Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “CATALOGING”

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 1,315 records · Page 73Linked to original sources
PubMedDate not supplied

Revolution through genomics in investigative and discovery toxicology.

The remarkable technologic and methodologic advances spurred on by the Human Genome Project are being applied throughout the life sciences. In the field of toxicology, high-resolution assays now make it possible to discover virtually all the differences in gene expression brought on by exposure to a particular xenobiotic. There are 2 principal approaches used to build a catalog of changes in gene expression: hybridization microarrays and gel-based methods, such as differential display and AFLP-based mRNA finger-printing. The power of such approaches is exemplified by the identification of more than 300 genes that differ in expression level by at least 2-fold in response to the nongenotoxic rodent liver carcinogen phenobarbital.

Animals↗
PubMedDate not supplied

Injuries among world-class professional beach volleyball players. The Fédération Internationale de Volleyball beach volleyball injury study.

BACKGROUND: Very little is known about the injury characteristics of beach volleyball. PURPOSE: To describe the incidence and pattern of injuries among professional male and female beach volleyball players. STUDY DESIGN: Cohort study--retrospective injury recall and prospective registration. METHODS: Injuries occurring over a 7.5-week interval of the summer season were retrospectively registered by interviewing 178 of the 188 participating players (95%) in the 2001 Beach Volleyball World Championships. Injuries were also cataloged prospectively during five of the tournaments held during this interval. RESULTS: Fifty-four acute injuries was recorded, of which 23 (43%) resulted in 1 or more days of missed practice or competition. The incidence of acute time-loss injuries was estimated to be 3.1 per 1000 competition hours and 0.8 per 1000 training hours. Knee (30%), ankle (17%), and finger injuries (17%) accounted for more than half of all acute time-loss injuries. In addition, 67 players reported 79 overuse injuries for which they received medical attention during the study period. The three most common overuse conditions were low back pain (19%), knee pain (12%), and shoulder problems (10%). Similar results were observed in the prospective portion of the study. CONCLUSIONS: The rate of acute time-loss injuries in beach volleyball is considerably lower than that in most other team sports, but overuse injuries affecting the low back, knees, and shoulder represent a significant source of disability and impaired performance for professional beach volleyball players.

Acute Disease↗
PubMed2003

A content analysis of Web sites promoting smoking culture and lifestyle.

The present study examined smoking culture and lifestyle Web sites listed on Yahoo!, a popular Internet search catalog, to determine whether the sites were easily accessible to youth, featured age or health warnings, and mentioned specific tobacco brands. A content analysis of photographs on these sites assessed the demographics of individuals depicted and the amount of smoking and nudity in the photographs. The sample included 30 Web sites, all of which were accessible to youth and did not require age verification services to enter them. Cigarette brand names were mentioned in writing on 35% of the sites, and brand images were present on 24% of the sites. Nearly all of the photographs (95%) depicted smoking, 92% featured women, and 7% contained partial or full nudity. These results underscore the need for greater research and monitoring of smoking-related Internet content by health educators and tobacco control advocates.

Adolescent↗
PubMed2003

New challenges for public health care: biological and chemical weapons awareness, surveillance, and response.

Recent events in the United States have demonstrated a critical need for recognizing nurses and emergency health care providers as important elements of the nation's first line of defense and response against terrorist attacks involving biological, chemical, or radiological weapons. The anthrax letter attacks of September/October 2001 demonstrate the importance of vigilance and attention to detail while interviewing and attending patients and when entering, reviewing, and cataloging patient records. Nursing professionals, emergency care responders, and physicians can perform a crucial role in our first-line defense against terrorism by detecting and reporting unusual or anomalous illness(es) consistent with possible exposure to biological or chemical agents. Nursing professionals should become more familiar with the etiology and clinical symptoms of biological agents of greatest current concern (smallpox, anthrax, tularemia, plague) and be alert for potentially anomalous or unfamiliar combinations of symptoms that could point to unwitting exposure to biological toxins, toxic chemicals, or cryptic radiological agents. Public health surveillance systems must be developed that encourage and facilitate the rapid reporting and follow-up investigation of suspect illnesses and potential disease outbreaks that will ensure early identification and response for covert attacks involving biological, chemical, or radiological weapons.

