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At least 73 records · Page 4Linked to original sources
PubMed1996

A Web-based repository manager for brain mapping data.

The Web provides a rapid prototyping environment for building platform-independent graphical user interfaces. A Web-based console can be implemented as a suite of CGI scripts that generate HTML code, manipulate files, execute system commands, and invoke external tools. Often these tools share data by reading and writing flat files, which must be explicitly maintained by the CGI programmer. In a repository system, meta-data about each file object are maintained in a database, and access to all data is regulated by a layer of control services. This paper describes the design and implementation of a Web-based Repository Manager (WRM), which provides an application programmer's interface for controlling applications, generating HTML documents, handling Web forms, and managing multi-media data. The WRM is being used to develop a console for the Brain Mapping Framework, a system for visualizing cortical stimulation data obtained during neurosurgery.

Brain Mapping↗
PubMed1997

Large scale protein modelling and model repository.

Knowledge-based molecular modelling of proteins has proven useful in many instances including the rational design of mutagenesis experiments, but it has been generally limited by the availability of expensive computer hardware and software. To overcome these limitations, we have developed the SWISS-MODEL server for automated knowledge-based protein modelling. The SWISS-MODEL server uses the Brookhaven Protein Data Bank as a source of structural information and automatically generates protein models for sequences which share significant similarities with at least one protein of known 3D-structure. We now use the software framework of the server to generate large collections of protein models. To store these models, we have established the SWISS-MODEL Repository, a new database for protein models generated by theoretical approaches. This repository is directly integrated with SWISS-PROT and other databases through the ExPASy World-Wide Web server (URL is http:(/)/www.expasy.ch).

Amino Acid Sequence↗
PubMed1997

A virtual repository approach to clinical and utilization studies: application in mammography as alternative to a national database.

A national mammography database was proposed, based on a centralized architecture for collecting, monitoring, and auditing mammography data. We have developed an alternative architecture relying on Internet-based distributed queries to heterogeneous databases. This architecture creates a "virtual repository", or a federated database which is constructed dynamically, for each query and makes use of data available in legacy systems. It allows the construction of custom-tailored databases at individual sites that can serve the dual purposes of providing data (a) to researchers through a common mammography repository and (b) to clinicians and administrators at participating institutions. We implemented this architecture in a prototype system at the Brigham and Women's Hospital to show its feasibility. Common queries are translated dynamically into database-specific queries, and the results are aggregated for immediate display or download by the user. Data reside in two different databases and consist of structured mammography reports, coded per BIRADS Standardized Mammography Lexicon, as well as pathology results. We prospectively collected data on 213 patients, and showed that our system can perform distributed queries effectively. We also implemented graphical exploratory analysis tools to allow visualization of results. Our findings indicate that the architecture is not only feasible, but also flexible and scaleable, constituting a good alternative to a national mammography database.

Computer Communication Networks↗
PubMed2003

Genetics of recurrent early-onset depression (GenRED): design and preliminary clinical characteristics of a repository sample for genetic linkage studies.

This is an initial report on a six-site collaborative project, Genetics of Recurrent Early-Onset Depression (GenRED). This is a study of a large sample of families with recurrent major depressive disorder (DSM-IV) beginning by the age 30 in probands or 40 in relatives. Evidence suggests that early onset and recurrence of depressive episodes predict substantially increased risk of depression in first-degree relatives compared with the general population, suggesting that susceptibility genes might be mapped with this phenotype. The projected sample of 800-1,000 affected sibling pairs (ASPs) and other relatives will be studied using genome scan methods. Biological materials and blinded clinical data will be made available through the NIMH cell repository program. The sample should have good-to-excellent power to detect a locus associated with a 24% or greater population-wide increase in risk to siblings. We describe 838 affected individuals from the first 305 families containing 434 independent ASPs, or 613 ASPs counting all possible pairs. The mean age at the onset was 18.5 years, with a mean of 7.3 episodes and longest episode of 655 days. Almost all subjects had experienced at least 4 weeks of depression with five or more additional symptom criteria. Frequencies of symptoms and psychiatric and medical comorbid are provided. Substance use was more common in males, and panic disorder in females. Within pairs of affected siblings, correlations were significant for age at onset, substance abuse/dependence, panic disorder, obsessive-compulsive disorder and nicotine initiation and persistence. We replicated previously reported associations among comorbid panic disorder and social phobia, chronicity of depression and suicidal behavior. This suggests comparability of our cases to those in earlier large family studies. This dataset should prove useful for genetic studies of a highly familial form of major depressive disorder.

