Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “data integration”

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 685 records · Page 38Linked to original sources

In vivo animal models for investigating potential CYP3A- and Pgp-mediated drug-drug interactions.

With the advent of polytherapy it has become prudent to minimize, as much as possible, the potential for drug-drug interactions. Towards this end, the metabolic and transporter pathways involved in the disposition of a drug candidate (phenotyping) are evaluated in vitro employing available human tissue and specific reagents. Likewise, in vitro screening for inhibition and induction of drug-metabolizing enzymes and transporters is conducted also. Such in vitro human data can be made available prior to human dosing and enable in vitro to in vivo-based predictions of clinical outcomes. Despite some success, however, in vitro systems are not dynamic and sometimes fail to predict drug-drug interactions for a variety of reasons. In comparison, relatively less effort has been made to evaluate predictions based on data derived from in vivo animal models. This review will attempt to summarize different examples from the literature where animal models have been used to predict cytochrome P450 3A (CYP3A)- and P-glycoprotein (Pgp)-based drug-drug interactions. When employing data from animal models one needs to be aware of species differences in pharmacokinetics, clearance pathways and selectivity and affinity of probe substrates and inhibitors. Because of these differences, in vivo animal studies alone, cannot be predictive of human drug-drug interactions. Despite these caveats, the information obtained from validated in vivo animal models may prove useful when used in conjunction with in vitro-in vivo extrapolation methods. Such an integrated data set can be used to select drug candidates with a reduced drug interaction potential.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

Computed tomographic evaluation of morphological and functional condition of left ventricle in heart aneurysm.

Computed tomography is a valuable method for the diagnosis of post-infarction aneurysm of the left ventricle of the heart. It gives additional information concerning the morphological and functional condition of the left ventricle. The suggested method of layer-by-layer scanning improves the diagnostic efficiency of CT during examination of patients with heart aneurysm and is noninvasive. Precise individual calculation of the peak concentration of contrast medium, defined by dynamic scanning, optimises the process of gated CT. CT makes it possible to study changes in cavity configuration, left ventricle wall thinning, induration and calcification of the myocardium, changes in left ventricle wall mobility, decreased thickening of the myocardium at systole and left ventricle cavity thrombosis--all changes characteristic of left ventricular aneurysm. CT provides important additional information about the condition of the inter-ventricular septum. EDV, ESV and EF data obtained using CT produce important information about the functional state of the left ventricle. Computed tomography can be used as an independent method of left ventricle aneurysm detection, especially in those institutions where more complicated investigation methods are not used and interventional cardiac procedures are not practised. Complex use of computed tomography and left ventriculography in cardiosurgical institutions makes it possible to improve significantly the diagnosis of cardiac aneurysm. Calculation of integral data about left ventricle pumping function based on CT and LVG data gives proper evaluation of the indications for operative intervention in left ventricular aneurysm.

Adult↗

Strategies for success when medical groups participate in CHINs.

A community health information network (CHIN) is a group of health care providers and others interested in health care in a community who share computerized patient information and medical records to provide comprehensive quality care at a lower cost. To protect confidential patient data, all CHIN members should sign a confidentiality agreement describing how and for what purposes health information may be used and incorporating adequate indemnification provisions for unauthorized disclosure. Further, CHIN members should implement practical security passwords which are periodically changed, and the rapid deactivation of the user identification of terminated employees. To ensure data integrity, clear policies should be established for recording, amending and destroying information stored in patient records. To preserve the availability of the network's essential software, CHIN members also should enter into software license agreements which will allow for uninterrupted use of the network software following the addition of a new member or the departure on an existing member. Medical groups participating in CHINs can utilize these strategies to minimize their liability exposure from patient data confidentiality lapses and to promote proper data management and software availability for the smooth functioning of the network.

Community Networks↗

Sensor fusion by pseudo information measure: a mobile robot application.

