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Sample records for medline prioritizing genes

  1. Biomedical hypothesis generation by text mining and gene prioritization.

    Science.gov (United States)

    Petric, Ingrid; Ligeti, Balazs; Gyorffy, Balazs; Pongor, Sandor

    2014-01-01

    Text mining methods can facilitate the generation of biomedical hypotheses by suggesting novel associations between diseases and genes. Previously, we developed a rare-term model called RaJoLink (Petric et al, J. Biomed. Inform. 42(2): 219-227, 2009) in which hypotheses are formulated on the basis of terms rarely associated with a target domain. Since many current medical hypotheses are formulated in terms of molecular entities and molecular mechanisms, here we extend the methodology to proteins and genes, using a standardized vocabulary as well as a gene/protein network model. The proposed enhanced RaJoLink rare-term model combines text mining and gene prioritization approaches. Its utility is illustrated by finding known as well as potential gene-disease associations in ovarian cancer using MEDLINE abstracts and the STRING database.

  2. Scuba: scalable kernel-based gene prioritization.

    Science.gov (United States)

    Zampieri, Guido; Tran, Dinh Van; Donini, Michele; Navarin, Nicolò; Aiolli, Fabio; Sperduti, Alessandro; Valle, Giorgio

    2018-01-25

    The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity of the available information. Computational methods for the prioritization of candidate genes can help to cope with these problems. In particular, kernel-based methods are a powerful resource for the integration of heterogeneous biological knowledge, however, their practical implementation is often precluded by their limited scalability. We propose Scuba, a scalable kernel-based method for gene prioritization. It implements a novel multiple kernel learning approach, based on a semi-supervised perspective and on the optimization of the margin distribution. Scuba is optimized to cope with strongly unbalanced settings where known disease genes are few and large scale predictions are required. Importantly, it is able to efficiently deal both with a large amount of candidate genes and with an arbitrary number of data sources. As a direct consequence of scalability, Scuba integrates also a new efficient strategy to select optimal kernel parameters for each data source. We performed cross-validation experiments and simulated a realistic usage setting, showing that Scuba outperforms a wide range of state-of-the-art methods. Scuba achieves state-of-the-art performance and has enhanced scalability compared to existing kernel-based approaches for genomic data. This method can be useful to prioritize candidate genes, particularly when their number is large or when input data is highly heterogeneous. The code is freely available at https://github.com/gzampieri/Scuba .

  3. Text mining in cancer gene and pathway prioritization.

    Science.gov (United States)

    Luo, Yuan; Riedlinger, Gregory; Szolovits, Peter

    2014-01-01

    Prioritization of cancer implicated genes has received growing attention as an effective way to reduce wet lab cost by computational analysis that ranks candidate genes according to the likelihood that experimental verifications will succeed. A multitude of gene prioritization tools have been developed, each integrating different data sources covering gene sequences, differential expressions, function annotations, gene regulations, protein domains, protein interactions, and pathways. This review places existing gene prioritization tools against the backdrop of an integrative Omic hierarchy view toward cancer and focuses on the analysis of their text mining components. We explain the relatively slow progress of text mining in gene prioritization, identify several challenges to current text mining methods, and highlight a few directions where more effective text mining algorithms may improve the overall prioritization task and where prioritizing the pathways may be more desirable than prioritizing only genes.

  4. Prioritizing genes associated with prostate cancer development

    International Nuclear Information System (INIS)

    Gorlov, Ivan P; Logothetis, Christopher J; Sircar, Kanishka; Zhao, Hongya; Maity, Sankar N; Navone, Nora M; Gorlova, Olga Y; Troncoso, Patricia; Pettaway, Curtis A; Byun, Jin Young

    2010-01-01

    The genetic control of prostate cancer development is poorly understood. Large numbers of gene-expression datasets on different aspects of prostate tumorigenesis are available. We used these data to identify and prioritize candidate genes associated with the development of prostate cancer and bone metastases. Our working hypothesis was that combining meta-analyses on different but overlapping steps of prostate tumorigenesis will improve identification of genes associated with prostate cancer development. A Z score-based meta-analysis of gene-expression data was used to identify candidate genes associated with prostate cancer development. To put together different datasets, we conducted a meta-analysis on 3 levels that follow the natural history of prostate cancer development. For experimental verification of candidates, we used in silico validation as well as in-house gene-expression data. Genes with experimental evidence of an association with prostate cancer development were overrepresented among our top candidates. The meta-analysis also identified a considerable number of novel candidate genes with no published evidence of a role in prostate cancer development. Functional annotation identified cytoskeleton, cell adhesion, extracellular matrix, and cell motility as the top functions associated with prostate cancer development. We identified 10 genes--CDC2, CCNA2, IGF1, EGR1, SRF, CTGF, CCL2, CAV1, SMAD4, and AURKA--that form hubs of the interaction network and therefore are likely to be primary drivers of prostate cancer development. By using this large 3-level meta-analysis of the gene-expression data to identify candidate genes associated with prostate cancer development, we have generated a list of candidate genes that may be a useful resource for researchers studying the molecular mechanisms underlying prostate cancer development

  5. Automatically identifying gene/protein terms in MEDLINE abstracts.

    Science.gov (United States)

    Yu, Hong; Hatzivassiloglou, Vasileios; Rzhetsky, Andrey; Wilbur, W John

    2002-01-01

    Natural language processing (NLP) techniques are used to extract information automatically from computer-readable literature. In biology, the identification of terms corresponding to biological substances (e.g., genes and proteins) is a necessary step that precedes the application of other NLP systems that extract biological information (e.g., protein-protein interactions, gene regulation events, and biochemical pathways). We have developed GPmarkup (for "gene/protein-full name mark up"), a software system that automatically identifies gene/protein terms (i.e., symbols or full names) in MEDLINE abstracts. As a part of marking up process, we also generated automatically a knowledge source of paired gene/protein symbols and full names (e.g., LARD for lymphocyte associated receptor of death) from MEDLINE. We found that many of the pairs in our knowledge source do not appear in the current GenBank database. Therefore our methods may also be used for automatic lexicon generation. GPmarkup has 73% recall and 93% precision in identifying and marking up gene/protein terms in MEDLINE abstracts. A random sample of gene/protein symbols and full names and a sample set of marked up abstracts can be viewed at http://www.cpmc.columbia.edu/homepages/yuh9001/GPmarkup/. Contact. hy52@columbia.edu. Voice: 212-939-7028; fax: 212-666-0140.

  6. Disease candidate gene identification and prioritization using protein interaction networks

    Directory of Open Access Journals (Sweden)

    Aronow Bruce J

    2009-02-01

    Full Text Available Abstract Background Although most of the current disease candidate gene identification and prioritization methods depend on functional annotations, the coverage of the gene functional annotations is a limiting factor. In the current study, we describe a candidate gene prioritization method that is entirely based on protein-protein interaction network (PPIN analyses. Results For the first time, extended versions of the PageRank and HITS algorithms, and the K-Step Markov method are applied to prioritize disease candidate genes in a training-test schema. Using a list of known disease-related genes from our earlier study as a training set ("seeds", and the rest of the known genes as a test list, we perform large-scale cross validation to rank the candidate genes and also evaluate and compare the performance of our approach. Under appropriate settings – for example, a back probability of 0.3 for PageRank with Priors and HITS with Priors, and step size 6 for K-Step Markov method – the three methods achieved a comparable AUC value, suggesting a similar performance. Conclusion Even though network-based methods are generally not as effective as integrated functional annotation-based methods for disease candidate gene prioritization, in a one-to-one comparison, PPIN-based candidate gene prioritization performs better than all other gene features or annotations. Additionally, we demonstrate that methods used for studying both social and Web networks can be successfully used for disease candidate gene prioritization.

  7. A large-scale benchmark of gene prioritization methods.

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    Guala, Dimitri; Sonnhammer, Erik L L

    2017-04-21

    In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. While prospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate the performance of gene prioritization tools, a strategy for retrospective benchmarking has been missing, and new tools usually only provide internal validations. The Gene Ontology(GO) contains genes clustered around annotation terms. This intrinsic property of GO can be utilized in construction of robust benchmarks, objective to the problem domain. We demonstrate how this can be achieved for network-based gene prioritization tools, utilizing the FunCoup network. We use cross-validation and a set of appropriate performance measures to compare state-of-the-art gene prioritization algorithms: three based on network diffusion, NetRank and two implementations of Random Walk with Restart, and MaxLink that utilizes network neighborhood. Our benchmark suite provides a systematic and objective way to compare the multitude of available and future gene prioritization tools, enabling researchers to select the best gene prioritization tool for the task at hand, and helping to guide the development of more accurate methods.

  8. Gene prioritization for livestock diseases by data integration

    DEFF Research Database (Denmark)

    Jiang, Li; Sørensen, Peter; Thomsen, Bo Stjerne

    2012-01-01

    in bovine mastitis. Gene-associated phenome profile and transcriptome profile in response to Escherichia coli infection in the mammary gland were integrated to make a global inference of bovine genes involved in mastitis. The top ranked genes were highly enriched for pathways and biological processes...... underlying inflammation and immune responses, which supports the validity of our approach for identifying genes that are relevant to animal health and disease. These gene-associated phenotypes were used for a local prioritization of candidate genes located in a QTL affecting the susceptibility to mastitis...

  9. Web tools for the prioritization of candidate disease genes.

    NARCIS (Netherlands)

    Oti, M.O.; Ballouz, S.; Wouters, M.A.

    2011-01-01

    Despite increasing sequencing capacity, genetic disease investigation still frequently results in the identification of loci containing multiple candidate disease genes that need to be tested for involvement in the disease. This process can be expedited by prioritizing the candidates prior to

  10. Genomic dissection and prioritizing of candidate genes of QTL for ...

    Indian Academy of Sciences (India)

    Genomic dissection and prioritizing of candidate genes of QTL for regulating spontaneous arthritis on chromosome 1 in mice deficient for interleukin-1 receptor antagonist. Yanhong Cao, Jifei Zhang, Yan Jiao, Jian Yan, Feng Jiao, XiaoYun Liu, Robert W. Williams, Karen A. Hasty,. John M. Stuart and Weikuan Gu. J. Genet.

  11. Speeding disease gene discovery by sequence based candidate prioritization

    Directory of Open Access Journals (Sweden)

    Porteous David J

    2005-03-01

    Full Text Available Abstract Background Regions of interest identified through genetic linkage studies regularly exceed 30 centimorgans in size and can contain hundreds of genes. Traditionally this number is reduced by matching functional annotation to knowledge of the disease or phenotype in question. However, here we show that disease genes share patterns of sequence-based features that can provide a good basis for automatic prioritization of candidates by machine learning. Results We examined a variety of sequence-based features and found that for many of them there are significant differences between the sets of genes known to be involved in human hereditary disease and those not known to be involved in disease. We have created an automatic classifier called PROSPECTR based on those features using the alternating decision tree algorithm which ranks genes in the order of likelihood of involvement in disease. On average, PROSPECTR enriches lists for disease genes two-fold 77% of the time, five-fold 37% of the time and twenty-fold 11% of the time. Conclusion PROSPECTR is a simple and effective way to identify genes involved in Mendelian and oligogenic disorders. It performs markedly better than the single existing sequence-based classifier on novel data. PROSPECTR could save investigators looking at large regions of interest time and effort by prioritizing positional candidate genes for mutation detection and case-control association studies.

  12. Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information.

    Directory of Open Access Journals (Sweden)

    Xinyan Wang

    Full Text Available Chronic obstructive pulmonary disease (COPD is a multi-factor disease, in which metabolic disturbances played important roles. In this paper, functional information was integrated into a COPD-related metabolic network to assess similarity between genes. Then a gene prioritization method was applied to the COPD-related metabolic network to prioritize COPD candidate genes. The gene prioritization method was superior to ToppGene and ToppNet in both literature validation and functional enrichment analysis. Top-ranked genes prioritized from the metabolic perspective with functional information could promote the better understanding about the molecular mechanism of this disease. Top 100 genes might be potential markers for diagnostic and effective therapies.

  13. Network Diffusion-Based Prioritization of Autism Risk Genes Identifies Significantly Connected Gene Modules

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    Ettore Mosca

    2017-09-01

    Full Text Available Autism spectrum disorder (ASD is marked by a strong genetic heterogeneity, which is underlined by the low overlap between ASD risk gene lists proposed in different studies. In this context, molecular networks can be used to analyze the results of several genome-wide studies in order to underline those network regions harboring genetic variations associated with ASD, the so-called “disease modules.” In this work, we used a recent network diffusion-based approach to jointly analyze multiple ASD risk gene lists. We defined genome-scale prioritizations of human genes in relation to ASD genes from multiple studies, found significantly connected gene modules associated with ASD and predicted genes functionally related to ASD risk genes. Most of them play a role in synapsis and neuronal development and function; many are related to syndromes that can be in comorbidity with ASD and the remaining are involved in epigenetics, cell cycle, cell adhesion and cancer.

  14. Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes

    KAUST Repository

    AlShahrani, Mona; Hoehndorf, Robert

    2018-01-01

    In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease's (or patient's) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse. Results: We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprising of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.

  15. Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes

    KAUST Repository

    Alshahrani, Mona

    2018-04-30

    In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease\\'s (or patient\\'s) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse. Results: We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprising of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.

  16. Integrative mining of traditional Chinese medicine literature and MEDLINE for functional gene networks.

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    Zhou, Xuezhong; Liu, Baoyan; Wu, Zhaohui; Feng, Yi

    2007-10-01

    The amount of biomedical data in different disciplines is growing at an exponential rate. Integrating these significant knowledge sources to generate novel hypotheses for systems biology research is difficult. Traditional Chinese medicine (TCM) is a completely different discipline, and is a complementary knowledge system to modern biomedical science. This paper uses a significant TCM bibliographic literature database in China, together with MEDLINE, to help discover novel gene functional knowledge. We present an integrative mining approach to uncover the functional gene relationships from MEDLINE and TCM bibliographic literature. This paper introduces TCM literature (about 50,000 records) as one knowledge source for constructing literature-based gene networks. We use the TCM diagnosis, TCM syndrome, to automatically congregate the related genes. The syndrome-gene relationships are discovered based on the syndrome-disease relationships extracted from TCM literature and the disease-gene relationships in MEDLINE. Based on the bubble-bootstrapping and relation weight computing methods, we have developed a prototype system called MeDisco/3S, which has name entity and relation extraction, and online analytical processing (OLAP) capabilities, to perform the integrative mining process. We have got about 200,000 syndrome-gene relations, which could help generate syndrome-based gene networks, and help analyze the functional knowledge of genes from syndrome perspective. We take the gene network of Kidney-Yang Deficiency syndrome (KYD syndrome) and the functional analysis of some genes, such as CRH (corticotropin releasing hormone), PTH (parathyroid hormone), PRL (prolactin), BRCA1 (breast cancer 1, early onset) and BRCA2 (breast cancer 2, early onset), to demonstrate the preliminary results. The underlying hypothesis is that the related genes of the same syndrome will have some biological functional relationships, and will constitute a functional network. This paper presents

  17. Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks.

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    Zhang, Yihua; Li, Wan; Feng, Yuyan; Guo, Shanshan; Zhao, Xilei; Wang, Yahui; He, Yuehan; He, Weiming; Chen, Lina

    2017-11-28

    Chronic obstructive pulmonary disease (COPD) is a multi-factor disease, which could be caused by many factors, including disturbances of metabolism and protein-protein interactions (PPIs). In this paper, a weighted COPD-related metabolic network and a weighted COPD-related PPI network were constructed base on COPD disease genes and functional information. Candidate genes in these weighted COPD-related networks were prioritized by making use of a gene prioritization method, respectively. Literature review and functional enrichment analysis of the top 100 genes in these two networks suggested the correlation of COPD and these genes. The performance of our gene prioritization method was superior to that of ToppGene and ToppNet for genes from the COPD-related metabolic network or the COPD-related PPI network after assessing using leave-one-out cross-validation, literature validation and functional enrichment analysis. The top-ranked genes prioritized from COPD-related metabolic and PPI networks could promote the better understanding about the molecular mechanism of this disease from different perspectives. The top 100 genes in COPD-related metabolic network or COPD-related PPI network might be potential markers for the diagnosis and treatment of COPD.

  18. Consensus strategy in genes prioritization and combined bioinformatics analysis for preeclampsia pathogenesis.

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    Tejera, Eduardo; Cruz-Monteagudo, Maykel; Burgos, Germán; Sánchez, María-Eugenia; Sánchez-Rodríguez, Aminael; Pérez-Castillo, Yunierkis; Borges, Fernanda; Cordeiro, Maria Natália Dias Soeiro; Paz-Y-Miño, César; Rebelo, Irene

    2017-08-08

    Preeclampsia is a multifactorial disease with unknown pathogenesis. Even when recent studies explored this disease using several bioinformatics tools, the main objective was not directed to pathogenesis. Additionally, consensus prioritization was proved to be highly efficient in the recognition of genes-disease association. However, not information is available about the consensus ability to early recognize genes directly involved in pathogenesis. Therefore our aim in this study is to apply several theoretical approaches to explore preeclampsia; specifically those genes directly involved in the pathogenesis. We firstly evaluated the consensus between 12 prioritization strategies to early recognize pathogenic genes related to preeclampsia. A communality analysis in the protein-protein interaction network of previously selected genes was done including further enrichment analysis. The enrichment analysis includes metabolic pathways as well as gene ontology. Microarray data was also collected and used in order to confirm our results or as a strategy to weight the previously enriched pathways. The consensus prioritized gene list was rationally filtered to 476 genes using several criteria. The communality analysis showed an enrichment of communities connected with VEGF-signaling pathway. This pathway is also enriched considering the microarray data. Our result point to VEGF, FLT1 and KDR as relevant pathogenic genes, as well as those connected with NO metabolism. Our results revealed that consensus strategy improve the detection and initial enrichment of pathogenic genes, at least in preeclampsia condition. Moreover the combination of the first percent of the prioritized genes with protein-protein interaction network followed by communality analysis reduces the gene space. This approach actually identifies well known genes related with pathogenesis. However, genes like HSP90, PAK2, CD247 and others included in the first 1% of the prioritized list need to be further

  19. Systematically characterizing and prioritizing chemosensitivity related gene based on Gene Ontology and protein interaction network

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    Chen Xin

    2012-10-01

    Full Text Available Abstract Background The identification of genes that predict in vitro cellular chemosensitivity of cancer cells is of great importance. Chemosensitivity related genes (CRGs have been widely utilized to guide clinical and cancer chemotherapy decisions. In addition, CRGs potentially share functional characteristics and network features in protein interaction networks (PPIN. Methods In this study, we proposed a method to identify CRGs based on Gene Ontology (GO and PPIN. Firstly, we documented 150 pairs of drug-CCRG (curated chemosensitivity related gene from 492 published papers. Secondly, we characterized CCRGs from the perspective of GO and PPIN. Thirdly, we prioritized CRGs based on CCRGs’ GO and network characteristics. Lastly, we evaluated the performance of the proposed method. Results We found that CCRG enriched GO terms were most often related to chemosensitivity and exhibited higher similarity scores compared to randomly selected genes. Moreover, CCRGs played key roles in maintaining the connectivity and controlling the information flow of PPINs. We then prioritized CRGs using CCRG enriched GO terms and CCRG network characteristics in order to obtain a database of predicted drug-CRGs that included 53 CRGs, 32 of which have been reported to affect susceptibility to drugs. Our proposed method identifies a greater number of drug-CCRGs, and drug-CCRGs are much more significantly enriched in predicted drug-CRGs, compared to a method based on the correlation of gene expression and drug activity. The mean area under ROC curve (AUC for our method is 65.2%, whereas that for the traditional method is 55.2%. Conclusions Our method not only identifies CRGs with expression patterns strongly correlated with drug activity, but also identifies CRGs in which expression is weakly correlated with drug activity. This study provides the framework for the identification of signatures that predict in vitro cellular chemosensitivity and offers a valuable

  20. Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene-based networks.

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    Nolan Priedigkeit

    2015-02-01

    Full Text Available Genes involved in the same function tend to have similar evolutionary histories, in that their rates of evolution covary over time. This coevolutionary signature, termed Evolutionary Rate Covariation (ERC, is calculated using only gene sequences from a set of closely related species and has demonstrated potential as a computational tool for inferring functional relationships between genes. To further define applications of ERC, we first established that roughly 55% of genetic diseases posses an ERC signature between their contributing genes. At a false discovery rate of 5% we report 40 such diseases including cancers, developmental disorders and mitochondrial diseases. Given these coevolutionary signatures between disease genes, we then assessed ERC's ability to prioritize known disease genes out of a list of unrelated candidates. We found that in the presence of an ERC signature, the true disease gene is effectively prioritized to the top 6% of candidates on average. We then apply this strategy to a melanoma-associated region on chromosome 1 and identify MCL1 as a potential causative gene. Furthermore, to gain global insight into disease mechanisms, we used ERC to predict molecular connections between 310 nominally distinct diseases. The resulting "disease map" network associates several diseases with related pathogenic mechanisms and unveils many novel relationships between clinically distinct diseases, such as between Hirschsprung's disease and melanoma. Taken together, these results demonstrate the utility of molecular evolution as a gene discovery platform and show that evolutionary signatures can be used to build informative gene-based networks.

  1. An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods.

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    Valentini, Giorgio; Paccanaro, Alberto; Caniza, Horacio; Romero, Alfonso E; Re, Matteo

    2014-06-01

    In the context of "network medicine", gene prioritization methods represent one of the main tools to discover candidate disease genes by exploiting the large amount of data covering different types of functional relationships between genes. Several works proposed to integrate multiple sources of data to improve disease gene prioritization, but to our knowledge no systematic studies focused on the quantitative evaluation of the impact of network integration on gene prioritization. In this paper, we aim at providing an extensive analysis of gene-disease associations not limited to genetic disorders, and a systematic comparison of different network integration methods for gene prioritization. We collected nine different functional networks representing different functional relationships between genes, and we combined them through both unweighted and weighted network integration methods. We then prioritized genes with respect to each of the considered 708 medical subject headings (MeSH) diseases by applying classical guilt-by-association, random walk and random walk with restart algorithms, and the recently proposed kernelized score functions. The results obtained with classical random walk algorithms and the best single network achieved an average area under the curve (AUC) across the 708 MeSH diseases of about 0.82, while kernelized score functions and network integration boosted the average AUC to about 0.89. Weighted integration, by exploiting the different "informativeness" embedded in different functional networks, outperforms unweighted integration at 0.01 significance level, according to the Wilcoxon signed rank sum test. For each MeSH disease we provide the top-ranked unannotated candidate genes, available for further bio-medical investigation. Network integration is necessary to boost the performances of gene prioritization methods. Moreover the methods based on kernelized score functions can further enhance disease gene ranking results, by adopting both

  2. An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods

    Science.gov (United States)

    Valentini, Giorgio; Paccanaro, Alberto; Caniza, Horacio; Romero, Alfonso E.; Re, Matteo

    2014-01-01

    Objective In the context of “network medicine”, gene prioritization methods represent one of the main tools to discover candidate disease genes by exploiting the large amount of data covering different types of functional relationships between genes. Several works proposed to integrate multiple sources of data to improve disease gene prioritization, but to our knowledge no systematic studies focused on the quantitative evaluation of the impact of network integration on gene prioritization. In this paper, we aim at providing an extensive analysis of gene-disease associations not limited to genetic disorders, and a systematic comparison of different network integration methods for gene prioritization. Materials and methods We collected nine different functional networks representing different functional relationships between genes, and we combined them through both unweighted and weighted network integration methods. We then prioritized genes with respect to each of the considered 708 medical subject headings (MeSH) diseases by applying classical guilt-by-association, random walk and random walk with restart algorithms, and the recently proposed kernelized score functions. Results The results obtained with classical random walk algorithms and the best single network achieved an average area under the curve (AUC) across the 708 MeSH diseases of about 0.82, while kernelized score functions and network integration boosted the average AUC to about 0.89. Weighted integration, by exploiting the different “informativeness” embedded in different functional networks, outperforms unweighted integration at 0.01 significance level, according to the Wilcoxon signed rank sum test. For each MeSH disease we provide the top-ranked unannotated candidate genes, available for further bio-medical investigation. Conclusions Network integration is necessary to boost the performances of gene prioritization methods. Moreover the methods based on kernelized score functions can further

  3. Systematic Prioritization and Integrative Analysis of Copy Number Variations in Schizophrenia Reveal Key Schizophrenia Susceptibility Genes

    Science.gov (United States)

    Luo, Xiongjian; Huang, Liang; Han, Leng; Luo, Zhenwu; Hu, Fang; Tieu, Roger; Gan, Lin

    2014-01-01

    Schizophrenia is a common mental disorder with high heritability and strong genetic heterogeneity. Common disease-common variants hypothesis predicts that schizophrenia is attributable in part to common genetic variants. However, recent studies have clearly demonstrated that copy number variations (CNVs) also play pivotal roles in schizophrenia susceptibility and explain a proportion of missing heritability. Though numerous CNVs have been identified, many of the regions affected by CNVs show poor overlapping among different studies, and it is not known whether the genes disrupted by CNVs contribute to the risk of schizophrenia. By using cumulative scoring, we systematically prioritized the genes affected by CNVs in schizophrenia. We identified 8 top genes that are frequently disrupted by CNVs, including NRXN1, CHRNA7, BCL9, CYFIP1, GJA8, NDE1, SNAP29, and GJA5. Integration of genes affected by CNVs with known schizophrenia susceptibility genes (from previous genetic linkage and association studies) reveals that many genes disrupted by CNVs are also associated with schizophrenia. Further protein-protein interaction (PPI) analysis indicates that protein products of genes affected by CNVs frequently interact with known schizophrenia-associated proteins. Finally, systematic integration of CNVs prioritization data with genetic association and PPI data identifies key schizophrenia candidate genes. Our results provide a global overview of genes impacted by CNVs in schizophrenia and reveal a densely interconnected molecular network of de novo CNVs in schizophrenia. Though the prioritized top genes represent promising schizophrenia risk genes, further work with different prioritization methods and independent samples is needed to confirm these findings. Nevertheless, the identified key candidate genes may have important roles in the pathogenesis of schizophrenia, and further functional characterization of these genes may provide pivotal targets for future therapeutics and

  4. Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles.

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    Zhu, Jie; Qin, Yufang; Liu, Taigang; Wang, Jun; Zheng, Xiaoqi

    2013-01-01

    Identification of gene-phenotype relationships is a fundamental challenge in human health clinic. Based on the observation that genes causing the same or similar phenotypes tend to correlate with each other in the protein-protein interaction network, a lot of network-based approaches were proposed based on different underlying models. A recent comparative study showed that diffusion-based methods achieve the state-of-the-art predictive performance. In this paper, a new diffusion-based method was proposed to prioritize candidate disease genes. Diffusion profile of a disease was defined as the stationary distribution of candidate genes given a random walk with restart where similarities between phenotypes are incorporated. Then, candidate disease genes are prioritized by comparing their diffusion profiles with that of the disease. Finally, the effectiveness of our method was demonstrated through the leave-one-out cross-validation against control genes from artificial linkage intervals and randomly chosen genes. Comparative study showed that our method achieves improved performance compared to some classical diffusion-based methods. To further illustrate our method, we used our algorithm to predict new causing genes of 16 multifactorial diseases including Prostate cancer and Alzheimer's disease, and the top predictions were in good consistent with literature reports. Our study indicates that integration of multiple information sources, especially the phenotype similarity profile data, and introduction of global similarity measure between disease and gene diffusion profiles are helpful for prioritizing candidate disease genes. Programs and data are available upon request.

  5. Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes.

    Science.gov (United States)

    Hsu, Jacob Shujui; Kwan, Johnny S H; Pan, Zhicheng; Garcia-Barcelo, Maria-Mercè; Sham, Pak Chung; Li, Miaoxin

    2016-10-15

    Exome sequencing studies have facilitated the detection of causal genetic variants in yet-unsolved Mendelian diseases. However, the identification of disease causal genes among a list of candidates in an exome sequencing study is still not fully settled, and it is often difficult to prioritize candidate genes for follow-up studies. The inheritance mode provides crucial information for understanding Mendelian diseases, but none of the existing gene prioritization tools fully utilize this information. We examined the characteristics of Mendelian disease genes under different inheritance modes. The results suggest that Mendelian disease genes with autosomal dominant (AD) inheritance mode are more haploinsufficiency and de novo mutation sensitive, whereas those autosomal recessive (AR) genes have significantly more non-synonymous variants and regulatory transcript isoforms. In addition, the X-linked (XL) Mendelian disease genes have fewer non-synonymous and synonymous variants. As a result, we derived a new scoring system for prioritizing candidate genes for Mendelian diseases according to the inheritance mode. Our scoring system assigned to each annotated protein-coding gene (N = 18 859) three pathogenic scores according to the inheritance mode (AD, AR and XL). This inheritance mode-specific framework achieved higher accuracy (area under curve  = 0.84) in XL mode. The inheritance-mode specific pathogenicity prioritization (ISPP) outperformed other well-known methods including Haploinsufficiency, Recessive, Network centrality, Genic Intolerance, Gene Damage Index and Gene Constraint scores. This systematic study suggests that genes manifesting disease inheritance modes tend to have unique characteristics. ISPP is included in KGGSeq v1.0 (http://grass.cgs.hku.hk/limx/kggseq/), and source code is available from (https://github.com/jacobhsu35/ISPP.git). mxli@hku.hkSupplementary information: Supplementary data are available at Bioinformatics online. © The Author

  6. Prioritization of epilepsy associated candidate genes by convergent analysis.

    Science.gov (United States)

    Jia, Peilin; Ewers, Jeffrey M; Zhao, Zhongming

    2011-02-24

    Epilepsy is a severe neurological disorder affecting a large number of individuals, yet the underlying genetic risk factors for epilepsy remain unclear. Recent studies have revealed several recurrent copy number variations (CNVs) that are more likely to be associated with epilepsy. The responsible gene(s) within these regions have yet to be definitively linked to the disorder, and the implications of their interactions are not fully understood. Identification of these genes may contribute to a better pathological understanding of epilepsy, and serve to implicate novel therapeutic targets for further research. In this study, we examined genes within heterozygous deletion regions identified in a recent large-scale study, encompassing a diverse spectrum of epileptic syndromes. By integrating additional protein-protein interaction data, we constructed subnetworks for these CNV-region genes and also those previously studied for epilepsy. We observed 20 genes common to both networks, primarily concentrated within a small molecular network populated by GABA receptor, BDNF/MAPK signaling, and estrogen receptor genes. From among the hundreds of genes in the initial networks, these were designated by convergent evidence for their likely association with epilepsy. Importantly, the identified molecular network was found to contain complex interrelationships, providing further insight into epilepsy's underlying pathology. We further performed pathway enrichment and crosstalk analysis and revealed a functional map which indicates the significant enrichment of closely related neurological, immune, and kinase regulatory pathways. The convergent framework we proposed here provides a unique and powerful approach to screening and identifying promising disease genes out of typically hundreds to thousands of genes in disease-related CNV-regions. Our network and pathway analysis provides important implications for the underlying molecular mechanisms for epilepsy. The strategy can be

  7. Prioritization of epilepsy associated candidate genes by convergent analysis.

    Directory of Open Access Journals (Sweden)

    Peilin Jia

    2011-02-01

    Full Text Available Epilepsy is a severe neurological disorder affecting a large number of individuals, yet the underlying genetic risk factors for epilepsy remain unclear. Recent studies have revealed several recurrent copy number variations (CNVs that are more likely to be associated with epilepsy. The responsible gene(s within these regions have yet to be definitively linked to the disorder, and the implications of their interactions are not fully understood. Identification of these genes may contribute to a better pathological understanding of epilepsy, and serve to implicate novel therapeutic targets for further research.In this study, we examined genes within heterozygous deletion regions identified in a recent large-scale study, encompassing a diverse spectrum of epileptic syndromes. By integrating additional protein-protein interaction data, we constructed subnetworks for these CNV-region genes and also those previously studied for epilepsy. We observed 20 genes common to both networks, primarily concentrated within a small molecular network populated by GABA receptor, BDNF/MAPK signaling, and estrogen receptor genes. From among the hundreds of genes in the initial networks, these were designated by convergent evidence for their likely association with epilepsy. Importantly, the identified molecular network was found to contain complex interrelationships, providing further insight into epilepsy's underlying pathology. We further performed pathway enrichment and crosstalk analysis and revealed a functional map which indicates the significant enrichment of closely related neurological, immune, and kinase regulatory pathways.The convergent framework we proposed here provides a unique and powerful approach to screening and identifying promising disease genes out of typically hundreds to thousands of genes in disease-related CNV-regions. Our network and pathway analysis provides important implications for the underlying molecular mechanisms for epilepsy. The

  8. Comparison of two schemes for automatic keyword extraction from MEDLINE for functional gene clustering.

    Science.gov (United States)

    Liu, Ying; Ciliax, Brian J; Borges, Karin; Dasigi, Venu; Ram, Ashwin; Navathe, Shamkant B; Dingledine, Ray

    2004-01-01

    One of the key challenges of microarray studies is to derive biological insights from the unprecedented quatities of data on gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the nature of the functional links among genes within the derived clusters. However, the quality of the keyword lists extracted from biomedical literature for each gene significantly affects the clustering results. We extracted keywords from MEDLINE that describes the most prominent functions of the genes, and used the resulting weights of the keywords as feature vectors for gene clustering. By analyzing the resulting cluster quality, we compared two keyword weighting schemes: normalized z-score and term frequency-inverse document frequency (TFIDF). The best combination of background comparison set, stop list and stemming algorithm was selected based on precision and recall metrics. In a test set of four known gene groups, a hierarchical algorithm correctly assigned 25 of 26 genes to the appropriate clusters based on keywords extracted by the TDFIDF weighting scheme, but only 23 og 26 with the z-score method. To evaluate the effectiveness of the weighting schemes for keyword extraction for gene clusters from microarray profiles, 44 yeast genes that are differentially expressed during the cell cycle were used as a second test set. Using established measures of cluster quality, the results produced from TFIDF-weighted keywords had higher purity, lower entropy, and higher mutual information than those produced from normalized z-score weighted keywords. The optimized algorithms should be useful for sorting genes from microarray lists into functionally discrete clusters.

  9. FUN-L: gene prioritization for RNAi screens.

    Science.gov (United States)

    Lees, Jonathan G; Hériché, Jean-Karim; Morilla, Ian; Fernández, José M; Adler, Priit; Krallinger, Martin; Vilo, Jaak; Valencia, Alfonso; Ellenberg, Jan; Ranea, Juan A; Orengo, Christine

    2015-06-15

    Most biological processes remain only partially characterized with many components still to be identified. Given that a whole genome can usually not be tested in a functional assay, identifying the genes most likely to be of interest is of critical importance to avoid wasting resources. Given a set of known functionally related genes and using a state-of-the-art approach to data integration and mining, our Functional Lists (FUN-L) method provides a ranked list of candidate genes for testing. Validation of predictions from FUN-L with independent RNAi screens confirms that FUN-L-produced lists are enriched in genes with the expected phenotypes. In this article, we describe a website front end to FUN-L. The website is freely available to use at http://funl.org © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. A meta-analysis based method for prioritizing candidate genes involved in a pre-specific function

    Directory of Open Access Journals (Sweden)

    Jingjing Zhai

    2016-12-01

    Full Text Available The identification of genes associated with a given biological function in plants remains a challenge, although network-based gene prioritization algorithms have been developed for Arabidopsis thaliana and many non-model plant species. Nevertheless, these network-based gene prioritization algorithms have encountered several problems; one in particular is that of unsatisfactory prediction accuracy due to limited network coverage, varying link quality, and/or uncertain network connectivity. Thus a model that integrates complementary biological data may be expected to increase the prediction accuracy of gene prioritization. Towards this goal, we developed a novel gene prioritization method named RafSee, to rank candidate genes using a random forest algorithm that integrates sequence, evolutionary, and epigenetic features of plants. Subsequently, we proposed an integrative approach named RAP (Rank Aggregation-based data fusion for gene Prioritization, in which an order statistics-based meta-analysis was used to aggregate the rank of the network-based gene prioritization method and RafSee, for accurately prioritizing candidate genes involved in a pre-specific biological function. Finally, we showcased the utility of RAP by prioritizing 380 flowering-time genes in Arabidopsis. The ‘leave-one-out’ cross-validation experiment showed that RafSee could work as a complement to a current state-of-art network-based gene prioritization system (AraNet v2. Moreover, RAP ranked 53.68% (204/380 flowering-time genes higher than AraNet v2, resulting in an 39.46% improvement in term of the first quartile rank. Further evaluations also showed that RAP was effective in prioritizing genes-related to different abiotic stresses. To enhance the usability of RAP for Arabidopsis and non-model plant species, an R package implementing the method is freely available at http://bioinfo.nwafu.edu.cn/software.

  11. PINTA: a web server for network-based gene prioritization from expression data

    DEFF Research Database (Denmark)

    Nitsch, Daniela; Tranchevent, Léon-Charles; Goncalves, Joana P.

    2011-01-01

    PINTA (available at http://www.esat.kuleuven.be/ pinta/; this web site is free and open to all users and there is no login requirement) is a web resource for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein–protein interaction...

  12. Genomic dissection and prioritizing of candidate genes of QTL for ...

    Indian Academy of Sciences (India)

    of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA. 5Mudanjiang ..... Fragile X mental retardation gene 1,. −2.1 ... stimulus/stress and signalling associated with acute-phase response were .... This work was supported by the Center of Genomics and Bioinfor- matics and ...

  13. Investigation of the molecular relationship between breast cancer and obesity by candidate gene prioritization methods

    Directory of Open Access Journals (Sweden)

    Saba Garshasbi

    2015-10-01

    Full Text Available Background: Cancer and obesity are two major public health concerns. More than 12 million cases of cancer are reported annually. Many reports confirmed obesity as a risk factor for cancer. The molecular relationship between obesity and breast cancer has not been clear yet. The purpose of this study was to investigate priorities of effective genes in the molecular relationship between obesity and breast cancer. Methods: In this study, computer simulation method was used for prioritizing the genes that involved in the molecular links between obesity and breast cancer in laboratory of systems biology and bioinformatics (LBB, Tehran University, Tehran, Iran, from March to July 2014. In this study, ENDEAVOUR software was used for prioritizing the genes and integrating multiple data sources was used for data analysis. Training genes were selected from effective genes in obesity and/or breast cancer. Two groups of candidate genes were selected. The first group was included the existential genes in 5 common region chromosomes (between obesity and breast cancer and the second group was included the results of genes microarray data analysis of research Creighton, et al (In 2012 on patients with breast cancer. The microarray data were analyzed with GER2 software (R online software on GEO website. Finally, both training and candidate genes were entered in ENDEAVOUR software package. Results: The candidate genes were prioritized to four style and five genes in ten of the first priorities were repeated twice. In other word, the outcome of prioritizing of 72 genes (Product of microarray data analysis and genes of 5 common chromosome regions (Between obesity and breast cancer showed, 5 genes (TNFRSF10B, F2, IGFALS, NTRK3 and HSP90B1 were the priorities in the molecular connection between obesity and breast cancer. Conclusion: There are some common genes between breast cancer and obesity. So, molecular relationship is confirmed. In this study the possible effect

  14. Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts

    Directory of Open Access Journals (Sweden)

    Spackman K

    2005-04-01

    Full Text Available Abstract Background Text-mining can assist biomedical researchers in reducing information overload by extracting useful knowledge from large collections of text. We developed a novel text-mining method based on analyzing the network structure created by symbol co-occurrences as a way to extend the capabilities of knowledge extraction. The method was applied to the task of automatic gene and protein name synonym extraction. Results Performance was measured on a test set consisting of about 50,000 abstracts from one year of MEDLINE. Synonyms retrieved from curated genomics databases were used as a gold standard. The system obtained a maximum F-score of 22.21% (23.18% precision and 21.36% recall, with high efficiency in the use of seed pairs. Conclusion The method performs comparably with other studied methods, does not rely on sophisticated named-entity recognition, and requires little initial seed knowledge.

  15. Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor

    Directory of Open Access Journals (Sweden)

    Takano Eriko

    2011-09-01

    Full Text Available Abstract Background Streptomyces coelicolor, a model organism of antibiotic producing bacteria, has one of the largest genomes of the bacterial kingdom, including 7825 predicted protein coding genes. A large number of these genes, nearly 34%, are functionally orphan (hypothetical proteins with unknown function. However, in gene expression time course data, many of these functionally orphan genes show interesting expression patterns. Results In this paper, we analyzed all functionally orphan genes of Streptomyces coelicolor and identified a list of "high priority" orphans by combining gene expression analysis and additional phylogenetic information (i.e. the level of evolutionary conservation of each protein. Conclusions The prioritized orphan genes are promising candidates to be examined experimentally in the lab for further characterization of their function.

  16. Prioritization of gene regulatory interactions from large-scale modules in yeast

    Directory of Open Access Journals (Sweden)

    Bringas Ricardo

    2008-01-01

    Full Text Available Abstract Background The identification of groups of co-regulated genes and their transcription factors, called transcriptional modules, has been a focus of many studies about biological systems. While methods have been developed to derive numerous modules from genome-wide data, individual links between regulatory proteins and target genes still need experimental verification. In this work, we aim to prioritize regulator-target links within transcriptional modules based on three types of large-scale data sources. Results Starting with putative transcriptional modules from ChIP-chip data, we first derive modules in which target genes show both expression and function coherence. The most reliable regulatory links between transcription factors and target genes are established by identifying intersection of target genes in coherent modules for each enriched functional category. Using a combination of genome-wide yeast data in normal growth conditions and two different reference datasets, we show that our method predicts regulatory interactions with significantly higher predictive power than ChIP-chip binding data alone. A comparison with results from other studies highlights that our approach provides a reliable and complementary set of regulatory interactions. Based on our results, we can also identify functionally interacting target genes, for instance, a group of co-regulated proteins related to cell wall synthesis. Furthermore, we report novel conserved binding sites of a glycoprotein-encoding gene, CIS3, regulated by Swi6-Swi4 and Ndd1-Fkh2-Mcm1 complexes. Conclusion We provide a simple method to prioritize individual TF-gene interactions from large-scale transcriptional modules. In comparison with other published works, we predict a complementary set of regulatory interactions which yields a similar or higher prediction accuracy at the expense of sensitivity. Therefore, our method can serve as an alternative approach to prioritization for

  17. Finding new genes for non-syndromic hearing loss through an in silico prioritization study.

    Directory of Open Access Journals (Sweden)

    Matteo Accetturo

    Full Text Available At present, 51 genes are already known to be responsible for Non-Syndromic hereditary Hearing Loss (NSHL, but the knowledge of 121 NSHL-linked chromosomal regions brings to the hypothesis that a number of disease genes have still to be uncovered. To help scientists to find new NSHL genes, we built a gene-scoring system, integrating Gene Ontology, NCBI Gene and Map Viewer databases, which prioritizes the candidate genes according to their probability to cause NSHL. We defined a set of candidates and measured their functional similarity with respect to the disease gene set, computing a score ( S S M avg that relies on the assumption that functionally related genes might contribute to the same (disease phenotype. A Kolmogorov-Smirnov test, comparing the pair-wise distribution on the disease gene set with the distribution on the remaining human genes, provided a statistical assessment of this assumption. We found at a p-value 0.99. The twenty top-scored genes were finally examined to evaluate their possible involvement in NSHL. We found that half of them are known to be expressed in human inner ear or cochlea and are mainly involved in remodeling and organization of actin formation and maintenance of the cilia and the endocochlear potential. These findings strongly indicate that our metric was able to suggest excellent NSHL candidates to be screened in patients and controls for causative mutations.

  18. Prioritization of Contaminants of Emerging Concern in Wastewater Treatment Plant Discharges using Chemical:Gene Interactions in Caged Fish.

    Data.gov (United States)

    U.S. Environmental Protection Agency — We examined whether contaminants present in surface waters could be prioritized for further assessment by linking the presence of specific chemicals to gene...

  19. A Gene Module-Based eQTL Analysis Prioritizing Disease Genes and Pathways in Kidney Cancer

    Directory of Open Access Journals (Sweden)

    Mary Qu Yang

    Full Text Available Clear cell renal cell carcinoma (ccRCC is the most common and most aggressive form of renal cell cancer (RCC. The incidence of RCC has increased steadily in recent years. The pathogenesis of renal cell cancer remains poorly understood. Many of the tumor suppressor genes, oncogenes, and dysregulated pathways in ccRCC need to be revealed for improvement of the overall clinical outlook of the disease. Here, we developed a systems biology approach to prioritize the somatic mutated genes that lead to dysregulation of pathways in ccRCC. The method integrated multi-layer information to infer causative mutations and disease genes. First, we identified differential gene modules in ccRCC by coupling transcriptome and protein-protein interactions. Each of these modules consisted of interacting genes that were involved in similar biological processes and their combined expression alterations were significantly associated with disease type. Then, subsequent gene module-based eQTL analysis revealed somatic mutated genes that had driven the expression alterations of differential gene modules. Our study yielded a list of candidate disease genes, including several known ccRCC causative genes such as BAP1 and PBRM1, as well as novel genes such as NOD2, RRM1, CSRNP1, SLC4A2, TTLL1 and CNTN1. The differential gene modules and their driver genes revealed by our study provided a new perspective for understanding the molecular mechanisms underlying the disease. Moreover, we validated the results in independent ccRCC patient datasets. Our study provided a new method for prioritizing disease genes and pathways. Keywords: ccRCC, Causative mutation, Pathways, Protein-protein interaction, Gene module, eQTL

  20. Network Based Integrated Analysis of Phenotype-Genotype Data for Prioritization of Candidate Symptom Genes

    Directory of Open Access Journals (Sweden)

    Xing Li

    2014-01-01

    Full Text Available Background. Symptoms and signs (symptoms in brief are the essential clinical manifestations for individualized diagnosis and treatment in traditional Chinese medicine (TCM. To gain insights into the molecular mechanism of symptoms, we develop a computational approach to identify the candidate genes of symptoms. Methods. This paper presents a network-based approach for the integrated analysis of multiple phenotype-genotype data sources and the prediction of the prioritizing genes for the associated symptoms. The method first calculates the similarities between symptoms and diseases based on the symptom-disease relationships retrieved from the PubMed bibliographic database. Then the disease-gene associations and protein-protein interactions are utilized to construct a phenotype-genotype network. The PRINCE algorithm is finally used to rank the potential genes for the associated symptoms. Results. The proposed method gets reliable gene rank list with AUC (area under curve 0.616 in classification. Some novel genes like CALCA, ESR1, and MTHFR were predicted to be associated with headache symptoms, which are not recorded in the benchmark data set, but have been reported in recent published literatures. Conclusions. Our study demonstrated that by integrating phenotype-genotype relationships into a complex network framework it provides an effective approach to identify candidate genes of symptoms.

