Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “data sharing”

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 1,243 records · Page 69Linked to original sources
PubMed2005

An international otology database.

There are many reports in the literature on the outcome of ear surgery. However, it is difficult to make comparisons from these reports because of a lack of uniformity in the way in which outcomes are reported. At the same time, the general public expects doctors to provide them with information regarding the benefits and risks of surgery. Many ear surgeons will not be able to provide this information because few have an up-to-date database. A group of otologists in Europe has attempted to establish a common otology database. The aim is to create a framework whereby surgeons in Europe can contribute to a common ear database using a web-based system. The proposed methodology involves two levels of data entry. Level 1 is a minimal database where the main outcomes are included. Level 2 is a comprehensive database where detailed information on pathologies, risk factors, and surgical procedures is also recorded. As both databases share the same core data, clinicians using database 1 can still compare their outcomes with those using database 2. Clinicians will be able to input and retrieve ear data onto or from the web-based database. There has already been an international consensus on the content of the common ear database. The website address is www.ear-audit.net. The international project has now been in operation for more than 6 months, and Ear UK has already given its endorsement. The founder members include 27 otologists from 12 European countries. The cumulative outcome from this group of surgeons will be used as the benchmark for the purpose of comparative audit. These benchmark sites will be subjected to regular external validation. The web-based system is interactive and gives instant feedback to individual surgeons who wish to compare their results to the benchmark. Therefore, it can be a good learning tool for trainees or less experienced surgeons. The common data entry system also provides an opportunity for clinicians to collaborate in clinical research.

Databases, Factual↗
PubMed2006

Consequences of heterogeneity in survival probability in a population of Florida scrub-jays.

1. Using data on breeding birds from a 35-year study of Florida scrub-jays Aphelocoma coerulescens (Bosc 1795), we show that survival probabilities are structured by age, birth cohort, and maternal family, but not by sex. Using both accelerated failure time (AFT) and Cox proportional hazard models, the data are best described by models incorporating variation among birth cohorts and greater mortality hazard with increasing age. AFT models using Weibull distributions with the shape parameter > 1 were always the best-fitting models. 2. Shared frailty models allowing for family structure greatly reduce model deviance. The best-fitting models included a term for frailty shared by maternal families. 3. To ask how long a data set must be to reach qualitatively the same conclusions, we repeated the analyses for all possible truncated data sets of 2 years in length or greater. Length of the data set affects the parameter estimates, but not the qualitative conclusions. In all but three of 337 truncated data sets the best-fitting models pointed to same conclusions as the full data set. Shared frailty models appear to be quite robust. 4. The data are not adequate for testing hypotheses as to whether variation in frailty is heritable. 5. Substantial structured heterogeneity for survival exists in this population. Such structured heterogeneity has been shown to have substantial effects in reducing demographic stochasticity.

Aging↗
PubMed2005

Deciphering structure and topology of conserved COG2042 orphan proteins.

BACKGROUND: The cluster of orthologous group COG2042 has members in all sequenced Eukaryota as well as in many Archaea. The cellular function of these proteins of ancient origin remains unknown. PSI-BLAST analysis does not indicate a possible link with even remotely-related proteins that have been functionally or structurally characterized. As a prototype among COG2042 orthologs, SSO0551 protein from the hyperthermophilic archaeon Sulfolobus solfataricus was purified to homogeneity for biophysical characterization. RESULTS: The untagged protein is thermostable and behaves as a monomeric protein in gel filtration experiment. Several mass spectrometry-based strategies were combined to obtain a set of low resolution structural information. Kinetic data from limited proteolysis with various endoproteases are concordant in pointing out that region Glu73-Arg78 is hyper-sensitive, and thus accessible and flexible. Lysine labeling with NHS-biotin and cross-linking with DTSSP revealed that the 35 amino acid RLI motif at the N terminus is solvent exposed. Cross-links between Lys10-Lys14 and Lys23-Lys25 indicate that these residues are spatially close and in adequate conformation to be cross-linked. These experimental data have been used to rank multiple three-dimensional models generated by a de novo procedure. CONCLUSION: Our data indicate that COG2042 proteins may share a novel fold. Combining biophysical, mass-spectrometry data and molecular model is a useful strategy to obtain structural information and to help in prioritizing targets in structural genomics programs.

Amino Acid Sequence↗
PubMedDate not supplied

IVE (Image Visualization Environment): a software platform for all three-dimensional microscopy applications.

IVE (Image Visualization Environment) is a software platform designed from the outset to handle all aspects of modern computerized multidimensional microscopy. This platform provides users with an execution environment in which 5D data (XYZ, wavelength, and time) can be easily manipulated for the purpose of data collection, processing, display, and analysis. During the entire process, powerful data display functions are readily available for extracting complicated three-dimensional information through data visualization. By employing both the shared memory and multitasking features of the UNIX operation system, individual functions can be implemented as separate programs, and multiple programs can access the same data pool simultaneously. This enables users to combine the functionalities of different programs to facilitate each unique data analysis task. Furthermore, by defining an appropriate program execution model, commonly shared functional components such as data display, data I/O and user interface, etc. can be implemented using simple IVE library calls. This dramatically reduces the program development time and ensures consistency throughout the entire software system. As a result, users can quickly master the microscopy software system and new functions can be easily integrated, as different functional requirements arise for different research projects.

