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PubMed2006

Metrics in the science of surge.

Metrics are the driver to positive change toward better patient care. However, the research into the metrics of the science of surge is incomplete, research funding is inadequate, and we lack a criterion standard metric for identifying and quantifying surge capacity. Therefore, a consensus working group was formed through a "viral invitation" process. With a combination of online discussion through a group e-mail list and in-person discussion at a breakout session of the Academic Emergency Medicine 2006 Consensus Conference, "The Science of Surge," seven consensus statements were generated. These statements emphasize the importance of funded research in the area of surge capacity metrics; the utility of an emergency medicine research registry; the need to make the data available to clinicians, administrators, public health officials, and internal and external systems; the importance of real-time data, data standards, and electronic transmission; seamless integration of data capture into the care process; the value of having data available from a single point of access through which data mining, forecasting, and modeling can be performed; and the basic necessity of a criterion standard metric for quantifying surge capacity. Further consensus work is needed to select a criterion standard metric for quantifying surge capacity. These consensus statements cover the future research needs, the infrastructure needs, and the data that are needed for a state-of-the-art approach to surge and surge capacity.

Consensus↗
PubMed2001

Pharmacokinetics and pharmacodynamics of danofloxacin in serum and tissue fluids of goats following intravenous and intramuscular administration.

OBJECTIVE: To determine the pharmacokinetics and pharmacodynamics of danofloxacin in goats and the concentrations required to induce bacteriostasis, bactericidal activity, and bacterial elimination. ANIMALS: 6 healthy British Saanen goats. PROCEDURE: Danofloxacin (1.25 mg/kg of body weight) was administered i.v. and i.m. in a cross-over design with 14 days between treatments. A tissue cage was used for evaluation of drug distribution into transudate and exudate. The ex vivo antibacterial activity of danofloxacin in serum, exudate, and transudate against a caprine isolate of Mannheimia haemolytica was determined. Pharmacokinetic and pharmacodynamic data were integrated to determine the ratio of the area under the concentration versus time curve to the minimum inhibitory concentration of danofloxacin (AUIC). RESULTS: Elimination half-lives of danofloxacin in serum were 4.67 and 4.41 hours after i.v. and i.m. administration, respectively. Volume of distribution was high after administration via either route, and bioavailability was 100% after i.m. administration. Rate of penetration into exudate and transudate was slow, but elimination half-lives from both fluids were approximately twice that from serum. Drug concentrations in serum, exudate, and transudate for 9 to 12 hours after administration induced marked ex vivo antibacterial activity. For serum, AUIC24h values required for bacteriostasis, bactericidal effect, and bacterial elimination were 22.6, 29.6, and 52.4, respectively. Similar values were obtained for exudate and transudate. CONCLUSIONS AND CLINICAL RELEVANCE: Integration of danofloxacin pharmacokinetic and pharmacodynamic data obtained in goats may provide a new approach on which to base recommendations for therapeutic dosages.

Animals↗
PubMed1999

Integrating integrated laboratory information into health care delivery systems.

Attention to integration of laboratory data and its integration into clinical processes and enterprises can help make the laboratory's work a more integral part of clinical practice. The resulting integration holds great potential for improving the quality and effectiveness of care and adding to the clinical value of the laboratory work.

Clinical Laboratory Information Systems↗
PubMed2000

Defining the role of anatomic pathology images in the multimedia electronic medical record--a preliminary report.

The development of the Multimedia Electronic Medical Record System (MEMRS) offers new opportunities for integrating medical imaging data with text-based clinical data. The effective integration of pathology images into the patient's medical record poses some significant technical and organizational challenges. Before these challenges can be met, it is imperative that we investigate the value and utility of providing these images to clinicians. In this study we examined attitudes towards use of pathology images in Image Engine, a MEMRS under development at the University of Pittsburgh Cancer Institute (UPCI). We conducted semi-structured standardized interviews with a cohort of practicing oncologists, all of whom had significant experience with Image Engine. This study is a first step towards elucidating the potential barriers, uses, and value of anatomic pathology images in the MEMRS.

Attitude of Health Personnel↗
PubMed2005

Syndromic surveillance on the epidemiologist's desktop: making sense of much data.