In any autonomous mobile robot, one of the most important issues to be designed and implemented is environment perception. In this paper, a new approach is formulated in order to perform sensory data integration for generation of an occupancy grid map of the environment. This method is an extended version of the Bayesian fusion method for independent sources of information. The performance of the proposed method of fusion and its sensitivity are discussed. Map building simulation for a cylindrical robot with eight ultrasonic sensors and mapping implementation for a Khepera robot have been separately tried in simulation and experimental works. A new neural structure is introduced for conversion of proximity data that are given by Khepera IR sensors to occupancy probabilities. Path planning experiments have also been applied to the resulting maps. For each map, two factors are considered and calculated: the fitness and the augmented occupancy of the map with respect to the ideal map. The length and the least distance to obstacles were the other two factors that were calculated for the routes that are resulted by path planning experiments. Experimental and simulation results show that by using the new fusion formulas, more informative maps of the environment are obtained. By these maps more appropriate routes could be achieved. Actually, there is a tradeoff between the length of the resulting routes and their safety and by choosing the proper fusion function, this tradeoff is suitably tuned for different map building applications.

Algorithms↗

Emerging neurochemical concepts in the actions of ethanol at ligand-gated ion channels.

Both data and opinion are beginning to unify a consensus concerning the neurochemical mediation of the effects of ethanol in the CNS. This review of the literature is offered as an introduction to the molecular and cellular aspects of the neurochemical effects of ethanol for behavioral pharmacologists. As such, this review emphasizes the receptor pharmacology of ethanol over its behavioral effects. The unifying principle throughout the review is that ethanol has selective effects at particular ionotropic receptors, including GABA(A), NMDA and 5-HT(3) receptors. Current concepts of how ethanol may selectively interact with these receptor systems are discussed. In particular, the molecular characterizations of these receptors are reviewed to provide a foundation for understanding the differential interaction of ethanol with particular receptor subtypes and integrating data addressing the behavioral actions of ethanol. Extension of the neurochemical effects to behavioral outcomes is explored primarily via drug discrimination procedures. The recent advances that are highlighted include the receptor basis for regional sensitivity to ethanol and potential interactions of ethanol-induced neurochemical activity associated with alcohol intoxication. The integration and understanding of how multiple receptor systems interact to influence a behavioral outcome will remain an important challenge for behavioral pharmacologists interested in the effects of ethanol.

Journal Article↗

Leveraging single-cell and spatial omics for brain tumour insights to improve therapeutic strategies.

Single-cell and spatial omics (SPOs) technologies have advanced how healthcare physicians characterise brain tumours by enabling detailed understanding of their cellular architecture, functional states, and microenvironmental dynamics. These approaches provide high-resolution detection of tumour heterogeneity and allow precise analysis of the brain tumour microenvironment. Their application has also led to the discovery of novel biomarkers used for early brain tumour detection, prognosis, and improved tumour stratification. Furthermore, integrative multi-omic analyses have revealed new therapeutic targets, clarified mechanisms of drug resistance, and uncovered molecular pathways underpinning treatment failure. By bridging cellular-level insights with spatial context, SPOs hold significant promise for advancing personalised diagnostics, predicting therapeutic response, and guiding the development of targeted interventions for brain tumours. Despite these advances, several limitations constrain the full translational potential of SPOs, including high experimental costs, substantial computational demands, lack of standardised protocols, and challenges in data integration and reproducibility. Addressing these barriers through scalable bioinformatic pipelines, consensus experimental frameworks, and cost-effective platforms remains critical for broadening accessibility and enabling clinical adoption.

Brain Neoplasms↗

Integrating forward and reverse proteomics to unravel protein function.

