bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Microbial Ecology of Bacterial Vaginosis: A Fine Scale Resolution Metagenomic Analysis
Authors: Ravel Jacques , Forney Larry 
Published: October 2010

AbstractThe vaginal microbiota play an important protective role in maintaining the health of women. Disruption of the mutualistic relationship that exists between bacterial communities in the vagina and their hosts can lead to bacterial vaginosis (BV), a condition in which lactic acid producing bacteria are supplanted by a diverse array of strictly anaerobic bacteria. BV has been shown to be an independent risk factor for adverse outcomes including preterm delivery and low infant birth weight, acquisition of sexually transmitted infections and HIV, and development of pelvic inflammatory disease. National surveys indicate the prevalence of BV among U.S. women is 29.2%, and yet, despite considerable effort, the etiology of BV remains unknown. Moreover, there are no broadly effective therapies for the treatment of BV, and reoccurrence is common. In the proposed research we will test the overarching hypothesis that vaginal microbial community dynamics and activities are indicators of risk to BV. To do this, we propose to conduct a high resolution prospective study in which samples collected daily from 200 reproductive-age women over two menstrual cycles are used to capture molecular events that take place before, during, and after the spontaneous remission of BV episodes. We will use modern genomic technologies to obtain the data needed to correlate shifts in vaginal microbial community composition and function, metabolomes, and epidemiological and behavioral metadata with the occurrence of BV to better define the syndrome itself and identify patterns that are predictive of BV. The three specific aims of the research are: (1) Evaluate the association between the dynamics of vaginal microbial communities and risk to BV by characterizing the community composition of vaginal specimens archived from a vaginal douching cessation study in which 33 women self-collected vaginal swabs twice-weekly for 16 weeks; (2) Enroll 135 women in a prospective study in which self-collected vaginal swab samples and secretions are collected daily along with data on the occurrence of BV, vaginal pH, and information on time varying habits and practices; (3) Apply model-based statistical clustering and classification approaches to associate the microbial community composition and function, with metadata and clinical diagnoses of BV. The large body of information generated will facilitate understanding vaginal microbial community dynamics, the etiology of BV, and drive the development of better diagnostic tools for BV. Furthermore, the information will enable a more personalized and effective treatment of BV and ultimately help prevent adverse sequelae associated with this highly prevalent disruption of the vaginal microbiome.
KaPPA-View4: A Pathway Database for Gene Co-expression and Metabolite Co-accumulation Analysis
Authors: Sakurai Nozomu 
Published: October 2010

AbstractCorrelations of gene-to-gene co-expression and metabolite-to-metabolite co-accumulation are considered to be useful for uncovering unknown functions of genes and regulatory systems of the metabolic pathways. Although many databases and tools are available to interpret quantitative data of transcriptome and metabolome, there are only limited ones that connect correlation data to biological knowledge and can be utilized to find biological significance of it. We developed a new metabolic pathway database, KaPPA-View4 ("http://kpv.kazusa.or.jp/kpv4/":http://kpv.kazusa.or.jp/kpv4/), that enables to overlay gene-to-gene and/or metabolite-to-metabolite relationships as quadratic Bezíer curves on metabolic pathway maps. For up to 4 maps including pathway maps, gene category maps, and user created maps can be analyzed on a single browser window, the representation would help to discover, for example, novel functions of a transcription factor that regulates genes on a metabolic pathway. Pathway maps of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and maps generated from their gene classifications are available at KaPPA-View4 KEGG ("http://kpv.kazusa.or.jp/kpv4-kegg/":http://kpv.kazusa.or.jp/kpv4-kegg/). One of the major advanteges of utilizing KEGG pathway maps is that we can share the latest results of KEGG's continuous effort for curation of gene descriptions, categorizations, and assignment on the maps for various organisms. We currently provide pathway map data for 20 species including animals, plants and microorganisms, and gene co-expression data for 12 species that are retrieved from ATTED-II, COXPRESdb, CoP and MiBase.This work was supported by the New Energy and Industrial Technology Development Organization (NEDO, Japan).
The Latest Information and Perspective of Human Gene and Protein Database (HGPD) as Human Proteome Study
Authors: Maruyama Yukio , Kawamura Yoshifumi , Isogai Takao , Nomura Nobuo , Goshima Naoki 
Published: October 2010