Biological Warfare↗
PubMed2002

Clinical proteomics for cancer biomarker discovery and therapeutic targeting.

As we emerge into the post-genome era, proteomics finds itself as the driving force field as we translate the nucleic acid information archive into understanding how the cell actually works and how disease processes operate. Even so, the traditionally held view of proteomics as simply cataloging and developing lists of the cellular protein repertoire of a cell are now changing, especially in the sub-discipline of clinical proteomics. The most relevant information archive to clinical applications and drug development involves the elucidation of the information flow of the cell; the "software" of protein pathway networks and circuitry. The deranged circuitry of the cell as the drug target itself as well as the effect of the drug on not just the target, but also the entire network, is what we now are striving towards. Clinical proteomics, as a new and most exciting sub-discipline of proteomics, involves the bench-to-bedside clinical application of proteomic tools. Unlike the genome, there are potentially thousands of proteomes: each cell type has its own unique proteome. Moreover, each cell type can alter its proteome depending on the unique tissue microenvironment in which it resides, giving rise to multiple permutations of a single proteome. Since there is no polymerase chain reaction equivalent to proteomics- identifying and discovering the "wiring diagram" of a human diseased cell in a biopsy specimen remains a daunting challenge. New micro-proteomic technologies are being and still need to be developed to drill down into the proteomes of clinically relevant material. Cancer, as a model disease, provides a fertile environment to study the application of proteomics at the bedside. The promise of clinical proteomics and the new technologies that are developed is that we will detect cancer earlier through discovery of biomarkers, we will discover the next generation of targets and imaging biomarkers, and we can then apply this knowledge to patient-tailored therapy.

Algorithms↗
PubMed2002

Variants in the VCAM1 gene and risk for symptomatic stroke in sickle cell disease.

Stroke is a major cause of morbidity and mortality in sickle cell (SS) disease. Genetic risk factors have been postulated to contribute to this clinical outcome. The human genome project has substantially increased the catalog of variations in genes, many of which could modify the risk for manifestations of disease outcome in a monogenic disease, namely SS. VCAM1 is a cell adhesion molecule postulated to play a critical role in the pathogenesis of SS disease. We identified a total of 33 single nucleotide polymorphisms (SNPs) by sequencing the entire coding region, 2134 bp upstream of the 5' end of the published cDNA, 217 bp downstream of the 3' end of the cDNA, and selected intronic regions of the VCAM1 locus. Allelic frequencies for selected SNPs were determined in a healthy population. We subsequently analyzed 4 nonsynonymous coding, 2 synonymous coding, and 4 common promoter SNPs in a genetic association study of clinically apparent stroke in SS disease conducted in a cohort derived from a single institution in Jamaica (51 symptomatic cases and 51 matched controls). Of the 10 candidate SNPs analyzed in this pilot study, the variant allele of the nonsynonymous SNP, VCAM1 G1238C, may be associated with protection from stroke (odds ratio [OR] 0.35, 95% confidence interval [CI] 0.15-0.83, P =.04). Further study is required to confirm the importance of this variant in VCAM1 as a clinically useful modifier of outcome in SS disease.

Alleles↗
PubMed2002

A molecular compendium of genes expressed in multiple myeloma.