To date, proteomics approaches have aimed to either identify novel proteins or change in protein expression/modification in various organisms under normal or disease conditions. One major aspect of functional proteomics is to identify protein biological properties in a given context, however, forward proteomics approaches alone cannot complete this goal. Indeed, with the increasing successes of such proteomics-based research strategies and the subsequent increasing amounts of proteins identified with unknown molecular functions, approaches allowing for systematic analyses of protein functions are desired. In this review, we propose to depict the complementarities of forward and reverse proteomics approaches in the definite understanding of protein functions. This dual strategy requires a data integration loop which allows for systematic characterization of protein function(s). The details of the integrative process combining both in silico and experimental resources and tools are presented. Altogether, we believe that the integration of forward and reverse proteomics approaches supported by bioinformatics will provide an efficient path towards systems biology.

Animals↗

An improved procedure for the preparation of rat uterine cell suspensions.

In the present paper we report on an improved procedure for the preparation of free uterine cells which avoids the use of trypsin and employs very low concentration of collagenase. The cells released mechanically from the digested tissue are constantly removed from the enzyme containing medium, thus minimizing exposure to collagenase. 60%-70% of the cells which make up the intact uterus are obtained as free cells and 95% of these cells are viable for at least 15 hours at 37 degrees. Metabolic integrity was assessed by measuring the cell's ability to oxidize glucose and synthesize proteins over extended periods of time. The membrane leucine carrier protein and the membrane Na+/K+ ATPase were found to be fully functional. Electron microscopic analysis of the cells confirmed their structural integrity. Data are presented illustrating that with this system the estrogen binding protein is stable at physiological temperatures. The cells contain approximately 30,000 specific estrogen binding sites, with an apparent KA of 5--6 x 10(9) M-1. At 37 degrees 80% of the hormone receptor complexes were in the nuclear fraction, 20% in the cytoplasm. The similarity of the estrogen receptor binding parameters with those measured in the intact tissue after in vivo hormone adminsistration, together with the cells' structural and metabolic integrity make this procedure for the preparation of uterine cell suspensions in high yields particularly suitable for studies in which minimal cell injury is an essential prerequisite.

Animals↗

Online data collection with special populations over the World Wide Web.

The quick ascendance of the World Wide Web as the dominant vehicle for internet communication has recently made experimentation in a multimedia environment feasible on the Internet. Although web sites containing online psychology demonstrations and experiments for non-handicapped individuals have appeared in recent years (especially in the areas of cognitive and social psychology), there appear to have been few attempts to conduct online experimentation with special populations. We recently completed two online pilot studies of families with Down syndrome or Williams syndrome members: a) A survey that asks (via Likert rating scales, adjective checklists, multiple-choice style questions, and text-entry boxes) about family background, computer use, and temperament of the special needs family member; and b) An experiment (completed by an individual with special needs) that includes auditory and visual digit span tasks and a memory-for-orientation task in which responses are entered via mouse clicks. Recruiting began with e-mail announcements to representative Down syndrome and Williams syndrome discussion groups, listserves, and bulletin boards, and submission of the project's URL (http://www.cofc.edu/~marcellm/testaw.htm) and key indexing terms to selected search engines. This paper reviews technical aspects of developing the online programmes as well as the strengths and weaknesses of online vs. traditional laboratory-based research in relation to issues such as experimental control, delivery of instructions, experimenter bias, participant recruitment, sample heterogeneity, generalization, attrition, privacy, financial costs, data integrity, and ethics. We conclude by offering our thoughts on two ways of implementing online experimentation with special populations: a) Using a remote parent 'helper' as a proxy to work with the target individual; and b) Collaborating with professional colleagues in Web-based projects conducted in traditional laboratory settings.

Child, Preschool↗

Computer-administered bath ankylosing spondylitis and Quebec Scale outcome questionnaires for low back pain: agreement with traditional paper format.

