Mutations in the human UBR1 gene and the associated phenotypic spectrum.

PubMed

Sukalo, Maja; Fiedler, Ariane; Guzmán, Celina; Spranger, Stephanie; Addor, Marie-Claude; McHeik, Jiad N; Oltra Benavent, Manuel; Cobben, Jan M; Gillis, Lynette A; Shealy, Amy G; Deshpande, Charu; Bozorgmehr, Bita; Everman, David B; Stattin, Eva-Lena; Liebelt, Jan; Keller, Klaus-Michael; Bertola, Débora Romeo; van Karnebeek, Clara D M; Bergmann, Carsten; Liu, Zhifeng; Düker, Gesche; Rezaei, Nima; Alkuraya, Fowzan S; Oğur, Gönül; Alrajoudi, Abdullah; Venegas-Vega, Carlos A; Verbeek, Nienke E; Richmond, Erick J; Kirbiyik, Ozgür; Ranganath, Prajnya; Singh, Ankur; Godbole, Koumudi; Ali, Fouad A M; Alves, Crésio; Mayerle, Julia; Lerch, Markus M; Witt, Heiko; Zenker, Martin

2014-05-01

Johanson-Blizzard syndrome (JBS) is a rare, autosomal recessive disorder characterized by exocrine pancreatic insufficiency, typical facial features, dental anomalies, hypothyroidism, sensorineural hearing loss, scalp defects, urogenital and anorectal anomalies, short stature, and cognitive impairment of variable degree. This syndrome is caused by a defect of the E3 ubiquitin ligase UBR1, which is part of the proteolytic N-end rule pathway. Herein, we review previously reported (n = 29) and a total of 31 novel UBR1 mutations in relation to the associated phenotype in patients from 50 unrelated families. Mutation types include nonsense, frameshift, splice site, missense, and small in-frame deletions consistent with the hypothesis that loss of UBR1 protein function is the molecular basis of JBS. There is an association of missense mutations and small in-frame deletions with milder physical abnormalities and a normal intellectual capacity, thus suggesting that at least some of these may represent hypomorphic UBR1 alleles. The review of clinical data of a large number of molecularly confirmed JBS cases allows us to define minimal clinical criteria for the diagnosis of JBS. For all previously reported and novel UBR1 mutations together with their clinical data, a mutation database has been established at LOVD. © 2014 WILEY PERIODICALS, INC.

NR2E3 mutations in enhanced S-cone sensitivity syndrome (ESCS), Goldmann-Favre syndrome (GFS), clumped pigmentary retinal degeneration (CPRD), and retinitis pigmentosa (RP).

PubMed

Schorderet, Daniel F; Escher, Pascal

2009-11-01

NR2E3, also called photoreceptor-specific nuclear receptor (PNR), is a transcription factor of the nuclear hormone receptor superfamily whose expression is uniquely restricted to photoreceptors. There, its physiological activity is essential for proper rod and cone photoreceptor development and maintenance. Thirty-two different mutations in NR2E3 have been identified in either homozygous or compound heterozygous state in the recessively inherited enhanced S-cone sensitivity syndrome (ESCS), Goldmann-Favre syndrome (GFS), and clumped pigmentary retinal degeneration (CPRD). The clinical phenotype common to all these patients is night blindness, rudimental or absent rod function, and hyperfunction of the "blue" S-cones. A single p.G56R mutation is inherited in a dominant manner and causes retinitis pigmentosa (RP). We have established a new locus-specific database for NR2E3 (www.LOVD.nl/eye), containing all reported mutations, polymorphisms, and unclassified sequence variants, including novel ones. A high proportion of mutations are located in the evolutionarily-conserved DNA-binding domains (DBDs) and ligand-binding domains (LBDs) of NR2E3. Based on homology modeling of these NR2E3 domains, we propose a structural localization of mutated residues. The high variability of clinical phenotypes observed in patients affected by NR2E3-linked retinal degenerations may be caused by different disease mechanisms, including absence of DNA-binding, altered interactions with transcriptional coregulators, and differential activity of modifier genes.

A novel pathogenic splice acceptor site germline mutation in intron 14 of the APC gene in a Chinese family with familial adenomatous polyposis.

PubMed

Wang, Dan; Liang, Shengyun; Zhang, Zhao; Zhao, Guoru; Hu, Yuan; Liang, Shengran; Zhang, Xipeng; Banerjee, Santasree

2017-03-28

Familial adenomatous polyposis (FAP) is an autosomal dominant precancerous condition, clinically characterized by the presence of multiple colorectal adenomas or polyps. Patients with FAP has a high risk of developing colorectal cancer (CRC) from these colorectal adenomatous polyps by the mean age of diagnosis at 40 years. Germline mutations of the APC gene cause familial adenomatous polyposis (FAP). Colectomy has recommended for the FAP patients with significant polyposis. Here, we present a clinical molecular study of a four generation Chinese family with FAP. Clinical diagnosis of FAP has been done according to the phenotype, family history and medical records. Patient's blood samples were collected and genomic DNA was extracted. In order to identify the pathogenic mutation underlying the disease phenotype targeted next-generation sequencing and confirmatory sanger sequencing has undertaken. Targeted next generation sequencing identified a novel heterozygous splice-acceptor site mutation [c.1744-1G>A] in intron 14 of APC gene, which is co-segregated with the FAP phenotypes in the proband and amongst all the affected family members. This mutation is not present in unaffected family members and in normal healthy controls of same ethnic origin. According to the LOVD database for Chinese colorectal cancer patients, in Chinese population, 60% of the previously reported APC gene mutations causes FAP, are missense mutations. This novel splice-acceptor site mutation causing FAP in this Chinese family expands the germline mutation spectrum of the APC gene in the Chinese population.

Amelogenesis Imperfecta; Genes, Proteins, and Pathways

PubMed Central

Smith, Claire E. L.; Poulter, James A.; Antanaviciute, Agne; Kirkham, Jennifer; Brookes, Steven J.; Inglehearn, Chris F.; Mighell, Alan J.

2017-01-01

Amelogenesis imperfecta (AI) is the name given to a heterogeneous group of conditions characterized by inherited developmental enamel defects. AI enamel is abnormally thin, soft, fragile, pitted and/or badly discolored, with poor function and aesthetics, causing patients problems such as early tooth loss, severe embarrassment, eating difficulties, and pain. It was first described separately from diseases of dentine nearly 80 years ago, but the underlying genetic and mechanistic basis of the condition is only now coming to light. Mutations in the gene AMELX, encoding an extracellular matrix protein secreted by ameloblasts during enamel formation, were first identified as a cause of AI in 1991. Since then, mutations in at least eighteen genes have been shown to cause AI presenting in isolation of other health problems, with many more implicated in syndromic AI. Some of the encoded proteins have well documented roles in amelogenesis, acting as enamel matrix proteins or the proteases that degrade them, cell adhesion molecules or regulators of calcium homeostasis. However, for others, function is less clear and further research is needed to understand the pathways and processes essential for the development of healthy enamel. Here, we review the genes and mutations underlying AI presenting in isolation of other health problems, the proteins they encode and knowledge of their roles in amelogenesis, combining evidence from human phenotypes, inheritance patterns, mouse models, and in vitro studies. An LOVD resource (http://dna2.leeds.ac.uk/LOVD/) containing all published gene mutations for AI presenting in isolation of other health problems is described. We use this resource to identify trends in the genes and mutations reported to cause AI in the 270 families for which molecular diagnoses have been reported by 23rd May 2017. Finally we discuss the potential value of the translation of AI genetics to clinical care with improved patient pathways and speculate on the possibility of novel treatments and prevention strategies for AI. PMID:28694781

Amelogenesis Imperfecta; Genes, Proteins, and Pathways.

PubMed

Smith, Claire E L; Poulter, James A; Antanaviciute, Agne; Kirkham, Jennifer; Brookes, Steven J; Inglehearn, Chris F; Mighell, Alan J

2017-01-01

Amelogenesis imperfecta (AI) is the name given to a heterogeneous group of conditions characterized by inherited developmental enamel defects. AI enamel is abnormally thin, soft, fragile, pitted and/or badly discolored, with poor function and aesthetics, causing patients problems such as early tooth loss, severe embarrassment, eating difficulties, and pain. It was first described separately from diseases of dentine nearly 80 years ago, but the underlying genetic and mechanistic basis of the condition is only now coming to light. Mutations in the gene AMELX , encoding an extracellular matrix protein secreted by ameloblasts during enamel formation, were first identified as a cause of AI in 1991. Since then, mutations in at least eighteen genes have been shown to cause AI presenting in isolation of other health problems, with many more implicated in syndromic AI. Some of the encoded proteins have well documented roles in amelogenesis, acting as enamel matrix proteins or the proteases that degrade them, cell adhesion molecules or regulators of calcium homeostasis. However, for others, function is less clear and further research is needed to understand the pathways and processes essential for the development of healthy enamel. Here, we review the genes and mutations underlying AI presenting in isolation of other health problems, the proteins they encode and knowledge of their roles in amelogenesis, combining evidence from human phenotypes, inheritance patterns, mouse models, and in vitro studies. An LOVD resource (http://dna2.leeds.ac.uk/LOVD/) containing all published gene mutations for AI presenting in isolation of other health problems is described. We use this resource to identify trends in the genes and mutations reported to cause AI in the 270 families for which molecular diagnoses have been reported by 23rd May 2017. Finally we discuss the potential value of the translation of AI genetics to clinical care with improved patient pathways and speculate on the possibility of novel treatments and prevention strategies for AI.

Coffin-Siris syndrome and the BAF complex: genotype-phenotype study in 63 patients.

PubMed

Santen, Gijs W E; Aten, Emmelien; Vulto-van Silfhout, Anneke T; Pottinger, Caroline; van Bon, Bregje W M; van Minderhout, Ivonne J H M; Snowdowne, Ronelle; van der Lans, Christian A C; Boogaard, Merel; Linssen, Margot M L; Vijfhuizen, Linda; van der Wielen, Michiel J R; Vollebregt, M J Ellen; Breuning, Martijn H; Kriek, Marjolein; van Haeringen, Arie; den Dunnen, Johan T; Hoischen, Alexander; Clayton-Smith, Jill; de Vries, Bert B A; Hennekam, Raoul C M; van Belzen, Martine J

2013-11-01

De novo germline variants in several components of the SWI/SNF-like BAF complex can cause Coffin-Siris syndrome (CSS), Nicolaides-Baraitser syndrome (NCBRS), and nonsyndromic intellectual disability. We screened 63 patients with a clinical diagnosis of CSS for these genes (ARID1A, ARID1B, SMARCA2, SMARCA4, SMARCB1, and SMARCE1) and identified pathogenic variants in 45 (71%) patients. We found a high proportion of variants in ARID1B (68%). All four pathogenic variants in ARID1A appeared to be mosaic. By using all variants from the Exome Variant Server as test data, we were able to classify variants in ARID1A, ARID1B, and SMARCB1 reliably as being pathogenic or nonpathogenic. For SMARCA2, SMARCA4, and SMARCE1 several variants in the EVS remained unclassified, underlining the importance of parental testing. We have entered all variant and clinical information in LOVD-powered databases to facilitate further genotype-phenotype correlations, as these will become increasingly important because of the uptake of targeted and untargeted next generation sequencing in diagnostics. The emerging phenotype-genotype correlation is that SMARCB1 patients have the most marked physical phenotype and severe cognitive and growth delay. The variability in phenotype seems most marked in ARID1A and ARID1B patients. Distal limbs anomalies are most marked in ARID1A patients and least in SMARCB1 patients. Numbers are small however, and larger series are needed to confirm this correlation. © 2013 WILEY PERIODICALS, INC.

PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.

PubMed

Kumar, Pankaj; Chaitanya, Pasumarthy S; Nagarajaram, Hampapathalu A

2011-01-01

PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1-6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in some bacteria. Although SSR-mediated phase variation and antigenic variations have been well-studied in some bacteria there seems a lot of other species of prokaryotes yet to be investigated for SSR mediated adaptive and other evolutionary advantages. As a part of our on-going studies on SSR polymorphism in prokaryotes we compared the genome sequences of various strains and isolates available for 85 different species of prokaryotes and extracted a number of SSRs showing length variations and created a relational database called PSSRdb. This database gives useful information such as location of PSSRs in genomes, length variation across genomes, the regions harboring PSSRs, etc. The information provided in this database is very useful for further research and analysis of SSRs in prokaryotes.

Establishment of an international database for genetic variants in esophageal cancer.

PubMed

Vihinen, Mauno

2016-10-01

The establishment of a database has been suggested in order to collect, organize, and distribute genetic information about esophageal cancer. The World Organization for Specialized Studies on Diseases of the Esophagus and the Human Variome Project will be in charge of a central database of information about esophageal cancer-related variations from publications, databases, and laboratories; in addition to genetic details, clinical parameters will also be included. The aim will be to get all the central players in research, clinical, and commercial laboratories to contribute. The database will follow established recommendations and guidelines. The database will require a team of dedicated curators with different backgrounds. Numerous layers of systematics will be applied to facilitate computational analyses. The data items will be extensively integrated with other information sources. The database will be distributed as open access to ensure exchange of the data with other databases. Variations will be reported in relation to reference sequences on three levels--DNA, RNA, and protein-whenever applicable. In the first phase, the database will concentrate on genetic variations including both somatic and germline variations for susceptibility genes. Additional types of information can be integrated at a later stage. © 2016 New York Academy of Sciences.

Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers

PubMed Central

2011-01-01

Background Most information on genomic variations and their associations with phenotypes are covered exclusively in scientific publications rather than in structured databases. These texts commonly describe variations using natural language; database identifiers are seldom mentioned. This complicates the retrieval of variations, associated articles, as well as information extraction, e. g. the search for biological implications. To overcome these challenges, procedures to map textual mentions of variations to database identifiers need to be developed. Results This article describes a workflow for normalization of variation mentions, i.e. the association of them to unique database identifiers. Common pitfalls in the interpretation of single nucleotide polymorphism (SNP) mentions are highlighted and discussed. The developed normalization procedure achieves a precision of 98.1 % and a recall of 67.5% for unambiguous association of variation mentions with dbSNP identifiers on a text corpus based on 296 MEDLINE abstracts containing 527 mentions of SNPs. The annotated corpus is freely available at http://www.scai.fraunhofer.de/snp-normalization-corpus.html. Conclusions Comparable approaches usually focus on variations mentioned on the protein sequence and neglect problems for other SNP mentions. The results presented here indicate that normalizing SNPs described on DNA level is more difficult than the normalization of SNPs described on protein level. The challenges associated with normalization are exemplified with ambiguities and errors, which occur in this corpus. PMID:21992066

Human Variome Project Quality Assessment Criteria for Variation Databases.

PubMed

Vihinen, Mauno; Hancock, John M; Maglott, Donna R; Landrum, Melissa J; Schaafsma, Gerard C P; Taschner, Peter

2016-06-01

Numerous databases containing information about DNA, RNA, and protein variations are available. Gene-specific variant databases (locus-specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research, and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. This report elaborates on the developed quality criteria and how implementation of the quality scheme can be achieved. Examples are provided for the current status of the quality items in two different databases, BTKbase, an LSDB, and ClinVar, a central archive of submissions about variants and their clinical significance. © 2016 WILEY PERIODICALS, INC.

GALT protein database: querying structural and functional features of GALT enzyme.

PubMed

d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

2014-09-01

Knowledge of the impact of variations on protein structure can enhance the comprehension of the mechanisms of genetic diseases related to that protein. Here, we present a new version of GALT Protein Database, a Web-accessible data repository for the storage and interrogation of structural effects of variations of the enzyme galactose-1-phosphate uridylyltransferase (GALT), the impairment of which leads to classic Galactosemia, a rare genetic disease. This new version of this database now contains the models of 201 missense variants of GALT enzyme, including heterozygous variants, and it allows users not only to retrieve information about the missense variations affecting this protein, but also to investigate their impact on substrate binding, intersubunit interactions, stability, and other structural features. In addition, it allows the interactive visualization of the models of variants collected into the database. We have developed additional tools to improve the use of the database by nonspecialized users. This Web-accessible database (http://bioinformatica.isa.cnr.it/GALT/GALT2.0) represents a model of tools potentially suitable for application to other proteins that are involved in human pathologies and that are subjected to genetic variations. © 2014 WILEY PERIODICALS, INC.

A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics*

PubMed Central

Li, Jing; Su, Zengliu; Ma, Ze-Qiang; Slebos, Robbert J. C.; Halvey, Patrick; Tabb, David L.; Liebler, Daniel C.; Pao, William; Zhang, Bing

2011-01-01

Shotgun proteomics data analysis usually relies on database search. However, commonly used protein sequence databases do not contain information on protein variants and thus prevent variant peptides and proteins from been identified. Including known coding variations into protein sequence databases could help alleviate this problem. Based on our recently published human Cancer Proteome Variation Database, we have created a protein sequence database that comprehensively annotates thousands of cancer-related coding variants collected in the Cancer Proteome Variation Database as well as noncancer-specific ones from the Single Nucleotide Polymorphism Database (dbSNP). Using this database, we then developed a data analysis workflow for variant peptide identification in shotgun proteomics. The high risk of false positive variant identifications was addressed by a modified false discovery rate estimation method. Analysis of colorectal cancer cell lines SW480, RKO, and HCT-116 revealed a total of 81 peptides that contain either noncancer-specific or cancer-related variations. Twenty-three out of 26 variants randomly selected from the 81 were confirmed by genomic sequencing. We further applied the workflow on data sets from three individual colorectal tumor specimens. A total of 204 distinct variant peptides were detected, and five carried known cancer-related mutations. Each individual showed a specific pattern of cancer-related mutations, suggesting potential use of this type of information for personalized medicine. Compatibility of the workflow has been tested with four popular database search engines including Sequest, Mascot, X!Tandem, and MyriMatch. In summary, we have developed a workflow that effectively uses existing genomic data to enable variant peptide detection in proteomics. PMID:21389108

Development of the Orion Crew Module Static Aerodynamic Database. Part 1; Hypersonic

NASA Technical Reports Server (NTRS)

Bibb, Karen L.; Walker, Eric L.; Robinson, Philip E.

2011-01-01

The Orion aerodynamic database provides force and moment coefficients given the velocity, attitude, configuration, etc. of the Crew Exploration Vehicle (CEV). The database is developed and maintained by the NASA CEV Aerosciences Project team from computational and experimental aerodynamic simulations. The database is used primarily by the Guidance, Navigation, and Control (GNC) team to design vehicle trajectories and assess flight performance. The initial hypersonic re-entry portion of the Crew Module (CM) database was developed in 2006. Updates incorporating additional data and improvements to the database formulation and uncertainty methodologies have been made since then. This paper details the process used to develop the CM database, including nominal values and uncertainties, for Mach numbers greater than 8 and angles of attack between 140deg and 180deg. The primary available data are more than 1000 viscous, reacting gas chemistry computational simulations using both the Laura and Dplr codes, over a range of Mach numbers from 2 to 37 and a range of angles of attack from 147deg to 172deg. Uncertainties were based on grid convergence, laminar-turbulent solution variations, combined altitude and code-to-code variations, and expected heatshield asymmetry. A radial basis function response surface tool, NEAR-RS, was used to fit the coefficient data smoothly in a velocity-angle-of-attack space. The resulting database is presented and includes some data comparisons and a discussion of the predicted variation of trim angle of attack and lift-to-drag ratio. The database provides a variation in trim angle of attack on the order of +/-2deg, and a range in lift-to-drag ratio of +/-0.035 for typical vehicle flight conditions.

Thailand mutation and variation database (ThaiMUT).

PubMed

Ruangrit, Uttapong; Srikummool, Metawee; Assawamakin, Anunchai; Ngamphiw, Chumpol; Chuechote, Suparat; Thaiprasarnsup, Vilasinee; Agavatpanitch, Gallissara; Pasomsab, Ekawat; Yenchitsomanus, Pa-Thai; Mahasirimongkol, Surakameth; Chantratita, Wasun; Palittapongarnpim, Prasit; Uyyanonvara, Bunyarit; Limwongse, Chanin; Tongsima, Sissades

2008-08-01

With the completion of the human genome project, novel sequencing and genotyping technologies had been utilized to detect mutations. Such mutations have continually been produced at exponential rate by researchers in various communities. Based on the population's mutation spectra, occurrences of Mendelian diseases are different across ethnic groups. A proportion of Mendelian diseases can be observed in some countries at higher rates than others. Recognizing the importance of mutation effects in Thailand, we established a National and Ethnic Mutation Database (NEMDB) for Thai people. This database, named Thailand Mutation and Variation database (ThaiMUT), offers a web-based access to genetic mutation and variation information in Thai population. This NEMDB initiative is an important informatics tool for both research and clinical purposes to retrieve and deposit human variation data. The mutation data cataloged in ThaiMUT database were derived from journal articles available in PubMed and local publications. In addition to collected mutation data, ThaiMUT also records genetic polymorphisms located in drug related genes. ThaiMUT could then provide useful information for clinical mutation screening services for Mendelian diseases and pharmacogenomic researches. ThaiMUT can be publicly accessed from http://gi.biotec.or.th/thaimut.

MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases.

PubMed

Townend, Gillian S; Ehrhart, Friederike; van Kranen, Henk J; Wilkinson, Mark; Jacobsen, Annika; Roos, Marco; Willighagen, Egon L; van Enckevort, David; Evelo, Chris T; Curfs, Leopold M G

2018-04-27

Rett syndrome (RTT) is a monogenic rare disorder that causes severe neurological problems. In most cases, it results from a loss-of-function mutation in the gene encoding methyl-CPG-binding protein 2 (MECP2). Currently, about 900 unique MECP2 variations (benign and pathogenic) have been identified and it is suspected that the different mutations contribute to different levels of disease severity. For researchers and clinicians, it is important that genotype-phenotype information is available to identify disease-causing mutations for diagnosis, to aid in clinical management of the disorder, and to provide counseling for parents. In this study, 13 genotype-phenotype databases were surveyed for their general functionality and availability of RTT-specific MECP2 variation data. For each database, we investigated findability and interoperability alongside practical user functionality, and type and amount of genetic and phenotype data. The main conclusions are that, as well as being challenging to find these databases and specific MECP2 variants held within, interoperability is as yet poorly developed and requires effort to search across databases. Nevertheless, we found several thousand online database entries for MECP2 variations and their associated phenotypes, diagnosis, or predicted variant effects, which is a good starting point for researchers and clinicians who want to provide, annotate, and use the data. © 2018 The Authors. Human Mutation published by Wiley Periodicals, Inc.

The first Malay database toward the ethnic-specific target molecular variation.

PubMed

Halim-Fikri, Hashim; Etemad, Ali; Abdul Latif, Ahmad Zubaidi; Merican, Amir Feisal; Baig, Atif Amin; Annuar, Azlina Ahmad; Ismail, Endom; Salahshourifar, Iman; Liza-Sharmini, Ahmad Tajudin; Ramli, Marini; Shah, Mohamed Irwan; Johan, Muhammad Farid; Hassan, Nik Norliza Nik; Abdul-Aziz, Noraishah Mydin; Mohd Noor, Noor Haslina; Nur-Shafawati, Ab Rajab; Hassan, Rosline; Bahar, Rosnah; Zain, Rosnah Binti; Yusoff, Shafini Mohamed; Yusoff, Surini; Tan, Soon Guan; Thong, Meow-Keong; Wan-Isa, Hatin; Abdullah, Wan Zaidah; Mohamed, Zahurin; Abdul Latiff, Zarina; Zilfalil, Bin Alwi

2015-04-30

The Malaysian Node of the Human Variome Project (MyHVP) is one of the eighteen official Human Variome Project (HVP) country-specific nodes. Since its inception in 9(th) October 2010, MyHVP has attracted the significant number of Malaysian clinicians and researchers to participate and contribute their data to this project. MyHVP also act as the center of coordination for genotypic and phenotypic variation studies of the Malaysian population. A specialized database was developed to store and manage the data based on genetic variations which also associated with health and disease of Malaysian ethnic groups. This ethnic-specific database is called the Malaysian Node of the Human Variome Project database (MyHVPDb). Currently, MyHVPDb provides only information about the genetic variations and mutations found in the Malays. In the near future, it will expand for the other Malaysian ethnics as well. The data sets are specified based on diseases or genetic mutation types which have three main subcategories: Single Nucleotide Polymorphism (SNP), Copy Number Variation (CNV) followed by the mutations which code for the common diseases among Malaysians. MyHVPDb has been open to the local researchers, academicians and students through the registration at the portal of MyHVP ( http://hvpmalaysia.kk.usm.my/mhgvc/index.php?id=register ). This database would be useful for clinicians and researchers who are interested in doing a study on genomics population and genetic diseases in order to obtain up-to-date and accurate information regarding the population-specific variations and also useful for those in countries with similar ethnic background.

Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies.

PubMed

Yang, Tsun-Po; Beazley, Claude; Montgomery, Stephen B; Dimas, Antigone S; Gutierrez-Arcelus, Maria; Stranger, Barbara E; Deloukas, Panos; Dermitzakis, Emmanouil T

2010-10-01

Genevar (GENe Expression VARiation) is a database and Java tool designed to integrate multiple datasets, and provides analysis and visualization of associations between sequence variation and gene expression. Genevar allows researchers to investigate expression quantitative trait loci (eQTL) associations within a gene locus of interest in real time. The database and application can be installed on a standard computer in database mode and, in addition, on a server to share discoveries among affiliations or the broader community over the Internet via web services protocols. http://www.sanger.ac.uk/resources/software/genevar.

Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database.

PubMed

Brandstätter, Anita; Peterson, Christine T; Irwin, Jodi A; Mpoke, Solomon; Koech, Davy K; Parson, Walther; Parsons, Thomas J

2004-10-01

Large forensic mtDNA databases which adhere to strict guidelines for generation and maintenance, are not available for many populations outside of the United States and western Europe. We have established a high quality mtDNA control region sequence database for urban Nairobi as both a reference database for forensic investigations, and as a tool to examine the genetic variation of Kenyan sequences in the context of known African variation. The Nairobi sequences exhibited high variation and a low random match probability, indicating utility for forensic testing. Haplogroup identification and frequencies were compared with those reported from other published studies on African, or African-origin populations from Mozambique, Sierra Leone, and the United States, and suggest significant differences in the mtDNA compositions of the various populations. The quality of the sequence data in our study was investigated and supported using phylogenetic measures. Our data demonstrate the diversity and distinctiveness of African populations, and underline the importance of establishing additional forensic mtDNA databases of indigenous African populations.

Towards linked open gene mutations data

PubMed Central

2012-01-01

Background With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework. In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data. Methods A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest. Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite. Results We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application. Conclusions This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development. The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine. PMID:22536974

Towards linked open gene mutations data.

PubMed

Zappa, Achille; Splendiani, Andrea; Romano, Paolo

2012-03-28

With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework. In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data. A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest. Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite. We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application. This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development.The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine.

The Moroccan Genetic Disease Database (MGDD): a database for DNA variations related to inherited disorders and disease susceptibility.

PubMed

Charoute, Hicham; Nahili, Halima; Abidi, Omar; Gabi, Khalid; Rouba, Hassan; Fakiri, Malika; Barakat, Abdelhamid

2014-03-01

National and ethnic mutation databases provide comprehensive information about genetic variations reported in a population or an ethnic group. In this paper, we present the Moroccan Genetic Disease Database (MGDD), a catalogue of genetic data related to diseases identified in the Moroccan population. We used the PubMed, Web of Science and Google Scholar databases to identify available articles published until April 2013. The Database is designed and implemented on a three-tier model using Mysql relational database and the PHP programming language. To date, the database contains 425 mutations and 208 polymorphisms found in 301 genes and 259 diseases. Most Mendelian diseases in the Moroccan population follow autosomal recessive mode of inheritance (74.17%) and affect endocrine, nutritional and metabolic physiology. The MGDD database provides reference information for researchers, clinicians and health professionals through a user-friendly Web interface. Its content should be useful to improve researches in human molecular genetics, disease diagnoses and design of association studies. MGDD can be publicly accessed at http://mgdd.pasteur.ma.

Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India.

PubMed

Pemberton, T J; Jakobsson, M; Conrad, D F; Coop, G; Wall, J D; Pritchard, J K; Patel, P I; Rosenberg, N A

2008-07-01

When performing association studies in populations that have not been the focus of large-scale investigations of haplotype variation, it is often helpful to rely on genomic databases in other populations for study design and analysis - such as in the selection of tag SNPs and in the imputation of missing genotypes. One way of improving the use of these databases is to rely on a mixture of database samples that is similar to the population of interest, rather than using the single most similar database sample. We demonstrate the effectiveness of the mixture approach in the application of African, European, and East Asian HapMap samples for tag SNP selection in populations from India, a genetically intermediate region underrepresented in genomic studies of haplotype variation.

[Genetic mutation databases: stakes and perspectives for orphan genetic diseases].

PubMed

Humbertclaude, V; Tuffery-Giraud, S; Bareil, C; Thèze, C; Paulet, D; Desmet, F-O; Hamroun, D; Baux, D; Girardet, A; Collod-Béroud, G; Khau Van Kien, P; Roux, A-F; des Georges, M; Béroud, C; Claustres, M

2010-10-01

New technologies, which constantly become available for mutation detection and gene analysis, have contributed to an exponential rate of discovery of disease genes and variation in the human genome. The task of collecting and documenting this enormous amount of data in genetic databases represents a major challenge for the future of biological and medical science. The Locus Specific Databases (LSDBs) are so far the most efficient mutation databases. This review presents the main types of databases available for the analysis of mutations responsible for genetic disorders, as well as open perspectives for new therapeutic research or challenges for future medicine. Accurate and exhaustive collection of variations in human genomes will be crucial for research and personalized delivery of healthcare. Copyright © 2009 Elsevier Masson SAS. All rights reserved.

Current databases on biological variation: pros, cons and progress.

PubMed

Ricós, C; Alvarez, V; Cava, F; García-Lario, J V; Hernández, A; Jiménez, C V; Minchinela, J; Perich, C; Simón, M

1999-11-01

A database with reliable information to derive definitive analytical quality specifications for a large number of clinical laboratory tests was prepared in this work. This was achieved by comparing and correlating descriptive data and relevant observations with the biological variation information, an approach that had not been used in the previous efforts of this type. The material compiled in the database was obtained from published articles referenced in BIOS, CURRENT CONTENTS, EMBASE and MEDLINE using "biological variation & laboratory medicine" as key words, as well as books and doctoral theses provided by their authors. The database covers 316 quantities and reviews 191 articles, fewer than 10 of which had to be rejected. The within- and between-subject coefficients of variation and the subsequent desirable quality specifications for precision, bias and total error for all the quantities accepted are presented. Sex-related stratification of results was justified for only four quantities and, in these cases, quality specifications were derived from the group with lower within-subject variation. For certain quantities, biological variation in pathological states was higher than in the healthy state. In these cases, quality specifications were derived only from the healthy population (most stringent). Several quantities (particularly hormones) have been treated in very few articles and the results found are highly discrepant. Therefore, professionals in laboratory medicine should be strongly encouraged to study the quantities for which results are discrepant, the 90 quantities described in only one paper and the numerous quantities that have not been the subject of study.

Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies

PubMed Central

Yang, Tsun-Po; Beazley, Claude; Montgomery, Stephen B.; Dimas, Antigone S.; Gutierrez-Arcelus, Maria; Stranger, Barbara E.; Deloukas, Panos; Dermitzakis, Emmanouil T.

2010-01-01

Summary: Genevar (GENe Expression VARiation) is a database and Java tool designed to integrate multiple datasets, and provides analysis and visualization of associations between sequence variation and gene expression. Genevar allows researchers to investigate expression quantitative trait loci (eQTL) associations within a gene locus of interest in real time. The database and application can be installed on a standard computer in database mode and, in addition, on a server to share discoveries among affiliations or the broader community over the Internet via web services protocols. Availability: http://www.sanger.ac.uk/resources/software/genevar Contact: emmanouil.dermitzakis@unige.ch PMID:20702402

Equivalent Indels – Ambiguous Functional Classes and Redundancy in Databases

PubMed Central

Assmus, Jens; Kleffe, Jürgen; Schmitt, Armin O.; Brockmann, Gudrun A.

2013-01-01

There is considerable interest in studying sequenced variations. However, while the positions of substitutions are uniquely identifiable by sequence alignment, the location of insertions and deletions still poses problems. Each insertion and deletion causes a change of sequence. Yet, due to low complexity or repetitive sequence structures, the same indel can sometimes be annotated in different ways. Two indels which differ in allele sequence and position can be one and the same, i.e. the alternative sequence of the whole chromosome is identical in both cases and, therefore, the two deletions are biologically equivalent. In such a case, it is impossible to identify the exact position of an indel merely based on sequence alignment. Thus, variation entries in a mutation database are not necessarily uniquely defined. We prove the existence of a contiguous region around an indel in which all deletions of the same length are biologically identical. Databases often show only one of several possible locations for a given variation. Furthermore, different data base entries can represent equivalent variation events. We identified 1,045,590 such problematic entries of insertions and deletions out of 5,860,408 indel entries in the current human database of Ensembl. Equivalent indels are found in sequence regions of different functions like exons, introns or 5' and 3' UTRs. One and the same variation can be assigned to several different functional classifications of which only one is correct. We implemented an algorithm that determines for each indel database entry its complete set of equivalent indels which is uniquely characterized by the indel itself and a given interval of the reference sequence. PMID:23658777

Infrared variation reduction by simultaneous background suppression and target contrast enhancement for deep convolutional neural network-based automatic target recognition

NASA Astrophysics Data System (ADS)

Kim, Sungho

2017-06-01

Automatic target recognition (ATR) is a traditionally challenging problem in military applications because of the wide range of infrared (IR) image variations and the limited number of training images. IR variations are caused by various three-dimensional target poses, noncooperative weather conditions (fog and rain), and difficult target acquisition environments. Recently, deep convolutional neural network-based approaches for RGB images (RGB-CNN) showed breakthrough performance in computer vision problems, such as object detection and classification. The direct use of RGB-CNN to the IR ATR problem fails to work because of the IR database problems (limited database size and IR image variations). An IR variation-reduced deep CNN (IVR-CNN) to cope with the problems is presented. The problem of limited IR database size is solved by a commercial thermal simulator (OKTAL-SE). The second problem of IR variations is mitigated by the proposed shifted ramp function-based intensity transformation. This can suppress the background and enhance the target contrast simultaneously. The experimental results on the synthesized IR images generated by the thermal simulator (OKTAL-SE) validated the feasibility of IVR-CNN for military ATR applications.

TRY – a global database of plant traits

PubMed Central

Kattge, J; Díaz, S; Lavorel, S; Prentice, I C; Leadley, P; Bönisch, G; Garnier, E; Westoby, M; Reich, P B; Wright, I J; Cornelissen, J H C; Violle, C; Harrison, S P; Van Bodegom, P M; Reichstein, M; Enquist, B J; Soudzilovskaia, N A; Ackerly, D D; Anand, M; Atkin, O; Bahn, M; Baker, T R; Baldocchi, D; Bekker, R; Blanco, C C; Blonder, B; Bond, W J; Bradstock, R; Bunker, D E; Casanoves, F; Cavender-Bares, J; Chambers, J Q; Chapin, F S; Chave, J; Coomes, D; Cornwell, W K; Craine, J M; Dobrin, B H; Duarte, L; Durka, W; Elser, J; Esser, G; Estiarte, M; Fagan, W F; Fang, J; Fernández-Méndez, F; Fidelis, A; Finegan, B; Flores, O; Ford, H; Frank, D; Freschet, G T; Fyllas, N M; Gallagher, R V; Green, W A; Gutierrez, A G; Hickler, T; Higgins, S I; Hodgson, J G; Jalili, A; Jansen, S; Joly, C A; Kerkhoff, A J; Kirkup, D; Kitajima, K; Kleyer, M; Klotz, S; Knops, J M H; Kramer, K; Kühn, I; Kurokawa, H; Laughlin, D; Lee, T D; Leishman, M; Lens, F; Lenz, T; Lewis, S L; Lloyd, J; Llusià, J; Louault, F; Ma, S; Mahecha, M D; Manning, P; Massad, T; Medlyn, B E; Messier, J; Moles, A T; Müller, S C; Nadrowski, K; Naeem, S; Niinemets, Ü; Nöllert, S; Nüske, A; Ogaya, R; Oleksyn, J; Onipchenko, V G; Onoda, Y; Ordoñez, J; Overbeck, G; Ozinga, W A; Patiño, S; Paula, S; Pausas, J G; Peñuelas, J; Phillips, O L; Pillar, V; Poorter, H; Poorter, L; Poschlod, P; Prinzing, A; Proulx, R; Rammig, A; Reinsch, S; Reu, B; Sack, L; Salgado-Negret, B; Sardans, J; Shiodera, S; Shipley, B; Siefert, A; Sosinski, E; Soussana, J-F; Swaine, E; Swenson, N; Thompson, K; Thornton, P; Waldram, M; Weiher, E; White, M; White, S; Wright, S J; Yguel, B; Zaehle, S; Zanne, A E; Wirth, C

2011-01-01

Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation

NASA Astrophysics Data System (ADS)

Sheynkman, Gloria M.; Shortreed, Michael R.; Cesnik, Anthony J.; Smith, Lloyd M.

2016-06-01

Mass spectrometry-based proteomics has emerged as the leading method for detection, quantification, and characterization of proteins. Nearly all proteomic workflows rely on proteomic databases to identify peptides and proteins, but these databases typically contain a generic set of proteins that lack variations unique to a given sample, precluding their detection. Fortunately, proteogenomics enables the detection of such proteomic variations and can be defined, broadly, as the use of nucleotide sequences to generate candidate protein sequences for mass spectrometry database searching. Proteogenomics is experiencing heightened significance due to two developments: (a) advances in DNA sequencing technologies that have made complete sequencing of human genomes and transcriptomes routine, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations. We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications.

Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation

PubMed Central

Sheynkman, Gloria M.; Shortreed, Michael R.; Cesnik, Anthony J.; Smith, Lloyd M.

2016-01-01

Mass spectrometry–based proteomics has emerged as the leading method for detection, quantification, and characterization of proteins. Nearly all proteomic workflows rely on proteomic databases to identify peptides and proteins, but these databases typically contain a generic set of proteins that lack variations unique to a given sample, precluding their detection. Fortunately, proteogenomics enables the detection of such proteomic variations and can be defined, broadly, as the use of nucleotide sequences to generate candidate protein sequences for mass spectrometry database searching. Proteogenomics is experiencing heightened significance due to two developments: (a) advances in DNA sequencing technologies that have made complete sequencing of human genomes and transcriptomes routine, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations. We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications. PMID:27049631

Using an international p53 mutation database as a foundation for an online laboratory in an upper level undergraduate biology class.

PubMed

Melloy, Patricia G

2015-01-01

A two-part laboratory exercise was developed to enhance classroom instruction on the significance of p53 mutations in cancer development. Students were asked to mine key information from an international database of p53 genetic changes related to cancer, the IARC TP53 database. Using this database, students designed several data mining activities to look at the changes in the p53 gene from a number of perspectives, including potential cancer-causing agents leading to particular changes and the prevalence of certain p53 variations in certain cancers. In addition, students gained a global perspective on cancer prevalence in different parts of the world. Students learned how to use the database in the first part of the exercise, and then used that knowledge to search particular cancers and cancer-causing agents of their choosing in the second part of the exercise. Students also connected the information gathered from the p53 exercise to a previous laboratory exercise looking at risk factors for cancer development. The goal of the experience was to increase student knowledge of the link between p53 genetic variation and cancer. Students also were able to walk a similar path through the website as a cancer researcher using the database to enhance bench work-based experiments with complementary large-scale database p53 variation information. © 2014 The International Union of Biochemistry and Molecular Biology.

RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation

PubMed Central

2009-01-01

Background Polymerase chain reaction (PCR) is very useful in many areas of molecular biology research. It is commonly observed that PCR success is critically dependent on design of an effective primer pair. Current tools for primer design do not adequately address the problem of PCR failure due to mis-priming on target-related sequences and structural variations in the genome. Methods We have developed an integrated graphical web-based application for primer design, called RExPrimer, which was written in Python language. The software uses Primer3 as the primer designing core algorithm. Locally stored sequence information and genomic variant information were hosted on MySQLv5.0 and were incorporated into RExPrimer. Results RExPrimer provides many functionalities for improved PCR primer design. Several databases, namely annotated human SNP databases, insertion/deletion (indel) polymorphisms database, pseudogene database, and structural genomic variation databases were integrated into RExPrimer, enabling an effective without-leaving-the-website validation of the resulting primers. By incorporating these databases, the primers reported by RExPrimer avoid mis-priming to related sequences (e.g. pseudogene, segmental duplication) as well as possible PCR failure because of structural polymorphisms (SNP, indel, and copy number variation (CNV)). To prevent mismatching caused by unexpected SNPs in the designed primers, in particular the 3' end (SNP-in-Primer), several SNP databases covering the broad range of population-specific SNP information are utilized to report SNPs present in the primer sequences. Population-specific SNP information also helps customize primer design for a specific population. Furthermore, RExPrimer offers a graphical user-friendly interface through the use of scalable vector graphic image that intuitively presents resulting primers along with the corresponding gene structure. In this study, we demonstrated the program effectiveness in successfully generating primers for strong homologous sequences. Conclusion The improvements for primer design incorporated into RExPrimer were demonstrated to be effective in designing primers for challenging PCR experiments. Integration of SNP and structural variation databases allows for robust primer design for a variety of PCR applications, irrespective of the sequence complexity in the region of interest. This software is freely available at http://www4a.biotec.or.th/rexprimer. PMID:19958502

Recognizing vocal emotions in Mandarin Chinese: a validated database of Chinese vocal emotional stimuli.

PubMed

Liu, Pan; Pell, Marc D

2012-12-01

To establish a valid database of vocal emotional stimuli in Mandarin Chinese, a set of Chinese pseudosentences (i.e., semantically meaningless sentences that resembled real Chinese) were produced by four native Mandarin speakers to express seven emotional meanings: anger, disgust, fear, sadness, happiness, pleasant surprise, and neutrality. These expressions were identified by a group of native Mandarin listeners in a seven-alternative forced choice task, and items reaching a recognition rate of at least three times chance performance in the seven-choice task were selected as a valid database and then subjected to acoustic analysis. The results demonstrated expected variations in both perceptual and acoustic patterns of the seven vocal emotions in Mandarin. For instance, fear, anger, sadness, and neutrality were associated with relatively high recognition, whereas happiness, disgust, and pleasant surprise were recognized less accurately. Acoustically, anger and pleasant surprise exhibited relatively high mean f0 values and large variation in f0 and amplitude; in contrast, sadness, disgust, fear, and neutrality exhibited relatively low mean f0 values and small amplitude variations, and happiness exhibited a moderate mean f0 value and f0 variation. Emotional expressions varied systematically in speech rate and harmonics-to-noise ratio values as well. This validated database is available to the research community and will contribute to future studies of emotional prosody for a number of purposes. To access the database, please contact pan.liu@mail.mcgill.ca.

DeitY-TU face database: its design, multiple camera capturing, characteristics, and evaluation

NASA Astrophysics Data System (ADS)

Bhowmik, Mrinal Kanti; Saha, Kankan; Saha, Priya; Bhattacharjee, Debotosh

2014-10-01

The development of the latest face databases is providing researchers different and realistic problems that play an important role in the development of efficient algorithms for solving the difficulties during automatic recognition of human faces. This paper presents the creation of a new visual face database, named the Department of Electronics and Information Technology-Tripura University (DeitY-TU) face database. It contains face images of 524 persons belonging to different nontribes and Mongolian tribes of north-east India, with their anthropometric measurements for identification. Database images are captured within a room with controlled variations in illumination, expression, and pose along with variability in age, gender, accessories, make-up, and partial occlusion. Each image contains the combined primary challenges of face recognition, i.e., illumination, expression, and pose. This database also represents some new features: soft biometric traits such as mole, freckle, scar, etc., and facial anthropometric variations that may be helpful for researchers for biometric recognition. It also gives an equivalent study of the existing two-dimensional face image databases. The database has been tested using two baseline algorithms: linear discriminant analysis and principal component analysis, which may be used by other researchers as the control algorithm performance score.

HormoneBase, a population-level database of steroid hormone levels across vertebrates

PubMed Central

Vitousek, Maren N.; Johnson, Michele A.; Donald, Jeremy W.; Francis, Clinton D.; Fuxjager, Matthew J.; Goymann, Wolfgang; Hau, Michaela; Husak, Jerry F.; Kircher, Bonnie K.; Knapp, Rosemary; Martin, Lynn B.; Miller, Eliot T.; Schoenle, Laura A.; Uehling, Jennifer J.; Williams, Tony D.

2018-01-01

Hormones are central regulators of organismal function and flexibility that mediate a diversity of phenotypic traits from early development through senescence. Yet despite these important roles, basic questions about how and why hormone systems vary within and across species remain unanswered. Here we describe HormoneBase, a database of circulating steroid hormone levels and their variation across vertebrates. This database aims to provide all available data on the mean, variation, and range of plasma glucocorticoids (both baseline and stress-induced) and androgens in free-living and un-manipulated adult vertebrates. HormoneBase (www.HormoneBase.org) currently includes >6,580 entries from 476 species, reported in 648 publications from 1967 to 2015, and unpublished datasets. Entries are associated with data on the species and population, sex, year and month of study, geographic coordinates, life history stage, method and latency of hormone sampling, and analysis technique. This novel resource could be used for analyses of the function and evolution of hormone systems, and the relationships between hormonal variation and a variety of processes including phenotypic variation, fitness, and species distributions. PMID:29786693

System for face recognition under expression variations of neutral-sampled individuals using recognized expression warping and a virtual expression-face database

NASA Astrophysics Data System (ADS)

Petpairote, Chayanut; Madarasmi, Suthep; Chamnongthai, Kosin

2018-01-01

The practical identification of individuals using facial recognition techniques requires the matching of faces with specific expressions to faces from a neutral face database. A method for facial recognition under varied expressions against neutral face samples of individuals via recognition of expression warping and the use of a virtual expression-face database is proposed. In this method, facial expressions are recognized and the input expression faces are classified into facial expression groups. To aid facial recognition, the virtual expression-face database is sorted into average facial-expression shapes and by coarse- and fine-featured facial textures. Wrinkle information is also employed in classification by using a process of masking to adjust input faces to match the expression-face database. We evaluate the performance of the proposed method using the CMU multi-PIE, Cohn-Kanade, and AR expression-face databases, and we find that it provides significantly improved results in terms of face recognition accuracy compared to conventional methods and is acceptable for facial recognition under expression variation.

Mutation databases and other online sites as a resource for transfusion medicine: history and attributes.

PubMed

Blumenfeld, Olga O

2002-04-01

Recent advances in molecular biology and technology have provided evidence, at a molecular level, for long-known observations that the human genome is not unique but is characterized by individual sequence variation. At the present time, documentation of genetic variation occurring in a large number of genes is increasing exponentially. The characterization of alleles that encode a variety of blood group antigens has been particularly fruitful for transfusion medicine. Phenotypic variation, as identified by the serologic study of blood group variants, is required to identify the presence of a variant allele. Many of the other alleles currently recorded have been selected and identified on the basis of inherited disease traits. New approaches document single nucleotide polymorphisms that occur throughout the genome and best show how the DNA sequence varies in the human population. The primary data dealing with variant alleles or more general genomic variation are scattered throughout the scientific literature and only within the last few years has information begun to be organized into databases. This article provides guidance on how to access those databases online as a source of information about genetic variation for purposes of molecular, clinical, and diagnostic medicine, research, and teaching. The attributes of the sites are described. A more detailed view of the database dealing specifically with alleles of genes encoding the blood group antigens includes a brief preliminary analysis of the molecular basis for observed polymorphisms. Other online sites that may be particularly useful to the transfusion medicine readership as well as a brief historical account are also presented. Copyright 2002, Elsevier Science (USA). All rights reserved.

Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach.

PubMed

Giardine, Belinda; Borg, Joseph; Higgs, Douglas R; Peterson, Kenneth R; Philipsen, Sjaak; Maglott, Donna; Singleton, Belinda K; Anstee, David J; Basak, A Nazli; Clark, Barnaby; Costa, Flavia C; Faustino, Paula; Fedosyuk, Halyna; Felice, Alex E; Francina, Alain; Galanello, Renzo; Gallivan, Monica V E; Georgitsi, Marianthi; Gibbons, Richard J; Giordano, Piero C; Harteveld, Cornelis L; Hoyer, James D; Jarvis, Martin; Joly, Philippe; Kanavakis, Emmanuel; Kollia, Panagoula; Menzel, Stephan; Miller, Webb; Moradkhani, Kamran; Old, John; Papachatzopoulou, Adamantia; Papadakis, Manoussos N; Papadopoulos, Petros; Pavlovic, Sonja; Perseu, Lucia; Radmilovic, Milena; Riemer, Cathy; Satta, Stefania; Schrijver, Iris; Stojiljkovic, Maja; Thein, Swee Lay; Traeger-Synodinos, Jan; Tully, Ray; Wada, Takahito; Waye, John S; Wiemann, Claudia; Zukic, Branka; Chui, David H K; Wajcman, Henri; Hardison, Ross C; Patrinos, George P

2011-03-20

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases.

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

PubMed

Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

2014-01-01

Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http://hive.biochemistry.gwu.edu/tools/biomuta/index.php; CSR: http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr; HIVE: http://hive.biochemistry.gwu.edu.

Image ratio features for facial expression recognition application.

PubMed

Song, Mingli; Tao, Dacheng; Liu, Zicheng; Li, Xuelong; Zhou, Mengchu

2010-06-01

Video-based facial expression recognition is a challenging problem in computer vision and human-computer interaction. To target this problem, texture features have been extracted and widely used, because they can capture image intensity changes raised by skin deformation. However, existing texture features encounter problems with albedo and lighting variations. To solve both problems, we propose a new texture feature called image ratio features. Compared with previously proposed texture features, e.g., high gradient component features, image ratio features are more robust to albedo and lighting variations. In addition, to further improve facial expression recognition accuracy based on image ratio features, we combine image ratio features with facial animation parameters (FAPs), which describe the geometric motions of facial feature points. The performance evaluation is based on the Carnegie Mellon University Cohn-Kanade database, our own database, and the Japanese Female Facial Expression database. Experimental results show that the proposed image ratio feature is more robust to albedo and lighting variations, and the combination of image ratio features and FAPs outperforms each feature alone. In addition, we study asymmetric facial expressions based on our own facial expression database and demonstrate the superior performance of our combined expression recognition system.

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

PubMed

Yang, Jin Ok; Hwang, Sohyun; Oh, Jeongsu; Bhak, Jong; Sohn, Tae-Kwon

2008-12-12

Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases. To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS) for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC) and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page http://diseasome.kobic.re.kr/, and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes. Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for evaluation in both epidemiological and molecular biological approaches to diseases-gene association studies. Furthermore, researchers then can decide semi-automatically the data set for association studies while considering the relationships between genetic variation and diseases. The database can also be economical for disease-association studies, as well as to facilitate an understanding of the processes which cause disease. Currently, the database contains 14,674 SNP records and 109,715 gene records associated with human diseases and it is updated at regular intervals.

Big Data and Total Hip Arthroplasty: How Do Large Databases Compare?

PubMed

Bedard, Nicholas A; Pugely, Andrew J; McHugh, Michael A; Lux, Nathan R; Bozic, Kevin J; Callaghan, John J

2018-01-01

Use of large databases for orthopedic research has become extremely popular in recent years. Each database varies in the methods used to capture data and the population it represents. The purpose of this study was to evaluate how these databases differed in reported demographics, comorbidities, and postoperative complications for primary total hip arthroplasty (THA) patients. Primary THA patients were identified within National Surgical Quality Improvement Programs (NSQIP), Nationwide Inpatient Sample (NIS), Medicare Standard Analytic Files (MED), and Humana administrative claims database (HAC). NSQIP definitions for comorbidities and complications were matched to corresponding International Classification of Diseases, 9th Revision/Current Procedural Terminology codes to query the other databases. Demographics, comorbidities, and postoperative complications were compared. The number of patients from each database was 22,644 in HAC, 371,715 in MED, 188,779 in NIS, and 27,818 in NSQIP. Age and gender distribution were clinically similar. Overall, there was variation in prevalence of comorbidities and rates of postoperative complications between databases. As an example, NSQIP had more than twice the obesity than NIS. HAC and MED had more than 2 times the diabetics than NSQIP. Rates of deep infection and stroke 30 days after THA had more than 2-fold difference between all databases. Among databases commonly used in orthopedic research, there is considerable variation in complication rates following THA depending upon the database used for analysis. It is important to consider these differences when critically evaluating database research. Additionally, with the advent of bundled payments, these differences must be considered in risk adjustment models. Copyright © 2017 Elsevier Inc. All rights reserved.

Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification.

PubMed

Schuemie, Martijn J; Mons, Barend; Weeber, Marc; Kors, Jan A

2007-06-01

Gene and protein name identification in text requires a dictionary approach to relate synonyms to the same gene or protein, and to link names to external databases. However, existing dictionaries are incomplete. We investigate two complementary methods for automatic generation of a comprehensive dictionary: combination of information from existing gene and protein databases and rule-based generation of spelling variations. Both methods have been reported in literature before, but have hitherto not been combined and evaluated systematically. We combined gene and protein names from several existing databases of four different organisms. The combined dictionaries showed a substantial increase in recall on three different test sets, as compared to any single database. Application of 23 spelling variation rules to the combined dictionaries further increased recall. However, many rules appeared to have no effect and some appear to have a detrimental effect on precision.

In Situ Global Sea Surface Salinity and Variability from the NCEI Global Thermosalinograph Database

NASA Astrophysics Data System (ADS)

Wang, Z.; Boyer, T.; Zhang, H. M.

2017-12-01

Sea surface salinity (SSS) plays an important role in the global ocean circulations. The variations of sea surface salinity are key indicators of changes in air-sea water fluxes. Using nearly 30 years of in situ measurements of sea surface salinity from thermosalinographs, we will evaluate the variations of the sea surface salinity in the global ocean. The sea surface salinity data used are from our newly-developed NCEI Global Thermosalinograph Database - NCEI-TSG. This database provides a comprehensive set of quality-controlled in-situ sea-surface salinity and temperature measurements collected from over 340 vessels during the period 1989 to the present. The NCEI-TSG is the world's most complete TSG dataset, containing all data from the different TSG data assembly centers, e.g. COAPS (SAMOS), IODE (GOSUD) and AOML, with more historical data from NCEI's archive to be added. Using this unique dataset, we will investigate the spatial variations of the global SSS and its variability. Annual and interannual variability will also be studied at selected regions.

Yaquina Bay, Oregon, Intertidal Sediment Temperature Database, 1998 - 2006.

EPA Science Inventory

Detailed, long term sediment temperature records were obtained and compiled in a database to determine the influence of daily, monthly, seasonal and annual temperature variation on eelgrass distribution across the intertidal habitat in Yaquina Bay, Oregon. Both currently and hi...

Genetic Variation in Cardiomyopathy and Cardiovascular Disorders.

PubMed

McNally, Elizabeth M; Puckelwartz, Megan J

2015-01-01

With the wider deployment of massively-parallel, next-generation sequencing, it is now possible to survey human genome data for research and clinical purposes. The reduced cost of producing short-read sequencing has now shifted the burden to data analysis. Analysis of genome sequencing remains challenged by the complexity of the human genome, including redundancy and the repetitive nature of genome elements and the large amount of variation in individual genomes. Public databases of human genome sequences greatly facilitate interpretation of common and rare genetic variation, although linking database sequence information to detailed clinical information is limited by privacy and practical issues. Genetic variation is a rich source of knowledge for cardiovascular disease because many, if not all, cardiovascular disorders are highly heritable. The role of rare genetic variation in predicting risk and complications of cardiovascular diseases has been well established for hypertrophic and dilated cardiomyopathy, where the number of genes that are linked to these disorders is growing. Bolstered by family data, where genetic variants segregate with disease, rare variation can be linked to specific genetic variation that offers profound diagnostic information. Understanding genetic variation in cardiomyopathy is likely to help stratify forms of heart failure and guide therapy. Ultimately, genetic variation may be amenable to gene correction and gene editing strategies.

A global Fine-Root Ecology Database to address below-ground challenges in plant ecology

DOE PAGES

Iversen, Colleen M.; McCormack, M. Luke; Powell, A. Shafer; ...

2017-02-28

Variation and tradeoffs within and among plant traits are increasingly being harnessed by empiricists and modelers to understand and predict ecosystem processes under changing environmental conditions. And while fine roots play an important role in ecosystem functioning, fine-root traits are underrepresented in global trait databases. This has hindered efforts to analyze fine-root trait variation and link it with plant function and environmental conditions at a global scale. This Viewpoint addresses the need for a centralized fine-root trait database, and introduces the Fine-Root Ecology Database (FRED, http://roots.ornl.gov) which so far includes > 70 000 observations encompassing a broad range of rootmore » traits and also includes associated environmental data. FRED represents a critical step toward improving our understanding of below-ground plant ecology. For example, FRED facilitates the quantification of variation in fine-root traits across root orders, species, biomes, and environmental gradients while also providing a platform for assessments of covariation among root, leaf, and wood traits, the role of fine roots in ecosystem functioning, and the representation of fine roots in terrestrial biosphere models. There has been a continued input of observations into FRED to fill gaps in trait coverage will improve our understanding of changes in fine-root traits across space and time.« less

A global Fine-Root Ecology Database to address below-ground challenges in plant ecology

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

Iversen, Colleen M.; McCormack, M. Luke; Powell, A. Shafer

Variation and tradeoffs within and among plant traits are increasingly being harnessed by empiricists and modelers to understand and predict ecosystem processes under changing environmental conditions. And while fine roots play an important role in ecosystem functioning, fine-root traits are underrepresented in global trait databases. This has hindered efforts to analyze fine-root trait variation and link it with plant function and environmental conditions at a global scale. This Viewpoint addresses the need for a centralized fine-root trait database, and introduces the Fine-Root Ecology Database (FRED, http://roots.ornl.gov) which so far includes > 70 000 observations encompassing a broad range of rootmore » traits and also includes associated environmental data. FRED represents a critical step toward improving our understanding of below-ground plant ecology. For example, FRED facilitates the quantification of variation in fine-root traits across root orders, species, biomes, and environmental gradients while also providing a platform for assessments of covariation among root, leaf, and wood traits, the role of fine roots in ecosystem functioning, and the representation of fine roots in terrestrial biosphere models. There has been a continued input of observations into FRED to fill gaps in trait coverage will improve our understanding of changes in fine-root traits across space and time.« less

Spatial variation of volcanic rock geochemistry in the Virunga Volcanic Province: Statistical analysis of an integrated database

NASA Astrophysics Data System (ADS)

Barette, Florian; Poppe, Sam; Smets, Benoît; Benbakkar, Mhammed; Kervyn, Matthieu

2017-10-01

We present an integrated, spatially-explicit database of existing geochemical major-element analyses available from (post-) colonial scientific reports, PhD Theses and international publications for the Virunga Volcanic Province, located in the western branch of the East African Rift System. This volcanic province is characterised by alkaline volcanism, including silica-undersaturated, alkaline and potassic lavas. The database contains a total of 908 geochemical analyses of eruptive rocks for the entire volcanic province with a localisation for most samples. A preliminary analysis of the overall consistency of the database, using statistical techniques on sets of geochemical analyses with contrasted analytical methods or dates, demonstrates that the database is consistent. We applied a principal component analysis and cluster analysis on whole-rock major element compositions included in the database to study the spatial variation of the chemical composition of eruptive products in the Virunga Volcanic Province. These statistical analyses identify spatially distributed clusters of eruptive products. The known geochemical contrasts are highlighted by the spatial analysis, such as the unique geochemical signature of Nyiragongo lavas compared to other Virunga lavas, the geochemical heterogeneity of the Bulengo area, and the trachyte flows of Karisimbi volcano. Most importantly, we identified separate clusters of eruptive products which originate from primitive magmatic sources. These lavas of primitive composition are preferentially located along NE-SW inherited rift structures, often at distance from the central Virunga volcanoes. Our results illustrate the relevance of a spatial analysis on integrated geochemical data for a volcanic province, as a complement to classical petrological investigations. This approach indeed helps to characterise geochemical variations within a complex of magmatic systems and to identify specific petrologic and geochemical investigations that should be tackled within a study area.

Genome-wide association as a means to understanding the mammary gland

USDA-ARS?s Scientific Manuscript database

Next-generation sequencing and related technologies have facilitated the creation of enormous public databases that catalogue genomic variation. These databases have facilitated a variety of approaches to discover new genes that regulate normal biology as well as disease. Genome wide association (...

VarioML framework for comprehensive variation data representation and exchange.

PubMed

Byrne, Myles; Fokkema, Ivo Fac; Lancaster, Owen; Adamusiak, Tomasz; Ahonen-Bishopp, Anni; Atlan, David; Béroud, Christophe; Cornell, Michael; Dalgleish, Raymond; Devereau, Andrew; Patrinos, George P; Swertz, Morris A; Taschner, Peter Em; Thorisson, Gudmundur A; Vihinen, Mauno; Brookes, Anthony J; Muilu, Juha

2012-10-03

Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.

VarioML framework for comprehensive variation data representation and exchange

PubMed Central

2012-01-01

Background Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. Results The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. Conclusions VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity. PMID:23031277

PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations

PubMed Central

Zhang, Chao; Gao, Yang; Liu, Jiaojiao; Xue, Zhe; Lu, Yan; Deng, Lian; Tian, Lei; Feng, Qidi

2018-01-01

Abstract There are a growing number of studies focusing on delineating genetic variations that are associated with complex human traits and diseases due to recent advances in next-generation sequencing technologies. However, identifying and prioritizing disease-associated causal variants relies on understanding the distribution of genetic variations within and among populations. The PGG.Population database documents 7122 genomes representing 356 global populations from 107 countries and provides essential information for researchers to understand human genomic diversity and genetic ancestry. These data and information can facilitate the design of research studies and the interpretation of results of both evolutionary and medical studies involving human populations. The database is carefully maintained and constantly updated when new data are available. We included miscellaneous functions and a user-friendly graphical interface for visualization of genomic diversity, population relationships (genetic affinity), ancestral makeup, footprints of natural selection, and population history etc. Moreover, PGG.Population provides a useful feature for users to analyze data and visualize results in a dynamic style via online illustration. The long-term ambition of the PGG.Population, together with the joint efforts from other researchers who contribute their data to our database, is to create a comprehensive depository of geographic and ethnic variation of human genome, as well as a platform bringing influence on future practitioners of medicine and clinical investigators. PGG.Population is available at https://www.pggpopulation.org. PMID:29112749

A global Fine-Root Ecology Database to address below-ground challenges in plant ecology.

PubMed

Iversen, Colleen M; McCormack, M Luke; Powell, A Shafer; Blackwood, Christopher B; Freschet, Grégoire T; Kattge, Jens; Roumet, Catherine; Stover, Daniel B; Soudzilovskaia, Nadejda A; Valverde-Barrantes, Oscar J; van Bodegom, Peter M; Violle, Cyrille

2017-07-01

Variation and tradeoffs within and among plant traits are increasingly being harnessed by empiricists and modelers to understand and predict ecosystem processes under changing environmental conditions. While fine roots play an important role in ecosystem functioning, fine-root traits are underrepresented in global trait databases. This has hindered efforts to analyze fine-root trait variation and link it with plant function and environmental conditions at a global scale. This Viewpoint addresses the need for a centralized fine-root trait database, and introduces the Fine-Root Ecology Database (FRED, http://roots.ornl.gov) which so far includes > 70 000 observations encompassing a broad range of root traits and also includes associated environmental data. FRED represents a critical step toward improving our understanding of below-ground plant ecology. For example, FRED facilitates the quantification of variation in fine-root traits across root orders, species, biomes, and environmental gradients while also providing a platform for assessments of covariation among root, leaf, and wood traits, the role of fine roots in ecosystem functioning, and the representation of fine roots in terrestrial biosphere models. Continued input of observations into FRED to fill gaps in trait coverage will improve our understanding of changes in fine-root traits across space and time. © 2017 UT-Battelle LLC. New Phytologist © 2017 New Phytologist Trust.

Practice databases and their uses in clinical research.

PubMed

Tierney, W M; McDonald, C J

1991-04-01

A few large clinical information databases have been established within larger medical information systems. Although they are smaller than claims databases, these clinical databases offer several advantages: accurate and timely data, rich clinical detail, and continuous parameters (for example, vital signs and laboratory results). However, the nature of the data vary considerably, which affects the kinds of secondary analyses that can be performed. These databases have been used to investigate clinical epidemiology, risk assessment, post-marketing surveillance of drugs, practice variation, resource use, quality assurance, and decision analysis. In addition, practice databases can be used to identify subjects for prospective studies. Further methodologic developments are necessary to deal with the prevalent problems of missing data and various forms of bias if such databases are to grow and contribute valuable clinical information.

Stylistic Variations in Science Lectures: Teaching Vocabulary.

ERIC Educational Resources Information Center

Jackson, Jane; Bilton, Linda

1994-01-01

Twenty lectures by native speaker geology lecturers to nonnative speaker students were transcribed, and 921 instances of vocabulary elaboration were coded into a computer database according to 20 linguistic features. Analysis revealed noticeable variation among lecturers in language range/technicality, vocabulary elaboration, signalling, and use…

NOAA Data Rescue of Key Solar Databases and Digitization of Historical Solar Images

NASA Astrophysics Data System (ADS)

Coffey, H. E.

2006-08-01

Over a number of years, the staff at NOAA National Geophysical Data Center (NGDC) has worked to rescue key solar databases by converting them to digital format and making them available via the World Wide Web. NOAA has had several data rescue programs where staff compete for funds to rescue important and critical historical data that are languishing in archives and at risk of being lost due to deteriorating condition, loss of any metadata or descriptive text that describe the databases, lack of interest or funding in maintaining databases, etc. The Solar-Terrestrial Physics Division at NGDC was able to obtain funds to key in some critical historical tabular databases. Recently the NOAA Climate Database Modernization Program (CDMP) funded a project to digitize historical solar images, producing a large online database of historical daily full disk solar images. The images include the wavelengths Calcium K, Hydrogen Alpha, and white light photos, as well as sunspot drawings and the comprehensive drawings of a multitude of solar phenomena on one daily map (Fraunhofer maps and Wendelstein drawings). Included in the digitization are high resolution solar H-alpha images taken at the Boulder Solar Observatory 1967-1984. The scanned daily images document many phases of solar activity, from decadal variation to rotational variation to daily changes. Smaller versions are available online. Larger versions are available by request. See http://www.ngdc.noaa.gov/stp/SOLAR/ftpsolarimages.html. The tabular listings and solar imagery will be discussed.

Detection and quantification of creep strain using process compensated resonance testing (PCRT) sorting modules trained with modeled resonance spectra

NASA Astrophysics Data System (ADS)

Heffernan, Julieanne; Biedermann, Eric; Mayes, Alexander; Livings, Richard; Jauriqui, Leanne; Goodlet, Brent; Aldrin, John C.; Mazdiyasni, Siamack

2018-04-01

Process Compensated Resonant Testing (PCRT) is a full-body nondestructive testing (NDT) method that measures the resonance frequencies of a part and correlates them to the part's material and/or damage state. PCRT testing is used in the automotive, aerospace, and power generation industries via automated PASS/FAIL inspections to distinguish parts with nominal process variation from those with the defect(s) of interest. Traditional PCRT tests are created through the statistical analysis of populations of "good" and "bad" parts. However, gathering a statistically significant number of parts can be costly and time-consuming, and the availability of defective parts may be limited. This work uses virtual databases of good and bad parts to create two targeted PCRT inspections for single crystal (SX) nickel-based superalloy turbine blades. Using finite element (FE) models, populations were modeled to include variations in geometric dimensions, material properties, crystallographic orientation, and creep damage. Model results were verified by comparing the frequency variation in the modeled populations with the measured frequency variations of several physical blade populations. Additionally, creep modeling results were verified through the experimental evaluation of coupon geometries. A virtual database of resonance spectra was created from the model data. The virtual database was used to create PCRT inspections to detect crystallographic defects and creep strain. Quantification of creep strain values using the PCRT inspection results was also demonstrated.

Why a Data-Based Decision-Making Intervention Works in Some Schools and Not in Others

ERIC Educational Resources Information Center

Keuning, Trynke; Van Geel, Marieke; Visscher, Adrie

2017-01-01

The use of data for adaptive, tailor-made education can be beneficial for students with learning difficulties. While evaluating the effects of a data-based decision-making (DBDM) intervention on student outcomes, considerable variation between intervention effects, ranging from high-intervention effects to small or even negative intervention…

A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS.

PubMed

Veloo, A C M; Jean-Pierre, H; Justesen, U S; Morris, T; Urban, E; Wybo, I; Shah, H N; Friedrich, A W; Morris, T; Shah, H N; Jean-Pierre, H; Justesen, U S; Nagy, E; Urban, E; Kostrzewa, M; Veloo, A; Friedrich, A W

2017-12-01

Inter-laboratory reproducibility of Matrix Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of anaerobic bacteria has not been shown before. Therefore, ten anonymized anaerobic strains were sent to seven participating laboratories, an initiative of the European Network for the Rapid Identification of Anaerobes (ENRIA). On arrival the strains were cultured and identified using MALDI-TOF MS. The spectra derived were compared with two different Biotyper MALDI-TOF MS databases, the db5627 and the db6903. The results obtained using the db5627 shows a reasonable variation between the different laboratories. However, when a more optimized database is used, the variation is less pronounced. In this study we show that an optimized database not only results in a higher number of strains which can be identified using MALDI-TOF MS, but also corrects for differences in performance between laboratories. Copyright © 2017 Elsevier Ltd. All rights reserved.

Joint seismic-infrasonic processing of recordings from a repeating source of atmospheric explosions.

PubMed

Gibbons, Steven J; Ringdal, Frode; Kvaerna, Tormod

2007-11-01

A database has been established of seismic and infrasonic recordings from more than 100 well-constrained surface explosions, conducted by the Finnish military to destroy old ammunition. The recorded seismic signals are essentially identical and indicate that the variation in source location and magnitude is negligible. In contrast, the infrasonic arrivals on both seismic and infrasound sensors exhibit significant variation both with regard to the number of detected phases, phase travel times, and phase amplitudes, which would be attributable to atmospheric factors. This data set provides an excellent database for studies in sound propagation, infrasound array detection, and direction estimation.

Inter-state Variation in the Burden of Fragility Fractures

USDA-ARS?s Scientific Manuscript database

Demographic differences may produce inter-state variation in the burden of osteoporosis. The objective of this study was to estimate the burden of fragility fractures by race/ethnicity, age, sex, and service site across 5 diverse and populous states. State inpatient databases for 2000 were used to ...

PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations.

PubMed

Zhang, Chao; Gao, Yang; Liu, Jiaojiao; Xue, Zhe; Lu, Yan; Deng, Lian; Tian, Lei; Feng, Qidi; Xu, Shuhua

2018-01-04

There are a growing number of studies focusing on delineating genetic variations that are associated with complex human traits and diseases due to recent advances in next-generation sequencing technologies. However, identifying and prioritizing disease-associated causal variants relies on understanding the distribution of genetic variations within and among populations. The PGG.Population database documents 7122 genomes representing 356 global populations from 107 countries and provides essential information for researchers to understand human genomic diversity and genetic ancestry. These data and information can facilitate the design of research studies and the interpretation of results of both evolutionary and medical studies involving human populations. The database is carefully maintained and constantly updated when new data are available. We included miscellaneous functions and a user-friendly graphical interface for visualization of genomic diversity, population relationships (genetic affinity), ancestral makeup, footprints of natural selection, and population history etc. Moreover, PGG.Population provides a useful feature for users to analyze data and visualize results in a dynamic style via online illustration. The long-term ambition of the PGG.Population, together with the joint efforts from other researchers who contribute their data to our database, is to create a comprehensive depository of geographic and ethnic variation of human genome, as well as a platform bringing influence on future practitioners of medicine and clinical investigators. PGG.Population is available at https://www.pggpopulation.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation.

PubMed

Komaki, Shohei; Shiwa, Yuh; Furukawa, Ryohei; Hachiya, Tsuyoshi; Ohmomo, Hideki; Otomo, Ryo; Satoh, Mamoru; Hitomi, Jiro; Sobue, Kenji; Sasaki, Makoto; Shimizu, Atsushi

2018-01-01

We launched an integrative multi-omics database, iMETHYL (http://imethyl.iwate-megabank.org). iMETHYL provides whole-DNA methylation (~24 million autosomal CpG sites), whole-genome (~9 million single-nucleotide variants), and whole-transcriptome (>14 000 genes) data for CD4 + T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. These data were obtained from whole-genome bisulfite sequencing, whole-genome sequencing, and whole-transcriptome sequencing, making iMETHYL a comprehensive database.

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

PubMed Central

Paila, Umadevi; Chapman, Brad A.; Kirchner, Rory; Quinlan, Aaron R.