We have created a molecular resource of genes expressed in primary malignant plasma cells using a combination of cDNA library construction, 5' end single-pass sequencing, bioinformatics, and microarray analysis. In total, we identified 9732 nonredundant expressed genes. This dataset is available as the Myeloma Gene Index (www.uhnres.utoronto.ca/akstewart_lab).Predictably, the sequenced profile of myeloma cDNAs mirrored the known function of immunoglobulin-producing, high-respiratory rate, low-cycling, terminally differentiated plasma cells. Nevertheless, approximately 10% of myeloma-expressed sequences matched only entries in the database of Expressed Sequence Tags (dbEST) or the high-throughput genomic sequence (htgs) database. Numerous novel genes of potential biologic significance were identified. We therefore spotted 4300 sequenced cDNAs on glass slides creating a myeloma-enriched microarray. Several of the most highly expressed genes identified by sequencing, such as a novel putative disulfide isomerase (MGC3178), tumor rejection antigen TRA1, heat shock 70-kDa protein 5, and annexin A2, were also differentially expressed between myeloma and B lymphoma cell lines using this myeloma-enriched microarray. Furthermore, a defined subset of 34 up-regulated and 18 down-regulated genes on the array were able to differentiate myeloma from nonmyeloma cell lines. These not only include genes involved in B-cell biology such as syndecan, BCMA, PIM2, MUM1/IRF4, and XBP1, but also novel uncharacterized genes matching sequences only in the public databases. In summary, our expressed gene catalog and myeloma-enriched microarray contains numerous genes of unknown function and may complement other commercially available arrays in defining the molecular portrait of this hematopoietic malignancy. GenBank Accession numbers include BF169967-BF176369, BF185966-BF185969, and BF177280-BF177455.

Amino Acid Sequence↗
PubMed2001

Genomic and proteomic analysis of the myeloid differentiation program.

Although the mature neutrophil is one of the better characterized mammalian cell types, the mechanisms of myeloid differentiation are incompletely understood at the molecular level. A mouse promyelocytic cell line (MPRO), derived from murine bone marrow cells and arrested developmentally by a dominant-negative retinoic acid receptor, morphologically differentiates to mature neutrophils in the presence of 10 microM retinoic acid. An extensive catalog was prepared of the gene expression changes that occur during morphologic maturation. To do this, 3'-end differential display, oligonucleotide chip array hybridization, and 2-dimensional protein electrophoresis were used. A large number of genes whose mRNA levels are modulated during differentiation of MPRO cells were identified. The results suggest the involvement of several transcription regulatory factors not previously implicated in this process, but they also emphasize the importance of events other than the production of new transcription factors. Furthermore, gene expression patterns were compared at the level of mRNA and protein, and the correlation between 2 parameters was studied. (Blood. 2001;98:513-524)

Animals↗
PubMed2005

Benzodiazepines and anxiety disorders: a review for the practicing physician.

UNLABELLED: OBJECTIVES AND SCOPE: The objective of this article is to briefly review for practicing clinicians differences among the benzodiazepines (BZDs) that are commonly used to treat anxiety, the efficacy of BZDs in various anxiety disorders, and potential safety issues associated with BZDs, including adverse events, tolerance, dependence, and withdrawal. METHODOLOGY: Information for this review was obtained using literature searches through PubMed (1966-2004), Google, and the Food and Drug Administration Catalog of Approved Drugs. Data sources were searched for information regarding anxiety disorders and the safety and efficacy of BZDs. Wherever possible and appropriate, information from randomized controlled trials was given priority. FINDINGS: Benzodiazepines have demonstrated efficacy in treating patients with anxiety disorders, with varying degrees of efficacy. Use of BZDs is advantageous because they have a quick onset of action and are generally well tolerated. Extended-release formulations of BZDs may be particularly advantageous in some patients with anxiety as they allow for maximization of a drug's therapeutic window with consistent serum drug concentrations. CONCLUSIONS: BZDs remain a mainstay in the treatment of anxiety, as both monotherapy and adjunctive therapy. Factors to consider prior to prescribing a BZD include the patient's diagnosis, as well as drug characteristics, including the potential for interactions with other drugs, the risk of dependence and withdrawal, and the required frequency of dosing.