Chromosomes↗
PubMed2001

The lod score method.

The lod score method originated in a seminal article by Newton Morton in 1955. The method is broadly concerned with issues of power and the posterior probability of linkage, ensuring that a reported linkage has a high probability of being a true linkage. In addition, the method is sequential, so that pedigrees or lod curves may be combined from published reports to pool data for analysis. This approach has been remarkably successful for 50 years in identifying disease genes for Mendelian disorders. After discussing these issues, we consider the situation for complex disorders, where the maximum lod score (MLS) statistic shares some of the advantages of the traditional lod score approach but is limited by unknown power and the lack of sharing of the primary data needed to optimally combine analytic results. We may still learn from the lod score method as we explore new methods in molecular biology and genetic analysis to utilize the complete human DNA sequence and the cataloging of all human genes.

Genetic Linkage↗
PubMed2004

The prevalence and characteristics associated with parent-infant bed-sharing in England.

AIMS: To investigate the characteristics of parent-infant bed-sharing prevalence in England. METHODS: Data on night-time sleeping practices from a two year, local, longitudinal study and a three-year, national, cross-sectional study were obtained. A total of 261 infants in North Tees were followed up at 1 and 3 months of age, as were 1095 infants aged 1 week to 1 year from five English health regions. RESULTS: Data from both studies found that almost half of all neonates bed-shared at some time with their parents (local = 47%, 95% CI 41 to 54; national = 46%, 95% CI 34 to 58), and on any one night in the first month over a quarter of parents slept with their baby (local = 27%, 95% CI 22 to 33; national = 30%, 95% CI 20 to 42). Bed-sharing was not related to younger mothers, single mothers, or larger families, and was not more common in the colder months, at weekends, or among the more socially deprived families; in fact bed-sharing was more common among the least deprived in the first months of life. Breast feeding was strongly associated with bed-sharing, both at birth and at 3 months. Bed-sharing prevalence was uniform with infant age from 3 to 12 months; on any one night over a fifth of parents (national = 21%, 95% CI 18 to 24) slept with their infants. CONCLUSION: Bed-sharing is a relatively common practice in England, not specific to class, but strongly related to breast feeding.

Adult↗
PubMed1984

Risk estimates for neonatal myotonic dystrophy.

Children who inherit the autosomal dominant gene for myotonic dystrophy from their mother rather than their father may develop the severe neonatal type rather than the late onset type. The families of 22 neonatal type probands and 59 late onset type probands were studied to determine the risk of occurrence and recurrence of the neonatal type. The frequency of the neonatal type in sibs of neonatal type probands was 29%, or 37% if cases of neonatal deaths are counted as affected. This is significantly higher than the 6% of the neonatal type found in the offspring of affected women not ascertained through a child with the neonatal type. These data suggest that certain women carrying the gene for myotonic dystrophy are predisposed to have children affected with the neonatal type rather than the late onset type. The female near relatives of these women do not seem to share this predisposition. The data should be useful for genetic counseling.

Adult↗
PubMed2026

Machine learning-integrated multi-omics risk prediction for pulmonary fungal infection in COPD and lung cancer: a transcriptomic and immune profiling study.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) and lung cancer are major risk factors for invasive pulmonary fungal infection (IPFI), carrying an attributable mortality of 30%-80%. Their coexistence further amplifies immunosuppression, while current diagnostic criteria remain inadequate for early risk identification. METHODS: Transcriptomic data from the GEO dataset GSE296912 (scRNA-seq; 12,078 cells from normal and COPD lung tissue) and The Cancer Genome Atlas (TCGA)-lung adenocarcinoma (LUAD) bulk RNA-seq cohort (539 tumor and 59 normal samples) underwent differential expression and cross-omics integration analysis. Five machine learning models were constructed: logistic regression, SVM, random forest, XGBoost, and LASSO. Candidate genes were validated by qRT-PCR in A549 cells and THP-1-derived macrophages stimulated with heat-inactivated Aspergillus fumigatus conidia, a protocol selected to ensure BSL-2 biosafety compliance and isolate PAMP-mediated innate immune signaling. Model performance was evaluated using 5-fold stratified cross-validation with AUC, calibration curves, and decision curve analysis. RESULTS: Single-cell transcriptomic analysis of 12,078 cells identified 14 distinct cell populations, with marked myeloid expansion and immune dysregulation in COPD lung tissue. Cross-omics integration with TCGA-LUAD data identified 1,145 shared genes (79 immune-related), converging on NF-κB, TLR4, and cytokine receptor signaling. The random forest model achieved excellent discriminative performance (5-fold CV AUC = 0.988), with Treg infiltration, TLR4, and MMP9 as the top predictors. qRT-PCR confirmed significant upregulation of all five candidate genes (DEFB4A, S100A8, IL-8, MMP9, and TLR4) in both A549 and THP-1 cells following fungal stimulation. CONCLUSION: This multi-omics machine learning model integrating scRNA-seq and TCGA transcriptomic data demonstrates excellent discriminative performance (AUC = 0.988), with mechanistic convergence of NF-κB, TLR4, and oncogenic signaling pathways identified across shared immune gene signatures. In vitro qRT-PCR validation confirms the biological relevance of five key antifungal immune genes, providing a transcriptomic foundation for future prospective IPFI risk stratification in patients with COPD and lung cancer.