2013-01-01

Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics. PMID:23874191

A web accessible resource for investigating cassava phenomics and genomics information: BIOGEN BASE

PubMed Central

Jayakodi, Murukarthick; selvan, Sreedevi Ghokhilamani; Natesan, Senthil; Muthurajan, Raveendran; Duraisamy, Raghu; Ramineni, Jana Jeevan; Rathinasamy, Sakthi Ambothi; Karuppusamy, Nageswari; Lakshmanan, Pugalenthi; Chokkappan, Mohan

2011-01-01

The goal of our research is to establish a unique portal to bring out the potential outcome of the research in the Casssava crop. The Biogen base for cassava clearly brings out the variations of different traits of the germplasms, maintained at the Tapioca and Castor Research Station, Tamil Nadu Agricultural University. Phenotypic and genotypic variations of the accessions are clearly depicted, for the users to browse and interpret the variations using the microsatellite markers. Database (BIOGEN BASE ‐ CASSAVA) is designed using PHP and MySQL and is equipped with extensive search options. It is more user-friendly and made publicly available, to improve the research and development of cassava by making a wealth of genetics and genomics data available through open, common, and worldwide forum for all individuals interested in the field. Availability The database is available for free at http://www.tnaugenomics.com/biogenbase/casava.php PMID:21904428

A web accessible resource for investigating cassava phenomics and genomics information: BIOGEN BASE.

PubMed

Jayakodi, Murukarthick; Selvan, Sreedevi Ghokhilamani; Natesan, Senthil; Muthurajan, Raveendran; Duraisamy, Raghu; Ramineni, Jana Jeevan; Rathinasamy, Sakthi Ambothi; Karuppusamy, Nageswari; Lakshmanan, Pugalenthi; Chokkappan, Mohan

2011-01-01

The goal of our research is to establish a unique portal to bring out the potential outcome of the research in the Casssava crop. The Biogen base for cassava clearly brings out the variations of different traits of the germplasms, maintained at the Tapioca and Castor Research Station, Tamil Nadu Agricultural University. Phenotypic and genotypic variations of the accessions are clearly depicted, for the users to browse and interpret the variations using the microsatellite markers. Database (BIOGEN BASE - CASSAVA) is designed using PHP and MySQL and is equipped with extensive search options. It is more user-friendly and made publicly available, to improve the research and development of cassava by making a wealth of genetics and genomics data available through open, common, and worldwide forum for all individuals interested in the field. The database is available for free at http://www.tnaugenomics.com/biogenbase/casava.php.

Subscribing to Databases: How Important Is Depth and Quality of Indexing?

ERIC Educational Resources Information Center

Delong, Linwood

2007-01-01

This paper compares the subject indexing on articles pertaining to Immanuel Kant, agriculture, and aging that are found simultaneously in Humanities Index, Academic Search Elite (EBSCO) and Periodicals Research II (Micromedia ProQuest), in order to show that there are substantial variations in the depth and quality of indexing in these databases.…

Mitigating component performance variation

DOEpatents

Gara, Alan G.; Sylvester, Steve S.; Eastep, Jonathan M.; Nagappan, Ramkumar; Cantalupo, Christopher M.

2018-01-09

Apparatus and methods may provide for characterizing a plurality of similar components of a distributed computing system based on a maximum safe operation level associated with each component and storing characterization data in a database and allocating non-uniform power to each similar component based at least in part on the characterization data in the database to substantially equalize performance of the components.

Registering Students from Language Backgrounds Other Than English. Issues & Answers. REL 2007-No. 025

ERIC Educational Resources Information Center

Marcus, Nicole; Adger, Carolyn Temple; Arteagoitia, Igone

2007-01-01

This report seeks to alert administrators, school staff, and database managers to variations in the naming systems of other cultures; to help these groups accommodate other cultures and identify students consistently in school databases; and to provide knowledge of other cultures' naming conventions and forms of address to assist in interacting…

The CoFactor database: organic cofactors in enzyme catalysis.

PubMed

Fischer, Julia D; Holliday, Gemma L; Thornton, Janet M

2010-10-01

Organic enzyme cofactors are involved in many enzyme reactions. Therefore, the analysis of cofactors is crucial to gain a better understanding of enzyme catalysis. To aid this, we have created the CoFactor database. CoFactor provides a web interface to access hand-curated data extracted from the literature on organic enzyme cofactors in biocatalysis, as well as automatically collected information. CoFactor includes information on the conformational and solvent accessibility variation of the enzyme-bound cofactors, as well as mechanistic and structural information about the hosting enzymes. The database is publicly available and can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/CoFactor.

DbMap: improving database interoperability issues in medical software using a simple, Java-Xml based solution.

PubMed Central

Karadimas, H.; Hemery, F.; Roland, P.; Lepage, E.

2000-01-01

In medical software development, the use of databases plays a central role. However, most of the databases have heterogeneous encoding and data models. To deal with these variations in the application code directly is error-prone and reduces the potential reuse of the produced software. Several approaches to overcome these limitations have been proposed in the medical database literature, which will be presented. We present a simple solution, based on a Java library, and a central Metadata description file in XML. This development approach presents several benefits in software design and development cycles, the main one being the simplicity in maintenance. PMID:11079915

A framework for the use of agent based modeling to simulate inter- and intraindividual variation in human behaviors

EPA Science Inventory

Simulation of human behavior in exposure modeling is a complex task. Traditionally, inter-individual variation in human activity has been modeled by drawing from a pool of single day time-activity diaries such as the US EPA Consolidated Human Activity Database (CHAD). Here, an ag...

Nationwide Databases in Orthopaedic Surgery Research.

PubMed

Bohl, Daniel D; Singh, Kern; Grauer, Jonathan N

2016-10-01

The use of nationwide databases to conduct orthopaedic research has expanded markedly in recent years. Nationwide databases offer large sample sizes, sampling of patients who are representative of the country as a whole, and data that enable investigation of trends over time. The most common use of nationwide databases is to study the occurrence of postoperative adverse events. Other uses include the analysis of costs and the investigation of critical hospital metrics, such as length of stay and readmission rates. Although nationwide databases are powerful research tools, readers should be aware of the differences between them and their limitations. These include variations and potential inaccuracies in data collection, imperfections in patient sampling, insufficient postoperative follow-up, and lack of orthopaedic-specific outcomes.

Ensembl variation resources

PubMed Central

2010-01-01

Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org. PMID:20459805

Federated Search Tools in Fusion Centers: Bridging Databases in the Information Sharing Environment

DTIC Science & Technology

2012-09-01

considerable variation in how fusion centers plan for, gather requirements, select and acquire federated search tools to bridge disparate databases...centers, when considering integrating federated search tools; by evaluating the importance of the planning, requirements gathering, selection and...acquisition processes for integrating federated search tools; by acknowledging the challenges faced by some fusion centers during these integration processes

ETHNOS: A versatile electronic tool for the development and curation of national genetic databases

PubMed Central

2010-01-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation. PMID:20650823

ETHNOS : A versatile electronic tool for the development and curation of national genetic databases.

PubMed

van Baal, Sjozef; Zlotogora, Joël; Lagoumintzis, George; Gkantouna, Vassiliki; Tzimas, Ioannis; Poulas, Konstantinos; Tsakalidis, Athanassios; Romeo, Giovanni; Patrinos, George P

2010-06-01

National and ethnic mutation databases (NEMDBs) are emerging online repositories, recording extensive information about the described genetic heterogeneity of an ethnic group or population. These resources facilitate the provision of genetic services and provide a comprehensive list of genomic variations among different populations. As such, they enhance awareness of the various genetic disorders. Here, we describe the features of the ETHNOS software, a simple but versatile tool based on a flat-file database that is specifically designed for the development and curation of NEMDBs. ETHNOS is a freely available software which runs more than half of the NEMDBs currently available. Given the emerging need for NEMDB in genetic testing services and the fact that ETHNOS is the only off-the-shelf software available for NEMDB development and curation, its adoption in subsequent NEMDB development would contribute towards data content uniformity, unlike the diverse contents and quality of the available gene (locus)-specific databases. Finally, we allude to the potential applications of NEMDBs, not only as worldwide central allele frequency repositories, but also, and most importantly, as data warehouses of individual-level genomic data, hence allowing for a comprehensive ethnicity-specific documentation of genomic variation.

Compression technique for large statistical data bases

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

Eggers, S.J.; Olken, F.; Shoshani, A.

1981-03-01

The compression of large statistical databases is explored and are proposed for organizing the compressed data, such that the time required to access the data is logarithmic. The techniques exploit special characteristics of statistical databases, namely, variation in the space required for the natural encoding of integer attributes, a prevalence of a few repeating values or constants, and the clustering of both data of the same length and constants in long, separate series. The techniques are variations of run-length encoding, in which modified run-lengths for the series are extracted from the data stream and stored in a header, which ismore » used to form the base level of a B-tree index into the database. The run-lengths are cumulative, and therefore the access time of the data is logarithmic in the size of the header. The details of the compression scheme and its implementation are discussed, several special cases are presented, and an analysis is given of the relative performance of the various versions.« less

Thirty-day Readmission Rates and Associated Factors: A Multilevel Analysis of Practice Variations in French Public Psychiatry.

PubMed

Gandré, Coralie; Gervaix, Jeanne; Thillard, Julien; Macé, Jean-Marc; Roelandt, Jean-Luc; Chevreul, Karine

2018-03-01

Inpatient psychiatric readmissions are often used as an indicator of the quality of care and their reduction is in line with international recommendations for mental health care. Research on variations in inpatient readmission rates among mental health care providers is therefore of key importance as these variations can impact equity, quality and efficiency of care when they do not result from differences in patients' needs. Our objectives were first to describe variations in inpatient readmission rates between public mental health care providers in France on a nationwide scale, and second, to identify their association with patient, health care providers and environment characteristics. We carried out a study for the year 2012 using data from ten administrative national databases. 30-day readmissions in inpatient care were identified in the French national psychiatric discharge database. Variations were described numerically and graphically between French psychiatric sectors and factors associated with these variations were identified by carrying out a multi-level logistic regression accounting for the hierarchical structure of the data. Significant practice variations in 30-day inpatient readmission rates were observed with a coefficient of variation above 50%. While a majority of those variations was related to differences within sectors, individual patient characteristics explained a lower part of the variations resulting from differences between sectors than the characteristics of sectors and of their environment. In particular, an increase in the mortality rate and in the acute admission rate for somatic disorders in sectors' catchment area was associated with a decrease in the probability of 30-day readmission. Similarly, an increase in the number of psychiatric inpatient beds in private for-profit hospitals per 1,000 inhabitants in sectors' catchment area was associated with a decrease in this probability, which also varied with overall sectors' case-mix characteristics and with the level of urbanisation of the area. The extent of the variations and the factors associated with it question the adequacy of care and suggest that some of them may be unwarranted. Our findings should however be interpreted in consideration of several limits inherent to data quality and availability as we relied on information from administrative databases. While we considered a wide range of factors potentially associated with variations in 30-day readmissions, our model indeed only explained a limited part of the variations resulting from differences between sectors. Our findings underscored that practice variations in psychiatry are a reality that merits the full attention of decision makers as they can impact the quality, equity and efficiency of care. A specific data system should be established to monitor practice variations in routine to promote transparency and accountability. Few associations were found between variations in 30-day inpatient readmissions and the supply of care. The routine collection of detailed organizational characteristics of health care providers at a national level should be supported to facilitate additional research work, both in France and in other contexts.

Inter- and intraspecific variation in leaf economic traits in wheat and maize

PubMed Central

Hale, Christine E; Cerabolini, Bruno E L; Cornelissen, Johannes H C; Craine, Joseph; Gough, William A; Kattge, Jens; Tirona, Cairan K F

2018-01-01

Abstract Leaf Economics Spectrum (LES) trait variation underpins multiple agroecological processes and many prominent crop yield models. While there are numerous independent studies assessing trait variation in crops, to date there have been no comprehensive assessments of intraspecific trait variation (ITV) in LES traits for wheat and maize: the world’s most widespread crops. Using trait databases and peer-reviewed literature, we compiled over 700 records of specific leaf area (SLA), maximum photosynthetic rates (Amax) and leaf nitrogen (N) concentrations, for wheat and maize. We evaluated intraspecific LES trait variation, and intraspecific trait–environment relationships. While wheat and maize occupy the upper 90th percentile of LES trait values observed across a global species pool, ITV ranged widely across the LES in wheat and maize. Fertilization treatments had strong impacts on leaf N, while plant developmental stage (here standardized as the number of days since planting) had strong impacts on Amax; days since planting, N fertilization and irrigation all influenced SLA. When controlling for these factors, intraspecific responses to temperature and precipitation explained 39.4 and 43.7 % of the variation in Amax and SLA, respectively, but only 5.4 % of the variation in leaf N. Despite a long history of domestication in these species, ITV in wheat and maize among and within cultivars remains large. Intraspecific trait variation is a critical consideration to refine regional to global models of agroecosystem structure, function and food security. Considerable opportunities and benefits exist for consolidating a crop trait database for a wider range of domesticated plant species. PMID:29484152

Inter- and intraspecific variation in leaf economic traits in wheat and maize.

PubMed

Martin, Adam R; Hale, Christine E; Cerabolini, Bruno E L; Cornelissen, Johannes H C; Craine, Joseph; Gough, William A; Kattge, Jens; Tirona, Cairan K F

2018-02-01

Leaf Economics Spectrum (LES) trait variation underpins multiple agroecological processes and many prominent crop yield models. While there are numerous independent studies assessing trait variation in crops, to date there have been no comprehensive assessments of intraspecific trait variation (ITV) in LES traits for wheat and maize: the world's most widespread crops. Using trait databases and peer-reviewed literature, we compiled over 700 records of specific leaf area (SLA), maximum photosynthetic rates ( A max ) and leaf nitrogen (N) concentrations, for wheat and maize. We evaluated intraspecific LES trait variation, and intraspecific trait-environment relationships. While wheat and maize occupy the upper 90th percentile of LES trait values observed across a global species pool, ITV ranged widely across the LES in wheat and maize. Fertilization treatments had strong impacts on leaf N, while plant developmental stage (here standardized as the number of days since planting) had strong impacts on A max ; days since planting, N fertilization and irrigation all influenced SLA. When controlling for these factors, intraspecific responses to temperature and precipitation explained 39.4 and 43.7 % of the variation in A max and SLA, respectively, but only 5.4 % of the variation in leaf N. Despite a long history of domestication in these species, ITV in wheat and maize among and within cultivars remains large. Intraspecific trait variation is a critical consideration to refine regional to global models of agroecosystem structure, function and food security. Considerable opportunities and benefits exist for consolidating a crop trait database for a wider range of domesticated plant species.

Effects of Fertile Mantle Compositional Variation and Spreading Rate Variation on the Working of Global Ocean Ridges

NASA Astrophysics Data System (ADS)

Niu, Y.; O'Hara, M. J.

2014-12-01

Mantle temperature variation, plate spreading rate variation and mantle compositional variation have been considered to be the three fundamental variables that govern the working of global ocean ridges [1]. An analysis demonstrates that mantle compositional variation exerts the primary control on ocean ridge processes; it determines (1) variation in both composition and mode of mantle mineralogy, (2) variation of mantle density, (3) variation of ridge axial depth, (4) source-inherited MORB compositional variation, (4) density-controlled variation in the amplitude of mantle upwelling, (5) apparent variation in the extent of melting, and (6) the correlated variation of MORB chemistry with ridge axial depth [2]. The above interpretations are reinforced by the updated MORB database [3]. The new database also confirms spreading rate control on the extent of melting as shown previously [4]. Mantle temperature variation could play a part, but its overstated role [3,5] results from a basic error (1) in treating ridge axial depth variation as evidence of mantle temperature variation by ignoring the intrinsic control of mantle composition, (2) in treating "mantle plume" influenced ridges (e.g., Iceland) as normal ridges of plate spreading origin, and (3) in treating low Vs at greater depths (> 300 km vs. < 200 km beneath ridges) beneath these "mantle plume" influenced ridges as evidence for hot ridge mantle. In order to understand the working of global ocean ridges, we must avoid plume-influenced ridges (e.g., in the vicinity of Iceland) and remove/average out data from such ridges. As a result, the correlations (e.g., between ridge axial depth, mantle low Vs anomaly, and some geochemical parameters) required for the interpretation of mantle temperature control all disappear. There is thus no evidence for large mantle temperature variation away from ridges influenced by "mantle plumes". References: [1] Niu et al., 2001, Earth Planet Sci. Lett., 186, 383-399; [2] Niu & O'Hara, 2008, J. Petrol., 49, 633-664; [3] Gale et al., 2014, J. Petrol, 55, 1051-1082; [4] Niu & Hékinian, 1997, Nature, 385, 326-329; [5] Dalton et al., 2014, Science, 334, 80-83; [6]Niu & Hékinian, 2004, In Oceanic Hotspots, Springer-Verlag, 285-307.

PoPoolation DB: a user-friendly web-based database for the retrieval of natural polymorphisms in Drosophila.

PubMed

Pandey, Ram Vinay; Kofler, Robert; Orozco-terWengel, Pablo; Nolte, Viola; Schlötterer, Christian

2011-03-02

The enormous potential of natural variation for the functional characterization of genes has been neglected for a long time. Only since recently, functional geneticists are starting to account for natural variation in their analyses. With the new sequencing technologies it has become feasible to collect sequence information for multiple individuals on a genomic scale. In particular sequencing pooled DNA samples has been shown to provide a cost-effective approach for characterizing variation in natural populations. While a range of software tools have been developed for mapping these reads onto a reference genome and extracting SNPs, linking this information to population genetic estimators and functional information still poses a major challenge to many researchers. We developed PoPoolation DB a user-friendly integrated database. Popoolation DB links variation in natural populations with functional information, allowing a wide range of researchers to take advantage of population genetic data. PoPoolation DB provides the user with population genetic parameters (Watterson's θ or Tajima's π), Tajima's D, SNPs, allele frequencies and indels in regions of interest. The database can be queried by gene name, chromosomal position, or a user-provided query sequence or GTF file. We anticipate that PoPoolation DB will be a highly versatile tool for functional geneticists as well as evolutionary biologists. PoPoolation DB, available at http://www.popoolation.at/pgt, provides an integrated platform for researchers to investigate natural polymorphism and associated functional annotations from UCSC and Flybase genome browsers, population genetic estimators and RNA-seq information.

A Knowledge Database on Thermal Control in Manufacturing Processes

NASA Astrophysics Data System (ADS)

Hirasawa, Shigeki; Satoh, Isao

A prototype version of a knowledge database on thermal control in manufacturing processes, specifically, molding, semiconductor manufacturing, and micro-scale manufacturing has been developed. The knowledge database has search functions for technical data, evaluated benchmark data, academic papers, and patents. The database also displays trends and future roadmaps for research topics. It has quick-calculation functions for basic design. This paper summarizes present research topics and future research on thermal control in manufacturing engineering to collate the information to the knowledge database. In the molding process, the initial mold and melt temperatures are very important parameters. In addition, thermal control is related to many semiconductor processes, and the main parameter is temperature variation in wafers. Accurate in-situ temperature measurment of wafers is important. And many technologies are being developed to manufacture micro-structures. Accordingly, the knowledge database will help further advance these technologies.

Developing an A Priori Database for Passive Microwave Snow Water Retrievals Over Ocean

NASA Astrophysics Data System (ADS)

Yin, Mengtao; Liu, Guosheng

2017-12-01

A physically optimized a priori database is developed for Global Precipitation Measurement Microwave Imager (GMI) snow water retrievals over ocean. The initial snow water content profiles are derived from CloudSat Cloud Profiling Radar (CPR) measurements. A radiative transfer model in which the single-scattering properties of nonspherical snowflakes are based on the discrete dipole approximate results is employed to simulate brightness temperatures and their gradients. Snow water content profiles are then optimized through a one-dimensional variational (1D-Var) method. The standard deviations of the difference between observed and simulated brightness temperatures are in a similar magnitude to the observation errors defined for observation error covariance matrix after the 1D-Var optimization, indicating that this variational method is successful. This optimized database is applied in a Bayesian retrieval snow water algorithm. The retrieval results indicated that the 1D-Var approach has a positive impact on the GMI retrieved snow water content profiles by improving the physical consistency between snow water content profiles and observed brightness temperatures. Global distribution of snow water contents retrieved from the a priori database is compared with CloudSat CPR estimates. Results showed that the two estimates have a similar pattern of global distribution, and the difference of their global means is small. In addition, we investigate the impact of using physical parameters to subset the database on snow water retrievals. It is shown that using total precipitable water to subset the database with 1D-Var optimization is beneficial for snow water retrievals.

Antiepileptic drug use in seven electronic health record databases in Europe: a methodologic comparison.

PubMed

de Groot, Mark C H; Schuerch, Markus; de Vries, Frank; Hesse, Ulrik; Oliva, Belén; Gil, Miguel; Huerta, Consuelo; Requena, Gema; de Abajo, Francisco; Afonso, Ana S; Souverein, Patrick C; Alvarez, Yolanda; Slattery, Jim; Rottenkolber, Marietta; Schmiedl, Sven; Van Dijk, Liset; Schlienger, Raymond G; Reynolds, Robert; Klungel, Olaf H

2014-05-01

The annual prevalence of antiepileptic drug (AED) prescribing reported in the literature differs considerably among European countries due to use of different type of data sources, time periods, population distribution, and methodologic differences. This study aimed to measure prevalence of AED prescribing across seven European routine health care databases in Spain, Denmark, The Netherlands, the United Kingdom, and Germany using a standardized methodology and to investigate sources of variation. Analyses on the annual prevalence of AEDs were stratified by sex, age, and AED. Overall prevalences were standardized to the European 2008 reference population. Prevalence of any AED varied from 88 per 10,000 persons (The Netherlands) to 144 per 10,000 in Spain and Denmark in 2001. In all databases, prevalence increased linearly: from 6% in Denmark to 15% in Spain each year since 2001. This increase could be attributed entirely to an increase in "new," recently marketed AEDs while prevalence of AEDs that have been available since the mid-1990s, hardly changed. AED use increased with age for both female and male patients up to the ages of 80 to 89 years old and tended to be somewhat higher in female than in male patients between the ages of 40 and 70. No differences between databases in the number of AEDs used simultaneously by a patient were found. We showed that during the study period of 2001-2009, AED prescribing increased in five European Union (EU) countries and that this increase was due entirely to the newer AEDs marketed since the 1990s. Using a standardized methodology, we showed consistent trends across databases and countries over time. Differences in age and sex distribution explained only part of the variation between countries. Therefore, remaining variation in AED use must originate from other differences in national health care systems. Wiley Periodicals, Inc. © 2014 International League Against Epilepsy.

Harmonizing the interpretation of genetic variants across the world: the Malaysian experience.

PubMed

Hassan, Nik Norliza Nik; Plazzer, John-Paul; Smith, Timothy D; Halim-Fikri, Hashim; Macrae, Finlay; Zubaidi, A A L; Zilfalil, Bin Alwi

2016-02-26

Databases for gene variants are very useful for sharing genetic data and to facilitate the understanding of the genetic basis of diseases. This report summarises the issues surrounding the development of the Malaysian Human Variome Project Country Node. The focus is on human germline variants. Somatic variants, mitochondrial variants and other types of genetic variation have corresponding databases which are not covered here, as they have specific issues that do not necessarily apply to germline variations. The ethical, legal, social issues, intellectual property, ownership of the data, information technology implementation, and efforts to improve the standards and systems used in data sharing are discussed. An overarching framework such as provided by the Human Variome Project to co-ordinate activities is invaluable. Country Nodes, such as MyHVP, enable human gene variation associated with human diseases to be collected, stored and shared by all disciplines (clinicians, molecular biologists, pathologists, bioinformaticians) for a consistent interpretation of genetic variants locally and across the world.

Variation in the Use of Federal and State Civil Money Penalties for Nursing Homes

ERIC Educational Resources Information Center

Harrington, Charlene; Tsoukalas, Theodore; Rudder, Cynthia; Mollot, Richard J.; Carrillo, Helen

2008-01-01

Purpose: The study examined factors associated with state variations in the use of federal and state civil money penalties (CMPs) for nursing homes. Design and Methods: We collected federal and state CMP data from state survey and certification agencies for 2004. We also used federal CMP data from the federal enforcement action database for…

The Advanced Learner's Sociolinguistic Profile: On Issues of Individual Differences, Second Language Exposure Conditions, and Type of Sociolinguistic Variable

ERIC Educational Resources Information Center

Howard, Martin

2012-01-01

Situated within the recent new wave of second language acquisition studies investigating the acquisition of sociolinguistic variation, this article draws on a longitudinal database of advanced French interlanguage to explore a number of issues that have not yet been extensively investigated. They concern the issue of individual variation in the…

Human phoneme recognition depending on speech-intrinsic variability.

PubMed

Meyer, Bernd T; Jürgens, Tim; Wesker, Thorsten; Brand, Thomas; Kollmeier, Birger

2010-11-01

The influence of different sources of speech-intrinsic variation (speaking rate, effort, style and dialect or accent) on human speech perception was investigated. In listening experiments with 16 listeners, confusions of consonant-vowel-consonant (CVC) and vowel-consonant-vowel (VCV) sounds in speech-weighted noise were analyzed. Experiments were based on the OLLO logatome speech database, which was designed for a man-machine comparison. It contains utterances spoken by 50 speakers from five dialect/accent regions and covers several intrinsic variations. By comparing results depending on intrinsic and extrinsic variations (i.e., different levels of masking noise), the degradation induced by variabilities can be expressed in terms of the SNR. The spectral level distance between the respective speech segment and the long-term spectrum of the masking noise was found to be a good predictor for recognition rates, while phoneme confusions were influenced by the distance to spectrally close phonemes. An analysis based on transmitted information of articulatory features showed that voicing and manner of articulation are comparatively robust cues in the presence of intrinsic variations, whereas the coding of place is more degraded. The database and detailed results have been made available for comparisons between human speech recognition (HSR) and automatic speech recognizers (ASR).

Robust Optical Recognition of Cursive Pashto Script Using Scale, Rotation and Location Invariant Approach

PubMed Central

Ahmad, Riaz; Naz, Saeeda; Afzal, Muhammad Zeshan; Amin, Sayed Hassan; Breuel, Thomas

2015-01-01

The presence of a large number of unique shapes called ligatures in cursive languages, along with variations due to scaling, orientation and location provides one of the most challenging pattern recognition problems. Recognition of the large number of ligatures is often a complicated task in oriental languages such as Pashto, Urdu, Persian and Arabic. Research on cursive script recognition often ignores the fact that scaling, orientation, location and font variations are common in printed cursive text. Therefore, these variations are not included in image databases and in experimental evaluations. This research uncovers challenges faced by Arabic cursive script recognition in a holistic framework by considering Pashto as a test case, because Pashto language has larger alphabet set than Arabic, Persian and Urdu. A database containing 8000 images of 1000 unique ligatures having scaling, orientation and location variations is introduced. In this article, a feature space based on scale invariant feature transform (SIFT) along with a segmentation framework has been proposed for overcoming the above mentioned challenges. The experimental results show a significantly improved performance of proposed scheme over traditional feature extraction techniques such as principal component analysis (PCA). PMID:26368566

Effect of database profile variation on drug safety assessment: an analysis of spontaneous adverse event reports of Japanese cases

PubMed Central

Nomura, Kaori; Takahashi, Kunihiko; Hinomura, Yasushi; Kawaguchi, Genta; Matsushita, Yasuyuki; Marui, Hiroko; Anzai, Tatsuhiko; Hashiguchi, Masayuki; Mochizuki, Mayumi

2015-01-01

Background The use of a statistical approach to analyze cumulative adverse event (AE) reports has been encouraged by regulatory authorities. However, data variations affect statistical analyses (eg, signal detection). Further, differences in regulations, social issues, and health care systems can cause variations in AE data. The present study examined similarities and differences between two publicly available databases, ie, the Japanese Adverse Drug Event Report (JADER) database and the US Food and Drug Administration Adverse Event Reporting System (FAERS), and how they affect signal detection. Methods Two AE data sources from 2010 were examined, ie, JADER cases (JP) and Japanese cases extracted from the FAERS (FAERS-JP). Three methods for signals of disproportionate reporting, ie, the reporting odds ratio, Bayesian confidence propagation neural network, and Gamma Poisson Shrinker (GPS), were used on drug-event combinations for three substances frequently recorded in both systems. Results The two databases showed similar elements of AE reports, but no option was provided for a shareable case identifier. The average number of AEs per case was 1.6±1.3 (maximum 37) in the JP and 3.3±3.5 (maximum 62) in the FAERS-JP. Between 5% and 57% of all AEs were signaled by three quantitative methods for etanercept, infliximab, and paroxetine. Signals identified by GPS for the JP and FAERS-JP, as referenced by Japanese labeling, showed higher positive sensitivity than was expected. Conclusion The FAERS-JP was different from the JADER. Signals derived from both datasets identified different results, but shared certain signals. Discrepancies in type of AEs, drugs reported, and average number of AEs per case were potential contributing factors. This study will help those concerned with pharmacovigilance better understand the use and pitfalls of using spontaneous AE data. PMID:26109846

VCGDB: a dynamic genome database of the Chinese population

PubMed Central

2014-01-01

Background The data released by the 1000 Genomes Project contain an increasing number of genome sequences from different nations and populations with a large number of genetic variations. As a result, the focus of human genome studies is changing from single and static to complex and dynamic. The currently available human reference genome (GRCh37) is based on sequencing data from 13 anonymous Caucasian volunteers, which might limit the scope of genomics, transcriptomics, epigenetics, and genome wide association studies. Description We used the massive amount of sequencing data published by the 1000 Genomes Project Consortium to construct the Virtual Chinese Genome Database (VCGDB), a dynamic genome database of the Chinese population based on the whole genome sequencing data of 194 individuals. VCGDB provides dynamic genomic information, which contains 35 million single nucleotide variations (SNVs), 0.5 million insertions/deletions (indels), and 29 million rare variations, together with genomic annotation information. VCGDB also provides a highly interactive user-friendly virtual Chinese genome browser (VCGBrowser) with functions like seamless zooming and real-time searching. In addition, we have established three population-specific consensus Chinese reference genomes that are compatible with mainstream alignment software. Conclusions VCGDB offers a feasible strategy for processing big data to keep pace with the biological data explosion by providing a robust resource for genomics studies; in particular, studies aimed at finding regions of the genome associated with diseases. PMID:24708222

A population health approach to reducing observational intensity bias in health risk adjustment: cross sectional analysis of insurance claims.

PubMed

Wennberg, David E; Sharp, Sandra M; Bevan, Gwyn; Skinner, Jonathan S; Gottlieb, Daniel J; Wennberg, John E

2014-04-10

To compare the performance of two new approaches to risk adjustment that are free of the influence of observational intensity with methods that depend on diagnoses listed in administrative databases. Administrative data from the US Medicare program for services provided in 2007 among 306 US hospital referral regions. Cross sectional analysis. 20% sample of fee for service Medicare beneficiaries residing in one of 306 hospital referral regions in the United States in 2007 (n = 5,153,877). The effect of health risk adjustment on age, sex, and race adjusted mortality and spending rates among hospital referral regions using four indices: the standard Centers for Medicare and Medicaid Services--Hierarchical Condition Categories (HCC) index used by the US Medicare program (calculated from diagnoses listed in Medicare's administrative database); a visit corrected HCC index (to reduce the effects of observational intensity on frequency of diagnoses); a poverty index (based on US census); and a population health index (calculated using data on incidence of hip fractures and strokes, and responses from a population based annual survey of health from the Centers for Disease Control and Prevention). Estimated variation in age, sex, and race adjusted mortality rates across hospital referral regions was reduced using the indices based on population health, poverty, and visit corrected HCC, but increased using the standard HCC index. Most of the residual variation in age, sex, and race adjusted mortality was explained (in terms of weighted R2) by the population health index: R2=0.65. The other indices explained less: R2=0.20 for the visit corrected HCC index; 0.19 for the poverty index, and 0.02 for the standard HCC index. The residual variation in age, sex, race, and price adjusted spending per capita across the 306 hospital referral regions explained by the indices (in terms of weighted R2) were 0.50 for the standard HCC index, 0.21 for the population health index, 0.12 for the poverty index, and 0.07 for the visit corrected HCC index, implying that only a modest amount of the variation in spending can be explained by factors most closely related to mortality. Further, once the HCC index is visit corrected it accounts for almost none of the residual variation in age, sex, and race adjusted spending. Health risk adjustment using either the poverty index or the population health index performed substantially better in terms of explaining actual mortality than the indices that relied on diagnoses from administrative databases; the population health index explained the majority of residual variation in age, sex, and race adjusted mortality. Owing to the influence of observational intensity on diagnoses from administrative databases, the standard HCC index over-adjusts for regional differences in spending. Research to improve health risk adjustment methods should focus on developing measures of risk that do not depend on observation influenced diagnoses recorded in administrative databases.

Critically evaluated/distributed database of IRAS LRS spectra

NASA Technical Reports Server (NTRS)

Stencel, R. E.

1993-01-01

Accomplishments under this grant effort include: successful scientific utilization of the IRAS Low Resolution Spectrometer (LRS) database of over 150,000 scans of 7-23 micron spectra for over 50,000 celestial sources; publication in refereed journal of an additional 486 critically evaluated spectra of sources brighter than 20 Jy, completing the LRS ATLAS (Olnon and Raimond 1986 A&A) uniformly to that level, and production of an additional 1,830 critically evaluated spectra of sources brighter than 10 Jy; creation and maintenance of on-line, remotely accessible LRS spectra of over 7500 sources; cooperation with Astrophysics Data System personnel for transitioning this LRS database to the ADS access system after funding for this project expires; and publication of research highlights, which include a systematic variation of the shapes of LRS silicate features among stars of differing IRAS broad-band colors, maser characteristics and light curve asymmetries, all correlated with the chemical and physical development and processing of solid phase materials, and preliminary evidence for silicate profile variations in individual stars as a function of visual light curve phase.

sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins.

PubMed

Meslamani, Jamel; Rognan, Didier; Kellenberger, Esther

2011-05-01

The sc-PDB database is an annotated archive of druggable binding sites extracted from the Protein Data Bank. It contains all-atoms coordinates for 8166 protein-ligand complexes, chosen for their geometrical and physico-chemical properties. The sc-PDB provides a functional annotation for proteins, a chemical description for ligands and the detailed intermolecular interactions for complexes. The sc-PDB now includes a hierarchical classification of all the binding sites within a functional class. The sc-PDB entries were first clustered according to the protein name indifferent of the species. For each cluster, we identified dissimilar sites (e.g. catalytic and allosteric sites of an enzyme). SCOPE AND APPLICATIONS: The classification of sc-PDB targets by binding site diversity was intended to facilitate chemogenomics approaches to drug design. In ligand-based approaches, it avoids comparing ligands that do not share the same binding site. In structure-based approaches, it permits to quantitatively evaluate the diversity of the binding site definition (variations in size, sequence and/or structure). The sc-PDB database is freely available at: http://bioinfo-pharma.u-strasbg.fr/scPDB.

LenVarDB: database of length-variant protein domains.

PubMed

Mutt, Eshita; Mathew, Oommen K; Sowdhamini, Ramanathan

2014-01-01

Protein domains are functionally and structurally independent modules, which add to the functional variety of proteins. This array of functional diversity has been enabled by evolutionary changes, such as amino acid substitutions or insertions or deletions, occurring in these protein domains. Length variations (indels) can introduce changes at structural, functional and interaction levels. LenVarDB (freely available at http://caps.ncbs.res.in/lenvardb/) traces these length variations, starting from structure-based sequence alignments in our Protein Alignments organized as Structural Superfamilies (PASS2) database, across 731 structural classification of proteins (SCOP)-based protein domain superfamilies connected to 2 730 625 sequence homologues. Alignment of sequence homologues corresponding to a structural domain is available, starting from a structure-based sequence alignment of the superfamily. Orientation of the length-variant (indel) regions in protein domains can be visualized by mapping them on the structure and on the alignment. Knowledge about location of length variations within protein domains and their visual representation will be useful in predicting changes within structurally or functionally relevant sites, which may ultimately regulate protein function. Non-technical summary: Evolutionary changes bring about natural changes to proteins that may be found in many organisms. Such changes could be reflected as amino acid substitutions or insertions-deletions (indels) in protein sequences. LenVarDB is a database that provides an early overview of observed length variations that were set among 731 protein families and after examining >2 million sequences. Indels are followed up to observe if they are close to the active site such that they can affect the activity of proteins. Inclusion of such information can aid the design of bioengineering experiments.

Epigenetic hereditary transcription profiles III, evidence for an epigenetic network resulting in gender, tissue and age-specific variation in overall transcription

PubMed Central

Simons, Johannes WIM

2009-01-01

Background We have previously shown that deviations from the average transcription profile of a group of functionally related genes are not only heritable, but also demonstrate specific patterns associated with age, gender and differentiation, thereby implicating genome-wide nuclear programming as the cause. To determine whether these results could be reproduced, a different micro-array database (obtained from two types of muscle tissue, derived from 81 human donors aged between 16 to 89 years) was studied. Results This new database also revealed the existence of age, gender and tissue-specific features in a small group of functionally related genes. In order to further analyze this phenomenon, a method was developed for quantifying the contribution of different factors to the variability in gene expression, and for generating a database limited to residual values reflecting constitutional differences between individuals. These constitutional differences, presumably epigenetic in origin, contribute to about 50% of the observed residual variance which is connected with a network of interrelated changes in gene expression with some genes displaying a decrease or increase in residual variation with age. Conclusion Epigenetic variation in gene expression without a clear concomitant relation to gene function appears to be a widespread phenomenon. This variation is connected with interactions between genes, is gender and tissue specific and is related to cellular aging. This finding, together with the method developed for analysis, might contribute to the elucidation of the role of nuclear programming in differentiation, aging and carcinogenesis Reviewers This article was reviewed by Thiago M. Venancio (nominated by Aravind Iyer), Hua Li (nominated by Arcady Mushegian) and Arcady Mushegian and J.P.de Magelhaes (nominated by G. Church). PMID:19796384

The Global Survey Method Applied to Ground-level Cosmic Ray Measurements

NASA Astrophysics Data System (ADS)

Belov, A.; Eroshenko, E.; Yanke, V.; Oleneva, V.; Abunin, A.; Abunina, M.; Papaioannou, A.; Mavromichalaki, H.

2018-04-01

The global survey method (GSM) technique unites simultaneous ground-level observations of cosmic rays in different locations and allows us to obtain the main characteristics of cosmic-ray variations outside of the atmosphere and magnetosphere of Earth. This technique has been developed and applied in numerous studies over many years by the Institute of Terrestrial Magnetism, Ionosphere and Radiowave Propagation (IZMIRAN). We here describe the IZMIRAN version of the GSM in detail. With this technique, the hourly data of the world-wide neutron-monitor network from July 1957 until December 2016 were processed, and further processing is enabled upon the receipt of new data. The result is a database of homogeneous and continuous hourly characteristics of the density variations (an isotropic part of the intensity) and the 3D vector of the cosmic-ray anisotropy. It includes all of the effects that could be identified in galactic cosmic-ray variations that were caused by large-scale disturbances of the interplanetary medium in more than 50 years. These results in turn became the basis for a database on Forbush effects and interplanetary disturbances. This database allows correlating various space-environment parameters (the characteristics of the Sun, the solar wind, et cetera) with cosmic-ray parameters and studying their interrelations. We also present features of the coupling coefficients for different neutron monitors that enable us to make a connection from ground-level measurements to primary cosmic-ray variations outside the atmosphere and the magnetosphere. We discuss the strengths and weaknesses of the current version of the GSM as well as further possible developments and improvements. The method developed allows us to minimize the problems of the neutron-monitor network, which are typical for experimental physics, and to considerably enhance its advantages.

Seasonal Variations in the Risk of Reoperation for Surgical Site Infection Following Elective Spinal Fusion Surgery: A Retrospective Study Using the Japanese Diagnosis Procedure Combination Database.

PubMed

Ohya, Junichi; Chikuda, Hirotaka; Oichi, Takeshi; Kato, So; Matsui, Hiroki; Horiguchi, Hiromasa; Tanaka, Sakae; Yasunaga, Hideo

2017-07-15

A retrospective study of data abstracted from the Diagnosis Procedure Combination (DPC) database, a national representative database in Japan. The aim of this study was to examine seasonal variations in the risk of reoperation for surgical site infection (SSI) following spinal fusion surgery. Although higher rates of infection in the summer than in other seasons were thought to be caused by increasing inexperience of new staff, high temperature, and high humidity, no studies have examined seasonal variations in the risk of SSI following spinal fusion surgery in the country where medical staff rotation timing is not in summer season. In Japan, medical staff rotation starts in April. We retrospectively extracted the data of patients who were admitted between July 2010 and March 2013 from the DPC database. Patients were included if they were aged 20 years or older and underwent elective spinal fusion surgery. The primary outcome was reoperation for SSI during hospitalization. We performed multivariate analysis to clarify the risk factors of primary outcome with adjustment for patient background characteristics. We identified 47,252 eligible patients (23,659 male, 23,593 female). The mean age of the patients was 65.4 years (range, 20-101 yrs). Overall, reoperation for SSI occurred in 0.93% of the patients during hospitalization. The risk of reoperation for SSI was significantly higher in April (vs. February; odds ratio, 1.93; 95% confidence interval, 1.09-3.43, P = 0.03) as well as other known risk factors. In subgroup analysis with stratification for type of hospital, month of surgery was identified as an independent risk factor of reoperation for SSI among cases in an academic hospital, although there was no seasonal variation among those in a nonacademic hospital. This study showed that month of surgery is a risk factor of reoperation for SSI following elective spinal fusion surgery, nevertheless, in the country where medical staff rotation timing is not in summer season. 3.

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

PubMed Central

Pruitt, Kim D.; Tatusova, Tatiana; Maglott, Donna R.

2005-01-01

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff. PMID:15608248

A Statistical Model of the Fluctuations in the Geomagnetic Field from Paleosecular Variation to Reversal

PubMed

Camps; Prevot

1996-08-09

The statistical characteristics of the local magnetic field of Earth during paleosecular variation, excursions, and reversals are described on the basis of a database that gathers the cleaned mean direction and average remanent intensity of 2741 lava flows that have erupted over the last 20 million years. A model consisting of a normally distributed axial dipole component plus an independent isotropic set of vectors with a Maxwellian distribution that simulates secular variation fits the range of geomagnetic fluctuations, in terms of both direction and intensity. This result suggests that the magnitude of secular variation vectors is independent of the magnitude of Earth's axial dipole moment and that the amplitude of secular variation is unchanged during reversals.

Mass Spectra-Based Framework for Automated Structural Elucidation of Metabolome Data to Explore Phytochemical Diversity

PubMed Central

Matsuda, Fumio; Nakabayashi, Ryo; Sawada, Yuji; Suzuki, Makoto; Hirai, Masami Y.; Kanaya, Shigehiko; Saito, Kazuki

2011-01-01

A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method. PMID:22645535

Development of the Orion Crew Module Static Aerodynamic Database. Par 2; Supersonic/Subsonic

NASA Technical Reports Server (NTRS)

Bibb, Karen L.; Walker, Eric L.; Brauckmann, Gregory J.; Robinson, Phil

2011-01-01

This work describes the process of developing the nominal static aerodynamic coefficients and associated uncertainties for the Orion Crew Module for Mach 8 and below. The database was developed from wind tunnel test data and computational simulations of the smooth Crew Module geometry, with no asymmetries or protuberances. The database covers the full range of Reynolds numbers seen in both entry and ascent abort scenarios. The basic uncertainties were developed as functions of Mach number and total angle of attack from variations in the primary data as well as computations at lower Reynolds numbers, on the baseline geometry, and using different flow solvers. The resulting aerodynamic database represents the Crew Exploration Vehicle Aerosciences Project's best estimate of the nominal aerodynamics for the current Crew Module vehicle.

Practical guidelines addressing ethical issues pertaining to the curation of human locus-specific variation databases (LSDBs)

PubMed Central

Povey, Sue; Al Aqeel, Aida I; Cambon-Thomsen, Anne; Dalgleish, Raymond; den Dunnen, Johan T; Firth, Helen V; Greenblatt, Marc S; Barash, Carol Isaacson; Parker, Michael; Patrinos, George P; Savige, Judith; Sobrido, Maria-Jesus; Winship, Ingrid; Cotton, Richard GH

2010-01-01

More than 1,000 Web-based locus-specific variation databases (LSDBs) are listed on the Website of the Human Genetic Variation Society (HGVS). These individual efforts, which often relate phenotype to genotype, are a valuable source of information for clinicians, patients, and their families, as well as for basic research. The initiators of the Human Variome Project recently recognized that having access to some of the immense resources of unpublished information already present in diagnostic laboratories would provide critical data to help manage genetic disorders. However, there are significant ethical issues involved in sharing these data worldwide. An international working group presents second-generation guidelines addressing ethical issues relating to the curation of human LSDBs that provide information via a Web-based interface. It is intended that these should help current and future curators and may also inform the future decisions of ethics committees and legislators. These guidelines have been reviewed by the Ethics Committee of the Human Genome Organization (HUGO). Hum Mutat 31:–6, 2010. © 2010 Wiley-Liss, Inc. PMID:20683926

Tracking and recognition face in videos with incremental local sparse representation model

NASA Astrophysics Data System (ADS)

Wang, Chao; Wang, Yunhong; Zhang, Zhaoxiang

2013-10-01

This paper addresses the problem of tracking and recognizing faces via incremental local sparse representation. First a robust face tracking algorithm is proposed via employing local sparse appearance and covariance pooling method. In the following face recognition stage, with the employment of a novel template update strategy, which combines incremental subspace learning, our recognition algorithm adapts the template to appearance changes and reduces the influence of occlusion and illumination variation. This leads to a robust video-based face tracking and recognition with desirable performance. In the experiments, we test the quality of face recognition in real-world noisy videos on YouTube database, which includes 47 celebrities. Our proposed method produces a high face recognition rate at 95% of all videos. The proposed face tracking and recognition algorithms are also tested on a set of noisy videos under heavy occlusion and illumination variation. The tracking results on challenging benchmark videos demonstrate that the proposed tracking algorithm performs favorably against several state-of-the-art methods. In the case of the challenging dataset in which faces undergo occlusion and illumination variation, and tracking and recognition experiments under significant pose variation on the University of California, San Diego (Honda/UCSD) database, our proposed method also consistently demonstrates a high recognition rate.

Rebelling for a Reason: Protein Structural “Outliers”

PubMed Central

Arumugam, Gandhimathi; Nair, Anu G.; Hariharaputran, Sridhar; Ramanathan, Sowdhamini

2013-01-01

Analysis of structural variation in domain superfamilies can reveal constraints in protein evolution which aids protein structure prediction and classification. Structure-based sequence alignment of distantly related proteins, organized in PASS2 database, provides clues about structurally conserved regions among different functional families. Some superfamily members show large structural differences which are functionally relevant. This paper analyses the impact of structural divergence on function for multi-member superfamilies, selected from the PASS2 superfamily alignment database. Functional annotations within superfamilies, with structural outliers or ‘rebels’, are discussed in the context of structural variations. Overall, these data reinforce the idea that functional similarities cannot be extrapolated from mere structural conservation. The implication for fold-function prediction is that the functional annotations can only be inherited with very careful consideration, especially at low sequence identities. PMID:24073209

Emotion-independent face recognition

NASA Astrophysics Data System (ADS)

De Silva, Liyanage C.; Esther, Kho G. P.

2000-12-01

Current face recognition techniques tend to work well when recognizing faces under small variations in lighting, facial expression and pose, but deteriorate under more extreme conditions. In this paper, a face recognition system to recognize faces of known individuals, despite variations in facial expression due to different emotions, is developed. The eigenface approach is used for feature extraction. Classification methods include Euclidean distance, back propagation neural network and generalized regression neural network. These methods yield 100% recognition accuracy when the training database is representative, containing one image representing the peak expression for each emotion of each person apart from the neutral expression. The feature vectors used for comparison in the Euclidean distance method and for training the neural network must be all the feature vectors of the training set. These results are obtained for a face database consisting of only four persons.

Improving the Automatic Inversion of Digital Alouette/ISIS Ionogram Reflection Traces into Topside Electron Density Profiles

NASA Technical Reports Server (NTRS)

Benson, Robert F.; Truhlik, Vladimir; Huang, Xueqin; Wang, Yongli; Bilitza, Dieter

2012-01-01

The topside sounders of the International Satellites for Ionospheric Studies (ISIS) program were designed as analog systems. The resulting ionograms were displayed on 35 mm film for analysis by visual inspection. Each of these satellites, launched between 1962 and 1971, produced data for 10 to 20 years. A number of the original telemetry tapes from this large data set have been converted directly into digital records. Software, known as the Topside Ionogram Scalar With True-Height (TOPIST) algorithm, has been produced and used for the automatic inversion of the ionogram reflection traces on more than 100,000 ISIS-2 digital topside ionograms into topside vertical electron density profiles Ne(h). Here we present some topside ionospheric solar cycle variations deduced from the TOPIST database to illustrate the scientific benefit of improving and expanding the topside ionospheric Ne(h) database. The profile improvements will be based on improvements in the TOPIST software motivated by direct comparisons between TOPIST profiles and profiles produced by manual scaling in the early days of the ISIS program. The database expansion will be based on new software designed to overcome limitations in the original digital topside ionogram database caused by difficulties encountered during the analog-to-digital conversion process in the detection of the ionogram frame sync pulse and/or the frequency markers. This improved and expanded TOPIST topside Ne(h) database will greatly enhance investigations into both short- and long-term ionospheric changes, e.g., the observed topside ionospheric responses to magnetic storms, induced by interplanetary magnetic clouds, and solar cycle variations, respectively.

Multi-stream face recognition for crime-fighting

NASA Astrophysics Data System (ADS)

Jassim, Sabah A.; Sellahewa, Harin

2007-04-01

Automatic face recognition (AFR) is a challenging task that is increasingly becoming the preferred biometric trait for identification and has the potential of becoming an essential tool in the fight against crime and terrorism. Closed-circuit television (CCTV) cameras have increasingly been used over the last few years for surveillance in public places such as airports, train stations and shopping centers. They are used to detect and prevent crime, shoplifting, public disorder and terrorism. The work of law-enforcing and intelligence agencies is becoming more reliant on the use of databases of biometric data for large section of the population. Face is one of the most natural biometric traits that can be used for identification and surveillance. However, variations in lighting conditions, facial expressions, face size and pose are a great obstacle to AFR. This paper is concerned with using waveletbased face recognition schemes in the presence of variations of expressions and illumination. In particular, we will investigate the use of a combination of wavelet frequency channels for a multi-stream face recognition using various wavelet subbands as different face signal streams. The proposed schemes extend our recently developed face veri.cation scheme for implementation on mobile devices. We shall present experimental results on the performance of our proposed schemes for a number of face databases including a new AV database recorded on a PDA. By analyzing the various experimental data, we shall demonstrate that the multi-stream approach is robust against variations in illumination and facial expressions than the previous single-stream approach.

ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins

PubMed Central

Krassowski, Michal; Paczkowska, Marta; Cullion, Kim; Huang, Tina; Dzneladze, Irakli; Ouellette, B F Francis; Yamada, Joseph T; Fradet-Turcotte, Amelie

2018-01-01

Abstract Interpretation of genetic variation is needed for deciphering genotype-phenotype associations, mechanisms of inherited disease, and cancer driver mutations. Millions of single nucleotide variants (SNVs) in human genomes are known and thousands are associated with disease. An estimated 21% of disease-associated amino acid substitutions corresponding to missense SNVs are located in protein sites of post-translational modifications (PTMs), chemical modifications of amino acids that extend protein function. ActiveDriverDB is a comprehensive human proteo-genomics database that annotates disease mutations and population variants through the lens of PTMs. We integrated >385,000 published PTM sites with ∼3.6 million substitutions from The Cancer Genome Atlas (TCGA), the ClinVar database of disease genes, and human genome sequencing projects. The database includes site-specific interaction networks of proteins, upstream enzymes such as kinases, and drugs targeting these enzymes. We also predicted network-rewiring impact of mutations by analyzing gains and losses of kinase-bound sequence motifs. ActiveDriverDB provides detailed visualization, filtering, browsing and searching options for studying PTM-associated mutations. Users can upload mutation datasets interactively and use our application programming interface in pipelines. Integrative analysis of mutations and PTMs may help decipher molecular mechanisms of phenotypes and disease, as exemplified by case studies of TP53, BRCA2 and VHL. The open-source database is available at https://www.ActiveDriverDB.org. PMID:29126202

Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement

PubMed Central

Govindaraj, Mahalingam

2015-01-01

The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away. PMID:25874133

Relational-database model for improving quality assurance and process control in a composite manufacturing environment

NASA Astrophysics Data System (ADS)

Gentry, Jeffery D.

2000-05-01

A relational database is a powerful tool for collecting and analyzing the vast amounts of inner-related data associated with the manufacture of composite materials. A relational database contains many individual database tables that store data that are related in some fashion. Manufacturing process variables as well as quality assurance measurements can be collected and stored in database tables indexed according to lot numbers, part type or individual serial numbers. Relationships between manufacturing process and product quality can then be correlated over a wide range of product types and process variations. This paper presents details on how relational databases are used to collect, store, and analyze process variables and quality assurance data associated with the manufacture of advanced composite materials. Important considerations are covered including how the various types of data are organized and how relationships between the data are defined. Employing relational database techniques to establish correlative relationships between process variables and quality assurance measurements is then explored. Finally, the benefits of database techniques such as data warehousing, data mining and web based client/server architectures are discussed in the context of composite material manufacturing.

A population health approach to reducing observational intensity bias in health risk adjustment: cross sectional analysis of insurance claims

PubMed Central

Sharp, Sandra M; Bevan, Gwyn; Skinner, Jonathan S; Gottlieb, Daniel J

2014-01-01

Objective To compare the performance of two new approaches to risk adjustment that are free of the influence of observational intensity with methods that depend on diagnoses listed in administrative databases. Setting Administrative data from the US Medicare program for services provided in 2007 among 306 US hospital referral regions. Design Cross sectional analysis. Participants 20% sample of fee for service Medicare beneficiaries residing in one of 306 hospital referral regions in the United States in 2007 (n=5 153 877). Main outcome measures The effect of health risk adjustment on age, sex, and race adjusted mortality and spending rates among hospital referral regions using four indices: the standard Centers for Medicare and Medicaid Services—Hierarchical Condition Categories (HCC) index used by the US Medicare program (calculated from diagnoses listed in Medicare’s administrative database); a visit corrected HCC index (to reduce the effects of observational intensity on frequency of diagnoses); a poverty index (based on US census); and a population health index (calculated using data on incidence of hip fractures and strokes, and responses from a population based annual survey of health from the Centers for Disease Control and Prevention). Results Estimated variation in age, sex, and race adjusted mortality rates across hospital referral regions was reduced using the indices based on population health, poverty, and visit corrected HCC, but increased using the standard HCC index. Most of the residual variation in age, sex, and race adjusted mortality was explained (in terms of weighted R2) by the population health index: R2=0.65. The other indices explained less: R2=0.20 for the visit corrected HCC index; 0.19 for the poverty index, and 0.02 for the standard HCC index. The residual variation in age, sex, race, and price adjusted spending per capita across the 306 hospital referral regions explained by the indices (in terms of weighted R2) were 0.50 for the standard HCC index, 0.21 for the population health index, 0.12 for the poverty index, and 0.07 for the visit corrected HCC index, implying that only a modest amount of the variation in spending can be explained by factors most closely related to mortality. Further, once the HCC index is visit corrected it accounts for almost none of the residual variation in age, sex, and race adjusted spending. Conclusion Health risk adjustment using either the poverty index or the population health index performed substantially better in terms of explaining actual mortality than the indices that relied on diagnoses from administrative databases; the population health index explained the majority of residual variation in age, sex, and race adjusted mortality. Owing to the influence of observational intensity on diagnoses from administrative databases, the standard HCC index over-adjusts for regional differences in spending. Research to improve health risk adjustment methods should focus on developing measures of risk that do not depend on observation influenced diagnoses recorded in administrative databases. PMID:24721838

Cordova: Web-based management of genetic variation data

PubMed Central

Ephraim, Sean S.; Anand, Nikhil; DeLuca, Adam P.; Taylor, Kyle R.; Kolbe, Diana L.; Simpson, Allen C.; Azaiez, Hela; Sloan, Christina M.; Shearer, A. Eliot; Hallier, Andrea R.; Casavant, Thomas L.; Scheetz, Todd E.; Smith, Richard J. H.; Braun, Terry A.

2014-01-01

Summary: Cordova is an out-of-the-box solution for building and maintaining an online database of genetic variations integrated with pathogenicity prediction results from popular algorithms. Our primary motivation for developing this system is to aid researchers and clinician–scientists in determining the clinical significance of genetic variations. To achieve this goal, Cordova provides an interface to review and manually or computationally curate genetic variation data as well as share it for clinical diagnostics and the advancement of research. Availability and implementation: Cordova is open source under the MIT license and is freely available for download at https://github.com/clcg/cordova. Contact: sean.ephraim@gmail.com or terry-braun@uiowa.edu PMID:25123904

Geographic variations in involuntary care and associations with the supply of health and social care: results from a nationwide study.

PubMed

Gandré, Coralie; Gervaix, Jeanne; Thillard, Julien; Macé, Jean-Marc; Roelandt, Jean-Luc; Chevreul, Karine

2018-04-06

Involuntary psychiatric care remains controversial. Geographic disparities in its use can challenge the appropriateness of the care provided when they do not result from different health needs of the population. These disparities should be reduced through dedicated health policies. However, their association with the supply of health and social care, which could be targeted by such policies, has been insufficiently studied. Our objectives were therefore to describe geographic variations in involuntary admission rates across France and to identify the characteristics of the supply of care which were associated with these variations. Involuntary admission rate per 100,000 adult inhabitants was calculated in French psychiatric sectors' catchment areas using 2012 data from the national psychiatric discharge database. Its variations were first described numerically and graphically. Several factors potentially associated with these variations were then considered in a negative binomial regression with an offset term accounting for the size of catchment areas. They included characteristics of the supply of care (public and private care, health and social care, hospital and community-based care, specialised and non-specialised care) as well as adjustment factors related to epidemiological characteristics of the population of each sector's catchment area and its level of urbanization. Such variables were extracted from complementary administrative databases. Supply characteristics associated with geographic variations were identified using a significance level of 0.05. Significant variations in involuntary admission rates were observed between psychiatric sectors' catchment areas with a coefficient of variation close to 80%. These variations were associated with some characteristics of the supply of health and social care in the sectors' catchment areas. Notably, an increase in the availability of community-based private psychiatrists and the capacity of housing institutions for disabled individuals was associated with a decrease in involuntary admission rates while an increase in the availability of general practitioners was associated with an increase in those rates. There is evidence of considerable variations in involuntary admission rates between psychiatric sectors' catchment areas. Our results provide lines of thoughts to reduce such variations, in particular by supporting an increase in the availability of upstream and downstream care in the community.

How to explain variations in sea cliff erosion rate?

NASA Astrophysics Data System (ADS)

Prémaillon, Melody; Regard, Vincent; Dewez, Thomas

2017-04-01

Every rocky coast of the world is eroding at different rate (cliff retreat rates). Erosion is caused by a complex interaction of multiple sea weather factors. While numerous local studies exist and explain erosion processes on specific sites, global studies lack. We started to compile many of those local studies and analyse their results with a global point of view in order to quantify the various parameters influencing erosion rates. In other words: is erosion more important in energetic seas? Are chalk cliff eroding faster in rainy environment? etc. In order to do this, we built a database based on literature and national erosion databases. It now contains 80 publications which represents 2500 cliffs studied and more than 3500 erosion rate estimates. A statistical analysis was conducted on this database. On a first approximation, cliff lithology is the only clear signal explaining erosion rate variation: hard lithologies are eroding at 1cm/y or less, whereas unconsolidated lithologies commonly erode faster than 10cm/y. No clear statistical relation were found between erosion rate and external parameters such as sea energy (swell, tide) or weather condition, even on cliff with similar lithology.

Korean Variant Archive (KOVA): a reference database of genetic variations in the Korean population.

PubMed

Lee, Sangmoon; Seo, Jihae; Park, Jinman; Nam, Jae-Yong; Choi, Ahyoung; Ignatius, Jason S; Bjornson, Robert D; Chae, Jong-Hee; Jang, In-Jin; Lee, Sanghyuk; Park, Woong-Yang; Baek, Daehyun; Choi, Murim

2017-06-27

Despite efforts to interrogate human genome variation through large-scale databases, systematic preference toward populations of Caucasian descendants has resulted in unintended reduction of power in studying non-Caucasians. Here we report a compilation of coding variants from 1,055 healthy Korean individuals (KOVA; Korean Variant Archive). The samples were sequenced to a mean depth of 75x, yielding 101 singleton variants per individual. Population genetics analysis demonstrates that the Korean population is a distinct ethnic group comparable to other discrete ethnic groups in Africa and Europe, providing a rationale for such independent genomic datasets. Indeed, KOVA conferred 22.8% increased variant filtering power in addition to Exome Aggregation Consortium (ExAC) when used on Korean exomes. Functional assessment of nonsynonymous variant supported the presence of purifying selection in Koreans. Analysis of copy number variants detected 5.2 deletions and 10.3 amplifications per individual with an increased fraction of novel variants among smaller and rarer copy number variable segments. We also report a list of germline variants that are associated with increased tumor susceptibility. This catalog can function as a critical addition to the pre-existing variant databases in pursuing genetic studies of Korean individuals.

The BIG Data Center: from deposition to integration to translation

PubMed Central

2017-01-01

Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn. PMID:27899658

A review on quantum search algorithms

NASA Astrophysics Data System (ADS)

Giri, Pulak Ranjan; Korepin, Vladimir E.

2017-12-01

The use of superposition of states in quantum computation, known as quantum parallelism, has significant advantage in terms of speed over the classical computation. It is evident from the early invented quantum algorithms such as Deutsch's algorithm, Deutsch-Jozsa algorithm and its variation as Bernstein-Vazirani algorithm, Simon algorithm, Shor's algorithms, etc. Quantum parallelism also significantly speeds up the database search algorithm, which is important in computer science because it comes as a subroutine in many important algorithms. Quantum database search of Grover achieves the task of finding the target element in an unsorted database in a time quadratically faster than the classical computer. We review Grover's quantum search algorithms for a singe and multiple target elements in a database. The partial search algorithm of Grover and Radhakrishnan and its optimization by Korepin called GRK algorithm are also discussed.

Challenges to the Standardization of Burn Data Collection: A Call for Common Data Elements for Burn Care.

PubMed

Schneider, Jeffrey C; Chen, Liang; Simko, Laura C; Warren, Katherine N; Nguyen, Brian Phu; Thorpe, Catherine R; Jeng, James C; Hickerson, William L; Kazis, Lewis E; Ryan, Colleen M

2018-02-20

The use of common data elements (CDEs) is growing in medical research; CDEs have demonstrated benefit in maximizing the impact of existing research infrastructure and funding. However, the field of burn care does not have a standard set of CDEs. The objective of this study is to examine the extent of common data collected in current burn databases.This study examines the data dictionaries of six U.S. burn databases to ascertain the extent of common data. This was assessed from a quantitative and qualitative perspective. Thirty-two demographic and clinical data elements were examined. The number of databases that collect each data element was calculated. The data values for each data element were compared across the six databases for common terminology. Finally, the data prompts of the data elements were examined for common language and structure.Five (16%) of the 32 data elements are collected by all six burn databases; additionally, five data elements (16%) are present in only one database. Furthermore, there are considerable variations in data values and prompts used among the burn databases. Only one of the 32 data elements (age) contains the same data values across all databases.The burn databases examined show minimal evidence of common data. There is a need to develop CDEs and standardized coding to enhance interoperability of burn databases.

Wavelet filtered shifted phase-encoded joint transform correlation for face recognition

NASA Astrophysics Data System (ADS)

Moniruzzaman, Md.; Alam, Mohammad S.

2017-05-01

A new wavelet-filtered-based Shifted- phase-encoded Joint Transform Correlation (WPJTC) technique has been proposed for efficient face recognition. The proposed technique uses discrete wavelet decomposition for preprocessing and can effectively accommodate various 3D facial distortions, effects of noise, and illumination variations. After analyzing different forms of wavelet basis functions, an optimal method has been proposed by considering the discrimination capability and processing speed as performance trade-offs. The proposed technique yields better correlation discrimination compared to alternate pattern recognition techniques such as phase-shifted phase-encoded fringe-adjusted joint transform correlator. The performance of the proposed WPJTC has been tested using the Yale facial database and extended Yale facial database under different environments such as illumination variation, noise, and 3D changes in facial expressions. Test results show that the proposed WPJTC yields better performance compared to alternate JTC based face recognition techniques.

Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

PubMed Central

Viennas, Emmanouil; Komianou, Angeliki; Mizzi, Clint; Stojiljkovic, Maja; Mitropoulou, Christina; Muilu, Juha; Vihinen, Mauno; Grypioti, Panagiota; Papadaki, Styliani; Pavlidis, Cristiana; Zukic, Branka; Katsila, Theodora; van der Spek, Peter J.; Pavlovic, Sonja; Tzimas, Giannis; Patrinos, George P.

2017-01-01

FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnic mutation databases, all built around Microsoft's PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The abovementioned updates further enhance the impact of FINDbase, as a key resource for Genomic Medicine applications. PMID:27924022

Genomic Sequence Variation Markup Language (GSVML).

PubMed

Nakaya, Jun; Kimura, Michio; Hiroi, Kaei; Ido, Keisuke; Yang, Woosung; Tanaka, Hiroshi

2010-02-01

With the aim of making good use of internationally accumulated genomic sequence variation data, which is increasing rapidly due to the explosive amount of genomic research at present, the development of an interoperable data exchange format and its international standardization are necessary. Genomic Sequence Variation Markup Language (GSVML) will focus on genomic sequence variation data and human health applications, such as gene based medicine or pharmacogenomics. We developed GSVML through eight steps, based on case analysis and domain investigations. By focusing on the design scope to human health applications and genomic sequence variation, we attempted to eliminate ambiguity and to ensure practicability. We intended to satisfy the requirements derived from the use case analysis of human-based clinical genomic applications. Based on database investigations, we attempted to minimize the redundancy of the data format, while maximizing the data covering range. We also attempted to ensure communication and interface ability with other Markup Languages, for exchange of omics data among various omics researchers or facilities. The interface ability with developing clinical standards, such as the Health Level Seven Genotype Information model, was analyzed. We developed the human health-oriented GSVML comprising variation data, direct annotation, and indirect annotation categories; the variation data category is required, while the direct and indirect annotation categories are optional. The annotation categories contain omics and clinical information, and have internal relationships. For designing, we examined 6 cases for three criteria as human health application and 15 data elements for three criteria as data formats for genomic sequence variation data exchange. The data format of five international SNP databases and six Markup Languages and the interface ability to the Health Level Seven Genotype Model in terms of 317 items were investigated. GSVML was developed as a potential data exchanging format for genomic sequence variation data exchange focusing on human health applications. The international standardization of GSVML is necessary, and is currently underway. GSVML can be applied to enhance the utilization of genomic sequence variation data worldwide by providing a communicable platform between clinical and research applications. Copyright 2009 Elsevier Ireland Ltd. All rights reserved.

Expanding the Range of Plant Functional Diversity Represented in Global Vegetation Models: Towards Lineage-based Plant Functional Types

NASA Astrophysics Data System (ADS)

Still, C. J.; Griffith, D.; Edwards, E.; Forrestel, E.; Lehmann, C.; Anderson, M.; Craine, J.; Pau, S.; Osborne, C.

2014-12-01

Variation in plant species traits, such as photosynthetic and hydraulic properties, can indicate vulnerability or resilience to climate change, and feed back to broad-scale spatial and temporal patterns in biogeochemistry, demographics, and biogeography. Yet, predicting how vegetation will respond to future environmental changes is severely limited by the inability of our models to represent species-level trait variation in processes and properties, as current generation process-based models are mostly based on the generalized and abstracted concept of plant functional types (PFTs) which were originally developed for hydrological modeling. For example, there are close to 11,000 grass species, but most vegetation models have only a single C4 grass and one or two C3 grass PFTs. However, while species trait databases are expanding rapidly, they have been produced mostly from unstructured research, with a focus on easily researched traits that are not necessarily the most important for determining plant function. Additionally, implementing realistic species-level trait variation in models is challenging. Combining related and ecologically similar species in these models might ameliorate this limitation. Here we argue for an intermediate, lineage-based approach to PFTs, which draws upon recent advances in gene sequencing and phylogenetic modeling, and where trait complex variations and anatomical features are constrained by a shared evolutionary history. We provide an example of this approach with grass lineages that vary in photosynthetic pathway (C3 or C4) and other functional and structural traits. We use machine learning approaches and geospatial databases to infer the most important environmental controls and climate niche variation for the distribution of grass lineages, and utilize a rapidly expanding grass trait database to demonstrate examples of lineage-based grass PFTs. For example, grasses in the Andropogoneae are typically tall species that dominate wet and seasonally burned ecosystems, whereas Chloridoideae grasses are associated with semi-arid regions. These two C4 lineages are expected to respond quite differently to climate change, but are often modelled as a single PFT.

Extending Glacier Monitoring into the Little Ice Age and Beyond

NASA Astrophysics Data System (ADS)

Nussbaumer, S. U.; Gärtner-Roer, I.; Zemp, M.; Zumbühl, H. J.; Masiokas, M. H.; Espizua, L. E.; Pitte, P.

2011-12-01

Glaciers are among the best natural proxies of climatic changes and, as such, a key variable within the international climate observing system. The worldwide monitoring of glacier distribution and fluctuations has been internationally coordinated for more than a century. Direct measurements of seasonal and annual glacier mass balance are available for the past six decades. Regular observations of glacier front variations have been carried out since the late 19th century. Information on glacier fluctuations before the onset of regular in situ measurements have to be reconstructed from moraines, historical evidence, and a wide range of dating methods. The majority of corresponding data is not available to the scientific community which challenges the reproducibility and direct comparison of the results. Here, we present a first approach towards the standardization of reconstructed Holocene glacier front variations as well as the integration of the corresponding data series into the database of the World Glacier Monitoring Service (www.wgms.ch), within the framework of the Global Terrestrial Network for Glaciers (www.gtn-g.org). The concept for the integration of these reconstructed front variations into the relational glacier database of the WGMS was jointly elaborated and tested by experts of both fields (natural and historical sciences), based on reconstruction series of 15 glaciers in Europe (western/central Alps and southern Norway) and 9 in southern South America. The reconstructed front variation series extend the direct measurements of the 20th century by two centuries in Norway and by four in the Alps and in South America. The storage of the records within the international glacier databases guarantees the long-term availability of the data series and increases the visibility of the scientific research which - in historical glaciology - is often the work of a lifetime. The standardized collection of reconstructed glacier front variations from southern Norway, the western Alps and the southern Andes allows a direct comparison between different glaciers. It is a first step towards a worldwide compilation and free dissemination of Holocene glacier fluctuation series within the internationally coordinated glacier monitoring.

The Basel Face Database: A validated set of photographs reflecting systematic differences in Big Two and Big Five personality dimensions

PubMed Central

Schönborn, Sandro; Greifeneder, Rainer; Vetter, Thomas

2018-01-01

Upon a first encounter, individuals spontaneously associate faces with certain personality dimensions. Such first impressions can strongly impact judgments and decisions and may prove highly consequential. Researchers investigating the impact of facial information often rely on (a) real photographs that have been selected to vary on the dimension of interest, (b) morphed photographs, or (c) computer-generated faces (avatars). All three approaches have distinct advantages. Here we present the Basel Face Database, which combines these advantages. In particular, the Basel Face Database consists of real photographs that are subtly, but systematically manipulated to show variations in the perception of the Big Two and the Big Five personality dimensions. To this end, the information specific to each psychological dimension is isolated and modeled in new photographs. Two studies serve as systematic validation of the Basel Face Database. The Basel Face Database opens a new pathway for researchers across psychological disciplines to investigate effects of perceived personality. PMID:29590124

The Basel Face Database: A validated set of photographs reflecting systematic differences in Big Two and Big Five personality dimensions.

PubMed

Walker, Mirella; Schönborn, Sandro; Greifeneder, Rainer; Vetter, Thomas

2018-01-01

Upon a first encounter, individuals spontaneously associate faces with certain personality dimensions. Such first impressions can strongly impact judgments and decisions and may prove highly consequential. Researchers investigating the impact of facial information often rely on (a) real photographs that have been selected to vary on the dimension of interest, (b) morphed photographs, or (c) computer-generated faces (avatars). All three approaches have distinct advantages. Here we present the Basel Face Database, which combines these advantages. In particular, the Basel Face Database consists of real photographs that are subtly, but systematically manipulated to show variations in the perception of the Big Two and the Big Five personality dimensions. To this end, the information specific to each psychological dimension is isolated and modeled in new photographs. Two studies serve as systematic validation of the Basel Face Database. The Basel Face Database opens a new pathway for researchers across psychological disciplines to investigate effects of perceived personality.

