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Current medicolegal and confidentiality issues in large, multicenter research programs.

The convenience of fast computers and the Internet have encouraged large collaborative research efforts by allowing transfers of data from multiple sites to a single data repository; however, standards for managing data security are needed to protect the confidentiality of participants. Through Dartmouth Medical School, in 1996-1998, the authors conducted a medicolegal analysis of federal laws, state statutes, and institutional policies in eight states and three different types of health care settings, which are part of a breast cancer surveillance consortium contributing data electronically to a centralized data repository. They learned that a variety of state and federal laws are available to protect confidentiality of professional and lay research participants. The strongest protection available is the Federal Certificate of Confidentiality, which supersedes state statutory protection, has been tested in court, and extends protection from forced disclosure (in litigation) to health care providers as well as patients. This paper describes the careful planning necessary to ensure adequate legal protection and data security, which must include a comprehensive understanding of state and federal protections applicable to medical research. Researchers must also develop rules or guidelines to ensure appropriate collection, use, and sharing of data. Finally, systems for the storage of both paper and electronic records must be as secure as possible.

Confidentiality↗

A natural language parsing system for encoding admitting diagnoses.

Free-text or natural language documents make up an increasing part of the computerized medical record. While they do provide accessible clinical information to health care personnel, they fail to support processes that require clinical data coded according to a shared lexicon and data structure. We have developed a natural language parser that converts free-text admitting diagnoses into a coded form. This application has proven acceptably accurate in the experimental laboratory to warrant a test in the target clinical environment. Here we describe an approach to moving this research application into a production environment where it can contribute to the efforts of the Health Information Services Department. This transition is essential if the products of natural language understanding research are to contribute to patient care in a routine and sustainable way.

Diagnosis-Related Groups↗

Do we need a uniform regulatory system for biobanks across Europe?

Within Europe, there is currently no uniform regulatory system that applies to human biobanks used for genetic research purposes. This has resulted in considerable variation in the national law that applies to the use of DNA samples, personal information and medical records in the countries across Europe. This could result in a situation where researchers collaborating across Europe may be operating unlawfully if they share research data and samples across borders where different laws are in operation. There are also concerns that the lack of standardised guidelines inhibits cooperation among researchers across Europe but also restricts the sharing of DNA samples and information across national borders, which is problematic for multinational companies and institutions carrying out collaborative research. Ultimately, the lack of a uniform regulatory system may have implications for the viability and long-term competitiveness of collaborative European research. The purpose of this paper is to discuss some of the preliminary issues that would need to be considered before such a regulatory system for biobanks could be developed within Europe.

Biological Specimen Banks↗

Clinical interpretation of reference intervals and reference limits. A plea for assay harmonization.

Reference intervals for healthy subjects and diseased populations are important benchmarks for the clinical interpretation of laboratory test values. It is important that the testing conditions used to collect the reference data be closely matched with the testing conditions used for patient data. Interlaboratory differences and intralaboratory changes, especially changes in analytic set-points, can markedly affect the clinical interpretation of tests. If laboratory testing methods could be harmonized, laboratories could potentially share reference data to make these data more reliable. This chapter illustrates the use of reference intervals for healthy subjects and reference data from diseased populations for medical decisions. One example illustrates the effects of age differences on test result interpretation. Other examples illustrate use of thyroid-stimulating hormone (TSH) and combinations of TSH with free thyroxine measurements for diagnosing thyroid diseases. Both univariate and multivariate reference intervals are discussed. Model systems for using disease prevalence and cost utility functions are provided to illustrate optimization of medical decisions.

Age Factors↗

The "latent membrane permeability" concept: QSPR analysis of inter/intralaboratory variable Caco-2 permeability.

Caco-2 cell monolayers grown on a filter support are the most widely used systems for predicting intestinal absorption. However, inter- and intralaboratory variability in Caco-2 permeability makes it difficult to analyze any QSPR relationship for a large number of compounds. We proposed the "latent membrane permeability" concept, assuming that all Caco-2 permeability data sets share a hidden, common relationship between their membrane permeability and physicochemical properties. An iterative calculation method was developed to handle this conceptual approach and applied to the analysis of Caco-2 permeability data sets from different sources. A thorough statistical analysis revealed that the "latent membrane permeability" concept be reasonable.

