Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Repositories”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,099 records · Page 61Linked to original sources
PubMed2002

Mitochondria, Ca2+ and neurodegenerative disease.

Mitochondria play a central role in cell biology not only as producers of ATP, but also in the sequestration of Ca(2+) and the generation of free radicals. They are also repositories of several proteins which regulate apoptosis. Perturbations in the normal functions of mitochondria will inevitably disturb cell function, may sensitise cells to neurotoxic insults and may initiate cell death. Neuronal Ca(2+) overload, such as follows excessive stimulation of Ca(2+) permeant excitatory amino acid receptors, can cause cell death. Recent evidence suggests that the accumulation of Ca(2+) into mitochondria during episodes of cellular Ca(2+) overload initiates a cascade of events that culminate in cell death. Cell death appears to require not only mitochondrial Ca(2+) overload, but rather a combination of raised intramitochondrial Ca(2+) concentration with increased production of nitric oxide and possibly other oxyradical species. Cell death may proceed through either necrotic or apoptotic mechanisms, depending on the rate of consumption and depletion of ATP. Evidence is also accumulating to suggest that more subtle alterations in mitochondrial function may serve as predisposing factors in the pathogenesis of a number of neurodegenerative disorders.

Animals↗
PubMed1995

Automating the sleep laboratory: implementation and validation of digital recording and analysis.

OBJECTIVES: We report on the implementation of digital processing in a large clinical and research sleep laboratory. The system includes the digital collection, display, analysis, and repository of physiological signals collected during sleep. METHODS: After describing the original analog system, the computer equipment and software necessary for the digital implementation are presented and we explain our algorithms for rapid eye movement (REM) and delta-wave detection. Finally, we describe an experiment validating the digital system of display and analyses. CONCLUSIONS: The digital processing of sleep signals saves computer operator, polysomnographic technologist, and computer time. It also saves resources such as polysomnographic paper and FM tape. The digital signals lend themselves to a large array of analysis techniques and result in improved signal quality. Automated REM and delta-wave detection via digital processing correlate highly with visual counts of rapid eye movements and delta waves.

Algorithms↗
PubMed2000

The African trypanosome genome.

The haploid nuclear genome of the African trypanosome, Trypanosoma brucei, is about 35 Mb and varies in size among different trypanosome isolates by as much as 25%. The nuclear DNA of this diploid organism is distributed among three size classes of chromosomes: the megabase chromosomes of which there are at least 11 pairs ranging from 1 Mb to more than 6 Mb (numbered I-XI from smallest to largest); several intermediate chromosomes of 200-900 kb and uncertain ploidy; and about 100 linear minichromosomes of 50-150 kb. Size differences of as much as four-fold can occur, both between the two homologues of a megabase chromosome pair in a specific trypanosome isolate and among chromosome pairs in different isolates. The genomic DNA sequences determined to date indicated that about 50% of the genome is coding sequence. The chromosomal telomeres possess TTAGGG repeats and many, if not all, of the telomeres of the megabase and intermediate chromosomes are linked to expression sites for genes encoding variant surface glycoproteins (VSGs). The minichromosomes serve as repositories for VSG genes since some but not all of their telomeres are linked to unexpressed VSG genes. A gene discovery program, based on sequencing the ends of cloned genomic DNA fragments, has generated more than 20 Mb of discontinuous single-pass genomic sequence data during the past year, and the complete sequences of chromosomes I and II (about 1 Mb each) in T. brucei GUTat 10.1 are currently being determined. It is anticipated that the entire genomic sequence of this organism will be known in a few years. Analysis of a test microarray of 400 cDNAs and small random genomic DNA fragments probed with RNAs from two developmental stages of T. brucei demonstrates that the microarray technology can be used to identify batteries of genes differentially expressed during the various life cycle stages of this parasite.

Animals↗
PubMed1992

Applications of DNA fingerprinting in pediatric practice.

Pediatric cases have played historic and precedent-setting roles in DNA forensics. DNA fingerprinting is a powerful tool for the pediatrician in cases of physical and sexual abuse and when issues arise regarding identification and familial relationships. If this technology is to be utilized effectively, the physician must know how to collect and document specimens. The pediatrician needs to be cautious in making referrals for commercial DNA banking. Whereas well-maintained and protected DNA repositories can be extremely valuable when there are medical and other appropriate indications, there are very real concerns about commercial DNA banking solely for purposes of identification. Pediatricians should recognize that this technology can be applied in novel but important new ways in their practices. For example, at the first indication of a possible mix-up of babies in the nursery, this should be acknowledged and rapidly resolved through DNA profiling of the parents and the neonates.