Anti-Anxiety Agents↗
PubMed2005

Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

BACKGROUND: To date, 35 human diseases, some of which also exhibit anticipation, have been associated with unstable repeats. Anticipation has been reported in a number of diseases in which repeat expansion may have a role in etiology. Despite the growing importance of unstable repeats in disease, currently no resource exists for the prioritization of repeats. Here we present Satellog, a database that catalogs all pure 1-16 repeat unit satellite repeats in the human genome along with supplementary data. Satellog analyzes each pure repeat in UniGene clusters for evidence of repeat polymorphism. RESULTS: A total of 5,546 such repeats were identified, providing the first indication of many novel polymorphic sites in the genome. Overall, polymorphic repeats were over-represented within 3'-UTR sequence relative to 5'-UTR and coding sequence. Interestingly, we observed that repeat polymorphism within coding sequence is restricted to trinucleotide repeats whereas UTR sequence tolerated a wider range of repeat period polymorphisms. For each pure repeat we also calculate its repeat length percentile rank, its location either within or adjacent to EnsEMBL genes, and its expression profile in normal tissues according to the GeneNote database. CONCLUSION: Satellog provides the ability to dynamically prioritize repeats based on any of their characteristics (i.e. repeat unit, class, period, length, repeat length percentile rank, genomic co-ordinates), polymorphism profile within UniGene, proximity to or presence within gene regions (i.e. cds, UTR, 15 kb upstream etc.), metadata of the genes they are detected within and gene expression profiles within normal human tissues. Unstable repeats associated with 31 diseases were analyzed in Satellog to evaluate their common repeat properties. The utility of Satellog was highlighted by prioritizing repeats for Huntington's disease and schizophrenia. Satellog is available online at http://satellog.bcgsc.ca.

3' Untranslated Regions↗
PubMed2005

Micro-Mar: a database for dynamic representation of marine microbial biodiversity.

BACKGROUND: The cataloging of marine prokaryotic DNA sequences is a fundamental aspect for bioprospecting and also for the development of evolutionary and speciation models. However, large amount of DNA sequences used to quantify prokaryotic biodiversity requires proper tools for storing, managing and analyzing these data for research purposes. DESCRIPTION: The Micro-Mar database has been created to collect DNA diversity information from marine prokaryotes for biogeographical and ecological analyses. The database currently includes 11874 sequences corresponding to high resolution taxonomic genes (16S rRNA, ITS and 23S rRNA) and many other genes including CDS of marine prokaryotes together with available biogeographical and ecological information. CONCLUSION: The database aims to integrate molecular data and taxonomic affiliation with biogeographical and ecological features that will allow to have a dynamic representation of the marine microbial diversity embedded in a user friendly web interface. It is available online at http://egg.umh.es/micromar/.

Base Sequence↗
PubMed2005

Sequence variation in ligand binding sites in proteins.

BACKGROUND: The recent explosion in the availability of complete genome sequences has led to the cataloging of tens of thousands of new proteins and putative proteins. Many of these proteins can be structurally or functionally categorized from sequence conservation alone. In contrast, little attention has been given to the meaning of poorly-conserved sites in families of proteins, which are typically assumed to be of little structural or functional importance. RESULTS: Recently, using statistical free energy analysis of tetratricopeptide repeat (TPR) domains, we observed that positions in contact with peptide ligands are more variable than surface positions in general. Here we show that statistical analysis of TPRs, ankyrin repeats, Cys2His2 zinc fingers and PDZ domains accurately identifies specificity-determining positions by their sequence variation. Sequence variation is measured as deviation from a neutral reference state, and we present probabilistic and information theory formalisms that improve upon recently suggested methods such as statistical free energies and sequence entropies. CONCLUSION: Sequence variation has been used to identify functionally-important residues in four selected protein families. With TPRs and ankyrin repeats, protein families that bind highly diverse ligands, the effect is so pronounced that sequence "hypervariation" alone can be used to predict ligand binding sites.

Binding Sites↗
PubMed2005

Computational identification of strain-, species- and genus-specific proteins.