Feedforward object-vision models only tolerate small image variations compared to human

PubMed Central

Ghodrati, Masoud; Farzmahdi, Amirhossein; Rajaei, Karim; Ebrahimpour, Reza; Khaligh-Razavi, Seyed-Mahdi

2014-01-01

Invariant object recognition is a remarkable ability of primates' visual system that its underlying mechanism has constantly been under intense investigations. Computational modeling is a valuable tool toward understanding the processes involved in invariant object recognition. Although recent computational models have shown outstanding performances on challenging image databases, they fail to perform well in image categorization under more complex image variations. Studies have shown that making sparse representation of objects by extracting more informative visual features through a feedforward sweep can lead to higher recognition performances. Here, however, we show that when the complexity of image variations is high, even this approach results in poor performance compared to humans. To assess the performance of models and humans in invariant object recognition tasks, we built a parametrically controlled image database consisting of several object categories varied in different dimensions and levels, rendered from 3D planes. Comparing the performance of several object recognition models with human observers shows that only in low-level image variations the models perform similar to humans in categorization tasks. Furthermore, the results of our behavioral experiments demonstrate that, even under difficult experimental conditions (i.e., briefly presented masked stimuli with complex image variations), human observers performed outstandingly well, suggesting that the models are still far from resembling humans in invariant object recognition. Taken together, we suggest that learning sparse informative visual features, although desirable, is not a complete solution for future progresses in object-vision modeling. We show that this approach is not of significant help in solving the computational crux of object recognition (i.e., invariant object recognition) when the identity-preserving image variations become more complex. PMID:25100986

The National Eutrophication Survey: lake characteristics and historical nutrient concentrations

NASA Astrophysics Data System (ADS)

Stachelek, Joseph; Ford, Chanse; Kincaid, Dustin; King, Katelyn; Miller, Heather; Nagelkirk, Ryan

2018-01-01

Historical ecological surveys serve as a baseline and provide context for contemporary research, yet many of these records are not preserved in a way that ensures their long-term usability. The National Eutrophication Survey (NES) database is currently only available as scans of the original reports (PDF files) with no embedded character information. This limits its searchability, machine readability, and the ability of current and future scientists to systematically evaluate its contents. The NES data were collected by the US Environmental Protection Agency between 1972 and 1975 as part of an effort to investigate eutrophication in freshwater lakes and reservoirs. Although several studies have manually transcribed small portions of the database in support of specific studies, there have been no systematic attempts to transcribe and preserve the database in its entirety. Here we use a combination of automated optical character recognition and manual quality assurance procedures to make these data available for analysis. The performance of the optical character recognition protocol was found to be linked to variation in the quality (clarity) of the original documents. For each of the four archival scanned reports, our quality assurance protocol found an error rate between 5.9 and 17 %. The goal of our approach was to strike a balance between efficiency and data quality by combining entry of data by hand with digital transcription technologies. The finished database contains information on the physical characteristics, hydrology, and water quality of about 800 lakes in the contiguous US (Stachelek et al.(2017), https://doi.org/10.5063/F1639MVD). Ultimately, this database could be combined with more recent studies to generate meta-analyses of water quality trends and spatial variation across the continental US.

Updating the French archeomagnetic directional database for the past two millennia

NASA Astrophysics Data System (ADS)

Le Goff, M.; Warmé, N.; Gallet, Y.; Genevey, A.

2009-04-01

Research in archeomagnetism began in France during the 1930's with the pioneering work of Emile Thellier. Combining instrumental and methodological developments, together with the patient establishment of a collaboration with archeologists, Thellier's activity led to the construction of the first directional secular variation curve in France spanning the past two millennia. After Thellier's retirement, Ileana Bucur continued this work, enriching the French archeomagnetic database up to more than 200 directional data, among which 120 dated results were used to construct in 1994 a revised version of the French directional secular variation curve, which is still considered as a reference today. Since 1994, the acquisition of archeomagnetic directional data has been continuously pursued at IPGP and the present study aims to update the French archeomagnetic dataset for the past two millennia. We have sampled about 400 burned structures from more than sixty different archeological sites mostly located near Paris, in the Ile-de-France region. Domestic kilns here represent approximately 2/3 of those structures, which were found in ancient agricultural settlements generally dated to the High Middle Ages. More than one hundred structures were dated using archeological constraints, such as the typo-morphology of ceramics, coins or archives, with enough precision and accuracy to be considered for improving the French reference directional secular variation curve over the past two millennia. We will discuss the present status of the French archeomagnetic directional database, which thus contains more than 600 data, 90% of which are defined with an a95 of less than 2°. We will also illustrate its increasingly potential as a dating tool for archeological purposes.

POLICY VARIATION, LABOR SUPPLY ELASTICITIES, AND A STRUCTURAL MODEL OF RETIREMENT

PubMed Central

MANOLI, DAY; MULLEN, KATHLEEN J.; WAGNER, MATHIS

2015-01-01

This paper exploits a combination of policy variation from multiple pension reforms in Austria and administrative data from the Austrian Social Security Database. Using the policy changes for identification, we estimate social security wealth and accrual elasticities in individuals’ retirement decisions. Next, we use these elasticities to estimate a dynamic programming model of retirement decisions. Finally, we use the estimated model to examine the labor supply and welfare consequences of potential social security reforms. PMID:26472916

An Overview of Genomic Sequence Variation Markup Language (GSVML)

PubMed Central

Nakaya, Jun; Hiroi, Kaei; Ido, Keisuke; Yang, Woosung; Kimura, Michio

2006-01-01

Internationally accumulated genomic sequence variation data on human requires the interoperable data exchanging format. We developed the GSVML as the data exchanging format. The GSVML is human health oriented and has three categories. Analyses on the use case in human health domain and the investigation on the databases and markup languages were conducted. An interface ability to Health Level Seven Genotype Model was examined. GSVML provides a sharable platform for both clinical and research applications.

DNA barcode reference data for the Korean herpetofauna and their applications.

PubMed

Jeong, Tae Jin; Jun, Jumin; Han, Sanghoon; Kim, Hyun Tae; Oh, Kyunghee; Kwak, Myounghai

2013-11-01

Recently, amphibians and reptiles have drawn attention because of declines in species and populations caused mainly by habitat loss, overexploitation and climate change. This study constructed a DNA barcode database for the Korean herpetofauna, including all the recorded amphibians and 68% of the recorded reptiles, to provide a useful, standardized tool for species identification in monitoring and management. A total of 103 individuals from 18 amphibian and 17 reptile species were used to generate barcode sequences using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and to compare it with other suggested barcode loci. Comparing 16S rRNA, cytochrome b (Cytb) and COI for amphibians and 12S rRNA, Cytb and COI for reptiles, our results revealed that COI is better than the other markers in terms of a high level of sequence variation without length variation and moderate amplification success. Although the COI marker had no clear barcoding gap because of the high level of intraspecific variation, all of the analysed individuals from the same species clustered together in a neighbour-joining tree. High intraspecific variation suggests the possibility of cryptic species. Finally, using this database, confiscated snakes were identified as Elaphe schrenckii, designated as endangered in Korea and a food contaminant was identified as the lizard Takydromus amurensis. © 2013 John Wiley & Sons Ltd.

Mitochondrial DNA haplogroup variation of contemporary mixed South Americans reveals prehistoric displacements linked to archaeologically-derived culture history.

PubMed

Rothhammer, Francisco; Fehren-Schmitz, Lars; Puddu, Giannina; Capriles, José

2017-11-01

The purpose of this study was to examine South American population structure and prehistoric population displacements prior to the Spanish conquest, utilizing mitochondrial DNA haplogroups of extant mixed populations from Mexico, Costa Rica, Venezuela, Colombia, Ecuador, Peru, Bolivia, Brazil, Argentina, and Chile. Relative frequencies of four pan-American haplogroups, obtained from published databases, were analyzed to evaluate patterns of variations, population structure and possible prehistoric migration pathways. Patterns of mtDNA variation verify biogeographic drift processes and possible migratory pathways. We propose an updated model of South American colonization that is fully compatible with previous studies based on autosomal, mtDNA, and Y chromosome variation and with archaeologically-derived culture history. © 2017 Wiley Periodicals, Inc.

Cordova: web-based management of genetic variation data.

PubMed

Ephraim, Sean S; Anand, Nikhil; DeLuca, Adam P; Taylor, Kyle R; Kolbe, Diana L; Simpson, Allen C; Azaiez, Hela; Sloan, Christina M; Shearer, A Eliot; Hallier, Andrea R; Casavant, Thomas L; Scheetz, Todd E; Smith, Richard J H; Braun, Terry A

2014-12-01

Cordova is an out-of-the-box solution for building and maintaining an online database of genetic variations integrated with pathogenicity prediction results from popular algorithms. Our primary motivation for developing this system is to aid researchers and clinician-scientists in determining the clinical significance of genetic variations. To achieve this goal, Cordova provides an interface to review and manually or computationally curate genetic variation data as well as share it for clinical diagnostics and the advancement of research. Cordova is open source under the MIT license and is freely available for download at https://github.com/clcg/cordova. Published by Oxford University Press. This work is written by US Government employees and is in the public domain in the US.

The Main Anatomic Variations of the Hepatic Artery and Their Importance in Surgical Practice: Review of the Literature.

PubMed

Noussios, George; Dimitriou, Ioannis; Chatzis, Iosif; Katsourakis, Anastasios

2017-04-01

Anatomical variations of the hepatic artery are important in the planning and performance of abdominal surgical procedures. Normal hepatic anatomy occurs in approximately 80% of cases, for the remaining 20% multiple variations have been described. The purpose of this study was to review the existing literature on the hepatic anatomy and to stress out its importance in surgical practice. Two main databases were searched for eligible articles during the period 2000 - 2015, and results concerning more than 19,000 patients were included in the study. The most common variation was the replaced right hepatic artery (type III according to Michels classification) which is the chief source of blood supply to the bile duct.

Building a database for long-term monitoring of benthic macrofauna in the Pertuis-Charentais (2004-2014).

PubMed

Philippe, Anne S; Plumejeaud-Perreau, Christine; Jourde, Jérôme; Pineau, Philippe; Lachaussée, Nicolas; Joyeux, Emmanuel; Corre, Frédéric; Delaporte, Philippe; Bocher, Pierrick

2017-01-01

Long-term benthic monitoring is rewarding in terms of science, but labour-intensive, whether in the field, the laboratory, or behind the computer. Building and managing databases require multiple skills, including consistency over time as well as organisation via a systematic approach. Here, we introduce and share our spatially explicit benthic database, comprising 11 years of benthic data. It is the result of intensive benthic sampling that has been conducted on a regular grid (259 stations) covering the intertidal mudflats of the Pertuis-Charentais (Marennes-Oléron Bay and Aiguillon Bay). Samples were taken by foot or by boats during winter depending on tidal height, from December 2003 to February 2014. The present dataset includes abundances and biomass densities of all mollusc species of the study regions and principal polychaetes as well as their length, accessibility to shorebirds, energy content and shell mass when appropriate and available. This database has supported many studies dealing with the spatial distribution of benthic invertebrates and temporal variations in food resources for shorebird species as well as latitudinal comparisons with other databases. In this paper, we introduce our benthos monitoring, share our data, and present a "guide of good practices" for building, cleaning and using it efficiently, providing examples of results with associated R code. The dataset has been formatted into a geo-referenced relational database, using PostgreSQL open-source DBMS. We provide density information, measurements, energy content and accessibility of thirteen bivalve, nine gastropod and two polychaete taxa (a total of 66,620 individuals)​ for 11 consecutive winters. Figures and maps are provided to describe how the dataset was built, cleaned, and how it can be used. This dataset can again support studies concerning spatial and temporal variations in species abundance, interspecific interactions as well as evaluations of the availability of food resources for small- and medium size shorebirds and, potentially, conservation and impact assessment studies.

X-Linked and Autosomal Recessive Alport Syndrome: Pathogenic Variant Features and Further Genotype-Phenotype Correlations

PubMed Central

Savige, Judith; Storey, Helen; Il Cheong, Hae; Gyung Kang, Hee; Park, Eujin; Hilbert, Pascale; Persikov, Anton; Torres-Fernandez, Carmen; Ars, Elisabet; Torra, Roser; Hertz, Jens Michael; Thomassen, Mads; Shagam, Lev; Wang, Dongmao; Wang, Yanyan; Flinter, Frances; Nagel, Mato

2016-01-01

Alport syndrome results from mutations in the COL4A5 (X-linked) or COL4A3/COL4A4 (recessive) genes. This study examined 754 previously- unpublished variants in these genes from individuals referred for genetic testing in 12 accredited diagnostic laboratories worldwide, in addition to all published COL4A5, COL4A3 and COL4A4 variants in the LOVD databases. It also determined genotype-phenotype correlations for variants where clinical data were available. Individuals were referred for genetic testing where Alport syndrome was suspected clinically or on biopsy (renal failure, hearing loss, retinopathy, lamellated glomerular basement membrane), variant pathogenicity was assessed using currently-accepted criteria, and variants were examined for gene location, and age at renal failure onset. Results were compared using Fisher’s exact test (DNA Stata). Altogether 754 new DNA variants were identified, an increase of 25%, predominantly in people of European background. Of the 1168 COL4A5 variants, 504 (43%) were missense mutations, 273 (23%) splicing variants, 73 (6%) nonsense mutations, 169 (14%) short deletions and 76 (7%) complex or large deletions. Only 135 of the 432 Gly residues in the collagenous sequence were substituted (31%), which means that fewer than 10% of all possible variants have been identified. Both missense and nonsense mutations in COL4A5 were not randomly distributed but more common at the 70 CpG sequences (p<10−41 and p<0.001 respectively). Gly>Ala substitutions were underrepresented in all three genes (p< 0.0001) probably because of an association with a milder phenotype. The average age at end-stage renal failure was the same for all mutations in COL4A5 (24.4 ±7.8 years), COL4A3 (23.3 ± 9.3) and COL4A4 (25.4 ± 10.3) (COL4A5 and COL4A3, p = 0.45; COL4A5 and COL4A4, p = 0.55; COL4A3 and COL4A4, p = 0.41). For COL4A5, renal failure occurred sooner with non-missense than missense variants (p<0.01). For the COL4A3 and COL4A4 genes, age at renal failure occurred sooner with two non-missense variants (p = 0.08, and p = 0.01 respectively). Thus DNA variant characteristics that predict age at renal failure appeared to be the same for all three Alport genes. Founder mutations (with the pathogenic variant in at least 5 apparently- unrelated individuals) were not necessarily associated with a milder phenotype. This study illustrates the benefits when routine diagnostic laboratories share and analyse their data. PMID:27627812

X-Linked and Autosomal Recessive Alport Syndrome: Pathogenic Variant Features and Further Genotype-Phenotype Correlations.

PubMed

Savige, Judith; Storey, Helen; Il Cheong, Hae; Gyung Kang, Hee; Park, Eujin; Hilbert, Pascale; Persikov, Anton; Torres-Fernandez, Carmen; Ars, Elisabet; Torra, Roser; Hertz, Jens Michael; Thomassen, Mads; Shagam, Lev; Wang, Dongmao; Wang, Yanyan; Flinter, Frances; Nagel, Mato

2016-01-01

Alport syndrome results from mutations in the COL4A5 (X-linked) or COL4A3/COL4A4 (recessive) genes. This study examined 754 previously- unpublished variants in these genes from individuals referred for genetic testing in 12 accredited diagnostic laboratories worldwide, in addition to all published COL4A5, COL4A3 and COL4A4 variants in the LOVD databases. It also determined genotype-phenotype correlations for variants where clinical data were available. Individuals were referred for genetic testing where Alport syndrome was suspected clinically or on biopsy (renal failure, hearing loss, retinopathy, lamellated glomerular basement membrane), variant pathogenicity was assessed using currently-accepted criteria, and variants were examined for gene location, and age at renal failure onset. Results were compared using Fisher's exact test (DNA Stata). Altogether 754 new DNA variants were identified, an increase of 25%, predominantly in people of European background. Of the 1168 COL4A5 variants, 504 (43%) were missense mutations, 273 (23%) splicing variants, 73 (6%) nonsense mutations, 169 (14%) short deletions and 76 (7%) complex or large deletions. Only 135 of the 432 Gly residues in the collagenous sequence were substituted (31%), which means that fewer than 10% of all possible variants have been identified. Both missense and nonsense mutations in COL4A5 were not randomly distributed but more common at the 70 CpG sequences (p<10-41 and p<0.001 respectively). Gly>Ala substitutions were underrepresented in all three genes (p< 0.0001) probably because of an association with a milder phenotype. The average age at end-stage renal failure was the same for all mutations in COL4A5 (24.4 ±7.8 years), COL4A3 (23.3 ± 9.3) and COL4A4 (25.4 ± 10.3) (COL4A5 and COL4A3, p = 0.45; COL4A5 and COL4A4, p = 0.55; COL4A3 and COL4A4, p = 0.41). For COL4A5, renal failure occurred sooner with non-missense than missense variants (p<0.01). For the COL4A3 and COL4A4 genes, age at renal failure occurred sooner with two non-missense variants (p = 0.08, and p = 0.01 respectively). Thus DNA variant characteristics that predict age at renal failure appeared to be the same for all three Alport genes. Founder mutations (with the pathogenic variant in at least 5 apparently- unrelated individuals) were not necessarily associated with a milder phenotype. This study illustrates the benefits when routine diagnostic laboratories share and analyse their data.

Database Resources of the BIG Data Center in 2018

PubMed Central

Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

2018-01-01

Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

Health Information-Seeking Patterns of the General Public and Indications for Disease Surveillance: Register-Based Study Using Lyme Disease.

PubMed

Pesälä, Samuli; Virtanen, Mikko J; Sane, Jussi; Mustonen, Pekka; Kaila, Minna; Helve, Otto

2017-11-06

People using the Internet to find information on health issues, such as specific diseases, usually start their search from a general search engine, for example, Google. Internet searches such as these may yield results and data of questionable quality and reliability. Health Library is a free-of-charge medical portal on the Internet providing medical information for the general public. Physician's Databases, an Internet evidence-based medicine source, provides medical information for health care professionals (HCPs) to support their clinical practice. Both databases are available throughout Finland, but the latter is used only by health professionals and pharmacies. Little is known about how the general public seeks medical information from medical sources on the Internet, how this behavior differs from HCPs' queries, and what causes possible differences in behavior. The aim of our study was to evaluate how the general public's and HCPs' information-seeking trends from Internet medical databases differ seasonally and temporally. In addition, we aimed to evaluate whether the general public's information-seeking trends could be utilized for disease surveillance and whether media coverage could affect these seeking trends. Lyme disease, serving as a well-defined disease model with distinct seasonal variation, was chosen as a case study. Two Internet medical databases, Health Library and Physician's Databases, were used. We compared the general public's article openings on Lyme disease from Health Library to HCPs' article openings on Lyme disease from Physician's Databases seasonally across Finland from 2011 to 2015. Additionally, media publications related to Lyme disease were searched from the largest and most popular media websites in Finland. Both databases, Health Library and Physician's Databases, show visually similar patterns in temporal variations of article openings on Lyme disease in Finland from 2011 to 2015. However, Health Library openings show not only an increasing trend over time but also greater fluctuations, especially during peak opening seasons. Outside these seasons, publications in the media coincide with Health Library article openings only occasionally. Lyme disease-related information-seeking behaviors between the general public and HCPs from Internet medical portals share similar temporal variations, which is consistent with the trend seen in epidemiological data. Therefore, the general public's article openings could be used as a supplementary source of information for disease surveillance. The fluctuations in article openings appeared stronger among the general public, thus, suggesting that different factors such as media coverage, affect the information-seeking behaviors of the public versus professionals. However, media coverage may also have an influence on HCPs. Not every publication was associated with an increase in openings, but the higher the media coverage by some publications, the higher the general public's access to Health Library. ©Samuli Pesälä, Mikko J Virtanen, Jussi Sane, Pekka Mustonen, Minna Kaila, Otto Helve. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 06.11.2017.

Health Information–Seeking Patterns of the General Public and Indications for Disease Surveillance: Register-Based Study Using Lyme Disease

PubMed Central

Virtanen, Mikko J; Sane, Jussi; Mustonen, Pekka; Kaila, Minna; Helve, Otto

2017-01-01

Background People using the Internet to find information on health issues, such as specific diseases, usually start their search from a general search engine, for example, Google. Internet searches such as these may yield results and data of questionable quality and reliability. Health Library is a free-of-charge medical portal on the Internet providing medical information for the general public. Physician’s Databases, an Internet evidence-based medicine source, provides medical information for health care professionals (HCPs) to support their clinical practice. Both databases are available throughout Finland, but the latter is used only by health professionals and pharmacies. Little is known about how the general public seeks medical information from medical sources on the Internet, how this behavior differs from HCPs’ queries, and what causes possible differences in behavior. Objective The aim of our study was to evaluate how the general public’s and HCPs’ information-seeking trends from Internet medical databases differ seasonally and temporally. In addition, we aimed to evaluate whether the general public’s information-seeking trends could be utilized for disease surveillance and whether media coverage could affect these seeking trends. Methods Lyme disease, serving as a well-defined disease model with distinct seasonal variation, was chosen as a case study. Two Internet medical databases, Health Library and Physician’s Databases, were used. We compared the general public’s article openings on Lyme disease from Health Library to HCPs’ article openings on Lyme disease from Physician’s Databases seasonally across Finland from 2011 to 2015. Additionally, media publications related to Lyme disease were searched from the largest and most popular media websites in Finland. Results Both databases, Health Library and Physician’s Databases, show visually similar patterns in temporal variations of article openings on Lyme disease in Finland from 2011 to 2015. However, Health Library openings show not only an increasing trend over time but also greater fluctuations, especially during peak opening seasons. Outside these seasons, publications in the media coincide with Health Library article openings only occasionally. Conclusions Lyme disease–related information-seeking behaviors between the general public and HCPs from Internet medical portals share similar temporal variations, which is consistent with the trend seen in epidemiological data. Therefore, the general public’s article openings could be used as a supplementary source of information for disease surveillance. The fluctuations in article openings appeared stronger among the general public, thus, suggesting that different factors such as media coverage, affect the information-seeking behaviors of the public versus professionals. However, media coverage may also have an influence on HCPs. Not every publication was associated with an increase in openings, but the higher the media coverage by some publications, the higher the general public’s access to Health Library. PMID:29109071

Seasonal variation of fecal indicator bacteria in storm events within the US stormwater database.

PubMed

Pan, Xubin; Jones, Kim D

2012-01-01

Bacteria are one of the major causes of surface water impairments in the USA. Over the past several years, best management practices, including detention basins, manufactured devices, grass swales, filters and bioretention cells have been used to remove bacteria and other pollutants from stormwater runoff. However, there are data gaps in the comprehensive studies of bacteria concentrations in stormwater runoff. In this paper, the event mean concentration (EMC) of fecal indicator bacteria (Enterococcus, Escherichia coli, fecal Streptococcus group bacteria, and fecal coliform) across the USA was retrieved from the international stormwater best management practices database to analyze the seasonal variations of inflow and outflow event mean concentrations and removal efficiencies. The Kruskal-Wallis test was employed to determine the seasonal variations of bacteria indicator concentrations and removals, and the two-sample Kolmogorov-Smirnov test was used for comparing different seasonal outcomes. The results indicate that all the inflow EMC of FIB in stormwater runoff is above the water quality criteria. The seasonal differences of fecal Streptococcus group bacteria and fecal coliform are significant. Summer has the potential to increase the bacteria EMC and illustrate the seasonal differences.

Radiobiological Implications of Fukushima Nuclear Accident for Personalized Medical Approach.

PubMed

Fukunaga, Hisanori; Yokoya, Akinari; Taki, Yasuyuki; Prise, Kevin M

2017-05-01

On March 11, 2011, a devastating earthquake and subsequent tsunami caused serious damage to areas of the Pacific coast in Fukushima prefecture and prompted fears among the residents about a possible meltdown of the Fukushima Daiichi Nuclear Power Plant reactors. As of 2017, over six years have passed since the Fukushima nuclear crisis and yet the full ramifications of the biological exposures to this accidental release of radioactive substances remain unclear. Furthermore, although several genetic studies have determined that the variation in radiation sensitivity among different individuals is wider than expected, personalized medical approaches for Fukushima victims have seemed to be insufficient. In this commentary, we discuss radiobiological issues arising from low-dose radiation exposure, from the cell-based to the population level. We also introduce the scientific utility of the Integrative Japanese Genome Variation Database (iJGVD), an online database released by the Tohoku Medical Megabank Organization, Tohoku University that covered the whole genome sequences of 2,049 healthy individuals in the northeastern part of Japan in 2016. Here we propose a personalized radiation risk assessment and medical approach, which considers the genetic variation of radiation sensitivity among individuals, for next-step developments in radiological protection.

BioQ: tracing experimental origins in public genomic databases using a novel data provenance model.

PubMed

Saccone, Scott F; Quan, Jiaxi; Jones, Peter L

2012-04-15

Public genomic databases, which are often used to guide genetic studies of human disease, are now being applied to genomic medicine through in silico integrative genomics. These databases, however, often lack tools for systematically determining the experimental origins of the data. We introduce a new data provenance model that we have implemented in a public web application, BioQ, for assessing the reliability of the data by systematically tracing its experimental origins to the original subjects and biologics. BioQ allows investigators to both visualize data provenance as well as explore individual elements of experimental process flow using precise tools for detailed data exploration and documentation. It includes a number of human genetic variation databases such as the HapMap and 1000 Genomes projects. BioQ is freely available to the public at http://bioq.saclab.net.

Application of cytochrome b DNA sequences for the authentication of endangered snake species.

PubMed

Wong, Ka-Lok; Wang, Jun; But, Paul Pui-Hay; Shaw, Pang-Chui

2004-01-06

In order to enforce the conservation program and curbing the illegal trading and consumption of endangered snake species, the value of cytochrome b sequence in the authentication of snake species was evaluated. As an illustration, DNA was extracted, selected cytochrome b DNA sequences amplified and sequenced from six snakes commonly consumed in Hong Kong. Cataloging with sequences available in public, a cytochrome b database containing 90 species of snakes was constructed. In this database, sequence homology between snakes ranged from 70.68 to 95.11%. On the other hand, intraspecific variation of three tested snakes was 0-0.98%. Using the database, we were able to determine the identity of six meat samples confiscated by the Agriculture, Fisheries and Conservation Department, HKSAR.

Prices For Common Medical Services Vary Substantially Among The Commercially Insured.

PubMed

Newman, David; Parente, Stephen T; Barrette, Eric; Kennedy, Kevin

2016-05-01

Using a national multipayer commercial claims database containing allowed amounts, we examined variations in the prices for 242 common medical services in forty-one states and the District of Columbia. Ratios of average state prices to national prices ranged from a low of 0.79 in Florida to a high of 2.64 in Alaska. Two- to threefold variations in prices were identified within some states and Metropolitan Statistical Areas. Project HOPE—The People-to-People Health Foundation, Inc.

Differentiation of several interstitial lung disease patterns in HRCT images using support vector machine: role of databases on performance

NASA Astrophysics Data System (ADS)

Kale, Mandar; Mukhopadhyay, Sudipta; Dash, Jatindra K.; Garg, Mandeep; Khandelwal, Niranjan

2016-03-01

Interstitial lung disease (ILD) is complicated group of pulmonary disorders. High Resolution Computed Tomography (HRCT) considered to be best imaging technique for analysis of different pulmonary disorders. HRCT findings can be categorised in several patterns viz. Consolidation, Emphysema, Ground Glass Opacity, Nodular, Normal etc. based on their texture like appearance. Clinician often find it difficult to diagnosis these pattern because of their complex nature. In such scenario computer-aided diagnosis system could help clinician to identify patterns. Several approaches had been proposed for classification of ILD patterns. This includes computation of textural feature and training /testing of classifier such as artificial neural network (ANN), support vector machine (SVM) etc. In this paper, wavelet features are calculated from two different ILD database, publically available MedGIFT ILD database and private ILD database, followed by performance evaluation of ANN and SVM classifiers in terms of average accuracy. It is found that average classification accuracy by SVM is greater than ANN where trained and tested on same database. Investigation continued further to test variation in accuracy of classifier when training and testing is performed with alternate database and training and testing of classifier with database formed by merging samples from same class from two individual databases. The average classification accuracy drops when two independent databases used for training and testing respectively. There is significant improvement in average accuracy when classifiers are trained and tested with merged database. It infers dependency of classification accuracy on training data. It is observed that SVM outperforms ANN when same database is used for training and testing.

Population and forensic genetic analyses of mitochondrial DNA control region variation from six major provinces in the Korean population.

PubMed

Hong, Seung Beom; Kim, Ki Cheol; Kim, Wook

2015-07-01

We generated complete mitochondrial DNA (mtDNA) control region sequences from 704 unrelated individuals residing in six major provinces in Korea. In addition to our earlier survey of the distribution of mtDNA haplogroup variation, a total of 560 different haplotypes characterized by 271 polymorphic sites were identified, of which 473 haplotypes were unique. The gene diversity and random match probability were 0.9989 and 0.0025, respectively. According to the pairwise comparison of the 704 control region sequences, the mean number of pairwise differences between individuals was 13.47±6.06. Based on the result of mtDNA control region sequences, pairwise FST genetic distances revealed genetic homogeneity of the Korean provinces on a peninsular level, except in samples from Jeju Island. This result indicates there may be a need to formulate a local mtDNA database for Jeju Island, to avoid bias in forensic parameter estimates caused by genetic heterogeneity of the population. Thus, the present data may help not only in personal identification but also in determining maternal lineages to provide an expanded and reliable Korean mtDNA database. These data will be available on the EMPOP database via accession number EMP00661. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

The BIG Data Center: from deposition to integration to translation.

PubMed

2017-01-04

Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Main Anatomical Variations of the Pancreatic Duct System: Review of the Literature and Its Importance in Surgical Practice.

PubMed

Dimitriou, Ioannis; Katsourakis, Anastasios; Nikolaidou, Eirini; Noussios, George

2018-05-01

Anatomical variations or anomalies of the pancreatic ducts are important in the planning and performance of endoscopic retrograde cholangiopancreatography (ERCP) and surgical procedures of the pancreas. Normal pancreatic duct anatomy occurs in approximately 94.3% of cases, and multiple variations have been described for the remaining 5.7%. The purpose of this study was to review the literature on the pancreatic duct anatomy and to underline its importance in daily invasive endoscopic and surgical practice. Two main databases were searched for suitable articles published from 2000 to 2017, and results concerning more than 8,200 patients were included in the review. The most common anatomical variation was that of pancreas divisum, which appeared in approximately 4.5% of cases.

aCGH-MAS: Analysis of aCGH by means of Multiagent System

PubMed Central

Benito, Rocío; Bajo, Javier; Rodríguez, Ana Eugenia; Abáigar, María

2015-01-01

There are currently different techniques, such as CGH arrays, to study genetic variations in patients. CGH arrays analyze gains and losses in different regions in the chromosome. Regions with gains or losses in pathologies are important for selecting relevant genes or CNVs (copy-number variations) associated with the variations detected within chromosomes. Information corresponding to mutations, genes, proteins, variations, CNVs, and diseases can be found in different databases and it would be of interest to incorporate information of different sources to extract relevant information. This work proposes a multiagent system to manage the information of aCGH arrays, with the aim of providing an intuitive and extensible system to analyze and interpret the results. The agent roles integrate statistical techniques to select relevant variations and visualization techniques for the interpretation of the final results and to extract relevant information from different sources of information by applying a CBR system. PMID:25874203

RICD: a rice indica cDNA database resource for rice functional genomics.

PubMed

Lu, Tingting; Huang, Xuehui; Zhu, Chuanrang; Huang, Tao; Zhao, Qiang; Xie, Kabing; Xiong, Lizhong; Zhang, Qifa; Han, Bin

2008-11-26

The Oryza sativa L. indica subspecies is the most widely cultivated rice. During the last few years, we have collected over 20,000 putative full-length cDNAs and over 40,000 ESTs isolated from various cDNA libraries of two indica varieties Guangluai 4 and Minghui 63. A database of the rice indica cDNAs was therefore built to provide a comprehensive web data source for searching and retrieving the indica cDNA clones. Rice Indica cDNA Database (RICD) is an online MySQL-PHP driven database with a user-friendly web interface. It allows investigators to query the cDNA clones by keyword, genome position, nucleotide or protein sequence, and putative function. It also provides a series of information, including sequences, protein domain annotations, similarity search results, SNPs and InDels information, and hyperlinks to gene annotation in both The Rice Annotation Project Database (RAP-DB) and The TIGR Rice Genome Annotation Resource, expression atlas in RiceGE and variation report in Gramene of each cDNA. The online rice indica cDNA database provides cDNA resource with comprehensive information to researchers for functional analysis of indica subspecies and for comparative genomics. The RICD database is available through our website http://www.ncgr.ac.cn/ricd.

HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server.

PubMed

Hardison, Ross C; Chui, David H K; Giardine, Belinda; Riemer, Cathy; Patrinos, George P; Anagnou, Nicholas; Miller, Webb; Wajcman, Henri

2002-03-01

We have constructed a relational database of hemoglobin variants and thalassemia mutations, called HbVar, which can be accessed on the web at http://globin.cse.psu.edu. Extensive information is recorded for each variant and mutation, including a description of the variant and associated pathology, hematology, electrophoretic mobility, methods of isolation, stability information, ethnic occurrence, structure studies, functional studies, and references. The initial information was derived from books by Dr. Titus Huisman and colleagues [Huisman et al., 1996, 1997, 1998]. The current database is updated regularly with the addition of new data and corrections to previous data. Queries can be formulated based on fields in the database. Tables of common categories of variants, such as all those involving the alpha1-globin gene (HBA1) or all those that result in high oxygen affinity, are maintained by automated queries on the database. Users can formulate more precise queries, such as identifying "all beta-globin variants associated with instability and found in Scottish populations." This new database should be useful for clinical diagnosis as well as in fundamental studies of hemoglobin biochemistry, globin gene regulation, and human sequence variation at these loci. Copyright 2002 Wiley-Liss, Inc.

A comparison of database systems for XML-type data.

PubMed

Risse, Judith E; Leunissen, Jack A M

2010-01-01

In the field of bioinformatics interchangeable data formats based on XML are widely used. XML-type data is also at the core of most web services. With the increasing amount of data stored in XML comes the need for storing and accessing the data. In this paper we analyse the suitability of different database systems for storing and querying large datasets in general and Medline in particular. All reviewed database systems perform well when tested with small to medium sized datasets, however when the full Medline dataset is queried a large variation in query times is observed. There is not one system that is vastly superior to the others in this comparison and, depending on the database size and the query requirements, different systems are most suitable. The best all-round solution is the Oracle 11~g database system using the new binary storage option. Alias-i's Lingpipe is a more lightweight, customizable and sufficiently fast solution. It does however require more initial configuration steps. For data with a changing XML structure Sedna and BaseX as native XML database systems or MySQL with an XML-type column are suitable.

Risks associated with clinical databases.

PubMed

Eleazar, P Y

1991-11-01

Providers will succeed who are evaluating themselves, and who are continuously striving to examine who they are and where they are going. Conscientious providers know that countless other agencies have them under the microscope and that they have to work to stay ahead in assessing their actions through their clinical database. "Medical care value purchasing" is what every employer and payor is looking for, and providers need to find ways to illustrate cost in relation to quality. The basics of data security and protection should be in place in order to concentrate on the bigger picture. The knowledge of the risk associated with individual hospital databases as well as the risk associated with comparative databases is critical. The hospital-level clinical database is the hub of the wheel. If the risk there can be minimized, the data headed for various investigative sites will have less inherent risk. When it is really recognized and accepted that all financial decisions are made based upon the clinical data generated at the site of care, then data integrity will become a strategic advantage for the industry. Clinical database goals will, over time, cause minimization of risk at all levels. As this occurs, variation in treatment will be explained artfully.

SIDD: A Semantically Integrated Database towards a Global View of Human Disease

PubMed Central

Cheng, Liang; Wang, Guohua; Li, Jie; Zhang, Tianjiao; Xu, Peigang; Wang, Yadong

2013-01-01

Background A number of databases have been developed to collect disease-related molecular, phenotypic and environmental features (DR-MPEs), such as genes, non-coding RNAs, genetic variations, drugs, phenotypes and environmental factors. However, each of current databases focused on only one or two DR-MPEs. There is an urgent demand to develop an integrated database, which can establish semantic associations among disease-related databases and link them to provide a global view of human disease at the biological level. This database, once developed, will facilitate researchers to query various DR-MPEs through disease, and investigate disease mechanisms from different types of data. Methodology To establish an integrated disease-associated database, disease vocabularies used in different databases are mapped to Disease Ontology (DO) through semantic match. 4,284 and 4,186 disease terms from Medical Subject Headings (MeSH) and Online Mendelian Inheritance in Man (OMIM) respectively are mapped to DO. Then, the relationships between DR-MPEs and diseases are extracted and merged from different source databases for reducing the data redundancy. Conclusions A semantically integrated disease-associated database (SIDD) is developed, which integrates 18 disease-associated databases, for researchers to browse multiple types of DR-MPEs in a view. A web interface allows easy navigation for querying information through browsing a disease ontology tree or searching a disease term. Furthermore, a network visualization tool using Cytoscape Web plugin has been implemented in SIDD. It enhances the SIDD usage when viewing the relationships between diseases and DR-MPEs. The current version of SIDD (Jul 2013) documents 4,465,131 entries relating to 139,365 DR-MPEs, and to 3,824 human diseases. The database can be freely accessed from: http://mlg.hit.edu.cn/SIDD. PMID:24146757

A novel processed food classification system applied to Australian food composition databases.

PubMed

O'Halloran, S A; Lacy, K E; Grimes, C A; Woods, J; Campbell, K J; Nowson, C A

2017-08-01

The extent of food processing can affect the nutritional quality of foodstuffs. Categorising foods by the level of processing emphasises the differences in nutritional quality between foods within the same food group and is likely useful for determining dietary processed food consumption. The present study aimed to categorise foods within Australian food composition databases according to the level of food processing using a processed food classification system, as well as assess the variation in the levels of processing within food groups. A processed foods classification system was applied to food and beverage items contained within Australian Food and Nutrient (AUSNUT) 2007 (n = 3874) and AUSNUT 2011-13 (n = 5740). The proportion of Minimally Processed (MP), Processed Culinary Ingredients (PCI) Processed (P) and Ultra Processed (ULP) by AUSNUT food group and the overall proportion of the four processed food categories across AUSNUT 2007 and AUSNUT 2011-13 were calculated. Across the food composition databases, the overall proportions of foods classified as MP, PCI, P and ULP were 27%, 3%, 26% and 44% for AUSNUT 2007 and 38%, 2%, 24% and 36% for AUSNUT 2011-13. Although there was wide variation in the classifications of food processing within the food groups, approximately one-third of foodstuffs were classified as ULP food items across both the 2007 and 2011-13 AUSNUT databases. This Australian processed food classification system will allow researchers to easily quantify the contribution of processed foods within the Australian food supply to assist in assessing the nutritional quality of the dietary intake of population groups. © 2017 The British Dietetic Association Ltd.

The utility of international shoulder joint replacement registries and databases: a comparative analytic review of two hundred and sixty one thousand, four hundred and eighty four cases.

PubMed

Bayona, Carlos Eduardo Afanador; Somerson, Jeremy S; Matsen, Frederick A

2018-02-01

National registries are valuable tools for understanding the results of shoulder arthroplasty across populations. These databases provide an unselected view of shoulder joint replacement within geographical areas that cannot be obtained from case series or prospective studies. They can be particularly helpful in determining which diagnoses, patients, procedures, and prostheses have higher than expected rates of revision. In an attempt to determine the generalizability of registry data, we asked, 'how similar are the patients and procedures among the different national registries?' We analyzed national shoulder arthroplasty registries and databases accessed via Internet portals and through a PubMed literature search. Seven national/regional registries and five publications regarding national shoulder arthroplasty data were identified; these sources contained a combined total of 261,484 shoulder arthroplasty cases. The percentages of hemiarthroplasty, anatomic (aTSA) and reverse total shoulders (rTSA), the diagnoses leading to arthroplasty, the mean patient age, and the distribution of patient gender varied significantly among these different databases. This study indicates that the indications for and application of shoulder arthroplasty have important geographical variations and that these variations must be considered when comparing outcomes of shoulder arthroplasty from different locations. Without controlling for age, gender, diagnosis and procedure type, the results from one national registry may not be applicable to patients from a different location. In that national data provide the opportunity to reduce costs by identifying implants and procedures with higher failure rates, the funding of registries needs to be free of conflicts of interest.

Time Trends of Period Prevalence Rates of Patients with Inhaled Long-Acting Beta-2-Agonists-Containing Prescriptions: A European Comparative Database Study

PubMed Central

Rottenkolber, Marietta; Voogd, Eef; van Dijk, Liset; Primatesta, Paola; Becker, Claudia; Schlienger, Raymond; de Groot, Mark C. H.; Alvarez, Yolanda; Durand, Julie; Slattery, Jim; Afonso, Ana; Requena, Gema; Gil, Miguel; Alvarez, Arturo; Hesse, Ulrik; Gerlach, Roman; Hasford, Joerg; Fischer, Rainald; Klungel, Olaf H.; Schmiedl, Sven

2015-01-01

Background Inhaled, long-acting beta-2-adrenoceptor agonists (LABA) have well-established roles in asthma and/or COPD treatment. Drug utilisation patterns for LABA have been described, but few studies have directly compared LABA use in different countries. We aimed to compare the prevalence of LABA-containing prescriptions in five European countries using a standardised methodology. Methods A common study protocol was applied to seven European healthcare record databases (Denmark, Germany, Spain, the Netherlands (2), and the UK (2)) to calculate crude and age- and sex-standardised annual period prevalence rates (PPRs) of LABA-containing prescriptions from 2002–2009. Annual PPRs were stratified by sex, age, and indication (asthma, COPD, asthma and COPD). Results From 2002–2009, age- and sex-standardised PPRs of patients with LABA-containing medications increased in all databases (58.2%–185.1%). Highest PPRs were found in men ≥ 80 years old and women 70–79 years old. Regarding the three indications, the highest age- and sex-standardised PPRs in all databases were found in patients with “asthma and COPD” but with large inter-country variation. In those with asthma or COPD, lower PPRs and smaller inter-country variations were found. For all three indications, PPRs for LABA-containing prescriptions increased with age. Conclusions Using a standardised protocol that allowed direct inter-country comparisons, we found highest rates of LABA-containing prescriptions in elderly patients and distinct differences in the increased utilisation of LABA-containing prescriptions within the study period throughout the five European countries. PMID:25706152

Database Resources of the BIG Data Center in 2018.

PubMed

2018-01-04

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Generating Shifting Workloads to Benchmark Adaptability in Relational Database Systems

NASA Astrophysics Data System (ADS)

Rabl, Tilmann; Lang, Andreas; Hackl, Thomas; Sick, Bernhard; Kosch, Harald

A large body of research concerns the adaptability of database systems. Many commercial systems already contain autonomic processes that adapt configurations as well as data structures and data organization. Yet there is virtually no possibility for a just measurement of the quality of such optimizations. While standard benchmarks have been developed that simulate real-world database applications very precisely, none of them considers variations in workloads produced by human factors. Today’s benchmarks test the performance of database systems by measuring peak performance on homogeneous request streams. Nevertheless, in systems with user interaction access patterns are constantly shifting. We present a benchmark that simulates a web information system with interaction of large user groups. It is based on the analysis of a real online eLearning management system with 15,000 users. The benchmark considers the temporal dependency of user interaction. Main focus is to measure the adaptability of a database management system according to shifting workloads. We will give details on our design approach that uses sophisticated pattern analysis and data mining techniques.

Variations in clinicopathologic characteristics of thyroid cancer among racial ethnic groups: analysis of a large public city hospital and the SEER database.

PubMed

Moo-Young, Tricia A; Panergo, Jessel; Wang, Chih E; Patel, Subhash; Duh, Hong Yan; Winchester, David J; Prinz, Richard A; Fogelfeld, Leon

2013-11-01

Clinicopathologic variables influence the treatment and prognosis of patients with thyroid cancer. A retrospective analysis of public hospital thyroid cancer database and the Surveillance, Epidemiology and End Results 17 database was conducted. Demographic, clinical, and pathologic data were compared across ethnic groups. Within the public hospital database, Hispanics versus non-Hispanic whites were younger and had more lymph node involvement (34% vs 17%, P < .001). Median tumor size was not statistically different across ethnic groups. Similar findings were demonstrated within the Surveillance, Epidemiology and End Results database. African Americans aged <45 years had the largest tumors but were least likely to have lymph node involvement. Asians had the most stage IV disease despite having no differences in tumor size, lymph node involvement, and capsular invasion. There is considerable variability in the clinical presentation of thyroid cancer across ethnic groups. Such disparities persist within an equal-access health care system. These findings suggest that factors beyond socioeconomics may contribute to such differences. Copyright © 2013 Elsevier Inc. All rights reserved.

Quantitative assessment of the facial features of a Mexican population dataset.

PubMed

Farrera, Arodi; García-Velasco, Maria; Villanueva, Maria

2016-05-01

The present study describes the morphological variation of a large database of facial photographs. The database comprises frontal (386 female, 764 males) and lateral (312 females, 666 males) images of Mexican individuals aged 14-69 years that were obtained under controlled conditions. We used geometric morphometric methods and multivariate statistics to describe the phenotypic variation within the dataset as well as the variation regarding sex and age groups. In addition, we explored the correlation between facial traits in both views. We found a spectrum of variation that encompasses broad and narrow faces. In frontal view, the latter is associated to a longer nose, a thinner upper lip, a shorter lower face and to a longer upper face, than individuals with broader faces. In lateral view, antero-posteriorly shortened faces are associated to a longer profile and to a shortened helix, than individuals with longer faces. Sexual dimorphism is found in all age groups except for individuals above 39 years old in lateral view. Likewise, age-related changes are significant for both sexes, except for females above 29 years old in both views. Finally, we observed that the pattern of covariation between views differs in males and females mainly in the thickness of the upper lip and the angle of the facial profile and the auricle. The results of this study could contribute to the forensic practices as a complement for the construction of biological profiles, for example, to improve facial reconstruction procedures. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Recent Variations of The Italian Glaciers: Qualitative and Quantitative Data-base and Processings On A Fundamental Water Resource

NASA Astrophysics Data System (ADS)

Diolaiuti, G.; D'Agata, C.; Stella, G.; Apadula, F.; Smiraglia, C.

This paper introduces the preliminary results of a project applied primarily to the compilation of the first general and complete data-base of all Italian glaciers, avail- able to the scientific community, and secondly to the elaboration of the information contained in the data base to supply a strong contribution to the study of the spatial and temporal variabilities of the climatic signal inside the alpine glacier historical series. The project started in the year 2000 as a convention between Università degli Studi di Milano (Italy) and CESI (Italian Electrical Sperimental Center) and gives the first results and the free use by people in the 2002, the International Year of Mountains. Fundamental for the development of the project was the collaboration of the Italian Glaciological Committee (CGI) with its publications (from 1914 to 1977 SBollettino & cedil;del Comitato Glaciologico ItalianoT and from 1978 to 2000 SGeografia Fisica e Di- & cedil;namica Quaternaria). The data-base collects qualitative and quantitative information on glaciers monitored by the Italian Glaciological CommitteeSs operators during the century of their activity for a total of 902 glaciers (901 alpine glaciers and only Ap- pennine one, the Calderone Glacier). For every glacier were inserted in the data-base: 1) data about the glacial terminus elevations, date and method of the measure 2) name and position of the signals used by the operators in order to verify the variations of extension of glacial terminus 3) distance between the signal and the glacier terminus and relative angle of measure 4) operatorSs name 5) bibliographical source of the information 6) qualitative data (on cartographic material, photographies and papers). Currently only a part of the data collected in the data-base is directly available in the web site: www.cesi.it/greeninfo/i ghiacciai Italiani/. Here the users are able to find, for every glacier, a table with all the references of qualitative (as cartography and iconog- raphy) data and diagrams of the frontal variations (both annual and cumulated) and of the glacier terminus elevations. For each diagram it is possible to evidence different temporal range (according to the usersS interest) by means of appropriate interroga- tion. It is possible to use all tha data base (and not only the diagrams and the qualitative table) by compiling appropriate request. The second phase consisted in the data pro- cessing. For all the glaciers collected in the database the data are processed in order to supply time-distance diagrams of the annual and cumulated frontal variations. The 1 comparison of the curves allowed to appreciate the common glacial trend differenti- ated from a glacial body to another in function of the multiple influential factors on frontal dynamics. All the monitored glaciers have in fact a phase of progress in the 20s of XXth century, a hard frontal retreat after the 30s and a new generalized progress be- tween the end of the 60s and the half of the 80s of XXth century and a general retreat from 1985 up to now. This is according to the climatic dynamics of the XX century (a general warming tendence with short periods of thermal reduction in the 20s and in 60s-.80s). For a sample of glacier were available complete data set for over a period of twenty years (without gaps) or not complete data set but with little gap of about 5 years or less that were possible to fulfill. For these data series were possible to cal- culate the correlation with the other glaciers. This type of analysis allowed to prepare correlation matrices for different temporal periods that allow to visualize the space and temporal variations of the climatic signal of the Italian glaciers frontal variations. It was possible to notice that glaciers located in close areas often do not manifest an strong correlation, while sometimes glaciers located far but with morphometric characteristics (dimensions) and geographic ones (aspect) similar were meaningfully correlated. This result is particularly interesting because it was quite different from the result obtained by various authors processing an other important glaciological param- eter, the glacier mass balances data. The large sample of data used in thi study allowed to notice that the regionalism rule is not valid for the frontal variations and that on the space variability of this glaciological parameter are instead influential the similarity of geometric and geographic factors (dimension and aspect), so glaciers far, but in the same physical conditions, answer in a similar way to the climatic variations. 2

Faculty Turnover: Discipline-Specific Attention Is Warranted

ERIC Educational Resources Information Center

Xu, Yonghong Jade

2008-01-01

This study investigated the importance of discipline variations in understanding faculty turnover behaviors. A representative sample of university faculty in Research and Doctoral universities was obtained from a national database. Faculty members, self-identified into a primary academic area, were grouped into eight discipline clusters according…

Pair Identity and Smooth Variation Rules Applicable for the Spectroscopic Parameters of H2O Transitions Involving High-J States

NASA Technical Reports Server (NTRS)

Ma, Q.; Tipping, R. H.; Lavrentieva, N. N.

2010-01-01

Two basic rules (i.e. the pair identity and the smooth variation) applicable for H2O transitions involving high-J states have been discovered. The origins of these rules are the properties of the energy levels and wavefunctions of H2O states with the quantum number J above certain boundaries. As a result, for lines involving high-J states in individually defined groups, all their spectroscopic parameters (i.e. the transition wavenumber, intensity, pressure-broadened half-width, pressure-induced shift, and temperature exponent) must follow these rules. One can use these rules to screen spectroscopic data provided by databases and to identify possible errors. In addition, by using extrapolation methods within the individual groups, one is able to predict the spectroscopic parameters for lines in this group involving very high-J states. The latter are required in developing high-temperature molecular spectroscopic databases such as HITEMP.

Determination of absorption coefficient based on laser beam thermal blooming in gas-filled tube.

PubMed

Hafizi, B; Peñano, J; Fischer, R; DiComo, G; Ting, A

2014-08-01

Thermal blooming of a laser beam propagating in a gas-filled tube is investigated both analytically and experimentally. A self-consistent formulation taking into account heating of the gas and the resultant laser beam spreading (including diffraction) is presented. The heat equation is used to determine the temperature variation while the paraxial wave equation is solved in the eikonal approximation to determine the temporal and spatial variation of the Gaussian laser spot radius, Gouy phase (longitudinal phase delay), and wavefront curvature. The analysis is benchmarked against a thermal blooming experiment in the literature using a CO₂ laser beam propagating in a tube filled with air and propane. New experimental results are presented in which a CW fiber laser (1 μm) propagates in a tube filled with nitrogen and water vapor. By matching laboratory and theoretical results, the absorption coefficient of water vapor is found to agree with calculations using MODTRAN (the MODerate-resolution atmospheric TRANsmission molecular absorption database) and HITRAN (the HIgh-resolution atmospheric TRANsmission molecular absorption database).

Variation in ventilation time after coronary artery bypass grafting: an analysis from the society of thoracic surgeons adult cardiac surgery database.

PubMed

Jacobs, Jeffrey P; He, Xia; O'Brien, Sean M; Welke, Karl F; Filardo, Giovanni; Han, Jane M; Ferraris, Victor A; Prager, Richard L; Shahian, David M

2013-09-01

Short postoperative ventilation times are accepted as a marker of quality. This analysis assesses center level variation in postoperative ventilation time in a subset of patients undergoing isolated coronary artery bypass grafting (CABG). In 2009 and 2010, 325,129 patients in the STS Adult Cardiac Surgery Database underwent isolated CABG. Patients were excluded if they were intubated before entering the operating room, required ventilation for greater than 24 hours, or had missing data on key covariates. The final study cohort was 274,231 isolated CABG patients from 1,008 centers. Bayesian hierarchical models were used to assess between-center variation in ventilation time and to explore the effect of center-level covariates. Analyses were performed with and without adjusting for case mix. After adjusting for case mix, the ratio of median ventilator time at the 90th percentile of the center-level distribution compared with the tenth percentile was 9.0:5.0=1.8 (95% credible interval: 1.79 to 1.85). This ratio illustrates the scale of between-center differences: centers above the 90th percentile have a ventilation time of at least 1.8 times that of centers below the tenth percentile. Smaller hospital volume, presence of a residency program, and some census regions were associated with longer ventilation times. After adjustment for severity of illness, substantial inter-center variation exists in postoperative ventilation time in this subset of patients undergoing isolated CABG. This finding represents an opportunity for multi-institutional quality improvement initiatives designed to limit variations in ventilator management and achieve the shortest possible ventilation times for all patients, thus benefiting both clinical outcomes and resource utilization. Copyright © 2013 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Holocene geomagnetic secular variation recorded by volcanic deposits at Mount St. Helens, Washington

USGS Publications Warehouse

Hagstrum, J.T.; Hoblitt, R.P.; Gardner, C.A.; Gray, T.E.

2002-01-01

A compilation of paleomagnetic data from volcanic deposits of Mount St. Helens is presented in this report. The database is used to determine signature paleomagnetic directions of products from its Holocene eruptive events, to assign sampled units to their proper eruptive period, and to begin the assembly of a much larger database of paleomagnetic directions from Holocene volcanic rocks in western North America. The paleomagnetic results from Mount St. Helens are mostly of high quality, and generally agree with the division of its volcanic deposits into eruptive episodes based on previous geologic mapping and radiocarbon dates. The Muddy River andesite's paleomagnetic direction, however, indicates that it is more likely part of the Pine Creek eruptive period rather than the Castle Creek period. In addition, the Two-Fingers andesite flow is more likely part of the Middle Kalama eruptive period and not part of the Goat Rocks period. The paleomagnetic data from Mount St. Helens and Mount Hood document variation in the geomagnetic field's pole position over the last ~2,500 years. A distinct feature of the new paleosecular variation (PSV) record, similar to the Fish Lake record (Oregon), indicates a sudden change from rapid clockwise movement of the pole about the Earth's spin axis to relatively slow counterclockwise movement at ???800 to 900 years B.P.

Multi-Directional Multi-Level Dual-Cross Patterns for Robust Face Recognition.

PubMed

Ding, Changxing; Choi, Jonghyun; Tao, Dacheng; Davis, Larry S

2016-03-01

To perform unconstrained face recognition robust to variations in illumination, pose and expression, this paper presents a new scheme to extract "Multi-Directional Multi-Level Dual-Cross Patterns" (MDML-DCPs) from face images. Specifically, the MDML-DCPs scheme exploits the first derivative of Gaussian operator to reduce the impact of differences in illumination and then computes the DCP feature at both the holistic and component levels. DCP is a novel face image descriptor inspired by the unique textural structure of human faces. It is computationally efficient and only doubles the cost of computing local binary patterns, yet is extremely robust to pose and expression variations. MDML-DCPs comprehensively yet efficiently encodes the invariant characteristics of a face image from multiple levels into patterns that are highly discriminative of inter-personal differences but robust to intra-personal variations. Experimental results on the FERET, CAS-PERL-R1, FRGC 2.0, and LFW databases indicate that DCP outperforms the state-of-the-art local descriptors (e.g., LBP, LTP, LPQ, POEM, tLBP, and LGXP) for both face identification and face verification tasks. More impressively, the best performance is achieved on the challenging LFW and FRGC 2.0 databases by deploying MDML-DCPs in a simple recognition scheme.

A framework to evaluate the effects of small area variations in healthcare infrastructure on diagnostics and patient outcomes of rare diseases based on administrative data.

PubMed

Stargardt, Tom; Schreyögg, Jonas

2012-05-01

Small area variations in healthcare infrastructure may result in differences in early detection and outcomes for patients with rare diseases. It is our aim to provide a framework for evaluating small area variations in healthcare infrastructure on the diagnostics and health outcomes of rare diseases. We focus on administrative data as it allows (a) for relatively large sample sizes even though the prevalence of rare diseases is very low, and (b) makes it possible to link information on healthcare infrastructure to morbidity, mortality, and utilization. For identifying patients with a rare disease in a database, a combination of different classification systems has to be used due to usually multiple diseases sharing one ICD code. Outcomes should be chosen that are (a) appropriate for the disease, (b) identifiable and reliably coded in the administrative database, and (c) observable during the limited time period of the follow-up. Risk adjustment using summary scores of disease-specific or comprehensive risk adjustment instruments might be preferable over empirical weights because of the lower number of variables needed. The proposed framework will help to identify differences in time to diagnosis and treatment outcomes across areas in the context of rare diseases. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Spanish personal name variations in national and international biomedical databases: implications for information retrieval and bibliometric studies

PubMed Central

Ruiz-Pérez, R.; López-Cózar, E. Delgado; Jiménez-Contreras, E.

2002-01-01

Objectives: The study sought to investigate how Spanish names are handled by national and international databases and to identify mistakes that can undermine the usefulness of these databases for locating and retrieving works by Spanish authors. Methods: The authors sampled 172 articles published by authors from the University of Granada Medical School between 1987 and 1996 and analyzed the variations in how each of their names was indexed in Science Citation Index (SCI), MEDLINE, and Índice Médico Español (IME). The number and types of variants that appeared for each author's name were recorded and compared across databases to identify inconsistencies in indexing practices. We analyzed the relationship between variability (number of variants of an author's name) and productivity (number of items the name was associated with as an author), the consequences for retrieval of information, and the most frequent indexing structures used for Spanish names. Results: The proportion of authors who appeared under more then one name was 48.1% in SCI, 50.7% in MEDLINE, and 69.0% in IME. Productivity correlated directly with variability: more than 50% of the authors listed on five to ten items appeared under more than one name in any given database, and close to 100% of the authors listed on more than ten items appeared under two or more variants. Productivity correlated inversely with retrievability: as the number of variants for a name increased, the number of items retrieved under each variant decreased. For the most highly productive authors, the number of items retrieved under each variant tended toward one. The most frequent indexing methods varied between databases. In MEDLINE and IME, names were indexed correctly as “first surname second surname, first name initial middle name initial” (if present) in 41.7% and 49.5% of the records, respectively. However, in SCI, the most frequent method was “first surname, first name initial second name initial” (48.0% of the records) and first surname and second surname run together, first name initial (18.3%). Conclusions: Retrievability on the basis of author's name was poor in all three databases. Each database uses accurate indexing methods, but these methods fail to result in consistency or coherence for specific entries. The likely causes of inconsistency are: (1) use by authors of variants of their names during their publication careers, (2) lack of authority control in all three databases, (3) the use of an inappropriate indexing method for Spanish names in SCI, (4) authors' inconsistent behaviors, and (5) possible editorial interventions by some journals. We offer some suggestions as to how to avert the proliferation of author name variants in the databases. PMID:12398248

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

PubMed

Cole, Charles; Krampis, Konstantinos; Karagiannis, Konstantinos; Almeida, Jonas S; Faison, William J; Motwani, Mona; Wan, Quan; Golikov, Anton; Pan, Yang; Simonyan, Vahan; Mazumder, Raja

2014-01-27

Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available from the CSR website (http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr). Availability of thousands of sequenced samples from patients provides a rich repository of sequence information that can be utilized to identify individual level SNVs and their effect on the human proteome beyond what the dbSNP database provides.

Variation in population levels of physical activity in European children and adolescents according to cross-European studies: a systematic literature review within DEDIPAC.

PubMed

Van Hecke, Linde; Loyen, Anne; Verloigne, Maïté; van der Ploeg, Hidde P; Lakerveld, Jeroen; Brug, Johannes; De Bourdeaudhuij, Ilse; Ekelund, Ulf; Donnelly, Alan; Hendriksen, Ingrid; Deforche, Benedicte

2016-06-28

Regular physical activity is associated with physical, social and mental health benefits, whilst insufficient physical activity is associated with several negative health outcomes (e.g. metabolic problems). Population monitoring of physical activity is important to gain insight into prevalence of compliance to physical activity recommendations, groups at risk and changes in physical activity patterns. This review aims to provide an overview of all existing studies that measure physical activity in youth, in cross-European studies, to describe the variation in population levels of physical activity and to describe and define challenges regarding assessment methods that are used. A systematic search was performed on six databases (PubMed, EMBASE, CINAHL, PsycINFO, SportDiscus and OpenGrey), supplemental forward- and backward tracking was done and authors' and experts' literature databases were searched to identify relevant articles. Journal articles or reports that reported levels of physical activity in the general population of youth from cross-European studies were included. Data were reviewed, extracted and assessed by two researchers, with disagreements being resolved by a third researcher. The review protocol of this review is published under registration number CRD42014010684 in the PROSPERO database. The search resulted in 9756 identified records of which 30 articles were included in the current review. This review revealed large differences between countries in prevalence of compliance to physical activity recommendations (i.e. 60 min of daily moderate- to vigorous-intensity physical activity (MVPA)) measured subjectively (5-47%) and accelerometer measured minutes of MVPA (23-200 min). Overall boys and children were more active than girls and adolescents. Different measurement methods (subjective n = 12, objective n = 18) and reported outcome variables (n = 17) were used in the included articles. Different accelerometer intensity thresholds used to define MVPA resulted in substantial differences in MVPA between studies conducted in the same countries when assessed objectively. Reported levels of physical activity and prevalence of compliance to physical activity recommendations in youth showed large variation across European countries. This may reflect true variation in physical activity as well as variation in assessment methods and reported outcome variables. Standardization across Europe, of methods to assess physical activity in youth and reported outcome variables is warranted, preferably moving towards a pan-European surveillance system combining objective and self-report methods.

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data

PubMed Central

2014-01-01

Background Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. Results To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available from the CSR website (http://hive.biochemistry.gwu.edu/dna.cgi?cmd=csr). Conclusions Availability of thousands of sequenced samples from patients provides a rich repository of sequence information that can be utilized to identify individual level SNVs and their effect on the human proteome beyond what the dbSNP database provides. PMID:24467687

Global Soil Respiration: Interaction with Environmental Variables and Response to Climate Change

NASA Astrophysics Data System (ADS)

Jian, J.; Steele, M.

2016-12-01

Background, methods, objectivesTerrestrial ecosystems take up around 1.7 Pg C per year; however, the role of terrestrial ecosystems as a carbon sink may change to carbon source by 2050, as a result of positive feedback of soil respiration response to global warming. Nevertheless, limited evidence shows that soil carbon is decreasing and the role of terrestrial ecosystems is changing under warming. One possibility is the positive feedback may slow due to the acclimation of soil respiration as a result of decreasing temperature sensitivity (Q10) with warming. To verify and quantify the uncertainty in soil carbon cycling and feedbacks to climate change, we assembled soil respiration observations from 1961 to 2014 from 724 publications into a monthly global soil respiration database (MSRDB), which included 13482 soil respiration measurements together with 38 other ancillary measurements from 538 sites. Using this database we examined macroscale variation in the relationship between soil respiration and air temperature, precipitation, leaf area index and soil properties. We also quantified global soil respiration, the sources of uncertainty, and its feedback to warming based on climate region-oriented models with variant Q10function. Results and ConclusionsOur results showed substantial heterogeneity in the relationship between soil respiration and environmental factors across different climate regions. For example, soil respiration was strongly related to vegetation (via leaf area index) in colder regions, but not in tropical region. Only in tropical and arid regions did soil properties explain any variation in soil respiration. Global annual mean soil respiration from 1961 to 2014 was estimated to be 72.41 Pg C yr-1 based on monthly global soil respiration database, 25 Pg lower than estimated based on yearly soil respiration database. By using the variable Q10 models, we estimated that global soil respiration increased at a rate of 0.03 Pg C yr-1 from 1961 to 2014, smaller than previous studies ( 0.1 Pg C yr-1). The substantial variations in these relationships suggest that regional scales is important for understanding and prediction of global carbon cycling and how it response to climate change.

Validity of registration of ICD codes and prescriptions in a research database in Swedish primary care: a cross-sectional study in Skaraborg primary care database

PubMed Central

2010-01-01

Background In recent years, several primary care databases recording information from computerized medical records have been established and used for quality assessment of medical care and research. However, to be useful for research purposes, the data generated routinely from every day practice require registration of high quality. In this study we aimed to investigate (i) the frequency and validity of ICD code and drug prescription registration in the new Skaraborg primary care database (SPCD) and (ii) to investigate the sources of variation in this registration. Methods SPCD contains anonymous electronic medical records (ProfDoc III) automatically retrieved from all 24 public health care centres (HCC) in Skaraborg, Sweden. The frequencies of ICD code registration for the selected diagnoses diabetes mellitus, hypertension and chronic cardiovascular disease and the relevant drug prescriptions in the time period between May 2002 and October 2003 were analysed. The validity of data registration in the SPCD was assessed in a random sample of 50 medical records from each HCC (n = 1200 records) using the medical record text as gold standard. The variance of ICD code registration was studied with multi-level logistic regression analysis and expressed as median odds ratio (MOR). Results For diabetes mellitus and hypertension ICD codes were registered in 80-90% of cases, while for congestive heart failure and ischemic heart disease ICD codes were registered more seldom (60-70%). Drug prescription registration was overall high (88%). A correlation between the frequency of ICD coded visits and the sensitivity of the ICD code registration was found for hypertension and congestive heart failure but not for diabetes or ischemic heart disease. The frequency of ICD code registration varied from 42 to 90% between HCCs, and the greatest variation was found at the physician level (MORPHYSICIAN = 4.2 and MORHCC = 2.3). Conclusions Since the frequency of ICD code registration varies between different diagnoses, each diagnosis must be separately validated. Improved frequency and quality of ICD code registration might be achieved by interventions directed towards the physicians where the greatest amount of variation was found. PMID:20416069

Validity of registration of ICD codes and prescriptions in a research database in Swedish primary care: a cross-sectional study in Skaraborg primary care database.

PubMed

Hjerpe, Per; Merlo, Juan; Ohlsson, Henrik; Bengtsson Boström, Kristina; Lindblad, Ulf

2010-04-23

In recent years, several primary care databases recording information from computerized medical records have been established and used for quality assessment of medical care and research. However, to be useful for research purposes, the data generated routinely from every day practice require registration of high quality. In this study we aimed to investigate (i) the frequency and validity of ICD code and drug prescription registration in the new Skaraborg primary care database (SPCD) and (ii) to investigate the sources of variation in this registration. SPCD contains anonymous electronic medical records (ProfDoc III) automatically retrieved from all 24 public health care centres (HCC) in Skaraborg, Sweden. The frequencies of ICD code registration for the selected diagnoses diabetes mellitus, hypertension and chronic cardiovascular disease and the relevant drug prescriptions in the time period between May 2002 and October 2003 were analysed. The validity of data registration in the SPCD was assessed in a random sample of 50 medical records from each HCC (n = 1200 records) using the medical record text as gold standard. The variance of ICD code registration was studied with multi-level logistic regression analysis and expressed as median odds ratio (MOR). For diabetes mellitus and hypertension ICD codes were registered in 80-90% of cases, while for congestive heart failure and ischemic heart disease ICD codes were registered more seldom (60-70%). Drug prescription registration was overall high (88%). A correlation between the frequency of ICD coded visits and the sensitivity of the ICD code registration was found for hypertension and congestive heart failure but not for diabetes or ischemic heart disease.The frequency of ICD code registration varied from 42 to 90% between HCCs, and the greatest variation was found at the physician level (MORPHYSICIAN = 4.2 and MORHCC = 2.3). Since the frequency of ICD code registration varies between different diagnoses, each diagnosis must be separately validated. Improved frequency and quality of ICD code registration might be achieved by interventions directed towards the physicians where the greatest amount of variation was found.

Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders and/or congenital anomalies.

PubMed

Willemsen, Marjolein H; de Leeuw, Nicole; de Brouwer, Arjan P M; Pfundt, Rolph; Hehir-Kwa, Jayne Y; Yntema, Helger G; Nillesen, Willy M; de Vries, Bert B A; van Bokhoven, Hans; Kleefstra, Tjitske

2012-11-01

Genome-wide array studies are now routinely being used in the evaluation of patients with cognitive disorders (CD) and/or congenital anomalies (CA). Therefore, inevitably each clinician is confronted with the challenging task of the interpretation of copy number variations detected by genome-wide array platforms in a diagnostic setting. Clinical interpretation of autosomal copy number variations is already challenging, but assessment of the clinical relevance of copy number variations of the X-chromosome is even more complex. This study provides an overview of the X-Chromosome copy number variations that we have identified by genome-wide array analysis in a large cohort of 4407 male and female patients. We have made an interpretation of the clinical relevance of each of these copy number variations based on well-defined criteria and previous reports in literature and databases. The prevalence of X-chromosome copy number variations in this cohort was 57/4407 (∼1.3%), of which 15 (0.3%) were interpreted as (likely) pathogenic. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

TBC1D24 genotype–phenotype correlation

PubMed Central

Balestrini, Simona; Milh, Mathieu; Castiglioni, Claudia; Lüthy, Kevin; Finelli, Mattea J.; Verstreken, Patrik; Cardon, Aaron; Stražišar, Barbara Gnidovec; Holder, J. Lloyd; Lesca, Gaetan; Mancardi, Maria M.; Poulat, Anne L.; Repetto, Gabriela M.; Banka, Siddharth; Bilo, Leonilda; Birkeland, Laura E.; Bosch, Friedrich; Brockmann, Knut; Cross, J. Helen; Doummar, Diane; Félix, Temis M.; Giuliano, Fabienne; Hori, Mutsuki; Hüning, Irina; Kayserili, Hulia; Kini, Usha; Lees, Melissa M.; Meenakshi, Girish; Mewasingh, Leena; Pagnamenta, Alistair T.; Peluso, Silvio; Mey, Antje; Rice, Gregory M.; Rosenfeld, Jill A.; Taylor, Jenny C.; Troester, Matthew M.; Stanley, Christine M.; Ville, Dorothee; Walkiewicz, Magdalena; Falace, Antonio; Fassio, Anna; Lemke, Johannes R.; Biskup, Saskia; Tardif, Jessica; Ajeawung, Norbert F.; Tolun, Aslihan; Corbett, Mark; Gecz, Jozef; Afawi, Zaid; Howell, Katherine B.; Oliver, Karen L.; Berkovic, Samuel F.; Scheffer, Ingrid E.; de Falco, Fabrizio A.; Oliver, Peter L.; Striano, Pasquale; Zara, Federico

2016-01-01

Objective: To evaluate the phenotypic spectrum associated with mutations in TBC1D24. Methods: We acquired new clinical, EEG, and neuroimaging data of 11 previously unreported and 37 published patients. TBC1D24 mutations, identified through various sequencing methods, can be found online (http://lovd.nl/TBC1D24). Results: Forty-eight patients were included (28 men, 20 women, average age 21 years) from 30 independent families. Eighteen patients (38%) had myoclonic epilepsies. The other patients carried diagnoses of focal (25%), multifocal (2%), generalized (4%), and unclassified epilepsy (6%), and early-onset epileptic encephalopathy (25%). Most patients had drug-resistant epilepsy. We detail EEG, neuroimaging, developmental, and cognitive features, treatment responsiveness, and physical examination. In silico evaluation revealed 7 different highly conserved motifs, with the most common pathogenic mutation located in the first. Neuronal outgrowth assays showed that some TBC1D24 mutations, associated with the most severe TBC1D24-associated disorders, are not necessarily the most disruptive to this gene function. Conclusions: TBC1D24-related epilepsy syndromes show marked phenotypic pleiotropy, with multisystem involvement and severity spectrum ranging from isolated deafness (not studied here), benign myoclonic epilepsy restricted to childhood with complete seizure control and normal intellect, to early-onset epileptic encephalopathy with severe developmental delay and early death. There is no distinct correlation with mutation type or location yet, but patterns are emerging. Given the phenotypic breadth observed, TBC1D24 mutation screening is indicated in a wide variety of epilepsies. A TBC1D24 consortium was formed to develop further research on this gene and its associated phenotypes. PMID:27281533

Improving past sea surface temperature reconstructions from the Southern Hemisphere oceans using planktonic foraminiferal census data

NASA Astrophysics Data System (ADS)

Haddam, N. A.; Michel, E.; Siani, G.; Cortese, G.; Bostock, H. C.; Duprat, J. M.; Isguder, G.