  1. A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records.

    Science.gov (United States)

    Jiang, Li; Edwards, Stefan M; Thomsen, Bo; Workman, Christopher T; Guldbrandtsen, Bernt; Sørensen, Peter

    2014-09-24

    Prioritizing genetic variants is a challenge because disease susceptibility loci are often located in genes of unknown function or the relationship with the corresponding phenotype is unclear. A global data-mining exercise on the biomedical literature can establish the phenotypic profile of genes with respect to their connection to disease phenotypes. The importance of protein-protein interaction networks in the genetic heterogeneity of common diseases or complex traits is becoming increasingly recognized. Thus, the development of a network-based approach combined with phenotypic profiling would be useful for disease gene prioritization. We developed a random-set scoring model and implemented it to quantify phenotype relevance in a network-based disease gene-prioritization approach. We validated our approach based on different gene phenotypic profiles, which were generated from PubMed abstracts, OMIM, and GeneRIF records. We also investigated the validity of several vocabulary filters and different likelihood thresholds for predicted protein-protein interactions in terms of their effect on the network-based gene-prioritization approach, which relies on text-mining of the phenotype data. Our method demonstrated good precision and sensitivity compared with those of two alternative complex-based prioritization approaches. We then conducted a global ranking of all human genes according to their relevance to a range of human diseases. The resulting accurate ranking of known causal genes supported the reliability of our approach. Moreover, these data suggest many promising novel candidate genes for human disorders that have a complex mode of inheritance. We have implemented and validated a network-based approach to prioritize genes for human diseases based on their phenotypic profile. We have devised a powerful and transparent tool to identify and rank candidate genes. Our global gene prioritization provides a unique resource for the biological interpretation of data

  2. GeneEd—A Genetics Educational Resource | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... of this page please turn Javascript on. Feature: Genetics 101 GeneEd — A Genetics Educational Resource Past Issues / Summer 2013 Table of ... GeneEd website as part of her lessons on genetics. A recently developed educational website about genetics— GeneEd. ...

  3. GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS.

    Directory of Open Access Journals (Sweden)

    Anselm S Hoppmann

    Full Text Available Genome-wide association studies (GWAS evaluate associations between genetic variants and a trait or disease of interest free of prior biological hypotheses. GWAS require stringent correction for multiple testing, with genome-wide significance typically defined as association p-value <5*10-8. This study presents a new tool that uses external information about genes to prioritize SNP associations (GenToS. For a given list of candidate genes, GenToS calculates an appropriate statistical significance threshold and then searches for trait-associated variants in summary statistics from human GWAS. It thereby allows for identifying trait-associated genetic variants that do not meet genome-wide significance. The program additionally tests for enrichment of significant candidate gene associations in the human GWAS data compared to the number expected by chance. As proof of principle, this report used external information from a comprehensive resource of genetically manipulated and systematically phenotyped mice. Based on selected murine phenotypes for which human GWAS data for corresponding traits were publicly available, several candidate gene input lists were derived. Using GenToS for the investigation of candidate genes underlying murine skeletal phenotypes in data from a large human discovery GWAS meta-analysis of bone mineral density resulted in the identification of significantly associated variants in 29 genes. Index variants in 28 of these loci were subsequently replicated in an independent GWAS replication step, highlighting that they are true positive associations. One signal, COL11A1, has not been discovered through GWAS so far and represents a novel human candidate gene for altered bone mineral density. The number of observed genes that contained significant SNP associations in human GWAS based on murine candidate gene input lists was much greater than the number expected by chance across several complex human traits (enrichment p-value as

  4. Prioritization of contaminants of emerging concern in wastewater treatment plant discharges using chemical: Gene interactions in caged fish

    Science.gov (United States)

    We examined whether contaminants present in surface waters could be prioritized for further assessment by linking the presence of specific chemicals to gene expression changes in exposed fish. Fathead minnows were deployed in cages for 2, 4, or 8 days at three locations near two ...

  5. Text analysis of MEDLINE for discovering functional relationships among genes: evaluation of keyword extraction weighting schemes.

    Science.gov (United States)

    Liu, Ying; Navathe, Shamkant B; Pivoshenko, Alex; Dasigi, Venu G; Dingledine, Ray; Ciliax, Brian J

    2006-01-01

    One of the key challenges of microarray studies is to derive biological insights from the gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the functional links among genes. However, the quality of the keyword lists significantly affects the clustering results. We compared two keyword weighting schemes: normalised z-score and term frequency-inverse document frequency (TFIDF). Two gene sets were tested to evaluate the effectiveness of the weighting schemes for keyword extraction for gene clustering. Using established measures of cluster quality, the results produced from TFIDF-weighted keywords outperformed those produced from normalised z-score weighted keywords. The optimised algorithms should be useful for partitioning genes from microarray lists into functionally discrete clusters.

  6. A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records

    DEFF Research Database (Denmark)

    Jiang, Li; Edwards, Stefan M.; Thomsen, Bo

    2014-01-01

    from PubMed abstracts, OMIM, and GeneRIF records. We also investigated the validity of several vocabulary filters and different likelihood thresholds for predicted protein-protein interactions in terms of their effect on the network-based gene-prioritization approach, which relies on text-mining......Background: Prioritizing genetic variants is a challenge because disease susceptibility loci are often located in genes of unknown function or the relationship with the corresponding phenotype is unclear. A global data-mining exercise on the biomedical literature can establish the phenotypic...

  7. A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records

    DEFF Research Database (Denmark)

    Jiang, Li; Edwards, Stefan M.; Thomsen, Bo

    2014-01-01

    from PubMed abstracts, OMIM, and GeneRIF records. We also investigated the validity of several vocabulary filters and different likelihood thresholds for predicted protein-protein interactions in terms of their effect on the network-based gene-prioritization approach, which relies on text...

  8. Using rule-based machine learning for candidate disease gene prioritization and sample classification of cancer gene expression data.

    Directory of Open Access Journals (Sweden)

    Enrico Glaab

    Full Text Available Microarray data analysis has been shown to provide an effective tool for studying cancer and genetic diseases. Although classical machine learning techniques have successfully been applied to find informative genes and to predict class labels for new samples, common restrictions of microarray analysis such as small sample sizes, a large attribute space and high noise levels still limit its scientific and clinical applications. Increasing the interpretability of prediction models while retaining a high accuracy would help to exploit the information content in microarray data more effectively. For this purpose, we evaluate our rule-based evolutionary machine learning systems, BioHEL and GAssist, on three public microarray cancer datasets, obtaining simple rule-based models for sample classification. A comparison with other benchmark microarray sample classifiers based on three diverse feature selection algorithms suggests that these evolutionary learning techniques can compete with state-of-the-art methods like support vector machines. The obtained models reach accuracies above 90% in two-level external cross-validation, with the added value of facilitating interpretation by using only combinations of simple if-then-else rules. As a further benefit, a literature mining analysis reveals that prioritizations of informative genes extracted from BioHEL's classification rule sets can outperform gene rankings obtained from a conventional ensemble feature selection in terms of the pointwise mutual information between relevant disease terms and the standardized names of top-ranked genes.

  9. Using rule-based machine learning for candidate disease gene prioritization and sample classification of cancer gene expression data.

    Science.gov (United States)

    Glaab, Enrico; Bacardit, Jaume; Garibaldi, Jonathan M; Krasnogor, Natalio

    2012-01-01

    Microarray data analysis has been shown to provide an effective tool for studying cancer and genetic diseases. Although classical machine learning techniques have successfully been applied to find informative genes and to predict class labels for new samples, common restrictions of microarray analysis such as small sample sizes, a large attribute space and high noise levels still limit its scientific and clinical applications. Increasing the interpretability of prediction models while retaining a high accuracy would help to exploit the information content in microarray data more effectively. For this purpose, we evaluate our rule-based evolutionary machine learning systems, BioHEL and GAssist, on three public microarray cancer datasets, obtaining simple rule-based models for sample classification. A comparison with other benchmark microarray sample classifiers based on three diverse feature selection algorithms suggests that these evolutionary learning techniques can compete with state-of-the-art methods like support vector machines. The obtained models reach accuracies above 90% in two-level external cross-validation, with the added value of facilitating interpretation by using only combinations of simple if-then-else rules. As a further benefit, a literature mining analysis reveals that prioritizations of informative genes extracted from BioHEL's classification rule sets can outperform gene rankings obtained from a conventional ensemble feature selection in terms of the pointwise mutual information between relevant disease terms and the standardized names of top-ranked genes.

  10. Analysis of the robustness of network-based disease-gene prioritization methods reveals redundancy in the human interactome and functional diversity of disease-genes.

    Directory of Open Access Journals (Sweden)

    Emre Guney

    Full Text Available Complex biological systems usually pose a trade-off between robustness and fragility where a small number of perturbations can substantially disrupt the system. Although biological systems are robust against changes in many external and internal conditions, even a single mutation can perturb the system substantially, giving rise to a pathophenotype. Recent advances in identifying and analyzing the sequential variations beneath human disorders help to comprehend a systemic view of the mechanisms underlying various disease phenotypes. Network-based disease-gene prioritization methods rank the relevance of genes in a disease under the hypothesis that genes whose proteins interact with each other tend to exhibit similar phenotypes. In this study, we have tested the robustness of several network-based disease-gene prioritization methods with respect to the perturbations of the system using various disease phenotypes from the Online Mendelian Inheritance in Man database. These perturbations have been introduced either in the protein-protein interaction network or in the set of known disease-gene associations. As the network-based disease-gene prioritization methods are based on the connectivity between known disease-gene associations, we have further used these methods to categorize the pathophenotypes with respect to the recoverability of hidden disease-genes. Our results have suggested that, in general, disease-genes are connected through multiple paths in the human interactome. Moreover, even when these paths are disturbed, network-based prioritization can reveal hidden disease-gene associations in some pathophenotypes such as breast cancer, cardiomyopathy, diabetes, leukemia, parkinson disease and obesity to a greater extend compared to the rest of the pathophenotypes tested in this study. Gene Ontology (GO analysis highlighted the role of functional diversity for such diseases.

  11. Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method

    Directory of Open Access Journals (Sweden)

    Carlos Roberto Arias

    2012-01-01

    Full Text Available Finding a genetic disease-related gene is not a trivial task. Therefore, computational methods are needed to present clues to the biomedical community to explore genes that are more likely to be related to a specific disease as biomarker. We present biomarker identification problem using gene prioritization method called gene prioritization from microarray data based on shortest paths, extended with structural and biological properties and edge flux using voting scheme (GP-MIDAS-VXEF. The method is based on finding relevant interactions on protein interaction networks, then scoring the genes using shortest paths and topological analysis, integrating the results using a voting scheme and a biological boosting. We applied two experiments, one is prostate primary and normal samples and the other is prostate primary tumor with and without lymph nodes metastasis. We used 137 truly prostate cancer genes as benchmark. In the first experiment, GP-MIDAS-VXEF outperforms all the other state-of-the-art methods in the benchmark by retrieving the truest related genes from the candidate set in the top 50 scores found. We applied the same technique to infer the significant biomarkers in prostate cancer with lymph nodes metastasis which is not established well.

  12. SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS.

    Science.gov (United States)

    Merelli, Ivan; Calabria, Andrea; Cozzi, Paolo; Viti, Federica; Mosca, Ettore; Milanesi, Luciano

    2013-01-01

    The capability of correlating specific genotypes with human diseases is a complex issue in spite of all advantages arisen from high-throughput technologies, such as Genome Wide Association Studies (GWAS). New tools for genetic variants interpretation and for Single Nucleotide Polymorphisms (SNPs) prioritization are actually needed. Given a list of the most relevant SNPs statistically associated to a specific pathology as result of a genotype study, a critical issue is the identification of genes that are effectively related to the disease by re-scoring the importance of the identified genetic variations. Vice versa, given a list of genes, it can be of great importance to predict which SNPs can be involved in the onset of a particular disease, in order to focus the research on their effects. We propose a new bioinformatics approach to support biological data mining in the analysis and interpretation of SNPs associated to pathologies. This system can be employed to design custom genotyping chips for disease-oriented studies and to re-score GWAS results. The proposed method relies (1) on the data integration of public resources using a gene-centric database design, (2) on the evaluation of a set of static biomolecular annotations, defined as features, and (3) on the SNP scoring function, which computes SNP scores using parameters and weights set by users. We employed a machine learning classifier to set default feature weights and an ontological annotation layer to enable the enrichment of the input gene set. We implemented our method as a web tool called SNPranker 2.0 (http://www.itb.cnr.it/snpranker), improving our first published release of this system. A user-friendly interface allows the input of a list of genes, SNPs or a biological process, and to customize the features set with relative weights. As result, SNPranker 2.0 returns a list of SNPs, localized within input and ontologically enriched genes, combined with their prioritization scores. Different

  13. Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology.

    Science.gov (United States)

    Masino, Aaron J; Dechene, Elizabeth T; Dulik, Matthew C; Wilkens, Alisha; Spinner, Nancy B; Krantz, Ian D; Pennington, Jeffrey W; Robinson, Peter N; White, Peter S

    2014-07-21

    Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging variants that must be individually assessed to establish clear association with patient phenotype. To assist interpretation, we implemented an algorithm that ranks a given set of genes relative to patient phenotype. The algorithm orders genes by the semantic similarity computed between phenotypic descriptors associated with each gene and those describing the patient. Phenotypic descriptor terms are taken from the Human Phenotype Ontology (HPO) and semantic similarity is derived from each term's information content. Model validation was performed via simulation and with clinical data. We simulated 33 Mendelian diseases with 100 patients per disease. We modeled clinical conditions by adding noise and imprecision, i.e. phenotypic terms unrelated to the disease and terms less specific than the actual disease terms. We ranked the causative gene against all 2488 HPO annotated genes. The median causative gene rank was 1 for the optimal and noise cases, 12 for the imprecision case, and 60 for the imprecision with noise case. Additionally, we examined a clinical cohort of subjects with hearing impairment. The disease gene median rank was 22. However, when also considering the patient's exome data and filtering non-exomic and common variants, the median rank improved to 3. Semantic similarity can rank a causative gene highly within a gene list relative to patient phenotype characteristics, provided that imprecision is mitigated. The clinical case results suggest that phenotype rank combined with variant analysis provides significant improvement over the individual approaches. We expect that this combined prioritization approach may increase accuracy and decrease effort for

  14. Prioritization of candidate disease genes by combining topological similarity and semantic similarity.

    Science.gov (United States)

    Liu, Bin; Jin, Min; Zeng, Pan

    2015-10-01

    The identification of gene-phenotype relationships is very important for the treatment of human diseases. Studies have shown that genes causing the same or similar phenotypes tend to interact with each other in a protein-protein interaction (PPI) network. Thus, many identification methods based on the PPI network model have achieved good results. However, in the PPI network, some interactions between the proteins encoded by candidate gene and the proteins encoded by known disease genes are very weak. Therefore, some studies have combined the PPI network with other genomic information and reported good predictive performances. However, we believe that the results could be further improved. In this paper, we propose a new method that uses the semantic similarity between the candidate gene and known disease genes to set the initial probability vector of a random walk with a restart algorithm in a human PPI network. The effectiveness of our method was demonstrated by leave-one-out cross-validation, and the experimental results indicated that our method outperformed other methods. Additionally, our method can predict new causative genes of multifactor diseases, including Parkinson's disease, breast cancer and obesity. The top predictions were good and consistent with the findings in the literature, which further illustrates the effectiveness of our method. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Prioritization of Candidate Genes in QTL Regions for Physiological and Biochemical Traits Underlying Drought Response in Barley (Hordeum vulgare L.

    Directory of Open Access Journals (Sweden)

    Kornelia Gudys

    2018-06-01

    Full Text Available Drought is one of the most adverse abiotic factors limiting growth and productivity of crops. Among them is barley, ranked fourth cereal worldwide in terms of harvested acreage and production. Plants have evolved various mechanisms to cope with water deficit at different biological levels, but there is an enormous challenge to decipher genes responsible for particular complex phenotypic traits, in order to develop drought tolerant crops. This work presents a comprehensive approach for elucidation of molecular mechanisms of drought tolerance in barley at the seedling stage of development. The study includes mapping of QTLs for physiological and biochemical traits associated with drought tolerance on a high-density function map, projection of QTL confidence intervals on barley physical map, and the retrievement of positional candidate genes (CGs, followed by their prioritization based on Gene Ontology (GO enrichment analysis. A total of 64 QTLs for 25 physiological and biochemical traits that describe plant water status, photosynthetic efficiency, osmoprotectant and hormone content, as well as antioxidant activity, were positioned on a consensus map, constructed using RIL populations developed from the crosses between European and Syrian genotypes. The map contained a total of 875 SNP, SSR and CGs, spanning 941.86 cM with resolution of 1.1 cM. For the first time, QTLs for ethylene, glucose, sucrose, maltose, raffinose, α-tocopherol, γ-tocotrienol content, and catalase activity, have been mapped in barley. Based on overlapping confidence intervals of QTLs, 11 hotspots were identified that enclosed more than 60% of mapped QTLs. Genetic and physical map integration allowed the identification of 1,101 positional CGs within the confidence intervals of drought response-specific QTLs. Prioritization resulted in the designation of 143 CGs, among them were genes encoding antioxidants, carboxylic acid biosynthesis enzymes, heat shock proteins, small auxin

  16. Tissue-specific functional networks for prioritizing phenotype and disease genes.

    Directory of Open Access Journals (Sweden)

    Yuanfang Guan

    Full Text Available Integrated analyses of functional genomics data have enormous potential for identifying phenotype-associated genes. Tissue-specificity is an important aspect of many genetic diseases, reflecting the potentially different roles of proteins and pathways in diverse cell lineages. Accounting for tissue specificity in global integration of functional genomics data is challenging, as "functionality" and "functional relationships" are often not resolved for specific tissue types. We address this challenge by generating tissue-specific functional networks, which can effectively represent the diversity of protein function for more accurate identification of phenotype-associated genes in the laboratory mouse. Specifically, we created 107 tissue-specific functional relationship networks through integration of genomic data utilizing knowledge of tissue-specific gene expression patterns. Cross-network comparison revealed significantly changed genes enriched for functions related to specific tissue development. We then utilized these tissue-specific networks to predict genes associated with different phenotypes. Our results demonstrate that prediction performance is significantly improved through using the tissue-specific networks as compared to the global functional network. We used a testis-specific functional relationship network to predict genes associated with male fertility and spermatogenesis phenotypes, and experimentally confirmed one top prediction, Mbyl1. We then focused on a less-common genetic disease, ataxia, and identified candidates uniquely predicted by the cerebellum network, which are supported by both literature and experimental evidence. Our systems-level, tissue-specific scheme advances over traditional global integration and analyses and establishes a prototype to address the tissue-specific effects of genetic perturbations, diseases and drugs.

  17. Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing

    NARCIS (Netherlands)

    I. Jansen (Iris); Ye, H. (Hui); Heetveld, S. (Sasja); Lechler, M.C. (Marie C.); Michels, H. (Helen); Seinstra, R.I. (Renée I.); Lubbe, S.J. (Steven J.); Drouet, V. (Valérie); S. Lesage (Suzanne); E. Majounie (Elisa); Gibbs, J.R. (J.Raphael); M.A. Nalls (Michael); M. Ryten (Mina); Botia, J.A. (Juan A.); J. Vandrovcova (Jana); J. Simón-Sánchez (Javier); Castillo-Lizardo, M. (Melissa); P. Rizzu (Patrizia); Blauwendraat, C. (Cornelis); Chouhan, A.K. (Amit K.); Li, Y. (Yarong); Yogi, P. (Puja); N. Amin (Najaf); C.M. van Duijn (Cornelia); Morris, H.R. (Huw R.); Brice, A. (Alexis); A. Singleton (Andrew); David, D.C. (Della C.); Nollen, E.A. (Ellen A.); A. Jain (Ashok); J.M. Shulman; P. Heutink (Peter); D.G. Hernandez (Dena); S. Arepalli (Sampath); J. Brooks (Janet); Price, R. (Ryan); Nicolas, A. (Aude); S. Chong (Sean); M.R. Cookson (Mark); A. Dillman (Allissa); M. Moore (Matt); B.J. Traynor (Bryan); A. Singleton (Andrew); V. Plagnol (Vincent); Nicholas W Wood,; U.-M. Sheerin (Una-Marie); Jose M Bras,; K. Charlesworth (Kate); M. Gardner (Mac); R. Guerreiro (Rita); D. Trabzuni (Danyah); Hardy, J. (John); M. Sharma; M. Saad (Mohamad); Javier Simón-Sánchez,; C. Schulte (Claudia); J.C. Corvol (Jean-Christophe); Dürr, A. (Alexandra); M. Vidailhet (M.); S. Sveinbjörnsdóttir (Sigurlaug); R.A. Barker (Roger); Caroline H Williams-Gray,; Y. Ben-Shlomo; H.W. Berendse (Henk W.); K.D. van Dijk (Karin); D. Berg (Daniela); K. Brockmann; K.D. Wurster (Kathrin); Mätzler, W. (Walter); Gasser, T. (Thomas); M. Martinez (Maria); R.M.A. de Bie (Rob); A. Biffi (Alessandro); D. Velseboer (Daan); B.R. Bloem (Bastiaan); B. Post (Bart); M. Wickremaratchi (Mirdhu); B. van de Warrenburg (Bart); Z. Bochdanovits (Zoltan); M. von Bonin (Malte); H. Pétursson (Hjörvar); O. Riess (Olaf); D.J. Burn (David); Lubbe, S. (Steven); Cooper, J.M. (J Mark); N.H. McNeill (Nathan); Schapira, A. (Anthony); Lungu, C. (Codrin); Chen, H. (Honglei); Dong, J. (Jing); Chinnery, P.F. (Patrick F.); G. Hudson (Gavin); Clarke, C.E. (Carl E.); C. Moorby (Catriona); C. Counsell (Carl); P. Damier (Philippe); J.-F. Dartigues; P. Deloukas (Panagiotis); E. Gray (Emma); T. Edkins (Ted); Hunt, S.E. (Sarah E.); S.C. Potter (Simon); A. Tashakkori-Ghanbaria (Avazeh); G. Deuschl (Günther); D. Lorenz (Delia); D.T. Dexter (David); F. Durif (Frank); J. Evans (Jonathan Mark); Langford, C. (Cordelia); T. Foltynie (Thomas); A.M. Goate (Alison); C. Harris (Clare); J.J. van Hilten (Jacobus); A. Hofman (Albert); J.R. Hollenbeck (John R.); J.L. Holton (Janice); Hu, M. (Michele); X. Huang (Xiaohong); Illig, T. (Thomas); P.V. Jónsson (Pálmi); J.-C. Lambert; S.S. O'Sullivan (Sean); T. Revesz (Tamas); K. Shaw (Karen); A.J. Lees (Andrew); P. Lichtner (Peter); P. Limousin (Patricia); G. Lopez; Escott-Price, V. (Valentina); J. Pearson (Justin); N. Williams (Nigel); E. Mudanohwo (Ese); J.S. Perlmutter (Joel); Pollak, P. (Pierre); F. Rivadeneira Ramirez (Fernando); A.G. Uitterlinden (André); S.J. Sawcer (Stephen); H. Scheffer (Hans); I. Shoulson (Ira); L. Shulman (Lee); Smith, C. (Colin); R. Walker (Robert); C.C.A. Spencer (Chris C.); A. Strange (Amy); H. Stefansson (Hreinn); F. Bettella (Francesco); J-A. Zwart (John-Anker); Stockton, J.D. (Joanna D.); D. Talbot; C.M. Tanner (Carlie); F. Tison (François); S. Winder-Rhodes (Sophie); K.P. Bhatia (Kailash)

    2017-01-01

    textabstractBackground: Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we

  18. Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS.

    Science.gov (United States)

    Pan, David Z; Garske, Kristina M; Alvarez, Marcus; Bhagat, Yash V; Boocock, James; Nikkola, Elina; Miao, Zong; Raulerson, Chelsea K; Cantor, Rita M; Civelek, Mete; Glastonbury, Craig A; Small, Kerrin S; Boehnke, Michael; Lusis, Aldons J; Sinsheimer, Janet S; Mohlke, Karen L; Laakso, Markku; Pajukanta, Päivi; Ko, Arthur

    2018-04-17

    Increased adiposity is a hallmark of obesity and overweight, which affect 2.2 billion people world-wide. Understanding the genetic and molecular mechanisms that underlie obesity-related phenotypes can help to improve treatment options and drug development. Here we perform promoter Capture Hi-C in human adipocytes to investigate interactions between gene promoters and distal elements as a transcription-regulating mechanism contributing to these phenotypes. We find that promoter-interacting elements in human adipocytes are enriched for adipose-related transcription factor motifs, such as PPARG and CEBPB, and contribute to heritability of cis-regulated gene expression. We further intersect these data with published genome-wide association studies for BMI and BMI-related metabolic traits to identify the genes that are under genetic cis regulation in human adipocytes via chromosomal interactions. This integrative genomics approach identifies four cis-eQTL-eGene relationships associated with BMI or obesity-related traits, including rs4776984 and MAP2K5, which we further confirm by EMSA, and highlights 38 additional candidate genes.

  19. Medical Movies on the Web Debuts with Gene Kelly's "Combat Fatigue Irritability" 1945 Film | NIH MedlinePlus the ...

    Science.gov (United States)

    ... National Library of Medicine (NLM) is a World War II U.S. Navy training film directed by and starring Gene Kelly, who was then a rising Hollywood star. Combat Fatigue Irritability is a historically significant, yet ...

  20. Prioritization of candidate genes for cattle reproductive traits, based on protein-protein interactions, gene expression, and text-mining

    DEFF Research Database (Denmark)

    Hulsegge, Ina; Woelders, Henri; Smits, Mari

    2013-01-01

    Reproduction is of significant economic importance in dairy cattle. Improved understanding of mechanisms that control estrous behavior and other reproduction traits could help in developing strategies to improve and/or monitor these traits. The objective of this study was to predict and rank gene...

  1. An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility Loci for osteoporosis-related traits.

    Directory of Open Access Journals (Sweden)

    Yi-Hsiang Hsu

    2010-06-01

    Full Text Available Osteoporosis is a complex disorder and commonly leads to fractures in elderly persons. Genome-wide association studies (GWAS have become an unbiased approach to identify variations in the genome that potentially affect health. However, the genetic variants identified so far only explain a small proportion of the heritability for complex traits. Due to the modest genetic effect size and inadequate power, true association signals may not be revealed based on a stringent genome-wide significance threshold. Here, we take advantage of SNP and transcript arrays and integrate GWAS and expression signature profiling relevant to the skeletal system in cellular and animal models to prioritize the discovery of novel candidate genes for osteoporosis-related traits, including bone mineral density (BMD at the lumbar spine (LS and femoral neck (FN, as well as geometric indices of the hip (femoral neck-shaft angle, NSA; femoral neck length, NL; and narrow-neck width, NW. A two-stage meta-analysis of GWAS from 7,633 Caucasian women and 3,657 men, revealed three novel loci associated with osteoporosis-related traits, including chromosome 1p13.2 (RAP1A, p = 3.6x10(-8, 2q11.2 (TBC1D8, and 18q11.2 (OSBPL1A, and confirmed a previously reported region near TNFRSF11B/OPG gene. We also prioritized 16 suggestive genome-wide significant candidate genes based on their potential involvement in skeletal metabolism. Among them, 3 candidate genes were associated with BMD in women. Notably, 2 out of these 3 genes (GPR177, p = 2.6x10(-13; SOX6, p = 6.4x10(-10 associated with BMD in women have been successfully replicated in a large-scale meta-analysis of BMD, but none of the non-prioritized candidates (associated with BMD did. Our results support the concept of our prioritization strategy. In the absence of direct biological support for identified genes, we highlighted the efficiency of subsequent functional characterization using publicly available expression profiling relevant

  2. Gene Prioritization by Integrated Analysis of Protein Structural and Network Topological Properties for the Protein-Protein Interaction Network of Neurological Disorders

    Directory of Open Access Journals (Sweden)

    Yashna Paul

    2016-01-01

    Full Text Available Neurological disorders are known to show similar phenotypic manifestations like anxiety, depression, and cognitive impairment. There is a need to identify shared genetic markers and molecular pathways in these diseases, which lead to such comorbid conditions. Our study aims to prioritize novel genetic markers that might increase the susceptibility of patients affected with one neurological disorder to other diseases with similar manifestations. Identification of pathways involving common candidate markers will help in the development of improved diagnosis and treatments strategies for patients affected with neurological disorders. This systems biology study for the first time integratively uses 3D-structural protein interface descriptors and network topological properties that characterize proteins in a neurological protein interaction network, to aid the identification of genes that are previously not known to be shared between these diseases. Results of protein prioritization by machine learning have identified known as well as new genetic markers which might have direct or indirect involvement in several neurological disorders. Important gene hubs have also been identified that provide an evidence for shared molecular pathways in the neurological disease network.

  3. MedlinePlus

    Data.gov (United States)

    U.S. Department of Health & Human Services — MedlinePlus is the National Institutes of Health's Web site for patients and their families and friends. Produced by the National Library of Medicine, the world’s...

  4. MedlinePlus Tour

    Science.gov (United States)

    ... captioning, click the CC button on the lower right-hand corner of the player. Video player keyboard shortcuts Transcript Welcome to MedlinePlus, the consumer health information website from the National Library of ...

  5. MedlinePlus FAQ: MedlinePlus and MEDLINE/PubMed

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    ... What is the difference between MedlinePlus and MEDLINE/PubMed? To use the sharing features on this page, ... latest health professional articles on your topic. MEDLINE/PubMed: Is a database of professional biomedical literature Is ...

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    ... want to link patients or healthcare providers from electronic health record (EHR) systems to relevant MedlinePlus information, use MedlinePlus ... updates Subscribe to RSS Follow us Disclaimers Copyright Privacy Accessibility Quality Guidelines Viewers & Players MedlinePlus Connect for ...

  7. Articles about MedlinePlus

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    ... MedlinePlus → Articles about MedlinePlus URL of this page: https://medlineplus.gov/bibliography.html Articles about MedlinePlus To ... Dec 29]; 3(5):256-60. Available from: http://ecp.acponline.org/sepoct00/nlm.htm . Marill JL, ...

  8. MedlinePlus FAQ: What's the difference between MedlinePlus and MedlinePlus Connect?

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    ... MedlinePlus Connect is a free service that allows electronic health record (EHR) systems to easily link users to MedlinePlus, ... updates Subscribe to RSS Follow us Disclaimers Copyright Privacy Accessibility Quality Guidelines Viewers & Players MedlinePlus Connect for ...

  9. IT Project Prioritization Process

    DEFF Research Database (Denmark)

    Shollo, Arisa; Constantiou, Ioanna

    2013-01-01

    In most of the large companies IT project prioritization process is designed based on principles of evidencebased management. We investigate a case of IT project prioritization in a financial institution, and in particular, how managers practice evidence-based management during this process. We use...... a rich dataset built from a longitudinal study of the prioritization process for the IT projects. Our findings indicate that managers reach a decision not only by using evidence but from the interplay between the evidence and the judgment devices that managers employ. The interplay between evidence...

  10. Prioritization of Capital Projects

    National Research Council Canada - National Science Library

    LaVielle, Michael

    2002-01-01

    Public works capital projects in the U,S, naval forces are not prioritized and funded in a way that best uses limited operations resources and maintenance dollars, This thesis develops a linear model...

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    ... version of this page please turn Javascript on. Mobile MedlinePlus Past Issues / Spring 2013 Table of Contents Trusted medical information on your mobile phone http://m.medlineplus.gov Wondering what the ...

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  13. Search Tips: MedlinePlus

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  17. Prioritized Abduction with CHR

    DEFF Research Database (Denmark)

    Christiansen, Henning

    2008-01-01

    A class of Prioritized Abductive Logic Programs (PrioALPs) is introduced and an implementation is developed in CHR for solving abductive problems, providing minimal explanations with best-first search. Priorities may represent probabilities or a cost function to be optimized. Compared with other...

  18. Beyond MEDLINE for literature searches.

    Science.gov (United States)

    Conn, Vicki S; Isaramalai, Sang-arun; Rath, Sabyasachi; Jantarakupt, Peeranuch; Wadhawan, Rohini; Dash, Yashodhara

    2003-01-01

    To describe strategies for a comprehensive literature search. MEDLINE searches result in limited numbers of studies that are often biased toward statistically significant findings. Diversified search strategies are needed. Empirical evidence about the recall and precision of diverse search strategies is presented. Challenges and strengths of each search strategy are identified. Search strategies vary in recall and precision. Often sensitivity and specificity are inversely related. Valuable search strategies include examination of multiple diverse computerized databases, ancestry searches, citation index searches, examination of research registries, journal hand searching, contact with the "invisible college," examination of abstracts, Internet searches, and contact with sources of synthesized information. Extending searches beyond MEDLINE enables researchers to conduct more systematic comprehensive searches.

  19. Prioritizing equipment for replacement.

    Science.gov (United States)

    Capuano, Mike

    2010-01-01

    It is suggested that clinical engineers take the lead in formulating evaluation processes to recommend equipment replacement. Their skill, knowledge, and experience, combined with access to equipment databases, make them a logical choice. Based on ideas from Fennigkoh's scheme, elements such as age, vendor support, accumulated maintenance cost, and function/risk were used.6 Other more subjective criteria such as cost benefits and efficacy of newer technology were not used. The element of downtime was also omitted due to the data element not being available. The resulting Periop Master Equipment List and its rationale was presented to the Perioperative Services Program Council. They deemed the criteria to be robust and provided overwhelming acceptance of the list. It was quickly put to use to estimate required capital funding, justify items already thought to need replacement, and identify high-priority ranked items for replacement. Incorporating prioritization criteria into an existing equipment database would be ideal. Some commercially available systems do have the basic elements of this. Maintaining replacement data can be labor-intensive regardless of the method used. There is usually little time to perform the tasks necessary for prioritizing equipment. However, where appropriate, a clinical engineering department might be able to conduct such an exercise as shown in the following case study.

  20. Prioritized Contact Transport Stream

    Science.gov (United States)

    Hunt, Walter Lee, Jr. (Inventor)

    2015-01-01

    A detection process, contact recognition process, classification process, and identification process are applied to raw sensor data to produce an identified contact record set containing one or more identified contact records. A prioritization process is applied to the identified contact record set to assign a contact priority to each contact record in the identified contact record set. Data are removed from the contact records in the identified contact record set based on the contact priorities assigned to those contact records. A first contact stream is produced from the resulting contact records. The first contact stream is streamed in a contact transport stream. The contact transport stream may include and stream additional contact streams. The contact transport stream may be varied dynamically over time based on parameters such as available bandwidth, contact priority, presence/absence of contacts, system state, and configuration parameters.

  1. MedlinePlus Milestones: 1998-present

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  4. Place prioritization for biodiversity content

    Indian Academy of Sciences (India)

    The prioritization of places on the basis of biodiversity content is part of any systematic biodiversity conservation planning process. The place prioritization procedure implemented in the ResNet software package is described. This procedure is primarily based on the principles of rarity and complementarity. Application of the ...

  5. MedlinePlus XML Data Sources

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    ... on MedlinePlus health topic pages. With the Web service, software developers can build applications that leverage the authoritative, reliable health information in MedlinePlus. The MedlinePlus Web service is free of charge and does not require ...

  6. Self-Prioritization Beyond Perception.

    Science.gov (United States)

    Schäfer, Sarah; Wentura, Dirk; Frings, Christian

    2015-01-01

    Recently, Sui, He, and Humphreys (2012) introduced a new paradigm to measure perceptual self-prioritization processes. It seems that arbitrarily tagging shapes to self-relevant words (I, my, me, and so on) leads to speeded verification times when matching self-relevant word shape pairings (e.g., me - triangle) as compared to non-self-relevant word shape pairings (e.g., stranger - circle). In order to analyze the level at which self-prioritization takes place we analyzed whether the self-prioritization effect is due to a tagging of the self-relevant label and the particular associated shape or due to a tagging of the self with an abstract concept. In two experiments participants showed standard self-prioritization effects with varying stimulus features or different exemplars of a particular stimulus-category suggesting that self-prioritization also works at a conceptual level.

  7. Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico

    Science.gov (United States)

    Maga, A. Murat; Navarro, Nicolas; Cunningham, Michael L.; Cox, Timothy C.

    2015-01-01

    We describe the first application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to map QTL responsible for variation in skull shape and size using a backcross between C57BL/6J and A/J inbred strains. Using 433 animals, 53 3D landmarks, and 882 SNPs from autosomes, we identified seven QTL responsible for the skull size (SCS.qtl) and 30 QTL responsible for the skull shape (SSH.qtl). Size, sex, and direction-of-cross were all significant factors and included in the analysis as covariates. All autosomes harbored at least one SSH.qtl, sometimes up to three. Effect sizes of SSH.qtl appeared to be small, rarely exceeding 1% of the overall shape variation. However, they account for significant amount of variation in some specific directions of the shape space. Many QTL have stronger effect on the neurocranium than expected from a random vector that will parcellate uniformly across the four cranial regions. On the contrary, most of QTL have an effect on the palate weaker than expected. Combined interval length of 30 SSH.qtl was about 315 MB and contained 2476 known protein coding genes. We used a bioinformatics approach to filter these candidate genes and identified 16 high-priority candidates that are likely to play a role in the craniofacial development and disorders. Thus, coupling the QTL mapping approach in model organisms with candidate gene enrichment approaches appears to be a feasible way to identify high-priority candidates genes related to the structure or tissue of interest. PMID:25859222

  8. Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico.

    Directory of Open Access Journals (Sweden)

    A. Murat eMaga

    2015-03-01

    Full Text Available We describe the first application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to map QTL responsible for variation in skull shape and size using a backcross between C57BL/6J and A/J inbred strains. Using 433 animals, 53 3D landmarks, and 882 SNPs from autosomes, we identified seven QTL responsible for the skull size (SCS.qtl and 30 QTL responsible for the skull shape (SSH.qtl. Size, sex and direction-of-cross were all significant factors and included in the analysis as covariates. All autosomes harbored at least one SSH.qtl, sometimes up to three. Effect sizes of SSH.qtl appeared to be small, rarely exceeding 1% of the overall shape variation. However, they account for significant amount of variation in some specific directions of the shape space. Many QTL have stronger effect on the neurocranium than expected from a random vector that will parcellate uniformly across the four cranial regions. On the contrary, most of QTL have an effect on the palate weaker than expected. Combined interval length of 30 SSH.qtl was about 315MB and contained 2,476 known protein coding genes. We used a bioinformatics approach to filter these candidate genes and identified 16 high-priority candidates that are likely to play a role in the craniofacial development and disorders. Thus, coupling the QTL mapping approach in model organisms with candidate gene enrichment approaches appears to be a feasible way to identify high-priority candidates genes related to the structure or tissue of interest.

  9. PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm

    Directory of Open Access Journals (Sweden)

    Chuong Cheng-Ming

    2006-10-01

    Full Text Available Abstract Background Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts. Results PubFocus web server automates analysis of MEDLINE/PubMed search queries by enriching them with two widely used human factor-based bibliometric indicators of publication quality: journal impact factor and volume of forward references. In addition to providing basic volumetric statistics, PubFocus also prioritizes citations and evaluates authors' impact on the field of search. PubFocus also analyses presence and occurrence of biomedical key terms within citations by utilizing controlled vocabularies. Conclusion We have developed citations' prioritisation algorithm based on journal impact factor, forward referencing volume, referencing dynamics, and author's contribution level. It can be applied either to the primary set of PubMed search results or to the subsets of these results identified through key terms from controlled biomedical vocabularies and ontologies. NCI (National Cancer Institute thesaurus and MGD (Mouse Genome Database mammalian gene orthology have been implemented for key terms analytics. PubFocus provides a scalable platform for the integration of multiple available ontology databases. PubFocus analytics can be adapted for input sources of biomedical citations other than PubMed.

  10. Prioritizing like nuclear smugglers

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, S A

    1999-07-01

    An individual or group attempting to smuggle nuclear material out of a country has a choice of what border crossing to use and how to do it. If it is possible to think like a smuggler and determine what preferences one would have, then we could protect those smuggler-preferred border crossings first. Thinking like a smuggler requires that one understand a host of things: who is likely to smuggle and what might they have obtained, where they might have gotten it, and where they would like to deliver or sell it, how they will attempt to pass customs, how they might travel on both sides of the border, and what influences they might have on customs officials. After collecting data on criminology, geography, and much else, it is necessary to paste the data together into scenarios to ensure that self-consistent smuggling plans are created. These lead to counter-smuggling opportunities. Smuggling by amateurs turns out to be of a different class than professional smuggling, and needs to be countered differently. This work also assists in formulating key policy questions useful to guide counter-smuggling efforts. This methodology was developed for DOE/NN-43 for assistance with prioritization within the Second Line of Defense program.

  11. Prioritizing like nuclear smugglers

    International Nuclear Information System (INIS)

    Erickson, S.A.

    1999-01-01

    An individual or group attempting to smuggle nuclear material out of a country has a choice of what border crossing to use and how to do it. If it is possible to think like a smuggler and determine what preferences one would have, then we could protect those smuggler-preferred border crossings first. Thinking like a smuggler requires that one understand a host of things: who is likely to smuggle and what might they have obtained, where they might have gotten it, and where they would like to deliver or sell it, how they will attempt to pass customs, how they might travel on both sides of the border, and what influences they might have on customs officials. After collecting data on criminology, geography, and much else, it is necessary to paste the data together into scenarios to ensure that self-consistent smuggling plans are created. These lead to counter-smuggling opportunities. Smuggling by amateurs turns out to be of a different class than professional smuggling, and needs to be countered differently. This work also assists in formulating key policy questions useful to guide counter-smuggling efforts. This methodology was developed for DOE/NN-43 for assistance with prioritization within the Second Line of Defense program

  12. A prioritization of research activities

    International Nuclear Information System (INIS)

    Pittman, J.W.

    1988-12-01

    This report presents the results of the efforts in prioritizing the activities in the Office of Research. The purpose of this prioritization is to provide a basis on which to make management decisions. The report describes also the methodology and criteria upon which the priority rankings are based. Each activity was evaluated against four attributes. These attributes are: safety assurance, usefulness, appropriateness and resources. This report will be periodically revised to include the prioritization of new activities, deletion of completed activities and to reflect changes in budget allocations and projections. 3 refs., 5 figs

  13. Neutrosophy for software requirement prioritization

    Directory of Open Access Journals (Sweden)

    Ronald Barriga Dias

    2017-09-01

    Full Text Available Software engineers are involved in complex decisions that require multiples viewpoints. A specific case is the requirement prioritization process. This process is used to decide which software requirement to develop in certain release from a group of candidate requirements. Criteria involved in this process can involve indeterminacy. In this paper a software requirement prioritization model is develop based SVN numbers. Finally, an illustrative example is presented in order to show the proposed model.

  14. OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants

    KAUST Repository

    Boudellioua, Imene; Kulmanov, Maxat; Schofield, Paul N; Gkoutos, Georgios V; Hoehndorf, Robert

    2018-01-01

    patient phenotypes to databases of gene-phenotype associations observed in clinical research can provide useful information and improve variant prioritization for Mendelian diseases. Additionally, background knowledge about interactions between genes can

  15. MedlinePlus Connect: Web Service

    Science.gov (United States)

    ... MedlinePlus Connect → Web Service URL of this page: https://medlineplus.gov/connect/service.html MedlinePlus Connect: Web ... will change.) Old URLs New URLs Web Application https://apps.nlm.nih.gov/medlineplus/services/mpconnect.cfm? ...

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    Science.gov (United States)

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  17. MedlinePlus Connect: Technical Information

    Science.gov (United States)

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  18. MedlinePlus Connect: Email List

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  19. MedlinePlus.gov on Twitter

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    ... page please turn Javascript on. MedlinePlus.gov on Twitter Past Issues / Fall 2009 Table of Contents You can now follow MedlinePlus.gov on Twitter: twitter.com/medlineplus4you The medlineplus4you Twitter feed provides ...

  20. Finding biomedical categories in Medline®

    Directory of Open Access Journals (Sweden)

    Yeganova Lana

    2012-10-01

    Full Text Available Abstract Background There are several humanly defined ontologies relevant to Medline. However, Medline is a fast growing collection of biomedical documents which creates difficulties in updating and expanding these humanly defined ontologies. Automatically identifying meaningful categories of entities in a large text corpus is useful for information extraction, construction of machine learning features, and development of semantic representations. In this paper we describe and compare two methods for automatically learning meaningful biomedical categories in Medline. The first approach is a simple statistical method that uses part-of-speech and frequency information to extract a list of frequent nouns from Medline. The second method implements an alignment-based technique to learn frequent generic patterns that indicate a hyponymy/hypernymy relationship between a pair of noun phrases. We then apply these patterns to Medline to collect frequent hypernyms as potential biomedical categories. Results We study and compare these two alternative sets of terms to identify semantic categories in Medline. We find that both approaches produce reasonable terms as potential categories. We also find that there is a significant agreement between the two sets of terms. The overlap between the two methods improves our confidence regarding categories predicted by these independent methods. Conclusions This study is an initial attempt to extract categories that are discussed in Medline. Rather than imposing external ontologies on Medline, our methods allow categories to emerge from the text.

  1. Automatic inference of indexing rules for MEDLINE

    Directory of Open Access Journals (Sweden)

    Shooshan Sonya E

    2008-11-01

    Full Text Available Abstract Background: Indexing is a crucial step in any information retrieval system. In MEDLINE, a widely used database of the biomedical literature, the indexing process involves the selection of Medical Subject Headings in order to describe the subject matter of articles. The need for automatic tools to assist MEDLINE indexers in this task is growing with the increasing number of publications being added to MEDLINE. Methods: In this paper, we describe the use and the customization of Inductive Logic Programming (ILP to infer indexing rules that may be used to produce automatic indexing recommendations for MEDLINE indexers. Results: Our results show that this original ILP-based approach outperforms manual rules when they exist. In addition, the use of ILP rules also improves the overall performance of the Medical Text Indexer (MTI, a system producing automatic indexing recommendations for MEDLINE. Conclusion: We expect the sets of ILP rules obtained in this experiment to be integrated into MTI.

  2. NIH Institutes and MLN MedlinePlus Advisory Board | NIH MedlinePlus the Magazine

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    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [3.1 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  3. Developing optimized prioritizing road maintenance

    Directory of Open Access Journals (Sweden)

    Ewadh Hussein Ali

    2018-01-01

    Full Text Available Increased demand for efficient maintenance of the existing roadway system needs optimal usage of the allocated funds. The paper demonstrates optimized methods for prioritizing maintenance implementation projects. A selected zone of roadway system in Kerbala city represents the study area to demonstrate the application of the developed prioritization process. Paver system PAVER integrated with GIS is used to estimate and display the pavement condition index PCI, thereby to establish a priority of maintenance. In addition to simple ranking method by PCI produced by the output of PAVER, the paper introduces PCI measure for each section of roadway. The paper introduces ranking by multiple measures investigated through expert knowledge about measures that affect prioritization and their irrespective weights due to a predesigned questionnaire. The maintenance priority index (MPI is related to cost of suitable proposed maintenance, easiness of proposed maintenance, average daily traffic and functional classification of the roadway in addition to PCI. Further, incremental benefit-cost analysis ranking provide an optimized process due to benefit and cost of maintenance. The paper introduces efficient display of layout and ranking for the selected zone of roadway system based on MPI index and incremental BCR method. Although the two developed methods introduce different layout display for priority, statistical test shows that no significant difference between ranking of all methods of prioritization.

