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At least 667 records · Page 37Linked to original sources
PubMed2002

Radiosensitivity of subterranean bacteria in the Hungarian Upper Permian Siltstone Formation.

The main purpose of this work was to study the radioresistance of subterranean aerobic and anaerobic isolates from the Hungarian Upper Permian Siltstone (Aleurolite) Formation, in order to assess the safety of potential sites of future underground repositories for nuclear waste. A total of 93 isolates were studied. The radiosensitivities of these aerobic and anaerobic bacteria isolates were determined: the D10 values (decimal reducing doses) of the aerobic spore-formers lay in the range 0.80 -2.44 kGy, and those of the anaerobic spore-formers lay in the range 1.86 4.93 kGy. The D10 values of the aerobic and anaerobic vegetative isolates were much lower, in the ranges 0.11 0.57 and 0.22-0.40 kGy. respectively. The variability in bacterial radioresistance indicates the biodiversity at this potential disposal site. These results can affect the construction of a future underground repository, since knowledge of the most resistant microorganism may be of importance as concerns calculation of the time required to inactivate the bacteria surrounding the containers.

Bacteria, Anaerobic↗
PubMed2005

Human embryonic stem cell lines with genetic disorders.

A previous study described the establishment of human embryonic stem cell (ESC) lines from different sources of embryonic material, including morula, whole blastocyst and isolated inner cell mass. Using these methods, a repository of ESC lines has been established with different genetic abnormalities, which provides an unlimited source of disease cells in culture for undertaking research on the primary disturbances of the cellular processes in the genetically abnormal cells. ESC lines with genetic disorders were derived from the mutant embryos detected and avoided from transfer in the ongoing practice of preimplantation genetic diagnosis (PGD). The current repository contains 18 ESC lines with genetic disorders, including adrenoleukodystrophy, Duchenne and Becker muscular dystrophy, Fanconi anaemia, complementation group A, fragile-X syndrome, Huntington disease (three lines), Marfan syndrome, myotonic dystrophy (two lines), neurofibromatosis type I (five lines) and thalassaemia (two lines). These ESC lines are presently used for research purposes and may be available on request.

Cell Line↗
PubMed2026

ProteoParc: A Reference Protein Database Builder for Ancient and Nonmodel Organisms.

Over the past few years, the increasing interest in analyzing the proteome of extinct and nonmodel organisms has generated a new field of research expanding the scope of proteomics. The lack of curated databases and/or molecular data from these organisms forces researchers to manually search in different public repositories for related protein sequences, either for MS/MS peptide identification or ZooMS marker annotation. This can lead to format incongruences and hinder reproducibility between studies. To address this issue, we introduce ProteoParc, a user-friendly software that builds reference databases by systematically downloading and processing protein sequences from the most widely used public repositories. The pipeline's output is a nonredundant protein database, formatted in a way to be interpreted by typical peptide identification software. Moreover, the user can adjust the database dimension and composition by applying different criteria to include only a certain number of genes or species. Thus, ProteoParc is an easy and fast, custom-made bioinformatic tool useful for future paleoproteomics analysis in ancient samples related to understudied organisms.

Databases, Protein↗
PubMedDate not supplied

An e-science environment for service crystallography--from submission to dissemination.

The U.K. National Crystallography Service (NCS) has developed a prototype e-science infrastructure for the provision of a small molecule crystallography service from sample receipt to results dissemination. This paper outlines the two strands of this service, which (a) enable a user to contribute in the conduction of an experiment and (b) provide an effective route for the archival and dissemination of the arising results. Access to use the NCS facilities and expertise and a mechanism to submit samples is granted through a secure Grid infrastructure, which seamlessly provides instantaneous feedback and the ability to remotely monitor and guide diffraction experiments and stage the diffraction data to a securely accessible location. Publication of all the data and results generated during the course of the experiment, from processed data to analyzed structures, is then enabled by means of an open access data repository. The repository publishes its content through established digital libraries' protocols, which enable harvester and aggregator services to make the data searchable and accessible.

