algorithm that relates patterns of gene expression in a set of microarray experiments to functional groups in one step. Our only assumption is that patterns co-occur frequently. The effectiveness of the algorithm is demonstrated as part of a study of regulation by two-component systems in Escherichia coli. The significance of the relationships between expression data and functional annotations is evaluated based on density histograms that are constructed using product similarity among expression vectors. We present a biological analysis of three of the resulting functional groups of proteins, develop hypotheses for further biological studies, and test one of these hypotheses experimentally. A comparison with other algorithms and a different data set is presented. Conclusion Our new algorithm is able to find interesting and biologically meaningful relationships, not found by other algorithms, in previously analyzed data sets. Scaling of the algorithm to large data sets can be achieved based on a theoretical model.

  12. Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB

    Directory of Open Access Journals (Sweden)

    Antoni Hermoso

    2007-01-01

    Full Text Available Loops represent an important part of protein structures. The study of loop is critical for two main reasons: First, loops are often involved in protein function, stability and folding. Second, despite improvements in experimental and computational structure prediction methods, modeling the conformation of loops remains problematic. Here, we present a structural classification of loops, ArchDB, a mine of information with application in both mentioned fields: loop structure prediction and function prediction. ArchDB (http://sbi.imim.es/archdb is a database of classified protein loop motifs. The current database provides four different classification sets tailored for different purposes. ArchDB-40, a loop classification derived from SCOP40, well suited for modeling common loop motifs. Since features relevant to loop structure or function can be more easily determined on well-populated clusters, we have developed ArchDB-95, a loop classification derived from SCOP95. This new classification set shows a ∼40% increase in the number of subclasses, and a large 7-fold increase in the number of putative structure/function-related subclasses. We also present ArchDB-EC, a classification of loop motifs from enzymes, and ArchDB-KI, a manually annotated classification of loop motifs from kinases. Information about ligand contacts and PDB sites has been included in all classification sets. Improvements in our classification scheme are described, as well as several new database features, such as the ability to query by conserved annotations, sequence similarity, or uploading 3D coordinates of a protein. The lengths of classified loops range between 0 and 36 residues long. ArchDB offers an exhaustive sampling of loop structures. Functional information about loops and links with related biological databases are also provided. All this information and the possibility to browse/query the database through a web-server outline an useful tool with application in the

  13. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

    Directory of Open Access Journals (Sweden)

    Baseler Michael W

    2007-11-01

    Full Text Available Abstract Background Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.

  14. Human cell adhesion molecules: annotated functional subtypes and overrepresentation of addiction-associated genes.

    Science.gov (United States)

    Zhong, Xiaoming; Drgonova, Jana; Li, Chuan-Yun; Uhl, George R

    2015-09-01

    Human cell adhesion molecules (CAMs) are essential for proper development, modulation, and maintenance of interactions between cells and cell-to-cell (and matrix-to-cell) communication about these interactions. Despite the differential functional significance of these roles, there have been surprisingly few systematic studies to enumerate the universe of CAMs and identify specific CAMs in distinct functions. In this paper, we update and review the set of human genes likely to encode CAMs with searches of databases, literature reviews, and annotations. We describe likely CAMs and functional subclasses, including CAMs that have a primary function in information exchange (iCAMs), CAMs involved in focal adhesions, CAM gene products that are preferentially involved with stereotyped and morphologically identifiable connections between cells (e.g., adherens junctions, gap junctions), and smaller numbers of CAM genes in other classes. We discuss a novel proposed mechanism involving selective anchoring of the constituents of iCAM-containing lipid rafts in zones of close neuronal apposition to membranes expressing iCAM binding partners. We also discuss data from genetic and genomic studies of addiction in humans and mouse models to highlight the ways in which CAM variation may contribute to a specific brain-based disorder such as addiction. Specific examples include changes in CAM mRNA splicing mediated by differences in the addiction-associated splicing regulator RBFOX1/A2BP1 and CAM expression in dopamine neurons. PMID:25988664

  15. Exploratory Analysis of Biological Networks through Visualization, Clustering, and Functional Annotation in Cytoscape.

    Science.gov (United States)

    Baryshnikova, Anastasia

    2016-01-01

    Biological networks define how genes, proteins, and other cellular components interact with one another to carry out specific functions, providing a scaffold for understanding cellular organization. Although in-depth network analysis requires advanced mathematical and computational knowledge, a preliminary visual exploration of biological networks is accessible to anyone with basic computer skills. Visualization of biological networks is used primarily to examine network topology, identify functional modules, and predict gene functions based on gene connectivity within the network. Networks are excellent at providing a bird's-eye view of data sets and have the power of illustrating complex ideas in simple and intuitive terms. In addition, they enable exploratory analysis and generation of new hypotheses, which can then be tested using rigorous statistical and experimental tools. This protocol describes a simple procedure for visualizing a biological network using the genetic interaction similarity network for Saccharomyces cerevisiae as an example. The visualization procedure described here relies on the open-source network visualization software Cytoscape and includes detailed instructions on formatting and loading the data, clustering networks, and overlaying functional annotations. PMID:26988373

  16. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

    DEFF Research Database (Denmark)

    Huerta-Cepas, Jaime; Szklarczyk, Damian; Forslund, Kristoffer;

    2016-01-01

    eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making ...

  17. Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven approach

    Directory of Open Access Journals (Sweden)

    Bárcena José A

    2008-12-01

    Full Text Available Abstract Background Annotation of protein-coding genes is a key step in sequencing projects. Protein functions are mainly assigned on the basis of the amino acid sequence alone by searching of homologous proteins. However, fully automated annotation processes often lead to wrong prediction of protein functions, and therefore time-intensive manual curation is often essential. Here we describe a fast and reliable way to correct function annotation in sequencing projects, focusing on surface proteomes. We use a proteomics approach, previously proven to be very powerful for identifying new vaccine candidates against Gram-positive pathogens. It consists of shaving the surface of intact cells with two proteases, the specific cleavage-site trypsin and the unspecific proteinase K, followed by LC/MS/MS analysis of the resulting peptides. The identified proteins are contrasted by computational analysis and their sequences are inspected to correct possible errors in function prediction. Results When applied to the zoonotic pathogen Streptococcus suis, of which two strains have been recently sequenced and annotated, we identified a set of surface proteins without cytoplasmic contamination: all the proteins identified had exporting or retention signals towards the outside and/or the cell surface, and viability of protease-treated cells was not affected. The combination of both experimental evidences and computational methods allowed us to determine that two of these proteins are putative extracellular new adhesins that had been previously attributed a wrong cytoplasmic function. One of them is a putative component of the pilus of this bacterium. Conclusion We illustrate the complementary nature of laboratory-based and computational methods to examine in concert the localization of a set of proteins in the cell, and demonstrate the utility of this proteomics-based strategy to experimentally correct function annotation errors in sequencing projects. This

  18. Gene Ontology annotation quality analysis in model eukaryotes

    Science.gov (United States)

    Buza, Teresia J.; McCarthy, Fiona M.; Wang, Nan; Bridges, Susan M.; Burgess, Shane C.

    2008-01-01

    Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different sets of gene products. In many cases the source of the GO annotations and the date the GO annotations were last updated is not apparent, further complicating a researchers’ ability to assess the quality of the GO data provided. Moreover, GO biocurators need to ensure that the GO quality is maintained and optimal for the functional processes that are most relevant for their research community. We report the GO Annotation Quality (GAQ) score, a quantitative measure of GO quality that includes breadth of GO annotation, the level of detail of annotation and the type of evidence used to make the annotation. As a case study, we apply the GAQ scoring method to a set of diverse eukaryotes and demonstrate how the GAQ score can be used to track changes in GO annotations over time and to assess the quality of GO annotations available for specific biological processes. The GAQ score also allows researchers to quantitatively assess the functional data available for their experimental systems (arrays or databases). PMID:18187504

  19. ARC: Automated Resource Classifier for agglomerative functional classification of prokaryotic proteins using annotation texts

    Indian Academy of Sciences (India)

    Muthiah Gnanamani; Naveen Kumar; Srinivasan Ramachandran

    2007-08-01

    Functional classification of proteins is central to comparative genomics. The need for algorithms tuned to enable integrative interpretation of analytical data is felt globally. The availability of a general, automated software with built-in flexibility will significantly aid this activity. We have prepared ARC (Automated Resource Classifier), which is an open source software meeting the user requirements of flexibility. The default classification scheme based on keyword match is agglomerative and directs entries into any of the 7 basic non-overlapping functional classes: Cell wall, Cell membrane and Transporters ($\\mathcal{C}$), Cell division ($\\mathcal{D}$), Information ($\\mathcal{I}$), Translocation ($\\mathcal{L}$), Metabolism ($\\mathcal{M}$), Stress($\\mathcal{R}$), Signal and communication($\\mathcal{S}$) and 2 ancillary classes: Others ($\\mathcal{O}$) and Hypothetical ($\\mathcal{H}$). The keyword library of ARC was built serially by first drawing keywords from Bacillus subtilis and Escherichia coli K12. In subsequent steps, this library was further enriched by collecting terms from archaeal representative Archaeoglobus fulgidus, Gene Ontology, and Gene Symbols. ARC is 94.04% successful on 6,75,663 annotated proteins from 348 prokaryotes. Three examples are provided to illuminate the current perspectives on mycobacterial physiology and costs of proteins in 333 prokaryotes. ARC is available at http://arc.igib.res.in.

  20. Gene expression and functional annotation of the human ciliary body epithelia.

    Directory of Open Access Journals (Sweden)

    Sarah F Janssen

    Full Text Available PURPOSE: The ciliary body (CB of the human eye consists of the non-pigmented (NPE and pigmented (PE neuro-epithelia. We investigated the gene expression of NPE and PE, to shed light on the molecular mechanisms underlying the most important functions of the CB. We also developed molecular signatures for the NPE and PE and studied possible new clues for glaucoma. METHODS: We isolated NPE and PE cells from seven healthy human donor eyes using laser dissection microscopy. Next, we performed RNA isolation, amplification, labeling and hybridization against 44×k Agilent microarrays. For microarray conformations, we used a literature study, RT-PCRs, and immunohistochemical stainings. We analyzed the gene expression data with R and with the knowledge database Ingenuity. RESULTS: The gene expression profiles and functional annotations of the NPE and PE were highly similar. We found that the most important functionalities of the NPE and PE were related to developmental processes, neural nature of the tissue, endocrine and metabolic signaling, and immunological functions. In total 1576 genes differed statistically significantly between NPE and PE. From these genes, at least 3 were cell-specific for the NPE and 143 for the PE. Finally, we observed high expression in the (NPE of 35 genes previously implicated in molecular mechanisms related to glaucoma. CONCLUSION: Our gene expression analysis suggested that the NPE and PE of the CB were quite similar. Nonetheless, cell-type specific differences were found. The molecular machineries of the human NPE and PE are involved in a range of neuro-endocrinological, developmental and immunological functions, and perhaps glaucoma.

  1. On Anomalies in Annotation Systems

    CERN Document Server

    Brust, Matthias R

    2007-01-01

    Today's computer-based annotation systems implement a wide range of functionalities that often go beyond those available in traditional paper-and-pencil annotations. Conceptually, annotation systems are based on thoroughly investigated psycho-sociological and pedagogical learning theories. They offer a huge diversity of annotation types that can be placed in textual as well as in multimedia format. Additionally, annotations can be published or shared with a group of interested parties via well-organized repositories. Although highly sophisticated annotation systems exist both conceptually as well as technologically, we still observe that their acceptance is somewhat limited. In this paper, we argue that nowadays annotation systems suffer from several fundamental problems that are inherent in the traditional paper-and-pencil annotation paradigm. As a solution, we propose to shift the annotation paradigm for the implementation of annotation system.

  2. RNA-seq analysis of Quercus pubescens Leaves: de novo transcriptome assembly, annotation and functional markers development.

    Directory of Open Access Journals (Sweden)

    Sara Torre

    Full Text Available Quercus pubescens Willd., a species distributed from Spain to southwest Asia, ranks high for drought tolerance among European oaks. Q. pubescens performs a role of outstanding significance in most Mediterranean forest ecosystems, but few mechanistic studies have been conducted to explore its response to environmental constrains, due to the lack of genomic resources. In our study, we performed a deep transcriptomic sequencing in Q. pubescens leaves, including de novo assembly, functional annotation and the identification of new molecular markers. Our results are a pre-requisite for undertaking molecular functional studies, and may give support in population and association genetic studies. 254,265,700 clean reads were generated by the Illumina HiSeq 2000 platform, with an average length of 98 bp. De novo assembly, using CLC Genomics, produced 96,006 contigs, having a mean length of 618 bp. Sequence similarity analyses against seven public databases (Uniprot, NR, RefSeq and KOGs at NCBI, Pfam, InterPro and KEGG resulted in 83,065 transcripts annotated with gene descriptions, conserved protein domains, or gene ontology terms. These annotations and local BLAST allowed identify genes specifically associated with mechanisms of drought avoidance. Finally, 14,202 microsatellite markers and 18,425 single nucleotide polymorphisms (SNPs were, in silico, discovered in assembled and annotated sequences. We completed a successful global analysis of the Q. pubescens leaf transcriptome using RNA-seq. The assembled and annotated sequences together with newly discovered molecular markers provide genomic information for functional genomic studies in Q. pubescens, with special emphasis to response mechanisms to severe constrain of the Mediterranean climate. Our tools enable comparative genomics studies on other Quercus species taking advantage of large intra-specific ecophysiological differences.

  3. RNA-Seq Analysis of Quercus pubescens Leaves: De Novo Transcriptome Assembly, Annotation and Functional Markers Development

    Science.gov (United States)

    Torre, Sara; Tattini, Massimiliano; Brunetti, Cecilia; Fineschi, Silvia; Fini, Alessio; Ferrini, Francesco; Sebastiani, Federico

    2014-01-01

    Quercus pubescens Willd., a species distributed from Spain to southwest Asia, ranks high for drought tolerance among European oaks. Q. pubescens performs a role of outstanding significance in most Mediterranean forest ecosystems, but few mechanistic studies have been conducted to explore its response to environmental constrains, due to the lack of genomic resources. In our study, we performed a deep transcriptomic sequencing in Q. pubescens leaves, including de novo assembly, functional annotation and the identification of new molecular markers. Our results are a pre-requisite for undertaking molecular functional studies, and may give support in population and association genetic studies. 254,265,700 clean reads were generated by the Illumina HiSeq 2000 platform, with an average length of 98 bp. De novo assembly, using CLC Genomics, produced 96,006 contigs, having a mean length of 618 bp. Sequence similarity analyses against seven public databases (Uniprot, NR, RefSeq and KOGs at NCBI, Pfam, InterPro and KEGG) resulted in 83,065 transcripts annotated with gene descriptions, conserved protein domains, or gene ontology terms. These annotations and local BLAST allowed identify genes specifically associated with mechanisms of drought avoidance. Finally, 14,202 microsatellite markers and 18,425 single nucleotide polymorphisms (SNPs) were, in silico, discovered in assembled and annotated sequences. We completed a successful global analysis of the Q. pubescens leaf transcriptome using RNA-seq. The assembled and annotated sequences together with newly discovered molecular markers provide genomic information for functional genomic studies in Q. pubescens, with special emphasis to response mechanisms to severe constrain of the Mediterranean climate. Our tools enable comparative genomics studies on other Quercus species taking advantage of large intra-specific ecophysiological differences. PMID:25393112

  4. Cellular functions of genetically imprinted genes in human and mouse as annotated in the gene ontology.

    Science.gov (United States)

    Hamed, Mohamed; Ismael, Siba; Paulsen, Martina; Helms, Volkhard

    2012-01-01

    By analyzing the cellular functions of genetically imprinted genes as annotated in the Gene Ontology for human and mouse, we found that imprinted genes are often involved in developmental, transport and regulatory processes. In the human, paternally expressed genes are enriched in GO terms related to the development of organs and of anatomical structures. In the mouse, maternally expressed genes regulate cation transport as well as G-protein signaling processes. Furthermore, we investigated if imprinted genes are regulated by common transcription factors. We identified 25 TF families that showed an enrichment of binding sites in the set of imprinted genes in human and 40 TF families in mouse. In general, maternally and paternally expressed genes are not regulated by different transcription factors. The genes Nnat, Klf14, Blcap, Gnas and Ube3a contribute most to the enrichment of TF families. In the mouse, genes that are maternally expressed in placenta are enriched for AP1 binding sites. In the human, we found that these genes possessed binding sites for both, AP1 and SP1. PMID:23226257

  5. Cellular functions of genetically imprinted genes in human and mouse as annotated in the gene ontology.

    Directory of Open Access Journals (Sweden)

    Mohamed Hamed

    Full Text Available By analyzing the cellular functions of genetically imprinted genes as annotated in the Gene Ontology for human and mouse, we found that imprinted genes are often involved in developmental, transport and regulatory processes. In the human, paternally expressed genes are enriched in GO terms related to the development of organs and of anatomical structures. In the mouse, maternally expressed genes regulate cation transport as well as G-protein signaling processes. Furthermore, we investigated if imprinted genes are regulated by common transcription factors. We identified 25 TF families that showed an enrichment of binding sites in the set of imprinted genes in human and 40 TF families in mouse. In general, maternally and paternally expressed genes are not regulated by different transcription factors. The genes Nnat, Klf14, Blcap, Gnas and Ube3a contribute most to the enrichment of TF families. In the mouse, genes that are maternally expressed in placenta are enriched for AP1 binding sites. In the human, we found that these genes possessed binding sites for both, AP1 and SP1.

  6. De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome

    Science.gov (United States)

    Muñoz-Mérida, Antonio; González-Plaza, Juan José; Cañada, Andrés; Blanco, Ana María; García-López, Maria del Carmen; Rodríguez, José Manuel; Pedrola, Laia; Sicardo, M. Dolores; Hernández, M. Luisa; De la Rosa, Raúl; Belaj, Angjelina; Gil-Borja, Mayte; Luque, Francisco; Martínez-Rivas, José Manuel; Pisano, David G.; Trelles, Oswaldo; Valpuesta, Victoriano; Beuzón, Carmen R.

    2013-01-01

    Olive breeding programmes are focused on selecting for traits as short juvenile period, plant architecture suited for mechanical harvest, or oil characteristics, including fatty acid composition, phenolic, and volatile compounds to suit new markets. Understanding the molecular basis of these characteristics and improving the efficiency of such breeding programmes require the development of genomic information and tools. However, despite its economic relevance, genomic information on olive or closely related species is still scarce. We have applied Sanger and 454 pyrosequencing technologies to generate close to 2 million reads from 12 cDNA libraries obtained from the Picual, Arbequina, and Lechin de Sevilla cultivars and seedlings from a segregating progeny of a Picual × Arbequina cross. The libraries include fruit mesocarp and seeds at three relevant developmental stages, young stems and leaves, active juvenile and adult buds as well as dormant buds, and juvenile and adult roots. The reads were assembled by library or tissue and then assembled together into 81 020 unigenes with an average size of 496 bases. Here, we report their assembly and their functional annotation. PMID:23297299

  7. Automated annotation of functional imaging experiments via multi-label classification

    Directory of Open Access Journals (Sweden)

    MatthewDTurner

    2013-12-01

    Full Text Available Identifying the experimental methods in human neuroimaging papers is important for grouping meaningfully similar experiments for meta-analyses. Currently, this can only be done by human readers. We present the performance of common machine learning (text mining methods applied to the problem of automatically classifying or labeling this literature. Labeling terms are from the Cognitive Paradigm Ontology (CogPO, the text corpora are abstracts of published functional neuroimaging papers, and the methods use the performance of a human expert as training data. We aim to replicate the expert's annotation of multiple labels per abstract identifying the experimental stimuli, cognitive paradigms, response types, and other relevant dimensions of the experiments. We use several standard machine learning methods: naive Bayes, k-nearest neighbor, and support vector machines (specifically SMO or sequential minimal optimization. Exact match performance ranged from only 15% in the worst cases to 78% in the best cases. Naive Bayes methods combined with binary relevance transformations performed strongly and were robust to overfitting. This collection of results demonstrates what can be achieved with off-the-shelf software components and little to no pre-processing of raw text.

  8. Comparative annotation of functional regions in the human genome using epigenomic data.

    Science.gov (United States)

    Won, Kyoung-Jae; Zhang, Xian; Wang, Tao; Ding, Bo; Raha, Debasish; Snyder, Michael; Ren, Bing; Wang, Wei

    2013-04-01

    Epigenetic regulation is dynamic and cell-type dependent. The recently available epigenomic data in multiple cell types provide an unprecedented opportunity for a comparative study of epigenetic landscape. We developed a machine-learning method called ChroModule to annotate the epigenetic states in eight ENCyclopedia Of DNA Elements cell types. The trained model successfully captured the characteristic histone-modification patterns associated with regulatory elements, such as promoters and enhancers, and showed superior performance on identifying enhancers compared with the state-of-art methods. In addition, given the fixed number of epigenetic states in the model, ChroModule allows straightforward illustration of epigenetic variability in multiple cell types. Using this feature, we found that invariable and variable epigenetic states across cell types correspond to housekeeping functions and stimulus response, respectively. Especially, we observed that enhancers, but not the other regulatory elements, dictate cell specificity, as similar cell types share common enhancers, and cell-type-specific enhancers are often bound by transcription factors playing critical roles in that cell type. More interestingly, we found some genomic regions are dormant in cell type but primed to become active in other cell types. These observations highlight the usefulness of ChroModule in comparative analysis and interpretation of multiple epigenomes. PMID:23482391

  9. Annotated English

    CERN Document Server

    Hernandez-Orallo, Jose

    2010-01-01

    This document presents Annotated English, a system of diacritical symbols which turns English pronunciation into a precise and unambiguous process. The annotations are defined and located in such a way that the original English text is not altered (not even a letter), thus allowing for a consistent reading and learning of the English language with and without annotations. The annotations are based on a set of general rules that make the frequency of annotations not dramatically high. This makes the reader easily associate annotations with exceptions, and makes it possible to shape, internalise and consolidate some rules for the English language which otherwise are weakened by the enormous amount of exceptions in English pronunciation. The advantages of this annotation system are manifold. Any existing text can be annotated without a significant increase in size. This means that we can get an annotated version of any document or book with the same number of pages and fontsize. Since no letter is affected, the ...

  10. Annotations for Intersection Typechecking

    Directory of Open Access Journals (Sweden)

    Joshua Dunfield

    2013-07-01

    Full Text Available In functional programming languages, the classic form of annotation is a single type constraint on a term. Intersection types add complications: a single term may have to be checked several times against different types, in different contexts, requiring annotation with several types. Moreover, it is useful (in some systems, necessary to indicate the context in which each such type is to be used. This paper explores the technical design space of annotations in systems with intersection types. Earlier work (Dunfield and Pfenning 2004 introduced contextual typing annotations, which we now tease apart into more elementary mechanisms: a "right hand" annotation (the standard form, a "left hand" annotation (the context in which a right-hand annotation is to be used, a merge that allows for multiple annotations, and an existential binder for index variables. The most novel element is the left-hand annotation, which guards terms (and right-hand annotations with a judgment that must follow from the current context.

  11. Generation, analysis and functional annotation of expressed sequence tags from the ectoparasitic mite Psoroptes ovis

    Directory of Open Access Journals (Sweden)

    Kenyon Fiona

    2011-07-01

    Full Text Available Abstract Background Sheep scab is caused by Psoroptes ovis and is arguably the most important ectoparasitic disease affecting sheep in the UK. The disease is highly contagious and causes and considerable pruritis and irritation and is therefore a major welfare concern. Current methods of treatment are unsustainable and in order to elucidate novel methods of disease control a more comprehensive understanding of the parasite is required. To date, no full genomic DNA sequence or large scale transcript datasets are available and prior to this study only 484 P. ovis expressed sequence tags (ESTs were accessible in public databases. Results In order to further expand upon the transcriptomic coverage of P. ovis thus facilitating novel insights into the mite biology we undertook a larger scale EST approach, incorporating newly generated and previously described P. ovis transcript data and representing the largest collection of P. ovis ESTs to date. We sequenced 1,574 ESTs and assembled these along with 484 previously generated P. ovis ESTs, which resulted in the identification of 1,545 unique P. ovis sequences. BLASTX searches identified 961 ESTs with significant hits (E-value P. ovis ESTs. Gene Ontology (GO analysis allowed the functional annotation of 880 ESTs and included predictions of signal peptide and transmembrane domains; allowing the identification of potential P. ovis excreted/secreted factors, and mapping of metabolic pathways. Conclusions This dataset currently represents the largest collection of P. ovis ESTs, all of which are publicly available in the GenBank EST database (dbEST (accession numbers FR748230 - FR749648. Functional analysis of this dataset identified important homologues, including house dust mite allergens and tick salivary factors. These findings offer new insights into the underlying biology of P. ovis, facilitating further investigations into mite biology and the identification of novel methods of intervention.

  12. Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid

    Directory of Open Access Journals (Sweden)

    Kumari Sunita

    2011-10-01

    expression and functional annotation in response to drought.

  13. De novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Wen Dee Ong

    Full Text Available BACKGROUND: Pineapple (Ananas comosus var. comosus, is an important tropical non-climacteric fruit with high commercial potential. Understanding the mechanism and processes underlying fruit ripening would enable scientists to enhance the improvement of quality traits such as, flavor, texture, appearance and fruit sweetness. Although, the pineapple is an important fruit, there is insufficient transcriptomic or genomic information that is available in public databases. Application of high throughput transcriptome sequencing to profile the pineapple fruit transcripts is therefore needed. METHODOLOGY/PRINCIPAL FINDINGS: To facilitate this, we have performed transcriptome sequencing of ripe yellow pineapple fruit flesh using Illumina technology. About 4.7 millions Illumina paired-end reads were generated and assembled using the Velvet de novo assembler. The assembly produced 28,728 unique transcripts with a mean length of approximately 200 bp. Sequence similarity search against non-redundant NCBI database identified a total of 16,932 unique transcripts (58.93% with significant hits. Out of these, 15,507 unique transcripts were assigned to gene ontology terms. Functional annotation against Kyoto Encyclopedia of Genes and Genomes pathway database identified 13,598 unique transcripts (47.33% which were mapped to 126 pathways. The assembly revealed many transcripts that were previously unknown. CONCLUSIONS: The unique transcripts derived from this work have rapidly increased of the number of the pineapple fruit mRNA transcripts as it is now available in public databases. This information can be further utilized in gene expression, genomics and other functional genomics studies in pineapple.

  14. Integrative analysis of functional genomic annotations and sequencing data to identify rare causal variants via hierarchical modeling

    Directory of Open Access Journals (Sweden)

    Marinela eCapanu

    2015-05-01

    Full Text Available Identifying the small number of rare causal variants contributing to disease has beena major focus of investigation in recent years, but represents a formidable statisticalchallenge due to the rare frequencies with which these variants are observed. In thiscommentary we draw attention to a formal statistical framework, namely hierarchicalmodeling, to combine functional genomic annotations with sequencing data with theobjective of enhancing our ability to identify rare causal variants. Using simulations weshow that in all configurations studied, the hierarchical modeling approach has superiordiscriminatory ability compared to a recently proposed aggregate measure of deleteriousness,the Combined Annotation-Dependent Depletion (CADD score, supportingour premise that aggregate functional genomic measures can more accurately identifycausal variants when used in conjunction with sequencing data through a hierarchicalmodeling approach

  15. FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression

    OpenAIRE

    Kolell Kevin J; Wyckoff Gerald J; Whitehead J Andrew; Roach Jennifer L; VanWye Jeffrey D; Oleksiak Marjorie F; Paschall Justin E; Crawford Douglas L

    2004-01-01

    Abstract Background While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to...

  16. RNA-Seq Analysis of Quercus pubescens Leaves: De Novo Transcriptome Assembly, Annotation and Functional Markers Development

    OpenAIRE

    Sara Torre; Massimiliano Tattini; Cecilia Brunetti; Silvia Fineschi; Alessio Fini; Francesco Ferrini; Federico Sebastiani

    2014-01-01

    Quercus pubescens Willd., a species distributed from Spain to southwest Asia, ranks high for drought tolerance among European oaks. Q. pubescens performs a role of outstanding significance in most Mediterranean forest ecosystems, but few mechanistic studies have been conducted to explore its response to environmental constrains, due to the lack of genomic resources. In our study, we performed a deep transcriptomic sequencing in Q. pubescens leaves, including de novo assembly, functional annot...

  17. Functional assessment of time course microarray data

    Science.gov (United States)

    Nueda, María José; Sebastián, Patricia; Tarazona, Sonia; García-García, Francisco; Dopazo, Joaquín; Ferrer, Alberto; Conesa, Ana

    2009-01-01

    Motivation Time-course microarray experiments study the progress of gene expression along time across one or several experimental conditions. Most developed analysis methods focus on the clustering or the differential expression analysis of genes and do not integrate functional information. The assessment of the functional aspects of time-course transcriptomics data requires the use of approaches that exploit the activation dynamics of the functional categories to where genes are annotated. Methods We present three novel methodologies for the functional assessment of time-course microarray data. i) maSigFun derives from the maSigPro method, a regression-based strategy to model time-dependent expression patterns and identify genes with differences across series. maSigFun fits a regression model for groups of genes labeled by a functional class and selects those categories which have a significant model. ii) PCA-maSigFun fits a PCA model of each functional class-defined expression matrix to extract orthogonal patterns of expression change, which are then assessed for their fit to a time-dependent regression model. iii) ASCA-functional uses the ASCA model to rank genes according to their correlation to principal time expression patterns and assess functional enrichment on a GSA fashion. We used simulated and experimental datasets to study these novel approaches. Results were compared to alternative methodologies. Results Synthetic and experimental data showed that the different methods are able to capture different aspects of the relationship between genes, functions and co-expression that are biologically meaningful. The methods should not be considered as competitive but they provide different insights into the molecular and functional dynamic events taking place within the biological system under study. PMID:19534758

  18. Use of Modern Chemical Protein Synthesis and Advanced Fluorescent Assay Techniques to Experimentally Validate the Functional Annotation of Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kent, Stephen [University of Chicago

    2012-07-20

    The objective of this research program was to prototype methods for the chemical synthesis of predicted protein molecules in annotated microbial genomes. High throughput chemical methods were to be used to make large numbers of predicted proteins and protein domains, based on microbial genome sequences. Microscale chemical synthesis methods for the parallel preparation of peptide-thioester building blocks were developed; these peptide segments are used for the parallel chemical synthesis of proteins and protein domains. Ultimately, it is envisaged that these synthetic molecules would be ‘printed’ in spatially addressable arrays. The unique ability of total synthesis to precision label protein molecules with dyes and with chemical or biochemical ‘tags’ can be used to facilitate novel assay technologies adapted from state-of-the art single molecule fluorescence detection techniques. In the future, in conjunction with modern laboratory automation this integrated set of techniques will enable high throughput experimental validation of the functional annotation of microbial genomes.

  19. MicroRNA expression profiling and functional annotation analysis of their targets in patients with type 1 diabetes mellitus.

    Science.gov (United States)

    Takahashi, Paula; Xavier, Danilo J; Evangelista, Adriane F; Manoel-Caetano, Fernanda S; Macedo, Claudia; Collares, Cristhianna V A; Foss-Freitas, Maria C; Foss, Milton C; Rassi, Diane M; Donadi, Eduardo A; Passos, Geraldo A; Sakamoto-Hojo, Elza T

    2014-04-15

    Type 1 diabetes mellitus (T1DM) results from an autoimmune attack against the insulin-producing pancreatic β-cells, leading to elimination of insulin production. The exact cause of this disorder is still unclear. Although the differential expression of microRNAs (miRNAs), small non-coding RNAs that control gene expression in a post-transcriptional manner, has been identified in many diseases, including T1DM, only scarce information exists concerning miRNA expression profile in T1DM. Thus, we employed the microarray technology to examine the miRNA expression profiles displayed by peripheral blood mononuclear cells (PBMCs) from T1DM patients compared with healthy subjects. Total RNA extracted from PBMCs from 11 T1DM patients and nine healthy subjects was hybridized onto Agilent human miRNA microarray slides (V3), 8x15K, and expression data were analyzed on R statistical environment. After applying the rank products statistical test, the receiver-operating characteristic (ROC) curves were generated and the areas under the ROC curves (AUC) were calculated. To examine the functions of the differentially expressed (p-value<0.01, percentage of false-positives <0.05) miRNAs that passed the AUC cutoff value ≥ 0.90, the database miRWalk was used to predict their potential targets, which were afterwards submitted to the functional annotation tool provided by the Database for Annotation, Visualization, and Integrated Discovery (DAVID), version 6.7, using annotations from the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found 57 probes, corresponding to 44 different miRNAs (35 up-regulated and 9 down-regulated), that were differentially expressed in T1DM and passed the AUC threshold of 0.90. The hierarchical clustering analysis indicated the discriminatory power of those miRNAs, since they were able to clearly distinguish T1DM patients from healthy individuals. Target prediction indicated that 47 candidate genes for T1DM are potentially regulated by

  20. Improving microbial genome annotations in an integrated database context.

    Directory of Open Access Journals (Sweden)

    I-Min A Chen

    Full Text Available Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.

  1. The Genome Sequence of Leishmania (Leishmania) amazonensis: Functional Annotation and Extended Analysis of Gene Models

    OpenAIRE

    Real, Fernando; Vidal, Ramon Oliveira; Carazzolle, Marcelo Falsarella; Mondego, Jorge Maurício Costa; Costa, Gustavo Gilson Lacerda; Herai, Roberto Hirochi; Würtele, Martin; de Carvalho, Lucas Miguel; e Ferreira, Renata Carmona; Mortara, Renato Arruda; Barbiéri, Clara Lucia; Mieczkowski, Piotr; da Silveira, José Franco; Briones, Marcelo Ribeiro da Silva; Pereira, Gonçalo Amarante Guimarães

    2013-01-01

    We present the sequencing and annotation of the Leishmania (Leishmania) amazonensis genome, an etiological agent of human cutaneous leishmaniasis in the Amazon region of Brazil. L. (L.) amazonensis shares features with Leishmania (L.) mexicana but also exhibits unique characteristics regarding geographical distribution and clinical manifestations of cutaneous lesions (e.g. borderline disseminated cutaneous leishmaniasis). Predicted genes were scored for orthologous gene families and conserved...

  2. Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors

    Directory of Open Access Journals (Sweden)

    Wuyi Liu

    2013-01-01

    Full Text Available The previous survey identified 70 basic helix-loop-helix (bHLH proteins, but it was proved to be incomplete, and the functional information and regulatory networks of frog bHLH transcription factors were not fully known. Therefore, we conducted an updated genome-wide survey in the Xenopus tropicalis genome project databases and identified 105 bHLH sequences. Among the retrieved 105 sequences, phylogenetic analyses revealed that 103 bHLH proteins belonged to 43 families or subfamilies with 46, 26, 11, 3, 15, and 4 members in the corresponding supergroups. Next, gene ontology (GO enrichment analyses showed 65 significant GO annotations of biological processes and molecular functions and KEGG pathways counted in frequency. To explore the functional pathways, regulatory gene networks, and/or related gene groups coding for Xenopus tropicalis bHLH proteins, the identified bHLH genes were put into the databases KOBAS and STRING to get the signaling information of pathways and protein interaction networks according to available public databases and known protein interactions. From the genome annotation and pathway analysis using KOBAS, we identified 16 pathways in the Xenopus tropicalis genome. From the STRING interaction analysis, 68 hub proteins were identified, and many hub proteins created a tight network or a functional module within the protein families.

  3. Non-gaussian distributions affect identification of expression patterns, functional annotation, and prospective classification in human cancer genomes.

    Directory of Open Access Journals (Sweden)

    Nicholas F Marko

    Full Text Available INTRODUCTION: Gene expression data is often assumed to be normally-distributed, but this assumption has not been tested rigorously. We investigate the distribution of expression data in human cancer genomes and study the implications of deviations from the normal distribution for translational molecular oncology research. METHODS: We conducted a central moments analysis of five cancer genomes and performed empiric distribution fitting to examine the true distribution of expression data both on the complete-experiment and on the individual-gene levels. We used a variety of parametric and nonparametric methods to test the effects of deviations from normality on gene calling, functional annotation, and prospective molecular classification using a sixth cancer genome. RESULTS: Central moments analyses reveal statistically-significant deviations from normality in all of the analyzed cancer genomes. We observe as much as 37% variability in gene calling, 39% variability in functional annotation, and 30% variability in prospective, molecular tumor subclassification associated with this effect. CONCLUSIONS: Cancer gene expression profiles are not normally-distributed, either on the complete-experiment or on the individual-gene level. Instead, they exhibit complex, heavy-tailed distributions characterized by statistically-significant skewness and kurtosis. The non-Gaussian distribution of this data affects identification of differentially-expressed genes, functional annotation, and prospective molecular classification. These effects may be reduced in some circumstances, although not completely eliminated, by using nonparametric analytics. This analysis highlights two unreliable assumptions of translational cancer gene expression analysis: that "small" departures from normality in the expression data distributions are analytically-insignificant and that "robust" gene-calling algorithms can fully compensate for these effects.

  4. Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

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    Chuming Chen

    Full Text Available The accelerating growth in the number of protein sequences taxes both the computational and manual resources needed to analyze them. One approach to dealing with this problem is to minimize the number of proteins subjected to such analysis in a way that minimizes loss of information. To this end we have developed a set of Representative Proteomes (RPs, each selected from a Representative Proteome Group (RPG containing similar proteomes calculated based on co-membership in UniRef50 clusters. A Representative Proteome is the proteome that can best represent all the proteomes in its group in terms of the majority of the sequence space and information. RPs at 75%, 55%, 35% and 15% co-membership threshold (CMT are provided to allow users to decrease or increase the granularity of the sequence space based on their requirements. We find that a CMT of 55% (RP55 most closely follows standard taxonomic classifications. Further analysis of this set reveals that sequence space is reduced by more than 80% relative to UniProtKB, while retaining both sequence diversity (over 95% of InterPro domains and annotation information (93% of experimentally characterized proteins. All sets can be browsed and are available for sequence similarity searches and download at http://www.proteininformationresource.org/rps, while the set of 637 RPs determined using a 55% CMT are also available for text searches. Potential applications include sequence similarity searches, protein classification and targeted protein annotation and characterization.

  5. Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation.

    Science.gov (United States)

    Chen, Chuming; Natale, Darren A; Finn, Robert D; Huang, Hongzhan; Zhang, Jian; Wu, Cathy H; Mazumder, Raja

    2011-01-01

    The accelerating growth in the number of protein sequences taxes both the computational and manual resources needed to analyze them. One approach to dealing with this problem is to minimize the number of proteins subjected to such analysis in a way that minimizes loss of information. To this end we have developed a set of Representative Proteomes (RPs), each selected from a Representative Proteome Group (RPG) containing similar proteomes calculated based on co-membership in UniRef50 clusters. A Representative Proteome is the proteome that can best represent all the proteomes in its group in terms of the majority of the sequence space and information. RPs at 75%, 55%, 35% and 15% co-membership threshold (CMT) are provided to allow users to decrease or increase the granularity of the sequence space based on their requirements. We find that a CMT of 55% (RP55) most closely follows standard taxonomic classifications. Further analysis of this set reveals that sequence space is reduced by more than 80% relative to UniProtKB, while retaining both sequence diversity (over 95% of InterPro domains) and annotation information (93% of experimentally characterized proteins). All sets can be browsed and are available for sequence similarity searches and download at http://www.proteininformationresource.org/rps, while the set of 637 RPs determined using a 55% CMT are also available for text searches. Potential applications include sequence similarity searches, protein classification and targeted protein annotation and characterization. PMID:21556138

  6. An in silico Approach for Structural and Functional Annotation of Salmonella enterica serovar typhimurium Hypothetical Protein R_27

    Directory of Open Access Journals (Sweden)

    Arif Khan

    2016-03-01

    Full Text Available Typhoid fever is a major cause of illness in most developing countries, including Bangladesh. In quest of new potential drug against Typhoid fever, the current study was designed to elucidate structural and functional details of S. typhi hypothetical protein (HP R_27. HP R_27 has the primary amino acid sequences available only. The structural annotation was determined by ProtParam, SOPMA, and CELLO. The three-dimensional (3D structure of HP R_27 predicted through homology modeling by using Phyre2. The 3D structure then refined and verified by ModRefiner, PROCHECK, ERRAT, QMEAN. The functional annotation was also performed by InterProScan, SMART, Pfam, NCBI-CDD and found Phospholipase D-like and DNA repair activity. Multiple sequence alignment also supported the existence of PLD-like domain and DNA repair protein domain in the selected hypothetical protein sequences. Finally, the cavity of drug binding was also identified to assist further molecular docking study and potent inhibitor identification. This in silico approach can be further utilized in molecular drug design for other clinically significant pathogens.

  7. Lost in Translation: Using Video Annotation Software to Examine How a Clinical Supervisor Interprets and Applies a State-Mandated Teacher Assessment Instrument

    Science.gov (United States)

    Miller, Matthew James; Carney, Joanne

    2009-01-01

    This case study examines the reasoning of a clinical supervisor as she assesses preservice teacher candidates with a state-mandated performance assessment instrument. The supervisor's evaluations were recorded using video annotation software, which allowed her to record her observations in real-time. The study reveals some of the inherent…

  8. The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment.

    Science.gov (United States)

    Eisenhaber, Birgit; Kuchibhatla, Durga; Sherman, Westley; Sirota, Fernanda L; Berezovsky, Igor N; Wong, Wing-Cheong; Eisenhaber, Frank

    2016-01-01

    As biomolecular sequencing is becoming the main technique in life sciences, functional interpretation of sequences in terms of biomolecular mechanisms with in silico approaches is getting increasingly significant. Function prediction tools are most powerful for protein-coding sequences; yet, the concepts and technologies used for this purpose are not well reflected in bioinformatics textbooks. Notably, protein sequences typically consist of globular domains and non-globular segments. The two types of regions require cardinally different approaches for function prediction. Whereas the former are classic targets for homology-inspired function transfer based on remnant, yet statistically significant sequence similarity to other, characterized sequences, the latter type of regions are characterized by compositional bias or simple, repetitive patterns and require lexical analysis and/or empirical sequence pattern-function correlations. The recipe for function prediction recommends first to find all types of non-globular segments and, then, to subject the remaining query sequence to sequence similarity searches. We provide an updated description of the ANNOTATOR software environment as an advanced example of a software platform that facilitates protein sequence-based function prediction. PMID:27115649

  9. The genome sequence of Leishmania (Leishmania) amazonensis: functional annotation and extended analysis of gene models.

    Science.gov (United States)

    Real, Fernando; Vidal, Ramon Oliveira; Carazzolle, Marcelo Falsarella; Mondego, Jorge Maurício Costa; Costa, Gustavo Gilson Lacerda; Herai, Roberto Hirochi; Würtele, Martin; de Carvalho, Lucas Miguel; Carmona e Ferreira, Renata; Mortara, Renato Arruda; Barbiéri, Clara Lucia; Mieczkowski, Piotr; da Silveira, José Franco; Briones, Marcelo Ribeiro da Silva; Pereira, Gonçalo Amarante Guimarães; Bahia, Diana

    2013-12-01

    We present the sequencing and annotation of the Leishmania (Leishmania) amazonensis genome, an etiological agent of human cutaneous leishmaniasis in the Amazon region of Brazil. L. (L.) amazonensis shares features with Leishmania (L.) mexicana but also exhibits unique characteristics regarding geographical distribution and clinical manifestations of cutaneous lesions (e.g. borderline disseminated cutaneous leishmaniasis). Predicted genes were scored for orthologous gene families and conserved domains in comparison with other human pathogenic Leishmania spp. Carboxypeptidase, aminotransferase, and 3'-nucleotidase genes and ATPase, thioredoxin, and chaperone-related domains were represented more abundantly in L. (L.) amazonensis and L. (L.) mexicana species. Phylogenetic analysis revealed that these two species share groups of amastin surface proteins unique to the genus that could be related to specific features of disease outcomes and host cell interactions. Additionally, we describe a hypothetical hybrid interactome of potentially secreted L. (L.) amazonensis proteins and host proteins under the assumption that parasite factors mimic their mammalian counterparts. The model predicts an interaction between an L. (L.) amazonensis heat-shock protein and mammalian Toll-like receptor 9, which is implicated in important immune responses such as cytokine and nitric oxide production. The analysis presented here represents valuable information for future studies of leishmaniasis pathogenicity and treatment. PMID:23857904

  10. Characterization of Liaoning cashmere goat transcriptome: sequencing, de novo assembly, functional annotation and comparative analysis.

    Directory of Open Access Journals (Sweden)

    Hongliang Liu

    Full Text Available BACKGROUND: Liaoning cashmere goat is a famous goat breed for cashmere wool. In order to increase the transcriptome data and accelerate genetic improvement for this breed, we performed de novo transcriptome sequencing to generate the first expressed sequence tag dataset for the Liaoning cashmere goat, using next-generation sequencing technology. RESULTS: Transcriptome sequencing of Liaoning cashmere goat on a Roche 454 platform yielded 804,601 high-quality reads. Clustering and assembly of these reads produced a non-redundant set of 117,854 unigenes, comprising 13,194 isotigs and 104,660 singletons. Based on similarity searches with known proteins, 17,356 unigenes were assigned to 6,700 GO categories, and the terms were summarized into three main GO categories and 59 sub-categories. 3,548 and 46,778 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Comparative analysis revealed that 42,254 unigenes were aligned to 17,532 different sequences in NCBI non-redundant nucleotide databases. 97,236 (82.51% unigenes were mapped to the 30 goat chromosomes. 35,551 (30.17% unigenes were matched to 11,438 reported goat protein-coding genes. The remaining non-matched unigenes were further compared with cattle and human reference genes, 67 putative new goat genes were discovered. Additionally, 2,781 potential simple sequence repeats were initially identified from all unigenes. CONCLUSION: The transcriptome of Liaoning cashmere goat was deep sequenced, de novo assembled, and annotated, providing abundant data to better understand the Liaoning cashmere goat transcriptome. The potential simple sequence repeats provide a material basis for future genetic linkage and quantitative trait loci analyses.

  11. The Ensembl gene annotation system.

    Science.gov (United States)

    Aken, Bronwen L; Ayling, Sarah; Barrell, Daniel; Clarke, Laura; Curwen, Valery; Fairley, Susan; Fernandez Banet, Julio; Billis, Konstantinos; García Girón, Carlos; Hourlier, Thibaut; Howe, Kevin; Kähäri, Andreas; Kokocinski, Felix; Martin, Fergal J; Murphy, Daniel N; Nag, Rishi; Ruffier, Magali; Schuster, Michael; Tang, Y Amy; Vogel, Jan-Hinnerk; White, Simon; Zadissa, Amonida; Flicek, Paul; Searle, Stephen M J

    2016-01-01

    The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html. PMID:27337980

  12. Annotated Answer Set Programming

    OpenAIRE

    Straccia, Umberto

    2005-01-01

    We present Annotated Answer Set Programming, that extends the ex pressive power of disjunctive logic programming with annotation terms, taken from the generalized annotated logic programming framework.