  4. Prioritization of generic safety issues

    International Nuclear Information System (INIS)

    Emrit, R.; Minners, W.; VanderMolen, H.

    1983-12-01

    This report presents the priority rankings for generic safety issues related to nuclear power plants. The purpose of these rankings is to assist in the timely and efficient allocation of NRC resources for the resolution of those safety issues that have a significant potential for reducing risk. The report focuses on the prioritization of generic safety issues. Issues primarily concerned with the licensing process or environmental protection and not directly related to safety have been excluded from prioritization. The prioritized issues include: TMI Action Plan items under development; previously proposed issues covered by Task Action Plans, except issues designated at Unresolved Safety Issues (USIs) which had already been assigned high priority; and newly-proposed issues. Future supplements to this report will include the prioritization of additional issues. The safety priority rankings are HIGH, MEDIUM, LOW, and DROP and have been assigned on the basis of risk significance estimates, the ratio of risk to costs and other impacts estimated to result if resolutions of the safety issues were implemented, and the consideration of uncertainties and other quantitative or qualitative factors. To the extent practical, estimates are quantitative

  5. Antibiotic Resistance: MedlinePlus Health Topic

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    ... GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español You Are Here: Home → Health Topics → Antibiotic Resistance URL of this page: https://medlineplus.gov/antibioticresistance. ...

  6. Newborn Screening: MedlinePlus Health Topic

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    ... more articles Reference Desk Glossary (National Center for Biotechnology Information) Find an Expert Eunice Kennedy Shriver National ... other than English on Newborn Screening NIH MedlinePlus Magazine Hearing Loss: Screening Newborns Screening Newborns' Hearing Now ...

  7. MedlinePlus: Awards and Recognition

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    ... winner of the 2005 World Summit on the Information Society Awards for e-health. Winner of the Thomas Reuters/Frank Bradway Rogers Information Advancement Award in 2014 for MedlinePlus Connect and ...

  8. MedlinePlus Connect: How it Works

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  9. Liver Transplantation: MedlinePlus Health Topic

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    ... Statistics and Research The SRTR/OPTN Annual Data Report (Scientific Registry of Transplant Recipients) Clinical Trials ClinicalTrials.gov: Liver Transplantation (National Institutes of Health) Journal Articles References and abstracts from MEDLINE/PubMed (National ...

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    ... Bar Home Current Issue Past Issues NIH MedlinePlus Salud Past Issues / Winter 2009 Table of Contents For ... this page please turn Javascript on. ¡A su salud! Los Institutos Nacionales de la Salud (NIH, por ...

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  14. Folic Acid: MedlinePlus Health Topic

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  15. Pneumococcal Infections: MedlinePlus Health Topic

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  18. Child Safety: MedlinePlus Health Topic

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  19. Diets: MedlinePlus Health Topic

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    ... Spanish Mediterranean diet (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Diets updates by ... foods Diet-busting foods Mediterranean diet Related Health Topics Child Nutrition DASH Eating Plan Diabetic Diet Nutrition ...

  20. Colonoscopy: MedlinePlus Health Topic

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    ... Spanish Virtual colonoscopy (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Colonoscopy updates by ... Colonoscopy Colonoscopy discharge Sigmoidoscopy Virtual colonoscopy Related Health Topics Colonic Diseases Colonic Polyps Colorectal Cancer National Institutes ...

  1. Pneumocystis Infections: MedlinePlus Health Topic

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    ... Pneumocystis jiroveci pneumonia (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Pneumocystis Infections updates ... GO MEDICAL ENCYCLOPEDIA Pneumocystis jiroveci pneumonia Related Health Topics HIV/AIDS HIV/AIDS and Infections Pneumonia National ...

  2. Collapsed Lung: MedlinePlus Health Topic

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  3. Male Infertility: MedlinePlus Health Topic

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    ... Spanish Testicular biopsy (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Male Infertility updates ... analysis Sperm release pathway Testicular biopsy Related Health Topics Assisted Reproductive Technology Female Infertility Infertility National Institutes ...

  4. Prediabetes:MedlinePlus Health Topic

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  5. Healthy Aging: MedlinePlus Health Topic

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  6. Psoriatic Arthritis: MedlinePlus Health Topic

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    ... Handouts Psoriatic arthritis (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Psoriatic Arthritis updates ... this? GO MEDICAL ENCYCLOPEDIA Psoriatic arthritis Related Health Topics Arthritis Psoriasis National Institutes of Health The primary ...

  7. Hip Replacement: MedlinePlus Health Topic

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    ... invasive hip replacement (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Hip Replacement updates ... replacement - precautions Minimally invasive hip replacement Related Health Topics Hip Injuries and Disorders National Institutes of Health ...

  8. Diabetes: MedlinePlus Health Topic

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    ... High blood sugar (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Diabetes updates by ... ketones test Show More Show Less Related Health Topics A1C Blood Sugar Diabetes and Pregnancy Diabetes Complications ...

  9. Platelet Disorders: MedlinePlus Health Topic

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    ... Thromobocytopenia - drug-induced (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Platelet Disorders updates ... Willebrand disease Show More Show Less Related Health Topics Bleeding Disorders Blood Clots Blood Count Tests Blood ...

  10. Cardiac Rehabilitation: MedlinePlus Health Topic

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    ... in Spanish Electrocardiogram (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Cardiac Rehabilitation updates ... How to take your pulse Pulse Related Health Topics Heart Attack Heart Diseases How to Prevent Heart ...

  11. Dialysis: MedlinePlus Health Topic

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    ... access for hemodialysis (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Dialysis updates by ... for hemodialysis Show More Show Less Related Health Topics Creatinine Kidney Cysts Kidney Failure Peritoneal Disorders National ...

  12. Eye Wear: MedlinePlus Health Topic

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    ... When You Exercise (National Institute on Aging) - PDF Topic Image MedlinePlus Email Updates Get Eye Wear updates by email What's this? GO Related Health Topics Refractive Errors National Institutes of Health The primary ...

  13. Cardiac Arrest: MedlinePlus Health Topic

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    ... Handouts Cardiac arrest (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Cardiac Arrest updates ... this? GO MEDICAL ENCYCLOPEDIA Cardiac arrest Related Health Topics Arrhythmia CPR Pacemakers and Implantable Defibrillators National Institutes ...

  14. Kawasaki Disease: MedlinePlus Health Topic

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    ... Spanish Kawasaki disease (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Kawasaki Disease updates ... GO MEDICAL ENCYCLOPEDIA Electrocardiogram Kawasaki disease Related Health Topics Vasculitis National Institutes of Health The primary NIH ...

  15. Diabetic Diet: MedlinePlus Health Topic

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  16. Infection Control: MedlinePlus Health Topic

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  17. Menopause: MedlinePlus Health Topic

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  18. Vaginitis: MedlinePlus Health Topic

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  19. Hearing Aids: MedlinePlus Health Topic

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  20. Kidney Tests: MedlinePlus Health Topic

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  1. Ischemic Stroke: MedlinePlus Health Topic

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  2. Pulmonary Rehabilitation: MedlinePlus Health Topic

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  3. Savannah River Site prioritization of transition activities

    International Nuclear Information System (INIS)

    Finley, R.H.

    1993-11-01

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D ampersand D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities

  4. The Medline/full-text research project.

    Science.gov (United States)

    McKinin, E J; Sievert, M; Johnson, E D; Mitchell, J A

    1991-05-01

    This project was designed to test the relative efficacy of index terms and full-text for the retrieval of documents in those MEDLINE journals for which full-text searching was also available. The full-text files used were MEDIS from Mead Data Central and CCML from BRS Information Technologies. One hundred clinical medical topics were searched in these two files as well as the MEDLINE file to accumulate the necessary data. It was found that full-text identified significantly more relevant articles than did the indexed file, MEDLINE. The full-text searches, however, lacked the precision of searches done in the indexed file. Most relevant items missed in the full-text files, but identified in MEDLINE, were missed because the searcher failed to account for some aspect of natural language, used a logical or positional operator that was too restrictive, or included a concept which was implied, but not expressed in the natural language. Very few of the unique relevant full-text citations would have been retrieved by title or abstract alone. Finally, as of July, 1990 the more current issue of a journal was just as likely to appear in MEDLINE as in one of the full-text files.

  5. Pain Relievers: MedlinePlus Health Topic

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    ... Health) ClinicalTrials.gov: Narcotics (National Institutes of Health) Journal Articles References and abstracts from MEDLINE/PubMed (National ... Concentration Before Giving Acetaminophen to Infants (Food and Drug Administration) ... Related Health Topics Chronic Pain Medicines Opioid Abuse and Addiction Over-the-Counter Medicines Pain Other ...

  6. Heart Surgery: MedlinePlus Health Topic

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    ... Living With Related Issues Specifics See, Play and Learn Videos and Tutorials Research Clinical Trials Journal Articles Resources ... Also in Spanish Videos and Tutorials MedlinePlus: Surgery Videos ... strategy is better to reduce postoperative stroke... Article: Ferumoxtyol-enhanced MR ...

  7. A remedial alternative prioritization method

    International Nuclear Information System (INIS)

    Richter, S.A.; Travis, C.C.

    1987-01-01

    This study develops and tests a technique for evaluating and prioritizing alternative remedial actions for hazardous waste sites. The method is based on criteria involving risk, benefit and cost, and identifies the most cost-effective solution to a given remedial problem. Four sites on the Department of Energy's Oak Ridge National Laboratory (ORNL) property in Oak Ridge, Tennessee, were used in a case study to develop and test the method. Results of the case study indicate that even if the cap providing in situ containment must be replaced every 10 years, it is a superior alternative to total excavation of the waste sites

  8. Prioritization methodology for chemical replacement

    Science.gov (United States)

    Cruit, Wendy; Goldberg, Ben; Schutzenhofer, Scott

    1995-01-01

    Since United States of America federal legislation has required ozone depleting chemicals (class 1 & 2) to be banned from production, The National Aeronautics and Space Administration (NASA) and industry have been required to find other chemicals and methods to replace these target chemicals. This project was initiated as a development of a prioritization methodology suitable for assessing and ranking existing processes for replacement 'urgency.' The methodology was produced in the form of a workbook (NASA Technical Paper 3421). The final workbook contains two tools, one for evaluation and one for prioritization. The two tools are interconnected in that they were developed from one central theme - chemical replacement due to imposed laws and regulations. This workbook provides matrices, detailed explanations of how to use them, and a detailed methodology for prioritization of replacement technology. The main objective is to provide a GUIDELINE to help direct the research for replacement technology. The approach for prioritization called for a system which would result in a numerical rating for the chemicals and processes being assessed. A Quality Function Deployment (QFD) technique was used in order to determine numerical values which would correspond to the concerns raised and their respective importance to the process. This workbook defines the approach and the application of the QFD matrix. This technique: (1) provides a standard database for technology that can be easily reviewed, and (2) provides a standard format for information when requesting resources for further research for chemical replacement technology. Originally, this workbook was to be used for Class 1 and Class 2 chemicals, but it was specifically designed to be flexible enough to be used for any chemical used in a process (if the chemical and/or process needs to be replaced). The methodology consists of comparison matrices (and the smaller comparison components) which allow replacement technology

  9. Grand Gulf-prioritization of regulatory requirements

    International Nuclear Information System (INIS)

    Meisner, M.J.

    1993-01-01

    As cost pressures mount, Grand Gulf nuclear station (GGNS) is relying increasingly on various prioritization approaches to implement, modify, eliminate, or defer regulatory requirements. Regulatory requirements can be prioritized through the use of three measures: (1) safety (or risk) significance; (2) cost; and (3) public policy (or political) significance. This paper summarizes GGNS' efforts to implement solutions to regulatory issues using these three prioritization schemes to preserve a balance between cost and safety benefit

  10. NLM MedlinePlus Magazine Team | NIH MedlinePlus the Magazine

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    ... Home Current issue contents Magazine Team Follow us Magazine Team National Library of Medicine at the National ... MLS, MA TREASURER Dennis Cryer, MD NIH MedlinePlus magazine is published by Friends of the NLM in ...

  11. MedlinePlus FAQ: Can you tell me how to cite MedlinePlus pages?

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    ... MedlinePlus, the National Library of Medicine recommends the citation style below, based upon Citing Medicine . This style, like many other citation styles, requires that for online references you include the ...

  12. MedlinePlus FAQ: Will MedlinePlus work on my mobile device?

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    ... mobile.html Question: Will MedlinePlus work on my mobile device? To use the sharing features on this page, ... Some video content might not play on your mobile device. See our FAQ on playing videos on phones ...

  13. NLM MedlinePlus Magazine Team | NIH MedlinePlus the Magazine

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  14. Problem Prioritization in Usability Evaluation:

    DEFF Research Database (Denmark)

    Hertzum, Morten

    2006-01-01

    Severity assessments enable prioritization of problems encountered during usability evaluations and thereby provide a device for guiding the utilization of design resources. However, designers' response to usability evaluations is also influenced by other factors, which may overshadow severity....... With the purpose of enhancing the impact of severity assessments, this study combines a field study of factors that influence the impact of evaluations with an experimental study of severity assessments made during usability inspections. The results show that even in a project receptive to input from evaluations...... their impact was highly dependent on conducting evaluations early. This accorded with an informal method that blended elements of usability evaluation and participatory design and could be extended with user-made severity assessments. The major cost associated with the evaluations was not finding but fixing...

  15. Modeling accidents for prioritizing prevention

    International Nuclear Information System (INIS)

    Hale, A.R.; Ale, B.J.M.; Goossens, L.H.J.; Heijer, T.; Bellamy, L.J; Mud, M.L.; Roelen, A.; Baksteen, H.; Post, J.; Papazoglou, I.A.; Bloemhoff, A.; Oh, J.I.H.

    2007-01-01

    The Workgroup Occupational Risk Model (WORM) project in the Netherlands is developing a comprehensive set of scenarios to cover the full range of occupational accidents. The objective is to support companies in their risk analysis and prioritization of prevention. This paper describes how the modeling has developed through projects in the chemical industry, to this one in general industry and how this is planned to develop further in the future to model risk prevention in air transport. The core modeling technique is based on the bowtie, with addition of more explicit modeling of the barriers needed for risk control, the tasks needed to ensure provision, use, monitoring and maintenance of the barriers, and the management resources and tasks required to ensure that these barrier life cycle tasks are carried out effectively. The modeling is moving from a static notion of barriers which can fail, to seeing risk control dynamically as (fallible) means for staying within a safe envelope. The paper shows how concepts develop slowly over a series of projects as a core team works continuously together. It concludes with some results of the WORM project and some indications of how the modeling is raising fundamental questions about the conceptualization of system safety, which need future resolution

  16. Combating HIV/AIDS | NIH MedlinePlus the Magazine

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  17. Helping others hear better | NIH MedlinePlus the Magazine

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  18. Mary Tyler Moore Helps Launch NIH MedlinePlus Magazine

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  1. Exploring Graphic Medicine | NIH MedlinePlus the Magazine

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  2. The Opioid Crisis | NIH MedlinePlus the Magazine

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  14. Use of prioritization in meeting regulatory requirements

    International Nuclear Information System (INIS)

    Bowling, M.L.; Sommers, D.A.; Girvin, L.M.

    1993-01-01

    The use of prioritization in the allocation of resources is certainly not a new idea. However, the degree to which prioritization must now be used is much greater than ever before. In the past, utilities generally allocated the necessary resources to meet all regulatory requirements and commitments. Prioritization was then applied to the remaining nonregulatory but required needs. This approach to resource allocation is no longer appropriate for the current and projected economic and operating environment. Key reasons for this conclusion are discussed in this paper by staff from Virginia Power

  15. Subscribe to NIH MedlinePlus the Magazine

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  16. Behavioral Correlates of Prioritizing Popularity in Adolescence

    NARCIS (Netherlands)

    van Den Broek, Nina; Deutz, Marike H F; Schoneveld, Elke A.; Burk, William J.; Cillessen, Antonius H N

    2016-01-01

    Little is known about individual differences in adolescents’ motivation to achieve and maintain popularity. This study examined the moderating effects of prioritizing popularity on the associations between popularity and adjustment outcomes in late adolescence. Participants were 314 Dutch

  17. Child Nutrition: MedlinePlus Health Topic

    Science.gov (United States)

    ... status, and HFE gene alterations during... Article: Breaking Habits: The Effect of the French Vending Machine Ban... ... Also in Spanish Energy Drinks and Food Bars: Power or Hype? (Nemours Foundation) Also in Spanish Figuring ...

  18. MetaRanker 2.0: a web server for prioritization of genetic variation data.

    Science.gov (United States)

    Pers, Tune H; Dworzyński, Piotr; Thomas, Cecilia Engel; Lage, Kasper; Brunak, Søren

    2013-07-01

    MetaRanker 2.0 is a web server for prioritization of common and rare frequency genetic variation data. Based on heterogeneous data sets including genetic association data, protein-protein interactions, large-scale text-mining data, copy number variation data and gene expression experiments, MetaRanker 2.0 prioritizes the protein-coding part of the human genome to shortlist candidate genes for targeted follow-up studies. MetaRanker 2.0 is made freely available at www.cbs.dtu.dk/services/MetaRanker-2.0.

  19. Test case prioritization using Cuscuta search

    Directory of Open Access Journals (Sweden)

    Mukesh Mann

    2014-12-01

    Full Text Available Most companies are under heavy time and resource constraints when it comes to testing a software system. Test prioritization technique(s allows the most useful tests to be executed first, exposing faults earlier in the testing process. Thus makes software testing more efficient and cost effective by covering maximum faults in minimum time. But test case prioritization is not an easy and straightforward process and it requires huge efforts and time. Number of approaches is available with their proclaimed advantages and limitations, but accessibility of any one of them is a subject dependent. In this paper, artificial Cuscuta search algorithm (CSA inspired by real Cuscuta parasitism is used to solve time constraint prioritization problem. We have applied CSA for prioritizing test cases in an order of maximum fault coverage with minimum test suite execution and compare its effectiveness with different prioritization ordering. Taking into account the experimental results, we conclude that (i The average percentage of faults detection (APFD is 82.5% using our proposed CSA ordering which is equal to the APFD of optimal and ant colony based ordering whereas No ordering, Random ordering and Reverse ordering has 76.25%, 75%, 68.75% of APFD respectively.

  20. Behavioral Correlates of Prioritizing Popularity in Adolescence.

    Science.gov (United States)

    van den Broek, Nina; Deutz, Marike H F; Schoneveld, Elke A; Burk, William J; Cillessen, Antonius H N

    2016-12-01

    Little is known about individual differences in adolescents' motivation to achieve and maintain popularity. This study examined the moderating effects of prioritizing popularity on the associations between popularity and adjustment outcomes in late adolescence. Participants were 314 Dutch eleventh-grade students (M age  = 16.83 years; 52 % male) who completed measures of popularity, prioritizing popularity, and prosocial, antisocial, and risk behaviors. It was hypothesized that associations between popularity and adjustment outcomes are stronger for adolescents who prioritize popularity. The results indicate that the combination of being popular and valuing popularity was strongly related to antisocial and risk behaviors, but not to prosocial behaviors. Adolescents' social status motivations thus play an important role in the association of popularity with antisocial and risk behaviors in late adolescence.

  1. MetaRanker 2.0: a web server for prioritization of genetic variation data

    DEFF Research Database (Denmark)

    Pers, Tune Hannes; Dworzynski, Piotr; Thomas, Cecilia Engel

    2013-01-01

    MetaRanker 2.0 is a web server for prioritization of common and rare frequency genetic variation data. Based on heterogeneous data sets including genetic association data, protein–protein interactions, large-scale text-mining data, copy number variation data and gene expression experiments, Meta...

  2. NIH Institutes and MLN MedlinePlus Advisory Board

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    ... main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [1.9 mb] ... nih.gov (301) 496-7301 National Institute of Mental Health (NIMH) www.nimh.nih.gov 1-866- ...

  3. MedlinePlus FAQ: Listing Your Web Site

    Science.gov (United States)

    ... JavaScript. Answer: MedlinePlus is a selected list of authoritative resources. MedlinePlus uses quality guidelines to evaluate Web ... ensure that the information we link to is authoritative, accurate, up-to-date, educational and available at ...

  4. A prioritization of generic safety issues

    International Nuclear Information System (INIS)

    Emrit, R.; Riggs, R.; Milstead, W.; Pittman, J.

    1991-07-01

    This report presents the priority rankings for generic safety issues and related to nuclear power plants. The purpose of these rankings is to assist in the timely and efficient allocation of NRC resources for the resolution of those safety issues that have a significant potential for reducing risk. The report focuses on the prioritization of generic safety issues. Issues primarily concerned with the licensing process or environmental protection and not directly related to safety have been excluded from prioritization. The prioritized issues include: TMI Action Plan items under development; previously proposed issues covered by Task Action Plans, except issues designated as Un-resolved Safety Issues (USIs) which had already been assigned high priority; and newly-proposed issues. Future supplements to this report will include the prioritization of additional issues. The safety priority rankings are High, Medium, Low, and Drop and have been assigned on the basis of risk significance estimates, the ratio of risk to costs and other impacts estimated to result if resolutions of the safety issues were implemented, and the consideration of uncertainties and other quantitative or qualitative factors. To the extent practical, estimates are quantitative. 1310 refs

  5. Prioritization of Programmer's Productivity Using Analytic Hierarchy ...

    African Journals Online (AJOL)

    This paper focuses on the application of Analytic Hierarchy Process (AHP) model in the context of prioritizing programmer's productivity in University of Benin, Benin City Nigeria. This is achieved by evaluating the way in which the AHP model can be used to select the best programmer for the purpose of developing software ...

  6. A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data.

    Science.gov (United States)

    Stark, Zornitza; Dashnow, Harriet; Lunke, Sebastian; Tan, Tiong Y; Yeung, Alison; Sadedin, Simon; Thorne, Natalie; Macciocca, Ivan; Gaff, Clara; Oshlack, Alicia; White, Susan M; James, Paul A

    2017-11-01

    Rapid identification of clinically significant variants is key to the successful application of next generation sequencing technologies in clinical practice. The Melbourne Genomics Health Alliance (MGHA) variant prioritization framework employs a gene prioritization index based on clinician-generated a priori gene lists, and a variant prioritization index (VPI) based on rarity, conservation and protein effect. We used data from 80 patients who underwent singleton whole exome sequencing (WES) to test the ability of the framework to rank causative variants highly, and compared it against the performance of other gene and variant prioritization tools. Causative variants were identified in 59 of the patients. Using the MGHA prioritization framework the average rank of the causative variant was 2.24, with 76% ranked as the top priority variant, and 90% ranked within the top five. Using clinician-generated gene lists resulted in ranking causative variants an average of 8.2 positions higher than prioritization based on variant properties alone. This clinically driven prioritization approach significantly outperformed purely computational tools, placing a greater proportion of causative variants top or in the top 5 (permutation P-value=0.001). Clinicians included 40 of the 49 WES diagnoses in their a priori list of differential diagnoses (81%). The lists generated by PhenoTips and Phenomizer contained 14 (29%) and 18 (37%) of these diagnoses respectively. These results highlight the benefits of clinically led variant prioritization in increasing the efficiency of singleton WES data analysis and have important implications for developing models for the funding and delivery of genomic services.

  7. Air pollution and vulnerability: solving the puzzle of prioritization

    CSIR Research Space (South Africa)

    Wright, CY

    2011-01-01

    Full Text Available conditions exacerbates the problem. Air quality management plans identify prioritized strategies for improved air quality independent of consideration of vulnerability. A population exposure and vulnerability risk prioritization framework comprising five...

  8. PRIORITIZING ECONOMIC GROWTH: ENHANCING MACROECONOMIC POLICY CHOICE

    OpenAIRE

    Colin I. BRADFORD, Jr.

    2005-01-01

    This paper spells out a logic for increasing macroeconomic policy space in order to prioritize the goals of growth, employment creation and poverty reduction. First, there is the need to create additional policy instruments so that a greater number of policy goals can be addressed. Frequently, real economy goals get partly crowded out by financial objectives because there are too few instruments for too many goals. Second, the calibrated use of policy tools by degrees of commitment, deploymen...

  9. Welcome to NIH MedlinePlus, the magazine

    Science.gov (United States)

    ... from the world's largest medical library, NIH's National Library of Medicine. MedlinePlus has extensive information from the NIH and other trusted sources on more than 700 diseases and conditions. There ...

  10. Traumatic Brain Injury: MedlinePlus Health Topic

    Science.gov (United States)

    ... injury - discharge (Medical Encyclopedia) Also in Spanish Chronic subdural hematoma (Medical Encyclopedia) Also in Spanish EEG (Medical Encyclopedia) ... Intracranial pressure monitoring (Medical Encyclopedia) Also in Spanish Subdural hematoma (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus ...

  11. Treating Cataracts | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... Claudine Klose, 63, lives on a farm in New York's Hudson Valley. She had successful cataract surgery in 2013 and shared her experience recently with NIH MedlinePlus magazine. What did you notice about your vision that ...

  12. A1C: MedlinePlus Health Topic

    Science.gov (United States)

    ... Numbers: Use Them to Manage Your Diabetes (National Diabetes Education Program) Also in Spanish Clinical Trials ClinicalTrials.gov: Hemoglobin A, Glycosylated (National Institutes of Health) Journal Articles References and abstracts from MEDLINE/PubMed ( ...

  13. To Your Health: NLM Update—MedlinePlus

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    ... illustrate health care May 7 2018 Transcript Genetic architecture of mental disorders April 30 2018 Transcript Why ... MedlinePlus Connect for EHRs For Developers U.S. National Library of Medicine 8600 Rockville Pike, Bethesda, MD 20894 ...

  14. Mentoring in Medicine | NIH MedlinePlus the Magazine

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    ... front is Andrew Morrison, MIM vice president of marketing. Giving Students a Vision of Healthcare Careers Research ... federal tax purposes. Web site: www.fnlm.org Mobile MedlinePlus! Trusted medical information on your mobile phone. ...

  15. MedlinePlus Connect: Frequently Asked Questions (FAQs)

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    ... topic data in XML format. Using the Web service, software developers can build applications that utilize MedlinePlus health topic information. The service accepts keyword searches as requests and returns relevant ...

  16. Kids Create Healthy Comics | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... School Students Using Medline Plus Kids Create Healthy Comics Past Issues / Fall 2015 Table of Contents Fresh, ... use of reliable health information resources." The Four Comic Books Are: The Expert Investigator explores the impact ...

  17. Sexual Problems in Men: MedlinePlus Health Topic

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    ... Spanish Retrograde ejaculation (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Sexual Problems in ... Premature ejaculation Reifenstein syndrome Retrograde ejaculation Related Health Topics Erectile Dysfunction Penis Disorders Prostate Diseases Testicular Disorders ...

  18. Baby Health Checkup: MedlinePlus Health Topic

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    ... Know (Centers for Disease Control and Prevention) - PDF Topic Image MedlinePlus Email Updates Get Baby Health Checkup ... GO MEDICAL ENCYCLOPEDIA Well-child visits Related Health Topics Childhood Immunization Common Infant and Newborn Problems Infant ...

  19. Cancer--Living with Cancer: MedlinePlus Health Topic

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    ... during cancer treatment (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Cancer--Living with ... care plan Show More Show Less Related Health Topics Cancer Cancer Chemotherapy Palliative Care National Institutes of ...

  20. How to Prevent Heart Disease: MedlinePlus Health Topic

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    ... and your heart (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get How to Prevent ... your heart Stress and your heart Related Health Topics Blood Thinners Cholesterol Heart Diseases Heart Health Tests ...

  1. Tetanus, Diphtheria, and Pertussis Vaccines: MedlinePlus Health Topic

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    ... Know (Centers for Disease Control and Prevention) - PDF Topic Image MedlinePlus Email Updates Get Tetanus, Diphtheria, and ... updates by email What's this? GO Related Health Topics Childhood Immunization Diphtheria Immunization Tetanus Whooping Cough National ...

  2. Laser Eye Surgery: MedlinePlus Health Topic

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    ... corneal surgery - discharge (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Laser Eye Surgery ... surgery - what to ask your doctor Related Health Topics Refractive Errors National Institutes of Health The primary ...

  3. Child Mental Health: MedlinePlus Health Topic

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    ... events and children (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Child Mental Health ... in childhood Traumatic events and children Related Health Topics Bullying Child Behavior Disorders Mental Disorders Mental Health ...

  4. Bone Marrow Transplantation: MedlinePlus Health Topic

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    ... marrow transplant - discharge (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Bone Marrow Transplantation ... transplant - slideshow Graft-versus-host disease Related Health Topics Bone Marrow Diseases Stem Cells National Institutes of ...

  5. Nutrition for Seniors: MedlinePlus Health Topic

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    ... America) National Institute on Aging Also in Spanish Topic Image MedlinePlus Email Updates Get Nutrition for Seniors updates by email What's this? GO Related Health Topics Nutrition Seniors' Health National Institutes of Health The ...

  6. Blood Count Tests: MedlinePlus Health Topic

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  7. Hormone Replacement Therapy: MedlinePlus Health Topic

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    ... of hormone therapy (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Hormone Replacement Therapy ... Estrogen overdose Types of hormone therapy Related Health Topics Menopause National Institutes of Health The primary NIH ...

  8. Improved Prioritization Criteria for Road Infrastructure Projects

    Directory of Open Access Journals (Sweden)

    Ionescu Heroiu Marcel

    2016-12-01

    Full Text Available This report’s main aim is to propose a methodology for assessing state-budget-funded projects based on a rigorous selection model, including clear and effective prioritization criteria. This report first argues that project prioritization and selection should be optimized against four dimensions: absorption, impact, legitimacy, and capacity. Second, it provides a diagnostic of the National Program for Local Development (PNDL, managed by the Ministry of Regional Development and Public Administration (MRDPA, as the most significant source of state-budget funding for local infrastructure projects. The PNDL’s current design and implementation leaves room for improvement, as reflected by the lack of strategic direction in allocating funds and the continued rise in the number of projects that get started without a feasible timeline for their completion. Further, this report makes recommendations for improvement of project evaluation and selection procedures for local infrastructure development projects, with a special focus on prioritization criteria and viable funding sources for each type of investment. The practical purpose is to enhance the efficiency and effectiveness of proposed investments, maximizing impact in the context of inherently limited available financial resources. A complementary focus is on opportunities for harmonizing and better coordinating investments across various sources of funding, in the context of nearly EUR 40 billion available to Romania from the EU for the 2014-2020 programming period.

  9. Multi-Stakeholder Case Prioritization in Digital Investigations

    Directory of Open Access Journals (Sweden)

    Joshua I. James

    2014-09-01

    Full Text Available This work examines the problem of case prioritization in digital investigations for better utilization of limited criminal investigation resources. Current methods of case prioritization, as well as observed prioritization methods used in digital forensic investigation laboratories are examined. After, a multi-stakeholder approach to case prioritization is given that may help reduce reputational risk to digital forensic laboratories while improving resource allocation. A survey is given that shows differing opinions of investigation priority between Law Enforcement and the public that is used in the development of a prioritization model. Finally, an example case is given to demonstrate the practicality of the proposed method.

  10. Identifying and Prioritizing Genes involved in Bovine Mastitis

    DEFF Research Database (Denmark)

    Jiang, Li

    In the "omics" era, identification of biological entities underlying complex traits or common diseases is characterized by the integration of high-throughput experiments and knowledge that have benn published or refined in biomedical repositories. Studies in this thesis generate, collect and inte......In the "omics" era, identification of biological entities underlying complex traits or common diseases is characterized by the integration of high-throughput experiments and knowledge that have benn published or refined in biomedical repositories. Studies in this thesis generate, collect...

  11. PubMed alternatives to search MEDLINE: An environmental scan

    Directory of Open Access Journals (Sweden)

    Arun Keepanasseril

    2014-01-01

    Full Text Available The prime objective of this article is to introduce the newer methods to access, search and process MEDLINE citations. It also aims to provide a brief overview of each service′s salient features. A targeted search was conducted in MEDLINE through the OVID gateway. This was followed with a search in Google Scholar as well as Google and Bing. Ninety-two web-based services that can be used to search MEDLINE were identified. The list was shortened to 24 by applying a set of relevancy criteria to select those services more relevant to general medical and dental users. Salient features of the selected services are outlined and a use case based classification of the system has been proposed to help dental practitioners and researchers select the appropriate service for a given purpose.

  12. From Prioritizing Objects to Prioritizing Cues: A Developmental Shift for Cognitive Control

    Science.gov (United States)

    Chevalier, Nicolas; Dauvier, Bruno; Blaye, Agnès

    2018-01-01

    Emerging cognitive control supports increasingly adaptive behaviors and predicts life success, while low cognitive control is a major risk factor during childhood. It is therefore essential to understand how it develops. The present study provides evidence for an age-related shift in the type of information that children prioritize in their…

  13. Semantic prioritization of novel causative genomic variants

    KAUST Repository

    Boudellioua, Imene

    2017-04-17

    Discriminating the causative disease variant(s) for individuals with inherited or de novo mutations presents one of the main challenges faced by the clinical genetics community today. Computational approaches for variant prioritization include machine learning methods utilizing a large number of features, including molecular information, interaction networks, or phenotypes. Here, we demonstrate the PhenomeNET Variant Predictor (PVP) system that exploits semantic technologies and automated reasoning over genotype-phenotype relations to filter and prioritize variants in whole exome and whole genome sequencing datasets. We demonstrate the performance of PVP in identifying causative variants on a large number of synthetic whole exome and whole genome sequences, covering a wide range of diseases and syndromes. In a retrospective study, we further illustrate the application of PVP for the interpretation of whole exome sequencing data in patients suffering from congenital hypothyroidism. We find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants.

  14. Semantic prioritization of novel causative genomic variants

    KAUST Repository

    Boudellioua, Imene; Mohamad Razali, Rozaimi; Kulmanov, Maxat; Hashish, Yasmeen; Bajic, Vladimir B.; Goncalves-Serra, Eva; Schoenmakers, Nadia; Gkoutos, Georgios V.; Schofield, Paul N.; Hoehndorf, Robert

    2017-01-01

    Discriminating the causative disease variant(s) for individuals with inherited or de novo mutations presents one of the main challenges faced by the clinical genetics community today. Computational approaches for variant prioritization include machine learning methods utilizing a large number of features, including molecular information, interaction networks, or phenotypes. Here, we demonstrate the PhenomeNET Variant Predictor (PVP) system that exploits semantic technologies and automated reasoning over genotype-phenotype relations to filter and prioritize variants in whole exome and whole genome sequencing datasets. We demonstrate the performance of PVP in identifying causative variants on a large number of synthetic whole exome and whole genome sequences, covering a wide range of diseases and syndromes. In a retrospective study, we further illustrate the application of PVP for the interpretation of whole exome sequencing data in patients suffering from congenital hypothyroidism. We find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants.

  15. Prioritization of environmental cleanup problems at Hanford

    International Nuclear Information System (INIS)

    Fassbender, L.L.

    1994-01-01

    New technologies and scientific research are needed to clean up the Hanford Site. However, there is insufficient funding to develop every technology that is identified or to undertake every scientific research project that is proposed. Thus, the Department of Energy (DOE) must focus its resources on science and technology (S ampersand T) that will have the most significant impacts on the overall cleanup effort. Hanford has recognized the importance of identifying and prioritizing its most critical problems and the most promising solutions to them. Hanford cleanup will require numerous decisions about technology development and implementation, which will be complicated because there are substantial uncertainties about the risks and the costs of new technologies. Further, the choice of a specific technology for a specific application must be evaluated with respect to multiple (and often conflicting) objectives (e.g., risk reduction, increasing effectiveness, cost reduction, increasing public acceptability, regulatory compliance). This paper provides an overview of the decision analysis methodology that was used to prioritize S ampersand T needs for Hanford cleanup

  16. Supplementary searches of PubMed to improve currency of MEDLINE and MEDLINE In-Process searches via Ovid.

    Science.gov (United States)

    Duffy, Steven; de Kock, Shelley; Misso, Kate; Noake, Caro; Ross, Janine; Stirk, Lisa

    2016-10-01

    The research investigated whether conducting a supplementary search of PubMed in addition to the main MEDLINE (Ovid) search for a systematic review is worthwhile and to ascertain whether this PubMed search can be conducted quickly and if it retrieves unique, recently published, and ahead-of-print studies that are subsequently considered for inclusion in the final systematic review. Searches of PubMed were conducted after MEDLINE (Ovid) and MEDLINE In-Process (Ovid) searches had been completed for seven recent reviews. The searches were limited to records not in MEDLINE or MEDLINE In-Process (Ovid). Additional unique records were identified for all of the investigated reviews. Search strategies were adapted quickly to run in PubMed, and reviewer screening of the results was not time consuming. For each of the investigated reviews, studies were ordered for full screening; in six cases, studies retrieved from the supplementary PubMed searches were included in the final systematic review. Supplementary searching of PubMed for studies unavailable elsewhere is worthwhile and improves the currency of the systematic reviews.

  17. MeSHmap: a text mining tool for MEDLINE.

    OpenAIRE

    Srinivasan, P.

    2001-01-01

    Our research goal is to explore text mining from the metadata included in MEDLINE documents. We present MeSHmap our prototype text mining system that exploits the MeSH indexing accompanying MEDLINE records. MeSHmap supports searches via PubMed followed by user driven exploration of the MeSH terms and subheadings in the retrieved set. The potential of the system goes beyond text retrieval. It may also be used to compare entities of the same type such as pairs of drugs or pairs of procedures et...

  18. A PERSPECTIVE ON PRIORITIZATION IN PROJECT PORTFOLIO ENVIRONMENT

    OpenAIRE

    Eberhardt, Henrik; Lindblom, David

    2011-01-01

    The overbridging aspect of this interpretative master thesis is the implementation of a project prioritizing strategy. The concept is subdivided into three processes and entities, which could be seen as tools; project management office(PMO), project evaluation and project selection, which in turn are discussed separately. The thesis investigates how the tools impact the prioritizing strategy and why a company must follow a certain prioritizing strategy. The primary focus has been an IS/IT dep...

  19. Pacemakers and Implantable Defibrillators: MedlinePlus Health Topic

    Science.gov (United States)

    ... ClinicalTrials.gov: Pacemaker, Artificial (National Institutes of Health) Journal Articles References and abstracts from MEDLINE/PubMed (National ... Leadless Cardiac Pacemakers: The Next Evolution in Pacemaker Technology. ... on Pacemakers and Implantable Defibrillators is the National Heart, Lung, and Blood Institute Other Languages Find health information in languages other than English on Pacemakers and ...

  20. Welcome to MedlinePlus en español

    Science.gov (United States)

    ... para el público de la Biblioteca Nacional de Medicina, la biblioteca médica más grande del mundo. Los ... B. Lindberg, M.D. Director, Biblioteca Nacional de Medicina MedlinePlus.gov/salud Spring 2007 Issue: Volume 2 ...

  1. Comparing Medline citations using modified N-grams

    Science.gov (United States)

    Nawab, Rao Muhammad Adeel; Stevenson, Mark; Clough, Paul

    2014-01-01

    Objective We aim to identify duplicate pairs of Medline citations, particularly when the documents are not identical but contain similar information. Materials and methods Duplicate pairs of citations are identified by comparing word n-grams in pairs of documents. N-grams are modified using two approaches which take account of the fact that the document may have been altered. These are: (1) deletion, an item in the n-gram is removed; and (2) substitution, an item in the n-gram is substituted with a similar term obtained from the Unified Medical Language System  Metathesaurus. N-grams are also weighted using a score derived from a language model. Evaluation is carried out using a set of 520 Medline citation pairs, including a set of 260 manually verified duplicate pairs obtained from the Deja Vu database. Results The approach accurately detects duplicate Medline document pairs with an F1 measure score of 0.99. Allowing for word deletions and substitution improves performance. The best results are obtained by combining scores for n-grams of length 1–5 words. Discussion Results show that the detection of duplicate Medline citations can be improved by modifying n-grams and that high performance can also be obtained using only unigrams (F1=0.959), particularly when allowing for substitutions of alternative phrases. PMID:23715801

  2. Death, dying and informatics: misrepresenting religion on MedLine.

    Science.gov (United States)

    Rodríguez Del Pozo, Pablo; Fins, Joseph J

    2005-07-01

    The globalization of medical science carries for doctors worldwide a correlative duty to deepen their understanding of patients' cultural contexts and religious backgrounds, in order to satisfy each as a unique individual. To become better informed, practitioners may turn to MedLine, but it is unclear whether the information found there is an accurate representation of culture and religion. To test MedLine's representation of this field, we chose the topic of death and dying in the three major monotheistic religions. We searched MedLine using PubMed in order to retrieve and thematically analyze full-length scholarly journal papers or case reports dealing with religious traditions and end-of-life care. Our search consisted of a string of words that included the most common denominations of the three religions, the standard heading terms used by the National Reference Center for Bioethics Literature (NRCBL), and the Medical Subject Headings (MeSH) used by the National Library of Medicine. Eligible articles were limited to English-language papers with an abstract. We found that while a bibliographic search in MedLine on this topic produced instant results and some valuable literature, the aggregate reflected a selection bias. American writers were over-represented given the global prevalence of these religious traditions. Denominationally affiliated authors predominated in representing the Christian traditions. The Islamic tradition was under-represented. MedLine's capability to identify the most current, reliable and accurate information about purely scientific topics should not be assumed to be the same case when considering the interface of religion, culture and end-of-life care.

  3. Death, dying and informatics: misrepresenting religion on MedLine

    Directory of Open Access Journals (Sweden)

    Fins Joseph J

    2005-07-01

    Full Text Available Abstract Background The globalization of medical science carries for doctors worldwide a correlative duty to deepen their understanding of patients' cultural contexts and religious backgrounds, in order to satisfy each as a unique individual. To become better informed, practitioners may turn to MedLine, but it is unclear whether the information found there is an accurate representation of culture and religion. To test MedLine's representation of this field, we chose the topic of death and dying in the three major monotheistic religions. Methods We searched MedLine using PubMed in order to retrieve and thematically analyze full-length scholarly journal papers or case reports dealing with religious traditions and end-of-life care. Our search consisted of a string of words that included the most common denominations of the three religions, the standard heading terms used by the National Reference Center for Bioethics Literature (NRCBL, and the Medical Subject Headings (MeSH used by the National Library of Medicine. Eligible articles were limited to English-language papers with an abstract. Results We found that while a bibliographic search in MedLine on this topic produced instant results and some valuable literature, the aggregate reflected a selection bias. American writers were over-represented given the global prevalence of these religious traditions. Denominationally affiliated authors predominated in representing the Christian traditions. The Islamic tradition was under-represented. Conclusion MedLine's capability to identify the most current, reliable and accurate information about purely scientific topics should not be assumed to be the same case when considering the interface of religion, culture and end-of-life care.

  4. Prioritizing conservation investments for mammal species globally

    Science.gov (United States)

    Wilson, Kerrie A.; Evans, Megan C.; Di Marco, Moreno; Green, David C.; Boitani, Luigi; Possingham, Hugh P.; Chiozza, Federica; Rondinini, Carlo

    2011-01-01

    We need to set priorities for conservation because we cannot do everything, everywhere, at the same time. We determined priority areas for investment in threat abatement actions, in both a cost-effective and spatially and temporally explicit way, for the threatened mammals of the world. Our analysis presents the first fine-resolution prioritization analysis for mammals at a global scale that accounts for the risk of habitat loss, the actions required to abate this risk, the costs of these actions and the likelihood of investment success. We evaluated the likelihood of success of investments using information on the past frequency and duration of legislative effectiveness at a country scale. The establishment of new protected areas was the action receiving the greatest investment, while restoration was never chosen. The resolution of the analysis and the incorporation of likelihood of success made little difference to this result, but affected the spatial location of these investments. PMID:21844046

  5. Data Partitioning Technique for Improved Video Prioritization

    Directory of Open Access Journals (Sweden)

    Ismail Amin Ali

    2017-07-01

    Full Text Available A compressed video bitstream can be partitioned according to the coding priority of the data, allowing prioritized wireless communication or selective dropping in a congested channel. Known as data partitioning in the H.264/Advanced Video Coding (AVC codec, this paper introduces a further sub-partition of one of the H.264/AVC codec’s three data-partitions. Results show a 5 dB improvement in Peak Signal-to-Noise Ratio (PSNR through this innovation. In particular, the data partition containing intra-coded residuals is sub-divided into data from: those macroblocks (MBs naturally intra-coded, and those MBs forcibly inserted for non-periodic intra-refresh. Interactive user-to-user video streaming can benefit, as then HTTP adaptive streaming is inappropriate and the High Efficiency Video Coding (HEVC codec is too energy demanding.

  6. A prioritization methodology to strategic planning process

    International Nuclear Information System (INIS)

    Rondinelli Junior, Francisco; Cherif, Hadj Slimane

    2009-01-01

    In the process of formulation of a Strategic Plan, there is always a step that deals with choices among different options and strategies. To do that a prioritization methodology has to be applied in order to achieve the higher needs identified along the analysis and evaluation of problems. To assign priorities within a set of needs/problems of a strategic nature and identified within various areas of activity or different sectors, it is proposed a methodology that envisage the use of specific attributes for which a graded scale of values is established for each need/problem, which, at the end of the process, allows a quantitative comparison among them. The methodology presented in this paper was developed following an approach that has been used in many areas over the last 20 years by various public and private institutions, and also by international organizations involved in promotion and development work. (author)

  7. Krsko periodic safety review project prioritization process

    International Nuclear Information System (INIS)

    Basic, I.; Vrbanic, I.; Spiler, J.; Lambright, J.

    2004-01-01

    Definition of a Krsko Periodic Safety Review (PSR) project is a comprehensive safety review of a plant after last ten years of operation. The objective is a verification by means of a comprehensive review using current methods that Krsko NPP remains safety when judged against current safety objectives and practices and that adequate arrangements are in place to maintain plant safety. This objective encompasses the three main criteria or goals: confirmation that the plant is as safe as originally intended, determination if there are any structures, systems or components that could limit the life of the plant in the foreseeable future, and comparison the plant against modern safety standards and to identify where improvements would be beneficial at justifiable cost. Krsko PSR project is structured in the three phases: Phase 1: Preparation of Detailed 10-years PSR Program, Phase 2: Performing of 10-years PSR Program and preparing of associated documents (2001-2003), and Phase 3: Implementation of the prioritized compensatory measures and modifications (development of associated EEAR, DMP, etc.) after agreement with the SNSA on the design, procedures and time-scales (2004-2008). This paper presents the NEK PSR results of work performed under Phase 2 focused on the ranking of safety issues and prioritization of corrective measures needed for establishing an efficient action plan. Safety issues were identified in Phase 2 during the following review processes: Periodic Safety Review (PSR) task; Krsko NPP Regulatory Compliance Program (RCP) review; Westinghouse Owner Group (WOG) catalog items screening/review; SNSA recommendations (including IAEA RAMP mission suggestions/recommendations).(author)

  8. Prioritization of design changes based on PSA

    International Nuclear Information System (INIS)

    Krajnc, B.; Mavko, B.