Caco-2 Cells↗

Evolution of web services in bioinformatics.

Bioinformaticians have developed large collections of tools to make sense of the rapidly growing pool of molecular biological data. Biological systems tend to be complex and in order to understand them, it is often necessary to link many data sets and use more than one tool. Therefore, bioinformaticians have experimented with several strategies to try to integrate data sets and tools. Owing to the lack of standards for data sets and the interfaces of the tools this is not a trivial task. Over the past few years building services with web-based interfaces has become a popular way of sharing the data and tools that have resulted from many bioinformatics projects. This paper discusses the interoperability problem and how web services are being used to try to solve it, resulting in the evolution of tools with web interfaces from HTML/web form-based tools not suited for automatic workflow generation to a dynamic network of XML-based web services that can easily be used to create pipelines.

Computational Biology↗

Delivery and interactive processing of visual data for a cooperative telemedicine environment.

Cooperative telemedicine environments are required for many situations such as consultations between residents and senior doctors, case correlations, and for teaching and research purposes. The mode of collaboration may vary with different situations, in terms of the synchronisation of tasks, the sharing of data and the extent of collaboration among participants. It is essential for participants to be able to remotely view and manipulate visual data (images, two-dimensional and three-dimensional graphics, animation, and video) as well as interactively run application programs that involve visual data in real-time. However, this is not possible with current network bandwidth limitations when large amount of visual data are involved. In this article, we first provide an analysis of functional requirements by participants in cooperative diagnosis in different types of situations, before discussing technical requirements, which form the basis for our system architecture design. A new approach is also presented for efficient handling of programs, which involve visual data in real time. This is achieved via the construction and transmission of small messages that encapsulate the operations in a pipelined or hierarchical fashion.

Computer Graphics↗

Why the poor pay more: household curative expenditures in rural Sierra Leone.

This paper draws on data from Sierra Leone, and secondary data from elsewhere, to show that the rural poor can be disproportionately disadvantaged by user charges for health care, paying a higher percentage of their incomes for health care than wealthier households. Cost sharing systems at primary care level should include exemptions for the poor, but rarely succeed in consistently protecting them. The regressivity of health expenditures also results from lack of protection from the higher costs of less-frequently used, expensive providers. In Sierra Leone, the burden of curative treatment costs for all groups came mainly from private and NGO providers. Proximity to facilities appeared a more important factor in their use than average price levels. Even if a perfect exemption system existed at government primary care facilities, it would not have had much overall effect because of their relatively small contribution to household health expenditures. The financial burden on households could be relieved by making basic health facilities more accessible and at hospital level using additional resources generated through improved efficiency and cross-subsidization to provide exemptions. Also, pricing policy should take into account local economic conditions. Insurance/prepayment schemes covering the cost of hospitalization would come closer to an ideal solution, but have been implemented in very few of the poorer countries.

Cost Sharing↗

Enabling high-throughput discovery.

During the past few years, the introduction of ultra-high-throughput screening and new assay design and detection technologies has exponentially increased the amount and complexity of screening data. Effective use of this data implies a process that begins with assay design. An effective data management system should control a range of processes, from the initial selection of compounds and storage and mining of the assay result to more complex tasks, such as extracting patterns from these data. Remarkable advances have been made during the last year to increase efficiency at different phases of the screening, shifting the bottleneck of this process to data analysis. The challenge facing drug discovery today is to extract knowledge from these data. Knowledge discovery is defined as 'the non-trivial extraction of implicit, unknown, and potentially useful information from data'. A large amount of research is being devoted to optimize the extraction of knowledge from screening data. In this review, we discuss the screening process and its progress during the last year. Some of the challenges for the future, such as optimization of the knowledge discovery process and the sharing of data across an organization, will also be presented.

Databases, Factual↗

HGVbase: a curated resource describing human DNA variation and phenotype relationships.