INTRODUCTION: Syndromic surveillance systems are becoming increasingly common in health departments. These systems represent a substantial improvement in the timeliness of ascertainment of community health status. For the value of such systems to be realized, protocols are needed for review and analysis of the findings that these systems produce. METHODS: A workgroup of experienced syndromic surveillance users and developers was convened to discuss approaches to data review and analyses. The discussion was structured to include general principles of the use of syndromic surveillance; how and why specific data are reviewed; integration of multiple data sources; daily versus research uses of systems; how data anomalies are identified by users and surveillance systems; the relative merits of anomalies; how a data anomaly is investigated to determine if it warrants a public health response; and how such a public health response should be framed. RESULTS: From this discussion, a generalized and more detailed process was documented that describes the common elements of analysis used by the workgroup participants. CONCLUSION: Establishment of a framework for evaluation and response to syndromic surveillance data will facilitate the implementation of these systems and standardization of procedures for validation of system findings. Careful development of an evaluation and response framework should be undertaken to assess whether use of syndromic surveillance systems requires excess work to distinguish between statistical anomalies and important public health events.

Data Interpretation, Statistical↗
PubMed1995

An analysis of the paper-based health record: information content and its implications for electronic patient records.

An analysis of paper-based charting was carried out at Sunnybrook Health Sciences Center as a prelude to developing a strategic plan to implement an electronic patient record. A relational model of the Sunnybrook paper chart was developed, describing each of its forms in terms of specific data fields. Three hundred and forty nine different forms are in current use at Sunnybrook, containing 64 types of data fields such as Patient Demographics, Vital Signs, and Doctor's Orders. The extent of data field duplication at the level of hospital forms was significant. A Patient Demographics field was present on all forms and on all pages of a patient's chart, as would be expected. Twenty seven other fields were duplicated on more than ten different forms, including Working Diagnosis which was present on 110 forms, History of Past Illness on 42 forms, and History of Present Illness on 32 forms. Current Medications were recorded on 32 forms and Allergy fields were present on 29 separate forms. Only five data fields of the total 64 were present on only one form. The duplication of data fields within complete patient charts was then examined to confirm that data field duplication was occurring within the actual healthcare delivery process. Using the relational model of the charting system, 143 acute care in-patient encounters were abstracted into the database. The charts were selected randomly from each of the hospital inpatient services. The numbers and types of forms within each chart were recorded, amounting to 18,654 physical pages and using 165 of the different forms. The average in-patient encounter within the model was 130.4 pages long, with a minimum of 27 pages, a maximum of 559 pages, and containing on average 25.8 different forms. The duplication of data fields within actual charts followed a pattern similar to the duplication found on the forms. Initial diagnosis was present on an average of 20.4 pages within the charts, with a minimum of 2 pages and a maximum of 152 pages containing this data field. Other frequently occurring data fields included History of Past Illness present on an average of 12.2 pages per chart, History of present illness on 10.2 pages per chart, and allergies on an average of 9.1 pages per chart. The results obtained through the examination of Sunnybrook charts should be generalizable to most paper-based systems. This study did not measure the workload associated with duplicating chart data. however, the magnitude of the duplication seen in this study leaves little doubt that significant amounts of time could be saved with appropriate modification of health care delivery processes. Multiple copies of the same data field within a database are referred to as aliases of each other. This study demonstrates that hospital charts contain many copies of the same information, such as medication lists, allergies etc. Due to manual replication of data fields, there is no mechanism to ensure that each copy of a data element within a chart actually contains the same information. This aliasing of data through manual duplication compromises the integrity of data within paper-based charts. Decisions and therapy based upon contradictory or inaccurate data are likely to lead to inefficient or erroneous care delivery; this has significant implications for hospital liability and quality of patient care. A growing recognition of the costs and risks of data replication within paper-based charting systems is driving the healthcare industry toward Electronic Patient Record systems. Better quality patient care data, provided by computerized records, is likely to be necessary but not sufficient to improving the efficiency and effectiveness of the healthcare system. Intelligent application of this information will be essential.

