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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↗

Online retrieval, processing, and visualization of primate connectivity data from the CoCoMac database.

Connectivity is the key to understanding distributed and cooperative brain functions. Detailed and comprehensive data on large-scale connectivity between primate brain areas have been collated systematically from published reports of experimental tracing studies. Although the majority of the data have been made easily available for online retrieval, the multiplicity of brain maps and the precise requirements of anatomical naming limit the intuitive access to the data. The quality of data retrieval can be improved by observing a small set of conventions in data representation. Standardized interfaces open up further opportunities for automated search and retrieval, for flexible visualization of data, and for interoperability with other databases. This article provides a discussion and examples in text and image of the capabilities of the online interface to the CoCoMac database of primate connectivity. These serve to point out sources of potential confusion and failure, and to demonstrate the automated interfacing with other neuroinformatics resources that facilitate selection and processing of connectivity data, for example, for computational modelling and interpretation of functional imaging studies.

Animals↗

[AIDS and HIV infection in Poland in 1999].

After gradual increasing in the number of annually diagnosed AIDS cases in the last years these numbers remained relatively stable (nearly 120). The biggest number of newly discovered HIV infections (809) was reported in 1990. Next years these numbers ranged from 384 in 1993 to 637 in 1998. Majority of AIDS cases and HIV-infected persons in Poland were drug users, respectively 50% and 60%. Between 1985 and 1999 some important changes have been observed in Polish data collection system concerning for example: anonimity of reported HIV infections, data completeness and reporting of AIDS indicator diseases. Quality of collected epidemiological data will depend--among others things--on: easy access to HIV testing, data completeness and diagnosis of AIDS indicator diseases by definitive methods.

Acquired Immunodeficiency Syndrome↗

Opinion paper. Resistance to new anti-HIV agents: problems in the pathway of drug registration.

Resistance data are now requested by the regulatory agencies as an integral part of the approval process of new antiretroviral drugs. We examined the means by which resistance data was gathered during pre-clinical and clinical Phases I, II and III of drug development, and how the public and academic experts access these proprietary data. The analysis identified various opportunities for improvement of the current process, in particular the need for standards in generating and reporting resistance data on new antiretroviral drugs, and the need to enforce warnings in the product labelling on the drug combinations that can potentially lead to resistance and treatment failure.

Anti-HIV Agents↗

Research and Social Security policy in the United States.

This article is adapted from a paper presented at a conference that investigated the role of policy research in shaping public policy. The conference focused on how studies of economic and social forces and their relationship with public problems and programs affect the decisions of public policymakers. The author contends that research has the potential to inform policy-making in any of its five stages: problem identification, option development, passage of new laws or development of new procedures, implementation, and evaluation. She notes that different players in the policy-making process use research differently, from the senior government official who needs a quick review of what is known relating to a "hot" issue to the interest group lobbyist who wants access to raw data. The article concludes that research can best achieve its potential when (1) it anticipates policymakers' information needs, (2) it is disseminated in an accessible form understandable to nonresearchers, and (3) the policy analyst is willing to engage in the policy process as an advocate for efficiency.

Eligibility Determination↗

Integration of pharmacy into the computerized problem-oriented medical information system (PROMIS)--a demonstration project.

The integration of pharmacy into the computerized problem-oriented medical information system (PROMIS) at the Medical Center Hospital of Vermont is discussed. Practioners who generate and retrieve information communicate directly with the computer without intermediary personnel. Touch-screen cathode-ray tube terminals are used for data input. Under PROMIS, the pharmacist has two new resources which better integrate his services into total patient care: (1) the ability to directly access online patient data in the pharmacy, and (2) the ability to directly couple online current drug information to a specific patient's computerized medical record in the pharmacy. The PROMIS solutions to pharmacy problems in drug ordering, drug distribution and drug therapy audit are discussed; In a demonstration project on a 20-bed unit, PROMIS made the medical record readily available to all health care providers, reduced reliance on memory, preserved the logic of medical action, and provided feedback loops for corrective action in everyday medical practice. Also discussed are user acceptance of the system, effect on pharmacy staffing, and implications for pharmacy.

Computers↗

IsoSVM--distinguishing isoforms and paralogs on the protein level.

BACKGROUND: Recent progress in cDNA and EST sequencing is yielding a deluge of sequence data. Like database search results and proteome databases, this data gives rise to inferred protein sequences without ready access to the underlying genomic data. Analysis of this information (e.g. for EST clustering or phylogenetic reconstruction from proteome data) is hampered because it is not known if two protein sequences are isoforms (splice variants) or not (i.e. paralogs/orthologs). However, even without knowing the intron/exon structure, visual analysis of the pattern of similarity across the alignment of the two protein sequences is usually helpful since paralogs and orthologs feature substitutions with respect to each other, as opposed to isoforms, which do not. RESULTS: The IsoSVM tool introduces an automated approach to identifying isoforms on the protein level using a support vector machine (SVM) classifier. Based on three specific features used as input of the SVM classifier, it is possible to automatically identify isoforms with little effort and with an accuracy of more than 97%. We show that the SVM is superior to a radial basis function network and to a linear classifier. As an example application we use IsoSVM to estimate that a set of Xenopus laevis EST clusters consists of approximately 81% cases where sequences are each other's paralogs and 19% cases where sequences are each other's isoforms. The number of isoforms and paralogs in this allotetraploid species is of interest in the study of evolution. CONCLUSION: We developed an SVM classifier that can be used to distinguish isoforms from paralogs with high accuracy and without access to the genomic data. It can be used to analyze, for example, EST data and database search results. Our software is freely available on the Web, under the name IsoSVM.