  13. Annotated Videography.

    Science.gov (United States)

    United States Holocaust Memorial Museum, Washington, DC.

    This annotated list of 43 videotapes recommended for classroom use addresses various themes for teaching about the Holocaust, including: (1) overviews of the Holocaust; (2) life before the Holocaust; (3) propaganda; (4) racism, anti-Semitism; (5) "enemies of the state"; (6) ghettos; (7) camps; (8) genocide; (9) rescue; (10) resistance; (11)…

  14. Functional annotation of native enhancers with a Cas9 -histone demethylase fusion

    OpenAIRE

    Kearns, Nicola A; Pham, Hannah; Tabak, Barbara; Genga, Ryan M; Silverstein, Noah J; Garber, Manuel; Maehr, René

    2015-01-01

    Understanding of mammalian enhancer function is limited by the lack of a technology to rapidly and thoroughly test their cell type-specific function. Here, we use a nuclease-deficient (d)Cas9 histone demethylase fusion to functionally characterize previously described and novel enhancer elements for their roles in the embryonic stem cell state. Further, we distinguish the mechanism of action of dCas9-LSD1 at enhancers from previous dCas9-effectors.

  15. The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation

    OpenAIRE

    Stevens Fred J; Johnson Seth; Desai Valmik; Zavaljevski Nela; Yu Chenggang; Reifman Jaques

    2008-01-01

    Abstract Background Automated protein function prediction methods are needed to keep pace with high-throughput sequencing. With the existence of many programs and databases for inferring different protein functions, a pipeline that properly integrates these resources will benefit from the advantages of each method. However, integrated systems usually do not provide mechanisms to generate customized databases to predict particular protein functions. Here, we describe a tool termed PIPA (Pipeli...

  16. Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation

    OpenAIRE

    Wilkins, A D; Lua, R.; Erdin, S; Ward, R M; LICHTARGE, O

    2010-01-01

    Protein functional sites control most biological processes and are important targets for drug design and protein engineering. To characterize them, the evolutionary trace (ET) ranks the relative importance of residues according to their evolutionary variations. Generally, top-ranked residues cluster spatially to define evolutionary hotspots that predict functional sites in structures. Here, various functions that measure the physical continuity of ET ranks among neighboring residues in the st...

  17. Functional annotation of native enhancers with a Cas9-histone demethylase fusion.

    Science.gov (United States)

    Kearns, Nicola A; Pham, Hannah; Tabak, Barbara; Genga, Ryan M; Silverstein, Noah J; Garber, Manuel; Maehr, René

    2015-05-01

    Understanding of mammalian enhancers is limited by the lack of a technology to rapidly and thoroughly test the cell type-specific function. Here, we use a nuclease-deficient Cas9 (dCas9)-histone demethylase fusion to functionally characterize previously described and new enhancer elements for their roles in the embryonic stem cell state. Further, we distinguish the mechanism of action of dCas9-LSD1 at enhancers from previous dCas9-effectors. PMID:25775043

  18. Annotated bibliography: hazard assessments for the geologic isolation of nuclear wastes. Final report. Center for Resource and Environmental Systems Studies report No. 41

    International Nuclear Information System (INIS)

    This report presents an annotated bibliography of risk assessments that are pertinent to constructing, operating, and decommissioning a federal repository for the underground storage of radioactive waste. This might be considered as a first phase in an assessment of the risks associated with radioactive waste storage. Only those documents judged to be the more pertinent are abstracted. The abstracts are grouped under 13 classifications. A subject and author index is provided

  19. Modeling Loosely Annotated Images with Imagined Annotations

    CERN Document Server

    Tang, Hong; Chen, Yunhao

    2008-01-01

    In this paper, we present an approach to learning latent semantic analysis models from loosely annotated images for automatic image annotation and indexing. The given annotation in training images is loose due to: (1) ambiguous correspondences between visual features and annotated keywords; (2) incomplete lists of annotated keywords. The second reason motivates us to enrich the incomplete annotation in a simple way before learning topic models. In particular, some imagined keywords are poured into the incomplete annotation through measuring similarity between keywords. Then, both given and imagined annotations are used to learning probabilistic topic models for automatically annotating new images. We conduct experiments on a typical Corel dataset of images and loose annotations, and compare the proposed method with state-of-the-art discrete annotation methods (using a set of discrete blobs to represent an image). The proposed method improves word-driven probability Latent Semantic Analysis (PLSA-words) up to ...

  20. A combined approach for genome wide protein function annotation/prediction

    DEFF Research Database (Denmark)

    Benso, Alfredo; Di Carlo, Stefano; Ur Rehman, Hafeez;

    2013-01-01

    predictive power of our model we also compute and integrate term specific relationships among functional terms based on Gene Ontology (GO). RESULTS: We tested our method on Saccharomyces Cerevisiae and Homo sapiens species proteins. The aggregation of different structural and functional evidence with GO...... relationships outperforms, in terms of precision and accuracy of prediction than the other methods reported in literature. The predicted precision and accuracy is 100% for more than half of the input set for both species; overall, we obtained 85.38% precision and 81.95% accuracy for Homo sapiens and 79...

  1. Functional annotation of rare gene aberration drivers of pancreatic cancer | Office of Cancer Genomics

    Science.gov (United States)

    As we enter the era of precision medicine, characterization of cancer genomes will directly influence therapeutic decisions in the clinic. Here we describe a platform enabling functionalization of rare gene mutations through their high-throughput construction, molecular barcoding and delivery to cancer models for in vivo tumour driver screens. We apply these technologies to identify oncogenic drivers of pancreatic ductal adenocarcinoma (PDAC).

  2. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions.

    OpenAIRE

    Adam Deutschbauer; Price, Morgan N.; Kelly M. Wetmore; Wenjun Shao; Baumohl, Jason K; Zhuchen Xu; Michelle Nguyen; Raquel Tamse; Davis, Ronald W; Arkin, Adam P.

    2011-01-01

    Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron ...

  3. A new approach to assess and predict the functional roles of proteins across all known structures.

    Science.gov (United States)

    Julfayev, Elchin S; McLaughlin, Ryan J; Tao, Yi-Ping; McLaughlin, William A

    2011-03-01

    The three dimensional atomic structures of proteins provide information regarding their function; and codified relationships between structure and function enable the assessment of function from structure. In the current study, a new data mining tool was implemented that checks current gene ontology (GO) annotations and predicts new ones across all the protein structures available in the Protein Data Bank (PDB). The tool overcomes some of the challenges of utilizing large amounts of protein annotation and measurement information to form correspondences between protein structure and function. Protein attributes were extracted from the Structural Biology Knowledgebase and open source biological databases. Based on the presence or absence of a given set of attributes, a given protein's functional annotations were inferred. The results show that attributes derived from the three dimensional structures of proteins enhanced predictions over that using attributes only derived from primary amino acid sequence. Some predictions reflected known but not completely documented GO annotations. For example, predictions for the GO term for copper ion binding reflected used information a copper ion was known to interact with the protein based on information in a ligand interaction database. Other predictions were novel and require further experimental validation. These include predictions for proteins labeled as unknown function in the PDB. Two examples are a role in the regulation of transcription for the protein AF1396 from Archaeoglobus fulgidus and a role in RNA metabolism for the protein psuG from Thermotoga maritima. PMID:21445639

  4. Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

    Directory of Open Access Journals (Sweden)

    Haznedaroglu Berat Z

    2012-07-01

    Full Text Available Abstract Background The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k-mer selection on the annotation output. This study provides an in-depth k-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k-mers and clustered assemblies (CA were considered using three representative software packages. Pair-wise comparison analyses (between individual k-mers and CAs were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG ortholog identifiers (KOIs, and to determine a strategy that maximizes the recovery of biological information in a de novo transcriptome assembly. Results Analyses of single k-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of k-mers (k-19 to k-63. For each k-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other k-mer assemblies. Producing a non-redundant CA of k-mers 19 to 63 resulted in a more complete functional annotation than any single k-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs in the assemblies of individual k-mers (k-19 to k-63 that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented. Conclusions This study demonstrated that different k-mer choices result in various quantities

  5. Annotation of gene function in citrus using gene expression information and co-expression networks

    OpenAIRE

    Wong, Darren CJ; Sweetman, Crystal; Ford, Christopher M

    2014-01-01

    Background The genus Citrus encompasses major cultivated plants such as sweet orange, mandarin, lemon and grapefruit, among the world’s most economically important fruit crops. With increasing volumes of transcriptomics data available for these species, Gene Co-expression Network (GCN) analysis is a viable option for predicting gene function at a genome-wide scale. GCN analysis is based on a “guilt-by-association” principle whereby genes encoding proteins involved in similar and/or related bi...

  6. River Lune juvenile fish stock assessment 2002 (annotated draft copy, Site Reports only)

    OpenAIRE

    2003-01-01

    This draft copy of the River Lune juvenile fish stock assessment from 2000 provides "Site Reports" from different water bodies in the Lune catchment. These Site Reports provide brief information on habitat features, fishery classification and comments on species caught and stocking. This document provides no summary or interpretation of the given data.

  7. IsoSeq analysis and functional annotation of the infratentorial ependymoma tumor tissue on PacBio RSII platform.

    Science.gov (United States)

    Singh, Neetu; Sahu, Dinesh Kumar; Chowdhry, Rebecca; Mishra, Archana; Goel, Madhu Mati; Faheem, Mohd; Srivastava, Chhitij; Ojha, Bal Krishna; Gupta, Devendra Kumar; Kant, Ravi

    2016-02-01

    Here, we sequenced and functionally annotated the long reads (1-2 kb) cDNAs library of an infratentorial ependymoma tumor tissue on PacBio RSII by Iso-Seq protocol using SMRT technology. 577 MB, data was generated from the brain tissues of ependymoma tumor patient, producing 1,19,313 high-quality reads assembled into 19,878 contigs using Celera assembler followed by Quiver pipelines, which produced 2952 unique protein accessions in the nr protein database and 307 KEGG pathways. Additionally, when we compared GO terms of second and third level with alternative splicing data obtained through HTA Array2.0. We identified four and twelve transcript cluster IDs in Level-2 and Level-3 scores respectively with alternative splicing index predicting mainly the major pathways of hallmarks of cancer. Out of these transcript cluster IDs only transcript cluster IDs of gene PNMT, SNN and LAMB1 showed Reads Per Kilobase of exon model per Million mapped reads (RPKM) values at gene-level expression (GE) and transcript-level (TE) track. Most importantly, brain-specific genes--PNMT, SNN and LAMB1 show their involvement in Ependymoma. PMID:26862483

  8. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions.

    Directory of Open Access Journals (Sweden)

    Adam Deutschbauer

    2011-11-01

    Full Text Available Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acceptors, stresses, and motility. We find that 2,350 genes have a pattern of fitness that is significantly different from random and 1,230 of these genes (37% of our total assayed genes have enough signal to show strong biological correlations. We find that genes in all functional categories have phenotypes, including hundreds of hypotheticals, and that potentially redundant genes (over 50% amino acid identity to another gene in the genome are also likely to have distinct phenotypes. Using fitness patterns, we were able to propose specific molecular functions for 40 genes or operons that lacked specific annotations or had incomplete annotations. In one example, we demonstrate that the previously hypothetical gene SO_3749 encodes a functional acetylornithine deacetylase, thus filling a missing step in S. oneidensis metabolism. Additionally, we demonstrate that the orphan histidine kinase SO_2742 and orphan response regulator SO_2648 form a signal transduction pathway that activates expression of acetyl-CoA synthase and is required for S. oneidensis to grow on acetate as a carbon source. Lastly, we demonstrate that gene expression and mutant fitness are poorly correlated and that mutant fitness generates more confident predictions of gene function than does gene expression. The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes.

  9. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions.

    Science.gov (United States)

    Deutschbauer, Adam; Price, Morgan N; Wetmore, Kelly M; Shao, Wenjun; Baumohl, Jason K; Xu, Zhuchen; Nguyen, Michelle; Tamse, Raquel; Davis, Ronald W; Arkin, Adam P

    2011-11-01

    Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acceptors, stresses, and motility. We find that 2,350 genes have a pattern of fitness that is significantly different from random and 1,230 of these genes (37% of our total assayed genes) have enough signal to show strong biological correlations. We find that genes in all functional categories have phenotypes, including hundreds of hypotheticals, and that potentially redundant genes (over 50% amino acid identity to another gene in the genome) are also likely to have distinct phenotypes. Using fitness patterns, we were able to propose specific molecular functions for 40 genes or operons that lacked specific annotations or had incomplete annotations. In one example, we demonstrate that the previously hypothetical gene SO_3749 encodes a functional acetylornithine deacetylase, thus filling a missing step in S. oneidensis metabolism. Additionally, we demonstrate that the orphan histidine kinase SO_2742 and orphan response regulator SO_2648 form a signal transduction pathway that activates expression of acetyl-CoA synthase and is required for S. oneidensis to grow on acetate as a carbon source. Lastly, we demonstrate that gene expression and mutant fitness are poorly correlated and that mutant fitness generates more confident predictions of gene function than does gene expression. The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes. PMID:22125499

  10. TreeQ-VISTA: An Interactive Tree Visualization Tool withFunctional Annotation Query Capabilities

    Energy Technology Data Exchange (ETDEWEB)

    Gu, Shengyin; Anderson, Iain; Kunin, Victor; Cipriano, Michael; Minovitsky, Simon; Weber, Gunther; Amenta, Nina; Hamann, Bernd; Dubchak,Inna

    2007-05-07

    Summary: We describe a general multiplatform exploratorytool called TreeQ-Vista, designed for presenting functional annotationsin a phylogenetic context. Traits, such as phenotypic and genomicproperties, are interactively queried from a relational database with auser-friendly interface which provides a set of tools for users with orwithout SQL knowledge. The query results are projected onto aphylogenetic tree and can be displayed in multiple color groups. A richset of browsing, grouping and query tools are provided to facilitatetrait exploration, comparison and analysis.Availability: The program,detailed tutorial and examples are available online athttp://genome-test.lbl.gov/vista/TreeQVista.

  11. Analysis and functional annotation of expressed sequence tags from the fall armyworm Spodoptera frugiperda

    Directory of Open Access Journals (Sweden)

    Clem Rollie J

    2006-10-01

    Full Text Available Abstract Background Little is known about the genome sequences of lepidopteran insects, although this group of insects has been studied extensively in the fields of endocrinology, development, immunity, and pathogen-host interactions. In addition, cell lines derived from Spodoptera frugiperda and other lepidopteran insects are routinely used for baculovirus foreign gene expression. This study reports the results of an expressed sequence tag (EST sequencing project in cells from the lepidopteran insect S. frugiperda, the fall armyworm. Results We have constructed an EST database using two cDNA libraries from the S. frugiperda-derived cell line, SF-21. The database consists of 2,367 ESTs which were assembled into 244 contigs and 951 singlets for a total of 1,195 unique sequences. Conclusion S. frugiperda is an agriculturally important pest insect and genomic information will be instrumental for establishing initial transcriptional profiling and gene function studies, and for obtaining information about genes manipulated during infections by insect pathogens such as baculoviruses.

  12. Array2BIO: from microarray expression data to functional annotation of co-regulated genes

    Directory of Open Access Journals (Sweden)

    Rasley Amy

    2006-06-01

    Full Text Available Abstract Background There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility. Results Array2BIO converts raw intensities into probe expression values, automatically maps those to genes, and subsequently identifies groups of co-expressed genes using two complementary approaches: (1 comparative analysis of signal versus control and (2 clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on Gene Ontology classification and KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods for quantifying expression levels, including Benjamini-Hochberg and Bonferroni multiple testing corrections. An automated interface with the ECR Browser provides evolutionary conservation analysis for the identified gene loci while the interconnection with Crème allows prediction of gene regulatory elements that underlie observed expression patterns. Conclusion We have developed Array2BIO – a web based tool for rapid comprehensive analysis of Affymetrix microarray expression data, which also allows users to link expression data to Dcode.org comparative genomics tools and integrates a system for translating co-expression data into mechanisms of gene co-regulation. Array2BIO is publicly available at http://array2bio.dcode.org.

  13. Functional Annotation of Two New Carboxypeptidases from the Amidohydrolase Superfamily of Enzymes

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, D.; Xu, C; Kumaran, D; Brown, A; Sauder, M; Burley, S; Swaminathan, S; Raushel, F

    2009-01-01

    Two proteins from the amidohydrolase superfamily of enzymes were cloned, expressed, and purified to homogeneity. The first protein, Cc0300, was from Caulobacter crescentus CB-15 (Cc0300), while the second one (Sgx9355e) was derived from an environmental DNA sequence originally isolated from the Sargasso Sea (gi|44371129). The catalytic functions and the substrate profiles for the two enzymes were determined with the aid of combinatorial dipeptide libraries. Both enzymes were shown to catalyze the hydrolysis of l-Xaa-l-Xaa dipeptides in which the amino acid at the N-terminus was relatively unimportant. These enzymes were specific for hydrophobic amino acids at the C-terminus. With Cc0300, substrates terminating in isoleucine, leucine, phenylalanine, tyrosine, valine, methionine, and tryptophan were hydrolyzed. The same specificity was observed with Sgx9355e, but this protein was also able to hydrolyze peptides terminating in threonine. Both enzymes were able to hydrolyze N-acetyl and N-formyl derivatives of the hydrophobic amino acids and tripeptides. The best substrates identified for Cc0300 were l-Ala-l-Leu with kcat and kcat/Km values of 37 s-1 and 1.1 x 105 M-1 s-1, respectively, and N-formyl-l-Tyr with kcat and kcat/Km values of 33 s-1 and 3.9 x 105 M-1 s-1, respectively. The best substrate identified for Sgx9355e was l-Ala-l-Phe with kcat and kcat/Km values of 0.41 s-1 and 5.8 x 103 M-1 s-1. The three-dimensional structure of Sgx9355e was determined to a resolution of 2.33 Angstroms with l-methionine bound in the active site. The a-carboxylate of the methionine is ion-paired to His-237 and also hydrogen bonded to the backbone amide groups of Val-201 and Leu-202. The a-amino group of the bound methionine interacts with Asp-328. The structural determinants for substrate recognition were identified and compared with other enzymes in this superfamily that hydrolyze dipeptides with different specificities.

  14. Annotated bibliography

    International Nuclear Information System (INIS)

    Under a cooperative agreement with the U.S. Department of Energy's Office of Science and Technology, Waste Policy Institute (WPI) is conducting a five-year research project to develop a research-based approach for integrating communication products in stakeholder involvement related to innovative technology. As part of the research, WPI developed this annotated bibliography which contains almost 100 citations of articles/books/resources involving topics related to communication and public involvement aspects of deploying innovative cleanup technology. To compile the bibliography, WPI performed on-line literature searches (e.g., Dialog, International Association of Business Communicators Public Relations Society of America, Chemical Manufacturers Association, etc.), consulted past years proceedings of major environmental waste cleanup conferences (e.g., Waste Management), networked with professional colleagues and DOE sites to gather reports or case studies, and received input during the August 1996 Research Design Team meeting held to discuss the project's research methodology. Articles were selected for annotation based upon their perceived usefulness to the broad range of public involvement and communication practitioners

  15. Transcriptome Analysis of the Emerald Ash Borer (EAB), Agrilus planipennis: De Novo Assembly, Functional Annotation and Comparative Analysis

    Science.gov (United States)

    Duan, Jun; Ladd, Tim; Doucet, Daniel; Cusson, Michel; vanFrankenhuyzen, Kees; Mittapalli, Omprakash; Krell, Peter J.; Quan, Guoxing

    2015-01-01

    Background The Emerald ash borer (EAB), Agrilus planipennis, is an invasive phloem-feeding insect pest of ash trees. Since its initial discovery near the Detroit, US- Windsor, Canada area in 2002, the spread of EAB has had strong negative economic, social and environmental impacts in both countries. Several transcriptomes from specific tissues including midgut, fat body and antenna have recently been generated. However, the relatively low sequence depth, gene coverage and completeness limited the usefulness of these EAB databases. Methodology and Principal Findings High-throughput deep RNA-Sequencing (RNA-Seq) was used to obtain 473.9 million pairs of 100 bp length paired-end reads from various life stages and tissues. These reads were assembled into 88,907 contigs using the Trinity strategy and integrated into 38,160 unigenes after redundant sequences were removed. We annotated 11,229 unigenes by searching against the public nr, Swiss-Prot and COG. The EAB transcriptome assembly was compared with 13 other sequenced insect species, resulting in the prediction of 536 unigenes that are Coleoptera-specific. Differential gene expression revealed that 290 unigenes are expressed during larval molting and 3,911 unigenes during metamorphosis from larvae to pupae, respectively (FDR2). In addition, 1,167 differentially expressed unigenes were identified from larval and adult midguts, 435 unigenes were up-regulated in larval midgut and 732 unigenes were up-regulated in adult midgut. Most of the genes involved in RNA interference (RNAi) pathways were identified, which implies the existence of a system RNAi in EAB. Conclusions and Significance This study provides one of the most fundamental and comprehensive transcriptome resources available for EAB to date. Identification of the tissue- stage- or species- specific unigenes will benefit the further study of gene functions during growth and metamorphosis processes in EAB and other pest insects. PMID:26244979

  16. GIFtS: annotation landscape analysis with GeneCards

    Directory of Open Access Journals (Sweden)

    Dalah Irina

    2009-10-01

    Full Text Available Abstract Background Gene annotation is a pivotal component in computational genomics, encompassing prediction of gene function, expression analysis, and sequence scrutiny. Hence, quantitative measures of the annotation landscape constitute a pertinent bioinformatics tool. GeneCards® is a gene-centric compendium of rich annotative information for over 50,000 human gene entries, building upon 68 data sources, including Gene Ontology (GO, pathways, interactions, phenotypes, publications and many more. Results We present the GeneCards Inferred Functionality Score (GIFtS which allows a quantitative assessment of a gene's annotation status, by exploiting the unique wealth and diversity of GeneCards information. The GIFtS tool, linked from the GeneCards home page, facilitates browsing the human genome by searching for the annotation level of a specified gene, retrieving a list of genes within a specified range of GIFtS value, obtaining random genes with a specific GIFtS value, and experimenting with the GIFtS weighting algorithm for a variety of annotation categories. The bimodal shape of the GIFtS distribution suggests a division of the human gene repertoire into two main groups: the high-GIFtS peak consists almost entirely of protein-coding genes; the low-GIFtS peak consists of genes from all of the categories. Cluster analysis of GIFtS annotation vectors provides the classification of gene groups by detailed positioning in the annotation arena. GIFtS also provide measures which enable the evaluation of the databases that serve as GeneCards sources. An inverse correlation is found (for GIFtS>25 between the number of genes annotated by each source, and the average GIFtS value of genes associated with that source. Three typical source prototypes are revealed by their GIFtS distribution: genome-wide sources, sources comprising mainly highly annotated genes, and sources comprising mainly poorly annotated genes. The degree of accumulated knowledge for a

  17. Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

    Energy Technology Data Exchange (ETDEWEB)

    Rutledge, Alexandra C.; Jones, Marcus B.; Chauhan, Sadhana; Purvine, Samuel O.; Sanford, James; Monroe, Matthew E.; Brewer, Heather M.; Payne, Samuel H.; Ansong, Charles; Frank, Bryan C.; Smith, Richard D.; Peterson, Scott; Motin, Vladimir L.; Adkins, Joshua N.

    2012-03-27

    Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. To date, the perceived value of manual curation for genome annotations is not offset by the real cost and time associated with the process. In order to balance the large number of sequences generated, the annotation process is now performed almost exclusively in an automated fashion for most genome sequencing projects. One possible way to reduce errors inherent to automated computational annotations is to apply data from 'omics' measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. This approach does require additional experimental and bioinformatics methods to include omics technologies; however, the approach is readily automatable and can benefit from rapid developments occurring in those research domains as well. The annotation process can be improved by experimental validation of transcription and translation and aid in the discovery of annotation errors. Here the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species, as is becoming common in sequencing efforts. Transcriptomic and proteomic data derived from three highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 previously incorrect protein-coding sequences (e.g., observed frameshifts, extended start sites, and translated pseudogenes) within the three current Yersinia genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent

  18. Gene Ontology annotations and resources.

    Science.gov (United States)

    Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources. PMID:23161678

  19. Comparative omics-driven genome annotation refinement: application across Yersiniae.

    Directory of Open Access Journals (Sweden)

    Alexandra C Schrimpe-Rutledge

    Full Text Available Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. The annotation process is now performed almost exclusively in an automated fashion to balance the large number of sequences generated. One possible way of reducing errors inherent to automated computational annotations is to apply data from omics measurements (i.e. transcriptional and proteomic to the un-annotated genome with a proteogenomic-based approach. Here, the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species. Transcriptomic and proteomic data derived from highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis Pestoides F, and Y. pseudotuberculosis PB1/+ was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 incorrect (i.e., observed frameshifts, extended start sites, and translated pseudogenes protein-coding sequences within the three current genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus the discovery of many translated pseudogenes, including the insertion-ablated argD, underscores a need for functional analyses to investigate hypotheses related to divergence. Refinements included the discovery of a seemingly essential ribosomal protein, several virulence-associated factors, a transcriptional regulator, and many hypothetical proteins that were missed during annotation.

  20. Annotating Enzymes of Uncertain Function: The Deacylation of d-Amino Acids by Members of the Amidohydrolase Superfamily†

    OpenAIRE

    Cummings, Jennifer; Fedorov, Alexander A.; Xu, Chengfu; Brown, Shoshana; Fedorov, Elena; Patricia C Babbitt; Almo, Steven C.; Raushel, Frank M.

    2009-01-01

    The catalytic activities of three members of the amidohydrolase superfamily were discovered using amino acid substrate libraries. Bb3285 from Bordetella bronchiseptica, Gox1177 from Gluconobacter oxydans, and Sco4986 from Streptomyces coelicolor are currently annotated as d-aminoacylases or N-acetyl-d-glutamate deacetylases. These three enzymes are 22−34% identical to one another in amino acid sequence. Substrate libraries containing nearly all combinations of N-formyl-d-Xaa, N-acetyl-d-Xaa, ...

  1. NCBI prokaryotic genome annotation pipeline.

    Science.gov (United States)

    Tatusova, Tatiana; DiCuccio, Michael; Badretdin, Azat; Chetvernin, Vyacheslav; Nawrocki, Eric P; Zaslavsky, Leonid; Lomsadze, Alexandre; Pruitt, Kim D; Borodovsky, Mark; Ostell, James

    2016-08-19

    Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ and the NCBI Handbook, https://www.ncbi.nlm.nih.gov/books/NBK174280/. PMID:27342282

  2. Estimating the annotation error rate of curated GO database sequence annotations

    Directory of Open Access Journals (Sweden)

    Brown Alfred L

    2007-05-01

    Full Text Available Abstract Background Annotations that describe the function of sequences are enormously important to researchers during laboratory investigations and when making computational inferences. However, there has been little investigation into the data quality of sequence function annotations. Here we have developed a new method of estimating the error rate of curated sequence annotations, and applied this to the Gene Ontology (GO sequence database (GOSeqLite. This method involved artificially adding errors to sequence annotations at known rates, and used regression to model the impact on the precision of annotations based on BLAST matched sequences. Results We estimated the error rate of curated GO sequence annotations in the GOSeqLite database (March 2006 at between 28% and 30%. Annotations made without use of sequence similarity based methods (non-ISS had an estimated error rate of between 13% and 18%. Annotations made with the use of sequence similarity methodology (ISS had an estimated error rate of 49%. Conclusion While the overall error rate is reasonably low, it would be prudent to treat all ISS annotations with caution. Electronic annotators that use ISS annotations as the basis of predictions are likely to have higher false prediction rates, and for this reason designers of these systems should consider avoiding ISS annotations where possible. Electronic annotators that use ISS annotations to make predictions should be viewed sceptically. We recommend that curators thoroughly review ISS annotations before accepting them as valid. Overall, users of curated sequence annotations from the GO database should feel assured that they are using a comparatively high quality source of information.

  3. Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitus

    Directory of Open Access Journals (Sweden)

    Farrall Martin

    2009-07-01

    Full Text Available Abstract Background Hyperglycaemia in diabetes mellitus (DM alters gene expression regulation in various organs and contributes to long term vascular and renal complications. We aimed to generate novel renal genome-wide gene transcription data in rat models of diabetes in order to test the responsiveness to hyperglycaemia and renal structural changes of positional candidate genes at selected diabetic nephropathy (DN susceptibility loci. Methods Both Affymetrix and Illumina technologies were used to identify significant quantitative changes in the abundance of over 15,000 transcripts in kidney of models of spontaneous (genetically determined mild hyperglycaemia and insulin resistance (Goto-Kakizaki-GK and experimentally induced severe hyperglycaemia (Wistar-Kyoto-WKY rats injected with streptozotocin [STZ]. Results Different patterns of transcription regulation in the two rat models of diabetes likely underlie the roles of genetic variants and hyperglycaemia severity. The impact of prolonged hyperglycaemia on gene expression changes was more profound in STZ-WKY rats than in GK rats and involved largely different sets of genes. These included genes already tested in genetic studies of DN and a large number of protein coding sequences of unknown function which can be considered as functional and, when they map to DN loci, positional candidates for DN. Further expression analysis of rat orthologs of human DN positional candidate genes provided functional annotations of known and novel genes that are responsive to hyperglycaemia and may contribute to renal functional and/or structural alterations. Conclusion Combining transcriptomics in animal models and comparative genomics provides important information to improve functional annotations of disease susceptibility loci in humans and experimental support for testing candidate genes in human genetics.

  4. BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal Matoq Saeed

    2015-08-18

    Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

  5. Interlinking Multimedia Annotations

    OpenAIRE

    Li, Yunjia; Wald, Mike; Wills, Gary

    2011-01-01

    With the fast growth of multimedia sharing and annotating applications on the Web, there is an increasing research interests in semantic annotations of multimedia. However, applying linked data principles in multimedia annotations is a relatively new topic, especially when annotations are related to media fragments. This paper, therefore, discusses this problem and further breaks it down into three fundamental sub-questions: 1) choosing media fragment URIs 2) Dereferencing media fragment URIs...

  6. Annotating Enzymes of Uncertain Function: The Deacylation of d-Amino Acids by Members of the Amidohydrolase Superfamily

    Energy Technology Data Exchange (ETDEWEB)

    Cummings, J.; Fedorov, A; Xu, C; Brown, S; Fedorov, E; Babbitt, P; Almo, S; Raushel, F

    2009-01-01

    The catalytic activities of three members of the amidohydrolase superfamily were discovered using amino acid substrate libraries. Bb3285 from Bordetella bronchiseptica, Gox1177 from Gluconobacter oxidans, and Sco4986 from Streptomyces coelicolor are currently annotated as d-aminoacylases or N-acetyl-d-glutamate deacetylases. These three enzymes are 22-34% identical to one another in amino acid sequence. Substrate libraries containing nearly all combinations of N-formyl-d-Xaa, N-acetyl-d-Xaa, N-succinyl-d-Xaa, and l-Xaa-d-Xaa were used to establish the substrate profiles for these enzymes. It was demonstrated that Bb3285 is restricted to the hydrolysis of N-acyl-substituted derivatives of d-glutamate. The best substrates for this enzyme are N-formyl-d-glutamate (k{sub cat}/K{sub m} = 5.8 x 10{sup 6} M{sup -1} s{sup -1}), N-acetyl-d-glutamate (k{sub cat}/K{sub m} = 5.2 x 10{sup 6} M{sup -1} s{sup -1}), and l-methionine-d-glutamate (k{sub cat}/K{sub m} = 3.4 x 10{sup 5} M{sup -1} s{sup -1}). Gox1177 and Sco4986 preferentially hydrolyze N-acyl-substituted derivatives of hydrophobic d-amino acids. The best substrates for Gox1177 are N-acetyl-d-leucine (k{sub cat}/K{sub m} = 3.2 x 104 M{sup -1} s-1), N-acetyl-d-tryptophan (kcat/Km = 4.1 x 104 M-1 s-1), and l-tyrosine-d-leucine (kcat/Km = 1.5 x 104 M-1 s-1). A fourth protein, Bb2785 from B. bronchiseptica, did not have d-aminoacylase activity. The best substrates for Sco4986 are N-acetyl-d-phenylalanine and N-acetyl-d-tryptophan. The three-dimensional structures of Bb3285 in the presence of the product acetate or a potent mimic of the tetrahedral intermediate were determined by X-ray diffraction methods. The side chain of the d-glutamate moiety of the inhibitor is ion-paired to Arg-295, while the {alpha}-carboxylate is ion-paired with Lys-250 and Arg-376. These results have revealed the chemical and structural determinants for substrate specificity in this protein. Bioinformatic analyses of an additional {approx}250

  7. Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily.

    Science.gov (United States)

    Cummings, Jennifer A; Fedorov, Alexander A; Xu, Chengfu; Brown, Shoshana; Fedorov, Elena; Babbitt, Patricia C; Almo, Steven C; Raushel, Frank M

    2009-07-14

    The catalytic activities of three members of the amidohydrolase superfamily were discovered using amino acid substrate libraries. Bb3285 from Bordetella bronchiseptica, Gox1177 from Gluconobacter oxidans, and Sco4986 from Streptomyces coelicolor are currently annotated as d-aminoacylases or N-acetyl-d-glutamate deacetylases. These three enzymes are 22-34% identical to one another in amino acid sequence. Substrate libraries containing nearly all combinations of N-formyl-d-Xaa, N-acetyl-d-Xaa, N-succinyl-d-Xaa, and l-Xaa-d-Xaa were used to establish the substrate profiles for these enzymes. It was demonstrated that Bb3285 is restricted to the hydrolysis of N-acyl-substituted derivatives of d-glutamate. The best substrates for this enzyme are N-formyl-d-glutamate (k(cat)/K(m) = 5.8 x 10(6) M(-1) s(-1)), N-acetyl-d-glutamate (k(cat)/K(m) = 5.2 x 10(6) M(-1) s(-1)), and l-methionine-d-glutamate (k(cat)/K(m) = 3.4 x 10(5) M(-1) s(-1)). Gox1177 and Sco4986 preferentially hydrolyze N-acyl-substituted derivatives of hydrophobic d-amino acids. The best substrates for Gox1177 are N-acetyl-d-leucine (k(cat)/K(m) = 3.2 x 10(4) M(-1) s(-1)), N-acetyl-d-tryptophan (k(cat)/K(m) = 4.1 x 10(4) M(-1) s(-1)), and l-tyrosine-d-leucine (k(cat)/K(m) = 1.5 x 10(4) M(-1) s(-1)). A fourth protein, Bb2785 from B. bronchiseptica, did not have d-aminoacylase activity. The best substrates for Sco4986 are N-acetyl-d-phenylalanine and N-acetyl-d-tryptophan. The three-dimensional structures of Bb3285 in the presence of the product acetate or a potent mimic of the tetrahedral intermediate were determined by X-ray diffraction methods. The side chain of the d-glutamate moiety of the inhibitor is ion-paired to Arg-295, while the alpha-carboxylate is ion-paired with Lys-250 and Arg-376. These results have revealed the chemical and structural determinants for substrate specificity in this protein. Bioinformatic analyses of an additional approximately 250 sequences identified as members of this group

  8. Annotation of Regular Polysemy

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector

    Regular polysemy has received a lot of attention from the theory of lexical semantics and from computational linguistics. However, there is no consensus on how to represent the sense of underspecified examples at the token level, namely when annotating or disambiguating senses of metonymic words...... like “London” (Location/Organization) or “cup” (Container/Content). The goal of this dissertation is to assess whether metonymic sense underspecification justifies incorporating a third sense into our sense inventories, thereby treating the underspecified sense as independent from the literal and...... metonymic. We have conducted an analysis in English, Danish and Spanish. Later on, we have tried to replicate the human judgments by means of unsupervised and semi-supervised sense prediction. The automatic sense-prediction systems have been unable to find empiric evidence for the underspecified sense, even...

  9. Functional Fuzzy Based Autism Assessment Support System

    Directory of Open Access Journals (Sweden)

    Anju Pratap

    2014-10-01

    Full Text Available Childhood autism is one of the most common developmental disorders in children, whose disabilities generally tend to follow through adulthood. The therapy given to an autistic child depends on its accurate assessment, which is a challenging clinical decision making problem. This paper describes the application of functional fuzzy model in autism assessment support systems. The fuzzy model uses Takagi-Sugeno Kang (TSK type of inference mechanism for supporting the assessment. A rule based single input-single output first order functional fuzzy model has been applied to a set of real world data and the experimental results were compared with the conventional autism assessment method. The results demonstrate that the proposed method works better in putting the borderline between autistic grades in terms of accuracy. Thus the functional fuzzy model can support in assessing the grade of childhood autism with certainty.

  10. Assessment of right atrial function analysis

    International Nuclear Information System (INIS)

    To assess the potential utility of right atrial function analysis in cardiac disease, reservoir function, pump function, and right atrial peak emptying rate (RAPER) were compared in 10 normal subjects, 32 patients with coronary artery disease, and 4 patients with primary pulmonary hypertension. Right atrial volume curves were obtained using cardiac radionuclide method with Kr-81m. In normal subjects, reservoir function index was 0.41+-0.05; pump function index was 0.25+-0.05. Both types of patients has decreased reservoir funcion and increased pump function. Pump function tended to decrease with an increase of right ventricular end-diastolic pressure. RAPER correlated well with right ventricular peak filling rate, probably reflecting right ventricular diastolic function. Analysis of right atrial function seemed to be of value in evaluating factors regulating right ventricular contraction and diastolic function, and cardiac output. (Namekawa, K)

  11. The assessment of executive functioning in children

    OpenAIRE

    Henry, L.; Bettenay, C.

    2010-01-01

    Background: Executive functioning is increasingly seen as incorporating several component sub-skills and clinical assessments should reflect this complexity. Method: Tools for assessing executive functioning in children are reviewed within five key areas, across verbal and visuospatial abilities, with emphasis on batteries of tests. Results: There are many appropriate tests for children, although the choice is more limited for those under the age of 8 years. Conclusions: Whilst...

  12. Annotated Stack Trees

    OpenAIRE

    Hague, Matthew; Penelle, Vincent

    2015-01-01

    Annotated pushdown automata provide an automaton model of higher-order recursion schemes, which may in turn be used to model higher-order programs for the purposes of verification. We study Ground Annotated Stack Tree Rewrite Systems -- a tree rewrite system where each node is labelled by the configuration of an annotated pushdown automaton. This allows the modelling of fork and join constructs in higher-order programs and is a generalisation of higher-order stack trees recently introduced by...

  13. Imaging and assessment of placental function.

    LENUS (Irish Health Repository)

    Moran, Mary

    2011-09-01

    The placenta is the vital support organ for the developing fetus. This article reviews current ultrasound (US) methods of assessing placental function. The ability of ultrasound to detect placental pathology is discussed. Doppler technology to investigate the fetal, placental, and maternal circulations in both high-risk and uncomplicated pregnancies is discussed and the current literature on the value of three-dimensional power Doppler studies to assess placental volume and vascularization is also evaluated. The article highlights the need for further research into three-dimensional ultrasound and alternative methods of placental evaluation if progress is to be made in optimizing placental function assessment.

  14. Computing human image annotation.

    Science.gov (United States)

    Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Rubin, Daniel L

    2009-01-01

    An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human (or machine) observer. An image markup is the graphical symbols placed over the image to depict an annotation. In the majority of current, clinical and research imaging practice, markup is captured in proprietary formats and annotations are referenced only in free text radiology reports. This makes these annotations difficult to query, retrieve and compute upon, hampering their integration into other data mining and analysis efforts. This paper describes the National Cancer Institute's Cancer Biomedical Informatics Grid's (caBIG) Annotation and Image Markup (AIM) project, focusing on how to use AIM to query for annotations. The AIM project delivers an information model for image annotation and markup. The model uses controlled terminologies for important concepts. All of the classes and attributes of the model have been harmonized with the other models and common data elements in use at the National Cancer Institute. The project also delivers XML schemata necessary to instantiate AIMs in XML as well as a software application for translating AIM XML into DICOM S/R and HL7 CDA. Large collections of AIM annotations can be built and then queried as Grid or Web services. Using the tools of the AIM project, image annotations and their markup can be captured and stored in human and machine readable formats. This enables the inclusion of human image observation and inference as part of larger data mining and analysis activities. PMID:19964202

  15. Functional assessment of time course microarray data

    OpenAIRE

    Dopazo Joaquín; García-García Francisco; Tarazona Sonia; Sebastián Patricia; Nueda María; Ferrer Alberto; Conesa Ana

    2009-01-01

    Abstract Motivation Time-course microarray experiments study the progress of gene expression along time across one or several experimental conditions. Most developed analysis methods focus on the clustering or the differential expression analysis of genes and do not integrate functional information. The assessment of the functional aspects of time-course transcriptomics data requires the use of approaches that exploit the activation dynamics of the functional categories to where genes are ann...

  16. Agroecosystem functional assessment and its difficulties

    Institute of Scientific and Technical Information of China (English)

    CAO Zhi-Ping; Richard Dawson1

    2004-01-01

    Agroecosystem functional assessment indicators provide a necessary bridge between decision-makers and scientists. The development of acceptable indicators, however, remains a difficult task because the current knowledge and understanding of ecosystems is not sufficient to allow an objective assessment of all ecosystem functions. These difficulties were summarized from three perspectives. First, there are difficulties in individual function assessment. Of the four functions associated with agroecosystems-energy flow, materials cycling, information flow and value flow - data on material cycling and information flow remain difficult to obtain and the indicators relatively immature. Secondly, there are difficulties of integration. During the assessment process, the integration of the agroecosystem functions remains the biggest obstacle. Until now, there has been no practical or effective methodology established to resolve the problem. At present, the makeshift approach has been to weight the various indicators and then add them together. Thirdly, there is the problem of obscure concepts and concept confusion. When assessments of agroecosystems are conducted, concepts such as structure, function, benefit, and resource utilization are used extensively. To date, no logical relationship(either real or implied) has been developed between any of these concepts. Are they causes and results such that the relationship between them is linear, or are they independent from one another such that the relationship is parallel? Thus far, the essence of this question is yet to be explored.

  17. Genome-wide and functional annotation of human E3 ubiquitin ligases identifies MULAN, a mitochondrial E3 that regulates the organelle's dynamics and signaling.

    Directory of Open Access Journals (Sweden)

    Wei Li

    Full Text Available Specificity of protein ubiquitylation is conferred by E3 ubiquitin (Ub ligases. We have annotated approximately 617 putative E3s and substrate-recognition subunits of E3 complexes encoded in the human genome. The limited knowledge of the function of members of the large E3 superfamily prompted us to generate genome-wide E3 cDNA and RNAi expression libraries designed for functional screening. An imaging-based screen using these libraries to identify E3s that regulate mitochondrial dynamics uncovered MULAN/FLJ12875, a RING finger protein whose ectopic expression and knockdown both interfered with mitochondrial trafficking and morphology. We found that MULAN is a mitochondrial protein - two transmembrane domains mediate its localization to the organelle's outer membrane. MULAN is oriented such that its E3-active, C-terminal RING finger is exposed to the cytosol, where it has access to other components of the Ub system. Both an intact RING finger and the correct subcellular localization were required for regulation of mitochondrial dynamics, suggesting that MULAN's downstream effectors are proteins that are either integral to, or associated with, mitochondria and that become modified with Ub. Interestingly, MULAN had previously been identified as an activator of NF-kappaB, thus providing a link between mitochondrial dynamics and mitochondria-to-nucleus signaling. These findings suggest the existence of a new, Ub-mediated mechanism responsible for integration of mitochondria into the cellular environment.

  18. Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases

    OpenAIRE

    Gobeill, Julien; Pasche, Emilie; Vishnyakova, Dina; Ruch, Patrick

    2013-01-01

    The available curated data lag behind current biological knowledge contained in the literature. Text mining can assist biologists and curators to locate and access this knowledge, for instance by characterizing the functional profile of publications. Gene Ontology (GO) category assignment in free text already supports various applications, such as powering ontology-based search engines, finding curation-relevant articles (triage) or helping the curator to identify and encode functions. Popula...

  19. Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region.

    Science.gov (United States)

    Lapidus, A; Galleron, N; Sorokin, A; Ehrlich, S D

    1997-11-01

    The 200 kb region of the Bacillus subtilis chromosome spanning from 255 to 275 degrees on the genetic map was sequenced. The strategy applied, based on use of yeast artificial chromosomes and multiplex Long Accurate PCR, proved to be very efficient for sequencing a large bacterial chromosome area. A total of 193 genes of this part of the chromosome was classified by level of knowledge and biological category of their functions. Five levels of gene function understanding are defined. These are: (i) experimental evidence is available of gene product or biological function; (ii) strong homology exists for the putative gene product with proteins from other organisms; (iii) some indication of the function can be derived from homologies with known proteins; (iv) the gene product can be clustered with hypothetical proteins; (v) no indication on the gene function exists. The percentage of detected genes in each category was: 20, 28, 20, 15 and 17, respectively. In the sequenced region, a high percentage of genes are implicated in transport and metabolic linking of glycolysis and the citric acid cycle. A functional connection of several genes from this region and the genes close to 140 degrees in the chromosome was also observed. PMID:9387221

  20. Annotating user-defined abstractions for optimization

    Energy Technology Data Exchange (ETDEWEB)

    Quinlan, D; Schordan, M; Vuduc, R; Yi, Q

    2005-12-05

    This paper discusses the features of an annotation language that we believe to be essential for optimizing user-defined abstractions. These features should capture semantics of function, data, and object-oriented abstractions, express abstraction equivalence (e.g., a class represents an array abstraction), and permit extension of traditional compiler optimizations to user-defined abstractions. Our future work will include developing a comprehensive annotation language for describing the semantics of general object-oriented abstractions, as well as automatically verifying and inferring the annotated semantics.