Adult↗
PubMed1985

Cellular repository for blood histamine in normal and nematode-infected rats.

Infections with the nematode N. brasiliensis is associated with a recruitment of intestinal mucosal mast cells (MMC) which increase greatly in numbers. We have studied histamine levels in the gut, whole blood and plasma in relation to MMC of the gut and blood cell morphology during the course of the infection in an attempt to clarify possible relations between circulating blood basophils and MMC. The results show a parallel increase in MMC numbers and histamine content of the gut, remaining high to day 20 after infection. Blood histamine increased from a control level of 30-40 ng/ml to a maximum of 200 ng/ml on day 12 to 14, but returned towards the control level already on day 16 after infection. There was a corresponding increase in plasma histamine to a maximum of 80 ng/ml. The total number of blood neutrophils increased during the early phase of the infection and there was a pronounced eosinophilia from day 10 to 16. No cells containing metachromatic granules were found in a screening comprised of 10,000 cells per specimen. During day 10 to 16 we found a number of coarsely granuled and vacuolated cells. The granules stained darkly by the Giemsa stain but not metachromatically with Toluidine Blue or with Alcian Blue at a low pH. We interpret this as an equivalent to the so-called toxic granulation occurring in human neutrophils. These cells may have been mistaken for basophils by previous investigators. The cellular repository for the high concentration of histamine in the blood is unknown. We suggest, as a working hypothesis, that it is contained in a circulating progenitor for MMC which has the ability to synthesize and, in a loosely bound state store, histamine, but which has not yet acquired the ability to assemble the specific metachromatic granules.

Animals↗
PubMed1990

The development of the U.S. EPA health effects research laboratory frozen blood cell repository program.

We have suggested that proper blood-cell freezing and storage is necessary in longitudinal studies with reduced between tests error, for specimen sharing between laboratories and for convenient scheduling of assays. Our present purpose is to describe the design and use of a prototype computer program, Cryovial, for data-based management of frozen cell repositories. We are pleased to provide, free of charge upon request, a 5.25" (specify 0.36 or 1.2 MB) disk containing all files required to run Cryovial.

Blood Preservation↗
PubMed2004

Protein expression clone repositories for functional proteomics.

The information generated from the sequence of the human genome has inspired efforts to systematically develop organized collections of human cDNA clones for use in expression screens in mammalian cells. These high-throughput cloning initiatives offer significant advantages over the cDNA libraries that have been used in the past, including greater experimental flexibility, immediate identification of hits, information regarding all tested proteins (even for those giving no response) and eventually more comprehensive coverage. Some of the lessons learned and the considerations that underlie the creation of genome-wide cDNA repositories are discussed here. Although still inchoate, these resources are already impacting the manner in which high-throughput functional screens are performed.

Animals↗
PubMed1978

Protocol for a computed tomography scanner performance repository.

An argument is presented for organization of a Computed Tomography Scanner Performance Repository. Performance data on CT scanners would be distributed in statistical form to the radiological community. A Protocol is presented for the uniform collection of data. Results of exposure, resolution and visibility measurements made by the authors are presented for the EMI 5005/U, Pfizer 0200 FS and General Electric CT/T scanners.

Humans↗
PubMed2003

Generation and stability of bentonite colloids at the bentonite/granite interface of a deep geological radioactive waste repository.