Crystallography, X-Ray↗
PubMed2002

Aqueous solubility diagrams for cementitious waste stabilization systems. 4. A carbonation model for Zn-doped calcium silicate hydrate by Gibbs energy minimization.

A thermodynamic Gibbs energy minimization (GEM) solid solution-aqueous solution (SSAS) equilibrium model was used to determine the solubility of Zn from calcium silicate hydrate (CSH) phases doped with 0, 0.1, 1, 5, and 10% Zn at a unity (Ca+Zn)/Si molar ratio. Both the stoichiometry and standard molar Gibbs energy (G(o)298) of the Zn-bearing end-member in the ideal ternary Zn-bearing calcium silicate hydrate (CZSH) solid solution were determined by a "dual-thermodynamic" (GEM-DT) estimation technique. The SSAS model reproduces a complex sequence of reactions suggested to occur in a long-term weathering scenario of cementitious waste forms at subsurface repository conditions. The GEM model of CZSH leaching at several Zn loadings and solid/water (s/w) ratios in a C02-free system showed that, upon complete dissolution of portlandite and calcium zincate phases at decreasing s/w < 0.01 mol x kg(H2O)(-1), the total dissolved concentrations Si(aq), Ca(aq), and Zn(aq) are controlled by a CZSH solid solution of changing composition, with a trough-like Znaq drop by 2-3 orders of magnitude. Carbonation was simulated in another GEM model run series by CO2 titration of the system with initial s/w approximately 0.9 mol/kg(H2O). Formation of (Ca,Zn)-CO3 nonideal solid solution was predicted already at early reaction stage in the presence of both portlandite and calcium zincate hydrate phases. Upon their disappearance, pH, Zn(aq), C(aq), and fCO2 were predicted to change due to the incongruent dissolution of two concurrent CZSH-I and CZSH-II solid solutions, until the total re-partitioning of Ca and Zn into a carbonate solid solution coexisting with amorphous silica at fCO2 > 0.1 bar. Along this solid-phase transition, dissolved Zn(aq) concentrations follow a highly nonlinear trend. The model results predict that at low to moderate Zn loading (< or = 1% per mole Si), CZSH-type compounds can efficiently immobilize Zn in the near field of a cement-stabilized waste repository.

Calcium Compounds↗
PubMed1999

The role of performance assessment in the regulation of underground disposal of radioactive wastes: an international perspective.

Much has been written about the development and application of quantitative methods for estimating under uncertainty the long-term radiological performance of underground disposal of radioactive wastes. Until recently, interest has been focused almost entirely on the technical challenges regardless of the role of the organization responsible for these analyses. Now the dialogue between regulators, the repository developer or operator, and other interested parties in the decision-making process receives increasing attention, especially in view of some current difficulties in obtaining approvals to construct or operate deep facilities for intermediate or high-level wastes. Consequently, it is timely to consider the options for regulators' review and evaluation of safety submissions, at the various stages in the site selection to repository closure process, and to consider, especially, the role for performance assessment (PA) within the programs of a regulator both before and after delivery of such a submission. The origins and broad character of present regulations in the European Union (EU) and in the OECD countries are outlined and some regulatory PA reviewed. The issues raised are discussed, especially in regard to the interpretation of regulations, the dangers from the desire for simplicity in argument, the use of regulatory PA to review and challenge the PA in the safety case, and the effects of the relationship between proponent and regulator. Finally, a very limited analysis of the role of PA in public hearings is outlined and recommendations are made, together with proposals for improving the mechanisms for international collaboration on technical issues of regulatory concern.

Ethics↗
PubMed2004

Development of national animal genetic resource programs.