AbstractHGPD ("http://www.HGPD.jp/":http://www.HGPD.jp/) is a unique database that stores information on a set of human Gateway entry clones in addition to protein expression data. HGPD was launched in November 2008 and, since then, 33,275 human Gateway entry clones have been constructed from ORFs of full-length cDNAs, thus representing the largest collection in the world. Sequence information and protein expression of Gateway entry clones can also be retrieved from HGPD. The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database ("http://flj.hinv.jp/v01/cgi/index.cgi":http://flj.hinv.jp/v01/cgi/index.cgi), which was constructed as human cDNA sequence analysis database focusing on mRNA varieties resulting from variations in transcription start site (TSS) and splicing.In this update, we constructed an additional 9,974 Gateway entry clones, giving a total of 43,249, corresponding to approximately 2,000 loci. Sequence summary, nucleotide and amino acid sequence data for these clones (v 2.0) can be obtained from download site. We named this human Gateway entry clone resource “HUPEX” (Human Proteome Expression-resource). And, we expressed 4,457 human proteins with a C-terminal V5 and His tag and analyzed them using SDS-PAGE, giving a total of 17,821. In the near future, we will construct 11,000 image data of subcellular localization of the proteins with fluorescent proteins at the N- or C-terminal which are expressed in HeLa cells by using Gateway entry clones. And, we will link ESPRESSO ("http://mbs.cbrc.jp/ESPRESSO/":http://mbs.cbrc.jp/ESPRESSO/) using ORF sequences of the entry clones, allowing us to acquire predictional protein expression and solubility results. Moreover, we will redesign the web interface.
Logical Operation Based Literature Association with Genes and its application, PosMed.
Authors: Makita Yuko , Bhatia Rinki , Deshpande Mrinalini , Matsushima Akihiro , Ishii Manabu , Mochizuki Yoshiki , Yoshida Yuko , Kobayashi Norio , Toyoda Testuro 
Published: October 2010

AbstractPosMed prioritizes candidate genes for positional cloning by employing our original database search engine GRASE, which uses an inferential process similar to an artificial neural network comprising documental neurons (or 'documentrons') that represent each document contained in databases such as MEDLINE and OMIM (Yoshida, et al. 2009, Makita, et al. 2009). PosMed immediately ranks the candidate genes by connecting phenotypic keywords to the genes through connections representing gene–gene interactions other biological relationships, such as metabolite–gene, mutant mouse–gene, drug–gene, disease–gene, and protein–protein interactions, ortholog data, and gene–literature connections.To make proper relationships between genes and literature, we manually curate queries, which are defined by logical operation rules, against MEDLINE. For example, to detect a set of MEDLINE documents for the AT1G03880 gene in A. thaliana, we applied the following logical query: (‘AT1G03880’ OR ‘CRU2’ OR ‘CRB’ OR ‘CRUCIFERIN 2' OR ‘CRUCIFERIN B’) AND (‘Arabidopsis’) NOT (‘chloroplast RNA binding’). Curators refined these queries in mouse, rice and A. thaliana. For human and rat genes, we use mouse curation results via ortholog genes in PosMed.PosMed is available at "http://omicspace.riken.jp/PosMed":http://omicspace.riken.jp/PosMed References:Yoshida Y, et al. Nucleic Acids Res. 37(Web Server issue):W147-52. 2009.Makita Y, et al. Plant Cell Physiol. 2009 Jul;50(7):1249-59.
RDF Curator: A Novel Workflow that Generates Semantic Graph from Literature for Curation Using Text Mining
Authors: Komiyama Yusuke , Gotoh Osamu 
Published: October 2010