Algorithms↗

Information access at the point of care: what can we learn for designing a mobile CPR system?

OBJECTIVES: Hospitals have started to migrate their paper-based records to computerized patient records (CPR). The majority of today's CPR systems are stationary, which means that physicians use a clinical workstation to access CPR information. But health care professionals need to request and enter information at different locations, for example, on their daily ward round. This suggests the use of mobile computers, enabling an ubiquitous access to needed data. Different studies show that health care professionals are reluctant to use poorly designed mobile CPR systems, as the work at the point of care is very time-pressured and hectic. To design a system with high acceptance, it is essential to obtain empirical insight into the work practices and context in which the mobile CPR system will be used. METHOD: We investigated the physicians' work with the patient record during their daily round. With the help of a compact notation method, the physicians' interaction with the information system was recorded in real time. Fourteen physicians from three different departments (internal medicine, surgery, and geriatrics) of a middle-sized Swiss hospital participated in our study. RESULTS: Physicians have clear access preferences when they interact with the patient record during their daily round. There exists a clear profile of access frequencies and patterns, respectively. As an example, approximately 50% of all patient record accesses concern information about medications, vital signs and lab test results. DISCUSSION/CONCLUSION: A CPR system which is designed to reflect the access frequencies and patterns should improve the efficiency of data entry and retrieval and thus result in a system with high acceptance among physicians in the demanding environment during hospital rounds.

Access to Information↗

Innovations in user-defined analysis: dynamic grouping and customized user datasets in VistaPHw.

Flexible, ready access to community health assessment data is a feature of innovative Web-based data query systems. An example is VistaPHw, which provides access to Washington state data and statistics used in community health assessment. Because of its flexible analysis options, VistaPHw customizes local, population-based results to be relevant to public health decision-making. The advantages of two innovations, dynamic grouping and the Custom Data Module, are described. Dynamic grouping permits the creation of user-defined aggregations of geographic areas, age groups, race categories, and years. Standard VistaPHw measures such as rates, confidence intervals, and other statistics may then be calculated for the new groups. Dynamic grouping has provided data for major, successful grant proposals, building partnerships with local governments and organizations, and informing program planning for community organizations. The Custom Data Module allows users to prepare virtually any dataset so it may be analyzed in VistaPHw. Uses for this module may include datasets too sensitive to be placed on a Web server or datasets that are not standardized across the state. Limitations and other system needs are also discussed.

Community Health Planning↗

Promoting standardized nursing language using an electronic medical record system.

Paper-based medical record systems are becoming obsolete with the advent of electronic medical record (EMR) systems. With EMRs, patient data can be accessed instantly, patients can be tracked intelligently, and safeguards can help prevent medical errors. By integrating a universal nursing language, such as the Perioperative Nursing Data Set (PNDS), into EMR systems, nurses can document the nursing care they give to patients. This allows nurses to show the value of their role in the OR, promote nursing, and explain how their actions help meet National Patient Safety Goals. The transition to an EMR system for Jackson Health System, Miami, is discussed, including integration of the PNDS into the EMR system.

Documentation↗

The information content of high-frequency environmental monitoring data signals pollution events in the coastal ocean.

There are an increasing number of coastal ocean observing systems that deploy new technology for environmental sensing and stream these data in near-real-time to end-users (e.g., scientists and coastal managers) via the worldwide web. The temporal resolution, spatial coverage, and accessibility of these data open up new opportunities for better understanding and managing the coastal ocean, but they also present enormous challenges relative to data processing and data interpretation, particularly in cases where these data are to inform rapid management decision making. Here we demonstrate that changes in surf zone water quality at a popular beach in southern California are signaled by changes in the Fisher Information and Shannon Entropy of high frequency (1/4 min(-1)) measurements of salinity and temperature in the surf zone. These results support the hypothesis that the information content of environmental signals, such as salinity and temperature, can be used to identify changes in the water quality of the coastal ocean. More generally, the approach described here-of using information theory indices calculated from monitoring data as real-time indicators of environmental change-is quite general, and may therefore be applicable to other situations where rapid management decisions are based on high-frequency measurements of environmental parameters.

Algorithms↗

Safety of low-dose radiocontrast for interventional AV fistula salvage in stage 4 chronic kidney disease patients.