  1. The effect of different types of image annotations in a scientific text on different learning outcomes in multimedia learning environments

    Science.gov (United States)

    Hamilton, Heather Suzanne

    The purpose of this research was to extend the current theoretical understanding of multimedia learning by assigning a specific function to visual information as an aid to learning and comprehension. This research was designed to determine if differences could be found in a learner's comprehension of a scientific text when the learner was presented with visual annotations that served to aid in selecting, organizing, or integrating content information. Learners were assessed in terms of their abilities to recognize, comprehend, and transfer knowledge dependent on the function of the visual annotations provided in a treatment lesson. The hypothesis was that presenting visual annotations that independently supported each of the three aforementioned processes would cause different learning outcomes. A series of tests were conducted to assess different types of learning. A Word Recognition Test and a Word Definition Test were designed to measure Knowledge. In addition, a Comprehension Test was designed to measure Comprehension. Further, a Transfer Test was designed to measure Application, Analysis, Synthesis and Evaluation (Bloom, 1956). In the experiment carried out for this study, participants read a text describing how cell phones work and viewed either no annotations (text-only group), or annotations designed to support the selection (selection group), organization (organization group), or integration (integration group) of information. As predicted, participants who viewed the visual annotations designed to support the selection process (selection group) scored higher on the Word Recognition Test than all other groups. These findings indicate that visual annotations can be designed to support Knowledge. In addition, while not predicted, participants who viewed the visual annotations designed to support the integration process (integration group) scored higher on the Comprehension Test than individuals in the selection group and the text-only group. These findings

  2. Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery

    Science.gov (United States)

    Kang, Se Won; Hwang, Hee-Ju; Park, So Young; Park, Eun Bi; Chung, Jong Min; Song, Dae Kwon; Kim, Changmu; Kim, Soonok; Lee, Jun Sang; Han, Yeon Soo; Park, Hong Seog; Lee, Yong Seok

    2016-01-01

    Background The freshwater mussel Cristaria plicata (Bivalvia: Eulamellibranchia: Unionidae), is an economically important species in molluscan aquaculture due to its use in pearl farming. The species have been listed as endangered in South Korea due to the loss of natural habitats caused by anthropogenic activities. The decreasing population and a lack of genomic information on the species is concerning for environmentalists and conservationists. In this study, we conducted a de novo transcriptome sequencing and annotation analysis of C. plicata using Illumina HiSeq 2500 next-generation sequencing (NGS) technology, the Trinity assembler, and bioinformatics databases to prepare a sustainable resource for the identification of candidate genes involved in immunity, defense, and reproduction. Results The C. plicata transcriptome analysis included a total of 286,152,584 raw reads and 281,322,837 clean reads. The de novo assembly identified a total of 453,931 contigs and 374,794 non-redundant unigenes with average lengths of 731.2 and 737.1 bp, respectively. Furthermore, 100% coverage of C. plicata mitochondrial genes within two unigenes supported the quality of the assembler. In total, 84,274 unigenes showed homology to entries in at least one database, and 23,246 unigenes were allocated to one or more Gene Ontology (GO) terms. The most prominent GO biological process, cellular component, and molecular function categories (level 2) were cellular process, membrane, and binding, respectively. A total of 4,776 unigenes were mapped to 123 biological pathways in the KEGG database. Based on the GO terms and KEGG annotation, the unigenes were suggested to be involved in immunity, stress responses, sex-determination, and reproduction. A total of 17,251 cDNA simple sequence repeats (cSSRs) were identified from 61,141 unigenes (size of >1 kb) with the most abundant being dinucleotide repeats. Conclusions This dataset represents the first transcriptome analysis of the endangered

  3. Making web annotations persistent over time

    Energy Technology Data Exchange (ETDEWEB)

    Sanderson, Robert [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory

    2010-01-01

    As Digital Libraries (DL) become more aligned with the web architecture, their functional components need to be fundamentally rethought in terms of URIs and HTTP. Annotation, a core scholarly activity enabled by many DL solutions, exhibits a clearly unacceptable characteristic when existing models are applied to the web: due to the representations of web resources changing over time, an annotation made about a web resource today may no longer be relevant to the representation that is served from that same resource tomorrow. We assume the existence of archived versions of resources, and combine the temporal features of the emerging Open Annotation data model with the capability offered by the Memento framework that allows seamless navigation from the URI of a resource to archived versions of that resource, and arrive at a solution that provides guarantees regarding the persistence of web annotations over time. More specifically, we provide theoretical solutions and proof-of-concept experimental evaluations for two problems: reconstructing an existing annotation so that the correct archived version is displayed for all resources involved in the annotation, and retrieving all annotations that involve a given archived version of a web resource.

  4. PSSP-RFE: accurate prediction of protein structural class by recursive feature extraction from PSI-BLAST profile, physical-chemical property and functional annotations.

    Directory of Open Access Journals (Sweden)

    Liqi Li

    Full Text Available Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM in conjunction with integrated features from position-specific score matrix (PSSM, PROFEAT and Gene Ontology (GO. A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets.

  5. Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation

    Directory of Open Access Journals (Sweden)

    Papaloukas Costas

    2009-04-01

    Full Text Available Abstract Background Polypeptides are composed of amino acids covalently bonded via a peptide bond. The majority of peptide bonds in proteins is found to occur in the trans conformation. In spite of their infrequent occurrence, cis peptide bonds play a key role in the protein structure and function, as well as in many significant biological processes. Results We perform a systematic analysis of regions in protein sequences that contain a proline cis peptide bond in order to discover non-random associations between the primary sequence and the nature of proline cis/trans isomerization. For this purpose an efficient pattern discovery algorithm is employed which discovers regular expression-type patterns that are overrepresented (i.e. appear frequently repeated in a set of sequences. Four types of pattern discovery are performed: i exact pattern discovery, ii pattern discovery using a chemical equivalency set, iii pattern discovery using a structural equivalency set and iv pattern discovery using certain amino acids' physicochemical properties. The extracted patterns are carefully validated using a specially implemented scoring function and a significance measure (i.e. log-probability estimate indicative of their specificity. The score threshold for the first three types of pattern discovery is 0.90 while for the last type of pattern discovery 0.80. Regarding the significance measure, all patterns yielded values in the range [-9, -31] which ensure that the derived patterns are highly unlikely to have emerged by chance. Among the highest scoring patterns, most of them are consistent with previous investigations concerning the neighborhood of cis proline peptide bonds, and many new ones are identified. Finally, the extracted patterns are systematically compared against the PROSITE database, in order to gain insight into the functional implications of cis prolyl bonds. Conclusion Cis patterns with matches in the PROSITE database fell mostly into two

  6. In silico Sequence Analysis, Homology Modeling and Function Annotation of Ocimum basilicum Hypothetical Protein G1CT28_OCIBA

    Directory of Open Access Journals (Sweden)

    Sobia Idrees

    2012-07-01

    Full Text Available Ocimum basilicum is commonly known as sweet basil and belongs to the Lamiaceae Family. Ocimum basilicum has great therapeutic benefits and can be used for lowering blood pressure, as an antispasmodic as well as cleansing the blood. In the present study, subcellular localization prediction suggested that it is a cytoplasmic protein. We predicted the 3D structure of protein using homology modeling as 3D structure prediction approach. 3D structure of the protein was determined using Protein Structure Prediction Server (PS2 selecting MODELLER as 3D structure prediction method. Quality analysis of the model indicated that it is a reliable model. Furthermore, it was discovered that Ocimum basilicum hypothetical protein G1CT28_OCIBA is involved in two biological processes, oxidation reduction and metabolic process and the biochemical function of the protein is acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, catalytic activity and oxidoreductase.

  7. Personnalisation de Syst\\`emes OLAP Annot\\'es

    CERN Document Server

    Jerbi, Houssem; Ravat, Franck; Teste, Olivier

    2010-01-01

    This paper deals with personalization of annotated OLAP systems. Data constellation is extended to support annotations and user preferences. Annotations reflect the decision-maker experience whereas user preferences enable users to focus on the most interesting data. User preferences allow annotated contextual recommendations helping the decision-maker during his/her multidimensional navigations.

  8. Cross genome phylogenetic analysis of human and Drosophila G protein-coupled receptors: application to functional annotation of orphan receptors

    Directory of Open Access Journals (Sweden)

    Sowdhamini Ramanathan

    2005-08-01

    Full Text Available Abstract Background The cell-membrane G-protein coupled receptors (GPCRs are one of the largest known superfamilies and are the main focus of intense pharmaceutical research due to their key role in cell physiology and disease. A large number of putative GPCRs are 'orphans' with no identified natural ligands. The first step in understanding the function of orphan GPCRs is to identify their ligands. Phylogenetic clustering methods were used to elucidate the chemical nature of receptor ligands, which led to the identification of natural ligands for many orphan receptors. We have clustered human and Drosophila receptors with known ligands and orphans through cross genome phylogenetic analysis and hypothesized higher relationship of co-clustered members that would ease ligand identification, as related receptors share ligands with similar structure or class. Results Cross-genome phylogenetic analyses were performed to identify eight major groups of GPCRs dividing them into 32 clusters of 371 human and 113 Drosophila proteins (excluding olfactory, taste and gustatory receptors and reveal unexpected levels of evolutionary conservation across human and Drosophila GPCRs. We also observe that members of human chemokine receptors, involved in immune response, and most of nucleotide-lipid receptors (except opsins do not have counterparts in Drosophila. Similarly, a group of Drosophila GPCRs (methuselah receptors, associated in aging, is not present in humans. Conclusion Our analysis suggests ligand class association to 52 unknown Drosophila receptors and 95 unknown human GPCRs. A higher level of phylogenetic organization was revealed in which clusters with common domain architecture or cellular localization or ligand structure or chemistry or a shared function are evident across human and Drosophila genomes. Such analyses will prove valuable for identifying the natural ligands of Drosophila and human orphan receptors that can lead to a better understanding

  9. Detection and functional annotation of misregulated microRNAs in the brain of the Ts65Dn mouse model of Down syndrome

    Institute of Scientific and Technical Information of China (English)

    HE Xiang-jun; XIAO Yun; ZHANG Qi; MA Li-ping; LI Na; YANG Jing

    2013-01-01

    Background Brain hypoplasia and mental retardation in Down syndrome (DS) can be attributed to a severe and selective disruption of neurogenesis.Secondary disruption of the transcriptome,as well as primary gene dosage imbalance,is responsible for the phenotype.MicroRNA (miRNA) expression is relatively abundant in brain tissue.Perturbed miRNA expression might contribute to the cellular events underlying the pathology in DS.Methods MiRNA expression profiles in the cerebrum of Ts65Dn mice,a DS model,were examined with a real-time RT-PCR array.MiRNA target gene expression was detected by real-time quantitative PCR and Western blotting.Based on the prediction of their cerebrum-specific targets,the functions of the misregulated miRNAs were annotated by Gene Ontology (GO) enrichment analysis.Results A total of 342 miRNAs were examined.Among them,20 miRNAs showed decreased expression in the brains of Ts65Dn mice,and some of these belonged to the same family.Two known targets of the miR-200 family,Lfng and Zeb2,were specifically selected to compare their expression in the cerebrum of Ts65Dn mice with those of euploids.However,no significant difference was found in terms of mRNA and protein expression levels of these genes.By enrichment analysis of the cerebrum-specific targets of each miRNA,we found that 15 of the differential miRNAs could significantly affect target genes that were enriched in the GO biological processes related to nervous system development.Conclusion Perturbed expression of multiple functionally cooperative miRNAs contributes to the cellular events underlying the pathogenesis of DS.

  10. Conservation, sex-biased expression and functional annotation of microRNAs in the gonad of Amur sturgeon (Acipenser schrenckii).

    Science.gov (United States)

    Zhang, Xiujuan; Yuan, Lihong; Li, Linmiao; Jiang, Haiying; Chen, Jinping

    2016-06-01

    MicroRNAs (miRNAs) are involved in post-transcriptional gene regulation and have crucial roles in regulating the expression of gametogenesis-related genes in animals. However, the mechanism of sex determination and differentiation in the sturgeon has remained unclear. Identifying miRNAs and characterizing sex-biased miRNA expression is therefore critical for understanding the role of miRNAs during sexual differentiation in sturgeon. In this study, five different tissues from sturgeon before sex differentiation and the gonads were used for miRNA expression profiling. We screened 1037 miRNAs in miRBase 20.0 and an additional 103 sturgeon miRNAs using microarray and real-time PCR. We found that the sequences of 477 miRNAs out of a total of 1140 miRNAs were highly conserved (100%) among different fish species. From a total of 663 non-redundant miRNA probes, 481 miRNAs were detected in the gonads of both sexes. Of the 148 miRNAs that were identified to have sex-biased expression patterns between the testis and the ovary (P2. The microarray expression patterns of 13 randomly selected sex-biased miRNAs were validated using real-time PCR. Target gene prediction revealed a significant enrichment of functional groups (88 GO terms) and 18 KEGG pathways (P<0.05) and suggested that there are interactions between sex-biased miRNAs and 25 putative gametogenesis-related targets. Therefore, our miRNA expression analysis in juvenile A. schrenckii establishes a foundation for understanding and further investigating the role of miRNAs in sturgeon sex differentiation. PMID:27089517

  11. Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries

    Science.gov (United States)

    Kurita, Kenji L.; Glassey, Emerson; Linington, Roger G.

    2015-01-01

    Traditional natural products discovery using a combination of live/dead screening followed by iterative bioassay-guided fractionation affords no information about compound structure or mode of action until late in the discovery process. This leads to high rates of rediscovery and low probabilities of finding compounds with unique biological and/or chemical properties. By integrating image-based phenotypic screening in HeLa cells with high-resolution untargeted metabolomics analysis, we have developed a new platform, termed Compound Activity Mapping, that is capable of directly predicting the identities and modes of action of bioactive constituents for any complex natural product extract library. This new tool can be used to rapidly identify novel bioactive constituents and provide predictions of compound modes of action directly from primary screening data. This approach inverts the natural products discovery process from the existing ‟grind and find” model to a targeted, hypothesis-driven discovery model where the chemical features and biological function of bioactive metabolites are known early in the screening workflow, and lead compounds can be rationally selected based on biological and/or chemical novelty. We demonstrate the utility of the Compound Activity Mapping platform by combining 10,977 mass spectral features and 58,032 biological measurements from a library of 234 natural products extracts and integrating these two datasets to identify 13 clusters of fractions containing 11 known compound families and four new compounds. Using Compound Activity Mapping we discovered the quinocinnolinomycins, a new family of natural products with a unique carbon skeleton that cause endoplasmic reticulum stress. PMID:26371303

  12. Creating Annotation Tools with the Annotation Graph Toolkit

    OpenAIRE

    Maeda, Kazuaki; Bird, Steven; Ma, Xiaoyi; Lee, Haejoong

    2002-01-01

    The Annotation Graph Toolkit is a collection of software supporting the development of annotation tools based on the annotation graph model. The toolkit includes application programming interfaces for manipulating annotation graph data and for importing data from other formats. There are interfaces for the scripting languages Tcl and Python, a database interface, specialized graphical user interfaces for a variety of annotation tasks, and several sample applications. This paper describes all ...

  13. Assessing functional diversity by program slicing

    International Nuclear Information System (INIS)

    A responsibility of the Nuclear Regulatory Commission auditors is to provide assessments of the quality of the safety systems. For software, the audit process as currently implemented is a slow, tedious, manual process prone to human errors. While auditors cannot possibly examine all components of the system in complete detail, they do check for implementation of specific principles like functional diversity. This paper describes an experimental prototype Computer Aided Software Engineering (CASE) tool, UNRAVEL, designed to enable auditors to check for functional diversity and aid an auditor in examining software by extracting all code relevant to a computation identified for detailed inspection

  14. COMPLEX FUNCTIONAL ASSESSMENT OF THE HIP JOINT.

    Directory of Open Access Journals (Sweden)

    Maya S. Krastanova

    2015-09-01

    Full Text Available Introduction: In relation to the study reporting the effects of applying phased complex rehabilitation in patients with total hip arthroplasty, it has been concluded that the everyday clinical practice in Bulgaria does not apply complex examination, giving an objective picture about the extent of functional status of patients with trauma and diseases of the hip. Aim: The main goal of this report is to present a test which incorporates all known and routine research and in which the total number of points determines the functional status of patients with trauma and diseases of the hip. Material and Methods: Based on the Hip dysfunction and Osteoarthritis Outcome Score, the Harris Hip Score modified test, scale D’Aubigne and Postel and Iowa’s test for complex functional evaluation of the hip joint, we have developed a test including information about the degree of pain; goniometry and manual muscle testing of the hip; locomotor test – type of gait and adjuvants; test for Daily Activities of Life. The test has been developed on the basis of expert assessment by doctors and physiotherapists of the proposed indicators for evaluation and determination of the weighting factors’ contribution to the general condition of the patient. Conclusion: The developed and tested method of complex functional assessment of the hip joint enables our colleagues, dealing with trauma and diseases of the hip, to use it in various research and scientific projects, as well as in general medical practice.

  15. Quantitative assessment of protein function prediction programs.

    Science.gov (United States)

    Rodrigues, B N; Steffens, M B R; Raittz, R T; Santos-Weiss, I C R; Marchaukoski, J N

    2015-01-01

    Fast prediction of protein function is essential for high-throughput sequencing analysis. Bioinformatic resources provide cheaper and faster techniques for function prediction and have helped to accelerate the process of protein sequence characterization. In this study, we assessed protein function prediction programs that accept amino acid sequences as input. We analyzed the classification, equality, and similarity between programs, and, additionally, compared program performance. The following programs were selected for our assessment: Blast2GO, InterProScan, PANTHER, Pfam, and ScanProsite. This selection was based on the high number of citations (over 500), fully automatic analysis, and the possibility of returning a single best classification per sequence. We tested these programs using 12 gold standard datasets from four different sources. The gold standard classification of the databases was based on expert analysis, the Protein Data Bank, or the Structure-Function Linkage Database. We found that the miss rate among the programs is globally over 50%. Furthermore, we observed little overlap in the correct predictions from each program. Therefore, a combination of multiple types of sources and methods, including experimental data, protein-protein interaction, and data mining, may be the best way to generate more reliable predictions and decrease the miss rate. PMID:26782400

  16. Semantic annotation of mutable data.

    Directory of Open Access Journals (Sweden)

    Robert A Morris

    Full Text Available Electronic annotation of scientific data is very similar to annotation of documents. Both types of annotation amplify the original object, add related knowledge to it, and dispute or support assertions in it. In each case, annotation is a framework for discourse about the original object, and, in each case, an annotation needs to clearly identify its scope and its own terminology. However, electronic annotation of data differs from annotation of documents: the content of the annotations, including expectations and supporting evidence, is more often shared among members of networks. Any consequent actions taken by the holders of the annotated data could be shared as well. But even those current annotation systems that admit data as their subject often make it difficult or impossible to annotate at fine-enough granularity to use the results in this way for data quality control. We address these kinds of issues by offering simple extensions to an existing annotation ontology and describe how the results support an interest-based distribution of annotations. We are using the result to design and deploy a platform that supports annotation services overlaid on networks of distributed data, with particular application to data quality control. Our initial instance supports a set of natural science collection metadata services. An important application is the support for data quality control and provision of missing data. A previous proof of concept demonstrated such use based on data annotations modeled with XML-Schema.

  17. Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Deng Jixin

    2009-02-01

    Full Text Available Abstract Background Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly. Methods A similarity-based (i.e., computational GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked. Results In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO. In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57% being annotated with 1,957 distinct and specific GO terms. Unannotated proteins

  18. Clinical Assessment of Cardiovascular and Autonomic Function

    Directory of Open Access Journals (Sweden)

    Diego Benitez

    2004-10-01

    Full Text Available This paper presents a non-invasive virtual medical instrument for the clinical assessment of cardiovascular and autonomic function. The virtual instrument was developed with the aim of analysing and understanding the physiological changes that occurs in the heart and circulation during vasovagal blackout attacks. The automated virtual instrument allows impedance cardiography analysis, time and frequency heart rate and blood pressure variability analysis, invasive and non-invasive baroreflex sensitivity assessment and forearm blood flow measurements. Using this virtual instrument five control subjects (3 male, mean age 30.6 ± 5.4 and five vasovagal syncope suffers (2 male, mean age 38.6 ± 6.3 were used in a study to try to identify the differences between the two groups to tilt induced syncope. The results obtained suggest that there are fundamental differences in the physiological responses to orthostatic stress between vasovagal patients and controls, which are evident before the onset of major haemodynamic changes.

  19. The GOA database: gene Ontology annotation updates for 2015.

    Science.gov (United States)

    Huntley, Rachael P; Sawford, Tony; Mutowo-Meullenet, Prudence; Shypitsyna, Aleksandra; Bonilla, Carlos; Martin, Maria J; O'Donovan, Claire

    2015-01-01

    The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups. GOA currently supplies 368 million GO annotations to almost 54 million proteins in more than 480,000 taxonomic groups. The resource now provides annotations to five times the number of proteins it did 4 years ago. As a member of the GO Consortium, we adhere to the most up-to-date Consortium-agreed annotation guidelines via the use of quality control checks that ensures that the GOA resource supplies high-quality functional information to proteins from a wide range of species. Annotations from GOA are freely available and are accessible through a powerful web browser as well as a variety of annotation file formats. PMID:25378336

  20. Sensory Dissociation in Vestibular Function Assessment

    Directory of Open Access Journals (Sweden)

    Tolmachev Ivan

    2016-01-01

    Full Text Available The project aims to create а solution to the problem of early diagnostics of neurodegenerative disorders, accompanied by imbalance, and to develop rehabilitation methods for patients with vestibular disorders. The balanced upright position is a result of interaction between vestibular system, skeleton and muscles, visual, and proprioceptive systems. Postural abnormalities are caused by morphological or functional alteration of the components of the equilibrioception system. These disorders weaken the ability of the central nervous system to process vestibular, visual and proprioceptive signals, which are responsible for the sense of balance. Moreover, it also decreases the plasticity of the nervous system, resulting in adaptation disfunctionality. Unfortunately, premorbid detection of vestibular dysfunctions is quite a complicated test because available methods to evaluate postural reflexes have low sensitivity and specifity. Consequently, the development of methods to assess functional state of the equilibrioception system becoming viable in order to detect neurodegenerative disorders as early as possible, to control treatment and rehabilitation procedures.

  1. All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs

    DEFF Research Database (Denmark)

    Schork, Andrew J; Thompson, Wesley K; Pham, Phillip;

    2013-01-01

    Recent results indicate that genome-wide association studies (GWAS) have the potential to explain much of the heritability of common complex phenotypes, but methods are lacking to reliably identify the remaining associated single nucleotide polymorphisms (SNPs). We applied stratified False...... Discovery Rate (sFDR) methods to leverage genic enrichment in GWAS summary statistics data to uncover new loci likely to replicate in independent samples. Specifically, we use linkage disequilibrium-weighted annotations for each SNP in combination with nominal p-values to estimate the True Discovery Rate...... (TDR = 1-FDR) for strata determined by different genic categories. We show a consistent pattern of enrichment of polygenic effects in specific annotation categories across diverse phenotypes, with the greatest enrichment for SNPs tagging regulatory and coding genic elements, little enrichment in...

  2. Collaborative Movie Annotation

    Science.gov (United States)

    Zad, Damon Daylamani; Agius, Harry

    In this paper, we focus on metadata for self-created movies like those found on YouTube and Google Video, the duration of which are increasing in line with falling upload restrictions. While simple tags may have been sufficient for most purposes for traditionally very short video footage that contains a relatively small amount of semantic content, this is not the case for movies of longer duration which embody more intricate semantics. Creating metadata is a time-consuming process that takes a great deal of individual effort; however, this effort can be greatly reduced by harnessing the power of Web 2.0 communities to create, update and maintain it. Consequently, we consider the annotation of movies within Web 2.0 environments, such that users create and share that metadata collaboratively and propose an architecture for collaborative movie annotation. This architecture arises from the results of an empirical experiment where metadata creation tools, YouTube and an MPEG-7 modelling tool, were used by users to create movie metadata. The next section discusses related work in the areas of collaborative retrieval and tagging. Then, we describe the experiments that were undertaken on a sample of 50 users. Next, the results are presented which provide some insight into how users interact with existing tools and systems for annotating movies. Based on these results, the paper then develops an architecture for collaborative movie annotation.

  3. Annotated bibliography traceability

    NARCIS (Netherlands)

    Narain, G.

    2006-01-01

    This annotated bibliography contains summaries of articles and chapters of books, which are relevant to traceability. After each summary there is a part about the relevancy of the paper for the LEI project. The aim of the LEI-project is to gain insight in several aspects of traceability in order to

  4. Annotation: The Savant Syndrome

    Science.gov (United States)

    Heaton, Pamela; Wallace, Gregory L.

    2004-01-01

    Background: Whilst interest has focused on the origin and nature of the savant syndrome for over a century, it is only within the past two decades that empirical group studies have been carried out. Methods: The following annotation briefly reviews relevant research and also attempts to address outstanding issues in this research area.…

  5. Beyond genomic variation - comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage

    OpenAIRE

    Lin, Ke; Zhang, Ningwen; Severing, Edouard I.; Nijveen, Harm; Cheng, Feng; Visser, Richard GF; Wang, Xiaowu; de Ridder, Dick; Bonnema, Guusje

    2014-01-01

    Background Brassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops. Results To investigate the genetic variation underlying this morphological variation, we re-sequenced, assembled and annotated the genomes of two B. rapa subspecies, turnip crops (turnip) and a rapid cycling. We then analysed the two resulting ge...

  6. Beyond genomic variation - comparison and functional annotation in three Brassica rapa genotypes: a turnip, a rapid cycling and a Chinese cabbage

    OpenAIRE

    Lin, K.; Zhang, N.; Severing, E.I.; Nijveen, H.; Cheng, F; Visser, R.G.F.; Wang, X.; De, Ridder, G.; Bonnema, A.B.

    2014-01-01

    Background - Brassica rapa is an economically important crop species. During its long breeding history, a large number of morphotypes have been generated, including leafy vegetables such as Chinese cabbage and pakchoi, turnip tuber crops and oil crops. Results - To investigate the genetic variation underlying this morphological variation, we re-sequenced, assembled and annotated the genomes of two B. rapa subspecies, turnip crops (turnip) and a rapid cycling. We then analysed the two resultin...

  7. Bioinformatics Assisted Gene Discovery and Annotation of Human Genome

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    As the sequencing stage of human genome project is near the end, the work has begun for discovering novel genes from genome sequences and annotating their biological functions. Here are reviewed current major bioinformatics tools and technologies available for large scale gene discovery and annotation from human genome sequences. Some ideas about possible future development are also provided.

  8. The UniProt-GO Annotation database in 2011

    Science.gov (United States)

    Dimmer, Emily C.; Huntley, Rachael P.; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria J.; Bely, Benoit; Browne, Paul; Mun Chan, Wei; Eberhardt, Ruth; Gardner, Michael; Laiho, Kati; Legge, Duncan; Magrane, Michele; Pichler, Klemens; Poggioli, Diego; Sehra, Harminder; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Bridge, Alan; Coudert, Elizabeth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Lemercier, Phillippe; Lieberherr, Damien; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michael; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Bougueleret, Lydie; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek- Roggli, Paula; Xenarios, Ioannis; Apweiler, Rolf

    2012-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set. PMID:22123736

  9. The UniProt-GO Annotation database in 2011.

    Science.gov (United States)

    Dimmer, Emily C; Huntley, Rachael P; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria J; Bely, Benoit; Browne, Paul; Mun Chan, Wei; Eberhardt, Ruth; Gardner, Michael; Laiho, Kati; Legge, Duncan; Magrane, Michele; Pichler, Klemens; Poggioli, Diego; Sehra, Harminder; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Bridge, Alan; Coudert, Elizabeth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Lemercier, Phillippe; Lieberherr, Damien; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michael; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Bougueleret, Lydie; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek-Roggli, Paula; Xenarios, Ioannis; Apweiler, Rolf

    2012-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360,000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set. PMID:22123736

  10. MPEG-7 based video annotation and browsing

    Science.gov (United States)

    Hoeynck, Michael; Auweiler, Thorsten; Wellhausen, Jens

    2003-11-01

    The huge amount of multimedia data produced worldwide requires annotation in order to enable universal content access and to provide content-based search-and-retrieval functionalities. Since manual video annotation can be time consuming, automatic annotation systems are required. We review recent approaches to content-based indexing and annotation of videos for different kind of sports and describe our approach to automatic annotation of equestrian sports videos. We especially concentrate on MPEG-7 based feature extraction and content description, where we apply different visual descriptors for cut detection. Further, we extract the temporal positions of single obstacles on the course by analyzing MPEG-7 edge information. Having determined single shot positions as well as the visual highlights, the information is jointly stored with meta-textual information in an MPEG-7 description scheme. Based on this information, we generate content summaries which can be utilized in a user-interface in order to provide content-based access to the video stream, but further for media browsing on a streaming server.

  11. A Factor Graph Approach to Automated GO Annotation.

    Science.gov (United States)

    Spetale, Flavio E; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

    2016-01-01

    As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum. PMID:26771463

  12. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations

    OpenAIRE

    Bastian F.B.; Chibucos M.C.; Gaudet P.; Giglio M.; Holliday G.L.; Huang H; Lewis S.E.; Niknejad A.; Orchard S.; Poux S.; Skunca N.; Robinson-Rechavi M.

    2015-01-01

    Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations has considerably grown in recent years. However, the reliability of these annotations varies; it has thus become necessary to be able to assess the confidence in annotations. Although several resources already provide confidence information about the annotations that they produce, a standard way of providing such information has yet to be defined. This lack of standardization undermines ...

  13. Implementation of functional assessment scales in geriatric practice

    DEFF Research Database (Denmark)

    Poulsen, Ingrid; Hesselbo, Bjørn; Pietersen, Inge; Schroll, Marianne

    2005-01-01

    A study was undertaken to evaluate the feasibility of functional assessment scales regarding completion rate and ability to document functional changes in geriatric rehabilitation patients.......A study was undertaken to evaluate the feasibility of functional assessment scales regarding completion rate and ability to document functional changes in geriatric rehabilitation patients....

  14. EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

    Directory of Open Access Journals (Sweden)

    Hamilton John P

    2007-10-01

    Full Text Available Abstract Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging knowledge from a dispersed community of scientists is a demonstrated way of improving a genome annotation. This requires tools that facilitate 1 the submission of gene annotation to an annotation project, 2 the review of the submitted models by project annotators, and 3 the incorporation of the submitted models in the ongoing annotation effort. Results We have developed the Eukaryotic Community Annotation Package (EuCAP, an annotation tool, and have applied it to the rice genome. The primary level of curation by community annotators (CA has been the annotation of gene families. Annotation can be submitted by email or through the EuCAP Web Tool. The CA models are aligned to the rice pseudomolecules and the coordinates of these alignments, along with functional annotation, are stored in the MySQL EuCAP Gene Model database. Web pages displaying the alignments of the CA models to the Osa1 Genome models are automatically generated from the EuCAP Gene Model database. The alignments are reviewed by the project annotators (PAs in the context of experimental evidence. Upon approval by the PAs, the CA models, along with the corresponding functional annotations, are integrated into the Osa1 Genome Annotation. The CA annotations, grouped by family, are displayed on the Community Annotation pages of the project website http://rice.tigr.org, as well as in the Community Annotation track of the Genome Browser. Conclusion We have applied EuCAP to rice. As of July 2007, the

  15. Evaluating techniques for metagenome annotation using simulated sequence data.

    Science.gov (United States)

    Randle-Boggis, Richard J; Helgason, Thorunn; Sapp, Melanie; Ashton, Peter D

    2016-07-01

    The advent of next-generation sequencing has allowed huge amounts of DNA sequence data to be produced, advancing the capabilities of microbial ecosystem studies. The current challenge is to identify from which microorganisms and genes the DNA originated. Several tools and databases are available for annotating DNA sequences. The tools, databases and parameters used can have a significant impact on the results: naïve choice of these factors can result in a false representation of community composition and function. We use a simulated metagenome to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast. This simulated metagenome allowed the recovery of known organism and function abundances to be quantitatively evaluated, which is not possible for environmental metagenomes. The performance of each program and database varied, e.g. One Codex correctly annotated many sequences at the genus level, whereas MG-RAST RefSeq produced many false positive annotations. This effect decreased as the taxonomic level investigated increased. Selecting more stringent parameters decreases the annotation sensitivity, but increases precision. Ultimately, there is a trade-off between taxonomic resolution and annotation accuracy. These results should be considered when annotating metagenomes and interpreting results from previous studies. PMID:27162180

  16. Statistical mechanics of ontology based annotations

    Science.gov (United States)

    Hoyle, David C.; Brass, Andrew

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.

  17. EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

    OpenAIRE

    Hamilton John P; Campbell Matthew; Thibaud-Nissen Françoise; Zhu Wei; Buell C

    2007-01-01

    Abstract Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation) is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging k...

  18. The GATO gene annotation tool for research laboratories

    Directory of Open Access Journals (Sweden)

    A. Fujita

    2005-11-01

    Full Text Available Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

  19. The GATO gene annotation tool for research laboratories.

    Science.gov (United States)

    Fujita, A; Massirer, K B; Durham, A M; Ferreira, C E; Sogayar, M C

    2005-11-01

    Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB. PMID:16258624

  20. Assessing Executive Functioning: A Pragmatic Review

    Science.gov (United States)

    Hass, Michael R.; Patterson, Ashlea; Sukraw, Jocelyn; Sullivan, Brianna M.

    2014-01-01

    Despite the common usage of the term "executive functioning" in neuropsychology, several aspects of this concept remain unsettled. In this paper, we will address some of the issues surrounding the notion of executive functioning and how an understanding of executive functioning and its components might assist school-based practitioners…

  1. Predicting word sense annotation agreement

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector; Johannsen, Anders Trærup; Lopez de Lacalle, Oier;

    2015-01-01

    High agreement is a common objective when annotating data for word senses. However, a number of factors make perfect agreement impossible, e.g. the limitations of the sense inventories, the difficulty of the examples or the interpretation preferences of the annotations. Estimating potential...... agreement is thus a relevant task to supplement the evaluation of sense annotations. In this article we propose two methods to predict agreement on word-annotation instances. We experiment with a continuous representation and a three-way discretization of observed agreement. In spite of the difficulty of...

  2. Statistical mechanics of ontology based annotations

    CERN Document Server

    Hoyle, David C

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotate...

  3. MimoSA: a system for minimotif annotation

    Directory of Open Access Journals (Sweden)

    Kundeti Vamsi

    2010-06-01

    Full Text Available Abstract Background Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature. Results We have built the MimoSA application for minimotif annotation. The application supports management of the Minimotif Miner database, literature tracking, and annotation of new minimotifs. MimoSA enables the visualization, organization, selection and editing functions of minimotifs and their attributes in the MnM database. For the literature components, Mimosa provides paper status tracking and scoring of papers for annotation through a freely available machine learning approach, which is based on word correlation. The paper scoring algorithm is also available as a separate program, TextMine. Form-driven annotation of minimotif attributes enables entry of new minimotifs into the MnM database. Several supporting features increase the efficiency of annotation. The layered architecture of MimoSA allows for extensibility by separating the functions of paper scoring, minimotif visualization, and database management. MimoSA is readily adaptable to other annotation efforts that manually curate literature into a MySQL database. Conclusions MimoSA is an extensible application that facilitates minimotif annotation and integrates with the Minimotif Miner database. We have built MimoSA as an application that integrates dynamic abstract scoring with a high performance relational model of minimotif syntax. MimoSA's TextMine, an efficient paper-scoring algorithm, can be used to

  4. Computational evaluation of TIS annotation for prokaryotic genomes

    OpenAIRE

    Zhu Huaiqiu; Ju Li-Ning; Zheng Xiaobin; Hu Gang-Qing; She Zhen-Su

    2008-01-01

    Abstract Background Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks. Results Based on a homogeneity assumption that gene translation-related signals are uniformly distributed across a genome, we have established a computational method for a large-scale quantitative assessment o...

  5. Collective dynamics of social annotation

    CERN Document Server

    Cattuto, Ciro; Baldassarri, Andrea; Schehr, G; Loreto, Vittorio

    2009-01-01

    The enormous increase of popularity and use of the WWW has led in the recent years to important changes in the ways people communicate. An interesting example of this fact is provided by the now very popular social annotation systems, through which users annotate resources (such as web pages or digital photographs) with text keywords dubbed tags. Understanding the rich emerging structures resulting from the uncoordinated actions of users calls for an interdisciplinary effort. In particular concepts borrowed from statistical physics, such as random walks, and the complex networks framework, can effectively contribute to the mathematical modeling of social annotation systems. Here we show that the process of social annotation can be seen as a collective but uncoordinated exploration of an underlying semantic space, pictured as a graph, through a series of random walks. This modeling framework reproduces several aspects, so far unexplained, of social annotation, among which the peculiar growth of the size of the...

  6. De novo assembly, functional annotation and comparative analysis of Withania somnifera leaf and root transcriptomes to identify putative genes involved in the withanolides biosynthesis.

    Directory of Open Access Journals (Sweden)

    Parul Gupta

    Full Text Available Withania somnifera is one of the most valuable medicinal plants used in Ayurvedic and other indigenous medicine systems due to bioactive molecules known as withanolides. As genomic information regarding this plant is very limited, little information is available about biosynthesis of withanolides. To facilitate the basic understanding about the withanolide biosynthesis pathways, we performed transcriptome sequencing for Withania leaf (101L and root (101R which specifically synthesize withaferin A and withanolide A, respectively. Pyrosequencing yielded 8,34,068 and 7,21,755 reads which got assembled into 89,548 and 1,14,814 unique sequences from 101L and 101R, respectively. A total of 47,885 (101L and 54,123 (101R could be annotated using TAIR10, NR, tomato and potato databases. Gene Ontology and KEGG analyses provided a detailed view of all the enzymes involved in withanolide backbone synthesis. Our analysis identified members of cytochrome P450, glycosyltransferase and methyltransferase gene families with unique presence or differential expression in leaf and root and might be involved in synthesis of tissue-specific withanolides. We also detected simple sequence repeats (SSRs in transcriptome data for use in future genetic studies. Comprehensive sequence resource developed for Withania, in this study, will help to elucidate biosynthetic pathway for tissue-specific synthesis of secondary plant products in non-model plant organisms as well as will be helpful in developing strategies for enhanced biosynthesis of withanolides through biotechnological approaches.

  7. Treatment assessment of radiotherapy using MR functional quantitative imaging

    Institute of Scientific and Technical Information of China (English)

    Zheng; Chang; Chunhao; Wang

    2015-01-01

    Recent developments in magnetic resonance(MR) functional quantitative imaging have made it a potentially powerful tool to assess treatment response in radiation therapy. With its abilities to capture functional information on underlying tissue characteristics, MR functional quantitative imaging can be valuable in assessing treatment response and as such to optimize therapeutic outcome. Various MR quantitative imaging techniques, including diffusion weighted imaging, diffusion tensor imaging, MR spectroscopy and dynamic contrastenhanced imaging, have been investigated and found useful for assessment of radiotherapy. However, various aspects including data reproducibility, interpretation of biomarkers, image quality and data analysis impose challenges on applications of MR functional quantitative imaging in radiotherapy assessment. All of these challenging issues shall be addressed to help us understand whether MR functional quantitative imaging is truly beneficial and contributes to future development of radiotherapy. It is evident that individualized therapy is the future direction of patient care. MR functional quantitative imaging might serves as an indispensable tool towards this promising direction.

  8. Lyapunov Functions Family Approach to Transient Stability Assessment

    OpenAIRE

    Vu, Thanh Long; Turitsyn, Konstantin

    2014-01-01

    Analysis of transient stability of strongly nonlinear post-fault dynamics is one of the most computationally challenging parts of Dynamic Security Assessment. This paper proposes a novel approach for assessment of transient stability of the system. The approach generalizes the idea of energy methods, and extends the concept of energy function to a more general Lyapunov Functions Family (LFF) constructed via Semi-Definite-Programming techniques. Unlike the traditional energy function and its v...

  9. The scintigraphic assessment of adrenocortical function

    International Nuclear Information System (INIS)

    The adrenal gland uptake of the radiopharmaceutical 131I-6#betta#-iodomethylnorcholesterol (NP-59) was used to localize diseases of the adrenal cortex and to functionally characterize abnormal cortisol secretion in Cushing's syndrome, adrenal hyperandrogenism and aldosterone secretion in an animal model

  10. Sensory Dissociation in Vestibular Function Assessment

    OpenAIRE

    Tolmachev Ivan; Brazovsky Konstantin; Schadenko Sergey; Korzhenkova Ekaterina

    2016-01-01

    The project aims to create а solution to the problem of early diagnostics of neurodegenerative disorders, accompanied by imbalance, and to develop rehabilitation methods for patients with vestibular disorders. The balanced upright position is a result of interaction between vestibular system, skeleton and muscles, visual, and proprioceptive systems. Postural abnormalities are caused by morphological or functional alteration of the components of the equilibrioception system. These disorders we...

  11. Brain function assessment in different conscious states

    OpenAIRE

    Ozgoren, Murat; Bayazit, Onur; Kocaaslan, Sibel; Gokmen, Necati; Oniz, Adile

    2010-01-01

    Background The study of brain functioning is a major challenge in neuroscience fields as human brain has a dynamic and ever changing information processing. Case is worsened with conditions where brain undergoes major changes in so-called different conscious states. Even though the exact definition of consciousness is a hard one, there are certain conditions where the descriptions have reached a consensus. The sleep and the anesthesia are different conditions which are separable from each oth...

  12. Cost Functions for Assessment of Vehicle Dynamics

    Czech Academy of Sciences Publication Activity Database

    Savitski, D.; Plíhal, Jiří; Nedoma, P.; Machan, J.; Ivanov, V.; Augsburg, K.

    Piscataway : IEEE, 2013, s. 48-55. ISBN 978-1-4673-5851-4. [IEEE Symposium Series on Computational Intelligence (SSCI) 2013. Singapore (SG), 16.04.2013-19.04.2013] Grant ostatní: EU commisions(XE) FP7-284708 (2007-2013) Institutional support: RVO:67985556 Keywords : vehicle dynamics * cost functions * weighting factors Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering http://library.utia.cas.cz/separaty/2013/AS/plihal-0392091.pdf

  13. Year 2 Report: Protein Function Prediction Platform

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, C E

    2012-04-27

    Upon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. The PFP platform is a multi-scale computational modeling system for protein structure-function annotation and function prediction. As of this writing, PFP is the only existing fully automated, high-throughput, multi-scale modeling, whole-proteome annotation platform, and represents a significant advance in the field of genome annotation (Fig. 1). PFP modules perform protein functional annotations at the sequence, systems biology, protein structure, and atomistic levels of biological complexity (Fig. 2). Because these approaches provide orthogonal means of characterizing proteins and suggesting protein function, PFP processing maximizes the protein functional information that can currently be gained by computational means. Comprehensive annotation of pathogen genomes is essential for bio-defense applications in pathogen characterization, threat assessment, and medical countermeasure design and development in that it can short-cut the time and effort required to select and characterize protein biomarkers.

  14. Functional criteria for assessing pointe-readiness.

    Science.gov (United States)

    Richardson, Megan; Liederbach, Marijeanne; Sandow, Emily

    2010-01-01

    The most popular criterion cited in the dance literature for advancement to pointe work is attainment of the chronological age of 12 years. However, dancers at this age vary greatly in terms of musculoskeletal maturity and motor skill development. The purpose of this study was to investigate whether objective, functional tests could be used in conjunction with dance teacher expertise to determine pointe-readiness. It was hypothesized that dynamic tests of motor control can better indicate pointe-readiness than chronological age alone or in combination with static musculoskeletal measurements. Thirty-seven pre-pointe students from two professional ballet schools were tested for muscular strength, ankle joint range of motion, single leg standing balance, dynamic alignment, and turning skill. In addition, the participating students' ballet teachers independently graded each student on her readiness to begin dancing en pointe. Performance on three functional tests (the Airplane test, Sauté test, and Topple test) was closely associated with teacher subjective rating for pointe-readiness. It is concluded that these tests may be more useful for gauging acquisition of the skills required for safe and successful performance than the traditionally accepted indicators of chronological age, years of dance training, and ankle joint range of motion. PMID:21067685

  15. Accountability for Early Childhood Education (Assessing Global Functioning).

    Science.gov (United States)

    Cassel, Russell N.

    1995-01-01

    Discusses the pacing of learning activity, knowledge of progress in student learning, teacher role, accountability in learning, feedback on knowledge of success, the global functioning assessment concept, and the mother surrogate. (RS)

  16. Assessing functional impairment in individuals with mild cognitive impairment

    Directory of Open Access Journals (Sweden)

    Patrícia Belchior

    2016-04-01

    Full Text Available To date, there is no consensus on how to assess functional impairment in individuals with mild cognitive impairment (MCI, and this lack of consensus is reflected in the clinical practice. Since the criterion used in the literature is very vague, clinicians are still left without much guidance in this area. Thus, the main goal of this study was to examine how functional impairment in individuals with MCI has been assessed in the literature. An electronic database search strategy was developed in consultation with an experienced librarian. Four databases (CINAHL, PsycINFO, PubMed, and MEDLINE were searched from 2000 to May 2014 to provide a comprehensive coverage of the literature. The literature search yielded 14 tools that assessed functional impairment in MCI. Among those, nine tools were performance-based measures in which participants were observed while executing a task in a simulated environment using real life material. In terms of questionnaires (either informant- or self-reports, five tools were found. Different functional domains have been assessed in each tool. According to this review, the characteristics of the instruments used in the literature to assess functional impairment in individuals with MCI vary greatly. Nonetheless, results of this study allow clinicians to make better-informed decisions when choosing a functional assessment for this population.

  17. Reliability of the Hazelbaker Assessment Tool for Lingual Frenulum Function

    OpenAIRE

    James Jennifer P; Amir Lisa H; Donath Susan M

    2006-01-01

    Abstract Background About 3% of infants are born with a tongue-tie which may lead to breastfeeding problems such as ineffective latch, painful attachment or poor weight gain. The Hazelbaker Assessment Tool for Lingual Frenulum Function (HATLFF) has been developed to give a quantitative assessment of the tongue-tie and recommendation about frenotomy (release of the frenulum). The aim of this study was to assess the inter-rater reliability of the HATLFF. Methods Fifty-eight infants referred to ...

  18. Semantic annotation of biological concepts interplaying microbial cellular responses

    Directory of Open Access Journals (Sweden)

    Carreira Rafael

    2011-11-01

    Full Text Available Abstract Background Automated extraction systems have become a time saving necessity in Systems Biology. Considerable human effort is needed to model, analyse and simulate biological networks. Thus, one of the challenges posed to Biomedical Text Mining tools is that of learning to recognise a wide variety of biological concepts with different functional roles to assist in these processes. Results Here, we present a novel corpus concerning the integrated cellular responses to nutrient starvation in the model-organism Escherichia coli. Our corpus is a unique resource in that it annotates biomedical concepts that play a functional role in expression, regulation and metabolism. Namely, it includes annotations for genetic information carriers (genes and DNA, RNA molecules, proteins (transcription factors, enzymes and transporters, small metabolites, physiological states and laboratory techniques. The corpus consists of 130 full-text papers with a total of 59043 annotations for 3649 different biomedical concepts; the two dominant classes are genes (highest number of unique concepts and compounds (most frequently annotated concepts, whereas other important cellular concepts such as proteins account for no more than 10% of the annotated concepts. Conclusions To the best of our knowledge, a corpus that details such a wide range of biological concepts has never been presented to the text mining community. The inter-annotator agreement statistics provide evidence of the importance of a consolidated background when dealing with such complex descriptions, the ambiguities naturally arising from the terminology and their impact for modelling purposes. Availability is granted for the full-text corpora of 130 freely accessible documents, the annotation scheme and the annotation guidelines. Also, we include a corpus of 340 abstracts.

  19. FINDING GENERIFS VIA GENE ONTOLOGY ANNOTATIONS

    OpenAIRE

    Lu, Zhiyong; Cohen, K Bretonnel; Hunter, Lawrence

    2006-01-01

    A Gene Reference Into Function (GeneRIF) is a concise phrase describing a function of a gene in the Entrez Gene database. Applying techniques from the area of natural language processing known as automatic summarization, it is possible to link the Entrez Gene database, the Gene Ontology, and the biomedical literature. A system was implemented that automatically suggests a sentence from a PubMed/MEDLINE abstract as a candidate GeneRIF by exploiting a gene’s GO annotations along with location f...