The possible mechanisms of colloid generation at the near field/far field interface of a radioactive repository have been investigated by means of novel column experiments simulating the granite/bentonite boundary, both in dynamic and in quasi-static water flow conditions. It has been shown that solid particles and colloids can be detached from the bulk and mobilised by the water flow. The higher the flow rate, the higher the concentration of particles found in the water, according to an erosion process. However, the gel formation and the intrinsic tactoid structure of the clay play an important role in the submicron particle generation even in the compacted clay and in a confined system. In fact, once a bentonite gel is formed, in the regions where the clay is contacted with water, clay colloids can be formed even in quasi-static flow conditions. The potential relevance of these colloids in radionuclide transport has been studied by evaluating their stability in different chemical environments. The coagulation kinetics of natural bentonite colloids was experimentally studied as a function of the ionic strength and pH, by means of time-resolved light scattering techniques. It has been shown that these colloids are very stable in low saline (approximately 1 x 10(-3) M) and alkaline (pH > or = 8) waters.

Aluminum Silicates↗
PubMedDate not supplied

Effect of heterogeneity in fracture permeability on the potential for liquid seepage into a heated emplacement drift of the potential repository.

A numerical model was used to investigate the effect of spatial variability in fracture permeability on liquid seepage and moisture distribution in the vicinity of a waste emplacement drift in the unsaturated zone (UZ) of Yucca Mountain. The model is based on a two-dimensional, cross-sectional, dual-permeability model of the unsaturated zone at Yucca Mountain and uses a stochastic approach to investigate the effect of small-scale heterogeneous features. The studies were conducted using one uniform fracture permeability case, three realizations of stochastically generated fracture permeability, one discrete permeability feature case, and one increased ambient liquid flux case. In all cases, the models predict that completely dry drift conditions will develop above and below the drift in 10-100 years and remain dry for 1000-2000 years. During this period, the models predict no seepage into drifts, although liquid flux above the drifts and within the drift pillars may increase by up to two orders of magnitude above ambient flux. This is because the heat released by the emplaced waste is sufficient to vaporize liquid flux of one to two orders of magnitude higher than present-day ambient flux for over 1000 years. The results also show that unsaturated zone thermal-hydrological (TH) models with uniform layer permeability can adequately predict the evolution of seepage and moisture distribution in the rock mass surrounding the repository drifts. The models further show that although variability in fracture permeability may focus and enhance liquid flow in regions of enhanced liquid saturation (due to condensation above the drifts), vaporization and vapor diffusion can maintain a dry environment within the drifts for thousands of years.

Geological Phenomena↗
PubMed2003

Generic performance assessment for a deep repository for low and intermediate level waste in the UK--a case study in assessing radiological impacts on the natural environment.

Concentrations of radionuclides in soil and surface water, taken from a generic performance assessment of a repository for low and intermediate level radioactive waste, assumed to be located in the UK, have been used as the basis for a case study in assessing radiological impacts on the natural environment. Simplified descriptions of the terrestrial and aquatic ecosystem types likely to be impacted have been developed. A scoping assessment has identified (226)Ra, (210)Po, (234)U, (230)Th and (238)U as having the highest potential for impact, with doses from internally incorporated alpha emitters as being potentially of particular importance. These nuclides, together with (36)Cl and (129)I (which have proved to be of importance in radiological risk assessments for humans) were included in a more detailed dose assessment. A basic methodology for dose assessment of ecosystems is described, and has been applied for the defined impacted ecosystems. Paucity of published data on concentration factors prevented a more detailed assessment for terrestrial ecosystems. For the aquatic ecosystem, a more detailed assessment was possible and highest calculated absorbed dose rates (weighted for the likely higher biological effectiveness of alpha radiation) were about 6.5 microGy h(-1). We conclude that harm to the impacted ecosystems is unlikely and make the observation that the lack of concentration factor or transfer factor data for a sufficiently wide range of species, ecosystems and nuclides appears to be the principal obstacle to establishing a comprehensive framework for the application of radiological protection to ecosystems.

Animals↗
PubMed2001

Development and application of a sorption data base for the performance assessment of a radwaste repository.

A sorption data base (SDB) provides readily available data for the performance assessment of a radwaste repository when site-specific and/or reference data are needed. The software developed at KAERI, SDB-21C, is a graphic user interface (GUI) program that provides efficient and user-friendly tools for evaluating large amount of sorption data. In addition, the most comprehensive sorption data base that contains about 11,000 NEA data and 2,000 KAERI data was compiled in the program. Besides the simple Kd approach, a parametric model and its compiled data sets are also included in the SDB-21C. In order to evaluate the versatility of SDB-21C, several applications were performed for relevant hypothetical situations.

