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At least 127 records · Page 7Linked to original sources
PubMed2006

A repository of ENU mutant mouse lines and their potential for male fertility research.

Many of the proteins and their encoding genes involved in spermatogenesis are unknown, making the specific diagnosis and treatment of infertility in males difficult and highlighting the importance of identifying new genes that are involved in spermatogenesis. Through genome-wide chemical mutagenesis using N-ethyl-N-nitrosourea (ENU) and a three-generation breeding scheme to isolate recessive mutations, we have identified mouse lines with a range of abnormalities relevant to human male fertility. Abnormal phenotypes included hypospermatogenesis, Sertoli cell-only (SCO) seminiferous tubules, germ-cell arrest and abnormal spermiogenesis and were accompanied, in some, with abnormal serum levels of reproductive hormones. In total, from 65 mouse lines, 14 showed a reproductive phenotype consistent with a recessive mutation. This study shows that it is feasible to use ENU mutagenesis as an effective and rapid means of generating mouse models relevant to furthering our understanding of human male infertility. Spermatozoa and genomic DNA from all mouse lines, including those with abnormal reproductive tract parameters, have been cryopreserved for the regeneration of lines as required. This repository will form a valuable resource for the identification and analysis of key regulators of multiple aspects of male fertility.

Activins↗
PubMed1999

Extension of CyanoBase. CyanoMutants: repository of mutant information on Synechocystis sp. strain PCC6803.

CyanoBase provides internet access to the complete genomic information of the cyanobacterium Synechocystis sp. strain PCC6803. CyanoBase contains annotations to each protein-coding gene, deduced from the entire nucleotide sequence of the genome, gene classification lists, keywords and similarity search engines. The present paper describes a recent extension of CyanoBase, named CyanoMutants. CyanoMutants is a repository database of mutant information on PCC6803. Each entry contains a dataset which describes a gene identifier, mutant information, and an address for correspondence. Two closely-linked databases, CyanoBase and CyanoMutants, connect information obtained from computational analysis to experimental analysis resulting in the clarification of the functions of hypothetical genes of the cyanobacterial genome. CyanoMutants can be accessed at http://www.kazusa.or. jp/cyano/mutants/

Computational Biology↗
PubMed2005

ArrayExpress--a public repository for microarray gene expression data at the EBI.

ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Information About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from approximately 12,000 hybridizations covering 35 species. Data can be submitted online or directly from local databases or LIMS in a standard format, and password-protected access to prepublication data is provided for reviewers and authors. The data can be retrieved by accession number or queried by various parameters such as species, author and array platform. A facility to query experiments by gene and sample properties is provided for a growing subset of curated data that is loaded in to the ArrayExpress data warehouse. Data can be visualized and analysed using Expression Profiler, the integrated data analysis tool. ArrayExpress is available at http://www.ebi.ac.uk/arrayexpress.

Animals↗
PubMed2005

The Yeast Resource Center Public Data Repository.

The Yeast Resource Center Public Data Repository (YRC PDR) serves as a single point of access for the experimental data produced from many collaborations typically studying Saccharomyces cerevisiae (baker's yeast). The experimental data include large amounts of mass spectrometry results from protein co-purification experiments, yeast two-hybrid interaction experiments, fluorescence microscopy images and protein structure predictions. All of the data are accessible via searching by gene or protein name, and are available on the Web at http://www.yeastrc.org/pdr/.

Databases, Protein↗
PubMed2005

SpliceInfo: an information repository for mRNA alternative splicing in human genome.

We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein sequences available for a given gene for evidence of AS. Additional features such as the tissue specificity of the mRNA, the protein domain contained by exons, the GC-ratio of exons, the repeats contained within the exons, and the Gene Ontology are annotated computationally for each exonic region that is alternatively spliced. Motivated by a previous investigation of AS-related motifs such as exonic splicing enhancer and exonic splicing silencer, this resource also provides a means of identifying motifs candidates and this should help to identify potential regulatory mechanisms within a particular exonic sequence set and its two flanking intronic sequence sets. This is carried out using motif discovery tools to identify motif candidates related to alternative splicing regulation and together with a secondary structure prediction tool, will help in the identification of the structural properties of such regulatory motifs. The integrated resource is now available on http://SpliceInfo.mbc.NCTU.edu.tw/.

Alternative Splicing↗
PubMed2006

Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community.