    1996-01-01

    Effective use of Probabilistic Safety Analyses (PSA) in the day to day plant operation is subject of intensive discussions among plant operators and regulators. There are several possible applications in which the PSA can be used, among those also to use the PSA approach for the quantification of influence of different proposed design changes to nuclear safety - influence on public safety - health. NPP Krsko is one of those plants that successfully completed its PSA project, with Level 1 and Level 2 analyses and effective know-how transfer. It also faces a number of regulatory and internally generated requirements for different design changes, mainly due to the fact that the plant is committed to continuous augmentation of nuclear safety. It is considered that the available tools and knowledge should be used and therefore applicable methodology should be developed for effective prioritization of proposed design changes by performing cost-benefit analyses for all major modifications - focusing on their influence on nuclear safety. Based on the above a new method for prioritization of design changes is proposed. The method uses Level 1 results (in the sense of plant damage states and their frequencies) directly as an input for further processing - first decision step to decide whether the proposed modification has or has no influence on nuclear safety. In Level 2 analyses the combination of probabilistic and deterministic approach was adopted. In fact the results of the deterministic analyses of severe accidents are treated in probabilistic manner due to large uncertainty of results. Finally to be able to perform plant specific cost benefit analyses so called partial Level 3 was defined. The proposed methods was preliminary tested and it gave favorable results. (author)

  9. ExpoCast: Exposure Science for Prioritization and Toxicity Testing

    Science.gov (United States)

    The US EPA is completing the Phase I pilot for a chemical prioritization research program, called ToxCastTM. Here EPA is developing methods for using computational chemistry, high-throughput screening, and toxicogenomic technologies to predict potential toxicity and prioritize l...

  10. 78 FR 69839 - Building Technologies Office Prioritization Tool

    Science.gov (United States)

    2013-11-21

    ... standards and building codes to ensure energy savings within buildings. BTO has developed a new technology... DEPARTMENT OF ENERGY Building Technologies Office Prioritization Tool AGENCY: Office of Energy....S. Department of Energy's (DOE) Building Technologies Office (BTO) developed the Prioritization Tool...

  11. False memory and importance: can we prioritize encoding without consequence?

    Science.gov (United States)

    Bui, Dung C; Friedman, Michael C; McDonough, Ian M; Castel, Alan D

    2013-10-01

    Given the large amount of information that we encounter, we often must prioritize what information we attempt to remember. Although critical for everyday functioning, relatively little research has focused on how people prioritize the encoding of information. Recent research has shown that people can and do selectively remember information assigned with higher, relative to lower, importance. However, the mechanisms underlying this prioritization process and the consequences of these processes are still not well understood. In the present study, we sought to better understand these prioritization processes and whether implementing these processes comes at the cost of memory accuracy, by increasing false memories. We used a modified form of the Deese/Roediger-McDermott (DRM) paradigm, in which participants studied DRM lists, with each list paired with low, medium, or high point values. In Experiment 1, encoding higher values led to more false memories than did encoding lower values, possibly because prioritizing information enhanced relational processing among high-value words. In Experiment 2, disrupting relational processing selectively reduced false memories for high-value words. Finally, in Experiment 3, facilitating relational processing selectively increased false memories for low-value words. These findings suggest that while prioritizing information can enhance true memory, this process concomitantly increases false memories. Furthermore, the mechanism underlying these prioritization processes depends on the ability to successfully engage in relational processing. Thus, how we prioritize the encoding of incoming information can come at a cost in terms of accurate memory.

  12. Contextual Requirements Prioritization and its Application to Smart Homes

    NARCIS (Netherlands)

    Sernani, Paolo; Dragoni, Aldo Franco; Serral, Estefanía; Dalpiaz, Fabiano

    2017-01-01

    When many requirements co-exist for a given system, prioritization is essential to determine which ones have higher priority. While the basic prioritization algorithms result in a total or partial order of the requirements, it is often the case that the priority of the requirements depends on the

  13. Cost-Prioritized Droop Schemes for Autonomous AC Microgrids

    DEFF Research Database (Denmark)

    Nutkani, Inam Ullah; Loh, Poh Chiang; Wang, Peng

    2015-01-01

    This paper presents two cost-prioritized droop sche- mes for distributed generators (DGs) in a rural or islanded microgrid. Dispatch prioritization of the schemes allows autonomous identification of the appropriate DGs for generation, in accordance to the overall load conditions of the microgrid....

  14. Asymptotic performance modelling of DCF protocol with prioritized channel access

    Science.gov (United States)

    Choi, Woo-Yong

    2017-11-01

    Recently, the modification of the DCF (Distributed Coordination Function) protocol by the prioritized channel access was proposed to resolve the problem that the DCF performance worsens exponentially as more nodes exist in IEEE 802.11 wireless LANs. In this paper, an asymptotic analytical performance model is presented to analyze the MAC performance of the DCF protocol with the prioritized channel access.

  15. Decision making in prioritization of required operational capabilities

    Science.gov (United States)

    Andreeva, P.; Karev, M.; Kovacheva, Ts.

    2015-10-01

    The paper describes an expert heuristic approach to prioritization of required operational capabilities in the field of defense. Based on expert assessment and by application of the method of Analytical Hierarchical Process, a methodology for their prioritization has been developed. It has been applied to practical simulation decision making games.

  16. Sensitivity and uncertainty analyses in aging risk-based prioritizations

    International Nuclear Information System (INIS)

    Hassan, M.; Uryas'ev, S.; Vesely, W.E.

    1993-01-01

    Aging risk evaluations of nuclear power plants using Probabilistic Risk Analyses (PRAs) involve assessments of the impact of aging structures, systems, and components (SSCs) on plant core damage frequency (CDF). These assessments can be used to prioritize the contributors to aging risk reflecting the relative risk potential of the SSCs. Aging prioritizations are important for identifying the SSCs contributing most to plant risk and can provide a systematic basis on which aging risk control and management strategies for a plant can be developed. However, these prioritizations are subject to variabilities arising from uncertainties in data, and/or from various modeling assumptions. The objective of this paper is to present an evaluation of the sensitivity of aging prioritizations of active components to uncertainties in aging risk quantifications. Approaches for robust prioritization of SSCs also are presented which are less susceptible to the uncertainties

  17. Aggressive effects of prioritizing popularity in early adolescence.

    Science.gov (United States)

    Cillessen, Antonius H N; Mayeux, Lara; Ha, Thao; de Bruyn, Eddy H; LaFontana, Kathryn M

    2014-01-01

    This study examined the moderating effects of prioritizing popularity on the association between early adolescents' popularity and their aggressive, leadership, and prosocial behaviors with peers. Participants were 288 14-year-olds from The Netherlands who completed a sociometric instrument and an assessment of how much they prioritized popularity over other personal goals. Results indicated that prioritizing popularity was distinct from actual popularity in the peer group. Further, prioritizing popularity moderated the association of popularity with aggressive and leadership behaviors, with adolescents who were both popular and who prioritized popularity being particularly aggressive and scoring high on leadership behaviors. This trend was especially true for boys. The same moderating effect was not found for prosocial behaviors. Motivational and social-cognitive factors in the dynamics of peer popularity are highlighted. © 2013 Wiley Periodicals, Inc.

  18. Systematic integration of biomedical knowledge prioritizes drugs for repurposing.

    Science.gov (United States)

    Himmelstein, Daniel Scott; Lizee, Antoine; Hessler, Christine; Brueggeman, Leo; Chen, Sabrina L; Hadley, Dexter; Green, Ari; Khankhanian, Pouya; Baranzini, Sergio E

    2017-09-22

    The ability to computationally predict whether a compound treats a disease would improve the economy and success rate of drug approval. This study describes Project Rephetio to systematically model drug efficacy based on 755 existing treatments. First, we constructed Hetionet (neo4j.het.io), an integrative network encoding knowledge from millions of biomedical studies. Hetionet v1.0 consists of 47,031 nodes of 11 types and 2,250,197 relationships of 24 types. Data were integrated from 29 public resources to connect compounds, diseases, genes, anatomies, pathways, biological processes, molecular functions, cellular components, pharmacologic classes, side effects, and symptoms. Next, we identified network patterns that distinguish treatments from non-treatments. Then, we predicted the probability of treatment for 209,168 compound-disease pairs (het.io/repurpose). Our predictions validated on two external sets of treatment and provided pharmacological insights on epilepsy, suggesting they will help prioritize drug repurposing candidates. This study was entirely open and received realtime feedback from 40 community members.

  19. Prioritizing emerging zoonoses in the Netherlands.

    Directory of Open Access Journals (Sweden)

    Arie H Havelaar

    Full Text Available BACKGROUND: To support the development of early warning and surveillance systems of emerging zoonoses, we present a general method to prioritize pathogens using a quantitative, stochastic multi-criteria model, parameterized for the Netherlands. METHODOLOGY/PRINCIPAL FINDINGS: A risk score was based on seven criteria, reflecting assessments of the epidemiology and impact of these pathogens on society. Criteria were weighed, based on the preferences of a panel of judges with a background in infectious disease control. CONCLUSIONS/SIGNIFICANCE: Pathogens with the highest risk for the Netherlands included pathogens in the livestock reservoir with a high actual human disease burden (e.g. Campylobacter spp., Toxoplasma gondii, Coxiella burnetii or a low current but higher historic burden (e.g. Mycobacterium bovis, rare zoonotic pathogens in domestic animals with severe disease manifestations in humans (e.g. BSE prion, Capnocytophaga canimorsus as well as arthropod-borne and wildlife associated pathogens which may pose a severe risk in future (e.g. Japanese encephalitis virus and West-Nile virus. These agents are key targets for development of early warning and surveillance.

  20. Prioritizing Environmental Chemicals for Obesity and Diabetes ...

    Science.gov (United States)

    Background: Diabetes and obesity are major threats to public health in the US and abroad. Understanding the role chemicals in our environment play in the development of these conditions is an emerging issue in environmental health, although identifying and prioritizing chemicals for testing beyond those already implicated in the literature is a challenge. This review is intended to help researchers generate hypotheses about chemicals potentially contributing to diabetes and obesity-related health outcomes by summarizing relevant findings from the US Environmental Protection Agency (EPA) ToxCast high-throughput screening (HTS) program. Objectives: To develop new hypotheses around environmental chemicals of potential interest for diabetes- or obesity-related outcomes using high throughput screening data. Methods: Identify ToxCast assay targets relevant to several biological processes related to diabetes and obesity (insulin sensitivity in peripheral tissue, pancreatic islet and beta cell function, adipocyte dierentiation, and feeding behavior) and present chemical screening data against those assay targets to identify chemicals of potential interest. Discussion: Results of this screening-level analysis suggest that the spectrum of environmental chemicals to consider in research related to diabetes and obesity is much broader than indicated from research papers and reviews published in the peer-reviewed literature. Testing of hypotheses based on ToxCast data will a

  1. Prioritizing pesticide compounds for analytical methods development

    Science.gov (United States)

    Norman, Julia E.; Kuivila, Kathryn; Nowell, Lisa H.

    2012-01-01

    The U.S. Geological Survey (USGS) has a periodic need to re-evaluate pesticide compounds in terms of priorities for inclusion in monitoring and studies and, thus, must also assess the current analytical capabilities for pesticide detection. To meet this need, a strategy has been developed to prioritize pesticides and degradates for analytical methods development. Screening procedures were developed to separately prioritize pesticide compounds in water and sediment. The procedures evaluate pesticide compounds in existing USGS analytical methods for water and sediment and compounds for which recent agricultural-use information was available. Measured occurrence (detection frequency and concentrations) in water and sediment, predicted concentrations in water and predicted likelihood of occurrence in sediment, potential toxicity to aquatic life or humans, and priorities of other agencies or organizations, regulatory or otherwise, were considered. Several existing strategies for prioritizing chemicals for various purposes were reviewed, including those that identify and prioritize persistent, bioaccumulative, and toxic compounds, and those that determine candidates for future regulation of drinking-water contaminants. The systematic procedures developed and used in this study rely on concepts common to many previously established strategies. The evaluation of pesticide compounds resulted in the classification of compounds into three groups: Tier 1 for high priority compounds, Tier 2 for moderate priority compounds, and Tier 3 for low priority compounds. For water, a total of 247 pesticide compounds were classified as Tier 1 and, thus, are high priority for inclusion in analytical methods for monitoring and studies. Of these, about three-quarters are included in some USGS analytical method; however, many of these compounds are included on research methods that are expensive and for which there are few data on environmental samples. The remaining quarter of Tier 1

  2. Prioritizing tiger conservation through landscape genetics and habitat linkages.

    Science.gov (United States)

    Yumnam, Bibek; Jhala, Yadvendradev V; Qureshi, Qamar; Maldonado, Jesus E; Gopal, Rajesh; Saini, Swati; Srinivas, Y; Fleischer, Robert C

    2014-01-01

    Even with global support for tiger (Panthera tigris) conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km(2) of forest habitat was found to be only 21,290 km(2). After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (FST) between populations were better explained by modeled linkage costs (r>0.5, p<0.05) compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should provide legal status

  3. Prioritizing tiger conservation through landscape genetics and habitat linkages.

    Directory of Open Access Journals (Sweden)

    Bibek Yumnam

    Full Text Available Even with global support for tiger (Panthera tigris conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km(2 of forest habitat was found to be only 21,290 km(2. After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (FST between populations were better explained by modeled linkage costs (r>0.5, p<0.05 compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should

  4. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  5. A protein prioritization approach tailored for the FA/BRCA pathway.

    Directory of Open Access Journals (Sweden)

    Anneke Haitjema

    Full Text Available Fanconi anemia (FA is a heterogeneous recessive disorder associated with a markedly elevated risk to develop cancer. To date sixteen FA genes have been identified, three of which predispose heterozygous mutation carriers to breast cancer. The FA proteins work together in a genome maintenance pathway, the so-called FA/BRCA pathway which is important during the S phase of the cell cycle. Since not all FA patients can be linked to (one of the sixteen known complementation groups, new FA genes remain to be identified. In addition the complex FA network remains to be further unravelled. One of the FA genes, FANCI, has been identified via a combination of bioinformatic techniques exploiting FA protein properties and genetic linkage. The aim of this study was to develop a prioritization approach for proteins of the entire human proteome that potentially interact with the FA/BRCA pathway or are novel candidate FA genes. To this end, we combined the original bioinformatics approach based on the properties of the first thirteen FA proteins identified with publicly available tools for protein-protein interactions, literature mining (Nermal and a protein function prediction tool (FuncNet. Importantly, the three newest FA proteins FANCO/RAD51C, FANCP/SLX4, and XRCC2 displayed scores in the range of the already known FA proteins. Likewise, a prime candidate FA gene based on next generation sequencing and having a very low score was subsequently disproven by functional studies for the FA phenotype. Furthermore, the approach strongly enriches for GO terms such as DNA repair, response to DNA damage stimulus, and cell cycle-regulated genes. Additionally, overlaying the top 150 with a haploinsufficiency probability score, renders the approach more tailored for identifying breast cancer related genes. This approach may be useful for prioritization of putative novel FA or breast cancer genes from next generation sequencing efforts.

  6. Health technology prioritization: which criteria for prioritizing new technologies and what are their relative weights?

    Science.gov (United States)

    Golan, Ofra; Hansen, Paul; Kaplan, Giora; Tal, Orna

    2011-10-01

    To review the criteria and 'other' considerations used internationally for prioritizing new health technologies, and to demonstrate a conjoint-analysis methodology (also known as discrete choice experiments) for deriving relative weights for the criteria. We searched the literature for criteria and other considerations for prioritizing new technologies. A convenience sample of 74 respondents completed a conjoint-analysis survey involving criteria related to technologies' 'benefits'. Encompassing 11 countries and the US state of Oregon, we were able to distinguish three main groups of criteria: (a) Need, appropriateness and clinical benefits; (b) Efficiency (including cost-effectiveness); and (c) Equality, solidarity and other ethical or social values. For several countries, the quality of the clinical and economic evidence and factors related to strategic issues and procedural justice respectively are also considered. The criteria and their weights from the conjoint-analysis survey are: 'Lives saved'=0.343, 'Life-prolongation benefits'=0.243, 'Quality-of-life gains'=0.217, a criterion representing the availability of alternative treatments=0.107, and 'Other important social/ethical benefits'=0.087. The criteria represent a pluralistic combination of needs-based, maximizing and egalitarian principles, and we demonstrated a methodology for deriving the weights for criteria related to technologies' 'benefits'. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  7. Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research.

    Science.gov (United States)

    Bravo, Àlex; Piñero, Janet; Queralt-Rosinach, Núria; Rautschka, Michael; Furlong, Laura I

    2015-02-21

    small fraction of MEDLINE results in a large dataset of gene-disease associations, and only a small proportion of this dataset is actually recorded in curated resources (2%), raising several issues on data prioritization and curation. We propose that joint analysis of text mined data with data curated by experts appears as a suitable approach to both assess data quality and highlight novel and interesting information.

  8. Cross-modal project prioritization : a TPCB peer exchange.

    Science.gov (United States)

    2015-05-01

    This report highlights key recommendations and best practices identified at the peer exchange on Cross-Modal Project Prioritization, held on December 16 and 17, 2014, in Raleigh, North Carolina. This event was sponsored by the Transportation Planning...

  9. Prioritizing connection requests in GMPLS-controlled optical networks

    DEFF Research Database (Denmark)

    Ruepp, Sarah Renée; Koster, A.; Andriolli, N.

    2009-01-01

    We prioritize bidirectional connection requests by combining dynamic connection provisioning with off-line optimization. Results show that the proposed approach decreases wavelength-converter usage, thereby allowing operators to reduce blocking-probably under bulk connection assignment or network...

  10. On the query reformulation technique for effective MEDLINE document retrieval.

    Science.gov (United States)

    Yoo, Sooyoung; Choi, Jinwook

    2010-10-01

    Improving the retrieval accuracy of MEDLINE documents is still a challenging issue due to low retrieval precision. Focusing on a query expansion technique based on pseudo-relevance feedback (PRF), this paper addresses the problem by systematically examining the effects of expansion term selection and adjustment of the term weights of the expanded query using a set of MEDLINE test documents called OHSUMED. Implementing a baseline information retrieval system based on the Okapi BM25 retrieval model, we compared six well-known term ranking algorithms for useful expansion term selection and then compared traditional term reweighting algorithms with our new variant of the standard Rocchio's feedback formula, which adopts a group-based weighting scheme. Our experimental results on the OHSUMED test collection showed a maximum improvement of 20.2% and 20.4% for mean average precision and recall measures over unexpanded queries when terms were expanded using a co-occurrence analysis-based term ranking algorithm in conjunction with our term reweighting algorithm (p-valueretrieval.

  11. Patient-centered prioritization of bladder cancer research.

    Science.gov (United States)

    Smith, Angela B; Chisolm, Stephanie; Deal, Allison; Spangler, Alejandra; Quale, Diane Z; Bangs, Rick; Jones, J Michael; Gore, John L

    2018-05-04

    Patient-centered research requires the meaningful involvement of patients and caregivers throughout the research process. The objective of this study was to create a process for sustainable engagement for research prioritization within oncology. From December 2014 to 2016, a network of engaged patients for research prioritization was created in partnership with the Bladder Cancer Advocacy Network (BCAN): the BCAN Patient Survey Network (PSN). The PSN leveraged an online bladder cancer community with additional recruitment through print advertisements and social media campaigns. Prioritized research questions were developed through a modified Delphi process and were iterated through multidisciplinary working groups and a repeat survey. In year 1 of the PSN, 354 patients and caregivers responded to the research prioritization survey; the number of responses increased to 1034 in year 2. The majority of respondents had non-muscle-invasive bladder cancer (NMIBC), and the mean time since diagnosis was 5 years. Stakeholder-identified questions for noninvasive, invasive, and metastatic disease were prioritized by the PSN. Free-text questions were sorted with thematic mapping. Several questions submitted by respondents were among the prioritized research questions. A final prioritized list of research questions was disseminated to various funding agencies, and a highly ranked NMIBC research question was included as a priority area in the 2017 Patient-Centered Outcomes Research Institute announcement of pragmatic trial funding. Patient engagement is needed to identify high-priority research questions in oncology. The BCAN PSN provides a successful example of an engagement infrastructure for annual research prioritization in bladder cancer. The creation of an engagement network sets the groundwork for additional phases of engagement, including design, conduct, and dissemination. Cancer 2018. © 2018 American Cancer Society. © 2018 American Cancer Society.

  12. Stroke: Working toward a Prioritized World Agenda

    Science.gov (United States)

    Hachinski, Vladimir; Donnan, Geoffrey A.; Gorelick, Philip B.; Hacke, Werner; Cramer, Steven C.; Kaste, Markku; Fisher, Marc; Brainin, Michael; Buchan, Alastair M.; Lo, Eng H.; Skolnick, Brett E.; Furie, Karen L.; Hankey, Graeme J.; Kivipelto, Miia; Morris, John; Rothwell, Peter M.; Sacco, Ralph L.; Smith, Jr., Sidney C.; Wang, Yulun; Bryer, Alan; Ford, Gary A.; Iadecola, Costantino; Martins, Sheila C.O.; Saver, Jeff; Skvortsova, Veronika; Bayley, Mark; Bednar, Martin M.; Duncan, Pamela; Enney, Lori; Finklestein, Seth; Jones, Theresa A.; Kalra, Lalit; Kleim, Jeff; Nitkin, Ralph; Teasell, Robert; Weiller, Cornelius; Desai, Bhupat; Goldberg, Mark P.; Heiss, Wolf-Dieter; Saarelma, Osmo; Schwamm, Lee H.; Shinohara, Yukito; Trivedi, Bhargava; Wahlgren, Nils; Wong, Lawrence K.; Hakim, Antoine; Norrving, Bo; Prudhomme, Stephen; Bornstein, Natan M.; Davis, Stephen M.; Goldstein, Larry B.; Leys, Didier; Tuomilehto, Jaakko

    2010-01-01

    Background and Purpose The aim of the Synergium was to devise and prioritize new ways of accelerating progress in reducing the risks, effects, and consequences of stroke. Methods Preliminary work was performed by 7 working groups of stroke leaders followed by a synergium (a forum for working synergistically together) with approximately 100 additional participants. The resulting draft document had further input from contributors outside the synergium. Results Recommendations of the Synergium are: Basic Science, Drug Development and Technology: There is a need to develop: (1) New systems of working together to break down the prevalent ‘silo’ mentality; (2) New models of vertically integrated basic, clinical, and epidemiological disciplines; and (3) Efficient methods of identifying other relevant areas of science. Stroke Prevention: (1) Establish a global chronic disease prevention initiative with stroke as a major focus. (2) Recognize not only abrupt clinical stroke, but subtle subclinical stroke, the commonest type of cerebrovascular disease, leading to impairments of executive function. (3) Develop, implement and evaluate a population approach for stroke prevention. (4) Develop public health communication strategies using traditional and novel (e.g., social media/marketing) techniques. Acute Stroke Management: Continue the establishment of stroke centers, stroke units, regional systems of emergency stroke care and telestroke networks. Brain Recovery and Rehabilitation: (1) Translate best neuroscience, including animal and human studies, into poststroke recovery research and clinical care. (2) Standardize poststroke rehabilitation based on best evidence. (3) Develop consensus on, then implementation of, standardized clinical and surrogate assessments. (4) Carry out rigorous clinical research to advance stroke recovery. Into the 21st Century: Web, Technology and Communications: (1) Work toward global unrestricted access to stroke-related information. (2) Build

  13. Stroke: working toward a prioritized world agenda.

    Science.gov (United States)

    Hachinski, Vladimir; Donnan, Geoffrey A; Gorelick, Philip B; Hacke, Werner; Cramer, Steven C; Kaste, Markku; Fisher, Marc; Brainin, Michael; Buchan, Alastair M; Lo, Eng H; Skolnick, Brett E; Furie, Karen L; Hankey, Graeme J; Kivipelto, Miia; Morris, John; Rothwell, Peter M; Sacco, Ralph L; Smith, Sidney C; Wang, Yulun; Bryer, Alan; Ford, Gary A; Iadecola, Costantino; Martins, Sheila C O; Saver, Jeff; Skvortsova, Veronika; Bayley, Mark; Bednar, Martin M; Duncan, Pamela; Enney, Lori; Finklestein, Seth; Jones, Theresa A; Kalra, Lalit; Kleim, Jeff; Nitkin, Ralph; Teasell, Robert; Weiller, Cornelius; Desai, Bhupat; Goldberg, Mark P; Heiss, Wolf-Dieter; Saarelma, Osmo; Schwamm, Lee H; Shinohara, Yukito; Trivedi, Bhargava; Wahlgren, Nils; Wong, Lawrence K; Hakim, Antoine; Norrving, Bo; Prudhomme, Stephen; Bornstein, Natan M; Davis, Stephen M; Goldstein, Larry B; Leys, Didier; Tuomilehto, Jaakko

    2010-01-01

    The aim of the Synergium was to devise and prioritize new ways of accelerating progress in reducing the risks, effects, and consequences of stroke. Preliminary work was performed by 7 working groups of stroke leaders followed by a synergium (a forum for working synergistically together) with approximately 100 additional participants. The resulting draft document had further input from contributors outside the synergium. Recommendations of the Synergium are: Basic Science, Drug Development and Technology: There is a need to develop: (1) New systems of working together to break down the prevalent 'silo' mentality; (2) New models of vertically integrated basic, clinical, and epidemiological disciplines; and (3) Efficient methods of identifying other relevant areas of science. Stroke Prevention: (1) Establish a global chronic disease prevention initiative with stroke as a major focus. (2) Recognize not only abrupt clinical stroke, but subtle subclinical stroke, the commonest type of cerebrovascular disease, leading to impairments of executive function. (3) Develop, implement and evaluate a population approach for stroke prevention. (4) Develop public health communication strategies using traditional and novel (e.g., social media/marketing) techniques. Acute Stroke Management: Continue the establishment of stroke centers, stroke units, regional systems of emergency stroke care and telestroke networks. Brain Recovery and Rehabilitation: (1) Translate best neuroscience, including animal and human studies, into poststroke recovery research and clinical care. (2) Standardize poststroke rehabilitation based on best evidence. (3) Develop consensus on, then implementation of, standardized clinical and surrogate assessments. (4) Carry out rigorous clinical research to advance stroke recovery. Into the 21st Century: Web, Technology and Communications: (1) Work toward global unrestricted access to stroke-related information. (2) Build centralized electronic archives and

  14. Stroke: working toward a prioritized world agenda.

    Science.gov (United States)

    Hachinski, Vladimir; Donnan, Geoffrey A; Gorelick, Philip B; Hacke, Werner; Cramer, Steven C; Kaste, Markku; Fisher, Marc; Brainin, Michael; Buchan, Alastair M; Lo, Eng H; Skolnick, Brett E; Furie, Karen L; Hankey, Graeme J; Kivipelto, Miia; Morris, John; Rothwell, Peter M; Sacco, Ralph L; Smith, Sidney C; Wang, Yulun; Bryer, Alan; Ford, Gary A; Iadecola, Costantino; Martins, Sheila C O; Saver, Jeff; Skvortsova, Veronika; Bayley, Mark; Bednar, Martin M; Duncan, Pamela; Enney, Lori; Finklestein, Seth; Jones, Theresa A; Kalra, Lalit; Kleim, Jeff; Nitkin, Ralph; Teasell, Robert; Weiller, Cornelius; Desai, Bhupat; Goldberg, Mark P; Heiss, Wolf-Dieter; Saarelma, Osmo; Schwamm, Lee H; Shinohara, Yukito; Trivedi, Bhargava; Wahlgren, Nils; Wong, Lawrence K; Hakim, Antoine; Norrving, Bo; Prudhomme, Stephen; Bornstein, Natan M; Davis, Stephen M; Goldstein, Larry B; Leys, Didier; Tuomilehto, Jaakko

    2010-08-01

    The aim of the Synergium was to devise and prioritize new ways of accelerating progress in reducing the risks, effects, and consequences of stroke. Preliminary work was performed by seven working groups of stroke leaders followed by a synergium (a forum for working synergistically together) with approximately 100 additional participants. The resulting draft document had further input from contributors outside the synergium. Recommendations of the Synergium are: Basic Science, Drug Development and Technology: There is a need to develop: (1) New systems of working together to break down the prevalent 'silo' mentality; (2) New models of vertically integrated basic, clinical, and epidemiological disciplines; and (3) Efficient methods of identifying other relevant areas of science. Stroke Prevention: (1) Establish a global chronic disease prevention initiative with stroke as a major focus. (2) Recognize not only abrupt clinical stroke, but subtle subclinical stroke, the commonest type of cerebrovascular disease, leading to impairments of executive function. (3) Develop, implement and evaluate a population approach for stroke prevention. (4) Develop public health communication strategies using traditional and novel (eg, social media/marketing) techniques. Acute Stroke Management: Continue the establishment of stroke centers, stroke units, regional systems of emergency stroke care and telestroke networks. Brain Recovery and Rehabilitation: (1) Translate best neuroscience, including animal and human studies, into poststroke recovery research and clinical care. (2) Standardize poststroke rehabilitation based on best evidence. (3) Develop consensus on, then implementation of, standardized clinical and surrogate assessments. (4) Carry out rigorous clinical research to advance stroke recovery. Into the 21st Century: Web, Technology and Communications: (1) Work toward global unrestricted access to stroke-related information. (2) Build centralized electronic archives and

  15. A network-based approach to prioritize results from genome-wide association studies.

    Directory of Open Access Journals (Sweden)

    Nirmala Akula

    Full Text Available Genome-wide association studies (GWAS are a valuable approach to understanding the genetic basis of complex traits. One of the challenges of GWAS is the translation of genetic association results into biological hypotheses suitable for further investigation in the laboratory. To address this challenge, we introduce Network Interface Miner for Multigenic Interactions (NIMMI, a network-based method that combines GWAS data with human protein-protein interaction data (PPI. NIMMI builds biological networks weighted by connectivity, which is estimated by use of a modification of the Google PageRank algorithm. These weights are then combined with genetic association p-values derived from GWAS, producing what we call 'trait prioritized sub-networks.' As a proof of principle, NIMMI was tested on three GWAS datasets previously analyzed for height, a classical polygenic trait. Despite differences in sample size and ancestry, NIMMI captured 95% of the known height associated genes within the top 20% of ranked sub-networks, far better than what could be achieved by a single-locus approach. The top 2% of NIMMI height-prioritized sub-networks were significantly enriched for genes involved in transcription, signal transduction, transport, and gene expression, as well as nucleic acid, phosphate, protein, and zinc metabolism. All of these sub-networks were ranked near the top across all three height GWAS datasets we tested. We also tested NIMMI on a categorical phenotype, Crohn's disease. NIMMI prioritized sub-networks involved in B- and T-cell receptor, chemokine, interleukin, and other pathways consistent with the known autoimmune nature of Crohn's disease. NIMMI is a simple, user-friendly, open-source software tool that efficiently combines genetic association data with biological networks, translating GWAS findings into biological hypotheses.

  16. A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies

    Science.gov (United States)

    Akula, Nirmala; Baranova, Ancha; Seto, Donald; Solka, Jeffrey; Nalls, Michael A.; Singleton, Andrew; Ferrucci, Luigi; Tanaka, Toshiko; Bandinelli, Stefania; Cho, Yoon Shin; Kim, Young Jin; Lee, Jong-Young; Han, Bok-Ghee; McMahon, Francis J.

    2011-01-01

    Genome-wide association studies (GWAS) are a valuable approach to understanding the genetic basis of complex traits. One of the challenges of GWAS is the translation of genetic association results into biological hypotheses suitable for further investigation in the laboratory. To address this challenge, we introduce Network Interface Miner for Multigenic Interactions (NIMMI), a network-based method that combines GWAS data with human protein-protein interaction data (PPI). NIMMI builds biological networks weighted by connectivity, which is estimated by use of a modification of the Google PageRank algorithm. These weights are then combined with genetic association p-values derived from GWAS, producing what we call ‘trait prioritized sub-networks.’ As a proof of principle, NIMMI was tested on three GWAS datasets previously analyzed for height, a classical polygenic trait. Despite differences in sample size and ancestry, NIMMI captured 95% of the known height associated genes within the top 20% of ranked sub-networks, far better than what could be achieved by a single-locus approach. The top 2% of NIMMI height-prioritized sub-networks were significantly enriched for genes involved in transcription, signal transduction, transport, and gene expression, as well as nucleic acid, phosphate, protein, and zinc metabolism. All of these sub-networks were ranked near the top across all three height GWAS datasets we tested. We also tested NIMMI on a categorical phenotype, Crohn’s disease. NIMMI prioritized sub-networks involved in B- and T-cell receptor, chemokine, interleukin, and other pathways consistent with the known autoimmune nature of Crohn’s disease. NIMMI is a simple, user-friendly, open-source software tool that efficiently combines genetic association data with biological networks, translating GWAS findings into biological hypotheses. PMID:21915301

  17. Use of a quality improvement tool, the prioritization matrix, to identify and prioritize triage software algorithm enhancement.

    Science.gov (United States)

    North, Frederick; Varkey, Prathiba; Caraballo, Pedro; Vsetecka, Darlene; Bartel, Greg

    2007-10-11

    Complex decision support software can require significant effort in maintenance and enhancement. A quality improvement tool, the prioritization matrix, was successfully used to guide software enhancement of algorithms in a symptom assessment call center.

  18. We’re All in This Together | NIH MedlinePlus the Magazine

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  19. Achoo! Cold, Flu, or Something Else? | NIH MedlinePlus the Magazine

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  20. Psoriasis: On the Road to Discovery | NIH MedlinePlus the Magazine

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  1. Nick Jonas on Type 1 Diabetes | NIH MedlinePlus the Magazine

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  2. Asthma: What You Need to Know | NIH MedlinePlus the Magazine

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  3. Preventing Pregnancy with a Gel for Men? | NIH MedlinePlus the Magazine

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  4. Caregiving: It Takes a Village | NIH MedlinePlus the Magazine

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  5. Breathtaking: Managing a COPD Diagnosis | NIH MedlinePlus the Magazine

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  6. Understanding and preventing tick bites | NIH MedlinePlus the Magazine

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  7. Battling C. Difficile: Don’t Delay | NIH MedlinePlus the Magazine

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  8. From the lab - Exercise Key to Keeping Weight Off | NIH MedlinePlus the Magazine

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  9. From the lab - Can Potassium Help Your Heart? | NIH MedlinePlus the Magazine

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  10. Sickle Cell Disease: What You Should Know | NIH MedlinePlus the Magazine

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  11. A Journey with Mid-life Hearing Loss | NIH MedlinePlus the Magazine

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  12. Joint Replacement Surgery: What you Need to Know | NIH MedlinePlus the Magazine

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  13. The Future of Asthma Monitoring | NIH MedlinePlus the Magazine

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  14. Too ‘Stubborn’ to Give in to COPD | NIH MedlinePlus the Magazine

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  15. Cholesterol: The Good, the Bad, and the Unhealthy | NIH MedlinePlus the Magazine

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  16. Palliative Care: A Spectrum of Support | NIH MedlinePlus the Magazine

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  17. Confronting 9/11 Trauma from Childhood into Adulthood | NIH MedlinePlus the Magazine

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  18. Solving the Undiagnosed Disease Puzzle at NIH | NIH MedlinePlus the Magazine

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  19. Love and Life without Gluten | NIH MedlinePlus the Magazine

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  20. A Couple’s Caregiving Journey | NIH MedlinePlus the Magazine

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  1. Surgeon General Outlines Opioid Plan | NIH MedlinePlus the Magazine

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  2. From the lab - Testing Malaria-Resistant Mosquitoes | NIH MedlinePlus the Magazine

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  3. A Path to Hope for Sickle Cell Disease | NIH MedlinePlus the Magazine

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  4. Step Inside NIH’s Sickle Cell Branch | NIH MedlinePlus the Magazine

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  5. From the lab - Progress Against Zika | NIH MedlinePlus the Magazine

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  6. A Closer Look at Cancer Imaging Tools | NIH MedlinePlus the Magazine

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  7. Exploring the Celiac Disease Mystery | NIH MedlinePlus the Magazine

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  8. Beyond Pain Relief: Total Knee Replacement Surgery | NIH MedlinePlus the Magazine

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  9. TV Star Jim Parsons Shines Light on NIH Research | NIH MedlinePlus the Magazine

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  10. Advance Care Plan: A Checklist for the Future | NIH MedlinePlus the Magazine

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  11. Understanding Asthma from the Inside Out | NIH MedlinePlus the Magazine

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  12. Keys to Recovery after Knee Replacement Surgery | NIH MedlinePlus the Magazine

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  13. Fighting the Flu with a Universal Vaccine | NIH MedlinePlus the Magazine

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  14. Using incomplete citation data for MEDLINE results ranking.

    Science.gov (United States)

    Herskovic, Jorge R; Bernstam, Elmer V

    2005-01-01

    Information overload is a significant problem for modern medicine. Searching MEDLINE for common topics often retrieves more relevant documents than users can review. Therefore, we must identify documents that are not only relevant, but also important. Our system ranks articles using citation counts and the PageRank algorithm, incorporating data from the Science Citation Index. However, citation data is usually incomplete. Therefore, we explore the relationship between the quantity of citation information available to the system and the quality of the result ranking. Specifically, we test the ability of citation count and PageRank to identify "important articles" as defined by experts from large result sets with decreasing citation information. We found that PageRank performs better than simple citation counts, but both algorithms are surprisingly robust to information loss. We conclude that even an incomplete citation database is likely to be effective for importance ranking.

  15. 76 FR 18399 - Changes To Implement the Prioritized Examination Track (Track I) of the Enhanced Examination...

    Science.gov (United States)

    2011-04-04

    ... prioritized examination fee, processing fee, and publication fee. Therefore, the fee amount due on filing for...) the $4,000 prioritized examination fee; (3) the $130 processing fee; and (4) the $300 publication fee...) prioritized examination fee; (3) the $130 processing fee; and (4) the $300 publication fee. Under prioritized...

  16. Friends of the National Library of Medicine, Welcome to NIH MedlinePlus, the magazine | NIH MedlinePlus the Magazine

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    ... Contents Dear Readers, WELCOME to NIH MedlinePlus , the magazine. The purpose of NIH MedlinePlus , the magazine, is to provide you with a FREE , trusted ... medical information. Published four times a year, the magazine showcases the National Institutes of Health's (NIH) latest ...

  17. Consequence Prioritization Process for Potential High Consequence Events (HCE)

    Energy Technology Data Exchange (ETDEWEB)

    Freeman, Sarah G. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2016-10-31

    This document describes the process for Consequence Prioritization, the first phase of the Consequence-Driven Cyber-Informed Engineering (CCE) framework. The primary goal of Consequence Prioritization is to identify potential disruptive events that would significantly inhibit an organization’s ability to provide the critical services and functions deemed fundamental to their business mission. These disruptive events, defined as High Consequence Events (HCE), include both events that have occurred or could be realized through an attack of critical infrastructure owner assets. While other efforts have been initiated to identify and mitigate disruptive events at the national security level, such as Presidential Policy Directive 41 (PPD-41), this process is intended to be used by individual organizations to evaluate events that fall below the threshold for a national security. Described another way, Consequence Prioritization considers threats greater than those addressable by standard cyber-hygiene and includes the consideration of events that go beyond a traditional continuity of operations (COOP) perspective. Finally, Consequence Prioritization is most successful when organizations adopt a multi-disciplinary approach, engaging both cyber security and engineering expertise, as in-depth engineering perspectives are required to recognize and characterize and mitigate HCEs. Figure 1 provides a high-level overview of the prioritization process.

  18. Using citation data to improve retrieval from MEDLINE.

    Science.gov (United States)

    Bernstam, Elmer V; Herskovic, Jorge R; Aphinyanaphongs, Yindalon; Aliferis, Constantin F; Sriram, Madurai G; Hersh, William R

    2006-01-01

    To determine whether algorithms developed for the World Wide Web can be applied to the biomedical literature in order to identify articles that are important as well as relevant. DESIGN AND MEASUREMENTS A direct comparison of eight algorithms: simple PubMed queries, clinical queries (sensitive and specific versions), vector cosine comparison, citation count, journal impact factor, PageRank, and machine learning based on polynomial support vector machines. The objective was to prioritize important articles, defined as being included in a pre-existing bibliography of important literature in surgical oncology. RESULTS Citation-based algorithms were more effective than noncitation-based algorithms at identifying important articles. The most effective strategies were simple citation count and PageRank, which on average identified over six important articles in the first 100 results compared to 0.85 for the best noncitation-based algorithm (p PageRank more than simple citation count. However, in spite of citation lag, citation-based algorithms remain more effective than noncitation-based algorithms. CONCLUSION Algorithms that have proved successful on the World Wide Web can be applied to biomedical information retrieval. Citation-based algorithms can help identify important articles within large sets of relevant results. Further studies are needed to determine whether citation-based algorithms can effectively meet actual user information needs.

  19. Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence

    Directory of Open Access Journals (Sweden)

    Yunus E. Tuncil

    2017-10-01

    Full Text Available When presented with nutrient mixtures, several human gut Bacteroides species exhibit hierarchical utilization of glycans through a phenomenon that resembles catabolite repression. However, it is unclear how closely these observed physiological changes, often measured by altered transcription of glycan utilization genes, mirror actual glycan depletion. To understand the glycan prioritization strategies of two closely related human gut symbionts, Bacteroides ovatus and Bacteroides thetaiotaomicron, we performed a series of time course assays in which both species were individually grown in a medium with six different glycans that both species can degrade. Disappearance of the substrates and transcription of the corresponding polysaccharide utilization loci (PULs were measured. Each species utilized some glycans before others, but with different priorities per species, providing insight into species-specific hierarchical preferences. In general, the presence of highly prioritized glycans repressed transcription of genes involved in utilizing lower-priority nutrients. However, transcriptional sensitivity to some glycans varied relative to the residual concentration in the medium, with some PULs that target high-priority substrates remaining highly expressed even after their target glycan had been mostly depleted. Coculturing of these organisms in the same mixture showed that the hierarchical orders generally remained the same, promoting stable coexistence. Polymer length was found to be a contributing factor for glycan utilization, thereby affecting its place in the hierarchy. Our findings not only elucidate how B. ovatus and B. thetaiotaomicron strategically access glycans to maintain coexistence but also support the prioritization of carbohydrate utilization based on carbohydrate structure, advancing our understanding of the relationships between diet and the gut microbiome.

  20. Scientists’ Prioritization of Communication Objectives for Public Engagement

    Science.gov (United States)

    2016-01-01

    Amid calls from scientific leaders for their colleagues to become more effective public communicators, this study examines the objectives that scientists’ report drive their public engagement behaviors. We explore how scientists evaluate five specific communication objectives, which include informing the public about science, exciting the public about science, strengthening the public’s trust in science, tailoring messages about science, and defending science from misinformation. We use insights from extant research, the theory of planned behavior, and procedural justice theory to identify likely predictors of scientists' views about these communication objectives. Results show that scientists most prioritize communication designed to defend science from misinformation and educate the public about science, and least prioritize communication that seeks to build trust and establish resonance with the public. Regression analyses reveal factors associated with scientists who prioritize each of the five specific communication objectives. Our findings highlight the need for communication trainers to help scientists select specific communication objectives for particular contexts and audiences. PMID:26913869

  1. Prioritizing Information during Working Memory: Beyond Sustained Internal Attention.

    Science.gov (United States)

    Myers, Nicholas E; Stokes, Mark G; Nobre, Anna C

    2017-06-01

    Working memory (WM) has limited capacity. This leaves attention with the important role of allowing into storage only the most relevant information. It is increasingly evident that attention is equally crucial for prioritizing representations within WM as the importance of individual items changes. Retrospective prioritization has been proposed to result from a focus of internal attention highlighting one of several representations. Here, we suggest an updated model, in which prioritization acts in multiple steps: first orienting towards and selecting a memory, and then reconfiguring its representational state in the service of upcoming task demands. Reconfiguration sets up an optimized perception-action mapping, obviating the need for sustained attention. This view is consistent with recent literature, makes testable predictions, and links WM with task switching and action preparation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Scientists' Prioritization of Communication Objectives for Public Engagement.

    Directory of Open Access Journals (Sweden)

    Anthony Dudo

    Full Text Available Amid calls from scientific leaders for their colleagues to become more effective public communicators, this study examines the objectives that scientists' report drive their public engagement behaviors. We explore how scientists evaluate five specific communication objectives, which include informing the public about science, exciting the public about science, strengthening the public's trust in science, tailoring messages about science, and defending science from misinformation. We use insights from extant research, the theory of planned behavior, and procedural justice theory to identify likely predictors of scientists' views about these communication objectives. Results show that scientists most prioritize communication designed to defend science from misinformation and educate the public about science, and least prioritize communication that seeks to build trust and establish resonance with the public. Regression analyses reveal factors associated with scientists who prioritize each of the five specific communication objectives. Our findings highlight the need for communication trainers to help scientists select specific communication objectives for particular contexts and audiences.

  3. Prioritizing veterinary pharmaceuticals for aquatic environment in Korea.

    Science.gov (United States)

    Kim, Younghee; Jung, Jinyong; Kim, Myunghyun; Park, Jeongim; Boxall, Alistair B A; Choi, Kyungho

    2008-09-01

    Pharmaceutical residues may have serious impacts on nontarget biological organisms in aquatic ecosystems, and have therefore precipitated numerous investigations worldwide. Many pharmaceutical compounds available on the market need to be prioritized based on their potential ecological and human health risks in order to develop sound management decisions. We prioritized veterinary pharmaceuticals in Korea by their usage, potential to enter the environment, and toxicological hazard. Twenty compounds were identified in the top priority class, most of which were antibiotics. Among these compounds, 8 were identified as deserving more immediate attention: amoxicillin, enramycin, fenbendazole, florfenicol, ivermectin, oxytetracycline, tylosin, and virginiamycin. A limitation of this study is that we initially screened veterinary pharmaceuticals by sales tonnage for veterinary use only. However, this is the first attempt to prioritize veterinary pharmaceuticals in Korea, and it provides important concepts for developing environmental risk management plans for such contaminants in aquatic systems. Copyright © 2008 Elsevier B.V. All rights reserved.

  4. Prioritizing Positivity: An Effective Approach to Pursuing Happiness?

    Science.gov (United States)

    Catalino, Lahnna I.; Algoe, Sara B.; Fredrickson, Barbara L.

    2017-01-01

    A decade of research reveals the benefits of positive emotions for mental and physical health; however, recent empirical work suggests the explicit pursuit of happiness may backfire. The present study hypothesized that the pursuit of happiness is not inherently self-defeating; in particular, individuals who seek positivity, as exemplified by how they make decisions about how to organize their day-to-day lives, may be happier. This individual difference is labeled prioritizing positivity. In a community sample of young to older adults (N = 233), prioritizing positivity predicted a host of well-being outcomes (positive emotions, depressive symptomology). In addition, people high in prioritizing positivity have greater resources, and these links are explained by more frequent experiences of positive emotions. In sum, the present study suggests that seeking happiness, although a delicate art, may be a worthwhile pursuit. PMID:25401290

  5. Hanford Mission Plan risk-based prioritization methodologies

    International Nuclear Information System (INIS)

    Hesser, W.A.; Madden, M.S.; Pyron, N.M.; Butcher, J.L.