Adolescent↗
PubMed1974

Plasma lead levels in normal and lead-intoxicated children.

Lead reaches tissues through the plasma, where the concentration of this ion is characteristically low. Little information exists on the mechanisms which determine the dynamics of lead in plasma. Measurement of plasma lead levels have been determined in normal and lead-intoxicated children, newborn infants, and children with sickle-cell disease. The results in all groups were remarkably similar and constant over a wide range of blood lead concentration and regardless of hematocrit. These results lend further support to the postulate that the red cell represents a repository for lead, maintaining plasma lead concentration within closely defined limits, and that methods other than an isolated measurement of plasma lead will be necessary to uncover a presumably dynamic transport system between red cell and plasma.

Anemia, Sickle Cell↗
PubMed1989

Pharmacokinetics of benzathine penicillin G: serum levels during the 28 days after intramuscular injection of 1,200,000 units.

Because of published data suggesting the inadequacy of once-every-4-weeks intramuscular injections of benzathine penicillin G for secondary rheumatic fever prevention, serum penicillin levels were determined at 1, 3, 10, 21, and 28 days after administration of 1,200,000 units of this repository penicillin. A total of 193 samples were studied. Mean serum penicillin levels remained greater than or equal to 0.02 micrograms/ml for 21 days, but by 28 days only 44% of the serum samples had detectable levels of penicillin and only 36% had levels greater than or equal to 0.02 micrograms/ml. Patients weighing more than 45 kg had significantly lower serum penicillin levels than did those who weighed less. There were similar correlations with body surface area and with age. These data indicate that a significant percentage of patients receiving benzathine penicillin G prophylaxis for prevention of recurrent attacks of rheumatic fever are not protected during the fourth week. More frequent administration of benzathine penicillin G should be considered in instances of high risk of recurrence of rheumatic fever.

Adolescent↗
PubMed1996

Utility of the National Cooperative Growth Study database for safety reporting.

The National Cooperative Growth Study (NCGS) maintains the largest database in the world, collecting information on patients with growth disorders treated with growth hormone (GH). More than 24,000 children have been monitored during its first decade (1985 through 1995). The database provides unique opportunities to learn about effectiveness of GH therapy in a real-world context. Its size also makes it possible to investigate rare adverse reactions, which is not reasonable in a randomized controlled trial (RCT). The frequency of adverse experiences reported in an observational study like the NCGS is lower than in an RCT, because the investigators in an observational study typically do not report events that they believe are clearly unrelated to the study drug. Nevertheless the NCGS has greatly facilitated collecting adverse-event data; approximately 75% of all adverse-event reports for GH received by the manufacturer are through NCGS data-collection forms. The NCGS has thus amassed a repository of GH safety data that is unparalleled. Furthermore, in contrast to an RCT, the NCGS database reflects real-world experience with long-term GH therapy in North America. Although the advantages of an observational study such as the NCGS must be recognized, such a study does differ from an RCT in important ways. For example, because the NCGS protocol allows customized patient treatment and individualization of GH therapy, it may be difficult to use the database to address questions (e. g., estimation of dose-response relationships, true incidence of adverse events) that require RCT designs.

Adverse Drug Reaction Reporting Systems↗
PubMed2006

Renal and extrarenal predictors of nephrectomy from the national trauma data bank.

PURPOSE: The kidney is injured in 1.4% to 3.0% of all trauma cases. The management of renal injuries is controversial, as reflected in regional and institutional variations in treatment preferences. Using a national trauma database we identified independent risk factors for nephrectomy. MATERIALS AND METHODS: The population was selected from the National Trauma Data Bank, a voluntary data repository containing all trauma admissions to 268 participating trauma centers. Patients with renal injuries were identified by Abbreviated Injury Scale codes. Patient demographic, associated injuries and facility characteristics were recorded. Univariate and Poisson regression analysis with clustering by facility was performed. RESULTS: Renal injury was present in 8,465 patients. Nephrectomy was performed in 4% of all blunt and 21% of all cases of penetrating renal injuries. Only 0.5% of blunt renal injury cases underwent repair compared with 15% of those of penetrating injuries. On multivariate analysis renal injury severity was the strongest predictor of nephrectomy. The relative risk of nephrectomy for grade V renal injuries was 146 (95% CI 74 to 289) and 33 (95% CI 13 to 89) in the blunt and penetrating models, respectively. The need for laparotomy and surgery on other intra-abdominal organs predicted nephrectomy in patients with blunt and penetrating injuries. Hospital trauma designation did not statistically impact nephrectomy rates. CONCLUSIONS: The severity of renal injury based on the AAST organ injury scale for Renal Trauma is the strongest risk factor for nephrectomy. The need for surgery on other intra-abdominal injuries increases the risk of nephrectomy to a lesser extent. In cases of blunt trauma severe renal injury usually necessitates nephrectomy.

