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.

SourceResearch connectionFrom yearThrough year

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

At least 1,729 records · Page 96Linked to original sources

PubMed2006

Inflammatory bowel disease characteristics among African Americans, Hispanics, and non-Hispanic Whites: characterization of a large North American cohort.

OBJECTIVES: Inflammatory bowel disease (IBD), comprising primarily of Crohn's disease (CD) and ulcerative colitis (UC), is increasingly prevalent in racial and ethnic minorities. This study was undertaken to characterize racial differences in disease phenotype in a predominantly adult population. METHODS: Phenotype data on 830 non-Hispanic white, 127 non-Hispanic African American, and 169 Hispanic IBD patients, recruited from six academic centers, were abstracted from medical records and compiled in the NIDDK-IBD Genetics Consortium repository. We characterized racial differences in family history, disease location and behavior, surgical history, and extraintestinal manifestations (EIMs) using standardized definitions. RESULTS: African American CD patients were more likely than whites to develop esophagogastroduodenal CD (OR = 2.8; 95% CI: 1.4-5.5), colorectal disease (OR = 1.9; 95% CI: 1.1-3.4), perianal disease (OR = 1.7; 95% CI: 1.03-2.8), but less likely to have ileal involvement (OR = 0.55; 95% CI: 0.32-0.96). They were also at higher risk for uveitis (OR = 5.5; 95% CI: 2.3-13.0) and sacroiliitis (OR = 4.0; 95% CI: 1.55-10.1). Hispanics had higher prevalence of perianal CD (OR = 2.9; 95% CI: 1.8-4.6) and erythema nodosum (3.3; 95% CI: 1.7-6.4). Among UC patients, Hispanics had more proximal disease extent. Both African American and Hispanic CD patients, but not UC patients, had lower prevalences of family history of IBD than their white counterparts. CONCLUSIONS: There are racial differences in IBD family history, disease location, and EIMs that may reflect underlying genetic variations and have important implications for diagnosis and management of disease. These findings underscore the need for further studies in minority populations.

Adult↗

PubMed2000

Analysis of the morphologic changes of Monascus sp. J101 cells cocultured with Saccharomyces cerevisiae.

Changes in cell life cycle and intracellular structure of Monascus sp. J101 by coculture with Saccharomyces cerevisiae were investigated. Cocultured Monascus cells showed accelerated cell growth and reproduction. Production of asexual and sexual spores was used as an efficient method of cell proliferation. Formation of meiotic (sexual) spores was more frequently observed in the cocultured Monascus cells. The interior structure of a cocultured cell was characterized by increased numbers and sizes of vacuoles. The vacuoles probably serve as repositories for pigment storage. Pigments produced by the cocultured Monascus cells were more hydrophobic than pigments produced by control cells with no coculture.

Ascomycota↗

PubMed2005

Medication utilization behavior in patients receiving phosphodiesterase type 5 inhibitors for erectile dysfunction.

INTRODUCTION: A number of preference studies have been conducted with phosphodiesterase type 5 (PDE5) inhibitor medications demonstrating inconsistent findings. Additionally, limited information is available regarding real-world utilization patterns of PDE5 inhibitors. AIM: To evaluate treatment patterns using real-world data for patients initiating erectile dysfunction (ED) therapy with Viagra (sildenafil citrate), Levitra (vardenafil), or Cialis (tadalafil). METHODS: Patients with an initial prescription claim for sildenafil, vardenafil, or tadalafil were identified in NDCHealth's Intelligent Health Repository. Medication refills, medication switching, and dose titration were analyzed. Logistic regression on the odds of refilling initial PDE5 medications was conducted controlling for patient age, presence of common comorbidities, initial number of tablets, and copay. RESULTS: A higher percentage of patients receiving sildenafil (52%) refilled their ED medication during the study period than patients receiving vardenafil (30%) or tadalafil (29%) (P<0.001). A smaller percentage of patients in the sildenafil cohort (6.4%) switched medication than in the tadalafil (9.0%) or vardenafil (10.4%) cohorts (P<0.001); the difference between the tadalafil and vardenafil cohorts in switching medications was also significant (P<0.001). There were no statistically significant differences between cohorts in dose titration frequency, which was low in all three treatment cohorts. Using logistic regression, the odds of refilling initial PDE5 therapy was significantly lower for vardenafil (odds ratio [OR]: 0.39, 95% confidence interval [CI]: 0.38-0.40; P<0.0001) and tadalafil (OR: 0.38, 95% CI: 0.37-0.40; P<0.0001) compared with sildenafil. CONCLUSIONS: Patients who were initially prescribed sildenafil were significantly more likely to refill their medication and significantly less likely to switch medications during the study period compared with patients who were initially prescribed vardenafil or tadalafil. These findings may indicate greater treatment satisfaction in patients receiving sildenafil, although future prospective evaluation is required.