Medical Records↗
PubMed1998

The geographical distribution of diagnostic medical and dental X-ray services in South Africa

AIM: The aim of this study was threefold, viz.: (i) to evaluate the availability and accessiblity of medical and dental X-ray services in South Africa; (ii) to evaluate geographical information systems (GIS) as a tool for management of health care technologies; and (iii) to guide policy and develop a process to provide optimal utilisation of X-ray services in South Africa. METHODS: Information supplied by the Department of Health on licensed X-ray equipment was integrated with census data and processed with GIS. Four key areas were assessed, viz. distribution, accessibility, age and availability of X-ray services in South Africa. RESULTS: The analysis shows a vast inequity in the distribution of X-ray services on a provincial as well as a district level, although on the national level the distribution of X-ray services meets the World health Organisation criteria. CONCLUSION: GIS is a useful tool in evaluating and planning of essential health services/techniques. However, care must be taken in interpreting the data on a macro level, as this masks vast inequities on the district level. RECOMMENDATIONS: The indicators of coverage should be expanded, similar reports should be prepared for the nine provinces, and these data should be integrated into the clinic planning programme. Radiological services should be added to and managed as part of an essential district health care technology package.

Journal Article↗
PubMed2004

Integrated wavelet processing and spatial statistical testing of fMRI data.

We introduce an integrated framework for detecting brain activity from fMRI data, which is based on a spatial discrete wavelet transform. Unlike the standard wavelet-based approach for fMRI analysis, we apply the suitable statistical test procedure in the spatial domain. For a desired significance level, this scheme has one remaining degree of freedom, characterizing the wavelet processing, which is optimized according to the principle of minimal approximation error. This allows us to determine the threshold values in a way that does not depend on data. While developing our framework, we make only conservative assumptions. Consequently, the detection of activation is based on strong evidence. We have implemented this framework as a toolbox (WSPM) for the SPM2 software, taking advantage of multiple options and functions of SPM such as the setup of the linear model and the use of the hemodynamic response function. We show by experimental results that our method is able to detect activation patterns; the results are comparable to those obtained by SPM even though statistical assumptions are more conservative.

Attention↗
PubMed1993

User evaluation of an integrated medical workstation for clinical data analysis.

Results are presented of the user evaluation of an integrated medical workstation for support of clinical research. Twenty-seven users were recruited from medical and scientific staff of the University Hospital Dijkzigt, the Faculty of Medicine of the Erasmus University Rotterdam, and from other Dutch medical institutions; and all were given a written, self-contained tutorial. Subsequently, an experiment was done in which six clinical data analysis problems had to be solved and an evaluation form was filled out. The aim of this user evaluation was to obtain insight in the benefits of integration for support of clinical data analysis for clinicians and biomedical researchers. The problems were divided into two sets, with gradually more complex problems. In the first set users were guided in a stepwise fashion to solve the problems. In the second set each stepwise problem had an open counterpart. During the evaluation, the workstation continuously recorded the user's actions. From these results significant differences became apparent between clinicians and non-clinicians for the correctness (means 54% and 81%, respectively, p = 0.04), completeness (means 64% and 88%, respectively, p = 0.01), and number of problems solved (means 67% and 90%, respectively, p = 0.02). These differences were absent for the stepwise problems. Physicians tend to skip more problems than biomedical researchers. No statistically significant differences were found between users with and without clinical data analysis experience, for correctness (means 74% and 72%, respectively, p = 0.95), and completeness (means 82% and 79%, respectively, p = 0.40).(ABSTRACT TRUNCATED AT 250 WORDS)

Computer Systems↗
PubMed2004

SCOP database in 2004: refinements integrate structure and sequence family data.

The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of sequence and structural data allows more rigorous analysis and provides important information for understanding the protein world and its evolutionary repertoire. SCOP participates in a project that aims to rationalize and integrate the data on proteins held in several sequence and structure databases. As part of this project, starting with release 1.63, we have initiated a refinement of the SCOP classification, which introduces a number of changes mostly at the levels below superfamily. The pending SCOP reclassification will be carried out gradually through a number of future releases. In addition to the expanded set of static links to external resources, available at the level of domain entries, we have started modernization of the interface capabilities of SCOP allowing more dynamic links with other databases. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.

