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At least 757 records · Page 42Linked to original sources
PubMed2007

TBestDB: a taxonomically broad database of expressed sequence tags (ESTs).

The TBestDB database contains approximately 370,000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and includes experimental information, consensus sequences, gene annotations and metabolic pathway predictions. Most of these ESTs have been generated by the Protist EST Program, a collaboration among six Canadian research groups. EST sequences are read from trace files up to a minimum quality cut-off, vector and linker sequence is masked, and the ESTs are clustered using phrap. The resulting consensus sequences are automatically annotated by using the AutoFACT program. The datasets are automatically checked for clustering errors due to chimerism and potential cross-contamination between organisms, and suspect data are flagged in or removed from the database. Access to data deposited in TBestDB by individual users can be restricted to those users for a limited period. With this first report on TBestDB, we open the database to the research community for free processing, annotation, interspecies comparisons and GenBank submission of EST data generated in individual laboratories. For instructions on submission to TBestDB, contact tbestdb@bch.umontreal.ca. The database can be queried at http://tbestdb.bcm.umontreal.ca/.

Animals↗
PubMed1987

What knowledge-accessing modes tell administrators about interdisciplinary crises and conflicts.

In hospitals administrators work with two major groups of medical professionals: physicians and nurses. Together, these three groups of professionals are primarily responsible for the care of patients. The quality of the service they provide is dependent on the working relationships among these disciplines. Potentially, the more harmony among administrators, physicians, and nurses, the better care patients can receive. The research reported in this article addresses the issue of interdisciplinary misunderstanding among these groups of professionals. The research was premised on the assumption that hospital administrators, physicians, and nurses differ in the way they access knowledge. That is, administrators, physicians, and nurses access knowledge in dissimilar ways and, by doing so, set the stage for crises and conflicts. Using a standardized instrument to assess knowledge-accessing modes, data were collected from samples of health administration, medical, and nursing students. The data indicated that the three groups did differ in the way they accessed knowledge. The individual discipline profiles generated from the data also revealed a finding common to the three disciplines, a finding may help resolve a very real problem for hospital patients. Based on the research results, the article discusses ways that administrators may be able to prevent crises and conflicts and enhance harmonious relations among the three disciplines, and thereby improve patient care. Avenues for further research are also suggested.

Attitude of Health Personnel↗
PubMed1997

The Danish Cancer Registry--history, content, quality and use.

The Danish Cancer Registry is a population-based registry containing data on the incidence of cancer throughout Denmark since 1943. Reporting of cancer was made mandatory by administrative order in 1987. Details of individual cases of cancer are available according to the 7th revision of the International Classification of Diseases (ICD) for all years, and according to the ICD-O since 1978. A core data set is kept on each individual which includes date of birth, sex, date of cancer diagnosis, method of verification, date of death and cause of death. This paper describes the history of the registry, its data sources and its procedures, including quality control and access to data. Integration of both research activities and registration since the inception of the Registry has maintained the completeness and validity of the data for 1943-1996.

Databases, Factual↗
PubMed1984

The national profile of access to medical care: where do we stand?

This paper presents analyses of recent national survey data on access to medical care. In particular, information on major access indicators and special problems associated with the economic and political climate of the 1980s collected in a 1982 national telephone survey of 6,610 United States adults and children, representing some 4,802 families, is compared with previous national surveys for key population subgroups--by age, place of residence, income, race, insurance coverage, and type of regular source of care. In general, the findings show that favorable progress has been made, but some inequities continue to persist. Some traditionally disadvantaged groups are more likely to have a regular family doctor, private insurance coverage, have been to a doctor, or had certain preventive tests and procedures than was true for them in the past. On the other hand, compared to the more economically and/or socially advantaged groups in 1982, they have still not "caught up" entirely. There also is evidence that they may be hardest hit by the exacerbation of the financial barriers to care that result from unemployment, inflation, and cutbacks in health program eligibility and benefits that have characterized the decade of the 1980s.

Adolescent↗
PubMed2004

Security middleware infrastructure for DICOM images in health information systems.

In health care, it is mandatory to maintain the privacy and confidentiality of medical data. To achieve this, a fine-grained access control and an access log for accessing medical images are two important aspects that need to be considered in health care systems. Fine-grained access control provides access to medical data only to authorized persons based on priority, location, and content. A log captures each attempt to access medical data. This article describes an overall middleware infrastructure required for secure access to Digital Imaging and Communication in Medicine (DICOM) images, with an emphasis on access control and log maintenance. We introduce a hybrid access control model that combines the properties of two existing models. A trust relationship between hospitals is used to make the hybrid access control model scalable across hospitals. We also discuss events that have to be logged and where the log has to be maintained. A prototype of security middleware infrastructure is implemented.

