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At least 883 records · Page 49Linked to original sources
PubMed2002

Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data.

Microarray analyses are providing a plethora of data concerning transcriptional responses to specific gene regulators and their inducers but do not distinguish between direct and indirect responses. Here, we identify directly activated promoters of the overlapping marA, soxS and rob regulon(s) of Escherichia coli by applying informatics, genomics and molecular genetics to microarray data obtained by others. Those studies found that overexpression of marA, or the treatment of cells with salicylate to derepress marA, or treatment with paraquat to induce soxS, resulted in elevated transcription of 153 genes. However, only 27 out of the promoters showed increased transcription under at least two of the aforementioned conditions and eight of those were previously known to be directly activated. A computer algorithm was used to identify potential activator binding sites located upstream of the remaining 19 promoters of this subset, and conventional genetic and biochemical approaches were applied to test whether these sites are critical for activation by the homologous MarA, SoxS and Rob transcriptional activators. Only seven out of the 19 promoters were found to be activated when fused to lacZ and tested as single lysogens. All seven contained an essential activator binding site. The remaining promoters were insensitive to stimulation by the inducers suggesting that the great majority of elevated microarray transcripts either were misidentified or resulted from indirect effects requiring sequences outside of the promoter region. We estimate that the total number of directly activated promoters in the regulon is less than 40.

Bacterial Proteins↗
PubMed2000

The role of informatics to support evidence-based practice and clinician education.

This paper reports the results of a national event held during November 1998 to educate health professionals representing multiple disciplines about evidence-based practice (EBP), its implementation and the use of informatics to support EBP. A combination of educational delivery methods and multimedia was used. Through local group work, participants identified obstacles to EBP implementation and developed strategies to overcome these in their own local environments. Major and common findings were a lack of management support and infrastructures needed for the successful adoption of evidence-based practices by all.

Australia↗
PubMed2006

Consideration of future requirements for Raman microbiology as an examplar for the ab initio development of informatics frameworks for emergent OMICS technologies.

Raman spectroscopy of single bacteria provides an OMIC-like view of the chemical status of individual cells, reporting on metabolism, cell stress and growth, and is likely to become a significant tool in environmental and medical microbiology. We advocate the early development of integrated data models and informatics frameworks, in parallel with the development of Raman hardware and experimental protocols, in order to maximize the benefits of this emerging OMIC technology to the research community.

Computational Biology↗
PubMed2006

caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid.

MOTIVATION: The complexity of cancer is prompting researchers to find new ways to synthesize information from diverse data sources and to carry out coordinated research efforts that span multiple institutions. There is a need for standard applications, common data models, and software infrastructure to enable more efficient access to and sharing of distributed computational resources in cancer research. To address this need the National Cancer Institute (NCI) has initiated a national-scale effort, called the cancer Biomedical Informatics Grid (caBIGtrade mark), to develop a federation of interoperable research information systems. RESULTS: At the heart of the caBIG approach to federated interoperability effort is a Grid middleware infrastructure, called caGrid. In this paper we describe the caGrid framework and its current implementation, caGrid version 0.5. caGrid is a model-driven and service-oriented architecture that synthesizes and extends a number of technologies to provide a standardized framework for the advertising, discovery, and invocation of data and analytical resources. We expect caGrid to greatly facilitate the launch and ongoing management of coordinated cancer research studies involving multiple institutions, to provide the ability to manage and securely share information and analytic resources, and to spur a new generation of research applications that empower researchers to take a more integrative, trans-domain approach to data mining and analysis. AVAILABILITY: The caGrid version 0.5 release can be downloaded from https://cabig.nci.nih.gov/workspaces/Architecture/caGrid/. The operational test bed Grid can be accessed through the client included in the release, or through the caGrid-browser web application http://cagrid-browser.nci.nih.gov.

Biomarkers, Tumor↗
PubMed2000

The phytophthora genome initiative database: informatics and analysis for distributed pathogenomic research.