The Human Genome Variation Database (HGVbase; http://hgvbase.cgb.ki.se) has provided a curated summary of human DNA variation for more than 5 years, thus facilitating research into DNA sequence variation and human phenotypes. The database has undergone many changes and improvements to accommodate increasing volumes and new types of data. The focus of HGVbase has recently shifted towards information on haplotypes and phenotypes, relationships between phenotypes and DNA variation, and collaborative efforts to provide a global resource for genome-phenome data. Open sharing and precise phenotype definitions are necessary to advance the current understanding of common diseases that are typified by complex aetiologies, small genetic effect sizes and multiple confounding factors that obscure positive study results. Association data will increasingly be collected as part of this new project thrust. This report describes the evolving features of HGVbase, and covers in detail the technological choices we have made to enable efficient storage and data mining of increasingly large and complex data sets.

Computational Biology↗

Creating the gene ontology resource: design and implementation.

The exponential growth in the volume of accessible biological information has generated a confusion of voices surrounding the annotation of molecular information about genes and their products. The Gene Ontology (GO) project seeks to provide a set of structured vocabularies for specific biological domains that can be used to describe gene products in any organism. This work includes building three extensive ontologies to describe molecular function, biological process, and cellular component, and providing a community database resource that supports the use of these ontologies. The GO Consortium was initiated by scientists associated with three model organism databases: SGD, the Saccharomyces Genome database; FlyBase, the Drosophila genome database; and MGD/GXD, the Mouse Genome Informatics databases. Additional model organism database groups are joining the project. Each of these model organism information systems is annotating genes and gene products using GO vocabulary terms and incorporating these annotations into their respective model organism databases. Each database contributes its annotation files to a shared GO data resource accessible to the public at http://www.geneontology.org/. The GO site can be used by the community both to recover the GO vocabularies and to access the annotated gene product data sets from the model organism databases. The GO Consortium supports the development of the GO database resource and provides tools enabling curators and researchers to query and manipulate the vocabularies. We believe that the shared development of this molecular annotation resource will contribute to the unification of biological information.

Animals↗

Unifying multimodal single-cell data with a mixture-of-experts β-variational autoencoder framework.

Multimodal single-cell assays profile complementary layers of cell state, but integration is complicated by modality mismatch, sparsity, and uneven cohort coverage. Here, we present Unified Variational Inference (UniVI), a scalable mixture-of-experts β-variational autoencoder that learns a shared latent space while preserving modality-specific structure. UniVI couples modality-specific encoders/decoders with a shared latent prior and a symmetric cross-modal alignment objective, enabling consistent integration of paired measurements without curated feature-link graphs or preannotated reference atlases; optional supervised heads can be added when labels are available. Across paired RNA-protein (CITE-seq) and RNA-chromatin (10x Genomics Multiome, SHARE-seq) data spanning human PBMCs and mouse back skin-a nonhematopoietic tissue with continuous differentiation hierarchies-UniVI produces coherent embeddings, improves label transfer, and enables cross-modal reconstruction and denoising. Extending to trimodal measurements, UniVI maintains robust three-way alignment among RNA, chromatin accessibility, and surface proteins (TEA-seq), and accommodates DNA methylation in a paired scNMT-seq mouse gastrulation proof-of-concept under beta-binomial likelihoods. Performance degrades gracefully under severe cell type imbalance and in the presence of modality-exclusive populations. In an acute myeloid leukemia mosaic design, a paired RNA-protein bridge anchors independent RNA-only and protein+genotype cohorts, revealing genotype-associated neighborhoods that sharpen with mutation-aware fine-tuning. UniVI thus provides a flexible, interpretable framework for multimodal integration across paired, trimodal, and mosaic study designs and supports practical reference-to-query projection in partially observed studies.

Journal Article↗

Public release of cardiac surgery outcomes data in New York: what do New York state cardiologists think of it?

BACKGROUND AND OBJECTIVE: Since 1990, risk-adjusted outcomes for patients undergoing coronary artery bypass graft surgery in New York state have been released to the public. The purpose of this study was to assess the extent to which referring cardiologists share these data with patients and use these data to make referrals. METHODS: A survey questionnaire was sent to all cardiologists in New York in the New York State Chapter of the American College of Cardiology. RESULTS: Four hundred fifty cardiologists responded to the survey. Most (94%) found the report "easy to read." A majority (67%) found the report to be "very accurate" or "somewhat accurate" in capturing differences in the performance of cardiac surgeons, whereas 33% found it to be "not at all accurate." Twenty-two percent reported that they "routinely discuss the reports with their patients," and 38% responded that the information has affected their referrals to surgeons "very much" or "somewhat." CONCLUSIONS: A majority of cardiologists has not generally changed their well-established referral patterns as a result of the New York coronary artery bypass graft surgery reports. However, there has been a modest impact on referrals resulting from the distribution of these reports. The findings also suggest that increased dialogue between clinicians and policy makers regarding the format and structure of public releases would be a valuable undertaking.