The Hedgehog Signaling Pathway Database is a curated repository of information pertaining to the Hedgehog developmental pathway. It was designed to provide centralized access to a wide range of relevant information in an organism-agnostic manner. Data are provided for all genes and gene targets known to be involved in the Hh pathway across various organisms. The data provided include DNA and protein sequences as well as domain structure motifs. All known human diseases associated with the Hh pathway are indexed including experimental data on therapeutic agents and their molecular targets. Hh researchers will find useful information on relevant protocols, tissue cell lines and reagents used in current Hh research projects. Curated content is also provided for publications, grants and patents relating to the Hh pathway. The database can be accessed at http://www.hedgehog.sfsu.edu.

Animals↗
PubMed1990

The skin as a repository and masker of evidence.

The role of the skin as a repository and masker of evidence is evaluated. Skin examination and testing are very important in the (a) identification of victims and suspects (for example, by fingerprints, lip prints, and fingernail marks), (b) recognition of patterns and shape of injurious energy impacts (for instance, recognition of type of injury and particular weapon), and (c) recovery of embedded evidence (for example, glass, wood, powder, explosives, and paint). It is also important to realize that the skin may conceal evidence by masking significant and/or lethal internal injuries.

Bites, Human↗
PubMed1982

Extreme scenarios for nuclear waste repositories.

Two extreme scenarios for release of radioactive waste have been constructed. In the first, a volcanic eruption releases 1 km2 of an underground nuclear waste repository, while in the second, waste enters the drinking water reservoir of a major city. With pessimistic assumptions, upper bounds on the number of cancers due to radiation are calculated. In the volcano scenario, the effects of the water are smaller than the effects of natural radioactivity in the volcanic dust if the delay between emplacement and eruption exceeds 2000 yr. The consequences of the waste in drinking water depend on the survival time of the canisters and the rate of leaching of the nuclides from the waste matrix. For a canister life of 400 yr and a leach time of 6300 yr the cancer rate in the affected area would increase by 25%.

Air Pollution, Radioactive↗
PubMed1986

A generic probabilistic risk analysis for a high-level waste repository.

A generic probabilistic risk analysis (PRA) is developed for high-level radioactive waste buried in a repository. The basic assumption is that an atom of buried waste has the same probability of escape as an atom of average rock at the same depth. Corrections are applied for variation of ground-water flow with depth, and for the fraction of ingested material derived from rock versus from soil. The final result is that we may eventually expect 0.012 deaths/GWe-yr. It is shown that this analysis is a PRA, and that the basic assumption is a conservative one--more likely to overestimate than to underestimate the hazard. This health impact is compared with those from other wastes generated in producing electricity.

Food↗
PubMed1995

A sensitivity study of the SCK.CEN BIOSPHERE model for performance assessment of near-surface repositories.

At SCK.CEN a model has been developed on behalf of NIRAS/ONDRAF for the performance assessment of near-surface repositories, consisting of several submodels. This article deals with the submodels BIOSPHERE, describing the transfer and accumulation of the radionuclides in the biosphere and DOSE, calculating effective individual doses to the critical group. An extensive literature review was performed in order to determine best-estimate values and uncertainty ranges (probability density functions) of biosphere parameter values, specific to conditions that may prevail at potential disposal sites in Belgium. In this paper the BIOSPHERE and DOSE models are described and default and site-specific values (probability density functions where appropriate) of the parameters involved are indicated for the radionuclides 129I, 239Pu, and 94Nb. A combined uncertainty/sensitivity analysis based on the pdf of the site-specific parameter values has been carried out. Median values and 95% confidence intervals of the site-specific doses are indicated and most influential parameters to the uncertainty identified. Site-specific median dose values are also compared with generic doses.

Air Pollutants, Radioactive↗
PubMedDate not supplied

Sex differences in mortality after burn injury: results of analysis of the National Burn Repository of the American Burn Association.

Clinical and experimental studies have shown a decreased mortality for women after nonthermal injury. However, recently published data from this institution showed an increased mortality for female patients younger than 60 years of age with thermal injury. This study extended these observations to evaluate outcomes related to sex in thermal injury in a larger population of patients. The National Burn Repository (NBR) was used for this analysis. Patients admitted to burn centers between 1991 and 2001 were selected for inclusion (n = 49,079). Sex differences in demographic, injury, clinical, and outcome characteristics were compared. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated for the association between mortality and sex, both overall and stratified by age. In total, 34,470 men and 14,609 women were included in this study. Women had a 50% increased risk of death when compared with men (OR 1.5; 95% CI 1.3-1.6), which diminished slightly when adjustments were made for age, race, TBSA burn, and inhalation injury (OR 1.3; 95% CI 1.2-1.5). When stratified by age, women had an increased risk of death for all age groups between 10 and 70 years. This study confirmed earlier studies showing an association between sex and burn mortality. Further prospective studies analyzing differences in immune responses between men and women after burn injury may provide insight into the mechanism behind these divergent outcomes and identify targets for future therapy.