2016-06-01

We present an improved database of planktonic foraminiferal census counts from the Southern Hemisphere oceans (SHO) from 15°S to 64°S. The SHO database combines three existing databases. Using this SHO database, we investigated dissolution biases that might affect faunal census counts. We suggest a depth/ΔCO32- threshold of ~3800 m/ΔCO32- = ~ -10 to -5 µmol/kg for the Pacific and Indian Oceans and ~4000 m/ΔCO32- = ~0 to 10 µmol/kg for the Atlantic Ocean, under which core-top assemblages can be affected by dissolution and are less reliable for paleo-sea surface temperature (SST) reconstructions. We removed all core tops beyond these thresholds from the SHO database. This database has 598 core tops and is able to reconstruct past SST variations from 2° to 25.5°C, with a root mean square error of 1.00°C, for annual temperatures. To inspect how dissolution affects SST reconstruction quality, we tested the data base with two "leave-one-out" tests, with and without the deep core tops. We used this database to reconstruct summer SST (SSST) over the last 20 ka, using the Modern Analog Technique method, on the Southeast Pacific core MD07-3100. This was compared to the SSST reconstructed using the three databases used to compile the SHO database, thus showing that the reconstruction using the SHO database is more reliable, as its dissimilarity values are the lowest. The most important aspect here is the importance of a bias-free, geographic-rich database. We leave this data set open-ended to future additions; the new core tops must be carefully selected, with their chronological frameworks, and evidence of dissolution assessed.

Regional Variation in Causes of Injuries among Terrorism Victims for Mass Casualty Events

PubMed Central

Regens, James L.; Schultheiss, Amy; Mould, Nick

2015-01-01

The efficient allocation of medical resources to prepare for and respond to mass casualty events (MCEs) attributable to intentional acts of terrorism is a major challenge confronting disaster planners and emergency personnel. This research article examines variation in regional patterns in the causes of injures associated with 77,258 successful terrorist attacks that occurred between 1970 and 2013 involving the use of explosives, firearms, and/or incendiaries. The objective of this research is to estimate regional variation in the use of different conventional weapons in successful terrorist attacks in each world region on variation in injury cause distributions. Indeed, we find that the distributions of the number of injuries attributable to specific weapons types (i.e., by cause) vary greatly among the 13 world regions identified within the Global Terrorism Database. PMID:26347857

Analyses of some exoplanets' transits and transit timing variations

NASA Astrophysics Data System (ADS)

Püsküllü, ćaǧlar; Soydugan, Faruk

2017-02-01

We present solutions of the transit light curves and transit timing variations (TTVs) analyses of the exoplanets HAT-P-5b, HAT-P-9b and HAT-P-25b. Transit light curves were collected at Çanakkale Onsekiz Mart University Observatory and TUBITAK National Observatory. The models were produced by WINFITTER program and stellar, planetary and orbital properties were obtained and discussed. We gave new transit times and generated TTVs with them by appending additional data based on Exoplanet Transit Database (ETD). Significant signals at the TTVs were also investigated.

A signal detection method for temporal variation of adverse effect with vaccine adverse event reporting system data.

PubMed

Cai, Yi; Du, Jingcheng; Huang, Jing; Ellenberg, Susan S; Hennessy, Sean; Tao, Cui; Chen, Yong

2017-07-05

To identify safety signals by manual review of individual report in large surveillance databases is time consuming; such an approach is very unlikely to reveal complex relationships between medications and adverse events. Since the late 1990s, efforts have been made to develop data mining tools to systematically and automatically search for safety signals in surveillance databases. Influenza vaccines present special challenges to safety surveillance because the vaccine changes every year in response to the influenza strains predicted to be prevalent that year. Therefore, it may be expected that reporting rates of adverse events following flu vaccines (number of reports for a specific vaccine-event combination/number of reports for all vaccine-event combinations) may vary substantially across reporting years. Current surveillance methods seldom consider these variations in signal detection, and reports from different years are typically collapsed together to conduct safety analyses. However, merging reports from different years ignores the potential heterogeneity of reporting rates across years and may miss important safety signals. Reports of adverse events between years 1990 to 2013 were extracted from the Vaccine Adverse Event Reporting System (VAERS) database and formatted into a three-dimensional data array with types of vaccine, groups of adverse events and reporting time as the three dimensions. We propose a random effects model to test the heterogeneity of reporting rates for a given vaccine-event combination across reporting years. The proposed method provides a rigorous statistical procedure to detect differences of reporting rates among years. We also introduce a new visualization tool to summarize the result of the proposed method when applied to multiple vaccine-adverse event combinations. We applied the proposed method to detect safety signals of FLU3, an influenza vaccine containing three flu strains, in the VAERS database. We showed that it had high statistical power to detect the variation in reporting rates across years. The identified vaccine-event combinations with significant different reporting rates over years suggested potential safety issues due to changes in vaccines which require further investigation. We developed a statistical model to detect safety signals arising from heterogeneity of reporting rates of a given vaccine-event combinations across reporting years. This method detects variation in reporting rates over years with high power. The temporal trend of reporting rate across years may reveal the impact of vaccine update on occurrence of adverse events and provide evidence for further investigations.

BioQ: tracing experimental origins in public genomic databases using a novel data provenance model

PubMed Central

Saccone, Scott F.; Quan, Jiaxi; Jones, Peter L.

2012-01-01

Motivation: Public genomic databases, which are often used to guide genetic studies of human disease, are now being applied to genomic medicine through in silico integrative genomics. These databases, however, often lack tools for systematically determining the experimental origins of the data. Results: We introduce a new data provenance model that we have implemented in a public web application, BioQ, for assessing the reliability of the data by systematically tracing its experimental origins to the original subjects and biologics. BioQ allows investigators to both visualize data provenance as well as explore individual elements of experimental process flow using precise tools for detailed data exploration and documentation. It includes a number of human genetic variation databases such as the HapMap and 1000 Genomes projects. Availability and implementation: BioQ is freely available to the public at http://bioq.saclab.net Contact: ssaccone@wustl.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22426342

Relax with CouchDB - Into the non-relational DBMS era of Bioinformatics

PubMed Central

Manyam, Ganiraju; Payton, Michelle A.; Roth, Jack A.; Abruzzo, Lynne V.; Coombes, Kevin R.

2012-01-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. PMID:22609849

The Molecular Signatures Database (MSigDB) hallmark gene set collection.

PubMed

Liberzon, Arthur; Birger, Chet; Thorvaldsdóttir, Helga; Ghandi, Mahmoud; Mesirov, Jill P; Tamayo, Pablo

2015-12-23

The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, here we use a combination of automated approaches and expert curation to develop a collection of "hallmark" gene sets as part of MSigDB. Each hallmark in this collection consists of a "refined" gene set, derived from multiple "founder" sets, that conveys a specific biological state or process and displays coherent expression. The hallmarks effectively summarize most of the relevant information of the original founder sets and, by reducing both variation and redundancy, provide more refined and concise inputs for gene set enrichment analysis.

Generation and validation of a universal perinatal database and biospecimen repository: PeriBank.

PubMed

Antony, K M; Hemarajata, P; Chen, J; Morris, J; Cook, C; Masalas, D; Gedminas, M; Brown, A; Versalovic, J; Aagaard, K

2016-11-01

There is a dearth of biospecimen repositories available to perinatal researchers. In order to address this need, here we describe the methodology used to establish such a resource. With the collaboration of MedSci.net, we generated an online perinatal database with 847 fields of clinical information. Simultaneously, we established a biospecimen repository of the same clinical participants. The demographic and clinical outcomes data are described for the first 10 000 participants enrolled. The demographic characteristics are consistent with the demographics of the delivery hospitals. Quality analysis of the biospecimens reveals variation in very few analytes. Furthermore, since the creation of PeriBank, we have demonstrated validity of the database and tissue integrity of the biospecimen repository. Here we establish that the creation of a universal perinatal database and biospecimen collection is not only possible, but allows for the performance of state-of-the-science translational perinatal research and is a potentially valuable resource to academic perinatal researchers.

1-CMDb: A Curated Database of Genomic Variations of the One-Carbon Metabolism Pathway.

PubMed

Bhat, Manoj K; Gadekar, Veerendra P; Jain, Aditya; Paul, Bobby; Rai, Padmalatha S; Satyamoorthy, Kapaettu

2017-01-01

The one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded. Hence, we designed the one-carbon metabolism database (1-CMDb) as a platform to interrogate its association with a host of human disorders. DNA sequence and network information of a total of 48 genes were extracted from a literature survey and KEGG pathway that are involved in the one-carbon folate-mediated pathway. The information generated, collected, and compiled for all these genes from the UCSC genome browser included the single nucleotide polymorphisms (SNPs), CpGs, copy number variations (CNVs), and miRNAs, and a comprehensive database was created. Furthermore, a significant correlation analysis was performed for SNPs in the pathway genes. Detailed data of SNPs, CNVs, CpG islands, and miRNAs for 48 folate pathway genes were compiled. The SNPs in CNVs (9670), CpGs (984), and miRNAs (14) were also compiled for all pathway genes. The SIFT score, the prediction and PolyPhen score, as well as the prediction for each of the SNPs were tabulated and represented for folate pathway genes. Also included in the database for folate pathway genes were the links to 124 various phenotypes and disease associations as reported in the literature and from publicly available information. A comprehensive database was generated consisting of genomic elements within and among SNPs, CNVs, CpGs, and miRNAs of one-carbon metabolism pathways to facilitate (a) single source of information and (b) integration into large-genome scale network analysis to be developed in the future by the scientific community. The database can be accessed at http://slsdb.manipal.edu/ocm/. © 2017 S. Karger AG, Basel.

Addressing unwarranted clinical variation: A rapid review of current evidence.

PubMed

Harrison, Reema; Manias, Elizabeth; Mears, Stephen; Heslop, David; Hinchcliff, Reece; Hay, Liz

2018-05-15

Unwarranted clinical variation (UCV) can be described as variation that can only be explained by differences in health system performance. There is a lack of clarity regarding how to define and identify UCV and, once identified, to determine whether it is sufficiently problematic to warrant action. As such, the implementation of systemic approaches to reducing UCV is challenging. A review of approaches to understand, identify, and address UCV was undertaken to determine how conceptual and theoretical frameworks currently attempt to define UCV, the approaches used to identify UCV, and the evidence of their effectiveness. Rapid evidence assessment (REA) methodology was used. A range of text words, synonyms, and subject headings were developed for the major concepts of unwarranted clinical variation, standards (and deviation from these standards), and health care environment. Two electronic databases (Medline and Pubmed) were searched from January 2006 to April 2017, in addition to hand searching of relevant journals, reference lists, and grey literature. Results were merged using reference-management software (Endnote) and duplicates removed. Inclusion criteria were independently applied to potentially relevant articles by 3 reviewers. Findings were presented in a narrative synthesis to highlight key concepts addressed in the published literature. A total of 48 relevant publications were included in the review; 21 articles were identified as eligible from the database search, 4 from hand searching published work and 23 from the grey literature. The search process highlighted the voluminous literature reporting clinical variation internationally; yet, there is a dearth of evidence regarding systematic approaches to identifying or addressing UCV. Wennberg's classification framework is commonly cited in relation to classifying variation, but no single approach is agreed upon to systematically explore and address UCV. The instances of UCV that warrant investigation and action are largely determined at a systems level currently, and stakeholder engagement in this process is limited. Lack of consensus on an evidence-based definition for UCV remains a substantial barrier to progress in this field. © 2018 John Wiley & Sons, Ltd.

Regional geographic variations in kidney cancer incidence rates in European countries.

PubMed

Li, Peng; Znaor, Ariana; Holcatova, Ivana; Fabianova, Eleonora; Mates, Dana; Wozniak, Magdalena B; Ferlay, Jacques; Scelo, Ghislaine

2015-06-01

Marked unexplained national variations in incidence rates of kidney cancer have been observed for decades in Europe. To investigate geographic variations at the regional level and identify European regions with high incidence rates of kidney cancer. Regional- and national-level incidence data were extracted from the Cancer Incidence in Five Continents databases, local cancer registry databases, and local published reports. World population age-standardised rates (ASRs) were calculated for the periods 2003-2007 and 1988-1992. Rates by period and sex were compared using map visualisation. During 2003-2007, the highest ASR was found in the Plzen region, Czech Republic (31.4/100,000 person-years in men). Other regions of the Czech Republic had ASRs of 18.6-27.5/100,000 in men, with a tendency for higher rates in regions south of Prague. Surrounding regions, including eastern Germany and regions of Slovakia and Austria, had medium-to-high incidence rates (13.0-16.8/100,000 in men). Three other areas in Europe showed higher incidence rates in men compared with the rest of the continent: Lithuania, Estonia, Latvia, and Belarus (15.0-17.6/100,000); Iceland (13.5/100,000), and northern Italy (up to 16.0/100,000). Similar regional differences were observed among women, with rates approximately half of those observed in men in the same region. In general, these regional geographic variations remained stable over the periods 1988-1992 and 2003-2007, although higher incidence rates were detected in the Baltic countries in 2003-2007. Several European regions show particularly high rates of kidney cancer incidence. Large variations were observed within countries covered by national health-care systems, implying that overdetection is not the major factor. We present regional geographic variations in kidney cancer incidence rates in Europe. We highlight several regions with high incidence rates where further studies should be conducted for cancer control and prevention. Copyright © 2014 European Association of Urology. Published by Elsevier B.V. All rights reserved.

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement.

PubMed

Sandhu, Maninder; Sureshkumar, V; Prakash, Chandra; Dixit, Rekha; Solanke, Amolkumar U; Sharma, Tilak Raj; Mohapatra, Trilochan; S V, Amitha Mithra

2017-09-30

Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice. RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. 'Physical position search' is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the 'common genes across varieties' search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search. The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype. Database URL: http://14.139.229.201.

Linkage of the Canadian Study of Health and Aging to provincial administrative health care databases in Nova Scotia.

PubMed

Yip, A M; Kephart, G; Rockwood, K

2001-01-01

The Canadian Study of Health and Aging (CSHA) was a cohort study that included 528 Nova Scotian community-dwelling participants. Linkage of CSHA and provincial Medical Services Insurance (MSI) data enabled examination of health care utilization in this subsample. This article discusses methodological and ethical issues of database linkage and explores variation in the use of health services by demographic variables and health status. Utilization over 24 months following baseline was extracted from MSI's physician claims, hospital discharge abstracts, and Pharmacare claims databases. Twenty-nine subjects refused consent for access to their MSI file; health card numbers for three others could not be retrieved. A significant difference in healthcare use by age and self-rated health was revealed. Linkage of population-based data with provincial administrative health care databases has the potential to guide health care planning and resource allocation. This process must include steps to ensure protection of confidentiality. Standard practices for linkage consent and routine follow-up should be adopted. The Canadian Study of Health and Aging (CSHA) began in 1991-92 to explore dementia, frailty, and adverse health outcomes (Canadian Study of Health and Aging Working Group, 1994). The original CSHA proposal included linkage to provincial administrative health care databases by the individual CSHA study centers to enhance information on health care utilization and outcomes of study participants. In Nova Scotia, the Medical Services Insurance (MSI) administration, which drew the sampling frame for the original CSHA, did not retain the list of corresponding health card numbers. Furthermore, consent for this access was not asked of participants at the time of the first interview. The objectives of this study reported here were to examine the feasibility and ethical considerations of linking data from the CSHA to MSI utilization data, and to explore variation in health services use by demographic and health status characteristics in the Nova Scotia community cohort.

Seasonal evolution of soil and plant parameters on the agricultural Gebesee test site: a database for the set-up and validation of EO-LDAS and satellite-aided retrieval models

NASA Astrophysics Data System (ADS)

Truckenbrodt, Sina C.; Schmullius, Christiane C.

2018-03-01

Ground reference data are a prerequisite for the calibration, update, and validation of retrieval models facilitating the monitoring of land parameters based on Earth Observation data. Here, we describe the acquisition of a comprehensive ground reference database which was created to test and validate the recently developed Earth Observation Land Data Assimilation System (EO-LDAS) and products derived from remote sensing observations in the visible and infrared range. In situ data were collected for seven crop types (winter barley, winter wheat, spring wheat, durum, winter rape, potato, and sugar beet) cultivated on the agricultural Gebesee test site, central Germany, in 2013 and 2014. The database contains information on hyperspectral surface reflectance factors, the evolution of biophysical and biochemical plant parameters, phenology, surface conditions, atmospheric states, and a set of ground control points. Ground reference data were gathered at an approximately weekly resolution and on different spatial scales to investigate variations within and between acreages. In situ data collected less than 1 day apart from satellite acquisitions (RapidEye, SPOT 5, Landsat-7 and -8) with a cloud coverage ≤ 25 % are available for 10 and 15 days in 2013 and 2014, respectively. The measurements show that the investigated growing seasons were characterized by distinct meteorological conditions causing interannual variations in the parameter evolution. Here, the experimental design of the field campaigns, and methods employed in the determination of all parameters, are described in detail. Insights into the database are provided and potential fields of application are discussed. The data will contribute to a further development of crop monitoring methods based on remote sensing techniques. The database is freely available at PANGAEA (https://doi.org/10.1594/PANGAEA.874251).

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi.

PubMed

Irinyi, Laszlo; Serena, Carolina; Garcia-Hermoso, Dea; Arabatzis, Michael; Desnos-Ollivier, Marie; Vu, Duong; Cardinali, Gianluigi; Arthur, Ian; Normand, Anne-Cécile; Giraldo, Alejandra; da Cunha, Keith Cassia; Sandoval-Denis, Marcelo; Hendrickx, Marijke; Nishikaku, Angela Satie; de Azevedo Melo, Analy Salles; Merseguel, Karina Bellinghausen; Khan, Aziza; Parente Rocha, Juliana Alves; Sampaio, Paula; da Silva Briones, Marcelo Ribeiro; e Ferreira, Renata Carmona; de Medeiros Muniz, Mauro; Castañón-Olivares, Laura Rosio; Estrada-Barcenas, Daniel; Cassagne, Carole; Mary, Charles; Duan, Shu Yao; Kong, Fanrong; Sun, Annie Ying; Zeng, Xianyu; Zhao, Zuotao; Gantois, Nausicaa; Botterel, Françoise; Robbertse, Barbara; Schoch, Conrad; Gams, Walter; Ellis, David; Halliday, Catriona; Chen, Sharon; Sorrell, Tania C; Piarroux, Renaud; Colombo, Arnaldo L; Pais, Célia; de Hoog, Sybren; Zancopé-Oliveira, Rosely Maria; Taylor, Maria Lucia; Toriello, Conchita; de Almeida Soares, Célia Maria; Delhaes, Laurence; Stubbe, Dirk; Dromer, Françoise; Ranque, Stéphane; Guarro, Josep; Cano-Lira, Jose F; Robert, Vincent; Velegraki, Aristea; Meyer, Wieland

2015-05-01

Human and animal fungal pathogens are a growing threat worldwide leading to emerging infections and creating new risks for established ones. There is a growing need for a rapid and accurate identification of pathogens to enable early diagnosis and targeted antifungal therapy. Morphological and biochemical identification methods are time-consuming and require trained experts. Alternatively, molecular methods, such as DNA barcoding, a powerful and easy tool for rapid monophasic identification, offer a practical approach for species identification and less demanding in terms of taxonomical expertise. However, its wide-spread use is still limited by a lack of quality-controlled reference databases and the evolving recognition and definition of new fungal species/complexes. An international consortium of medical mycology laboratories was formed aiming to establish a quality controlled ITS database under the umbrella of the ISHAM working group on "DNA barcoding of human and animal pathogenic fungi." A new database, containing 2800 ITS sequences representing 421 fungal species, providing the medical community with a freely accessible tool at http://www.isham.org/ and http://its.mycologylab.org/ to rapidly and reliably identify most agents of mycoses, was established. The generated sequences included in the new database were used to evaluate the variation and overall utility of the ITS region for the identification of pathogenic fungi at intra-and interspecies level. The average intraspecies variation ranged from 0 to 2.25%. This highlighted selected pathogenic fungal species, such as the dermatophytes and emerging yeast, for which additional molecular methods/genetic markers are required for their reliable identification from clinical and veterinary specimens. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes.

PubMed

Chetal, Kashish; Janga, Sarath Chandra

2015-01-01

Background. In prokaryotic organisms, a substantial fraction of adjacent genes are organized into operons-codirectionally organized genes in prokaryotic genomes with the presence of a common promoter and terminator. Although several available operon databases provide information with varying levels of reliability, very few resources provide experimentally supported results. Therefore, we believe that the biological community could benefit from having a new operon prediction database with operons predicted using next-generation RNA-seq datasets. Description. We present operomeDB, a database which provides an ensemble of all the predicted operons for bacterial genomes using available RNA-sequencing datasets across a wide range of experimental conditions. Although several studies have recently confirmed that prokaryotic operon structure is dynamic with significant alterations across environmental and experimental conditions, there are no comprehensive databases for studying such variations across prokaryotic transcriptomes. Currently our database contains nine bacterial organisms and 168 transcriptomes for which we predicted operons. User interface is simple and easy to use, in terms of visualization, downloading, and querying of data. In addition, because of its ability to load custom datasets, users can also compare their datasets with publicly available transcriptomic data of an organism. Conclusion. OperomeDB as a database should not only aid experimental groups working on transcriptome analysis of specific organisms but also enable studies related to computational and comparative operomics.

Plant Genome Resources at the National Center for Biotechnology Information

PubMed Central

Wheeler, David L.; Smith-White, Brian; Chetvernin, Vyacheslav; Resenchuk, Sergei; Dombrowski, Susan M.; Pechous, Steven W.; Tatusova, Tatiana; Ostell, James

2005-01-01

The National Center for Biotechnology Information (NCBI) integrates data from more than 20 biological databases through a flexible search and retrieval system called Entrez. A core Entrez database, Entrez Nucleotide, includes GenBank and is tightly linked to the NCBI Taxonomy database, the Entrez Protein database, and the scientific literature in PubMed. A suite of more specialized databases for genomes, genes, gene families, gene expression, gene variation, and protein domains dovetails with the core databases to make Entrez a powerful system for genomic research. Linked to the full range of Entrez databases is the NCBI Map Viewer, which displays aligned genetic, physical, and sequence maps for eukaryotic genomes including those of many plants. A specialized plant query page allow maps from all plant genomes covered by the Map Viewer to be searched in tandem to produce a display of aligned maps from several species. PlantBLAST searches against the sequences shown in the Map Viewer allow BLAST alignments to be viewed within a genomic context. In addition, precomputed sequence similarities, such as those for proteins offered by BLAST Link, enable fluid navigation from unannotated to annotated sequences, quickening the pace of discovery. NCBI Web pages for plants, such as Plant Genome Central, complete the system by providing centralized access to NCBI's genomic resources as well as links to organism-specific Web pages beyond NCBI. PMID:16010002

Genome Variation Map: a data repository of genome variations in BIG Data Center

PubMed Central

Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang

2018-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473

Assembly: a resource for assembled genomes at NCBI

PubMed Central

Kitts, Paul A.; Church, Deanna M.; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G.; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D.; Pruitt, Kim D.; Kimchi, Avi

2016-01-01

The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site. PMID:26578580

Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices.

PubMed

Dececchi, T Alex; Mabee, Paula M; Blackburn, David C

2016-01-01

Databases of organismal traits that aggregate information from one or multiple sources can be leveraged for large-scale analyses in biology. Yet the differences among these data streams and how well they capture trait diversity have never been explored. We present the first analysis of the differences between phenotypes captured in free text of descriptive publications ('monographs') and those used in phylogenetic analyses ('matrices'). We focus our analysis on osteological phenotypes of the limbs of four extinct vertebrate taxa critical to our understanding of the fin-to-limb transition. We find that there is low overlap between the anatomical entities used in these two sources of phenotype data, indicating that phenotypes represented in matrices are not simply a subset of those found in monographic descriptions. Perhaps as expected, compared to characters found in matrices, phenotypes in monographs tend to emphasize descriptive and positional morphology, be somewhat more complex, and relate to fewer additional taxa. While based on a small set of focal taxa, these qualitative and quantitative data suggest that either source of phenotypes alone will result in incomplete knowledge of variation for a given taxon. As a broader community develops to use and expand databases characterizing organismal trait diversity, it is important to recognize the limitations of the data sources and develop strategies to more fully characterize variation both within species and across the tree of life.

Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices

PubMed Central

Dececchi, T. Alex; Mabee, Paula M.; Blackburn, David C.

2016-01-01

Databases of organismal traits that aggregate information from one or multiple sources can be leveraged for large-scale analyses in biology. Yet the differences among these data streams and how well they capture trait diversity have never been explored. We present the first analysis of the differences between phenotypes captured in free text of descriptive publications (‘monographs’) and those used in phylogenetic analyses (‘matrices’). We focus our analysis on osteological phenotypes of the limbs of four extinct vertebrate taxa critical to our understanding of the fin-to-limb transition. We find that there is low overlap between the anatomical entities used in these two sources of phenotype data, indicating that phenotypes represented in matrices are not simply a subset of those found in monographic descriptions. Perhaps as expected, compared to characters found in matrices, phenotypes in monographs tend to emphasize descriptive and positional morphology, be somewhat more complex, and relate to fewer additional taxa. While based on a small set of focal taxa, these qualitative and quantitative data suggest that either source of phenotypes alone will result in incomplete knowledge of variation for a given taxon. As a broader community develops to use and expand databases characterizing organismal trait diversity, it is important to recognize the limitations of the data sources and develop strategies to more fully characterize variation both within species and across the tree of life. PMID:27191170

UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.

PubMed

Lua, Rhonald C; Wilson, Stephen J; Konecki, Daniel M; Wilkins, Angela D; Venner, Eric; Morgan, Daniel H; Lichtarge, Olivier

2016-01-04

The structure and function of proteins underlie most aspects of biology and their mutational perturbations often cause disease. To identify the molecular determinants of function as well as targets for drugs, it is central to characterize the important residues and how they cluster to form functional sites. The Evolutionary Trace (ET) achieves this by ranking the functional and structural importance of the protein sequence positions. ET uses evolutionary distances to estimate functional distances and correlates genotype variations with those in the fitness phenotype. Thus, ET ranks are worse for sequence positions that vary among evolutionarily closer homologs but better for positions that vary mostly among distant homologs. This approach identifies functional determinants, predicts function, guides the mutational redesign of functional and allosteric specificity, and interprets the action of coding sequence variations in proteins, people and populations. Now, the UET database offers pre-computed ET analyses for the protein structure databank, and on-the-fly analysis of any protein sequence. A web interface retrieves ET rankings of sequence positions and maps results to a structure to identify functionally important regions. This UET database integrates several ways of viewing the results on the protein sequence or structure and can be found at http://mammoth.bcm.tmc.edu/uet/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Participation Patterns of Korean Adolescents in School-Based Career Exploration Activities

ERIC Educational Resources Information Center

Rojewski, Jay W.; Lee, In Heok; Hill, Roger B.

2014-01-01

Variations in the school-based career exploration activities of Korean high school students were examined. Data represented 5,227 Korean adolescents in Grade 11 contained in the Korean Education Longitudinal Study of 2005, a nationally representative longitudinal database administered by the Korean Educational Development Institute. Latent class…

PMHOME: A DATABASE OF CONTINUOUS PARTICLE MEASUREMENTS IN AN OCCUPIED HOUSE OVER A FOUR-YEAR PERIOD

EPA Science Inventory

Although considerable data exist on 24-hour integrated measurements of fine and coarse particles indoors, much less information is available on moment-to-moment variation for a full range of particle sizes including ultrafine particles. Also, information is limited on the rela...

Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection

USDA-ARS?s Scientific Manuscript database

Current advances in sequencing technologies and bioinformatics allow to determine a nearly complete genomic background of rice, a staple food for the poor people. Consequently, comprehensive databases of variation among thousands of varieties is currently being assembled and released. Proper analysi...

A Climatological Study of Cloud to Ground Lightning Strikes in the Vicinity of the Kennedy Space Center

NASA Technical Reports Server (NTRS)

Burns, Lee; Decker, Ryan

2004-01-01

Lightning strike location and peak current are monitored operationally in the Kennedy Space Center (KSC)/Cape Canaveral Air Force Station (CCAFS) area by the Cloud to Ground Lightning Surveillance System (CGLSS). The present study compiles ten years of CGLSS data into a climatological database of all strikes recorded within a 20-mile radius of space shuttle launch platform LP39A, which serves as a convenient central point. The period of record (POR) for the database runs from January 1, 1993 to December 31, 2002. Histograms and cumulative probability curves are produced to determine the distribution of occurrence rates for the spectrum of strike intensities (given in kA). Further analysis of the database provides a description of both seasonal and interannual variations in the lightning distribution.

Dietary choline and betaine intakes vary in an adult multiethnic population.

PubMed

Yonemori, Kim M; Lim, Unhee; Koga, Karin R; Wilkens, Lynne R; Au, Donna; Boushey, Carol J; Le Marchand, Loïc; Kolonel, Laurence N; Murphy, Suzanne P

2013-06-01

Choline and betaine are important nutrients for human health, but reference food composition databases for these nutrients became available only recently. We tested the feasibility of using these databases to estimate dietary choline and betaine intakes among ethnically diverse adults who participated in the Multiethnic Cohort (MEC) Study. Of the food items (n = 965) used to quantify intakes for the MEC FFQ, 189 items were exactly matched with items in the USDA Database for the Choline Content of Common Foods for total choline, choline-containing compounds, and betaine, and 547 items were matched to the USDA National Nutrient Database for Standard Reference for total choline (n = 547) and 148 for betaine. When a match was not found, choline and betaine values were imputed based on the same food with a different form (124 food items for choline, 300 for choline compounds, 236 for betaine), a similar food (n = 98, 284, and 227, respectively) or the closest item in the same food category (n = 6, 191, and 157, respectively), or the values were assumed to be zero (n = 1, 1, and 8, respectively). The resulting mean intake estimates for choline and betaine among 188,147 MEC participants (aged 45-75) varied by sex (372 and 154 mg/d in men, 304 and 128 mg/d in women, respectively; P-heterogeneity < 0.0001) and by race/ethnicity among Caucasians, African Americans, Japanese Americans, Latinos, and Native Hawaiians (P-heterogeneity < 0.0001), largely due to the variation in energy intake. Our findings demonstrate the feasibility of assessing choline and betaine intake and characterize the variation in intake that exists in a multiethnic population.

Variation in choice of study design: findings from the Epidemiology Design Decision Inventory and Evaluation (EDDIE) survey.

PubMed

Stang, Paul E; Ryan, Patrick B; Overhage, J Marc; Schuemie, Martijn J; Hartzema, Abraham G; Welebob, Emily

2013-10-01

Researchers using observational data to understand drug effects must make a number of analytic design choices that suit the characteristics of the data and the subject of the study. Review of the published literature suggests that there is a lack of consistency even when addressing the same research question in the same database. To characterize the degree of similarity or difference in the method and analysis choices made by observational database research experts when presented with research study scenarios. On-line survey using research scenarios on drug-effect studies to capture method selection and analysis choices that follow a dependency branching based on response to key questions. Voluntary participants experienced in epidemiological study design solicited for participation through registration on the Observational Medical Outcomes Partnership website, membership in particular professional organizations, or links in relevant newsletters. Description (proportion) of respondents selecting particular methods and making specific analysis choices based on individual drug-outcome scenario pairs. The number of questions/decisions differed based on stem questions of study design, time-at-risk, outcome definition, and comparator. There is little consistency across scenarios, by drug or by outcome of interest, in the decisions made for design and analyses in scenarios using large healthcare databases. The most consistent choice was the cohort study design but variability in the other critical decisions was common. There is great variation among epidemiologists in the design and analytical choices that they make when implementing analyses in observational healthcare databases. These findings confirm that it will be important to generate empiric evidence to inform these decisions and to promote a better understanding of the impact of standardization on research implementation.

The identification of incident cancers in UK primary care databases: a systematic review.

PubMed

Rañopa, Michael; Douglas, Ian; van Staa, Tjeerd; Smeeth, Liam; Klungel, Olaf; Reynolds, Robert; Bhaskaran, Krishnan

2015-01-01

UK primary care databases are frequently used in observational studies with cancer outcomes. We aimed to systematically review methods used by such studies to identify and validate incident cancers of the breast, colorectum, and prostate. Medline and Embase (1980-2013) were searched for UK primary care database studies with incident breast, colorectal, or prostate cancer outcomes. Data on the methods used for case ascertainment were extracted and summarised. Questionnaires were sent to corresponding authors to obtain details about case ascertainment. Eighty-four studies of breast (n = 51), colorectal (n = 54), and prostate cancer (n = 31) were identified; 30 examined >1 cancer type. Among the 84 studies, 57 defined cancers using only diagnosis codes, while 27 required further evidence such as chemotherapy. Few studies described methods used to create cancer code lists (n = 5); or made lists available directly (n = 5). Twenty-eight code lists were received on request from study authors. All included malignant neoplasm diagnosis codes, but there was considerable variation in the specific codes included which was not explained by coding dictionary changes. Code lists also varied in terms of other types of codes included, such as in-situ, cancer morphology, history of cancer, and secondary/suspected/borderline cancer codes. In UK primary care database studies, methods for identifying breast, colorectal, and prostate cancers were often unclear. Code lists were often unavailable, and where provided, we observed variation in the individual codes and types of codes included. Clearer reporting of methods and publication of code lists would improve transparency and reproducibility of studies. Copyright © 2014 John Wiley & Sons, Ltd.

Dietary Choline and Betaine Intakes Vary in an Adult Multiethnic Population123

PubMed Central

Yonemori, Kim M.; Lim, Unhee; Koga, Karin R.; Wilkens, Lynne R.; Au, Donna; Boushey, Carol J.; Le Marchand, Loïc; Kolonel, Laurence N.; Murphy, Suzanne P.

2013-01-01

Choline and betaine are important nutrients for human health, but reference food composition databases for these nutrients became available only recently. We tested the feasibility of using these databases to estimate dietary choline and betaine intakes among ethnically diverse adults who participated in the Multiethnic Cohort (MEC) Study. Of the food items (n = 965) used to quantify intakes for the MEC FFQ, 189 items were exactly matched with items in the USDA Database for the Choline Content of Common Foods for total choline, choline-containing compounds, and betaine, and 547 items were matched to the USDA National Nutrient Database for Standard Reference for total choline (n = 547) and 148 for betaine. When a match was not found, choline and betaine values were imputed based on the same food with a different form (124 food items for choline, 300 for choline compounds, 236 for betaine), a similar food (n = 98, 284, and 227, respectively) or the closest item in the same food category (n = 6, 191, and 157, respectively), or the values were assumed to be zero (n = 1, 1, and 8, respectively). The resulting mean intake estimates for choline and betaine among 188,147 MEC participants (aged 45–75) varied by sex (372 and 154 mg/d in men, 304 and 128 mg/d in women, respectively; P-heterogeneity < 0.0001) and by race/ethnicity among Caucasians, African Americans, Japanese Americans, Latinos, and Native Hawaiians (P-heterogeneity < 0.0001), largely due to the variation in energy intake. Our findings demonstrate the feasibility of assessing choline and betaine intake and characterize the variation in intake that exists in a multiethnic population. PMID:23616508

New data-driven estimation of terrestrial CO2 fluxes in Asia using a standardized database of eddy covariance measurements, remote sensing data, and support vector regression

NASA Astrophysics Data System (ADS)

Ichii, Kazuhito; Ueyama, Masahito; Kondo, Masayuki; Saigusa, Nobuko; Kim, Joon; Alberto, Ma. Carmelita; Ardö, Jonas; Euskirchen, Eugénie S.; Kang, Minseok; Hirano, Takashi; Joiner, Joanna; Kobayashi, Hideki; Marchesini, Luca Belelli; Merbold, Lutz; Miyata, Akira; Saitoh, Taku M.; Takagi, Kentaro; Varlagin, Andrej; Bret-Harte, M. Syndonia; Kitamura, Kenzo; Kosugi, Yoshiko; Kotani, Ayumi; Kumar, Kireet; Li, Sheng-Gong; Machimura, Takashi; Matsuura, Yojiro; Mizoguchi, Yasuko; Ohta, Takeshi; Mukherjee, Sandipan; Yanagi, Yuji; Yasuda, Yukio; Zhang, Yiping; Zhao, Fenghua

2017-04-01

The lack of a standardized database of eddy covariance observations has been an obstacle for data-driven estimation of terrestrial CO2 fluxes in Asia. In this study, we developed such a standardized database using 54 sites from various databases by applying consistent postprocessing for data-driven estimation of gross primary productivity (GPP) and net ecosystem CO2 exchange (NEE). Data-driven estimation was conducted by using a machine learning algorithm: support vector regression (SVR), with remote sensing data for 2000 to 2015 period. Site-level evaluation of the estimated CO2 fluxes shows that although performance varies in different vegetation and climate classifications, GPP and NEE at 8 days are reproduced (e.g., r2 = 0.73 and 0.42 for 8 day GPP and NEE). Evaluation of spatially estimated GPP with Global Ozone Monitoring Experiment 2 sensor-based Sun-induced chlorophyll fluorescence shows that monthly GPP variations at subcontinental scale were reproduced by SVR (r2 = 1.00, 0.94, 0.91, and 0.89 for Siberia, East Asia, South Asia, and Southeast Asia, respectively). Evaluation of spatially estimated NEE with net atmosphere-land CO2 fluxes of Greenhouse Gases Observing Satellite (GOSAT) Level 4A product shows that monthly variations of these data were consistent in Siberia and East Asia; meanwhile, inconsistency was found in South Asia and Southeast Asia. Furthermore, differences in the land CO2 fluxes from SVR-NEE and GOSAT Level 4A were partially explained by accounting for the differences in the definition of land CO2 fluxes. These data-driven estimates can provide a new opportunity to assess CO2 fluxes in Asia and evaluate and constrain terrestrial ecosystem models.

Influence of rumen protozoa on methane emission in ruminants: a meta-analysis approach.

PubMed

Guyader, J; Eugène, M; Nozière, P; Morgavi, D P; Doreau, M; Martin, C

2014-11-01

A meta-analysis was conducted to evaluate the effects of protozoa concentration on methane emission from ruminants. A database was built from 59 publications reporting data from 76 in vivo experiments. The experiments included in the database recorded methane production and rumen protozoa concentration measured on the same groups of animals. Quantitative data such as diet chemical composition, rumen fermentation and microbial parameters, and qualitative information such as methane mitigation strategies were also collected. In the database, 31% of the experiments reported a concomitant reduction of both protozoa concentration and methane emission (g/kg dry matter intake). Nearly all of these experiments tested lipids as methane mitigation strategies. By contrast, 21% of the experiments reported a variation in methane emission without changes in protozoa numbers, indicating that methanogenesis is also regulated by other mechanisms not involving protozoa. Experiments that used chemical compounds as an antimethanogenic treatment belonged to this group. The relationship between methane emission and protozoa concentration was studied with a variance-covariance model, with experiment as a fixed effect. The experiments included in the analysis had a within-experiment variation of protozoa concentration higher than 5.3 log10 cells/ml corresponding to the average s.e.m. of the database for this variable. To detect potential interfering factors for the relationship, the influence of several qualitative and quantitative secondary factors was tested. This meta-analysis showed a significant linear relationship between methane emission and protozoa concentration: methane (g/kg dry matter intake)=-30.7+8.14×protozoa (log10 cells/ml) with 28 experiments (91 treatments), residual mean square error=1.94 and adjusted R 2=0.90. The proportion of butyrate in the rumen positively influenced the least square means of this relationship.

Choice of treatment modalities was not influenced by pain, severity or co-morbidity in patients with knee osteoarthritis.

PubMed

Jamtvedt, Gro; Dahm, Kristin Thuve; Holm, Inger; Odegaard-Jensen, Jan; Flottorp, Signe

2010-03-01

Patients with knee osteoarthritis (OA) are commonly treated by physiotherapists in primary care. The physiotherapists use different treatment modalities. In a previous study, we identified variation in the use of transcutaneous electrical nerve stimulation (TENS), low level laser or acupuncture, massage and weight reduction advice for patients with knee OA. The purpose of this study was to examine factors that might explain variation in treatment modalities for patients with knee OA. Practising physiotherapists prospectively collected data for one patient with knee osteoarthritis each through 12 treatment sessions.We chose to examine factors that might explain variation in the choice of treatment modalities supported by high or moderate quality evidence, and modalities which were frequently used but which were not supported by evidence from systematic reviews. Experienced clinicians proposed factors that they thought might explain the variation in the choice of these specific treatments. We used these factors in explanatory analyses. Using TENS, low level laser or acupuncture was significantly associated with having searched databases to help answer clinical questions in the last six months (odds ratio [OR] = 1.93, 95% confidence interval [CI] = 1.08-3.42). Not having Internet access at work and using more than four treatment modalities were significant determinants for giving massage (OR = 0.36, 95% CI = 0.19-0.68 and OR = 8.92, 95% CI = 4.37-18.21, respectively). Being a female therapist significantly increased the odds for providing weight reduction advice (OR = 3.60, 95% CI = 1.12-11.57). No patient characteristics, such as age, pain or co-morbidity, were significantly associated with variation in practice. Factors related to patient characteristics, such as pain severity and co-morbidity, did not seem to explain variation in treatment modalities for patients with knee OA. Variation was associated with the following factors: physiotherapists having Internet access at work, physiotherapists having searched databases for the last six months and the gender of the therapist. There is a need for more studies of determinants for physiotherapy practice. (c) 2009 John Wiley & Sons, Ltd.

State-by-state variations in cardiac rehabilitation participation are associated with educational attainment, income, and program availability.

PubMed

Gaalema, Diann E; Higgins, Stephen T; Shepard, Donald S; Suaya, Jose A; Savage, Patrick D; Ades, Philip A

2014-01-01

Wide geographic variations in cardiac rehabilitation (CR) participation in the United States have been demonstrated but are not well understood. Socioeconomic factors such as educational attainment are robust predictors of many health-related behaviors, including smoking, obesity, physical activity, substance abuse, and cardiovascular disease. We investigated potential associations between state-level differences in educational attainment, other socioeconomic factors, CR program availability, and variations in CR participation. A retrospective database analysis was conducted using data from the US Census Bureau, the Centers for Disease Control and Prevention, and the 1997 Medicare database. The outcome of interest was CR participation rates by state, and predictors included state-level high school (HS) graduation rates (in 2001 and 1970), median household income, smoking rates, density of CR program (programs per square mile and per state population), sex and race ratios, and median age. The relationship between HS graduation rates and CR participation by state was significant for both 2001 and 1970 (r = 0.64 and 0.44, respectively, P < .01). Adding the density of CR programs (per population) and income contributed significantly with a cumulative r value of 0.74 and 0.71 for the models using 2001 and 1970, respectively (Ps < .01). The amount of variance accounted for by each of the 3 variables differed between the 2000 and 1970 graduation rates, but both models were unaltered by including additional variables. State-level HS graduation rates, CR programs expressed as programs per population, and median income were strongly associated with geographic variations in CR participation rates.

On Quasi-biennial Oscillations in Chromospheric Macrospicules and Their Potential Relation to the Global Solar Magnetic Field

NASA Astrophysics Data System (ADS)

Kiss, T. S.; Erdélyi, R.

2018-04-01

This study aims to provide further evidence for the potential influence of the global solar magnetic field on localized chromospheric jets, the macrospicules (MS). To find a connection between the long-term variation of properties of MS and other solar activity proxies, including, e.g., the temporal variation of the frequency shift of solar global oscillations, sunspot area, etc., a database overarching seven years of observations was compiled. This database contains 362 MS, based on observations at the 30.4 nm of the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory. Three of the five investigated physical properties of MS show a clear long-term temporal variation after smoothing the raw data. Wavelet analysis of the temporal variation of maximum length, maximum area, and average velocity is carried out. The results reveal a strong pattern of periodicities at around 2 years (also referred to as quasi-biennial oscillations—QBOs). A comparison with solar activity proxies that also possess the properties of QBOs provides some interesting features: the minima and maxima of QBOs of MS properties occur at around the same epoch as the minima and maxima of these activity proxies. For most of the time span investigated, the oscillations are out of phase. This out-of-phase behavior was also corroborated by a cross-correlation analysis. These results suggest that the physical processes that generate and drive the long-term evolution of the global solar activity proxies may be coupled to the short-term local physical processes driving the macrospicules, and, therefore modulate the properties of local dynamics.

Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains.

PubMed

Solano-Román, Antonio; Alfaro-Arias, Verónica; Cruz-Castillo, Carlos; Orozco-Solano, Allan

2018-03-15

VizGVar was designed to meet the growing need of the research community for improved genomic and proteomic data viewers that benefit from better information visualization. We implemented a new information architecture and applied user centered design principles to provide a new improved way of visualizing genetic information and protein data related to human disease. VizGVar connects the entire database of Ensembl protein motifs, domains, genes and exons with annotated SNPs and somatic variations from PharmGKB and COSMIC. VizGVar precisely represents genetic variations and their respective location by colored curves to designate different types of variations. The structured hierarchy of biological data is reflected in aggregated patterns through different levels, integrating several layers of information at once. VizGVar provides a new interactive, web-based JavaScript visualization of somatic mutations and protein variation, enabling fast and easy discovery of clinically relevant variation patterns. VizGVar is accessible at http://vizport.io/vizgvar; http://vizport.io/vizgvar/doc/. asolano@broadinstitute.org or allan.orozcosolano@ucr.ac.cr.

Variations of archived static-weight data and WIM

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

Elliott, C.J.; Gillmann, R.; Kent, P.M.

1998-12-01

Using seven-card archived, static-weight and weigh-in-motion (WIM), truck data received by FHWA for 1966--1992, the authors examine the fluctuations of four fiducial weight measures reported at weight sites in the 50 states. The reduced 172 MB Class 9 (332000) database was prepared and ordered from 2 CD-ROMS with duplicate records removed. Front-axle weight and gross-vehicle weight (GVW) are combined conceptually by determining the front axle weight in four-quartile GVW categories. The four categories of front axle weight from the four GVW categories are combined in four ways. Three linear combinations are with fixed-coefficient fiducials and one is that optimal linearmore » combination producing the smallest standard deviation to mean value ratio. The best combination gives coefficients of variation of 2--3% for samples of 100 trucks, below the expected accuracy of single-event WIM measurements. Time tracking of data shows some high-variation sites have seasonal variations, or linear variations over the time-ordered samples. Modeling of these effects is very site specific but provides a way to reduce high variations. Some automatic calibration schemes would erroneously remove such seasonal or linear variations were they static effects.« less

Mapping the influence of the deep Nazca slab on the geometry of the 660-km discontinuity beneath stable South America

NASA Astrophysics Data System (ADS)

Bianchi, M. B. D.; Assumpcao, M.; Julià, J.

2017-12-01

The fate of the deep Nazca subducted plate is poorly mapped under stable South America. Transition zone thickness and position is greatly dependent on mantle temperature and so is influenced by the colder Nazca plate position. We use a database of 35,000 LQT deconvolved receiver function traces to image the mantle transition zone and other upper mantle discontinuities under different terranes of stable South American continent. Data from the entire Brazilian Seismographic Network database, consisting of more than 80 broadband stations supplemented by 35 temporary stations deployed in west Brazil, Argentina, Paraguay, Bolivia and Uruguay were processed. Our results indicates that upper mantle velocities are faster than average under stable cratons and that most of the discontinuities are positioned with small variations in respect to nominal depths, except in places were the Nazca plate interacts with the transition zone. Under the Chaco-Pantanal basin the Nazca plate appears to be trapped in the transition zone for more than 1000 km with variations of up to 30 km in 660 km discontinuity topography under this region consistent with global tomographic models. Additional results obtained from SS precursor analysis of South Sandwich Islands teleseismic events recorded at USArray stations indicates that variations of transition zones thickness occur where the Nazca plate interacts with the upper mantle discontinuities in the northern part of Stable South American continent.

Global Survey Method for the World Network of Neutron Monitors

NASA Astrophysics Data System (ADS)

Belov, A. V.; Eroshenko, E. A.; Yanke, V. G.; Oleneva, V. A.; Abunina, M. A.; Abunin, A. A.

2018-05-01

One of the variants of the global survey method developed and used for many years at the Institute of Terrestrial Magnetism, Ionosphere, and Radio Wave Propagation of the Russian Academy of Sciences is described. Data from the world network of neutron monitors for every hour from July 1957 to the present has been processed by this method. A consistent continuous series of hourly characteristics of variation of the density and vector anisotropy of cosmic rays with a rigidity of 10 GV is obtained. A database of Forbush decreases in galactic cosmic rays caused by large-scale disturbances of the interplanetary medium for more than half a century has been created based on this series. The capabilities of the database make it possible to perform a correlation analysis of various parameters of the space environment (characteristics of the Sun, solar wind, and interplanetary magnetic field) with the parameters of cosmic rays and to study their interrelationships in the solar-terrestrial space. The features of reception coefficients for different stations are considered, which allows the transition from variations according to ground measurements to variations of primary cosmic rays. The advantages and disadvantages of this variant of the global survey method and the opportunities for its development and improvement are assessed. The developed method makes it possible to minimize the problems of the network of neutron monitors and to make significant use of its advantages.

Global Analysis, Interpretation, and Modelling: First Science Conference

NASA Technical Reports Server (NTRS)

Sahagian, Dork

1995-01-01

Topics considered include: Biomass of termites and their emissions of methane and carbon dioxide - A global database; Carbon isotope discrimination during photosynthesis and the isotope ratio of respired CO2 in boreal forest ecosystems; Estimation of methane emission from rice paddies in mainland China; Climate and nitrogen controls on the geography and timescales of terrestrial biogeochemical cycling; Potential role of vegetation feedback in the climate sensitivity of high-latitude regions - A case study at 6000 years B.P.; Interannual variation of carbon exchange fluxes in terrestrial ecosystems; and Variations in modeled atmospheric transport of carbon dioxide and the consequences for CO2 inversions.

BIOFRAG - a new database for analyzing BIOdiversity responses to forest FRAGmentation

Treesearch

M. Pfeifer; Tamara Heartsill Scalley

2014-01-01

Habitat fragmentation studies have produced complex results that are challenging to synthesize. Inconsistencies among studies may result from variation in the choice of landscape metrics and response variables, which is often compounded by a lack of key statistical or methodological information. Collating primary datasets on biodiversity responses to fragmentation in a...

Assessing variability in chemical acute toxicity of unionid mussels: Influence of intra- and inter-laboratory testing, life stage, and species

EPA Science Inventory

The authors developed a toxicity database for unionid mussels to examine the extent of intra- and interlaboratory variability in acute toxicity tests with mussel larvae (glochidia) and juveniles; the extent of differential sensitivity of the 2 life stages; and the variation in se...

Spoken Words. Technical Report No. 177.

ERIC Educational Resources Information Center

Hall, William S.; And Others

The word frequency lists presented in this publication were compiled to create a database for further research into vocabulary use, especially the variation in vocabulary due to differences in situation and social group membership. Taken from the natural conversations of 40 target children (four and a half to five years old) with their families,…

Social Change and Anomie: A Cross-National Study

ERIC Educational Resources Information Center

Zhao, Ruohui; Cao, Liqun

2010-01-01

We apply Durkheim's social transitional theory to explain the variation of anomie in 30 nations in the world. Combining data from two sources--the 1995 "World Values Survey and the United Nations University's World Income Inequality Database" or WIID--we test the hypothesis that rapid sociopolitical change at the structural level disrupts social…

Voxel-Based Morphometry ALE meta-analysis of Bipolar Disorder

NASA Astrophysics Data System (ADS)

Magana, Omar; Laird, Robert

2012-03-01

A meta-analysis was performed independently to view the changes in gray matter (GM) on patients with Bipolar disorder (BP). The meta-analysis was conducted on a Talairach Space using GingerALE to determine the voxels and their permutation. In order to achieve the data acquisition, published experiments and similar research studies were uploaded onto the online Voxel-Based Morphometry database (VBM). By doing so, coordinates of activation locations were extracted from Bipolar disorder related journals utilizing Sleuth. Once the coordinates of given experiments were selected and imported to GingerALE, a Gaussian was performed on all foci points to create the concentration points of GM on BP patients. The results included volume reductions and variations of GM between Normal Healthy controls and Patients with Bipolar disorder. A significant amount of GM clusters were obtained in Normal Healthy controls over BP patients on the right precentral gyrus, right anterior cingulate, and the left inferior frontal gyrus. In future research, more published journals could be uploaded onto the database and another VBM meta-analysis could be performed including more activation coordinates or a variation of age groups.

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.

PubMed

Wen, Bo; Xu, Shaohang; Sheynkman, Gloria M; Feng, Qiang; Lin, Liang; Wang, Quanhui; Xu, Xun; Wang, Jun; Liu, Siqi

2014-11-01

Single nucleotide variations (SNVs) located within a reading frame can result in single amino acid polymorphisms (SAPs), leading to alteration of the corresponding amino acid sequence as well as function of a protein. Accurate detection of SAPs is an important issue in proteomic analysis at the experimental and bioinformatic level. Herein, we present sapFinder, an R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. This package automates the construction of variation-associated databases from public SNV repositories or sample-specific next-generation sequencing (NGS) data and the identification of SAPs through database searching, post-processing and generation of HTML-based report with visualized interface. sapFinder is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at http://bioconductor.org/packages/devel/bioc/html/sapFinder.html and are provided under a GPL-2 license. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Developments in Post-marketing Comparative Effectiveness Research

PubMed Central

S, Schneeweiss

2010-01-01

Physicians and insurers need to weigh the effectiveness of new drugs against existing therapeutics in routine care to make decisions about treatment and formularies. Because Food and Drug Administration (FDA) approval of most new drugs requires demonstrating efficacy and safety against placebo, there is limited interest by manufacturers in conducting such head-to-head trials. Comparative effectiveness research seeks to provide head-to-head comparisons of treatment outcomes in routine care. Health-care utilization databases record drug use and selected health outcomes for large populations in a timely way and reflect routine care, and therefore may be the preferred data source for comparative effectiveness research. Confounding caused by selective prescribing based on indication, severity, and prognosis threatens the validity of non-randomized database studies that often have limited details on clinical information. Several recent developments may bring the field closer to acceptable validity, including approaches that exploit the concepts of proxy variables using high-dimensional propensity scores, within-patient variation of drug exposure using crossover designs, and between-provider variation in prescribing preference using instrumental variable (IV) analyses. PMID:17554243

Genetic diversity of Taenia asiatica from Thailand and other geographical locations as revealed by cytochrome c oxidase subunit 1 sequences.

PubMed

Anantaphruti, Malinee Thairungroj; Thaenkham, Urusa; Watthanakulpanich, Dorn; Phuphisut, Orawan; Maipanich, Wanna; Yoonuan, Tippayarat; Nuamtanong, Supaporn; Pubampen, Somjit; Sanguankiat, Surapol

2013-02-01

Twelve 924 bp cytochrome c oxidase subunit 1 (cox1) mitochondrial DNA sequences from Taenia asiatica isolates from Thailand were aligned and compared with multiple sequence isolates from Thailand and 6 other countries from the GenBank database. The genetic divergence of T. asiatica was also compared with Taenia saginata database sequences from 6 different countries in Asia, including Thailand, and 3 countries from other continents. The results showed that there were minor genetic variations within T. asiatica species, while high intraspecies variation was found in T. saginata. There were only 2 haplotypes and 1 polymorphic site found in T. asiatica, but 8 haplotypes and 9 polymorphic sites in T. saginata. Haplotype diversity was very low, 0.067, in T. asiatica and high, 0.700, in T. saginata. The very low genetic diversity suggested that T. asiatica may be at a risk due to the loss of potential adaptive alleles, resulting in reduced viability and decreased responses to environmental changes, which may endanger the species.

Genetic Diversity of Taenia asiatica from Thailand and Other Geographical Locations as Revealed by Cytochrome c Oxidase Subunit 1 Sequences

PubMed Central

Thaenkham, Urusa; Watthanakulpanich, Dorn; Phuphisut, Orawan; Maipanich, Wanna; Yoonuan, Tippayarat; Nuamtanong, Supaporn; Pubampen, Somjit; Sanguankiat, Surapol

2013-01-01

Twelve 924 bp cytochrome c oxidase subunit 1 (cox1) mitochondrial DNA sequences from Taenia asiatica isolates from Thailand were aligned and compared with multiple sequence isolates from Thailand and 6 other countries from the GenBank database. The genetic divergence of T. asiatica was also compared with Taenia saginata database sequences from 6 different countries in Asia, including Thailand, and 3 countries from other continents. The results showed that there were minor genetic variations within T. asiatica species, while high intraspecies variation was found in T. saginata. There were only 2 haplotypes and 1 polymorphic site found in T. asiatica, but 8 haplotypes and 9 polymorphic sites in T. saginata. Haplotype diversity was very low, 0.067, in T. asiatica and high, 0.700, in T. saginata. The very low genetic diversity suggested that T. asiatica may be at a risk due to the loss of potential adaptive alleles, resulting in reduced viability and decreased responses to environmental changes, which may endanger the species. PMID:23467439

Sequential Total Variation Denoising for the Extraction of Fetal ECG from Single-Channel Maternal Abdominal ECG

PubMed Central

Lee, Kwang Jin; Lee, Boreom

2016-01-01

Fetal heart rate (FHR) is an important determinant of fetal health. Cardiotocography (CTG) is widely used for measuring the FHR in the clinical field. However, fetal movement and blood flow through the maternal blood vessels can critically influence Doppler ultrasound signals. Moreover, CTG is not suitable for long-term monitoring. Therefore, researchers have been developing algorithms to estimate the FHR using electrocardiograms (ECGs) from the abdomen of pregnant women. However, separating the weak fetal ECG signal from the abdominal ECG signal is a challenging problem. In this paper, we propose a method for estimating the FHR using sequential total variation denoising and compare its performance with that of other single-channel fetal ECG extraction methods via simulation using the Fetal ECG Synthetic Database (FECGSYNDB). Moreover, we used real data from PhysioNet fetal ECG databases for the evaluation of the algorithm performance. The R-peak detection rate is calculated to evaluate the performance of our algorithm. Our approach could not only separate the fetal ECG signals from the abdominal ECG signals but also accurately estimate the FHR. PMID:27376296

Sequential Total Variation Denoising for the Extraction of Fetal ECG from Single-Channel Maternal Abdominal ECG.

PubMed

Lee, Kwang Jin; Lee, Boreom

2016-07-01

Fetal heart rate (FHR) is an important determinant of fetal health. Cardiotocography (CTG) is widely used for measuring the FHR in the clinical field. However, fetal movement and blood flow through the maternal blood vessels can critically influence Doppler ultrasound signals. Moreover, CTG is not suitable for long-term monitoring. Therefore, researchers have been developing algorithms to estimate the FHR using electrocardiograms (ECGs) from the abdomen of pregnant women. However, separating the weak fetal ECG signal from the abdominal ECG signal is a challenging problem. In this paper, we propose a method for estimating the FHR using sequential total variation denoising and compare its performance with that of other single-channel fetal ECG extraction methods via simulation using the Fetal ECG Synthetic Database (FECGSYNDB). Moreover, we used real data from PhysioNet fetal ECG databases for the evaluation of the algorithm performance. The R-peak detection rate is calculated to evaluate the performance of our algorithm. Our approach could not only separate the fetal ECG signals from the abdominal ECG signals but also accurately estimate the FHR.

Developments in post-marketing comparative effectiveness research.

PubMed

Schneeweiss, S

2007-08-01

Physicians and insurers need to weigh the effectiveness of new drugs against existing therapeutics in routine care to make decisions about treatment and formularies. Because Food and Drug Administration (FDA) approval of most new drugs requires demonstrating efficacy and safety against placebo, there is limited interest by manufacturers in conducting such head-to-head trials. Comparative effectiveness research seeks to provide head-to-head comparisons of treatment outcomes in routine care. Health-care utilization databases record drug use and selected health outcomes for large populations in a timely way and reflect routine care, and therefore may be the preferred data source for comparative effectiveness research. Confounding caused by selective prescribing based on indication, severity, and prognosis threatens the validity of non-randomized database studies that often have limited details on clinical information. Several recent developments may bring the field closer to acceptable validity, including approaches that exploit the concepts of proxy variables using high-dimensional propensity scores, within-patient variation of drug exposure using crossover designs, and between-provider variation in prescribing preference using instrumental variable (IV) analyses.

Promise and Limitations of Big Data Research in Plastic Surgery.

PubMed

Zhu, Victor Zhang; Tuggle, Charles Thompson; Au, Alexander Francis

2016-04-01

The use of "Big Data" in plastic surgery outcomes research has increased dramatically in the last 5 years. This article addresses some of the benefits and limitations of such research. This is a narrative review of large database studies in plastic surgery. There are several benefits to database research as compared with traditional forms of research, such as randomized controlled studies and cohort studies. These include the ease in patient recruitment, reduction in selection bias, and increased generalizability. As such, the types of outcomes research that are particularly suited for database studies include determination of geographic variations in practice, volume outcome analysis, evaluation of how sociodemographic factors affect access to health care, and trend analyses over time. The limitations of database research include data which are limited only to what was captured in the database, high power which can cause clinically insignificant differences to achieve statistical significance, and fishing which can lead to increased type I errors. The National Surgical Quality Improvement Project is an important general surgery database that may be useful for plastic surgeons because it is validated and has a large number of patients after over a decade of collecting data. The Tracking Operations and Outcomes for Plastic Surgeons Program is a newer database specific to plastic surgery. Databases are a powerful tool for plastic surgery outcomes research. It is critically important to understand their benefits and limitations when designing research projects or interpreting studies whose data have been drawn from them. For plastic surgeons, National Surgical Quality Improvement Project has a greater number of publications, but Tracking Operations and Outcomes for Plastic Surgeons Program is the most applicable database for plastic surgery research.

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation

PubMed Central

Kristensen, David M.; Wolf, Yuri I.; Koonin, Eugene V.

2017-01-01

The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e.g. species), whereas the entire collection of ATGCs is useful for macroevolutionary studies. The ATGC database includes many forms of pre-computed data, in particular ATGC-COGs (Clusters of Orthologous Genes), multiple sequence alignments, a set of ‘index’ orthologs representing the most well-conserved members of each ATGC-COG, the phylogenetic tree of the organisms within each ATGC, etc. Although the ATGC database contains several million proteins from thousands of genomes organized into hundreds of clusters (roughly a 4-fold increase since the last version of the ATGC database), it is now built with completely automated methods and will be regularly updated following new releases of the NCBI RefSeq database. The ATGC database is hosted jointly at the University of Iowa at dmk-brain.ecn.uiowa.edu/ATGC/ and the NCBI at ftp.ncbi.nlm.nih.gov/pub/kristensen/ATGC/atgc_home.html. PMID:28053163

Assessment of COPD-related outcomes via a national electronic medical record database.

PubMed

Asche, Carl; Said, Quayyim; Joish, Vijay; Hall, Charles Oaxaca; Brixner, Diana

2008-01-01

The technology and sophistication of healthcare utilization databases have expanded over the last decade to include results of lab tests, vital signs, and other clinical information. This review provides an assessment of the methodological and analytical challenges of conducting chronic obstructive pulmonary disease (COPD) outcomes research in a national electronic medical records (EMR) dataset and its potential application towards the assessment of national health policy issues, as well as a description of the challenges or limitations. An EMR database and its application to measuring outcomes for COPD are described. The ability to measure adherence to the COPD evidence-based practice guidelines, generated by the NIH and HEDIS quality indicators, in this database was examined. Case studies, before and after their publication, were used to assess the adherence to guidelines and gauge the conformity to quality indicators. EMR was the only source of information for pulmonary function tests, but low frequency in ordering by primary care was an issue. The EMR data can be used to explore impact of variation in healthcare provision on clinical outcomes. The EMR database permits access to specific lab data and biometric information. The richness and depth of information on "real world" use of health services for large population-based analytical studies at relatively low cost render such databases an attractive resource for outcomes research. Various sources of information exist to perform outcomes research. It is important to understand the desired endpoints of such research and choose the appropriate database source.

The Effect of Geographic Units of Analysis on Measuring Geographic Variation in Medical Services Utilization.

PubMed

Kim, Agnus M; Park, Jong Heon; Kang, Sungchan; Hwang, Kyosang; Lee, Taesik; Kim, Yoon

2016-07-01

We aimed to evaluate the effect of geographic units of analysis on measuring geographic variation in medical services utilization. For this purpose, we compared geographic variations in the rates of eight major procedures in administrative units (districts) and new areal units organized based on the actual health care use of the population in Korea. To compare geographic variation in geographic units of analysis, we calculated the age-sex standardized rates of eight major procedures (coronary artery bypass graft surgery, percutaneous transluminal coronary angioplasty, surgery after hip fracture, knee-replacement surgery, caesarean section, hysterectomy, computed tomography scan, and magnetic resonance imaging scan) from the National Health Insurance database in Korea for the 2013 period. Using the coefficient of variation, the extremal quotient, and the systematic component of variation, we measured geographic variation for these eight procedures in districts and new areal units. Compared with districts, new areal units showed a reduction in geographic variation. Extremal quotients and inter-decile ratios for the eight procedures were lower in new areal units. While the coefficient of variation was lower for most procedures in new areal units, the pattern of change of the systematic component of variation between districts and new areal units differed among procedures. Geographic variation in medical service utilization could vary according to the geographic unit of analysis. To determine how geographic characteristics such as population size and number of geographic units affect geographic variation, further studies are needed.

Rationale and uses of a public HIV drug-resistance database.

PubMed

Shafer, Robert W

2006-09-15

Knowledge regarding the drug resistance of human immunodeficiency virus (HIV) is critical for surveillance of drug resistance, development of antiretroviral drugs, and management of infections with drug-resistant viruses. Such knowledge is derived from studies that correlate genetic variation in the targets of therapy with the antiretroviral treatments received by persons from whom the variant was obtained (genotype-treatment), with drug-susceptibility data on genetic variants (genotype-phenotype), and with virological and clinical response to a new treatment regimen (genotype-outcome). An HIV drug-resistance database is required to represent, store, and analyze the diverse forms of data underlying our knowledge of drug resistance and to make these data available to the broad community of researchers studying drug resistance in HIV and clinicians using HIV drug-resistance tests. Such genotype-treatment, genotype-phenotype, and genotype-outcome correlations are contained in the Stanford HIV RT and Protease Sequence Database and have specific usefulness.

MSDB: A Comprehensive Database of Simple Sequence Repeats

PubMed Central

Avvaru, Akshay Kumar; Saxena, Saketh; Mishra, Rakesh Kumar

2017-01-01

Abstract Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1–6 nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of >650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb. PMID:28854643

Interactive DataBase of Cosmic Ray Anisotropy (DB A10)

NASA Astrophysics Data System (ADS)

Asipenka, A.S.; Belov, A.V.; Eroshenko, E.F.; Klepach, E.G.; Oleneva, V.A.; Yake, V.G.

Data on the hourly means of cosmic ray density and anisotropy derived by the GSM method over the 1957-2006 are introduced in to MySQL database. This format allowed an access to data both in local and in the Internet. Using the realized combination of script-language Php and My SQL database the Internet project was created on the access for users data on the CR anisotropy in different formats (http://cr20.izmiran.ru/AnisotropyCR/main.htm/). Usage the sheaf Php and MySQL provides fast receiving data even in the Internet since a request and following process of data are accomplished on the project server. Usage of MySQL basis for the storing data on cosmic ray variations give a possibility to construct requests of different structures, extends the variety of data reflection, makes it possible the conformity data to other systems and usage them in other projects.

Autonomous facial recognition system inspired by human visual system based logarithmical image visualization technique

NASA Astrophysics Data System (ADS)

Wan, Qianwen; Panetta, Karen; Agaian, Sos

2017-05-01

Autonomous facial recognition system is widely used in real-life applications, such as homeland border security, law enforcement identification and authentication, and video-based surveillance analysis. Issues like low image quality, non-uniform illumination as well as variations in poses and facial expressions can impair the performance of recognition systems. To address the non-uniform illumination challenge, we present a novel robust autonomous facial recognition system inspired by the human visual system based, so called, logarithmical image visualization technique. In this paper, the proposed method, for the first time, utilizes the logarithmical image visualization technique coupled with the local binary pattern to perform discriminative feature extraction for facial recognition system. The Yale database, the Yale-B database and the ATT database are used for computer simulation accuracy and efficiency testing. The extensive computer simulation demonstrates the method's efficiency, accuracy, and robustness of illumination invariance for facial recognition.

Geothermal Resource/Reservoir Investigations Based on Heat Flow and Thermal Gradient Data for the United States

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

D. D. Blackwell; K. W. Wisian; M. C. Richards

2000-04-01

Several activities related to geothermal resources in the western United States are described in this report. A database of geothermal site-specific thermal gradient and heat flow results from individual exploration wells in the western US has been assembled. Extensive temperature gradient and heat flow exploration data from the active exploration of the 1970's and 1980's were collected, compiled, and synthesized, emphasizing previously unavailable company data. Examples of the use and applications of the database are described. The database and results are available on the world wide web. In this report numerical models are used to establish basic qualitative relationships betweenmore » structure, heat input, and permeability distribution, and the resulting geothermal system. A series of steady state, two-dimensional numerical models evaluate the effect of permeability and structural variations on an idealized, generic Basin and Range geothermal system and the results are described.« less

Genome Variation Map: a data repository of genome variations in BIG Data Center.

PubMed

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2018-01-04

The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Hydrologic and landscape database for the Cache and White River National Wildlife Refuges and contributing watersheds in Arkansas, Missouri, and Oklahoma

USGS Publications Warehouse

Buell, Gary R.; Wehmeyer, Loren L.; Calhoun, Daniel L.

2012-01-01

A hydrologic and landscape database was developed by the U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, for the Cache River and White River National Wildlife Refuges and their contributing watersheds in Arkansas, Missouri, and Oklahoma. The database is composed of a set of ASCII files, Microsoft Access® files, Microsoft Excel® files, an Environmental Systems Research Institute (ESRI) ArcGIS® geodatabase, ESRI ArcGRID® raster datasets, and an ESRI ArcReader® published map. The database was developed as an assessment and evaluation tool to use in examining refuge-specific hydrologic patterns and trends as related to water availability for refuge ecosystems, habitats, and target species; and includes hydrologic time-series data, statistics, and hydroecological metrics that can be used to assess refuge hydrologic conditions and the availability of aquatic and riparian habitat. Landscape data that describe the refuge physiographic setting and the locations of hydrologic-data collection stations are also included in the database. Categories of landscape data include land cover, soil hydrologic characteristics, physiographic features, geographic and hydrographic boundaries, hydrographic features, regional runoff estimates, and gaging-station locations. The database geographic extent covers three hydrologic subregions—the Lower Mississippi–St Francis (0802), the Upper White (1101), and the Lower Arkansas (1111)—within which human activities, climatic variation, and hydrologic processes can potentially affect the hydrologic regime of the refuges and adjacent areas. Database construction has been automated to facilitate periodic updates with new data. The database report (1) serves as a user guide for the database, (2) describes the data-collection, data-reduction, and data-analysis methods used to construct the database, (3) provides a statistical and graphical description of the database, and (4) provides detailed information on the development of analytical techniques designed to assess water availability for ecological needs.

The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database

PubMed Central

Engel, Stacia R.; Cherry, J. Michael

2013-01-01

The first completed eukaryotic genome sequence was that of the yeast Saccharomyces cerevisiae, and the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the original model organism database. SGD remains the authoritative community resource for the S. cerevisiae reference genome sequence and its annotation, and continues to provide comprehensive biological information correlated with S. cerevisiae genes and their products. A diverse set of yeast strains have been sequenced to explore commercial and laboratory applications, and a brief history of those strains is provided. The publication of these new genomes has motivated the creation of new tools, and SGD will annotate and provide comparative analyses of these sequences, correlating changes with variations in strain phenotypes and protein function. We are entering a new era at SGD, as we incorporate these new sequences and make them accessible to the scientific community, all in an effort to continue in our mission of educating researchers and facilitating discovery. Database URL: http://www.yeastgenome.org/ PMID:23487186

Relax with CouchDB--into the non-relational DBMS era of bioinformatics.

PubMed

Manyam, Ganiraju; Payton, Michelle A; Roth, Jack A; Abruzzo, Lynne V; Coombes, Kevin R

2012-07-01

With the proliferation of high-throughput technologies, genome-level data analysis has become common in molecular biology. Bioinformaticians are developing extensive resources to annotate and mine biological features from high-throughput data. The underlying database management systems for most bioinformatics software are based on a relational model. Modern non-relational databases offer an alternative that has flexibility, scalability, and a non-rigid design schema. Moreover, with an accelerated development pace, non-relational databases like CouchDB can be ideal tools to construct bioinformatics utilities. We describe CouchDB by presenting three new bioinformatics resources: (a) geneSmash, which collates data from bioinformatics resources and provides automated gene-centric annotations, (b) drugBase, a database of drug-target interactions with a web interface powered by geneSmash, and (c) HapMap-CN, which provides a web interface to query copy number variations from three SNP-chip HapMap datasets. In addition to the web sites, all three systems can be accessed programmatically via web services. Copyright © 2012 Elsevier Inc. All rights reserved.

SparCLeS: dynamic l₁ sparse classifiers with level sets for robust beard/moustache detection and segmentation.

PubMed

Le, T Hoang Ngan; Luu, Khoa; Savvides, Marios

2013-08-01

Robust facial hair detection and segmentation is a highly valued soft biometric attribute for carrying out forensic facial analysis. In this paper, we propose a novel and fully automatic system, called SparCLeS, for beard/moustache detection and segmentation in challenging facial images. SparCLeS uses the multiscale self-quotient (MSQ) algorithm to preprocess facial images and deal with illumination variation. Histogram of oriented gradients (HOG) features are extracted from the preprocessed images and a dynamic sparse classifier is built using these features to classify a facial region as either containing skin or facial hair. A level set based approach, which makes use of the advantages of both global and local information, is then used to segment the regions of a face containing facial hair. Experimental results demonstrate the effectiveness of our proposed system in detecting and segmenting facial hair regions in images drawn from three databases, i.e., the NIST Multiple Biometric Grand Challenge (MBGC) still face database, the NIST Color Facial Recognition Technology FERET database, and the Labeled Faces in the Wild (LFW) database.