The Phytophthora Genome Initiative (PGI) is a distributed collaboration to study the genome and evolution of a particularly destructive group of plant pathogenic oomycete, with the goal of understanding the mechanisms of infection and resistance. NCGR provides informatics support for the collaboration as well as a centralized data repository. In the pilot phase of the project, several investigators prepared Phytophthora infestans and Phytophthora sojae EST and Phytophthora sojae BAC libraries and sent them to another laboratory for sequencing. Data from sequencing reactions were transferred to NCGR for analysis and curation. An analysis pipeline transforms raw data by performing simple analyses (i.e., vector removal and similarity searching) that are stored and can be retrieved by investigators using a web browser. Here we describe the database and access tools, provide an overview of the data therein and outline future plans. This resource has provided a unique opportunity for the distributed, collaborative study of a genus from which relatively little sequence data are available. Results may lead to insight into how better to control these pathogens. The homepage of PGI can be accessed at http:www.ncgr.org/pgi, with database access through the database access hyperlink.

Databases, Factual↗
PubMed2005

Farm animal genomics and informatics: an update.

Farm animal genomics is of interest to a wide audience of researchers because of the utility derived from understanding how genomics and proteomics function in various organisms. Applications such as xenotransplantation, increased livestock productivity, bioengineering new materials, products and even fabrics are several reasons for thriving farm animal genome activity. Currently mined in rapidly growing data warehouses, completed genomes of chicken, fish and cows are available but are largely stored in decentralized data repositories. In this paper, we provide an informatics primer on farm animal bioinformatics and genome project resources which drive attention to the most recent advances in the field. We hope to provide individuals in biotechnology and in the farming industry with information on resources and updates concerning farm animal genome projects.

Animals↗
PubMedDate not supplied

Nursing informatics: a model curriculum for an emerging role.

The authors delineate the emerging role of the nurse as Information Systems Specialist and describe a prototype educational program in Nursing Informatics which is designed to prepare nurses for this role. Major duties, knowledge required, and resulting interactions related to the role are discussed in relation to the curriculum design and course content. The projected impact of this model program is also addressed.

Curriculum↗
PubMed2004

Biodiversity informatics: managing and applying primary biodiversity data.

Recently, advances in information technology and an increased willingness to share primary biodiversity data are enabling unprecedented access to it. By combining presences of species data with electronic cartography via a number of algorithms, estimating niches of species and their areas of distribution becomes feasible at resolutions one to three orders of magnitude higher than it was possible a few years ago. Some examples of the power of that technique are presented. For the method to work, limitations such as lack of high-quality taxonomic determination, precise georeferencing of the data and availability of high-quality and updated taxonomic treatments of the groups must be overcome. These are discussed, together with comments on the potential of these biodiversity informatics techniques not only for fundamental studies but also as a way for developing countries to apply state of the art bioinformatic methods and large quantities of data, in practical ways, to tackle issues of biodiversity management.

Biodiversity↗
PubMed2000

The quiet revolution: biodiversity informatics and the internet.

The massive development of biodiversity-related information systems on the Internet has created much that appears exciting but chaotic, a diversity to match biodiversity itself. This richness and the arrays of new sources are counterbalanced by the maddening difficulty in knowing what is where, or of comparing like with like. But quietly, behind the first waves of exuberance, biologists and computer scientists have started to pull together in a rising tide of coherence and organization. The fledgling field of biodiversity informatics looks set to deliver major advances that could turn the Internet into a giant global biodiversity information system.

Animals↗
PubMedDate not supplied

HCFA's health care quality improvement program: the medical informatics challenge.

The peer-review organizations (PROs) were created by Congress in 1984 to monitor the cost and quality of care received by Medicare beneficiaries. In order to do this, the Health Care Financing Administration (HCFA) contracted with the PROs through a series of contracts referred to as "Scopes of Work." Under the Fourth Scope of Work, the HCFA initiated the Health Care Quality Improvement Program (HCQIP) in 1990, as an application of the principles of continuous quality improvement. Since then, the PROs have participated with health care providers in cooperative projects to improve the quality of primarily inpatient care provided to Medicare beneficiaries. Through HCFA-supplied administrative data and clinical data abstracted from patient records, the PROs have been able to identify opportunities for improvements in patient care. In May 1995, the HCFA proposed a new Fifth Scope of Work, which will shift the focus of HCQIP from inpatient care projects to projects in outpatient and managed care settings. This article describes the HCQIP process, the types of data used by the PROs to conduct cooperative projects with health care providers, and the informatics challenges in improving the quality of care received by Medicare beneficiaries.