TLR4↗
PubMed1979

Doctor patient relationships and the older patient.

The authority of physicians in patient encounters is posited by the sicrole and the professional-client models in sociology. Yet, public challenges to physician authority are currently occurring, as shown by self care movements, and by some empirical data. Whether the elderly share in such challenges is, however, an unresolved question. Will longer experience with health services produce skepticism about medicine's claims, or conversely will the aged's probable more authoritarina upbringing and concern about failing health produce acceptance of physician authority? Data from an interview survey of 640 randomly sampled persons in a midwestern state, reveal that the 153 respondents aged 60 and over are more likely to accept physician authority, both in terms of attitudes and behaviors, than are the younger groups. Moreover, the findings show that the level of older persons' challenging attitudes is affected by their health knowledge and general views on authority, while their challenging behaviors are influenced by belief in right to medical information and an experience factor. Implications of the findings for appropriate modes of doctor-patient relationships for the elderly are discussed.

Adult↗
PubMedDate not supplied

Roundtable on bioterrorism detection: information system-based surveillance.

During the 2001 AMIA Annual Symposium, the Anesthesia, Critical Care, and Emergency Medicine Working Group hosted the Roundtable on Bioterrorism Detection. Sixty-four people attended the roundtable discussion, during which several researchers discussed public health surveillance systems designed to enhance early detection of bioterrorism events. These systems make secondary use of existing clinical, laboratory, paramedical, and pharmacy data or facilitate electronic case reporting by clinicians. This paper combines case reports of six existing systems with discussion of some common techniques and approaches. The purpose of the roundtable discussion was to foster communication among researchers and promote progress by 1) sharing information about systems, including origins, current capabilities, stages of deployment, and architectures; 2) sharing lessons learned during the development and implementation of systems; and 3) exploring cooperation projects, including the sharing of software and data. A mailing list server for these ongoing efforts may be found at http://bt.cirg.washington.edu.

Bioterrorism↗
PubMed1998

HLA-DRB1 typing in rheumatoid arthritis: predicting response to specific treatments.

OBJECTIVE: To determine the predictive value of shared epitope alleles for response to treatment in patients with rheumatoid arthritis. METHODS: Patients from our previously published triple DMARD study were tested for the presence of shared epitope alleles (DRB1 *0401, 0404/0408, 0405, 0101, 1001, and 1402). Patients who were shared epitope positive were then compared with those who were negative to see if there was a differential effect on therapeutic response. RESULTS: Shared epitope positive patients were much more likely to achieve a 50% response if treated with methotrexate-sulphasalazine-hydroxychloroquine compared with methotrexate alone (94% responders versus 32%, p < 0.0001). In contrast shared epitope negative patients did equally well regardless of treatment (88% responders for methotrexate-sulphasalazine-hydroxychloroquine versus 83% for methotrexate). Additionally, a trend toward an inverse relation of the gene dose was seen for response to methotrexate treatment (p = 0.05). CONCLUSIONS: These data suggest that determining shared epitope status may provide clinical information useful in selecting among treatment options.

Adult↗
PubMed2004

Toxicogenomics in risk assessment: an overview of an HESI collaborative research program.

The value of genomic approaches in hypothesis generation is being realized as a tool for understanding toxicity and consequently contributing to an assessment of drug and chemical safety. In 1999 the membership of the International Life Sciences Institute Health and Environmental Sciences Institute formed a committee to develop a collaborative scientific program to address issues, challenges, and opportunities afforded by the emerging field of toxicogenomics. Experts and advisors from academia and government laboratories participate on the committee, along with approximately 30 corporate member organizations from the pharmaceutical, agrochemical, chemical, and consumer products industries. The committee has designed, conducted, and analyzed numerous toxicogenomic experiments within the broad fields of hepatotoxicity, nephrotoxicity, and genotoxicity. The considerable body of data generated by these programs has been instrumental in increasing understanding of sources of biological and technical variability in the alignment of toxicant-induced transcription changes with the accepted mechanism of action of these agents and the challenges in the consistent analysis and sharing of the voluminous data sets generated by these approaches. Recognizing the importance of standardized microarray data formats and public repository databases as the mechanism by which microarray data can be compared and interpreted by the scientific community, the committee has partnered with the European Bioinformatics Institute to develop a database to house the data generated by its collaborative research.

Gene Expression Profiling↗