Relation between Soil Order and Sorptive Capacity for Dissolved Organic Carbon

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

Heal, Katherine R; Brandt, Craig C; Mayes, Melanie

2012-01-01

Soils have historically been considered a temporary sink for organic C, but deeper soils may serve as longer term C sinks due to the sorption of dissolved organic C (DOC) onto Fe- and clay-rich mineral soil particles. This project provides an improved understanding and predictive capability of the physical and chemical properties of deep soils that control their sorptive capacities for DOC. Two hundred thirteen subsurface soil samples (72 series from five orders) were selected from the eastern and central United States. A characterized natural DOC source was added to the soils, and the Langmuir sorption equation was fitted tomore » the observed data by adjusting the maximum DOC sorption capacity (Q{sub max}) and the binding coefficient (k). Different isotherm shapes were observed for Ultisols, Alfisols, and Mollisols due to statistically significant differences in the magnitude of k, while Q{sub max} was statistically invariant among these three orders. Linear regressions were performed on the entire database and as a function of soil order to correlate Langmuir fitted parameters with measured soil properties, e.g., pH, clay content, total organic C (TOC), and total Fe oxide content. Together, textural clay and Fe oxide content accounted for 35% of the variation in Q{sub max} in the database, and clay was most important for Alfisols and Ultisols. The TOC content, however, accounted for 27% of the variation in Q{sub max} in Mollisols. Soil pH accounted for 45% of the variation in k for the entire database, 41% for Mollisols, and 22% for Alfisols. Our findings demonstrate that correlations between Langmuir parameters and soil properties are different for different soil orders and that k is a more sensitive parameter for DOC sorption than is Q{sub max} for temperate soils from the central and eastern United States.« less

Variability sensitivity of dynamic texture based recognition in clinical CT data

NASA Astrophysics Data System (ADS)

Kwitt, Roland; Razzaque, Sharif; Lowell, Jeffrey; Aylward, Stephen

2014-03-01

Dynamic texture recognition using a database of template models has recently shown promising results for the task of localizing anatomical structures in Ultrasound video. In order to understand its clinical value, it is imperative to study the sensitivity with respect to inter-patient variability as well as sensitivity to acquisition parameters such as Ultrasound probe angle. Fully addressing patient and acquisition variability issues, however, would require a large database of clinical Ultrasound from many patients, acquired in a multitude of controlled conditions, e.g., using a tracked transducer. Since such data is not readily attainable, we advocate an alternative evaluation strategy using abdominal CT data as a surrogate. In this paper, we describe how to replicate Ultrasound variabilities by extracting subvolumes from CT and interpreting the image material as an ordered sequence of video frames. Utilizing this technique, and based on a database of abdominal CT from 45 patients, we report recognition results on an organ (kidney) recognition task, where we try to discriminate kidney subvolumes/videos from a collection of randomly sampled negative instances. We demonstrate that (1) dynamic texture recognition is relatively insensitive to inter-patient variation while (2) viewing angle variability needs to be accounted for in the template database. Since naively extending the template database to counteract variability issues can lead to impractical database sizes, we propose an alternative strategy based on automated identification of a small set of representative models.

Variation in Outcomes for Risk-Stratified Pediatric Cardiac Surgical Operations: An Analysis of the STS Congenital Heart Surgery Database

PubMed Central

Jacobs, Jeffrey Phillip; O'Brien, Sean M.; Pasquali, Sara K.; Jacobs, Marshall Lewis; Lacour-Gayet, François G.; Tchervenkov, Christo I.; Austin III, Erle H.; Pizarro, Christian; Pourmoghadam, Kamal K.; Scholl, Frank G.; Welke, Karl F.; Gaynor, J. William; Clarke, David R.; Mayer, John E.; Mavroudis, Constantine

2013-01-01

Background. We evaluated outcomes for groups of risk-stratified operations in The Society of Thoracic Surgeons Congenital Heart Surgery Database to provide contemporary benchmarks and examine variation between centers. Methods. Patients undergoing surgery from 2005 to 2009 were included. Centers with more than 10% missing data were excluded. Discharge mortality and postoperative length of stay (PLOS) among patients discharged alive were calculated for groups of risk-stratified operations using the five Society of Thoracic Surgeons-European Association for Cardio-Thoracic Surgery Congenital Heart Surgery mortality categories (STAT Mortality Categories). Power for analyzing between-center differences in outcome was determined for each STAT Mortality Category. Variation was evaluated using funnel plots and Bayesian hierarchical modeling. Results. In this analysis of risk-stratified operations, 58,506 index operations at 73 centers were included. Overall discharge mortality (interquartile range among programs with more than 10 cases) was as follows: STAT Category 1 = 0.55% (0% to 1.0%), STAT Category 2 = 1.7% (1.0% to 2.2%), STAT Category 3 = 2.6% (1.1% to 4.4%), STAT Category 4 = 8.0% (6.3% to 11.1%), and STAT Category 5 = 18.4% (13.9% to 27.9%). Funnel plots with 95% prediction limits revealed the number of centers characterized as outliers by STAT Mortality Categories was as follows: Category 1 = 3 (4.1%), Category 2 = 1 (1.4%), Category 3 = 7 (9.7%), Category 4 = 13 (17.8%), and Category 5 = 13 (18.6%). Between-center variation in PLOS was analyzed for all STAT Categories and was greatest for STAT Category 5 operations. Conclusions. This analysis documents contemporary benchmarks for risk-stratified pediatric cardiac surgical operations grouped by STAT Mortality Categories and the range of outcomes among centers. Variation was greatest for the more complex operations. These data may aid in the design and planning of quality assessment and quality improvement initiatives. PMID:22704799

Are common names becoming less common? The rise in uniqueness and individualism in Japan.

PubMed

Ogihara, Yuji; Fujita, Hiroyo; Tominaga, Hitoshi; Ishigaki, Sho; Kashimoto, Takuya; Takahashi, Ayano; Toyohara, Kyoko; Uchida, Yukiko

2015-01-01

We examined whether Japanese culture has become more individualistic by investigating how the practice of naming babies has changed over time. Cultural psychology has revealed substantial cultural variation in human psychology and behavior, emphasizing the mutual construction of socio-cultural environment and mind. However, much of the past research did not account for the fact that culture is changing. Indeed, archival data on behavior (e.g., divorce rates) suggest a rise in individualism in the U.S. and Japan. In addition to archival data, cultural products (which express an individual's psyche and behavior outside the head; e.g., advertising) can also reveal cultural change. However, little research has investigated the changes in individualism in East Asia using cultural products. To reveal the dynamic aspects of culture, it is important to present temporal data across cultures. In this study, we examined baby names as a cultural product. If Japanese culture has become more individualistic, parents would be expected to give their children unique names. Using two databases, we calculated the rate of popular baby names between 2004 and 2013. Both databases released the rankings of popular names and their rates within the sample. As Japanese names are generally comprised of both written Chinese characters and their pronunciations, we analyzed these two separately. We found that the rate of popular Chinese characters increased, whereas the rate of popular pronunciations decreased. However, only the rate of popular pronunciations was associated with a previously validated collectivism index. Moreover, we examined the pronunciation variation of common combinations of Chinese characters and the written form variation of common pronunciations. We found that the variation of written forms decreased, whereas the variation of pronunciations increased over time. Taken together, these results showed that parents are giving their children unique names by pairing common Chinese characters with uncommon pronunciations, which indicates an increase in individualism in Japan.

Regional Differences in Case Mix and Peri-operative Outcome After Elective Abdominal Aortic Aneurysm Repair in the Vascunet Database.

PubMed

Mani, K; Venermo, M; Beiles, B; Menyhei, G; Altreuther, M; Loftus, I; Björck, M

2015-06-01

National differences exist in the outcome of elective abdominal aortic aneurysm (AAA) repair. The role of case mix variation was assessed based on an international vascular registry collaboration. All elective AAA repairs with aneurysm size data in the Vascunet database in the period 2005-09 were included. AAA size and peri-operative outcome (crude and age adjusted mortality) were analysed overall and in risk cohorts, as well as per country. Glasgow Aneurysm Score (GAS) was calculated as risk score, and patients were stratified in three equal sized risk cohorts based on GAS. Predictors of peri-operative mortality were analysed with multiple regression. Missing data were handled with multiple imputation. Patients from Australia, Finland, Hungary, Norway, Sweden and the UK (n = 5,895) were analysed; mean age was 72.7 years and 54% had endovascular repair (EVAR). There were significant variations in GAS (lowest = Finland [75.7], highest = UK [79.4], p for comparison of all regions < .001), proportion of AAA < 5.5 cm (lowest = UK [6.4%], highest = Hungary [29.0%]; p < .001), proportion undergoing EVAR (lowest = Finland [10.1%], highest = Australia [58.9%]; p < .001), crude mortality (lowest = Norway [2.0%], highest = Finland [5.0%]; p = .006), and age adjusted mortality (lowest = Norway [2.5%], highest = Finland [6.0%]; p = .048). Both aneurysm size and peri-operative mortality were highest among patients with a GAS >82. Of those with a GAS >82, 8.4% of men and 20.8% of women had an AAA <5.5 cm. Important regional differences exist in case selection for elective AAA repair, including variations in AAA size and patient risk profile. These differences partly explain the variations in peri-operative mortality. Further audit is warranted to assess the underlying reasons for the regional variation in case-mix. Copyright © 2015 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

Variation in outcomes for risk-stratified pediatric cardiac surgical operations: an analysis of the STS Congenital Heart Surgery Database.

PubMed

Jacobs, Jeffrey Phillip; O'Brien, Sean M; Pasquali, Sara K; Jacobs, Marshall Lewis; Lacour-Gayet, François G; Tchervenkov, Christo I; Austin, Erle H; Pizarro, Christian; Pourmoghadam, Kamal K; Scholl, Frank G; Welke, Karl F; Gaynor, J William; Clarke, David R; Mayer, John E; Mavroudis, Constantine

2012-08-01

We evaluated outcomes for groups of risk-stratified operations in The Society of Thoracic Surgeons Congenital Heart Surgery Database to provide contemporary benchmarks and examine variation between centers. Patients undergoing surgery from 2005 to 2009 were included. Centers with more than 10% missing data were excluded. Discharge mortality and postoperative length of stay (PLOS) among patients discharged alive were calculated for groups of risk-stratified operations using the five Society of Thoracic Surgeons-European Association for Cardio-Thoracic Surgery Congenital Heart Surgery mortality categories (STAT Mortality Categories). Power for analyzing between-center differences in outcome was determined for each STAT Mortality Category. Variation was evaluated using funnel plots and Bayesian hierarchical modeling. In this analysis of risk-stratified operations, 58,506 index operations at 73 centers were included. Overall discharge mortality (interquartile range among programs with more than 10 cases) was as follows: STAT Category 1=0.55% (0% to 1.0%), STAT Category 2=1.7% (1.0% to 2.2%), STAT Category 3=2.6% (1.1% to 4.4%), STAT Category 4=8.0% (6.3% to 11.1%), and STAT Category 5=18.4% (13.9% to 27.9%). Funnel plots with 95% prediction limits revealed the number of centers characterized as outliers by STAT Mortality Categories was as follows: Category 1=3 (4.1%), Category 2=1 (1.4%), Category 3=7 (9.7%), Category 4=13 (17.8%), and Category 5=13 (18.6%). Between-center variation in PLOS was analyzed for all STAT Categories and was greatest for STAT Category 5 operations. This analysis documents contemporary benchmarks for risk-stratified pediatric cardiac surgical operations grouped by STAT Mortality Categories and the range of outcomes among centers. Variation was greatest for the more complex operations. These data may aid in the design and planning of quality assessment and quality improvement initiatives. Copyright © 2012 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Are common names becoming less common? The rise in uniqueness and individualism in Japan

PubMed Central

Ogihara, Yuji; Fujita, Hiroyo; Tominaga, Hitoshi; Ishigaki, Sho; Kashimoto, Takuya; Takahashi, Ayano; Toyohara, Kyoko; Uchida, Yukiko

2015-01-01

We examined whether Japanese culture has become more individualistic by investigating how the practice of naming babies has changed over time. Cultural psychology has revealed substantial cultural variation in human psychology and behavior, emphasizing the mutual construction of socio-cultural environment and mind. However, much of the past research did not account for the fact that culture is changing. Indeed, archival data on behavior (e.g., divorce rates) suggest a rise in individualism in the U.S. and Japan. In addition to archival data, cultural products (which express an individual’s psyche and behavior outside the head; e.g., advertising) can also reveal cultural change. However, little research has investigated the changes in individualism in East Asia using cultural products. To reveal the dynamic aspects of culture, it is important to present temporal data across cultures. In this study, we examined baby names as a cultural product. If Japanese culture has become more individualistic, parents would be expected to give their children unique names. Using two databases, we calculated the rate of popular baby names between 2004 and 2013. Both databases released the rankings of popular names and their rates within the sample. As Japanese names are generally comprised of both written Chinese characters and their pronunciations, we analyzed these two separately. We found that the rate of popular Chinese characters increased, whereas the rate of popular pronunciations decreased. However, only the rate of popular pronunciations was associated with a previously validated collectivism index. Moreover, we examined the pronunciation variation of common combinations of Chinese characters and the written form variation of common pronunciations. We found that the variation of written forms decreased, whereas the variation of pronunciations increased over time. Taken together, these results showed that parents are giving their children unique names by pairing common Chinese characters with uncommon pronunciations, which indicates an increase in individualism in Japan. PMID:26557100

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.

PubMed

Pérez-Losada, Marcos; Castro-Nallar, Eduardo; Bendall, Matthew L; Freishtat, Robert J; Crandall, Keith A

2015-01-01

High-throughput sequencing (HTS) analysis of microbial communities from the respiratory airways has heavily relied on the 16S rRNA gene. Given the intrinsic limitations of this approach, airway microbiome research has focused on assessing bacterial composition during health and disease, and its variation in relation to clinical and environmental factors, or other microbiomes. Consequently, very little effort has been dedicated to describing the functional characteristics of the airway microbiota and even less to explore the microbe-host interactions. Here we present a simultaneous assessment of microbiome and host functional diversity and host-microbe interactions from the same RNA-seq experiment, while accounting for variation in clinical metadata. Transcriptomic (host) and metatranscriptomic (microbiota) sequences from the nasal epithelium of 8 asthmatics and 6 healthy controls were separated in silico and mapped to available human and NCBI-NR protein reference databases. Human genes differentially expressed in asthmatics and controls were then used to infer upstream regulators involved in immune and inflammatory responses. Concomitantly, microbial genes were mapped to metabolic databases (COG, SEED, and KEGG) to infer microbial functions differentially expressed in asthmatics and controls. Finally, multivariate analysis was applied to find associations between microbiome characteristics and host upstream regulators while accounting for clinical variation. Our study showed significant differences in the metabolism of microbiomes from asthmatic and non-asthmatic children for up to 25% of the functional properties tested. Enrichment analysis of 499 differentially expressed host genes for inflammatory and immune responses revealed 43 upstream regulators differentially activated in asthma. Microbial adhesion (virulence) and Proteobacteria abundance were significantly associated with variation in the expression of the upstream regulator IL1A; suggesting that microbiome characteristics modulate host inflammatory and immune systems during asthma.

Face recognition via edge-based Gabor feature representation for plastic surgery-altered images

NASA Astrophysics Data System (ADS)

Chude-Olisah, Chollette C.; Sulong, Ghazali; Chude-Okonkwo, Uche A. K.; Hashim, Siti Z. M.

2014-12-01

Plastic surgery procedures on the face introduce skin texture variations between images of the same person (intra-subject), thereby making the task of face recognition more difficult than in normal scenario. Usually, in contemporary face recognition systems, the original gray-level face image is used as input to the Gabor descriptor, which translates to encoding some texture properties of the face image. The texture-encoding process significantly degrades the performance of such systems in the case of plastic surgery due to the presence of surgically induced intra-subject variations. Based on the proposition that the shape of significant facial components such as eyes, nose, eyebrow, and mouth remains unchanged after plastic surgery, this paper employs an edge-based Gabor feature representation approach for the recognition of surgically altered face images. We use the edge information, which is dependent on the shapes of the significant facial components, to address the plastic surgery-induced texture variation problems. To ensure that the significant facial components represent useful edge information with little or no false edges, a simple illumination normalization technique is proposed for preprocessing. Gabor wavelet is applied to the edge image to accentuate on the uniqueness of the significant facial components for discriminating among different subjects. The performance of the proposed method is evaluated on the Georgia Tech (GT) and the Labeled Faces in the Wild (LFW) databases with illumination and expression problems, and the plastic surgery database with texture changes. Results show that the proposed edge-based Gabor feature representation approach is robust against plastic surgery-induced face variations amidst expression and illumination problems and outperforms the existing plastic surgery face recognition methods reported in the literature.

Meta-analysis of the performance variation in broilers experimentally challenged by Eimeria spp.

PubMed

Kipper, Marcos; Andretta, Ines; Lehnen, Cheila Roberta; Lovatto, Paulo Alberto; Monteiro, Silvia Gonzalez

2013-09-01

A meta-analysis was carried out to (1) study the relation of the variation in feed intake and weight gain in broilers infected with Eimeria acervulina, Eimeria maxima, Eimeria tenella, or a Pool of Eimeria species, and (2) to identify and to quantify the effects involved in the infection. A database of articles addressing the experimental infection with Coccidia in broilers was developed. These publications must present results of animal performance (weight gain, feed intake, and feed conversion ratio). The database was composed by 69 publications, totalling around 44 thousand animals. Meta-analysis followed three sequential analyses: graphical, correlation, and variance-covariance. The feed intake of the groups challenged by E. acervulina and E. tenella did not differ (P>0.05) to the control group. However, the feed intake in groups challenged by E. maxima and Pool showed an increase of 8% and 5% (P<0.05) in relation to the control group. Challenged groups presented a decrease (P<0.05) in weight gain compared with control groups. All challenged groups showed a reduction in weight gain, even when there was no reduction (P<0.05) in feed intake (adjustment through variance-covariance analysis). The feed intake variation in broilers infected with E. acervulina, E. maxima, E. tenella, or Pool showed a quadratic (P<0.05) influence over the variation in weight gain. In relation to the isolated effects, the challenges have an impact of less than 1% over the variance in feed intake and weight gain. However, the magnitude of the effects varied with Eimeria species, animal age, sex, and genetic line. In general the age effect is superior to the challenge effect, showing that age at the challenge is important to determine the impact of Eimeria infection. Copyright © 2013 Elsevier B.V. All rights reserved.

A regional study of the seasonal variation in the molecular composition of rainwater

NASA Astrophysics Data System (ADS)

Cottrell, Barbara A.; Gonsior, Michael; Isabelle, Lorne M.; Luo, W.; Perraud, Véronique; McIntire, Theresa M.; Pankow, James F.; Schmitt-Kopplin, Philippe; Cooper, William J.; Simpson, André J.

2013-10-01

Rainwater is not only a critical source of drinking and agricultural water but it plays a key role in the fate and transport of contaminants through their removal by wet deposition. Rainwater is a complex mixture of organic compounds yet despite its importance its spatial and temporal variability are not well understood and less than 50% of the organic matter has been characterized. In-depth analytical approaches were used in this study to characterize the seasonal variation in rainwater composition. Rainwater samples were collected over a one-year period in Scarborough, Ontario, Canada. The seasonal variation of atmospheric organic carbon (AOC) in rainwater was analyzed by excitation-emission matrix spectroscopy (EEMs), 1D and 2D NMR with compound identification by spectral database matching, GC-MS, FT-ICR-MS, and GC × GC-TOFMS. This combination of techniques provided four complementary datasets, with less than 10% overlap, of anthropogenic and biogenic AOC. NMR with database matching identified over 100 compounds, primarily carboxylic acids, carbohydrates, and nitrogen-containing compounds. GC × GC-TOFMS analysis identified 344 compounds in two rain events with 33% of the compounds common to both events. FT-ICR-MS generated a seasonally dependent profile of 1226-1575 molecular ions of CHO, CHOS, and CHON elemental composition. FT-ICR-MS and GC × GC-TOFMS datasets were compared using van Krevelen diagrams (H/C vs. O/C), the H/C ratio vs. mass/charge (m/z), and the carbon oxidation state/carbon number matrix. Fluorescence patterns were correlated with NMR results resulting in the identification one seasonally-dependent component of chromophoric dissolved organic matter (CDOM). This study demonstrated the importance of using of an integrated analytical approach to monitor the compositional variation of AOC.

Practice variation in the treatment of rheumatoid arthritis among German rheumatologists.

PubMed

Zink, A; Listing, J; Ziemer, S; Zeidler, H

2001-10-01

To describe practice variation in the treatment of rheumatoid arthritis (RA) among German rheumatologists with regard to drug and non-drug therapy. We used data of 7,326 patients with RA registered in a national German rheumatological database in 1998. In the database, every patient with an inflammatory rheumatic disease seen at one of the German Collaborative Arthritis Centres is registered once a year with a standard clinical data form and a patient questionnaire. We compared health care provided by 29 rheumatological outpatient units. For drug and non-drug treatment unit prescription rates, ranges and outliers were calculated. Logistic regression analysis was used for case mix adjustment and for the identification of practice patterns. We observed variation concerning the frequency of use of single disease modifying antirheumatic drugs (DMARD). The median of the prescription rates in the 29 units for methotrexate (MTX) was 55% in 1998 (1st quartile: 51%, 3rd quartile: 63%); sulfasalazine had a median of 15% (quartiles: 10%/19%), antimalarials a median of 8% (quartiles: 5%/21%). Combination DMARD therapy was used in 11% (quartiles: 6%/18%). Prescriptions of low dose steroids (< or = 7.5 mg) had a median of 45% (quartiles: 35%/55%), and nonsteroidal antiinflammatory drugs (NSAID) had a median prescription rate of 58% (quartiles: 50%/70%). High variation was also found concerning active physiotherapy (median: 41%; quartiles 34%/55%) and passive physical measures (median 14%, quartiles 9%/37%). Differences in case mix (age, sex, rheumatoid factor, disease duration, severity, disability) only explained a small proportion of the total variation. When the units were grouped according to the frequency of prescription of DMARD combination therapy, treatment patterns could be identified. Units with higher rates of DMARD combination therapy used more drugs for the prevention and treatment of osteoporosis, more active physiotherapy but fewer NSAID and fewer passive physical therapies. Variation in drug and non-drug treatment indicates significant differences in health care provision. Trends in the drug management of RA are adopted differentially by the members of the rheumatology community. The large variability in non-drug therapies may, apart from differences in availability, suggest a lack of agreement on therapeutic effectiveness.

Normal Databases for the Relative Quantification of Myocardial Perfusion

PubMed Central

Rubeaux, Mathieu; Xu, Yuan; Germano, Guido; Berman, Daniel S.; Slomka, Piotr J.

2016-01-01

Purpose of review Myocardial perfusion imaging (MPI) with SPECT is performed clinically worldwide to detect and monitor coronary artery disease (CAD). MPI allows an objective quantification of myocardial perfusion at stress and rest. This established technique relies on normal databases to compare patient scans against reference normal limits. In this review, we aim to introduce the process of MPI quantification with normal databases and describe the associated perfusion quantitative measures that are used. Recent findings New equipment and new software reconstruction algorithms have been introduced which require the development of new normal limits. The appearance and regional count variations of normal MPI scan may differ between these new scanners and standard Anger cameras. Therefore, these new systems may require the determination of new normal limits to achieve optimal accuracy in relative myocardial perfusion quantification. Accurate diagnostic and prognostic results rivaling those obtained by expert readers can be obtained by this widely used technique. Summary Throughout this review, we emphasize the importance of the different normal databases and the need for specific databases relative to distinct imaging procedures. use of appropriate normal limits allows optimal quantification of MPI by taking into account subtle image differences due to the hardware and software used, and the population studied. PMID:28138354

Food composition database development for between country comparisons.

PubMed

Merchant, Anwar T; Dehghan, Mahshid

2006-01-19

Nutritional assessment by diet analysis is a two-stepped process consisting of evaluation of food consumption, and conversion of food into nutrient intake by using a food composition database, which lists the mean nutritional values for a given food portion. Most reports in the literature focus on minimizing errors in estimation of food consumption but the selection of a specific food composition table used in nutrient estimation is also a source of errors. We are conducting a large prospective study internationally and need to compare diet, assessed by food frequency questionnaires, in a comparable manner between different countries. We have prepared a multi-country food composition database for nutrient estimation in all the countries participating in our study. The nutrient database is primarily based on the USDA food composition database, modified appropriately with reference to local food composition tables, and supplemented with recipes of locally eaten mixed dishes. By doing so we have ensured that the units of measurement, method of selection of foods for testing, and assays used for nutrient estimation are consistent and as current as possible, and yet have taken into account some local variations. Using this common metric for nutrient assessment will reduce differential errors in nutrient estimation and improve the validity of between-country comparisons.

Producing a Climate-Quality Database of Global Upper Ocean Profile Temperatures - The IQuOD (International Quality-controlled Ocean Database) Project.

NASA Astrophysics Data System (ADS)

Sprintall, J.; Cowley, R.; Palmer, M. D.; Domingues, C. M.; Suzuki, T.; Ishii, M.; Boyer, T.; Goni, G. J.; Gouretski, V. V.; Macdonald, A. M.; Thresher, A.; Good, S. A.; Diggs, S. C.

2016-02-01

Historical ocean temperature profile observations provide a critical element for a host of ocean and climate research activities. These include providing initial conditions for seasonal-to-decadal prediction systems, evaluating past variations in sea level and Earth's energy imbalance, ocean state estimation for studying variability and change, and climate model evaluation and development. The International Quality controlled Ocean Database (IQuOD) initiative represents a community effort to create the most globally complete temperature profile dataset, with (intelligent) metadata and assigned uncertainties. With an internationally coordinated effort organized by oceanographers, with data and ocean instrumentation expertise, and in close consultation with end users (e.g., climate modelers), the IQuOD initiative will assess and maximize the potential of an irreplaceable collection of ocean temperature observations (tens of millions of profiles collected at a cost of tens of billions of dollars, since 1772) to fulfil the demand for a climate-quality global database that can be used with greater confidence in a vast range of climate change related research and services of societal benefit. Progress towards version 1 of the IQuOD database, ongoing and future work will be presented. More information on IQuOD is available at www.iquod.org.

Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments.

PubMed

Linder, Suzanne K; Kamath, Geetanjali R; Pratt, Gregory F; Saraykar, Smita S; Volk, Robert J

2015-04-01

To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a health care decision-making instrument commonly used in clinical settings. We searched the literature using two methods: (1) keyword searching using variations of "Control Preferences Scale" and (2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, and Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Keyword searches in bibliographic databases yielded high average precision (90%) but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45-54%), but precision ranged from 35% to 75% with Scopus being the most precise. Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time, and resources should dictate the combination of which methods and databases are used. Copyright © 2015 Elsevier Inc. All rights reserved.

Citation searches are more sensitive than keyword searches to identify studies using specific measurement instruments

PubMed Central

Linder, Suzanne K.; Kamath, Geetanjali R.; Pratt, Gregory F.; Saraykar, Smita S.; Volk, Robert J.

2015-01-01

Objective To compare the effectiveness of two search methods in identifying studies that used the Control Preferences Scale (CPS), a healthcare decision-making instrument commonly used in clinical settings. Study Design & Setting We searched the literature using two methods: 1) keyword searching using variations of “control preferences scale” and 2) cited reference searching using two seminal CPS publications. We searched three bibliographic databases [PubMed, Scopus, Web of Science (WOS)] and one full-text database (Google Scholar). We report precision and sensitivity as measures of effectiveness. Results Keyword searches in bibliographic databases yielded high average precision (90%), but low average sensitivity (16%). PubMed was the most precise, followed closely by Scopus and WOS. The Google Scholar keyword search had low precision (54%) but provided the highest sensitivity (70%). Cited reference searches in all databases yielded moderate sensitivity (45–54%), but precision ranged from 35–75% with Scopus being the most precise. Conclusion Cited reference searches were more sensitive than keyword searches, making it a more comprehensive strategy to identify all studies that use a particular instrument. Keyword searches provide a quick way of finding some but not all relevant articles. Goals, time and resources should dictate the combination of which methods and databases are used. PMID:25554521

Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees, and whole-genome-based data

USDA-ARS?s Scientific Manuscript database

Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining data sets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data, and mol...

Assessing variability in chemical acute toxicity of unionid mussels: Influence of intra- and inter-laboratory testing, life stage, and species - SETAC Abstract

EPA Science Inventory

We developed a toxicity database for unionid mussels to examine the extent of intra- and inter-laboratory variability in acute toxicity tests with mussel larvae (glochidia) and juveniles; the extent of differential sensitivity of the two life stages; and the variation in sensitiv...

Characterization of Genome-Wide Variation in Four-Row Wax, a Waxy Maize Landrace with a Reduced Kernel Row Phenotype

PubMed Central

Liu, Hanmei; Wang, Xuewen; Wei, Bin; Wang, Yongbin; Liu, Yinghong; Zhang, Junjie; Hu, Yufeng; Yu, Guowu; Li, Jian; Xu, Zhanbin; Huang, Yubi

2016-01-01

In southwest China, some maize landraces have long been isolated geographically, and have phenotypes that differ from those of widely grown cultivars. These landraces may harbor rich genetic variation responsible for those phenotypes. Four-row Wax is one such landrace, with four rows of kernels on the cob. We resequenced the genome of Four-row Wax, obtaining 50.46 Gb sequence at 21.87× coverage, then identified and characterized 3,252,194 SNPs, 213,181 short InDels (1–5 bp) and 39,631 structural variations (greater than 5 bp). Of those, 312,511 (9.6%) SNPs were novel compared to the most detailed haplotype map (HapMap) SNP database of maize. Characterization of variations in reported kernel row number (KRN) related genes and KRN QTL regions revealed potential causal mutations in fea2, td1, kn1, and te1. Genome-wide comparisons revealed abundant genetic variations in Four-row Wax, which may be associated with environmental adaptation. The sequence and SNP variations described here enrich genetic resources of maize, and provide guidance into study of seed numbers for crop yield improvement. PMID:27242868

Global epidemiological trends and variations in the burden of gallbladder cancer.

PubMed

Are, Chandrakanth; Ahmad, Humera; Ravipati, Advaitaa; Croo, Darren; Clarey, Dillon; Smith, Lynette; Price, Ray R; Butte, Jean M; Gupta, Sameer; Chaturvedi, Arun; Chowdhury, Sanjib

2017-04-01

The aim of this study is to describe the trends and variations in the global burden of gallbladder cancer (GBC) with an emphasis on geographic variations and female gender. Data (2012-2030) relating to GBC was extracted from GLOBOCAN 2012 database and analyzed. The results of our study document a rising global burden of GBC with geographic and gender variations. The highest burden was noted in the WPRO region (based on WHO regions), Asia (based on continents) and India, Chile, and China (based on countries). The less developed regions of the world account for the majority of the global burden of GBC. The geographic variations are also present within individual countries such as in India and Chile. Females are afflicted at a much higher rate with GBC and this predilection is exaggerated in countries with higher incidence such as India and Chile. In females, people of certain ethnic groups and lower socio-economic standing are at a higher risk. Our study demonstrates a rising global burden of GBC with some specific data on geographic and gender-based variations which can be used to develop strategies at the global as well as the high-risk individual country level. © 2017 Wiley Periodicals, Inc.

Global variability in leaf respiration in relation to climate and leaf traits

NASA Astrophysics Data System (ADS)

Atkin, Owen K.

2015-04-01

Leaf respiration plays a vital role in regulating ecosystem functioning and the Earth's climate. Because of this, it is imperative that that Earth-system, climate and ecosystem-level models be able to accurately predict variations in rates of leaf respiration. In the field of photosynthesis research, the F/vC/B model has enabled modellers to accurately predict variations in photosynthesis through time and space. By contrast, we lack an equivalent biochemical model to predict variations in leaf respiration. Consequently, we need to rely on phenomenological approaches to model variations in respiration across the Earth's surface. Such approaches require that we develop a thorough understanding of how rates of respiration vary among species and whether global environmental gradients play a role in determining variations in leaf respiration. Dealing with these issues requires that data sets be assembled on rates of leaf respiration in biomes across the Earth's surface. In this talk, I will use a newly-assembled global database on leaf respiration and associated traits (including photosynthesis) to highlight variation in leaf respiration (and the balance between respiration and photosynthesis) across global gradients in growth temperature and aridity.

Riparian plant litter quality increases with latitude.

PubMed

Boyero, Luz; Graça, Manuel A S; Tonin, Alan M; Pérez, Javier; J Swafford, Andrew; Ferreira, Verónica; Landeira-Dabarca, Andrea; A Alexandrou, Markos; Gessner, Mark O; McKie, Brendan G; Albariño, Ricardo J; Barmuta, Leon A; Callisto, Marcos; Chará, Julián; Chauvet, Eric; Colón-Gaud, Checo; Dudgeon, David; Encalada, Andrea C; Figueroa, Ricardo; Flecker, Alexander S; Fleituch, Tadeusz; Frainer, André; Gonçalves, José F; Helson, Julie E; Iwata, Tomoya; Mathooko, Jude; M'Erimba, Charles; Pringle, Catherine M; Ramírez, Alonso; Swan, Christopher M; Yule, Catherine M; Pearson, Richard G

2017-09-05

Plant litter represents a major basal resource in streams, where its decomposition is partly regulated by litter traits. Litter-trait variation may determine the latitudinal gradient in decomposition in streams, which is mainly microbial in the tropics and detritivore-mediated at high latitudes. However, this hypothesis remains untested, as we lack information on large-scale trait variation for riparian litter. Variation cannot easily be inferred from existing leaf-trait databases, since nutrient resorption can cause traits of litter and green leaves to diverge. Here we present the first global-scale assessment of riparian litter quality by determining latitudinal variation (spanning 107°) in litter traits (nutrient concentrations; physical and chemical defences) of 151 species from 24 regions and their relationships with environmental factors and phylogeny. We hypothesized that litter quality would increase with latitude (despite variation within regions) and traits would be correlated to produce 'syndromes' resulting from phylogeny and environmental variation. We found lower litter quality and higher nitrogen:phosphorus ratios in the tropics. Traits were linked but showed no phylogenetic signal, suggesting that syndromes were environmentally determined. Poorer litter quality and greater phosphorus limitation towards the equator may restrict detritivore-mediated decomposition, contributing to the predominance of microbial decomposers in tropical streams.

Observational intensity bias associated with illness adjustment: cross sectional analysis of insurance claims

PubMed Central

Staiger, Douglas O; Sharp, Sandra M; Gottlieb, Daniel J; Bevan, Gwyn; McPherson, Klim; Welch, H Gilbert

2013-01-01

Objective To determine the bias associated with frequency of visits by physicians in adjusting for illness, using diagnoses recorded in administrative databases. Setting Claims data from the US Medicare program for services provided in 2007 among 306 US hospital referral regions. Design Cross sectional analysis. Participants 20% sample of fee for service Medicare beneficiaries residing in the United States in 2007 (n=5 153 877). Main outcome measures The effect of illness adjustment on regional mortality and spending rates using standard and visit corrected illness methods for adjustment. The standard method adjusts using comorbidity measures based on diagnoses listed in administrative databases; the modified method corrects these measures for the frequency of visits by physicians. Three conventions for measuring comorbidity are used: the Charlson comorbidity index, Iezzoni chronic conditions, and hierarchical condition categories risk scores. Results The visit corrected Charlson comorbidity index explained more of the variation in age, sex, and race mortality across the 306 hospital referral regions than did the standard index (R2=0.21 v 0.11, P<0.001) and, compared with sex and race adjusted mortality, reduced regional variation, whereas adjustment using the standard Charlson comorbidity index increased it. Although visit corrected and age, sex, and race adjusted mortality rates were similar in hospital referral regions with the highest and lowest fifths of visits, adjustment using the standard index resulted in a rate that was 18% lower in the highest fifth (46.4 v 56.3 deaths per 1000, P<0.001). Age, sex, and race adjusted spending as well as visit corrected spending was more than 30% greater in the highest fifth of visits than in the lowest fifth, but only 12% greater after adjustment using the standard index. Similar results were obtained using the Iezzoni and the hierarchical condition categories conventions for measuring comorbidity. Conclusion The rates of visits by physicians introduce substantial bias when regional mortality and spending rates are adjusted for illness using comorbidity measures based on the observed number of diagnoses recorded in Medicare’s administrative database. Adjusting without correction for regional variation in visit rates tends to make regions with high rates of visits seem to have lower mortality and lower costs, and vice versa. Visit corrected comorbidity measures better explain variation in age, sex, and race mortality than observed measures, and reduce observational intensity bias. PMID:23430282

Drug residues in urban water: A database for ecotoxicological risk management.

PubMed

Destrieux, Doriane; Laurent, François; Budzinski, Hélène; Pedelucq, Julie; Vervier, Philippe; Gerino, Magali

2017-12-31

Human-use drug residues (DR) are only partially eliminated by waste water treatment plants (WWTPs), so that residual amounts can reach natural waters and cause environmental hazards. In order to properly manage these hazards in the aquatic environment, a database is made available that integrates the concentration ranges for DR, which cause adverse effects for aquatic organisms, and the temporal variations of the ecotoxicological risks. To implement this database for the ecotoxicological risk assessment (ERA database), the required information for each DR is the predicted no effect concentrations (PNECs), along with the predicted environmental concentrations (PECs). The risk assessment is based on the ratio between the PNECs and the PECs. Adverse effect data or PNECs have been found in the publicly available literature for 45 substances. These ecotoxicity test data have been extracted from 125 different sources. This ERA database contains 1157 adverse effect data and 287 PNECs. The efficiency of this ERA database was tested with a data set coming from a simultaneous survey of WWTPs and the natural environment. In this data set, 26 DR were searched for in two WWTPs and in the river. On five sampling dates, concentrations measured in the river for 10 DR could pose environmental problems of which 7 were measured only downstream of WWTP outlets. From scientific literature and measurements, data implementation with unit homogenisation in a single database facilitates the actual ecotoxicological risk assessment, and may be useful for further risk coming from data arising from the future field survey. Moreover, the accumulation of a large ecotoxicity data set in a single database should not only improve knowledge of higher risk molecules but also supply an objective tool to help the rapid and efficient evaluation of the risk. Copyright © 2017 Elsevier B.V. All rights reserved.

The risk of paradoxical embolism (RoPE) study: initial description of the completed database.

PubMed

Thaler, David E; Di Angelantonio, Emanuele; Di Tullio, Marco R; Donovan, Jennifer S; Griffith, John; Homma, Shunichi; Jaigobin, Cheryl; Mas, Jean-Louis; Mattle, Heinrich P; Michel, Patrik; Mono, Marie-Luise; Nedeltchev, Krassen; Papetti, Federica; Ruthazer, Robin; Serena, Joaquín; Weimar, Christian; Elkind, Mitchell S V; Kent, David M

2013-12-01

Detecting a benefit from closure of patent foramen ovale in patients with cryptogenic stroke is hampered by low rates of stroke recurrence and uncertainty about the causal role of patent foramen ovale in the index event. A method to predict patent foramen ovale-attributable recurrence risk is needed. However, individual databases generally have too few stroke recurrences to support risk modeling. Prior studies of this population have been limited by low statistical power for examining factors related to recurrence. The aim of this study was to develop a database to support modeling of patent foramen ovale-attributable recurrence risk by combining extant data sets. We identified investigators with extant databases including subjects with cryptogenic stroke investigated for patent foramen ovale, determined the availability and characteristics of data in each database, collaboratively specified the variables to be included in the Risk of Paradoxical Embolism database, harmonized the variables across databases, and collected new primary data when necessary and feasible. The Risk of Paradoxical Embolism database has individual clinical, radiologic, and echocardiographic data from 12 component databases, including subjects with cryptogenic stroke both with (n = 1925) and without (n = 1749) patent foramen ovale. In the patent foramen ovale subjects, a total of 381 outcomes (stroke, transient ischemic attack, death) occurred (median follow-up 2·2 years). While there were substantial variations in data collection between studies, there was sufficient overlap to define a common set of variables suitable for risk modeling. While individual studies are inadequate for modeling patent foramen ovale-attributable recurrence risk, collaboration between investigators has yielded a database with sufficient power to identify those patients at highest risk for a patent foramen ovale-related stroke recurrence who may have the greatest potential benefit from patent foramen ovale closure. © 2012 The Authors. International Journal of Stroke © 2012 World Stroke Organization.

Statistical process control charts for attribute data involving very large sample sizes: a review of problems and solutions.

PubMed

Mohammed, Mohammed A; Panesar, Jagdeep S; Laney, David B; Wilson, Richard

2013-04-01

The use of statistical process control (SPC) charts in healthcare is increasing. The primary purpose of SPC is to distinguish between common-cause variation which is attributable to the underlying process, and special-cause variation which is extrinsic to the underlying process. This is important because improvement under common-cause variation requires action on the process, whereas special-cause variation merits an investigation to first find the cause. Nonetheless, when dealing with attribute or count data (eg, number of emergency admissions) involving very large sample sizes, traditional SPC charts often produce tight control limits with most of the data points appearing outside the control limits. This can give a false impression of common and special-cause variation, and potentially misguide the user into taking the wrong actions. Given the growing availability of large datasets from routinely collected databases in healthcare, there is a need to present a review of this problem (which arises because traditional attribute charts only consider within-subgroup variation) and its solutions (which consider within and between-subgroup variation), which involve the use of the well-established measurements chart and the more recently developed attribute charts based on Laney's innovative approach. We close by making some suggestions for practice.

Is there a species spectrum within the world-wide leaf economics spectrum? Major variations in leaf functional traits in the Mediterranean sclerophyll Quercus ilex.

PubMed

Niinemets, Ulo

2015-01-01

The leaf economics spectrum is a general concept describing coordinated variation in foliage structural, chemical and physiological traits across resource gradients. Yet, within this concept,the role of within-species variation, including ecotypic and plastic variation components, has been largely neglected. This study hypothesized that there is a within-species economics spectrum within the general spectrum in the evergreen sclerophyll Quercus ilex which dominates low resource ecosystems over an exceptionally wide range. An extensive database of foliage traits covering the full species range was constructed, and improved filtering algorithms were developed. Standardized data filtering was deemed absolutely essential as additional variation sources can result in trait variation of 10–300%,blurring the broad relationships. Strong trait variation, c. two-fold for most traits to up to almost an order of magnitude, was uncovered.Although the Q. ilex spectrum is part of the general spectrum, within-species trait and climatic relationships in this species partly differed from the overall spectrum. Contrary to world-wide trends, Q. ilex does not necessarily have a low nitrogen content per mass and can increase photosynthetic capacity with increasing foliage robustness. This study argues that the within-species economics spectrum needs to be considered in regional- to biome-level analyses.

Proteogenomic Analysis of Polymorphisms and Gene Annotation Divergences in Prokaryotes using a Clustered Mass Spectrometry-Friendly Database*

PubMed Central

de Souza, Gustavo A.; Arntzen, Magnus Ø.; Fortuin, Suereta; Schürch, Anita C.; Målen, Hiwa; McEvoy, Christopher R. E.; van Soolingen, Dick; Thiede, Bernd; Warren, Robin M.; Wiker, Harald G.

2011-01-01

Precise annotation of genes or open reading frames is still a difficult task that results in divergence even for data generated from the same genomic sequence. This has an impact in further proteomic studies, and also compromises the characterization of clinical isolates with many specific genetic variations that may not be represented in the selected database. We recently developed software called multistrain mass spectrometry prokaryotic database builder (MSMSpdbb) that can merge protein databases from several sources and be applied on any prokaryotic organism, in a proteomic-friendly approach. We generated a database for the Mycobacterium tuberculosis complex (using three strains of Mycobacterium bovis and five of M. tuberculosis), and analyzed data collected from two laboratory strains and two clinical isolates of M. tuberculosis. We identified 2561 proteins, of which 24 were present in M. tuberculosis H37Rv samples, but not annotated in the M. tuberculosis H37Rv genome. We were also able to identify 280 nonsynonymous single amino acid polymorphisms and confirm 367 translational start sites. As a proof of concept we applied the database to whole-genome DNA sequencing data of one of the clinical isolates, which allowed the validation of 116 predicted single amino acid polymorphisms and the annotation of 131 N-terminal start sites. Moreover we identified regions not present in the original M. tuberculosis H37Rv sequence, indicating strain divergence or errors in the reference sequence. In conclusion, we demonstrated the potential of using a merged database to better characterize laboratory or clinical bacterial strains. PMID:21030493

Measuring disease prevalence: a comparison of musculoskeletal disease using four general practice consultation databases

PubMed Central

Jordan, Kelvin; Clarke, Alexandra M; Symmons, Deborah PM; Fleming, Douglas; Porcheret, Mark; Kadam, Umesh T; Croft, Peter

2007-01-01

Background Primary care consultation data are an important source of information on morbidity prevalence. It is not known how reliable such figures are. Aim To compare annual consultation prevalence estimates for musculoskeletal conditions derived from four general practice consultation databases. Design of study Retrospective study of general practice consultation records. Setting Three national general practice consultation databases: i) Fourth Morbidity Statistics from General Practice (MSGP4, 1991/92), ii) Royal College of General Practitioners Weekly Returns Service (RCGP WRS, 2001), and iii) General Practice Research Database (GPRD, 1991 and 2001); and one regional database (Consultations in Primary Care Archive, 2001). Method Age-sex standardised persons consulting annual prevalence rates for musculoskeletal conditions overall, rheumatoid arthritis, osteoarthritis and arthralgia were derived for patients aged 15 years and over. Results GPRD prevalence of any musculoskeletal condition, rheumatoid arthritis and osteoarthritis was lower than that of the other databases. This is likely to be due to GPs not needing to record every consultation made for a chronic condition. MSGP4 gave the highest prevalence for osteoarthritis but low prevalence of arthralgia which reflects encouragement for GPs to use diagnostic rather than symptom codes. Conclusion Considerable variation exists in consultation prevalence estimates for musculoskeletal conditions. Researchers and health service planners should be aware that estimates of disease occurrence based on consultation will be influenced by choice of database. This is likely to be true for other chronic diseases and where alternative symptom labels exist for a disease. RCGP WRS may give the most reliable prevalence figures for musculoskeletal and other chronic diseases. PMID:17244418

Interpretation of Blazar Flux Variations as Music

NASA Astrophysics Data System (ADS)

Webb, J. R.

2003-12-01

Blazars are believed to be distant galaxies in the process of formation. They emit electromagnetic radiation (light) over the entire electromagnetic spectrum from radio waves to gamma-rays. The emission varies with time in most frequency ranges and the causes for the variation are yet to be adequately explained. Astronomers have been monitoring these objects with optical telescopes for over 50 years now and we have collected a large database of brightnesses over these fifty years. This paper presents some of these light curves, and adopts a computational method to translate the brightness fluctuations into musical tones. These tones are then converted to sound using a midi synthesizer on a PC.

Black-White variations in the lagged reciprocal relationship between religiosity and perceived control.

PubMed

Oates, Gary

2013-06-01

This national longitudinal data-based multi-population LISREL study, the most comprehensive assessment to date of racial variations in the (in)congruity between religiosity and perceived control, gauges variation among Black and White Americans in the lagged reciprocal relationship between religiosity dimensions and mastery. Racial variation in the reciprocal religiosity-perceived control relationship has hitherto gone un-addressed. Prior investigations have also typically utilised cross-sectional samples - often from regional or age-specific populations. The observed public religiosity-mastery relationship over time exhibits signs of mutual reinforcement among Blacks: public religiosity enhances Blacks' subsequent mastery, while prior mastery borderline-significantly enhances their public religiosity. The subjective religiosity-mastery relationship among Whites evinces a marginally countervailing pattern: Subjective religiosity diminishes Whites' mastery, while mastery borderline-significantly enhances their subjective religiosity. The inordinately positive public religiosity-effect on Blacks' mastery notably constitutes solid support for the " resource compensation " perspective on the impact of religiosity on mastery across dominant and subordinate groups.

A review of the surface and internal anatomy of the caudal canal in children.

PubMed

Lees, David; Frawley, Geoff; Taghavi, Kiarash; Mirjalili, Seyed Ali

2014-08-01

The anatomy of the sacral hiatus and caudal canal is prone to significant variation, yet studies assessing this in the pediatric population remain limited. Awareness of the possible anatomical variations is critical to the safety and success of caudal epidural blocks, particularly when image guidance is not employed. This systematic review analyzes the available evidence on the clinical anatomy of the caudal canal in pediatric patients, emphasizing surface anatomy and internal anatomical variations. A literature search using three electronic databases and standard pediatric and anatomy reference texts was conducted yielding 24 primary and seven secondary English-language sources. Appreciating that our current landmark-guided approaches to the caudal canal are not well studied in the pediatric population is important for both clinicians and researchers. © 2014 John Wiley & Sons Ltd.

Genovar: a detection and visualization tool for genomic variants.

PubMed

Jung, Kwang Su; Moon, Sanghoon; Kim, Young Jin; Kim, Bong-Jo; Park, Kiejung

2012-05-08

Along with single nucleotide polymorphisms (SNPs), copy number variation (CNV) is considered an important source of genetic variation associated with disease susceptibility. Despite the importance of CNV, the tools currently available for its analysis often produce false positive results due to limitations such as low resolution of array platforms, platform specificity, and the type of CNV. To resolve this problem, spurious signals must be separated from true signals by visual inspection. None of the previously reported CNV analysis tools support this function and the simultaneous visualization of comparative genomic hybridization arrays (aCGH) and sequence alignment. The purpose of the present study was to develop a useful program for the efficient detection and visualization of CNV regions that enables the manual exclusion of erroneous signals. A JAVA-based stand-alone program called Genovar was developed. To ascertain whether a detected CNV region is a novel variant, Genovar compares the detected CNV regions with previously reported CNV regions using the Database of Genomic Variants (DGV, http://projects.tcag.ca/variation) and the Single Nucleotide Polymorphism Database (dbSNP). The current version of Genovar is capable of visualizing genomic data from sources such as the aCGH data file and sequence alignment format files. Genovar is freely accessible and provides a user-friendly graphic user interface (GUI) to facilitate the detection of CNV regions. The program also provides comprehensive information to help in the elimination of spurious signals by visual inspection, making Genovar a valuable tool for reducing false positive CNV results. http://genovar.sourceforge.net/.

Validation of a common data model for active safety surveillance research

PubMed Central

Ryan, Patrick B; Reich, Christian G; Hartzema, Abraham G; Stang, Paul E

2011-01-01

Objective Systematic analysis of observational medical databases for active safety surveillance is hindered by the variation in data models and coding systems. Data analysts often find robust clinical data models difficult to understand and ill suited to support their analytic approaches. Further, some models do not facilitate the computations required for systematic analysis across many interventions and outcomes for large datasets. Translating the data from these idiosyncratic data models to a common data model (CDM) could facilitate both the analysts' understanding and the suitability for large-scale systematic analysis. In addition to facilitating analysis, a suitable CDM has to faithfully represent the source observational database. Before beginning to use the Observational Medical Outcomes Partnership (OMOP) CDM and a related dictionary of standardized terminologies for a study of large-scale systematic active safety surveillance, the authors validated the model's suitability for this use by example. Validation by example To validate the OMOP CDM, the model was instantiated into a relational database, data from 10 different observational healthcare databases were loaded into separate instances, a comprehensive array of analytic methods that operate on the data model was created, and these methods were executed against the databases to measure performance. Conclusion There was acceptable representation of the data from 10 observational databases in the OMOP CDM using the standardized terminologies selected, and a range of analytic methods was developed and executed with sufficient performance to be useful for active safety surveillance. PMID:22037893

Predictions of Control Inputs, Periodic Responses and Damping Levels of an Isolated Experimental Rotor in Trimmed Flight

NASA Technical Reports Server (NTRS)

Gaonkar, G. H.; Subramanian, S.

1996-01-01

Since the early 1990s the Aeroflightdynamics Directorate at the Ames Research Center has been conducting tests on isolated hingeless rotors in hover and forward flight. The primary objective is to generate a database on aeroelastic stability in trimmed flight for torsionally soft rotors at realistic tip speeds. The rotor test model has four soft inplane blades of NACA 0012 airfoil section with low torsional stiffness. The collective pitch and shaft tilt are set prior to each test run, and then the rotor is trimmed in the following sense: the longitudinal and lateral cyclic pitch controls are adjusted through a swashplate to minimize the 1/rev flapping moment at the 12 percent radial station. In hover, the database comprises lag regressive-mode damping with pitch variations. In forward flight the database comprises cyclic pitch controls, root flap moment and lag regressive-mode damping with advance ratio, shaft angle and pitch variations. This report presents the predictions and their correlation with the database. A modal analysis is used, in which nonrotating modes in flap bending, lag bending and torsion are computed from the measured blade mass and stiffness distributions. The airfoil aerodynamics is represented by the ONERA dynamic stall models of lift, drag and pitching moment, and the wake dynamics is represented by a state-space wake model. The trim analysis of finding, the cyclic controls and the corresponding, periodic responses is based on periodic shooting with damped Newton iteration; the Floquet transition matrix (FTM) comes out as a byproduct. The stabillty analysis of finding the frequencies and damping levels is based on the eigenvalue-eigenvector analysis of the FTM. All the structural and aerodynamic states are included from modeling to trim analysis. A major finding is that dynamic wake dramatically improves the correlation for the lateral cyclic pitch control. Overall, the correlation is fairly good.

Season plays a role in variability in vitamin C content of fresh fruits and vegetables in a local retail market

USDA-ARS?s Scientific Manuscript database

Seasonal variation of vitamin C in fresh fruits and vegetables is not reflected in food composition database average values, yet many factors influence content and retention. Fresh fruits and vegetables were sampled on three occasions in each season, from the same local retail outlets, for one or tw...

Urbanicity-Related Variation in Help-Seeking and Services Utilization among Preschool-Age Children with Autism in Taiwan

ERIC Educational Resources Information Center

Chen, Chuan-Yu; Liu, Chieh-Yu; Su, Wen-Chuan; Huang, Su-Ling; Lin, Keh-Ming

2008-01-01

The present study examines urbanicity-related differences in help-seeking process among preschool children with autism and investigates the factors associated with utilization of autism-related services within the year of diagnosis. Using the 1997-2004 National Health Insurance Research Database (NHIRD) in Taiwan, we identified a total of 3495…

Changes in wood product proportions in the Douglas-fir region with respect to size, age, and time.

Treesearch

R.A. Monserud; X. Zhou

2007-01-01

We examine both the variation and the changing proportions of different wood products obtained from trees and logs in the Douglas-fir region of the Northwestern United States. Analyses are based on a large product recovery database covering over 40 years of recovery studies; 13 studies are available for Douglas-fir (Pseudotsuga menziesii (Mirb.)...

Temporal variation in synchrony among chinook salmon (Oncorhynchus tshawytscha) redd counts from a wilderness area in central Idaho

Treesearch

D. J. Isaak; R. F. Thurow; B. E. Rieman; J. B. Dunham

2003-01-01

Metapopulation dynamics have emerged as a key consideration in conservation planning for salmonid fishes. Implicit to many models of spatially structured populations is a degree of synchrony, or correlation, among populations. We used a spatially and temporally extensive database of chinook salmon (Oncorhynchus tshawytscha) redd counts from a wilderness area in central...

Hospital Variation in Utilization of Life-Sustaining Treatments among Patients with Do Not Resuscitate Orders.

PubMed

Walkey, Allan J; Weinberg, Janice; Wiener, Renda Soylemez; Cooke, Colin R; Lindenauer, Peter K

2018-06-01

To determine between-hospital variation in interventions provided to patients with do not resuscitate (DNR) orders. United States Agency of Healthcare Research and Quality, Healthcare Cost and Utilization Project, California State Inpatient Database. Retrospective cohort study including hospitalized patients aged 40 and older with potential indications for invasive treatments: in-hospital cardiac arrest (indication for CPR), acute respiratory failure (mechanical ventilation), acute renal failure (hemodialysis), septic shock (central venous catheterization), and palliative care. Hierarchical logistic regression to determine associations of hospital "early" DNR rates (DNR order placed within 24 hours of admission) with utilization of invasive interventions. California State Inpatient Database, year 2011. Patients with DNR orders at high-DNR-rate hospitals were less likely to receive invasive mechanical ventilation for acute respiratory failure or hemodialysis for acute renal failure, but more likely to receive palliative care than DNR patients at low-DNR-rate hospitals. Patients without DNR orders experienced similar rates of invasive interventions regardless of hospital DNR rates. Hospitals vary widely in the scope of invasive or organ-supporting treatments provided to patients with DNR orders. © Health Research and Educational Trust.

Factors affecting variation in mortality of marine Atlantic salmon Salmo salar in Scotland.

PubMed

Soares, Silvia; Murray, Alexander G; Crumlish, Mags; Turnbull, James F; Green, Darren M

2013-03-26

Databases of site production have an important role to play in the investigation and understanding of diseases, since they store valuable amounts of disease and management data. Diseases pose an important constraint to economic expansion of aquaculture. They are dependent on the complex interacting factors of pathogen, environment, and host, and the causes of death can be related to nutritional, environmental, and genetic factors of the host or infectious agents. We examined the drivers of mortality from a single site-production database, which represented one-third of Scottish farmed salmon Salmo salar L. production in 2005, to determine whether mortality 'benchmarking' data could be generalised across sites and production cycles. We show that farm mortality records play an important role in studying mortality losses and identifying of management problems in production. We found that mortalities varied across the months of the year and with the time of year of initial stocking. Production cycles that started in the third quarter of the year had the highest mortality overall. Furthermore, we found site-to-site variation in mortality that may have been caused by either random occurrence of epidemics and environmental events or other local effects.

WGE: a CRISPR database for genome engineering.

PubMed

Hodgkins, Alex; Farne, Anna; Perera, Sajith; Grego, Tiago; Parry-Smith, David J; Skarnes, William C; Iyer, Vivek

2015-09-15

The rapid development of CRISPR-Cas9 mediated genome editing techniques has given rise to a number of online and stand-alone tools to find and score CRISPR sites for whole genomes. Here we describe the Wellcome Trust Sanger Institute Genome Editing database (WGE), which uses novel methods to compute, visualize and select optimal CRISPR sites in a genome browser environment. The WGE database currently stores single and paired CRISPR sites and pre-calculated off-target information for CRISPRs located in the mouse and human exomes. Scoring and display of off-target sites is simple, and intuitive, and filters can be applied to identify high-quality CRISPR sites rapidly. WGE also provides a tool for the design and display of gene targeting vectors in the same genome browser, along with gene models, protein translation and variation tracks. WGE is open, extensible and can be set up to compute and present CRISPR sites for any genome. The WGE database is freely available at www.sanger.ac.uk/htgt/wge : vvi@sanger.ac.uk or skarnes@sanger.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Gene: a gene-centered information resource at NCBI.

PubMed

Brown, Garth R; Hem, Vichet; Katz, Kenneth S; Ovetsky, Michael; Wallin, Craig; Ermolaeva, Olga; Tolstoy, Igor; Tatusova, Tatiana; Pruitt, Kim D; Maglott, Donna R; Murphy, Terence D

2015-01-01

The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.nih.gov/gene) integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that they form the critical association between sequence and a tracked gene upon which additional functional and descriptive content is anchored. Additional content is integrated based on the genomic location and RefSeq transcript and protein sequence data. The content of a Gene record represents the integration of curation and automated processing from RefSeq, collaborating model organism databases, consortia such as Gene Ontology, and other databases within NCBI. Records in Gene are assigned unique, tracked integers as identifiers. The content (citations, nomenclature, genomic location, gene products and their attributes, phenotypes, sequences, interactions, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities and Entrez Direct) and for bulk transfer by FTP. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Winnowing sequences from a database search.

PubMed

Berman, P; Zhang, Z; Wolf, Y I; Koonin, E V; Miller, W

2000-01-01

In database searches for sequence similarity, matches to a distinct sequence region (e.g., protein domain) are frequently obscured by numerous matches to another region of the same sequence. In order to cope with this problem, algorithms are developed to discard redundant matches. One model for this problem begins with a list of intervals, each with an associated score; each interval gives the range of positions in the query sequence that align to a database sequence, and the score is that of the alignment. If interval I is contained in interval J, and I's score is less than J's, then I is said to be dominated by J. The problem is then to identify each interval that is dominated by at least K other intervals, where K is a given level of "tolerable redundancy." An algorithm is developed to solve the problem in O(N log N) time and O(N*) space, where N is the number of intervals and N* is a precisely defined value that never exceeds N and is frequently much smaller. This criterion for discarding database hits has been implemented in the Blast program, as illustrated herein with examples. Several variations and extensions of this approach are also described.

JEnsembl: a version-aware Java API to Ensembl data systems.

PubMed

Paterson, Trevor; Law, Andy

2012-11-01

The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing 'through time' comparative analyses to be performed. Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net).

Phosphorus-containing food additives and the accuracy of nutrient databases: implications for renal patients.

PubMed

Sullivan, Catherine M; Leon, Janeen B; Sehgal, Ashwini R

2007-09-01

Phosphorus-containing additives are increasingly being added to food products. We sought to determine the potential impact of these additives. We focused on chicken products as an example. We purchased a variety of chicken products, prepared them according to package directions, and performed laboratory analyses to determine their actual phosphorus content. We used ESHA Food Processor SQL Software (version 9.8, ESHA Research, Salem, OR) to determine the expected phosphorus content of each product. Of 38 chicken products, 35 (92%) had phosphorus-containing additives listed among their ingredients. For every category of chicken products containing additives, the actual phosphorus content was greater than the content expected from nutrient database. For example, actual phosphorus content exceeded expected phosphorus content by an average of 84 mg/100 g for breaded breast strips. There was also a great deal of variation within each category. For example, the difference between actual and expected phosphorus content ranged from 59-165 mg/100 g for breast patties. Two 100-g servings of additive-containing products contained, on average, 440 mg of phosphorus, or about half the total daily recommended intake for dialysis patients. Phosphorus-containing additives significantly increase the amount of phosphorus in chicken products. Available nutrient databases do not reflect this higher phosphorus content, and the variation between similar products makes it impossible for patients and dietitians to accurately estimate phosphorus content. We recommend that dialysis patients limit their intake of additive-containing products, and that the phosphorus content of food products be included on nutrition facts labels.

PHOSPHORUS CONTAINING FOOD ADDITIVES AND THE ACCURACY OF NUTRIENT DATABASES: IMPLICATIONS FOR RENAL PATIENTS

PubMed Central

Sullivan, Catherine M.; Leon, Janeen B.; Sehgal, Ashwini R.

2007-01-01

Objective Phosphorus containing additives are increasingly added to food products. We sought to determine the potential impact of these additives. We focused on chicken products as an example. Methods We purchased a variety of chicken products, prepared them according to package directions, and performed laboratory analyses to determine their actual phosphorus content. We used ESHA Food Processor SQL Software to determine the expected phosphorus content of each product. Results Of 38 chicken products, 35 (92%) had phosphorus containing additives listed among their ingredients. For every category of chicken products containing additives, the actual phosphorus content was greater than the content expected from nutrient database. For example, actual phosphorus content exceeded expected phosphorus content by an average of 84 mg/100g for breaded breast strips. There was also a great deal of variation within each category. For example, the difference between actual and expected phosphorus content ranged from 59 to 165 mg/100g for breast patties. Two 100 g servings of additive containing products contain an average of 440 mg of phosphorus, or about half the total daily recommended intake for dialysis patients. Conclusion Phosphorus containing additives significantly increase the amount of phosphorus in chicken products. Available nutrient databases do not reflect this higher phosphorus content, and the variation between similar products makes it impossible for patients and dietitians to accurately estimate phosphorus content. We recommend that dialysis patients limit their intake of additive containing products and that the phosphorus content of food products be included on nutrition facts labels. PMID:17720105

Assessing the Variability in the Relationship Between the Particulate Backscattering Coefficient and the Chlorophyll a Concentration From a Global Biogeochemical-Argo Database

NASA Astrophysics Data System (ADS)

Barbieux, Marie; Uitz, Julia; Bricaud, Annick; Organelli, Emanuele; Poteau, Antoine; Schmechtig, Catherine; Gentili, Bernard; Obolensky, Grigor; Leymarie, Edouard; Penkerc'h, Christophe; D'Ortenzio, Fabrizio; Claustre, Hervé

2018-02-01

Characterizing phytoplankton distribution and dynamics in the world's open oceans requires in situ observations over a broad range of space and time scales. In addition to temperature/salinity measurements, Biogeochemical-Argo (BGC-Argo) profiling floats are capable of autonomously observing at high-frequency bio-optical properties such as the chlorophyll fluorescence, a proxy of the chlorophyll a concentration (Chla), the particulate backscattering coefficient (bbp), a proxy of the stock of particulate organic carbon, and the light available for photosynthesis. We analyzed an unprecedented BGC-Argo database of more than 8,500 multivariable profiles collected in various oceanic conditions, from subpolar waters to subtropical gyres. Our objective is to refine previously established Chla versus bbp relationships and gain insights into the sources of vertical, seasonal, and regional variability in this relationship. Despite some regional, seasonal and vertical variations, a general covariation occurs at a global scale. We distinguish two main contrasted situations: (1) concomitant changes in Chla and bbp that correspond to actual variations in phytoplankton biomass, e.g., in subpolar regimes; (2) a decoupling between the two variables attributed to photoacclimation or changes in the relative abundance of nonalgal particles, e.g., in subtropical regimes. The variability in the bbp:Chla ratio in the surface layer appears to be essentially influenced by the type of particles and by photoacclimation processes. The large BGC-Argo database helps identifying the spatial and temporal scales at which this ratio is predominantly driven by one or the other of these two factors.

Inaccurate Ascertainment of Morbidity and Mortality due to Influenza in Administrative Databases: A Population-Based Record Linkage Study

PubMed Central

Muscatello, David J.; Amin, Janaki; MacIntyre, C. Raina; Newall, Anthony T.; Rawlinson, William D.; Sintchenko, Vitali; Gilmour, Robin; Thackway, Sarah

2014-01-01

Background Historically, counting influenza recorded in administrative health outcome databases has been considered insufficient to estimate influenza attributable morbidity and mortality in populations. We used database record linkage to evaluate whether modern databases have similar limitations. Methods Person-level records were linked across databases of laboratory notified influenza, emergency department (ED) presentations, hospital admissions and death registrations, from the population (∼6.9 million) of New South Wales (NSW), Australia, 2005 to 2008. Results There were 2568 virologically diagnosed influenza infections notified. Among those, 25% of 40 who died, 49% of 1451 with a hospital admission and 7% of 1742 with an ED presentation had influenza recorded on the respective database record. Compared with persons aged ≥65 years and residents of regional and remote areas, respectively, children and residents of major cities were more likely to have influenza coded on their admission record. Compared with older persons and admitted patients, respectively, working age persons and non-admitted persons were more likely to have influenza coded on their ED record. On both ED and admission records, persons with influenza type A infection were more likely than those with type B infection to have influenza coded. Among death registrations, hospital admissions and ED presentations with influenza recorded as a cause of illness, 15%, 28% and 1.4%, respectively, also had laboratory notified influenza. Time trends in counts of influenza recorded on the ED, admission and death databases reflected the trend in counts of virologically diagnosed influenza. Conclusions A minority of the death, hospital admission and ED records for persons with a virologically diagnosed influenza infection identified influenza as a cause of illness. Few database records with influenza recorded as a cause had laboratory confirmation. The databases have limited value for estimating incidence of influenza outcomes, but can be used for monitoring variation in incidence over time. PMID:24875306

Challenges in developing medicinal plant databases for sharing ethnopharmacological knowledge.

PubMed

Ningthoujam, Sanjoy Singh; Talukdar, Anupam Das; Potsangbam, Kumar Singh; Choudhury, Manabendra Dutta

2012-05-07

Major research contributions in ethnopharmacology have generated vast amount of data associated with medicinal plants. Computerized databases facilitate data management and analysis making coherent information available to researchers, planners and other users. Web-based databases also facilitate knowledge transmission and feed the circle of information exchange between the ethnopharmacological studies and public audience. However, despite the development of many medicinal plant databases, a lack of uniformity is still discernible. Therefore, it calls for defining a common standard to achieve the common objectives of ethnopharmacology. The aim of the study is to review the diversity of approaches in storing ethnopharmacological information in databases and to provide some minimal standards for these databases. Survey for articles on medicinal plant databases was done on the Internet by using selective keywords. Grey literatures and printed materials were also searched for information. Listed resources were critically analyzed for their approaches in content type, focus area and software technology. Necessity for rapid incorporation of traditional knowledge by compiling primary data has been felt. While citation collection is common approach for information compilation, it could not fully assimilate local literatures which reflect traditional knowledge. Need for defining standards for systematic evaluation, checking quality and authenticity of the data is felt. Databases focussing on thematic areas, viz., traditional medicine system, regional aspect, disease and phytochemical information are analyzed. Issues pertaining to data standard, data linking and unique identification need to be addressed in addition to general issues like lack of update and sustainability. In the background of the present study, suggestions have been made on some minimum standards for development of medicinal plant database. In spite of variations in approaches, existence of many overlapping features indicates redundancy of resources and efforts. As the development of global data in a single database may not be possible in view of the culture-specific differences, efforts can be given to specific regional areas. Existing scenario calls for collaborative approach for defining a common standard in medicinal plant database for knowledge sharing and scientific advancement. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Knowledge Discovery in Variant Databases Using Inductive Logic Programming

PubMed Central

Nguyen, Hoan; Luu, Tien-Dao; Poch, Olivier; Thompson, Julie D.

2013-01-01

Understanding the effects of genetic variation on the phenotype of an individual is a major goal of biomedical research, especially for the development of diagnostics and effective therapeutic solutions. In this work, we describe the use of a recent knowledge discovery from database (KDD) approach using inductive logic programming (ILP) to automatically extract knowledge about human monogenic diseases. We extracted background knowledge from MSV3d, a database of all human missense variants mapped to 3D protein structure. In this study, we identified 8,117 mutations in 805 proteins with known three-dimensional structures that were known to be involved in human monogenic disease. Our results help to improve our understanding of the relationships between structural, functional or evolutionary features and deleterious mutations. Our inferred rules can also be applied to predict the impact of any single amino acid replacement on the function of a protein. The interpretable rules are available at http://decrypthon.igbmc.fr/kd4v/. PMID:23589683

Knowledge discovery in variant databases using inductive logic programming.

PubMed

Nguyen, Hoan; Luu, Tien-Dao; Poch, Olivier; Thompson, Julie D

2013-01-01

Understanding the effects of genetic variation on the phenotype of an individual is a major goal of biomedical research, especially for the development of diagnostics and effective therapeutic solutions. In this work, we describe the use of a recent knowledge discovery from database (KDD) approach using inductive logic programming (ILP) to automatically extract knowledge about human monogenic diseases. We extracted background knowledge from MSV3d, a database of all human missense variants mapped to 3D protein structure. In this study, we identified 8,117 mutations in 805 proteins with known three-dimensional structures that were known to be involved in human monogenic disease. Our results help to improve our understanding of the relationships between structural, functional or evolutionary features and deleterious mutations. Our inferred rules can also be applied to predict the impact of any single amino acid replacement on the function of a protein. The interpretable rules are available at http://decrypthon.igbmc.fr/kd4v/.

DataTri, a database of American triatomine species occurrence

NASA Astrophysics Data System (ADS)

Ceccarelli, Soledad; Balsalobre, Agustín; Medone, Paula; Cano, María Eugenia; Gurgel Gonçalves, Rodrigo; Feliciangeli, Dora; Vezzani, Darío; Wisnivesky-Colli, Cristina; Gorla, David E.; Marti, Gerardo A.; Rabinovich, Jorge E.

2018-04-01

Trypanosoma cruzi, the causative agent of Chagas disease, is transmitted to mammals - including humans - by insect vectors of the subfamily Triatominae. We present the results of a compilation of triatomine occurrence and complementary ecological data that represents the most complete, integrated and updated database (DataTri) available on triatomine species at a continental scale. This database was assembled by collecting the records of triatomine species published from 1904 to 2017, spanning all American countries with triatomine presence. A total of 21815 georeferenced records were obtained from published literature, personal fieldwork and data provided by colleagues. The data compiled includes 24 American countries, 14 genera and 135 species. From a taxonomic perspective, 67.33% of the records correspond to the genus Triatoma, 20.81% to Panstrongylus, 9.01% to Rhodnius and the remaining 2.85% are distributed among the other 11 triatomine genera. We encourage using DataTri information in various areas, especially to improve knowledge of the geographical distribution of triatomine species and its variations in time.

MSDB: A Comprehensive Database of Simple Sequence Repeats.

PubMed

Avvaru, Akshay Kumar; Saxena, Saketh; Sowpati, Divya Tej; Mishra, Rakesh Kumar

2017-06-01

Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6 nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of >650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Impact of dietary fiber energy on the calculation of food total energy value in the Brazilian Food Composition Database.