Animals↗
PubMed2005

The SET domain protein Metnase mediates foreign DNA integration and links integration to nonhomologous end-joining repair.

The molecular mechanism by which foreign DNA integrates into the human genome is poorly understood yet critical to many disease processes, including retroviral infection and carcinogenesis, and to gene therapy. We hypothesized that the mechanism of genomic integration may be similar to transposition in lower organisms. We identified a protein, termed Metnase, that has a SET domain and a transposase/nuclease domain. Metnase methylates histone H3 lysines 4 and 36, which are associated with open chromatin. Metnase increases resistance to ionizing radiation and increases nonhomologous end-joining repair of DNA doublestrand breaks. Most significantly, Metnase promotes integration of exogenous DNA into the genomes of host cells. Therefore, Metnase is a nonhomologous end-joining repair protein that regulates genomic integration of exogenous DNA and establishes a relationship among histone modification, DNA repair, and integration. The data suggest a model wherein Metnase promotes integration of exogenous DNA by opening chromatin and facilitating joining of DNA ends. This study demonstrates that eukaryotic transposase domains can have important cell functions beyond transposition of genetic elements.

Amino Acid Sequence↗
PubMed2002

Integration of genomic datasets to predict protein complexes in yeast.

The ultimate goal of functional genomics is to define the function of all the genes in the genome of an organism. A large body of information of the biological roles of genes has been accumulated and aggregated in the past decades of research, both from traditional experiments detailing the role of individual genes and proteins, and from newer experimental strategies that aim to characterize gene function on a genomic scale. It is clear that the goal of functional genomics can only be achieved by integrating information and data sources from the variety of these different experiments. Integration of different data is thus an important challenge for bioinformatics. The integration of different data sources often helps to uncover non-obvious relationships between genes, but there are also two further benefits. First, it is likely that whenever information from multiple independent sources agrees, it should be more valid and reliable. Secondly, by looking at the union of multiple sources, one can cover larger parts of the genome. This is obvious for integrating results from multiple single gene or protein experiments, but also necessary for many of the results from genome-wide experiments since they are often confined to certain (although sizable) subsets of the genome. In this paper, we explore an example of such a data integration procedure. We focus on the prediction of membership in protein complexes for individual genes. For this, we recruit six different data sources that include expression profiles, interaction data, essentiality and localization information. Each of these data sources individually contains some weakly predictive information with respect to protein complexes, but we show how this prediction can be improved by combining all of them. Supplementary information is available at http:// bioinfo.mbb.yale.edu/integrate/interactions/.

Cell Cycle↗
PubMed2003

Web-based exchange of biochemical information.

In this paper we present a web-based system for the semantic integration of biological data using a database model and an XML exchange format. The prototype developed integrates data related to enzymes.

Databases, Factual↗
PubMed1994

The ecological database VODE as the base for monitoring and the study of the water quality parameters correlation.

The ecological approach to the disease facilitates the understanding of the reasons for the multiplicity of causal factors and the finding of those on which the preventive measures will be easily and successfully directed. That is the reason why integration of space data for getting insight into the existing condition from ecological point of view is necessary. The ecological need to sum up the work of the water research and to estimate the future water quality trends by observing the relevant parameters as influential ecological factors for the health of the population resulted in relation data base VODE. Besides it integrates the data group of waters data and from the ecological standpoint is suitable for the several years study of trends of existing water supply system condition with special survey of the results of the water quality analyses in view of the recognition of the actual pollutions that are significant for the health problems of population, group and individuals. One gets informations by putting questions and than plans necessary interventions, what is the new significant contribution in the approach to the analytical and monitoring techniques, i.e., application of informatical techniques in water pollution control.

Croatia↗
PubMed1988

[Screening of thyroid function proper by calculating the integral index based on data from in vitro radioimmunological testing].

A total of 1494 patients were investigated: 803--with the euthyroid state and extrathyroid (nonthyroid) pathology, 493--with primary hyperthyroidism and 101--with primary hypothyroidism; 93 healthy donors (61 women and 32 men) were entered into the control group. The thyroid integral index (II) was used for the assessment of the level of function of the thyroid proper. Normal II values ranged within 0.6-5 rel. units hypothyroidism values were within 0.6 and below this value, hyperthyroidism values--within 5 and above tris value. II calculation made it possible to divide (with 100% accuracy) the patients into 3 groups of the thyroid state: eu-, hypo- and hyperthyroidism. Euthyroidism values by the TSH level were within 1.7-9 mU/l.

