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At least 235 records · Page 13Linked to original sources
PubMed2004

BioSimGrid: towards a worldwide repository for biomolecular simulations.

BioSimGrid is a database for biomolecular simulations, or, a "Protein Data Bank extended in time" for molecular dynamics trajectories. We describe the implementation details: architecture, data schema, deposition, and analysis modules. We encourage the simulation community to explore BioSimGrid and work towards a common trajectory exchange format.

Acetylcholinesterase↗
PubMed2001

Analysis of HBV infection after blood transfusion in Japan through investigation of a comprehensive donor specimen repository.

BACKGROUND: To understand the risk of transfusion-transmitted viral infection, it is important to precisely assess cases of infection that follow transfusion. STUDY DESIGN AND METHODS: HBV infections noted after transfusion in 1997, 1998, and 1999 were analyzed. Transfusion in all these cases was performed before NAT was adopted for donor screening. To detect viral infection, PCR and serologic tests for HBV were performed retrospectively on all blood samples from implicated donors that had been stored in a frozen state after each donation. The concentration of HBV genome was measured in HBV-positive blood samples. RESULTS: One hundred three cases of HBV infection were analyzed; of these, only 16, including at least 10 infections due to window-period (HBsAg-positive by reverse particle hemagglutination assay) donations, were confirmed by further testing to be related to transfusion. The concentrations of HBV genome were very low in four blood samples (<50, 400, 500, and 800 genome equivalents/mL of plasma). CONCLUSIONS: The remaining risk of transfusion transmission of HBV infection before the adoption of NAT was mainly due to window-period donations, including one that was made before the HBV genome was detectable by PCR. However, it was determined that transfusion was not responsible in many cases for HBV infection after transfusion.

Blood Donors↗
PubMed2004

Endoscopic evaluation of patients with dyspepsia: results from the national endoscopic data repository.

BACKGROUND & AIMS: Endoscopy is commonly performed to evaluate symptoms of dyspepsia. The aim of this study was to characterize patients who receive endoscopy for dyspepsia and measure predictors of primary endoscopic outcomes, utilizing a large national endoscopic database. METHODS: The Clinical Outcomes Research Initiative (CORI) receives endoscopy reports from a network of 74 sites in the United States. Sixty-one percent of reports come from private practice settings. Patients with reflux dyspepsia and nonreflux dyspepsia were identified from January 2000 to June 2002. Patients with dysphagia and known Barrett's esophagus were excluded. Primary endoscopic outcomes included esophageal inflammation and stricture, gastric ulcer, duodenal ulcer, suspected Barrett's esophagus (> or =2 cm), and suspected esophageal and gastric malignancy. The presence or absence of alarm symptoms (vomiting, weight loss, and evidence of GI blood loss) was determined. Adjusted relative risk (RR) for predicting serious outcomes was calculated in a multivariate model. RESULTS: We received 117,497 endoscopic reports, representing 99,558 unique patients. Dyspepsia, with and without reflux symptoms, accounted for 43% of upper endoscopies. Among dyspeptic patients, 36.5% were younger than 50 years of age without alarm symptoms. Esophageal or gastric malignancy in patients with dyspepsia was associated with increasing age, male sex, Asian race, Native American race, and symptoms of weight loss and vomiting. Suspected Barrett's esophagus (> or =2 cm) was associated with reflux symptoms, male sex, age, and white race. Ulcers were associated with evidence of bleeding, vomiting, male sex, black race, and Hispanic ethnicity. CONCLUSIONS: These practice-based data reveal important practice behaviors and outcomes.

Adult↗
PubMed1977

Shattuck lecture--The general medical journal: for readers or repositories?

General medical journals seek newsworthiness but face obstacles because of their usually slow publication schedules and because of contents that readers find either obscure or contradictory to long held beliefs. In addition, since medical news has become "big news," general medical journals find themselves in competition with both the lay press and the medical giveaways. One effect of the escalating public interest in medical news is that general medical journals that are reliable and have maintained their newsworthiness are increasingly cited. These journals thus eventually transmit research findings to the public as well as to the health-care professions. To help prevent exaggeration and misinterpretation by the lay press and by the public, general medical journals must evaluate submissions in a broader than traditional context. Nevertheless, newsworthiness is an appropiate goal for such journals.

Boston↗
PubMed2005

Building a human kinase gene repository: bioinformatics, molecular cloning, and functional validation.

Kinases catalyze the phosphorylation of proteins, lipids, sugars, nucleosides, and other important cellular metabolites and play key regulatory roles in all aspects of eukaryotic cell physiology. Here, we describe the mining of public databases to collect the sequence information of all identified human kinase genes and the cloning of the corresponding ORFs. We identified 663 genes, 511 encoding protein kinases, and 152 encoding nonprotein kinases. We describe the successful cloning and sequence verification of 270 of these genes. Subcloning of this gene set in mammalian expression vectors and their use in high-throughput cell-based screens allowed the validation of the clones at the level of expression and the identification of previously uncharacterized modulators of the survivin promoter. Moreover, expressions of the kinase genes in bacteria, followed by autophosphorylation assays, identified 21 protein kinases that showed autocatalytic activity. The work described here will facilitate the functional assaying of this important gene family in phenotypic screens and their use in biochemical and structural studies.

Animals↗
PubMed2003

Bioactive crude plant seed extracts from the NCAUR oilseed repository.

Over four-hundred crude extracts from 202 plant species distributed among 131 plant families were evaluated for their bioactivity against brine shrimp (Artemia salina). Activity was determined for both the organic (CH2Cl2:MeOH) and aqueous extracts against A. salina in a 96 well-plate assay. Of the greater than four-hundred extracts tested, 21 organic and 6 aqueous extracts demonstrated potent cytotoxic activity (LC50 = < 100 microg/ml). Three of these organic extracts (Crateva religiosa, Diospyros dichrophylla, and Olax subscorpioidea) were chosen for chemical investigations due to their high activity and a lack of prior investigations. Chemical analysis of these extracts resulted in the isolation of oleanolic acid (1) and 4-epi-hederagenin (2) from C. religiosa, isodiospyrin (3) from D. dichrophylla, and santalbic acid (4) from O. subscorpioidea.

Animals↗