  20. Reliability of the Hazelbaker Assessment Tool for Lingual Frenulum Function

    Directory of Open Access Journals (Sweden)

    James Jennifer P

    2006-03-01

    Full Text Available Abstract Background About 3% of infants are born with a tongue-tie which may lead to breastfeeding problems such as ineffective latch, painful attachment or poor weight gain. The Hazelbaker Assessment Tool for Lingual Frenulum Function (HATLFF has been developed to give a quantitative assessment of the tongue-tie and recommendation about frenotomy (release of the frenulum. The aim of this study was to assess the inter-rater reliability of the HATLFF. Methods Fifty-eight infants referred to the Breastfeeding Education and Support Services (BESS at The Royal Women's Hospital for assessment of tongue-tie and 25 control infants were assessed by two clinicians independently. Results The Appearance items received kappas between about 0.4 to 0.6, which represents "moderate" reliability. The first three Function items (lateralization, lift and extension of tongue had kappa values over 0.65 which indicates "substantial" agreement. The four Function items relating to infant sucking (spread, cupping, peristalsis and snapback received low kappa values with insignificant p values. There was 96% agreement between the two assessors on the recommendation for frenotomy (kappa 0.92, excellent agreement. The study found that the Function Score can be more simply assessed using only the first three function items (ie not scoring the sucking items, with a cut-off of ≤4 for recommendation of frenotomy. Conclusion We found that the HATLFF has a high reliability in a study of infants with tongue-tie and control infants

  1. Assessing Functional Performance in the Mdx Mouse Model

    OpenAIRE

    Aartsma-Rus, Annemieke; van Putten, Maaike

    2014-01-01

    Duchenne muscular dystrophy (DMD) is a severe and progressive muscle wasting disorder for which no cure is available. Nevertheless, several potential pharmaceutical compounds and gene therapy approaches have progressed into clinical trials. With improvement in muscle function being the most important end point in these trials, a lot of emphasis has been placed on setting up reliable, reproducible, and easy to perform functional tests to pre clinically assess muscle function, strength, conditi...

  2. Evidence-based Assessment of Cognitive Functioning in Pediatric Psychology

    OpenAIRE

    Campbell, Jonathan M.; Brown, Ronald T.; Cavanagh, Sarah E.; Vess, Sarah F.; Segall, Mathew J.

    2008-01-01

    Objective To review the evidence base for measures of cognitive functioning frequently used within the field of pediatric psychology. Methods From a list of 47 measures identified by the Society of Pediatric Psychology (Division 54) Evidence-Based Assessment Task Force Workgroup, 27 measures were included in the review. Measures were organized, reviewed, and evaluated according to general domains of functioning (e.g., attention/executive functioning, memory). Results Twenty-two of 27 measures...

  3. Defining and Assessing Public Health Functions: A Global Analysis.

    Science.gov (United States)

    Martin-Moreno, Jose M; Harris, Meggan; Jakubowski, Elke; Kluge, Hans

    2016-01-01

    Given the broad scope and intersectoral nature of public health structures and practices, there are inherent difficulties in defining which services fall under the public health remit and in assessing their capacity and performance. The aim of this study is to analyze how public health functions and practice have been defined and operationalized in different countries and regions around the world, with a specific focus on assessment tools that have been developed to evaluate the performance of essential public health functions, services, and operations. Our review has identified nearly 100 countries that have carried out assessments, using diverse analytical and methodological approaches. The assessment processes have evolved quite differently according to administrative arrangements and resource availability, but some key contextual factors emerge that seem to favor policy-oriented follow-up. These include local ownership of the assessment process, policymakers' commitment to reform, and expert technical advice for implementation. PMID:26789385

  4. A novel approach to the assessment of vascular endothelial function

    Energy Technology Data Exchange (ETDEWEB)

    Sathasivam, S; Siddiqui, Z; Greenwald, S [Pathology Group, Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London (United Kingdom); Phababpha, S; Sengmeuan, P; Detchaporn, P; Kukongviriyapan, U, E-mail: s.e.greenwald@qmul.ac.uk [Department of Physiology, Khon Kaen University, Khon Kaen (Thailand)

    2011-08-17

    Impaired endothelial function (EF) is associated with atherogenesis, and its quantitative assessment has prognostic value. Currently, methods based on assessing flow-mediated dilation (FMD) are technically difficult and expensive. We tested a novel way of assessing EF by measuring the time difference between pulses arriving at the middle fingers of each hand (f-f{Delta}T), whilst FMD is induced in one arm. We compared f-f{Delta}T with standard methods in healthy and diseased subjects. Our findings suggest that the proposed simple and inexpensive technique gives comparable results and has the potential to qualitatively assess EF in the clinical setting, although further work is required.

  5. Assessment of subjective and objective cognitive function in bipolar disorder

    DEFF Research Database (Denmark)

    Demant, Kirsa M; Vinberg, Maj; Kessing, Lars V;

    2015-01-01

    Cognitive dysfunction is prevalent in bipolar disorder (BD). However, the evidence regarding the association between subjective cognitive complaints, objective cognitive performance and psychosocial function is sparse and inconsistent. Seventy seven patients with bipolar disorder who presented...... cognitive complaints underwent assessment of objective and subjective cognitive function and psychosocial functioning as part of their participation in two clinical trials. We investigated the association between global and domain-specific objective and subjective cognitive function and between global...... cognitive function and psychosocial function. We also identified clinical variables that predicted objective and subjective cognitive function and psychosocial functioning. There was a correlation between global subjective and objective measures of cognitive dysfunction but not within the individual...

  6. APPRIS: annotation of principal and alternative splice isoforms.

    Science.gov (United States)

    Rodriguez, Jose Manuel; Maietta, Paolo; Ezkurdia, Iakes; Pietrelli, Alessandro; Wesselink, Jan-Jaap; Lopez, Gonzalo; Valencia, Alfonso; Tress, Michael L

    2013-01-01

    Here, we present APPRIS (http://appris.bioinfo.cnio.es), a database that houses annotations of human splice isoforms. APPRIS has been designed to provide value to manual annotations of the human genome by adding reliable protein structural and functional data and information from cross-species conservation. The visual representation of the annotations provided by APPRIS for each gene allows annotators and researchers alike to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, APPRIS also selects a single reference sequence for each gene, here termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. APPRIS identifies a principal isoform for 85% of the protein-coding genes in the GENCODE 7 release for ENSEMBL. Analysis of the APPRIS data shows that at least 70% of the alternative (non-principal) variants would lose important functional or structural information relative to the principal isoform. PMID:23161672

  7. AGeS: A Software System for Microbial Genome Sequence Annotation

    Science.gov (United States)

    Kumar, Kamal; Desai, Valmik; Cheng, Li; Khitrov, Maxim; Grover, Deepak; Satya, Ravi Vijaya; Yu, Chenggang; Zavaljevski, Nela; Reifman, Jaques

    2011-01-01

    Background The annotation of genomes from next-generation sequencing platforms needs to be rapid, high-throughput, and fully integrated and automated. Although a few Web-based annotation services have recently become available, they may not be the best solution for researchers that need to annotate a large number of genomes, possibly including proprietary data, and store them locally for further analysis. To address this need, we developed a standalone software application, the Annotation of microbial Genome Sequences (AGeS) system, which incorporates publicly available and in-house-developed bioinformatics tools and databases, many of which are parallelized for high-throughput performance. Methodology The AGeS system supports three main capabilities. The first is the storage of input contig sequences and the resulting annotation data in a central, customized database. The second is the annotation of microbial genomes using an integrated software pipeline, which first analyzes contigs from high-throughput sequencing by locating genomic regions that code for proteins, RNA, and other genomic elements through the Do-It-Yourself Annotation (DIYA) framework. The identified protein-coding regions are then functionally annotated using the in-house-developed Pipeline for Protein Annotation (PIPA). The third capability is the visualization of annotated sequences using GBrowse. To date, we have implemented these capabilities for bacterial genomes. AGeS was evaluated by comparing its genome annotations with those provided by three other methods. Our results indicate that the software tools integrated into AGeS provide annotations that are in general agreement with those provided by the compared methods. This is demonstrated by a >94% overlap in the number of identified genes, a significant number of identical annotated features, and a >90% agreement in enzyme function predictions. PMID:21408217

  8. Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study

    OpenAIRE

    Costanzo, Maria C.; Park, Julie; Balakrishnan, Rama; Cherry, J. Michael; Hong, Eurie L.

    2011-01-01

    Annotation using Gene Ontology (GO) terms is one of the most important ways in which biological information about specific gene products can be expressed in a searchable, computable form that may be compared across genomes and organisms. Because literature-based GO annotations are often used to propagate functional predictions between related proteins, their accuracy is critically important. We present a strategy that employs a comparison of literature-based annotations with computational pre...

  9. Comparative validation of the D. melanogaster modENCODE transcriptome annotation

    OpenAIRE

    Chen, Zhen-Xia; Sturgill, David; Qu, Jiaxin; Jiang, Huaiyang; Park, Soo; Boley, Nathan; Suzuki, Ana Maria; Anthony R. Fletcher; David C Plachetzki; FitzGerald, Peter C.; Artieri, Carlo G.; Atallah, Joel; Barmina, Olga; Brown, James B.; Blankenburg, Kerstin P

    2014-01-01

    Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the ...

  10. Collective dynamics of social annotation.

    Science.gov (United States)

    Cattuto, Ciro; Barrat, Alain; Baldassarri, Andrea; Schehr, Gregory; Loreto, Vittorio

    2009-06-30

    The enormous increase of popularity and use of the worldwide web has led in the recent years to important changes in the ways people communicate. An interesting example of this fact is provided by the now very popular social annotation systems, through which users annotate resources (such as web pages or digital photographs) with keywords known as "tags." Understanding the rich emergent structures resulting from the uncoordinated actions of users calls for an interdisciplinary effort. In particular concepts borrowed from statistical physics, such as random walks (RWs), and complex networks theory, can effectively contribute to the mathematical modeling of social annotation systems. Here, we show that the process of social annotation can be seen as a collective but uncoordinated exploration of an underlying semantic space, pictured as a graph, through a series of RWs. This modeling framework reproduces several aspects, thus far unexplained, of social annotation, among which are the peculiar growth of the size of the vocabulary used by the community and its complex network structure that represents an externalization of semantic structures grounded in cognition and that are typically hard to access. PMID:19506244

  11. SENTIMENT ANALYSIS OF DOCUMENT BASED ON ANNOTATION

    Directory of Open Access Journals (Sweden)

    Archana Shukla

    2011-11-01

    Full Text Available I present a tool which tells the quality of document or its usefulness based on annotations. Annotation mayinclude comments, notes, observation, highlights, underline, explanation, question or help etc. commentsare used for evaluative purpose while others are used for summarization or for expansion also. Furtherthese comments may be on another annotation. Such annotations are referred as meta-annotation. Allannotation may not get equal weightage. My tool considered highlights, underline as well as comments toinfer the collective sentiment of annotators. Collective sentiments of annotators are classified as positive,negative, objectivity. My tool computes collective sentiment of annotations in two manners. It counts all theannotation present on the documents as well as it also computes sentiment scores of all annotation whichincludes comments to obtain the collective sentiments about the document or to judge the quality ofdocument. I demonstrate the use of tool on research paper.

  12. Assessment of Cognitive Functions in Methadone Maintenance Patients

    OpenAIRE

    Mazhari, Shahrzad; Keshvari, Zeinab; Sabahi, Abdolreza; Mottaghian, Shirin

    2015-01-01

    Background Methadone maintenance has received little scientific attention regarding neurocognitive effects. This study is aimed to assess the neuropsychological performance of methadone maintenance patients (MMP) compared to those healthy controls. Methods Thirty-five MMP and 35 healthy controls, matched for age, gender, education and employment status, examined on a battery of tests aimed at assessing verbal fluency, executive functions, verbal memory, and working memory, using controlled or...

  13. Vcfanno: fast, flexible annotation of genetic variants.

    Science.gov (United States)

    Pedersen, Brent S; Layer, Ryan M; Quinlan, Aaron R

    2016-01-01

    The integration of genome annotations is critical to the identification of genetic variants that are relevant to studies of disease or other traits. However, comprehensive variant annotation with diverse file formats is difficult with existing methods. Here we describe vcfanno, which flexibly extracts and summarizes attributes from multiple annotation files and integrates the annotations within the INFO column of the original VCF file. By leveraging a parallel "chromosome sweeping" algorithm, we demonstrate substantial performance gains by annotating ~85,000 variants per second with 50 attributes from 17 commonly used genome annotation resources. Vcfanno is available at https://github.com/brentp/vcfanno under the MIT license. PMID:27250555

  14. Robot-aided assessment of lower extremity functions: a review.

    Science.gov (United States)

    Maggioni, Serena; Melendez-Calderon, Alejandro; van Asseldonk, Edwin; Klamroth-Marganska, Verena; Lünenburger, Lars; Riener, Robert; van der Kooij, Herman

    2016-01-01

    The assessment of sensorimotor functions is extremely important to understand the health status of a patient and its change over time. Assessments are necessary to plan and adjust the therapy in order to maximize the chances of individual recovery. Nowadays, however, assessments are seldom used in clinical practice due to administrative constraints or to inadequate validity, reliability and responsiveness. In clinical trials, more sensitive and reliable measurement scales could unmask changes in physiological variables that would not be visible with existing clinical scores.In the last decades robotic devices have become available for neurorehabilitation training in clinical centers. Besides training, robotic devices can overcome some of the limitations in traditional clinical assessments by providing more objective, sensitive, reliable and time-efficient measurements. However, it is necessary to understand the clinical needs to be able to develop novel robot-aided assessment methods that can be integrated in clinical practice.This paper aims at providing researchers and developers in the field of robotic neurorehabilitation with a comprehensive review of assessment methods for the lower extremities. Among the ICF domains, we included those related to lower extremities sensorimotor functions and walking; for each chapter we present and discuss existing assessments used in routine clinical practice and contrast those to state-of-the-art instrumented and robot-aided technologies. Based on the shortcomings of current assessments, on the identified clinical needs and on the opportunities offered by robotic devices, we propose future directions for research in rehabilitation robotics. The review and recommendations provided in this paper aim to guide the design of the next generation of robot-aided functional assessments, their validation and their translation to clinical practice. PMID:27485106

  15. Assessment of pulmonary function tests in cardiac patients

    OpenAIRE

    El-Sobkey, Salwa B.; Gomaa, Magdi

    2011-01-01

    This study was aimed to assess the pulmonary function tests (PFTs) in cardiac patients; with ischemic or rheumatic heart diseases as well as in patients who underwent coronary artery bypass graft (CABG) or valvular procedures. For the forty eligible participants, the pulmonary function was measured using the spirometry test before and after the cardiac surgery. Data collection sheet was used for the patient’s demographic and intra-operative information. Cardiac diseases and surgeries had rest...

  16. The DOE-JGI Standard Operating Procedure for the Annotations of the Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Mavromatis, Konstantinos; Ivanova, Natalia; Chen, I-Min A.; Szeto, Ernest; Markowitz, Victor; Kyrpides, Nikos C.

    2009-05-20

    The DOE-JGI Microbial Annotation Pipeline (DOE-JGI MAP) supports gene prediction and/or functional annotation of microbial genomes towards comparative analysis with the Integrated Microbial Genome (IMG) system. DOE-JGI MAP annotation is applied on nucleotide sequence datasets included in the IMG-ER (Expert Review) version of IMG via the IMG ER submission site. Users can submit the sequence datasets consisting of one or more contigs in a multi-fasta file. DOE-JGI MAP annotation includes prediction of protein coding and RNA genes, as well as repeats and assignment of product names to these genes.

  17. The DOE-JGI Standard Operating Procedure for the Annotations of the Microbial Genomes

    OpenAIRE

    Mavromatis, Konstantinos

    2010-01-01

    The DOE-JGI Microbial Annotation Pipeline (DOE-JGI MAP) supports gene prediction and/or functional annotation of microbial genomes towards comparative analysis with the Integrated Microbial Genome (IMG) system. DOE-JGI MAP annotation is applied on nucleotide sequence datasets included in the IMG-ER (Expert Review) version of IMG via the IMG ER submission site. Users can submit the sequence datasets consisting of one or more contigs in a multi-fasta file. DOE-JGI MAP annotation includes predic...

  18. The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes.

    Science.gov (United States)

    Mavromatis, Konstantinos; Ivanova, Natalia N; Chen, I-Min A; Szeto, Ernest; Markowitz, Victor M; Kyrpides, Nikos C

    2009-01-01

    The DOE-JGI Microbial Annotation Pipeline (DOE-JGI MAP) supports gene prediction and/or functional annotation of microbial genomes towards comparative analysis with the Integrated Microbial Genome (IMG) system. DOE-JGI MAP annotation is applied on nucleotide sequence datasets included in the IMG-ER (Expert Review) version of IMG via the IMG ER submission site. Users can submit the sequence datasets consisting of one or more contigs in a multi-fasta file. DOE-JGI MAP annotation includes prediction of protein coding and RNA genes, as well as repeats and assignment of product names to these genes. PMID:21304638

  19. The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes

    OpenAIRE

    Mavromatis, Konstantinos; Natalia N. Ivanova; Chen, I-Min A.; Szeto, Ernest; Markowitz, Victor M.; Kyrpides, Nikos C.

    2009-01-01

    The DOE-JGI Microbial Annotation Pipeline (DOE-JGI MAP) supports gene prediction and/or functional annotation of microbial genomes towards comparative analysis with the Integrated Microbial Genome (IMG) system. DOE-JGI MAP annotation is applied on nucleotide sequence datasets included in the IMG-ER (Expert Review) version of IMG via the IMG ER submission site. Users can submit the sequence datasets consisting of one or more contigs in a multi-fasta file. DOE-JGI MAP annotation includes predic...

  20. LNG annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Bomelburg, H.J.; Counts, C.A.; Cowan, C.E.; Davis, W.E.; DeSteese, J.G.; Pelto, P.J.

    1982-09-01

    This document updates the bibliography published in Liquefied Gaseous Fuels Safety and Environmental Control Assessment Program: third status report (PNL-4172) and is a complete listing of literature reviewed and reported under the LNG Technical Surveillance Task. The bibliography is organized alphabetically by author.

  1. Information Technologies in the Assessment of Violations of Cognitive Functions

    Directory of Open Access Journals (Sweden)

    Vitaly P. Omelchenko

    2013-01-01

    Full Text Available This article is about application of information technologies for an assessment of violations of cognitive functions at patients with diabetic and discirculatorencephalopathies. Results of the mathematical analysis of bioelectric activity of a brain of examinees are considered, the most significant factors reflecting existence of cognitive violations are revealed

  2. Assessing Students' Understanding of Functions in a Graphing Calculator Environment.

    Science.gov (United States)

    Beckmann, Charlene E.; Senk, Sharon L.; Thompson, Denisse R.

    1999-01-01

    In a classroom environment in which continual access to graphing calculators is assumed, items that have been used to assess students' understanding of functions often are no longer appropriate. Describes strategies for modifying such items including requiring students to explain their reasoning, using calculator-active items, analyzing graphs and…

  3. Upper Limb Assessment in Tetraplegia: Clinical, Functional and Kinematic Correlations

    Science.gov (United States)

    Cacho, Enio Walker Azevedo; de Oliveira, Roberta; Ortolan, Rodrigo L.; Varoto, Renato; Cliquet, Alberto

    2011-01-01

    The aim of this study was to correlate clinical and functional evaluations with kinematic variables of upper limp reach-to-grasp movement in patients with tetraplegia. Twenty chronic patients were selected to perform reach-to-grasp kinematic assessment using a target placed at a distance equal to the arm's length. Kinematic variables (hand peak…

  4. Systems Theory and Communication. Annotated Bibliography.

    Science.gov (United States)

    Covington, William G., Jr.

    This annotated bibliography presents annotations of 31 books and journal articles dealing with systems theory and its relation to organizational communication, marketing, information theory, and cybernetics. Materials were published between 1963 and 1992 and are listed alphabetically by author. (RS)

  5. International Standard for a Linguistic Annotation Framework

    CERN Document Server

    Romary, Laurent

    2004-01-01

    This paper describes the Linguistic Annotation Framework under development within ISO TC37 SC4 WG1. The Linguistic Annotation Framework is intended to serve as a basis for harmonizing existing language resources as well as developing new ones.

  6. Annotated Bibliography, Grades K-6.

    Science.gov (United States)

    Massachusetts Dept. of Education, Boston. Bureau of Nutrition Education and School Food Services.

    This annotated bibliography on nutrition is for the use of teachers at the elementary grade level. It contains a list of books suitable for reading about nutrition and foods for pupils from kindergarten through the sixth grade. Films and audiovisual presentations for classroom use are also listed. The names and addresses from which these materials…

  7. Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study.

    Science.gov (United States)

    Costanzo, Maria C; Park, Julie; Balakrishnan, Rama; Cherry, J Michael; Hong, Eurie L

    2011-01-01

    Annotation using Gene Ontology (GO) terms is one of the most important ways in which biological information about specific gene products can be expressed in a searchable, computable form that may be compared across genomes and organisms. Because literature-based GO annotations are often used to propagate functional predictions between related proteins, their accuracy is critically important. We present a strategy that employs a comparison of literature-based annotations with computational predictions to identify and prioritize genes whose annotations need review. Using this method, we show that comparison of manually assigned 'unknown' annotations in the Saccharomyces Genome Database (SGD) with InterPro-based predictions can identify annotations that need to be updated. A survey of literature-based annotations and computational predictions made by the Gene Ontology Annotation (GOA) project at the European Bioinformatics Institute (EBI) across several other databases shows that this comparison strategy could be used to maintain and improve the quality of GO annotations for other organisms besides yeast. The survey also shows that although GOA-assigned predictions are the most comprehensive source of functional information for many genomes, a large proportion of genes in a variety of different organisms entirely lack these predictions but do have manual annotations. This underscores the critical need for manually performed, literature-based curation to provide functional information about genes that are outside the scope of widely used computational methods. Thus, the combination of manual and computational methods is essential to provide the most accurate and complete functional annotation of a genome. Database URL: http://www.yeastgenome.org. PMID:21411447

  8. Concept annotation in the CRAFT corpus

    OpenAIRE

    Bada Michael; Eckert Miriam; Evans Donald; Garcia Kristin; Shipley Krista; Sitnikov Dmitry; Baumgartner William A; Cohen K; Verspoor Karin; Blake Judith A; Hunter Lawrence E

    2012-01-01

    Abstract Background Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. Results This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRA...

  9. Use of the catena principle in geomorphological impact assessment: a functional approach

    NARCIS (Netherlands)

    Wolfert, H.P.

    1995-01-01

    An integral method for assessing geomorphological landscape qualities is presented, to be used in environmental impact assessments. Five groups of landform functions are distinguished in the Netherlands, an area of low relief: orientation functions, information functions, ordering functions, regulat

  10. Annotating images by mining image search results

    NARCIS (Netherlands)

    X.J. Wang; L. Zhang; X. Li; W.Y. Ma

    2008-01-01

    Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search results

  11. Eight questions about semantic web annotations

    OpenAIRE

    Euzenat, Jérôme

    2002-01-01

    Improving information retrieval is annotation¹s central goal. However, without sufficient planning, annotation - especially when running a robot and attaching automatically extracted content - risks producing incoherent information. The author recommends answering eight questions before you annotate. He provides a practical application of this approach, and discusses applying the questions to other systems.

  12. Annotation and Classification of Argumentative Writing Revisions

    Science.gov (United States)

    Zhang, Fan; Litman, Diane

    2015-01-01

    This paper explores the annotation and classification of students' revision behaviors in argumentative writing. A sentence-level revision schema is proposed to capture why and how students make revisions. Based on the proposed schema, a small corpus of student essays and revisions was annotated. Studies show that manual annotation is reliable with…

  13. Genome re-annotation: a wiki solution?

    OpenAIRE

    Salzberg, Steven L.

    2007-01-01

    The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution.

  14. An automated system for assessing cognitive function in any environment

    Science.gov (United States)

    Wesnes, Keith A.

    2005-05-01

    The Cognitive Drug Research (CDR) computerized assessment system has been in use in worldwide clinical trials for over 20 years. It is a computer based system which assesses core aspects of human cognitive function including attention, information, working memory and long-term memory. It has been extensively validated and can be performed by a wide range of clinical populations including patients with various types of dementia. It is currently in worldwide use in clinical trials to evaluate new medicines, as well as a variety of programs involving the effects of age, stressors illnesses and trauma upon human cognitive function. Besides being highly sensitive to drugs which will impair or improve function, its utility has been maintained over the last two decades by constantly increasing the number of platforms upon which it can operate. Besides notebook versions, the system can be used on a wrist worn device, PDA, via tht telephone and over the internet. It is the most widely used automated cognitive function assessment system in worldwide clinical research. It has dozens of parallel forms and requires little training to use or administer. The basic development of the system wil be identified, and the huge databases (normative, patient population, drug effects) which have been built up from hundreds of clinical trials will be described. The system is available for use in virtually any environment or type of trial.

  15. Knee Function Assessment in Patients With Meniscus Injury

    Science.gov (United States)

    Naimark, Micah B.; Kegel, Gary; O’Donnell, Thomas; Lavigne, Stephanie; Heveran, Chelsea; Crawford, Dennis C.

    2014-01-01

    Background: Outcomes of meniscus surgery are typically assessed with patient questionnaires that help capture symptoms and functional limitations but may not provide an accurate representation of underlying joint health. There are currently no performance-based measures of knee function in patients with symptomatic meniscus injury. Purpose: To assess the reproducibility, response to partial meniscectomy, and correlation with patient-reported questionnaire outcomes of novel performance-based knee function tests. Study Design: Cohort study (diagnosis); Level of evidence, 2. Methods: A battery of 9 tests for activities that require knee movements essential for everyday living was developed. Intra- and interrater reproducibility was assessed in 50 meniscus tear patients completing the battery at 2 preoperative assessments with either the same or different examiners. Response to arthroscopic partial meniscectomy was evaluated in 35 of these patients 6 weeks after surgery. Subjects also completed the Knee Injury and Osteoarthritis Outcome Score (KOOS) and International Knee Documentation Committee (IKDC) questionnaires pre- and postoperatively. Results: The intrarater intraclass correlation coefficients (ICCs) were excellent for all tests (ICC > 0.8). Interrater ICC > 0.8 was observed for step-down, stair descent, star lunges, and timed treadmill travel. Performance on all tests improved significantly with surgery (P < .05), with the greatest improvement in sit-to-stand and stair ascent and descent. A greater percentage response to surgery was seen on questionnaire outcomes (20%-65%) than on performance-based tests (3%-15%). Moderate to poor correlations existed between the KOOS activities of daily living subscale and the performance-based tests (all ICCs ≤ 0.4). Conclusion: Performance-based knee function tests demonstrated good reproducibility and responsiveness in patients undergoing partial meniscectomy. Clinical Relevance: As both patient perception and functional

  16. Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks

    Directory of Open Access Journals (Sweden)

    Mazo Ilya

    2007-07-01

    Full Text Available Abstract Background Uncovering cellular roles of a protein is a task of tremendous importance and complexity that requires dedicated experimental work as well as often sophisticated data mining and processing tools. Protein functions, often referred to as its annotations, are believed to manifest themselves through topology of the networks of inter-proteins interactions. In particular, there is a growing body of evidence that proteins performing the same function are more likely to interact with each other than with proteins with other functions. However, since functional annotation and protein network topology are often studied separately, the direct relationship between them has not been comprehensively demonstrated. In addition to having the general biological significance, such demonstration would further validate the data extraction and processing methods used to compose protein annotation and protein-protein interactions datasets. Results We developed a method for automatic extraction of protein functional annotation from scientific text based on the Natural Language Processing (NLP technology. For the protein annotation extracted from the entire PubMed, we evaluated the precision and recall rates, and compared the performance of the automatic extraction technology to that of manual curation used in public Gene Ontology (GO annotation. In the second part of our presentation, we reported a large-scale investigation into the correspondence between communities in the literature-based protein networks and GO annotation groups of functionally related proteins. We found a comprehensive two-way match: proteins within biological annotation groups form significantly denser linked network clusters than expected by chance and, conversely, densely linked network communities exhibit a pronounced non-random overlap with GO groups. We also expanded the publicly available GO biological process annotation using the relations extracted by our NLP technology

  17. Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation.

    Science.gov (United States)

    Beijbom, Oscar; Edmunds, Peter J; Roelfsema, Chris; Smith, Jennifer; Kline, David I; Neal, Benjamin P; Dunlap, Matthew J; Moriarty, Vincent; Fan, Tung-Yung; Tan, Chih-Jui; Chan, Stephen; Treibitz, Tali; Gamst, Anthony; Mitchell, B Greg; Kriegman, David

    2015-01-01

    Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys. PMID:26154157

  18. Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation.

    Directory of Open Access Journals (Sweden)

    Oscar Beijbom

    Full Text Available Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys.

  19. IMG ER: A System for Microbial Genome Annotation Expert Review and Curation

    Energy Technology Data Exchange (ETDEWEB)

    Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.; Chu, Ken; Kyrpides, Nikos C.

    2009-05-25

    A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG's rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.

  20. Towards a more functional and dynamic assessment of children with special needs in function of more inclusive education

    OpenAIRE

    Lebeer, Jo; Partanen, P.; Candeias, A.A.; Grácio, L.; Bohacs, K.; Sonnesyn, G.; Van de Veire, H.; Van Trimpont, I.; Maior, E.; Szamoskozi, I.; Dawson, L.

    2010-01-01

    Towards a more functional and dynamic assessment of children with special needs in function of more inclusive education - We present the Guidelines for Inclusive Assessment of children that experiment Special Educational Needs, developed by the DAFFODIL project team.

  1. Effects of E-Textbook Instructor Annotations on Learner Performance

    Science.gov (United States)

    Dennis, Alan R.; Abaci, Serdar; Morrone, Anastasia S.; Plaskoff, Joshua; McNamara, Kelly O.

    2016-01-01

    With additional features and increasing cost advantages, e-textbooks are becoming a viable alternative to paper textbooks. One important feature offered by enhanced e-textbooks (e-textbooks with interactive functionality) is the ability for instructors to annotate passages with additional insights. This paper describes a pilot study that examines…

  2. Sequence-based feature prediction and annotation of proteins

    DEFF Research Database (Denmark)

    Juncker, Agnieszka; Jensen, Lars J.; Pierleoni, Andrea; Bernsel, Andreas; Tress, Michael L.; Bork, Peer; Von Heijne, Gunnar; Valencia, Alfonso; A Ouzounis, Christos; Casadio, Rita; Brunak, Søren

    2009-01-01

    A recent trend in computational methods for annotation of protein function is that many prediction tools are combined in complex workflows and pipelines to facilitate the analysis of feature combinations, for example, the entire repertoire of kinase-binding motifs in the human proteome....

  3. Assessing Executive Function components in 9 years old children

    OpenAIRE

    Sandra Reyes; Juan Pablo Barreyro; Irene Injoque-Ricle

    2014-01-01

    Executive Function (EF) is a multidimensional construct. It includes a set of abilities that allows to execute actions with a purpose, aimed to a goal, in an efficient way. The objective of this work is to explore some of the cognitive abilities that constitute a common factor for EF in 9 years-old children. The chosen instruments: Batería de Evaluación Neuropsicológica de la Función Ejecutiva en niños (ENFEN) (Battery of Neuropsychological Assessment for Executive Function in Children), alon...

  4. Annotating Coloured Petri Nets

    DEFF Research Database (Denmark)

    Lindstrøm, Bo; Wells, Lisa Marie

    2002-01-01

    Coloured Petri nets (CP-nets) can be used for several fundamentally different purposes like functional analysis, performance analysis, and visualisation. To be able to use the corresponding tool extensions and libraries it is sometimes necessary to include extra auxiliary information in the CP......-net. An example of such auxiliary information is a counter which is associated with a token to be able to do performance analysis. Modifying colour sets and arc inscriptions in a CP-net to support a specific use may lead to creation of several slightly different CP-nets – only to support the different...... uses of the same basic CP-net. One solution to this problem is that the auxiliary information is not integrated into colour sets and arc inscriptions of a CP-net, but is kept separately. This makes it easy to disable this auxiliary information if a CP-net is to be used for another purpose. This paper...

  5. ASAP: Amplification, sequencing & annotation of plastomes

    Directory of Open Access Journals (Sweden)

    Folta Kevin M

    2005-12-01

    Full Text Available Abstract Background Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate ~1 – 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera. Results 100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and

  6. Clinical assessment tools identify functional deficits in fragility fracture patients

    Science.gov (United States)

    Ames, Tyler D; Wee, Corinne E; Le, Khoi M; Wang, Tiffany L; Bishop, Julie Y; Phieffer, Laura S; Quatman, Carmen E

    2016-01-01

    Purpose To identify inexpensive, noninvasive, portable, clinical assessment tools that can be used to assess functional performance measures that may put older patients at risk for falls such as balance, handgrip strength, and lumbopelvic control. Patients and methods Twenty fragility fracture patients and 21 healthy control subjects were evaluated using clinical assessment tools (Nintendo Wii Balance Board [WBB], a handheld dynamometer, and an application for the Apple iPod Touch, the Level Belt) that measure functional performance during activity of daily living tasks. The main outcome measurements were balance (WBB), handgrip strength (handheld dynamometer), and lumbopelvic control (iPod Touch Level Belt), which were compared between fragility fracture patients and healthy controls. Results Fragility fracture patients had lower scores on the vertical component of the WBB Torso Twist task (P=0.042) and greater medial–lateral lumbopelvic sway during a 40 m walk (P=0.026) when compared to healthy controls. Unexpectedly, the fracture patients had significantly higher scores on the left leg (P=0.020) and total components (P=0.010) of the WBB Single Leg Stand task as well as less faults during the left Single Leg Stand task (P=0.003). Conclusion The clinical assessment tools utilized in this study are relatively inexpensive and portable tools of performance measures capable of detecting differences in postural sway between fragility fracture patients and controls.

  7. Werkzeuge zur Annotation diachroner Korpora

    OpenAIRE

    Burghardt, Manuel; Wolff, Christian

    2009-01-01

    Wir diskutieren zunächst die Problematik der (syntaktischen) Annotation diachroner Korpora und stellen anschließend eine Evaluationsstudie vor, bei der mehr als 50 Annotationswerkzeuge und -frameworks vor dem Hintergrund eines funktionalen und software-ergonomischen Anforderungsprofils nach dem Qualitätsmodell von ISO/IEC 9126-1:2001 (Software engineering – Product quality – Part 1: Quality model) und ISO/IEC 25000:2005 (Software Engineering – Software product Quality Requirements and Evaluat...

  8. Assessing functional performance in the mdx mouse model.

    Science.gov (United States)

    Aartsma-Rus, Annemieke; van Putten, Maaike

    2014-01-01

    Duchenne muscular dystrophy (DMD) is a severe and progressive muscle wasting disorder for which no cure is available. Nevertheless, several potential pharmaceutical compounds and gene therapy approaches have progressed into clinical trials. With improvement in muscle function being the most important end point in these trials, a lot of emphasis has been placed on setting up reliable, reproducible, and easy to perform functional tests to pre clinically assess muscle function, strength, condition, and coordination in the mdx mouse model for DMD. Both invasive and noninvasive tests are available. Tests that do not exacerbate the disease can be used to determine the natural history of the disease and the effects of therapeutic interventions (e.g. forelimb grip strength test, two different hanging tests using either a wire or a grid and rotarod running). Alternatively, forced treadmill running can be used to enhance disease progression and/or assess protective effects of therapeutic interventions on disease pathology. We here describe how to perform these most commonly used functional tests in a reliable and reproducible manner. Using these protocols based on standard operating procedures enables comparison of data between different laboratories. PMID:24747372

  9. Morphological filters for functional assessment of roundness profiles

    International Nuclear Information System (INIS)

    Filtration techniques are useful tools for analysing roundness profiles. The 2RC filter and Gaussian filter are commonly used to assess peripheral undulations of the roundness data. However they cannot do every aspect of functional prediction. Morphological filters are employed to characterize roundness profiles for functional assessment. Traditional computation methods for morphological filters are limited to planar surfaces and unable to be extended to roundness measurement. A novel method based on alpha shape theory is developed to break up the confinement. The morphological closing and opening envelopes are obtained by rolling a disk upon the roundness profile from the air and material side of the component respectively. They can be used to identify significant peaks and valleys on the profile respectively, which is vital to the functional performance of components, especially contact phenomenon. A case study is presented where various options of morphological filters and reference circles are applied to a roundness profile, delivering different functional meanings. An in-depth comparison of morphological filters and the Gaussian filter is followed to derive their pros and cons. (paper)

  10. The Effect of Human Genome Annotation Complexity on RNA-Seq Gene Expression Quantification

    Science.gov (United States)

    Wu, Po-Yen; Phan, John H.; Wang, May D.

    2016-01-01

    Next-generation sequencing (NGS) has brought human genomic research to an unprecedented era. RNA-Seq is a branch of NGS that can be used to quantify gene expression and depends on accurate annotation of the human genome (i.e., the definition of genes and all of their variants or isoforms). Multiple annotations of the human genome exist with varying complexity. However, it is not clear how the choice of genome annotation influences RNA-Seq gene expression quantification. We assess the effect of different genome annotations in terms of (1) mapping quality, (2) quantification variation, (3) quantification accuracy (i.e., by comparing to qRT-PCR data), and (4) the concordance of detecting differentially expressed genes. External validation with qRT-PCR suggests that more complex genome annotations result in higher quantification variation.

  11. Clinical assessment of social cognitive function in neurological disorders.

    Science.gov (United States)

    Henry, Julie D; von Hippel, William; Molenberghs, Pascal; Lee, Teresa; Sachdev, Perminder S

    2016-01-01

    Social cognition broadly refers to the processing of social information in the brain that underlies abilities such as the detection of others' emotions and responding appropriately to these emotions. Social cognitive skills are critical for successful communication and, consequently, mental health and wellbeing. Disturbances of social cognition are early and salient features of many neuropsychiatric, neurodevelopmental and neurodegenerative disorders, and often occur after acute brain injury. Its assessment in the clinic is, therefore, of paramount importance. Indeed, the most recent edition of the American Psychiatric Association's Diagnostic and Statistical Manual for Mental Disorders (DSM-5) introduced social cognition as one of six core components of neurocognitive function, alongside memory and executive control. Failures of social cognition most often present as poor theory of mind, reduced affective empathy, impaired social perception or abnormal social behaviour. Standard neuropsychological assessments lack the precision and sensitivity needed to adequately inform treatment of these failures. In this Review, we present appropriate methods of assessment for each of the four domains, using an example disorder to illustrate the value of these approaches. We discuss the clinical applications of testing for social cognitive function, and finally suggest a five-step algorithm for the evaluation and treatment of impairments, providing quantitative evidence to guide the selection of social cognitive measures in clinical practice. PMID:26670297

  12. Context Sampling Descriptive Assessment: A Pilot Study of a Further Approach to Functional Assessment

    Science.gov (United States)

    Garbutt, Nathalie; Furniss, Frederick

    2007-01-01

    Background: The ability of descriptive assessments to differentiate functions of problem behaviours might be increased by systematically sampling natural contexts characterized by different establishing operations. This study evaluated the stability of such characteristics, and variability in challenging behaviour, for three school contexts.…

  13. Aldo-keto reductase (AKR) superfamily: genomics and annotation.

    Science.gov (United States)

    Mindnich, Rebekka D; Penning, Trevor M

    2009-07-01

    Aldo-keto reductases (AKRs) are phase I metabolising enzymes that catalyse the reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H)-dependent reduction of carbonyl groups to yield primary and secondary alcohols on a wide range of substrates, including aliphatic and aromatic aldehydes and ketones, ketoprostaglandins, ketosteroids and xenobiotics. In so doing they functionalise the carbonyl group for conjugation (phase II enzyme reactions). Although functionally diverse, AKRs form a protein superfamily based on their high sequence identity and common protein fold, the (alpha/beta) 8 -barrel structure. Well over 150 AKR enzymes, from diverse organisms, have been annotated so far and given systematic names according to a nomenclature that is based on multiple protein sequence alignment and degree of identity. Annotation of non-vertebrate AKRs at the National Center for Biotechnology Information or Vertebrate Genome Annotation (vega) database does not often include the systematic nomenclature name, so the most comprehensive overview of all annotated AKRs is found on the AKR website (http://www.med.upenn.edu/akr/). This site also hosts links to more detailed and specialised information (eg on crystal structures, gene expression and single nucleotide polymorphisms [SNPs]). The protein-based AKR nomenclature allows unambiguous identification of a given enzyme but does not reflect the wealth of genomic and transcriptomic variation that exists in the various databases. In this context, identification of putative new AKRs and their distinction from pseudogenes are challenging. This review provides a short summary of the characteristic features of AKR biochemistry and structure that have been reviewed in great detail elsewhere, and focuses mainly on nomenclature and database entries of human AKRs that so far have not been subject to systematic annotation. Recent developments in the annotation of SNP and transcript variance in AKRs are also summarised. PMID:19706366

  14. Aldo-keto reductase (AKR superfamily: Genomics and annotation

    Directory of Open Access Journals (Sweden)

    Mindnich Rebekka D

    2009-07-01

    Full Text Available Abstract Aldo-keto reductases (AKRs are phase I metabolising enzymes that catalyse the reduced nicotinamide adenine dinucleotide (phosphate (NAD(PH-dependent reduction of carbonyl groups to yield primary and secondary alcohols on a wide range of substrates, including aliphatic and aromatic aldehydes and ketones, ketoprostaglan-dins, ketosteroids and xenobiotics. In so doing they functionalise the carbonyl group for conjugation (phase II enzyme reactions. Although functionally diverse, AKRs form a protein superfamily based on their high sequence identity and common protein fold, the (α/(β8-barrel structure. Well over 150 AKR enzymes, from diverse organisms, have been annotated so far and given systematic names according to a nomenclature that is based on multiple protein sequence alignment and degree of identity. Annotation of non-vertebrate AKRs at the National Center for Biotechnology Information or Vertebrate Genome Annotation (vega database does not often include the systematic nomenclature name, so the most comprehensive overview of all annotated AKRs is found on the AKR website (http://www.med.upenn.edu/akr/. This site also hosts links to more detailed and specialised information (eg on crystal structures, gene expression and single nucleotide polymorphisms [SNPs]. The protein-based AKR nomenclature allows unambiguous identification of a given enzyme but does not reflect the wealth of genomic and transcriptomic variation that exists in the various databases. In this context, identification of putative new AKRs and their distinction from pseudogenes are challenging. This review provides a short summary of the characteristic features of AKR biochemistry and structure that have been reviewed in great detail elsewhere, and focuses mainly on nomenclature and database entries of human AKRs that so far have not been subject to systematic annotation. Recent developments in the annotation of SNP and transcript variance in AKRs are also summarised.

  15. Text mining improves prediction of protein functional sites.

    Directory of Open Access Journals (Sweden)

    Karin M Verspoor

    Full Text Available We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites. The structure analysis was carried out using Dynamics Perturbation Analysis (DPA, which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions.

  16. MR urography for morphological and functional assessment of UT abnormalities

    International Nuclear Information System (INIS)

    Full text: Introduction: Magnetic resonance urography is a new, modern method in various urological conditions. The method is most often used for the evaluation of hydronephrosis and provides valuable information on a variety of obstructive uropathy, presenting both morphological and functional information about the urinary tract. What you will learn: The purpose of this presentation is to examine the current role of MR urography in evaluation of hydronephrosis and hydroureter, variants and congenital anomalies of the kidney, various causes of obstruction, tumor and inflammation, hematuria. Combining static and dynamic MR urography, yielding both morphological and functional information by using different sequences with and without the injection of contrast agents. Highlighted the advantages of the method in children and demonstrated software programs available for postprocessing in urodiagnostic illustrated with typical clinical cases. Discussion: MR urography is a promising method to diagnose a wide range of pathological conditions of the urogenital tract, with huge development opportunities in urogenital tract imaging. It integrates excellent anatomical informative in combination with various functional data in the absence of ionizing radiation. Postprocessing algorithms facilitate the assessment of differentiated renal function, by generating curves of signal intensity - time. Due to the risk of nephrogenic systemic fibrosis, using the contrast media requires caution, especially in cases of impaired renal function. Conclusion: MR urography is a highly informative method in the case of diagnostic difficulties using conventional techniques, overcoming their limitations and has the potential to become a future the leading method for diagnosing kidney disease, especially in infants and children

  17. Collaborative Design of an Image Annotation Tool for Oceanographic Imaging Systems

    Science.gov (United States)

    Futrelle, J.; York, A.

    2012-12-01

    We present a design for a web-based image annotation interface developed to assist in supervised classification of organisms and substrate for habitat assessment from multiple, heterogeneous oceanographic imaging systems. The interface enables human image annotators to count, identify, and measure targets and classify substrate in a variety of kinds of imagery including benthic surveys and imaging flow cytometry. These annotations are then used to build training sets for supervised classification algorithms for purposes of characterizing community structure and habitat assessment. The Ocean Imaging Informatics team at WHOI used the Tetherless World Constellation's collaborative design methodology to develop shared formal information model and system design that applies to a variety of image annotation use cases. Because the information model represents consensus between researchers with differing instrumentation and science needs, it assists with rapid prototyping and establishes a baseline against which existing and forthcoming image annotation tools can be evaluated. A technology review suggested that there are few general-purpose image annotation tools suitable for annotation of high-volume oceanographic imagery. Most tools require too many steps for operations that must be repeated thousands of times, and/or lack critical features such as display of instrument metadata, QA/QC, and management of annotator tasks. While some of these problems are user interface limitations, others suggest that existing tools are missing critically important concepts. For example, QA/QC appears in our information model as an "activity stream" associated with each image annotation, consisting of events indicating review status, specific image quality issues, etc. The model also includes "identification modes" that contextualize annotations according to the annotator's assigned task, assisting both with interpreting annotations and with providing contextual user interface shortcuts

  18. Assessing cognitive function and capacity in older adults with cancer.

    Science.gov (United States)

    McKoy, June M; Burhenn, Peggy S; Browner, Ilene S; Loeser, Kari L; Tulas, Katrina M; Oden, Megan R; Rupper, Randall W

    2014-01-01

    The number of older individuals with cancer is increasing exponentially, mandating that oncologists contemplate more comprehensive and multidisciplinary approaches to treatment of this cohort. Recruitment of assessment instruments validated in older patients can be invaluable for guiding treatment and decision-making by both patients and providers, and can arguably contribute to improving outcomes and health-related quality of life. The Comprehensive Geriatric Assessment is one such validated instrument that can be used by oncologists to assess patient readiness and appropriateness for prescribed cancer therapy. As a multidisciplinary diagnostic and treatment process, it comprises functional status, cognitive status, social support, and advance care preferences, and is an ideal instrument for evaluating complex older individuals. It is well established that many older individuals with cancer travel with multiple comorbid illnesses, including cognitive impairment, and when presented with a cancer diagnosis struggle to choose from multiple treatment options. In addition to the complete medical history, the ability of patients to decide on a course of therapy in concert with their oncologist is critically important. Alternatively, many oncologists are conflicted as to whether true informed consent for treatment can be obtained from many older patients. Having a roadmap to decision-making capacity is therefore an inescapable imperative in geriatric oncology, because careful attention must be directed at identifying older patients with cancer who might benefit from these assessments and the individualized treatment plans that emerge. PMID:24453297

  19. Cine-oesophago-gastroscintigraphy: assessment of digestive function in paediatrics

    Energy Technology Data Exchange (ETDEWEB)

    Guillet, J. (Hopital Pellegrin, 33 - Bordeaux (France))

    1984-05-15

    Cine-oesophago-gastroscintigraphy (COGS) can assess structure and function of the oesophagogastrointestinal tract. With this non-invasive method, the dosimetry is very low and quantification is easy. Milk or water labelled by sup(99m)Tc sulfocolloids are drunk by the patient. The transit is continuously monitored by a gamma camera and a computer. The esophageal transit time is useful in studying impairment of peristaltic motion. Fistula, diverticula and stenosis are easily detected. The sensitivity of this technique for the search of gastroesophageal reflux is as great as pH-metry. The quantification is of great interest to assess the severity of the reflux and to measure treatment efficacity. Slow rates of gastric emptying are associated with some of the reflux, and pyloric stenosis. Pulmonary contamination can be discovered in patients with gastro oesophageal reflux.