Adult↗
PubMed2003

Promoting good clinical practices in the conduct of clinical trials: experiences in the Department of Veterans Affairs Cooperative Studies Program.

The ever-increasing concern for the welfare of volunteers participating in clinical trials and for the integrity of the data derived from those trials has generated the concept of Good Clinical Practice (GCP). The Veterans Affairs Cooperative Studies Program, in anticipation of the need to comply with GCP guidelines, developed a Site Monitoring and Review Team (SMART), which consists of a Good Clinical Practice Monitoring Group and a Good Clinical Practice Review Group. The review group conducted 335 site reviews from fiscal years (FY) 1999 through 2001 to assess and encourage adherence to GCP. Data from reviews were compared for two time periods, a 2-year implementation period (FYs 1999/2000, n=204) and a continuing follow-up period (FY 2001, n=131). Overall, high GCP adherence was exhibited by 11.3% (n=23) of study sites in FY 1999/2000 versus 20.6% (n=27) in FY 2001, average to good adherence was exhibited by 84.3% (n=172) in FY 1999/2000 versus 77.0% (n=101) in FY 2001, and below average adherence was exhibited by 4.4% (n=9) versus 1.5% (n=3) in these two periods. These changes were statistically significant by chi square analysis (p=0.029). Moreover, GCP adherence was assessed within eight GCP focus areas: patient informed consent, protocol adherence, safety monitoring, institutional review board interactions, regulatory document management, patient records in investigator file, drug/device accountability, and general site operations. Median assessment scores for all 62 GCP review elements improved from 0.82 to 0.89 (p<0.001). Median assessment scores for the 14 selected critical GCP items improved from 0.78 to 0.89 (p<0.001). Median scores for five of the eight GCP focus areas improved significantly (p<0.001) between the two time periods. These data suggest that the site-oriented activities of SMART combined with centralized quality assurance activities of the coordinating centers represent an integrated, versatile program to promote and assure GCP adherence and data integrity in Cooperative Studies Program trials.

Clinical Trials as Topic↗
PubMed2002

Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline.

By integrating functional genomic and proteomic mapping approaches, biological hypotheses should be formulated with increasing levels of confidence. For example, yeast interactome and transcriptome data can be correlated in biologically meaningful ways. Here, we combine interactome mapping data generated for a multicellular organism with data from both large-scale phenotypic analysis ("phenome mapping") and transcriptome profiling. First, we generated a two-hybrid interactome map of the Caenorhabditis elegans germline by using 600 transcripts enriched in this tissue. We compared this map to a phenome map of the germline obtained by RNA interference (RNAi) and to a transcriptome map obtained by clustering worm genes across 553 expression profiling experiments. In this dataset, we find that essential proteins have a tendency to interact with each other, that pairs of genes encoding interacting proteins tend to exhibit similar expression profiles, and that, for approximately 24% of germline interactions, both partners show overlapping embryonic lethal or high incidence of males RNAi phenotypes and similar expression profiles. We propose that these interactions are most likely to be relevant to germline biology. Similar integration of interactome, phenome, and transcriptome data should be possible for other biological processes in the nematode and for other organisms, including humans.

Animals↗
PubMed2006

Equilibrium dialysis data and the relationships between preferential interaction parameters for biological systems in terms of Kirkwood-Buff integrals.

Equilibrium dialysis data has provided valuable information concerning the preferential interaction of a cosolvent with a biomolecule in aqueous solutions. Here, we formulate the experimental data in terms of Kirkwood-Buff (KB) theory, resulting in equations that provide a simple physical picture of the dialysis experiment and thereby the interaction of a cosolvent with a biomolecule. These results are then used to establish exact relationships between preferential interaction coefficients, defined in different ensembles and/or using different concentration scales, in terms of KB integrals. It is then argued that the molality based equilibrium dialysis data represent the situation most relevant to computer simulations performed in either open or closed systems.

Computer Simulation↗