Adult↗

PubMedDate not supplied

Effect of heterogeneity on radionuclide retardation in the alluvial aquifer near Yucca Mountain, Nevada.

The U.S. Department of Energy is currently studying Yucca Mountain, Nevada, as a potential site for a geological high-level waste repository. In the current conceptual models of radionuclide transport at Yucca Mountain, part of the transport path to pumping locations would be through an alluvial aquifer. Interactions with minerals in the alluvium are expected to retard the downstream migration of radionuclides, thereby delaying arrival times and reducing ground water concentrations. We evaluate the effectiveness of the alluvial aquifer as a transport barrier using the stochastic Lagrangian framework. A transport model is developed to account for physical and chemical heterogeneities and rate-limited mass transfer between mobile and immobile zones. The latter process is caused by small-scale heterogeneity and is thought to control the macroscopic-scale retardation in some field experiments. A geostatistical model for the spatially varying sorption parameters is developed from a site-specific database created from hydrochemical measurements and a calibrated modeling approach (Turner and Pabalan 1999). Transport of neptunium is considered as an example. The results are sensitive to the rate of transfer between mobile and immobile zones, and to spatial variability in the hydraulic conductivity. Chemical heterogeneity has only a small effect, as does correlation between hydraulic conductivity and the neptunium distribution coefficient. These results illustrate how general sensitivities can be explored with modest effort within the Lagrangian framework. Such studies complement and guide the application of more detailed numerical simulations.

Actinoid Series Elements↗

PubMedDate not supplied

Stochastic study of solute transport in a nonstationary medium.

A Lagrangian stochastic approach is applied to develop a method of moment for solute transport in a physically and chemically nonstationary medium. Stochastic governing equations for mean solute flux and solute covariance are analytically obtained in the first-order accuracy of log conductivity and/or chemical sorption variances and solved numerically using the finite-difference method. The developed method, the numerical method of moments (NMM), is used to predict radionuclide solute transport processes in the saturated zone below the Yucca Mountain project area. The mean, variance, and upper bound of the radionuclide mass flux through a control plane 5 km downstream of the footprint of the repository are calculated. According to their chemical sorption capacities, the various radionuclear chemicals are grouped as nonreactive, weakly sorbing, and strongly sorbing chemicals. The NMM method is used to study their transport processes and influence factors. To verify the method of moments, a Monte Carlo simulation is conducted for nonreactive chemical transport. Results indicate the results from the two methods are consistent, but the NMM method is computationally more efficient than the Monte Carlo method. This study adds to the ongoing debate in the literature on the effect of heterogeneity on solute transport prediction, especially on prediction uncertainty, by showing that the standard derivation of solute flux is larger than the mean solute flux even when the hydraulic conductivity within each geological layer is mild. This study provides a method that may become an efficient calculation tool for many environmental projects.

Adsorption↗

PubMedDate not supplied

Local hydraulic gradient estimator analysis of long-term monitoring networks.

Three measurements of head at unique locations form a three-point estimator of the local magnitude and orientation of the hydraulic gradient. The relative head measurement error (RHME) is defined here as the measurement error normalized by the head drop across the three-point estimator. Monte Carlo simulation results show that estimators with base to height ratios between 0.5 and 5.0 and that are large enough to keep the RHME below 0.05 create the most accurate gradient estimates and provide criteria for identifying good estimators. These criteria are applied to an example ground water monitoring network design problem in the Culebra dolomite near the Waste Isolation Pilot Plant repository to both analyze temporal changes and modify and expand the current monitoring network. Limiting the three-point estimators to those that meet the shape and RHME criteria reduces the number of possible estimators by >50% and leads to approximately 1 order of magnitude decrease in the average estimated magnitude of the gradient relative to using all estimators. Application of these criteria also reduces the variability in estimated gradient magnitude and orientation between the two time periods of measurements. Redundant wells in the network are identified by removing each existing well in turn and determining which removals yield the smallest decrease in the number of acceptable estimators. Optimal new well locations are identified by mapping the increase in total number of acceptable estimators for a single new well placed in the study domain.

Computer Simulation↗

PubMed1993

Using portfolios to assess student performance in school health education.