Access to Information↗
PubMed1998

Development of a clinical event monitor for use with the Veterans Affairs Computerized Patient Record System and other data sources.

We are developing an event monitor to operate with the Veterans Affairs Computerized Patient Record System (CPRS). The event monitor is designed to receive messages when important patient events such as posting of new results, patient movement, and orders occur. Our design separates the event monitor from CPRS itself, using communication via a network connection to receive HL7 messages, to access other data needed to run rules, and to communicate with providers by message display, electronic mail and other mechanisms. Results from operation of the event monitor using patient data in our test account show that a wide variety of data can be accessed by the event monitor with acceptable response times.

Computer Communication Networks↗
PubMed1999

The Genome Sequence DataBase: towards an integrated functional genomics resource.

During 1998 the primary focus of the Genome Sequence DataBase (GSDB; http://www.ncgr.org/gsdb ) located at the National Center for Genome Resources (NCGR) has been to improve data quality, improve data collections, and provide new methods and tools to access and analyze data. Data quality has been improved by extensive curation of certain data fields necessary for maintaining data collections and for using certain tools. Data quality has also been increased by improvements to the suite of programs that import data from the International Nucleotide Sequence Database Collaboration (IC). The Sequence Tag Alignment and Consensus Knowledgebase (STACK), a database of human expressed gene sequences developed by the South African National Bioinformatics Institute (SANBI), became available within the last year, allowing public access to this valuable resource of expressed sequences. Data access was improved by the addition of the Sequence Viewer, a platform-independent graphical viewer for GSDB sequence data. This tool has also been integrated with other searching and data retrieval tools. A BLAST homology search service was also made available, allowing researchers to search all of the data, including the unique data, that are available from GSDB. These improvements are designed to make GSDB more accessible to users, extend the rich searching capability already present in GSDB, and to facilitate the transition to an integrated system containing many different types of biological data.

Animals↗
PubMed1996

Integrated access to metabolic and genomic data.

The EcoCyc system consists of a knowledge base (KB) that describes the genes and intermediary metabolism of Escherichia coli, and a graphical user interface (GUI) for accessing that knowledge. This paper addresses two problems: How can we create a GUI that provides integrated access to metabolic and genomic data? We describe the design and implementation of visual presentations that closely mimic those found in the biology literature, and that offer hypertext navigation among related entities, and multiple views of the same entity. We employ a frame knowledge representation system (FRS) called HyperTHEO to manage the EcoCyc knowledge base. Among the advantages of FRSs are an expressive data model for capturing the complexities of biological information, and schema-evolution capabilities that facilitate the constant schema changes that biological databases tend to undergo. HyperTHEO also includes rule-based inference facilities that are the foundation of expert systems, a constraint language for maintaining data integrity, and a declarative query language. A graphic KB editor and browser allow the EcoCyc developers to interactively inspect and modify this evolving KB.

Artificial Intelligence↗
PubMed1993

The GDB human genome data base anno 1993.

Version 5.0 of the Genome Data Base (GDB) was released in March 1993. This document describes some of the significant changes to the types of data which are stored within the GDB. In addition to handling a wider scope of data, the GDB 5.0 application software now supports the X-Windows protocol. Although the GDB software still remains the most widely utilized method for accessing the data, alternate methods of access are now available, including direct SQL (Structured Query Language) queries, FTP (Internet File Transfer Protocol), WAIS (Wide Area Information Server), and other tools produced by third-party developers.

Chromosome Mapping↗
PubMed2006

Integrated multimedia medical data agent in E-health.

E-Health is producing a great impact in the field of information distribution of the health services to the intra-hospital and the public. Previous researches have addressed the development of system architectures in the aim of integrating the distributed and heterogeneous medical information systems. The easing of difficulties in the sharing and management of medical data and the timely accessibility to these data is a critical need for health care providers. We have proposed a client-server agent that allows a portal to the every permitted Information System of the Hospital that consists of PACS, RIS and HIS via the Intranet and the Internet. Our proposed agent enables remote access into the usually closed information system of the hospital and a server that indexes all the medical data which allows for in-depth and complex search queries for data retrieval.

Computer Communication Networks↗
PubMed1997

Access to health care: bridging the gap between policy and research.