Attitude of Health Personnel↗

Public release of cardiac surgery outcomes data in New York: what do New York state cardiologists think of it?

BACKGROUND AND OBJECTIVE: Since 1990, risk-adjusted outcomes for patients undergoing coronary artery bypass graft surgery in New York state have been released to the public. The purpose of this study was to assess the extent to which referring cardiologists share these data with patients and use these data to make referrals. METHODS: A survey questionnaire was sent to all cardiologists in New York in the New York State Chapter of the American College of Cardiology. RESULTS: Four hundred fifty cardiologists responded to the survey. Most (94%) found the report "easy to read." A majority (67%) found the report to be "very accurate" or "somewhat accurate" in capturing differences in the performance of cardiac surgeons, whereas 33% found it to be "not at all accurate." Twenty-two percent reported that they "routinely discuss the reports with their patients," and 38% responded that the information has affected their referrals to surgeons "very much" or "somewhat." CONCLUSIONS: A majority of cardiologists has not generally changed their well-established referral patterns as a result of the New York coronary artery bypass graft surgery reports. However, there has been a modest impact on referrals resulting from the distribution of these reports. The findings also suggest that increased dialogue between clinicians and policy makers regarding the format and structure of public releases would be a valuable undertaking.

Adult↗

[Multilocus sequence typing: the molecular marker of the Internet era].

Global or longer term epidemiology track the spread of clonal lineages, associated with hipervirulence or resistance or multi-resistance to antimicrobial agents. Therefore, the application of a molecular typing system for this purpose should produce data easily shared by different and geographically distant laboratories, as well as distinguish those clonal lineages even with low levels of variability accumulated in the genome.A marker based on the DNA sequence will produce objective results easily organized in data bases accessible by Internet. The application of a similar strategy that was used in the analysis of isoenzymes, by sequencing variable fragments of selected housekeeping genes, will allow obtaining a general view of the distribution of the clonal lineages and tracking their spread.

Bacterial Infections↗

Social factors related to syringe sharing among injecting partners: a focus on gender.

The study of social networks has become an increasingly utilized method of examining the relationship between injection drug users' social environment and risk of HIV. This study examined relational aspects of two injection drug users (IDUs) within a single social network as they relate to sharing syringes. Data presented in this study were derived from baseline interviews of 508 IDUs from Baltimore, MD. Analyses were performed separately for male and female participants in an effort to understand gender differences in social aspects of syringe sharing. Among this sample, women shared syringes with a significantly higher percentage of injecting partners compared to men. In separate multilevel logistic regression models, significant variables associated with males' and females' syringe sharing were: sharing drugs daily with female injecting partners, injecting partners' provision of drugs when indexes' were withdrawing, being sexual partners, and injecting partners' injecting speedballs. Factors associated with male injecting dyads sharing of syringes were: being kin, injecting partners' injection of heroin and daily drug use, and drinking alcohol together. Results from this study demonstrate the usefulness of examining relationship characteristics of injecting dyads related to syringe sharing as they differ between men and women.

Acquired Immunodeficiency Syndrome↗

ABO incompatible kidney transplantation - an analysis of UNOS Registry data.