  20. Intra-species sequence comparisons for annotating genomes

    Energy Technology Data Exchange (ETDEWEB)

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

    2004-07-15

    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  1. Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

    DEFF Research Database (Denmark)

    Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim;

    2008-01-01

    Background: Since ancient times the filamentous fungus Aspergillus oryzae has been used in the fermentation industry for the production of fermented sauces and the production of industrial enzymes. Recently, the genome sequence of A. oryzae with 12,074 annotated genes was released but the number...... of hypothetical proteins accounted for more than 50% of the annotated genes. Considering the industrial importance of this fungus, it is therefore valuable to improve the annotation and further integrate genomic information with biochemical and physiological information available for this microorganism and other...... related fungi. Here we proposed the gene prediction by construction of an A. oryzae Expressed Sequence Tag (EST) library, sequencing and assembly. We enhanced the function assignment by our developed annotation strategy. The resulting better annotation was used to reconstruct the metabolic network leading...

  2. Clinical assessment tools identify functional deficits in fragility fracture patients

    Directory of Open Access Journals (Sweden)

    Ames TD

    2016-05-01

    Full Text Available Tyler D Ames,1 Corinne E Wee,1 Khoi M Le,1 Tiffany L Wang,1 Julie Y Bishop,2 Laura S Phieffer,2 Carmen E Quatman2 1The Ohio State University College of Medicine, 2Department of Orthopaedics, The Ohio State University Wexner Medical Center, Columbus, OH, USA Purpose: To identify inexpensive, noninvasive, portable, clinical assessment tools that can be used to assess functional performance measures that may put older patients at risk for falls such as balance, handgrip strength, and lumbopelvic control.Patients and methods: Twenty fragility fracture patients and 21 healthy control subjects were evaluated using clinical assessment tools (Nintendo Wii Balance Board [WBB], a handheld dynamometer, and an application for the Apple iPod Touch, the Level Belt that measure functional performance during activity of daily living tasks. The main outcome measurements were balance (WBB, handgrip strength (handheld dynamometer, and lumbopelvic control (iPod Touch Level Belt, which were compared between fragility fracture patients and healthy controls.Results: Fragility fracture patients had lower scores on the vertical component of the WBB Torso Twist task (P=0.042 and greater medial–lateral lumbopelvic sway during a 40 m walk (P=0.026 when compared to healthy controls. Unexpectedly, the fracture patients had significantly higher scores on the left leg (P=0.020 and total components (P=0.010 of the WBB Single Leg Stand task as well as less faults during the left Single Leg Stand task (P=0.003.Conclusion: The clinical assessment tools utilized in this study are relatively inexpensive and portable tools of performance measures capable of detecting differences in postural sway between fragility fracture patients and controls. Keywords: fall risk, geriatric fracture, Nintendo Wii Balance Board, Level Belt, fragility fracture

  3. ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins

    Science.gov (United States)

    Mall, Tarun; Eckstein, John; Norris, David; Vora, Hiral; Freese, Nowlan H.; Loraine, Ann E.

    2016-01-01

    Summary: One gene can produce multiple transcript variants encoding proteins with different functions. To facilitate visual analysis of transcript variants, we developed ProtAnnot, which shows protein annotations in the context of genomic sequence. ProtAnnot searches InterPro and displays profile matches (protein annotations) alongside gene models, exposing how alternative promoters, splicing and 3′ end processing add, remove, or remodel functional motifs. To draw attention to these effects, ProtAnnot color-codes exons by frame and displays a cityscape graphic summarizing exonic sequence at each position. These techniques make visual analysis of alternative transcripts faster and more convenient for biologists. Availability and implementation: ProtAnnot is a plug-in App for Integrated Genome Browser, an open source desktop genome browser available from http://www.bioviz.org. Contact: aloraine@uncc.edu PMID:27153567

  4. Assessment of luteal function after surgical tubal sterilization.

    Science.gov (United States)

    Garza-Flores, J; Vázquez-Estrada, L; Reyes, A; Valero, A; Morales del Olmo, A; Alba, V M; Bonilla, C

    1991-12-01

    To evaluate ovarian luteal function after tubal occlusion, a group of women who underwent Pomeroy sterilization were studied. A prospective group I (n = 16) were followed for one year and scheduled for blood sampling every other day during their luteal phase before surgical procedure and at 3 and 12 months thereafter. Group II (n = 15) included women who were studied during their luteal phase at 1 or 5 years post-surgery. Mid-luteal progesterone and estradiol serum levels were calculated by estimating the average of at least 3 values of serum samples obtained in days 20-25 of a menstrual cycle. The data suggest that no major changes occur in ovarian function after surgical tubal occlusion, as assessed by the mid-luteal hormone serum levels, and underscore the safety of this procedure. PMID:1776562

  5. ONEMercury: Towards Automatic Annotation of Earth Science Metadata

    Science.gov (United States)

    Tuarob, S.; Pouchard, L. C.; Noy, N.; Horsburgh, J. S.; Palanisamy, G.

    2012-12-01

    Earth sciences have become more data-intensive, requiring access to heterogeneous data collected from multiple places, times, and thematic scales. For example, research on climate change may involve exploring and analyzing observational data such as the migration of animals and temperature shifts across the earth, as well as various model-observation inter-comparison studies. Recently, DataONE, a federated data network built to facilitate access to and preservation of environmental and ecological data, has come to exist. ONEMercury has recently been implemented as part of the DataONE project to serve as a portal for discovering and accessing environmental and observational data across the globe. ONEMercury harvests metadata from the data hosted by multiple data repositories and makes it searchable via a common search interface built upon cutting edge search engine technology, allowing users to interact with the system, intelligently filter the search results on the fly, and fetch the data from distributed data sources. Linking data from heterogeneous sources always has a cost. A problem that ONEMercury faces is the different levels of annotation in the harvested metadata records. Poorly annotated records tend to be missed during the search process as they lack meaningful keywords. Furthermore, such records would not be compatible with the advanced search functionality offered by ONEMercury as the interface requires a metadata record be semantically annotated. The explosion of the number of metadata records harvested from an increasing number of data repositories makes it impossible to annotate the harvested records manually, urging the need for a tool capable of automatically annotating poorly curated metadata records. In this paper, we propose a topic-model (TM) based approach for automatic metadata annotation. Our approach mines topics in the set of well annotated records and suggests keywords for poorly annotated records based on topic similarity. We utilize the

  6. LeARN: a platform for detecting, clustering and annotating non-coding RNAs

    Directory of Open Access Journals (Sweden)

    Schiex Thomas

    2008-01-01

    Full Text Available Abstract Background In the last decade, sequencing projects have led to the development of a number of annotation systems dedicated to the structural and functional annotation of protein-coding genes. These annotation systems manage the annotation of the non-protein coding genes (ncRNAs in a very crude way, allowing neither the edition of the secondary structures nor the clustering of ncRNA genes into families which are crucial for appropriate annotation of these molecules. Results LeARN is a flexible software package which handles the complete process of ncRNA annotation by integrating the layers of automatic detection and human curation. Conclusion This software provides the infrastructure to deal properly with ncRNAs in the framework of any annotation project. It fills the gap between existing prediction software, that detect independent ncRNA occurrences, and public ncRNA repositories, that do not offer the flexibility and interactivity required for annotation projects. The software is freely available from the download section of the website http://bioinfo.genopole-toulouse.prd.fr/LeARN

  7. VariOtator, a Software Tool for Variation Annotation with the Variation Ontology.

    Science.gov (United States)

    Schaafsma, Gerard C P; Vihinen, Mauno

    2016-04-01

    The Variation Ontology (VariO) is used for describing and annotating types, effects, consequences, and mechanisms of variations. To facilitate easy and consistent annotations, the online application VariOtator was developed. For variation type annotations, VariOtator is fully automated, accepting variant descriptions in Human Genome Variation Society (HGVS) format, and generating VariO terms, either with or without full lineage, that is, all parent terms. When a coding DNA variant description with a reference sequence is provided, VariOtator checks the description first with Mutalyzer and then generates the predicted RNA and protein descriptions with their respective VariO annotations. For the other sublevels, function, structure, and property, annotations cannot be automated, and VariOtator generates annotation based on provided details. For VariO terms relating to structure and property, one can use attribute terms as modifiers and evidence code terms for annotating experimental evidence. There is an online batch version, and stand-alone batch versions to be used with a Leiden Open Variation Database (LOVD) download file. A SOAP Web service allows client programs to access VariOtator programmatically. Thus, systematic variation effect and type annotations can be efficiently generated to allow easy use and integration of variations and their consequences. PMID:26773573

  8. EST-PAC a web package for EST annotation and protein sequence prediction

    Directory of Open Access Journals (Sweden)

    Strahm Yvan

    2006-10-01

    Full Text Available Abstract With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1 searching local or remote biological databases for sequence similarities using Blast services, 2 predicting protein coding sequence from EST data and, 3 annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics.

  9. A collection of bioconductor methods to visualize gene-list annotations

    Directory of Open Access Journals (Sweden)

    Kibbe Warren A

    2010-01-01

    Full Text Available Abstract Background Gene-list annotations are critical for researchers to explore the complex relationships between genes and functionalities. Currently, the annotations of a gene list are usually summarized by a table or a barplot. As such, potentially biologically important complexities such as one gene belonging to multiple annotation categories are difficult to extract. We have devised explicit and efficient visualization methods that provide intuitive methods for interrogating the intrinsic connections between biological categories and genes. Findings We have constructed a data model and now present two novel methods in a Bioconductor package, "GeneAnswers", to simultaneously visualize genes, concepts (a.k.a. annotation categories, and concept-gene connections (a.k.a. annotations: the "Concept-and-Gene Network" and the "Concept-and-Gene Cross Tabulation". These methods have been tested and validated with microarray-derived gene lists. Conclusions These new visualization methods can effectively present annotations using Gene Ontology, Disease Ontology, or any other user-defined gene annotations that have been pre-associated with an organism's genome by human curation, automated pipelines, or a combination of the two. The gene-annotation data model and associated methods are available in the Bioconductor package called "GeneAnswers " described in this publication.

  10. Omics data management and annotation.

    Science.gov (United States)

    Harel, Arye; Dalah, Irina; Pietrokovski, Shmuel; Safran, Marilyn; Lancet, Doron

    2011-01-01

    Technological Omics breakthroughs, including next generation sequencing, bring avalanches of data which need to undergo effective data management to ensure integrity, security, and maximal knowledge-gleaning. Data management system requirements include flexible input formats, diverse data entry mechanisms and views, user friendliness, attention to standards, hardware and software platform definition, as well as robustness. Relevant solutions elaborated by the scientific community include Laboratory Information Management Systems (LIMS) and standardization protocols facilitating data sharing and managing. In project planning, special consideration has to be made when choosing relevant Omics annotation sources, since many of them overlap and require sophisticated integration heuristics. The data modeling step defines and categorizes the data into objects (e.g., genes, articles, disorders) and creates an application flow. A data storage/warehouse mechanism must be selected, such as file-based systems and relational databases, the latter typically used for larger projects. Omics project life cycle considerations must include the definition and deployment of new versions, incorporating either full or partial updates. Finally, quality assurance (QA) procedures must validate data and feature integrity, as well as system performance expectations. We illustrate these data management principles with examples from the life cycle of the GeneCards Omics project (http://www.genecards.org), a comprehensive, widely used compendium of annotative information about human genes. For example, the GeneCards infrastructure has recently been changed from text files to a relational database, enabling better organization and views of the growing data. Omics data handling benefits from the wealth of Web-based information, the vast amount of public domain software, increasingly affordable hardware, and effective use of data management and annotation principles as outlined in this chapter

  11. FUNCTIONAL ASSESSMENT OF OLDER OBESE PATIENTS CANDIDATES FOR BARIATRIC SURGERY

    Directory of Open Access Journals (Sweden)

    Denis PAJECKI

    2014-03-01

    Full Text Available Context Obesity in the elderly is associated with exacerbation of functional decline (dependency, that occurs with aging, because of decreased muscle mass and strength, and increased joint dysfunction. Consequently, there is progressive loss of independence, autonomy, chronic pain and impaired quality of life. The weight loss can bring benefits in all these aspects, especially when accompanied by exercises. Elderly patients with morbid obesity may be submitted to surgical treatment, taking into account that the massive weight loss, eventually caused by bariatric surgery, may exacerbate the loss of muscle mass and nutritional complications that may bring harm to the overall health and quality of life of these patients. The functional assessment of elderly patients, candidates for bariatric surgery and the extent to which surgery can bring benefits to the patients, in the field of functionality, has still to be determined. Objective To describe profile functionality in obese elderly referred to a bariatric surgery program. Methods Patients with age ≥60 and BMI ≥35 underwent comprehensive geriatric assessment that evaluates co morbidities, medication use, ability to perform basic activities of daily living and instrumental activities of daily living, and the “Timedupandgo” test to evaluate mobility, whose cut-off point was ≤10 seconds. Statistical analysis was performed in order to see if there is a positive correlation of dependency with BMI and age (over or under 65 years. Results Forty subjects have completed evaluation. The mean age was 64.1 years (60-72 and 75% were women. They had an average weight of 121.1 kg (72.7-204 and a mean BMI of 47.2 kg/m2 (35.8-68.9. 16 patients (40% have shown dependency for activities of daily living, 19 (47,5% for instrumental activities of daily living and 20 patients (50% had a “Timedupandgo” test over 10 seconds. Statistical analysis (t-Student, Mann-Whitney, Binary Logistic Regression has shown

  12. Project Aloha:indexing, highlighting and annotation

    OpenAIRE

    Fallahkhair, Sanaz; Kennedy, Ian

    2010-01-01

    Lifelong learning requires many skills that are often not taught or are poorly taught. Such skills include speed reading, critical analysis, creative thinking, active reading and even a “little” skill like annotation. There are many ways that readers annotate. A short classification of some ways that reader may annotate includes underlining, using coloured highlighters, interlinear notes, marginal notes, and disassociated notes. This paper presents an investigation into the use of a tool for ...

  13. Automatic Multilevel Medical Image Annotation and Retrieval

    OpenAIRE

    Mueen, A.; Zainuddin, R.; Baba, M. Sapiyan

    2007-01-01

    Image retrieval at the semantic level mostly depends on image annotation or image classification. Image annotation performance largely depends on three issues: (1) automatic image feature extraction; (2) a semantic image concept modeling; (3) algorithm for semantic image annotation. To address first issue, multilevel features are extracted to construct the feature vector, which represents the contents of the image. To address second issue, domain-dependent concept hierarchy is constructed for...

  14. Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes

    Directory of Open Access Journals (Sweden)

    Danchin Antoine

    2002-02-01

    Full Text Available Abstract Background Analysis of any newly sequenced bacterial genome starts with the identification of protein-coding genes. Despite the accumulation of multiple complete genome sequences, which provide useful comparisons with close relatives among other organisms during the annotation process, accurate gene prediction remains quite difficult. A major reason for this situation is that genes are tightly packed in prokaryotes, resulting in frequent overlap. Thus, detection of translation initiation sites and/or selection of the correct coding regions remain difficult unless appropriate biological knowledge (about the structure of a gene is imbedded in the approach. Results We have developed a new program that automatically identifies biologically significant candidate genes in a bacterial genome. Twenty-six complete prokaryotic genomes were analyzed using this tool, and the accuracy of gene finding was assessed by comparison with existing annotations. This analysis revealed that, despite the enormous effort of genome program annotators, a small but not negligible number of genes annotated within the framework of sequencing projects are likely to be partially inaccurate or plainly wrong. Moreover, the analysis of several putative new genes shows that, as expected, many short genes have escaped annotation. In most cases, these new genes revealed frameshifts that could be either artifacts or genuine frameshifts. Some entirely unexpected new genes have also been identified. This allowed us to get a more complete picture of prokaryotic genomes. The results of this procedure are progressively integrated into the SWISS-PROT reference databank. Conclusions The results described in the present study show that our procedure is very satisfactory in terms of gene finding accuracy. Except in few cases, discrepancies between our results and annotations provided by individual authors can be accounted for by the nature of each annotation process or by specific

  15. Phylogenetic and functional assessment of orthologs inference projects and methods.

    Directory of Open Access Journals (Sweden)

    Adrian M Altenhoff

    2009-01-01

    Full Text Available Accurate genome-wide identification of orthologs is a central problem in comparative genomics, a fact reflected by the numerous orthology identification projects developed in recent years. However, only a few reports have compared their accuracy, and indeed, several recent efforts have not yet been systematically evaluated. Furthermore, orthology is typically only assessed in terms of function conservation, despite the phylogeny-based original definition of Fitch. We collected and mapped the results of nine leading orthology projects and methods (COG, KOG, Inparanoid, OrthoMCL, Ensembl Compara, Homologene, RoundUp, EggNOG, and OMA and two standard methods (bidirectional best-hit and reciprocal smallest distance. We systematically compared their predictions with respect to both phylogeny and function, using six different tests. This required the mapping of millions of sequences, the handling of hundreds of millions of predicted pairs of orthologs, and the computation of tens of thousands of trees. In phylogenetic analysis or in functional analysis where high specificity is required, we find that OMA and Homologene perform best. At lower functional specificity but higher coverage level, OrthoMCL outperforms Ensembl Compara, and to a lesser extent Inparanoid. Lastly, the large coverage of the recent EggNOG can be of interest to build broad functional grouping, but the method is not specific enough for phylogenetic or detailed function analyses. In terms of general methodology, we observe that the more sophisticated tree reconstruction/reconciliation approach of Ensembl Compara was at times outperformed by pairwise comparison approaches, even in phylogenetic tests. Furthermore, we show that standard bidirectional best-hit often outperforms projects with more complex algorithms. First, the present study provides guidance for the broad community of orthology data users as to which database best suits their needs. Second, it introduces new methodology

  16. Knowledge Annotation maknig implicit knowledge explicit

    CERN Document Server

    Dingli, Alexiei

    2011-01-01

    Did you ever read something on a book, felt the need to comment, took up a pencil and scribbled something on the books' text'? If you did, you just annotated a book. But that process has now become something fundamental and revolutionary in these days of computing. Annotation is all about adding further information to text, pictures, movies and even to physical objects. In practice, anything which can be identified either virtually or physically can be annotated. In this book, we will delve into what makes annotations, and analyse their significance for the future evolutions of the web. We wil

  17. Analytical strategies to assess the functional metabolome of vitamin E.

    Science.gov (United States)

    Torquato, Pierangelo; Ripa, Orsola; Giusepponi, Danilo; Galarini, Roberta; Bartolini, Desirée; Wallert, Maria; Pellegrino, Roberto; Cruciani, Gabriele; Lorkowski, Stefan; Birringer, Marc; Mazzini, Francesco; Galli, Francesco

    2016-05-30

    After more than 90 years from its discovery and thousands of papers published, the physiological roles of vitamin E (tocopherols and tocotrienols) are still not fully clarified. In the last few decades, the enzymatic metabolism of this vitamin has represented a stimulating subject of research. Its elucidation has opened up new horizons to the interpretation of the biological function of that class of molecules. The identification of specific properties for some of the physiological metabolites and the definition of advanced analytical techniques to assess the human metabolome of this vitamin in vivo, have paved the way to a series of hypotheses on the functional implications that this metabolism may have far beyond its catabolic role. The present review collects the available information on the most relevant analytical strategies employed to assess the status and metabolism of vitamin E in humans as well as in other model systems. A particular focus is dedicated to the analytical methods used to measure vitamin E metabolites, and particularly long-chain metabolites, in biological fluids and tissues. Preliminary information on a new LC-APCI-MS/MS method to measure these metabolites in human serum is reported. PMID:26947319

  18. Development and Preliminary Reliability of a Multitasking Assessment for Executive Functioning After Concussion

    OpenAIRE

    Smith, Laurel B.; Radomski, Mary Vining; Davidson, Leslie Freeman; Finkelstein, Marsha; Weightman, Margaret M.; McCulloch, Karen L.; Scherer, Matthew R.

    2014-01-01

    Researchers found encouraging preliminary interrater reliability data for the Charge of Quarters Duty Task, a multitask assessment designed to assess executive functioning in servicemembers after concussion.

  19. Assessing cognitive function in clinical trials of schizophrenia.

    Science.gov (United States)

    Barnett, Jennifer H; Robbins, Trevor W; Leeson, Verity C; Sahakian, Barbara J; Joyce, Eileen M; Blackwell, Andrew D

    2010-07-01

    Cognitive dysfunction in schizophrenia is an important target for novel therapies. Effectively measuring the cognitive effects of compounds in clinical trials of schizophrenia could be a major barrier to drug development. The Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) programme produced a consensus cognitive battery which is now widely used, however alternative assessments have advantages and disadvantages when compared with MATRICS. The Cambridge Neuropsychological Test Automated Battery (CANTAB) is a computerised assessment developed from animal behaviour paradigms and human neuropsychology. We review the utility of CANTAB according to MATRICS and CNTRICS recommendations. CANTAB tests have been used in more than 60 studies of psychotic disorders. Their neural bases are well understood through patient and neuroimaging studies and directly equivalent tests in rodents and non-human primates. The tests' sensitivity to pharmacological manipulation is well established. Future studies should collect more data regarding psychometric properties in patients over short time periods, and should continue to study the tests' relationships to functional outcomes. Computerised cognitive assessment may optimise the statistical power of cognitive trials by reducing measurement error and between-site variability and decreasing patient attrition through increased tolerability. PMID:20105440

  20. Fast Arc-Annotated Subsequence Matching in Linear Space

    CERN Document Server

    Bille, Philip

    2009-01-01

    An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings $P$ and $Q$ the arc-preserving subsequence problem is to determine if $P$ can be obtained from $Q$ by deleting bases from $Q$. Whenever a base is deleted any arc with an endpoint in that base is also deleted. Arc-annotated strings where the arcs are "nested" are a natural model of RNA molecules that captures both the primary and secondary structure of these. The arc-preserving subsequence problem for nested arc-annotated strings is basic primitive for investigating the function of RNA molecules. Gramm et al. [ACM Trans. Algorithms 2006] gave an algorithm for this problem using $O(nm)$ time and space, where $m$ and $n$ are the lengths of $P$ and $Q$, respectively. In this paper we present a new algorithm using $O(nm)$ time and $O(n + m)$ space, thereby matching the previous time bound while significantly reducing the space from a quadratic term to l...

  1. Unsupervised Decoding of Long-Term, Naturalistic Human Neural Recordings with Automated Video and Audio Annotations

    Science.gov (United States)

    Wang, Nancy X. R.; Olson, Jared D.; Ojemann, Jeffrey G.; Rao, Rajesh P. N.; Brunton, Bingni W.

    2016-01-01

    Fully automated decoding of human activities and intentions from direct neural recordings is a tantalizing challenge in brain-computer interfacing. Implementing Brain Computer Interfaces (BCIs) outside carefully controlled experiments in laboratory settings requires adaptive and scalable strategies with minimal supervision. Here we describe an unsupervised approach to decoding neural states from naturalistic human brain recordings. We analyzed continuous, long-term electrocorticography (ECoG) data recorded over many days from the brain of subjects in a hospital room, with simultaneous audio and video recordings. We discovered coherent clusters in high-dimensional ECoG recordings using hierarchical clustering and automatically annotated them using speech and movement labels extracted from audio and video. To our knowledge, this represents the first time techniques from computer vision and speech processing have been used for natural ECoG decoding. Interpretable behaviors were decoded from ECoG data, including moving, speaking and resting; the results were assessed by comparison with manual annotation. Discovered clusters were projected back onto the brain revealing features consistent with known functional areas, opening the door to automated functional brain mapping in natural settings. PMID:27148018

  2. Unsupervised Decoding of Long-Term, Naturalistic Human Neural Recordings with Automated Video and Audio Annotations.

    Science.gov (United States)

    Wang, Nancy X R; Olson, Jared D; Ojemann, Jeffrey G; Rao, Rajesh P N; Brunton, Bingni W

    2016-01-01

    Fully automated decoding of human activities and intentions from direct neural recordings is a tantalizing challenge in brain-computer interfacing. Implementing Brain Computer Interfaces (BCIs) outside carefully controlled experiments in laboratory settings requires adaptive and scalable strategies with minimal supervision. Here we describe an unsupervised approach to decoding neural states from naturalistic human brain recordings. We analyzed continuous, long-term electrocorticography (ECoG) data recorded over many days from the brain of subjects in a hospital room, with simultaneous audio and video recordings. We discovered coherent clusters in high-dimensional ECoG recordings using hierarchical clustering and automatically annotated them using speech and movement labels extracted from audio and video. To our knowledge, this represents the first time techniques from computer vision and speech processing have been used for natural ECoG decoding. Interpretable behaviors were decoded from ECoG data, including moving, speaking and resting; the results were assessed by comparison with manual annotation. Discovered clusters were projected back onto the brain revealing features consistent with known functional areas, opening the door to automated functional brain mapping in natural settings. PMID:27148018

  3. Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

    Science.gov (United States)

    Chen, Zhen-Xia; Sturgill, David; Qu, Jiaxin; Jiang, Huaiyang; Park, Soo; Boley, Nathan; Suzuki, Ana Maria; Fletcher, Anthony R; Plachetzki, David C; FitzGerald, Peter C; Artieri, Carlo G; Atallah, Joel; Barmina, Olga; Brown, James B; Blankenburg, Kerstin P; Clough, Emily; Dasgupta, Abhijit; Gubbala, Sai; Han, Yi; Jayaseelan, Joy C; Kalra, Divya; Kim, Yoo-Ah; Kovar, Christie L; Lee, Sandra L; Li, Mingmei; Malley, James D; Malone, John H; Mathew, Tittu; Mattiuzzo, Nicolas R; Munidasa, Mala; Muzny, Donna M; Ongeri, Fiona; Perales, Lora; Przytycka, Teresa M; Pu, Ling-Ling; Robinson, Garrett; Thornton, Rebecca L; Saada, Nehad; Scherer, Steven E; Smith, Harold E; Vinson, Charles; Warner, Crystal B; Worley, Kim C; Wu, Yuan-Qing; Zou, Xiaoyan; Cherbas, Peter; Kellis, Manolis; Eisen, Michael B; Piano, Fabio; Kionte, Karin; Fitch, David H; Sternberg, Paul W; Cutter, Asher D; Duff, Michael O; Hoskins, Roger A; Graveley, Brenton R; Gibbs, Richard A; Bickel, Peter J; Kopp, Artyom; Carninci, Piero; Celniker, Susan E; Oliver, Brian; Richards, Stephen

    2014-07-01

    Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community. PMID:24985915

  4. Annotation an effective device for student feedback: a critical review of the literature.

    Science.gov (United States)

    Ball, Elaine C

    2010-05-01

    The paper examines hand-written annotation, its many features, difficulties and strengths as a feedback tool. It extends and clarifies what modest evidence is in the public domain and offers an evaluation of how to use annotation effectively in the support of student feedback [Marshall, C.M., 1998a. The Future of Annotation in a Digital (paper) World. Presented at the 35th Annual GLSLIS Clinic: Successes and Failures of Digital Libraries, June 20-24, University of Illinois at Urbana-Champaign, March 24, pp. 1-20; Marshall, C.M., 1998b. Toward an ecology of hypertext annotation. Hypertext. In: Proceedings of the Ninth ACM Conference on Hypertext and Hypermedia, June 20-24, Pittsburgh Pennsylvania, US, pp. 40-49; Wolfe, J.L., Nuewirth, C.M., 2001. From the margins to the centre: the future of annotation. Journal of Business and Technical Communication, 15(3), 333-371; Diyanni, R., 2002. One Hundred Great Essays. Addison-Wesley, New York; Wolfe, J.L., 2002. Marginal pedagogy: how annotated texts affect writing-from-source texts. Written Communication, 19(2), 297-333; Liu, K., 2006. Annotation as an index to critical writing. Urban Education, 41, 192-207; Feito, A., Donahue, P., 2008. Minding the gap annotation as preparation for discussion. Arts and Humanities in Higher Education, 7(3), 295-307; Ball, E., 2009. A participatory action research study on handwritten annotation feedback and its impact on staff and students. Systemic Practice and Action Research, 22(2), 111-124; Ball, E., Franks, H., McGrath, M., Leigh, J., 2009. Annotation is a valuable tool to enhance learning and assessment in student essays. Nurse Education Today, 29(3), 284-291]. Although a significant number of studies examine annotation, this is largely related to on-line tools and computer mediated communication and not hand-written annotation as comment, phrase or sign written on the student essay to provide critique. Little systematic research has been conducted to consider how this latter form

  5. Functional cardiac MRI for assessment of aortic valve disease

    International Nuclear Information System (INIS)

    Aortic valve disease shows a rising incidence with the increasing mean age of Western populations. The detection of hemodynamic parameters, which transcends the mere assessment of valve morphology, has an important future potential concerning classification of the severity of disease. MRI allows a non-invasive and a spatially flexible view of the aortic valve and the adjacent anatomic region, left ventricular outflow tract (LVOT) and ascending aorta. Moreover, the technique allows the determination of functional hemodynamic parameters, such as flow velocities and effective orifice areas. The new approach of a serial systolic planimetry velocity-encoded MRI sequence (VENC-MRI) facilitates the sizing of blood-filled cardiac structures with the registration of changes in magnitude during systole. Additionally, the subvalvular VENC-MRI measurements improve the clinically important exact determination of the LVOT area with respect to its specific eccentric configuration and its systolic deformity. (orig.)

  6. The surplus value of semantic annotations

    NARCIS (Netherlands)

    M. Marx

    2010-01-01

    We compare the costs of semantic annotation of textual documents to its benefits for information processing tasks. Semantic annotation can improve the performance of retrieval tasks and facilitates an improved search experience through faceted search, focused retrieval, better document summaries, an

  7. Towards an event annotated corpus of Polish

    Directory of Open Access Journals (Sweden)

    Michał Marcińczuk

    2015-12-01

    Full Text Available Towards an event annotated corpus of PolishThe paper presents a typology of events built on the basis of TimeML specification adapted to Polish language. Some changes were introduced to the definition of the event categories and a motivation for event categorization was formulated. The event annotation task is presented on two levels – ontology level (language independent and text mentions (language dependant. The various types of event mentions in Polish text are discussed. A procedure for annotation of event mentions in Polish texts is presented and evaluated. In the evaluation a randomly selected set of documents from the Corpus of Wrocław University of Technology (called KPWr was annotated by two linguists and the annotator agreement was calculated. The evaluation was done in two iterations. After the first evaluation we revised and improved the annotation procedure. The second evaluation showed a significant improvement of the agreement between annotators. The current work was focused on annotation and categorisation of event mentions in text. The future work will be focused on description of event with a set of attributes, arguments and relations.

  8. DIMA – Annotation guidelines for German intonation

    DEFF Research Database (Denmark)

    Kügler, Frank; Smolibocki, Bernadett; Arnold, Denis;

    2015-01-01

    easier since German intonation is currently annotated according to different models. To this end, we aim to provide guidelines that are easy to learn. The guidelines were evaluated running an inter-annotator reliability study on three different speech styles (read speech, monologue and dialogue...

  9. Creating Gaze Annotations in Head Mounted Displays

    DEFF Research Database (Denmark)

    Mardanbeigi, Diako; Qvarfordt, Pernilla

    To facilitate distributed communication in mobile settings, we developed GazeNote for creating and sharing gaze annotations in head mounted displays (HMDs). With gaze annotations it possible to point out objects of interest within an image and add a verbal description. To create an annota- tion, ...

  10. Crowdsourcing and annotating NER for Twitter #drift

    DEFF Research Database (Denmark)

    Fromreide, Hege; Hovy, Dirk; Søgaard, Anders

    2014-01-01

    We present two new NER datasets for Twitter; a manually annotated set of 1,467 tweets (kappa=0.942) and a set of 2,975 expert-corrected, crowdsourced NER annotated tweets from the dataset described in Finin et al. (2010). In our experiments with these datasets, we observe two important points: (a...

  11. Annotation of regular polysemy and underspecification

    DEFF Research Database (Denmark)

    Martínez Alonso, Héctor; Pedersen, Bolette Sandford; Bel, Núria

    2013-01-01

    We present the result of an annotation task on regular polysemy for a series of seman- tic classes or dot types in English, Dan- ish and Spanish. This article describes the annotation process, the results in terms of inter-encoder agreement, and the sense distributions obtained with two methods...

  12. Skype: a tool for functional assessment in orthopaedic research.

    LENUS (Irish Health Repository)

    Good, Daniel W

    2012-03-01

    Skype is a free program which enables PC users to make video calls to other users with Internet access. We carried out a prospective review of all acromioclavicular joint hook plates for lateral-third clavicle fractures over a five-year period. Functional assessment with Oxford and Constant shoulder scores were carried out using Skype and compared to outpatient review using the Bland-Altman method. Of 36 patients (mean age 36 years), 33 had a computer with a video camera, all 33 had Internet access and 22 were already users of Skype. In total 29 patients were happy to take part in Skype assessment (83%). In comparison with outpatient review, there was a mean difference in the Oxford score of -0.48 (95% confidence interval -0.84, -0.12); the mean difference for the Constant score was -0.68 (95% confidence interval -1.08, -0.29). These differences were not clinically significant, confirming that Skype can be used as an alternative to goniometry in this clinical setting. A survey showed that 93% of 29 patients surveyed preferred the use of Skype for follow-up, mainly due to the convenience and cost-saving involved. The study demonstrates the potential for this new technique in providing patients with more options for follow-up.

  13. Manual Annotation of Translational Equivalence The Blinker Project

    CERN Document Server

    Melamed, I D

    1998-01-01

    Bilingual annotators were paid to link roughly sixteen thousand corresponding words between on-line versions of the Bible in modern French and modern English. These annotations are freely available to the research community from http://www.cis.upenn.edu/~melamed . The annotations can be used for several purposes. First, they can be used as a standard data set for developing and testing translation lexicons and statistical translation models. Second, researchers in lexical semantics will be able to mine the annotations for insights about cross-linguistic lexicalization patterns. Third, the annotations can be used in research into certain recently proposed methods for monolingual word-sense disambiguation. This paper describes the annotated texts, the specially-designed annotation tool, and the strategies employed to increase the consistency of the annotations. The annotation process was repeated five times by different annotators. Inter-annotator agreement rates indicate that the annotations are reasonably rel...

  14. Computational annotation of genes differentially expressed along olive fruit development

    Directory of Open Access Journals (Sweden)

    Martinelli Federico

    2009-10-01

    Full Text Available Abstract Background Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software. Results mRNA from fruits of the cv. Leccino sampled at three different stages [i.e., initial fruit set (stage 1, completed pit hardening (stage 2 and veraison (stage 3] was used for the identification of differentially expressed genes putatively involved in main processes along fruit development. Four subtractive hybridization libraries were constructed: forward and reverse between stage 1 and 2 (libraries A and B, and 2 and 3 (libraries C and D. All sequenced clones (1,132 in total were analyzed through BlastX against non-redundant NCBI databases and about 60% of them showed similarity to known proteins. A total of 89 out of 642 differentially expressed unique sequences was further investigated by Real-Time PCR, showing a validation of the SSH results as high as 69%. Library-specific cDNA repertories were annotated according to the three main vocabularies of the gene ontology (GO: cellular component, biological process and molecular function. BlastX analysis, GO terms mapping and annotation analysis were performed using the Blast2GO software, a research tool designed with the main purpose of enabling GO based data mining on sequence sets for which no GO annotation is yet available. Bioinformatic analysis pointed out a significantly different distribution of the annotated sequences for each GO category, when comparing the three fruit developmental stages. The olive fruit-specific transcriptome dataset was

  15. Cardiac function during exercise in patients with coronary bypass surgery assessed by continuous ventricular function monitoring

    International Nuclear Information System (INIS)

    The response of left ventricular function during exercise and recovery after exercise was assessed in 52 patients with coronary artery bypass surgery by means of a radionuclide continuous ventricular function monitor. This system consists of 2 radionuclide detectors, recorder and a computer. After the equilibration of 20 mCi technetium 99m-labeled autologaous red blood cells into the intravascular space, the beat by beat radionuclide data were summed for 20-sec intervals to measure left ventricular ejection fraction (EF). Before surgery, the mean EF decreased with exercise from 51±9% to 45±11% (p<0.001). Cardiac response was divided into 4 types according to the profiles of the EFs during exercise. In 6 patients, EF continued to increase until maximal exercise (type A). In 10 patients, EF initially increased and then decreased in late exercise stages (type B). In 9 patients, EF did not change significantly during exercise (type C). In 27 patients, EF decreased throughout exercise (type D). After surgery, the mean EF increased with exercise from 53±10% to 60±13% (p<0.001). Thirty-five patients showed type A, 9 type B, 5 type C, and 3 type D. Two type D and 5 type B patients had occluded grafts or ungrafted coronary arteries. Four patients with complete revascularization including an internal thoracic artery and saphenous vein grafts showed type B. Three patients with extensive infarction and poor left ventricular function showed type C. The time interval between the end of exercise and the point of maximal EF during recovery after exercise was reduced from 168 sec before surgery to 98 sec after surgery (p<0.001). The continuous ventricular function monitor elucidated changes in left ventricular function during exercise and recovery after exercise and provided a new aspect of assessing the effects of coronary bypass surgery. (author)

  16. Relationship between functional connectivity and motor function assessment in stroke patients with hemiplegia: a resting-state functional MRI study

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ye; Wang, Li; Zhang, Jingna; Sang, Linqiong; Li, Pengyue; Qiu, Mingguo [Third Military Medical University, Department of Medical Imaging, College of Biomedical Engineering, Chongqing (China); Liu, Hongliang; Yan, Rubing [Third Military Medical University, Department of Rehabilitation, Southwest Hospital, Chongqing (China); Yang, Jun; Wang, Jian [Third Military Medical University, Department of Radiology, Southwest Hospital, Chongqing (China)

    2016-05-15

    Resting-state functional magnetic resonance imaging (fMRI) has been used to examine the brain mechanisms of stroke patients with hemiplegia, but the relationship between functional connectivity (FC) and treatment-induced motor function recovery has not yet been fully investigated. This study aimed to identify the brain FC changes in stroke patients and study the relationship between FC and motor function assessment using the resting-state fMRI. Seventeen stroke patients with hemiplegia and fifteen healthy control subjects (HCSs) were recruited in this study. We compared the FC between the ipsilesional primary motor cortex (M1) and the whole brain of the patients with the FC of the HCSs and studied the FC changes in the patients before and after conventional rehabilitation and motor imagery therapy. Additionally, correlations between the FC change and motor function of the patients were studied. Compared to the HCSs, the FC in the patient group was significantly increased between the ipsilesional M1 and the ipsilesional inferior parietal cortex, frontal gyrus, supplementary motor area (SMA), and contralesional angular and decreased between the ipsilesional M1 and bilateral M1. After the treatment, the FC between the ipsilesional M1 and contralesional M1 increased while the FC between the ipsilesional M1 and ipsilesional SMA and paracentral lobule decreased. A statistically significant correlation was found between the FC change in the bilateral M1 and the Fugl-Meyer assessment (FMA) score change. Our results revealed an abnormal motor network after stroke and suggested that the FC could serve as a biomarker of motor function recovery in stroke patients with hemiplegia. (orig.)

  17. Relationship between functional connectivity and motor function assessment in stroke patients with hemiplegia: a resting-state functional MRI study

    International Nuclear Information System (INIS)

    Resting-state functional magnetic resonance imaging (fMRI) has been used to examine the brain mechanisms of stroke patients with hemiplegia, but the relationship between functional connectivity (FC) and treatment-induced motor function recovery has not yet been fully investigated. This study aimed to identify the brain FC changes in stroke patients and study the relationship between FC and motor function assessment using the resting-state fMRI. Seventeen stroke patients with hemiplegia and fifteen healthy control subjects (HCSs) were recruited in this study. We compared the FC between the ipsilesional primary motor cortex (M1) and the whole brain of the patients with the FC of the HCSs and studied the FC changes in the patients before and after conventional rehabilitation and motor imagery therapy. Additionally, correlations between the FC change and motor function of the patients were studied. Compared to the HCSs, the FC in the patient group was significantly increased between the ipsilesional M1 and the ipsilesional inferior parietal cortex, frontal gyrus, supplementary motor area (SMA), and contralesional angular and decreased between the ipsilesional M1 and bilateral M1. After the treatment, the FC between the ipsilesional M1 and contralesional M1 increased while the FC between the ipsilesional M1 and ipsilesional SMA and paracentral lobule decreased. A statistically significant correlation was found between the FC change in the bilateral M1 and the Fugl-Meyer assessment (FMA) score change. Our results revealed an abnormal motor network after stroke and suggested that the FC could serve as a biomarker of motor function recovery in stroke patients with hemiplegia. (orig.)

  18. Assessing Executive Function components in 9 years old children

    Directory of Open Access Journals (Sweden)

    Sandra Reyes

    2014-05-01

    Full Text Available Executive Function (EF is a multidimensional construct. It includes a set of abilities that allows to execute actions with a purpose, aimed to a goal, in an efficient way. The objective of this work is to explore some of the cognitive abilities that constitute a common factor for EF in 9 years-old children. The chosen instruments: Batería de Evaluación Neuropsicológica de la Función Ejecutiva en niños (ENFEN (Battery of Neuropsychological Assessment for Executive Function in Children, along with the Backward Digits Subtestfrom the WISC-III, were administered to 101 children from private schools of Buenos Aires State, Argentina. The ENFEN consists on EF tasks, including Phonological and Semantic Fluency, Trail Making Test versions for children (gray and colored sets, Interference Task, and Planning disc movements according to a model. An initial confirmatory factor analysis didn’t show significant fit indexes, being the Inhibitory control the variable with the lower and non significant factorial weight. A second model excluding the Inhibitory control measure was conducted, and it showed excellent fit indexes. Therefore, it can be concluded that at this age, some of the cognitive abilities included on the EF are: Phonological and Semantic Fluency, Sustained and Selective attention, Planning and Working memory; which is not the case for Inhibitory Control (measured by the Interference Task in the ENFEN.

  19. Concept annotation in the CRAFT corpus

    Directory of Open Access Journals (Sweden)

    Bada Michael

    2012-07-01

    Full Text Available Abstract Background Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. Results This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released. Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. Conclusions As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens, our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection, the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are

  20. Critical Zone Experimental Design to Assess Soil Processes and Function

    Science.gov (United States)

    Banwart, Steve

    2010-05-01

    Through unsustainable land use practices, mining, deforestation, urbanisation and degradation by industrial pollution, soil losses are now hypothesized to be much faster (100 times or more) than soil formation - with the consequence that soil has become a finite resource. The crucial challenge for the international research community is to understand the rates of processes that dictate soil mass stocks and their function within Earth's Critical Zone (CZ). The CZ is the environment where soils are formed, degrade and provide their essential ecosystem services. Key among these ecosystem services are food and fibre production, filtering, buffering and transformation of water, nutrients and contaminants, storage of carbon and maintaining biological habitat and genetic diversity. We have initiated a new research project to address the priority research areas identified in the European Union Soil Thematic Strategy and to contribute to the development of a global network of Critical Zone Observatories (CZO) committed to soil research. Our hypothesis is that the combined physical-chemical-biological structure of soil can be assessed from first-principles and the resulting soil functions can be quantified in process models that couple the formation and loss of soil stocks with descriptions of biodiversity and nutrient dynamics. The objectives of this research are to 1. Describe from 1st principles how soil structure influences processes and functions of soils, 2. Establish 4 European Critical Zone Observatories to link with established CZOs, 3. Develop a CZ Integrated Model of soil processes and function, 4. Create a GIS-based modelling framework to assess soil threats and mitigation at EU scale, 5. Quantify impacts of changing land use, climate and biodiversity on soil function and its value and 6. Form with international partners a global network of CZOs for soil research and deliver a programme of public outreach and research transfer on soil sustainability. The

  1. Assessment of right ventricular systolic function by tissue Doppler echocardiography.

    Science.gov (United States)

    Kjærgaard, Jesper

    2012-03-01

    This thesis summarizes a series of studies performed in order to assess the clinical usefulness of a novel echocardiographic technology that allows non-invasive assessment of regional right ventricular myocardial velocities and deformation: tissue Doppler echocardiography. While the technology is a promising tool for improving our understanding of right ventricular hemodynamics, several aspects of the technology must be evaluated. The accuracy and reproducibility of the technology is evaluated in vitro, and normal values, impact of changes in loading of the right ventricle, response to exercise and pharmacological pulmonary vasodilatation is established in normal subjects. The diagnostic and prognostic importance of adding tissue Doppler echocardiography to conventional echocardiographic and clinical parameters was evaluated in studies on patients with diseases associated with different modes of impact on right ventricular hemodynamics: pulmonary embolism, Arrhythmogenic right ventricular cardiomyopathy and pulmonary regurgitation, the latter in an animal model. The conclusions of the thesis are: Color tissue Doppler echocardiography accurately measures velocities, SR and strain in vitro. No systematic bias between ultrasound systems can be found, and accuracy of the measurements is good. However, the reproducibility of measurements in a test-retest design can limit the usefulness of the technology in daily clinical use, as 25% to 80% of change would be needed for the technology to identify a change in individual patients [I]. Normal values of tissue Doppler based measurements of RV regional velocities, SR and strain exist, and apply to both sexes and in all age groups with the exception of slightly decreasing values in strain with increasing age. Increasing preload and afterload changes regional myocardial velocities, but no changes in SR, strain or isovolumic acceleration could be observed [II and III]. Tissue Doppler echocardiography of the RV free wall in non

  2. The GOA database: Gene Ontology annotation updates for 2015

    OpenAIRE

    Huntley, Rachael P; Sawford, Tony; Mutowo-Meullenet, Prudence; Shypitsyna, Aleksandra; Bonilla, Carlos; Martin, Maria J.; O'Donovan, Claire

    2014-01-01

    The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups. GOA currently supplies 368 million GO annotations to almost 54 million proteins in more than 480 000 taxonomic groups. The resource now provides annotat...