Access to care has long been studied by researchers, but emphasis has shifted recently from measuring whether access is worse for the poor and uninsured to monitoring how access is changing over time. Only a limited number of measures have been used consistently to monitor changes longitudinally, and these suggest that access by the uninsured is declining. There are potentially more valuable measures to track access, but data that are consistent over time have not been available. This Issue Brief, which is based on a seminar held by the Center for Studying Health System Change, discusses current research efforts to measure access to care.

Data Collection↗
PubMed1998

GenBank.

The GenBank(R) sequence database (http://www.ncbi.nlm.nih.gov/) incorporates DNA sequences from all available public sources, primarily through the direct submission of sequence data from individual laboratories and from large-scale sequencing projects. Most submitters use the BankIt (WWW) or Sequin programs to send their sequence data. Data exchange with the EMBL Data Library and the DNA Data Bank of Japan helps ensure comprehensive worldwide coverage. GenBank data is accessible through NCBI's integrated retrieval system, Entrez , which integrates data from the major DNA and protein sequence databases along with taxonomy, genome and protein structure information. MEDLINE(R) abstracts from published articles describing the sequences are also included as an additional source of biological annotation. Sequence similarity searching is offered through the BLAST series of database search programs. In addition to FTP, e-mail and server/client versions of Entrez and BLAST, NCBI offers a wide range of World Wide Web retrieval and analysis services of interest to biologists.

Animals↗
PubMed2004

Establishment and maintenance of vascular access in incident hemodialysis patients: a prospective cost analysis.

Despite the importance of hemodialysis vascular access, the cost of vascular access care has not been studied in detail. A prospective cost analysis was performed among incident hemodialysis patients to determine the cost of vascular access care overall and on the basis of access type. Detailed clinical and demographic information, as well as data on access type, was collected for all local incident hemodialysis patients between July 1, 1999, and November 1, 2001. A comprehensive measure of total vascular access costs, including surgery, radiology, hospitalization for access complications, physician costs, costs for management of outpatient bacteremia, and vascular access monitoring costs, was obtained. Costs are reported in 2002 Canadian dollars (1 CAN dollar = 0.69 US dollar). A total of 239 consecutive incident hemodialysis patients were identified, 49, 157, and 33 of whom were dialyzed exclusively with a catheter or had a native arteriovenous fistula or synthetic graft attempted, respectively. In year 1, 18.4% of all hospital admissions were for vascular access-related complications. The mean cost of all vascular access care in year 1 was 6890 CAN dollars(median 4020 dollars; interquartile range [IQR] 2440 dollars to 7540 dollars). The mean cost of access care per patient-year at risk for maintaining a catheter exclusively, attempting an arteriovenous fistula, or attempting a graft was 9180 dollars (median 3812 dollars; IQR 2250 dollars to 7762 dollars), 7989 dollars (median 4641 dollars ; IQR 3035 dollars to 8832 dollars), and 11,685 dollars (median 8152 dollars; IQR 3395 dollars to 12,908 dollars), respectively (P = 0.01). Vascular access care is responsible for a significant proportion of health care costs in the first year of hemodialysis. These results support clinical practice guidelines that recommend preferential placement of a native fistula.

Aged↗
PubMed2004

ComBase: a common database on microbial responses to food environments.

The advancement of predictive microbiology relies on available data that describe the behavior of microorganisms in different environmental matrices. For such information to be useful to the predictive microbiology research community, data must be organized in a manner that permits efficient access and data retrieval. Here, we describe a database protocol that encompasses observations of bacterial responses to food environments, resulting in a database (ComBase) for predictive microbiology purposes. The data included in ComBase were obtained from cooperating research institutes and from the literature and are publicly available via the Internet.

Bacteria↗
PubMed1999

Getting data out of the electronic patient record: critical steps in building a data warehouse for decision support.

Health care has taken advantage of computers to streamline many clinical and administrative processes. However, the potential of health care information technology as a source of data for clinical and administrative decision support has not been fully explored. This paper describes the process of developing on-line analytical processing (OLAP) capacity from data generated in an on-line transaction processing (OLTP) system (the electronic patient record). We discuss the steps used to evaluate the EPR system, retrieve the data, and create an analytical data warehouse accessible for analysis. We also summarize studies based on the data (lab re-engineering, practice variation in diagnostic decision-making and evaluation of a clinical alert). Besides producing a useful data warehouse, the process also increased understanding of organizational and cost considerations in purchasing OLAP tools. We discuss the limitations of our approach and ways in which these limitations can be addressed.