AbstractThere exist few databases that enable cross-reference among various research fields related to bioenergy. Cross-reference is highly desired among bioinformatics databases related to environment, energy, and agriculture for better mutual cooperation. By uniting Semantic Graph, we can economically construct a distributed database, regardless of the size of research laboratories and research endeavors.Our purpose is to design and develop a workflow based on RDF (Resource Description Framework) that generates Semantic Graph for a set of technical terms extracted from documents of various formats, such as PDF, HTML, and plain text. Our attempt is to generate Semantics Graph as a result of text mining including morphological analysis and syntax analysis.We have developed a prototype of workflow program named "RDF Curator". By using this system, various types of documents can be automatically converted into RDF. "RDF Curator" is composed of general tools and libraries so that no special environment is needed. Hence, “RDF Curator” can be used on many platforms, such as MacOSX, Linux, and Windows (Cygwin). We expect that our system can assist human curators in constructing Semantic Graph. Although fast and high throughput, the accuracy of the present version of "RDF Curator" is lower than that of human curators. As a future task, we have to improve the accuracy of the workflow. In addition, we also plan to apply our system to analysis of network similarity.
DDBJ Sequence Read Archive / DDBJ Omics Archive
Authors: Nakamura Yasukazu , Kodama Yuichi , Saruhashi Satoshi , Kaminuma Eli , Sugawara Hideaki , Takagi Toshihisa , Okubo Kousaku 
Published: October 2010

AbstractMassively parallel sequencers become widespread and produce unprecedented amounts of sequence reads in many biological fields. DNA Data Bank of Japan (DDBJ) has constructed the international sequence database collaboration (INSDC) together with EBI and NCBI. In 2008, DDBJ has established the DDBJ Read Archive (DRA) to archive raw output data from the new sequencing platforms. DRA archives and provides the raw data sets together with the other two INSDC partners the Sequence Read Archive (SRA) at NCBI and the European Sequence Read Archive (ERA) at EBI. These new sequencing platforms are also used to count DNA/RNA molecules instead of microarray experiment because of their higher accuracy. Since 2004, DDBJ has operated CIBEX as a repository database for the microarray data. In 2009, we decided to establish a new archive DDBJ Omics Archive (DOR) to efficiently accommodate the massive amounts of quantitative data. DOR integrates array-based CIBEX data. DOR accepts submissions of functional genomics data both from the array- and sequencing-based platforms in collaboration with EBI ArrayExpress. DOR uses the same standards with those of ArrayExpress, namely, MAGE-TAB file format for metadata, MIAME and MINSEQE guidelines for submissions. Thus, the data sets released from DOR are seamlessly exported to ArrayExpress. Moreover, entrances of the submission is unified between the DOR and DRA, in which the submitters once deposit their raw and processed data with necessary metadata, their data will be registered to both databases.DDBJ continues to serve the biological science with the primary archive databases of DDBJ, DRA and DOR.
Effects of the level of dietary valine supply on amino acids and urea concentration in milk and blood plasma of lactating sows
Authors: Roth‐Maier D. A. , Ott H. , Roth F. X. , Paulicks B. R. 
Published: October 2010

SummaryIn order to determine the valine (Val) requirement, suckling sows with 10–12 piglets were supplied with feed mixtures, which contained various levels of Val derived by adding crystalline l‐Val to the native diet (0.45% = native, 0.55, 0.65, 0.85, 1.05 and 1.45%) during a total of 72 lactations. Milk and blood plasma, taken after 3 weeks of lactation, was examined on the concentration of amino acids (total amino acids in milk, free amino acids in plasma) and urea by ion exchange chromatography or autoanalyzer, respectively. The contents of almost all amino acids in milk were significantly higher compared with the native diet, when Val was supplemented, reflecting increasing milk protein concentrations. Highest amino acid concentrations were observed with 0.85% dietary Val. Amino acid pattern in milk was not affected by the Val supply. In blood plasma the concentration of free Val rose with the dietary Val from 9 mg/l (0.45% dietary Val) to 132 mg/l (1.45% dietary Val). Several other amino acid contents were also higher when Val was added to the native diet, but there was no dose–response. Urea concentrations in milk and blood plasma were lowest with 0.65% and 0.85% dietary Val, respectively. Conclusively, for sows nursing litters with 10–12 piglets a dietary valine supply of 0.85% (0.75% apparent ileal digestible Val) can be recommended with a minimum requirement of 0.65% (0.55% apparent ileal digestible Val).
The Treatment of Auto‐erotic Asphyxiation in a Man with Severe Intellectual Disabilities: the Effectiveness of a Behavioural and Educational Programme
Authors: Thompson A. R. , Beail N. 
Published: October 2010