    1994-08-01

    Sites across the US Department (DOE) complex recognize the critical need for a systematic method for prioritizing among their work scope activities. Here at the Hanford Site, Pacific Northwest Laboratory and Westinghouse Hanford Company (WHC) conducted preliminary research into techniques to meet this need and assist managers in making financial resource allocation decisions. This research is a subtask of the risk management task of the Hanford Mission Plan as described in the WHC Integrated Planning Work Breakdown Structure 1.8.2 Fiscal Year 1994 Work Plan. The research team investigated prioritization techniques used at other DOE sites and compared them with the Priority Planning Grid (PPG), a tool used at Hanford. The authors concluded that the PPG could be used for prioritization of resource allocation, but it needed to be revised to better reflect the Site's priorities and objectives. The revised PPG was tested with three Hanford programs, the PPG was modified, and updated procedures were prepared

  6. Throughput centered prioritization of machines in transfer lines

    International Nuclear Information System (INIS)

    Pascual, R.; Godoy, D.; Louit, D.M.

    2011-01-01

    In an environment of scarce resources and complex production systems, prioritizing is key to confront the challenge of managing physical assets. In the literature, there exist a number of techniques to prioritize maintenance decisions that consider safety, technical and business perspectives. However, the effect of risk mitigating elements-such as intermediate buffers in production lines-on prioritization has not yet been investigated in depth. In this line, the work proposes a user-friendly graphical technique called the system efficiency influence diagram (SEID). Asset managers may use SEID to identify machines that have a greater impact on the system throughput, and thus set prioritized maintenance policies and/or redesign of buffers capacities. The tool provides insight to the analyst as it decomposes the influence of a given machine on the system throughput as a product of two elements: (1) system influence efficiency factor and (2) machine unavailability factor. We illustrate its applicability using three case studies: a four-machine transfer line, a vehicle assembly line, and an open-pit mining conveyor system. The results confirm that the machines with greater unavailability factors are not necessarily the most important for the efficiency of the production line, as it is the case when no intermediate buffers exist. As a decision aid tool, SEID emphasizes the need to move from a maintenance vision focused on machine availability, to a systems engineering perspective. - Highlights: → We propose a graphical technique to prioritize machines in production lines. → The tool is called 'system efficiency influence diagram' (SEID). → It helps setting prioritized maintenance policies and/or redesign of buffers. → The SEID technique focuses on system efficiency and throughput. → We illustrate its applicability using three case studies.

  7. Throughput centered prioritization of machines in transfer lines

    Energy Technology Data Exchange (ETDEWEB)

    Pascual, R., E-mail: rpascual@ing.puc.cl [Physical Asset Management Lab, Centro de Mineria, Pontificia Universidad Catolica de Chile, Av. Vicuna Mackenna 4860, Santiago (Chile); Godoy, D. [Physical Asset Management Lab, Centro de Mineria, Pontificia Universidad Catolica de Chile, Av. Vicuna Mackenna 4860, Santiago (Chile); Louit, D.M. [Komatsu Chile S.A., Av. Americo Vespucio 0631, Quilicura, Santiago (Chile)

    2011-10-15

    In an environment of scarce resources and complex production systems, prioritizing is key to confront the challenge of managing physical assets. In the literature, there exist a number of techniques to prioritize maintenance decisions that consider safety, technical and business perspectives. However, the effect of risk mitigating elements-such as intermediate buffers in production lines-on prioritization has not yet been investigated in depth. In this line, the work proposes a user-friendly graphical technique called the system efficiency influence diagram (SEID). Asset managers may use SEID to identify machines that have a greater impact on the system throughput, and thus set prioritized maintenance policies and/or redesign of buffers capacities. The tool provides insight to the analyst as it decomposes the influence of a given machine on the system throughput as a product of two elements: (1) system influence efficiency factor and (2) machine unavailability factor. We illustrate its applicability using three case studies: a four-machine transfer line, a vehicle assembly line, and an open-pit mining conveyor system. The results confirm that the machines with greater unavailability factors are not necessarily the most important for the efficiency of the production line, as it is the case when no intermediate buffers exist. As a decision aid tool, SEID emphasizes the need to move from a maintenance vision focused on machine availability, to a systems engineering perspective. - Highlights: > We propose a graphical technique to prioritize machines in production lines. > The tool is called 'system efficiency influence diagram' (SEID). > It helps setting prioritized maintenance policies and/or redesign of buffers. > The SEID technique focuses on system efficiency and throughput. > We illustrate its applicability using three case studies.

  8. Maximum flow approach to prioritize potential drug targets of Mycobacterium tuberculosis H37Rv from protein-protein interaction network.

    Science.gov (United States)

    Melak, Tilahun; Gakkhar, Sunita

    2015-12-01

    In spite of the implementations of several strategies, tuberculosis (TB) is overwhelmingly a serious global public health problem causing millions of infections and deaths every year. This is mainly due to the emergence of drug-resistance varieties of TB. The current treatment strategies for the drug-resistance TB are of longer duration, more expensive and have side effects. This highlights the importance of identification and prioritization of targets for new drugs. This study has been carried out to prioritize potential drug targets of Mycobacterium tuberculosis H37Rv based on their flow to resistance genes. The weighted proteome interaction network of the pathogen was constructed using a dataset from STRING database. Only a subset of the dataset with interactions that have a combined score value ≥770 was considered. Maximum flow approach has been used to prioritize potential drug targets. The potential drug targets were obtained through comparative genome and network centrality analysis. The curated set of resistance genes was retrieved from literatures. Detail literature review and additional assessment of the method were also carried out for validation. A list of 537 proteins which are essential to the pathogen and non-homologous with human was obtained from the comparative genome analysis. Through network centrality measures, 131 of them were found within the close neighborhood of the centre of gravity of the proteome network. These proteins were further prioritized based on their maximum flow value to resistance genes and they are proposed as reliable drug targets of the pathogen. Proteins which interact with the host were also identified in order to understand the infection mechanism. Potential drug targets of Mycobacterium tuberculosis H37Rv were successfully prioritized based on their flow to resistance genes of existing drugs which is believed to increase the druggability of the targets since inhibition of a protein that has a maximum flow to

  9. Spanish scientific output on Helicobacter pylori. A study through Medline.

    Science.gov (United States)

    Trapero-Marugán, M; Gisbert, J P; Pajares, J M

    2006-04-01

    to analyze scientific output from Spanish hospitals in relation to Helicobacter pylori infection. papers collected from the Medline database between January 1988 and December 2003 were selected. Our search strategy was: "Helicobacter pylori" [MeSH] AND ((Spain [AD] OR Espana [AD] OR Spanien [AD] OR Espagne [AD] OR Espanha [AD]) OR (Spanish [LA]) OR Spain). The following was analyzed: geographic area, Spanish or foreign publication, topic, and year of publication. Output and impact bibliometric markers were evaluated. in all, 691 papers were identified, of which 241 were excluded. Number of papers went from 2 in 1988 to 47 in 2002 and 13 in 2003. There were more reports in Spanish versus foreign journals (58 vs. 42%). In the first 5 years the areas with greater output were associated with diagnosis and microbiology (33 and 20%), whereas therapy was the predominating subject during the last 5 years (27%). Original papers were most common among publications (69%). Hospitals with highest output included La Princesa (24%) and Ramón y Cajal (17.6%) in Madrid, and Parc Taulí in Barcelona (6.4%). Mean impact factor progressively increased from 1.826 in 1988 to 2.142 in 2002 and 2.493 in 2003. the production and impact of documents published by Spanish scientists regarding H. pylori infection considerably increased during the past two decades.

  10. Optimizing the Prioritization of Natural Disaster Recovery Projects

    National Research Council Canada - National Science Library

    Aftanas, Jason M

    2007-01-01

    .... This work will focus on promoting objectivity in the project prioritizing process, improving the communication of the overall base recovery requirement, increasing efficiency in utilizing human and monetary resources, and the creation of a usable and repeatable decision-making tool based on Value-Focused Thinking and integer programming methods.

  11. A method for the efficient prioritization of infrastructure renewal projects

    International Nuclear Information System (INIS)

    Karydas, D.M.; Gifun, J.F.

    2006-01-01

    The infrastructure renewal program at MIT consists of a large number of projects with an estimated budget that could approach $1 billion. Infrastructure renewal at the Massachusetts Institute of Technology (MIT) is the process of evaluating and investing in the maintenance of facility systems and basic structure to preserve existing campus buildings. The selection and prioritization of projects must be addressed with a systematic method for the optimal allocation of funds and other resources. This paper presents a case study of a prioritization method utilizing multi-attribute utility theory. This method was developed at MIT's Department of Nuclear Engineering and was deployed by the Department of Facilities after appropriate modifications were implemented to address the idiosyncrasies of infrastructure renewal projects and the competing criteria and constraints that influence the judgment of the decision-makers. Such criteria include minimization of risk, optimization of economic impact, and coordination with academic policies, programs, and operations of the Institute. A brief overview of the method is presented, as well as the results of its application to the prioritization of infrastructure renewal projects. Results of workshops held at MIT with the participation of stakeholders demonstrate the feasibility of the prioritization method and the usefulness of this approach

  12. Prioritizing Training To Maximize Results: The 3 Box System.

    Science.gov (United States)

    Kearns, Paul

    2003-01-01

    Considers fundamentals of effective training and focuses on the evaluation of training. Describes the 3 Box System, which provides a framework for discussing: (1) basic training needs and priorities; (2) added value training, including ROI (return on investment); evaluation; and (3) prioritizing training budgets. (LRW)

  13. Aggressive effects of prioritizing popularity in early adolescence

    NARCIS (Netherlands)

    Cillessen, A.H.N.; Mayeux, L.; Ha, P.T.; Bruyn, E.H. de; LaFontana, K.M.

    2014-01-01

    This study examined the moderating effects of prioritizing popularity on the association between early adolescents' popularity and their aggressive, leadership, and prosocial behaviors with peers. Participants were 288 14-year-olds from The Netherlands who completed a sociometric instrument and an

  14. The noise control prioritizing index in a tire manufacturing company

    Directory of Open Access Journals (Sweden)

    Rostam Golmohammadi

    2017-11-01

    Conclusion; the results of the present study indicated that using an index resulted from a combination of various parameters affecting the noise pollution, we would be able to prioritize units for implementing noise pollution control confidently. The results of the present study are applicable to all similar industrial settings.

  15. Sensitivity-based research prioritization through stochastic characterization modeling

    DEFF Research Database (Denmark)

    Wender, Ben A.; Prado-Lopez, Valentina; Fantke, Peter

    2018-01-01

    to guide research efforts in data refinement and design of experiments for existing and emerging chemicals alike. This study presents a sensitivity-based approach for estimating toxicity characterization factors given high input data uncertainty and using the results to prioritize data collection according...

  16. A COMPARISON OF APPROACHES TO PRIORITIZING SITES FOR RIPARIAN RESTORATION

    Science.gov (United States)

    This study compares the results of Olson and Harris (1997) and Russell et al.(1997)in their work to prioritize sites for riparian restoration in the San Luis Rey River watershed. Olson and Harris defined reaches of the mainstem and evaluated the relative potential for restoration...

  17. An expert system for automated flavour matching - Prioritizer

    DEFF Research Database (Denmark)

    Silva, Bárbara Santos; Tøstesen, Marie; Petersen, Mikael Agerlin

    2017-01-01

    Flavour matching can be viewed as trying to reproduce a specific flavour. This is a time consuming task and may lead to flavour mixtures that are too complex or too expensive to be commercialized. In order to facilitate the matching, we have developed a new mathematical model, called Prioritizer....

  18. Prioritizing substitution of organic solvents in industrial cleaning processes

    DEFF Research Database (Denmark)

    Rasmussen, Pia Brunn; Jacobsen, Thomas

    1997-01-01

    A method for prioritizing the substitution of volatile organic compounds (VOC) used in industrial cleaning processes is developed. The result is a matrix, which, if all information can be obtained, gives a comprehensive description of the effects, exposure and emission of VOC, as well as the pros...

  19. The effect of requirements prioritization on avionics system conceptual design

    Science.gov (United States)

    Lorentz, John

    This dissertation will provide a detailed approach and analysis of a new collaborative requirements prioritization methodology that has been used successfully on four Coast Guard avionics acquisition and development programs valued at $400M+. A statistical representation of participant study results will be discussed and analyzed in detail. Many technically compliant projects fail to deliver levels of performance and capability that the customer desires. Some of these systems completely meet "threshold" levels of performance; however, the distribution of resources in the process devoted to the development and management of the requirements does not always represent the voice of the customer. This is especially true for technically complex projects such as modern avionics systems. A simplified facilitated process for prioritization of system requirements will be described. The collaborative prioritization process, and resulting artifacts, aids the systems engineer during early conceptual design. All requirements are not the same in terms of customer priority. While there is a tendency to have many thresholds inside of a system design, there is usually a subset of requirements and system performance that is of the utmost importance to the design. These critical capabilities and critical levels of performance typically represent the reason the system is being built. The systems engineer needs processes to identify these critical capabilities, the associated desired levels of performance, and the risks associated with the specific requirements that define the critical capability. The facilitated prioritization exercise is designed to collaboratively draw out these critical capabilities and levels of performance so they can be emphasized in system design. Developing the purpose, scheduling and process for prioritization events are key elements of systems engineering and modern project management. The benefits of early collaborative prioritization flow throughout the

  20. Risk-based prioritization of pharmaceuticals in the natural environment in Iraq.

    Science.gov (United States)

    Al-Khazrajy, Omar S A; Boxall, Alistair B A

    2016-08-01

    Numerous studies have demonstrated the occurrence of pharmaceuticals in the natural environment, raising concerns about their impact on non-target organisms or human health. One region where little is known about the exposure and effects of pharmaceuticals in the environment is Iraq. Due to the high number of pharmaceuticals used by the public health sector in Iraq (hospitals and care centres) and distributed over the counter, there is a need for a systematic approach for identifying substances that should be monitored in the environment in Iraq and assessed in terms of environmental risk. In this study, a risk-based prioritization approach was applied to 99 of the most dispensed pharmaceuticals in three Iraqi cities, Baghdad, Mosul and Basrah. Initially, information on the amounts of pharmaceuticals used in Iraq was obtained. The top used medicines were found to be paracetamol, amoxicillin and metformin with total annual consumption exceeding 1000 tonnes per year. Predicted environmental concentrations (PECs) and predicted no-effect concentrations (PNECs), derived from ecotoxicological end-points and effects related to the therapeutic mode of action, were then used to rank the pharmaceuticals in terms of risks to different environmental compartments. Active pharmaceutical ingredients used as antibiotics, antidepressants and analgesics were identified as the highest priority in surface water, sediment and the terrestrial environment. Antibiotics were also prioritized according to their susceptibility to kill or inhibit the growth of bacteria or to accelerate the evolution and dissemination of antibiotic-resistant genes in water. Future work will focus on understanding the occurrence, fate and effects of some of highly prioritized substances in the environment.

  1. The medline UK filter: development and validation of a geographic search filter to retrieve research about the UK from OVID medline.

    Science.gov (United States)

    Ayiku, Lynda; Levay, Paul; Hudson, Tom; Craven, Jenny; Barrett, Elizabeth; Finnegan, Amy; Adams, Rachel

    2017-07-13

    A validated geographic search filter for the retrieval of research about the United Kingdom (UK) from bibliographic databases had not previously been published. To develop and validate a geographic search filter to retrieve research about the UK from OVID medline with high recall and precision. Three gold standard sets of references were generated using the relative recall method. The sets contained references to studies about the UK which had informed National Institute for Health and Care Excellence (NICE) guidance. The first and second sets were used to develop and refine the medline UK filter. The third set was used to validate the filter. Recall, precision and number-needed-to-read (NNR) were calculated using a case study. The validated medline UK filter demonstrated 87.6% relative recall against the third gold standard set. In the case study, the medline UK filter demonstrated 100% recall, 11.4% precision and a NNR of nine. A validated geographic search filter to retrieve research about the UK with high recall and precision has been developed. The medline UK filter can be applied to systematic literature searches in OVID medline for topics with a UK focus. © 2017 Crown copyright. Health Information and Libraries Journal © 2017 Health Libraries GroupThis article is published with the permission of the Controller of HMSO and the Queen's Printer for Scotland.

  2. In vitro screening of environmental chemicals for targeted testing prioritization: the ToxCast project.

    Science.gov (United States)

    Judson, Richard S; Houck, Keith A; Kavlock, Robert J; Knudsen, Thomas B; Martin, Matthew T; Mortensen, Holly M; Reif, David M; Rotroff, Daniel M; Shah, Imran; Richard, Ann M; Dix, David J

    2010-04-01

    Chemical toxicity testing is being transformed by advances in biology and computer modeling, concerns over animal use, and the thousands of environmental chemicals lacking toxicity data. The U.S. Environmental Protection Agency's ToxCast program aims to address these concerns by screening and prioritizing chemicals for potential human toxicity using in vitro assays and in silico approaches. This project aims to evaluate the use of in vitro assays for understanding the types of molecular and pathway perturbations caused by environmental chemicals and to build initial prioritization models of in vivo toxicity. We tested 309 mostly pesticide active chemicals in 467 assays across nine technologies, including high-throughput cell-free assays and cell-based assays, in multiple human primary cells and cell lines plus rat primary hepatocytes. Both individual and composite scores for effects on genes and pathways were analyzed. Chemicals displayed a broad spectrum of activity at the molecular and pathway levels. We saw many expected interactions, including endocrine and xenobiotic metabolism enzyme activity. Chemicals ranged in promiscuity across pathways, from no activity to affecting dozens of pathways. We found a statistically significant inverse association between the number of pathways perturbed by a chemical at low in vitro concentrations and the lowest in vivo dose at which a chemical causes toxicity. We also found associations between a small set of in vitro assays and rodent liver lesion formation. This approach promises to provide meaningful data on the thousands of untested environmental chemicals and to guide targeted testing of environmental contaminants.

  3. MedlinePlus Connect: Linking Patient Portals and Electronic Health Records to Health Information

    Science.gov (United States)

    ... Here: Home → MedlinePlus Connect URL of this page: https://medlineplus.gov/connect/overview.html MedlinePlus Connect Linking ... will change.) Old URLs New URLs Web Application https://apps.nlm.nih.gov/medlineplus/services/mpconnect.cfm? ...

  4. Efficient population-scale variant analysis and prioritization with VAPr.

    Science.gov (United States)

    Birmingham, Amanda; Mark, Adam M; Mazzaferro, Carlo; Xu, Guorong; Fisch, Kathleen M

    2018-04-06

    With the growing availability of population-scale whole-exome and whole-genome sequencing, demand for reproducible, scalable variant analysis has spread within genomic research communities. To address this need, we introduce the Python package VAPr (Variant Analysis and Prioritization). VAPr leverages existing annotation tools ANNOVAR and MyVariant.info with MongoDB-based flexible storage and filtering functionality. It offers biologists and bioinformatics generalists easy-to-use and scalable analysis and prioritization of genomic variants from large cohort studies. VAPr is developed in Python and is available for free use and extension under the MIT License. An install package is available on PyPi at https://pypi.python.org/pypi/VAPr, while source code and extensive documentation are on GitHub at https://github.com/ucsd-ccbb/VAPr. kfisch@ucsd.edu.

  5. A weight restricted DEA model for FMEA risk prioritization

    Directory of Open Access Journals (Sweden)

    Pauli Adriano de Almada Garcia

    2012-01-01

    Full Text Available In this paper we present a linear programming (LP approach to risk prioritization in failure mode and effects analysis (FMEA. The LP is a data envelopment analysis (DEA-based model considering weight restriction. In a FMEA, we commonly consider three criteria to prioritize the failure modes, occurrence, severity and detectability. These criteria are in an ordinal scale commonly varying from 1 to 10, higher the figure worse the result. Considering the values established for each criteria, in traditional FMEA one adopts a Risk Priority Number, calculated considering the product of criteria, which has been very criticized due to its shortcoming. Through the proposed approach a frontier is established considering the less critical failure modes. Considering this frontier, one can establish how much each failure mode must be improved to become relatively acceptable. A simplified case concerning an AFWS of a two loops PWR power plant is presented to shows the applicability of the proposed approach.

  6. Modeling and prioritizing demand response programs in power markets

    International Nuclear Information System (INIS)

    Aalami, H.A.; Moghaddam, M. Parsa; Yousefi, G.R.

    2010-01-01

    One of the responsibilities of power market regulator is setting rules for selecting and prioritizing demand response (DR) programs. There are many different alternatives of DR programs for improving load profile characteristics and achieving customers' satisfaction. Regulator should find the optimal solution which reflects the perspectives of each DR stakeholder. Multi Attribute Decision Making (MADM) is a proper method for handling such optimization problems. In this paper, an extended responsive load economic model is developed. The model is based on price elasticity and customer benefit function. Prioritizing of DR programs can be realized by means of Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) method. Considerations of ISO/utility/customer regarding the weighting of attributes are encountered by entropy method. An Analytical Hierarchy Process (AHP) is used for selecting the most effective DR program. Numerical studies are conducted on the load curve of the Iranian power grid in 2007. (author)

  7. Effects of preference heterogeneity among landowners on spatial conservation prioritization

    DEFF Research Database (Denmark)

    Nielsen, Anne Sofie Elberg; Strange, Niels; Bruun, Hans Henrik

    2017-01-01

    The participation of private landowners in conservation is crucial to efficient biodiversity conservation. This is especially the case in settings where the share of private ownership is large and the economic costs associated with land acquisition are high. We used probit regression analysis...... into a spatial prioritization for conservation of unmanaged forests. The choice models are based on sociodemographic data on the entire population of Danish forest owners and historical data on their participation in conservation schemes. Inclusion in the model of information on private landowners' willingness...... to supply land for conservation yielded at intermediate budget levels up to 30% more expected species coverage than the uninformed prioritization scheme. Our landowner-choice model provides an example of moving toward more implementable conservation planning....

  8. Sustainability Decision Support Framework for Industrial System Prioritization

    DEFF Research Database (Denmark)

    Ren, Jingzheng; Wei, Shunan; Goodsite, Michael Evan

    2016-01-01

    A multicriteria decision-making methodology for the sustainability prioritization of industrial systems is proposed. The methodology incorporates a fuzzy Analytic Hierarchy Process method that allows the users to assess the soft criteria using linguistic terms. A fuzzy Analytic Network Process...... method is used to calculate the weights of each criterion, which can tackle the interdependencies and interactions among the criteria. The Preference Ranking Organization Method for Enrichment Evaluation approach is used to prioritize the sustainability sequence of the alternative systems. Moreover......, a sensitivity analysis method was developed to investigate the most critical and sensitive criteria. The developed methodology was illustrated by a case study to rank the sustainability of five alternative hydrogen production technologies. The advantages of the developed methodology over the previous approaches...

  9. Patient prioritization in medical emergencies: an ethical analysis.

    Science.gov (United States)

    Fortes, Paulo Antônio de Carvalho; Pereira, Patricia Cristina Andrade

    2012-01-01

    To identify and analyze, in the light of ethical considerations, the choices and justifications of public health professionals in hypothetical situations of patient prioritization in circumstances of limited resources during emergency medical care. Qualitative and quantitative study, carried out through interviews with 80 public health professionals, graduate students (MSc and PhD students) in public health who were faced with hypothetical situations involving the criteria of gender, age, and responsibility, asked to choose between alternatives that referred to the existence of people, equally submitted to life-threatening situations, who needed care in an emergency department. The choices prioritized children, young individuals, women, and married women, with decision-making invoking the ethical principles of vulnerability, social utility, and equity. The study shows a clear tendency to justify the choices that were made, guided by utilitarian ethics.

  10. Points to consider for prioritizing clinical genetic testing services

    DEFF Research Database (Denmark)

    Severin, Franziska; Borry, Pascal; Cornel, Martina C

    2015-01-01

    Given the cost constraints of the European health-care systems, criteria are needed to decide which genetic services to fund from the public budgets, if not all can be covered. To ensure that high-priority services are available equitably within and across the European countries, a shared set...... testing services available in the next decade. Ethically and economically reflected prioritization criteria are needed. Prioritization should be based on considerations of medical benefit, health need and costs. Medical benefit includes evidence of benefit in terms of clinical benefit, benefit......, following the principles of accountability for reasonableness. We provide points to consider to stimulate this debate across the EU and to serve as a reference for improving patient management.European Journal of Human Genetics advance online publication, 24 September 2014; doi:10.1038/ejhg.2014.190....

  11. Healthcare Analytics: Creating a Prioritized Improvement System with Performance Benchmarking.

    Science.gov (United States)

    Kolker, Eugene; Kolker, Evelyne

    2014-03-01

    The importance of healthcare improvement is difficult to overstate. This article describes our collaborative work with experts at Seattle Children's to create a prioritized improvement system using performance benchmarking. We applied analytics and modeling approaches to compare and assess performance metrics derived from U.S. News and World Report benchmarking data. We then compared a wide range of departmental performance metrics, including patient outcomes, structural and process metrics, survival rates, clinical practices, and subspecialist quality. By applying empirically simulated transformations and imputation methods, we built a predictive model that achieves departments' average rank correlation of 0.98 and average score correlation of 0.99. The results are then translated into prioritized departmental and enterprise-wide improvements, following a data to knowledge to outcomes paradigm. These approaches, which translate data into sustainable outcomes, are essential to solving a wide array of healthcare issues, improving patient care, and reducing costs.

  12. Comparison of methods for prioritizing risk in radiation oncology

    International Nuclear Information System (INIS)

    Biazotto, Bruna; Tokarski, Marcio

    2016-01-01

    Proactive risk management tools, such as Failure Mode and Effect Analysis (FEMA), were imported from engineering and have been widely used in Radiation Oncology. An important step in this process is the risk prioritization and there are many methods to do that. This paper compares the risk prioritization of computerized planning phase in interstitial implants with high dose rate brachytherapy performed with Health Care Failure Mode and Effect Analysis (HFMEA) and FMEA with guidelines given by the Task Group 100 (TG 100) of the American Association of Physicists in Medicine. Out of the 33 possible failure modes of this process, 21 require more attention when evaluated by HFMEA and 22, when evaluated by FMEA TG 100. Despite the high coincidence between the methods, the execution of HFMEA was simpler. (author)

  13. 13 CFR 107.1520 - How a Licensee computes and allocates Prioritized Payments to SBA.

    Science.gov (United States)

    2010-01-01

    ... Prioritized Payments, earned Adjustments and earned Charges. (3) Earned Payments Account. The Earned Payments... Distribution: (1) Bring the Accumulation Account up to date by adding to it all Prioritized Payments and... Payments to SBA. This section tells you how to compute Prioritized Payments, Adjustments and Charges on...

  14. Experimentation on accuracy of non functional requirement prioritization approaches for different complexity projects

    OpenAIRE

    Raj Kumar Chopra; Varun Gupta; Durg Singh Chauhan

    2016-01-01

    Non functional requirements must be selected for implementation together with functional requirements to enhance the success of software projects. Three approaches exist for performing the prioritization of non functional requirements using the suitable prioritization technique. This paper performs experimentation on three different complexity versions of the industrial software project using cost-value prioritization technique employing three approaches. Experimentation is conducted to analy...

  15. Consequences for diversity when prioritizing animals for conservation with pedigree or genomic information

    NARCIS (Netherlands)

    Engelsma, K.A.; Veerkamp, R.F.; Calus, M.P.L.; Windig, J.J.

    2011-01-01

    Up to now, prioritization of animals for conservation has been mainly based on pedigree information; however, genomic information may improve prioritization. In this study, we used two Holstein populations to investigate the consequences for genetic diversity when animals are prioritized with

  16. Prioritizing zoonotic diseases in Ethiopia using a one health approach

    Directory of Open Access Journals (Sweden)

    Emily G. Pieracci

    2016-12-01

    Discussion: Multi-sectoral collaborations strengthen disease surveillance system development in humans and animals, enhance laboratory capacity, and support implementation of prevention and control strategies. To facilitate this, the creation of a One Health-focused Zoonotic Disease Unit is recommended. Enhancement of public health and veterinary laboratories, joint outbreak and surveillance activities, and intersectoral linkages created to tackle the prioritized zoonotic diseases will undoubtedly prepare the country to effectively address newly emerging zoonotic diseases.

  17. Place prioritization for biodiversity content using species ecological niche modeling

    OpenAIRE

    Víctor Sánchez-Cordero; Verónica Cirelli; Mariana Munguial; Sahotra Sarkar

    2005-01-01

    Place prioritization for biodiversity representation is essential for conservation planning, particularly in megadiverse countries where high deforestation threatens biodiversity. Given the collecting biases and uneven sampling of biological inventories, there is a need to develop robust models of species’ distributions. By modeling species’ ecological niches using point occurrence data and digitized environmental feature maps, we can predict potential and extant distributions of species in u...

  18. Prioritizing lean management practices in public and private hospitals.

    Science.gov (United States)

    Hussain, Matloub; Malik, Mohsin

    2016-05-16

    Purpose - The purpose of this paper is to prioritize 21 healthcare wastes in public and private hospitals of United Arab Emirates (UAE). Design/methodology/approach - Seven healthcare wastes linked with lean management are further decomposed in to sub-criteria and to deal with this complexity of multi criteria decision-making process, analytical hierarchical process (AHP) method is used in this research. Findings - AHP framework for this study resulted in a ranking of 21 healthcare wastes in public and private hospitals of UAE. It has been found that management in private healthcare systems of UAE is putting more emphasis on the inventory waste. On the other hand, over processing waste has got highest weight in public hospitals of UAE. Research limitations/implications - The future directions of this research would be to apply a lean set of tools for the value stream optimization of the prioritized key improvement areas. Practical implications - This is a contribution to the continuing research into lean management, giving practitioners and designers a practical way for measuring and implementing lean practices across health organizations. Originality/value - The contribution of this research, through successive stages of data collection, measurement analysis and refinement, is a set of reliable and valid framework that can be subsequently used in conceptualization, prioritization of the waste reduction strategies in healthcare management.

  19. Data integration to prioritize drugs using genomics and curated data.

    Science.gov (United States)

    Louhimo, Riku; Laakso, Marko; Belitskin, Denis; Klefström, Juha; Lehtonen, Rainer; Hautaniemi, Sampsa

    2016-01-01

    Genomic alterations affecting drug target proteins occur in several tumor types and are prime candidates for patient-specific tailored treatments. Increasingly, patients likely to benefit from targeted cancer therapy are selected based on molecular alterations. The selection of a precision therapy benefiting most patients is challenging but can be enhanced with integration of multiple types of molecular data. Data integration approaches for drug prioritization have successfully integrated diverse molecular data but do not take full advantage of existing data and literature. We have built a knowledge-base which connects data from public databases with molecular results from over 2200 tumors, signaling pathways and drug-target databases. Moreover, we have developed a data mining algorithm to effectively utilize this heterogeneous knowledge-base. Our algorithm is designed to facilitate retargeting of existing drugs by stratifying samples and prioritizing drug targets. We analyzed 797 primary tumors from The Cancer Genome Atlas breast and ovarian cancer cohorts using our framework. FGFR, CDK and HER2 inhibitors were prioritized in breast and ovarian data sets. Estrogen receptor positive breast tumors showed potential sensitivity to targeted inhibitors of FGFR due to activation of FGFR3. Our results suggest that computational sample stratification selects potentially sensitive samples for targeted therapies and can aid in precision medicine drug repositioning. Source code is available from http://csblcanges.fimm.fi/GOPredict/.

  20. iLOCi: a SNP interaction prioritization technique for detecting epistasis in genome-wide association studies

    Directory of Open Access Journals (Sweden)

    Piriyapongsa Jittima

    2012-12-01

    Full Text Available Abstract Background Genome-wide association studies (GWAS do not provide a full account of the heritability of genetic diseases since gene-gene interactions, also known as epistasis are not considered in single locus GWAS. To address this problem, a considerable number of methods have been developed for identifying disease-associated gene-gene interactions. However, these methods typically fail to identify interacting markers explaining more of the disease heritability over single locus GWAS, since many of the interactions significant for disease are obscured by uninformative marker interactions e.g., linkage disequilibrium (LD. Results In this study, we present a novel SNP interaction prioritization algorithm, named iLOCi (Interacting Loci. This algorithm accounts for marker dependencies separately in case and control groups. Disease-associated interactions are then prioritized according to a novel ranking score calculated from the difference in marker dependencies for every possible pair between case and control groups. The analysis of a typical GWAS dataset can be completed in less than a day on a standard workstation with parallel processing capability. The proposed framework was validated using simulated data and applied to real GWAS datasets using the Wellcome Trust Case Control Consortium (WTCCC data. The results from simulated data showed the ability of iLOCi to identify various types of gene-gene interactions, especially for high-order interaction. From the WTCCC data, we found that among the top ranked interacting SNP pairs, several mapped to genes previously known to be associated with disease, and interestingly, other previously unreported genes with biologically related roles. Conclusion iLOCi is a powerful tool for uncovering true disease interacting markers and thus can provide a more complete understanding of the genetic basis underlying complex disease. The program is available for download at http://www4a.biotec.or.th/GI/tools/iloci.

  1. Intelligent system for topic survey in MEDLINE by keyword recommendation and learning text characteristics.

    Science.gov (United States)

    Tanaka, M; Nakazono, S; Matsuno, H; Tsujimoto, H; Kitamura, Y; Miyano, S

    2000-01-01

    We have implemented a system for assisting experts in selecting MEDLINE records for database construction purposes. This system has two specific features: The first is a learning mechanism which extracts characteristics in the abstracts of MEDLINE records of interest as patterns. These patterns reflect selection decisions by experts and are used for screening the records. The second is a keyword recommendation system which assists and supplements experts' knowledge in unexpected cases. Combined with a conventional keyword-based information retrieval system, this system may provide an efficient and comfortable environment for MEDLINE record selection by experts. Some computational experiments are provided to prove that this idea is useful.

  2. Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.

    Science.gov (United States)

    Kim, Sun; Kim, Won; Wei, Chih-Hsuan; Lu, Zhiyong; Wilbur, W John

    2012-01-01

    The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical-gene interactions, chemical-disease relationships and gene-disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein-protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team.

  3. OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants

    KAUST Repository

    Boudellioua, Imene

    2018-05-02

    Purpose: An increasing number of Mendelian disorders have been identified for which two or more variants in one or more genes are required to cause the disease, or significantly modify its severity or phenotype. It is difficult to discover such interactions using existing approaches. The purpose of our work is to develop and evaluate a system that can identify combinations of variants underlying oligogenic diseases in individual whole exome or whole genome sequences. Methods: Information that links patient phenotypes to databases of gene-phenotype associations observed in clinical research can provide useful information and improve variant prioritization for Mendelian diseases. Additionally, background knowledge about interactions between genes can be utilized to guide and restrict the selection of candidate disease modules. Results: We developed OligoPVP, an algorithm that can be used to identify variants in oligogenic diseases and their interactions, using whole exome or whole genome sequences together with patient phenotypes as input. We demonstrate that OligoPVP has significantly improved performance when compared to state of the art pathogenicity detection methods. Conclusions: Our results show that OligoPVP can efficiently detect oligogenic interactions using a phenotype-driven approach and identify etiologically important variants in whole genomes.

  4. Effect of risk aversion on prioritizing conservation projects.

    Science.gov (United States)

    Tulloch, Ayesha I T; Maloney, Richard F; Joseph, Liana N; Bennett, Joseph R; Di Fonzo, Martina M I; Probert, William J M; O'Connor, Shaun M; Densem, Jodie P; Possingham, Hugh P

    2015-04-01

    Conservation outcomes are uncertain. Agencies making decisions about what threat mitigation actions to take to save which species frequently face the dilemma of whether to invest in actions with high probability of success and guaranteed benefits or to choose projects with a greater risk of failure that might provide higher benefits if they succeed. The answer to this dilemma lies in the decision maker's aversion to risk--their unwillingness to accept uncertain outcomes. Little guidance exists on how risk preferences affect conservation investment priorities. Using a prioritization approach based on cost effectiveness, we compared 2 approaches: a conservative probability threshold approach that excludes investment in projects with a risk of management failure greater than a fixed level, and a variance-discounting heuristic used in economics that explicitly accounts for risk tolerance and the probabilities of management success and failure. We applied both approaches to prioritizing projects for 700 of New Zealand's threatened species across 8303 management actions. Both decision makers' risk tolerance and our choice of approach to dealing with risk preferences drove the prioritization solution (i.e., the species selected for management). Use of a probability threshold minimized uncertainty, but more expensive projects were selected than with variance discounting, which maximized expected benefits by selecting the management of species with higher extinction risk and higher conservation value. Explicitly incorporating risk preferences within the decision making process reduced the number of species expected to be safe from extinction because lower risk tolerance resulted in more species being excluded from management, but the approach allowed decision makers to choose a level of acceptable risk that fit with their ability to accommodate failure. We argue for transparency in risk tolerance and recommend that decision makers accept risk in an adaptive management

  5. Prioritizing land and sea conservation investments to protect coral reefs.

    Directory of Open Access Journals (Sweden)

    Carissa J Klein

    Full Text Available BACKGROUND: Coral reefs have exceptional biodiversity, support the livelihoods of millions of people, and are threatened by multiple human activities on land (e.g. farming and in the sea (e.g. overfishing. Most conservation efforts occur at local scales and, when effective, can increase the resilience of coral reefs to global threats such as climate change (e.g. warming water and ocean acidification. Limited resources for conservation require that we efficiently prioritize where and how to best sustain coral reef ecosystems. METHODOLOGY/PRINCIPAL FINDINGS: Here we develop the first prioritization approach that can guide regional-scale conservation investments in land- and sea-based conservation actions that cost-effectively mitigate threats to coral reefs, and apply it to the Coral Triangle, an area of significant global attention and funding. Using information on threats to marine ecosystems, effectiveness of management actions at abating threats, and the management and opportunity costs of actions, we calculate the rate of return on investment in two conservation actions in sixteen ecoregions. We discover that marine conservation almost always trumps terrestrial conservation within any ecoregion, but terrestrial conservation in one ecoregion can be a better investment than marine conservation in another. We show how these results could be used to allocate a limited budget for conservation and compare them to priorities based on individual criteria. CONCLUSIONS/SIGNIFICANCE: Previous prioritization approaches do not consider both land and sea-based threats or the socioeconomic costs of conserving coral reefs. A simple and transparent approach like ours is essential to support effective coral reef conservation decisions in a large and diverse region like the Coral Triangle, but can be applied at any scale and to other marine ecosystems.

  6. Prioritizing conservation areas for coastal plant diversity under increasing urbanization.

    Science.gov (United States)

    Doxa, Aggeliki; Albert, Cécile Hélène; Leriche, Agathe; Saatkamp, Arne

    2017-10-01

    Coastal urban expansion will continue to drive further biodiversity losses, if conservation targets for coastal ecosystems are not defined and met. Prioritizing areas for future protected area networks is thus an urgent task in such urbanization-threatened ecosystems. Our aim is to quantify past and future losses of coastal vegetation priority areas due to urbanization and assess the effectiveness of the existing protected area network for conservation. We conduct a prioritization analysis, based on 82 coastal plants, including common and IUCN red list species, in a highly-urbanized but biotically diverse region, in South-Eastern France. We evaluate the role of protected areas, by taking into account both strict and multi-use areas. We assess the impact of past and future urbanization on high priority areas, by combining prioritization analyses and urbanization models. We show that half of the highly diverse areas have already been lost due to urbanization. Remaining top priority areas are also among the most exposed to future urban expansion. The effectiveness of the existing protected area (PA) network is only partial. While strict PAs coincide well with top priority areas, they only represent less than one third of priority areas. The effectiveness of multi-use PAs, such as the Natura 2000 network, also remains limited. Our approach highlights the impact of urbanization on plant conservation targets. By modelling urbanization, we manage to identify those areas where protection could be more efficient to limit further losses. We suggest to use our approach in the future to expand the PA network in order to achieve the 2020 Aichi biodiversity targets. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Prioritization strategies in clinical practice guidelines development: a pilot study

    Directory of Open Access Journals (Sweden)

    Torres Marcela

    2010-03-01

    Full Text Available Abstract Objective Few methodological studies address the prioritization of clinical topics for the development of Clinical Practice Guidelines (CPGs. The aim of this study was to validate a methodology for Priority Determination of Topics (PDT of CPGs. Methods and results Firstly, we developed an instrument for PDT with 41 criteria that were grouped under 10 domains, based on a comprehensive systematic search. Secondly, we performed a survey of stakeholders involved in CPGs development, and end users of guidelines, using the instrument. Thirdly, a pilot testing of the PDT procedure was performed in order to choose 10 guideline topics among 34 proposed projects; using a multi-criteria analysis approach, we validated a mechanism that followed five stages: determination of the composition of groups, item/domain scoring, weights determination, quality of the information used to support judgments, and finally, topic selection. Participants first scored the importance of each domain, after which four different weighting procedures were calculated (including the survey results. The process of weighting was determined by correlating the data between them. We also reported the quality of evidence used for PDT. Finally, we provided a qualitative analysis of the process. The main domains used to support judgement, having higher quality scores and weightings, were feasibility, disease burden, implementation and information needs. Other important domains such as user preferences, adverse events, potential for health promotion, social effects, and economic impact had lower relevance for clinicians. Criteria for prioritization were mainly judged through professional experience, while good quality information was only used in 15% of cases. Conclusion The main advantages of the proposed methodology are supported by the use of a systematic approach to identify, score and weight guideline topics selection, limiting or exposing the influence of personal biases

  8. Enabling task-based information prioritization via semantic web encodings

    Science.gov (United States)

    Michaelis, James R.

    2016-05-01

    Modern Soldiers rely upon accurate and actionable information technology to achieve mission objectives. While increasingly rich sensor networks for Areas of Operation (AO) can offer many directions for aiding Soldiers, limitations are imposed by current tactical edge systems on the rate that content can be transmitted. Furthermore, mission tasks will often require very specific sets of information which may easily be drowned out by other content sources. Prior research on Quality and Value of Information (QoI/VoI) has aimed to define ways to prioritize information objects based on their intrinsic attributes (QoI) and perceived value to a consumer (VoI). As part of this effort, established ranking approaches for obtaining Subject Matter Expert (SME) recommendations, such as the Analytic Hierarchy Process (AHP) have been considered. However, limited work has been done to tie Soldier context - such as descriptions of their mission and tasks - back to intrinsic attributes of information objects. As a first step toward addressing the above challenges, this work introduces an ontology-backed approach - rooted in Semantic Web publication practices - for expressing both AHP decision hierarchies and corresponding SME feedback. Following a short discussion on related QoI/VoI research, an ontology-based data structure is introduced for supporting evaluation of Information Objects, using AHP rankings designed to facilitate information object prioritization. Consistent with alternate AHP approaches, prioritization in this approach is based on pairwise comparisons between Information Objects with respect to established criteria, as well as on pairwise comparison of the criteria to assess their relative importance. The paper concludes with a discussion of both ongoing and future work.

  9. Prioritizing land and sea conservation investments to protect coral reefs.

    Science.gov (United States)

    Klein, Carissa J; Ban, Natalie C; Halpern, Benjamin S; Beger, Maria; Game, Edward T; Grantham, Hedley S; Green, Alison; Klein, Travis J; Kininmonth, Stuart; Treml, Eric; Wilson, Kerrie; Possingham, Hugh P

    2010-08-30

    Coral reefs have exceptional biodiversity, support the livelihoods of millions of people, and are threatened by multiple human activities on land (e.g. farming) and in the sea (e.g. overfishing). Most conservation efforts occur at local scales and, when effective, can increase the resilience of coral reefs to global threats such as climate change (e.g. warming water and ocean acidification). Limited resources for conservation require that we efficiently prioritize where and how to best sustain coral reef ecosystems. Here we develop the first prioritization approach that can guide regional-scale conservation investments in land- and sea-based conservation actions that cost-effectively mitigate threats to coral reefs, and apply it to the Coral Triangle, an area of significant global attention and funding. Using information on threats to marine ecosystems, effectiveness of management actions at abating threats, and the management and opportunity costs of actions, we calculate the rate of return on investment in two conservation actions in sixteen ecoregions. We discover that marine conservation almost always trumps terrestrial conservation within any ecoregion, but terrestrial conservation in one ecoregion can be a better investment than marine conservation in another. We show how these results could be used to allocate a limited budget for conservation and compare them to priorities based on individual criteria. Previous prioritization approaches do not consider both land and sea-based threats or the socioeconomic costs of conserving coral reefs. A simple and transparent approach like ours is essential to support effective coral reef conservation decisions in a large and diverse region like the Coral Triangle, but can be applied at any scale and to other marine ecosystems.

  10. Sensory Prioritization in Rats: Behavioral Performance and Neuronal Correlates.

    Science.gov (United States)

    Lee, Conrad C Y; Diamond, Mathew E; Arabzadeh, Ehsan

    2016-03-16

    Operating with some finite quantity of processing resources, an animal would benefit from prioritizing the sensory modality expected to provide key information in a particular context. The present study investigated whether rats dedicate attentional resources to the sensory modality in which a near-threshold event is more likely to occur. We manipulated attention by controlling the likelihood with which a stimulus was presented from one of two modalities. In a whisker session, 80% of trials contained a brief vibration stimulus applied to whiskers and the remaining 20% of trials contained a brief change of luminance. These likelihoods were reversed in a visual session. When a stimulus was presented in the high-likelihood context, detection performance increased and was faster compared with the same stimulus presented in the low-likelihood context. Sensory prioritization was also reflected in neuronal activity in the vibrissal area of primary somatosensory cortex: single units responded differentially to the whisker vibration stimulus when presented with higher probability compared with lower probability. Neuronal activity in the vibrissal cortex displayed signatures of multiplicative gain control and enhanced response to vibration stimuli during the whisker session. In conclusion, rats allocate priority to the more likely stimulus modality and the primary sensory cortex may participate in the redistribution of resources. Detection of low-amplitude events is critical to survival; for example, to warn prey of predators. To formulate a response, decision-making systems must extract minute neuronal signals from the sensory modality that provides key information. Here, we identify the behavioral and neuronal correlates of sensory prioritization in rats. Rats were trained to detect whisker vibrations or visual flickers. Stimuli were embedded in two contexts in which either visual or whisker modality was more likely to occur. When a stimulus was presented in the high

  11. Robust and accurate multi-view reconstruction by prioritized matching

    DEFF Research Database (Denmark)

    Ylimaki, Markus; Kannala, Juho; Holappa, Jukka

    2012-01-01

    a prioritized matching method which expands the most promising seeds first. The output of the method is a three-dimensional point cloud. Unlike previous correspondence growing approaches our method allows to use the best-first matching principle in the generic multi-view stereo setting with arbitrary number...... of input images. Our experiments show that matching the most promising seeds first provides very robust point cloud reconstructions efficiently with just a single expansion step. A comparison to the current state-of-the-art shows that our method produces reconstructions of similar quality but significantly...