Globally, animal genetic resources are contracting due to economic forces. As a result, during the 1990s there was a dramatic increase in national animal genetic resource activities. Many national programmes were initiated and the Food and Agriculture Organisation of the United Nations played a prominent role in coalescing national actions. Nationally, programmes have been initiated that comprise of in situ, ex situ and information-exchange efforts. A critical element to national conservation efforts is the development of cryopreserved collections of germplasm. Several countries have initiated substantial multispecies collections of cryopreserved germplasm. The selection of animals within breeds of interest is an important consideration in building cryopreserved collections. Animal selection should be based on a lack of genetic relationship, with sufficient numbers of animals to ensure the capture of rare alleles. Major issues facing repository development and genetic conservation are: (1) that all breeds are in need of genetic diversity management; (2) a better understanding of in situ breed population dynamics is needed; and (3) the concept that repository collections can be used by a broad range of clientele across time as well as during emergency situations.

Animals↗
PubMedDate not supplied

56K fibroblast protein not specific for Duchenne muscular dystrophy but for skin biopsy site.

Recently, we reported the detection by two-dimensional gel electrophoresis of a 56,000 (56K)-molecular weight polypeptide that was present in cultured skin fibroblasts from normal males but was not detectable in fibroblasts from Duchenne muscular dystrophy (DMD) patients. Since then we have established that the 56K polypeptide is not present in skin fibroblasts from normal females, DMD carrier females, or in normal male fibroblasts obtained from sources other than the Repository for Mutant Human Cell Strains, Montreal. Further inquiry has led to the discovery that all the normal male fibroblast cultures obtained from the Montreal repository had been established from preputial skin. Fibroblast cultures from DMD patients, DMD carriers, as well as other normal individuals, had been derived from non-genital skin biopsies. Thus, the absence of the 56K polypeptide is not specific for DMD, but rather is related to the site of skin biopsy.

Biopsy↗
PubMed2025

Integrated genomic analysis of NF1-associated peripheral nerve sheath tumors: an updated biorepository dataset.

Neurofibromatosis type 1 (NF1) is an inherited neurocutaneous condition that predisposes to the development of peripheral nerve sheath tumors (PNST) including cutaneous neurofibromas (CNF), plexiform neurofibromas (PNF), atypical neurofibromatous neoplasms of uncertain biologic potential (ANNUBP), and malignant peripheral nerve sheath tumors (MPNST). The Johns Hopkins NF1 biospecimen repository promotes the successful advancement of therapeutic developments for NF1-associated PNST through acquisition and genomic analysis of human tumor specimens. RNA sequencing (RNAseq) and whole exome sequencing (WES) data were generated from 73 and 114 primary human tumor samples, respectively. These pre-processed data, standardized for immediate computational analysis, are accessible through the NF Data Portal, allowing immediate interrogation. This dataset combines new and previously released samples, offering a comprehensive view of the entire cohort sequenced. As a dedicated effort to systematically bank tumor samples from people with NF1, in collaboration with molecular geneticists and computational biologists, the Johns Hopkins NF1 biospecimen repository offers access to tissue samples and genomic data to promote the advancement of NF1-related tumor biologic insights and therapies.

Humans↗
PubMed2002

Developmental therapeutics program at the NCI: molecular target and drug discovery process.

As the drug discovery and developmental arm of the National Cancer Institute (NCI), the Developmental Therapeutics Program (DTP) plans, conducts and facilitates development of therapeutic agents for cancer and AIDS. DTP's goal is to turn 'molecules into medicine for the public health'. Areas of support by DTP are discovery, development and pathways to development for the intramural and the extramural community. The Developmental Therapeutics Program (DTP) operates a repository of synthetic and pure natural products, which are evaluated as potential anticancer agents. The repository derives from a historical database of greater than 600 000 compounds, which have been supplied to DTP from a variety of sources worldwide. The in vitro anti-cancer drug cell line screen established at DTP is unique in several respects. It has changed the NCI emphasis from a compound-oriented drug discovery effort to a disease-panel oriented exercise, emphasized human tumor cells derived from solid tumors, developed a high volume screening method that can adapt to processing of numerous chemical agents or natural source-derived extracts, that has minimized the use of animals, and saved on the amount of material required for the initial screening. The hollow fiber assay created at the DTP has demonstrated the ability to provide quantitative initial indices of in vivo drug efficacy, with minimum expenditures of time and materials and is currently being utilized as the initial in vivo experience for agents found to have reproducible activity in the in vitroanticancer drug screen. Drugs showing activity with unique mechanisms of actions are being further developed for treatment of hematopoietic neoplasms, prominent examples being flavopiridol, UCN-01 and depsipeptide among others.