OBJECTIVE: To measure the agreement between computer and paper-administered versions of Bath ankylosing spondylitis (AS) questionnaires and the Quebec Scale for low back pain (LBP). METHODS: Fifty patients with LBP completed the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Functional Index (BASFI), Global Score (BAS-G), and the Quebec Scale. Outcome measures were administered both in traditional paper format and by computerized touch-screen system. The order of completion was randomly assigned to each participant. The length of time required to complete each set of questionnaires was recorded and a "washout" period of at least 40 minutes was ensured between completion of the first and second set of outcome measures. RESULTS: There was no statistically significant difference in completion time between the 2 methods of administration. A small systematic difference between computer and paper-administered versions was observed in the Quebec Scale and in the BAS-G results. However, there was a high degree of agreement between paper and computer-administered versions of the Quebec Scale, the BASDAI, BASFI, and BAS-G. Out of the 50 subjects, 84% indicated a preference for the computer-administered method. CONCLUSION: The Bath AS questionnaires and the Quebec Scale can be reliably administered by a computerized touch-screen system. Given the ease of data integration and analysis supported by computer-administered versions of these outcome measures, their excellent reliability, and their popularity among study participants, the computerized versions of the BASDAI, BASFI, BAS-G, and Quebec Scale seem preferable to the traditional paper format.

Adult↗

From fragmentation to coordination: strengthening One Health research to support H5N1 preparedness in Cambodia.

OBJECTIVES: Highly pathogenic avian influenza A (H5N1) remains a major zoonotic threat, characterized by persistent transmission in Cambodia since its re-emergence in 2023. Despite strengthened surveillance and the establishment of the Inter-Ministerial Coordination Committee on One Health, limited integration of research across sectors constrains preparedness and response. This viewpoint examines how research supports the One Health system in Cambodia. METHODS: This viewpoint draws on insights obtained from the first national multistakeholder workshop on H5N1, held in March 2026. RESULTS: Fragmentation across epidemiological, clinical, behavioral, environmental, and genomic domains limits the generation of actionable evidence and delays its translation into policy. CONCLUSION: We propose the establishment of a multisectoral technical working group on H5N1 research embedded within the Inter-Ministerial Coordination Committee on One Health to align research priorities, strengthen data integration, and improve evidence-to-policy translation. This approach could enhance national preparedness while simultaneously positioning Cambodia as a model for coordinated One Health research in the Western Pacific region and beyond.

Avian influenza A (H5N1)↗

The Consortium on the Genetics of Endophenotypes in Schizophrenia: model recruitment, assessment, and endophenotyping methods for a multisite collaboration.

BACKGROUND: The Consortium on the Genetics of Schizophrenia (COGS) is an ongoing, National Institute of Mental Health-funded, 7-site collaboration investigating the occurrence and genetic architecture of quantitative endophenotypes related to schizophrenia. The purpose of this article is to provide a description of the COGS structure and methods, including participant recruitment and assessment. METHODS: The hypothesis-driven recruitment strategy ascertains families that include a proband with a Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition diagnosis of schizophrenia, and at least one unaffected full sibling available for genotyping and endophenotyping, along with parents available for genotyping and (optional depending on age) endophenotyping. The family structure is selected to provide contrast in quantitative endophenotypic traits and thus to maximize the power of the planned genetic analyses. Probands are recruited from many sources including clinician referrals, local National Alliance for the Mentally Ill chapters, and advertising via the media. All participants undergo a standardized protocol that includes clinical characterization, a blood draw for genotyping, and endophenotype assessments (P50 suppression, prepulse inhibition, antisaccade performance, continuous performance tasks, letter-number span, verbal memory, and a computerized neurocognitive battery). Investigators participate in weekly teleconferences to coordinate and evaluate recruitment, clinical assessment, endophenotyping, and continuous quality control of data gathering and analyses. Data integrity is maintained through use of a highly quality-assured, centralized web-based database. RESULTS: As of February 2006, 355 families have been enrolled and 688 participants have been endophenotyped, including schizophrenia probands (n = 154, M:F = 110:44), first-degree biological relatives (n = 343, M:F = 151:192), and community comparison subjects (n = 191, M:F = 81:110). DISCUSSION: Successful multisite genetics collaborations must institute standardized methodological criteria for assessment and recruitment that are clearly defined, well communicated, and uniformly applied. In parallel, studies utilizing endophenotypes require strict adherence to criteria for cross-site data acquisition, equipment calibration and testing and software equivalence, and continuous quality assurance for many measures obtained across sites. This report describes methods and presents the structure of the COGS as a model of multisite endophenotype genetic studies. It also provides demographic information after the first 2 years of data collection on a sample for whom the behavioral data and genetics of endophenotype performance will be fully characterized in future articles. Some issues discussed in the reviews that follow reflect the challenges of evaluating endophenotypes in studies of the genetic architecture of endophenotypes in schizophrenia.