  12. Neural Signature of Value-Based Sensorimotor Prioritization in Humans.

    Science.gov (United States)

    Blangero, Annabelle; Kelly, Simon P

    2017-11-01

    In situations in which impending sensory events demand fast action choices, we must be ready to prioritize higher-value courses of action to avoid missed opportunities. When such a situation first presents itself, stimulus-action contingencies and their relative value must be encoded to establish a value-biased state of preparation for an impending sensorimotor decision. Here, we sought to identify neurophysiological signatures of such processes in the human brain (both female and male). We devised a task requiring fast action choices based on the discrimination of a simple visual cue in which the differently valued sensory alternatives were presented 750-800 ms before as peripheral "targets" that specified the stimulus-action mapping for the upcoming decision. In response to the targets, we identified a discrete, transient, spatially selective signal in the event-related potential (ERP), which scaled with relative value and strongly predicted the degree of behavioral bias in the upcoming decision both across and within subjects. This signal is not compatible with any hitherto known ERP signature of spatial selection and also bears novel distinctions with respect to characterizations of value-sensitive, spatially selective activity found in sensorimotor areas of nonhuman primates. Specifically, a series of follow-up experiments revealed that the signal was reliably invoked regardless of response laterality, response modality, sensory feature, and reward valence. It was absent, however, when the response deadline was relaxed and the strategic need for biasing removed. Therefore, more than passively representing value or salience, the signal appears to play a versatile and active role in adaptive sensorimotor prioritization. SIGNIFICANCE STATEMENT In many situations such as fast-moving sports, we must be ready to act fast in response to sensory events and, in our preparation, prioritize courses of action that lead to greater rewards. Although behavioral effects of

  13. Prioritization of Workplace Practices: Evidence from Islamic financial institutions

    Directory of Open Access Journals (Sweden)

    Faizah Darus

    2016-01-01

    Full Text Available The aim of this study is to examine the prioritization of workplace practices among Islamic financial institutions in Malaysia for 2012. A content analysis of the annual and sustainability reports were carried out to examine the extensiveness of disclosure relating to information on workplace practices. An Islamic workplace index was used to evaluate the workplace disclosure. The results of the study revealed that skill enhancement and employees-management engagement were the focus for workplace environment among Islamic financial institutions. Particularly, information relating to incentives and bonuses were found to be the most extensively disclosed information.

  14. Interaction Matrices as a Tool for Prioritizing Radioecology Research

    Energy Technology Data Exchange (ETDEWEB)

    Mora, J.C.; Robles, Beatriz [Centro de Investigaciones Energeticas, Medioambientales y Tecnologicas - CIEMAT (Spain); Bradshaw, Clare; Stark, Karolina [Stockholm University (Sweden); Sweeck, Liev; Vives i Batlle, Jordi [Belgian Nuclear Research Centre SCK-CEN (Belgium); Beresford, Nick [Centre for Ecology and Hydrology - CEH (United Kingdom); Thoerring, Havard; Dowdall, Mark [Norwegian Radiation Protection Authority - NRPA (Norway); Outola, Iisa; Turtiainen, Tuukka; Vetikko, Virve [STUK - Radiation and Nuclear Safety Authority (Finland); Steiner, Martin [Federal Office for Radiation Protection - BfS (Germany); Beaugelin-Seiller, Karine; Fevrier, Laureline; Hurtevent, Pierre; Boyer, Patrick [Institut de Radioprotection et de Surete Nucleaire - IRSN (France)

    2014-07-01

    Interaction Matrices as a Tool for Prioritizing Radioecology Research J.C. Mora CIEMAT In 2010 the Strategy for Allied Radioecology (STAR) was launched with several objectives aimed towards integrating the radioecology research efforts of nine institutions in Europe. One of these objectives was the creation of European Radioecology Observatories. The Chernobyl Exclusion Zone (CEZ) and the Upper Silesian Coal Basin (USCB), a coal mining area in Poland, have been chosen after a selection process. A second objective was to develop a system for improving and validating the capabilities of predicting the behaviour of the main radionuclides existing at these observatories. Interaction Matrices (IM) have been used since the 1990's as a tool for developing ecological conceptual models and have also been used within radioecology. The Interaction Matrix system relies on expert judgement for structuring knowledge of a given ecosystem at the conceptual level and was selected for use in the STAR project. A group of experts, selected from each institution of STAR, designed two matrices with the main compartments for each ecosystem (a forest in CEZ and a lake in USCB). All the features, events and processes (FEPs) which could affect the behaviour of the considered radionuclides, focusing on radiocaesium in the Chernobyl forest and radium in the Rontok-Wielki lake, were also included in each IM. Two new sets of experts were appointed to review, improve and prioritize the processes included in each IM. A first processing of the various candidate interaction matrices produced a single interaction matrix for each ecosystem which incorporated all experts combined knowledge. During the prioritization of processes in the IMs, directed towards developing a whole predictive model of radionuclides behaviour in those ecosystems, raised interesting issues related to the processes and parameters involved, regarding the existing knowledge in them. This exercise revealed several processes

  15. MedlinePlus® Everywhere: Access from Your Phone, Tablet or Desktop

    Science.gov (United States)

    ... responsivefull.html MedlinePlus® Everywhere: Access from Your Phone, Tablet or Desktop To use the sharing features on ... provide a consistent user experience from a desktop, tablet, or phone. All users, regardless of how they ...

  16. A Leader in Clinical Trials, Medical Data, & Electronic Health Information | NIH MedlinePlus the Magazine

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    ... of C. Everett Koop, the former Surgeon General; Charles Drew, the “father of the blood bank”; Rosalind ... MedlinePlus information resources about prescriptions. Soon, such information will be available through one click on the name ...

  17. For Distinguished Public Service: Medical Library Association Honors FNLM and NIH MedlinePlus Magazine | NIH ...

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    ... Medical Library Association Honors FNLM and NIH MedlinePlus Magazine Past Issues / Summer 2011 Table of Contents MLA ... From You We want your feedback on the magazine and ideas for future issues, as well as ...

  18. The Match of Her Life | NIH MedlinePlus the Magazine

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    ... answer questions for this issue of NIH MedlinePlus magazine about her breast cancer. You discovered you had ... way of healing. As this issue of the magazine went to press, Navratilova was receiving radiation therapy ...

  19. FNLM 2013 Events & Programs Announced | NIH MedlinePlus the Magazine

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    ... study in their field of expertise. Annual Awards Dinner In 2013, the Awards Dinner to celebrate advances ... Mobile MedlinePlus! Trusted medical information on your mobile phone. http://m.medlineplus.gov and in Spanish at ...

  20. To Your Health: NLM update transcript - NIH MedlinePlus magazine Winter 2018

    Science.gov (United States)

    ... who is a star of 'The Big Bang Theory' television show, and the producer/narrator of a ... trials, NIH MedlinePlus magazine reports the current life expectancy of a person with sickle cell disease is ...

  1. NIH Launches National COPD Action Plan | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... COPD Action Plan Follow us NIH Launches National COPD Action Plan Photo: National Heart, Lung, and Blood ... questions for NIH MedlinePlus magazine. Why was the COPD National Action Plan created? The staggering numbers associated ...

  2. Annotating patents with Medline MeSH codes via citation mapping.

    Science.gov (United States)

    Griffin, Thomas D; Boyer, Stephen K; Councill, Isaac G

    2010-01-01

    Both patents and Medline are important document collections for discovering new relationships between chemicals and biology, searching for prior art for patent applications and retrieving background knowledge for current research activities. Finding relevance to a topic within patents is often made difficult by poor categorization, badly written descriptions, and even intentional obfuscation. Unlike patents, the Medline corpus has Medical Subject Heading (MeSH) keywords manually added to their articles, giving a medically relevant taxonomy to the 18 million article abstracts. Our work attempts to accurately recognize the citations made in patents to Medline-indexed articles, linking them to their corresponding PubMed ID and exploiting the associated MeSH to enhance patent search by annotating the referencing patents with their Medline citations' MeSH codes. The techniques, system features, and benefits are explained.

  3. Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

    OpenAIRE

    Muin, Michael; Fontelo, Paul

    2006-01-01

    Abstract Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhanci...

  4. Is a Widely Available Cure for Sickle Cell Disease on the Horizon? | NIH MedlinePlus the Magazine

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  5. Journalist Liz Hernandez hopes to make Alzheimer’s a thing of the past | NIH MedlinePlus the Magazine

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  6. Finding Better and More Personalized Ways to Diagnose Cancer at NIH | NIH MedlinePlus the Magazine

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  7. From the lab - CancerSEEK: Blood Test Could Detect Cancer Earlier | NIH MedlinePlus the Magazine

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  8. From Bench to Bedside: Researchers of NIH’s Clinical Center | NIH MedlinePlus the Magazine

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  9. From the lab - Brain Scan Technology Extends Treatment Window for Stroke | NIH MedlinePlus the Magazine

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  10. The prioritization of open innovation determinants in banking

    Directory of Open Access Journals (Sweden)

    Tornjanski Vesna

    2015-01-01

    Full Text Available The research scope of the paper is prioritization of open innovation determinants in banking industry using an integrated application of qualitative and quantitative methods in the evaluation process. The research methods were implemented to compound the depth of experts' knowledge and experience on the one hand, and the precise mathematical reasoning, on the other, thus creating the objective and accurate basis for effective decision making. The overview of determinants of open innovations in banking industry has been obtained from the literature overview and the Delphi study conducted among 51 experts from banks in Serbia. Fifteen significant determinants within five dimensions were further evaluated through AHP decision-making method to prioritize them toward the development of the open innovation in banking. The research results show that effective application of open innovation in banking lies in formal reinforcement by management to integrate innovation into organizational policies and in designing dual structures that facilitate the initiation and implementation of an innovation, i.e. building an ambidextrous organization. The research findings and results introduced in this paper can be usefully applied and widely used by both academics and practitioners who are interested in applying the open innovation concept in banking industry.

  11. Enhancing employee capacity to prioritize health insurance benefits.

    Science.gov (United States)

    Danis, Marion; Goold, Susan Dorr; Parise, Carol; Ginsburg, Marjorie

    2007-09-01

    To demonstrate that employees can gain understanding of the financial constraints involved in designing health insurance benefits. While employees who receive their health insurance through the workplace have much at stake as the cost of health insurance rises, they are not necessarily prepared to constructively participate in prioritizing their health insurance benefits in order to limit cost. Structured group exercises. Employees of 41 public and private organizations in Northern California. Administration of the CHAT (Choosing Healthplans All Together) exercise in which participants engage in deliberation to design health insurance benefits under financial constraints. Change in priorities and attitudes about the need to exercise insurance cost constraints. Participants (N = 744) became significantly more cognizant of the need to limit insurance benefits for the sake of affordability and capable of prioritizing benefit options. Those agreeing that it is reasonable to limit health insurance coverage given the cost increased from 47% to 72%. It is both possible and valuable to involve employees in priority setting regarding health insurance benefits through the use of structured decision tools.

  12. Application of risk-based methodologies to prioritize safety resources

    International Nuclear Information System (INIS)

    Rahn, F.J.; Sursock, J.P.; Hosler, J.

    1993-01-01

    The Electric Power Research Institute (EPRI) started a program entitled risk-based prioritization in 1992. The purpose of this program is to provide generic technical support to the nuclear power industry relative to its recent initiatives in the area of operations and maintenance (O ampersand M) cost control using state-of-the-art risk methods. The approach uses probabilistic risk assessment (PRA), or similar techniques, to allocate resources commensurate with the risk posed by nuclear plant operations. Specifically, those items or events that have high risk significance would receive the most attention, while those with little risk content would command fewer resources. As quantified in a companion paper,close-quote the potential O ampersand M cost reduction inherent in this approach is very large. Furthermore, risk-based methods should also lead to safety improvements. This paper outlines the way that the EPRI technical work complements the technical, policy, and regulatory initiatives taken by others in the industry and provides an example of the approach as used to prioritize motor-operated valve (MOV) testing in response to US Nuclear Regulatory Commission (NRC) Generic Letter 89-10

  13. Prioritizing ecological restoration among sites in multi-stressor landscapes.

    Science.gov (United States)

    Neeson, Thomas M; Smith, Sigrid D P; Allan, J David; McIntyre, Peter B

    2016-09-01

    Most ecosystems are impacted by multiple local and long-distance stressors, many of which interact in complex ways. We present a framework for prioritizing ecological restoration efforts among sites in multi-stressor landscapes. Using a simple model, we show that both the economic and sociopolitical costs of restoration will typically be lower at sites with a relatively small number of severe problems than at sites with numerous lesser problems. Based on these results, we propose using cumulative stress and evenness of stressor impact as complementary indices that together reflect key challenges of restoring a site to improved condition. To illustrate this approach, we analyze stressor evenness across the world's rivers and the Laurentian Great Lakes. This exploration reveals that evenness and cumulative stress are decoupled, enabling selection of sites where remediating a modest number of high-intensity stressors could substantially reduce cumulative stress. Just as species richness and species evenness are fundamental axes of biological diversity, we argue that cumulative stress and stressor evenness constitute fundamental axes for identifying restoration opportunities in multi-stressor landscapes. Our results highlight opportunities to boost restoration efficiency through strategic use of multi-stressor datasets to identify sites that maximize ecological response per stressor remediated. This prioritization framework can also be expanded to account for the feasibility of remediation and the expected societal benefits of restoration projects. © 2016 by the Ecological Society of America.

  14. Split diversity in constrained conservation prioritization using integer linear programming.

    Science.gov (United States)

    Chernomor, Olga; Minh, Bui Quang; Forest, Félix; Klaere, Steffen; Ingram, Travis; Henzinger, Monika; von Haeseler, Arndt

    2015-01-01

    Phylogenetic diversity (PD) is a measure of biodiversity based on the evolutionary history of species. Here, we discuss several optimization problems related to the use of PD, and the more general measure split diversity (SD), in conservation prioritization.Depending on the conservation goal and the information available about species, one can construct optimization routines that incorporate various conservation constraints. We demonstrate how this information can be used to select sets of species for conservation action. Specifically, we discuss the use of species' geographic distributions, the choice of candidates under economic pressure, and the use of predator-prey interactions between the species in a community to define viability constraints.Despite such optimization problems falling into the area of NP hard problems, it is possible to solve them in a reasonable amount of time using integer programming. We apply integer linear programming to a variety of models for conservation prioritization that incorporate the SD measure.We exemplarily show the results for two data sets: the Cape region of South Africa and a Caribbean coral reef community. Finally, we provide user-friendly software at http://www.cibiv.at/software/pda.

  15. Prioritization of sediment management alternatives using stochastic multicriteria acceptability analysis

    International Nuclear Information System (INIS)

    Alvarez-Guerra, Manuel; Canis, Laure; Voulvoulis, Nikolaos; Viguri, Javier R.; Linkov, Igor

    2010-01-01

    Decision-making for sediment management is a complex task that requires the consideration of temporal and spatial impacts of several remedial alternatives as well as the associated economic, social and political impact. Multicriteria decision analysis (MCDA) is becoming increasingly recognized as an important environmental management tool that can be used to support the selection of suitable remediation alternatives and prioritization of management units in space and time. This paper proposes an MCDA framework for prioritizing sediment management alternatives. This framework involves identifying of a set of feasible options, as well as defining and evaluating criteria which integrate relevant technical, economic, social and environmental aspects of remedies. The methodology allows an explicit consideration of uncertainty in criteria scores and weights by assigning probability distributions and analyzing subsequent Monte-Carlo simulations. The consideration of different stakeholder simulated values is used to assess the robustness of alternative rankings and to guide the selection of remediation options. An application of this methodology to a case study in the Bay of Santander, Spain, is presented. An assessment is conducted for the case of unknown preferences as well as for hypothetical preferences profiles for four types of stakeholders: Idealist, Politician, Environmentalist and Balanced. The results are used to visualize stakeholder positions and potential disagreements, allowing for the identification of a group of least preferred alternatives for each stakeholder. Stakeholder involvement has the potential to ease the remedy selection process during all stages of the decision-making process and to eventually remedy implementation.

  16. A risk-based approach to prioritize underground storage tanks

    International Nuclear Information System (INIS)

    Chidambariah, V.; Travis, C.C.; Trabalka, J.R.; Thomas, J.K.

    1992-01-01

    The purpose of this paper is to present a risk-based approach for rapid prioritization of low level liquid radioactive waste underground storage tanks (LLLW USTs) for possible interim corrective measures and/or ultimate closure. The ranking of LLLW USTs is needed to ensure that tanks with the greatest potential for adverse impact on the environment and human health receive top priority for further evaluation and remediation. Wastes from the LLLW USTs at the Oak Ridge National Laboratory (ORNL) were pumped out at the time the tanks were removed from service. The residual liquids and sludge contain a mixture of radionuclides and chemicals. Contaminants of concern that were identified in the liquid phase of the inactive LLLW USTs include, the radionuclides, 9O Sr, 137 Cs and 233 U and the chemicals, carbon tetrachloride, trichloroethene, tetrachloroethene, methyl ethyl ketone, mercury, lead and chromium. The risk-based approach for prioritization of the LLLW USTs is based upon three major criteria: (1) leaking characteristics of the tank; (2) location of the tanks; and (3) toxic potential of the tank contents

  17. Prioritizing Acquisition Pathways in the State Level Concept

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, Chantell L. [Los Alamos National Laboratory; Budlong-Sylvester, Kory [Los Alamos National Laboratory; Pilat, Joseph F. [Los Alamos National Laboratory

    2012-06-27

    The International Atomic Energy Agency's (IAEA) Department of Safeguards has launched a project to further develop the State-level concept for the planning, implementation, and evaluation of safeguards activities. In order to further evolve the safeguards system an emphasis is placed on integrating inspection-related activities and the State evaluation process to draw safeguards conclusions in the most efficient way. The credible implementation of acquisition pathway analysis is central to the success of the IAEA's State-level concept. NNSA's Office of Nuclear Safeguards and Security (NA-241) The Next Generation Safeguards Initiative (NGSI) is sponsoring Los Alamos National Laboratory (LANL) to produce a study that will examine the use of acquisition pathway analysis in: (1) Developing a State-specific, State-level approach (SLA) and Annual Implementation Plan (AIP); (2) Maximizing the utility of the physical model; and (3) Supporting resource allocation decisions through a pathway prioritization. To deal with the challenge of developing an effective and efficient SLA, this study looks at: (1) Prioritizing proliferation pathways based on an assessment of a State's capabilities and assumed proliferation strategies; and (2) Relevant State behavior (e.g., transparency, cooperation, etc.) while avoiding subjective judgments about States themselves. The study makes use of case studies and concrete examples in order to illustrate how new concepts and approaches will be implemented, and how they may differ from more traditional safeguards approaches.

  18. Effects of preference heterogeneity among landowners on spatial conservation prioritization.

    Science.gov (United States)

    Nielsen, Anne Sofie Elberg; Strange, Niels; Bruun, Hans Henrik; Jacobsen, Jette Bredahl

    2017-06-01

    The participation of private landowners in conservation is crucial to efficient biodiversity conservation. This is especially the case in settings where the share of private ownership is large and the economic costs associated with land acquisition are high. We used probit regression analysis and historical participation data to examine the likelihood of participation of Danish forest owners in a voluntary conservation program. We used the results to spatially predict the likelihood of participation of all forest owners in Denmark. We merged spatial data on the presence of forest, cadastral information on participation contracts, and individual-level socioeconomic information about the forest owners and their households. We included predicted participation in a probability model for species survival. Uninformed and informed (included land owner characteristics) models were then incorporated into a spatial prioritization for conservation of unmanaged forests. The choice models are based on sociodemographic data on the entire population of Danish forest owners and historical data on their participation in conservation schemes. Inclusion in the model of information on private landowners' willingness to supply land for conservation yielded at intermediate budget levels up to 30% more expected species coverage than the uninformed prioritization scheme. Our landowner-choice model provides an example of moving toward more implementable conservation planning. © 2016 Society for Conservation Biology.

  19. IMRT treatment planning based on prioritizing prescription goals

    International Nuclear Information System (INIS)

    Wilkens, Jan J; Alaly, James R; Zakarian, Konstantin; Thorstad, Wade L; Deasy, Joseph O

    2007-01-01

    Determining the 'best' optimization parameters in IMRT planning is typically a time-consuming trial-and-error process with no unambiguous termination point. Recently we and others proposed a goal-programming approach which better captures the desired prioritization of dosimetric goals. Here, individual prescription goals are addressed stepwise in their order of priority. In the first step, only the highest order goals are considered (target coverage and dose-limiting normal structures). In subsequent steps, the achievements of the previous steps are turned into hard constraints and lower priority goals are optimized, in turn, subject to higher priority constraints. So-called 'slip' factors were introduced to allow for slight, clinically acceptable violations of the constraints. Focusing on head and neck cases, we present several examples for this planning technique. The main advantages of the new optimization method are (i) its ability to generate plans that meet the clinical goals, as well as possible, without tuning any weighting factors or dose-volume constraints, and (ii) the ability to conveniently include more terms such as fluence map smoothness. Lower level goals can be optimized to the achievable limit without compromising higher order goals. The prioritized prescription-goal planning method allows for a more intuitive and human-time-efficient way of dealing with conflicting goals compared to the conventional trial-and-error method of varying weighting factors and dose-volume constraints

  20. Research prioritization of men’s health and urologic diseases

    Directory of Open Access Journals (Sweden)

    Tyler Okland

    Full Text Available ABSTRACT Objectives We sought to determine whether disease representation in the Cochrane Database of Systematic Reviews (CDSR reflects disease burden, measured by the Global Burden of Disease (GBD Study as disability-adjusted life-years (DALYs. Materials and Methods Two investigators performed independent assessment of ten men’s health and urologic diseases (MHUDs in CDSR for systematic review and protocol representation, which were compared with percentage of total 2010 DALYs for the ten conditions. Data were analyzed for correlation using Spearman rank analysis. Results Nine of ten MHUDs were represented by at least one CDSR review. There was a poor and statistically insignificant positive correlation between CDSR representation and disease burden (rho = 0.42, p = 0.23. CDSR representation was aligned with disease burden for three conditions, greater than disease burden for one condition, and less than disease burden for six conditions. Conclusions These results yield high-quality estimates to inform future research prioritization for MHUDs. While prioritization processes are complex and multi-faceted, disease burden should be strongly considered. Awareness of research priority setting has the potential to minimize research disparities on a global scale.

  1. A study on prioritizing typical women’s entrepreneur characteristics

    Directory of Open Access Journals (Sweden)

    Ebrahim Ramezani

    2014-07-01

    Full Text Available Entrepreneurship is one of the main pivot of progress and growth of every country. The spread of entrepreneurship particularly the role of women in this category has speeded up today more than any other times. Many of researchers believe that attention to women entrepreneurship plays remarkable role in soundness and safety of nation’s economy. Maybe in Iran less attention has been paid to this matter in proportion to other countries and due to various reasons, there are not many entrepreneur woman. However, employing typical entrepreneur women in various fields of productivity, industrial, commercial, social and cultural and even higher than these, in country’s political issue proves that women’s role is magnificent and in many cases they enjoy higher abilities in portion to men. In this paper, using additive ratio assessment (ARAS as a prioritizing method, eleven entrepreneur women were chosen for prioritizing criteria for measuring a typical women’s entrepreneurship characteristics. The results show that the balance between work and family among criteria are propounded as the highest weight and fulfilling different jobs simultaneously as the lowest weight.

  2. Harnessing Omics Big Data in Nine Vertebrate Species by Genome-Wide Prioritization of Sequence Variants with the Highest Predicted Deleterious Effect on Protein Function.

    Science.gov (United States)

    Rozman, Vita; Kunej, Tanja

    2018-05-10

    Harnessing the genomics big data requires innovation in how we extract and interpret biologically relevant variants. Currently, there is no established catalog of prioritized missense variants associated with deleterious protein function phenotypes. We report in this study, to the best of our knowledge, the first genome-wide prioritization of sequence variants with the most deleterious effect on protein function (potentially deleterious variants [pDelVars]) in nine vertebrate species: human, cattle, horse, sheep, pig, dog, rat, mouse, and zebrafish. The analysis was conducted using the Ensembl/BioMart tool. Genes comprising pDelVars in the highest number of examined species were identified using a Python script. Multiple genomic alignments of the selected genes were built to identify interspecies orthologous potentially deleterious variants, which we defined as the "ortho-pDelVars." Genome-wide prioritization revealed that in humans, 0.12% of the known variants are predicted to be deleterious. In seven out of nine examined vertebrate species, the genes encoding the multiple PDZ domain crumbs cell polarity complex component (MPDZ) and the transforming acidic coiled-coil containing protein 2 (TACC2) comprise pDelVars. Five interspecies ortho-pDelVars were identified in three genes. These findings offer new ways to harness genomics big data by facilitating the identification of functional polymorphisms in humans and animal models and thus provide a future basis for optimization of protocols for whole genome prioritization of pDelVars and screening of orthologous sequence variants. The approach presented here can inform various postgenomic applications such as personalized medicine and multiomics study of health interventions (iatromics).

  3. In Silico Systems Biology Analysis of Variants of Uncertain Significance in Lynch Syndrome Supports the Prioritization of Functional Molecular Validation.

    Science.gov (United States)

    Borras, Ester; Chang, Kyle; Pande, Mala; Cuddy, Amanda; Bosch, Jennifer L; Bannon, Sarah A; Mork, Maureen E; Rodriguez-Bigas, Miguel A; Taggart, Melissa W; Lynch, Patrick M; You, Y Nancy; Vilar, Eduardo

    2017-10-01

    Lynch syndrome (LS) is a genetic condition secondary to germline alterations in the DNA mismatch repair (MMR) genes with 30% of changes being variants of uncertain significance (VUS). Our aim was to perform an in silico reclassification of VUS from a large single institutional cohort that will help prioritizing functional validation. A total of 54 VUS were detected with 33 (61%) novel variants. We integrated family history, pathology, and genetic information along with supporting evidence from eight different in silico tools at the RNA and protein level. Our assessment allowed us to reclassify 54% (29/54) of the VUS as probably damaging, 13% (7/54) as possibly damaging, and 28% (15/54) as probably neutral. There are more than 1,000 VUS reported in MMR genes and our approach facilitates the prioritization of further functional efforts to assess the pathogenicity to those classified as probably damaging. Cancer Prev Res; 10(10); 580-7. ©2017 AACR . ©2017 American Association for Cancer Research.

  4. A concern-based method to prioritize spill response activities

    International Nuclear Information System (INIS)

    Lamarche, A.; Bart, H.

    2002-01-01

    The Shoreline Cleanup Assessment Team (SCAT) of the Emergencies Division of Environment Canada in the Ontario Region developed a computerized method to help rank segments of shoreline according to levels of concern in the event of an oil spill. The original SCAT approach was designed to allow survey teams to acquire information about the state of shoreline spills so that assessments of oilings would be comparable in time and space. The SCAT method, which allows several decision makers to obtain an unbiased evaluation of the oiling situation, has been recognized in both Canada and the United States as a method that ensures the consistency of data gathering and processing for prioritization purposes. The concern-based prioritization system was integrated within the computerized response tools used by the SCAT team using tools such as the Great Lakes Electronic Environmental Sensitivities Atlas (GLEESA), a geographic information system (GIS) of environmental data, and Shore Assess, a GIS based computerized system used to provide support during a response phase of a spill. It was noted that this method is considered to be a practical response tool designed around the principles of performance support and cybernetics to help decision makers set priorities. It is not designed for pre-impact assessment. Instead, it ensures that existing knowledge of the spill characteristics and environmental conditions are used in a consistent and logical method to prioritize contingency plans. The factors used to evaluate concern for oiling, shoreline type and land use were described. Factors for concern assessment of biological organisms include the status of organisms as being either endangered, threatened, vulnerable, special concern, or not at risk. Characteristics of the species, potential effect of the pollutant and potential effect from response activities are other factors for concern. The method evaluates the concern for every category using a simple algorithm which is

  5. Sustainability as the key to prioritize investments in public infrastructures

    International Nuclear Information System (INIS)

    Pardo-Bosch, Francesc; Aguado, Antonio

    2016-01-01

    Infrastructure construction, one of the biggest driving forces of the economy nowadays, requires a huge analysis and clear transparency to decide what projects have to be executed with the few resources available. With the aim to provide the public administrations a tool with which they can make their decisions easier, the Sustainability Index of Infrastructure Projects (SIIP) has been defined, with a multi-criteria decision system called MIVES, in order to classify non-uniform investments. This index evaluates, in two inseparable stages, the contribution to the sustainable development of each infrastructure project, analyzing its social, environmental and economic impact. The result of the SIIP allows to decide the order with which projects will be prioritized. The case of study developed proves the adaptability and utility of this tool for the ordinary budget management.

  6. Sustainability as the key to prioritize investments in public infrastructures

    Energy Technology Data Exchange (ETDEWEB)

    Pardo-Bosch, Francesc, E-mail: francesc.pardo@upc.edu [Departament d' Enginyeria Civil i Ambiental, Universitat Politècnica de Catalunya - Barcelona Tech. (Spain); Political Science Department, University of California - Berkeley (United States); Aguado, Antonio, E-mail: antonio.aguado@upc.edu [Departament d' Enginyeria Civil i Ambiental, Universitat Politècnica de Catalunya - Barcelona Tech. (Spain)

    2016-09-15

    Infrastructure construction, one of the biggest driving forces of the economy nowadays, requires a huge analysis and clear transparency to decide what projects have to be executed with the few resources available. With the aim to provide the public administrations a tool with which they can make their decisions easier, the Sustainability Index of Infrastructure Projects (SIIP) has been defined, with a multi-criteria decision system called MIVES, in order to classify non-uniform investments. This index evaluates, in two inseparable stages, the contribution to the sustainable development of each infrastructure project, analyzing its social, environmental and economic impact. The result of the SIIP allows to decide the order with which projects will be prioritized. The case of study developed proves the adaptability and utility of this tool for the ordinary budget management.

  7. Prioritizing Signaling Information Transmission in Next Generation Networks

    Directory of Open Access Journals (Sweden)

    Jasmina Baraković

    2011-01-01

    Full Text Available Next generation transport network is characterized by the use of in-band signaling, where Internet Protocol (IP packets carrying signaling or media information are mixed in transmission. Since transport resources are limited, when any segment of access or core network is congested, IP packets carrying signaling information may be discarded. As a consequence, it may be impossible to implement reachability and quality of service (QoS. Since present approaches are insufficient to completely address this problem, a novel approach is proposed, which is based on prioritizing signaling information transmission. To proof the concept, a simulation study was performed using Network Simulator version 2 (ns-2 and independently developed Session Initiation Protocol (SIP module. The obtained results were statistically processed using Statistical Package for the Social Sciences (SPSS version 15.0. Summarizing our research results, several issues are identified for future work.

  8. Task-relevant information is prioritized in spatiotemporal contextual cueing.

    Science.gov (United States)

    Higuchi, Yoko; Ueda, Yoshiyuki; Ogawa, Hirokazu; Saiki, Jun

    2016-11-01

    Implicit learning of visual contexts facilitates search performance-a phenomenon known as contextual cueing; however, little is known about contextual cueing under situations in which multidimensional regularities exist simultaneously. In everyday vision, different information, such as object identity and location, appears simultaneously and interacts with each other. We tested the hypothesis that, in contextual cueing, when multiple regularities are present, the regularities that are most relevant to our behavioral goals would be prioritized. Previous studies of contextual cueing have commonly used the visual search paradigm. However, this paradigm is not suitable for directing participants' attention to a particular regularity. Therefore, we developed a new paradigm, the "spatiotemporal contextual cueing paradigm," and manipulated task-relevant and task-irrelevant regularities. In four experiments, we demonstrated that task-relevant regularities were more responsible for search facilitation than task-irrelevant regularities. This finding suggests our visual behavior is focused on regularities that are relevant to our current goal.

  9. Prioritization of motor operated valves based on risk importances

    International Nuclear Information System (INIS)

    Vesely, W.E.; Weidenhamer, G.H.

    1994-01-01

    The plant Probabilistic Risk Assessment (PRA) can be a potentially useful and powerful tool for helping to define an effective response to GL 89-10. The plant PRA can be used to prioritize the Motor Operated Valves (MOV) dynamic test. The plant PRA can also be used to determine test schedules for the MOVs. In order for the PRA to be validly used to respond to GL 89-10, various issues need to be validly addressed. Eleven issues are specifically identified and responses to these issues are outlined. The issues of joint MOV importance, PRA truncation, and validation of the proposed approach are specifically highlighted and more detailed response considerations are described. As in all PRA applications, sensitivity studies and uncertainty considerations should be incorporated in the PRA evaluations. 4 refs, 3 tabs

  10. Threat Prioritization Process for the Czech Security Strategy Making

    Directory of Open Access Journals (Sweden)

    Milos Balaban

    2012-06-01

    Full Text Available This article offers systematic view of a process of identification of security threats and, subsequently, their use in the making of strategic documents, notably the Security Strategy of the Czech Republic. It is not the aim of the authors to name or define such threats, but to present the process itself. It is paramount to any credible security strategy that it deals with the threat identification in the most precise fashion. The authors take reservations against the “catalogue” approach and claim the processes of prioritization and categorization to be essential for any policies derived from the security strategy, especially in times of economic need. It is also the 2011 final paper of the project “Trends, Risks, and Scenarios of the Security Developments in the World, Europe, and the Czech Republic – Impacts on the Policy and Security System of the Czech Republic” (TRS / VG20102013009.

  11. Spatially explicit prioritization of human antibiotics and antineoplastics in Europe.

    Science.gov (United States)

    Oldenkamp, Rik; Huijbregts, Mark A J; Hollander, Anne; Versporten, Ann; Goossens, Herman; Ragas, Ad M J

    2013-01-01

    This paper presents a screening tool for the location-specific prioritization of human pharmaceutical emissions in Europe, based on risk quotients for the aquatic environment and human health. The tool provides direction towards either monitoring activities or additional research. Its application is illustrated for a set of 11 human antibiotics and 7 antineoplastics. Risk quotients for the aquatic environment were highest for levofloxacin, doxycycline and ciprofloxacin, located in Northern Italy (Milan region; particularly levofloxacin) and other densely populated areas in Europe (e.g. London, Krakow and the Ruhr area). Risk quotients for human health not only depend on pharmaceutical and location, but also on behavioral characteristics, such as consumption patterns. Infants in eastern Spain that consume locally produced food and conventionally treated drinking water were predicted to run the highest risks. A limited comparison with measured concentrations in surface water showed that predicted and measured concentrations are approximately within one order of magnitude. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Place prioritization for biodiversity content using species ecological niche modeling

    Directory of Open Access Journals (Sweden)

    Víctor Sánchez-Cordero

    2005-01-01

    Full Text Available Place prioritization for biodiversity representation is essential for conservation planning, particularly in megadiverse countries where high deforestation threatens biodiversity. Given the collecting biases and uneven sampling of biological inventories, there is a need to develop robust models of species’ distributions. By modeling species’ ecological niches using point occurrence data and digitized environmental feature maps, we can predict potential and extant distributions of species in untransformed landscapes, as well as in those transformed by vegetation change (including deforestation. Such distributional predictions provide a framework for use of species as biodiversity surrogates in place prioritization procedures such as those based on rarity and complementarity. Beyond biodiversity conservation, these predictions can also be used for place prioritization for ecological restoration under current conditions and under future scenarios of habitat change (e.g., deforestation scenarios. To illustrate these points, we (1 predict distributions under current and future deforestation scenarios for the Mexican endemic mammal Dipodomys phillipsii, and show how areas for restoration may be selected; and (2 propose conservation areas by combining nonvolant mammal distributional predictions as biodiversity surrogates with place prioritization procedures, to connect decreed natural protected areas in a region holding exceptional biodiversity: the Transvolcanic Belt in central Mexico. La selección de áreas prioritarias de conservación es fundamental en la planeación sistemática de la conservación, particularmente en países de mega-diversidad, en donde la alta deforestación es una de las amenazas a la biodiversidad. Debido a los sesgos taxonómicos y geográficos de colecta de los inventarios biológicos, es indispensable generar modelos robustos de distribución de especies. Al modelar el nicho ecológico de especies usando localidades de

  13. Prioritization of natural phenomena hazards evaluations for CHG facilities

    International Nuclear Information System (INIS)

    GRAVES, C.E.

    2001-01-01

    Natural phenomena hazards (NPH) are unexpected acts of nature that pose a threat or danger to workers, the public or to the environment by potential damage to structures, systems and components (SSCs). Earthquakes, extreme winds (hurricane and tornado), flood, volcanic eruption, lightning strike, or extreme cold or heat are examples of NPH. This document outlines the method used to prioritize buildings for inspection following an NPH event and contains the priority list for CH2M HILL Hanford Group, Inc. (CHG) buildings. Once an NPH event occurs and the Hanford Emergency Operations Center (EOC) is activated, this document will be used by the EOC to assign building inspections for the trained evaluators, barring any information from the field

  14. Prioritization of R and D programs on probabilistic reactor safety

    International Nuclear Information System (INIS)

    Husseiny, A.A.

    1982-01-01

    An interactive computer code based on the multiattribute utility theory has been developed with graphic capabilities to use in selection of probabilistic reactor safety RandD programs. Utility values and proper graphic representation are made through lottery games on the computer terminal. The code is applied to prioritize a set of RandD programs on LWR safety based on attributes including regulatory issues, institutional issues and operation problems. The methodology is described here in detail with its applications. Some of the input includes statistical distributions and subjective judgments on institutional issues. The flexibility of the approach provides a tool for decision makers whether on individual or group level to assess LWR safety priorities and continuously update their strategies

  15. Prioritized Main Potential Solutions for the e-Navigation Concept

    Directory of Open Access Journals (Sweden)

    Adam Weintrit

    2013-03-01

    Full Text Available In the paper the Author, a member of the International Maritime Organization’s Correspondence Group on e-Navigation, outlines the prioritized solutions for e-Navigation concept formulated at the beginning of 2013. He presents the details of internal CG’s discussions, different national positions after the announcement by the chairman of the group, Mr John Erik Hagen, the working material in this case. The hidden purpose of this study is to show the style and pace of the IMO working group, details regarding the exchange of posts and the formation of a final common position. Author presents just three weeks working with the CG on e-Nav in the lens, doing it with the consent of all participants in this discussion.

  16. Considerations on the selection and prioritization of information security solutions

    Directory of Open Access Journals (Sweden)

    Maria Cristina RĂDULESCU

    2016-05-01

    Full Text Available This paper provides a set of guidelines that can be used for prescribing a methodology or a detailed process for selecting and prioritizing security projects or solutions. It is based on the idea that costs of security solutions should be justified by their contribution to ensuring adequate protection of information resources in the organization which implements them. The article reviews general issues of security risks and costs, arguing the need for explicit consideration of information resources security requirements in order to validate decisions concerning security projects implementation. In such an approach, security requirements of information resources are used as a reference system to quantify the benefits and limitations of security solutions defined as alternative or complementary responses to certain security risks as their implementation faces budget constraints.

  17. Prioritizing research to reduce youth suicide and suicidal behavior.

    Science.gov (United States)

    Bridge, Jeffrey A; Horowitz, Lisa M; Fontanella, Cynthia A; Grupp-Phelan, Jackie; Campo, John V

    2014-09-01

    The goal of the National Action Alliance for Suicide Prevention is to reduce suicide and suicide attempts in the U.S. by 40% in the next decade. In this paper, a public health approach is applied to suicide prevention to illustrate how reductions in youth suicide and suicidal behavior might be achieved by prioritizing research in two areas: (1) increasing access to primary care-based behavioral health interventions for depressed youth and (2) improving continuity of care for youth who present to emergency departments after a suicide attempt. Finally, some scientific, clinical, and methodologic breakthroughs needed to achieve rapid, substantial, and sustained reductions in youth suicide and suicidal behavior are discussed. Copyright © 2014 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

  18. Prioritization of natural phenomena hazards evaluations for CHG facilities

    CERN Document Server

    Graves, C E

    2001-01-01

    Natural phenomena hazards (NPH) are unexpected acts of nature that pose a threat or danger to workers, the public or to the environment by potential damage to structures, systems and components (SSCs). Earthquakes, extreme winds (hurricane and tornado), flood, volcanic eruption, lightning strike, or extreme cold or heat are examples of NPH. This document outlines the method used to prioritize buildings for inspection following an NPH event and contains the priority list for CH2M HILL Hanford Group, Inc. (CHG) buildings. Once an NPH event occurs and the Hanford Emergency Operations Center (EOC) is activated, this document will be used by the EOC to assign building inspections for the trained evaluators, barring any information from the field.

  19. A methodology for comprehensive strategic planning and program prioritization

    Science.gov (United States)

    Raczynski, Christopher Michael

    2008-10-01

    This process developed in this work, Strategy Optimization for the Allocation of Resources (SOAR), is a strategic planning methodology based off Integrated Product and Process Development and systems engineering techniques. Utilizing a top down approach, the process starts with the creation of the organization vision and its measures of effectiveness. These measures are prioritized based on their application to external world scenarios which will frame the future. The programs which will be used to accomplish this vision are identified by decomposing the problem. Information is gathered on the programs as to the application, cost, schedule, risk, and other pertinent information. The relationships between the levels of the hierarchy are mapped utilizing subject matter experts. These connections are then utilized to determine the overall benefit of the programs to the vision of the organization. Through a Multi-Objective Genetic Algorithm a tradespace of potential program portfolios can be created amongst which the decision maker can allocate resources. The information and portfolios are presented to the decision maker through the use of a Decision Support System which collects and visualizes all the data in a single location. This methodology was tested utilizing a science and technology planning exercise conducted by the United States Navy. A thorough decomposition was defined and technology programs identified which had the potential to provide benefit to the vision. The prioritization of the top level capabilities was performed through the use of a rank ordering scheme and a previous naval application was used to demonstrate a cumulative voting scheme. Voting was performed utilizing the Nominal Group Technique to capture the relationships between the levels of the hierarchy. Interrelationships between the technologies were identified and a MOGA was utilized to optimize portfolios with respect to these constraints and information was placed in a DSS. This

  20. A Bayesian variable selection procedure for ranking overlapping gene sets

    DEFF Research Database (Denmark)

    Skarman, Axel; Mahdi Shariati, Mohammad; Janss, Luc

    2012-01-01

    Background Genome-wide expression profiling using microarrays or sequence-based technologies allows us to identify genes and genetic pathways whose expression patterns influence complex traits. Different methods to prioritize gene sets, such as the genes in a given molecular pathway, have been de...

  1. NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease.

    Science.gov (United States)

    Iyappan, Anandhi; Kawalia, Shweta Bagewadi; Raschka, Tamara; Hofmann-Apitius, Martin; Senger, Philipp

    2016-07-08

    Neurodegenerative diseases are incurable and debilitating indications with huge social and economic impact, where much is still to be learnt about the underlying molecular events. Mechanistic disease models could offer a knowledge framework to help decipher the complex interactions that occur at molecular and cellular levels. This motivates the need for the development of an approach integrating highly curated and heterogeneous data into a disease model of different regulatory data layers. Although several disease models exist, they often do not consider the quality of underlying data. Moreover, even with the current advancements in semantic web technology, we still do not have cure for complex diseases like Alzheimer's disease. One of the key reasons accountable for this could be the increasing gap between generated data and the derived knowledge. In this paper, we describe an approach, called as NeuroRDF, to develop an integrative framework for modeling curated knowledge in the area of complex neurodegenerative diseases. The core of this strategy lies in the usage of well curated and context specific data for integration into one single semantic web-based framework, RDF. This increases the probability of the derived knowledge to be novel and reliable in a specific disease context. This infrastructure integrates highly curated data from databases (Bind, IntAct, etc.), literature (PubMed), and gene expression resources (such as GEO and ArrayExpress). We illustrate the effectiveness of our approach by asking real-world biomedical questions that link these resources to prioritize the plausible biomarker candidates. Among the 13 prioritized candidate genes, we identified MIF to be a potential emerging candidate due to its role as a pro-inflammatory cytokine. We additionally report on the effort and challenges faced during generation of such an indication-specific knowledge base comprising of curated and quality-controlled data. Although many alternative approaches

  2. Impact of SciELO and MEDLINE indexing on submissions to Jornal de Pediatria.

    Science.gov (United States)

    Blank, Danilo; Buchweitz, Claudia; Procianoy, Renato S

    2005-01-01

    To evaluate the impact of SciELO and MEDLINE indexing on the number of articles submitted to Jornal de Pediatria. Analysis of total article submission, submission of articles from foreign countries and acceptance figures in the following periods: stage I - pre-website (Jan 2000-Mar 2001); stage II - website (Apr 2001-Jul 2002); stage III - SciELO (Aug 2002-Aug 2003); stage IV - MEDLINE (Sep 2003-Dec 2004). There was a significant trend toward linear increase in the number of submissions along the study period (p = 0.009). The number of manuscripts submitted in stages I through IV was 184, 240, 297, and 482, respectively. The number of submissions was similar in stages I and II (p = 0.148), but statistically higher in Stage III (p SciELO indexing was associated with an increase in Brazilian manuscript submissions to Jornal de Pediatria, whereas MEDLINE indexing led to an increase in both Brazilian and foreign submissions.

  3. The MedlinePlus public user interface: studies of design challenges and opportunities

    Science.gov (United States)

    Marill, Jennifer L.; Miller, Naomi; Kitendaugh, Paula

    2006-01-01

    Question: What are the challenges involved in designing, modifying, and improving a major health information portal that serves over sixty million page views a month? Setting: MedlinePlus, the National Library of Medicine's (NLM's) consumer health Website, is examined. Method: Challenges are presented as six “studies,” which describe selected design issues and how NLM staff resolved them. Main Result: Improving MedlinePlus is an iterative process. Changes in the public user interface are ongoing, reflecting Web design trends, usability testing recommendations, user survey results, new technical requirements, and the need to grow the site in an orderly way. Conclusion: Testing and analysis should accompany Website design modifications. New technologies may enhance a site but also introduce problems. Further modifications to MedlinePlus will be informed by the experiences described here. PMID:16404467

  4. ExpoCast: Exposure Science for Prioritization and Toxicity Testing (S)

    Science.gov (United States)

    The US EPA is completing the Phase I pilot for a chemical prioritization research program, called ToxCast. Here EPA is developing methods for using computational chemistry, high-throughput screening, and toxicogenomic technologies to predict potential toxicity and prioritize limi...

  5. The Effect of a Workload-Preview on Task-Prioritization and Task-Performance

    Science.gov (United States)

    Minotra, Dev

    2012-01-01

    With increased volume and sophistication of cyber attacks in recent years, maintaining situation awareness and effective task-prioritization strategy is critical to the task of cybersecurity analysts. However, high levels of mental-workload associated with the task of cybersecurity analyst's limits their ability to prioritize tasks.…

  6. Arts and Humanities Research, Redefining Public Benefit, and Research Prioritization in Ireland

    Science.gov (United States)

    Gibson, Andrew G.; Hazelkorn, Ellen

    2017-01-01

    This article looks at the effects of a national policy of research prioritization in the years following Ireland's economic crisis. A national research prioritization exercise initiated by policymakers redefined the purpose of higher education research, and designed policies in line with this approach. Placing research for enterprise to the fore,…

  7. Married...with Food Allergies | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... this page please turn Javascript on. Feature: Food Allergies Married...with Food Allergies Past Issues / Spring 2011 Table of Contents Photo: ... life together and a common problem—severe food allergies. NIH MedlinePlus magazine’s Naomi Miller caught up with ...

  8. Parkinson's Disease Research at NIH | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... of this page please turn JavaScript on. Feature: Parkinson's Disease Parkinson's Disease Research at NIH Past Issues / Winter 2014 ... areas of its research: MedlinePlus . medlineplus.gov . Type "Parkinson's disease" in the Search box. NIHSeniorHealth —Parkinson's Disease ...