Adsorption↗
PubMed2001

Colloids in the mortar backfill of a cementitious repository for radioactive waste.

Colloids are present in groundwater aquifers and water-permeable engineered barrier systems and may facilitate the migration of radionuclides. A highly permeable mortar is foreseen to be used as backfill for the engineered barrier of the Swiss repository for low- and intermediate-level waste. The backfill is considered to be a chemical environment with some potential for colloid generation and, due to its high porosity, for colloid mobility. Colloid concentration measurements were carried out using an in-situ liquid particle counting system. The in-house developed counting system with three commercially available sensors allowed the detection of single particles and colloids at low concentrations in the size range 50-5000 nm. The counting system was tested using suspensions prepared from certified size standards. The concentrations of colloids with size range 50-1000 nm were measured in cement pore water, which was collected from a column filled with a highly permeable backfill mortar. The chemical composition of the pore water corresponded to a Ca(OH)2-controlled cement system. Colloid concentrations in the backfill pore water were found to be typically lower than approximately 0.1 ppm. The specific (geometric) surface areas of the colloid populations were in the range 240 m2 g(-1) to 770 m2 g(-1). The low colloid inventories observed in this study can be explained by the high ionic strength and Ca concentrations of the cement pore water. These conditions are favourable for colloid-colloid and colloid-backfill interactions and unfavourable for colloid-enhanced nuclide transport.

Colloids↗
PubMed1995

Developing and using a data repository for quality improvement: the genesis of IRIS.

BACKGROUND: In 1991 the Inova Health System, a regional hospital system in Fairfax, Virginia, started developing a patient data repository, the Inova Research Information System (IRIS), to support clinical quality improvement, managed care contracting, and technology assessment. BUILDING A DATABASE PROTOTYPE: The prototype was built with the help of five key early user groups; each group, led by an influential physician, was eager to have access to data important to their work in an integrated and standardized electronic format. USING THE DATABASE: IRIS serves as the principal resource that QI committees, risk managers, managed care contracting officers, and others turn to for data to support their studies of the processes of care used and patient outcomes. Clinicians should use data analysis to identify opportunities for QI and implement change in their processes of care as a result. IRIS has already been used to make selected comparisons of patient management. For example, at Inova's largest hospital, for patients with a primary diagnosis of acute myocardial infarction (but without any unrelated secondary diagnoses), the length of stay was significantly shorter (5.5 days) when the attending physician was a cardiologist rather than an internist (7.5 days) or family practitioner (7.7 days). SUMMARY: IRIS represents an architecture of study of patients, clinicians, and administrators--and the outcomes and the results produced. By the end of 1995 three years of integrated clinical and financial data on inpatients will be available, permitting creation of a feed-back loop for continuous clinical and managerial learning.

Confidentiality↗
PubMed1993

Rapid freezing of whole blood or buffy coat samples for polymerase chain reaction and cell culture analysis: application to detection of human immunodeficiency virus in blood donor and recipient repositories. The Transfusion Safety Study Group.

Storage of lymphocytes for later use in prospective epidemiologic studies of blood donors and transfusion recipients has been limited by the cost of separating peripheral blood mononuclear cells (PBMCs). When the Transfusion Safety Study began in 1985, it was decided to establish a cell repository of cryopreserved buffy coat (BC) samples, and thus far over 20,000 samples have been accumulated from enrolled subjects. To determine if these specimens could be used for polymerase chain reaction, a simple thawing and pelleting technique for recovering hemoglobin-free total white cells (WBCs) was developed. To validate the technique, parallel analysis was conducted of BCs, whole blood (WB), and PBMC samples from human immunodeficiency virus type 1 (HIV-1)-seropositive subjects. Immediate postthaw cell courts of 29 frozen-thawed (F-T) WB and BC samples averaged 90 percent of the prefreeze (input) values. Representative WBC populations were obtained by immediate pelleting. Amplification of HIV-1 gag sequences from F-T BCs and F-T WB was 94 and 75 percent, respectively, which is as sensitive as that obtained with freshly separated PBMC lysates. Quantitative HIV-1 proviral load analysis by serial dilution of 23 F-T BCs and 8 WB lysates showed results comparable to those obtained with lysates of fresh PBMCs. Values for WBC differential and immunophenotyping could be applied to express viral load relative to total WBCs, PBMCs, or CD4+ cells. These results establish the basis for simplified virologic analysis of cryopreserved BC or WB specimens.