PubMed

Menezes, Elizabete Wenzel de; Grande, Fernanda; Giuntini, Eliana Bistriche; Lopes, Tássia do Vale Cardoso; Dan, Milana Cara Tanasov; Prado, Samira Bernardino Ramos do; Franco, Bernadette Dora Gombossy de Melo; Charrondière, U Ruth; Lajolo, Franco Maria

2016-02-15

Dietary fiber (DF) contributes to the energy value of foods and including it in the calculation of total food energy has been recommended for food composition databases. The present study aimed to investigate the impact of including energy provided by the DF fermentation in the calculation of food energy. Total energy values of 1753 foods from the Brazilian Food Composition Database were calculated with or without the inclusion of DF energy. The energy values were compared, through the use of percentage difference (D%), in individual foods and in daily menus. Appreciable energy D% (⩾10) was observed in 321 foods, mainly in the group of vegetables, legumes and fruits. However, in the Brazilian typical menus containing foods from all groups, only D%<3 was observed. In mixed diets, the DF energy may cause slight variations in total energy; on the other hand, there is appreciable energy D% for certain foods, when individually considered. Copyright © 2015 Elsevier Ltd. All rights reserved.

DataTri, a database of American triatomine species occurrence.

PubMed

Ceccarelli, Soledad; Balsalobre, Agustín; Medone, Paula; Cano, María Eugenia; Gurgel Gonçalves, Rodrigo; Feliciangeli, Dora; Vezzani, Darío; Wisnivesky-Colli, Cristina; Gorla, David E; Marti, Gerardo A; Rabinovich, Jorge E

2018-04-24

Trypanosoma cruzi, the causative agent of Chagas disease, is transmitted to mammals - including humans - by insect vectors of the subfamily Triatominae. We present the results of a compilation of triatomine occurrence and complementary ecological data that represents the most complete, integrated and updated database (DataTri) available on triatomine species at a continental scale. This database was assembled by collecting the records of triatomine species published from 1904 to 2017, spanning all American countries with triatomine presence. A total of 21815 georeferenced records were obtained from published literature, personal fieldwork and data provided by colleagues. The data compiled includes 24 American countries, 14 genera and 135 species. From a taxonomic perspective, 67.33% of the records correspond to the genus Triatoma, 20.81% to Panstrongylus, 9.01% to Rhodnius and the remaining 2.85% are distributed among the other 11 triatomine genera. We encourage using DataTri information in various areas, especially to improve knowledge of the geographical distribution of triatomine species and its variations in time.

CFTR-France, a national relational patient database for sharing genetic and phenotypic data associated with rare CFTR variants.

PubMed

Claustres, Mireille; Thèze, Corinne; des Georges, Marie; Baux, David; Girodon, Emmanuelle; Bienvenu, Thierry; Audrezet, Marie-Pierre; Dugueperoux, Ingrid; Férec, Claude; Lalau, Guy; Pagin, Adrien; Kitzis, Alain; Thoreau, Vincent; Gaston, Véronique; Bieth, Eric; Malinge, Marie-Claire; Reboul, Marie-Pierre; Fergelot, Patricia; Lemonnier, Lydie; Mekki, Chadia; Fanen, Pascale; Bergougnoux, Anne; Sasorith, Souphatta; Raynal, Caroline; Bareil, Corinne

2017-10-01

Most of the 2,000 variants identified in the CFTR (cystic fibrosis transmembrane regulator) gene are rare or private. Their interpretation is hampered by the lack of available data and resources, making patient care and genetic counseling challenging. We developed a patient-based database dedicated to the annotations of rare CFTR variants in the context of their cis- and trans-allelic combinations. Based on almost 30 years of experience of CFTR testing, CFTR-France (https://cftr.iurc.montp.inserm.fr/cftr) currently compiles 16,819 variant records from 4,615 individuals with cystic fibrosis (CF) or CFTR-RD (related disorders), fetuses with ultrasound bowel anomalies, newborns awaiting clinical diagnosis, and asymptomatic compound heterozygotes. For each of the 736 different variants reported in the database, patient characteristics and genetic information (other variations in cis or in trans) have been thoroughly checked by a dedicated curator. Combining updated clinical, epidemiological, in silico, or in vitro functional data helps to the interpretation of unclassified and the reassessment of misclassified variants. This comprehensive CFTR database is now an invaluable tool for diagnostic laboratories gathering information on rare variants, especially in the context of genetic counseling, prenatal and preimplantation genetic diagnosis. CFTR-France is thus highly complementary to the international database CFTR2 focused so far on the most common CF-causing alleles. © 2017 Wiley Periodicals, Inc.

Prevalence of physical inactivity in Iran: a systematic review.

PubMed

Fakhrzadeh, Hossein; Djalalinia, Shirin; Mirarefin, Mojdeh; Arefirad, Tahereh; Asayesh, Hamid; Safiri, Saeid; Samami, Elham; Mansourian, Morteza; Shamsizadeh, Morteza; Qorbani, Mostafa

2016-01-01

Introduction: Physical inactivity is one of the most important risk factors for chronic diseases, including cardiovascular disease, cancer, and stroke. We aim to conduct a systematic review of the prevalence of physical inactivity in Iran. Methods: We searched international databases; ISI, PubMed/Medline, Scopus, and national databases Irandoc, Barakat knowledge network system, and Scientific Information Database (SID). We collected data for outcome measures of prevalence of physical inactivity by sex, age, province, and year. Quality assessment and data extraction has been conducted independently by two independent research experts. There were no limitations for time and language. Results: We analyzed data for prevalence of physical inactivity in Iranian population. According to our search strategy we found 254 records; of them 185 were from international databases and the remaining 69 were obtained from national databases after refining the data, 34 articles that met eligible criteria remained for data extraction. From them respectively; 9, 20, 2 and 3 studies were at national, provincial, regional and local levels. The estimates for inactivity ranged from approximately 30% to almost 70% and had considerable variation between sexes and studied sub-groups. Conclusion: In Iran, most of studies reported high prevalence of physical inactivity. Our findings reveal a heterogeneity of reported values, often from differences in study design, measurement tools and methods, different target groups and sub-population sampling. These data do not provide the possibility of aggregation of data for a comprehensive inference.

The Role of Data Archives in Synoptic Solar Physics

NASA Astrophysics Data System (ADS)

Reardon, Kevin

The detailed study of solar cycle variations requires analysis of recorded datasets spanning many years of observations, that is, a data archive. The use of digital data, combined with powerful database server software, gives such archives new capabilities to provide, quickly and flexibly, selected pieces of information to scientists. Use of standardized protocols will allow multiple databases, independently maintained, to be seamlessly joined, allowing complex searches spanning multiple archives. These data archives also benefit from being developed in parallel with the telescope itself, which helps to assure data integrity and to provide close integration between the telescope and archive. Development of archives that can guarantee long-term data availability and strong compatibility with other projects makes solar-cycle studies easier to plan and realize.

Analysis of a Meteorological Database for London Heathrow in the Context of Wake Vortex Hazards

NASA Astrophysics Data System (ADS)

Agnew, P.; Ogden, D. J.; Hoad, D. J.

2003-04-01

A database of meteorological parameters collected by aircraft arriving at LHR has recently been compiled. We have used the recorded variation of temperature and wind with height to deduce the 'wake vortex behaviour class' (WVBC) along the glide slope, as experienced by each flight. The integrated state of the glide slope has been investigated, allowing us to estimate the proportion of time for which the wake vortex threat is reduced, due to either rapid decay or transport off the glide slope. A numerical weather prediction model was used to forecast the meteorological parameters for periods coinciding with the aircraft data. This allowed us to perform a comparison of forecast WVBC with those deduced from the aircraft measurements.

Understanding sources of uncertainty and bias error in models of human response to low amplitude sonic booms

NASA Astrophysics Data System (ADS)

Collmar, M.; Cook, B. G.; Cowart, R.; Freund, D.; Gavin, J.

2015-10-01

A pool of 240 subjects was exposed to a library of waveforms consisting of example signatures of low boom aircraft. The signature library included intentional variations in both loudness and spectral content, and were auralized using the Gulfstream SASS-II sonic boom simulator. Post-processing was used to quantify the impacts of test design decisions on the "quality" of the resultant database. Specific lessons learned from this study include insight regarding potential for bias error due to variations in loudness or peak over-pressure, sources of uncertainty and their relative importance on objective measurements and robustness of individual metrics to wide variations in spectral content. Results provide clear guidance for design of future large scale community surveys, where one must optimize the complex tradeoffs between the size of the surveyed population, spatial footprint of those participants, and the fidelity/density of objective measurements.

Patterns of breast cancer mortality trends in Europe.

PubMed

Amaro, Joana; Severo, Milton; Vilela, Sofia; Fonseca, Sérgio; Fontes, Filipa; La Vecchia, Carlo; Lunet, Nuno

2013-06-01

To identify patterns of variation in breast cancer mortality in Europe (1980-2010), using a model-based approach. Mortality data were obtained from the World Health Organization database and mixed models were used to describe the time trends in the age-standardized mortality rates (ASMR). Model-based clustering was used to identify clusters of countries with homogeneous variation in ASMR. Three patterns were identified. Patterns 1 and 2 are characterized by stable or slightly increasing trends in ASMR in the first half of the period analysed, and a clear decline is observed thereafter; in pattern 1 the median of the ASMR is higher, and the highest rates were achieved sooner. Pattern 3 is characterised by a rapid increase in mortality until 1999, declining slowly thereafter. This study provides a general model for the description and interpretation of the variation in breast cancer mortality in Europe, based in three main patterns. Copyright © 2013 Elsevier Ltd. All rights reserved.

Evaluation of Long-term Soil Moisture Proxies in the U.S. Great Plains

NASA Astrophysics Data System (ADS)

Yuan, S.; Quiring, S. M.

2016-12-01

Soil moisture plays an important role in land-atmosphere interactions through both surface energy and water balances. However, despite its importance, there are few long-term records of observed soil moisture for investigating long-term spatial and temporal variations of soil moisture. Hence, it is necessary to find suitable approximations of soil moisture observations. 5 drought indices will be compared with simulated and observed soil moisture over the U.S. Great Plains during two time periods (1980 - 2012 and 2003 - 2012). Standardized Precipitation Index (SPI), Standardized Precipitation-Evapotranspiration Index (SPEI), Palmer Z Index (zindex) and Crop Moisture Index (CMI) will be calculated by PRISM data. The soil moisture simulations will be derived from NLDAS. In situ soil moisture will be obtained from North American Soil Moisture Database. The evaluation will focus on three main aspects: trends, variations and persistence. The results will support further research investigating long-term variations in soil moisture-climate interactions.

Magnetic activity of red secondaries: clues from the outburst cycle variations of dwarf novae

NASA Astrophysics Data System (ADS)

Chinarova, L. L.

Photometric variations of 6 dwarf novae stars are studied based on the photographic observations from the Odessa, Moscow and Sonneberg plate collections and published visual monitoring data from the AFOEV database (Schweitzer E.: 1993, Bull. AFOEV, 64, 14). The moments of maxima are determined by using the "running parabola" fit (Andronov I.L., 1990, Kinematika Fizika Nebesn. Tel., v.6,,N 6, 87) with automatically determined filter half-width (Andronov I.L., 1997, As.Ap. Suppl., in press). All investigated stars exhibit significant changes not only from cycle-to-cycle, but from season-to-season as well. Secondary decade-scale cycles of smooth variations (Bianchini A., 1990, AJ 99, 1941) and abrupt switchings (Andronov I.L., Shakun L.I., 1990, ASS 169, 237) were interpreted by a solar-type activity of the red dwarf secondary in a binary system and may argue for existence of two different subgroups of the dwarf novae.

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.

PubMed

Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

2017-01-04

The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e.g. species), whereas the entire collection of ATGCs is useful for macroevolutionary studies. The ATGC database includes many forms of pre-computed data, in particular ATGC-COGs (Clusters of Orthologous Genes), multiple sequence alignments, a set of 'index' orthologs representing the most well-conserved members of each ATGC-COG, the phylogenetic tree of the organisms within each ATGC, etc. Although the ATGC database contains several million proteins from thousands of genomes organized into hundreds of clusters (roughly a 4-fold increase since the last version of the ATGC database), it is now built with completely automated methods and will be regularly updated following new releases of the NCBI RefSeq database. The ATGC database is hosted jointly at the University of Iowa at dmk-brain.ecn.uiowa.edu/ATGC/ and the NCBI at ftp.ncbi.nlm.nih.gov/pub/kristensen/ATGC/atgc_home.html. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions

PubMed Central

Kuang, Xingyan; Dhroso, Andi; Han, Jing Ginger; Shyu, Chi-Ren; Korkin, Dmitry

2016-01-01

Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction’s mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein–protein interactions or protein–DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1 040 000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43 000 RNA-mediated interactions, and ∼12 000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N- termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network, binary interaction and interaction interface. Database URL: http://dommino.org PMID:26827237

Stable orthogonal local discriminant embedding for linear dimensionality reduction.

PubMed

Gao, Quanxue; Ma, Jingjie; Zhang, Hailin; Gao, Xinbo; Liu, Yamin

2013-07-01

Manifold learning is widely used in machine learning and pattern recognition. However, manifold learning only considers the similarity of samples belonging to the same class and ignores the within-class variation of data, which will impair the generalization and stableness of the algorithms. For this purpose, we construct an adjacency graph to model the intraclass variation that characterizes the most important properties, such as diversity of patterns, and then incorporate the diversity into the discriminant objective function for linear dimensionality reduction. Finally, we introduce the orthogonal constraint for the basis vectors and propose an orthogonal algorithm called stable orthogonal local discriminate embedding. Experimental results on several standard image databases demonstrate the effectiveness of the proposed dimensionality reduction approach.

Travel Distance and the Use of Inpatient Care among Patients with Schizophrenia

PubMed Central

Hemenway, David; Kawachi, Ichiro; Subramanian, S. V.; Chen, Wei J.

2009-01-01

This study examines the variations in the use of inpatient care that can be explained by travel distance among patients with schizophrenia living in Taiwan. Data were drawn from the Psychiatric Inpatient Medical Claims Database. We used mediation analysis and multilevel analysis to identify associations. Travel distance did not significantly account for lower readmission rates after an index admission, but significantly explained the longer length of stay of an index admission by 9.3 days (P < 0.001, 85% of variation) between remote and non-remote regions. Policies are discussed aimed at reducing the impact of travel distance on rural mental health care through inter-disciplinary collaboration and telepsychiatry. PMID:18512144

A Supplement to the 1995 Matched Anthropometric Database of U.S. Marine Corps Personnel: Summary Statistics

DTIC Science & Technology

1997-06-01

4.53 110.00 Maximum 4.33 Symmetry- Veta I 5.00 Symmetry- Veta I 1.20 Kurtosis- Veta II 6.70 Kurtosis- Veta II 1.40 Coeff. of Variation 33.2% Coeff of...Mean) 0.64 0.62 SE(SD) 0.02 0.62 SE(SD) 0.02 277.00 Minimum 10.91 264.00 Minimum 10.39 408.00 Maximum 16.06 379.00 Maximum 14.92 Symmetry- Veta I...0.60 Symmetry- Veta I 1.3{) Kurtosis- Veta II -0.40 Kurtosis- Veta II 0.30 Coeff. ofV ariation 4.9% Coeff. of Variation 5.2% Sample Size 4447 Sarn_ple

Comprehensive List of Cancer-Related Genetic Variations of the NCI-60 Panel | Center for Cancer Research

Cancer.gov

The NCI-60 cell lines are the most frequently studied human tumor cell lines in cancer research. The panel of cell lines represents nine different types of cancer: breast, ovary, prostate, colon, lung, kidney, brain, leukemia, and melanoma. Originally developed to screen anticancer compounds by the NCI Developmental Therapeutics Program (DTP), the NCI-60 panel has generated the most extensive cancer pharmacology database worldwide. The 60 cell lines have also been extensively analyzed for their gene and microRNA expression levels, DNA mutation status, and DNA copy number variations. These findings have provided the groundwork for research centered on increasing our understanding of tumor biology and drug activity.

Constitutional pericentric inversion 9 in Korean patients with chronic myelogenous leukemia.

PubMed

Suh, Borum; Song, Jaewoo; Kim, Juwon; Park, Tae Sung; Choi, Jong Rak

2010-06-01

Although the pericentric inversion of chromosome 9, inv(9)(p11q13), is generally considered a normal variation, it is also associated with solid tumors and several hematologic malignancies such as biphenotypic acute leukemia, ALL, AML, and myeloproliferative neoplasms. However, to the best of our knowledge, there have been no reports that suggest an association between CML and constitutional pericentric inversion of chromosome 9. The purpose of this retrospective study was to investigate the frequency and clinical features of CML patients with concomitant inv(9) and t(9;22)(q34;q11.2) variation at our institution. We reviewed the bone marrow chromosome database entries between October 2006 and December 2008 to identify patients with concomitant inv(9) and t(9;22) variations. Laboratory and clinical data of the patients were obtained from the electronic medical record system. Among the 51 CML patients, 4 (7.8%) had concomitant inv(9) and t(9;22) variations. Although the association between inv(9) variation and CML is still controversial, we believe that hematologists should consider the role of constitutional inv(9) variation in CML patients to avoid overlooking the impaired engraftment potential of hematopoietic stem cells harboring inv(9). Therefore, we suggest that more effort should be invested to develop cytogenetic tests for detecting constitutional inv(9) variation in CML patients.

Anatomical variations of mandibular canal detected by panoramic radiography and CT: a systematic review and meta-analysis

PubMed Central

Dutra, Kamile; Porporatti, André Luís; Mezzomo, Luis A; De Luca Canto, Graziela; Flores-Mir, Carlos; Corrêa, Márcio

2016-01-01

Objectives: To investigate the anatomical variations of the mandibular canal through assessment in situ, panoramic radiography, CT or CBCT and assess their frequency. Methods: Articles were selected from databases (Cochrane Library, LILACS, ProQuest, PubMed, Scopus, Web of Science and Google Scholar), articles without limitations of language, in which the main objective was to evaluate the frequency of bifurcation of the mandibular canal through assessment in situ, panoramic radiography, CT or CBCT were selected. A meta-analysis of prevalence using random effects was performed. Results: Using a selection process in two phases, 15 articles were identified, and a meta-analysis was conducted. The results from these meta-analyses showed that the overall prevalence of anatomical variations for in situ studies was 6.46%, and through assessment of panoramic radiography and CT or CBCT the overall prevalence shown was 4.20% and 16.25%, respectively. Conclusions: There are two types of variations of the mandibular canal: the retromolar canal and bifid mandibular canal. The frequency variations through assessing in situ, panoramic radiography and CT or CBCT were 6.46%, 4.20% and 16.25%, respectively. PMID:26576624

Attenuated total reflectance spectroscopy of plant leaves: A tool for ecological and botanical studies

USGS Publications Warehouse

Ribeiro da Luz, B.

2006-01-01

??? Attenuated total reflectance (ATR) spectra of plant leaves display complex absorption features related to organic constituents of leaf surfaces. The spectra can be recorded rapidly, both in the field and in the laboratory, without special sample preparation. ??? This paper explores sources of ATR spectral variation in leaves, including compositional, positional and temporal variations. Interspecific variations are also examined, including the use of ATR spectra as a tool for species identification. ??? Positional spectral variations generally reflected the abundance of cutin and the epicuticular wax thickness and composition. For example, leaves exposed to full sunlight commonly showed more prominent cutin- and wax-related absorption features compared with shaded leaves. Adaxial vs. abaxial leaf surfaces displayed spectral variations reflecting differences in trichome abundance and wax composition. Mature vs. young leaves showed changes in absorption band position and intensity related to cutin, polysaccharide, and possibly amorphous silica development on and near the leaf surfaces. ??? Provided that similar samples are compared (e.g. adaxial surfaces of mature, sun-exposed leaves) same-species individuals display practically identical ATR spectra. Using spectral matching procedures to analyze an ATR database containing 117 individuals, including 32 different tree species, 83% of the individuals were correctly identified. ?? The Authors (2006).

Ecology has contrasting effects on genetic variation within species versus rates of molecular evolution across species in water beetles.

PubMed

Fujisawa, Tomochika; Vogler, Alfried P; Barraclough, Timothy G

2015-01-22

Comparative analysis is a potentially powerful approach to study the effects of ecological traits on genetic variation and rate of evolution across species. However, the lack of suitable datasets means that comparative studies of correlates of genetic traits across an entire clade have been rare. Here, we use a large DNA-barcode dataset (5062 sequences) of water beetles to test the effects of species ecology and geographical distribution on genetic variation within species and rates of molecular evolution across species. We investigated species traits predicted to influence their genetic characteristics, such as surrogate measures of species population size, latitudinal distribution and habitat types, taking phylogeny into account. Genetic variation of cytochrome oxidase I in water beetles was positively correlated with occupancy (numbers of sites of species presence) and negatively with latitude, whereas substitution rates across species depended mainly on habitat types, and running water specialists had the highest rate. These results are consistent with theoretical predictions from nearly-neutral theories of evolution, and suggest that the comparative analysis using large databases can give insights into correlates of genetic variation and molecular evolution.

Comparing tree foliage biomass models fitted to a multispecies, felled-tree biomass dataset for the United States

Treesearch

Brian J. Clough; Matthew B. Russell; Grant M. Domke; Christopher W. Woodall; Philip J. Radtke

2016-01-01

tEstimation of live tree biomass is an important task for both forest carbon accounting and studies of nutri-ent dynamics in forest ecosystems. In this study, we took advantage of an extensive felled-tree database(with 2885 foliage biomass observations) to compare different models and grouping schemes based onphylogenetic and geographic variation for predicting foliage...

A Possible Literary Canon in Upper School English Literature in Various Australian States, 1945-2005

ERIC Educational Resources Information Center

Yiannakis, John

2014-01-01

Using information gathered from a specifically created database, ALIAS, this paper sets out to examine the variations and changes to the works that appeared on the English reading lists of the different Australian states in their literature course(s) between 1945 and 2005. All those states which offered a set of public examinations at the end of…

Variation in Citational Practice in a Corpus of Student Biology Papers: From Parenthetical Plonking to Intertextual Storytelling

ERIC Educational Resources Information Center

Swales, John M.

2014-01-01

This is a corpus-based study of a key aspect of academic writing in one discipline (biology) by final-year undergraduates and first-, second-, and third-year graduate students. The papers come from the Michigan Corpus of Upper-level Student Papers, a freely available electronic database. The principal aim of the study is to examine the extent of…

Future Naval Use of COTS Networking Infrastructure

DTIC Science & Technology

2009-07-01

user to benefit from Google’s vast databases and computational resources. Obviously, the ability to harness the full power of the Cloud could be... Computing Impact Findings Action Items Take-Aways Appendices: Pages 54-68 A. Terms of Reference Document B. Sample Definitions of Cloud ...and definition of Cloud Computing . While Cloud Computing is developing in many variations – including Infrastructure as a Service (IaaS), Platform as

Variation in population levels of physical activity in European adults according to cross-European studies: a systematic literature review within DEDIPAC.

PubMed

Loyen, Anne; Van Hecke, Linde; Verloigne, Maïté; Hendriksen, Ingrid; Lakerveld, Jeroen; Steene-Johannessen, Jostein; Vuillemin, Anne; Koster, Annemarie; Donnelly, Alan; Ekelund, Ulf; Deforche, Benedicte; De Bourdeaudhuij, Ilse; Brug, Johannes; van der Ploeg, Hidde P

2016-06-28

Physical inactivity is a well-known public health risk that should be monitored at the population level. Physical activity levels are often surveyed across Europe. This systematic literature review aims to provide an overview of all existing cross-European studies that assess physical activity in European adults, describe the variation in population levels according to these studies, and discuss the impact of the assessment methods. Six literature databases (PubMed, EMBASE, CINAHL, PsycINFO, SportDiscus and OpenGrey) were searched, supplemented with backward- and forward tracking and searching authors' and experts' literature databases. Articles were included if they reported on observational studies measuring total physical activity and/or physical activity in leisure time in the general population in two or more European countries. Each record was reviewed, extracted and assessed by two independent researchers and disagreements were resolved by a third researcher. The review protocol of this review is registered in the PROSPERO database under registration number CRD42014010334. Of the 9,756 unique identified articles, twenty-five were included in this review, reporting on sixteen different studies, including 2 to 35 countries and 321 to 274,740 participants. All but two of the studies used questionnaires to assess physical activity, with the majority of studies using the IPAQ-short questionnaire. The remaining studies used accelerometers. The percentage of participants who either were or were not meeting the physical activity recommendations was the most commonly reported outcome variable, with the percentage of participants meeting the recommendations ranging from 7% to 96% across studies and countries. The included studies showed substantial variation in the assessment methods, reported outcome variables and, consequently, the presented physical activity levels. Because of this, absolute population levels of physical activity in European adults are currently unknown. However, when ranking countries, Ireland, Italy, Malta, Portugal, and Spain generally appear to be among the less active countries. Objective data of adults across Europe is currently limited. These findings highlight the need for standardisation of the measurement methods, as well as cross-European monitoring of physical activity levels.

Comprehensive Analysis of Non-Synonymous Natural Variants of G Protein-Coupled Receptors.

PubMed

Kim, Hee Ryung; Duc, Nguyen Minh; Chung, Ka Young

2018-03-01

G protein-coupled receptors (GPCRs) are the largest superfamily of transmembrane receptors and have vital signaling functions in various organs. Because of their critical roles in physiology and pathology, GPCRs are the most commonly used therapeutic target. It has been suggested that GPCRs undergo massive genetic variations such as genetic polymorphisms and DNA insertions or deletions. Among these genetic variations, non-synonymous natural variations change the amino acid sequence and could thus alter GPCR functions such as expression, localization, signaling, and ligand binding, which may be involved in disease development and altered responses to GPCR-targeting drugs. Despite the clinical importance of GPCRs, studies on the genotype-phenotype relationship of GPCR natural variants have been limited to a few GPCRs such as β-adrenergic receptors and opioid receptors. Comprehensive understanding of non-synonymous natural variations within GPCRs would help to predict the unknown genotype-phenotype relationship and yet-to-be-discovered natural variants. Here, we analyzed the non-synonymous natural variants of all non-olfactory GPCRs available from a public database, UniProt. The results suggest that non-synonymous natural variations occur extensively within the GPCR superfamily especially in the N-terminus and transmembrane domains. Within the transmembrane domains, natural variations observed more frequently in the conserved residues, which leads to disruption of the receptor function. Our analysis also suggests that only few non-synonymous natural variations have been studied in efforts to link the variations with functional consequences.

Variation in Nephrologist Visits to Patients on Hemodialysis across Dialysis Facilities and Geographic Locations

PubMed Central

Tan, Kelvin B.; Winkelmayer, Wolfgang C.; Chertow, Glenn M.; Bhattacharya, Jay

2013-01-01

Summary Background and objectives Geographic and other variations in medical practices lead to differences in medical costs, often without a clear link to health outcomes. This work examined variation in the frequency of physician visits to patients receiving hemodialysis to measure the relative importance of provider practice patterns (including those patterns linked to geographic region) and patient health in determining visit frequency. Design, setting, participants, & measurements This work analyzed a nationally representative 2006 database of patients receiving hemodialysis in the United States. A variation decomposition analysis of the relative importance of facility, geographic region, and patient characteristics—including demographics, socioeconomic status, and indicators of health status—in explaining physician visit frequency variation was conducted. Finally, the associations between facility, geographic and patient characteristics, and provider visit frequency were measured using multivariable regression. Results Patient characteristics accounted for only 0.9% of the total visit frequency variation. Accounting for case-mix differences, patients’ hemodialysis facilities explained about 24.9% of visit frequency variation, of which 9.3% was explained by geographic region. Visit frequency was more closely associated with many facility and geographic characteristics than indicators of health status. More recent dialysis initiation and recent hospitalization were associated with decreased visit frequency. Conclusions In hemodialysis, provider visit frequency depends more on geography and facility location and characteristics than patients’ health status or acuity of illness. The magnitude of variation unrelated to patient health suggests that provider visit frequency practices do not reflect optimal management of patients on dialysis. PMID:23430207

Changes in geographic variation in the use of percutaneous coronary intervention for stable ischemic heart disease after publication of the Clinical Outcomes Utilizing Revascularization and Aggressive Drug Evaluation (COURAGE) trial.

PubMed

Mohan, Arun V; Fazel, Reza; Huang, Pei-Hsiu; Shen, Yu-Chu; Howard, David

2014-01-01

Clinical uncertainty is cited as a cause of geographic variation. However, little is known about the effect of comparative effectiveness research on variation. We examined whether geographic variation in the use of percutaneous coronary intervention (PCI) for stable ischemic heart disease (SIHD) declined after publication of the Clinical Outcomes Utilizing Revascularization and Aggressive Drug Evaluation (COURAGE) trial. We examined changes in utilization and geographic variation in 67 hospital referral regions using the State Inpatient Databases. We compared age- and sex-adjusted rates of PCI for SIHD before (2006) and after (2008) publication of the COURAGE trial and compared those with contemporaneous changes in PCI volume for acute coronary syndrome. A total of 272,659 PCIs for SIHD from 526 hospitals were included in the analysis. After the publication of the COURAGE trial, PCI volume for SIHD declined by 25% (P<0.001) and decreased by 12% for acute coronary syndrome (P<0.001). This was predominantly attributable to changes in hospital referral regions with the highest levels of utilization pre-COURAGE trial (35% decline in the highest tertile versus 18% in the lowest). As measured by the systematic component of variation, there was substantial geographic variation in the use of PCI for SIHD preceding the publication of the COURAGE trial. Variation declined by 28% (0.53 versus 0.40) after publication, but geographic variation remained higher for SIHD than acute coronary syndrome (0.40 versus 0.17). There was a substantial decline in the use of and geographic variation in PCI for SIHD after the publication of the COURAGE trial. However, geographic variation in the use of PCI for SIHD remained high.

Data-based estimates of the ocean carbon sink variability - results of the Surface Ocean pCO2 Mapping intercomparison (SOCOM)

NASA Astrophysics Data System (ADS)

Rödenbeck, Christian; Bakker, Dorothee; Gruber, Nicolas; Iida, Yosuke; Jacobson, Andy; Jones, Steve; Landschützer, Peter; Metzl, Nicolas; Nakaoka, Shin-ichiro; Olsen, Are; Park, Geun-Ha; Peylin, Philippe; Rodgers, Keith; Sasse, Tristan; Schuster, Ute; Shutler, James; Valsala, Vinu; Wanninkhof, Rik; Zeng, Jiye

2016-04-01

Using measurements of the surface-ocean COtwo partial pressure (pCOtwo) from the SOCAT and LDEO data bases and 14 different pCOtwo mapping methods recently collated by the Surface Ocean pCOtwo Mapping intercomparison (SOCOM) initiative, variations in regional and global sea-air COtwo fluxes are investigated. Though the available mapping methods use widely different approaches, we find relatively consistent estimates of regional pCOtwo seasonality, in line with previous estimates. In terms of interannual variability (IAV), all mapping methods estimate the largest variations to occur in the Eastern equatorial Pacific. Despite considerable spread in the detailed variations, mapping methods that fit the data more closely also tend to agree more closely with each other in regional averages. Encouragingly, this includes mapping methods belonging to complementary types - taking variability either directly from the pCOtwo data or indirectly from driver data via regression. From a weighted ensemble average, we find an IAV amplitude of the global sea-air COtwo flux of IAVampl (standard deviation over AnalysisPeriod), which is larger than simulated by biogeochemical process models. On a decadal perspective, the global ocean COtwo uptake is estimated to have gradually increased since about 2000, with little decadal change prior to that. The weighted mean net global ocean COtwo sink estimated by the SOCOM ensemble is -1.75 UPgCyr (AnalysisPeriod), consistent within uncertainties with estimates from ocean-interior carbon data or atmospheric oxygen trends. Using data-based sea-air COtwo fluxes in atmospheric COtwo inversions also helps to better constrain land-atmosphere COtwo fluxes.

The geometrical precision of virtual bone models derived from clinical computed tomography data for forensic anthropology.

PubMed

Colman, Kerri L; Dobbe, Johannes G G; Stull, Kyra E; Ruijter, Jan M; Oostra, Roelof-Jan; van Rijn, Rick R; van der Merwe, Alie E; de Boer, Hans H; Streekstra, Geert J

2017-07-01

Almost all European countries lack contemporary skeletal collections for the development and validation of forensic anthropological methods. Furthermore, legal, ethical and practical considerations hinder the development of skeletal collections. A virtual skeletal database derived from clinical computed tomography (CT) scans provides a potential solution. However, clinical CT scans are typically generated with varying settings. This study investigates the effects of image segmentation and varying imaging conditions on the precision of virtual modelled pelves. An adult human cadaver was scanned using varying imaging conditions, such as scanner type and standard patient scanning protocol, slice thickness and exposure level. The pelvis was segmented from the various CT images resulting in virtually modelled pelves. The precision of the virtual modelling was determined per polygon mesh point. The fraction of mesh points resulting in point-to-point distance variations of 2 mm or less (95% confidence interval (CI)) was reported. Colour mapping was used to visualise modelling variability. At almost all (>97%) locations across the pelvis, the point-to-point distance variation is less than 2 mm (CI = 95%). In >91% of the locations, the point-to-point distance variation was less than 1 mm (CI = 95%). This indicates that the geometric variability of the virtual pelvis as a result of segmentation and imaging conditions rarely exceeds the generally accepted linear error of 2 mm. Colour mapping shows that areas with large variability are predominantly joint surfaces. Therefore, results indicate that segmented bone elements from patient-derived CT scans are a sufficiently precise source for creating a virtual skeletal database.

Analysis of Family Structures Reveals Robustness or Sensitivity of Bursting Activity to Parameter Variations in a Half-Center Oscillator (HCO) Model.

PubMed

Doloc-Mihu, Anca; Calabrese, Ronald L

2016-01-01

The underlying mechanisms that support robustness in neuronal networks are as yet unknown. However, recent studies provide evidence that neuronal networks are robust to natural variations, modulation, and environmental perturbations of parameters, such as maximal conductances of intrinsic membrane and synaptic currents. Here we sought a method for assessing robustness, which might easily be applied to large brute-force databases of model instances. Starting with groups of instances with appropriate activity (e.g., tonic spiking), our method classifies instances into much smaller subgroups, called families, in which all members vary only by the one parameter that defines the family. By analyzing the structures of families, we developed measures of robustness for activity type. Then, we applied these measures to our previously developed model database, HCO-db, of a two-neuron half-center oscillator (HCO), a neuronal microcircuit from the leech heartbeat central pattern generator where the appropriate activity type is alternating bursting. In HCO-db, the maximal conductances of five intrinsic and two synaptic currents were varied over eight values (leak reversal potential also varied, five values). We focused on how variations of particular conductance parameters maintain normal alternating bursting activity while still allowing for functional modulation of period and spike frequency. We explored the trade-off between robustness of activity type and desirable change in activity characteristics when intrinsic conductances are altered and identified the hyperpolarization-activated (h) current as an ideal target for modulation. We also identified ensembles of model instances that closely approximate physiological activity and can be used in future modeling studies.

Performance of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Identifying Clinical Malassezia Isolates

PubMed Central

Machouart, Marie; Morio, Florent; Sabou, Marcela; Kauffmann-LaCroix, Catherine; Contet-Audonneau, Nelly; Candolfi, Ermanno; Letscher-Bru, Valérie

2016-01-01

ABSTRACT The genus Malassezia comprises commensal yeasts on human skin. These yeasts are involved in superficial infections but are also isolated in deeper infections, such as fungemia, particularly in certain at-risk patients, such as neonates or patients with parenteral nutrition catheters. Very little is known about Malassezia epidemiology and virulence. This is due mainly to the difficulty of distinguishing species. Currently, species identification is based on morphological and biochemical characteristics. Only molecular biology techniques identify species with certainty, but they are time-consuming and expensive. The aim of this study was to develop and evaluate a matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) database for identifying Malassezia species by mass spectrometry. Eighty-five Malassezia isolates from patients in three French university hospitals were investigated. Each strain was identified by internal transcribed spacer sequencing. Forty-five strains of the six species Malassezia furfur, M. sympodialis, M. slooffiae, M. globosa, M. restricta, and M. pachydermatis allowed the creation of a MALDI-TOF database. Forty other strains were used to test this database. All strains were identified by our Malassezia database with log scores of >2.0, according to the manufacturer's criteria. Repeatability and reproducibility tests showed a coefficient of variation of the log score values of <10%. In conclusion, our new Malassezia database allows easy, fast, and reliable identification of Malassezia species. Implementation of this database will contribute to a better, more rapid identification of Malassezia species and will be helpful in gaining a better understanding of their epidemiology. PMID:27795342

Performance of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identifying Clinical Malassezia Isolates.

PubMed

Denis, Julie; Machouart, Marie; Morio, Florent; Sabou, Marcela; Kauffmann-LaCroix, Catherine; Contet-Audonneau, Nelly; Candolfi, Ermanno; Letscher-Bru, Valérie

2017-01-01

The genus Malassezia comprises commensal yeasts on human skin. These yeasts are involved in superficial infections but are also isolated in deeper infections, such as fungemia, particularly in certain at-risk patients, such as neonates or patients with parenteral nutrition catheters. Very little is known about Malassezia epidemiology and virulence. This is due mainly to the difficulty of distinguishing species. Currently, species identification is based on morphological and biochemical characteristics. Only molecular biology techniques identify species with certainty, but they are time-consuming and expensive. The aim of this study was to develop and evaluate a matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) database for identifying Malassezia species by mass spectrometry. Eighty-five Malassezia isolates from patients in three French university hospitals were investigated. Each strain was identified by internal transcribed spacer sequencing. Forty-five strains of the six species Malassezia furfur, M. sympodialis, M. slooffiae, M. globosa, M. restricta, and M. pachydermatis allowed the creation of a MALDI-TOF database. Forty other strains were used to test this database. All strains were identified by our Malassezia database with log scores of >2.0, according to the manufacturer's criteria. Repeatability and reproducibility tests showed a coefficient of variation of the log score values of <10%. In conclusion, our new Malassezia database allows easy, fast, and reliable identification of Malassezia species. Implementation of this database will contribute to a better, more rapid identification of Malassezia species and will be helpful in gaining a better understanding of their epidemiology. Copyright © 2016 Denis et al.

The TERRA-PNW Dataset: A New Source for Standardized Plant Trait, Forest Carbon Cycling, and Soil Properties Measurements from the Pacific Northwest US, 2000-2014.

NASA Astrophysics Data System (ADS)

Berner, L. T.; Law, B. E.

2015-12-01

Plant traits include physiological, morphological, and biogeochemical characteristics that in combination determine a species sensitivity to environmental conditions. Standardized, co-located, and geo-referenced species- and plot-level measurements are needed to address variation in species sensitivity to climate change impacts and for ecosystem process model development, parameterization and testing. We present a new database of plant trait, forest carbon cycling, and soil property measurements derived from multiple TERRA-PNW projects in the Pacific Northwest US, spanning 2000-2014. The database includes measurements from over 200 forest plots across Oregon and northern California, where the data were explicitly collected for scaling and modeling regional terrestrial carbon processes with models such as Biome-BGC and the Community Land Model. Some of the data are co-located at AmeriFlux sites in the region. The database currently contains leaf trait measurements (specific leaf area, leaf longevity, leaf carbon and nitrogen) from over 1,200 branch samples and 30 species, as well as plot-level biomass and productivity components, and soil carbon and nitrogen. Standardized protocols were used across projects, as summarized in an FAO protocols document. The database continues to expand and will include agricultural crops. The database will be hosted by the Oak Ridge National Laboratory (ORLN) Distributed Active Archive Center (DAAC). We hope that other regional databases will become publicly available to help enable Earth System Modeling to simulate species-level sensitivity to climate at regional to global scales.

The influence of soil properties and nutrients on conifer forest growth in Sweden, and the first steps in developing a nutrient availability metric

NASA Astrophysics Data System (ADS)

Van Sundert, Kevin; Horemans, Joanna A.; Stendahl, Johan; Vicca, Sara

2018-06-01

The availability of nutrients is one of the factors that regulate terrestrial carbon cycling and modify ecosystem responses to environmental changes. Nonetheless, nutrient availability is often overlooked in climate-carbon cycle studies because it depends on the interplay of various soil factors that would ideally be comprised into metrics applicable at large spatial scales. Such metrics do not currently exist. Here, we use a Swedish forest inventory database that contains soil data and tree growth data for > 2500 forests across Sweden to (i) test which combination of soil factors best explains variation in tree growth, (ii) evaluate an existing metric of constraints on nutrient availability, and (iii) adjust this metric for boreal forest data. With (iii), we thus aimed to provide an adjustable nutrient metric, applicable for Sweden and with potential for elaboration to other regions. While taking into account confounding factors such as climate, N deposition, and soil oxygen availability, our analyses revealed that the soil organic carbon concentration (SOC) and the ratio of soil carbon to nitrogen (C : N) were the most important factors explaining variation in normalized (climate-independent) productivity (mean annual volume increment - m3 ha-1 yr-1) across Sweden. Normalized forest productivity was significantly negatively related to the soil C : N ratio (R2 = 0.02-0.13), while SOC exhibited an empirical optimum (R2 = 0.05-0.15). For the metric, we started from a (yet unvalidated) metric for constraints on nutrient availability that was previously developed by the International Institute for Applied Systems Analysis (IIASA - Laxenburg, Austria) for evaluating potential productivity of arable land. This IIASA metric requires information on soil properties that are indicative of nutrient availability (SOC, soil texture, total exchangeable bases - TEB, and pH) and is based on theoretical considerations that are also generally valid for nonagricultural ecosystems. However, the IIASA metric was unrelated to normalized forest productivity across Sweden (R2 = 0.00-0.01) because the soil factors under consideration were not optimally implemented according to the Swedish data, and because the soil C : N ratio was not included. Using two methods (each one based on a different way of normalizing productivity for climate), we adjusted this metric by incorporating soil C : N and modifying the relationship between SOC and nutrient availability in view of the observed relationships across our database. In contrast to the IIASA metric, the adjusted metrics explained some variation in normalized productivity in the database (R2 = 0.03-0.21; depending on the applied method). A test for five manually selected local fertility gradients in our database revealed a significant and stronger relationship between the adjusted metrics and productivity for each of the gradients (R2 = 0.09-0.38). This study thus shows for the first time how nutrient availability metrics can be evaluated and adjusted for a particular ecosystem type, using a large-scale database.

[Relationship between cost systems and hospital expenditure].

PubMed

García-Cornejo, Beatriz; Pérez-Méndez, José A

To analyze the relationship between the degree of development of hospital cost systems (CS) implemented by the regional health services (RHS) and the variation in unit cost of hospitals in Spanish National Health Service (NHS) between 2010 and 2013 and to identify other explanatory factors of this variation. A database of NHS hospitals was constructed from exclusively public sources. Using a multilevel regression model, explaining factors of the variation in unit cost (cost per weighted unit of activity [WAU]) of a sample of 170 hospitals were analyzed. The variables representative of the degree of development of CS are associated in a negative and significant way with the variation of the cost per WAU. It is observed that if a high-level development CS is used the cost variation per WAU would be reduced by close to 3.2%. There is also a negative and significant relationship between the variation in the cost per WAU and the variations in the percentage of high technology and the hospital occupancy rate. On the other hand, the variations in the average cost of personnel and in the number of workers per 100 beds are associated in a positive and significant way with the variation of the cost per WAU. In the period analysed, during which the main health expenditure adjustment was made, the control in hospital unit cost is associated not only with spending cuts but also with aspects related to their management, such as the implementation of more developed CS. Copyright © 2017 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

[Variations in patient data coding affect hospital standardized mortality ratio (HSMR)].

PubMed

van den Bosch, Wim F; Silberbusch, Joseph; Roozendaal, Klaas J; Wagner, Cordula

2010-01-01

To investigate the impact of coding variations on 'hospital standardized mortality ratio' (HSMR) and to define variation reduction measures. Retrospective, descriptive. We analysed coding variations in HSMR parameters for main diagnosis, urgency of the admission and comorbidity in the national medical registration (LMR) database of admissions in 6 Dutch top clinical hospitals during 2003-2007. More than a quarter of these admission records had been included in the HSMR calculation. Admissions with ICD-9 main diagnosis codes that were excluded from HSMR calculations were investigated for inter-hospital variability and correct exclusion. Variation in coding admission type was signalled by analyzing admission records with diagnoses that had an emergency nature by their title. Variation in the average number of comorbidity diagnoses per admission was determined as an indicator for coding variation. Interviews with coding teams were used to check whether the conclusions of the analysis were correct. Over 165,000 admissions that were excluded from HSMR calculations showed large variability between hospitals. This figure was 40% of all admissions that were included. Of the admissions with a main diagnosis indicating an emergency, 34% to 93% were recorded as an emergency. The average number of comorbidity diagnoses varied between hospitals from 0.9 to 3.0 per admission. Coding of main diagnoses, urgency of admission and comorbidities showed strong inter-hospital variation with a potentially large impact on the HSMR outcomes of the hospitals. Coding variations originated from differences in interpretation of coding rules, differences in coding capacity, quality of patient records and discharge documentation and timely delivery of these.

The methane distribution on Titan: high resolution spectroscopy in the near-IR with Keck NIRSPEC/AO

NASA Astrophysics Data System (ADS)

Adamkovics, Mate; Mitchell, Jonathan L.

2014-11-01

The distribution of methane on Titan is a diagnostic of regional scale meteorology and large scale atmospheric circulation. The observed formation of clouds and the transport of heat through the atmosphere both depend on spatial and temporal variations in methane humidity. We have performed observations to measure the the distribution on methane Titan using high spectral resolution near-IR (H-band) observations made with NIRSPEC, with adaptive optics, at Keck Observatory in July 2014. This work builds on previous attempts at this measurement with improvement in the observing protocol and data reduction, together with increased integration times. Radiative transfer models using line-by-line calculation of methane opacities from the HITRAN2012 database are used to retrieve methane abundances. We will describe analysis of the reduced observations, which show latitudinal spatial variation in the region the spectrum that is thought to be sensitive to methane abundance. Quantifying the methane abundance variation requires models that include the spatial variation in surface albedo and meridional haze gradient; we will describe (currently preliminary) analysis of the the methane distribution and uncertainties in the retrieval.

Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations.

PubMed

Teo, Yik-Ying; Sim, Xueling; Ong, Rick T H; Tan, Adrian K S; Chen, Jieming; Tantoso, Erwin; Small, Kerrin S; Ku, Chee-Seng; Lee, Edmund J D; Seielstad, Mark; Chia, Kee-Seng

2009-11-01

The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser.

Singapore Genome Variation Project: A haplotype map of three Southeast Asian populations

PubMed Central

Teo, Yik-Ying; Sim, Xueling; Ong, Rick T.H.; Tan, Adrian K.S.; Chen, Jieming; Tantoso, Erwin; Small, Kerrin S.; Ku, Chee-Seng; Lee, Edmund J.D.; Seielstad, Mark; Chia, Kee-Seng

2009-01-01

The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser. PMID:19700652

Single-Nucleotide Polymorphism and Copy Number Variation of the Multidrug Resistance-1 Locus of Plasmodium vivax: Local and Global Patterns

PubMed Central

Vargas-Rodríguez, Rosa del Carmen Miluska; da Silva Bastos, Melissa; Menezes, Maria José; Orjuela-Sánchez, Pamela; Ferreira, Marcelo U.

2012-01-01

Emerging resistance to chloroquine (CQ) poses a major challenge for Plasmodium vivax malaria control, and nucleotide substitutions and copy number variation in the P. vivax multidrug resistance 1 (pvmdr-1) locus, which encodes a digestive vacuole membrane transporter, may modulate this phenotype. We describe patterns of genetic variation in pvmdr-1 alleles from Acre and Amazonas in northwestern Brazil, and compare then with those reported in other malaria-endemic regions. The pvmdr-1 mutation Y976F, which is associated with CQ resistance in Southeast Asia and Oceania, remains rare in northwestern Brazil (1.8%) and its prevalence mirrors that of CQ resistance worldwide. Gene amplification of pvmdr-1, which is associated with mefloquine resistance but increased susceptibility to CQ, remains relatively rare in northwestern Brazil (0.9%) and globally (< 4%), but became common (> 10%) in Tak Province, Thailand, possibly because of drug-mediated selection. The global database we have assembled provides a baseline for further studies of genetic variation in pvmdr-1 and drug resistance in P. vivax malaria. PMID:22949516

Single-nucleotide polymorphism and copy number variation of the multidrug resistance-1 locus of Plasmodium vivax: local and global patterns.

PubMed

Vargas-Rodríguez, Rosa del Carmen Miluska; da Silva Bastos, Melissa; Menezes, Maria José; Orjuela-Sánchez, Pamela; Ferreira, Marcelo U

2012-11-01

Emerging resistance to chloroquine (CQ) poses a major challenge for Plasmodium vivax malaria control, and nucleotide substitutions and copy number variation in the P. vivax multidrug resistance 1 (pvmdr-1) locus, which encodes a digestive vacuole membrane transporter, may modulate this phenotype. We describe patterns of genetic variation in pvmdr-1 alleles from Acre and Amazonas in northwestern Brazil, and compare then with those reported in other malaria-endemic regions. The pvmdr-1 mutation Y976F, which is associated with CQ resistance in Southeast Asia and Oceania, remains rare in northwestern Brazil (1.8%) and its prevalence mirrors that of CQ resistance worldwide. Gene amplification of pvmdr-1, which is associated with mefloquine resistance but increased susceptibility to CQ, remains relatively rare in northwestern Brazil (0.9%) and globally (< 4%), but became common (> 10%) in Tak Province, Thailand, possibly because of drug-mediated selection. The global database we have assembled provides a baseline for further studies of genetic variation in pvmdr-1 and drug resistance in P. vivax malaria.

Variations in data collection methods between national databases affect study results: a comparison of the nationwide inpatient sample and national surgical quality improvement program databases for lumbar spine fusion procedures.

PubMed

Bohl, Daniel D; Russo, Glenn S; Basques, Bryce A; Golinvaux, Nicholas S; Fu, Michael C; Long, William D; Grauer, Jonathan N

2014-12-03

There has been an increasing use of national databases to conduct orthopaedic research. Questions regarding the validity and consistency of these studies have not been fully addressed. The purpose of this study was to test for similarity in reported measures between two national databases commonly used for orthopaedic research. A retrospective cohort study of patients undergoing lumbar spinal fusion procedures during 2009 to 2011 was performed in two national databases: the Nationwide Inpatient Sample and the National Surgical Quality Improvement Program. Demographic characteristics, comorbidities, and inpatient adverse events were directly compared between databases. The total numbers of patients included were 144,098 from the Nationwide Inpatient Sample and 8434 from the National Surgical Quality Improvement Program. There were only small differences in demographic characteristics between the two databases. There were large differences between databases in the rates at which specific comorbidities were documented. Non-morbid obesity was documented at rates of 9.33% in the Nationwide Inpatient Sample and 36.93% in the National Surgical Quality Improvement Program (relative risk, 0.25; p < 0.05). Peripheral vascular disease was documented at rates of 2.35% in the Nationwide Inpatient Sample and 0.60% in the National Surgical Quality Improvement Program (relative risk, 3.89; p < 0.05). Similarly, there were large differences between databases in the rates at which specific inpatient adverse events were documented. Sepsis was documented at rates of 0.38% in the Nationwide Inpatient Sample and 0.81% in the National Surgical Quality Improvement Program (relative risk, 0.47; p < 0.05). Acute kidney injury was documented at rates of 1.79% in the Nationwide Inpatient Sample and 0.21% in the National Surgical Quality Improvement Program (relative risk, 8.54; p < 0.05). As database studies become more prevalent in orthopaedic surgery, authors, reviewers, and readers should view these studies with caution. This study shows that two commonly used databases can identify demographically similar patients undergoing a common orthopaedic procedure; however, the databases document markedly different rates of comorbidities and inpatient adverse events. The differences are likely the result of the very different mechanisms through which the databases collect their comorbidity and adverse event data. Findings highlight concerns regarding the validity of orthopaedic database research. Copyright © 2014 by The Journal of Bone and Joint Surgery, Incorporated.

NR4A2 genetic variation and Parkinson's disease: Evidence from a systematic review and meta-analysis.

PubMed

Liu, Hongmei; Liu, Hongbo; Li, Ting; Cui, Jiayi; Fu, Yingmei; Ren, Juanjuan; Sun, Xiujia; Jiang, Ping; Yu, Shunying; Li, Chunbo

2017-05-22

The homo sapiens nuclear receptor subfamily 4, group A (NR4A2) genetic variation has been implicated as a risk factor for Parkinson's disease (PD). Nevertheless, the results are inconclusive. We conducted a comprehensive systematic review and meta-analysis to quantify the impact of NR4A2 variation on the risk of PD. All eligible case-control studies published up to June 2016 by searching Pubmed, OVID, EBSCO, PsycINFO, ISI Web of Knowledge, Chinese Biomedical Literature Database and China Academic Journals Database were identified. Pooled odds ratio (OR) with 95% confidence interval (CI) were used to access the strength of the association in fixed- or random-effects model. Eighteen studies reported 24 genetic variants with a total of 6150 cases and 5919 controls were included. Twelve studies for NR4A2 rs35479735 polymorphism and 4 studies for rs12803 were available for meta-analysis. A significant association was observed for rs35479735 under the homozygous model (OR=1.31, 95% CI: 1.10-1.56, P=0.003), whereas no significant association for rs12803 was detected. In subgroup analysis stratified by ethnicity, age onset and familial history, we found no significant association except one in sporadic PD subgroup under the recessive (OR=3.30, 95% CI: 1.23-8.84, P=0.02) and homozygous model (OR=3.43, 95% CI: 1.26-9.33, P=0.02) for rs35479735. The study comprehensively evaluated the association of NR4A2 variation with PD, and the results failed to demonstrate that the NR4A2 polymorphisms significantly associated with PD except for rs35479735, suggesting that more studies are needed to elucidate if NR4A2 is a risk of PD. Copyright © 2017 Elsevier B.V. All rights reserved.

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.

PubMed

Piro, Vitor C; Matschkowski, Marcel; Renard, Bernhard Y

2017-08-14

Many metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g., read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations. All this variation creates a complicated scenario to researchers to decide which methods to use. Installation, configuration and execution can also be difficult especially when dealing with multiple datasets and tools. We propose MetaMeta: a pipeline to execute and integrate results from metagenome analysis tools. MetaMeta provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample. MetaMeta includes a database generation, pre-processing, execution, and integration steps, allowing easy execution and parallelization. The integration relies on the co-occurrence of organisms from different methods as the main feature to improve community profiling while accounting for differences in their databases. In a controlled case with simulated and real data, we show that the integrated profiles of MetaMeta overcome the best single profile. Using the same input data, it provides more sensitive and reliable results with the presence of each organism being supported by several methods. MetaMeta uses Snakemake and has six pre-configured tools, all available at BioConda channel for easy installation (conda install -c bioconda metameta). The MetaMeta pipeline is open-source and can be downloaded at: https://gitlab.com/rki_bioinformatics .

RECENT DEVELOPMENTS IN HYDROWEB DATABASE Water level time series on lakes and reservoirs (Invited)

NASA Astrophysics Data System (ADS)

Cretaux, J.; Arsen, A.; Calmant, S.

2013-12-01

We present the current state of the Hydroweb database as well as developments in progress. It provides offline water level time series on rivers, reservoirs and lakes based on altimetry data from several satellites (Topex/Poseidon, ERS, Jason-1&2, GFO and ENVISAT). The major developments in Hydroweb concerns the development of an operational data centre with automatic acquisition and processing of IGDR data for updating time series in near real time (both for lakes & rivers) and also use of additional remote sensing data, like satellite imagery allowing the calculation of lake's surfaces. A lake data centre is under development at the Legos in coordination with Hydrolare Project leaded by SHI (State Hydrological Institute of the Russian Academy of Science). It will provide the level-surface-volume variations of about 230 lakes and reservoirs, calculated through combination of various satellite images (Modis, Asar, Landsat, Cbers) and radar altimetry (Topex / Poseidon, Jason-1 & 2, GFO, Envisat, ERS2, AltiKa). The final objective is to propose a data centre fully based on remote sensing technique and controlled by in situ infrastructure for the Global Terrestrial Network for Lakes (GTN-L) under the supervision of WMO and GCOS. In a longer perspective, the Hydroweb database will integrate data from future missions (Jason-3, Jason-CS, Sentinel-3A/B) and finally will serve for the design of the SWOT mission. The products of hydroweb will be used as input data for simulation of the SWOT products (water height and surface variations of lakes and rivers). In the future, the SWOT mission will allow to monitor on a sub-monthly basis the worldwide lakes and reservoirs bigger than 250 * 250 m and Hydroweb will host water level and extent products from this

Lack of Detectable Allergenicity in Genetically Modified Maize Containing “Cry” Proteins as Compared to Native Maize Based on In Silico & In Vitro Analysis

PubMed Central

Mathur, Chandni; Kathuria, Pooran C.; Dahiya, Pushpa; Singh, Anand B.

2015-01-01

Background Genetically modified, (GM) crops with potential allergens must be evaluated for safety and endogenous IgE binding pattern compared to native variety, prior to market release. Objective To compare endogenous IgE binding proteins of three GM maize seeds containing Cry 1Ab,1Ac,1C transgenic proteins with non GM maize. Methods An integrated approach of in silico & in vitro methods was employed. Cry proteins were tested for presence of allergen sequence by FASTA in allergen databases. Biochemical assays for maize extracts were performed. Specific IgE (sIgE) and Immunoblot using food sensitized patients sera (n = 39) to non GM and GM maize antigens was performed. Results In silico approaches, confirmed for non sequence similarity of stated transgenic proteins in allergen databases. An insignificant (p> 0.05) variation in protein content between GM and non GM maize was observed. Simulated Gastric Fluid (SGF) revealed reduced number of stable protein fractions in GM then non GM maize which might be due to shift of constituent protein expression. Specific IgE values from patients showed insignificant difference in non GM and GM maize extracts. Five maize sensitized cases, recognized same 7 protein fractions of 88-28 kD as IgE bindng in both GM and non-GM maize, signifying absence of variation. Four of the reported IgE binding proteins were also found to be stable by SGF. Conclusion Cry proteins did not indicate any significant similarity of >35% in allergen databases. Immunoassays also did not identify appreciable differences in endogenous IgE binding in GM and non GM maize. PMID:25706412

Global distribution of soil organic carbon, based on the Harmonized World Soil Database - Part 1: Masses and frequency distribution of SOC stocks for the tropics, permafrost regions, wetlands, and the world

NASA Astrophysics Data System (ADS)

Köchy, M.; Hiederer, R.; Freibauer, A.

2014-09-01

The global soil organic carbon (SOC) mass is relevant for the carbon cycle budget. We review current estimates of soil organic carbon stocks (mass/area) and mass (stock × area) in wetlands, permafrost and tropical regions and the world in the upper 1 m of soil. The Harmonized World Soil Database (HWSD) v.1.2 provides one of the most recent and coherent global data sets of SOC, giving a total mass of 2476 Pg. Correcting the HWSD's bulk density of organic soils, especially Histosols, results in a mass of 1062 Pg. The uncertainty of bulk density of Histosols alone introduces a range of -56 to +180 Pg for the estimate of global SOC in the top 1 m, larger than estimates of global soil respiration. We report the spatial distribution of SOC stocks per 0.5 arc minutes, the areal masses of SOC and the quantiles of SOC stocks by continents, wetland types, and permafrost types. Depending on the definition of "wetland", wetland soils contain between 82 and 158 Pg SOC. Incorporating more detailed estimates for permafrost from the Northern Circumpolar Soil Carbon Data Base (496 Pg SOC) and tropical peatland carbon, global soils contain 1324 Pg SOC in the upper 1 m including 421 Pg in tropical soils, whereof 40 Pg occur in tropical wetlands. Global SOC amounts to just under 3000 Pg when estimates for deeper soil layers are included. Variability in estimates is due to variation in definitions of soil units, differences in soil property databases, scarcity of information about soil carbon at depths > 1 m in peatlands, and variation in definitions of "peatland".

Filipino DNA variation at 12 X-chromosome short tandem repeat markers.

PubMed

Salvador, Jazelyn M; Apaga, Dame Loveliness T; Delfin, Frederick C; Calacal, Gayvelline C; Dennis, Sheila Estacio; De Ungria, Maria Corazon A

2018-06-08

Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database. This population database is also used for statistical evaluation of DNA typing results. Here, we report X-STR data from 143 unrelated Filipino male individuals who were genotyped via conventional polymerase chain reaction-capillary electrophoresis (PCR-CE) using the 12 X-STR loci included in the Investigator ® Argus X-12 kit (Qiagen) and via massively parallel sequencing (MPS) of seven X-STR loci included in the ForenSeq ™ DNA Signature Prep kit of the MiSeq ® FGx ™ Forensic Genomics System (Illumina). Allele calls between PCR-CE and MPS systems were consistent (100% concordance) across seven overlapping X-STRs. Allele and haplotype frequencies and other parameters of forensic interest were calculated based on length (PCR-CE, 12 X-STRs) and sequence (MPS, seven X-STRs) variations observed in the population. Results of our study indicate that the 12 X-STRs in the PCR-CE system are highly informative for the Filipino population. MPS of seven X-STR loci identified 73 X-STR alleles compared with 55 X-STR alleles that were identified solely by length via PCR-CE. Of the 73 sequence-based alleles observed, six alleles have not been reported in the literature. The population data presented here may serve as a reference Philippine frequency database of X-STRs for forensic casework applications. Copyright © 2018 Elsevier B.V. All rights reserved.

The Saccharomyces Genome Database Variant Viewer

PubMed Central

Sheppard, Travis K.; Hitz, Benjamin C.; Engel, Stacia R.; Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C.; Dalusag, Kyla S.; Demeter, Janos; Hellerstedt, Sage T.; Karra, Kalpana; Nash, Robert S.; Paskov, Kelley M.; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Cherry, J. Michael

2016-01-01

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer. PMID:26578556

[The National Database of the Regional Collaborative Rheumatic Centers as a tool for clinical epidemiology and quality assessment in rheumatology].

PubMed

Zink, Angela; Huscher, Dörte; Listing, Joachim

2003-01-01

The national database of the German Collaborative Arthritis Centres is a well-established tool for the observation and assessment of health care delivery to patients with rheumatic diseases in Germany. The discussion of variations in treatment practices contributes to the internal quality assessment in the participating arthritis centres. This documentation has shown deficits in primary health care including late referral to a rheumatologist, undertreatment with disease-modifying drugs and complementary therapies. In rheumatology, there is a trend towards early, intensive medical treatment including combination therapy. The frequency and length of inpatient hospital and rehabilitation treatments is decreasing, while active physiotherapy in outpatient care has been increased. Specific deficits have been identified concerning the provision of occupational therapy services and patient education.

JEnsembl: a version-aware Java API to Ensembl data systems

PubMed Central

Paterson, Trevor; Law, Andy

2012-01-01

Motivation: The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. Results: The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing ‘through time’ comparative analyses to be performed. Availability: Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net). Contact: jensembl-develop@lists.sf.net, andy.law@roslin.ed.ac.uk, trevor.paterson@roslin.ed.ac.uk PMID:22945789

Leaf respiration ( GlobResp) - global trait database supports Earth System Models

DOE PAGES

Wullschleger, Stan D.; Warren, Jeffrey; Thornton, Peter E.

2015-03-20

Here we detail how Atkin and his colleagues compiled a global database (GlobResp) that details rates of leaf dark respiration and associated traits from sites that span Arctic tundra to tropical forests. This compilation builds upon earlier research (Reich et al., 1998; Wright et al., 2006) and was supplemented by recent field campaigns and unpublished data.In keeping with other trait databases, GlobResp provides insights on how physiological traits, especially rates of dark respiration, vary as a function of environment and how that variation can be used to inform terrestrial biosphere models and land surface components of Earth System Models. Althoughmore » an important component of plant and ecosystem carbon (C) budgets (Wythers et al., 2013), respiration has only limited representation in models. Seen through the eyes of a plant scientist, Atkin et al. (2015) give readers a unique perspective on the climatic controls on respiration, thermal acclimation and evolutionary adaptation of dark respiration, and insights into the covariation of respiration with other leaf traits. We find there is ample evidence that once large databases are compiled, like GlobResp, they can reveal new knowledge of plant function and provide a valuable resource for hypothesis testing and model development.« less

WormQTLHD—a web database for linking human disease to natural variation data in C. elegans

PubMed Central

van der Velde, K. Joeri; de Haan, Mark; Zych, Konrad; Arends, Danny; Snoek, L. Basten; Kammenga, Jan E.; Jansen, Ritsert C.; Swertz, Morris A.; Li, Yang

2014-01-01

Interactions between proteins are highly conserved across species. As a result, the molecular basis of multiple diseases affecting humans can be studied in model organisms that offer many alternative experimental opportunities. One such organism—Caenorhabditis elegans—has been used to produce much molecular quantitative genetics and systems biology data over the past decade. We present WormQTLHD (Human Disease), a database that quantitatively and systematically links expression Quantitative Trait Loci (eQTL) findings in C. elegans to gene–disease associations in man. WormQTLHD, available online at http://www.wormqtl-hd.org, is a user-friendly set of tools to reveal functionally coherent, evolutionary conserved gene networks. These can be used to predict novel gene-to-gene associations and the functions of genes underlying the disease of interest. We created a new database that links C. elegans eQTL data sets to human diseases (34 337 gene–disease associations from OMIM, DGA, GWAS Central and NHGRI GWAS Catalogue) based on overlapping sets of orthologous genes associated to phenotypes in these two species. We utilized QTL results, high-throughput molecular phenotypes, classical phenotypes and genotype data covering different developmental stages and environments from WormQTL database. All software is available as open source, built on MOLGENIS and xQTL workbench. PMID:24217915

WormQTLHD--a web database for linking human disease to natural variation data in C. elegans.

PubMed

van der Velde, K Joeri; de Haan, Mark; Zych, Konrad; Arends, Danny; Snoek, L Basten; Kammenga, Jan E; Jansen, Ritsert C; Swertz, Morris A; Li, Yang

2014-01-01

Interactions between proteins are highly conserved across species. As a result, the molecular basis of multiple diseases affecting humans can be studied in model organisms that offer many alternative experimental opportunities. One such organism-Caenorhabditis elegans-has been used to produce much molecular quantitative genetics and systems biology data over the past decade. We present WormQTL(HD) (Human Disease), a database that quantitatively and systematically links expression Quantitative Trait Loci (eQTL) findings in C. elegans to gene-disease associations in man. WormQTL(HD), available online at http://www.wormqtl-hd.org, is a user-friendly set of tools to reveal functionally coherent, evolutionary conserved gene networks. These can be used to predict novel gene-to-gene associations and the functions of genes underlying the disease of interest. We created a new database that links C. elegans eQTL data sets to human diseases (34 337 gene-disease associations from OMIM, DGA, GWAS Central and NHGRI GWAS Catalogue) based on overlapping sets of orthologous genes associated to phenotypes in these two species. We utilized QTL results, high-throughput molecular phenotypes, classical phenotypes and genotype data covering different developmental stages and environments from WormQTL database. All software is available as open source, built on MOLGENIS and xQTL workbench.

EuPathDB: the eukaryotic pathogen genomics database resource

PubMed Central

Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S.; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C.; Lawrence, Cris; Li, Wei; Pinney, Deborah F.; Pulman, Jane A.; Roos, David S.; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J.; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

2017-01-01

The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions. PMID:27903906

BRCA Share: A Collection of Clinical BRCA Gene Variants.

PubMed

Béroud, Christophe; Letovsky, Stanley I; Braastad, Corey D; Caputo, Sandrine M; Beaudoux, Olivia; Bignon, Yves Jean; Bressac-De Paillerets, Brigitte; Bronner, Myriam; Buell, Crystal M; Collod-Béroud, Gwenaëlle; Coulet, Florence; Derive, Nicolas; Divincenzo, Christina; Elzinga, Christopher D; Garrec, Céline; Houdayer, Claude; Karbassi, Izabela; Lizard, Sarab; Love, Angela; Muller, Danièle; Nagan, Narasimhan; Nery, Camille R; Rai, Ghadi; Revillion, Françoise; Salgado, David; Sévenet, Nicolas; Sinilnikova, Olga; Sobol, Hagay; Stoppa-Lyonnet, Dominique; Toulas, Christine; Trautman, Edwin; Vaur, Dominique; Vilquin, Paul; Weymouth, Katelyn S; Willis, Alecia; Eisenberg, Marcia; Strom, Charles M

2016-12-01

As next-generation sequencing increases access to human genetic variation, the challenge of determining clinical significance of variants becomes ever more acute. Germline variants in the BRCA1 and BRCA2 genes can confer substantial lifetime risk of breast and ovarian cancer. Assessment of variant pathogenicity is a vital part of clinical genetic testing for these genes. A database of clinical observations of BRCA variants is a critical resource in that process. This article describes BRCA Share™, a database created by a unique international alliance of academic centers and commercial testing laboratories. By integrating the content of the Universal Mutation Database generated by the French Unicancer Genetic Group with the testing results of two large commercial laboratories, Quest Diagnostics and Laboratory Corporation of America (LabCorp), BRCA Share™ has assembled one of the largest publicly accessible collections of BRCA variants currently available. Although access is available to academic researchers without charge, commercial participants in the project are required to pay a support fee and contribute their data. The fees fund the ongoing curation effort, as well as planned experiments to functionally characterize variants of uncertain significance. BRCA Share™ databases can therefore be considered as models of successful data sharing between private companies and the academic world. © 2016 WILEY PERIODICALS, INC.

Review of availability of food composition data for fish and shellfish.

PubMed

Rittenschober, Doris; Nowak, Verena; Charrondiere, U Ruth

2013-12-15

The FAO/INFOODS database on fish and shellfish (aFiSh) is a collection of analytical data from primary sources and holds values for 2,277 entries on raw and processed food with sufficient quality. Most data were entered on fatty acids (60%), followed by macronutrients and their fractions (16%), minerals (10%), amino acids (7%), (pro)vitamins (2%), heavy metals (2%) and other components (3%). Information on several factors that contribute to the variation of compositional data (e.g., biodiversity, catch season, habitat, size and part of fish/shellfish analysed) as well as the bibliographic references are presented alongside with each food entry. The data were published in the FAO/INFOODS Food Composition Database for Biodiversity (BioFoodComp2.0) and in the FAO/INFOODS Analytical Food Composition Database (AnFooD1.0), freely available at the INFOODS webpage http://www.fao.org/infoods/biodiversity/index_en.stm. The provision of easy accessible, analytical compositional data should be seen as stimulation for researchers and compilers to incorporate more analytical and detailed data of fish and shellfish into future food composition tables and databases and to improve dietary assessment tools. Copyright © 2013 Food and Agriculture Organization of the United Nations. Published by Elsevier Ltd.. All rights reserved.

Gaps in sampling and limitations to tree biomass estimation: a review of past sampling efforts over the past 50 years

Treesearch

Aaron Weiskittel; Jereme Frank; James Westfall; David Walker; Phil Radtke; David Affleck; David Macfarlane

2015-01-01

Tree biomass models are widely used but differ due to variation in the quality and quantity of data used in their development. We reviewed over 250 biomass studies and categorized them by species, location, sampled diameter distribution, and sample size. Overall, less than half of the tree species in Forest Inventory and Analysis database (FIADB) are without a...

Host allometry influences the evolution of parasite host-generalism: theory and meta-analysis

PubMed Central

Hurford, Amy; Ellison, Amy R.

2017-01-01

Parasites vary widely in the diversity of hosts they infect: some parasite species are specialists—infecting just a single host species, while others are generalists, capable of infecting many. Understanding the factors that drive parasite host-generalism is of basic biological interest, but also directly relevant to predicting disease emergence in new host species, identifying parasites that are likely to have unidentified additional hosts, and assessing transmission risk. Here, we use mathematical models to investigate how variation in host body size and environmental temperature affect the evolution of parasite host-generalism. We predict that parasites are more likely to evolve a generalist strategy when hosts are large-bodied, when variation in host body size is large, and in cooler environments. We then explore these predictions using a newly updated database of over 20 000 fish–macroparasite associations. Within the database we see some evidence supporting these predictions, but also highlight mismatches between theory and data. By combining these two approaches, we establish a theoretical basis for interpreting empirical data on parasites' host specificity and identify key areas for future work that will help untangle the drivers of parasite host-generalism. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’. PMID:28289257

Host allometry influences the evolution of parasite host-generalism: theory and meta-analysis.

PubMed

Walker, Josephine G; Hurford, Amy; Cable, Jo; Ellison, Amy R; Price, Stephen J; Cressler, Clayton E

2017-05-05

Parasites vary widely in the diversity of hosts they infect: some parasite species are specialists-infecting just a single host species, while others are generalists, capable of infecting many. Understanding the factors that drive parasite host-generalism is of basic biological interest, but also directly relevant to predicting disease emergence in new host species, identifying parasites that are likely to have unidentified additional hosts, and assessing transmission risk. Here, we use mathematical models to investigate how variation in host body size and environmental temperature affect the evolution of parasite host-generalism. We predict that parasites are more likely to evolve a generalist strategy when hosts are large-bodied, when variation in host body size is large, and in cooler environments. We then explore these predictions using a newly updated database of over 20 000 fish-macroparasite associations. Within the database we see some evidence supporting these predictions, but also highlight mismatches between theory and data. By combining these two approaches, we establish a theoretical basis for interpreting empirical data on parasites' host specificity and identify key areas for future work that will help untangle the drivers of parasite host-generalism.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'. © 2017 The Authors.