Background The treatment of individuals with severe intellectual disabilities who engage in self‐injurious sexual practices and are incapable of giving consent poses a significant challenge to health care services. Treatment options can be highly personal and intrusive, and potentially pose a risk of litigation. However, there is also a risk of being prosecuted for negligence if necessary treatment is not pursued. This paper discusses the treatment of an individual engaged in such a behaviour – auto‐erotic asphyxiation. It describes how the legal aspects of the design and implementation of the treatment approach were handled.Methods The treatment approach involved a behavioural and psycho‐educational programme. A single case study methodology was utilized in order to assess the effectiveness of the intervention.Results The intervention led to the learning of new adaptive behaviour. Auto‐erotic asphyxiation ceased and the individual's masturbatory behaviour changed sufficiently to reduce the threat of mortality. Qualitatively, a significant reduction in the level of stress experienced by the individual's family was reported.Conclusions It is concluded that behavioural and educational techniques may be effective in the management of such cases. Further research replicating such techniques with similar cases is required prior to the efficacy of this treatment becoming established.
Grandparent Support for Families of Children with Down's Syndrome
Authors: Hastings Richard P. , Thomas Hannah , Delwiche Nicole 
Published: October 2010

Background  Although grandparents are recognized as an important source of support for families of children with intellectual and other disabilities, there has been very little research in this area. The aim of the present paper is to present a brief overview of the literature, and to present data from a preliminary study of relationships between parental stress and grandparent support and conflict.Methods  Sixty‐one parents of children with Down's syndrome (34 mothers and 27 fathers) completed questionnaires on grandparent support and conflict. Parents also completed the Friedrich Short Form of the Questionnaire on Resources and Stress (QRS) with scoring amended to include a depression sub‐scale.Results  The main findings were: (1) grandparent support and conflict were associated with mothers' but not fathers' ratings of stress on the QRS, and (2) both grandparent support and conflict made independent contributions to the prediction of mothers' stress on at least one dimension of the QRS.Conclusions  Practical implications of the results for interventions designed to encourage grandparent support for families are discussed. Issues for further research and methodological problems with the study are also identified.
Mortality of Parents of People with Intellectual Disabilities
Authors: Hill‐Smith Andrew J. , Hollins Sheila C. 
Published: October 2010

Background  The experience of caring for a son or daughter with an intellectual disability has long been recognized as stressful. The long‐term health costs for parents of people with intellectual disability have attracted some recent research attention, but mortality has not been studied.Methods  The present authors examined mortality as measured by the standardized mortality ratio (SMR), and cause of death for parents of people with intellectual disability, identified through an intellectual disability register in Merton, south London.Results  Although there was a trend for lower SMRs particularly for mothers, SMRs were not significantly different from unity. Subgroups of parents whose child was cared for predominantly in an institution, or in the family home were analysed and similarly showed no significant difference from unity. The same applied to cause of death analyses.Conclusions  These findings offer some reassurance to parents of people with intellectual disability. There is an urgent need for further research in this area.
A semi‐empirical velocity‐porosity‐clay model for petrophysical interpretation of P‐ and S‐velocities
Authors: Goldberg Igor , Gurevich Boris 
Published: October 2010