Blood Donors↗
PubMed2001

A genomewide scan for loci predisposing to type 2 diabetes in a U.K. population (the Diabetes UK Warren 2 Repository): analysis of 573 pedigrees provides independent replication of a susceptibility locus on chromosome 1q.

Improved molecular understanding of the pathogenesis of type 2 diabetes is essential if current therapeutic and preventative options are to be extended. To identify diabetes-susceptibility genes, we have completed a primary (418-marker, 9-cM) autosomal-genome scan of 743 sib pairs (573 pedigrees) with type 2 diabetes who are from the Diabetes UK Warren 2 repository. Nonparametric linkage analysis of the entire data set identified seven regions showing evidence for linkage, with allele-sharing LOD scores > or =1.18 (P< or =.01). The strongest evidence was seen on chromosomes 8p21-22 (near D8S258 [LOD score 2.55]) and 10q23.3 (near D10S1765 [LOD score 1.99]), both coinciding with regions identified in previous scans in European subjects. This was also true of two lesser regions identified, on chromosomes 5q13 (D5S647 [LOD score 1.22] and 5q32 (D5S436 [LOD score 1.22]). Loci on 7p15.3 (LOD score 1.31) and 8q24.2 (LOD score 1.41) are novel. The final region showing evidence for linkage, on chromosome 1q24-25 (near D1S218 [LOD score 1.50]), colocalizes with evidence for linkage to diabetes found in Utah, French, and Pima families and in the GK rat. After dense-map genotyping (mean marker spacing 4.4 cM), evidence for linkage to this region increased to a LOD score of 1.98. Conditional analyses revealed nominally significant interactions between this locus and the regions on chromosomes 10q23.3 (P=.01) and 5q32 (P=.02). These data, derived from one of the largest genome scans undertaken in this condition, confirm that individual susceptibility-gene effects for type 2 diabetes are likely to be modest in size. Taken with genome scans in other populations, they provide both replication of previous evidence indicating the presence of a diabetes-susceptibility locus on chromosome 1q24-25 and support for the existence of additional loci on chromosomes 5, 8, and 10. These data should accelerate positional cloning efforts in these regions of interest.

Chromosome Mapping↗
PubMed2002

A model for evaluating radiological impacts on organisms other than man for use in post-closure assessments of geological repositories for radioactive wastes.

Bioaccumulation and dosimetric models have been developed that allow the computation of dose rates to a wide variety of plants and animals in the context of the deep geological disposal of solid radioactive wastes. These dose rates can be compared with the threshold dose rates at which significant deleterious effects have been observed in field and laboratory observations. This provides a general indication of whether effects on ecosystems could be observable, but does not quantify the level of those effects. To address this latter issue, two indicator organisms were identified and exposure-response relationships were developed for endpoints of potential interest (mortality in conifers and the induction of skeletal malformations in rodents irradiated in utero). The bioaccumulation, dosimetry and exposure-response models were implemented and used to evaluate the potential significance of radionuclide releases from a proposed deep geological repository for radioactive wastes in France. This evaluation was undertaken in the context of a programme of assessment studies being performed by the Agence nationale pour la gestion des déchets radioactifs (ANDRA).

Animals↗
PubMed2001

Progenetix.net: an online repository for molecular cytogenetic aberration data.

UNLABELLED: Through sequencing projects and, more recently, array-based expression analysis experiments, a wealth of genetic data has become accessible via online resources. In contrast, few of the (molecular-) cytogenetic aberration data collected in the last decades are available in a format suitable for data mining procedures. www.progenetix.net is a new online repository for previously published chromosomal aberration data, allowing the addition of band-specific information about chromosomal imbalances to oncologic data analysis efforts. AVAILABILITY: http://www.progenetix.net CONTACT: mbaudis@stanford.edu

Chromosome Aberrations↗