  3. Investigating the impact of nicotine on executive functions using a novel virtual reality assessment

    OpenAIRE

    Jansari, Ashok S.; Froggatt, Daniel; Edginton, Trudi; Dawkins, Lynne

    2013-01-01

    Aims Nicotine is known to enhance aspects of cognitive functioning in abstinent smokers but the effects on specific areas of executive functions, and in non-smokers are inconclusive. This may be due in part to the poor sensitivity of tests used to assess executive functions. This study used a new virtual reality assessment of executive functions known as JEF (the Jansari assessment of Executive Functions) to address this issue. Design 2x2 design manipulating group (smokers and never-smokers)...

  4. svm PRAT: SVM-based Protein Residue Annotation Toolkit

    OpenAIRE

    Rangwala, Huzefa; Kauffman, Christopher; Karypis, George

    2009-01-01

    Background Over the last decade several prediction methods have been developed for determining the structural and functional properties of individual protein residues using sequence and sequence-derived information. Most of these methods are based on support vector machines as they provide accurate and generalizable prediction models. Results We present a general purpose protein residue annotation toolkit (svm PRAT) to allow biologists to formulate residue-wise prediction problems. svm PRAT f...

  5. Learning a Hybrid Architecture for Sequence Regression and Annotation

    OpenAIRE

    Zhang, Yizhe; Henao, Ricardo; Carin, Lawrence; Zhong, Jianling; Hartemink, Alexander J.

    2015-01-01

    When learning a hidden Markov model (HMM), sequen- tial observations can often be complemented by real-valued summary response variables generated from the path of hid- den states. Such settings arise in numerous domains, includ- ing many applications in biology, like motif discovery and genome annotation. In this paper, we present a flexible frame- work for jointly modeling both latent sequence features and the functional mapping that relates the summary response variables to the hidden stat...

  6. The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4).

    Science.gov (United States)

    Huntemann, Marcel; Ivanova, Natalia N; Mavromatis, Konstantinos; Tripp, H James; Paez-Espino, David; Tennessen, Kristin; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M; Kyrpides, Nikos C

    2016-01-01

    The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provided via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation is followed by functional annotation including assignment of protein product names and connection to various protein family databases. PMID:26918089

  7. A Common XML-based Framework for Syntactic Annotations

    CERN Document Server

    Ide, Nancy; Erjavec, Tomaz

    2009-01-01

    It is widely recognized that the proliferation of annotation schemes runs counter to the need to re-use language resources, and that standards for linguistic annotation are becoming increasingly mandatory. To answer this need, we have developed a framework comprised of an abstract model for a variety of different annotation types (e.g., morpho-syntactic tagging, syntactic annotation, co-reference annotation, etc.), which can be instantiated in different ways depending on the annotator's approach and goals. In this paper we provide an overview of the framework, demonstrate its applicability to syntactic annotation, and show how it can contribute to comparative evaluation of parser output and diverse syntactic annotation schemes.

  8. Refining Inquiry with Multi-Form Assessment: Formative and summative assessment functions for flexible inquiry

    Science.gov (United States)

    Zuiker, Steven; Reid Whitaker, J.

    2014-04-01

    This paper describes the 5E+I/A inquiry model and reports a case study of one curricular enactment by a US fifth-grade classroom. A literature review establishes the model's conceptual adequacy with respect to longstanding research related to both the 5E inquiry model and multiple, incremental innovations of it. As a collective line of research, the review highlights a common emphasis on formative assessment, at times coupled either with differentiated instruction strategies or with activities that target the generalization of learning. The 5E+I/A model contributes a multi-level assessment strategy that balances formative and summative functions of multiple forms of assessment in order to support classroom participation while still attending to individual achievement. The case report documents the enactment of a weeklong 5E+I/A curricular design as a preliminary account of the model's empirical adequacy. A descriptive and analytical narrative illustrates variable ways that multi-level assessment makes student thinking visible and pedagogical decision-making more powerful. In light of both, it also documents productive adaptations to a flexible curricular design and considers future research to advance this collective line of inquiry.

  9. A large-scale evaluation of computational protein function prediction.

    Science.gov (United States)

    Radivojac, Predrag; Clark, Wyatt T; Oron, Tal Ronnen; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; Pandey, Gaurav; Yunes, Jeffrey M; Talwalkar, Ameet S; Repo, Susanna; Souza, Michael L; Piovesan, Damiano; Casadio, Rita; Wang, Zheng; Cheng, Jianlin; Fang, Hai; Gough, Julian; Koskinen, Patrik; Törönen, Petri; Nokso-Koivisto, Jussi; Holm, Liisa; Cozzetto, Domenico; Buchan, Daniel W A; Bryson, Kevin; Jones, David T; Limaye, Bhakti; Inamdar, Harshal; Datta, Avik; Manjari, Sunitha K; Joshi, Rajendra; Chitale, Meghana; Kihara, Daisuke; Lisewski, Andreas M; Erdin, Serkan; Venner, Eric; Lichtarge, Olivier; Rentzsch, Robert; Yang, Haixuan; Romero, Alfonso E; Bhat, Prajwal; Paccanaro, Alberto; Hamp, Tobias; Kaßner, Rebecca; Seemayer, Stefan; Vicedo, Esmeralda; Schaefer, Christian; Achten, Dominik; Auer, Florian; Boehm, Ariane; Braun, Tatjana; Hecht, Maximilian; Heron, Mark; Hönigschmid, Peter; Hopf, Thomas A; Kaufmann, Stefanie; Kiening, Michael; Krompass, Denis; Landerer, Cedric; Mahlich, Yannick; Roos, Manfred; Björne, Jari; Salakoski, Tapio; Wong, Andrew; Shatkay, Hagit; Gatzmann, Fanny; Sommer, Ingolf; Wass, Mark N; Sternberg, Michael J E; Škunca, Nives; Supek, Fran; Bošnjak, Matko; Panov, Panče; Džeroski, Sašo; Šmuc, Tomislav; Kourmpetis, Yiannis A I; van Dijk, Aalt D J; ter Braak, Cajo J F; Zhou, Yuanpeng; Gong, Qingtian; Dong, Xinran; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Di Camillo, Barbara; Toppo, Stefano; Lan, Liang; Djuric, Nemanja; Guo, Yuhong; Vucetic, Slobodan; Bairoch, Amos; Linial, Michal; Babbitt, Patricia C; Brenner, Steven E; Orengo, Christine; Rost, Burkhard; Mooney, Sean D; Friedberg, Iddo

    2013-03-01

    Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools. PMID:23353650

  10. A brief assessment of physical functioning for prostate cancer patients

    Directory of Open Access Journals (Sweden)

    Jin-Shei Lai

    2010-06-01

    Full Text Available Jin-Shei Lai1, Rita Bode2, Hwee-Lin Wee3, David Eton4, David Cella11Department of Medical Social Sciences, 2Department of Physical Medicine and Rehabilitation, Feinberg School of Medicine, Northwestern University, IL USA; 3Department of Pharmacy, National University of Singapore, Singapore; 4Division of Health Care Policy and Research, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USAAbstract: We aimed to validate a more rapid, yet reliable means of assessing physical function (PF for patients with prostate cancer. The sample included 128 prostate cancer patients recruited from urology and general oncology clinics at two Chicago-area hospitals. The main outcome measures were: A 36-item PF item bank that included a 5-item short form (BriefPF and the 10-item PF subscale (PF-10 from the Medical Outcomes Study SF-36. Validity, information function, and relative precision (calculated using Rasch analysis and raw scores of the BriefPF were compared to the PF-10 and the full PF item bank. We found that the BriefPF and PF-10 were strongly correlated (r = 0.85 with the PF bank, and all three scales differentiated patients according to performance status (FPF bank(2,124 = 32.51 P < 0.001, FPF-10(2,121 = 27.35 P < 0.001, FBriefPF (2,123 = 38.40 P < 0.001. BriefPF has excellent precision relative to the PF-10 in measuring patients with different performance status levels. The Rasch-based information function indicated that the BriefPF was more informative than PF-10 in measuring moderate to higher functioning patients. Hence, the BriefPF offers a parsimonious and precise measure of PF for use among men with prostate cancer, and may aid in the timely inclusion of patient-reported outcomes in treatment decision-making.Keywords: quality-of-life, item bank, short-form, Medical Outcomes Study

  11. Using the Gene Ontology to Annotate Key Players in Parkinson's Disease.

    Science.gov (United States)

    Foulger, R E; Denny, P; Hardy, J; Martin, M J; Sawford, T; Lovering, R C

    2016-07-01

    The Gene Ontology (GO) is widely recognised as the gold standard bioinformatics resource for summarizing functional knowledge of gene products in a consistent and computable, information-rich language. GO describes cellular and organismal processes across all species, yet until now there has been a considerable gene annotation deficit within the neurological and immunological domains, both of which are relevant to Parkinson's disease. Here we introduce the Parkinson's disease GO Annotation Project, funded by Parkinson's UK and supported by the GO Consortium, which is addressing this deficit by providing GO annotation to Parkinson's-relevant human gene products, principally through expert literature curation. We discuss the steps taken to prioritise proteins, publications and cellular processes for annotation, examples of how GO annotations capture Parkinson's-relevant information, and the advantages that a topic-focused annotation approach offers to users. Building on the existing GO resource, this project collates a vast amount of Parkinson's-relevant literature into a set of high-quality annotations to be utilized by the research community. PMID:26825309

  12. Polymorphism Identification and Improved Genome Annotation of Brassica rapa Through Deep RNA Sequencing

    OpenAIRE

    Devisetty, Upendra Kumar; Covington, Michael F.; An V Tat; Lekkala, Saradadevi; Maloof, Julin N.

    2014-01-01

    The mapping and functional analysis of quantitative traits in Brassica rapa can be greatly improved with the availability of physically positioned, gene-based genetic markers and accurate genome annotation. In this study, deep transcriptome RNA sequencing (RNA-Seq) of Brassica rapa was undertaken with two objectives: SNP detection and improved transcriptome annotation. We performed SNP detection on two varieties that are parents of a mapping population to aid in development of a marker system...

  13. Recent improvements to the SMART domain-based sequence annotation resource

    OpenAIRE

    Letunic, I.; Goodstadt, L.; Dickens, N.J.; Doerks, T.; Schultz, J; R. Mott; Ciccarelli, F.; Copley, R. R.; Ponting, C. P.; Bork, P.

    2002-01-01

    SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with particular emphasis on mobile eukaryotic domains. Extensive annotation for each domain family is available, providing information relating to function, subcellular localization, phyletic distribution and tertiary structure. The January 2002 release has added more than 200 hand-curated domain models....

  14. Use of Gene Ontology Annotation to understand the peroxisome proteome in humans

    OpenAIRE

    Mutowo-Meullenet, Prudence; Huntley, Rachael P; Dimmer, Emily C.; Alam-Faruque, Yasmin; Sawford, Tony; Jesus Martin, Maria; O’Donovan, Claire; Apweiler, Rolf

    2013-01-01

    The Gene Ontology (GO) is the de facto standard for the functional description of gene products, providing a consistent, information-rich terminology applicable across species and information repositories. The UniProt Consortium uses both manual and automatic GO annotation approaches to curate UniProt Knowledgebase (UniProtKB) entries. The selection of a protein set prioritized for manual annotation has implications for the characteristics of the information provided to users working in a spe...

  15. Open-Source Toolkit for Simple XML Annotation: AMIA 2003 Open Source Expo

    OpenAIRE

    Mamlin, Burke W; SCHADOW, Gunther; Overhage, J. Marc

    2003-01-01

    Use of Extensible Markup Language (XML) is increasingly prevalent among medical informatics projects. Many of these projects involve, at some point, the interaction between a researcher and specialized XML documents for the purpose of annotating the XML data. We offer a simple toolkit to assist these researchers. Our solution is a simple, yet fully functional, annotation system that can easily be adapted to the needs of the researcher. All of the materials for this toolkit are freely available.

  16. D4.5 Final Report on the Corpus Acquisition & Annotation subsystem and its components

    OpenAIRE

    Prokopidis, Prokopis; Papavassiliou, Vassilis; Toral, Antonio; Poch Riera, Marc; Frontini, Francesca; Rubino, Francesco; Thurmair, Gregor

    2012-01-01

    PANACEA WP4 targets the creation of a Corpus Acquisition and Annotation (CAA) subsystem for the acquisition and processing of monolingual and bilingual language resources (LRs). The CAA subsystem consists of tools that have been integrated as web services in the PANACEA platform of LR production. D4.2 Initial functional prototype and documentation in T13 and D4.4 Report on the revised Corpus Acquisition & Annotation subsystem and its components in T23 provided initial and updated documentatio...

  17. Final Report on the Corpus Acquisition & Annotation subsystem and its components

    OpenAIRE

    Prokopidis, Prokopis; Papavassiliou, Vassilis; Toral, Antonio; Poch, Marc; Frontini, Francesca; Rubino, Francesco; Thurmair, Gregor

    2012-01-01

    PANACEA WP4 targets the creation of a Corpus Acquisition and Annotation (CAA) subsystem for the acquisition and processing of monolingual and bilingual language resources (LRs). The CAA subsystem consists of tools that have been integrated as web services in the PANACEA platform of LR production. D4.2 Initial functional prototype and documentation in T13 and D4.4 Report on the revised Corpus Acquisition & Annotation subsystem and its components in T23 provided initial and updated documenta...

  18. Plethyzmography in assessment of hemodynamic results of pacemaker functions programming

    Science.gov (United States)

    Wojciechowski, Dariusz; Sionek, Piotr; Peczalski, Kazimierz; Janusek, Dariusz

    2011-01-01

    The paper presents potential role of plethyzmography in optimization of heart hemodynamic function during pacemaker programming. The assessment of optimal stroke volume in patients, with implanted dual chamber pacemaker (DDD), by plethyzmography was a goal of the study. The data were collected during pacing rhythm. 20 patients (8 female and 12 male, average 77.4+/-4.6 years) with dual chamber pacemaker (DDD) and with pacing rhythm during routine pacemaker control and study tests were incorporated in the study group. Hemodynamic parameters were assessed during modification of atrio-ventricular delay (AVD) for pacing rhythm of 70 bpm and 90 bpm. The time of atrioventricular was programmed with 20 ms steps within range 100-200 ms and data were recorded with two minutes delay between two consecutive measurements. Stroke volume (SV) and cardiac output (CO) were calculated from plethyzmographic signal by using Beatscope software (TNO Holand). Highest SV calculated for given pacing rhythm was named optimal stroke volume (OSV) and consequently highest cardiac output was named maximal cardiac output (MCO). The time of atrio-ventricular delay for OSV was named optimal atrioventricular delay (OAVD). The results have showed: mean values of OAVD for 70 bpm - 152+/-33 ms and for 90 bpm -149+/-35 ms, shortening of the mean OAVD time caused by increase of pacing rate from 70 bpm to 90 bpm what resulted in statistically significant decrease of OSV with not statistically significant increase of MCO. The analysis of consecutive patients revealed three types of response to increase of pacing rhythm: 1. typical-shortening of OAVD, 2. neutral-no change of OAVD and 3.atypical-lengthening of OAVD.

  19. Guidelines for rating Global Assessment of Functioning (GAF

    Directory of Open Access Journals (Sweden)

    Aas IH Monrad

    2011-01-01

    Full Text Available Abstract Background Global Assessment of Functioning (GAF is a scoring system for the severity of illness in psychiatry. It is used clinically in many countries, as well as in research, but studies have shown several problems with GAF, for example concerning its validity and reliability. Guidelines for rating are important. The present study aimed to identify the current status of guidelines for rating GAF, and relevant factors and gaps in knowledge for the development of improved guidelines. Methods A thorough literature search was conducted. Results Few studies of existing guidelines have been conducted; existing guidelines are short; and rating has a subjective element. Seven main categories were identified as being important in relation to further development of guidelines: (1 general points about guidelines for rating GAF; (2 introduction to guidelines, with ground rules; (3 starting scoring at the top, middle or bottom level of the scale; (4 scoring for different time periods and of different values (highest, lowest or average; (5 the finer grading of the scale; (6 different guidelines for different conditions; and (7 different languages and cultures. Little information is available about how rules for rating are understood by different raters: the final score may be affected by whether the rater starts at the top, middle or bottom of the scale; there is little data on which value/combination of GAF values to record; guidelines for scoring within 10-point intervals are limited; there is little empirical information concerning the suitability of existing guidelines for different conditions and patient characteristics; and little is known about the effects of translation into different languages or of different cultural understanding. Conclusions Few studies have dealt specifically with guidelines for rating GAF. Current guidelines for rating GAF are not comprehensive, and relevant points for new guidelines are presented. Theoretical and

  20. Balance Functional Assessment in People with Visual Impairment

    Directory of Open Access Journals (Sweden)

    Rutkowska Izabela

    2015-12-01

    Full Text Available The aims of this study were twofold: to assess the level of balance of people with visual impairment against the BOT-2 standard scores for the able-bodied, and to identify in which trials subjects had the greatest difficulties in maintaining balance with respect to the degree of vision loss and age categories. One hundred twenty-seven subjects with visual impairment aged 6-16 years, participated in the study (68 girls and 59 boys. The division for partially sighted people (61 and the blind (66 was made according to the WHO classification. Functional balance assessment was made using a balance subtest from the Bruininks-Oseretsky test. Significant relationships were noticed between age and the level of balance (χ2 = 8.35 p <0,05, as well as between the degree of vision loss and the level of balance (χ2 = 24.53 p <0,001. The level of balance of almost all blind subjects was below (20% or well-below (60% the average for the able-bodied. The subjects’ ability to maintain balance was not dependent on gender and was associated primarily with the degree of visual impairment and age. Partially sighted people had better balance than the blind and the decrease in visual acuity resulted in reduction of balance skills. The lowest level of balance was observed in blind students aged 7-11 years. Elaborating physical fitness improvement programs for children and adolescents with visual impairment, diversity of age, the degree of vision loss and limitations of ablility to maintain balance should be taken into account.

  1. Expectation-Maximization Binary Clustering for Behavioural Annotation.

    Science.gov (United States)

    Garriga, Joan; Palmer, John R B; Oltra, Aitana; Bartumeus, Frederic

    2016-01-01

    The growing capacity to process and store animal tracks has spurred the development of new methods to segment animal trajectories into elementary units of movement. Key challenges for movement trajectory segmentation are to (i) minimize the need of supervision, (ii) reduce computational costs, (iii) minimize the need of prior assumptions (e.g. simple parametrizations), and (iv) capture biologically meaningful semantics, useful across a broad range of species. We introduce the Expectation-Maximization binary Clustering (EMbC), a general purpose, unsupervised approach to multivariate data clustering. The EMbC is a variant of the Expectation-Maximization Clustering (EMC), a clustering algorithm based on the maximum likelihood estimation of a Gaussian mixture model. This is an iterative algorithm with a closed form step solution and hence a reasonable computational cost. The method looks for a good compromise between statistical soundness and ease and generality of use (by minimizing prior assumptions and favouring the semantic interpretation of the final clustering). Here we focus on the suitability of the EMbC algorithm for behavioural annotation of movement data. We show and discuss the EMbC outputs in both simulated trajectories and empirical movement trajectories including different species and different tracking methodologies. We use synthetic trajectories to assess the performance of EMbC compared to classic EMC and Hidden Markov Models. Empirical trajectories allow us to explore the robustness of the EMbC to data loss and data inaccuracies, and assess the relationship between EMbC output and expert label assignments. Additionally, we suggest a smoothing procedure to account for temporal correlations among labels, and a proper visualization of the output for movement trajectories. Our algorithm is available as an R-package with a set of complementary functions to ease the analysis. PMID:27002631

  2. Video Quality Assessment Using Spatio-Velocity Contrast Sensitivity Function

    Science.gov (United States)

    Hirai, Keita; Tumurtogoo, Jambal; Kikuchi, Ayano; Tsumura, Norimichi; Nakaguchi, Toshiya; Miyake, Yoichi

    Due to the development and popularization of high-definition televisions, digital video cameras, Blu-ray discs, digital broadcasting, IP television and so on, it plays an important role to identify and quantify video quality degradations. In this paper, we propose SV-CIELAB which is an objective video quality assessment (VQA) method using a spatio-velocity contrast sensitivity function (SV-CSF). In SV-CIELAB, motion information in videos is effectively utilized for filtering unnecessary information in the spatial frequency domain. As the filter to apply videos, we used the SV-CSF. It is a modulation transfer function of the human visual system, and consists of the relationship among contrast sensitivities, spatial frequencies and velocities of perceived stimuli. In the filtering process, the SV-CSF cannot be directly applied in the spatial frequency domain because spatial coordinate information is required when using velocity information. For filtering by the SV-CSF, we obtain video frames separated in spatial frequency domain. By using velocity information, the separated frames with limited spatial frequencies are weighted by contrast sensitivities in the SV-CSF model. In SV-CIELAB, the criteria are obtained by calculating image differences between filtered original and distorted videos. For the validation of SV-CIELAB, subjective evaluation experiments were conducted. The subjective experimental results were compared with SV-CIELAB and the conventional VQA methods such as CIELAB color difference, Spatial-CIELAB, signal to noise ratio and so on. From the experimental results, it was shown that SV-CIELAB is a more efficient VQA method than the conventional methods.

  3. Assessment of Dengue Fever Severity Through Liver Function Tests

    International Nuclear Information System (INIS)

    Objective: To assess the utility of liver function tests (LFTs) for early recognition and prediction of severity of Dengue fever in hospitalized patients. Study Design: An analytical study. Place and Duration of Study: Services Institute of Medical Science and Fatima Memorial Hospital, Lahore, from September - December 2010. Methodology: Admitted cases of Dengue fever were divided into 3 groups; mild, moderate and severe increases in aminotransferases. Elevation in LFTs was co-related with good or bad outcome i.e. (survival or complication free stay) or (death or complications). Results were analyzed in SPSS version 18. Results: Out of the 353 patients with mean age of 37.12 +- 15.45 years, 245 (69.4%) were males and 108 (30.6%) were females. Seventy five patients (21.2%) had mild elevation of aminotransferases (2 fold increases), 265 patients (75.1%) had moderate increases (3 to 4 fold) and 13 (3.7%) had severe (> 4 fold increase). ALT was statistically higher in patients with septicemia, hepatic and renal failure (p-value 0.05). AST was higher in almost all complications. Prolonged hospital stay was associated with raised LFTs and greater complications and mortality. AST was found to be twice as much raised as ALT. Conclusion: AST and ALT were statistically higher in patients with worse outcome thus can lead to early recognition of high risk cases. (author)

  4. Visualization and quality assessment of the contrast transfer function estimation.

    Science.gov (United States)

    Sheth, Lisa K; Piotrowski, Angela L; Voss, Neil R

    2015-11-01

    The contrast transfer function (CTF) describes an undesirable distortion of image data from a transmission electron microscope. Many users of full-featured processing packages are often new to electron microscopy and are unfamiliar with the CTF concept. Here we present a common graphical output to clearly demonstrate the CTF fit quality independent of estimation software. Separately, many software programs exist to estimate the four CTF parameters, but their results are difficult to compare across multiple runs and it is all but impossible to select the best parameters to use for further processing. A new measurement is presented based on the correlation falloff of the calculated CTF oscillations against the normalized oscillating signal of the data, called the CTF resolution. It was devised to provide a robust numerical quality metric of every CTF estimation for high-throughput screening of micrographs and to select the best parameters for each micrograph. These new CTF visualizations and quantitative measures will help users better assess the quality of their CTF parameters and provide a mechanism to choose the best CTF tool for their data. PMID:26080023

  5. Assessment of cardiac function by an ambulatory ventricular function monitor (VEST), (2)

    International Nuclear Information System (INIS)

    To assess incidence of ischemic episodes in patients with coronary artery disease (CAD), left ventricular function and electrocardiogram (ECG) were continuously monitored by an ambulatory ventricular function monitor (VEST) during daily activities for a mean of 2.1 hours in 13 patients with CAD. Nine were patients with unstable angina. This VEST detected 20 episodes of transient decrease in ejection fraction ( ≥ 6 % below the baseline) in 8 patients. Five were symptomatic and 15 were symptom free. Among 5 symptomatic episodes, four were typical ischemic ones accompanied with ST segment depression on ECG. Among 15 asymptomatic episodes, 4 were associated with ST depression, which was highly suggestive of silent ischemia. However, 11 episodes of transient decrease in ejection fraction were not accompanied with either symptoms or ECG changes. On the other hand, the VEST detected 10 periods of ST depression, among which two were not associated with transient decrease in ejection fraction. We conclude that monitoring both ventricular function and ECG by the VEST is valuable for detecting and evaluating various episodes in patients with CAD. (author)

  6. Annotation of glycoproteins in the SWISS-PROT database.

    Science.gov (United States)

    Jung, E; Veuthey, A L; Gasteiger, E; Bairoch, A

    2001-02-01

    SWISS-PROT is a protein sequence database, which aims to be nonredundant, fully annotated and highly cross-referenced. Most eukaryotic gene products undergo co- and/or post-translational modifications, and these need to be included in the database in order to describe the mature protein. SWISS-PROT includes information on many types of different protein modifications. As glycosylation is the most common type of post-translational protein modification, we are currently placing an emphasis on annotation of protein glycosylation in SWISS-PROT. Information on the position of the sugar within the polypeptide chain, the reducing terminal linkage as well as additional information on biological function of the sugar is included in the database. In this paper we describe how we account for the different types of protein glycosylation, namely N-linked glycosylation, O-linked glycosylation, proteoglycans, C-linked glycosylation and the attachment of glycosyl-phosphatidylinosital anchors to proteins. PMID:11680872

  7. SVA: software for annotating and visualizing sequenced human genomes

    Science.gov (United States)

    Ge, Dongliang; Ruzzo, Elizabeth K.; Shianna, Kevin V.; He, Min; Pelak, Kimberly; Heinzen, Erin L.; Need, Anna C.; Cirulli, Elizabeth T.; Maia, Jessica M.; Dickson, Samuel P.; Zhu, Mingfu; Singh, Abanish; Allen, Andrew S.; Goldstein, David B.

    2011-01-01

    Summary: Here we present Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits. We illustrate the annotation features of SVA using two simple examples of sequenced genomes that harbor Mendelian mutations. Availability and implementation: Freely available on the web at http://www.svaproject.org. Contact: d.ge@duke.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21624899

  8. Meteor showers an annotated catalog

    CERN Document Server

    Kronk, Gary W

    2014-01-01

    Meteor showers are among the most spectacular celestial events that may be observed by the naked eye, and have been the object of fascination throughout human history. In “Meteor Showers: An Annotated Catalog,” the interested observer can access detailed research on over 100 annual and periodic meteor streams in order to capitalize on these majestic spectacles. Each meteor shower entry includes details of their discovery, important observations and orbits, and gives a full picture of duration, location in the sky, and expected hourly rates. Armed with a fuller understanding, the amateur observer can better view and appreciate the shower of their choice. The original book, published in 1988, has been updated with over 25 years of research in this new and improved edition. Almost every meteor shower study is expanded, with some original minor showers being dropped while new ones are added. The book also includes breakthroughs in the study of meteor showers, such as accurate predictions of outbursts as well ...

  9. FolksAnnotation: A Semantic Metadata Tool for Annotating Learning Resources Using Folksonomies and Domain Ontologies

    OpenAIRE

    Hend S. Al-Khalifa; Davis, Hugh C.

    2006-01-01

    There are many resources on the Web which are suitable for educational purposes. Unfortunately the task of identifying suitable resources for a particular educational purpose is difficult as they have not typically been annotated with educational metadata. However, many resources have now been annotated in an unstructured manner within contemporary social bookmaking services. This paper describes a novel tool called ‘FolksAnnotation’ that creates annotations with educational semantics from th...

  10. SASL: A Semantic Annotation System for Literature

    Science.gov (United States)

    Yuan, Pingpeng; Wang, Guoyin; Zhang, Qin; Jin, Hai

    Due to ambiguity, search engines for scientific literatures may not return right search results. One efficient solution to the problems is to automatically annotate literatures and attach the semantic information to them. Generally, semantic annotation requires identifying entities before attaching semantic information to them. However, due to abbreviation and other reasons, it is very difficult to identify entities correctly. The paper presents a Semantic Annotation System for Literature (SASL), which utilizes Wikipedia as knowledge base to annotate literatures. SASL mainly attaches semantic to terminology, academic institutions, conferences, and journals etc. Many of them are usually abbreviations, which induces ambiguity. Here, SASL uses regular expressions to extract the mapping between full name of entities and their abbreviation. Since full names of several entities may map to a single abbreviation, SASL introduces Hidden Markov Model to implement name disambiguation. Finally, the paper presents the experimental results, which confirm SASL a good performance.

  11. Modeling Social Annotation: a Bayesian Approach

    CERN Document Server

    Plangprasopchok, Anon

    2008-01-01

    Collaborative tagging systems, such as del.icio.us, CiteULike, and others, allow users to annotate objects, e.g., Web pages or scientific papers, with descriptive labels called tags. The social annotations, contributed by thousands of users, can potentially be used to infer categorical knowledge, classify documents or recommend new relevant information. Traditional text inference methods do not make best use of socially-generated data, since they do not take into account variations in individual users' perspectives and vocabulary. In a previous work, we introduced a simple probabilistic model that takes interests of individual annotators into account in order to find hidden topics of annotated objects. Unfortunately, our proposed approach had a number of shortcomings, including overfitting, local maxima and the requirement to specify values for some parameters. In this paper we address these shortcomings in two ways. First, we extend the model to a fully Bayesian framework. Second, we describe an infinite ver...

  12. Annotation sémantique par classification

    OpenAIRE

    Toussaint, Yannick; Tenier, Sylvain

    2007-01-01

    Les systèmes actuels d'annotation sémantique exploitent peu les connaissances du domaine et fonctionnent essentiellement du texte vers l'ontologie. Pourtant, il est fréquent qu'un élément dans une page doive être annoté par un concept parce que certains autres éléments de cette même page sont annotés par d'autres concepts. Cet article propose une méthode d'annotation prenant en compte cette dépendance entre concepts, exprimée dans une ontologie sous forme de concepts définis. L'utilisation de...

  13. GRADUATE AND PROFESSIONAL EDUCATION, AN ANNOTATED BIBLIOGRAPHY.

    Science.gov (United States)

    HEISS, ANN M.; AND OTHERS

    THIS ANNOTATED BIBLIOGRAPHY CONTAINS REFERENCES TO GENERAL GRADUATE EDUCATION AND TO EDUCATION FOR THE FOLLOWING PROFESSIONAL FIELDS--ARCHITECTURE, BUSINESS, CLINICAL PSYCHOLOGY, DENTISTRY, ENGINEERING, LAW, LIBRARY SCIENCE, MEDICINE, NURSING, SOCIAL WORK, TEACHING, AND THEOLOGY. (HW)

  14. SNPsnap: a Web-based tool for identification and annotation of matched SNPs

    DEFF Research Database (Denmark)

    Pers, Tune Hannes; Timshel, Pascal; Hirschhorn, Joel N.

    2015-01-01

    Summary : An important computational step following genome-wide association studies (GWAS) is to assess whether disease or trait-associated single-nucleotide polymorphisms (SNPs) enrich for particular biological annotations. SNP-based enrichment analysis needs to account for biases such as co......-localization of GWAS signals to gene-dense and high linkage disequilibrium (LD) regions, and correlations of gene size, location and function. The SNPsnap Web server enables SNP-based enrichment analysis by providing matched sets of SNPs that can be used to calibrate background expectations. Specifically, SNPsnap...... efficiently identifies sets of randomly drawn SNPs that are matched to a set of query SNPs based on allele frequency, number of SNPs in LD, distance to nearest gene and gene density. Availability and implementation : SNPsnap server is available at http://www.broadinstitute.org/mpg/snpsnap/. Contact: joelh...

  15. Services for annotation of biomedical text

    OpenAIRE

    Hakenberg, Jörg

    2008-01-01

    Motivation: Text mining in the biomedical domain in recent years has focused on the development of tools for recognizing named entities and extracting relations. Such research resulted from the need for such tools as basic components for more advanced solutions. Named entity recognition, entity mention normalization, and relationship extraction now have reached a stage where they perform comparably to human annotators (considering inter--annotator agreement, measured in many studies to be aro...

  16. Multimedia Annotations on the Semantic Web

    OpenAIRE

    Stamou, G.; Ossenbruggen, J.R.; Pan, J; Schreiber, A.T.

    2006-01-01

    Multimedia in all forms (images, video, graphics, music, speech) is exploding on the Web. The content needs to be annotated and indexed to enable effective search and retrieval. However, recent standards and best practices for multimedia metadata don't provide semantically rich descriptions of multimedia content. On the other hand, the World Wide Web Consortium's (W3C's) Semantic Web effort has been making great progress in advancing techniques for annotating semantics of Web resources. To br...

  17. Fluid Annotations in a Open World

    DEFF Research Database (Denmark)

    Zellweger, Polle Trescott; Bouvin, Niels Olof; Jehøj, Henning;

    2001-01-01

    Fluid Documents use animated typographical changes to provide a novel and appealing user experience for hypertext browsing and for viewing document annotations in context. This paper describes an effort to broaden the utility of Fluid Documents by using the open hypermedia Arakne Environment to l...... layer fluid annotations and links on top of abitrary HTML pages on the World Wide Web. Changes to both Fluid Documents and Arakne are required....

  18. Learning Object Annotation for Agricultural Learning Repositories

    OpenAIRE

    Ebner, Hannes; Manouselis, Nikos; Palmér, Matthias; Enoksson, Fredrik; Palavitsinis, Nikos; Kastrantas, Kostas; Naeve, Ambjörn

    2009-01-01

    This paper introduces a Web-based tool that has been developed to facilitate learning object annotation in agricultural learning repositories with IEEE LOM-compliant metadata. More specifically, it presents how an application profile of the IEEE LOM standard has been developed for the description of learning objects on organic agriculture and agroecology. Then, it describes the design and prototype development of the Organic.Edunet repository tool: a Web-based for annotating learning objects ...

  19. Instantiation of relations for semantic annotation

    OpenAIRE

    Tenier, Sylvain; Toussaint, Yannick; Napoli, Amedeo; Polanco, Xavier

    2006-01-01

    This paper presents a methodology for the semantic annotation of web pages with individuals of a domain ontology. While most semantic annotation systems can recognize knowledge units, they usually do not establish explicit relations between them. The method presented identifies the individuals which should be related among the whole set of individuals and codes them as role instances within an OWL ontology. This is done by using a correspondence between the tree structure of a web page and th...

  20. Instructions for Temporal Annotation of Scheduling Dialogs

    OpenAIRE

    O'Hara, Tom; Wiebe, Janyce; Payne, Karen

    1997-01-01

    Human annotation of natural language facilitates standardized evaluation of natural language processing systems and supports automated feature extraction. This document consists of instructions for annotating the temporal information in scheduling dialogs, dialogs in which the participants schedule a meeting with one another. Task-oriented dialogs, such as these are, would arise in many useful applications, for instance, automated information providers and automated phone operators. Explicit ...

  1. DIMA – Annotation guidelines for German intonation

    OpenAIRE

    Kügler, Frank; Smolibocki, Bernadett; Arnold, Denis; Baumann, Stefan; Braun, Bettina; Grice, Martine; Jannedy, Stefanie; Michalsky, Jan; Niebuhr, Oliver; Peters, Jörg; Ritter, Simon; Röhr, Christine T.; Schweitzer, Antje; Schweitzer, Katrin; Wagner, Petra

    2015-01-01

    This paper presents newly developed guidelines for prosodic annotation of German as a consensus system agreed upon by German intonologists. The DIMA system is rooted in the framework of autosegmental-metrical phonology. One important goal of the consensus is to make exchanging data between groups easier since German intonation is currently annotated according to different models. To this end, we aim to provide guidelines that are easy to learn. The guidelines were e...

  2. Annotating Honorifics Denoting Social Ranking of Referents

    OpenAIRE

    Nariyama, Shigeko; Nakaiwa, Hiromi; Siegel, Melanie

    2011-01-01

    This paper proposes an annotating scheme that encodes honorifics (respectful words). Honorifics are used extensively in Japanese, reflecting the social relationship (e.g. social ranks and age) of the referents. This referential information is vital for resolving zero pronouns and improving machine translation outputs. Annotating honorifics is a complex task that involves identifying a predicate with honorifics, assigning ranks to referents of the predicate, calibrating the ranks, and co...

  3. Assessment of autonomic function in untreated adult coeliac disease

    Institute of Scientific and Technical Information of China (English)

    Gian Marco Giorgetti; Antonio Tursi; Cesare Iani; Flavio Arciprete; Giovanni Brandimarte; Ambrogio Capria; Luigi Fontana

    2004-01-01

    AIM: Some recent studies showed that alteration of upper-gut motility in coeliac disease may be related to dysfunction of autonomic nervous system. The aim of our study was to investigate whether autonomic nervous system was altered in untreated and unselected coeliac disease patients.METHODS: We studied 8 untreated and consecutive coeliac disease patients (2 males and 6 females, age range 37±14.5 years). Histological evaluation of duodenal mucosa, anti-gliadin antibodies (AGA), antiendomysial antibodies (EMA) and anti-tTG antibodies and sorbitol H2 breath test were performed in all patients. Extrinsic autonomic neuropathy was assessed by the standardized measurement of cardiovascular reflexes (lying-to-standing, Valsalva manoeuvre, deep breathing, sustained handgrip). The results obtained were compared with a healthy, asymptomatic control group (6 males and 7females, age range 42.3±13.5 years). RESULTS: Coeliac patients exhibited a lower increase of PAS as a response to isometric effort, a reduction of spectral power LF as a response to clinostatic position, but without statistical significance. Also they showed a lower tolerance to orthostatic position, associated with a latent disequilibrium of sympathetic-vagal balance, a relative prevalence of parasympathetic component of the autonomic function. However, these results were not statistically significant when compared with control group (P = n.s.). And they were unchanged after 6 and 12 mo of gluten-free diet.CONCLUSION: This study failed to confirm a significant correlation between autonomic dysfunction and coeliac disease, yet we could not exclude a role of autonomic dysfunction in the genesis of systemic symptoms in some coeliacs.

  4. Assessing and Treating Stereotypical Behaviors in Classrooms Using a Functional Approach

    Science.gov (United States)

    Bruhn, Allison L.; Balint-Langel, Kinga; Troughton, Leonard; Langan, Sean; Lodge, Kelsey; Kortemeyer, Sara

    2015-01-01

    For years, the assumption has been that stereotypical behaviors functioned only to provide sensory or automatic reinforcement. However, these behaviors also may serve social functions. Given the unsettled debate, functional behavior assessment and functional analysis can be used to identify the exact function of stereotypical behavior and design…

  5. 20 CFR 404.1546 - Responsibility for assessing your residual functional capacity.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Responsibility for assessing your residual functional capacity. 404.1546 Section 404.1546 Employees' Benefits SOCIAL SECURITY ADMINISTRATION FEDERAL OLD... Functional Capacity § 404.1546 Responsibility for assessing your residual functional capacity....

  6. Related Documents Search Using User Created Annotations

    Directory of Open Access Journals (Sweden)

    Jakub Sevcech

    2013-01-01

    Full Text Available We often use various services for creating bookmarks,tags, highlights and other types of annotations while surf-ing the Internet or when reading electronic documentsas well. These services allows us to create a number oftypes of annotation that we are commonly creating intoprinted documents. Annotations attached to electronicdocuments however can be used for other purposes suchas navigation support, text summarization etc. We pro-posed a method for searching related documents to cur-rently studied document using annotations created by thedocument reader as indicators of user's interest in par-ticular parts of the document. The method is based onspreading activation in text transformed into graph. Forevaluation we created a service called Annota, which al-lows users to insert various types of annotations into webpages and PDF documents displayed in the web browser.We analyzed properties of various types of annotations in-serted by users of Annota into documents. Based on thesewe evaluated our method by simulation and we comparedit against commonly used TF-IDF based method.

  7. JGI Plant Genomics Gene Annotation Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

  8. BG7: a new approach for bacterial genome annotation designed for next generation sequencing data.

    Directory of Open Access Journals (Sweden)

    Pablo Pareja-Tobes

    Full Text Available BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version - which is developed in Java, takes advantage of Amazon Web Services (AWS cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future.

  9. BG7: a new approach for bacterial genome annotation designed for next generation sequencing data.

    Science.gov (United States)

    Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Pareja, Eduardo; Tobes, Raquel

    2012-01-01

    BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version - which is developed in Java, takes advantage of Amazon Web Services (AWS) cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future. PMID:23185310

  10. An annotation based approach to support design communication

    CERN Document Server

    Hisarciklilar, Onur

    2007-01-01

    The aim of this paper is to propose an approach based on the concept of annotation for supporting design communication. In this paper, we describe a co-operative design case study where we analyse some annotation practices, mainly focused on design minutes recorded during project reviews. We point out specific requirements concerning annotation needs. Based on these requirements, we propose an annotation model, inspired from the Speech Act Theory (SAT) to support communication in a 3D digital environment. We define two types of annotations in the engineering design context, locutionary and illocutionary annotations. The annotations we describe in this paper are materialised by a set of digital artefacts, which have a semantic dimension allowing express/record elements of technical justifications, traces of contradictory debates, etc. In this paper, we first clarify the semantic annotation concept, and we define general properties of annotations in the engineering design context, and the role of annotations in...

  11. Ecological assessment of executive functions: a new virtual reality paradigm

    OpenAIRE

    Jansari, Ashok S.; Devlin, Alex; Agnew, Robert; Akesson, Katarina; Murphy, Lesley; Leadbetter, Tony

    2014-01-01

    Acquired brain injury (ABI) can lead to a constellation of higher-order executive problems, which can impact significantly on everyday behaviour. While some neuropsychological assessments are able to objectively assess these impairments, increasingly, clinicians are finding that a subset of their patients pass these tests whilst still exhibiting difficulties in day-to-day living. Calls have therefore been made to develop assessments that are more sensitive and that are more ecologically-valid...

  12. The Annotation of RNA Motifs

    Directory of Open Access Journals (Sweden)

    Eric Westhof

    2006-04-01

    Full Text Available The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNA–RNA and quaternary RNA–protein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-Watson–Crick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s. The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a decomposition of each motif into non-Watson–Crick base-pairs; (b geometric classification of each basepair; (c identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e acceptance or rejection of the null hypothesis that the motif is conserved.

  13. Computational analyses and annotations of the Arabidopsis peroxidasegene family

    DEFF Research Database (Denmark)

    Østergaard, Lars; Pedersen, Anders Gorm; Jespersen, Hans M.;

    1998-01-01

    Classical heme-containing plant peroxidases have been ascribed a wide variety of functional roles related to development, defense, lignification and hormonal signaling. More than 40 peroxidase genes are now known in Arabidopsis thaliana for which functional association is complicated by a general...... lack of peroxidase substrate specificity. Computational analysis was performed on 30 near full-length Arabidopsis peroxidase cDNAs for annotation of start codons and signal peptide cleavage sites. A compositional analysis revealed that 23 of the 30 peroxidase cDNAs have 5' untranslated regions...

  14. GOAnnotator: linking protein GO annotations to evidence text

    OpenAIRE

    Couto, Francisco M.; Silva, Mário J.; Lee, Vivian; Dimmer, Emily; Camon, Evelyn; Apweiler, Rolf; Kirsch, Harald; Rebholz-Schuhmann, Dietrich

    2006-01-01

    Background Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators. Results In this paper we describe an ...

  15. Web Database Query Interface Annotation Based on User Collaboration

    Institute of Scientific and Technical Information of China (English)

    LIU Wei; LIN Can; MENG Xiaofeng

    2006-01-01

    A vision based query interface annotation method is used to relate attributes and form elements in form-based web query interfaces, this method can reach accuracy of 82%.And a user participation method is used to tune the result; user can answer "yes" or "no" for existing annotations, or manually annotate form elements.Mass feedback is added to the annotation algorithm to produce more accurate result.By this approach, query interface annotation can reach a perfect accuracy.

  16. Unravelling peer assessment : Methodological, functional, and conceptual developments

    NARCIS (Netherlands)

    Strijbos, Jan-Willem; Sluijsmans, Dominique

    2010-01-01

    Peer assessment is an educational arrangement where students judge a peer's performance quantitatively and/or qualitatively and which stimulates students to reflect, discuss and collaborate. However, empirical evidence for peer assessment effects on learning is scarce, mostly based on student self-r

  17. Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome

    Science.gov (United States)

    Ernst, Jason; Kellis, Manolis

    A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation and the onset of disease. Although individual modifications have been linked to the activity levels of various genetic functional elements, their combinatorial patterns are still unresolved and their potential for systematic de novo genome annotation remains untapped. Here, we use a multivariate Hidden Markov Model to reveal chromatin states in human T cells, based on recurrent and spatially coherent combinations of chromatin marks.We define 51 distinct chromatin states, including promoter-associated, transcription-associated, active intergenic, largescale repressed and repeat-associated states. Each chromatin state shows specific enrichments in functional annotations, sequence motifs and specific experimentally observed characteristics, suggesting distinct biological roles. This approach provides a complementary functional annotation of the human genome that reveals the genome-wide locations of diverse classes of epigenetic function.

  18. Functional assessment of ubiquitin-depended processes under microgravity conditions

    Science.gov (United States)

    Zhabereva, Anastasia; Shenkman, Boris S.; Gainullin, Murat; Gurev, Eugeny; Kondratieva, Ekaterina; Kopylov, Arthur

    , were separated by SDS-PAGE and subjected for mass spectrometry-based analysis.With the described workflow, we identified more than 200 proteins including of 26S proteasome subunits, members of SUMO (Small Ubiquitin-like Modifier) family and ubiquitylated substrates. On the whole, our results provide an unbiased view of ubiquitylation state under microgravity conditions and thereby demonstrate the utility of proposed combination of analytical methods for functional assessment of ubiquitin-depended processes. Acknowledgment - We thank teams of Institute of Biomedical Problems of Russian Academy of Sciences and TsSKB “Progress” Samara for organization and preparation for spaceflight. This work is partially supported by the Russian Foundation for Basic Research (grant12-04-01836).