Adult↗
PubMed2002

Distributed structure-searchable toxicity (DSSTox) public database network: a proposal.

The ability to assess the potential genotoxicity, carcinogenicity, or other toxicity of pharmaceutical or industrial chemicals based on chemical structure information is a highly coveted and shared goal of varied academic, commercial, and government regulatory groups. These diverse interests often employ different approaches and have different criteria and use for toxicity assessments, but they share a need for unrestricted access to existing public toxicity data linked with chemical structure information. Currently, there exists no central repository of toxicity information, commercial or public, that adequately meets the data requirements for flexible analogue searching, Structure-Activity Relationship (SAR) model development, or building of chemical relational databases (CRD). The distributed structure-searchable toxicity (DSSTox) public database network is being proposed as a community-supported, web-based effort to address these shared needs of the SAR and toxicology communities. The DSSTox project has the following major elements: (1) to adopt and encourage the use of a common standard file format (structure data file (SDF)) for public toxicity databases that includes chemical structure, text and property information, and that can easily be imported into available CRD applications; (2) to implement a distributed source approach, managed by a DSSTox Central Website, that will enable decentralized, free public access to structure-toxicity data files, and that will effectively link knowledgeable toxicity data sources with potential users of these data from other disciplines (such as chemistry, modeling, and computer science); and (3) to engage public/commercial/academic/industry groups in contributing to and expanding this community-wide, public data sharing and distribution effort. The DSSTox project's overall aims are to effect the closer association of chemical structure information with existing toxicity data, and to promote and facilitate structure-based exploration of these data within a common chemistry-based framework that spans toxicological disciplines.

Carcinogens↗
PubMedDate not supplied

Limbal stem cells of the corneal epithelium.

Stem cells have certain unique characteristics, which include longevity, high capacity of self-renewal with a long cell cycle time and a short S-phase duration, increased potential for error-free proliferation, and poor differentiation. The ocular surface is made up of two distinct types of epithelial cells, constituting the conjunctival and the corneal epithelia. Although anatomically continuous with each other at the corneoscleral limbus, the two cell phenotypes represent quite distinct subpopulations. Stem cells for the cornea reside at the corneoscleral limbus. The limbal palisades of Vogt and the interpalisade rete ridges are believed to be repositories of stem cells. The microenvironment of the limbus is considered to be important in maintaining the stemness of stem cells. Limbal stem cells also act as a "barrier" to conjunctival epithelial cells and normally prevent them from migrating on to the corneal surface. Under certain conditions, however, the limbal stem cells may be partially or totally depleted, resulting in varying degrees of stem cell deficiency with resulting abnormalities in the corneal surface. Such deficiency of limbal stem cells leads to "conjunctivalization" of the cornea with vascularization, appearance of goblet cells, and an irregular and unstable epithelium. This results in ocular discomfort and reduced vision. Partial stem cell deficiency can be managed by removing the abnormal epithelium and allowing the denuded cornea, especially the visual axis, to resurface with cells derived from the remaining intact limbal epithelium. In total stem cell deficiency, autologous limbus from the opposite normal eye or homologous limbus from living related or cadaveric donors can be transplanted on to the affected eye. With the latter option, systemic immunosuppression is required. Amniotic membrane transplantation is a useful adjunct to the above procedures in some instances.

Cell Movement↗
PubMed1988

Pathologic features of extraosseous Ewing's sarcoma: a report from the Intergroup Rhabdomyosarcoma Study.

Eighty-four cases of extraosseous Ewing's sarcoma (EOE) were found during the pathology review of the Intergroup Rhabdomyosarcoma Study I and II. Patients commonly presented during or after adolescence with the most common primary sites including the trunk, extremities, and retroperitoneum. Males were slightly more affected. Histologic sections of 74 tumors in the pathology repository were re-reviewed with attention to rosette formation (positive in 18 cases) and glycogen deposition (++ in 21, + in 36, +/- in 11, and - in 2 of 70 cases examined). Fourteen tumors (7 with rosettes and 7 without) were selected for immunohistochemical and ultrastructural studies, and 13 showed single or multiple neural markers (neuron-specific enolase in 8, S-100 protein in 6, and neurosecretory-type granules in 9). These possible cases of neural EOE could be divided into three subgroups: tumor with bidirectional neuroblastic and schwannian differentiation (5 cases), tumor with monodirectional neuroblastic differentiation (7 cases), and tumor with monodirectional schwannian differentiation (1 case). EOE with a neural nature may be categorized into a spectrum of peripheral primitive neuroectodermal tumors. Clinical, histopathologic, and biologic differences between this disease and conventional sympathetic neuroblastoma are discussed.