Outcome-based education is a topic of growing interest in educational circles today. More performance-oriented than traditional learning approaches, outcome-based education requires students to demonstrate what they know and what they can do. Because of this emphasis, outcome-based curricula will require new methods to assess student achievement. One approach is the portfolio, a repository that enables students to document authentic examples of academic work and presentations as well as nonschool accomplishments. The possibility of using portfolio-based assessment as a viable mechanism to promote comprehensive school health education is examined. Practical recommendations concerning portfolio development and evaluation are offered.

Health Education↗

PubMed1991

Platelet protease nexin-2/amyloid beta-protein precursor. Possible pathologic and physiologic functions.

The amyloid beta-protein and its parent protein, amyloid beta-protein precursor (APP), are major constituents of neuritic plaques and cerebrovascular deposits in Alzheimer's disease and Down's syndrome. We reported that the protease inhibitor protease nexin-2 (PN-2) is the secreted form of APP that contains the Kunitz protease inhibitor domain. Previous studies suggested that circulating forms of PN-2/APP exist. Recently, we reported that PN-2/APP is a platelet alpha granule protein and is secreted upon platelet activation. Subsequent studies revealed that platelets are the major circulating repository for PN-2/APP and may contribute to its deposition in Alzheimer's disease. Protease inhibition measurements demonstrated that PN-2/APP is a potent inhibitor of certain serine proteases, particularly intrinsic blood coagulation factor XIa. Together, these findings indicate that PN-2/APP regulates blood coagulation, and possibly other proteolytic events, at sites of vascular injury.

Alzheimer Disease↗

PubMed2000

The role of the World Reference Laboratories for Foot-and-Mouth Disease and for Rinderpest.

The World Reference Laboratories for Foot-and-Mouth Disease and for Rinderpest provide a worldwide diagnostic and surveillance service for these disease for FAO and OIE. Both laboratories are housed within the high security facility of the Institute for Animal Health, Pirbright, UK. Foot-and-mouth disease (FMD) and rinderpest (RP) are OIE List A diseases and historically have caused huge losses to agricultural economies around the world, prompting the establishment of veterinary colleges in Europe and environmentally controversial control programs in Africa. FMD and RP have now been geographically restricted, but the large legal and illegal world trade in live animals and animal products constantly threatens to allow them to spread back into disease-free areas. The Reference Laboratories provide a center of excellence for the development of improved diagnostic techniques and a repository of isolates collected over many years. These libraries provide material for investigations of the molecular epidemiology and evolution of the viruses and a data base against which new isolates can be compared. Thus it is possible to individually characterize new outbreak strains, identify their likely origin and provide the most up-to-date support for their control.

Africa↗

PubMed2001

Proteomic approaches within the NCI early detection research network for the discovery and identification of cancer biomarkers.

In the postgenome era, proteomics provides a powerful approach for the analysis of normal and transformed cell functions, for the identification of disease-specific targets, and for uncovering novel endpoints for the evaluation of chemoprevention agents and drug toxicity. Unfortunately, the genomic information that has greatly expounded the genetic basis of cancer does not allow an accurate prediction of what is actually occurring at the protein level within a given cell type at any given time. The gene expression program of a given cell is affected by numerous factors in the in vivo environment resulting from tissue complexity and organ system orchestration, with cells acting in concert with each other and responding to changes in their microenvironment. Repositories of genomic information can be considered master "inventory lists" of genes and their maps, which need to be supplemented with protein-derived information. The National Cancer Institute's Early Detection Research Network is employing proteomics, or "protein walking", in the discovery and evaluation of biomarkers for cancer detection and for the identification of high-risk subjects. Armed with microdissection techniques, including the use of Laser Capture Microdissection (LCM) to procure pure populations of cells directly from human tissue, the Network is facilitating the development of technologies that can overcome the problem of tissue heterogeneity and address the need to identify markers in easily accessible biological fluids. Proteomic approaches complement plasma-based assays of circulating DNA for cancer detection and risk assessment. LCM, coupled with downstream proteomics applications, such as two-dimensional polyacrylamide gel electrophoresis and SELDI (surface enhanced laser desorption ionization) separation followed by mass spectrometry (MS) analysis, may greatly facilitate the characterization and identification of protein expression changes that track normal and disease phenotypes. We highlight recent work from Network investigators to demonstrate the potential of proteomics to identify proteins present in cancer tissues and body fluids that are relevant for cancer screening.

Biomarkers, Tumor↗

PubMed2002

Automated biological sequence description by genetic multiobjective generalized clustering.