  9. The development of search filters for adverse effects of surgical interventions in medline and Embase.

    Science.gov (United States)

    Golder, Su; Wright, Kath; Loke, Yoon Kong

    2018-03-31

    Search filter development for adverse effects has tended to focus on retrieving studies of drug interventions. However, a different approach is required for surgical interventions. To develop and validate search filters for medline and Embase for the adverse effects of surgical interventions. Systematic reviews of surgical interventions where the primary focus was to evaluate adverse effect(s) were sought. The included studies within these reviews were divided randomly into a development set, evaluation set and validation set. Using word frequency analysis we constructed a sensitivity maximising search strategy and this was tested in the evaluation and validation set. Three hundred and fifty eight papers were included from 19 surgical intervention reviews. Three hundred and fifty two papers were available on medline and 348 were available on Embase. Generic adverse effects search strategies in medline and Embase could achieve approximately 90% relative recall. Recall could be further improved with the addition of specific adverse effects terms to the search strategies. We have derived and validated a novel search filter that has reasonable performance for identifying adverse effects of surgical interventions in medline and Embase. However, we appreciate the limitations of our methods, and recommend further research on larger sample sizes and prospective systematic reviews. © 2018 The Authors Health Information and Libraries Journal published by John Wiley & Sons Ltd on behalf of Health Libraries Group.

  10. High school peer tutors teach MedlinePlus: a model for Hispanic outreach*

    Science.gov (United States)

    Warner, Debra G.; Olney, Cynthia A.; Wood, Fred B.; Hansen, Lucille; Bowden, Virginia M.

    2005-01-01

    Objectives: The objective was to introduce the MedlinePlus Website to the predominantly Hispanic residents of the Lower Rio Grande Valley region of Texas by partnering with a health professions magnet high school (known as Med High). Methods: Community assessment was used in the planning stages and included pre-project focus groups with students and teachers. Outreach methods included peer tutor selection, train-the-trainer sessions, school and community outreach, and pre- and posttests of MedlinePlus training sessions. Evaluation methods included Web statistics; end-of-project interviews; focus groups with students, faculty, and librarians; and end-of-project surveys of students and faculty. Results: Four peer tutors reached more than 2,000 people during the project year. Students and faculty found MedlinePlus to be a useful resource. Faculty and librarians developed new or revised teaching methods incorporating MedlinePlus. The project enhanced the role of school librarians as agents of change at Med High. The project continues on a self-sustaining basis. Conclusions: Using peer tutors is an effective way to educate high school students about health information resources and, through the students, to reach families and community members. PMID:15858628

  11. Use of the critical incident technique to evaluate the impact of MEDLINE

    International Nuclear Information System (INIS)

    Wilson, S.R.; Starr-Schneidkraut, N.; Cooper, M.D.

    1989-01-01

    The NLM has an ongoing responsibility to assess the extent to which its information products and services support the requirements of its users. This enables the Library to craft ever more responsive systems that capitalize on the latest advances in information and computer technology and, when necessary, to modify existing systems whose performance may no longer be optimal or consistent with the functions intended. The importance of this requirement was underscored in the recent report of the Outreach Planning Panel to the NLM Board of regents. A fundamental concern is the need to identify the impact of MEDLINE-derived information--i.e., does the use of MEDLINE ''make a difference''? In what ways is it used, and with what effect? In particular, is information retrieved from MEDLINE used successfully by health professionals to support medical decision-making and patient care? Previous efforts to address this question have been limited to the collection of available anecdotal reports. Traditional survey methodology, with pre-defined response categories, while used effectively to determine general areas in which MEDLINE information is used, is not well suited to developing a detailed understanding of user motivation, behavior, and resulting consequences. 8 refs., 6 figs., 2 tab

  12. A novel algorithm for analyzing drug-drug interactions from MEDLINE literature.

    Science.gov (United States)

    Lu, Yin; Shen, Dan; Pietsch, Maxwell; Nagar, Chetan; Fadli, Zayd; Huang, Hong; Tu, Yi-Cheng; Cheng, Feng

    2015-11-27

    Drug-drug interaction (DDI) is becoming a serious clinical safety issue as the use of multiple medications becomes more common. Searching the MEDLINE database for journal articles related to DDI produces over 330,000 results. It is impossible to read and summarize these references manually. As the volume of biomedical reference in the MEDLINE database continues to expand at a rapid pace, automatic identification of DDIs from literature is becoming increasingly important. In this article, we present a random-sampling-based statistical algorithm to identify possible DDIs and the underlying mechanism from the substances field of MEDLINE records. The substances terms are essentially carriers of compound (including protein) information in a MEDLINE record. Four case studies on warfarin, ibuprofen, furosemide and sertraline implied that our method was able to rank possible DDIs with high accuracy (90.0% for warfarin, 83.3% for ibuprofen, 70.0% for furosemide and 100% for sertraline in the top 10% of a list of compounds ranked by p-value). A social network analysis of substance terms was also performed to construct networks between proteins and drug pairs to elucidate how the two drugs could interact.

  13. Usefulness of systematic review search strategies in finding child health systematic reviews in MEDLINE

    NARCIS (Netherlands)

    Boluyt, Nicole; Tjosvold, Lisa; Lefebvre, Carol; Klassen, Terry P.; Offringa, Martin

    2008-01-01

    OBJECTIVE: To determine the sensitivity and precision of existing search strategies for retrieving child health systematic reviews in MEDLINE using PubMed. DESIGN: Filter (diagnostic) accuracy study. We identified existing search strategies for systematic reviews, combined them with a filter that

  14. Meta-analysis of Cancer Gene Profiling Data.

    Science.gov (United States)

    Roy, Janine; Winter, Christof; Schroeder, Michael

    2016-01-01

    The simultaneous measurement of thousands of genes gives the opportunity to personalize and improve cancer therapy. In addition, the integration of meta-data such as protein-protein interaction (PPI) information into the analyses helps in the identification and prioritization of genes from these screens. Here, we describe a computational approach that identifies genes prognostic for outcome by combining gene profiling data from any source with a network of known relationships between genes.

  15. MetaCompare: A computational pipeline for prioritizing environmental resistome risk.

    Science.gov (United States)

    Oh, Min; Pruden, Amy; Chen, Chaoqi; Heath, Lenwood S; Xia, Kang; Zhang, Liqing

    2018-04-26

    The spread of antibiotic resistance is a growing public health concern. While numerous studies have highlighted the importance of environmental sources and pathways of the spread of antibiotic resistance, a systematic means of comparing and prioritizing risks represented by various environmental compartments is lacking. Here we introduce MetaCompare, a publicly-available tool for ranking 'resistome risk,' which we define as the potential for antibiotic resistance genes (ARGs) to be associated with mobile genetic elements (MGEs) and mobilize to pathogens based on metagenomic data. A computational pipeline was developed in which each ARG is evaluated based on relative abundance, mobility, and presence within a pathogen. This is determined through assembly of shotgun sequencing data and analysis of contigs containing ARGs to determine if they contain sequence similarity to MGEs or human pathogens. Based on the assembled metagenomes, samples are projected into a 3-D hazard space and assigned resistome risk scores. To validate, we tested previously published metagenomic data derived from distinct aquatic environments. Based on unsupervised machine learning, the test samples clustered in the hazard space in a manner consistent with their origin. The derived scores produced a well-resolved ascending resistome risk ranking of: wastewater treatment plant effluent, dairy lagoon, hospital sewage.

  16. A method to prioritize quantitative traits and individuals for sequencing in family-based studies.

    Directory of Open Access Journals (Sweden)

    Kaanan P Shah

    Full Text Available Owing to recent advances in DNA sequencing, it is now technically feasible to evaluate the contribution of rare variation to complex traits and diseases. However, it is still cost prohibitive to sequence the whole genome (or exome of all individuals in each study. For quantitative traits, one strategy to reduce cost is to sequence individuals in the tails of the trait distribution. However, the next challenge becomes how to prioritize traits and individuals for sequencing since individuals are often characterized for dozens of medically relevant traits. In this article, we describe a new method, the Rare Variant Kinship Test (RVKT, which leverages relationship information in family-based studies to identify quantitative traits that are likely influenced by rare variants. Conditional on nuclear families and extended pedigrees, we evaluate the power of the RVKT via simulation. Not unexpectedly, the power of our method depends strongly on effect size, and to a lesser extent, on the frequency of the rare variant and the number and type of relationships in the sample. As an illustration, we also apply our method to data from two genetic studies in the Old Order Amish, a founder population with extensive genealogical records. Remarkably, we implicate the presence of a rare variant that lowers fasting triglyceride levels in the Heredity and Phenotype Intervention (HAPI Heart study (p = 0.044, consistent with the presence of a previously identified null mutation in the APOC3 gene that lowers fasting triglyceride levels in HAPI Heart study participants.

  17. Developing optimal search strategies for detecting clinically sound prognostic studies in MEDLINE: an analytic survey

    Directory of Open Access Journals (Sweden)

    Haynes R Brian

    2004-06-01

    Full Text Available Abstract Background Clinical end users of MEDLINE have a difficult time retrieving articles that are both scientifically sound and directly relevant to clinical practice. Search filters have been developed to assist end users in increasing the success of their searches. Many filters have been developed for the literature on therapy and reviews but little has been done in the area of prognosis. The objective of this study is to determine how well various methodologic textwords, Medical Subject Headings, and their Boolean combinations retrieve methodologically sound literature on the prognosis of health disorders in MEDLINE. Methods An analytic survey was conducted, comparing hand searches of journals with retrievals from MEDLINE for candidate search terms and combinations. Six research assistants read all issues of 161 journals for the publishing year 2000. All articles were rated using purpose and quality indicators and categorized into clinically relevant original studies, review articles, general papers, or case reports. The original and review articles were then categorized as 'pass' or 'fail' for methodologic rigor in the areas of prognosis and other clinical topics. Candidate search strategies were developed for prognosis and run in MEDLINE – the retrievals being compared with the hand search data. The sensitivity, specificity, precision, and accuracy of the search strategies were calculated. Results 12% of studies classified as prognosis met basic criteria for scientific merit for testing clinical applications. Combinations of terms reached peak sensitivities of 90%. Compared with the best single term, multiple terms increased sensitivity for sound studies by 25.2% (absolute increase, and increased specificity, but by a much smaller amount (1.1% when sensitivity was maximized. Combining terms to optimize both sensitivity and specificity achieved sensitivities and specificities of approximately 83% for each. Conclusion Empirically derived

  18. Integrating conservation costs into sea level rise adaptive conservation prioritization

    Directory of Open Access Journals (Sweden)

    Mingjian Zhu

    2015-07-01

    Full Text Available Biodiversity conservation requires strategic investment as resources for conservation are often limited. As sea level rises, it is important and necessary to consider both sea level rise and costs in conservation decision making. In this study, we consider costs of conservation in an integrated modeling process that incorporates a geomorphological model (SLAMM, species habitat models, and conservation prioritization (Zonation to identify conservation priorities in the face of landscape dynamics due to sea level rise in the Matanzas River basin of northeast Florida. Compared to conservation priorities that do not consider land costs in the analysis process, conservation priorities that consider costs in the planning process change significantly. The comparison demonstrates that some areas with high conservation values might be identified as lower priorities when integrating economic costs in the planning process and some areas with low conservation values might be identified as high priorities when considering costs in the planning process. This research could help coastal resources managers make informed decisions about where and how to allocate conservation resources more wisely to facilitate biodiversity adaptation to sea level rise.

  19. Prioritizing research needs: insights from a healthcare organization in Iran

    Directory of Open Access Journals (Sweden)

    Mohammadkarim Bahadori 1*, Ehsan Teimourzadeh 1, Ali Farzaneh 1, Mostafa Nejati 2

    2011-09-01

    Full Text Available Objectives: The goal of this study was to identify the priorityof research needs in a healthcare organization in Iran, based onidentification of the problems faced by patients, as the mainrecipients of healthcare services.Method: A cross -sectional descriptive study was planned toachieve the objectives of study. The service recipients sampleconsisted of 400 patients. Given the necessity to gain in-depthinsights of the subject matter, a qualitative research design waschosen. A number of 50 interviews were conducted withindividuals from among 400 patients. The data was analyzedusing ATLAS.ti softwarePrioritizing of the topics was doneusing Analytical Hierarchy Process (AHP method and theExpert Choice software.Results: Based on the issues extracted from the interviews anddiscourses, 13 research topics were proposed by experts.Among these, the topics “designing the model of premium andcomplementary franchise payment, proportional to theincome, access and enjoyment”, “designing the dental servicespackage with specific premium in three basic, complementaryand optional levels” and “Presenting the model of diseaseprevention in healthcare organizations” acquired the highestpriority ranked 1 to 3 and earning the scores of 0.63, 0.61 and0.41, respectively.Conclusion: Because resources are limited and needs areunlimited, in order to avoid wasting research resources inhealthcare organizations, allocating the resources must bebased on the extracted priorities; and this is vital to fulfill theorganizational objectives.

  20. Levelized cost-risk reduction prioritization of waste disposal options

    International Nuclear Information System (INIS)

    Wilkinson, V.K.; Young, J.M.

    1992-01-01

    The prioritization of solid waste disposal options in terms of reduced risk to workers, the public, and the environment has recently generated considerable governmental and public interest. In this paper we address the development of a methodology to establish priorities for waste disposal options, such as incineration, landfills, long-term storage, waste minimization, etc. The study is one result of an overall project to develop methodologies for Probabilistic Risk Assessments (PRAs) of non-reactor nuclear facilities for the US Department of Energy. Option preferences are based on a levelized cost-risk reduction analysis. Option rankings are developed as functions of disposal option cost and timing, relative long- and short-term risks, and possible accident scenarios. We examine the annual costs and risks for each option over a large number of years. Risk, in this paper, is defined in terms of annual fatalities (both prompt and long-term) and environmental restoration costs that might result from either an accidental release or long-term exposure to both plant workers and the public near the site or facility. We use event timing to weigh both costs and risks; near-term costs and risks are discounted less than future expenditures and fatalities. This technique levels the timing of cash flows and benefits by converting future costs and benefits to present value costs and benefits. We give an example Levelized Cost-Benefit Analysis of incinerator location options to demonstrate the methodology and required data

  1. A Process for Technology Prioritization in a Competitive Environment

    Science.gov (United States)

    Stephens, Karen; Herman, Melody; Griffin, Brand

    2006-01-01

    This slide presentation reviews NASA's process for prioritizing technology requirements where there is a competitive environment. The In-Space Propulsion Technology (ISPT) project is used to exemplify the process. The ISPT project focuses on the mid level Technology Readiness Level (TRL) for development. These are TRL's 4 through 6, (i.e. Technology Development and Technology Demonstration. The objective of the planning activity is to identify the current most likely date each technology is needed and create ISPT technology development schedules based on these dates. There is a minimum of 4 years between flight and pacing mission. The ISPT Project needed to identify the "pacing mission" for each technology in order to provide funding for each area. Graphic representations show the development of the process. A matrix shows which missions are currently receiving pull from the both the Solar System Exploration and the Sun-Solar System Connection Roadmaps. The timeframes of the pacing missions technologies are shown for various types of propulsion. A pacing mission that was in the near future serves to increase the priority for funding. Adaptations were made when budget reductions precluded the total implementation of the plan.

  2. Business-oriented prioritization: A novel graphical technique

    International Nuclear Information System (INIS)

    Pascual, R.; Del Castillo, G.; Louit, D.; Knights, P.

    2009-01-01

    Traditionally, Pareto analysis has been used to select the most critical components and failure modes of a system. A clear disadvantage of this technique is that it requires preselecting a single criterion to establish priorities. More recently, a graphical log-scatter diagram technique has been proposed. It considers three key performance indicators simultaneously: reliability (MTBF), maintainability (MTTR), and unavailability (D). This technique considers only times and does not include economical effects explicitly. This article extends both techniques to explicitly consider both direct and indirect costs to prioritize from the point of view of an asset manager or from a maintenance decision-maker, as required. Due to the economic-based approach of this article, cost discounting is also considered inside financial costs such as-but not limited to-reliability-related investments. Also, the results are displayed on simple and accessible graphs which make them particularly useful for conveying results to non-technical managers. The methodology is illustrated by analyzing a shovel from the copper mine industry, and it clearly shows how the proposed technique facilitates business oriented decisions and how they should change under different market conditions.

  3. Business-oriented prioritization: A novel graphical technique

    Energy Technology Data Exchange (ETDEWEB)

    Pascual, R. [Centro de Mineria, Pontificia Universidad Catolica de Chile, Av. Vicuna Mackenna 4860, Santiago (Chile)], E-mail: rpascual@ing.puc.cl; Del Castillo, G. [Department of Mechanical Engineering, Universidad de Chile, Casilla 2777, Santiago (Chile); Louit, D. [Komatsu Chile, Av. Americo Vespucio 0631, Quilicura, Santiago (Chile); Centro de Mineria, Pontificia Universidad Catolica de Chile, Av. Vicuna Mackenna 4860, Santiago (Chile); Knights, P. [Division of Mining Engineering, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Brisbane, 4072 (Australia)

    2009-08-15

    Traditionally, Pareto analysis has been used to select the most critical components and failure modes of a system. A clear disadvantage of this technique is that it requires preselecting a single criterion to establish priorities. More recently, a graphical log-scatter diagram technique has been proposed. It considers three key performance indicators simultaneously: reliability (MTBF), maintainability (MTTR), and unavailability (D). This technique considers only times and does not include economical effects explicitly. This article extends both techniques to explicitly consider both direct and indirect costs to prioritize from the point of view of an asset manager or from a maintenance decision-maker, as required. Due to the economic-based approach of this article, cost discounting is also considered inside financial costs such as-but not limited to-reliability-related investments. Also, the results are displayed on simple and accessible graphs which make them particularly useful for conveying results to non-technical managers. The methodology is illustrated by analyzing a shovel from the copper mine industry, and it clearly shows how the proposed technique facilitates business oriented decisions and how they should change under different market conditions.

  4. Prioritizing Test Cases for Memory Leaks in Android Applications

    Institute of Scientific and Technical Information of China (English)

    Ju Qian; Di Zhou

    2016-01-01

    Mobile applications usually can only access limited amount of memory. Improper use of the memory can cause memory leaks, which may lead to performance slowdowns or even cause applications to be unexpectedly killed. Although a large body of research has been devoted into the memory leak diagnosing techniques after leaks have been discovered, it is still challenging to find out the memory leak phenomena at first. Testing is the most widely used technique for failure discovery. However, traditional testing techniques are not directed for the discovery of memory leaks. They may spend lots of time on testing unlikely leaking executions and therefore can be inefficient. To address the problem, we propose a novel approach to prioritize test cases according to their likelihood to cause memory leaks in a given test suite. It firstly builds a prediction model to determine whether each test can potentially lead to memory leaks based on machine learning on selected code features. Then, for each input test case, we partly run it to get its code features and predict its likelihood to cause leaks. The most suspicious test cases will be suggested to run at first in order to reveal memory leak faults as soon as possible. Experimental evaluation on several Android applications shows that our approach is effective.

  5. On Energy Efficiency of Prioritized IoT Systems

    KAUST Repository

    Alabbasi, Abdulrahman

    2018-01-15

    The inevitable deployment of 5G and the Internet of Things (IoT) sheds the light on the importance of the energy efficiency (EE) performance of Device-to- Device (DD) communication systems. In this work, we address a potential IoT application, where different prioritized DD system, i.e., Low-Priority (LP) and High-Priority (HP) systems, co-exist and share the spectrum. We maximize the EE of each system by proposing two schemes. The first scheme optimizes the individual transmission power and the spatial density of each system. The second scheme optimizes the transmission power ratio of both systems and the spatial density of each one. We also construct and analytically solve a multi- objective optimization problem that combines and jointly maximizes both HP and LP EE performance. Unique structures of the addressed problems are verified. Via numerical results we show that the system which dominates the overall EE (combined EEs of both HP and LP) is the system corresponding to the lowest power for low/high power ratio (between HP and LP systems). However, if the power ratio is close to one, the dominating EE corresponds to the system with higher weight.

  6. Component Fragility Research Program: Phase 1 component prioritization

    International Nuclear Information System (INIS)

    Holman, G.S.; Chou, C.K.

    1987-06-01

    Current probabilistic risk assessment (PRA) methods for nuclear power plants utilize seismic ''fragilities'' - probabilities of failure conditioned on the severity of seismic input motion - that are based largely on limited test data and on engineering judgment. Under the NRC Component Fragility Research Program (CFRP), the Lawrence Livermore National Laboratory (LLNL) has developed and demonstrated procedures for using test data to derive probabilistic fragility descriptions for mechanical and electrical components. As part of its CFRP activities, LLNL systematically identified and categorized components influencing plant safety in order to identify ''candidate'' components for future NRC testing. Plant systems relevant to safety were first identified; within each system components were then ranked according to their importance to overall system function and their anticipated seismic capacity. Highest priority for future testing was assigned to those ''very important'' components having ''low'' seismic capacity. This report describes the LLNL prioritization effort, which also included application of ''high-level'' qualification data as an alternate means of developing probabilistic fragility descriptions for PRA applications

  7. An Intuitionistic Multiplicative ORESTE Method for Patients’ Prioritization of Hospitalization

    Directory of Open Access Journals (Sweden)

    Cheng Zhang

    2018-04-01

    Full Text Available The tension brought about by sickbeds is a common and intractable issue in public hospitals in China due to the large population. Assigning the order of hospitalization of patients is difficult because of complex patient information such as disease type, emergency degree, and severity. It is critical to rank the patients taking full account of various factors. However, most of the evaluation criteria for hospitalization are qualitative, and the classical ranking method cannot derive the detailed relations between patients based on these criteria. Motivated by this, a comprehensive multiple criteria decision making method named the intuitionistic multiplicative ORESTE (organísation, rangement et Synthèse dedonnées relarionnelles, in French was proposed to handle the problem. The subjective and objective weights of criteria were considered in the proposed method. To do so, first, considering the vagueness of human perceptions towards the alternatives, an intuitionistic multiplicative preference relation model is applied to represent the experts’ preferences over the pairwise alternatives with respect to the predetermined criteria. Then, a correlation coefficient-based weight determining method is developed to derive the objective weights of criteria. This method can overcome the biased results caused by highly-related criteria. Afterwards, we improved the general ranking method, ORESTE, by introducing a new score function which considers both the subjective and objective weights of criteria. An intuitionistic multiplicative ORESTE method was then developed and further highlighted by a case study concerning the patients’ prioritization.

  8. PubMed had a higher sensitivity than Ovid-MEDLINE in the search for systematic reviews.

    Science.gov (United States)

    Katchamart, Wanruchada; Faulkner, Amy; Feldman, Brian; Tomlinson, George; Bombardier, Claire

    2011-07-01

    To compare the performance of Ovid-MEDLINE vs. PubMed for identifying randomized controlled trials of methotrexate (MTX) in patients with rheumatoid arthritis (RA). We created search strategies for Ovid-MEDLINE and PubMed for a systematic review of MTX in RA. Their performance was evaluated using sensitivity, precision, and number needed to read (NNR). Comparing searches in Ovid-MEDLINE vs. PubMed, PubMed retrieved more citations overall than Ovid-MEDLINE; however, of the 20 citations that met eligibility criteria for the review, Ovid-MEDLINE retrieved 17 and PubMed 18. The sensitivity was 85% for Ovid-MEDLINE vs. 90% for PubMed, whereas the precision and NNR were comparable (precision: 0.881% for Ovid-MEDLINE vs. 0.884% for PubMed and NNR: 114 for Ovid-MEDLINE vs. 113 for PubMed). In systematic reviews of RA, PubMed has higher sensitivity than Ovid-MEDLINE with comparable precision and NNR. This study highlights the importance of well-designed database-specific search strategies. Copyright © 2010 Elsevier Inc. All rights reserved.

  9. An Approach for Integrating the Prioritization of Functional and Nonfunctional Requirements

    Directory of Open Access Journals (Sweden)

    Mohammad Dabbagh

    2014-01-01

    Full Text Available Due to the budgetary deadlines and time to market constraints, it is essential to prioritize software requirements. The outcome of requirements prioritization is an ordering of requirements which need to be considered first during the software development process. To achieve a high quality software system, both functional and nonfunctional requirements must be taken into consideration during the prioritization process. Although several requirements prioritization methods have been proposed so far, no particular method or approach is presented to consider both functional and nonfunctional requirements during the prioritization stage. In this paper, we propose an approach which aims to integrate the process of prioritizing functional and nonfunctional requirements. The outcome of applying the proposed approach produces two separate prioritized lists of functional and non-functional requirements. The effectiveness of the proposed approach has been evaluated through an empirical experiment aimed at comparing the approach with the two state-of-the-art-based approaches, analytic hierarchy process (AHP and hybrid assessment method (HAM. Results show that our proposed approach outperforms AHP and HAM in terms of actual time-consumption while preserving the quality of the results obtained by our proposed approach at a high level of agreement in comparison with the results produced by the other two approaches.

  10. An approach for integrating the prioritization of functional and nonfunctional requirements.

    Science.gov (United States)

    Dabbagh, Mohammad; Lee, Sai Peck

    2014-01-01

    Due to the budgetary deadlines and time to market constraints, it is essential to prioritize software requirements. The outcome of requirements prioritization is an ordering of requirements which need to be considered first during the software development process. To achieve a high quality software system, both functional and nonfunctional requirements must be taken into consideration during the prioritization process. Although several requirements prioritization methods have been proposed so far, no particular method or approach is presented to consider both functional and nonfunctional requirements during the prioritization stage. In this paper, we propose an approach which aims to integrate the process of prioritizing functional and nonfunctional requirements. The outcome of applying the proposed approach produces two separate prioritized lists of functional and non-functional requirements. The effectiveness of the proposed approach has been evaluated through an empirical experiment aimed at comparing the approach with the two state-of-the-art-based approaches, analytic hierarchy process (AHP) and hybrid assessment method (HAM). Results show that our proposed approach outperforms AHP and HAM in terms of actual time-consumption while preserving the quality of the results obtained by our proposed approach at a high level of agreement in comparison with the results produced by the other two approaches.

  11. Methodology for national risk analysis and prioritization of toxic industrial chemicals.

    Science.gov (United States)

    Taxell, Piia; Engström, Kerstin; Tuovila, Juha; Söderström, Martin; Kiljunen, Harri; Vanninen, Paula; Santonen, Tiina

    2013-01-01

    The identification of chemicals that pose the greatest threat to human health from incidental releases is a cornerstone in public health preparedness for chemical threats. The present study developed and applied a methodology for the risk analysis and prioritization of industrial chemicals to identify the most significant chemicals that pose a threat to public health in Finland. The prioritization criteria included acute and chronic health hazards, physicochemical and environmental hazards, national production and use quantities, the physicochemical properties of the substances, and the history of substance-related incidents. The presented methodology enabled a systematic review and prioritization of industrial chemicals for the purpose of national public health preparedness for chemical incidents.

  12. Prioritization Assessment for Capability Gaps in Weapon System of Systems Based on the Conditional Evidential Network

    Directory of Open Access Journals (Sweden)

    Dong Pei

    2018-02-01

    Full Text Available The prioritization of capability gaps for weapon system of systems is the basis for design and capability planning in the system of systems development process. In order to address input information uncertainties, the prioritization of capability gaps is computed in two steps using the conditional evidential network method. First, we evaluated the belief distribution of degree of required satisfaction for capabilities, and then calculated the reverse conditional belief function between capability hierarchies. We also provided verification for the feasibility and effectiveness of the proposed method through a prioritization of capability gaps calculation using an example of a spatial-navigation-and-positioning system of systems.

  13. Prioritizing and scheduling Portsmouth Gaseous Diffusion Plant safeguards upgrades

    International Nuclear Information System (INIS)

    Edmunds, T.; Saleh, R.; Zevanove, S.

    1992-02-01

    As part of the Site Safeguards and Security Plan (SSSP), facilities are required to develop a Resource Plan (RP). The Resource Plan provides documentation and justification for the facility's planned upgrades, including the schedule, priority, and cost estimates for the safeguards and security upgrades. Portsmouth Gaseous Diffusion Plant (PORTS) management has identified and obtained funding approval for a number of safeguards and security upgrades, including line-item construction projects. These upgrade projects were selected to address a variety of concerns identified in the PORTS vulnerability assessments and other reviews performed in support of the SSSP process. However, budgeting and scheduling constraints do not make it possible to simultaneously begin implementation of all of the upgrade projects. A formal methodology and analysis are needed to explicitly address the trade-offs between competing safeguards objectives, and to prioritize and schedule the upgrade projects to ensure that the maximum benefit can be realized in the shortest possible time frame. The purpose of this report is to describe the methodology developed to support these upgrade project scheduling decisions. The report also presents the results obtained from applying the methodology to a set of the upgrade projects selected by PORTS S ampersand S management. Data for the analysis are based on discussions with personnel familiar with the PORTS safeguards and security needs, the requirements for implementing these upgrades, and upgrade funding limitations. The analysis results presented here assume continued highly enriched uranium (HEU) operations at PORTS. However, the methodology developed is readily adaptable for the evaluation of other operational scenarios and other resource allocation issues relevant to PORTS

  14. Misleading prioritizations from modelling range shifts under climate change

    Science.gov (United States)

    Sofaer, Helen R.; Jarnevich, Catherine S.; Flather, Curtis H.

    2018-01-01

    AimConservation planning requires the prioritization of a subset of taxa and geographical locations to focus monitoring and management efforts. Integration of the threats and opportunities posed by climate change often relies on predictions from species distribution models, particularly for assessments of vulnerability or invasion risk for multiple taxa. We evaluated whether species distribution models could reliably rank changes in species range size under climate and land use change.LocationConterminous U.S.A.Time period1977–2014.Major taxa studiedPasserine birds.MethodsWe estimated ensembles of species distribution models based on historical North American Breeding Bird Survey occurrences for 190 songbirds, and generated predictions to recent years given c. 35 years of observed land use and climate change. We evaluated model predictions using standard metrics of discrimination performance and a more detailed assessment of the ability of models to rank species vulnerability to climate change based on predicted range loss, range gain, and overall change in range size.ResultsSpecies distribution models yielded unreliable and misleading assessments of relative vulnerability to climate and land use change. Models could not accurately predict range expansion or contraction, and therefore failed to anticipate patterns of range change among species. These failures occurred despite excellent overall discrimination ability and transferability to the validation time period, which reflected strong performance at the majority of locations that were either always or never occupied by each species.Main conclusionsModels failed for the questions and at the locations of greatest interest to conservation and management. This highlights potential pitfalls of multi-taxa impact assessments under global change; in our case, models provided misleading rankings of the most impacted species, and spatial information about range changes was not credible. As modelling methods and

  15. Online Impact Prioritization of Essential Climate Variables on Climate Change

    Science.gov (United States)

    Forsythe-Newell, S. P.; Barkstrom, B. B.; Roberts, K. P.

    2007-12-01

    The National Oceanic & Atmospheric Administration (NOAA)'s NCDC Scientific Data Stewardship (SDS) Team has developed an online prototype that is capable of displaying the "big picture" perspective of all Essential Climate Variable (ECV) impacts on society and value to the IPCC. This prototype ECV-Model provides the ability to visualize global ECV information with options to drill down in great detail. It offers a quantifiable prioritization of ECV impacts that potentially may significantly enhance collaboration with respect to dealing effectively with climate change. The ECV-Model prototype assures anonymity and provides an online input mechanism for subject matter experts and decision makers to access, review and submit: (1) ranking of ECV"s, (2) new ECV's and associated impact categories and (3) feedback about ECV"s, satellites, etc. Input and feedback are vetted by experts before changes or additions are implemented online. The SDS prototype also provides an intuitive one-stop web site that displays past, current and planned launches of satellites; and general as well as detailed information in conjunction with imagery. NCDC's version 1.0 release will be available to the public and provide an easy "at-a-glance" interface to rapidly identify gaps and overlaps of satellites and associated instruments monitoring climate change ECV's. The SDS version 1.1 will enhance depiction of gaps and overlaps with instruments associated with In-Situ and Satellites related to ECVs. NOAA's SDS model empowers decision makers and the scientific community to rapidly identify weaknesses and strengths in monitoring climate change ECV's and potentially significantly enhance collaboration.

  16. Use of risk importance measures in maintenance prioritization

    International Nuclear Information System (INIS)

    Dubreil Chambardel, A.; Ardorino, F.; Mauger, P.

    1997-01-01

    A RCM method has been developed at EDF since 1990 to optimize maintenance through a prioritization of resources for equipment that are important in terms of safety, availability and maintenance costs. In 1994, the Nuclear Power Plant Operations Division decided to apply this method to the most important systems of the French PWRs. About 50 systems are in the scope of the RCM. Those that have a role in safety were ranked depending on their contribution to the risk of core melt provided by PSAs. The RCM studies on the 20 most important to safety systems are performed by the Nuclear Power Plant Operations division, the other 30 systems are studied on sites. The RCM study consists first in the research of equipment and failures modes significant to safety, availability or maintenance costs and the evaluation of the performance of those equipment. Those studies lead to the distinction of equipment and failure modes that are critical or non critical to safety, availability and costs. The last part of the study consists in optimizing maintenance on those equipment. In this process, risk measures are used to help defining equipment and failure modes critical to safety. This is done by calculation of risk importance measures provided by PSAs. We explain in this paper which measures of risk have been defined, how PSAs allow calculation of those measures, and how we used those results in the RCM studies we processed. We give also extensions of the use of those measures in the process of defining optimized maintenance tasks. After having defined a RCM method for the French PWRs, the Nuclear Power plant Operations Division decided to start a generalized program of maintenance optimization for the most important systems. The three criteria on which the method relies are: safety, unit availability and maintenance costs. We present here the safety aspect of the method and more precisely these of risk importance measures in the RCM process. (author)

  17. Implied reading direction and prioritization of letter encoding.

    Science.gov (United States)

    Holcombe, Alex O; Nguyen, Elizabeth H L; Goodbourn, Patrick T

    2017-10-01

    Capacity limits hinder processing of multiple stimuli, contributing to poorer performance for identifying two briefly presented letters than for identifying a single letter. Higher accuracy is typically found for identifying the letter on the left, which has been attributed to a right-hemisphere dominance for selective attention. Here, we use rapid serial visual presentation (RSVP) of letters in two locations at once. The letters to be identified are simultaneous and cued by rings. In the first experiment, we manipulated implied reading direction by rotating or mirror-reversing the letters to face to the left rather than to the right. The left-side performance advantage was eliminated. In the second experiment, letters were positioned above and below fixation, oriented such that they appeared to face downward (90° clockwise rotation) or upward (90° counterclockwise rotation). Again consistent with an effect of implied reading direction, performance was better for the top position in the downward condition, but not in the upward condition. In both experiments, mixture modeling of participants' report errors revealed that attentional sampling from the two locations was approximately simultaneous, ruling out the theory that the letter on one side was processed first, followed by a shift of attention to sample the other letter. Thus, the orientation of the letters apparently controls not when the letters are sampled from the scene, but rather the dynamics of a subsequent process, such as tokenization or memory consolidation. Implied reading direction appears to determine the letter prioritized at a high-level processing bottleneck. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  18. Operationalizing Semantic Medline for meeting the information needs at point of care

    Science.gov (United States)

    Rastegar-Mojarad, Majid; Li, Dingcheng; Liu, Hongfang

    2015-01-01

    Scientific literature is one of the popular resources for providing decision support at point of care. It is highly desirable to bring the most relevant literature to support the evidence-based clinical decision making process. Motivated by the recent advance in semantically enhanced information retrieval, we have developed a system, which aims to bring semantically enriched literature, Semantic Medline, to meet the information needs at point of care. This study reports our work towards operationalizing the system for real time use. We demonstrate that the migration of a relational database implementation to a NoSQL (Not only SQL) implementation significantly improves the performance and makes the use of Semantic Medline at point of care decision support possible. PMID:26306259

  19. An IR-Based Approach Utilizing Query Expansion for Plagiarism Detection in MEDLINE.

    Science.gov (United States)

    Nawab, Rao Muhammad Adeel; Stevenson, Mark; Clough, Paul

    2017-01-01

    The identification of duplicated and plagiarized passages of text has become an increasingly active area of research. In this paper, we investigate methods for plagiarism detection that aim to identify potential sources of plagiarism from MEDLINE, particularly when the original text has been modified through the replacement of words or phrases. A scalable approach based on Information Retrieval is used to perform candidate document selection-the identification of a subset of potential source documents given a suspicious text-from MEDLINE. Query expansion is performed using the ULMS Metathesaurus to deal with situations in which original documents are obfuscated. Various approaches to Word Sense Disambiguation are investigated to deal with cases where there are multiple Concept Unique Identifiers (CUIs) for a given term. Results using the proposed IR-based approach outperform a state-of-the-art baseline based on Kullback-Leibler Distance.

  20. Operationalizing Semantic Medline for meeting the information needs at point of care.

    Science.gov (United States)

    Rastegar-Mojarad, Majid; Li, Dingcheng; Liu, Hongfang

    2015-01-01

    Scientific literature is one of the popular resources for providing decision support at point of care. It is highly desirable to bring the most relevant literature to support the evidence-based clinical decision making process. Motivated by the recent advance in semantically enhanced information retrieval, we have developed a system, which aims to bring semantically enriched literature, Semantic Medline, to meet the information needs at point of care. This study reports our work towards operationalizing the system for real time use. We demonstrate that the migration of a relational database implementation to a NoSQL (Not only SQL) implementation significantly improves the performance and makes the use of Semantic Medline at point of care decision support possible.

  1. A short guide to peer-reviewed, MEDLINE-indexed complementary and alternative medicine journals.

    Science.gov (United States)

    Morgan, Sherry; Littman, Lynn; Palmer, Christina; Singh, Gurneet; LaRiccia, Patrick J

    2012-01-01

    Complementary and alternative medicine (CAM) comprises a multitude of disciplines, for example, acupuncture, ayurvedic medicine, biofeedback, herbal medicine, and homeopathic medicine. While research on CAM interventions has increased and the CAM literature has proliferated since the mid-1990s, a number of our colleagues have expressed difficulties in deciding where to publish CAM articles. In response, we created a short guide to peer-reviewed MEDLINE-indexed journals that publish CAM articles. We examined numerous English-language sources to identify titles that met our criteria, whether specific to or overlapping CAM. A few of the resources in which we found the journal titles that we included are Alternative Medicine Foundation, American Holistic Nurses Association, CINAHL/Nursing Database, Journal Citation Reports database, MEDLINE, PubMed, and Research Council for Complementary Medicine. We organized the 69 selected titles for easy use by creating 2 user-friendly tables, one listing titles in alphabetical order and one listing them in topical categories. A few examples of the topical categories are Acupuncture, CAM (general), Chinese Medicine, Herbal/Plant/Phytotherapy, Neuroscience/Psychology, Nursing/Clinical Care. Our study is the first to list general CAM journals, specialty CAM journals, and overlapping mainstream journals that are peer reviewed, in English, and indexed in MEDLINE. Our goal was to assist both authors seeking publication and mainstream journal editors who receive an overabundance of publishable articles but must recommend that authors seek publication elsewhere due to space and priority issues. Publishing in journals indexed by and included in MEDLINE (or PubMed) ensures that citations to articles will be found easily. Copyright © 2012 Lippincott Williams & Wilkins.

  2. Data mart construction based on semantic annotation of scientific articles: A case study for the prioritization of drug targets.

    Science.gov (United States)

    Teixeira, Marlon Amaro Coelho; Belloze, Kele Teixeira; Cavalcanti, Maria Cláudia; Silva-Junior, Floriano P

    2018-04-01

    Semantic text annotation enables the association of semantic information (ontology concepts) to text expressions (terms), which are readable by software agents. In the scientific scenario, this is particularly useful because it reveals a lot of scientific discoveries that are hidden within academic articles. The Biomedical area has more than 300 ontologies, most of them composed of over 500 concepts. These ontologies can be used to annotate scientific papers and thus, facilitate data extraction. However, in the context of a scientific research, a simple keyword-based query using the interface of a digital scientific texts library can return more than a thousand hits. The analysis of such a large set of texts, annotated with such numerous and large ontologies, is not an easy task. Therefore, the main objective of this work is to provide a method that could facilitate this task. This work describes a method called Text and Ontology ETL (TOETL), to build an analytical view over such texts. First, a corpus of selected papers is semantically annotated using distinct ontologies. Then, the annotation data is extracted, organized and aggregated into the dimensional schema of a data mart. Besides the TOETL method, this work illustrates its application through the development of the TaP DM (Target Prioritization data mart). This data mart has focus on the research of gene essentiality, a key concept to be considered when searching for genes showing potential as anti-infective drug targets. This work reveals that the proposed approach is a relevant tool to support decision making in the prioritization of new drug targets, being more efficient than the keyword-based traditional tools. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. Evaluation of Term Ranking Algorithms for Pseudo-Relevance Feedback in MEDLINE Retrieval.

    Science.gov (United States)

    Yoo, Sooyoung; Choi, Jinwook

    2011-06-01

    The purpose of this study was to investigate the effects of query expansion algorithms for MEDLINE retrieval within a pseudo-relevance feedback framework. A number of query expansion algorithms were tested using various term ranking formulas, focusing on query expansion based on pseudo-relevance feedback. The OHSUMED test collection, which is a subset of the MEDLINE database, was used as a test corpus. Various ranking algorithms were tested in combination with different term re-weighting algorithms. Our comprehensive evaluation showed that the local context analysis ranking algorithm, when used in combination with one of the reweighting algorithms - Rocchio, the probabilistic model, and our variants - significantly outperformed other algorithm combinations by up to 12% (paired t-test; p algorithm pairs, at least in the context of the OHSUMED corpus. Comparative experiments on term ranking algorithms were performed in the context of a subset of MEDLINE documents. With medical documents, local context analysis, which uses co-occurrence with all query terms, significantly outperformed various term ranking methods based on both frequency and distribution analyses. Furthermore, the results of the experiments demonstrated that the term rank-based re-weighting method contributed to a remarkable improvement in mean average precision.

  4. Knowledge production status of Iranian researchers in the gastric cancer area: based on the medline database.

    Science.gov (United States)

    Ghojazadeh, Morteza; Naghavi-Behzad, Mohammad; Nasrolah-Zadeh, Raheleh; Bayat-Khajeh, Parvaneh; Piri, Reza; Mirnia, Keyvan; Azami-Aghdash, Saber

    2014-01-01

    Scientometrics is a useful method for management of financial and human resources and has been applied many times in medical sciences during recent years. The aim of this study was to investigate the status of science production by Iranian scientists in the gastric cancer field based on the Medline database. In this descriptive-cross sectional study Iranian science production concerning gastric cancer during 2000-2011 was investigated based on Medline. After two stages of searching, 121 articles were found, then we reviewed publication date, authors names, journal title, impact factor (IF), and cooperation coefficient between researchers. SPSS.19 was used for statistical analysis. There was a significant increase in published articles about gastric cancer by Iranian researchers in Medline database during 2006-2011. Mean cooperation coefficient between researchers was 6.14±3.29 person per article. Articles of this field were published in 19 countries and 56 journals. Those basex in Thailand, England, and America had the most published Iranian articles. Tehran University of Medical Sciences and Mohammadreza Zali had the most outstanding role in publishing scientific articles. According to results of this study, improving cooperation of researchers in conducting research and scientometric studies about other fields may have an important role in increasing both quality and quantity of published studies.

  5. Dialysis search filters for PubMed, Ovid MEDLINE, and Embase databases.

    Science.gov (United States)

    Iansavichus, Arthur V; Haynes, R Brian; Lee, Christopher W C; Wilczynski, Nancy L; McKibbon, Ann; Shariff, Salimah Z; Blake, Peter G; Lindsay, Robert M; Garg, Amit X

    2012-10-01

    Physicians frequently search bibliographic databases, such as MEDLINE via PubMed, for best evidence for patient care. The objective of this study was to develop and test search filters to help physicians efficiently retrieve literature related to dialysis (hemodialysis or peritoneal dialysis) from all other articles indexed in PubMed, Ovid MEDLINE, and Embase. A diagnostic test assessment framework was used to develop and test robust dialysis filters. The reference standard was a manual review of the full texts of 22,992 articles from 39 journals to determine whether each article contained dialysis information. Next, 1,623,728 unique search filters were developed, and their ability to retrieve relevant articles was evaluated. The high-performance dialysis filters consisted of up to 65 search terms in combination. These terms included the words "dialy" (truncated), "uremic," "catheters," and "renal transplant wait list." These filters reached peak sensitivities of 98.6% and specificities of 98.5%. The filters' performance remained robust in an independent validation subset of articles. These empirically derived and validated high-performance search filters should enable physicians to effectively retrieve dialysis information from PubMed, Ovid MEDLINE, and Embase.

  6. Psoriasis Doesn't Slow Down Texan Brian LaFoy | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... willing to do. I'm one of the lucky ones." Find Out More National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) MedlinePlus-Psoriasis Clinical Trials Search Psoriasis Spring 2017 Issue: Volume 12 Number 1 Page 22 MedlinePlus Subscribe Magazine Information Contact ...

  7. Guidelines for nuclear power plant safety issue prioritization information development. Supplement 3

    International Nuclear Information System (INIS)

    Andrews, W.B.; Bickford, W.E.; Counts, C.A.; Gallucci, R.H.V.; Heaberlin, S.W.; Powers, T.B.; Weakley, S.A.

    1985-09-01

    This supplemental report is the fourth in a series that document and use methods developed to calculate, for prioritization purposes, the risk, dose and cost impacts of implementing resolutions to reactor safety issues. The initial report in this series was published by Andrews et al. in 1983 as NUREG/CR-2800. This supplement consists of two parts describing separate research efforts: (1) an alternative human factors methodology approach, and (2) a prioritization of the NRC's Human Factors Program Plan. The alternative human factors methodology approach may be used in specific future cases in which the methods identified in the initial report (NUREG/CR-2800) may not adequately assess the proper impact for resolution of new safety issues. The alternative methodology included in this supplement is entitled ''Methodology for Estimating the Public Risk Reduction Affected by Human Factors Improvement.'' The prioritization section of this report is entitled ''Prioritization of the US Nuclear Regulatory Commission Human Factors Program Plan.''

  8. Prioritizing quality over profit : Value trade-offs within architect-client relations

    NARCIS (Netherlands)

    Bos-De Vos, M.; Volker, L.; Wamelink, J.W.F.

    2015-01-01

    Architectural service delivery involves a complex system of economic and quality related value dimensions, which are mutually dependent and prioritized differently by actors. Responding to professional logics as well as organizational logics, value creation goals of architects and clients are

  9. Procedure for Prioritization of Natural Phenomena Hazards Evaluations for Existing DOE Facilities

    Energy Technology Data Exchange (ETDEWEB)

    Conrads, T.J., Westinghouse Hanford

    1996-05-07

    This document describes the procedure to be used for the prioritization for natural phenomena hazards evaluations of existing DOE facilities in conformance with DOE Order 5480.28, `Natural Phenomena Hazards Mitigation.`

  10. Developing a performance measurement approach to benefit/cost freight project prioritization.

    Science.gov (United States)

    2014-10-01

    Future reauthorizations of the federal transportation bill will require a comprehensive and quantitative analysis of the freight benefits : of proposed freight system projects. To prioritize public investments in freight systems and to insure conside...