Centers for Medicare and Medicaid Services, U.S.↗
PubMedDate not supplied

Q-methodology: definition and application in health care informatics.

OBJECTIVE: To introduce the Q-methodology research technique to the field of health informatics. Q-methodology--the systematic study of subjectivity--was used to identify and categorize the opinions of primary care physicians and medical students that contributed to our understanding of their reasons for acceptance of and/or resistance to adapting information technologies in the health care workplace. DESIGN: Thirty-four physicians and 25 medical students from the Chicago area were surveyed and asked to rank-order 30 opinion statements about information technologies within the health care workplace. The Q-methodology research technique was employed to structure an opinion typology from their rank-ordered statements. (The rank-ordered sorts were subjected to correlation and by-person factor analysis to obtain groupings of participants who sorted the opinion statements into similar arrangements.) RESULTS: The typology for this study revealed groupings of similar opinion-types associated with the likelihood of physicians and medical students to adapt information technology into their health care workplace. A typology of six opinions was identified in the following groups: (1) Full-Range Adopters; (2) Skills-Concerned Adopters; (3) Technology-Critical Adopters; (4) Independently-Minded and Concerned; (5) Inexperienced and Worried; and (6) Business-Minded and Adaptive. It is imperative to understand that in the application of Q-methodology, the domain is subjectivity and research is performed on small samples. The methodology is a combination of qualitative and quantitative research techniques that reveals dimensions of subjective phenomena from a perspective intrinsic to the individual to determine what is statistically different about the dimensions and to identify characteristics of individuals who share common viewpoints. Low response rates do not bias Q-methodology because the primary purpose is to identify a typology, not to test the typology's proportional distribution within the larger population. CONCLUSION: Q-methodology can allow for the simultaneous study of objective and subjective issues to determine an individual's opinion and forecast their likeliness to adapt information technologies in the health care workplace. This study suggests that an organization's system implementers could employ Q-methodology to individualize and customize their approach to understanding the personality complexities of physicians in their organization and their willingness to adapt and utilize information technologies within the workplace.

Attitude of Health Personnel↗
PubMedDate not supplied

An informatics-based chronic disease practice: case study of a 35-year computer-based longitudinal record system.

The authors present the case study of a 35-year informatics-based single subspecialty practice for the management of patients with chronic thyroid disease. This extensive experience provides a paradigm for the organization of longitudinal medical information by integrating individual patient care with clinical research and education. The kernel of the process is a set of worksheets easily completed by the physician during the patient encounter. It is a structured medical record that has been computerized since 1972, enabling analysis of different groups of patients to answer questions about chronic conditions and the effects of therapeutic interventions. The recording process and resulting studies serve as an important vehicle for medical education about the nuances of clinical practice. The authors suggest ways in which computerized medical records can become an integral part of medical practice, rather than a luxury or novelty.

Chronic Disease↗
PubMedDate not supplied

A framework for comprehensive health terminology systems in the United States: development guidelines, criteria for selection, and public policy implications. ANSI Healthcare Informatics Standards Board Vocabulary Working Group and the Computer-Based Patient Records Institute Working Group on Codes and Structures.

Health care in the United States has become an information-intensive industry, yet electronic health records represent patient data inconsistently for lack of clinical data standards. Classifications that have achieved common acceptance, such as the ICD-9-CM or ICD, aggregate heterogeneous patients into broad categories, which preclude their practical use in decision support, development of refined guidelines, or detailed comparison of patient outcomes or benchmarks. This document proposes a framework for the integration and maturation of clinical terminologies that would have practical applications in patient care, process management, outcome analysis, and decision support. Arising from the two working groups within the standards community--the ANSI (American National Standards Institute) Healthcare Informatics Standards Board Working Group and the Computer-based Patient Records Institute Working Group on Codes and Structures--it outlines policies regarding 1) functional characteristics of practical terminologies, 2) terminology models that can broaden their applications and contribute to their sustainability, 3) maintenance attributes that will enable terminologies to keep pace with rapidly changing health care knowledge and process, and 4) administrative issues that would facilitate their accessibility, adoption, and application to improve the quality and efficiency of American health care.