Average snowcover density values in Eastern Alps mountain

NASA Astrophysics Data System (ADS)

Valt, M.; Moro, D.

2009-04-01

The Italian Avalanche Warning Services monitor the snow cover characteristics through networks evenly distributed all over the alpine chain. Measurements of snow stratigraphy and density are very frequently performed with sampling rates of 1 -2 times per week. Snow cover density values are used to compute the dimensions of the building roofs as well as to design avalanche barriers. Based on the measured snow densities the Electricity Board can predict the amount of water resources deriving from snow melt in high relieves drainage basins. In this work it was possible to compute characteristic density values of the snow cover in the Eastern Alps using the information contained in the database from the ARPA (Agenzia Regionale Protezione Ambiente)-Centro Valanghe di Arabba, and Ufficio Valanghe- Udine. Among the other things, this database includes 15 years of stratigraphic measurements. More than 6,000 snow stratigraphic logs were analysed, in order to derive typical values as for geographical area, altitude, exposure, snow cover thickness and season. Computed values were compared to those established by the current Italian laws. Eventually, experts identified and evaluated the correlations between the seasonal variations of the average snow density and the variations related to the snowfall rate in the period 1994-2008 in the Eastern Alps mountain range

Resource utilization in primary repair of cleft lip.

PubMed

Owusu, James A; Liu, Meixia; Sidman, James D; Scott, Andrew R

2013-03-01

To determine national variations in resource utilization for primary repair of cleft lip, identify patient and institutional factors associated with high resource use, and estimate the current incidence of cleft lip in the United States. Retrospective analysis of a national, pediatric database (2009 Kids' Inpatient Database [KID]). Patients aged 1 year and younger were selected using international classification of disease codes for cleft lip and procedure codes for cleft lip repair. A number of demographic variables were analyzed, and hospital charges were considered as a measure of resource utilization. There were 1318 patients identified. The national incidence was 0.09%, with a male to female ratio of 1.8:1. Regional incidence varied from 0.07% (Northeast) to 0.10% (West). The mean age at surgery was 4.2 months. The average length of stay was 1.4 days. The national average hospital charge was $20,147, ranging from $14,635 (South) to $23,663 (West). Teaching hospitals charge an average of $9764 higher than nonteaching hospitals. The strongest predictor of charge was length of stay, increasing charge by $8102 for every additional hospital day (P < .01). Regional variations exist in resource utilization for primary cleft lip repair. Resource use is higher in the West and among teaching hospitals.

Concomitant prescription of non-steroidal anti-inflammatory drugs and antacids in the outpatient setting of a medical center in taiwan: a prescription database study.

PubMed

Liu, J Y; Chen, T J; Hwang, S J

2001-09-01

Although antacids were ineffective in preventing serious gastrointestinal complications caused by non-steroidal anti-inflammatory drugs (NSAIDs), many physicians in Taiwan still prescribe antacids concomitantly with NSAIDs. A survey of an outpatient prescription database was performed to measure the extent of such a combination and to explore its associated factors. One month of the outpatient prescription data in the polyclinic of a medical center in Taiwan served to estimate the frequency of concomitant antacid prescription with NSAIDs. The age of patients, duration of NSAID prescriptions, concomitant prescription of corticosteroid or ulcer-healing drugs, and inter-departmental variations were compared between the NSAID prescriptions with and without antacids. Antacids were present in 87.3% of prescriptions with NSAIDs but only in 34.4% of prescriptions without NSAIDs (P<0.001). The prescription of antacids was significantly associated with the prescription of NSAIDs. The age of patients and duration of NSAID prescriptions did not influence the co-prescription of NSAIDs and antacids. Significant inter-departmental variations were noted in which the surgeons and orthopedic doctors tended to co-prescribe antacids with NSAIDs more often than the internists. The physicians in Taiwan tended to prescribe NSAIDs together with antacids. The rationality of this co-prescription deserves further investigation.

Geostatistical analysis of effective vertical hydraulic conductivity and presence of confining layers in the Shallow Glacial Drift Aquifer, Oakland County, Michigan

USGS Publications Warehouse

Bissell, E.G.; Aichele, Stephen S.

2004-01-01

About 400,000 residents of Oakland County, Mich., rely on ground water for their primary drinking-water supply. More than 90 percent of these residents draw ground water from the shallow glacial drift aquifer. Understanding the vertical hydraulic conductivity of the shallow glacial drift aquifer is important both in identifying areas of ground-water recharge and in evaluating susceptibility to contamination. The geologic environment throughout much of the county, however, is poorly understood and heterogeneous, making conventional aquifer mapping techniques difficult. Geostatistical procedures are therefore used to describe the effective vertical hydraulic conductivity of the top 50 ft of the glacial deposits and to predict the probability of finding a potentially protective confining layer at a given location. The results presented synthesize the available well-log data; however, only about 40 percent of the explainable variation in the dataset is accounted for, making the results more qualitative than quantitative. Most of the variation in the effective vertical hydraulic conductivity cannot be explained with the well-log data currently available (as of 2004). Although the geologic environment is heterogeneous, the quality-assurance process indicated that more than half of the wells in the county’s Wellkey database (statewide database for monitoring drinking-water wells) had inconsistent identifications of lithology.

ALDB: a domestic-animal long noncoding RNA database.

PubMed

Li, Aimin; Zhang, Junying; Zhou, Zhongyin; Wang, Lei; Liu, Yujuan; Liu, Yajun

2015-01-01

Long noncoding RNAs (lncRNAs) have attracted significant attention in recent years due to their important roles in many biological processes. Domestic animals constitute a unique resource for understanding the genetic basis of phenotypic variation and are ideal models relevant to diverse areas of biomedical research. With improving sequencing technologies, numerous domestic-animal lncRNAs are now available. Thus, there is an immediate need for a database resource that can assist researchers to store, organize, analyze and visualize domestic-animal lncRNAs. The domestic-animal lncRNA database, named ALDB, is the first comprehensive database with a focus on the domestic-animal lncRNAs. It currently archives 12,103 pig intergenic lncRNAs (lincRNAs), 8,923 chicken lincRNAs and 8,250 cow lincRNAs. In addition to the annotations of lincRNAs, it offers related data that is not available yet in existing lncRNA databases (lncRNAdb and NONCODE), such as genome-wide expression profiles and animal quantitative trait loci (QTLs) of domestic animals. Moreover, a collection of interfaces and applications, such as the Basic Local Alignment Search Tool (BLAST), the Generic Genome Browser (GBrowse) and flexible search functionalities, are available to help users effectively explore, analyze and download data related to domestic-animal lncRNAs. ALDB enables the exploration and comparative analysis of lncRNAs in domestic animals. A user-friendly web interface, integrated information and tools make it valuable to researchers in their studies. ALDB is freely available from http://res.xaut.edu.cn/aldb/index.jsp.

Evaluation of Online Information Sources on Alien Species in Europe: The Need of Harmonization and Integration

NASA Astrophysics Data System (ADS)

Gatto, Francesca; Katsanevakis, Stelios; Vandekerkhove, Jochen; Zenetos, Argyro; Cardoso, Ana Cristina

2013-06-01

Europe is severely affected by alien invasions, which impact biodiversity, ecosystem services, economy, and human health. A large number of national, regional, and global online databases provide information on the distribution, pathways of introduction, and impacts of alien species. The sufficiency and efficiency of the current online information systems to assist the European policy on alien species was investigated by a comparative analysis of occurrence data across 43 online databases. Large differences among databases were found which are partially explained by variations in their taxonomical, environmental, and geographical scopes but also by the variable efforts for continuous updates and by inconsistencies on the definition of "alien" or "invasive" species. No single database covered all European environments, countries, and taxonomic groups. In many European countries national databases do not exist, which greatly affects the quality of reported information. To be operational and useful to scientists, managers, and policy makers, online information systems need to be regularly updated through continuous monitoring on a country or regional level. We propose the creation of a network of online interoperable web services through which information in distributed resources can be accessed, aggregated and then used for reporting and further analysis at different geographical and political scales, as an efficient approach to increase the accessibility of information. Harmonization, standardization, conformity on international standards for nomenclature, and agreement on common definitions of alien and invasive species are among the necessary prerequisites.

Development of a relational database to capture and merge clinical history with the quantitative results of radionuclide renography.

PubMed

Folks, Russell D; Savir-Baruch, Bital; Garcia, Ernest V; Verdes, Liudmila; Taylor, Andrew T

2012-12-01

Our objective was to design and implement a clinical history database capable of linking to our database of quantitative results from (99m)Tc-mercaptoacetyltriglycine (MAG3) renal scans and export a data summary for physicians or our software decision support system. For database development, we used a commercial program. Additional software was developed in Interactive Data Language. MAG3 studies were processed using an in-house enhancement of a commercial program. The relational database has 3 parts: a list of all renal scans (the RENAL database), a set of patients with quantitative processing results (the Q2 database), and a subset of patients from Q2 containing clinical data manually transcribed from the hospital information system (the CLINICAL database). To test interobserver variability, a second physician transcriber reviewed 50 randomly selected patients in the hospital information system and tabulated 2 clinical data items: hydronephrosis and presence of a current stent. The CLINICAL database was developed in stages and contains 342 fields comprising demographic information, clinical history, and findings from up to 11 radiologic procedures. A scripted algorithm is used to reliably match records present in both Q2 and CLINICAL. An Interactive Data Language program then combines data from the 2 databases into an XML (extensible markup language) file for use by the decision support system. A text file is constructed and saved for review by physicians. RENAL contains 2,222 records, Q2 contains 456 records, and CLINICAL contains 152 records. The interobserver variability testing found a 95% match between the 2 observers for presence or absence of ureteral stent (κ = 0.52), a 75% match for hydronephrosis based on narrative summaries of hospitalizations and clinical visits (κ = 0.41), and a 92% match for hydronephrosis based on the imaging report (κ = 0.84). We have developed a relational database system to integrate the quantitative results of MAG3 image processing with clinical records obtained from the hospital information system. We also have developed a methodology for formatting clinical history for review by physicians and export to a decision support system. We identified several pitfalls, including the fact that important textual information extracted from the hospital information system by knowledgeable transcribers can show substantial interobserver variation, particularly when record retrieval is based on the narrative clinical records.

A cross-cultural comparison of children's imitative flexibility.

PubMed

Clegg, Jennifer M; Legare, Cristine H

2016-09-01

Recent research with Western populations has demonstrated that children use imitation flexibly to engage in both instrumental and conventional learning. Evidence for children's imitative flexibility in non-Western populations is limited, however, and has only assessed imitation of instrumental tasks. This study (N = 142, 6- to 8-year-olds) demonstrates both cultural continuity and cultural variation in imitative flexibility. Children engage in higher imitative fidelity for conventional tasks than for instrumental tasks in both an industrialized, Western culture (United States), and a subsistence-based, non-Western culture (Vanuatu). Children in Vanuatu engage in higher imitative fidelity of instrumental tasks than in the United States, a potential consequence of cultural variation in child socialization for conformity. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Managing daily happiness: The relationship between selection, optimization, and compensation strategies and well-being in adulthood.

PubMed

Teshale, Salom M; Lachman, Margie E

2016-11-01

Past work on selective optimization and compensation (SOC) has focused on between-persons differences and its relationship with global well-being. However, less work examines within-person SOC variation. This study examined whether variation over 7 days in everyday SOC was associated with happiness in a sample of 145 adults ages 22-94. Age differences in this relationship, the moderating effects of health, and lagged effects were also examined. On days in which middle-age and older adults and individuals with lower health used more SOC, they also reported greater happiness. Lagged effects indicated lower happiness led to greater subsequent SOC usage. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

a Spatiotemporal Aggregation Query Method Using Multi-Thread Parallel Technique Based on Regional Division

NASA Astrophysics Data System (ADS)

Liao, S.; Chen, L.; Li, J.; Xiong, W.; Wu, Q.

2015-07-01

Existing spatiotemporal database supports spatiotemporal aggregation query over massive moving objects datasets. Due to the large amounts of data and single-thread processing method, the query speed cannot meet the application requirements. On the other hand, the query efficiency is more sensitive to spatial variation then temporal variation. In this paper, we proposed a spatiotemporal aggregation query method using multi-thread parallel technique based on regional divison and implemented it on the server. Concretely, we divided the spatiotemporal domain into several spatiotemporal cubes, computed spatiotemporal aggregation on all cubes using the technique of multi-thread parallel processing, and then integrated the query results. By testing and analyzing on the real datasets, this method has improved the query speed significantly.

Case-mix fails to explain variation in mastectomy rates: management of screen-detected breast cancer in a UK region 1997–2003

PubMed Central

Caldon, L J M; Walters, S J; Reed, J A; Murphy, A; Worley, A; Reed, M W R

2004-01-01

Wide variation in the surgical management of breast cancer exists at hospital, regional, national and international level. To demonstrate whether variation in surgical practice observed at aggregate level between breast units persists following adjustment for case-mix, individual patient-level data from the Trent Breast Screening Programme Quality Assurance database (1997–2003) was analysed. Expected case-mix adjusted mastectomy rates were derived by logistic regression using the variables tumour size, site and grade, patient age and year of presentation, employing the region's overall case-mix adjusted practice as the reference population. The region's 11 breast screening units detected 5109 (3989 invasive) surgically managed primary breast cancers over the 6-year period. A total of 1828 mastectomies (Mx) were performed (Mx rate 35.8%, 95% confidence interval: 34.5–37.1%). Significant variation in mastectomy rates were observed between units (range 25–45%, P<0.0001), and persists following case-mix adjustment (P<0.0001). Two-fold variation in observed to expected unit mastectomy rate coefficient is demonstrated overall (range 0.66–1.36), increasing to almost four-fold variation in cancers less than 15 mm diameter (range 0.55–1.95). Significant variation in surgery for screen-detected primary breast cancer is not explained by case-mix. Further research is required to investigate potential patient and professional causative factors. PMID:15611797

High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources

PubMed Central

2013-01-01

Background Little is known about the levels of variation in lignin or other wood related genes in Salix, a genus that is being increasingly used for biomass and biofuel production. The lignin biosynthesis pathway is well characterized in a number of species, including the model tree Populus. We aimed to transfer the genomic resources already available in Populus to its sister genus Salix to assess levels of variation within genes involved in wood formation. Results Amplification trials for 27 gene regions were undertaken in 40 Salix taxa. Twelve of these regions were sequenced. Alignment searches of the resulting sequences against reference databases, combined with phylogenetic analyses, showed the close similarity of these Salix sequences to Populus, confirming homology of the primer regions and indicating a high level of conservation within the wood formation genes. However, all sequences were found to vary considerably among Salix species, mainly as SNPs with a smaller number of insertions-deletions. Between 25 and 176 SNPs per kbp per gene region (in predicted exons) were discovered within Salix. Conclusions The variation found is sizeable but not unexpected as it is based on interspecific and not intraspecific comparison; it is comparable to interspecific variation in Populus. The characterisation of genetic variation is a key process in pre-breeding and for the conservation and exploitation of genetic resources in Salix. This study characterises the variation in several lignocellulose gene markers for such purposes. PMID:23924375

Spatio-Temporal Variability of the Phase of Total Ozone Quasi-Decennial Oscillations

NASA Astrophysics Data System (ADS)

Visheratin, K. N.

2017-12-01

The SBUV/SBUV2 (65° S-65° N) and Bodeker Scientific (90° S-90° N) satellite databases have been used for composite and cross-wavelet analyses of the spatio-temporal variability of phase relations between a 11-year cycle of solar activity (SA) and quasi-decennial oscillations (QDOs) of total ozone content (TOC). For globally average TOC values, the QDO maxima coincide in phase with the solar-activity maxima, and amplitude variations of TOC correlate with those of the 11-year solar cycle. According to the analysis of amplitude and phase of QDOs for the zonal average TOC fields, a QDO amplitude is about 6-7 Dobson Units (DU) in the high northern and southern latitudes, and it does not exceed 2-3 DU in the tropic regions. The latitudinal TOC variations are distinguished by a delay of the quasi-decennial oscillation phase in the southern latitudes in comparison with the northern latitudes. The TOC maxima phase coincides with the SA maxima phase in the tropic regions; the TOC variations go ahead of the SA variations, on average, in moderate and high latitudes of the Northern Hemisphere; the TOC variations are behind the SA variations in the Southern Hemisphere. The phase delay between TOC QDO maxima in the northern and southern latitudes appears to increase in the course of time, and the TOC quasi-decennial variations in the Arctic and Antarctic subpolar regions occur approximately in an antiphase over the last two decades.

Building a multi-scaled geospatial temporal ecology database from disparate data sources: fostering open science and data reuse.

PubMed

Soranno, Patricia A; Bissell, Edward G; Cheruvelil, Kendra S; Christel, Samuel T; Collins, Sarah M; Fergus, C Emi; Filstrup, Christopher T; Lapierre, Jean-Francois; Lottig, Noah R; Oliver, Samantha K; Scott, Caren E; Smith, Nicole J; Stopyak, Scott; Yuan, Shuai; Bremigan, Mary Tate; Downing, John A; Gries, Corinna; Henry, Emily N; Skaff, Nick K; Stanley, Emily H; Stow, Craig A; Tan, Pang-Ning; Wagner, Tyler; Webster, Katherine E

2015-01-01

Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km(2)). LAGOS includes two modules: LAGOSGEO, with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOSLIMNO, with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.

Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science through data reuse

USGS Publications Warehouse

Soranno, Patricia A.; Bissell, E.G.; Cheruvelil, Kendra S.; Christel, Samuel T.; Collins, Sarah M.; Fergus, C. Emi; Filstrup, Christopher T.; Lapierre, Jean-Francois; Lotting, Noah R.; Oliver, Samantha K.; Scott, Caren E.; Smith, Nicole J.; Stopyak, Scott; Yuan, Shuai; Bremigan, Mary Tate; Downing, John A.; Gries, Corinna; Henry, Emily N.; Skaff, Nick K.; Stanley, Emily H.; Stow, Craig A.; Tan, Pang-Ning; Wagner, Tyler; Webster, Katherine E.

2015-01-01

Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km2). LAGOS includes two modules: LAGOSGEO, with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOSLIMNO, with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.

NGS Catalog: A Database of Next Generation Sequencing Studies in Humans

PubMed Central

Xia, Junfeng; Wang, Qingguo; Jia, Peilin; Wang, Bing; Pao, William; Zhao, Zhongming

2015-01-01

Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages available human NGS data obtained from published literature. NGS Catalog deposits publication information of NGS studies and their mutation characteristics (SNVs, small insertions/deletions, copy number variations, and structural variants), as well as mutated genes and gene fusions detected by NGS. Other functions include user data upload, NGS general analysis pipelines, and NGS software. NGS Catalog is particularly useful for investigators who are new to NGS but would like to take advantage of these powerful technologies for their own research. Finally, based on the data deposited in NGS Catalog, we summarized features and findings from whole exome sequencing, whole genome sequencing, and transcriptome sequencing studies for human diseases or traits. PMID:22517761

Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer

PubMed Central

Lee, Ji-Hyun; You, Sungyong; Hyeon, Do Young; Kang, Byeongsoo; Kim, Hyerim; Park, Kyoung Mii; Han, Byungwoo; Hwang, Daehee; Kim, Sunghoon

2015-01-01

Mammalian cells have cytoplasmic and mitochondrial aminoacyl-tRNA synthetases (ARSs) that catalyze aminoacylation of tRNAs during protein synthesis. Despite their housekeeping functions in protein synthesis, recently, ARSs and ARS-interacting multifunctional proteins (AIMPs) have been shown to play important roles in disease pathogenesis through their interactions with disease-related molecules. However, there are lacks of data resources and analytical tools that can be used to examine disease associations of ARS/AIMPs. Here, we developed an Integrated Database for ARSs (IDA), a resource database including cancer genomic/proteomic and interaction data of ARS/AIMPs. IDA includes mRNA expression, somatic mutation, copy number variation and phosphorylation data of ARS/AIMPs and their interacting proteins in various cancers. IDA further includes an array of analytical tools for exploration of disease association of ARS/AIMPs, identification of disease-associated ARS/AIMP interactors and reconstruction of ARS-dependent disease-perturbed network models. Therefore, IDA provides both comprehensive data resources and analytical tools for understanding potential roles of ARS/AIMPs in cancers. Database URL: http://ida.biocon.re.kr/, http://ars.biocon.re.kr/ PMID:25824651

Tensor discriminant color space for face recognition.

PubMed

Wang, Su-Jing; Yang, Jian; Zhang, Na; Zhou, Chun-Guang

2011-09-01

Recent research efforts reveal that color may provide useful information for face recognition. For different visual tasks, the choice of a color space is generally different. How can a color space be sought for the specific face recognition problem? To address this problem, this paper represents a color image as a third-order tensor and presents the tensor discriminant color space (TDCS) model. The model can keep the underlying spatial structure of color images. With the definition of n-mode between-class scatter matrices and within-class scatter matrices, TDCS constructs an iterative procedure to obtain one color space transformation matrix and two discriminant projection matrices by maximizing the ratio of these two scatter matrices. The experiments are conducted on two color face databases, AR and Georgia Tech face databases, and the results show that both the performance and the efficiency of the proposed method are better than those of the state-of-the-art color image discriminant model, which involve one color space transformation matrix and one discriminant projection matrix, specifically in a complicated face database with various pose variations.

Empirical correction for earth sensor horizon radiance variation

NASA Technical Reports Server (NTRS)

Hashmall, Joseph A.; Sedlak, Joseph; Andrews, Daniel; Luquette, Richard

1998-01-01

A major limitation on the use of infrared horizon sensors for attitude determination is the variability of the height of the infrared Earth horizon. This variation includes a climatological component and a stochastic component of approximately equal importance. The climatological component shows regular variation with season and latitude. Models based on historical measurements have been used to compensate for these systematic changes. The stochastic component is analogous to tropospheric weather. It can cause extreme, localized changes that for a period of days, overwhelm the climatological variation. An algorithm has been developed to compensate partially for the climatological variation of horizon height and at least to mitigate the stochastic variation. This method uses attitude and horizon sensor data from spacecraft to update a horizon height history as a function of latitude. For spacecraft that depend on horizon sensors for their attitudes (such as the Total Ozone Mapping Spectrometer-Earth Probe-TOMS-EP) a batch least squares attitude determination system is used. It is assumed that minimizing the average sensor residual throughout a full orbit of data results in attitudes that are nearly independent of local horizon height variations. The method depends on the additional assumption that the mean horizon height over all latitudes is approximately independent of season. Using these assumptions, the method yields the latitude dependent portion of local horizon height variations. This paper describes the algorithm used to generate an empirical horizon height. Ideally, an international horizon height database could be established that would rapidly merge data from various spacecraft to provide timely corrections that could be used by all.

Variation in prostate cancer treatment associated with population density of the county of residence.

PubMed

Cary, C; Odisho, A Y; Cooperberg, M R

2016-06-01

We sought to assess variation in the primary treatment of prostate cancer by examining the effect of population density of the county of residence on treatment for clinically localized prostate cancer and quantify variation in primary treatment attributable to the county and state level. A total 138 226 men with clinically localized prostate cancer in the Surveillance, Epidemiology and End Result (SEER) database in 2005 through 2008 were analyzed. The main association of interest was between prostate cancer treatment and population density using multilevel hierarchical logit models while accounting for the random effects of counties nested within SEER regions. To quantify the effect of county and SEER region on individual treatment, the percent of total variance in treatment attributable to county of residence and SEER site was estimated with residual intraclass correlation coefficients. Men with localized prostate cancer in metropolitan counties had 23% higher odds of being treated with surgery or radiation compared with men in rural counties, controlling for number of urologists per county as well as clinical and sociodemographic characteristics. Three percent (95% confidence interval (CI): 1.2-6.2%) of the total variation in treatment was attributable to SEER site, while 6% (95% CI: 4.3-9.0%) of variation was attributable to county of residence, adjusting for clinical and sociodemographic characteristics. Variation in treatment for localized prostate cancer exists for men living in different population-dense counties of the country. These findings highlight the importance of comparative effectiveness research to improve understanding of this variation and lead to a reduction in unwarranted variation.

Seasonal Variation in Penicillin Use in Mexico and Brazil: Analysis of the Impact of Over-the-Counter Restrictions

PubMed Central

Santa-Ana-Tellez, Yared; Mantel-Teeuwisse, Aukje K.; Leufkens, Hubert G. M.

2014-01-01

During 2010, Mexico and Brazil implemented policies to enforce existing laws of restricting over-the-counter sales of antibiotics. We determined if the enforcement led to more appropriate antibiotic use by measuring changes in seasonal variation of penicillin use. We used retail quarterly sales data in defined daily doses per 1,000 inhabitant-days (DDD/TID) from IMS Health from the private sector in Mexico and Brazil from the first quarter of 2007 to the first quarter of 2013. This database contains information on volume of antibiotics sold in retail pharmacies using information from wholesalers. We used interrupted time-series models controlling for external factors with the use of antihypertensives with interaction terms to assess changes in trend, level, and variation in use between quarters for total penicillin use and by active substance. The most used penicillin was amoxicillin, followed by amoxicillin-clavulanic acid and ampicillin (minimal use in Brazil). Before the restrictions, the seasonal variation in penicillin use was 1.1 DDD/TID in Mexico and 0.8 DDD/TID in Brazil. In Mexico, we estimated a significant decrease in the seasonal variation of 0.4 DDD/TID after the restriction, mainly due to changes in seasonal variation of amoxicillin and ampicillin. In Brazil, the seasonal variation did not change significantly, overall and in the breakdown by individual active substances. For Mexico, inappropriate penicillin use may have diminished after the restrictions were enforced. For Brazil, increasing use and no change in seasonal variation suggest that further efforts are needed to reduce inappropriate penicillin use. PMID:25313222

Viability of in-house datamarting approaches for population genetics analysis of SNP genotypes

PubMed Central

Amigo, Jorge; Phillips, Christopher; Salas, Antonio; Carracedo, Ángel

2009-01-01

Background Databases containing very large amounts of SNP (Single Nucleotide Polymorphism) data are now freely available for researchers interested in medical and/or population genetics applications. While many of these SNP repositories have implemented data retrieval tools for general-purpose mining, these alone cannot cover the broad spectrum of needs of most medical and population genetics studies. Results To address this limitation, we have built in-house customized data marts from the raw data provided by the largest public databases. In particular, for population genetics analysis based on genotypes we have built a set of data processing scripts that deal with raw data coming from the major SNP variation databases (e.g. HapMap, Perlegen), stripping them into single genotypes and then grouping them into populations, then merged with additional complementary descriptive information extracted from dbSNP. This allows not only in-house standardization and normalization of the genotyping data retrieved from different repositories, but also the calculation of statistical indices from simple allele frequency estimates to more elaborate genetic differentiation tests within populations, together with the ability to combine population samples from different databases. Conclusion The present study demonstrates the viability of implementing scripts for handling extensive datasets of SNP genotypes with low computational costs, dealing with certain complex issues that arise from the divergent nature and configuration of the most popular SNP repositories. The information contained in these databases can also be enriched with additional information obtained from other complementary databases, in order to build a dedicated data mart. Updating the data structure is straightforward, as well as permitting easy implementation of new external data and the computation of supplementary statistical indices of interest. PMID:19344481

The total antioxidant content of more than 3100 foods, beverages, spices, herbs and supplements used worldwide

PubMed Central

2010-01-01

Background A plant-based diet protects against chronic oxidative stress-related diseases. Dietary plants contain variable chemical families and amounts of antioxidants. It has been hypothesized that plant antioxidants may contribute to the beneficial health effects of dietary plants. Our objective was to develop a comprehensive food database consisting of the total antioxidant content of typical foods as well as other dietary items such as traditional medicine plants, herbs and spices and dietary supplements. This database is intended for use in a wide range of nutritional research, from in vitro and cell and animal studies, to clinical trials and nutritional epidemiological studies. Methods We procured samples from countries worldwide and assayed the samples for their total antioxidant content using a modified version of the FRAP assay. Results and sample information (such as country of origin, product and/or brand name) were registered for each individual food sample and constitute the Antioxidant Food Table. Results The results demonstrate that there are several thousand-fold differences in antioxidant content of foods. Spices, herbs and supplements include the most antioxidant rich products in our study, some exceptionally high. Berries, fruits, nuts, chocolate, vegetables and products thereof constitute common foods and beverages with high antioxidant values. Conclusions This database is to our best knowledge the most comprehensive Antioxidant Food Database published and it shows that plant-based foods introduce significantly more antioxidants into human diet than non-plant foods. Because of the large variations observed between otherwise comparable food samples the study emphasizes the importance of using a comprehensive database combined with a detailed system for food registration in clinical and epidemiological studies. The present antioxidant database is therefore an essential research tool to further elucidate the potential health effects of phytochemical antioxidants in diet. PMID:20096093

Viability of in-house datamarting approaches for population genetics analysis of SNP genotypes.

PubMed

Amigo, Jorge; Phillips, Christopher; Salas, Antonio; Carracedo, Angel

2009-03-19

Databases containing very large amounts of SNP (Single Nucleotide Polymorphism) data are now freely available for researchers interested in medical and/or population genetics applications. While many of these SNP repositories have implemented data retrieval tools for general-purpose mining, these alone cannot cover the broad spectrum of needs of most medical and population genetics studies. To address this limitation, we have built in-house customized data marts from the raw data provided by the largest public databases. In particular, for population genetics analysis based on genotypes we have built a set of data processing scripts that deal with raw data coming from the major SNP variation databases (e.g. HapMap, Perlegen), stripping them into single genotypes and then grouping them into populations, then merged with additional complementary descriptive information extracted from dbSNP. This allows not only in-house standardization and normalization of the genotyping data retrieved from different repositories, but also the calculation of statistical indices from simple allele frequency estimates to more elaborate genetic differentiation tests within populations, together with the ability to combine population samples from different databases. The present study demonstrates the viability of implementing scripts for handling extensive datasets of SNP genotypes with low computational costs, dealing with certain complex issues that arise from the divergent nature and configuration of the most popular SNP repositories. The information contained in these databases can also be enriched with additional information obtained from other complementary databases, in order to build a dedicated data mart. Updating the data structure is straightforward, as well as permitting easy implementation of new external data and the computation of supplementary statistical indices of interest.

A taxonomy has been developed for outcomes in medical research to help improve knowledge discovery.

PubMed

Dodd, Susanna; Clarke, Mike; Becker, Lorne; Mavergames, Chris; Fish, Rebecca; Williamson, Paula R

2018-04-01

There is increasing recognition that insufficient attention has been paid to the choice of outcomes measured in clinical trials. The lack of a standardized outcome classification system results in inconsistencies due to ambiguity and variation in how outcomes are described across different studies. Being able to classify by outcome would increase efficiency in searching sources such as clinical trial registries, patient registries, the Cochrane Database of Systematic Reviews, and the Core Outcome Measures in Effectiveness Trials (COMET) database of core outcome sets (COS), thus aiding knowledge discovery. A literature review was carried out to determine existing outcome classification systems, none of which were sufficiently comprehensive or granular for classification of all potential outcomes from clinical trials. A new taxonomy for outcome classification was developed, and as proof of principle, outcomes extracted from all published COS in the COMET database, selected Cochrane reviews, and clinical trial registry entries were classified using this new system. Application of this new taxonomy to COS in the COMET database revealed that 274/299 (92%) COS include at least one physiological outcome, whereas only 177 (59%) include at least one measure of impact (global quality of life or some measure of functioning) and only 105 (35%) made reference to adverse events. This outcome taxonomy will be used to annotate outcomes included in COS within the COMET database and is currently being piloted for use in Cochrane Reviews within the Cochrane Linked Data Project. Wider implementation of this standard taxonomy in trial and systematic review databases and registries will further promote efficient searching, reporting, and classification of trial outcomes. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Fast 3D shape screening of large chemical databases through alignment-recycling

PubMed Central

Fontaine, Fabien; Bolton, Evan; Borodina, Yulia; Bryant, Stephen H

2007-01-01

Background Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes. Results Using a dataset of more than one million PubChem compounds of limited size (< 28 heavy atoms) and flexibility (< 6 rotatable bonds), we obtained a set of a few thousand diverse structures covering entirely the 3D shape space of the conformers of the dataset. Transformation matrices gathered from the overlays between these diverse structures and the 3D conformer dataset allowed us to drastically (100-fold) reduce the CPU time required for shape overlay. The alignment-recycling heuristic produces results consistent with de novo alignment calculation, with better than 80% hit list overlap on average. Conclusion Overlay-based 3D methods are computationally demanding when searching large databases. Alignment-recycling reduces the CPU time to perform shape similarity searches by breaking the alignment problem into three steps: selection of diverse shapes to describe the database shape-space; overlay of the database conformers to the diverse shapes; and non-optimized overlay of query and database conformers using common reference shapes. The precomputation, required by the first two steps, is a significant cost of the method; however, once performed, querying is two orders of magnitude faster. Extensions and variations of this methodology, for example, to handle more flexible and larger small-molecules are discussed. PMID:17880744

Photodissociation and photoionisation of atoms and molecules of astrophysical interest

NASA Astrophysics Data System (ADS)

Heays, A. N.; Bosman, A. D.; van Dishoeck, E. F.

2017-06-01

A new collection of photodissociation and photoionisation cross sections for 102 atoms and molecules of astrochemical interest has been assembled, along with a brief review of the basic physical processes involved. These have been used to calculate dissociation and ionisation rates, with uncertainties, in a standard ultraviolet interstellar radiation field (ISRF) and for other wavelength-dependent radiation fields, including cool stellar and solar radiation, Lyman-α dominated radiation, and a cosmic-ray induced ultraviolet flux. The new ISRF rates generally agree within 30% with our previous compilations, with a few notable exceptions. Comparison with other databases such as PHIDRATES is made. The reduction of rates in shielded regions was calculated as a function of dust, molecular and atomic hydrogen, atomic C, and self-shielding column densities. The relative importance of these shielding types depends on the atom or molecule in question and the assumed dust optical properties. All of the new data are publicly available from the Leiden photodissociation and ionisation database. Sensitivity of the calculated rates to variation of temperature and isotope, and uncertainties in measured or calculated cross sections, are tested and discussed. Tests were conducted on the new rates with an interstellar-cloud chemical model, and find general agreement (within a factor of two) in abundances obtained with the previous iteration of the Leiden database assuming an ISRF, and order-of-magnitude variations assuming various kinds of stellar radiation. The newly parameterised dust-shielding factors makes a factor-of-two difference to many atomic and molecular abundances relative to parameters currently in the UDfA and KIDA astrochemical reaction databases. The newly-calculated cosmic-ray induced photodissociation and ionisation rates differ from current standard values up to a factor of 5. Under high temperature and cosmic-ray-flux conditions the new rates alter the equilibrium abundances of abundant dark cloud abundances by up to a factor of two. The partial cross sections for H2O and NH3 photodissociation forming OH, O, NH2 and NH are also evaluated and lead to radiation-field-dependent branching ratios.

Screening of reproduction-related single-nucleotide variations from MeDIP-seq data in sheep.

PubMed

Cao, Jiaxue; Wei, Caihong; Zhang, Shuzhen; Capellini, Terence D; Zhang, Li; Zhao, Fuping; Li, Li; Zhong, Tao; Wang, Linjie; Du, Lixin; Zhang, Hongping

2016-11-01

Extensive variation in reproduction has arisen in Chinese Mongolian sheep during recent domestication. Hu and Small-tailed Han sheep, for example, have become non-seasonal breeders and exhibit higher fecundity than Tan and Ujumqin breeds. We therefore scanned reproduction-related single-nucleotide variations from methylated DNA-immunoprecipitation sequencing data generated from each of those four breeds to uncover potential mechanisms underlying this breed variation. We generated a high-quality map of single nucleotide variations (SNVs) in DNA methylation enriched regions, and found that the majority of variants are located within non-coding regions. We identified 359 SNVs within the Sheep Quantitative Trait Locus (QTL) database. Nineteen of these SNVs associated with the Aseasonal Reproduction QTL, and 10 out of the 19 reside close to genes with known reproduction functions. We also identified the well-known FecB mutation in high-fecundity sheep (Hu and Small-tailed Han sheep). When we applied these FecB finding to our breeding system, we improved lambing rate by 175%. In summary, this study provided strong candidate SNVs associated with sheep fecundity that can serve as targets for functional testing and to enhance selective breeding strategies. Mol. Reprod. Dev. 83: 958-967, 2016 © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Excess congenital non-synonymous variation in leukemia-associated genes in MLL− infant leukemia: a Children's Oncology Group report

PubMed Central

Valentine, M C; Linabery, A M; Chasnoff, S; Hughes, A E O; Mallaney, C; Sanchez, N; Giacalone, J; Heerema, N A; Hilden, J M; Spector, L G; Ross, J A; Druley, T E

2014-01-01

Infant leukemia (IL) is a rare sporadic cancer with a grim prognosis. Although most cases are accompanied by MLL rearrangements and harbor very few somatic mutations, less is known about the genetics of the cases without MLL translocations. We performed the largest exome-sequencing study to date on matched non-cancer DNA from pairs of mothers and IL patients to characterize congenital variation that may contribute to early leukemogenesis. Using the COSMIC database to define acute leukemia-associated candidate genes, we find a significant enrichment of rare, potentially functional congenital variation in IL patients compared with randomly selected genes within the same patients and unaffected pediatric controls. IL acute myeloid leukemia (AML) patients had more overall variation than IL acute lymphocytic leukemia (ALL) patients, but less of that variation was inherited from mothers. Of our candidate genes, we found that MLL3 was a compound heterozygote in every infant who developed AML and 50% of infants who developed ALL. These data suggest a model by which known genetic mechanisms for leukemogenesis could be disrupted without an abundance of somatic mutation or chromosomal rearrangements. This model would be consistent with existing models for the establishment of leukemia clones in utero and the high rate of IL concordance in monozygotic twins. PMID:24301523

A systematic review of global cultural variations in knowledge, attitudes and health responses to tuberculosis stigma.

PubMed

Chang, S-H; Cataldo, J K

2014-02-01

Tuberculosis (TB) related stigma is associated with lack of treatment adherence. Individual perceptions of stigma differ by societal context. Limited data are available on variations of TB stigma worldwide. To describe the influence of TB stigma on knowledge, attitudes and responses to TB and to identify similarities and differences across countries. Systematic review of international descriptive studies. A total of 1268 studies were identified from PubMed/Medline, Web of Science, Cochrane, PsycINFO and Cumulative Index to Nursing and Allied Health Literature database searches. Eighty-three studies from 35 countries met the inclusion criteria for English, peer-reviewed, original and non-interventional studies. Variation and similarities in the influence of TB stigma on knowledge, attitudes and responses to TB across countries were identified. Stigma antecedents included negative attitudes and misperceptions regarding the causes of TB and the association with the human immunodeficiency virus. Decisions about illness disclosure and choices between traditional healers and public or private providers were influenced by TB stigma. Sex-influenced perceptions and management of TB and public health responses contributed to TB stigma. Our findings confirm cultural variations with respect to TB and the potential for stigma. Cultural variations should be considered in the development of interventions aimed at reducing stigma and improving treatment adherence.

Deep Networks Can Resemble Human Feed-forward Vision in Invariant Object Recognition

PubMed Central

Kheradpisheh, Saeed Reza; Ghodrati, Masoud; Ganjtabesh, Mohammad; Masquelier, Timothée

2016-01-01

Deep convolutional neural networks (DCNNs) have attracted much attention recently, and have shown to be able to recognize thousands of object categories in natural image databases. Their architecture is somewhat similar to that of the human visual system: both use restricted receptive fields, and a hierarchy of layers which progressively extract more and more abstracted features. Yet it is unknown whether DCNNs match human performance at the task of view-invariant object recognition, whether they make similar errors and use similar representations for this task, and whether the answers depend on the magnitude of the viewpoint variations. To investigate these issues, we benchmarked eight state-of-the-art DCNNs, the HMAX model, and a baseline shallow model and compared their results to those of humans with backward masking. Unlike in all previous DCNN studies, we carefully controlled the magnitude of the viewpoint variations to demonstrate that shallow nets can outperform deep nets and humans when variations are weak. When facing larger variations, however, more layers were needed to match human performance and error distributions, and to have representations that are consistent with human behavior. A very deep net with 18 layers even outperformed humans at the highest variation level, using the most human-like representations. PMID:27601096

Variations in the anatomy of the celiac trunk: A systematic review and clinical implications.

PubMed

Panagouli, Eleni; Venieratos, Dionysios; Lolis, Evangelos; Skandalakis, Panagiotis

2013-12-01

The normal pattern of the celiac trunk (CT) implies its bifurcation to three branches, the common hepatic, the splenic and the left gastric artery. According to the available literature the CT presents several anatomical variations. The purpose of our study is to investigate the different types of these variations, the corresponding incidences and the probable influence of genetic factors, as they are presented in the existing literature. Four databases were searched for eligible articles for the period up to January 2013 and a total of 36 studies were collected. The CT was trifurcated into the three basic branches in the 89.42% (10,906/12,196) of the cases. Bifurcation of the CT occurred in the 7.40% of the pooled samples (903/12,196). Absence of the CT was the rarest variation with a percentage of 0.38% (46/12,196), hepatosplenomesenteric trunk was found in 49 out of the 12,196 cases (0.40%) and the celiacomesenteric trunk presented an incidence of 0.76% (93/12,196). Other variations of the CT were detected in the 1.64% of the pooled cases (199/12,196). The 14.9% of the cases in the cadaveric series (489/3278 specimens), the 10.5% in the imaging series (675/6501 specimens) and the 4.6% (104/2261) in the liver transplantation series presented variations. These differences are statistically significant (p<0.001). The Japanese and Korean populations presented more variations in the CT than Caucasians (p<0.05 and p<0.001). Negro, colored and black populations presented more variations of the CT than Indian ones (p>0.05). Using those data, a novel classification of CT variations is proposed. Copyright © 2013 Elsevier GmbH. All rights reserved.

Systematic variation in the temperature dependence of physiological and ecological traits.

PubMed

Dell, Anthony I; Pawar, Samraat; Savage, Van M

2011-06-28

To understand the effects of temperature on biological systems, we compile, organize, and analyze a database of 1,072 thermal responses for microbes, plants, and animals. The unprecedented diversity of traits (n = 112), species (n = 309), body sizes (15 orders of magnitude), and habitats (all major biomes) in our database allows us to quantify novel features of the temperature response of biological traits. In particular, analysis of the rising component of within-species (intraspecific) responses reveals that 87% are fit well by the Boltzmann-Arrhenius model. The mean activation energy for these rises is 0.66 ± 0.05 eV, similar to the reported across-species (interspecific) value of 0.65 eV. However, systematic variation in the distribution of rise activation energies is evident, including previously unrecognized right skewness around a median of 0.55 eV. This skewness exists across levels of organization, taxa, trophic groups, and habitats, and it is partially explained by prey having increased trait performance at lower temperatures relative to predators, suggesting a thermal version of the life-dinner principle-stronger selection on running for your life than running for your dinner. For unimodal responses, habitat (marine, freshwater, and terrestrial) largely explains the mean temperature at which trait values are optimal but not variation around the mean. The distribution of activation energies for trait falls has a mean of 1.15 ± 0.39 eV (significantly higher than rises) and is also right-skewed. Our results highlight generalities and deviations in the thermal response of biological traits and help to provide a basis to predict better how biological systems, from cells to communities, respond to temperature change.

Hospital and Community Characteristics Associated With Pediatric Direct Admission to Hospital.

PubMed

Leyenaar, JoAnna K; Shieh, Meng-Shiou; Lagu, Tara; Pekow, Penelope S; Lindenauer, Peter K

2017-10-27

One quarter of pediatric hospitalizations begin as direct admissions, defined as hospitalization without receiving care in the hospital's emergency department (ED). Direct admission rates are highly variable across hospitals, yet previous studies have not examined reasons for this variation. We aimed to determine the relationships between hospital and community factors and pediatric direct admission rates, and to evaluate the degree to which these characteristics explain variation in risk-adjusted direct admission rates. We conducted a cross-sectional study of the Healthcare Cost and Utilization Project's Kids Inpatient Database, American Hospital Association Database, and Area Health Resource File, including children <18 years of age who were admitted for a medical hospitalization in states contributing data to all data sets. Using hierarchical generalized linear modeling, we generated risk-adjusted direct admission rates and used generalized linear models to assess the association of hospital and community characteristics with these risk-adjusted rates. We included 211,458 children discharged from 933 hospitals and 26 states; 20.2% were admitted directly. One-fifth of the variance in risk-adjusted direct admission rates was attributed to observed hospital and community factors. The greatest proportion of this explained variance was related to ED volume (37%), volume of pediatric hospitalizations (27%), and size of the pediatrician workforce (12%). Direct admission rates were associated with several hospital and community characteristics, but the majority of variation in hospitals' direct admission rates was not explained by these factors. These findings suggest opportunities for diverse hospital types to develop the infrastructure and communication systems necessary to support pediatric direct admissions. Copyright © 2017 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

Systematic variation in the temperature dependence of physiological and ecological traits

PubMed Central

Dell, Anthony I.; Pawar, Samraat; Savage, Van M.

2011-01-01

To understand the effects of temperature on biological systems, we compile, organize, and analyze a database of 1,072 thermal responses for microbes, plants, and animals. The unprecedented diversity of traits (n = 112), species (n = 309), body sizes (15 orders of magnitude), and habitats (all major biomes) in our database allows us to quantify novel features of the temperature response of biological traits. In particular, analysis of the rising component of within-species (intraspecific) responses reveals that 87% are fit well by the Boltzmann–Arrhenius model. The mean activation energy for these rises is 0.66 ± 0.05 eV, similar to the reported across-species (interspecific) value of 0.65 eV. However, systematic variation in the distribution of rise activation energies is evident, including previously unrecognized right skewness around a median of 0.55 eV. This skewness exists across levels of organization, taxa, trophic groups, and habitats, and it is partially explained by prey having increased trait performance at lower temperatures relative to predators, suggesting a thermal version of the life-dinner principle—stronger selection on running for your life than running for your dinner. For unimodal responses, habitat (marine, freshwater, and terrestrial) largely explains the mean temperature at which trait values are optimal but not variation around the mean. The distribution of activation energies for trait falls has a mean of 1.15 ± 0.39 eV (significantly higher than rises) and is also right-skewed. Our results highlight generalities and deviations in the thermal response of biological traits and help to provide a basis to predict better how biological systems, from cells to communities, respond to temperature change. PMID:21606358

Sources of Variation in Hospital-level Infection Rates after Coronary Artery Bypass Grafting: An analysis of The Society of Thoracic Surgeons Adult Heart Surgery Database

PubMed Central

Likosky, Donald S.; Wallace, Amelia S.; Prager, Richard L.; Jacobs, Jeffrey P.; Zhang, Min; Harrington, Steven D.; Saha-Chaudhuri, Paramita; Theurer, Patricia F.; Fishstrom, Astrid; Dokholyan, Rachel S.; Shahian, David M.; Rankin, J. Scott

2016-01-01

Background Patients undergoing coronary artery bypass grafting (CABG) are at risk for developing a variety of infections. While investigators have focused on predictors of these adverse sequelae, less attention has been focused on characterizing hospital-level variability in these outcomes. Methods 365,686 patients in the STS Adult Cardiac Surgery Database underwent isolated CABG across 1084 hospitals between July 2011 and December 2013. Hospital-acquired infections (HAIs) were defined as: pneumonia, sepsis/septicemia, deep sternal wound infection/mediastinitis, vein harvest/cannulation, or thoracotomy. Hospitals were ranked based on their HAI rate: Low (≤10th Percentile) vs. Medium (10th–90th Percentile) and High (>90th Percentile). Differences in peri-operative factors and composite morbidity/mortality endpoints across these groups were determined using the Wilcoxon rank-sum and chi-square tests. Results HAIs occurred among 3.97% of patients overall, but rates varied across hospital groups (Low:<0.84%, Medium:0.84–8.41%, High:>8.41%). Pneumonia (2.98%) was the most common HAI, followed by sepsis/septicemia (0.84%). Patients at high rate hospitals more often smoked, had diabetes, chronic lung disease, NYHA Class III-IV, and received blood products, (p<0.001); however, they less often were prescribed the appropriate antibiotics (p<0.001). Major morbidity/mortality occurred among 12.3% of patients, although varied by hospital group (low: 8.6%, medium: 12.3%, high: 17.9%, p<0.001). Conclusions Substantial hospital-level variation exists in postoperative HAIs among patients undergoing CABG, driven predominantly by pneumonia. Given the relatively small absolute differences in comorbidities across hospital groups, our findings suggest factors other than case mix may explain the observed variation in HAI rates. PMID:26321440

A systematic review of variations of the recurrent laryngeal nerve.

PubMed

Ling, Xing Yao; Smoll, Nicolas Roydon

2016-01-01

With thyroid cancer fast becoming one of the most common endocrine cancers, the frequency of thyroid surgery has increased. A common and debilitating concern with thyroid surgery is recurrent laryngeal nerve (RLN) paralysis leading to glottal obstruction and airway compromise. A systematic review regarding the anatomical variation of the recurrent laryngeal nerve was performed to determine the position of anatomical variants of the RLN in relation to the inferior thyroid artery (ITA) as well as the prevalence of nonrecurrent laryngeal nerve (NRLN). MEDLINE, Web of Science, MEDITEXT, AMED, CINAHL, Cochrane, ProQuest, Pubmed, and ScienceDirect. Databases were searched using the search terms "inferior thyroid artery," "recurrent laryngeal nerve," "nonrecurrent laryngeal nerve," and "anatomical variation." The reference sections of the articles found were searched for additional reports. The references of all articles were searched to find articles missed in the database search. A total of 8,655 RLN sides were included in this study. One thousand eight hundred and thirteen (20.95%; 95% confidence interval (CI) 20.09, 2,182) showed a Type A configuration of RLN in relation to the ITA, 2,432 (28.10%; 95% CI 27.15, 29.06) showed a Type B configuration and 4,410 (50.95%; 95% CI 49.89, 52.01) showed a Type C configuration between the RLN and the ITA. The second search returned with 38,568 recurrent laryngeal sides and only 221 (0.57%; 95%CI 0.5, 0.65) NRLN documented. The RLN is most commonly found in the posterior position, relative to the ITA. The incidence of the NRLN is low, only occurring in 0.57% of people. © 2015 Wiley Periodicals, Inc.

The relationship between the number of cardiologists and clinical practice patterns in acute heart failure: a cross-sectional observational study

PubMed Central

Sasaki, Noriko; Kunisawa, Susumu; Otsubo, Tetsuya; Ikai, Hiroshi; Fushimi, Kiyohide; Yasumura, Yoshio; Kimura, Takeshi; Imanaka, Yuichi

2014-01-01

Objectives Despite the increasing burden of acute heart failure (AHF) on healthcare systems, the association between centralised cardiovascular specialist care and the quality of AHF care remains unknown. We examine the relationship between the number of cardiologists per hospital and hospital practice variations. Design, setting and participants In a retrospective observational study, we analysed 38 668 patients with AHF admitted to 546 Japanese acute care hospitals between 2010 and 2011 using the Diagnosis Procedure Combination administrative claims database. Sample hospitals were categorised into four groups according to the number of cardiologists per facility (none, 1–4, 5–9 and ≥10). To confirm the capability of administrative data to identify patients with AHF, the ≥10 cardiologists group was compared with two recent clinical registries in Japan. Main outcome measures Using multivariable logistic regression models, patient risk-adjusted in-hospital mortality rates and age-sex-adjusted ORs of various AHF therapies were calculated and compared among four hospital groups. Results The ≥10 cardiologists group of hospitals from the administrative database had similar major underlying disease incidence and therapeutic practices to those of the clinical registry hospitals. Age-adjusted and sex-adjusted ORs of various AHF therapies in the four hospital groups revealed wide practice variations associated with the number of cardiologists. Adjusted in-hospital mortality demonstrated a negative association with the number of cardiologists. In addition, the different hospital-level distribution patterns of specific therapeutic practices illustrated the diffusion process of therapies across facilities. Conclusions Wide practice variations in AHF care were associated with the number of cardiologists per facility, indicating a possible relationship between the quality of AHF care and manpower resources. The provision of recommended therapies increased together with the number of cardiologists. PMID:25550294

Regional variations of basal cell carcinoma incidence in the U.K. using The Health Improvement Network database (2004-10).

PubMed

Musah, A; Gibson, J E; Leonardi-Bee, J; Cave, M R; Ander, E L; Bath-Hextall, F

2013-11-01

Basal cell carcinoma (BCC) is one of the most common types of nonmelanoma skin cancer affecting the white population; however, little is known about how the incidence varies across the U.K. To determine the variation in BCC throughout the U.K. Data from 2004 to 2010 were obtained from The Health Improvement Network database. European and world age-standardized incidence rates (EASRs and WASRs, respectively) were obtained for country-level estimates and levels of socioeconomic deprivation, while strategic health-authority-level estimates were directly age and sex standardized to the U.K. standard population. Incidence-rate ratios were estimated using multivariable Poisson regression models. The overall EASR and WASR of BCC in the U.K. were 98.6 per 100,000 person-years and 66.9 per 100,000 person-years, respectively. Regional-level incidence rates indicated a significant geographical variation in the distribution of BCC, which was more pronounced in the southern parts of the country. The South East Coast had the highest BCC rate followed by South Central, Wales and the South West. Incidence rates were substantially higher in the least deprived groups and we observed a trend of decreasing incidence with increasing levels of deprivation (P < 0.001). Finally, in terms of age groups, the largest annual increase was observed among those aged 30-49 years. Basal cell carcinoma is an increasing health problem in the U.K.; the southern regions of the U.K. and those in the least deprived groups had a higher incidence of BCC. Our findings indicate an increased incidence of BCC for younger age groups below 49 years. © 2013 British Association of Dermatologists.

Structural diversity of domain superfamilies in the CATH database.

PubMed

Reeves, Gabrielle A; Dallman, Timothy J; Redfern, Oliver C; Akpor, Adrian; Orengo, Christine A

2006-07-14

The CATH database of domain structures has been used to explore the structural variation of homologous domains in 294 well populated domain structure superfamilies, each containing at least three sequence diverse relatives. Our analyses confirm some previously detected trends relating sequence divergence to structural variation but for a much larger dataset and in some superfamilies the new data reveal exceptional structural variation. Use of a new algorithm (2DSEC) to analyse variability in secondary structure compositions across a superfamily sheds new light on how structures evolve. 2DSEC detects inserted secondary structures that embellish the core of conserved secondary structures found throughout the superfamily. Analysis showed that for 56% of highly populated superfamilies (>9 sequence diverse relatives), there are twofold or more increases in the numbers of secondary structures in some relatives. In some families fivefold increases occur, sometimes modifying the fold of the domain. Manual inspection of secondary structure insertions or embellishments in 48 particularly variable superfamilies revealed that although these insertions were usually discontiguous in the sequence they were often co-located in 3D resulting in a larger structural motif that often modified the geometry of the active site or the surface conformation promoting diverse domain partnerships and protein interactions. These observations, supported by automatic analysis of all well populated CATH families, suggest that accretion of small secondary structure insertions may provide a simple mechanism for evolving new functions in diverse relatives. Some layered domain architectures (e.g. mainly-beta and alpha-beta sandwiches) that recur highly in the genomes more frequently exploit these types of embellishments to modify function. In these architectures, aggregation occurs most often at the edges, top or bottom of the beta-sheets. Information on structural variability across domain superfamilies has been made available through the CATH Dictionary of Homologous Structures (DHS).

Copy number variation in CEP57L1 predisposes to congenital absence of bilateral ACL and PCL ligaments.

PubMed

Liu, Yichuan; Li, Yun; March, Michael E; Nguyen, Kenny; Kenny, Nguyen; Xu, Kexiang; Wang, Fengxiang; Guo, Yiran; Keating, Brendan; Glessner, Joseph; Li, Jiankang; Ganley, Theodore J; Zhang, Jianguo; Deardorff, Matthew A; Xu, Xun; Hakonarson, Hakon

2015-11-11

Absence of the anterior (ACL) or posterior cruciate ligament (PCL) are rare congenital malformations that result in knee joint instability, with a prevalence of 1.7 per 100,000 live births and can be associated with other lower-limb abnormalities such as ACL agnesia and absence of the menisci of the knee. While a few cases of absence of ACL/PCL are reported in the literature, a number of large familial case series of related conditions such as ACL agnesia suggest a potential underlying monogenic etiology. We performed whole exome sequencing of a family with two individuals affected by ACL/PCL. We identified copy number variation (CNV) deletion impacting the exon sequences of CEP57L1, present in the affected mother and her affected daughter based on the exome sequencing data. The deletion was validated using quantitative PCR (qPCR), and the gene was confirmed to be expressed in ACL ligament tissue. Interestingly, we detected reduced expression of CEP57L1 in Epstein-Barr virus (EBV) cells from the two patients in comparison with healthy controls. Evaluation of 3D protein structure showed that the helix-binding sites of the protein remain intact with the deletion, but other functional binding sites related to microtubule attachment are missing. The specificity of the CNV deletion was confirmed by showing that it was absent in ~700 exome sequencing samples as well as in the database of genomic variations (DGV), a database containing large numbers of annotated CNVs from previous scientific reports. We identified a novel CNV deletion that was inherited through an autosomal dominant transmission from an affected mother to her affected daughter, both of whom suffered from the absence of the anterior and posterior cruciate ligaments of the knees.

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

PubMed Central

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

2010-01-01

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

Planning the Human Variome Project: The Spain Report†

PubMed Central

Kaput, Jim; Cotton, Richard G. H.; Hardman, Lauren; Al Aqeel, Aida I.; Al-Aama, Jumana Y.; Al-Mulla, Fahd; Aretz, Stefan; Auerbach, Arleen D.; Axton, Myles; Bapat, Bharati; Bernstein, Inge T.; Bhak, Jong; Bleoo, Stacey L.; Blöcker, Helmut; Brenner, Steven E.; Burn, John; Bustamante, Mariona; Calzone, Rita; Cambon-Thomsen, Anne; Cargill, Michele; Carrera, Paola; Cavedon, Lawrence; Cho, Yoon Shin; Chung, Yeun-Jun; Claustres, Mireille; Cutting, Garry; Dalgleish, Raymond; den Dunnen, Johan T.; Díaz, Carlos; Dobrowolski, Steven; dos Santos, M. Rosário N.; Ekong, Rosemary; Flanagan, Simon B.; Flicek, Paul; Furukawa, Yoichi; Genuardi, Maurizio; Ghang, Ho; Golubenko, Maria V.; Greenblatt, Marc S.; Hamosh, Ada; Hancock, John M.; Hardison, Ross; Harrison, Terence M.; Hoffmann, Robert; Horaitis, Rania; Howard, Heather J.; Barash, Carol Isaacson; Izagirre, Neskuts; Jung, Jongsun; Kojima, Toshio; Laradi, Sandrine; Lee, Yeon-Su; Lee, Jong-Young; Gil-da-Silva-Lopes, Vera L.; Macrae, Finlay A.; Maglott, Donna; Marafie, Makia J.; Marsh, Steven G.E.; Matsubara, Yoichi; Messiaen, Ludwine M.; Möslein, Gabriela; Netea, Mihai G.; Norton, Melissa L.; Oefner, Peter J.; Oetting, William S.; O’Leary, James C.; de Ramirez, Ana Maria Oller; Paalman, Mark H.; Parboosingh, Jillian; Patrinos, George P.; Perozzi, Giuditta; Phillips, Ian R.; Povey, Sue; Prasad, Suyash; Qi, Ming; Quin, David J.; Ramesar, Rajkumar S.; Richards, C. Sue; Savige, Judith; Scheible, Dagmar G.; Scott, Rodney J.; Seminara, Daniela; Shephard, Elizabeth A.; Sijmons, Rolf H.; Smith, Timothy D.; Sobrido, María-Jesús; Tanaka, Toshihiro; Tavtigian, Sean V.; Taylor, Graham R.; Teague, Jon; Töpel, Thoralf; Ullman-Cullere, Mollie; Utsunomiya, Joji; van Kranen, Henk J.; Vihinen, Mauno; Watson, Michael; Webb, Elizabeth; Weber, Thomas K.; Yeager, Meredith; Yeom, Young I.; Yim, Seon-Hee; Yoo, Hyang-Sook

2018-01-01

The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Since variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008. PMID:19306394

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

PubMed

Hart, Reece K; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A

2015-01-15

Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Planning the human variome project: the Spain report.

PubMed

Kaput, Jim; Cotton, Richard G H; Hardman, Lauren; Watson, Michael; Al Aqeel, Aida I; Al-Aama, Jumana Y; Al-Mulla, Fahd; Alonso, Santos; Aretz, Stefan; Auerbach, Arleen D; Bapat, Bharati; Bernstein, Inge T; Bhak, Jong; Bleoo, Stacey L; Blöcker, Helmut; Brenner, Steven E; Burn, John; Bustamante, Mariona; Calzone, Rita; Cambon-Thomsen, Anne; Cargill, Michele; Carrera, Paola; Cavedon, Lawrence; Cho, Yoon Shin; Chung, Yeun-Jun; Claustres, Mireille; Cutting, Garry; Dalgleish, Raymond; den Dunnen, Johan T; Díaz, Carlos; Dobrowolski, Steven; dos Santos, M Rosário N; Ekong, Rosemary; Flanagan, Simon B; Flicek, Paul; Furukawa, Yoichi; Genuardi, Maurizio; Ghang, Ho; Golubenko, Maria V; Greenblatt, Marc S; Hamosh, Ada; Hancock, John M; Hardison, Ross; Harrison, Terence M; Hoffmann, Robert; Horaitis, Rania; Howard, Heather J; Barash, Carol Isaacson; Izagirre, Neskuts; Jung, Jongsun; Kojima, Toshio; Laradi, Sandrine; Lee, Yeon-Su; Lee, Jong-Young; Gil-da-Silva-Lopes, Vera L; Macrae, Finlay A; Maglott, Donna; Marafie, Makia J; Marsh, Steven G E; Matsubara, Yoichi; Messiaen, Ludwine M; Möslein, Gabriela; Netea, Mihai G; Norton, Melissa L; Oefner, Peter J; Oetting, William S; O'Leary, James C; de Ramirez, Ana Maria Oller; Paalman, Mark H; Parboosingh, Jillian; Patrinos, George P; Perozzi, Giuditta; Phillips, Ian R; Povey, Sue; Prasad, Suyash; Qi, Ming; Quin, David J; Ramesar, Rajkumar S; Richards, C Sue; Savige, Judith; Scheible, Dagmar G; Scott, Rodney J; Seminara, Daniela; Shephard, Elizabeth A; Sijmons, Rolf H; Smith, Timothy D; Sobrido, María-Jesús; Tanaka, Toshihiro; Tavtigian, Sean V; Taylor, Graham R; Teague, Jon; Töpel, Thoralf; Ullman-Cullere, Mollie; Utsunomiya, Joji; van Kranen, Henk J; Vihinen, Mauno; Webb, Elizabeth; Weber, Thomas K; Yeager, Meredith; Yeom, Young I; Yim, Seon-Hee; Yoo, Hyang-Sook

2009-04-01

The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008. (c) 2009 Wiley-Liss, Inc.

Geomagnetic Jerks in the Swarm Era

NASA Astrophysics Data System (ADS)

Brown, William; Beggan, Ciaran; Macmillan, Susan

2016-08-01

The timely provision of geomagnetic observations as part of the European Space Agency (ESA) Swarm mission means up-to-date analysis and modelling of the Earth's magnetic field can be conducted rapidly in a manner not possible before. Observations from each of the three Swarm constellation satellites are available within 4 days and a database of close-to-definitive ground observatory measurements is updated every 3 months. This makes it possible to study very recent variations of the core magnetic field. Here we investigate rapid, unpredictable internal field variations known as geomagnetic jerks. Given that jerks represent (currently) unpredictable changes in the core field and have been identified to have happened in 2014 since Swarm was launched, we ask what impact this might have on the future accuracy of the International Geomagnetic Reference Field (IGRF). We assess the performance of each of the IGRF-12 secular variation model candidates in light of recent jerks, given that four of the nine candidates are novel physics-based predictive models.

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature

PubMed Central

Hart, Reece K.; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A.

2015-01-01

Summary: Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. Availability and implementation: The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Contact: reecehart@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25273102

Transit timing analysis of the exoplanet TrES-5 b. Possible existence of the exoplanet TrES-5 c

NASA Astrophysics Data System (ADS)

Sokov, Eugene N.; Sokova, Iraida A.; Dyachenko, Vladimir V.; Rastegaev, Denis A.; Burdanov, Artem; Rusov, Sergey A.; Benni, Paul; Shadick, Stan; Hentunen, Veli-Pekka; Salisbury, Mark; Esseiva, Nicolas; Garlitz, Joe; Bretton, Marc; Ogmen, Yenal; Karavaev, Yuri; Ayiomamitis, Anthony; Mazurenko, Oleg; Alonso, David Molina; Velichko, Sergey F.

2018-06-01

In this work, we present transit timing variations detected for the exoplanet TrES-5b. To obtain the necessary amount of photometric data for this exoplanet, we have organized an international campaign to search for exoplanets based on the Transit Timing Variation method (TTV) and as a result of this we collected 30 new light curves, 15 light curves from the Exoplanet Transit Database (ETD) and 8 light curves from the literature for the timing analysis of the exoplanet TrES-5b. We have detected timing variations with a semi-amplitude of A ≈ 0.0016 days and a period of P ≈ 99 days. We carried out the N-body modeling based on the three-body problem. The detected perturbation of TrES-5b may be caused by a second exoplanet in the TrES-5 system. We have calculated the possible mass and resonance of the object: M ≈ 0.24MJup at a 1:2 Resonance.

WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp

PubMed Central

Snoek, L. Basten; Van der Velde, K. Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O.; Poulin, Gino B.; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C.; Kammenga, Jan E.; Swertz, Morris A.

2013-01-01

Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype–phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers. PMID:23180786

WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

PubMed

Snoek, L Basten; Van der Velde, K Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O; Poulin, Gino B; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C; Kammenga, Jan E; Swertz, Morris A

2013-01-01

Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers.

Effect of temperature variations and thermal noise on the static and dynamic behavior of straintronics devices

NASA Astrophysics Data System (ADS)

Barangi, Mahmood; Mazumder, Pinaki

2015-11-01

A theoretical model quantifying the effect of temperature variations on the magnetic properties and static and dynamic behavior of the straintronics magnetic tunneling junction is presented. Four common magnetostrictive materials (Nickel, Cobalt, Terfenol-D, and Galfenol) are analyzed to determine their temperature sensitivity and to provide a comprehensive database for different applications. The variations of magnetic anisotropies are studied in detail for temperature levels up to the Curie temperature. The energy barrier of the free layer and the critical voltage required for flipping the magnetization vector are inspected as important metrics that dominate the energy requirements and noise immunity when the device is incorporated into large systems. To study the dynamic thermal noise, the effect of the Langevin thermal field on the free layer's magnetization vector is incorporated into the Landau-Lifshitz-Gilbert equation. The switching energy, flipping delay, write, and hold error probabilities are studied, which are important metrics for nonvolatile memories, an important application of the straintronics magnetic tunneling junctions.

A Forensic Workshop Report Concerning (1) The Measurement and Analysis of Energetic Materials and (2) Databasing

DTIC Science & Technology

1999-01-01

contaminating the surface. Research efforts to develop an improved sampling method have previously been limited to deposits made from solutions of explosives...explosive per fingerprint calculated in this way has too much variation to allow determination of sampling efficiency or to use this method to prepare...crystals is put into suspension, the actual amount is determined by usual methods including high-performance liquid chromatography (HPLC), gas

Building a Better Model: A Comprehensive Breast Cancer Risk Model Incorporating Breast Density to Stratify Risk and Apply Resources

DTIC Science & Technology

2014-10-01

variability with well trained readers. Figure 7: comparison between the PD (percent density using Cumulus area) and the automatic PD. The...evaluation of outlier correction, comparison of several different software methods, precision measurement, and evaluation of variation by mammography...chart review for selected cases (month 4-6). Comparison of information from the Breast Cancer Database and medical records showed good consistency

Investigation of mutations in the HBB gene using the 1,000 genomes database.

PubMed

Carlice-Dos-Reis, Tânia; Viana, Jaime; Moreira, Fabiano Cordeiro; Cardoso, Greice de Lemos; Guerreiro, João; Santos, Sidney; Ribeiro-Dos-Santos, Ândrea

2017-01-01

Mutations in the HBB gene are responsible for several serious hemoglobinopathies, such as sickle cell anemia and β-thalassemia. Sickle cell anemia is one of the most common monogenic diseases worldwide. Due to its prevalence, diverse strategies have been developed for a better understanding of its molecular mechanisms. In silico analysis has been increasingly used to investigate the genotype-phenotype relationship of many diseases, and the sequences of healthy individuals deposited in the 1,000 Genomes database appear to be an excellent tool for such analysis. The objective of this study is to analyze the variations in the HBB gene in the 1,000 Genomes database, to describe the mutation frequencies in the different population groups, and to investigate the pattern of pathogenicity. The computational tool SNPEFF was used to align the data from 2,504 samples of the 1,000 Genomes database with the HG19 genome reference. The pathogenicity of each amino acid change was investigated using the databases CLINVAR, dbSNP and HbVar and five different predictors. Twenty different mutations were found in 209 healthy individuals. The African group had the highest number of individuals with mutations, and the European group had the lowest number. Thus, it is concluded that approximately 8.3% of phenotypically healthy individuals from the 1,000 Genomes database have some mutation in the HBB gene. The frequency of mutated genes was estimated at 0.042, so that the expected frequency of being homozygous or compound heterozygous for these variants in the next generation is approximately 0.002. In total, 193 subjects had a non-synonymous mutation, which 186 (7.4%) have a deleterious mutation. Considering that the 1,000 Genomes database is representative of the world's population, it can be estimated that fourteen out of every 10,000 individuals in the world will have a hemoglobinopathy in the next generation.

BIOFRAG – a new database for analyzing BIOdiversity responses to forest FRAGmentation

PubMed Central

Pfeifer, Marion; Lefebvre, Veronique; Gardner, Toby A; Arroyo-Rodriguez, Victor; Baeten, Lander; Banks-Leite, Cristina; Barlow, Jos; Betts, Matthew G; Brunet, Joerg; Cerezo, Alexis; Cisneros, Laura M; Collard, Stuart; D'Cruze, Neil; da Silva Motta, Catarina; Duguay, Stephanie; Eggermont, Hilde; Eigenbrod, Felix; Hadley, Adam S; Hanson, Thor R; Hawes, Joseph E; Heartsill Scalley, Tamara; Klingbeil, Brian T; Kolb, Annette; Kormann, Urs; Kumar, Sunil; Lachat, Thibault; Lakeman Fraser, Poppy; Lantschner, Victoria; Laurance, William F; Leal, Inara R; Lens, Luc; Marsh, Charles J; Medina-Rangel, Guido F; Melles, Stephanie; Mezger, Dirk; Oldekop, Johan A; Overal, William L; Owen, Charlotte; Peres, Carlos A; Phalan, Ben; Pidgeon, Anna M; Pilia, Oriana; Possingham, Hugh P; Possingham, Max L; Raheem, Dinarzarde C; Ribeiro, Danilo B; Ribeiro Neto, Jose D; Douglas Robinson, W; Robinson, Richard; Rytwinski, Trina; Scherber, Christoph; Slade, Eleanor M; Somarriba, Eduardo; Stouffer, Philip C; Struebig, Matthew J; Tylianakis, Jason M; Tscharntke, Teja; Tyre, Andrew J; Urbina Cardona, Jose N; Vasconcelos, Heraldo L; Wearn, Oliver; Wells, Konstans; Willig, Michael R; Wood, Eric; Young, Richard P; Bradley, Andrew V; Ewers, Robert M

2014-01-01

Habitat fragmentation studies have produced complex results that are challenging to synthesize. Inconsistencies among studies may result from variation in the choice of landscape metrics and response variables, which is often compounded by a lack of key statistical or methodological information. Collating primary datasets on biodiversity responses to fragmentation in a consistent and flexible database permits simple data retrieval for subsequent analyses. We present a relational database that links such field data to taxonomic nomenclature, spatial and temporal plot attributes, and environmental characteristics. Field assessments include measurements of the response(s) (e.g., presence, abundance, ground cover) of one or more species linked to plots in fragments within a partially forested landscape. The database currently holds 9830 unique species recorded in plots of 58 unique landscapes in six of eight realms: mammals 315, birds 1286, herptiles 460, insects 4521, spiders 204, other arthropods 85, gastropods 70, annelids 8, platyhelminthes 4, Onychophora 2, vascular plants 2112, nonvascular plants and lichens 320, and fungi 449. Three landscapes were sampled as long-term time series (>10 years). Seven hundred and eleven species are found in two or more landscapes. Consolidating the substantial amount of primary data available on biodiversity responses to fragmentation in the context of land-use change and natural disturbances is an essential part of understanding the effects of increasing anthropogenic pressures on land. The consistent format of this database facilitates testing of generalizations concerning biologic responses to fragmentation across diverse systems and taxa. It also allows the re-examination of existing datasets with alternative landscape metrics and robust statistical methods, for example, helping to address pseudo-replication problems. The database can thus help researchers in producing broad syntheses of the effects of land use. The database is dynamic and inclusive, and contributions from individual and large-scale data-collection efforts are welcome. PMID:24967073

Subscale Test Methods for Combustion Devices

NASA Technical Reports Server (NTRS)

Anderson, W. E.; Sisco, J. C.; Long, M. R.; Sung, I.-K.