BACKGROUND: The identification of unique proteins at different taxonomic levels has both scientific and practical value. Strain-, species- and genus-specific proteins can provide insight into the criteria that define an organism and its relationship with close relatives. Such proteins can also serve as taxon-specific diagnostic targets. DESCRIPTION: A pipeline using a combination of computational and manual analyses of BLAST results was developed to identify strain-, species-, and genus-specific proteins and to catalog the closest sequenced relative for each protein in a proteome. Proteins encoded by a given strain are preliminarily considered to be unique if BLAST, using a comprehensive protein database, fails to retrieve (with an e-value better than 0.001) any protein not encoded by the query strain, species or genus (for strain-, species- and genus-specific proteins respectively), or if BLAST, using the best hit as the query (reverse BLAST), does not retrieve the initial query protein. Results are manually inspected for homology if the initial query is retrieved in the reverse BLAST but is not the best hit. Sequences unlikely to retrieve homologs using the default BLOSUM62 matrix (usually short sequences) are re-tested using the PAM30 matrix, thereby increasing the number of retrieved homologs and increasing the stringency of the search for unique proteins. The above protocol was used to examine several food- and water-borne pathogens. We find that the reverse BLAST step filters out about 22% of proteins with homologs that would otherwise be considered unique at the genus and species levels. Analysis of the annotations of unique proteins reveals that many are remnants of prophage proteins, or may be involved in virulence. The data generated from this study can be accessed and further evaluated from the CUPID (Core and Unique Protein Identification) system web site (updated semi-annually) at http://pir.georgetown.edu/cupid. CONCLUSION: CUPID provides a set of proteins specific to a genus, species or a strain, and identifies the most closely related organism.

Algorithms↗
PubMed2005

The Gene Set Builder: collation, curation, and distribution of sets of genes.

BACKGROUND: In bioinformatics and genomics, there are many applications designed to investigate the common properties for a set of genes. Often, these multi-gene analysis tools attempt to reveal sequential, functional, and expressional ties. However, while tremendous effort has been invested in developing tools that can analyze a set of genes, minimal effort has been invested in developing tools that can help researchers compile, store, and annotate gene sets in the first place. As a result, the process of making or accessing a set often involves tedious and time consuming steps such as finding identifiers for each individual gene. These steps are often repeated extensively to shift from one identifier type to another; or to recreate a published set. In this paper, we present a simple online tool which - with the help of the gene catalogs Ensembl and GeneLynx - can help researchers build and annotate sets of genes quickly and easily. DESCRIPTION: The Gene Set Builder is a database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored to facilitate easy access. Gene sets stored in the system can be "exported" in a variety of output formats - as lists of identifiers, in tables, or as sequences. In addition, gene sets can be "shared" with specific users to facilitate collaborations or fully released to provide access to published results. The application also features a Perl API (Application Programming Interface) for direct connectivity to custom analysis tools. A downloadable Quick Reference guide and an online tutorial are available to help new users learn its functionalities. CONCLUSION: The Gene Set Builder is an Ensembl-facilitated online tool designed to help researchers compile and manage sets of genes in a user-friendly environment. The application can be accessed via http://www.cisreg.ca/gsb/.

Computational Biology↗
PubMed2006

iHAP--integrated haplotype analysis pipeline for characterizing the haplotype structure of genes.

BACKGROUND: The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows that genotype data from the International HapMap Project have a high degree of transferability to the wider population. This implies that the design of genotyping studies on local populations may be facilitated through inferences drawn from information contained in HapMap populations. RESULTS: To facilitate analysis of HapMap data for characterizing the haplotype structure of genes or any chromosomal regions, we have developed an integrated web-based resource, iHAP. In addition to incorporating genotype and haplotype data from the International HapMap Project and gene information from the UCSC Genome Browser Database, iHAP also provides capabilities for inferring haplotype blocks and selecting tag SNPs that are representative of haplotype patterns. These include block partitioning algorithms, block definitions, tag SNP definitions, as well as SNPs to be "force included" as tags. Based on the parameters defined at the input stage, iHAP performs on-the-fly analysis and displays the result graphically as a webpage. To facilitate analysis, intermediate and final result files can be downloaded. CONCLUSION: The iHAP resource, available at http://ihap.bii.a-star.edu.sg, provides a convenient yet flexible approach for the user community to analyze HapMap data and identify candidate targets for genotyping studies.

Algorithms↗
PubMed2006

Comparative analysis of haplotype association mapping algorithms.