Recent advances in the accessibility of databases containing representations of complex objects-exemplified by repositories of time-series data, information about biological macromolecules, or knowledge about metabolic pathways-have not been matched by availability of tools that facilitate the retrieval of objects of particular interest and aid understanding their structure and relations. In applications, such as the analysis of DNA sequences, on the other hand, requirements to retrieve objects on the basis of qualitative characteristics are poorly met by descriptions that emphasize precision and detail rather than structural features. This paper presents a method for identification of interesting qualitative features in biological sequences. Our approach relies on a generalized clustering methodology in which the features being sought correspond to the solutions of a multivariable, multiobjective optimization problem with features generally corresponding to fuzzy subsets of the object being represented. Foremost among the optimization objectives being considered are measures of the degree by which features resemble prototypical structures deemed to be interesting by database users. Other objectives include feature size and, in some cases, performance criteria related to domain-specific constraints. Genetic-algorithm methods are employed to solve the multiobjective optimization problem. These optimization algorithms discover candidate features as subsets of the object being described and that lie in the set of all Pareto-optimal solutions-of that problem. These candidate features are then summarized, employing again evolutionary-computation methods, and interrelated by employing domain-specific relations of interest to the end users. We present results of the application of this two-step method to the recognition and summarization of interesting features in DNA sequences of Tripanosoma cruzi.

Algorithms↗

PubMed2002

An XML Gateway to Patient Data for Medical Research Applications.

As the medical environment becomes increasingly electronic, clinical databases are continually growing, accruing masses of patient information. This wealth of data is an invaluable source of information to researchers, serving as a testbed for the development of new information technologies and as a repository of real-world data for data mining and population-based studies. However, the true utility of this information is not fulfilled, in part because of issues pertaining to security and patient confidentiality, but also due to the lack of an effective infrastructure to access the data. This paper describes a system, DataServer, that permits researchers to query and retrieve data from multiple clinical data sources, automatically deidentifying patient data so that it can be used for research purposes. DataServer functions as an application framework, enabling extensible markup language (XML)-based querying of existing medical databases. Key aspects of DataServer include ready inclusion of new information resources, minimal processing impact on existing clinical systems via a distributed cache, and flexible output representation via XSL (eXtensible Style Language) transforms.

Databases, Factual↗

PubMedDate not supplied

Primary hypoadrenocorticism in ten cats.

Primary hypoadrenocorticism was diagnosed in ten young to middle-aged cats of mixed breeding. Five of the cats were male, and five were female. Historic signs included lethargy (n = 10), anorexia (n = 10), weight loss (n = 9), vomiting (n = 4), and polyuria (n = 3). Dehydration (n = 9), hypothermia (n = 8), prolonged capillary refill time (n = 5), weak pulse (n = 5), collapse (n = 3), and sinus bradycardia (n = 2) were found on physical examination. Results of initial laboratory tests revealed anemia (n = 3), absolute lymphocytosis (n = 2), absolute eosinophilia (n = 1), and azotemia and hyperphosphatemia (n = 10). Serum electrolyte changes included hyponatremia (n = 10), hyperkalemia (n = 9), hypochloremia (n = 9), and hypercalcemia (n = 1). The diagnosis of primary adrenocortical insufficiency was established on the basis of results of adrenocorticotropic hormone (ACTH) stimulation tests (n = 10) and endogenous plasma ACTH determinations (n = 7). Initial therapy for hypoadrenocorticism included intravenous administration of 0.9% saline and dexamethasone and intramuscular administration of desoxycorticosterone acetate in oil. Three cats were euthanatized shortly after diagnosis because of poor clinical response. Results of necropsy examination were unremarkable except for complete destruction of both adrenal cortices. Seven cats were treated chronically with oral prednisone or intramuscular methylprednisolone acetate for glucocorticoid supplementation and with oral fludrocortisone acetate or intramuscular injections of repository desoxycorticosterone pivalate for mineralocorticoid replacement. One cat died after 47 days of therapy from unknown causes; the other six cats are still alive and well after 3 to 70 months of treatment.

Addison Disease↗

PubMedDate not supplied

Using quality service analysts to streamline record reviews.

By using registered nurse quality service analysts (RN-QSAs), the United States Air Force Medical Center in Wiesbaden, Germany, which closed in 1993, reduced physician reviews of medical records in 1991-1992 to only the records that did not meet the preestablished screening criteria. The authors relate how the screening of records by RN-QSAs increased the number of records reviewed, reduced the number of people reviewing records, established the quality services department as a repository of patient care information, and markedly improved the quantity, quality, and reproducibility of patient care reviews.

Concurrent Review↗

PubMedDate not supplied

Barriers and solutions in implementing occupational health and safety services at a large nuclear weapons facility.