We design a velocity–porosity model for sand‐shale environments with the emphasis on its application to petrophysical interpretation of compressional and shear velocities. In order to achieve this objective, we extend the velocity–porosity model proposed by Krief et al., to account for the effect of clay content in sandstones, using the published laboratory experiments on rocks and well log data in a wide range of porosities and clay contents.The model of Krief et al. works well for clean compacted rocks. It assumes that compressional and shear velocities in a porous fluid‐saturated rock obey Gassmann formulae with the Biot compliance coefficient. In order to use this model for clay‐rich rocks, we assume that the bulk and shear moduli of the grain material, and the dependence of the compliance on porosity, are functions of the clay content.Statistical analysis of published laboratory data shows that the moduli of the matrix grain material are best defined by low Hashin–Shtrikman bounds. The parameters of the model include the bulk and shear moduli of the sand and clay mineral components as well as coefficients which define the dependence of the bulk and shear compliance on porosity and clay content. The constants of the model are determined by a multivariate non‐linear regression fit for P‐ and S‐velocities as functions of porosity and clay content using the data acquired in the area of interest.In order to demonstrate the potential application of the proposed model to petrophysical interpretation, we design an inversion procedure, which allows us to estimate porosity, saturation and/or clay content from compressional and shear velocities.Testing of the model on laboratory data and a set of well logs from Carnarvon Basin, Australia, shows good agreement between predictions and measurements. This simple velocity‐porosity‐clay semi‐empirical model could be used for more reliable petrophysical interpretation of compressional and shear velocities obtained from well logs or surface seismic data.
Evolutionary change in the use of skills within the district nursing team: a study in two Health Board areas in Scotland
Authors: McIntosh Jean , Moriarty Deirdre , Lugton Jean , Carney Orla 
Published: October 2010

Evolutionary change in the use of skills within the district nursing team: a study in two Health Board areas in Scotland Grade mix within the district nursing team in the United Kingdom has changed markedly over the last 10 years but the relationship between grade mix and skill mix has received only intermittent research attention. This study adopted an ethnographic approach and aimed to explore the way in which grade and skill are taken into account in the delegation of nursing care. After gaining ethical approval, a total of 76 members of 21 district nursing teams in two areas were observed and interviewed. Delegation practices were found to vary both within and between areas and considerable differences were uncovered in the responsibilities allocated to more junior and unqualified team members. The developing role of nursing auxiliaries is discussed in relation to the role of the G grade sister, resource constraints and the standards of patient care. The paper concludes by arguing that the supervision and leadership role provided by the G grade sister should be fully recognized and safeguarded.
Which terminally ill cancer patients in the United Kingdom receive care from community specialist palliative care nurses?
Authors: Addington‐Hall Julia , Altmann Dan 
Published: October 2010

Which terminally ill patients in the United Kingdom receive care from community specialist palliative care nurses? This study investigates how cancer patients who receive care from community specialist palliative care (CSPC) nurses differ from those who do not. This was achieved by secondary data analyses from the Regional Study of Care for the Dying, a retrospective interview survey of deaths in 1990 in 20 nationally representative health districts. Interviews were obtained for 2074/2915 (71%) of randomly selected cancer deaths; 574 (27·8%) were reported to have received care from a Macmillan nurse, hospice home‐care nurse, or other community specialist palliative care nurse. Using logistic regression analysis 10 factors were found to predict independently CSPC use. Being dependent with dressing/undressing, needing help at night, having constipation, experiencing vomiting/nausea, being mentally confused, having breast cancer and being under the age of 75 years increased the likelihood of receiving CSPC. Having a lymphoma, leukaemia or myeloma, a brain tumour and being dependent on others for help with self‐care for more than 1 year decreased the likelihood. The use of CSPC nurses to provide expertise in symptom control and to support families of dependent patients is consistent with the aims of palliative care, and therefore appears appropriate. Further research is, however, needed to investigate the apparent age bias in access to these services, and to ensure that CSPC services are provided on the basis of need, irrespective of patient age.
Nursing in the public sphere: breaching the boundary between research and policy
Authors: West Elizabeth , Scott Cherill 
Published: October 2010

Nursing in the public sphere: breaching the boundary between research and policy Nurses and nursing are associated traditionally with activities in a private sphere. This paper argues that, if clinical care is to be improved, nurses need to take a more active public role in making and implementing health policy at both local and national levels. In the current climate, empirical evidence is one of the most important tools for influencing health policy. This paper discusses contemporary models of the policy‐making process before outlining a number of strategies that could be used to increase the policy impact of nursing research. Finally, while the current climate in the United Kingdom health‐care arena presents opportunities for researchers to have an impact on policy, the growth of health policy research as a distinct field of scholarship also poses a number of challenges and dangers.