BACKGROUND: Finding the genetic causes of quantitative traits is a complex and difficult task. Classical methods for mapping quantitative trail loci (QTL) in miceuse an F2 cross between two strains with substantially different phenotype and an interval mapping method to compute confidence intervals at each position in the genome. This process requires significant resources for breeding and genotyping, and the data generated are usually only applicable to one phenotype of interest. Recently, we reported the application of a haplotype association mapping method which utilizes dense genotyping data across a diverse panel of inbred mouse strains and a marker association algorithm that is independent of any specific phenotype. As the availability of genotyping data grows in size and density, analysis of these haplotype association mapping methods should be of increasing value to the statistical genetics community. RESULTS: We describe a detailed comparative analysis of variations on our marker association method. In particular, we describe the use of inferred haplotypes from adjacent SNPs, parametric and nonparametric statistics, and control of multiple testing error. These results show that nonparametric methods are slightly better in the test cases we study, although the choice of test statistic may often be dependent on the specific phenotype and haplotype structure being studied. The use of multi-SNP windows to infer local haplotype structure is critical to the use of a diverse panel of inbred strains for QTL mapping. Finally, because the marginal effect of any single gene in a complex disease is often relatively small, these methods require the use of sensitive methods for controlling family-wise error. We also report our initial application of this method to phenotypes cataloged in the Mouse Phenome Database. CONCLUSION: The use of inbred strains of mice for QTL mapping has many advantages over traditional methods. However, there are also limitations in comparison to the traditional linkage analysis from F2 and RI lines. Application of these methods requires careful consideration of algorithmic choices based on both theoretical and practical factors. Our findings suggest general guidelines, though a complete evaluation of these methods can only be performed as more genetic data in complex diseases becomes available.

Algorithms↗
PubMed2004

Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line.

BACKGROUND: The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames (ORFs) and flanking untranslated regions. The best currently available chicken transcript catalog is the Ensembl build based on the mappings of a relatively small number of full length cDNAs and ESTs to the genome as well as genome sequence derived in silico gene predictions. RESULTS: We use Long Serial Analysis of Gene Expression (LongSAGE) in bursal lymphocytes and the DT40 cell line to verify the quality and completeness of the annotated transcripts. 53.6% of the more than 38,000 unique SAGE tags (unitags) match to full length bursal cDNAs, the Ensembl transcript build or the genome sequence. The majority of all matching unitags show single matches to the genome, but no matches to the genome derived Ensembl transcript build. Nevertheless, most of these tags map close to the 3' boundaries of annotated Ensembl transcripts. CONCLUSIONS: These results suggests that rather few genes are missing in the current Ensembl chicken transcript build, but that the 3' ends of many transcripts may not have been accurately predicted. The tags with no match in the transcript sequences can now be used to improve gene predictions, pinpoint the genomic location of entirely missed transcripts and optimize the accuracy of gene finder software.

Animals↗
PubMed2005

Specificity and overlap in gene segment-defined antibody repertoires.

BACKGROUND: To date several studies have sought to catalog the full suite of antibodies that humans naturally produce against single antigens or other specificities (repertoire). Here we analyze the properties of all sequenced repertoires in order to better understand the specificity of antibody responses. Specifically, we ask whether the large-scale sequencing of antibody repertoires might provide a diagnostic tool for detecting antigen exposure. We do this by examining the overlap in VH-, D-, and JH- segment usage among sequenced repertoires. RESULTS: We find that repertoire overlap in VH-, D-, and JH-segment use is least for VH segments and greatest for JH segments, consistent with there being more VH than JH segments in the human genome. We find that for any two antigens chosen at random, chances are 90 percent that their repertoires' VH segments will overlap by less than half, and 98 percent that their VDJH combinations will overlap by < or =10 percent. We ran computer simulations to test whether enrichment for specific VDJH combinations could be detected in "antigen-exposed" populations, and found that enrichment is detectable with moderate-to-high sensitivity and high specificity, even when some VDJH combinations are not represented at all in some test sets. CONCLUSION: Thus, as large-scale sequencing becomes cost-effective for clinical testing, we suggest that sequencing an individual's expressed antibody repertoire has the potential to become a useful diagnostic modality.

Algorithms↗