  11. Eliciting Preferences of Multimorbid Elderly Adults in Family Practice Using an Outcome Prioritization Tool

    NARCIS (Netherlands)

    van Summeren, Jojanneke J. G. T.; Haaijer-Ruskamp, Flora M.; Schuling, Jan

    2016-01-01

    ObjectivesTo explore an outcome prioritization tool (OPT) in eliciting individuals' preferred health outcomes (remaining alive, maintaining independence, reducing pain, reducing other symptoms) in the context of medication review in family practice. DesignCross-sectional pilot study with

  12. Prioritizing sewer rehabilitation projects using AHP-PROMETHEE II ranking method.

    Science.gov (United States)

    Kessili, Abdelhak; Benmamar, Saadia

    2016-01-01

    The aim of this paper is to develop a methodology for the prioritization of sewer rehabilitation projects for Algiers (Algeria) sewer networks to support the National Sanitation Office in its challenge to make decisions on prioritization of sewer rehabilitation projects. The methodology applies multiple-criteria decision making. The study includes 47 projects (collectors) and 12 criteria to evaluate them. These criteria represent the different issues considered in the prioritization of the projects, which are structural, hydraulic, environmental, financial, social and technical. The analytic hierarchy process (AHP) is used to determine weights of the criteria and the Preference Ranking Organization Method for Enrichment Evaluations (PROMETHEE II) method is used to obtain the final ranking of the projects. The model was verified using the sewer data of Algiers. The results have shown that the method can be used for prioritizing sewer rehabilitation projects.

  13. Evaluation of the Montana Department of Transportation's research project solicitation, prioritization, and selection process

    Science.gov (United States)

    2008-05-01

    The Montana Department of Transportation (MDT) contracted the Bureau of Business and Economic Research at the University of Montana Missoula to conduct research to determine how other states solicit, prioritize, and select research problem statem...

  14. DeepPVP: phenotype-based prioritization of causative variants using deep learning

    KAUST Repository

    Boudellioua, Imene

    2018-05-02

    Background: Prioritization of variants in personal genomic data is a major challenge. Recently, computational methods that rely on comparing phenotype similarity have shown to be useful to identify causative variants. In these methods, pathogenicity prediction is combined with a semantic similarity measure to prioritize not only variants that are likely to be dysfunctional but those that are likely involved in the pathogenesis of a patient\\'s phenotype. Results: We have developed DeepPVP, a variant prioritization method that combined automated inference with deep neural networks to identify the likely causative variants in whole exome or whole genome sequence data. We demonstrate that DeepPVP performs significantly better than existing methods, including phenotype-based methods that use similar features. DeepPVP is freely available at https://github.com/bio-ontology-research-group/phenomenet-vp Conclusions: DeepPVP further improves on existing variant prioritization methods both in terms of speed as well as accuracy.

  15. Getting the Policies Right: The Prioritization and Sequencing of Policies in Post-Conflict Countries

    National Research Council Canada - National Science Library

    Timilsina, Anga R

    2007-01-01

    ... (Cambodia, Mozambique, and Haiti) and expert opinions of 30 academicians and practitioners, this study identifies major reconstruction policies, outlines the preferred way to prioritize and sequence them, and develops a framework...

  16. Prioritization of pharmaceuticals for potential environmental hazard through leveraging a large scale mammalian pharmacological dataset

    Science.gov (United States)

    To proceed in the investigation of potential effects of thousands of active pharmaceutical ingredients (API) which may enter the aquatic environment, a cohesive research strategy, specifically a prioritization is paramount. API are biologically active, with specific physiologica...

  17. The prioritization and categorization method (PCM) process evaluation at Ericsson : a case study

    NARCIS (Netherlands)

    Ohlsson, Jens; Han, Shengnan; Bouwman, W.A.G.A.

    2017-01-01

    Purpose: The purpose of this paper is to demonstrate and evaluate the prioritization and categorization method (PCM), which facilitates the active participation of process stakeholders (managers, owners, customers) in process assessments. Stakeholders evaluate processes in terms of effectiveness,

  18. Modeling Personalized Email Prioritization: Classification-based and Regression-based Approaches

    Energy Technology Data Exchange (ETDEWEB)

    Yoo S.; Yang, Y.; Carbonell, J.

    2011-10-24

    Email overload, even after spam filtering, presents a serious productivity challenge for busy professionals and executives. One solution is automated prioritization of incoming emails to ensure the most important are read and processed quickly, while others are processed later as/if time permits in declining priority levels. This paper presents a study of machine learning approaches to email prioritization into discrete levels, comparing ordinal regression versus classier cascades. Given the ordinal nature of discrete email priority levels, SVM ordinal regression would be expected to perform well, but surprisingly a cascade of SVM classifiers significantly outperforms ordinal regression for email prioritization. In contrast, SVM regression performs well -- better than classifiers -- on selected UCI data sets. This unexpected performance inversion is analyzed and results are presented, providing core functionality for email prioritization systems.

  19. Updating and improving methodology for prioritizing highway project locations on the strategic intermodal system (SIS).

    Science.gov (United States)

    2016-04-01

    The Florida Department of Transportation (FDOT) District One developed the Congestion Management Process : (CMP) system to prioritize low-cost, near-term highway improvements on the Strategic Intermodal System (SIS). : The existing CMP system is desi...

  20. Evidence for a Selectively Regulated Prioritization Shift Depending on Walking Situations in Older Adults

    OpenAIRE

    Salkovic, Dina; Hobert, Markus A.; Bellut, Carolin; Funer, Florian; Renno, Sarah; Haertner, Linda; Hasmann, Sandra E.; Staebler, Jana; Geritz, Johanna; Suenkel, Ulrike; Fallgatter, Andreas J.; Eschweiler, Gerhard W.; Berg, Daniela; Maetzler, Walter

    2017-01-01

    Background: Older adults have increased risks of balance issues and falls when walking and performing turns in daily situations. Changes of prioritization during different walking situations associated with dual tasking may contribute to these deficits. The objective of this study was therefore to investigate whether older adults demonstrate changes of prioritization during different walking paths. Methods: In total, 1,054 subjects with an age range from 50 to 83 years were selected from t...

  1. RiskREP: Risk-Based Security Requirements Elicitation and Prioritization

    OpenAIRE

    Herrmann, Andrea; Morali, A.; Etalle, Sandro; Wieringa, Roelf J.; Niedrite, Laila; Strazdina, Renate; Wangler, Benkt

    2011-01-01

    Companies are under pressure to be in control of their assets but at the same time they must operate as efficiently as possible. This means that they aim to implement “good-enough security‿ but need to be able to justify their security investment plans. In this paper, we present a Risk-Based Requirements Prioritization method (RiskREP) that extends misuse case-based methods with IT architecture based risk assessment and countermeasure definition and prioritization. Countermeasure prioritizati...

  2. Multisectoral prioritization of zoonotic diseases in Uganda, 2017: A One Health perspective.

    Directory of Open Access Journals (Sweden)

    Musa Sekamatte

    Full Text Available Zoonotic diseases continue to be a public health burden globally. Uganda is especially vulnerable due to its location, biodiversity, and population. Given these concerns, the Ugandan government in collaboration with the Global Health Security Agenda conducted a One Health Zoonotic Disease Prioritization Workshop to identify zoonotic diseases of greatest national concern to the Ugandan government.The One Health Zoonotic Disease Prioritization tool, a semi-quantitative tool developed by the U.S. Centers for Disease Control and Prevention, was used for the prioritization of zoonoses. Workshop participants included voting members and observers representing multiple government and non-governmental sectors. During the workshop, criteria for prioritization were selected, and questions and weights relevant to each criterion were determined. We used a decision tree to provide a ranked list of zoonoses. Participants then established next steps for multisectoral engagement for the prioritized zoonoses. A sensitivity analysis demonstrated how criteria weights impacted disease prioritization.Forty-eight zoonoses were considered during the workshop. Criteria selected to prioritize zoonotic diseases were (1 severity of disease in humans in Uganda, (2 availability of effective control strategies, (3 potential to cause an epidemic or pandemic in humans or animals, (4 social and economic impacts, and (5 bioterrorism potential. Seven zoonotic diseases were identified as priorities for Uganda: anthrax, zoonotic influenza viruses, viral hemorrhagic fevers, brucellosis, African trypanosomiasis, plague, and rabies. Sensitivity analysis did not indicate significant changes in zoonotic disease prioritization based on criteria weights.One Health approaches and multisectoral collaborations are crucial to the surveillance, prevention, and control strategies for zoonotic diseases. Uganda used such an approach to identify zoonoses of national concern. Identifying these

  3. Prioritizing Zoonotic Diseases: Differences in Perspectives Between Human and Animal Health Professionals in North America.

    Science.gov (United States)

    Ng, V; Sargeant, J M

    2016-05-01

    Zoonoses pose a significant burden of illness in North America. Zoonoses represent an additional threat to public health because the natural reservoirs are often animals, particularly wildlife, thus eluding control efforts such as quarantine, vaccination and social distancing. As there are limited resources available, it is necessary to prioritize diseases in order to allocate resources to those posing the greatest public health threat. Many studies have attempted to prioritize zoonoses, but challenges exist. This study uses a quantitative approach, conjoint analysis (CA), to overcome some limitations of traditional disease prioritization exercises. We used CA to conduct a zoonoses prioritization study involving a range of human and animal health professionals across North America; these included epidemiologists, public health practitioners, research scientists, physicians, veterinarians, laboratory technicians and nurses. A total of 699 human health professionals (HHP) and 585 animal health professionals (AHP) participated in this study. We used CA to prioritize 62 zoonotic diseases using 21 criteria. Our findings suggest CA can be used to produce reasonable criteria scores for disease prioritization. The fitted models were satisfactory for both groups with a slightly better fit for AHP compared to HHP (84.4% certainty fit versus 83.6%). Human-related criteria were more influential for HHP in their decision to prioritize zoonoses, while animal-related criteria were more influential for AHP resulting in different disease priority lists. While the differences were not statistically significant, a difference of one or two ranks could be considered important for some individuals. A potential solution to address the varying opinions is discussed. The scientific framework for disease prioritization presented can be revised on a regular basis by updating disease criteria to reflect diseases as they evolve over time; such a framework is of value allowing diseases of

  4. Prioritization of Companion Animal Transmissible Diseases for Policy Intervention in Europe

    DEFF Research Database (Denmark)

    Cito, F.; Rijks, J.; Rantsios, A.T.

    2016-01-01

    A number of papers have been published on the prioritization of transmissible diseases in farm animals and wildlife, based either on semiquantitative or truly quantitative methods, but there is no published literature on the prioritization of transmissible diseases in companion animals. In this s...... reptiles. The methodology presented in this paper can be used to generate accurate priority lists according to narrower and more specific objectives....

  5. Research prioritization using the Analytic Hierarchy Process: basic methods. Volume 1

    International Nuclear Information System (INIS)

    Vesely, W.E.; Shafaghi, A.; Gary, I. Jr.; Rasmuson, D.M.

    1983-08-01

    This report describes a systematic approach for prioritizing research needs and research programs. The approach is formally called the Analytic Hierarchy Process which was developed by T.L. Saaty and is described in several of his texts referenced in the report. The Analytic Hierarchy Process, or AHP for short, has been applied to a wide variety of prioritization problems and has a good record of success as documented in Saaty's texts. The report develops specific guidelines for constructing the hierarchy and for prioritizing the research programs. Specific examples are given to illustrate the steps in the AHP. As part of the work, a computer code has been developed and the use of the code is described. The code allows the prioritizations to be done in a codified and efficient manner; sensitivity and parametric studies can also be straightforwardly performed to gain a better understanding of the prioritization results. Finally, as an important part of the work, an approach is developed which utilizes probabilistic risk analyses (PRAs) to systematically identify and prioritize research needs and research programs. When utilized in an AHP framework, the PRA's which have been performed to date provide a powerful information source for focusing research on those areas most impacting risk and risk uncertainty

  6. Do language fluency and other socioeconomic factors influence the use of PubMed and MedlinePlus?

    Science.gov (United States)

    Sheets, L; Gavino, A; Callaghan, F; Fontelo, P

    2013-01-01

    Increased usage of MedlinePlus by Spanish-speakers was observed after introduction of MedlinePlus in Spanish. This probably reflects increased usage of MEDLINE and PubMed by those with greater fluency in the language in which it is presented; but this has never been demonstrated in English speakers. Evidence that lack of English fluency deters international healthcare personnel from using PubMed could support the use of multi-language search tools like Babel-MeSH. This study aims to measure the effects of language fluency and other socioeconomic factors on PubMed MEDLINE and MedlinePlus access by international users. We retrospectively reviewed server pageviews of PubMed and MedlinePlus from various periods of time, and analyzed them against country statistics on language fluency, GDP, literacy rate, Internet usage, medical schools, and physicians per capita, to determine whether they were associated. We found fluency in English to be positively associated with pageviews of PubMed and MedlinePlus in countries with high literacy rates. Spanish was generally found to be positively associated with pageviews of MedlinePlus en Español. The other parameters also showed varying degrees of association with pageviews. After adjusting for the other factors investigated in this study, language fluency was a consistently significant predictor of the use of PubMed, MedlinePlus English and MedlinePlus en Español. This study may support the need for multi-language search tools and may increase access of health information resources from non-English speaking countries.

  7. An in vitro approach for prioritization and evaluation of chemical effects on glucocorticoid receptor mediated adipogenesis.

    Science.gov (United States)

    Hartman, Jessica K; Beames, Tyler; Parks, Bethany; Doheny, Daniel; Song, Gina; Efremenko, Alina; Yoon, Miyoung; Foley, Briana; Deisenroth, Chad; McMullen, Patrick D; Clewell, Rebecca A

    2018-05-18

    Rising obesity rates worldwide have socio-economic ramifications. While genetics, diet, and lack of exercise are major contributors to obesity, environmental factors may enhance susceptibility through disruption of hormone homeostasis and metabolic processes. The obesogen hypothesis contends that chemical exposure early in development may enhance adipocyte differentiation, thereby increasing the number of adipocytes and predisposing for obesity and metabolic disease. We previously developed a primary human adipose stem cell (hASC) assay to evaluate the effect of environmental chemicals on PPARG-dependent adipogenesis. Here, the assay was modified to determine the effects of chemicals on the glucocorticoid receptor (GR) pathway. In differentiation cocktail lacking the glucocorticoid agonist dexamethasone (DEX), hASCs do not differentiate into adipocytes. In the presence of GR agonists, adipocyte maturation was observed using phenotypic makers for lipid accumulation, adipokine secretion, and expression of key genes. To evaluate the role of environmental compounds on adipocyte differentiation, progenitor cells were treated with 19 prioritized compounds previously identified by ToxPi as having GR-dependent bioactivity, and multiplexed assays were used to confirm a GR-dependent mode of action. Five chemicals were found to be strong agonists. The assay was also modified to evaluate GR-antagonists, and 8/10 of the hypothesized antagonists inhibited adipogenesis. The in vitro bioactivity data was put into context with extrapolated human steady state concentrations (Css) and clinical exposure data (Cmax). These data support using a human adipose-derived stem cell differentiation assay to test the potential of chemicals to alter human GR-dependent adipogenesis. Copyright © 2017. Published by Elsevier Inc.

  8. Decision Support Tool for Prioritization of Surveillance and Maintenance Investment

    International Nuclear Information System (INIS)

    Velez, L.Y.; Conley, T.B.

    2009-01-01

    The Department of Energy (DOE) currently faces a difficult task in the disposition of the numerous excess or to-be excessed facilities owned by the Department. Many of these facilities are in various physical conditions and contain potentially hazardous nuclear, chemical, radiological or industrial materials left behind as a byproduct of nuclear weapons production, nuclear powered naval vessels and commercial nuclear energy production. During the last period of a facility's life cycle, it is important that surveillance and maintenance (S and M) be adequate to maintain the facility within an appropriate safety envelope. Inadequate investment in maintenance can cause facilities to deteriorate to the point they are unsafe for human entry. Too often this can mean tremendous increases to cost during deactivation and decommissioning (D and D). However, experiences often show that once buildings have been declared excess and enter the transition phase (as defined in DOE G 430.1-5 Transition Implementation Guide), maintenance budgets are drastically reduced. This is justified by the desire to not spend money 'on a building that is being torn down'. The objective of this study was to provide the U.S. Department of Energy (DOE) Environmental Management (EM) federal project directors and their contractors with a decision support tool to aid in prioritizing S and M investment across a site's excess facilities so that the limited budget available can be used most effectively. The analytical hierarchy process (AHP), a multi-criteria decision making method developed by Dr. Thomas Saaty in the 1970's, was used to derive the weight of importance of a defined list of risk-based criteria and typical S and M activities. A total of 10 facilities at the Oak Ridge National Laboratory (ORNL) varying in perceived hazards and conditions were chosen to test the tool by evaluating them with respect to each risk criterion and combining these results with the weight of importance of the S and M

  9. Constructing an integrated gene similarity network for the identification of disease genes.

    Science.gov (United States)

    Tian, Zhen; Guo, Maozu; Wang, Chunyu; Xing, LinLin; Wang, Lei; Zhang, Yin

    2017-09-20

    Discovering novel genes that are involved human diseases is a challenging task in biomedical research. In recent years, several computational approaches have been proposed to prioritize candidate disease genes. Most of these methods are mainly based on protein-protein interaction (PPI) networks. However, since these PPI networks contain false positives and only cover less half of known human genes, their reliability and coverage are very low. Therefore, it is highly necessary to fuse multiple genomic data to construct a credible gene similarity network and then infer disease genes on the whole genomic scale. We proposed a novel method, named RWRB, to infer causal genes of interested diseases. First, we construct five individual gene (protein) similarity networks based on multiple genomic data of human genes. Then, an integrated gene similarity network (IGSN) is reconstructed based on similarity network fusion (SNF) method. Finally, we employee the random walk with restart algorithm on the phenotype-gene bilayer network, which combines phenotype similarity network, IGSN as well as phenotype-gene association network, to prioritize candidate disease genes. We investigate the effectiveness of RWRB through leave-one-out cross-validation methods in inferring phenotype-gene relationships. Results show that RWRB is more accurate than state-of-the-art methods on most evaluation metrics. Further analysis shows that the success of RWRB is benefited from IGSN which has a wider coverage and higher reliability comparing with current PPI networks. Moreover, we conduct a comprehensive case study for Alzheimer's disease and predict some novel disease genes that supported by literature. RWRB is an effective and reliable algorithm in prioritizing candidate disease genes on the genomic scale. Software and supplementary information are available at http://nclab.hit.edu.cn/~tianzhen/RWRB/ .

  10. POINeT: protein interactome with sub-network analysis and hub prioritization

    Directory of Open Access Journals (Sweden)

    Lai Jin-Mei

    2009-04-01

    Full Text Available Abstract Background Protein-protein interactions (PPIs are critical to every aspect of biological processes. Expansion of all PPIs from a set of given queries often results in a complex PPI network lacking spatiotemporal consideration. Moreover, the reliability of available PPI resources, which consist of low- and high-throughput data, for network construction remains a significant challenge. Even though a number of software tools are available to facilitate PPI network analysis, an integrated tool is crucial to alleviate the burden on querying across multiple web servers and software tools. Results We have constructed an integrated web service, POINeT, to simplify the process of PPI searching, analysis, and visualization. POINeT merges PPI and tissue-specific expression data from multiple resources. The tissue-specific PPIs and the numbers of research papers supporting the PPIs can be filtered with user-adjustable threshold values and are dynamically updated in the viewer. The network constructed in POINeT can be readily analyzed with, for example, the built-in centrality calculation module and an integrated network viewer. Nodes in global networks can also be ranked and filtered using various network analysis formulas, i.e., centralities. To prioritize the sub-network, we developed a ranking filtered method (S3 to uncover potential novel mediators in the midbody network. Several examples are provided to illustrate the functionality of POINeT. The network constructed from four schizophrenia risk markers suggests that EXOC4 might be a novel marker for this disease. Finally, a liver-specific PPI network has been filtered with adult and fetal liver expression profiles. Conclusion The functionalities provided by POINeT are highly improved compared to previous version of POINT. POINeT enables the identification and ranking of potential novel genes involved in a sub-network. Combining with tissue-specific gene expression profiles, PPIs specific to

  11. Ranking candidate disease genes from gene expression and protein interaction: a Katz-centrality based approach.

    Directory of Open Access Journals (Sweden)

    Jing Zhao

    Full Text Available Many diseases have complex genetic causes, where a set of alleles can affect the propensity of getting the disease. The identification of such disease genes is important to understand the mechanistic and evolutionary aspects of pathogenesis, improve diagnosis and treatment of the disease, and aid in drug discovery. Current genetic studies typically identify chromosomal regions associated specific diseases. But picking out an unknown disease gene from hundreds of candidates located on the same genomic interval is still challenging. In this study, we propose an approach to prioritize candidate genes by integrating data of gene expression level, protein-protein interaction strength and known disease genes. Our method is based only on two, simple, biologically motivated assumptions--that a gene is a good disease-gene candidate if it is differentially expressed in cases and controls, or that it is close to other disease-gene candidates in its protein interaction network. We tested our method on 40 diseases in 58 gene expression datasets of the NCBI Gene Expression Omnibus database. On these datasets our method is able to predict unknown disease genes as well as identifying pleiotropic genes involved in the physiological cellular processes of many diseases. Our study not only provides an effective algorithm for prioritizing candidate disease genes but is also a way to discover phenotypic interdependency, cooccurrence and shared pathophysiology between different disorders.

  12. Genes and Gene Therapy

    Science.gov (United States)

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  13. Lack of support structures in prioritization decision making concerning patients and resources. Interviews with Swedish physicians.

    Science.gov (United States)

    Werntoft, Elisabet; Edberg, Anna-Karin

    2011-08-01

    To investigate physicians' experiences in relation to prioritization and financing in health care in order to gain a deeper understanding of the reasons behind their standpoints. Eighteen physicians, seven women and eleven men, aged 30 to 69 years were interviewed and the text was analyzed using an inductive approach, also described as conventional qualitative content analysis. Experience of setting healthcare priorities and difficult decision making differed widely among the physicians and seemed to be related to the number of years in professional practice. Their view of how resources should be allocated between disciplines/patients showed that they wanted politicians to make the decisions, with support from medical professions. The overwhelming impression of their reasoning showed that they lacked support structures for their decision making and could be understood under the following categories: prioritisation, easier in theory than in practice, and increasing costs threaten the Swedish welfare model. The findings of this study highlight the importance of practical national guidelines concerning vertical prioritization, also as an important measure to make prioritization more distinct and transparent. The physicians further had a need for tools to increase patients' awareness of their health. The findings of this study also showed that an awareness of the actual costs involved might increase the responsibility among both physicians and patients. The physicians' lack of support structures implies an urgent need for practical national guidelines, especially concerning vertical prioritization. This will also make prioritization appear clear and transparent for citizens.

  14. Prioritizing critical success factors for reverse logistics implementation using fuzzy-TOPSIS methodology

    Science.gov (United States)

    Agrawal, Saurabh; Singh, Rajesh K.; Murtaza, Qasim

    2016-03-01

    Electronics industry is one of the fastest growing industries in the world. In India also, there are high turnovers and growing demand of electronics product especially after post liberalization in early nineties. These products generate e-waste which has become big environmental issue. Industries can handle these e-waste and product returns efficiently by developing reverse logistics (RL) system. A thorough study of critical success factors (CSFs) and their ordered implementation is essential for successful RL implementation. The aim of the study is to review the CSFs, and to prioritize them for RL implementation in Indian electronics industry. Twelve CSFs were identified through literature review, and discussion with the experts from the Indian electronics industry. Fuzzy-Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) approach is proposed for prioritizing these CSFs. Perusal of literature indicates that fuzzy-TOPSIS has not been applied earlier for prioritization of CSFs in Indian electronics industry. Five Indian electronics companies were selected for evaluation of this methodology. Results indicate that most of the identified factors are crucial for the RL implementation. Top management awareness, resource management, economic factors, and contracts terms and conditions are top four prioritized factor, and process capabilities and skilled workers is the least prioritized factor. The findings will be useful for successful RL implementation in Indian electronics industry.

  15. Web-Scale Discovery Services Retrieve Relevant Results in Health Sciences Topics Including MEDLINE Content

    Directory of Open Access Journals (Sweden)

    Elizabeth Margaret Stovold

    2017-06-01

    Full Text Available A Review of: Hanneke, R., & O’Brien, K. K. (2016. Comparison of three web-scale discovery services for health sciences research. Journal of the Medical Library Association, 104(2, 109-117. http://dx.doi.org/10.3163/1536-5050.104.2.004 Abstract Objective – To compare the results of health sciences search queries in three web-scale discovery (WSD services for relevance, duplicate detection, and retrieval of MEDLINE content. Design – Comparative evaluation and bibliometric study. Setting – Six university libraries in the United States of America. Subjects – Three commercial WSD services: Primo, Summon, and EBSCO Discovery Service (EDS. Methods – The authors collected data at six universities, including their own. They tested each of the three WSDs at two data collection sites. However, since one of the sites was using a legacy version of Summon that was due to be upgraded, data collected for Summon at this site were considered obsolete and excluded from the analysis. The authors generated three questions for each of six major health disciplines, then designed simple keyword searches to mimic typical student search behaviours. They captured the first 20 results from each query run at each test site, to represent the first “page” of results, giving a total of 2,086 total search results. These were independently assessed for relevance to the topic. Authors resolved disagreements by discussion, and calculated a kappa inter-observer score. They retained duplicate records within the results so that the duplicate detection by the WSDs could be compared. They assessed MEDLINE coverage by the WSDs in several ways. Using precise strategies to generate a relevant set of articles, they conducted one search from each of the six disciplines in PubMed so that they could compare retrieval of MEDLINE content. These results were cross-checked against the first 20 results from the corresponding query in the WSDs. To aid investigation of overall

  16. Welcome from Library Director Donald A.B. Lindberg, M.D. | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... turn Javascript on. Welcome to the NIH MedlinePlus Magazine. Past Issues / Spring 2013 Table of Contents Donald ... about their efforts to cure disease. Lastly, the magazine's lively graphics, fun quizzes and practical tips have ...

  17. Milestones in Medical Research, The Human Genome and ClinicalTrials.gov | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... the information in this issue of NIH MedlinePlus magazine helps you and your loved ones stay healthier! ... From You! We want your feedback on the magazine, ideas for future issues, as well as questions ...

  18. National Library of Medicine Celebrates 30 Years of Progress and Charts the Future | NIH MedlinePlus the Magazine

    Science.gov (United States)

    ... described the genesis of the National Center for Biotechnology Information (NCBI); the Visible Human Project (a digital ... expand the publication and distribution of NIH MedlinePlus magazine, thousands and thousands more people will gain valuable, ...

  19. A Review of Published Articles in the Field of Biomedical Nanotechnology in Medline Database during 2000-2010

    OpenAIRE

    Peyman Sheikhzade

    2015-01-01

    Background and objectives : Nanotechnology is a new technology which is increasingly used over the past decade. Due to its great significance, governments are tending to invest greatly on the research and development on nanotechnology in various sectors and aspects. The purpose of this study was to determine the status of biomedical nanotechnology publications over the past ten years (2010-2000) in Medline/ PubMed. Material and Methods : This was a descriptive study. The Medline database wa...

  20. GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity.

    Science.gov (United States)

    Kim, Hyunjin; Choi, Sang-Min; Park, Sanghyun

    2018-01-01

    When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with the disease. By utilizing this gene expression heterogeneity, we can obtain additional information that abets discovery of disease-associated genes. In this study, we used collaborative filtering to calculate the degree of gene expression heterogeneity between classes and then scored the genes on the basis of the degree of gene expression heterogeneity to find "differentially predicted" genes. Through the proposed method, we discovered more prostate cancer-associated genes than 10 comparable methods. The genes prioritized by the proposed method are potentially significant to biological processes of a disease and can provide insight into them.

  1. Product prioritization in a two-stage food production system with intermediate storage

    DEFF Research Database (Denmark)

    Akkerman, Renzo; van Donk, Dirk Pieter

    2007-01-01

    In the food-processing industry, usually a limited number of storage tanks for intermediate storage is available, which are used for different products. The market sometimes requires extremely short lead times for some products, leading to prioritization of these products, partly through...... the performance improvements for the prioritized product, as well as the negative effects for the other products. We also show how the effect decreases with more storage tanks, and increases with more products....... the dedication of a storage tank. This type of situation has hardly been investigated, although planners struggle with it in practice. This paper aims at investigating the fundamental effect of prioritization and dedicated storage in a two-stage production system, for various product mixes. We show...

  2. Scenario-informed multiple criteria analysis for prioritizing investments in electricity capacity expansion

    International Nuclear Information System (INIS)

    Martinez, Lauro J.; Lambert, James H.; Karvetski, Christopher W.

    2011-01-01

    Planning the expansion and energy security of electricity capacity for a national electricity utility is a complex task in almost any economy. Planning is usually an iterative activity and can involve the use of large scale planning optimization systems accompanied by assessment of uncertain scenarios emerging from economic, technological, environmental, and regulatory developments. This paper applies a multiple criteria decision analysis to prioritize investment portfolios in capacity expansion and energy security while principally studying the robustness of the prioritization to multiple uncertain and emergent scenarios. The scenarios are identified through interaction with decision makers and stakeholders. The approach finds which scenarios most affect the prioritization of the portfolios and which portfolios have the greatest upside and downside potential across scenarios. The approach fosters innovation in the use of robust and efficient technologies, renewable energy sources, and cleaner energy fuels. A demonstration is provided for assessing the performance of technology portfolios constructed from investments in nine electricity generation technologies in Mexico.

  3. A Fuzzy Group Prioritization Method for Deriving Weights and its Software Implementation

    Directory of Open Access Journals (Sweden)

    Tarifa Almulhim

    2013-09-01

    Full Text Available Several Multi-Criteria Decision Making (MCDM methods involve pairwise comparisons to obtain the preferences of decision makers (DMs. This paper proposes a fuzzy group prioritization method for deriving group priorities/weights from fuzzy pairwise comparison matrices. The proposed method extends the Fuzzy Preferences Programming Method (FPP by considering the different importance weights of multiple DMs . The elements of the group pairwise comparison matrices are presented as fuzzy numbers rather than exact numerical values, in order to model the uncertainty and imprecision in the DMs’ judgments. Unlike the known fuzzy prioritization techniques, the proposed method is able to derive crisp weights from incomplete and fuzzy set of comparison judgments and does not require additional aggregation procedures. A prototype of a decision tool is developed to assist DMs to implement the proposed method for solving fuzzy group prioritization problems in MATLAB. Detailed numerical examples are used to illustrate the proposed approach.

  4. Risk-based prioritization of ground water threatening point sources at catchment and regional scales

    DEFF Research Database (Denmark)

    Overheu, Niels Døssing; Tuxen, Nina; Flyvbjerg, John

    2014-01-01

    framework has been developed to enable a systematic and transparent risk assessment and prioritization of contaminant point sources, considering the local, catchment, or regional scales (Danish EPA, 2011, 2012). The framework has been tested in several catchments in Denmark with different challenges...... and needs, and two of these are presented. Based on the lessons learned, the Danish EPA has prepared a handbook to guide the user through the steps in a risk-based prioritization (Danish EPA, 2012). It provides guidance on prioritization both in an administratively defined area such as a Danish Region...... of the results are presented using the case studies as examples. The methodology was developed by a broad industry group including the Danish EPA, the Danish Regions, the Danish Nature Agency, the Technical University of Denmark, and consultants — and the framework has been widely accepted by the professional...

  5. Experimentation on accuracy of non functional requirement prioritization approaches for different complexity projects

    Directory of Open Access Journals (Sweden)

    Raj Kumar Chopra

    2016-09-01

    Full Text Available Non functional requirements must be selected for implementation together with functional requirements to enhance the success of software projects. Three approaches exist for performing the prioritization of non functional requirements using the suitable prioritization technique. This paper performs experimentation on three different complexity versions of the industrial software project using cost-value prioritization technique employing three approaches. Experimentation is conducted to analyze the accuracy of individual approaches and the variation of accuracy with the complexity of the software project. The results indicate that selecting non functional requirements separately, but in accordance with functionality has higher accuracy amongst the other two approaches. Further, likewise other approaches, it witnesses the decrease in accuracy with increase in software complexity but the decrease is minimal.

  6. Determining and prioritizing competencies in the undergraduate internal medicine curriculum in Saudi Arabia.

    Science.gov (United States)

    Almoallim, H

    2011-08-01

    To determine knowledge and skills competencies in internal medicine for the undergraduate curriculum in Saudi Arabia, competencies were identified based on group work utilizing common textbooks. The Delphi Technique was used as a consensus method to determine and prioritize competencies in internal medicine. A group of 20 clinicians rated the identified competencies from 0-3 (0: no need to know, 1: interesting to know, 2: should know and 3: must know). After formulating the results, a second Delphi round was conducted with 5 experts in internal medicine. A total of 1513 knowledge competencies and 189 skills competencies were determined and prioritized. The competencies corresponded to the 12 systems in internal medicine. All competencies rated 2.2-3.0 were produced separately and considered core competencies for the undergraduate internal medicine curriculum. Determining and prioritizing competencies should influence the curriculum reform process.

  7. Program prioritization system user requirements document for Gas Cooled Reactor Associates

    International Nuclear Information System (INIS)

    1981-01-01

    Efficient management of the national HTGR program requires the establishment of an information system that will facilitate a more rational allocation of resources and task prioritization consistent with program policies. The system described in this document provides a data analysis mechanism for processing top level summary status and planning information in a rapid, timely and selective manner. Data produced by the system can be used by management to provide a rational basis for prioritizing tasks, evaluating program changes and program planning regarding costs, schedules and overall program development logic. The purpose of this document is to delineate the program prioritization system (PPS) requirements for use as a guide to acquiring and implementing the system

  8. Use of multiple patient simulators to enhance prioritizing and delegating skills for senior nursing students.

    Science.gov (United States)

    Kaplan, Barbara; Ura, Darla

    2010-07-01

    The student clinical experience is rich, yet challenges arise in providing experiences where leadership skills can be developed and used in nursing practice. To increase student confidence and enhance student ability to safely and effectively prioritize, delegate, and implement care for numerous patients, a simulation-based learning (SBL) experience was developed. The SBL experience involves multiple patient simulators, case study analysis, and a debriefing session. Ninety-seven senior nursing students participated in this program. Students reported through Likert surveys to either "agree" or "strongly agree" that the SBL was well organized (87%, n = 84), prompted realistic expectations (59%, n = 57), the scenarios were believable (73%, n = 71), case studies increased understanding (66%, n = 64), and that the SBL experience increased understanding of prioritizing and delegating care (69%, n = 67). Seventy-eight percent (n = 76) reported "more confidence in ability to work as a team" and 55% (n = 52) reported "more confidence in prioritizing and delegating care." Copyright 2010, SLACK Incorporated.

  9. Hesitant fuzzy linguistic multicriteria decision-making method based on generalized prioritized aggregation operator.

    Science.gov (United States)

    Wu, Jia-ting; Wang, Jian-qiang; Wang, Jing; Zhang, Hong-yu; Chen, Xiao-hong

    2014-01-01

    Based on linguistic term sets and hesitant fuzzy sets, the concept of hesitant fuzzy linguistic sets was introduced. The focus of this paper is the multicriteria decision-making (MCDM) problems in which the criteria are in different priority levels and the criteria values take the form of hesitant fuzzy linguistic numbers (HFLNs). A new approach to solving these problems is proposed, which is based on the generalized prioritized aggregation operator of HFLNs. Firstly, the new operations and comparison method for HFLNs are provided and some linguistic scale functions are applied. Subsequently, two prioritized aggregation operators and a generalized prioritized aggregation operator of HFLNs are developed and applied to MCDM problems. Finally, an illustrative example is given to illustrate the effectiveness and feasibility of the proposed method, which are then compared to the existing approach.

  10. From the lab - Eyes May be ‘Windows to the Brain’ in Stroke Patients | NIH MedlinePlus the Magazine

    Science.gov (United States)

    Skip to main content NIH MedlinePlus the Magazine NIH MedlinePlus Salud Download the Current Issue PDF [3.1 mb] Trusted Health Information from the National Institutes of Health Home Current Issue ...

  11. Environmental restoration risk-based prioritization work package planning and risk ranking methodology. Revision 2

    International Nuclear Information System (INIS)

    Dail, J.L.; Nanstad, L.D.; White, R.K.

    1995-06-01

    This document presents the risk-based prioritization methodology developed to evaluate and rank Environmental Restoration (ER) work packages at the five US Department of Energy, Oak Ridge Field Office (DOE-ORO) sites [i.e., Oak Ridge K-25 Site (K-25), Portsmouth Gaseous Diffusion Plant (PORTS), Paducah Gaseous Diffusion Plant (PGDP), Oak Ridge National Laboratory (ORNL), and the Oak Ridge Y-12 Plant (Y-12)], the ER Off-site Program, and Central ER. This prioritization methodology was developed to support the increased rigor and formality of work planning in the overall conduct of operations within the DOE-ORO ER Program. Prioritization is conducted as an integral component of the fiscal ER funding cycle to establish program budget priorities. The purpose of the ER risk-based prioritization methodology is to provide ER management with the tools and processes needed to evaluate, compare, prioritize, and justify fiscal budget decisions for a diverse set of remedial action, decontamination and decommissioning, and waste management activities. The methodology provides the ER Program with a framework for (1) organizing information about identified DOE-ORO environmental problems, (2) generating qualitative assessments of the long- and short-term risks posed by DOE-ORO environmental problems, and (3) evaluating the benefits associated with candidate work packages designed to reduce those risks. Prioritization is conducted to rank ER work packages on the basis of the overall value (e.g., risk reduction, stakeholder confidence) each package provides to the ER Program. Application of the methodology yields individual work package ''scores'' and rankings that are used to develop fiscal budget requests. This document presents the technical basis for the decision support tools and process

  12. PHIRST Trial - pharmacist consults: prioritization of HIV-patients with a referral screening tool.

    Science.gov (United States)

    Awad, Catherine; Canneva, Arnaud; Chiasson, Charles-Olivier; Galarneau, Annie; Schnitzer, Mireille E; Sheehan, Nancy L; Wong, Alison Yj

    2017-11-01

    The role of pharmacists in HIV outpatient clinics has greatly increased in the past decades. Given the limited resources of the health system, the prioritization of pharmacist consults is now a main concern. This study aimed to create a scoring system allowing for standardized prioritization of pharmacist consults for patients living with HIV. Data was retrospectively collected from 200 HIV patients attending the Chronic Viral Illness Service at the McGill University Health Center. An expert panel consisting of four pharmacists working in the field of HIV prioritized each patient individually, after which a consensus was established and was considered as the gold standard. In order to create a scoring system, two different methods (Delphi, statistical) were used to assign a weight to each characteristic considered to be important in patient prioritization. A third method (equal weight to each characteristic) was also evaluated. The total score per patient for each method was then compared to the expert consensus in order to establish the score cut-offs to indicate the appropriate categories of delay in which to see the patient. All three systems failed to accurately prioritize patients into urgency categories ("less than 48 h", "less than 1 month", "less than 3 months", "no consult required") according to expert pharmacist consensus. The presence of high level interactions between patient characteristics, the limited number of patients and the low prevalence of some characteristics were hypothesized as the main causes for the results. Creating a prioritization tool for pharmacy consults in HIV outpatient clinics is a complex task and developing a decision tree algorithm may be a more appropriate approach in the future to take into account the importance of combinations of patient characteristic.

  13. The Interplay Between Evidence and Judgment in the IT Project Prioritization Process

    DEFF Research Database (Denmark)

    Shollo, Arisa; Constantiou, Ioanna; Kreiner, Kristian

    2015-01-01

    Strategic decisions concerning IT investments are based on a project prioritization process designed to accommodate evidence-based management and rational decision-making. Our empirical study of IT project prioritization in a financial institution shows how managers reach decisions under norms...... of evidence-based management. We use a rich dataset derived from a longitudinal study. We analyze managers’ decision-making practices and identify four tactics of supplementing, substituting, interpreting, and reframing the available evidence. The choice of tactic depends on how decision makers perceive...

  14. Guidelines for nuclear power plant safety issue prioritization information development. Supplement 5

    International Nuclear Information System (INIS)

    Daling, P.M.; Lavender, J.C.

    1996-07-01

    This is the sixth in a series of reports to document the development and use of a methodology developed by the Pacific Northwest Laboratory (PNL) to calculate, for prioritization purposes, the risk, dose, and cost impacts of implementing potential resolutions to reactor safety issues (see NUREG/CR-2800, Andrews, et al., 1983). This report contains the results of issue-specific analyses for 34 generic issues. Each issue was considered within the constraints of available information at the time the issues were examined and approximately 2 staff-weeks of labor. The results are referenced as one consideration in NUREG-0933, A Prioritization of Generic Safety Issues (Emrit, et al., 1983)

  15. Guidelines for nuclear-power-plant safety-issue prioritization information development

    International Nuclear Information System (INIS)

    Andrews, W.B.; Gallucci, R.H.V.; Konzek, G.J.

    1983-05-01

    This is the second in a series of reports to document the use of a methodology developed by the Pacific Northwest Laboratory to calculate, for prioritization purposes, the risk, dose and cost impacts of implementing resolutions to reactor safety issues. This report contains results of issue-specific analyses for 15 issues. Each issue was considered within the contraints of available information as of September 1982 and two staff-weeks of labor. The results will be referenced, as one consideration in setting priorities for reactor safety issues, in an NRC prioritization report to be published at a future date

  16. Guidelines for nuclear power plant safety issue prioritization information development. Supplement 5

    Energy Technology Data Exchange (ETDEWEB)

    Daling, P.M.; Lavender, J.C. [Pacific Northwest National Lab., Richland, WA (United States)

    1996-07-01

    This is the sixth in a series of reports to document the development and use of a methodology developed by the Pacific Northwest Laboratory (PNL) to calculate, for prioritization purposes, the risk, dose, and cost impacts of implementing potential resolutions to reactor safety issues (see NUREG/CR-2800, Andrews, et al., 1983). This report contains the results of issue-specific analyses for 34 generic issues. Each issue was considered within the constraints of available information at the time the issues were examined and approximately 2 staff-weeks of labor. The results are referenced as one consideration in NUREG-0933, A Prioritization of Generic Safety Issues (Emrit, et al., 1983).

  17. Economic Functions Proposal of Urgency Prioritization of Investment Projects of Operated Railway Bridges

    Directory of Open Access Journals (Sweden)

    Pitoňák Martin

    2014-12-01

    Full Text Available The main objective of the article is to describe the proposals of economic functions within the prioritization of urgency investments of operated railway bridges within a comprehensive evaluation of existing bridges. The purpose of the paper is a comprehensive assessment of existing bridges and to define determinants and determinants of decision-making and designing a mechanism of decision-making procedures of prioritized infrastructure measures in the form of repairs and reconstructions of bridges resulting from the records of supervising activities based not only on technical but also economic aspects to the railway infrastructure manager.

  18. Guidelines for nuclear power plant safety issue prioritization information development. Supplement 2

    International Nuclear Information System (INIS)

    Andrews, W.B.; Gallucci, R.H.V.; Konzek, G.J.; Heaberlin, S.W.; Fecht, B.A.; Allen, C.H.; Allen, R.D.; Bickford, W.E.; Carbaugh, E.H.; Lewis, J.R.

    1983-12-01

    This is the third in a series of reports to document the use of a methodology developed by the Pacific Northwest Laboratory to calculate, for prioritization purposes, the risk, dose and cost impacts of implementing resolutions to reactor safety issues (NUREG/CR-2800, Andrews et al. 1983). This report contains results of issue-specific analyses for 31 issues. Each issue was considered within the constraints of available information as of summer 1983, and two staff-weeks of labor. The results are referenced, as one consideration in setting priorities for reactor safety issues, in NUREG-0933, A Prioritization of Generic Safety Issues

  19. Evaluating the MEDLINE Core Clinical Journals filter: data-driven evidence assessing clinical utility.

    Science.gov (United States)

    Klein-Fedyshin, Michele; Ketchum, Andrea M; Arnold, Robert M; Fedyshin, Peter J

    2014-12-01

    MEDLINE offers the Core Clinical Journals filter to limit to clinically useful journals. To determine its effectiveness for searching and patient-centric decision making, this study compared literature used for Morning Report in Internal Medicine with journals in the filter. An EndNote library with references answering 327 patient-related questions during Morning Report from 2007 to 2012 was exported to a file listing variables including designated Core Clinical Journal, Impact Factor, date used and medical subject. Bradford's law of scattering was applied ranking the journals and reflecting their clinical utility. Recall (sensitivity) and precision of the Core Morning Report journals and non-Core set was calculated. This study applied bibliometrics to compare the 628 articles used against these criteria to determine journals impacting decision making. Analysis shows 30% of clinically used articles are from the Core Clinical Journals filter and 16% of the journals represented are Core titles. When Bradford-ranked, 55% of the top 20 journals are Core. Articles sources used. Among the 63 Morning Report subjects, 55 have <50% precision and 41 have <50% recall including 37 subjects with 0% precision and 0% recall. Low usage of publications within the Core Clinical Journals filter indicates less relevance for hospital-based care. The divergence from high-impact medicine titles suggests clinically valuable journals differ from academically important titles. With few subjects demonstrating high recall or precision, the MEDLINE Core Clinical Journals filter may require a review and update to better align with current clinical needs. © 2014 John Wiley & Sons, Ltd.

  20. Strategies to optimize MEDLINE and EMBASE search strategies for anesthesiology systematic reviews. An experimental study.

    Science.gov (United States)

    Volpato, Enilze de Souza Nogueira; Betini, Marluci; Puga, Maria Eduarda; Agarwal, Arnav; Cataneo, Antônio José Maria; Oliveira, Luciane Dias de; Bazan, Rodrigo; Braz, Leandro Gobbo; Pereira, José Eduardo Guimarães; El Dib, Regina

    2018-01-15

    A high-quality electronic search is essential for ensuring accuracy and comprehensiveness among the records retrieved when conducting systematic reviews. Therefore, we aimed to identify the most efficient method for searching in both MEDLINE (through PubMed) and EMBASE, covering search terms with variant spellings, direct and indirect orders, and associations with MeSH and EMTREE terms (or lack thereof). Experimental study. UNESP, Brazil. We selected and analyzed 37 search strategies that had specifically been developed for the field of anesthesiology. These search strategies were adapted in order to cover all potentially relevant search terms, with regard to variant spellings and direct and indirect orders, in the most efficient manner. When the strategies included variant spellings and direct and indirect orders, these adapted versions of the search strategies selected retrieved the same number of search results in MEDLINE (mean of 61.3%) and a higher number in EMBASE (mean of 63.9%) in the sample analyzed. The numbers of results retrieved through the searches analyzed here were not identical with and without associated use of MeSH and EMTREE terms. However, association of these terms from both controlled vocabularies retrieved a larger number of records than did the use of either one of them. In view of these results, we recommend that the search terms used should include both preferred and non-preferred terms (i.e. variant spellings and direct/indirect order of the same term) and associated MeSH and EMTREE terms, in order to develop highly-sensitive search strategies for systematic reviews.