  19. Assessment of vascular function in systemic onset juvenile idiopathic arthritis.

    Science.gov (United States)

    Sozeri, Betul; Atikan, Basak Yildiz; Ozdemir, Kadriye; Mir, Sevgi

    2016-07-01

    An increased incidence of cardiovascular disease has been found in rheumatic disorders. Juvenile idiopathic arthritis (JIA) is the most common chronic rheumatic disease in children. Prolonged immunological inflammatory process leads these patients to an early onset of atherosclerosis. We aimed to assess the presence of early vascular dysfunction in patients with systemic onset juvenile idiopathic arthritis (sJIA) and investigate the role of therapy sJIA in vascular health. Thirty-three patients (22 males, 11 females) diagnosed with sJIA according to the International League of Associations for Rheumatology criteria were compared to 72 age- and sex-matched controls. None of the participants was overweight, obese, or had a history of hypertension, dyslipidemia, diabetes mellitus, or cardiovascular disease. Arterial stiffness (As) was evaluated by measurement of carotid-femoral pulse wave velocity (PWV) and augmentation index (AIx) with a Vicorder. The mean age of patients in this study was 9.96 ± 3.71 years (range 4-16 years) and the mean age of controls was 10.9 ± 3.52 years (range 4-19 years). These two groups were well matched for age, sex, and BMI. The mean age of patients at the onset of disease was 7.06 ± 3.9 years (range 3-15 years). The mean duration of disease and active disease was 79 ± 45 months (range 6-162 months) and 58 ± 49 months (range 1-101 months), respectively. The highest levels of PWV and AIx were found in the patient group. Seven patients had had macrophage activation syndrome at presentation. In these patients, vascular changes were higher than other patients (6.30 ± 0.42 m/s vs 5.17 ± 0.55 m/s, p = 0.01, respectively). The corticosteroid therapy was found associated with higher PWV, (p < 0.05), while there was no difference between vascular parameters and use of non-steroid therapies (methotrexate (MTX), anti-TNF alfa agents). We also find statistically significant correlation between PWV

  20. The assessment of functional communication in patients with acquired communication problems: the development of the Derby Functional Communication Scale

    OpenAIRE

    Ditchfield, Jennifer A.

    2008-01-01

    The Derby Functional Communication Scale (DFCS) was developed to assess functional communication in patients in hospital and rehabilitation settings. The validity of the DFCS and its sensitivity to low mood was also examined. In this study, correlation analysis was undertaken between DFCS and other existing measures of communication and mood. Assessments took place on local Stroke and Rehabilitation units. Sixteen hospital inpatients with acquired communication problems due to mixed aetiolog...

  1. Annotated chemical patent corpus: a gold standard for text mining.

    Directory of Open Access Journals (Sweden)

    Saber A Akhondi

    Full Text Available Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org.

  2. Supraclavicular scalenectomy for thoracic outlet syndrome--functional outcomes assessed using the DASH scoring system.

    LENUS (Irish Health Repository)

    Glynn, Ronan W

    2012-02-01

    To evaluate supraclavicular scalenectomy ± cervical rib excision for thoracic outlet syndrome (TOS), employing Disability of Arm, Shoulder, and Hand (DASH) scoring for functional assessment post-decompression.

  3. What we have learned from complex annotation of topic-focus articulation in a large Czech corpus

    Directory of Open Access Journals (Sweden)

    Eva Hajičová

    2012-09-01

    Full Text Available After a short summary of the theory of Topic-Focus Articulation (TFA the present contribution documents on several examples illustrating the annotation of the basic features of TFA on a large corpus (the Prague Dependency Treebank that corpus annotation brings an additional value to the corpus if the following two conditions are being met: (i the annotation scheme is based on a sound linguistic theory, and (ii the annotation scenario is carefully (i.e. systematically and consistently designed. Such an annotation is important not only for the surface shape of the sentence but even more for the underlying sentence structure: it may elucidate phenomena hidden on the surface but unavoidable for the representation of the meaning and functioning of the sentence.

  4. Gene Ontology annotations at SGD: new data sources and annotation methods.

    Science.gov (United States)

    Hong, Eurie L; Balakrishnan, Rama; Dong, Qing; Christie, Karen R; Park, Julie; Binkley, Gail; Costanzo, Maria C; Dwight, Selina S; Engel, Stacia R; Fisk, Dianna G; Hirschman, Jodi E; Hitz, Benjamin C; Krieger, Cynthia J; Livstone, Michael S; Miyasato, Stuart R; Nash, Robert S; Oughtred, Rose; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Zhu, Kathy K; Dolinski, Kara; Botstein, David; Cherry, J Michael

    2008-01-01

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current. PMID:17982175

  5. Proteogenomics: the needs and roles to be filled by proteomics in genome annotation

    Energy Technology Data Exchange (ETDEWEB)

    Ansong, Charles; Purvine, Samuel O.; Adkins, Joshua N.; Lipton, Mary S.; Smith, Richard D.

    2008-01-01

    While genome sequencing efforts reveal the basic building blocks of life, a genome sequence alone is insufficient for elucidating biological function. Genome annotation – the process of identifying genes and assigning function to each gene in a genome sequence – provides the means to elucidate biological function from sequence. Current state-of-the-art high throughput genome annotation uses a combination of comparative (sequence similarity data) and non-comparative (ab initio gene prediction algorithms) methods to identify open reading frames in genome sequences. Because approaches used to validate the presence of these open reading frames are typically based on the information derived from the annotated genomes, they cannot independently and unequivocally determine whether a predicted open reading frame is translated into a protein. With the ability to directly measure peptides arising from expressed proteins, high throughput liquid chromatography-tandem mass spectrometry-based proteomics, approaches can be used to verify coding regions of a genomic sequence. Here, we highlight several ways in which high throughput tandem mass spectrometry-based proteomics can improve the quality of genome annotations and suggest that it could be efficiently applied during the initial gene calling process so that the improvements are propagated through the subsequent functional annotation process.

  6. Assessing Pulmonary Pathology by Detailed Examination of Respiratory Function

    OpenAIRE

    Vaickus, Louis J; Bouchard, Jacqueline; Kim, Jiyoun; Natarajan, Sudha; Remick, Daniel G.

    2010-01-01

    Pulmonary inflammation causes multiple alterations within the lung, including mucus production, recruitment of inflammatory cells, and airway hyperreactivity (AHR). Measurement of AHR by direct, invasive means (eg, mechanical ventilation) or noninvasive techniques, like whole body plethysmography (WBP), assesses the severity of pulmonary inflammation in animal models of inflammatory lung disease. Direct measurement of AHR is acknowledged as the most accurate method for assessing airway mechan...

  7. Reliability and content validity of the Disability Assessment Structured Interview (DASI): A tool to assess functional limitations in claimants

    OpenAIRE

    Spanjer, Jerry; Krol, Boudien; Brouwer, Sandra; Popping, R.; Groothoff, J. W.; van der Klink, J. J. L.

    2010-01-01

    Objective The aim of this study is to investigate the reliability and validity of the Disability Assessment Structured Interview (DASI). The DASI is a semi-structured interview for assessing long-term functional limitations concerning the work disability assessment of claimants. Methods A randomized controlled trial was conducted. Patients applying for a work-disability pension after 21 months of sick leave were independently interviewed and examined either by two physicians who had completed...

  8. Towards a New Functional Assessment of Autistic Dysfunction in Children with Developmental Disorders: The Behaviour Function Inventory.

    Science.gov (United States)

    Adrien, Jean-Louis; Roux, Sylvie; Couturier, Guylene; Malvy, Joelle; Guerin, Pascaline; Debuly, Sabine; Lelord, Gilbert; Berthelemy, Catherine

    2001-01-01

    This paper describes the development of the Behaviour Function Inventory (BFI), an instrument designed to assess particular disorders of psychological development and functioning in children with developmental disorders including autism. A study of the reliability and validity of the scale indicated that the BFI provides precise information on the…

  9. Outpatient Assessment of Neurovisual Functions in Children with Cerebral Palsy

    Science.gov (United States)

    Barca, Laura; Cappelli, Francesca R.; Di Giulio, Paola; Staccioli, Susanna; Castelli, Enrico

    2010-01-01

    This study examined the feasibility of the Atkinson Battery for Child Development for Examining Functional Vision (Atkinson, Anker, Rae, et al., 2002) to evaluate neurovisual functions of children with neurodevelopmental disorders in outpatient setting. A total of 90 patients underwent a comprehensive evaluation. Among these, a group of 33…

  10. Assessing Executive Functions: A Life-Span Perspective

    Science.gov (United States)

    Reynolds, Cecil R.; Horton, Arthur MacNeill, Jr.

    2008-01-01

    Despite many disagreements on the utility of neuropsychological applications in schools, executive function measures have been found to be useful across a variety of areas and ages. In addition, many disagreements are extant in discussions of the maturational course of the development of executive functioning abilities that are dependent on…

  11. Metabolic Assessment of Suited Mobility Using Functional Tasks

    Science.gov (United States)

    Norcross, J. R.; McFarland, S. M.; Ploutz-Snyder, Robert

    2016-01-01

    Existing methods for evaluating extravehicular activity (EVA) suit mobility have typically focused on isolated joint range of motion or torque, but these techniques have little to do with how well a crewmember functionally performs in an EVA suit. To evaluate suited mobility at the system level through measuring metabolic cost (MC) of functional tasks.

  12. Platelet function testing: methods of assessment and clinical utility.

    LENUS (Irish Health Repository)

    Mylotte, Darren

    2012-02-01

    Platelets play a central role in the regulation of both thrombosis and haemostasis yet tests of platelet function have, until recently, been exclusively used in the diagnosis and management of bleeding disorders. Recent advances have demonstrated the clinical utility of platelet function testing in patients with cardiovascular disease. The ex vivo measurement of response to antiplatelet therapies (aspirin and clopidogrel), by an ever-increasing array of platelet function tests, is with some assays, predictive of adverse clinical events and thus, represents an emerging area of interest for both the clinician and basic scientist. This review article will describe the advantages and disadvantages of the currently available methods of measuring platelet function and discuss both the limitations and emerging data supporting the role of platelet function studies in clinical practice.

  13. Platelet function testing: methods of assessment and clinical utility.

    LENUS (Irish Health Repository)

    Mylotte, Darren

    2011-01-01

    Platelets play a central role in the regulation of both thrombosis and haemostasis yet tests of platelet function have, until recently, been exclusively used in the diagnosis and management of bleeding disorders. Recent advances have demonstrated the clinical utility of platelet function testing in patients with cardiovascular disease. The ex vivo measurement of response to antiplatelet therapies (aspirin and clopidogrel), by an ever-increasing array of platelet function tests, is with some assays, predictive of adverse clinical events and thus, represents an emerging area of interest for both the clinician and basic scientist. This review article will describe the advantages and disadvantages of the currently available methods of measuring platelet function and discuss both the limitations and emerging data supporting the role of platelet function studies in clinical practice.

  14. Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.

    Directory of Open Access Journals (Sweden)

    Anika Oellrich

    Full Text Available Electronic health records and scientific articles possess differing linguistic characteristics that may impact the performance of natural language processing tools developed for one or the other. In this paper, we investigate the performance of four extant concept recognition tools: the clinical Text Analysis and Knowledge Extraction System (cTAKES, the National Center for Biomedical Ontology (NCBO Annotator, the Biomedical Concept Annotation System (BeCAS and MetaMap. Each of the four concept recognition systems is applied to four different corpora: the i2b2 corpus of clinical documents, a PubMed corpus of Medline abstracts, a clinical trails corpus and the ShARe/CLEF corpus. In addition, we assess the individual system performances with respect to one gold standard annotation set, available for the ShARe/CLEF corpus. Furthermore, we built a silver standard annotation set from the individual systems' output and assess the quality as well as the contribution of individual systems to the quality of the silver standard. Our results demonstrate that mainly the NCBO annotator and cTAKES contribute to the silver standard corpora (F1-measures in the range of 21% to 74% and their quality (best F1-measure of 33%, independent from the type of text investigated. While BeCAS and MetaMap can contribute to the precision of silver standard annotations (precision of up to 42%, the F1-measure drops when combined with NCBO Annotator and cTAKES due to a low recall. In conclusion, the performances of individual systems need to be improved independently from the text types, and the leveraging strategies to best take advantage of individual systems' annotations need to be revised. The textual content of the PubMed corpus, accession numbers for the clinical trials corpus, and assigned annotations of the four concept recognition systems as well as the generated silver standard annotation sets are available from http://purl.org/phenotype/resources. The textual content

  15. Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.

    Science.gov (United States)

    Oellrich, Anika; Collier, Nigel; Smedley, Damian; Groza, Tudor

    2015-01-01

    Electronic health records and scientific articles possess differing linguistic characteristics that may impact the performance of natural language processing tools developed for one or the other. In this paper, we investigate the performance of four extant concept recognition tools: the clinical Text Analysis and Knowledge Extraction System (cTAKES), the National Center for Biomedical Ontology (NCBO) Annotator, the Biomedical Concept Annotation System (BeCAS) and MetaMap. Each of the four concept recognition systems is applied to four different corpora: the i2b2 corpus of clinical documents, a PubMed corpus of Medline abstracts, a clinical trails corpus and the ShARe/CLEF corpus. In addition, we assess the individual system performances with respect to one gold standard annotation set, available for the ShARe/CLEF corpus. Furthermore, we built a silver standard annotation set from the individual systems' output and assess the quality as well as the contribution of individual systems to the quality of the silver standard. Our results demonstrate that mainly the NCBO annotator and cTAKES contribute to the silver standard corpora (F1-measures in the range of 21% to 74%) and their quality (best F1-measure of 33%), independent from the type of text investigated. While BeCAS and MetaMap can contribute to the precision of silver standard annotations (precision of up to 42%), the F1-measure drops when combined with NCBO Annotator and cTAKES due to a low recall. In conclusion, the performances of individual systems need to be improved independently from the text types, and the leveraging strategies to best take advantage of individual systems' annotations need to be revised. The textual content of the PubMed corpus, accession numbers for the clinical trials corpus, and assigned annotations of the four concept recognition systems as well as the generated silver standard annotation sets are available from http://purl.org/phenotype/resources. The textual content of the Sh

  16. GPA: A Statistical Approach to Prioritizing GWAS Results by Integrating Pleiotropy and Annotation

    Science.gov (United States)

    Li, Cong; Gelernter, Joel; Zhao, Hongyu

    2014-01-01

    Results from Genome-Wide Association Studies (GWAS) have shown that complex diseases are often affected by many genetic variants with small or moderate effects. Identifications of these risk variants remain a very challenging problem. There is a need to develop more powerful statistical methods to leverage available information to improve upon traditional approaches that focus on a single GWAS dataset without incorporating additional data. In this paper, we propose a novel statistical approach, GPA (Genetic analysis incorporating Pleiotropy and Annotation), to increase statistical power to identify risk variants through joint analysis of multiple GWAS data sets and annotation information because: (1) accumulating evidence suggests that different complex diseases share common risk bases, i.e., pleiotropy; and (2) functionally annotated variants have been consistently demonstrated to be enriched among GWAS hits. GPA can integrate multiple GWAS datasets and functional annotations to seek association signals, and it can also perform hypothesis testing to test the presence of pleiotropy and enrichment of functional annotation. Statistical inference of the model parameters and SNP ranking is achieved through an EM algorithm that can handle genome-wide markers efficiently. When we applied GPA to jointly analyze five psychiatric disorders with annotation information, not only did GPA identify many weak signals missed by the traditional single phenotype analysis, but it also revealed relationships in the genetic architecture of these disorders. Using our hypothesis testing framework, statistically significant pleiotropic effects were detected among these psychiatric disorders, and the markers annotated in the central nervous system genes and eQTLs from the Genotype-Tissue Expression (GTEx) database were significantly enriched. We also applied GPA to a bladder cancer GWAS data set with the ENCODE DNase-seq data from 125 cell lines. GPA was able to detect cell lines that are

  17. Automated analysis and annotation of basketball video

    Science.gov (United States)

    Saur, Drew D.; Tan, Yap-Peng; Kulkarni, Sanjeev R.; Ramadge, Peter J.

    1997-01-01

    Automated analysis and annotation of video sequences are important for digital video libraries, content-based video browsing and data mining projects. A successful video annotation system should provide users with useful video content summary in a reasonable processing time. Given the wide variety of video genres available today, automatically extracting meaningful video content for annotation still remains hard by using current available techniques. However, a wide range video has inherent structure such that some prior knowledge about the video content can be exploited to improve our understanding of the high-level video semantic content. In this paper, we develop tools and techniques for analyzing structured video by using the low-level information available directly from MPEG compressed video. Being able to work directly in the video compressed domain can greatly reduce the processing time and enhance storage efficiency. As a testbed, we have developed a basketball annotation system which combines the low-level information extracted from MPEG stream with the prior knowledge of basketball video structure to provide high level content analysis, annotation and browsing for events such as wide- angle and close-up views, fast breaks, steals, potential shots, number of possessions and possession times. We expect our approach can also be extended to structured video in other domains.

  18. Biochemical functional predictions for protein structures of unknown or uncertain function

    Directory of Open Access Journals (Sweden)

    Caitlyn L. Mills

    2015-01-01

    Full Text Available With the exponential growth in the determination of protein sequences and structures via genome sequencing and structural genomics efforts, there is a growing need for reliable computational methods to determine the biochemical function of these proteins. This paper reviews the efforts to address the challenge of annotating the function at the molecular level of uncharacterized proteins. While sequence- and three-dimensional-structure-based methods for protein function prediction have been reviewed previously, the recent trends in local structure-based methods have received less attention. These local structure-based methods are the primary focus of this review. Computational methods have been developed to predict the residues important for catalysis and the local spatial arrangements of these residues can be used to identify protein function. In addition, the combination of different types of methods can help obtain more information and better predictions of function for proteins of unknown function. Global initiatives, including the Enzyme Function Initiative (EFI, COMputational BRidges to EXperiments (COMBREX, and the Critical Assessment of Function Annotation (CAFA, are evaluating and testing the different approaches to predicting the function of proteins of unknown function. These initiatives and global collaborations will increase the capability and reliability of methods to predict biochemical function computationally and will add substantial value to the current volume of structural genomics data by reducing the number of absent or inaccurate functional annotations.

  19. Methods to assess Drosophila heart development, function and aging

    OpenAIRE

    Ocorr, Karen; Vogler, Georg; Bodmer, Rolf

    2014-01-01

    In recent years the Drosophila heart has become an established model of many different aspects of human cardiac disease. This model has allowed identification of disease-causing mechanisms underlying congenital heart disease and cardiomyopathies and has permitted the study underlying genetic, metabolic and age-related contributions to heart function. In this review we discuss methods currently employed in the analysis of the Drosophila heart structure and function, such as optical methods to ...

  20. Outpatient assessment of neurovisual functions in children with Cerebral Palsy

    OpenAIRE

    Barca, Laura; Cappelli, Francesca R.; Di Giulio, Paola; Staccioli, Susanna; Castelli, Enrico

    2010-01-01

    This study examined the feasibility of the Atkinson Battery for Child development for Examining Functional Vision (Atkinson, Anker, Rae, et al., 2002) to evaluate neurovisual functions of children with neurodevelopmental disorders in outpatient setting. A total of 90 patients underwent a comprehensive evaluation. Among these, a group of 33 children with Cerebral Palsy (CP), mean age 6 years, with different types of CP (26% diplegic, 37% hemiplegic and 37% tetraplegic) were selected to constit...

  1. The Relationship between Functional Assessment and Treatment Selection for Aggressive Behaviors.

    Science.gov (United States)

    Hile, Matthew G.; Desrochers, Marcie N.

    1993-01-01

    This paper reviews the literature on functional assessment in the behavioral treatment of aggression in persons with mental retardation or developmental delays. Increased use of functional assessment and skill training is noted but no concomitant decrease in the use of intrusive procedures. (Author/DB)

  2. The Assessment of Executive Functioning in People with Intellectual Disabilities: An Exploratory Analysis

    Science.gov (United States)

    Bevins, Shelley; Hurse, Emily

    2016-01-01

    The following article details a piece of service development work undertaken as part of the Plymouth Down Syndrome Screening Programme. The work aimed to review the use of three measures assessing executive functioning skills used within the Programme as well as with people without Down syndrome. Three tasks assessing executive functioning (the…

  3. 20 CFR 416.946 - Responsibility for assessing your residual functional capacity.

    Science.gov (United States)

    2010-04-01

    ... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Responsibility for assessing your residual functional capacity. 416.946 Section 416.946 Employees' Benefits SOCIAL SECURITY ADMINISTRATION SUPPLEMENTAL... Capacity § 416.946 Responsibility for assessing your residual functional capacity. (a) Responsibility...

  4. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D

    Directory of Open Access Journals (Sweden)

    Meller Jaroslaw

    2007-08-01

    Full Text Available Abstract Background Macromolecular visualization as well as automated structural and functional annotation tools play an increasingly important role in the post-genomic era, contributing significantly towards the understanding of molecular systems and processes. For example, three dimensional (3D models help in exploring protein active sites and functional hot spots that can be targeted in drug design. Automated annotation and visualization pipelines can also reveal other functionally important attributes of macromolecules. These goals are dependent on the availability of advanced tools that integrate better the existing databases, annotation servers and other resources with state-of-the-art rendering programs. Results We present a new tool for protein structure analysis, with the focus on annotation and visualization of protein complexes, which is an extension of our previously developed POLYVIEW web server. By integrating the web technology with state-of-the-art software for macromolecular visualization, such as the PyMol program, POLYVIEW-3D enables combining versatile structural and functional annotations with a simple web-based interface for creating publication quality structure rendering, as well as animated images for Powerpoint™, web sites and other electronic resources. The service is platform independent and no plug-ins are required. Several examples of how POLYVIEW-3D can be used for structural and functional analysis in the context of protein-protein interactions are presented to illustrate the available annotation options. Conclusion POLYVIEW-3D server features the PyMol image rendering that provides detailed and high quality presentation of macromolecular structures, with an easy to use web-based interface. POLYVIEW-3D also provides a wide array of options for automated structural and functional analysis of proteins and their complexes. Thus, the POLYVIEW-3D server may become an important resource for researches and educators in

  5. Graph Annotations in Modeling Complex Network Topologies

    CERN Document Server

    Dimitropoulos, Xenofontas; Vahdat, Amin; Riley, George

    2007-01-01

    The coarsest approximation of the structure of a complex network, such as the Internet, is a simple undirected unweighted graph. This approximation, however, loses too much detail. In reality, objects represented by vertices and edges in such a graph possess some non-trivial internal structure that varies across and differentiates among distinct types of links or nodes. In this work, we abstract such additional information as network annotations. We introduce a network topology modeling framework that treats annotations as an extended correlation profile of a network. Assuming we have this profile measured for a given network, we present an algorithm to rescale it in order to construct networks of varying size that still reproduce the original measured annotation profile. Using this methodology, we accurately capture the network properties essential for realistic simulations of network applications and protocols, or any other simulations involving complex network topologies, including modeling and simulation ...

  6. Non-invasive Assessment of Microvascular and Endothelial Function

    OpenAIRE

    Cheng, Cynthia; Daskalakis, Constantine; Falkner, Bonita

    2013-01-01

    The authors have utilized capillaroscopy and forearm blood flow techniques to investigate the role of microvascular dysfunction in pathogenesis of cardiovascular disease. Capillaroscopy is a non-invasive, relatively inexpensive methodology for directly visualizing the microcirculation. Percent capillary recruitment is assessed by dividing the increase in capillary density induced by postocclusive reactive hyperemia (postocclusive reactive hyperemia capillary density minus baseline capillary d...

  7. Brazilian Version of the Functional Assessment Measure: Cross-Cultural Adaptation and Reliability Evaluation

    Science.gov (United States)

    Lourenco Jorge, Liliana; Garcia Marchi, Flavia Helena; Portela Hara, Ana Clara; Battistella, Linamara R.

    2011-01-01

    The objective of this prospective study was to perform a cross-cultural adaptation of the Functional Assessment Measure (FAM) into Brazilian Portuguese, and to assess the test-retest reliability. The instrument was translated, back-translated, pretested, and reviewed by a committee. The Brazilian version was assessed in 61 brain-injury patients.…

  8. Deep Question Answering for protein annotation.

    Science.gov (United States)

    Gobeill, Julien; Gaudinat, Arnaud; Pasche, Emilie; Vishnyakova, Dina; Gaudet, Pascale; Bairoch, Amos; Ruch, Patrick

    2015-01-01

    Biomedical professionals have access to a huge amount of literature, but when they use a search engine, they often have to deal with too many documents to efficiently find the appropriate information in a reasonable time. In this perspective, question-answering (QA) engines are designed to display answers, which were automatically extracted from the retrieved documents. Standard QA engines in literature process a user question, then retrieve relevant documents and finally extract some possible answers out of these documents using various named-entity recognition processes. In our study, we try to answer complex genomics questions, which can be adequately answered only using Gene Ontology (GO) concepts. Such complex answers cannot be found using state-of-the-art dictionary- and redundancy-based QA engines. We compare the effectiveness of two dictionary-based classifiers for extracting correct GO answers from a large set of 100 retrieved abstracts per question. In the same way, we also investigate the power of GOCat, a GO supervised classifier. GOCat exploits the GOA database to propose GO concepts that were annotated by curators for similar abstracts. This approach is called deep QA, as it adds an original classification step, and exploits curated biological data to infer answers, which are not explicitly mentioned in the retrieved documents. We show that for complex answers such as protein functional descriptions, the redundancy phenomenon has a limited effect. Similarly usual dictionary-based approaches are relatively ineffective. In contrast, we demonstrate how existing curated data, beyond information extraction, can be exploited by a supervised classifier, such as GOCat, to massively improve both the quantity and the quality of the answers with a +100% improvement for both recall and precision. Database URL: http://eagl.unige.ch/DeepQA4PA/. PMID:26384372

  9. SmashCommunity: A metagenomic annotation and analysis tool

    DEFF Research Database (Denmark)

    Arumugam, Manimozhiyan; Harrington, Eoghan D; Foerstner, Konrad U;

    2010-01-01

    SUMMARY: SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It supports state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction. It provides tools to estimate...... the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple metagenomes and to produce intuitive visual representations of such analyses. AVAILABILITY: SmashCommunity is freely available at http://www.bork.embl.de/software/smash CONTACT: bork@embl.de....

  10. An Annotated Dataset of 14 Meat Images

    DEFF Research Database (Denmark)

    Stegmann, Mikkel Bille

    2002-01-01

    This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given.......This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given....

  11. Software for computing and annotating genomic ranges.

    Directory of Open Access Journals (Sweden)

    Michael Lawrence

    Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  12. Knowledge-based annotation of small molecule binding sites in proteins

    Directory of Open Access Journals (Sweden)

    Panchenko Anna R

    2010-07-01

    Full Text Available Abstract Background The study of protein-small molecule interactions is vital for understanding protein function and for practical applications in drug discovery. To benefit from the rapidly increasing structural data, it is essential to improve the tools that enable large scale binding site prediction with greater emphasis on their biological validity. Results We have developed a new method for the annotation of protein-small molecule binding sites, using inference by homology, which allows us to extend annotation onto protein sequences without experimental data available. To ensure biological relevance of binding sites, our method clusters similar binding sites found in homologous protein structures based on their sequence and structure conservation. Binding sites which appear evolutionarily conserved among non-redundant sets of homologous proteins are given higher priority. After binding sites are clustered, position specific score matrices (PSSMs are constructed from the corresponding binding site alignments. Together with other measures, the PSSMs are subsequently used to rank binding sites to assess how well they match the query and to better gauge their biological relevance. The method also facilitates a succinct and informative representation of observed and inferred binding sites from homologs with known three-dimensional structures, thereby providing the means to analyze conservation and diversity of binding modes. Furthermore, the chemical properties of small molecules bound to the inferred binding sites can be used as a starting point in small molecule virtual screening. The method was validated by comparison to other binding site prediction methods and to a collection of manually curated binding site annotations. We show that our method achieves a sensitivity of 72% at predicting biologically relevant binding sites and can accurately discriminate those sites that bind biological small molecules from non-biological ones. Conclusions

  13. Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

    Energy Technology Data Exchange (ETDEWEB)

    Ansong, Charles; Tolic, Nikola; Purvine, Samuel O.; Porwollik, Steffen; Jones, Marcus B.; Yoon, Hyunjin; Payne, Samuel H.; Martin, Jessica L.; Burnet, Meagan C.; Monroe, Matthew E.; Venepally, Pratap; Smith, Richard D.; Peterson, Scott; Heffron, Fred; Mcclelland, Michael; Adkins, Joshua N.

    2011-08-25

    Complete and accurate genome annotation is crucial for comprehensive and systematic studies of biological systems. For example systems biology-oriented genome scale modeling efforts greatly benefit from accurate annotation of protein-coding genes to develop proper functioning models. However, determining protein-coding genes for most new genomes is almost completely performed by inference, using computational predictions with significant documented error rates (> 15%). Furthermore, gene prediction programs provide no information on biologically important post-translational processing events critical for protein function. With the ability to directly measure peptides arising from expressed proteins, mass spectrometry-based proteomics approaches can be used to augment and verify coding regions of a genomic sequence and importantly detect post-translational processing events. In this study we utilized “shotgun” proteomics to guide accurate primary genome annotation of the bacterial pathogen Salmonella Typhimurium 14028 to facilitate a systems-level understanding of Salmonella biology. The data provides protein-level experimental confirmation for 44% of predicted protein-coding genes, suggests revisions to 48 genes assigned incorrect translational start sites, and uncovers 13 non-annotated genes missed by gene prediction programs. We also present a comprehensive analysis of post-translational processing events in Salmonella, revealing a wide range of complex chemical modifications (70 distinct modifications) and confirming more than 130 signal peptide and N-terminal methionine cleavage events in Salmonella. This study highlights several ways in which proteomics data applied during the primary stages of annotation can improve the quality of genome annotations, especially with regards to the annotation of mature protein products.

  14. Assessment of the left ventricular function with the nuclear stethoscope

    International Nuclear Information System (INIS)

    The evaluation of the left ventricular function with the Nuclear Stethoscope was performed on 27 patients with heart diseases. The reproducibility of the measurements was good. Repetitions of EF, ER and EDV estimations yielded errors of 2.63%, 1.45% and 0.31%. The comparison with the results of camera ventriculography showed a good agreement of EF, contraction velocity parameters and relaxation velocity parameters, with a cor. coeff. of greater or equal to 0.750. A particularly high correlation was found between the NS EF and NS ER (r = 0.968). It was concluded that the Nuclear Stethoscope provides a reliable evaluation of left ventricular function. (orig.)

  15. Assessment of the left ventricular function with the nuclear stethoscope

    Energy Technology Data Exchange (ETDEWEB)

    Tarkowska, A.; Adam, W.E.; Bitter, F.

    1980-08-01

    The evaluation of the left ventricular function with the Nuclear Stethoscope was performed on 27 patients with heart diseases. The reproducibility of the measurements was good. Repetitions of EF, ER and EDV estimations yielded errors of 2.63%, 1.45% and 0.31%. The comparison with the results of camera ventriculography showed a good agreement of EF, contraction velocity parameters and relaxation velocity parameters, with a cor. coeff. of greater or equal to 0.750. A particularly high correlation was found between the NS EF and NS ER (r = 0.968). It was concluded that the Nuclear Stethoscope provides a reliable evaluation of left ventricular function.

  16. Assessment of right ventricular systolic function by tissue Doppler echocardiography

    DEFF Research Database (Denmark)

    Kjærgaard, Jesper

    2012-01-01

    right ventricular hemodynamics: pulmonary embolism, Arrhythmogenic right ventricular cardiomyopathy and pulmonary regurgitation, the latter in an animal model. The conclusions of the thesis are: Color tissue Doppler echocardiography accurately measures velocities, SR and strain in vitro. No systematic......This thesis summarizes a series of studies performed in order to assess the clinical usefulness of a novel echocardiographic technology that allows non-invasive assessment of regional right ventricular myocardial velocities and deformation: tissue Doppler echocardiography. While the technology is a...... promising tool for improving our understanding of right ventricular hemodynamics, several aspects of the technology must be evaluated. The accuracy and reproducibility of the technology is evaluated in vitro, and normal values, impact of changes in loading of the right ventricle, response to exercise and...

  17. Ecological risk assessment in the function of environmental protection

    Directory of Open Access Journals (Sweden)

    Saša T. Bakrač

    2012-10-01

    Full Text Available This paper proposes an appropriate methodology for ecological risk assessment. The methodology has been applied in the region of Boka Kotorska Bay (Bay, Montenegro. The emphasis of the research is on the analysis of the impact of various stressors on the ecological components of Bay. The consequences of that impact can be seen in an increased level of eutrophication of water environment, mostly through the influence of nitrogen and its compounds. The actual research at/about the region of Boka Kotorska Bay was performed in the period of 2008. The study emphasized the importance of the acquisition, processing and analysis of various ecologically related data for more efficient monitoring and management of the environment. The suggested methodology of the ecological risk assessment is, therefore, a remarkable scientific and expert contribution in the area of environmental protection in our country and in general.

  18. A purely functional combinator language for software quality assessment

    OpenAIRE

    Martins, Pedro; Fernandes, João Paulo; Saraiva, João

    2012-01-01

    Quality assessment of open source software is becoming an important and active research area. One of the reasons for this recent interest is the consequence of Internet popularity. Nowadays, programming also involves looking for the large set of open source libraries and tools that may be reused when developing our software applications. In order to reuse such open source software artifacts, programmers not only need the guarantee that the reused artifact is certified, but a...

  19. Assessment of Physical Functioning: A Conceptual Model Encompassing Environmental Factors and Individual Compensation Strategies

    OpenAIRE

    Tomey, Kristin M.; Sowers, MaryFran R.

    2009-01-01

    Commonly studied physical functions include activities such as walking and climbing stairs. Despite the acknowledged role of environmental factors and behavioral strategies to compensate for reduced performance capacity or environmental barriers in characterizing physical functioning, most assessments do not take these factors into account. This article presents a new conceptual model for assessment of relevant physical functioning while accounting for habitual environmental factors and compe...

  20. Assessment of organ function with digital subtraction angiography

    International Nuclear Information System (INIS)

    In the Vandebilt Radiological Sciences laboratories and the Center for Medical Imaging Research (CMIR), the authors have used digital subtraction techniques with intravenous injection of contrast media to investigate the methods by which DSA could be used to evaluate both organ anatomy and function. In this work they present some of their data from three organ systems: kidneys, lungs, and heart

  1. Radionuclide assessment of renal function in the transplanted kidney

    International Nuclear Information System (INIS)

    The ability of radionuclide renal function to detect rejection and to presume the prognosis of the transplanted kidney was evaluated in 70 patients. Effective renal plasma flow (ERPF), excretory index (EI) and perfusion index (PI) were examined by I-123 OIH and Tc-99 m DTPA. Numbers of the study in various status were as follows; 51 studies in good function, 43 in acute rejection and 18 in chronic rejection. Significant reduction in ERPF and EI and increase of PI were observed in the acute rejection (p<0.01). In the chronic rejection, there was a progressive decrease of ERPF (p<0.01). The patients were divided into two groups: group A; 46 patients with good function more than 9 months after transplantation and group B; 20 patients of whom recurrence of hemodialysis or nephectomy was done. In living transplantation, ERPF of group B at the first week after transplantation was remarkably lower than group A (p<0.05). In cadaveric transplantation, ERPF of group B at the sixth week was lower than that of group B (p<0.05). This study indicates that serial measurements of renal function by radionuclide methods may provide the state of rejection and prognosis of the transplanted kidney. (author)

  2. Capital yields assessment trough cross section production function

    Czech Academy of Sciences Publication Activity Database

    Kodera, Jan; Pánková, V.

    2001-01-01

    Roč. 8, č. 14 (2001), s. 79-87. ISSN 1212-074X R&D Projects: GA ČR GA402/00/0439 Institutional research plan: AV0Z1075907 Keywords : yield of capital * cross-section production function * maximisation of profit Subject RIV: AH - Economics

  3. LSCI in Functional Behavior Assessment and Positive Behavioral Intervention.

    Science.gov (United States)

    Marston, John R.

    2001-01-01

    The Individuals with Disabilities Education Act (IDEA) Amendments of 1997 mandated a shift from reactive strategies toward proactive interventions with students who experience both disability and behavioral challenges. The author describes how the methodology of Life Space Crisis Intervention can provide a source of data for functional assessment…

  4. Determinants and Functions of Standardized Assessment Use Among School Mental Health Clinicians: A Mixed Methods Evaluation.

    Science.gov (United States)

    Lyon, Aaron R; Ludwig, Kristy; Wasse, Jessica Knaster; Bergstrom, Alex; Hendrix, Ethan; McCauley, Elizabeth

    2016-01-01

    The current study evaluated why and how school mental health clinicians use standardized assessment tools in their work with youth and families. Quantitative and qualitative (focus group) data were collected prior to and following a training and consultation sequence as part of a trial program to assess school clinician's (n = 15) experiences administering standardized tools to youth on their caseloads (n = 191). Findings indicated that, although assessment use was initially somewhat low, clinicians used measures to conduct initial assessments with the bulk of their caseloads (average = 62.2%) during the implementation period. Clinicians also reported on factors influencing their use of assessments at the client, provider, and system levels; perceived functions of assessment; student responses to assessment use; and use of additional sources of clinically-relevant information (primarily educational data) for the purposes of assessment and progress monitoring. Implications for the contextual appropriateness of standardized assessment and training in assessment tools are discussed. PMID:25875325

  5. Protein annotation in the era of personal genomics

    DEFF Research Database (Denmark)

    Holberg Blicher, Thomas; Gupta, Ramneek; Wesolowska, Agata;

    2010-01-01

    the differences between many individuals of the same species-humans in particular-the focus needs be on the functional impact of individual residue variation. To fulfil the promises of personal genomics, we need to start asking not only what is in a genome but also how millions of small differences......Protein annotation provides a condensed and systematic view on the function of individual proteins. It has traditionally dealt with sorting proteins into functional categories, which for example has proven to be successful for the comparison of different species. However, if we are to understand...... between individual genomes affect protein function and in turn human health. Copyright © 2010 Elsevier Ltd. All rights reserved....

  6. Software tool for researching annotations of proteins: open-source protein annotation software with data visualization.

    Science.gov (United States)

    Bhatia, Vivek N; Perlman, David H; Costello, Catherine E; McComb, Mark E

    2009-12-01

    In order that biological meaning may be derived and testable hypotheses may be built from proteomics experiments, assignments of proteins identified by mass spectrometry or other techniques must be supplemented with additional notation, such as information on known protein functions, protein-protein interactions, or biological pathway associations. Collecting, organizing, and interpreting this data often requires the input of experts in the biological field of study, in addition to the time-consuming search for and compilation of information from online protein databases. Furthermore, visualizing this bulk of information can be challenging due to the limited availability of easy-to-use and freely available tools for this process. In response to these constraints, we have undertaken the design of software to automate annotation and visualization of proteomics data in order to accelerate the pace of research. Here we present the Software Tool for Researching Annotations of Proteins (STRAP), a user-friendly, open-source C# application. STRAP automatically obtains gene ontology (GO) terms associated with proteins in a proteomics results ID list using the freely accessible UniProtKB and EBI GOA databases. Summarized in an easy-to-navigate tabular format, STRAP results include meta-information on the protein in addition to complementary GO terminology. Additionally, this information can be edited by the user so that in-house expertise on particular proteins may be integrated into the larger data set. STRAP provides a sortable tabular view for all terms, as well as graphical representations of GO-term association data in pie charts (biological process, cellular component, and molecular function) and bar charts (cross comparison of sample sets) to aid in the interpretation of large data sets and differential analyses experiments. Furthermore, proteins of interest may be exported as a unique FASTA-formatted file to allow for customizable re-searching of mass spectrometry

  7. Predicting Emotions in Facial Expressions from the Annotations in Naturally Occurring First Encounters

    DEFF Research Database (Denmark)

    Navarretta, Costanza

    2014-01-01

    tokens. We also investigate the relation between emotions and the communicative functions of facial expressions. Both emotion labels and their values in a three dimensional space are identified. The three dimensions are Pleasure, Arousal and Dominance. The results of our experiments indicate that the......This paper deals with the automatic identification of emotions from the manual annotations of the shape and functions of facial expressions in a Danish corpus of video recorded naturally occurring first encounters. More specifically, a support vector classified is trained on the corpus annotations...... to identify emotions in facial expressions. In the classification experiments, we test to what extent emotions expressed in naturally-occurring conversations can be identified automatically by a classifier trained on the manual annotations of the shape of facial expressions and co-occurring speech...

  8. Assessment of right ventricular systolic function by tissue Doppler echocardiography

    DEFF Research Database (Denmark)

    Kjærgaard, Jesper

    2012-01-01

    pulmonary hypertension and exercise in normal individuals. Phosphodiestares-5 inhibition by sildenafil may predominantly be effective during hypoxia in resting conditions, and may improve the blunted response in RV contractility seen with exercise in hypoxia [VII]. Reduced RV free wall deformation can be...... promising tool for improving our understanding of right ventricular hemodynamics, several aspects of the technology must be evaluated. The accuracy and reproducibility of the technology is evaluated in vitro, and normal values, impact of changes in loading of the right ventricle, response to exercise and...... not add to the information gained from other quantitative echocardiographic measures of LV and RV function and pressure [VI]. Changes in tissue Doppler based measures of RV systolic function can be used to monitor the effect of selective vasodilation by phosphodiestares-5 inhibition in hypoxic...

  9. Assessment of ventricular function by radionuclide ventriculography in hyperthyroidism

    International Nuclear Information System (INIS)

    Left ventricular(LV) and right ventricular(RV) function were determined using radionuclide ventriculography in 50 patients with hyperthyroidism. LVEF, LVPFR, SV of the hyperthyroidism group were decreased in comparison with the normal group (P<0.01), whereas CO of the hyperthyroidism patients were higher than that of normal (P<0.01). Except LVPER, the LVEF, SV had significant difference between two groups. Compared to normal group, RVEF, RVPER, RVPFR were also decreased (P<0.01). Besides 30 cases of the hyperthyroidism were examined by impedance cardiogram (ICG) and impedance pulmonary rheogram (IPR), all showed closely correlation with the parameters determined by ventriculography. There was the involvement of right ventricular function insufficiency, especially in ejection phase. When compared with pre-therapy, pos-therapy cases showed significant improvement in EF, PER, PFR of left and right ventricular

  10. Functional assessment of high level ice-dancing.

    Science.gov (United States)

    Roi, G S; Mevio, M; Occhi, G; Gemma, S; Facchini, R

    1989-06-01

    In these studies the anthropometric characteristics and some functional characteristics of ice-dancers are analysed. It has been shown that the maximum oxygen uptake is similar to that of classical ballet dancers. Tests effected on the ice revealed a high production of lactate, the involvement of the anaerobic metabolism, and high heart rates. It is concluded that the high production of lactate during the free dance on ice is due to the isometric muscular contraction, necessary to maintain certain positions. PMID:2593659

  11. Stability Assessment of Flutter - Type Vibration Using Lyapunov Function

    Czech Academy of Sciences Publication Activity Database

    Náprstek, Jiří

    Žďár nad Sázavou : ŽĎAS, 2000 - (Náprstek, J.; Minster, J.), s. 17-24 ISBN 80-86246-03-5. [Engineering Mechanics 2000. Svratka (CZ), 15.05.2000-18.05.2000] R&D Projects: GA ČR GA103/99/0122 Keywords : bending - torsional flutter * nonlinear differential equations * Lyapunov function Subject RIV: JM - Building Engineering

  12. Assessment of pancreatic islet cell function and survival

    OpenAIRE

    Köhler, Martin

    2015-01-01

    Function and survival of pancreatic islet insulin-producing beta-cells (β-cells) and glucagonproducing alpha-cells (α-cells) were studied, and methods for this purpose were developed or refined. Dynamic control of glucose metabolism is essential for β-cell stimulus-secretion coupling. ATP is an important metabolic parameter and therefore we set up a technique to monitor dynamic changes of ATP in insulin-producing cells using luciferase bioluminescence at the level of single...

  13. Assessing dynamical correlations between functional and structural brain connectivity

    OpenAIRE

    Liegeois, Raphaël; Ziegler, Erik; Phillips, Christophe; Gomez, Francisco; Soddu, Andrea; Laureys, Steven; Sepulchre, Rodolphe

    2014-01-01

    The link between resting­‐state functional connectivity (FC), measured by the correlations of the fMRI BOLD time courses, and structural connectivity (SC) has been repeatedly investigated recently. Meanwhile, the importance of considering the dynamics of neuronal processes has also been highlighted. In this work we show how the classical static (i.e. considered as constant) relationship between SC and FC could be enriched when the FC dynamics are taken into account. We use a sliding window...

  14. Functional ability in a population: normative survey data and reliability for the ICF based Norwegian Function Assessment Scale

    Directory of Open Access Journals (Sweden)

    Natvig Bård

    2007-10-01

    Full Text Available Abstract Background The increasing focus on functional ability assessments in relation to sickness absence necessitates the measurement of population functional levels. This study assessed the reliability of the Norwegian Function Assessment Scale (NFAS and presents normative population data. Methods All inhabitants in seven birth cohorts in Ullensaker municipality in 2004 were approached by means of a postal questionnaire. The NFAS was included as part of The Ullensaker Study 2004. The instrument comprises 39 items derived from the activities/participation component in the International Classification for Functioning, Disabilities and Health (ICF. Based on the results of principal component analysis, these items comprise seven domains. Non-parametric tests for independent samples were used to compare subgroups. Internal consistency was assessed by Cronbach's alpha. Two-week test-retest reliability was assessed by total proportions of agreement, weighted kappa, and intraclass correlation coefficient (ICC. Results The response rate was 54% (1620 persons and 75.4% (101 persons for the retest. Items had low levels of missing data. Test-retest reliability was acceptable with high proportions of absolute agreement; kappa and ICC values ranged from 0.38 to 0.83 and 0.79 to 0.83, respectively. No difficulty on all 39 functional activities was reported by 33.1% of respondents. Females, older persons and persons with lower levels of education reported more functional problems than their respective counterparts (p Conclusion This study presents population based normative data on functional ability, as measured by the NFAS. These data will serve as basis for the development of national population norms and are necessary for score interpretation. Data quality and test-retest reliability of the NFAS were acceptable.

  15. Annotation Method (AM): SE22_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ether with predicted molecular formulae and putative structures, were provided as metabolite annotations. Comparison with public data...bases was performed. A grading system was introduced to describe the evidence supporting the annotations. ...

  16. Computer systems for annotation of single molecule fragments

    Science.gov (United States)

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  17. Drought impact functions as intermediate step towards drought damage assessment

    Science.gov (United States)

    Bachmair, Sophie; Svensson, Cecilia; Prosdocimi, Ilaria; Hannaford, Jamie; Helm Smith, Kelly; Svoboda, Mark; Stahl, Kerstin

    2016-04-01

    While damage or vulnerability functions for floods and seismic hazards have gained considerable attention, there is comparably little knowledge on drought damage or loss. On the one hand this is due to the complexity of the drought hazard affecting different domains of the hydrological cycle and different sectors of human activity. Hence, a single hazard indicator is likely not able to fully capture this multifaceted hazard. On the other hand, drought impacts are often non-structural and hard to quantify or monetize. Examples are impaired navigability of streams, restrictions on domestic water use, reduced hydropower production, reduced tree growth, and irreversible deterioration/loss of wetlands. Apart from reduced crop yield, data about drought damage or loss with adequate spatial and temporal resolution is scarce, making the development of drought damage functions difficult. As an intermediate step towards drought damage functions we exploit text-based reports on drought impacts from the European Drought Impact report Inventory and the US Drought Impact Reporter to derive surrogate information for drought damage or loss. First, text-based information on drought impacts is converted into timeseries of absence versus presence of impacts, or number of impact occurrences. Second, meaningful hydro-meteorological indicators characterizing drought intensity are identified. Third, different statistical models are tested as link functions relating drought hazard indicators with drought impacts: 1) logistic regression for drought impacts coded as binary response variable; and 2) mixture/hurdle models (zero-inflated/zero-altered negative binomial regression) and an ensemble regression tree approach for modeling the number of drought impact occurrences. Testing the predictability of (number of) drought impact occurrences based on cross-validation revealed a good agreement between observed and modeled (number of) impacts for regions at the scale of federal states or

  18. Multicultural Education: A Selected Annotated Bibliography.

    Science.gov (United States)

    Mathieson, Moira B.; Tatis, Rita M.