Cooperative Behavior↗

Correlation between serological and sequencing analyses of the PorB outer membrane protein in the Neisseria meningitidis serotyping system.

The current serological typing scheme for Neisseria meningitidis is not comprehensive; a proportion of isolates are not serotypeable. DNA sequence analysis and predicted amino acid sequences were used to characterize the structures of variable-region (VR) epitopes on N. meningitidis PorB proteins (PorB VR typing). Twenty-six porB gene sequences were obtained from GenBank and aligned with 41 new sequences. Primary amino acid structures predicted from those genes were grouped into 30 VR families of related variants that displayed at least 60% similarity. We correlated VR families with monoclonal antibody (MAb) reactivities, establishing a relationship between VR families and epitope locations for 15 serotype-defining MAbs. The current panel of serotype-defining MAbs underestimates by at least 50% the PorB VR variability because reagents for several major VR families are lacking or because a number of VR variants within some families are not recognized by serotype-defining MAbs. These difficulties, also reported for serosubtyping based on the PorA protein, are shown as inconsistent results between serological and sequence analyses, leading to inaccurate strain identification and incomplete epidemiological data. The information from this study enabled the expansion of the panel of MAbs currently available for serotyping, by including MAbs of previously undetermined specificities. Use of the expanded serotype panel enabled us to improve the sensitivity of serotyping by resolving a number of formerly nonserotypeable strains. In most cases, this information can be used to predict the VR family placement of unknown PorB proteins without sequencing the entire porB gene. PorB VR typing complements serotyping, and a combination of both techniques may be used for full characterization of meningococcal strains. The present work represents the most complete and integrated data set of PorB VR sequences and MAb reactivities of serogroup B and C meningococci produced to date.

Amino Acid Sequence↗

Making health data maps: a case study of a community/university research collaboration.

This paper presents the main findings from a collaborative community/university research project in Canada. The goal of the project was to improve access to community health information, and in so doing, enhance our knowledge of the development of community health information resources and community/university collaboration. The project built on a rich history of community/university collaboration in Southeast Toronto (SETO), and employed an interdisciplinary applied research and action design. Specific project objectives were to: (1) develop via active community/university collaboration a geographic information system (GIS) for ready access to routinely collected health data, and to study logistical, conceptual and technical problems encountered during system development; and (2) to document and analyze issues that can emerge in the process of community/university research collaboration. System development involved iteration through community user assessment of need, development or refinement of the GIS, and assessment of the GIS by community users. Collaborative process assessment entailed analysis of archival material, interviews with investigators and participant observation. Over the course of the project, a system was successfully developed, and favorably assessed by users. System development problems fell into four main areas: maintaining user involvement in system development, understanding and integrating data, bringing disparate data sources together, and making use of assembled data. Major themes emerging from the community/university collaborative research process included separate community and university cultures, time as an important issue for all involved, and the impact of uncertainty and ambiguity on the collaborative process.

Access to Information↗

Automated clinical annotation of tissue bank specimens.

Modern, molecular bio-medicine is driving a growing demand for extensively annotated tissue bank specimens. With careful clinical, pathologic and outcomes annotation, samples can be better matched to the research question at hand and experimental results better understood and verified. However, the difficulty and expense of detailed specimen annotation is well beyond the capability of most banks and has made access to well documented tissue a major limitation in medical re-search. In this context, we have implemented automated annotation of banked tissue by integrating data from three clinical systems--the cancer registry, the pathology LIS and the tissue bank inventory system--through a classical data warehouse environment. The project required modification of clinical systems, development of methods to identify patients between and map data elements across systems and the creation of de-identified data in data marts for use by researchers. The result has been much more extensive and accurate initial tissue annotation with less effort in the tissue bank, as well as dynamic ongoing annotation as the cancer registry follows patients over time.