Animals↗
PubMed1980

Dedicated-site, interim storage of high-level nuclear waste as part of the management system.

Dedicated-site interim storage of high-level reprocessed nuclear waste and of spent fuel rods is proposed as a long-term integral part of the systems approach of the national nuclear waste isolation program. Separation of interim sites for retrievable storage from permanent-disposal repositories should enhance ensurance of the performance of the latter; maintenance of retrievability at separate sites also has many advantages in both safety and possible use of waste as resources. Interim storage sites probably will not be needed beyond about 100 years from now, so the institutional and technical considerations involved in their choice should be much less stringent than those for the selection of permanent sites. Development of interim sites must be concurrent with unabated effort to identify and to develop permanent repositories.

Journal Article↗
PubMed1999

A physically based approach to modelling radionuclide transport in the biosphere.

Calculations of radiological risk are required to assess the safety of any potential future UK deep underground repository for intermediate-level and certain low-level solid radioactive wastes. In support of such calculations, contaminant movement and dilution in the terrestrial biosphere is investigated using the physically based modelling system SHETRAN. Two case studies are presented involving modelling of contaminants representing long-lived poorly sorbed radionuclides in the near-surface aquifers and surface waters of hypothetical catchments. The contaminants arise from diffuse sources at the base of the modelled aquifers. The catchments are characterised in terms of detailed spatial data for topography, the river network, soils and vegetation. Simulations are run for temperate and boreal climates representing possible future conditions at a repository site. Results are presented in terms of the concentration of contaminants in the aquifer, in soils and in surface waters; these are used to support the simpler models used in risk calculations.

Climate↗
PubMed2000

Current medicolegal and confidentiality issues in large, multicenter research programs.

The convenience of fast computers and the Internet have encouraged large collaborative research efforts by allowing transfers of data from multiple sites to a single data repository; however, standards for managing data security are needed to protect the confidentiality of participants. Through Dartmouth Medical School, in 1996-1998, the authors conducted a medicolegal analysis of federal laws, state statutes, and institutional policies in eight states and three different types of health care settings, which are part of a breast cancer surveillance consortium contributing data electronically to a centralized data repository. They learned that a variety of state and federal laws are available to protect confidentiality of professional and lay research participants. The strongest protection available is the Federal Certificate of Confidentiality, which supersedes state statutory protection, has been tested in court, and extends protection from forced disclosure (in litigation) to health care providers as well as patients. This paper describes the careful planning necessary to ensure adequate legal protection and data security, which must include a comprehensive understanding of state and federal protections applicable to medical research. Researchers must also develop rules or guidelines to ensure appropriate collection, use, and sharing of data. Finally, systems for the storage of both paper and electronic records must be as secure as possible.

Confidentiality↗
PubMed2004

Bioinformatics software resources.

This review looks at internet archives, repositories and lists for obtaining popular and useful biology and bioinformatics software. Resources include collections of free software, services for the collaborative development of new programs, software news media and catalogues of links to bioinformatics software and web tools. Problems with such resources arise from needs for continued curator effort to collect and update these, combined with less than optimal community support, funding and collaboration. Despite some problems, the available software repositories provide needed public access to many tools that are a foundation for analyses in bioscience research efforts.

Algorithms↗
PubMed2025

Gencube: centralized retrieval and integration of multi-omics resources from leading databases.