Adult↗
PubMedDate not supplied

National Burn Repository 2005: a ten-year review.

In the early 1990s, the American Burn Association (ABA) started its first burn registry development initiatives. The impetus for the registry development software originated from several directions, including the following: (1) the recognition that national registries were widespread and of proven benefit; (2) growing demands from accrediting institutions, payers, and patient advocacy groups for objective and verifiable data regarding patient costs, treatments, and outcomes; and (3) the shift toward "evidence-based" medicine and the ongoing analysis of treatment effectiveness. The ABA has issued three calls for burn registry data for its National Burn Repository (NBR): 1994, 2002, and 2005. In 1994, 28 burn centers contributed data for more than 6,400 patients treated from 1991 to 1993. The ABA announced its second call for data in 2001 and distributed the published results of more than 54,000 acute burn admissions treated from 1974 to 2002 at the Association's 2002 Annual Meeting. The third ABA call for data was issued in the Fall of 2005. The results are detailed in this report, which provides a summary of more than a quarter million acute burn admissions from 1995 to 2005, representing 70 hospitals from 30 states plus the District of Columbia. Statistics are presented in chart and table format to illustrate such key factors as patient age, burn size group, types of injuries, mortality rates, and average hospital charges by etiology and length of hospital stay. The data presented herein should help stimulate quality improvement programs in burn care, as burn centers compare their performance with the national data and as research is expanded using the NBR. The NBR will be published annually and, with continued refinements to the registry software, should become of increasing importance to clinicians, payers, researchers, and the public.

Adolescent↗
PubMedDate not supplied

Frequency and distribution of GJB2 (connexin 26) and GJB6 (connexin 30) mutations in a large North American repository of deaf probands.

PURPOSE: Profound hearing loss occurs with a frequency of 1 in 1000 live births, half of which is genetic in etiology. The past decade has witnessed rapid advances in determining the pathogenesis of both syndromic and nonsyndromic deafness. The most significant clinical finding to date has been the discovery that mutations of GJB2 at the DFNB1 locus are the major cause of profound prelingual deafness in many countries. 1 More recently, GJB2 mutations have been shown to cause deafness when present with a deletion of the GJB6 gene. We report on the prevalence of GJB2 and GJB6 mutations in a large North American Repository of DNA from deaf probands and document the profound effects of familial ethnicity and parental mating types on the frequency of these mutations in the population. METHODS: Deaf probands were ascertained through the Annual Survey of Deaf and Hard of Hearing Children and Youth, conducted at the Research Institute of Gallaudet University. Educational, etiologic, and audiologic information was collected after obtaining informed consent. DNA studies were performed for the GJB2 and GJB6 loci by sequencing and PCR methods. RESULTS: GJB2 mutations accounted for 22.2% of deafness in the overall sample but differed significantly among Asians, African-Americans and Hispanics and for probands from deaf by deaf and deaf by hearing matings, as well as probands from simplex and multiplex sibships of hearing parents. In our sample, the overall incidence of GJB2/GJB6 deafness was 2.57%. CONCLUSION: GJB2 mutations account for a large proportion of deafness in the US, with certain mutations having a high ethnic predilection. Heterozygotes at the GJB2 locus should be screened for the GJB6 deletion as a cause of deafness. Molecular testing for GJB2 and GJB6 should be offered to all patients with nonsyndromic hearing loss.

Alleles↗
PubMed2000

Computer-assisted discrimination among malignant lymphomas and leukemia using immunophenotyping, intelligent image repositories, and telemicroscopy.