Child↗
PubMed2002

A chemical and mineralogical reconstruction of Zn-smelter emissions in the Kempen region (Belgium), based on organic pool sediment cores.

The atmospheric pollution history of a former Belgian Zn-smelter complex is preserved in organic sediments of a nearby peat bog pool. The stratigraphy of trace metals, Pb-isotope ratios and mineralogy indicate extreme heavy metal pollution in recent sediments. In the pollutant trend, extremes coincide with maxima in 20th century metal production, minima during major war conflicts and the final shutdown of the smelter. Peak pollution concentrations measure up to 4.7 wt.% Zn, 1.1 wt.% Pb and 0.1 wt.% Cd, which correspond to calculated atmospheric deposition rates of 9.0, 1.6 and 0.16 g m(-2) yr(-1), respectively. 206Pb/207Pb isotope ratios show higher values in the polluted interval (1.135-1.162) relative to local geogenic values deeper down-core (1.194-1.215). Within the polluted interval, three significantly different 208Pb/206Pb plateaus are recognized and suggested to indicate changes in the origins of processed ores. Microprobe analyses on sediment thin sections show extensive in situ FeS2 and ZnS precipitation, which suggests that anoxic processes are responsible for the immobilization of the atmospheric metal inputs. The occurrence of oxidized smelter dusts in an independent surface soil sample indicates a rapid diagenetic transformation of metal oxides into sulfides. Morphology and chemical characteristics allow the distinction between smelter related and diagenetic mineral deposits, and give evidence for dust from open-air ore repositories, as well as smelter operation without dust filters.

Air Pollutants↗
PubMed2003

The Fungal Genetics Stock Center: from molds to molecules.

The FGSC, which began as a specialized repository for Neurospora and Aspergillus mutants, has grown to hold over 16,000 fungal strains as well as a variety of molecular genetics tools. The FGSC has expanded to include a variety of different fungi including Magnaporthe and Fusarium and is part of the Magnaporthe genome and knockout projects. The FGSC serves as a central clearing house for information in fungal genetics and has a role in facilitating the meetings of the Neurospora and fungal genetics communities. The FGSC is a model for the development of a culture collection much as Neurospora serves as a model organism.

Biological Specimen Banks↗
PubMed2004

Cell and molecular biology of nucleolar assembly and disassembly.

Nucleoli disassemble in prophase of the metazoan mitotic cycle, and they begin their reassembly (nucleologenesis) in late anaphase?early telophase. Nucleolar disassembly and reassembly were obvious to the early cytologists of the eighteenth and nineteenth centuries, and although this has lead to a plethora of literature describing these events, our understanding of the molecular mechanisms regulating nucleolar assembly and disassembly has expanded immensely just within the last 10-15 years. We briefly survey the findings of nineteenth-century cytologists on nucleolar assembly and disassembly, followed by the work of Heitz and McClintock on nucleolar organizers. A primer review of nucleolar structure and functions precedes detailed descriptions of modern molecular and microscopic studies of nucleolar assembly and disassembly. Nucleologenesis is concurrent with the reinitiation of rDNA transcription in telophase. The perichromosomal sheath, prenucleolar bodies, and nucleolar-derived foci serve as repositories for nucleolar processing components used in the previous interphase. Disassembly of the perichromosomal sheath along with the dynamic movements and compositional changes of the prenucleolar bodies and nucleolus-derived foci coincide with reactivation of rDNA synthesis within the chromosomal nucleolar organizers during telophase. Nucleologenesis is considered in various model organisms to provide breadth to our understanding. Nucleolar disassembly occurs at the onset of mitosis primarily as a result of the mitosis-specific phosphorylation of Pol I transcription factors and processing components. Although we have learned much regarding nucleolar assembly and disassembly, many questions still remain, and these questions are as vibrant for us today as early questions were for nineteenth- and early twentieth-century cytologists.

Animals↗
PubMed2006

Gene expression omnibus: microarray data storage, submission, retrieval, and analysis.