2005-01-01

Stated goals for long-life LRE s have been between 100 and 500 cycles: 1) Inherent technical difficulty of accurately defining the transient and steady state thermochemical environments and structural response (strain); 2) Limited statistical basis on failure mechanisms and effects of design and operational variability; and 3) Very high test costs and budget-driven need to protect test hardware (aversion to test-to-failure). Ambitious goals will require development of new databases: a) Advanced materials, e.g., tailored composites with virtually unlimited property variations; b) Innovative functional designs to exploit full capabilities of advanced materials; and c) Different cycles/operations. Subscale testing is one way to address technical and budget challenges: 1) Prototype subscale combustors exposed to controlled simulated conditions; 2) Complementary to conventional laboratory specimen database development; 3) Instrumented with sensors to measure thermostructural response; and 4) Coupled with analysis

RefSeq microbial genomes database: new representation and annotation strategy.

PubMed

Tatusova, Tatiana; Ciufo, Stacy; Fedorov, Boris; O'Neill, Kathleen; Tolstoy, Igor

2014-01-01

The source of the microbial genomic sequences in the RefSeq collection is the set of primary sequence records submitted to the International Nucleotide Sequence Database public archives. These can be accessed through the Entrez search and retrieval system at http://www.ncbi.nlm.nih.gov/genome. Next-generation sequencing has enabled researchers to perform genomic sequencing at rates that were unimaginable in the past. Microbial genomes can now be sequenced in a matter of hours, which has led to a significant increase in the number of assembled genomes deposited in the public archives. This huge increase in DNA sequence data presents new challenges for the annotation, analysis and visualization bioinformatics tools. New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks.

First archaeointensity catalogue and intensity secular variation curve for Iberia spanning the last 3000 years

NASA Astrophysics Data System (ADS)

Molina-Cardín, Alberto; Campuzano, Saioa A.; Rivero, Mercedes; Osete, María Luisa; Gómez-Paccard, Miriam; Pérez-Fuentes, José Carlos; Pavón-Carrasco, F. Javier; Chauvin, Annick; Palencia-Ortas, Alicia

2017-04-01

In this work we present the first archaeomagnetic intensity database for the Iberian Peninsula covering the last 3 millennia. In addition to previously published archaeointensities (about 100 data), we present twenty new high-quality archaeointensities. The new data have been obtained following the Thellier and Thellier method including pTRM-checks and have been corrected for the effect of the anisotropy of thermoremanent magnetization upon archaeointensity estimates. Importantly, about 50% of the new data obtained correspond to the first millennium BC, a period for which there was not possible to develop an intensity palaeosecular variation curve before due to the lack of high-quality archaeointensity data. The different qualities of the data included in the Iberian dataset have been evaluated following different palaeomagnetic criteria, such as the number of specimens analysed, the laboratory protocol applied and the kind of material analysed. Finally, we present the first intensity palaeosecular variation curve for the Iberian Peninsula centred at Madrid for the last 3000 years. In order to obtain the most reliable secular variation curve, it has been generated using only selected high-quality data from the catalogue.

Recommendations of the 2006 Human Variome Project meeting.

PubMed

Cotton, Richard G H; Appelbe, William; Auerbach, Arleen D; Becker, Kevin; Bodmer, Walter; Boone, D Joe; Boulyjenkov, Victor; Brahmachari, Samir; Brody, Lawrence; Brookes, Anthony; Brown, Alastair F; Byers, Peter; Cantu, Jose Maria; Cassiman, Jean-Jacques; Claustres, Mireille; Concannon, Patrick; Cotton, Richard G H; den Dunnen, Johan T; Flicek, Paul; Gibbs, Richard; Hall, Judith; Hasler, Julia; Katz, Michael; Kwok, Pui-Yan; Laradi, Sandrine; Lindblom, Annika; Maglott, Donna; Marsh, Steven; Masimirembwa, Collen Muto; Minoshima, Shinsei; de Ramirez, Ana Maria Oller; Pagon, Roberta; Ramesar, Raj; Ravine, David; Richards, Sue; Rimoin, David; Ring, Huijun Z; Scriver, Charles R; Sherry, Stephen; Shimizu, Nobuyoshi; Stein, Lincoln; Tadmouri, Ghazi Omar; Taylor, Graham; Watson, Michael

2007-04-01

Lists of variations in genomic DNA and their effects have been kept for some time and have been used in diagnostics and research. Although these lists have been carefully gathered and curated, there has been little standardization and coordination, complicating their use. Given the myriad possible variations in the estimated 24,000 genes in the human genome, it would be useful to have standard criteria for databases of variation. Incomplete collection and ascertainment of variants demonstrates a need for a universally accessible system. These and other problems led to the World Heath Organization-cosponsored meeting on June 20-23, 2006 in Melbourne, Australia, which launched the Human Variome Project. This meeting addressed all areas of human genetics relevant to collection of information on variation and its effects. Members of each of eight sessions (the clinic and phenotype, the diagnostic laboratory, the research laboratory, curation and collection, informatics, relevance to the emerging world, integration and federation and funding and sustainability) developed a number of recommendations that were then organized into a total of 96 recommendations to act as a foundation for future work worldwide. Here we summarize the background of the project, the meeting and its recommendations.

The behavioral ecology of cultural psychological variation.

PubMed

Sng, Oliver; Neuberg, Steven L; Varnum, Michael E W; Kenrick, Douglas T

2018-04-23

Recent work has documented a wide range of important psychological differences across societies. Multiple explanations have been offered for why such differences exist, including historical philosophies, subsistence methods, social mobility, social class, climactic stresses, and religion. With the growing body of theory and data, there is an emerging need for an organizing framework. We propose here that a behavioral ecological perspective, particularly the idea of adaptive phenotypic plasticity, can provide an overarching framework for thinking about psychological variation across cultures and societies. We focus on how societies vary as a function of six important ecological dimensions: density, relatedness, sex ratio, mortality likelihood, resources, and disease. This framework can: (a) highlight new areas of research, (b) integrate and ground existing cultural psychological explanations, (c) integrate research on variation across human societies with research on parallel variations in other animal species, (d) provide a way for thinking about multiple levels of culture and cultural change, and (e) facilitate the creation of an ecological taxonomy of societies, from which one can derive specific predictions about cultural differences and similarities. Finally, we discuss the relationships between the current framework and existing perspectives. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Recovery Act: An Integrated Experimental and Numerical Study: Developing a Reaction Transport Model that Couples Chemical Reactions of Mineral Dissolution/Precipitation with Spatial and Temporal Flow Variations.

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

Saar, Martin O.; Seyfried, Jr., William E.; Longmire, Ellen K.

2016-06-24

A total of 12 publications and 23 abstracts were produced as a result of this study. In particular, the compilation of a thermodynamic database utilizing consistent, current thermodynamic data is a major step toward accurately modeling multi-phase fluid interactions with solids. Existing databases designed for aqueous fluids did not mesh well with existing solid phase databases. Addition of a second liquid phase (CO2) magnifies the inconsistencies between aqueous and solid thermodynamic databases. Overall, the combination of high temperature and pressure lab studies (task 1), using a purpose built apparatus, and solid characterization (task 2), using XRCT and more developed technologies,more » allowed observation of dissolution and precipitation processes under CO2 reservoir conditions. These observations were combined with results from PIV experiments on multi-phase fluids (task 3) in typical flow path geometries. The results of the tasks 1, 2, and 3 were compiled and integrated into numerical models utilizing Lattice-Boltzmann simulations (task 4) to realistically model the physical processes and were ultimately folded into TOUGH2 code for reservoir scale modeling (task 5). Compilation of the thermodynamic database assisted comparisons to PIV experiments (Task 3) and greatly improved Lattice Boltzmann (Task 4) and TOUGH2 simulations (Task 5). PIV (Task 3) and experimental apparatus (Task 1) have identified problem areas in TOUGHREACT code. Additional lab experiments and coding work has been integrated into an improved numerical modeling code.« less

HEROD: a human ethnic and regional specific omics database.

PubMed

Zeng, Xian; Tao, Lin; Zhang, Peng; Qin, Chu; Chen, Shangying; He, Weidong; Tan, Ying; Xia Liu, Hong; Yang, Sheng Yong; Chen, Zhe; Jiang, Yu Yang; Chen, Yu Zong

2017-10-15

Genetic and gene expression variations within and between populations and across geographical regions have substantial effects on the biological phenotypes, diseases, and therapeutic response. The development of precision medicines can be facilitated by the OMICS studies of the patients of specific ethnicity and geographic region. However, there is an inadequate facility for broadly and conveniently accessing the ethnic and regional specific OMICS data. Here, we introduced a new free database, HEROD, a human ethnic and regional specific OMICS database. Its first version contains the gene expression data of 53 070 patients of 169 diseases in seven ethnic populations from 193 cities/regions in 49 nations curated from the Gene Expression Omnibus (GEO), the ArrayExpress Archive of Functional Genomics Data (ArrayExpress), the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Geographic region information of curated patients was mainly manually extracted from referenced publications of each original study. These data can be accessed and downloaded via keyword search, World map search, and menu-bar search of disease name, the international classification of disease code, geographical region, location of sample collection, ethnic population, gender, age, sample source organ, patient type (patient or healthy), sample type (disease or normal tissue) and assay type on the web interface. The HEROD database is freely accessible at http://bidd2.nus.edu.sg/herod/index.php. The database and web interface are implemented in MySQL, PHP and HTML with all major browsers supported. phacyz@nus.edu.sg. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Pitfalls of using administrative data sets to describe clinical outcomes in sickle cell disease.

PubMed

Claster, Susan; Termuhlen, Amanda; Schrager, Sheree M; Wolfson, Julie A; Iverson, Ellen

2013-12-01

Administrative data sets are increasingly being used to describe clinical care in sickle cell disease (SCD). We recently used such an administrative database to look at the frequency of acute chest syndrome (ACS) and the use of transfusion to treat this syndrome in California patients from 2005 to 2010. Our results revealed a surprisingly low rate of transfusion for this life-threatening situation. To validate these results, we compared California OSPHD (Office of Statewide Health Planning and Development) administrative data with medical record review of patients diagnosed with ACS identified by two pediatric and one adult hospital databases during 2009-2010. ACS or a related pulmonary process accounted for one-fifth of the inpatient hospital discharges associated with the diagnosis of SCD between 2005 and 2010. Only 47% of those discharges were associated with a transfusion. However, chart reviews found that hospital databases over-reported visits for ACS. OSHPD underreported transfusions compared to hospital data. The net effect was a markedly higher true rate of transfusion (40.7% vs. 70.2%). These results point out the difficulties in using this administrative data base to describe clinical care for ACS given the variation in clinician recognition of this entity. OSPHD is widely used to inform health care policy in California and contributes to national databases. Our study suggests that using this administrative database to assess clinical care for SCD may lead to inaccurate assumptions about quality of care for SCD patients in California. Future studies on health services in SCD may require a different methodology. © 2013 Wiley Periodicals, Inc.

Direct variational data assimilation algorithm for atmospheric chemistry data with transport and transformation model

NASA Astrophysics Data System (ADS)

Penenko, Alexey; Penenko, Vladimir; Nuterman, Roman; Baklanov, Alexander; Mahura, Alexander

2015-11-01

Atmospheric chemistry dynamics is studied with convection-diffusion-reaction model. The numerical Data Assimilation algorithm presented is based on the additive-averaged splitting schemes. It carries out ''fine-grained'' variational data assimilation on the separate splitting stages with respect to spatial dimensions and processes i.e. the same measurement data is assimilated to different parts of the split model. This design has efficient implementation due to the direct data assimilation algorithms of the transport process along coordinate lines. Results of numerical experiments with chemical data assimilation algorithm of in situ concentration measurements on real data scenario have been presented. In order to construct the scenario, meteorological data has been taken from EnviroHIRLAM model output, initial conditions from MOZART model output and measurements from Airbase database.

Systemic sclerosis: a world wide global analysis.

PubMed

Coral-Alvarado, Paola; Pardo, Aryce L; Castaño-Rodriguez, Natalia; Rojas-Villarraga, Adriana; Anaya, Juan-Manuel

2009-07-01

The objective of this study was to analyze epidemiological tendencies of systemic sclerosis (SSc) around the world in order to identify possible local variations in the presentation and occurrence of the disease. A systematic review of the literature was performed through electronic databases using the keywords "Systemic Sclerosis" and "Clinical Characteristics." Out of a total of 167 articles, 41 were included in the analysis. Significant differences in the mean age at the time of diagnosis, subsets of SSc, clinical characteristics, and presence of antibodies were found between different regions of the word. Because variations in both additive and nonadditive genetic factors and the environmental variance are specific to the investigated population, ethnicity and geography are important characteristics to be considered in the study of SSc and other autoimmune diseases.

Electrochemical measurements on a droplet using gold microelectrodes

NASA Astrophysics Data System (ADS)

Jenabi, Amin; Souri, Asma; Rastkhadiv, Ali

2016-03-01

Facile methods of ion recognition are important for the fabrication of electronic tongue systems. In this work, we demonstrate performing pulsed conductometry on microliter electrolyte droplets dropped on gold microelectrodes vapor deposited on soda lime glass slides. A droplet is dropped between two microelectrodes when a voltage waveform from a preprogramed power supply is applied on them. The temporal variation of the electric current passing through the droplet is recorded, digitized and stored. The obtained data are compared with the database formed out of the previous experiences for the classification of the sample electrolytes. It is shown that the shape of the voltage waveform is the important parameter of the process. We devised a method for the optimization of the voltage waveform profile for obtaining the maximum of discriminating information from the recorded current variations.

Annual and Semi-Annual Temperature Oscillations in the Upper Mesosphere

NASA Technical Reports Server (NTRS)

Niciejewski, R. J.; Killeen, T. L.

1995-01-01

Fourier transform spectrometer observations of the mesosphere have been performed at the University of Michigan (latitude: 42.5 N) on a long term basis. A database of near infrared Meinel hydroxyl spectra has been accumulated from which rotational temperatures have been determined. Harmonic analysis of one-day averaged temperatures for the period 1992.0 to 1994.5 has shown a distinct annual and semi-annual variation. Subsequent fitting of a five term periodic function characterizing the annual and semi-annual temperature oscillations to the daily averaged temperatures was performed. The resultant mean temperature and the amplitudes and phases of the annual and semi-annual variations are shown to coincide with an emission height slightly above 85 km which is consistent with the mean rocket derived altitude for peak nocturnal hydroxyl emission.

Universals and cultural variations in 22 emotional expressions across five cultures.

PubMed

Cordaro, Daniel T; Sun, Rui; Keltner, Dacher; Kamble, Shanmukh; Huddar, Niranjan; McNeil, Galen

2018-02-01

We collected and Facial Action Coding System (FACS) coded over 2,600 free-response facial and body displays of 22 emotions in China, India, Japan, Korea, and the United States to test 5 hypotheses concerning universals and cultural variants in emotional expression. New techniques enabled us to identify cross-cultural core patterns of expressive behaviors for each of the 22 emotions. We also documented systematic cultural variations of expressive behaviors within each culture that were shaped by the cultural resemblance in values, and identified a gradient of universality for the 22 emotions. Our discussion focused on the science of new expressions and how the evidence from this investigation identifies the extent to which emotional displays vary across cultures. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

A Call for Consensus on Methodology and Terminology to Improve Comparability in the Study of Preventable Prehospital Trauma Deaths: A Systematic Literature Review.

PubMed

Oliver, Govind J; Walter, Darren P

2016-04-01

The study of preventable deaths is essential to trauma research for measuring service quality and highlighting avenues for improving care and as a performance indicator. However, variations in the terminology and methodology of studies on preventable prehospital trauma death limit the comparability and wider application of data. The objective of this study was to describe the heterogeneity in terminology and methodology. We performed a systematic literature review and report this using the PRISMA guidelines. Searches were conducted using PubMed (including Medline), Ovid, and Embase databases. Studies, with a full text available in English published between 1990 and 2015, meeting the following inclusion criteria were included: analysis of 1) deaths from trauma, 2) occurring in the prehospital phase of care, and 3) application of criteria to ascertain whether deaths were preventable. One author screened database results for relevance by title and abstract. The full text of identified papers was reviewed for inclusion. The reference list of included papers was screened for studies not identified by the database search. Data were extracted on predefined core elements relating to preventability reporting and definitions using a standardized form. Twenty-seven studies meeting the inclusion criteria were identified: 12 studies used two categories to assess the preventability of death while 15 used three categories. Fifteen variations in the terminology of these categories and combination with death descriptors were found. Eleven different approaches were used in defining what constituted a preventable death. Twenty-one included survivability of injuries as a criterion. Methods used to determine survivability differed and eight variations in parameters for categorization of deaths were used. Nineteen used panel review in determining preventability with six implementing panel blinding. Panel composition varied greatly by expertise of personnel. Separation of prehospital deaths differed with 10 separating those dead at scene (DAS) and dead on arrival, three excluding those DAS, three excluding deaths prior to EMS arrival, and 11 not separating prehospital deaths. The heterogeneity in methodology, terminology, and definitions of "preventable" between studies render data incomparable. To facilitate common understanding, comparability, and analysis, a commonly agreed ontology by the prehospital research community is required. © 2016 by the Society for Academic Emergency Medicine.

Locus-Specific Mutation Databases for Neurodegenerative Brain Diseases

PubMed Central

Cruts, Marc; Theuns, Jessie; Van Broeckhoven, Christine

2012-01-01

The Alzheimer disease and frontotemporal dementia (AD&FTLD) and Parkinson disease (PD) Mutation Databases make available curated information of sequence variations in genes causing Mendelian forms of the most common neurodegenerative brain disease AD, frontotemporal lobar degeneration (FTLD), and PD. They are established resources for clinical geneticists, neurologists, and researchers in need of comprehensive, referenced genetic, epidemiologic, clinical, neuropathological, and/or cell biological information of specific gene mutations in these diseases. In addition, the aggregate analysis of all information available in the databases provides unique opportunities to extract mutation characteristics and genotype–phenotype correlations, which would be otherwise unnoticed and unexplored. Such analyses revealed that 61.4% of mutations are private to one single family, while only 5.7% of mutations occur in 10 or more families. The five mutations with most frequent independent observations occur in 21% of AD, 43% of FTLD, and 48% of PD families recorded in the Mutation Databases, respectively. Although these figures are inevitably biased by a publishing policy favoring novel mutations, they probably also reflect the occurrence of multiple rare and few relatively common mutations in the inherited forms of these diseases. Finally, with the exception of the PD genes PARK2 and PINK1, all other genes are associated with more than one clinical diagnosis or characteristics thereof. Hum Mutat 33:1340–1344, 2012. © 2012 Wiley Periodicals, Inc. PMID:22581678

The Amordad database engine for metagenomics.

PubMed

Behnam, Ehsan; Smith, Andrew D

2014-10-15

Several technical challenges in metagenomic data analysis, including assembling metagenomic sequence data or identifying operational taxonomic units, are both significant and well known. These forms of analysis are increasingly cited as conceptually flawed, given the extreme variation within traditionally defined species and rampant horizontal gene transfer. Furthermore, computational requirements of such analysis have hindered content-based organization of metagenomic data at large scale. In this article, we introduce the Amordad database engine for alignment-free, content-based indexing of metagenomic datasets. Amordad places the metagenome comparison problem in a geometric context, and uses an indexing strategy that combines random hashing with a regular nearest neighbor graph. This framework allows refinement of the database over time by continual application of random hash functions, with the effect of each hash function encoded in the nearest neighbor graph. This eliminates the need to explicitly maintain the hash functions in order for query efficiency to benefit from the accumulated randomness. Results on real and simulated data show that Amordad can support logarithmic query time for identifying similar metagenomes even as the database size reaches into the millions. Source code, licensed under the GNU general public license (version 3) is freely available for download from http://smithlabresearch.org/amordad andrewds@usc.edu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Seasonal variation in penicillin use in Mexico and Brazil: analysis of the impact of over-the-counter restrictions.

PubMed

Santa-Ana-Tellez, Yared; Mantel-Teeuwisse, Aukje K; Leufkens, Hubert G M; Wirtz, Veronika J

2015-01-01

During 2010, Mexico and Brazil implemented policies to enforce existing laws of restricting over-the-counter sales of antibiotics. We determined if the enforcement led to more appropriate antibiotic use by measuring changes in seasonal variation of penicillin use. We used retail quarterly sales data in defined daily doses per 1,000 inhabitant-days (DDD/TID) from IMS Health from the private sector in Mexico and Brazil from the first quarter of 2007 to the first quarter of 2013. This database contains information on volume of antibiotics sold in retail pharmacies using information from wholesalers. We used interrupted time-series models controlling for external factors with the use of antihypertensives with interaction terms to assess changes in trend, level, and variation in use between quarters for total penicillin use and by active substance. The most used penicillin was amoxicillin, followed by amoxicillin-clavulanic acid and ampicillin (minimal use in Brazil). Before the restrictions, the seasonal variation in penicillin use was 1.1 DDD/TID in Mexico and 0.8 DDD/TID in Brazil. In Mexico, we estimated a significant decrease in the seasonal variation of 0.4 DDD/TID after the restriction, mainly due to changes in seasonal variation of amoxicillin and ampicillin. In Brazil, the seasonal variation did not change significantly, overall and in the breakdown by individual active substances. For Mexico, inappropriate penicillin use may have diminished after the restrictions were enforced. For Brazil, increasing use and no change in seasonal variation suggest that further efforts are needed to reduce inappropriate penicillin use. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Incubator weaning in preterm infants and associated practice variation.

PubMed

Schneiderman, R; Kirkby, S; Turenne, W; Greenspan, J

2009-08-01

To evaluate the relationship of weight of preterm infants when first placed into an open crib with days to full oral feedings, growth velocity and length of stay (LOS), and to identify unwarranted variation in incubator weaning after adjusting for severity indices. A retrospective study using the ParadigmHealth neonatal database from 2003 to 2006 reviewed incubator weaning to an open crib in appropriate-for-gestational-age (AGA) infants from 22 to weeks gestation. Primary outcome measurements included days to full oral (PO) feeding, weight gain from open crib to discharge and length of stay. Models were severity adjusted. To understand hospital practice variation, we also used a regression model to estimate the weight at open crib for the top 10 volume hospitals. In all 2908 infants met the inclusion criteria for the study. Their mean weight at open crib was 1850 g. On average every additional 100 g an infant weighed at the open crib was associated with increased time to full PO feeding by 0.8 days, decreased weight gained per day by 1 gram and increased LOS by 0.9 days. For the top 10 volume hospitals, severity variables alone accounted for 9% of the variation in weight at open crib, whereas the hospital in which the baby was treated accounted for an additional 19% of the variation. Even after controlling for severity, significant practice variation exists in weaning to an open crib, leading to potential delays in achieving full-volume oral feeds, decreased growth velocity and prolonged LOS.

Dietary Polyphenol Intake Estimated by 7-Day Dietary Records among Japanese Male Workers: Evaluation of the Within- and Between-Individual Variation.

PubMed

Taguchi, Chie; Kishimoto, Yoshimi; Fukushima, Yoichi; Saita, Emi; Tanaka, Miori; Takahashi, Yoshinari; Masuda, Yasunobu; Goda, Toshinao; Kondo, Kazuo

2017-01-01

Polyphenol intake has been estimated in some populations; however, information about day-to-day and individual differences in polyphenol intake has not been well-evaluated. In this study, we aimed to examine within- and between-individual variation in polyphenol intake in Japanese male workers. First, 56 male subjects (aged 37.9±10.4 y) completed detailed 7-d dietary records (DR). We then calculated their total polyphenol intake using our polyphenol content database and the within- and between-individual variations. We also estimated the minimum number of days of dietary assessment required both to rank individuals within a group and to assess an individual's usual polyphenol intake with acceptable accuracy. The estimated daily total polyphenol intake was 965±471 mg/d, which was largely sourced from beverages. The day-to-day variation (CV w ) for polyphenol intake was 43.6%, and the variation between the individuals in the population (CV b ) for polyphenol intake was 45.9%. A 4-d DR was required to rank individuals within a group with high correlation coefficients (r=0.9), and a 19-d DR was required to assess the individual's usual polyphenol intake with 20% deviation. The CV w for polyphenol intake was intermediate between those of the other nutrients, but the CV b for polyphenol intake was largest among the nutrients. These results suggest that the dietary intake of polyphenols should be carefully estimated considering its within- and between-individual variation.

HECLIB. Volume 2: HECDSS Subroutines Programmer’s Manual

DTIC Science & Technology

1991-05-01

algorithm and hierarchical design for database accesses. This algorithm provides quick access to data sets and an efficient means of adding new data set...Description of How DSS Works DSS version 6 utilizes a modified hash algorithm based upon the pathname to store and retrieve data. This structure allows...balancing disk space and record access times. A variation in this algorithm is for "stable" files. In a stable file, a hash table is not utilized

Contribution for an African autosomic STR database (AmpF/STR Identifiler and Powerplex 16 System) and a report on genotypic variations.

PubMed

Alves, Cíntia; Gusmão, Leonor; Damasceno, Albertino; Soares, Benilde; Amorim, António

2004-01-28

Allele frequencies, together with some parameters of forensic interest, for 17 STRs included in the AmpF/STR Identifiler (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) and Powerplex 16 System (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, Penta D, Penta E, TH01, TPO and VWA) were estimated from a sample of 135-144 unrelated individuals from Mozambique. No deviations from Hardy-Weinberg equilibrium were observed with the exception of the FGA locus (using the Bonferroni correction for the number of loci analysed, the departure observed at this locus was not significant). Comparative analyses between our population data and other African databases, namely Promega's African-Americans, AB Applied Biosystems African-Americans and two other population samples from Mozambique and Guiné Bissau, are presented and discussed. Genotype inconsistencies between both commercial kits (for D16S539 and D8S1179) and other genotypic variations (three-banded allele patterns for TPO) are also reported.

What difference does a day make? Examining temporal variations in partner maltreatment.

PubMed

McCarthy, Randy J; Rabenhorst, Mandy M; Milner, Joel S; Travis, Wendy J; Collins, Pamela S

2014-06-01

Routine activities (RA) theory posits that changes in people's typical daily activities covary with increases or decreases in criminal behaviors, including, but not limited to, partner maltreatment. Using a large clinical database, we examined temporal variations among 24,460 incidents of confirmed partner maltreatment across an 11-year period within the U.S. Air Force (USAF). Specifically, we created regression models that predicted the number of partner maltreatment incidents per day. In addition to several control variables, we coded temporal variables for days of the week, month, year, and several significant days (e.g., holidays, Super Bowl Sunday), which allowed us to examine the independent influence of these variables on partner maltreatment prevalence. While accounting for the influence of all other study variables, we observed significant increases in partner maltreatment for weekend days, New Year's Day, Independence Day, and Super Bowl Sunday. Similar results were found for partner maltreatment incidents involving offender alcohol/drug use. Furthermore, the proportion of incidents involving offender alcohol/drug use increased on New Year's Day and Independence Day. Consistent with RA theory and data from civilian samples, the current results indicate that certain days are associated with increased incidents of partner maltreatment within the USAF. These findings should be used to inform future preventive efforts. PsycINFO Database Record (c) 2014 APA, all rights reserved.

A Combined Gravity Compensation Method for INS Using the Simplified Gravity Model and Gravity Database.

PubMed

Zhou, Xiao; Yang, Gongliu; Wang, Jing; Wen, Zeyang

2018-05-14

In recent decades, gravity compensation has become an important way to reduce the position error of an inertial navigation system (INS), especially for a high-precision INS, because of the extensive application of high precision inertial sensors (accelerometers and gyros). This paper first deducts the INS's solution error considering gravity disturbance and simulates the results. Meanwhile, this paper proposes a combined gravity compensation method using a simplified gravity model and gravity database. This new combined method consists of two steps all together. Step 1 subtracts the normal gravity using a simplified gravity model. Step 2 first obtains the gravity disturbance on the trajectory of the carrier with the help of ELM training based on the measured gravity data (provided by Institute of Geodesy and Geophysics; Chinese Academy of sciences), and then compensates it into the error equations of the INS, considering the gravity disturbance, to further improve the navigation accuracy. The effectiveness and feasibility of this new gravity compensation method for the INS are verified through vehicle tests in two different regions; one is in flat terrain with mild gravity variation and the other is in complex terrain with fierce gravity variation. During 2 h vehicle tests, the positioning accuracy of two tests can improve by 20% and 38% respectively, after the gravity is compensated by the proposed method.

A Combined Gravity Compensation Method for INS Using the Simplified Gravity Model and Gravity Database

PubMed Central

Zhou, Xiao; Yang, Gongliu; Wang, Jing; Wen, Zeyang

2018-01-01

In recent decades, gravity compensation has become an important way to reduce the position error of an inertial navigation system (INS), especially for a high-precision INS, because of the extensive application of high precision inertial sensors (accelerometers and gyros). This paper first deducts the INS’s solution error considering gravity disturbance and simulates the results. Meanwhile, this paper proposes a combined gravity compensation method using a simplified gravity model and gravity database. This new combined method consists of two steps all together. Step 1 subtracts the normal gravity using a simplified gravity model. Step 2 first obtains the gravity disturbance on the trajectory of the carrier with the help of ELM training based on the measured gravity data (provided by Institute of Geodesy and Geophysics; Chinese Academy of sciences), and then compensates it into the error equations of the INS, considering the gravity disturbance, to further improve the navigation accuracy. The effectiveness and feasibility of this new gravity compensation method for the INS are verified through vehicle tests in two different regions; one is in flat terrain with mild gravity variation and the other is in complex terrain with fierce gravity variation. During 2 h vehicle tests, the positioning accuracy of two tests can improve by 20% and 38% respectively, after the gravity is compensated by the proposed method. PMID:29757983

Carbon - Bulk Density Relationships for Highly Weathered Soils of the Americas

NASA Astrophysics Data System (ADS)

Nave, L. E.

2014-12-01

Soils are dynamic natural bodies composed of mineral and organic materials. As a result of this mixed composition, essential properties of soils such as their apparent density, organic and mineral contents are typically correlated. Negative relationships between bulk density (Db) and organic matter concentration provide well-known examples across a broad range of soils, and such quantitative relationships among soil properties are useful for a variety of applications. First, gap-filling or data interpolation often are necessary to develop large soil carbon (C) datasets; furthermore, limitations of access to analytical instruments may preclude C determinations for every soil sample. In such cases, equations to derive soil C concentrations from basic measures of soil mass, volume, and density offer significant potential for purposes of soil C stock estimation. To facilitate estimation of soil C stocks on highly weathered soils of the Americas, I used observations from the International Soil Carbon Network (ISCN) database to develop carbon - bulk density prediction equations for Oxisols and Ultisols. Within a small sample set of georeferenced Oxisols (n=89), 29% of the variation in A horizon C concentrations can be predicted from Db. Including the A-horizon sand content improves predictive capacity to 35%. B horizon C concentrations (n=285) were best predicted by Db and clay content, but were more variable than A-horizons (only 10% of variation explained by linear regression). Among Ultisols, a larger sample set allowed investigation of specific horizons of interest. For example, C concentrations of plowed A (Ap) horizons are predictable based on Db, sand and silt contents (n=804, r2=0.38); gleyed argillic (Btg) horizon concentrations are predictable from Db, sand and clay contents (n=190, r2=0.23). Because soil C stock estimates are more sensitive to variation in soil mass and volume determinations than to variation in C concentration, prediction equations such as these may be used on carefully collected samples to constrain soil C stocks. The geo-referenced ISCN database allows users the opportunity to derive similar predictive relationships among measured soil parameters; continued input of new datasets from highly weathered soils of the Americas will improve the precision of these prediction equations.

Season affects body composition and estimation of fluid overload in haemodialysis patients: variations in body composition; a survey from the European MONDO database.

PubMed

Broers, Natascha J H; Usvyat, Len A; Marcelli, Daniele; Bayh, Inga; Scatizzi, Laura; Canaud, Bernard; van der Sande, Frank M; Kotanko, Peter; Moissl, Ulrich; Kooman, Jeroen P

2015-04-01

Seasonal variations in blood pressure (BP) and inter-dialytic weight gain (IDWG) are well established in dialysis patients. However, no study has assessed changes in body composition (BC) in this population. In this survey, seasonal variations in fat mass (FM), lean tissue mass (LTM), extracellular water (ECW) and fluid overload (FO) were assessed in 42 099 dialysis patients (mean age 61.2 years, 58% males) from the Fresenius Medical Care Europe database, as part of the MONitoring Dialysis Outcomes (MONDO) consortium, in relation to other nutritional parameters, IDWG and BP. BC was assessed by a body composition monitor (BCM®, Fresenius Medical Care, Bad Homburg, Germany). FM was highest in winter and lowest in summer (▵FM -1.17 kg; P < 0.001), whereas LTM was lowest during winter and highest in summer (▵LTM 0.86 kg; P < 0.0001). ECW and FO were lowest in winter, and highest in spring (▵ECW: 0.13 L; P < 0.0001, ▵FO: 0.31 L; P < 0.0001) and summer (▵ECW: 0.15 L; P < 0.0001 and ▵FO: 0.2 L; P < 0.0001), despite a higher systolic blood pressure (SBP; 136.7 ± 17.4 mmHg) and IDWG (3.0 ± 1.1 kg) during winter. C-reactive protein (CRP), serum sodium and haemoglobin levels were highest in winter, whereas serum albumin was lowest in fall. Normalized protein catabolic rate (nPCR) was lowest in winter and matched variations in BC only to a minor degree. BC and hydration state, assessed by bio-impedance spectroscopy, follows a seasonal pattern which may be of relevance for the estimation of target weight, and for the interpretation of longitudinal studies including estimates of BC. Whether these changes should lead to therapeutic interventions could be the focus of future studies. © The Author 2014. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

A simple genetic architecture underlies morphological variation in dogs.

PubMed

Boyko, Adam R; Quignon, Pascale; Li, Lin; Schoenebeck, Jeffrey J; Degenhardt, Jeremiah D; Lohmueller, Kirk E; Zhao, Keyan; Brisbin, Abra; Parker, Heidi G; vonHoldt, Bridgett M; Cargill, Michele; Auton, Adam; Reynolds, Andy; Elkahloun, Abdel G; Castelhano, Marta; Mosher, Dana S; Sutter, Nathan B; Johnson, Gary S; Novembre, John; Hubisz, Melissa J; Siepel, Adam; Wayne, Robert K; Bustamante, Carlos D; Ostrander, Elaine A

2010-08-10

Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (< or = 3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species.

Variations in lake and reservoir storage associated with Middle East droughts

NASA Astrophysics Data System (ADS)

Marlier, M. E.; Kim, J.; Khandelwal, A.; Karpatne, A.; Kumar, V.; Zhou, T.; Lettenmaier, D. P.

2016-12-01

The Middle East experienced severe drought conditions from 1998-2000 and again from 2007-2009; during both periods cumulative monthly precipitation averaged over the Fertile Crescent fell below the 10th percentile of the 1940-2009 climatology. The severity of the drought has been linked to rising greenhouse gas concentrations and may have contributed to the conflict in Syria. We use multiple sources of satellite data to examine how these droughts impacted surface water storage in Turkey, Syria, Iran, and Iraq. We first apply a MODIS-based classification algorithm to map variations in the areal extent of lakes and reservoirs from 2000-2015 at 500 m spatial resolution and nominal eight-day intervals. We combine this information with estimates of changes in water levels from several archives of radar altimetry products (Global Reservoir and Lake Monitor (G-REALM), Database for Hydrological Time Series of Inland Waters (DAHITI), and HydroWeb) for 16 lakes and reservoirs across the region at 10-day and/or 35-day intervals, and then estimate storage variations as far back as the 1990s. We find strong correlations between surface areal extent and water level variations, with preliminary results for reservoirs ranging from R=0.30-0.98 (median R=0.84). Taken together, we use this information to explore variations in temporal trends in water storage across the region.

Seasonal variation in myocardial infarction is limited to patients with ST-elevations on admission.

PubMed

Leibowitz, David; Planer, David; Weiss, Teddy; Rott, David

2007-01-01

Previous studies have demonstrated seasonal variation in the incidence of acute myocardial infarction (AMI) with an increase in cases during the winter months. However, they did not assess whether ST-elevation MI (STEMI) and non-ST-elevation MI (NSTEMI) exhibit similar changes. The object of this study was to compare the seasonal variation of STEMI and NSTEMI. All patients who presented with AMI and underwent coronary angiography within seven days of admission were identified via the institutional database. STEMI diagnosis required admission ECG demonstrating ST elevation in at least two continguous leads. All AMIs not meeting criteria for STEMI were defined as NSTEMI. Patients were divided into monthly and seasonal groups based on the date of admission with MI. A total of 784 patients were included: 549 patients with STEMI and 235 with NSTEMI. When STEMI patients were analyzed by season, there were 170 patients (31%) in the winter months, a statistically significant difference of excess MI (p<0.005). When NSTEMI patients were analyzed, there were 62 patients (26%) in the winter with no statistically significant difference in the seasonal variation. Our findings suggest that the previously noted seasonal variation in the incidence of AMI is limited to patients presenting with STEMI, and that there are important physiological differences between STEMI and NSTEMI, the nature of which remains to be elucidated.

A Simple Genetic Architecture Underlies Morphological Variation in Dogs

PubMed Central

Schoenebeck, Jeffrey J.; Degenhardt, Jeremiah D.; Lohmueller, Kirk E.; Zhao, Keyan; Brisbin, Abra; Parker, Heidi G.; vonHoldt, Bridgett M.; Cargill, Michele; Auton, Adam; Reynolds, Andy; Elkahloun, Abdel G.; Castelhano, Marta; Mosher, Dana S.; Sutter, Nathan B.; Johnson, Gary S.; Novembre, John; Hubisz, Melissa J.; Siepel, Adam; Wayne, Robert K.; Bustamante, Carlos D.; Ostrander, Elaine A.

2010-01-01

Domestic dogs exhibit tremendous phenotypic diversity, including a greater variation in body size than any other terrestrial mammal. Here, we generate a high density map of canine genetic variation by genotyping 915 dogs from 80 domestic dog breeds, 83 wild canids, and 10 outbred African shelter dogs across 60,968 single-nucleotide polymorphisms (SNPs). Coupling this genomic resource with external measurements from breed standards and individuals as well as skeletal measurements from museum specimens, we identify 51 regions of the dog genome associated with phenotypic variation among breeds in 57 traits. The complex traits include average breed body size and external body dimensions and cranial, dental, and long bone shape and size with and without allometric scaling. In contrast to the results from association mapping of quantitative traits in humans and domesticated plants, we find that across dog breeds, a small number of quantitative trait loci (≤3) explain the majority of phenotypic variation for most of the traits we studied. In addition, many genomic regions show signatures of recent selection, with most of the highly differentiated regions being associated with breed-defining traits such as body size, coat characteristics, and ear floppiness. Our results demonstrate the efficacy of mapping multiple traits in the domestic dog using a database of genotyped individuals and highlight the important role human-directed selection has played in altering the genetic architecture of key traits in this important species. PMID:20711490

Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth.

PubMed

Gao, Lei; He, Chongbo; Bao, Xiangbo; Tian, Meilin; Ma, Zhen

2017-01-01

The sea cucumber (Apostichopus japonicus) is an economically important aquaculture species in China. However, the serious individual growth variation often caused financial losses to farmers and the genetic mechanisms are poorly understood. In the present study, the extensively analysis at the transcriptome level for individual growth variation in sea cucumber was carried out. A total of 118946 unigenes were assembled from 255861 transcripts, with N50 of 1700. Of all unigenes, about 23% were identified with at least one significant match to known databases. In all four pair of comparison, 1840 genes were found to be expressed differently. Global hypometabolism was found to be occurred in the slow growing population, based on which the hypothesis was raised that growth retardation in individual growth variation of sea cucumber is one type of dormancy which is used to be against to adverse circumstances. Besides, the pathways such as ECM-receptor interaction and focal adhesion were enriched in the maintenance of cell and tissue structure and communication. Further, 76645 SSRs, 765242 SNPs and 146886 ins-dels were detected in the current study providing an extensive set of data for future studies of genetic mapping and selective breeding. In summary, these results will provides deep insight into the molecular basis of individual growth variation in marine invertebrates, and be valuable for understanding the physiological differences of growth process.

Variations in measured performance of CAD schemes due to database composition and scoring protocol

NASA Astrophysics Data System (ADS)

Nishikawa, Robert M.; Yarusso, Laura M.

1998-06-01

There is now a large effort towards developing computer- aided diagnosis (CAD) techniques. It is important to be able to compare performance of different approaches to be able to determine which ones are the most efficacious. There are currently a number of barriers preventing meaningful (statistical) comparisons, two of which are discussed in this paper: database composition and scoring protocol. We have examined how the choice of cases used to test a CAD scheme can affect its performance. We found that our computer scheme varied between a sensitivity of 100% to 77%, at a false-positive rate of 1.0 per image, with only 100% change in the composition of the database. To evaluate the performance of a CAD scheme the output of the computer must be graded. There are a number of different criteria that are being used by different investigators. We have found that for the same set of detection results, the measured sensitivity can be between 40 - 90% depending on the scoring methodology. Clearly consensus must be reached on these two issues in order for the field to make rapid progress. As it stands now, it is not possible to make meaningful comparisons of different techniques.

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

PubMed

Barrett, Tanya; Troup, Dennis B; Wilhite, Stephen E; Ledoux, Pierre; Evangelista, Carlos; Kim, Irene F; Tomashevsky, Maxim; Marshall, Kimberly A; Phillippy, Katherine H; Sherman, Patti M; Muertter, Rolf N; Holko, Michelle; Ayanbule, Oluwabukunmi; Yefanov, Andrey; Soboleva, Alexandra

2011-01-01

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

Automatic image database generation from CAD for 3D object recognition

NASA Astrophysics Data System (ADS)

Sardana, Harish K.; Daemi, Mohammad F.; Ibrahim, Mohammad K.

1993-06-01

The development and evaluation of Multiple-View 3-D object recognition systems is based on a large set of model images. Due to the various advantages of using CAD, it is becoming more and more practical to use existing CAD data in computer vision systems. Current PC- level CAD systems are capable of providing physical image modelling and rendering involving positional variations in cameras, light sources etc. We have formulated a modular scheme for automatic generation of various aspects (views) of the objects in a model based 3-D object recognition system. These views are generated at desired orientations on the unit Gaussian sphere. With a suitable network file sharing system (NFS), the images can directly be stored on a database located on a file server. This paper presents the image modelling solutions using CAD in relation to multiple-view approach. Our modular scheme for data conversion and automatic image database storage for such a system is discussed. We have used this approach in 3-D polyhedron recognition. An overview of the results, advantages and limitations of using CAD data and conclusions using such as scheme are also presented.

STOPGAP: a database for systematic target opportunity assessment by genetic association predictions.

PubMed

Shen, Judong; Song, Kijoung; Slater, Andrew J; Ferrero, Enrico; Nelson, Matthew R

2017-09-01

We developed the STOPGAP (Systematic Target OPportunity assessment by Genetic Association Predictions) database, an extensive catalog of human genetic associations mapped to effector gene candidates. STOPGAP draws on a variety of publicly available GWAS associations, linkage disequilibrium (LD) measures, functional genomic and variant annotation sources. Algorithms were developed to merge the association data, partition associations into non-overlapping LD clusters, map variants to genes and produce a variant-to-gene score used to rank the relative confidence among potential effector genes. This database can be used for a multitude of investigations into the genes and genetic mechanisms underlying inter-individual variation in human traits, as well as supporting drug discovery applications. Shell, R, Perl and Python scripts and STOPGAP R data files (version 2.5.1 at publication) are available at https://github.com/StatGenPRD/STOPGAP . Some of the most useful STOPGAP fields can be queried through an R Shiny web application at http://stopgapwebapp.com . matthew.r.nelson@gsk.com. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Biosamples, genomics, and human rights: context and content of Iceland's Biobanks Act.

PubMed

Winickoff, D E

2001-01-01

In recent years, human DNA sampling and collection has accelerated without the development of enforceable rules protecting the human rights of donors. The need for regulation of biobanking is especially acute in Iceland, whose parliament has granted a for-profit corporation, deCODE Genetics, an exclusive license to create a centralized database of health records for studies on human genetic variation. Until recently, how deCODE Genetics would get genetic material for its genotypic-phenotypic database remained unclear. However, in May 2000, the Icelandic Parliament passed the Icelandic Biobanks Act, the world's earliest attempt to construct binding rules for the use of biobanks in scientific research. Unfortunately, Iceland has lost an opportunity for bringing clear and ethically sound standards to the use of human biological samples in deCODE's database and in other projects: the Biobanks Act has extended a notion of "presumed consent" from the use of medical records to the use of patients' biological samples; worse, the act has made it possible--perhaps likely--that a donor's wish to withdraw his/her sample will be ignored. Inadequacies in the Act's legislative process help account for these deficiencies in the protection of donor autonomy.

A solar radiation database for Chile.

PubMed

Molina, Alejandra; Falvey, Mark; Rondanelli, Roberto

2017-11-01

Chile hosts some of the sunniest places on earth, which has led to a growing solar energy industry in recent years. However, the lack of high resolution measurements of solar irradiance becomes a critical obstacle for both financing and design of solar installations. Besides the Atacama Desert, Chile displays a large array of "solar climates" due to large latitude and altitude variations, and so provides a useful testbed for the development of solar irradiance maps. Here a new public database for surface solar irradiance over Chile is presented. This database includes hourly irradiance from 2004 to 2016 at 90 m horizontal resolution over continental Chile. Our results are based on global reanalysis data to force a radiative transfer model for clear sky solar irradiance and an empirical model based on geostationary satellite data for cloudy conditions. The results have been validated using 140 surface solar irradiance stations throughout the country. Model mean percentage error in hourly time series of global horizontal irradiance is only 0.73%, considering both clear and cloudy days. The simplicity and accuracy of the model over a wide range of solar conditions provides confidence that the model can be easily generalized to other regions of the world.

A Southern Ocean variability study using the Argo-based Model for Investigation of the Global Ocean (AMIGO)

NASA Astrophysics Data System (ADS)

Lebedev, Konstantin

2017-04-01

The era of satellite observations of the ocean surface that started at the end of the 20th century and the development of the Argo project in the first years of the 21st century, designed to collect information of the upper 2000 m of the ocean using satellites, provides unique opportunities for continuous monitoring of the Global Ocean state. Starting from 2005, measurements with the Argo floats have been performed over the majority of the World Ocean. In November 2007, the Argo program reached coverage of 3000 simultaneously operating floats (one float in a three-degree square) planned during the development of the program. Currently, 4000 Argo floats autonomously profile the upper 2000-m water column of the ocean from Antarctica to Spitsbergen increasing World Ocean temperature and salinity databases by 12000 profiles per month. This makes it possible to solve problems on reconstructing and monitoring the ocean state on an almost real-time basis, study the ocean dynamics, obtain reasonable estimates of the climatic state of the ocean in the last decade and estimate existing intraclimatic trends. We present the newly developed Argo-Based Model for Investigation of the Global Ocean (AMIGO), which consists of a block for variational interpolation of the profiles of drifting Argo floats to a regular grid and a block for model hydrodynamic adjustment of variationally interpolated fields. Such a method makes it possible to obtain a full set of oceanographic characteristics - temperature, salinity, density, and current velocity - using irregularly located Argo measurements (the principle of the variational interpolation technique entails minimization of the misfit between the interpolated fields defined on the regular grid and irregularly distributed data; hence the optimal solution passes as close to the data as possible). The simulations were performed for the entire globe limited in the north by 85.5° N using 1° grid spacing in both longitude and latitude. At the depths exceeding 2000 m, in which Argo data are lacking, the temperature and salinity data were taken from the WOA-09 database. The constant temperature and salinity values from the Argo data for the corresponding month (year, season) derived using the variational technique described above were specified as the boundary conditions at the ocean surface. The constant wind stress in the corresponding month (year, season) was specified from the ECMWF ERA-Interim reanalysis data. The mass, salt, and heat transports over several regions of the Antarctic Circumpolar Current (ACC) and at its northern boundary (35° S) were calculated, seasonal and intra-decadal variation of the transports was studied. The calculations cover the 12-year period from 2005 to 2016. The AMIGO database enjoys free public access on the Internet at: http://argo.ocean.ru/. The results are represented as monthly, seasonal, and annual data and climatological mean fields. The spatial resolution of the data is one degree in latitude and longitude, and the temporal resolution is one month. The work was supported by the Russian Science Foundation (project 16-17-10149).

Drainage investment and wetland loss: an analysis of the national resources inventory data

USGS Publications Warehouse

Douglas, Aaron J.; Johnson, Richard L.

1994-01-01

The United States Soil Conservation Service (SCS) conducts a survey for the purpose of establishing an agricultural land use database. This survey is called the National Resources Inventory (NRI) database. The complex NRI land classification system, in conjunction with the quantitative information gathered by the survey, has numerous applications. The current paper uses the wetland area data gathered by the NRI in 1982 and 1987 to examine empirically the factors that generate wetland loss in the United States. The cross-section regression models listed here use the quantity of wetlands, the stock of drainage capital, the realty value of farmland and drainage costs to explain most of the cross-state variation in wetland loss rates. Wetlands preservation efforts by federal agencies assume that pecuniary economic factors play a decisive role in wetland drainage. The empirical models tested in the present paper validate this assumption.

Update on Genomic Databases and Resources at the National Center for Biotechnology Information.

PubMed

Tatusova, Tatiana

2016-01-01

The National Center for Biotechnology Information (NCBI), as a primary public repository of genomic sequence data, collects and maintains enormous amounts of heterogeneous data. Data for genomes, genes, gene expressions, gene variation, gene families, proteins, and protein domains are integrated with the analytical, search, and retrieval resources through the NCBI website, text-based search and retrieval system, provides a fast and easy way to navigate across diverse biological databases.Comparative genome analysis tools lead to further understanding of evolution processes quickening the pace of discovery. Recent technological innovations have ignited an explosion in genome sequencing that has fundamentally changed our understanding of the biology of living organisms. This huge increase in DNA sequence data presents new challenges for the information management system and the visualization tools. New strategies have been designed to bring an order to this genome sequence shockwave and improve the usability of associated data.

The Saccharomyces Genome Database Variant Viewer.

PubMed

Sheppard, Travis K; Hitz, Benjamin C; Engel, Stacia R; Song, Giltae; Balakrishnan, Rama; Binkley, Gail; Costanzo, Maria C; Dalusag, Kyla S; Demeter, Janos; Hellerstedt, Sage T; Karra, Kalpana; Nash, Robert S; Paskov, Kelley M; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Cherry, J Michael

2016-01-04

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Work measurement for estimating food preparation time of a bioregenerative diet

NASA Technical Reports Server (NTRS)

Olabi, Ammar; Hunter, Jean; Jackson, Peter; Segal, Michele; Spies, Rupert; Wang, Carolyn; Lau, Christina; Ong, Christopher; Alexander, Conor; Raskob, Evan;

A k-Vector Approach to Sampling, Interpolation, and Approximation

NASA Astrophysics Data System (ADS)

Mortari, Daniele; Rogers, Jonathan

2013-12-01

The k-vector search technique is a method designed to perform extremely fast range searching of large databases at computational cost independent of the size of the database. k-vector search algorithms have historically found application in satellite star-tracker navigation systems which index very large star catalogues repeatedly in the process of attitude estimation. Recently, the k-vector search algorithm has been applied to numerous other problem areas including non-uniform random variate sampling, interpolation of 1-D or 2-D tables, nonlinear function inversion, and solution of systems of nonlinear equations. This paper presents algorithms in which the k-vector search technique is used to solve each of these problems in a computationally-efficient manner. In instances where these tasks must be performed repeatedly on a static (or nearly-static) data set, the proposed k-vector-based algorithms offer an extremely fast solution technique that outperforms standard methods.

Mixing characterization of highly underexpanded fluid jets with real gas expansion

NASA Astrophysics Data System (ADS)

Förster, Felix J.; Baab, Steffen; Steinhausen, Christoph; Lamanna, Grazia; Ewart, Paul; Weigand, Bernhard

2018-03-01

We report a comprehensive speed of sound database for multi-component mixing of underexpanded fuel jets with real gas expansion. The paper presents several reference test cases with well-defined experimental conditions providing quantitative data for validation of computational simulations. Two injectant fluids, fundamentally different with respect to their critical properties, are brought to supercritical state and discharged into cold nitrogen at different pressures. The database features a wide range of nozzle pressure ratios covering the regimes that are generally classified as highly and extremely highly underexpanded jets. Further variation is introduced by investigating different injection temperatures. Measurements are obtained along the centerline at different axial positions. In addition, an adiabatic mixing model based on non-ideal thermodynamic mixture properties is used to extract mixture compositions from the experimental speed of sound data. The concentration data obtained are complemented by existing experimental data and represented by an empirical fit.

Cluster analysis of word frequency dynamics

NASA Astrophysics Data System (ADS)

Maslennikova, Yu S.; Bochkarev, V. V.; Belashova, I. A.

2015-01-01

This paper describes the analysis and modelling of word usage frequency time series. During one of previous studies, an assumption was put forward that all word usage frequencies have uniform dynamics approaching the shape of a Gaussian function. This assumption can be checked using the frequency dictionaries of the Google Books Ngram database. This database includes 5.2 million books published between 1500 and 2008. The corpus contains over 500 billion words in American English, British English, French, German, Spanish, Russian, Hebrew, and Chinese. We clustered time series of word usage frequencies using a Kohonen neural network. The similarity between input vectors was estimated using several algorithms. As a result of the neural network training procedure, more than ten different forms of time series were found. They describe the dynamics of word usage frequencies from birth to death of individual words. Different groups of word forms were found to have different dynamics of word usage frequency variations.

Global distribution of soil organic carbon - Part 1: Masses and frequency distributions of SOC stocks for the tropics, permafrost regions, wetlands, and the world

NASA Astrophysics Data System (ADS)

Köchy, M.; Hiederer, R.; Freibauer, A.

2015-04-01

The global soil organic carbon (SOC) mass is relevant for the carbon cycle budget and thus atmospheric carbon concentrations. We review current estimates of SOC stocks and mass (stock × area) in wetlands, permafrost and tropical regions and the world in the upper 1 m of soil. The Harmonized World Soil Database (HWSD) v.1.2 provides one of the most recent and coherent global data sets of SOC, giving a total mass of 2476 Pg when using the original values for bulk density. Adjusting the HWSD's bulk density (BD) of soil high in organic carbon results in a mass of 1230 Pg, and additionally setting the BD of Histosols to 0.1 g cm-3 (typical of peat soils), results in a mass of 1062 Pg. The uncertainty in BD of Histosols alone introduces a range of -56 to +180 Pg C into the estimate of global SOC mass in the top 1 m, larger than estimates of global soil respiration. We report the spatial distribution of SOC stocks per 0.5 arcminutes; the areal masses of SOC; and the quantiles of SOC stocks by continents, wetland types, and permafrost types. Depending on the definition of "wetland", wetland soils contain between 82 and 158 Pg SOC. With more detailed estimates for permafrost from the Northern Circumpolar Soil Carbon Database (496 Pg SOC) and tropical peatland carbon incorporated, global soils contain 1325 Pg SOC in the upper 1 m, including 421 Pg in tropical soils, whereof 40 Pg occurs in tropical wetlands. Global SOC amounts to just under 3000 Pg when estimates for deeper soil layers are included. Variability in estimates is due to variation in definitions of soil units, differences in soil property databases, scarcity of information about soil carbon at depths > 1 m in peatlands, and variation in definitions of "peatland".

SU-E-J-164: Estimation of DVH Variation for PTV Due to Interfraction Organ Motion in Prostate VMAT Using Gaussian Error Function

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

Lewis, C; Jiang, R; Chow, J

2015-06-15

Purpose: We developed a method to predict the change of DVH for PTV due to interfraction organ motion in prostate VMAT without repeating the CT scan and treatment planning. The method is based on a pre-calculated patient database with DVH curves of PTV modelled by the Gaussian error function (GEF). Methods: For a group of 30 patients with different prostate sizes, their VMAT plans were recalculated by shifting their PTVs 1 cm with 10 increments in the anterior-posterior, left-right and superior-inferior directions. The DVH curve of PTV in each replan was then fitted by the GEF to determine parameters describingmore » the shape of curve. Information of parameters, varying with the DVH change due to prostate motion for different prostate sizes, was analyzed and stored in a database of a program written by MATLAB. Results: To predict a new DVH for PTV due to prostate interfraction motion, prostate size and shift distance with direction were input to the program. Parameters modelling the DVH for PTV were determined based on the pre-calculated patient dataset. From the new parameters, DVH curves of PTVs with and without considering the prostate motion were plotted for comparison. The program was verified with different prostate cases involving interfraction prostate shifts and replans. Conclusion: Variation of DVH for PTV in prostate VMAT can be predicted using a pre-calculated patient database with DVH curve fitting. The computing time is fast because CT rescan and replan are not required. This quick DVH estimation can help radiation staff to determine if the changed PTV coverage due to prostate shift is tolerable in the treatment. However, it should be noted that the program can only consider prostate interfraction motions along three axes, and is restricted to prostate VMAT plan using the same plan script in the treatment planning system.« less

CFD in the 1980's from one point of view

NASA Technical Reports Server (NTRS)

Lomax, Harvard

1991-01-01

The present interpretive treatment of the development history of CFD in the 1980s gives attention to advancements in such algorithmic techniques as flux Jacobian-based upwind differencing, total variation-diminishing and essentially nonoscillatory schemes, multigrid methods, unstructured grids, and nonrectangular structured grids. At the same time, computational turbulence research gave attention to turbulence modeling on the bases of increasingly powerful supercomputers and meticulously constructed databases. The major future developments in CFD will encompass such capabilities as structured and unstructured three-dimensional grids.

The RAND Online Measure Repository for Evaluating Psychological Health and Traumatic Brain Injury Programs. The RAND Toolkit, Volume 2

DTIC Science & Technology

2014-01-01

tempo may raise the risk for mental health challenges. During this time, the U.S. Department of Defense (DoD) has implemented numerous programs to...and were based on the constraints of each electronic database. However, most searches were variations on a basic three-category format: The first...Gerontology, 1983, 38: 111–116. Iannuzzo RW, Jaeger J, Goldberg JF, Kafantaris V, Sublette ME. “Development and Reliability of the Ham-D/MADRS

Where does good quality qualitative health care research get published?

PubMed

Richardson, Jane C; Liddle, Jennifer

2017-09-01

This short report aims to give some insight into current publication patterns for high-quality qualitative health research, using the Research Excellence Framework (REF) 2014 database. We explored patterns of publication by range and type of journal, by date and by methodological focus. We also looked at variations between the publications submitted to different Units of Assessment, focussing particularly on the one most closely aligned with our own research area of primary care. Our brief analysis demonstrates that general medical/health journals with high impact factors are the dominant routes of publication, but there is variation according to the methodological approach adopted by articles. The number of qualitative health articles submitted to REF 2014 overall was small, and even more so for articles based on mixed methods research, qualitative methodology or reviews/syntheses that included qualitative articles.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

PubMed

Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

PubMed Central

Zheng, Wenning; Mutha, Naresh V.R.; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

Validation of the 'United Registries for Clinical Assessment and Research' [UR-CARE], a European Online Registry for Clinical Care and Research in Inflammatory Bowel Disease.

PubMed

Burisch, Johan; Gisbert, Javier P; Siegmund, Britta; Bettenworth, Dominik; Thomsen, Sandra Bohn; Cleynen, Isabelle; Cremer, Anneline; Ding, Nik John Sheng; Furfaro, Federica; Galanopoulos, Michail; Grunert, Philip Christian; Hanzel, Jurij; Ivanovski, Tamara Knezevic; Krustins, Eduards; Noor, Nurulamin; O'Morain, Neil; Rodríguez-Lago, Iago; Scharl, Michael; Tua, Julia; Uzzan, Mathieu; Ali Yassin, Nuha; Baert, Filip; Langholz, Ebbe

2018-04-27

The 'United Registries for Clinical Assessment and Research' [UR-CARE] database is an initiative of the European Crohn's and Colitis Organisation [ECCO] to facilitate daily patient care and research studies in inflammatory bowel disease [IBD]. Herein, we sought to validate the database by using fictional case histories of patients with IBD that were to be entered by observers of varying experience in IBD. Nineteen observers entered five patient case histories into the database. After 6 weeks, all observers entered the same case histories again. For each case history, 20 key variables were selected to calculate the accuracy for each observer. We assumed that the database was such that ≥ 90% of the entered data would be correct. The overall proportion of correctly entered data was calculated using a beta-binomial regression model to account for inter-observer variation and compared to the expected level of validity. Re-test reliability was assessed using McNemar's test. For all case histories, the overall proportion of correctly entered items and their confidence intervals included the target of 90% (Case 1: 92% [88-94%]; Case 2: 87% [83-91%]; Case 3: 93% [90-95%]; Case 4: 97% [94-99%]; Case 5: 91% [87-93%]). These numbers did not differ significantly from those found 6 weeks later [NcNemar's test p > 0.05]. The UR-CARE database appears to be feasible, valid and reliable as a tool and easy to use regardless of prior user experience and level of clinical IBD experience. UR-CARE has the potential to enhance future European collaborations regarding clinical research in IBD.

UMD-USHbases: a comprehensive set of databases to record and analyse pathogenic mutations and unclassified variants in seven Usher syndrome causing genes.

PubMed

Baux, David; Faugère, Valérie; Larrieu, Lise; Le Guédard-Méreuze, Sandie; Hamroun, Dalil; Béroud, Christophe; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

2008-08-01

Using the Universal Mutation Database (UMD) software, we have constructed "UMD-USHbases", a set of relational databases of nucleotide variations for seven genes involved in Usher syndrome (MYO7A, CDH23, PCDH15, USH1C, USH1G, USH3A and USH2A). Mutations in the Usher syndrome type I causing genes are also recorded in non-syndromic hearing loss cases and mutations in USH2A in non-syndromic retinitis pigmentosa. Usher syndrome provides a particular challenge for molecular diagnostics because of the clinical and molecular heterogeneity. As many mutations are missense changes, and all the genes also contain apparently non-pathogenic polymorphisms, well-curated databases are crucial for accurate interpretation of pathogenicity. Tools are provided to assess the pathogenicity of mutations, including conservation of amino acids and analysis of splice-sites. Reference amino acid alignments are provided. Apparently non-pathogenic variants in patients with Usher syndrome, at both the nucleotide and amino acid level, are included. The UMD-USHbases currently contain more than 2,830 entries including disease causing mutations, unclassified variants or non-pathogenic polymorphisms identified in over 938 patients. In addition to data collected from 89 publications, 15 novel mutations identified in our laboratory are recorded in MYO7A (6), CDH23 (8), or PCDH15 (1) genes. Information is given on the relative involvement of the seven genes, the number and distribution of variants in each gene. UMD-USHbases give access to a software package that provides specific routines and optimized multicriteria research and sorting tools. These databases should assist clinicians and geneticists seeking information about mutations responsible for Usher syndrome.

Large-scale mass spectrometric detection of variant peptides resulting from non-synonymous nucleotide differences

PubMed Central

Sheynkman, Gloria M.; Shortreed, Michael R.; Frey, Brian L.; Scalf, Mark; Smith, Lloyd M.

2013-01-01

Each individual carries thousands of non-synonymous single nucleotide variants (nsSNVs) in their genome, each corresponding to a single amino acid polymorphism (SAP) in the encoded proteins. It is important to be able to directly detect and quantify these variations at the protein level in order to study post-transcriptional regulation, differential allelic expression, and other important biological processes. However, such variant peptides are not generally detected in standard proteomic analyses, due to their absence from the generic databases that are employed for mass spectrometry searching. Here, we extend previous work that demonstrated the use of customized SAP databases constructed from sample-matched RNA-Seq data. We collected deep coverage RNA-Seq data from the Jurkat cell line, compiled the set of nsSNVs that are expressed, used this information to construct a customized SAP database, and searched it against deep coverage shotgun MS data obtained from the same sample. This approach enabled detection of 421 SAP peptides mapping to 395 nsSNVs. We compared these peptides to peptides identified from a large generic search database containing all known nsSNVs (dbSNP) and found that more than 70% of the SAP peptides from this dbSNP-derived search were not supported by the RNA-Seq data, and thus are likely false positives. Next, we increased the SAP coverage from the RNA-Seq derived database by utilizing multiple protease digestions, thereby increasing variant detection to 695 SAP peptides mapping to 504 nsSNV sites. These detected SAP peptides corresponded to moderate to high abundance transcripts (30+ transcripts per million, TPM). The SAP peptides included 192 allelic pairs; the relative expression levels of the two alleles were evaluated for 51 of those pairs, and found to be comparable in all cases. PMID:24175627

Developing STR databases on structured populations: the native South Siberian population versus the Russian population.

PubMed

Zhivotovsky, Lev A; Malyarchuk, Boris A; Derenko, Miroslava V; Wozniak, Marcin; Grzybowski, Tomasz

2009-09-01

Developing a forensic DNA database on a population that consists of local ethnic groups separated by physical and cultural barriers is questionable as it can be genetically subdivided. On the other side, small sizes of ethnic groups, especially in alpine regions where they are sub-structured further into small villages, prevent collecting a large sample from each ethnic group. For such situations, we suggest to obtain both a total population database on allele frequencies across ethnic groups and a list of theta-values between the groups and the total data. We have genotyped 558 individuals from the native population of South Siberia, consisting of nine ethnic groups, at 17 autosomal STR loci of the kit packages AmpFlSTR SGM Plus i, Cyrillic AmpFlSTR Profiler Plus. The groups differentiate from each other with average theta-values of around 1.1%, and some reach up to three to four percent at certain loci. There exists between-village differentiation as well. Therefore, a database for the population of South Siberia is composed of data on allele frequencies in the pool of ethnic groups and data on theta-values that indicate variation in allele frequencies across the groups. Comparison to additional data on northeastern Asia (the Chukchi and Koryak) shows that differentiation in allele frequencies among small groups that are separated by large geographic distance can be even greater. In contrast, populations of Russians that live in large cities of the European part of Russia are homogeneous in allele frequencies, despite large geographic distance between them, and thus can be described by a database on allele frequencies alone, without any specific information on theta-values.

The ALS patient care database: goals, design, and early results. ALS C.A.R.E. Study Group.

PubMed

Miller, R G; Anderson, F A; Bradley, W G; Brooks, B R; Mitsumoto, H; Munsat, T L; Ringel, S P

2000-01-11

The ALS Patient Care Database was created to improve the quality of care for patients with ALS by 1) providing neurologists with data to evaluate and improve their practices, 2) publishing data on temporal trends in the care of patients with ALS, and 3) developing hypotheses to be tested during formal clinical trials. Substantial variations exist in managing ALS, but there has been no North American database to measure outcomes in ALS until now. This observational database is open to all neurologists practicing in North America, who are encouraged to enroll both incident and prevalent ALS patients. Longitudinal data are collected at intervals of 3 to 6 months by using standard data collection instruments. Forms are submitted to a central data coordinating center, which mails quarterly reports to participating neurologists. Beginning in September 1996 through November 30, 1998, 1,857 patients were enrolled at 83 clinical sites. On enrollment, patients had a mean age of 58.6 years +/-12.9 (SD) years (range, 20.1 to 95.1 years), 92% were white, and 61% were men. The mean interval between onset of symptoms and diagnosis was 1.2+/-1.6 years (range, 0 to 31.9 years). Riluzole was the most frequently used disease-specific therapy (48%). Physical therapy was the most common nonpharmacologic intervention (45%). The primary caregiver was generally the spouse (77%). Advance directives were in place at the time of death for 70% of 213 enrolled patients who were reported to have died. The ALS Patient Care Database appears to provide valuable data on physician practices and patient-focused outcomes in ALS.

Improving Cardiac Surgical Site Infection Reporting and Prevention By Using Registry Data for Case Ascertainment.

PubMed

Nayar, Vaidehi; Kennedy, Andrea; Pappas, Janine; Atchley, Krista D; Field, Cynthia; Smathers, Sarah; Teszner, Eva E; Sammons, Julia S; Coffin, Susan E; Gerber, Jeffrey S; Spray, Thomas L; Steven, James M; Bell, Louis M; Forrer, Joan; Gonzalez, Fernando; Chi, Albert; Nieczpiel, William J; Martin, John N; Gaynor, J William

2016-01-01

The use of administrative data for surgical site infection (SSI) surveillance leads to inaccurate reporting of SSI rates [1]. A quality improvement (QI) initiative was conducted linking clinical registry and administrative databases to improve reporting and reduce the incidence of SSI [2]. At our institution, The Society of Thoracic Surgeons Congenital Heart Surgery Database (STS-CHSD) and infection surveillance database (ISD) were linked to the enterprise data warehouse containing electronic health record (EHR) billing data. A data visualization tool was created to (1) use the STS-CHSD for case ascertainment, (2) resolve discrepancies between the databases, and (3) assess impact of QI initiatives, including wound alert reports, bedside reviews, prevention bundles, and billing coder education. Over the 24-month study period, 1,715 surgical cases were ascertained according to the STS-CHSD clinical criteria, with 23 SSIs identified through the STS-CHSD, 20 SSIs identified through the ISD, and 32 SSIs identified through the billing database. The rolling 12-month STS-CHSD SSI rate decreased from 2.73% (21 of 769 as of January 2013) to 1.11% (9 of 813 as of December 2014). Thirty reporting discrepancies were reviewed to ensure accuracy. Workflow changes facilitated communication and improved adjudication of suspected SSIs. Billing coder education increased coding accuracy and narrowed variation between the 3 SSI sources. The data visualization tool demonstrated temporal relationships between QI initiatives and SSI rate reductions. Linkage of registry and infection control surveillance data with the EHR improves SSI surveillance. The visualization tool and workflow changes facilitated communication, SSI adjudication, and assessment of the QI initiatives. Implementation of these initiatives was associated with decreased SSI rates. Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

Multi-window detection for P-wave in electrocardiograms based on bilateral accumulative area.

PubMed

Chen, Riqing; Huang, Yingsong; Wu, Jian

2016-11-01

P-wave detection is one of the most challenging aspects in electrocardiograms (ECGs) due to its low amplitude, low frequency, and variable waveforms. This work introduces a novel multi-window detection method for P-wave delineation based on the bilateral accumulative area. The bilateral accumulative area is calculated by summing the areas covered by the P-wave curve with left and right sliding windows. The onset and offset of a positive P-wave correspond to the local maxima of the area detector. The position drift and difference in area variation of local extreme points with different windows are used to systematically combine multi-window and 12-lead synchronous detection methods, which are used to screen the optimization boundary points from all extreme points of different window widths and adaptively match the P-wave location. The proposed method was validated with ECG signals from various databases, including the Standard CSE Database, T-Wave Alternans Challenge Database, PTB Diagnostic ECG Database, and the St. Petersburg Institute of Cardiological Technics 12-Lead Arrhythmia Database. The average sensitivity Se was 99.44% with a positive predictivity P+ of 99.37% for P-wave detection. Standard deviations of 3.7 and 4.3ms were achieved for the onset and offset of P-waves, respectively, which is in agreement with the accepted tolerances required by the CSE committee. Compared with well-known delineation methods, this method can achieve high sensitivity and positive predictability using a simple calculation process. The experiment results suggest that the bilateral accumulative area could be an effective detection tool for ECG signal analysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Regional variation in thyroid cancer incidence in Belgium is associated with variation in thyroid imaging and thyroid disease management.

PubMed

Van den Bruel, Annick; Francart, Julie; Dubois, Cecile; Adam, Marielle; Vlayen, Joan; De Schutter, Harlinde; Stordeur, Sabine; Decallonne, Brigitte

2013-10-01

Increased thyroid cancer incidence is at least partially attributed to increased detection and shows considerable regional variation. We investigated whether regional variation in cancer incidence was associated with variations in thyroid disease management. We conducted a retrospective population-based cohort study that involved linking data from the Belgian Health Insurance database and the Belgian Cancer Registry to compare thyroid-related procedures between regions with high and low cancer incidence. Primary outcome measures were rates of TSH testing, imaging, fine-needle aspiration cytology (FNAC), and thyroid surgery. Secondary study outcomes were proportions of subjects with thyrotoxicosis and nodular disease treated with surgery, of subjects treated with surgery preceded by FNAC or with synchronous lymph node dissection, and of thyroid cancer diagnosis after surgery. The rate of TSH testing was similar, but the rate of imaging was lower in the low incidence region. The rate of FNAC was similar, whereas the rate of surgery was lower in the low incidence region (34 [95% CI 33; 35 ] vs 80 [95% CI 79; 81 ] per 100,000 person years in the high incidence region; P < .05). In the low incidence region compared to the high incidence region, surgery represented a less chosen therapy for euthyroid nodular disease patients (47% [95% CI 46; 48] vs 69% [95% CI 68; 70]; P < .05), proportionally more surgery was preceded by FNAC, more cancer was diagnosed after total thyroidectomy, and thyroid cancer patients had more preoperative FNAC and synchronous lymph node dissection. Regional variation in thyroid cancer incidence, most marked for low-risk disease, is associated with different usage of thyroid imaging and surgery, supporting variable detection as a key determinant in geographic variation.