MOTIVATION: The volume of multi-omics data for diverse species is growing at an unprecedented rate, with new genome assemblies, related annotations, and high-throughput sequencing resources being submitted daily to various genomic data repositories. In response to this data influx, both existing and new databases are establishing optimized hierarchical structures to manage the vast amount of information. However, the lack of accessible command-line tools, combined with the functional limitations and unintuitive design of existing options, presents significant challenges for researchers. This gap underscores a critical need for a tool that enables streamlined retrieval and integration of omics data across these diverse repositories. RESULTS: We have developed Gencube, a command-line tool that enables centralized retrieval and integration of a comprehensive set of six different data types-genome assemblies, gene sets, annotations, sequences, comparative genomic data, and NGS-based omics resources-from various leading databases. AVAILABILITY AND IMPLEMENTATION: Gencube is a free and open-source tool, with its code available on GitHub: https://github.com/snu-cdrc/gencube and also archived on Zenodo: https://doi.org/10.5281/zenodo.14607649.

Databases, Genetic↗
PubMed2026

Managing workflow executions with WESkit.

SUMMARY: In biomedical research, managing computational workflows across numerous projects-with varying parameters, tools, and environments-creates major challenges in scalability, reproducibility, and collaboration. Here, we present WESkit, an implementation of the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) interface, designed to streamline the execution, monitoring, and documentation of data processing workflows. It addresses the complexities involved in managing numerous executions with varying parameters across diverse research projects. Supporting both Snakemake and Nextflow, the system enables consistent automation and centralized monitoring, which benefits research groups aiming for long-term reproducibility and scalable collaboration. Its suitability for larger teams and service units is further enhanced by seamless integration into cloud environments, contributing to the GA4GH cloud framework. AVAILABILITY AND IMPLEMENTATION: The software WESkit is available under MIT license at the GitLab repository (https://gitlab.com/one-touch-pipeline/weskit). The WESkit main repository is archived at Software Heritage (https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://gitlab.com/one-touch-pipeline/weskit/api.git) and can be found using "one-touch-pipeline/weskit" term in the search section.

Workflow↗
PubMed2026

SeqUIaSCOPE: multi-omics data integration platform for single-patient clinical oncology pathway exploration.

SUMMARY: SeqUIaSCOPE is an open-source platform designed for routine clinical oncology diagnostics through case-centric integration and visualization of genomic variants, fusion events, and expression profiles. The platform combines molecular-level validation via embedded genome browsing with systems-level interpretation through dynamic pathway visualization, enabling geneticists to assess how alterations converge across biological networks. Flexible reporting with customizable templates accommodates diverse institutional requirements, while secure cluster-based or local deployment ensures compliance with data protection policies, making advanced multi-omics diagnostics accessible to academic and clinical institutions. AVAILABILITY AND IMPLEMENTATION: SeqUIaSCOPE is freely available on GitHub at https://github.com/BioIT-CEITEC/sequiascope under the MIT license and archived at Zenodo (https://zenodo.org/records/21338445). Due to the sensitive nature of patient data, the repository provides simulated datasets that mimic the structure of real clinical data for testing and exploration. Documentation and a live demo accompany these datasets, allowing users to explore the application without any prior setup. The repository also includes a Helm chart for Kubernetes deployment and Docker containers for local deployment, ensuring compatibility across Linux, macOS, and Windows. No user registration is required, and all data remains on local or institutional infrastructure.

Humans↗
PubMed2005

Gene-Expression Omnibus integration and clustering tools in SeqExpress.

UNLABELLED: SeqExpress, a gene-expression analysis suite, has been extended to offer a number of cluster generation, refinement and visualization techniques. The cluster generation methods have been specialized to deal with aspects of the sparseness and extreme values that occur within microarray data. The results of such cluster analysis can then be refined using either: a functional enrichment based procedure, which examines each cluster to see if it possesses an unusually high or low concentration of ontology terms; or by using Expectation-Maximization to find a mixture of model based distributions within the datasets. Visualizations are provided both to explore and compare the results of the cluster generation algorithms. In addition, a tool has been developed which integrates SeqExpress with the Gene-Expression Omnibus repository. The tool provides seamless access to the large number of experimental results in the repository, so that they can be visualized and analysed locally using SeqExpress. AVAILABILITY: SeqExpress is available as a 6 MB download from http://www.seqexpress.com and runs under Windows. A server-based version is available and is required for the GEO integration. SeqExpress is not affiliated with any academic institution, funding body or commercial organization and is free to use by all.

Algorithms↗