Clinical Laboratory Information Systems↗

CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based integrated database on cell cycle regulation in mammals in normal and pathological states (Cyclonet database). It integrates data obtained by 'omics' sciences and chemoinformatics on the basis of systems biology approach. Cyclonet is a specialized resource, which enables researchers working in the field of anticancer drug discovery to analyze the wealth of currently available information in a systematic way. Cyclonet contains information on relevant genes and molecules; diagrams and models of cell cycle regulation and results of their simulation; microarray data on cell cycle and on various types of cancer, information on drug targets and their ligands, as well as extensive bibliography on modelling of cell cycle and cancer-related gene expression data. The Cyclonet database is also accessible through the BioUML workbench, which allows flexible querying, analyzing and editing the data by means of visual modelling. Cyclonet aims to predict promising anticancer targets and their agents by application of Prediction of Activity Spectra for Substances. The Cyclonet database is available at http://cyclonet.biouml.org.

Animals↗

A framework for teaching medical students and residents about practice-based learning and improvement, synthesized from a literature review.

PURPOSE: To create a framework for teaching the knowledge and skills of practice-based learning and improvement to medical students and residents based on proven, effective strategies. METHOD: The authors conducted a Medline search of English-language articles published between 1996 and May 2001, using the term "quality improvement" (QI), and cross-matched it with "medical education" and "health professions education." A thematic-synthesis method of review was used to compile the information from the articles. Based on the literature review, an expert panel recommended educational objectives for practice-based learning and improvement. RESULTS: Twenty-seven articles met the inclusion criteria. The majority of studies were conducted in academic medical centers and medical schools and 40% addressed experiential learning of QI. More than 75% were qualitative case reports capturing educational outcomes, and 7% included an experimental study design. The expert panel integrated data from the literature review with the Dreyfus model of professional skill acquisition, the Institute for Healthcare Improvement's (IHI) knowledge domains for improving health care, and the ACGME competencies and generated a framework of core educational objectives about teaching practice-based learning and improvement to medical students and residents. CONCLUSION: Teaching the knowledge and skills of practice-based learning and improvement to medical students and residents is a necessary and important foundation for improving patient care. The authors present a framework of learning objectives-informed by the literature and synthesized by the expert panel-to assist educational leaders when integrating these objectives into a curriculum. This framework serves as a blueprint to bridge the gap between current knowledge and future practice needs.

Clinical Competence↗

Predictive models for protein crystallization.

Crystallization of proteins is a nontrivial task, and despite the substantial efforts in robotic automation, crystallization screening is still largely based on trial-and-error sampling of a limited subset of suitable reagents and experimental parameters. Funding of high throughput crystallography pilot projects through the NIH Protein Structure Initiative provides the opportunity to collect crystallization data in a comprehensive and statistically valid form. Data mining and machine learning algorithms thus have the potential to deliver predictive models for protein crystallization. However, the underlying complex physical reality of crystallization, combined with a generally ill-defined and sparsely populated sampling space, and inconsistent scoring and annotation make the development of predictive models non-trivial. We discuss the conceptual problems, and review strengths and limitations of current approaches towards crystallization prediction, emphasizing the importance of comprehensive and valid sampling protocols. In view of limited overlap in techniques and sampling parameters between the publicly funded high throughput crystallography initiatives, exchange of information and standardization should be encouraged, aiming to effectively integrate data mining and machine learning efforts into a comprehensive predictive framework for protein crystallization. Similar experimental design and knowledge discovery strategies should be applied to valid analysis and prediction of protein expression, solubilization, and purification, as well as crystal handling and cryo-protection.

Bayes Theorem↗