Delivery of Health Care↗
PubMedDate not supplied

Columbia University's Informatics for Diabetes Education and Telemedicine (IDEATel) project: technical implementation.

The Columbia University Informatics for Diabetes Education and Telemedicine IDEATel) project is a four-year demonstration project funded by the Centers for Medicare and Medicaid Services with the overall goal of evaluating the feasibility, acceptability, effectiveness, and cost-effectiveness of telemedicine. The focal point of the intervention is the home telemedicine unit (HTU), which provides four functions: synchronous videoconferencing over standard telephone lines, electronic transmission for fingerstick glucose and blood pressure readings, secure Web-based messaging and clinical data review, and access to Web-based educational materials. The HTU must be usable by elderly patients with no prior computer experience. Providing these functions through the HTU requires tight integration of six components: the HTU itself, case management software, a clinical information system, Web-based educational material, data security, and networking and telecommunications. These six components were integrated through a variety of interfaces, providing a system that works well for patients and providers. With more than 400 HTUs installed, IDEATel has demonstrated the feasibility of large-scale home telemedicine.

Case Management↗
PubMedDate not supplied

Columbia University's Informatics for Diabetes Education and Telemedicine (IDEATel) Project: rationale and design.

The Columbia University Informatics for Diabetes Education and Telemedicine (IDEATel) Project is a four-year demonstration project funded by the Centers for Medicare and Medicaid Services with the overall goals of evaluating the feasibility, acceptability, effectiveness, and cost-effectiveness of telemedicine in the management of older patients with diabetes. The study is designed as a randomized controlled trial and is being conducted by a state-wide consortium in New York. Eligibility requires that participants have diabetes, are Medicare beneficiaries, and reside in federally designated medically underserved areas. A total of 1,500 participants will be randomized, half in New York City and half in other areas of the state. Intervention participants receive a home telemedicine unit that provides synchronous videoconferencing with a project-based nurse, electronic transmission of home fingerstick glucose and blood pressure data, and Web access to a project Web site. End points include glycosylated hemoglobin, blood pressure, and lipid levels; patient satisfaction; health care service utilization; and costs. The project is intended to provide data to help inform regulatory and reimbursement policies for electronically delivered health care services.

Case Management↗
PubMed2003

Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone.

The postgenomic era, as manifest, inter alia, by proteomics, offers unparalleled opportunities for the efficient discovery of safe, efficacious, and novel subunit vaccines targeting a tranche of modern major diseases. A negative corollary of this opportunity is the risk of becoming overwhelmed by this embarrassment of riches. Informatics techniques, working to address issues of both data management and through prediction to shortcut the experimental process, can be of enormous benefit in leveraging the proteomic revolution. In this disquisition, we evaluate proteomic approaches to the discovery of subunit vaccines, focussing on viral, bacterial, fungal, and parasite systems. We also adumbrate the impact that proteomic analysis of host-pathogen interactions can have. Finally, we review relevant methods to the prediction of immunome, with special emphasis on quantitative methods, and the subcellular localization of proteins within bacteria.

Journal Article↗
PubMed2003

Genome informatics: current status and future prospects.

This article reviews recent advances in genomics and informatics relevant to cardiovascular research. In particular, we review the status of (1) whole genome sequencing efforts in human, mouse, rat, zebrafish, and dog; (2) the development of data mining and analysis tools; (3) the launching of the National Heart, Lung, and Blood Institute Programs for Genomics Applications and Proteomics Initiative; (4) efforts to characterize the cardiac transcriptome and proteome; and (5) the current status of computational modeling of the cardiac myocyte. In each instance, we provide links to relevant sources of information on the World Wide Web and critical appraisals of the promises and the challenges of an expanding and diverse information landscape.

Animals↗