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information archives and freely distributes high-throughput molecular abundance data, predominantly gene expression data generated by DNA microarray technology. The database has a flexible design that can handle diverse styles of both unprocessed and processed data in a Minimum Information About a Microarray Experiment-supportive infrastructure that promotes fully annotated submissions. GEO currently stores about a billion individual gene expression measurements, derived from over 100 organisms, submitted by over 1500 laboratories, addressing a wide range of biological phenomena. To maximize the utility of these data, several user-friendly web-based interfaces and applications have been implemented that enable effective exploration, query, and visualization of these data at the level of individual genes or entire studies. This chapter describes how data are stored, submission procedures, and mechanisms for data retrieval and query. GEO is publicly accessible at http://www.ncbi.nlm.nih.gov/projects/geo/.

Animals↗
PubMed2006

Clustering methods for analyzing large data sets: gonad development, a study case.

With the development of data set repositories, it is now possible to collate high numbers of related results by gathering data from experiments carried out in different laboratories and addressing similar questions or using a single type of biological material under different conditions. To address the challenge posed by the heterogeneous nature of multiple data sources, this chapter presents several methods used routinely for assessing the quality of data (i.e., reproducibility of replicates and similarity between experimental points obtained under identical or similar biological conditions). As gene clustering on large data sets is not straightforward, this chapter also presents a rapid gene clustering method that involves translating variation profiles from an ordered set of comparisons into chains of symbols. In addition, it shows that lists of genes assembled based on the presence of a common term in their functional description can be used to find the most informative comparisons and to construct from them exemplar chains of symbols that are useful for clustering similar genes. Finally, this symbolic approach is extended to the overall set of biological conditions under study and shows how the resultant collection of variation profiles can be used to construct transcriptional networks, which in turn can be used as powerful tools for gene clustering.

Animals↗
PubMed2006

Genetic approaches to autonomic dysreflexia.

Autonomic dysreflexia is a potentially life-threatening condition in which episodic hypertension occurs after injuries above the mid-thoracic segments of the spinal cord. Despite the seriousness of this condition, little is known of the molecular mechanisms that lead to its development. The completed sequencing of the mouse genome, its dense genetic map, and the large repository of engineered and spontaneous mouse mutants, make the mouse an ideal model organism in which to study the molecular mechanisms underlying autonomic dysreflexia. We subjected two wild-type strains of mice, 129Sv and C57BL/6, and one spontaneous mouse mutant, Wallerian degeneration slow (Wld s), to spinal cord transection and clip-compression injury. We found that the incidence of autonomic dysreflexia is greatly reduced, compared to spinal cord-transected wild-type mice, in Wld s mice after both injury paradigms and in 129Sv and C57BL/6 that have undergone the clip-compression injury. We also found that the amplitude of the dysreflexic response was greater in cord-compressed 129Sv than in C57BL/6 mice. These results implicate axonal degeneration as an important source of signals that trigger the development of autonomic dysreflexia and are discussed in the context of mouse genetics, interstrain differences and possible molecular mechanisms underlying autonomic dysreflexia after spinal cord injury.

Animals↗
PubMed1998

Vasopressin in the mammalian brain: the neurobiology of a mnemonic peptide.

We have sought to understand the mechanisms by which VP can enhance memory function and in the process determine whether VP fulfills the requirements for neurotransmitter status. The latter goal of proving the neurotransmitter status of VP has been achieved through our findings and the results of many of the scientists contributing to this volume. With respect to elucidating the mechanisms by which VP can enhance memory function, results of our work have shown that VP and its receptors are present in brain regions known to be involved in memory function, that release of VP is inhibited by a factor that inhibits memory function, that VP can significantly enhance the morphological complexity and outgrowth of neurons involved in memory function, that second messenger systems held to be involved in learning and memory, cyclic AMP and calcium signaling pathways, are potentiated and activated by VP, that electrophysiological models of memory function are induced by VP, and that when animals remember a learned association VP content in brain increases over time during the active phase of remembering. Collectively, these studies have taught us a great deal about the sites and mechanisms of VP action and have led us to pursue avenues of investigation that we would not have imagined 15 years ago when we began this work. We stand on the threshold of a new era in our research as we begin our studies of the role VP and its receptors play in the cerebral cortex. Thus far, results of these studies are quite exciting and promise to yield fascinating insights into the complexities of VP action in the most highly developed region of the mammalian brain, the cerebral cortex, the site of abstract reasoning, judgment, complex analysis and the repository of those memories that last a life-time.

Animals↗