    This annotated bibliography lists 70 documents dealing with cultural differences and cross-cultural educational problems on the elementary-secondary-collegiate level and does not include material on the economically disadvantaged or inner city problems as such. The first section reports citations drawn from Research in Education and the…

  19. Semantic Annotation to Support Automatic Taxonomy Classification

    DEFF Research Database (Denmark)

    Kim, Sanghee; Ahmed, Saeema; Wallace, Ken

    2006-01-01

    This paper presents a new taxonomy classification method that generates classification criteria from a small number of important sentences identified through semantic annotations, e.g. cause-effect. Rhetorical Structure Theory (RST) is used to discover the semantics (Mann et al. 1988). Specifically...

  20. Reflective Annotations: On Becoming a Scholar

    Science.gov (United States)

    Alexander, Mark; Taylor, Caroline; Greenberger, Scott; Watts, Margie; Balch, Riann

    2012-01-01

    This article presents the authors' reflective annotations on becoming a scholar. This paper begins with a discussion on socialization for teaching, followed by a discussion on socialization for service and sense of belonging. Then, it describes how the doctoral process evolves. Finally, it talks about adult learners who pursue doctoral education.

  1. Annotated Bibliography of EDGE2D Use

    International Nuclear Information System (INIS)

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables

  2. Studies of Scientific Disciplines. An Annotated Bibliography.

    Science.gov (United States)

    Weisz, Diane; Kruytbosch, Carlos

    Provided in this bibliography are annotated lists of social studies of science literature, arranged alphabetically by author in 13 disciplinary areas. These areas include astronomy; general biology; biochemistry and molecular biology; biomedicine; chemistry; earth and space sciences; economics; engineering; mathematics; physics; political science;…

  3. Food Habits: A Selected Annotated Bibliography

    Science.gov (United States)

    Wilson, Christine S.

    1973-01-01

    This is a selective annotated bibliography of material on food habits and factors affecting them, published during the period 1928-1972. References are mainly in English, although a few in European languages are included, and represent information primarily from scholarly and professional journals. Entries are organized by subject and author. (LK)

  4. An Annotated Publications List on Homelessness.

    Science.gov (United States)

    Tutunjian, Beth Ann

    This annotated publications list on homelessness contains citations for 19 publications, most of which deal with problems of alcohol or drug abuse among homeless persons. Citations are listed alphabetically by author and cover the topics of homelessness and alcoholism, drug abuse, public policy, research methodologies, mental illness, alcohol- and…

  5. SNAD: sequence name annotation-based designer

    Directory of Open Access Journals (Sweden)

    Gorbalenya Alexander E

    2009-08-01

    Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

  6. Law in the Classroom. An Annotated Bibliography.

    Science.gov (United States)

    Carsello, Carmen J.

    An annotated bibliography of some 236 items relevant to discussions of school law, from novels to government-published law and court reports. The material is listed alphabetically by author within each document type (books; periodicals; documents; monographs and special reports; law reports; digests; newsletters; dictionaries, directories, and…

  7. Organizational and Intercultural Communication: An Annotated Bibliography.

    Science.gov (United States)

    Constantinides, Helen; St. Amant, Kirk; Kampf, Connie

    2001-01-01

    Presents a 27-item annotated bibliography that overviews theories of organization from the viewpoint of culture, using five themes of organizational research as a framework. Notes that each section introduces specific theories of international, intercultural, or organizational communication, building upon them through a series of related articles,…

  8. Teleconferencing, an annotated bibliography, volume 3

    Science.gov (United States)

    Shervis, K.

    1971-01-01

    In this annotated and indexed listing of works on teleconferencing, emphasis has been placed upon teleconferencing as real-time, two way audio communication with or without visual aids. However, works on the use of television in two-way or multiway nets, data transmission, regional communications networks and on telecommunications in general are also included.

  9. Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.

    2006-06-06

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  10. Automating Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.

    2006-01-22

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  11. Kwanzaa: A Selective Annotated Bibliography for Teachers.

    Science.gov (United States)

    Dupree, Sandra K., Comp.; Gillum, Holly A., Comp.

    This annotated bibliography about Kwanzaa, an end-of-the-year holiday that emphasizes an appreciation for the culture of African Americans, aims to provide ready access to information for classroom teachers. Noting that Kwanzaa (celebrated from December 26 to January 1) is an important cultural event, the bibliography states that the festival…

  12. Skin Cancer Education Materials: Selected Annotations.

    Science.gov (United States)

    National Cancer Inst. (NIH), Bethesda, MD.

    This annotated bibliography presents 85 entries on a variety of approaches to cancer education. The entries are grouped under three broad headings, two of which contain smaller sub-divisions. The first heading, Public Education, contains prevention and general information, and non-print materials. The second heading, Professional Education,…

  13. College Students in Transition: An Annotated Bibliography

    Science.gov (United States)

    Foote, Stephanie M., Ed.; Hinkle, Sara M., Ed.; Kranzow, Jeannine, Ed.; Pistilli, Matthew D., Ed.; Miles, LaTonya Rease, Ed.; Simmons, Jannell G., Ed.

    2013-01-01

    The transition from high school to college is an important milestone, but it is only one of many steps in the journey through higher education. This volume is an annotated bibliography of the emerging literature examining the many other transitions students make beyond the first year, including the sophomore year, the transfer experience, and the…

  14. Annotated Bibliography of EDGE2D Use

    Energy Technology Data Exchange (ETDEWEB)

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  15. Assessment on the Ecosystem Service Functions of Nansi Lake in China

    Directory of Open Access Journals (Sweden)

    Zhongyu Wang

    2016-03-01

    Full Text Available The assessment of ecosystem service functions is one of the focused area in modern ecological and environmental research. As a typical shallow macrophytic lake in China, Nansi Lake is selected as the study area. Based the indicator system and assessment models established in this research, the ecosystem service functions of Nansi Lake are assessed. The results show that the ecosystem service function of drinking water source area/aquatic product supply/ecological habitat/entertainment and landscape/ water purification function of the lakeside zone for Nansi Lake is assessed as medium (2.2/good (3.5/medium (3/medium (2.55/medium (3, and the overall ecosystem service function of Nansi Lake can be considered as ―Medium‖. The eutrophication control and ecological restoration of lakeside wetland need to be enhanced in the future.

  16. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    Energy Technology Data Exchange (ETDEWEB)

    Grossman, Arthur R

    2007-04-13

    Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual

  17. Using Microbial Genome Annotation as a Foundation for Collaborative Student Research

    Science.gov (United States)

    Reed, Kelynne E.; Richardson, John M.

    2013-01-01

    We used the Integrated Microbial Genomes Annotation Collaboration Toolkit as a framework to incorporate microbial genomics research into a microbiology and biochemistry course in a way that promoted student learning of bioinformatics and research skills and emphasized teamwork and collaboration as evidenced through multiple assessment mechanisms.…

  18. Inter and intra-observer variability of time-lapse annotations

    DEFF Research Database (Denmark)

    Sundvall Germeys, Linda Karin M; Ingerslev, Hans Jakob; Knudsen, Ulla Breth;

    -lapse annotations. This provides the basis for further investigation of embryo assessment and selection by time-lapse imaging in prospective trials. Study funding/competing interest(s): Research at the Fertility Clinic was funded by an unrestricted grant from Ferring and MSD. The authors have no competing interests...

  19. Proteins of Unknown Function in the Protein Data Bank (PDB: An Inventory of True Uncharacterized Proteins and Computational Tools for Their Analysis

    Directory of Open Access Journals (Sweden)

    Nurul Nadzirin

    2012-10-01

    Full Text Available Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB. Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files that were categorized under “unknown function” are true examples of proteins of unknown function at this point in time. The remainder 1465 entries also annotated as such appear to be able to have their annotations re-assessed, based on the availability of direct functional characterization experiments for the protein itself, or for homologous sequences or structures thus enabling computational function inference.

  20. Classes d'annotation pour l'annotation sémantique

    OpenAIRE

    Tenier, Sylvain; Toussaint, Yannick

    2007-01-01

    Les classes d'annotation constituent une méthode d'annotation sémantique de pages web fondée sur les logiques de descriptions. Elles désignent l'annotation à la fois comme processus et comme résultat de ce processus. Cette approche est motivée par un parallèle entre la structure d'une page web et la sémantique qui lui est associée. Ces deux dimensions de structure et de sémantique sont formalisées en OWL-DL, un langage fondé sur les logiques de descriptions. L'annotation est ensuite traitée c...

  1. Ontology Learning and Semantic Annotation: a Necessary Symbiosis

    OpenAIRE

    Giovannetti, Emiliano; Marchi, Simone; Montemagni, Simonetta; Bartolini, Roberto

    2008-01-01

    Semantic annotation of text requires the dynamic merging of linguistically structured information and a ?world model?, usually represented as a domain-specific ontology. On the other hand, the process of engineering a domain-ontology through semi-automatic ontology learning system requires the availability of a considerable amount of semantically annotated documents. Facing this bootstrapping paradox requires an incremental process of annotation-acquisition-annotation, whereby domain-specific...

  2. A unified representation for morphological, syntactic, semantic, and referential annotations

    OpenAIRE

    Hinrichs, Erhard W.; Kübler, Sandra; Naumann, Karin

    2008-01-01

    This paper reports on the SYN-RA (SYNtax-based Reference Annotation) project, an on-going project of annotating German newspaper texts with referential relations. The project has developed an inventory of anaphoric and coreference relations for German in the context of a unified, XML-based annotation scheme for combining morphological, syntactic, semantic, and anaphoric information. The paper discusses how this unified annotation scheme relates to other formats currently discussed in the lite...

  3. AnnaBot: A Static Verifier for Java Annotation Usage

    OpenAIRE

    Ian Darwin

    2010-01-01

    This paper describes AnnaBot, one of the first tools to verify correct use of Annotation-based metadata in the Java programming language. These Annotations are a standard Java 5 mechanism used to attach metadata to types, methods, or fields without using an external configuration file. A binary representation of the Annotation becomes part of the compiled “.class” file, for inspection by another component or library at runtime. Java Annotations were introduced into the Java language in 2004 a...

  4. Assessment of results of functional units department of marketing

    Directory of Open Access Journals (Sweden)

    D.V. Raiko

    2011-12-01

    Full Text Available Improved methodological support of the evaluation of heads of departments of marketing, the distinction which is urahuvanni functional orientation of each department, the application of expert methods using universal scale Harinhtona for the quantitative determination of performance in two components: the results of the work and qualities of leaders (business, professional and personal. The total score corresponds to the head of qualitative features of the low to very high, which allows to make personnel decisions for the promotion of leaders and motivating material as well as identify priority areas to improve the results of their work and improving the professional, business, personal qualities.

  5. Assessment of Time Functions for Piles Driven in Clay

    DEFF Research Database (Denmark)

    Augustesen, Anders; Andersen, Lars; Sørensen, Carsten Steen

    The vertical bearing capacity of piles situated in clay is studied with regard to the long-term set-up. A statistical analysis is carried out on the basis of data from numerous static loading tests. The database covers a wide range of both soil and pile properties, which ensures a general...... alternative models. In the first of these models, the rate of set-up is independent of the soil properties, whereas the second function depends on the undrained shear strength. Based on the available data, there is no statistical evidence that the magnitude of set-up depends on the properties of the soil...

  6. Scintigraphic Assessment of Hepatobiliary Functions in Healthy Adult Dogs

    OpenAIRE

    SARIERLER, Murat

    2005-01-01

    Our objective was to investigate hepatobiliary functions in healthy dogs using 99mTc-mebrofenin hepatobiliary scintigraphy (HBS): 200 µCi/kg 99mTc-mebrofenin was injected intravenously into 12 healthy adult dogs. One-hour dynamic images and 2, 4 and 24 h static images were obtained. HBS was evaluated for 7 variables. Cardiac washout occurred within 3 min in all dogs. A photophenic area in the region of the gall bladder was seen in 3.03 ± 0.21 min. However, bile ducts were not identified as se...

  7. Assessing the functions and dimensions of visualizations in foresight

    DEFF Research Database (Denmark)

    Müller, Adrian W.; Schwarz, Jan Oliver

    trend- and futures-researchers, designers and innovation strategist, was to assess how visualization of foresight results can be applied, reflecting on different purposes and context. The study based insights are then applied to a comprehensive foresight project case in context of electromobility in......Visualizations have become a vital part of many foresight activities. In the realm of creating scenarios it is stressed to visualize the different scenario as alternative pictures of the future. Corporation such as Siemens for example have developed an own approach called “pictures of the future......” to disseminate their ideas on the future of a variety of technologies. And others have made the argument that through visualizing trends in their early stage, these weak signals of change can be injected into an organization. While visualization of foresight results is considered to be very relevant...

  8. Image quality influences the assessment of left ventricular function

    DEFF Research Database (Denmark)

    Grossgasteiger, Manuel; Hien, Maximilian D; Graser, Bastian;

    2014-01-01

    divided by the total endocardial border. These ratings were used to generate groups of poor (0%-40%), fair (41%-70%), and good (71%-100%) image quality. The ejection fraction (EF), end-diastolic volume, and end-systolic volume were analyzed by the Simpson method of disks (biplane and monoplane), eyeball......, with the Teichholz EF found to be most accurate with poor (r = 0.928) in contrast to good (r = 0.699) image quality. Conclusions: With good image quality, the Simpson biplane method is the most accurate 2-dimensional method for assessing the left ventricular EF. Short-axis view methods, especially the...... method, Teichholz method, and speckle-tracking method. Furthermore, the fractional area change was determined. Each correlation with real-time 3DE was evaluated. Results: Correlations of the EF and volumes, respectively, as determined by long-axis view methods increased with improving image quality: the...

  9. Assessment of subjective and objective cognitive function in bipolar disorder: Correlations, predictors and the relation to psychosocial function.

    Science.gov (United States)

    Demant, Kirsa M; Vinberg, Maj; Kessing, Lars V; Miskowiak, Kamilla W

    2015-09-30

    Cognitive dysfunction is prevalent in bipolar disorder (BD). However, the evidence regarding the association between subjective cognitive complaints, objective cognitive performance and psychosocial function is sparse and inconsistent. Seventy seven patients with bipolar disorder who presented cognitive complaints underwent assessment of objective and subjective cognitive function and psychosocial functioning as part of their participation in two clinical trials. We investigated the association between global and domain-specific objective and subjective cognitive function and between global cognitive function and psychosocial function. We also identified clinical variables that predicted objective and subjective cognitive function and psychosocial functioning. There was a correlation between global subjective and objective measures of cognitive dysfunction but not within the individual cognitive domains. However, the correlation was weak, suggesting that cognitive complaints are not an assay of cognition per se. Self-rated psychosocial difficulties were associated with subjective (but not objective) cognitive impairment and both subjective cognitive and psychosocial difficulties were predicted by depressive symptoms. Our findings indicate that adequate assessment of cognition in the clinical treatment of BD and in drug trials targeting cognition requires implementation of not only subjective measures but also of objective neuropsychological tests. PMID:26073281

  10. Automatic annotation of head velocity and acceleration in Anvil

    DEFF Research Database (Denmark)

    Jongejan, Bart

    2012-01-01

    We describe an automatic face tracker plugin for the ANVIL annotation tool. The face tracker produces data for velocity and for acceleration in two dimensions. We compare the annotations generated by the face tracking algorithm with independently made manual annotations for head movements. The...

  11. The Scientific and Historical Value of Annotations on Astronomical Photographic Plates

    CERN Document Server

    Schechner, Sara J

    2016-01-01

    The application of photography to astronomy was a critical step in the development of astrophysics at the end of the nineteenth century. Using custom-built photographic telescopes and objective prisms, astronomers took images of the sky on glass plates during a 100-year period from many observing stations around the globe. After each plate was developed, astronomers and their assistants studied and annotated the plates as they made astrometric, photometric and spectroscopic measurements, counted galaxies, observed stellar variability, tracked meteors, and calculated the ephemerides of asteroids and comets. In this paper, the authors assess the importance of the plate annotations for future scientific, historical, and educational programs. Unfortunately, many of these interesting annotations are now being erased when grime is removed from the plates before they are digitized to make the photometric data available for time-domain astrophysics. To see what professional astronomers and historians think about this...

  12. MOCAT2: a metagenomic assembly, annotation and profiling framework

    Science.gov (United States)

    Kultima, Jens Roat; Coelho, Luis Pedro; Forslund, Kristoffer; Huerta-Cepas, Jaime; Li, Simone S.; Driessen, Marja; Voigt, Anita Yvonne; Zeller, Georg; Sunagawa, Shinichi; Bork, Peer

    2016-01-01

    Summary: MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes. Availability and Implementation: MOCAT2 is implemented in Perl 5 and Python 2.7, designed for 64-bit UNIX systems and offers support for high-performance computer usage via LSF, PBS or SGE queuing systems; source code is freely available under the GPL3 license at http://mocat.embl.de. Contact: bork@embl.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153620

  13. Assessment of left ventricular function by noninvasive methods.

    Science.gov (United States)

    Luisada, A A; Singhal, A; Portaluppi, F

    1985-01-01

    The possibility of evaluating left ventricular function by noninvasive methods is discussed in detail. The methods that are considered are electrocardiograph, phonocardiography, apex cardiography, sphygmography, impedance cardiography, electrokymography, and echocardiography. Following a brief section of 'definitions', each method is described in detail including technical problems, difficulties, and results. The systolic time intervals and the stress tests are briefly discussed. Based on modern experimental studies, the stress test should include both an electro- and a phonocardiogram. In the latter, one would measure the amplitude of the first heart sound as an index of contractility. The conclusion is that combined methods give the best results. They are electrocardiography, phonocardiography, impedance cardiography, and echocardiography. An alternative, dictated by technical problems, is to use at first phonocardiography and impedance plus electrocardiography; then echocardiography plus electrocardiography; and then, if indicated, a stress test might complete the study; the latter should include both an electrocardiogram and a phonocardiogram. PMID:4003144

  14. Rorschach assessment of psychological functioning in sexually abused girls.

    Science.gov (United States)

    Leifer, M; Shapiro, J P; Martone, M W; Kassem, L

    1991-02-01

    We measured psychological functioning in a group of 79 Black females between the ages of 5 and 16 and a comparison group of nonabused girls using the Rorschach. In addition to Exner's (1985) Comprehensive System, the Elizur (1949) Rorschach Content Test Scale (RCT), the Mutuality of Autonomy Scale (MOA; Urist, 1977; Urist & Shill, 1982), and the Barrier and Penetration Scales (Fisher & Cleveland, 1968) were used. Sexually abused girls were found to show more disturbed thinking, to experience a higher level of stress relative to their adaptive abilities, to describe human relationships more negatively, and to show more preoccupation with sexuality than the comparison group. The distress experienced by the victimized children was more related to internal mediating variables then to abuse characteristics. Sexually abused girls who are cognitively and emotionally active also experienced high levels of distress compared to abused girls who are psychologically constricted. PMID:2002437

  15. Intelligent platforms for disease assessment: novel approaches in functional echocardiography.

    Science.gov (United States)

    Sengupta, Partho P

    2013-11-01

    Accelerating trends in the dynamic digital era (from 2004 onward) has resulted in the emergence of novel parametric imaging tools that allow easy and accurate extraction of quantitative information from cardiac images. This review principally attempts to heighten the awareness of newer emerging paradigms that may advance acquisition, visualization and interpretation of the large functional data sets obtained during cardiac ultrasound imaging. Incorporation of innovative cognitive software that allow advanced pattern recognition and disease forecasting will likely transform the human-machine interface and interpretation process to achieve a more efficient and effective work environment. Novel technologies for automation and big data analytics that are already active in other fields need to be rapidly adapted to the health care environment with new academic-industry collaborations to enrich and accelerate the delivery of newer decision making tools for enhancing patient care. PMID:24229773

  16. Assessment of cognitive function in patients with myasthenia gravis

    Directory of Open Access Journals (Sweden)

    Sherifa A Hamed

    2014-12-01

    Full Text Available Aim: During the past decade, there has been an increasing interest in the evaluation of cognitive function in myasthenia gravis (MG, neuromuscular transmission disorder caused by acetylcholine receptor auto-antibodies. However, the results of previous studies on cognition and MG are inconsistent and controversial. This study aimed to evaluate cognition in patients with mild/moderate grades of MG. Methods: This study included 20 patients with MG with a mean age of 28.45 ± 8.89 years and duration of illness of 3.52 ± 1.15 years. Cognition was tested using a sensitive battery of psychometric testing (Mini-mental State Examination [MMSE], Stanford-Binet Intelligence Scale 4 th edition [SBIS] and Wechsler Memory Scale-Revised [WMS-R] and by recording P300 component of event-related potentials (ERPs, a neurophysiological analog for cognitive function. Results: Compared with healthy subjects (n = 20, patients had lower total scores of cognitive testing (MMSE, SBIS and WMS-R (P = 0.001, higher Beck Depression Inventory 2 nd edition scores (P = 0.0001 and prolonged latencies (P = 0.01 and reduced amplitudes (P = 0.001 of P300 component of ERPs. Correlations were identified between total scores of cognitive testing and age (r = -0.470, P = 0.010, duration of illness (r = -0.788, P = 0.001 and depression scores (r = -0.323, P = 0.045. Using linear regression analysis and after controlling for age and depression scores, a significant correlation was identified between total scores of cognitive testing and duration of illness (β = -0.305, P = 0.045. Conclusion: Patients with mild/moderate MG may have cognitive dysfunction. This is important to determine prognosis and managing patients.

  17. Assessment of functional status in children with brain tumors

    International Nuclear Information System (INIS)

    Thirty children treated for brain tumors between 1978 - 1985 at Kurume university hospital were evaluated for alternation in intellectual, emotional, and social function. They were 15 males and 15 females, aged 3 to 16 years, on the averaged 1.7 years after treatment. Twenty-eight children had no neurological deficits and 2 children had slight neurological deficits. It was possible for twenty-eight children to be evaluated for intelligence quotient by Wechsler Intelligence Scale for Children-revised and Tanaka-Binet. The median score and standard deviation of intelligence quotient (IQ) test in children with brain tumors were as follows; verbal IQ: 84 ± 16, performance IQ: 77 ± 20, full scale IQ: 80 ± 20. There children with brain tumors obtained significant low IQ scores than children (t-test, P < 0.01). Twenty-one (72 %) children showed subnormal IQ scores (IQ < 90) and 7 children showed normal IQ scores (IQ ≥ 90). Concerning social and emotional function, twelve children (45.7 %) showed abnormal behaviour. The median scores and standard deviation of IQ scores in cranial irradiated patients were as follows; verbal IQ: 79 ± 13, performance IQ: 71 ± 15, full scale IQ: 71 ± 14. Especially, ten of twelve cranial irradiated patients showed subnormal IQ scores. Also, cranial irradiated patients obtained significant low IQ scores than non-cranial irradiated patients (t-test, P < 0.05). Serial evaluation of three cranial irradiated patients revealed further deterioration without recurrence of tumor and hydrocephalus. The results are discussed to: (1) the effects and mechanism of cranial irradiation on cognitive development: (2) the relationship between cognitive dysfunction and irradiation methods. The effects and mechanism of cranial irradiation on cognitive dysfunction is considered to be not only injury of cortex but also injury of fiber tracts. Also, cognitive dysfunction is apt to be related to age of irradiated patients. (J.P.N.)

  18. Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture

    OpenAIRE

    Ghaffari, Noushin; Sanchez-Flores, Alejandro; Doan, Ryan; Garcia-Orozco, Karina D.; Chen, Patricia L.; Ochoa-Leyva, Adrian; Lopez-Zavala, Alonso A.; Carrasco, J. Salvador; Hong, Chris; Brieba, Luis G.; Rudiño-Piñera, Enrique; Blood, Philip D; Jason E. Sawyer; Charles D Johnson; Dindot, Scott V.

    2014-01-01

    We present a new transcriptome assembly of the Pacific whiteleg shrimp (Litopenaeus vannamei), the species most farmed for human consumption. Its functional annotation, a substantial improvement over previous ones, is provided freely. RNA-Seq with Illumina HiSeq technology was used to analyze samples extracted from shrimp abdominal muscle, hepatopancreas, gills and pleopods. We used the Trinity and Trinotate software suites for transcriptome assembly and annotation, respectively. The quality ...

  19. Modular power system topology assessment using Gaussian potential functions

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Lagos, F.; Joya, G.; Sandoval, F. [Universidad de Malaga, ETSI Telecomunicacion (Spain). Dpto. Tecnologia Electronica; Marin, F.J. [Universidad de Malaga, ETSI Informatica (Spain). Dpto. Electronica

    2003-09-01

    A topology assessment system for power systems using active power measurements as input data is presented. The method is designed to be incorporated into a state estimator working with a bus-branch orientated network model. The system architecture contains two states: (i) the preprocessing state; and (ii) the classification stage. The preprocessing stage transforms each current measurement set to produce a vector in the [0.1]{sup n} space. This stage produces clusters of very similar preprocessing output vectors for each grid topology. The classification stage consists in a layer of Gaussian potential units with Mahalanobis distance, and classifies the preprocessing output vectors to identify the actual topology. The main features of this method are: (i) local topology identification; (ii) linear growth of the complexity with the power system size; (iii) correction of multiple errors; and (iv) insensitivity to bad data. Tests have been carried out using the IEEE 14, 30, 57, 118 and 300 standard networks and different topological and measurement configurations. These tests have demonstrated the successful application of the technique. (Author)

  20. HBVRegDB: Annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences

    Directory of Open Access Journals (Sweden)

    Firth Andrew E

    2007-12-01

    Full Text Available Abstract Background The many Hepadnaviridae sequences available have widely varied functional annotation. The genomes are very compact (~3.2 kb but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses. Results These genomic sequences have been organized into a structured database to facilitate research at the molecular level. HBVRegDB is a comparative genomic analysis tool with an integrated underlying sequence database. The database contains genomic sequence data from representative viruses. In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters and comparative genome analysis results (e.g. blastn, tblastx. It also contains analyses based on curated HBV alignments. Information about conserved regions – including primary conservation (e.g. CDS-Plotcon and RNA secondary structure predictions (e.g. Alidot – is integrated into the database. A large amount of data is graphically presented using the GBrowse (Generic Genome Browser adapted for analysis of viral genomes. Flexible query access is provided based on any annotated genomic feature. Novel regulatory motifs can be found by analysing the annotated sequences. Conclusion HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV. It is publicly available and complementary to other viral and HBV focused datasets and tools http://hbvregdb.otago.ac.nz. The availability of multiple and highly annotated sequences of viral genomes in one database combined with comparative analysis tools facilitates detection of novel genomic elements.

  1. A structural annotation resource for the selection of putative target proteins in the malaria parasite

    Directory of Open Access Journals (Sweden)

    Joubert Fourie

    2008-05-01

    Full Text Available Abstract Background Protein structure plays a pivotal role in elucidating mechanisms of parasite functioning and drug resistance. Moreover, protein structure aids the determination of protein function, which can together with the structure be used to identify novel drug targets in the parasite. However, various structural features in Plasmodium falciparum proteins complicate the experimental determination of protein structures. Limited similarity to proteins in the Protein Data Bank and the shortage of solved protein structures in the malaria parasite necessitate genome-scale structural annotation of P. falciparum proteins. Additionally, the annotation of a range of structural features facilitates the identification of suitable targets for experimental and computational studies. Methods An integrated structural annotation system was developed and applied to P. falciparum, Plasmodium vivax and Plasmodium yoelii. The annotation included searches for sequence similarity, patterns and domains in addition to the following predictions: secondary structure, transmembrane helices, protein disorder, low complexity, coiled-coils and small molecule interactions. Subsequently, candidate proteins for further structural studies were identified based on the annotated structural features. Results The annotation results are accessible through a web interface, enabling users to select groups of proteins which fulfil multiple criteria pertaining to structural and functional features 1. Analysis of features in the P. falciparum proteome showed that protein-interacting proteins contained a higher percentage of predicted disordered residues than non-interacting proteins. Proteins interacting with 10 or more proteins have a disordered content concentrated in the range of 60–100%, while the disorder distribution for proteins having only one interacting partner, was more evenly spread. Conclusion A series of P. falciparum protein targets for experimental structure

  2. Model and Interoperability using Meta Data Annotations

    Science.gov (United States)

    David, O.

    2011-12-01

    Software frameworks and architectures are in need for meta data to efficiently support model integration. Modelers have to know the context of a model, often stepping into modeling semantics and auxiliary information usually not provided in a concise structure and universal format, consumable by a range of (modeling) tools. XML often seems the obvious solution for capturing meta data, but its wide adoption to facilitate model interoperability is limited by XML schema fragmentation, complexity, and verbosity outside of a data-automation process. Ontologies seem to overcome those shortcomings, however the practical significance of their use remains to be demonstrated. OMS version 3 took a different approach for meta data representation. The fundamental building block of a modular model in OMS is a software component representing a single physical process, calibration method, or data access approach. Here, programing language features known as Annotations or Attributes were adopted. Within other (non-modeling) frameworks it has been observed that annotations lead to cleaner and leaner application code. Framework-supported model integration, traditionally accomplished using Application Programming Interfaces (API) calls is now achieved using descriptive code annotations. Fully annotated components for various hydrological and Ag-system models now provide information directly for (i) model assembly and building, (ii) data flow analysis for implicit multi-threading or visualization, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, calibration, and optimization, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Such a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework but a strong reference to its originating code. Since models and

  3. Assessment of carbon nanoparticle exposure on murine macrophage function

    Science.gov (United States)

    Suro-Maldonado, Raquel M.

    There is growing concern about the potential cytotoxicity of nanoparticles. Exposure to respirable ultrafine particles (2.5uM) can adversely affect human health and have been implicated with episodes of increased respiratory diseases such as asthma and allergies. Nanoparticles are of particular interest because of their ability to penetrate into the lung and potentially elicit health effects triggering immune responses. Nanoparticles are structures and devises with length scales in the 1 to 100-nanometer range. Black carbon (BC) nanoparticles have been observed to be products of combustion, especially flame combustion and multi-walled carbon nanotubes (MWCNT) have been shown to be found in both indoor and outdoor air. Furthermore, asbestos, which have been known to cause mesothelioma as well as lung cancer, have been shown to be structurally identical to MWCNTs. The aims of these studies were to examine the effects of carbon nanoparticles on murine macrophage function and clearance mechanisms. Macrophages are immune cells that function as the first line of defense against invading pathogens and are likely to be amongst the first cells affected by nanoparticles. Our research focused on two manufactured nanoparticles, MWCNT and BC. The two were tested against murine-derived macrophages in a chronic contact model. We hypothesized that long-term chronic exposure to carbon nanoparticles would decrease macrophages ability to effectively respond to immunological challenge. Production of nitric oxide (NO), tumor necrosis factor alpha (TNF-alpha), cell surface macrophage; activation markers, reactive oxygen species formation (ROS), and antigen processing and presentation were examined in response to lipopolysaccharide (LPS) following a 144hr exposure to the particulates. Data demonstrated an increase in TNF-alpha, and NO production; a decrease in phagocytosis and antigen processing and presentation; and a decrease in the expression levels of cell surface macrophage

  4. Annotations and the Collaborative Digital Library: Effects of an Aligned Annotation Interface on Student Argumentation and Reading Strategies

    Science.gov (United States)

    Wolfe, Joanna

    2008-01-01

    Recent research on annotation interfaces provides provocative evidence that anchored, annotation-based discussion environments may lead to better conversations about a text. However, annotation interfaces raise complicated tradeoffs regarding screen real estate and positioning. It is argued that solving this screen real estate problem requires…

  5. Assessment of Macular Function Using the SKILL Card in Adults With Type 2 Diabetes Mellitus

    OpenAIRE

    Dhamdhere, Kavita P.; Schneck, Marilyn E.; Bearse, Marcus A.; Lam, Wendy; Barez, Shirin; Adams, Anthony J.

    2014-01-01

    We assess vision function at reduced contrast and luminance in adult patients with type 2 diabetes mellitus using the SKILL Card. The SKILL Card discriminated patients having diabetes with or without retinopathy from the controls with high overall accuracy.

  6. Deep annotation of Populus trichocarpa microRNAs from diverse tissue sets.

    Directory of Open Access Journals (Sweden)

    Joshua R Puzey

    Full Text Available Populus trichocarpa is an important woody model organism whose entire genome has been sequenced. This resource has facilitated the annotation of microRNAs (miRNAs, which are short non-coding RNAs with critical regulatory functions. However, despite their developmental importance, P. trichocarpa miRNAs have yet to be annotated from numerous important tissues. Here we significantly expand the breadth of tissue sampling and sequencing depth for miRNA annotation in P. trichocarpa using high-throughput smallRNA (sRNA sequencing. miRNA annotation was performed using three individual next-generation sRNA sequencing runs from separate leaves, xylem, and mechanically treated xylem, as well as a fourth run using a pooled sample containing vegetative apices, male flowers, female flowers, female apical buds, and male apical and lateral buds. A total of 276 miRNAs were identified from these datasets, including 155 previously unannotated miRNAs, most of which are P. trichocarpa specific. Importantly, we identified several xylem-enriched miRNAs predicted to target genes known to be important in secondary growth, including the critical reaction wood enzyme xyloglucan endo-transglycosylase/hydrolase and vascular-related transcription factors. This study provides a thorough genome-wide annotation of miRNAs in P. trichocarpa through deep sRNA sequencing from diverse tissue sets. Our data significantly expands the P. trichocarpa miRNA repertoire, which will facilitate a broad range of research in this major model system.

  7. Dynamic Assessment of Functional Lipidomic Analysis in Human Urine.

    Science.gov (United States)

    Rockwell, Hannah E; Gao, Fei; Chen, Emily Y; McDaniel, Justice; Sarangarajan, Rangaprasad; Narain, Niven R; Kiebish, Michael A

    2016-07-01

    The development of enabling mass spectrometry platforms for the quantification of diverse lipid species in human urine is of paramount importance for understanding metabolic homeostasis in normal and pathophysiological conditions. Urine represents a non-invasive biofluid that can capture distinct differences in an individual's physiological status. However, currently there is a lack of quantitative workflows to engage in high throughput lipidomic analysis. This study describes the development of a MS/MS(ALL) shotgun lipidomic workflow and a micro liquid chromatography-high resolution tandem mass spectrometry (LC-MS/MS) workflow for urine structural and mediator lipid analysis, respectively. This workflow was deployed to understand biofluid sample handling and collection, extraction efficiency, and natural human variation over time. Utilization of 0.5 mL of urine for structural lipidomic analysis resulted in reproducible quantification of more than 600 lipid molecular species from over 20 lipid classes. Analysis of 1 mL of urine routinely quantified in excess of 55 mediator lipid metabolites comprised of octadecanoids, eicosanoids, and docosanoids generated by lipoxygenase, cyclooxygenase, and cytochrome P450 activities. In summary, the high-throughput functional lipidomics workflow described in this study demonstrates an impressive robustness and reproducibility that can be utilized for population health and precision medicine applications. PMID:27038173

  8. Assessment of the functional status of the pulmonary endothelium and the neuroadrenergic function of the airways with MIBG

    International Nuclear Information System (INIS)

    Only little attention is directed towards nonrespiratory functions of the lung in today's nuclear medicine. However, the metabolic performance of the lung (e.g. the handling of biologically active amines) is of major importance for the whole organism. The main site for metabolic lung functions is the endothelium. Nuclear medicine methods are suitable for the noninvasive evaluation of the functional status of endothelial cells. After i.v. injection, MIBG is taken up by the pulmonary endothelium analogous to norepinephrine. Consequently, dysfunction of the endothelium can be recognized early by lung scintigraphy with MIBG. Since MIBG competes with norepinephrine at the cellular up-take mechanism, MIBG scintigraphy of the lung gives also insight into the function of the systemic neuroadrenergic system. MIBG radioaerosol may be of potential use for the assessment of the neuroadrenergic function of the airways. Even though the feasibility of the method has been demonstrated, clinical studies are lacking so far. (orig.)

  9. Assessment of strontium oxide functionalized graphene nanoflakes for enhanced photocatalytic activity: A density functional theory approach

    Science.gov (United States)

    Divya, A.; Mathavan, T.; Asath, R. Mohamed; Archana, J.; Hayakawa, Y.; Benial, A. Milton Franklin

    2016-05-01

    A series of strontium oxide functionalized graphene nanoflakes were designed and their optoelectronic properties were studied for enhanced photocatalytic activity. The efficiency of designed molecules was studied using various parameters such as HOMO-LUMO energy gap, light harvesting efficiency and exciton binding energy. The computed results show that by increasing the degree of functionalization of strontium oxide leads to lowering the band gap of hydrogen terminated graphene nanoflakes. Furthermore, the study explores the role of strontium oxide functionalization in Frontier Molecular Orbitals, ionization potential, electron affinity, exciton binding energy and light harvesting efficiency of designed molecules. The infrared and Raman spectra were simulated for pure and SrO functionalized graphene nanoflakes. The electron rich and electron deficient regions which are favorable for electrophilic and nucleophilic attacks respectively were analyzed using molecular electrostatic potential surface analysis.

  10. The transcriptome pyrosequencing and gene function annotation of the green microalga Myrmecia incisa%缺刻缘绿藻转录组测序及脂质代谢相关基因注释

    Institute of Scientific and Technical Information of China (English)

    陈思弘; 周志刚

    2012-01-01

    In order to understand the metabolic pathway of arachidonic acid and other lipids in Myrmecia incisa,the transcriptome pyrosequencing of this microalga was conducted by use of the sequencer Roche 454 GS FLX.Totally 393 722 reads(minimal size〉29 bp) averaging 333 bp were generated from one consecutive pyrosequencing run.Cleaning of the raw sequences resulted in a total of 382 468 high quality reads with an average length of 322 nucleotides totalling 123 Mb.After clustering and assembly,these reads were assembled into 22 714 contigs and 25 621 singletons.The average length for contigs and singletons were 639 bp and 277 bp,respectively.By annotating the unisequences,the metabolic pathways of lipids were constructed.Fatty acid was de novo synthesized in chloroplasts,and free fatty acids were transported into cytosol where triacylglycerol was synthesized by endoplasmic reticulum.Oil bodies were formed possibly with the help of caleosins.Arachidonic acid was synthesized by desaturation for several times and elongation from oleic acid.Oleic acid was formed by stearoyl-ACP desaturase,whereas palmitoic acid bound with glucolipid was generated by Δ7 desaturase.This research lays a foundation for systematic investigation into the manipulation of lipid metabolism and gene modification for higher production of ArA in M.incisa.%为了能深入地了解缺刻缘绿藻花生四烯酸(ArA)和脂质的代谢过程,利用Roche 454 GS FLX测序仪对该藻转录组进行高通量的焦磷酸测序。得到高质量读序(read)382 468条,占原始读序的97.14%,平均每条读序长322 bp,总大小达123 Mb。经CAP3软件拼接得到22 714条重叠群、25 621条singleton。将这些序列与公共数据库进行同源性搜索、比较、基因功能注释和分类。基于转录组中所注释的基因构建缺刻缘绿藻脂质代谢途径:脂肪酸是在叶绿体内从头合成,然后游离脂肪酸进入胞质,由内质网进行三酰甘油的合成,最后可能在

  11. Diagnostic Efficiency of the Personality Assessment Inventory LOGIT Function for Posttraumatic Stress Disorder in Women

    OpenAIRE

    Calhoun, Patrick S.; Boggs, Christina D.; Crawford, Eric F.; Beckham, Jean C.

    2009-01-01

    In this study, we examined the diagnostic efficiency of the Personality Assessment Inventory (PAI; Morey, 1991) for the assessment of posttraumatic stress disorder (PTSD) in a community-based sample of women (n=128). Receiver operating characteristic curves (ROC) were generated to examine the efficiency of the PAI PTSD LOGIT function as a tool for diagnosing PTSD. Using the Clinician Administered PTSD Scale as the reference standard, the PTSD LOGIT function performed well (area under the curv...

  12. Non-invasive assessment of endothelial function. Intra and inter-observer variability

    OpenAIRE

    Sotomayor González,Arturo; Kostine,Andrea; Gómez-Flores,Jorge R; MANLIO F. MÁRQUEZ; Hermosillo,Antonio G; Verdejo París,Juan; Iturralde Torres,Pedro; Colin Lizalde,Luis; Nava Townsend,Santiago; Cárdenas , Manuel

    2006-01-01

    Background and objectives: Non-invasive evaluation of endothelial function with high resolution ultrasound has become a widely accepted tool in determination of high risk subjects for early atherosclerosis. Despite its simple appearance, ultrasonographic assessment of brachial artery changes, is technically challenging and has a significant learning curve. In the present study, we evaluate the intra and inter-observer variability in assessing peripheral endothelial function with high resoluti...

  13. Using Hausdorff Distance for New Medical Image Annotation

    CERN Document Server

    Bouslimi, Riadh

    2012-01-01

    Medical images annotation is most of the time a repetitive hard task. Collecting old similar annotations and assigning them to new medical images may not only enhance the annotation process, but also reduce ambiguity caused by repetitive annotations. The goal of this work is to propose an approach based on Hausdorff distance able to compute similarity between a new medical image and old stored images. User has to choose then one of the similar images and annotations related to the selected one are assigned to the new one.

  14. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation

    DEFF Research Database (Denmark)

    Panitz, Frank; Stengaard, Henrik; Hornshoj, Henrik; Gorodkin, Jan; Hedegaard, Jakob; Cirera, Susanne; Thomsen, Bo; Madsen, Lone B.; Hoj, Anette; Vingborg, Rikke K.; Zahn, Bujie; Wang, Xuegang; Wang, Xuefei; Wernersson, Rasmus; Jørgensen, Claus B.; Scheibye-Knudsen, Karsten; Arvin, Troels; Lumholdt, Steen; Sawera, Milena; Green, Trine; Nielsen, Bente J.; Havgaard, Jakob H.; Brunak, Søren; Fredholm, Merete; Bendixen, Christian

    MOTIVATION: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data in...... manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non......-synonymous SNPs were analyzed for their potential effect on the protein structure/function using the PolyPhen and SIFT prediction programs. Predicted SNPs and annotations are stored in a web-based database. Using MAVIANT SNPs can visually be verified based on the DNA sequencing traces. A subset of candidate SNPs...

  15. Ontology-Based Annotation of Multimedia Language Data for the Semantic Web

    CERN Document Server

    Chebotko, Artem; Fotouhi, Farshad; Aristar, Anthony

    2009-01-01

    There is an increasing interest and effort in preserving and documenting endangered languages. Language data are valuable only when they are well-cataloged, indexed and searchable. Many language data, particularly those of lesser-spoken languages, are collected as audio and video recordings. While multimedia data provide more channels and dimensions to describe a language's function, and gives a better presentation of the cultural system associated with the language of that community, they are not text-based or structured (in binary format), and their semantics is implicit in their content. The content is thus easy for a human being to understand, but difficult for computers to interpret. Hence, there is a great need for a powerful and user-friendly system to annotate multimedia data with text-based, well-structured and searchable metadata. This chapter describes an ontology-based multimedia annotation tool, OntoELAN, that enables annotation of language multimedia data with a linguistic ontology.

  16. The Educational Role of Zoos: A Synthesis of the Literature (1928-1987) with Annotated Bibliography.

    Science.gov (United States)

    Churchman, David

    Zoos generally claim their four purposes to be conservation, research, entertainment, and education. This paper is intended to synthesize the literature relevant to the educational function and provide an annotated bibliography of that literature. The first section of the synthesis, "Audiences," addresses staff, volunteers, outreach programs, and…

  17. User Education in the Academic Library: Media Methods for Reference Work. An Annotated Bibliography. Updated.

    Science.gov (United States)

    Wharton, Sika

    This annotated bibliography focuses on academic library usage of audiovisual (AV) methods of instruction, particularly for the enhancement of the reference teaching function. The bibliography's objectives are as follows: to identify current trends with regard to AV methods in library orientation and bibliographic instruction; to isolate instances…

  18. FragKB: structural and literature annotation resource of conserved peptide fragments and residues.

    Directory of Open Access Journals (Sweden)

    Ashish V Tendulkar

    Full Text Available BACKGROUND: FragKB (Fragment Knowledgebase is a repository of clusters of structurally similar fragments from proteins. Fragments are annotated with information at the level of sequence, structure and function, integrating biological descriptions derived from multiple existing resources and text mining. METHODOLOGY: FragKB contains approximately 400,000 conserved fragments from 4,800 representative proteins from PDB. Literature annotations are extracted from more than 1,700 articles and are available for over 12,000 fragments. The underlying systematic annotation workflow of FragKB ensures efficient update and maintenance of this database. The information in FragKB can be accessed through a web interface that facilitates sequence and structural visualization of fragments together with known literature information on the consequences of specific residue mutations and functional annotations of proteins and fragment clusters. FragKB is accessible online at http://ubio.bioinfo.cnio.es/biotools/fragkb/. SIGNIFICANCE: The information presented in FragKB can be used for modeling protein structures, for designing novel proteins and for functional characterization of related fragments. The current release is focused on functional characterization of proteins through inspection of conservation of the fragments.

  19. Systematic interpretation of microarray data using experiment annotations

    Directory of Open Access Journals (Sweden)

    Frohme Marcus

    2006-12-01

    Full Text Available Abstract Background Up to now, microarray data are mostly assessed in context with only one or few parameters characterizing the experimental conditions under study. More explicit experiment annotations, however, are highly useful for interpreting microarray data, when available in a statistically accessible format. Results We provide means to preprocess these additional data, and to extract relevant traits corresponding to the transcription patterns under study. We found correspondence analysis particularly well-suited for mapping such extracted traits. It visualizes associations both among and between the traits, the hereby annotated experiments, and the genes, revealing how they are all interrelated. Here, we apply our methods to the systematic interpretation of radioactive (single channel and two-channel data, stemming from model organisms such as yeast and drosophila up to complex human cancer samples. Inclusion of technical parameters allows for identification of artifacts and flaws in experimental design. Conclusion Biological and clinical traits can act as landmarks in transcription space, systematically mapping the variance of large datasets from the predominant changes down toward intricate details.

  20. Self-Report Assessment of Executive Functioning in College Students with Disabilities

    Science.gov (United States)

    Grieve, Adam; Webne-Behrman, Lisa; Couillou, Ryan; Sieben-Schneider, Jill

    2014-01-01

    This study presents a unique assessment of executive functioning (EF) among postsecondary students with disabilities, with the aim of understanding the extent to which students with different disabilities and in different age groups assess their own difficulties with relevant and educationally-adaptive skills such as planning, initiating, managing…