BACKGROUND: The ABO incompatible kidney transplants have been performed successfully from large numbers of living donors and some blood type A2 deceased donors. However, there are few reports to support the feasibility of ABO incompatible transplants from non-A2 deceased donors. This problem was examined in the United Network for Organ Sharing (UNOS) data file. PATIENTS AND METHODS: The UNOS Registry data of kidney transplants performed between 1995 and 2003 from 256 centers was utilized for Kaplan-Meier curves and log-rank tests to compare graft and functional graft survival rates. RESULTS: Deceased donor transplants from all ABO incompatible donors had the same graft survival rates, as that from ABO compatible donors regardless of whether the blood group incompatibility was A (A1), A2 or B. Graft survival from 201 ABO incompatible donors was 66.9% at 5 yr, compared with 66.7% for ABO compatible donors (p = 0.83). Non-A2 incompatible donors also yielded comparable survival rates to ABO compatible donors. From living donors, ABO incompatible donors yielded significantly lower graft survival rates than the ABO compatible group, although long-term graft survival rates of those who survived >1 yr did not differ significantly. CONCLUSION: Except higher initial graft loss possibility because of insufficient removal of antibodies, non-A2 kidneys yielded equivalent graft survival rates to ABO compatible transplants. In addition to A2 incompatibilities, Blood group A1 and B incompatibilities can also be considered in ABO incompatible transplants.

ABO Blood-Group System↗

Lithium for schizophrenia.

BACKGROUND: Many people with schizophrenia do not achieve a satisfactory treatment response with ordinary antipsychotic drug treatment. In these cases, various add-on medications are used, among them lithium. OBJECTIVES: To review the effects of lithium for the treatment of schizophrenia and schizophrenia-like psychoses. SEARCH STRATEGY: The reviewers searched the Cochrane Schizophrenia Group's register (March 2002). This register is compiled by methodical searches of BIOSIS, CINAHL, Dissertation abstracts, EMBASE, LILACS, MEDLINE, PSYNDEX, PsycINFO, RUSSMED, Sociofile, supplemented with hand searching of relevant journals and numerous conference proceedings. We also contacted pharmaceutical companies and authors of relevant studies to identify further trials and to obtain original patient data. SELECTION CRITERIA: All randomised controlled trials comparing lithium to antipsychotics or to placebo (or no intervention), whether as sole treatment or as an adjunct to antipsychotic medication for the treatment of schizophrenia and/or schizophrenia-like psychoses. DATA COLLECTION AND ANALYSIS: Citations and, where possible, abstracts were independently inspected by reviewers, papers ordered, re-inspected and quality assessed. Data were extracted independently by at least two reviewers. Dichotomous data were analysed using relative risks (RR) and the 95% confidence interval (CI) estimated. Where possible the number needed to treat (NNT) or number needed to harm statistics were calculated. Continuous data were analysed using weighted mean differences (WMD). MAIN RESULTS: The review currently includes 20 studies with a total of 611 participants. Most studies were small, of short duration and incompletely reported, but a number of authors were willing to share their data with us. Three studies comparing lithium with placebo as the sole treatment showed no difference in any of the outcomes we analysed. In eight studies comparing lithium with antipsychotic drugs as the sole treatment more participants in the lithium group left the studies early (n=270, RR 1.8, CI 1.2 to 2.9, NNT 9, CI 5 to 33). Several of the outcomes relating to these studies suggested that lithium is less effective than antipsychotic drugs, but it was difficult to summarise the data, because a variety of rating scales were used in the studies. Eleven studies examined whether the augmentation of antipsychotic drugs with lithium salts is more effective than antipsychotic drugs alone. More participants who received lithium augmentation had a clinically significant response (n=244, RR 0.8, CI 0.7 to 0.96, NNT 8, CI 4 to 33). However, statistical significance became borderline when participants with schizoaffective disorders were excluded in a sensitivity analysis (n=120, RR 0.8, CI 0.6 to 1.0, p=0.07). Furthermore, more participants in the lithium augmentation groups left the studies early (n=320, RR 2.0 CI 1.3 to 3.1, NNT 7, CI 4 to 14), suggesting a lower acceptability of lithium augmentation compared to those on antipsychotics alone. No superior efficacy of lithium augmentation in any specific aspect of the mental state was found. While based on very little data, there were no differences between groups for adverse events. REVIEWER'S CONCLUSIONS: There is no randomised trial based evidence that lithium on its own is an effective treatment for people with schizophrenia. The evidence available on augmentation of antipsychotics with lithium is inconclusive, but it justifies further, large, simple and well-designed trials. These should concentrate on two target groups: 1) people with no affective symptoms, so that trialists can determine whether lithium has an effect on the core symptoms of schizophrenia, 2) people with schizoaffective disorders for whom lithium is widely used in clinical practice, although there is no evidence to support this use.

Antipsychotic Agents↗