The process of discriminating among pathologies involving peripheral blood, bone marrow, and lymph node has traditionally begun with subjective morphological assessment of cellular materials viewed using light microscopy. The subtle visible differences exhibited by some malignant lymphomas and leukemia, however, give rise to a significant number of false negatives during microscopic evaluation by medical technologists. We have developed a distributed, clinical decision support prototype for distinguishing among hematologic malignancies. The system consists of two major components, a distributed telemicroscopy system and an intelligent image repository. The hybrid system enables individuals located at disparate clinical and research sites to engage in interactive consultation and to obtain computer-assisted decision support. Software, written in JAVA, allows primary users to control the specimen stage, objective lens, light levels, and focus of a robotic microscope remotely while a digital representation of the specimen is continuously broadcast to all session participants. Primary user status can be passed as a token. The system features shared graphical pointers, text messaging capability, and automated database management. Search engines for the database allow one to automatically identify and retrieve images, diagnoses, and correlated clinical data of cases from a "gold standard" database which exhibit spectral and spatial profiles which are most similar to a given query image. The system suggests the most likely diagnosis based on majority logic of the retrieved cases. The system was used to discriminate among three lymphoproliferative disorders and healthy cells. The system provided the correct classification in more than 83% of the cases studied. System performance was evaluated using rigorous statistical assessment and by comparison with human observers.

Decision Support Techniques↗
PubMed2004

Retrieval of images from artistic repositories using a decision fusion framework.

The large volumes of artistic visual data available to museums, art galleries, and online collections motivate the need for effective means to retrieve relevant information from such repositories. This paper proposes a decision making framework for content-based retrieval of art images based on a combination of low-level features. Traditionally, the similarity among two images has been calculated as a weighted distance between two feature vectors. This approach, however, may not be mathematically and computationally appropriate and does not provide enough flexibility in modeling user queries. This paper proposes a framework that generalizes a wide set of previous approaches to similarity calculation including the weighted distance approach. In this framework, image similarities are obtained through a decision making process based on low-level feature distances using fuzzy theory. The analysis and results of this paper indicate that the aggregation technique presented here provides an effective, general, and flexible tool for similarity calculation based on the combination of individual descriptors and features.

Algorithms↗
PubMed2002

Importance of transparency and traceability in building a safety case for high-level nuclear waste repositories.

The complexity of the safety case for a high-level nuclear waste repository makes it imperative that deliberate and significant effort be made to incorporate in it a high level of transparency and traceability. Diverse audiences, from interested members of the public to highly trained subject matter experts, make this task difficult. A systematic study of the meaning of transparency and traceability and the implementation of the associated principles in preparing the safety case is, therefore, required. In this article, we review the existing knowledge and propose topics for further investigation.

Humans↗
PubMedDate not supplied

The routine collation of health outcomes data from hospital treated subjects in the Health Outcomes Data Repository (HODaR): descriptive analysis from the first 20,000 subjects.

OBJECTIVES: Health technology assessment requires data covering many different facets of treatment. A new resource, the Health Outcomes Data Repository (HODaR), is described and evaluated for its use in the pharmaceutical research and development process. METHODS: Data were collated for subjects treated at Cardiff and Vale National Health Service (NHS) Hospitals Trust, United Kingdom. Inpatients are surveyed 6 weeks postdischarge by postal survey, whilst outpatients are handed a survey pack when they attend. Survey data cover sociodemographics, resource use, production losses, and quality of life. Electronic hospital data are available for all responders, and linked with survey returns. Sample characteristics, coverage of disease areas, and a more detailed description of data values for diabetes are described. RESULTS: Survey responses relating to 16,188 admissions and 4476 outpatient attendances were available relating to around 2000 different diagnoses. Over 5000 pharmacy items and 400,000 biochemistry test results were available. Analysis of utility data showed a broad coverage of diseases. For patients with diabetes the pattern of EQ-5D scores across subgroups is not clear. Health service resource use showed a linear relationship with respect to number of comorbidities. CONCLUSIONS: HODaR represents a new approach to accessing patient data, and gathers both routine and survey-based data. Although linking survey data to routine hospital systems is a complex task, which produces some limitations, it can produce health outcomes data at relatively low cost. Its performance within the pharmaceutical research and development process needs to be further evaluated in order to assess its most appropriate role.

Adult↗
PubMed1987

A review of the high-level nuclear waste repository siting analysis.

We critique two 1986 Department of Energy reports concerning the selection of sites for characterization as the nation's first high-level nuclear waste repository. We find that the multiattribute utility analysis of the five nominated sites was well done, although we express concern about the assessed probabilities, question the construction of two important attribute scales, and disagree with some of the value tradeoffs that were used. In contrast, we find the logic of the recommendations report to be weak and unconvincing.

Radioactive Waste↗