The Hanford Nuclear Reservation is one of the U.S. Department of Energy's largest nuclear weapons sites. The enormous changes experienced by Hanford over the last several years, as its mission has shifted from weapons production to cleanup, has profoundly affected its occupational health and safety services. Innovative programs and new initiatives hold promise for a safer workplace for the thousands of workers at Hanford and other DOE sites. However, occupational health and safety professionals continue to face multiple organizational, economic, and cultural challenges. A major problem identified during this review was the lack of coordination of onsite services. Because each health and safety program operates independently (albeit with the guidance of the Richland field operations office), many services are duplicative and the health and safety system is fragmented. The fragmentation is compounded by the lack of centralized data repositories for demographic and exposure data. Innovative measures such as a questionnaire-driven Employee Job Task Analysis linked to medical examinations has allowed the site to move from the inefficient and potentially dangerous administrative medical monitoring assignment to defensible risk-based assignments and could serve as a framework for improving centralized data management and service delivery.

Contract Services↗

PubMedDate not supplied

An informatics infrastructure for patient safety and evidence-based practice in home healthcare.

The informatics infrastructure for patient safety and evidence-based practice (EBP) in home healthcare comprises data acquisition methods, healthcare standards including standardized terminologies, data repositories and clinical event monitors, data-mining techniques, digital sources of evidence, and communication technologies. Although the components of an informatics infrastructure are available and applications that bring these components together to promote patient safety and enable EBP have demonstrated positive or promising results in the acute care setting, a number of challenges hinder implementation in home healthcare. Resolution of these challenges requires commitment and collaboration among key stakeholders.

Benchmarking↗

PubMed2025

The Mycobacterium tuberculosis Transposon Sequencing Database (MtbTnDB): A Large-Scale Guide to Genetic Conditional Essentiality.

Characterizing genetic essentiality across various conditions is fundamental for understanding gene function. Transposon sequencing (TnSeq) is a powerful technique to generate genome-wide essentiality profiles in bacteria and has been extensively applied to Mycobacterium tuberculosis (Mtb). Dozens of TnSeq screens have yielded valuable insights into the biology of Mtb in vitro, inside macrophages, and in model host organisms. Despite their value, these Mtb TnSeq profiles have not been standardized or collated into a single, easily searchable database. This results in significant challenges when attempting to query and compare these resources, limiting our ability to obtain a comprehensive and consistent understanding of genetic conditional essentiality in Mtb. We address this problem by building a central repository of publicly available Mtb TnSeq screens, the Mtb transposon sequencing database (MtbTnDB). The MtbTnDB is a living resource that encompasses to date ≈150 standardized TnSeq screens, enabling open access to data, visualizations, and functional predictions through an interactive web app (www.mtbtndb.app). We conduct several statistical analyses on the complete database, such as demonstrating that (i) genes in the same genomic neighborhood have similar TnSeq profiles, and (ii) clusters of genes with similar TnSeq profiles are enriched for genes from similar functional categories. We further analyze the performance of machine learning models trained on TnSeq profiles to predict the functional annotation of orphan genes in Mtb. By facilitating the comparison of TnSeq screens across conditions, the MtbTnDB will accelerate the exploration of conditional genetic essentiality, provide insights into the functional organization of Mtb genes, and help predict gene function in this important human pathogen.

DNA Transposable Elements↗

PubMed2025

Identification of potential cell surface targets in patient-derived cultures toward photoimmunotherapy of high-grade serous ovarian cancer.

Tumor-targeted, activatable photoimmunotherapy (taPIT) has shown promise in preclinical models to selectively eliminate drug-resistant micrometastases that evade standard treatments. Moreover, taPIT has the potential to resensitize chemo-resistant tumor cells to chemotherapy, making it a complementary modality for treating recurrent high-grade serous ovarian cancer (HGSOC). However, the established implementation of taPIT relies on the overexpression of EGFR in tumor cells, which is not universally observed in HGSOCs. Motivated by the need to expand taPIT applications beyond EGFR, we conducted mRNA-sequencing and proteomics to identify alternative cell surface targets for taPIT in patient-derived HGSOC cell cultures with weak EGFR expression and lacking expression of other cell surface proteins commonly reported in the literature as overexpressed in ovarian cancers, such as FOLR1 and EpCAM. Our findings highlight TFRC and LRP1 as promising alternative targets. Notably, TFRC was overexpressed in 100% (N = 5) of the patient-derived HGSOC models tested, whereas only 60% of models had high EpCAM expression, suggesting that future larger cohort studies should include TFRC. While this study focuses on target identification, future work will expand the approaches developed here to larger HGSOC biopsy repositories and will also develop and evaluate antibody-photosensitizer conjugates targeting these proteins for taPIT applications.

Humans↗