Database Management Systems↗
PubMed2000

Data acquisition, data storage, and data presentation in a modern genetics laboratory.

Modern genetic analysis can be divided into three main areas of investigation. The first is data acquisition, in the form of genomic sequence and the cataloguing of polymorphism data of the single nucleotide polymorphism variety (so called SNPs). Once identified, such genetic information can be adapted into high throughput tests to examine genetic information in large populations, making the analysis of sufficiently large numbers both cost and time effective so that relatively low-penetrant genetic effects can be accurately detected. The third step is correlating variation with phenotype (e.g. disease susceptibility or resistance) for a variety of disorders is paramount in our motivation and indeed is a common goal of modern human genetic analysis. While the technology to acquire vast amounts of genetic data is now well established and continues to expand, the ability to deal with such data, from the process of acquisition, storage, and analysis depends fundamentally on a solid informatics infrastructure as an essential component. Indeed, most of the major gains in productivity in this field are to be realized on the informatics front, and involve automating data acquisition, defining and sorting data in databases for quality control and analysis and facilitating access to data for the large variety of data analyses. Informatics-related issues including those relating to data acquisition, database structure, and analysis tools are summarized here in an effort to define some of the issues relevant to establishing informatics infrastructure in a small genetics laboratory focused on resequencing human immune response genes. From inherited diseases to drug efficacy to the specific genetic changes occurring during tumor development, this new field of medical genetics promises a profound impact on the state of human health. Ultimately, any and all advances in this field will continue to depend on major investments in informatics.

Computational Biology↗
PubMed1997

Long-term survival in acute myeloid leukemia: the Eastern Cooperative Oncology Group experience.

BACKGROUND: The data base of the Eastern Cooperative Oncology Group (ECOG) provides access to data on a large adult patient population drawn from more than 25 major university institutions and hundreds of participating hospitals. Extensive medical files are maintained at the ECOG Coordinating Center and are updated regularly. METHODS: Data on 1414 eligible patients with acute myeloid leukemia (AML), treated on 6 ECOG protocols during the period 1976-1994, were reviewed to determine the number of long-term survivors (LTS) and to identify factors that predicted LTS. Disease free survival and factors impacting quality of life were examined as well. RESULTS: Of the 1414 patients, 274 survived for > or = 3 years and were considered LTS. A logistic regression analysis revealed that factors predicting LTS included age < 55 years, female gender, treatment between 1985 and 1990, white blood cell count < 10,000 cells/mm3, and hemoglobin > 10 g/dL. Disease free survival improved with escalating intensity of therapy. Quality-of-life data showed that infections were fairly common. Significant graft-versus-host disease occurred in 6 of 40 patients who received allogeneic bone marrow transplantation and contributed to the deaths of 4 individuals. Information on employment, insurance, social or marital difficulties, and psychosocial issues was more difficult to obtain. CONCLUSIONS: Prognosis in AML is a complex interaction involving the cellular origin of the malignant clone, morphology, and evolving therapeutic strategies. The most recent ECOG studies incorporate these variables and should provide additional insights into factors affecting LTS in patients with AML.

Acute Disease↗
PubMed1995

Forensic DNA data banking by state crime laboratories.

This article reports the results of a survey of the responsible crime laboratories in the first 19 states with legislation establishing forensic DNA data banks. The survey inquired into the labs' policies and procedures regarding the collection, storage, and analysis of samples; the retention of samples and data; search protocols; access to samples and data by third parties; and related matters. The research suggests that (1) the number of samples collected from convicted offenders for DNA data banking has far surpassed the number that have been analyzed; (2) data banks have already been used in a small but growing number of cases, to locate suspects and to identify associations between unresolved cases; (3) crime labs currently plan to retain indefinitely the samples collected for their data banks; and (4) the nature and extent of security safeguards that crime labs have implemented for their data banks vary among states. The recently enacted DNA Identification Act (1994) will provide $40 million in federal matching grants to states for DNA analysis activities, so long as states comply with specified quality-assurance standards, submit to external proficiency testing, and limit access to DNA information. Although these additional funds should help to ease some sample backlogs, it remains unclear how labs will allocate the funds, as between analyzing samples for their data banks and testing evidence samples in cases without suspects. The DNA Identification Act provides penalties for the disclosure or obtaining of DNA data held by data banks that participate in CODIS, the FBI's evolving national network of DNA data banks, but individual crime labs must also develop stringent internal safeguards to prevent breaches of data-bank security.

Civil Rights↗