The Dialysis Outcomes Quality Initiative emphasizes increasing arteriovenous fistula prevalence, by promoting referral for fistula creation in patients with stage 4 chronic kidney disease (CKD). The aim is to provide an optimal access for initiation of dialysis, thus avoiding central venous catheter use. The endovascular management of nonmaturing fistulas is more complicated in these patients, where the expected benefit of catheter avoidance must be weighed against the risk of contrast induced nephropathy (CIN). This study reports on the safety of a low-dose radiocontrast regimen, used in performing endovascular fistula salvage procedures in patients with stage 4 CKD. All consecutive endovascular procedures performed over a 2-year period in patients with stage 4 CKD and nonmaturing access were identified. Data collected included the type of procedure, contrast volume per procedure, pre, 2- and 7-day creatinine, need for acute dialysis, and the type of access used to initiate dialysis. Total of 65 procedures were performed in 34 patients. The mean contrast volume was 7.8 ml per procedure. The incidence of CIN (25% increase in serum creatinine) was 4% at 2 days and 4.6% at 1 week. All values returned to baseline within 2 weeks, and no patient required acute dialysis. Among the 33 patients with nonmaturing fistulas, 20 initiated dialysis during the follow-up period, 15 (75%) using their fistula, and five (25%) using a catheter. This study demonstrates that in patients with advanced CKD, fistulas can be successfully salvaged using small contrast volumes with a low incidence of CIN.

Aged↗

Active site structures and the redox properties of blue copper proteins: atomic resolution structure of azurin II and electronic structure calculations of azurin, plastocyanin and stellacyanin.

Understanding how the active site structures of blue copper proteins determine their redox properties is the central structure-function relationship question of this important class of protein, also referred to as cupredoxins. We here describe both experimental and computational studies of azurin, plastocyanin and stellacyanin designed to define more accurately the geometric structures of the active site of the reduced and oxidized species, and thus to understand how these structures determine the redox potentials of these proteins. To this end the crystal structure of reduced azurin II has been determined at an atomic resolution of 1.13 Angstrom and is presented here. Co-ordinates and structure factors have been deposited in the RCSB Protein Data Bank with accession codes 2ccw and r2ccwsf respectively. The improved accuracy provided by the atomic resolution for the metal stereochemistry are utilised in conjunction with the EXAFS data for theoretical calculations. Multilevel calculations involving density functional theory and molecular mechanical potentials are used to predict both the geometric and electronic structure of the active sites of azurin, plastocyanin and stellacyanin and to estimate the relative redox potentials of these three proteins. We have also compared the relative energies of the structures obtained from experiment at varying resolutions, and from the isolated and embedded cluster calculations. We find significant energy differences between low and high (atomic) resolution structures arising primarily due to inaccuracies in the Cu-ligand distances in the lower resolution structures, emphasising the importance of accurate, very high resolution structural information. QM/MM structures are only approximately 1 kcal mol(-1) lower in energy than the 1.13 Angstrom structure while the optimized gas phase structure is 13.0 kcal mol(-1) lower in energy.

Alcaligenes↗

Autopsy data in the peer review process improves outcomes analysis.

BACKGROUND: The value of autopsy findings has been questioned in peer review at mature trauma centers. We sought to determine the impact of autopsy data on the peer-review process. METHODS: This was a retrospective study. Data analyzed included mortality type (immediate/dead on arrival [DOA]; early [< or =48 hours]; late [>48 hours]), Injury Severity Scale (ISS) score, Trauma and Injury Severity Score-generated probability of survival (PS), peer-review judgment of preventability, and findings at autopsy. Deaths were assigned to a category; then pre- and postautopsy ISS score, PS, and outcomes of the peer- review process (percent nonpreventable [%NP]) were compared. Paired t tests (alpha = 0.05) were performed to determine whether changes in ISS score and PS were statistically significant. All descriptive and inferential analyses were based on cases with pre- and postautopsy data for the relevant variables. RESULTS: Of the 170 deaths, 126 deaths had an autopsy performed (74.1%) and 112 autopsy reports were available (89.9%). Autopsy data resulted in statistically significant changes in ISS score for each mortality category and in PS for the immediate/DOA and early categories. There were also autopsy- related changes in peer-review outcomes for immediate/DOA and late deaths but not for early deaths. The proportion of overall agreement between pre- and postautopsy outcomes for the immediate/DOA category was 94.3% (50/53); three deaths initially deemed NP were reclassified as potentially preventable (PP) after autopsy. Overall agreement for the late category was 87% (20/23); one PP was reclassified as NP and two NPs were reclassified as PP. CONCLUSION: Autopsy data enhanced peer review in immediate/DOA and late death after injury but did not impact peer review in early deaths. Autopsy data were most important to the analysis of late deaths. Targeting autopsy performance to these mortality categories is an effective strategy for centers with constrained access to autopsy data.

Autopsy↗

Security and confidentiality in an electronic medical record.

The maintenance of privacy and confidentially must remain a core principle of the interaction between patients and medical staff. Traditionally, the single paper copy of the medical history has been treated with systematic handling, careful tracking, and respect for the integrity and confidentiality of the contents. The widespread availability of computerized information requires that these principles be maintained in the electronic environment. Security measures should protect sensitive data without hindering medical practice. At Mayo, we have established data security policies and standards for the handling of all electronic information. Dissemination and communication of these standards and guidelines are an ongoing challenge. Technical maneuvers can be employed to protect data integrity, identify users, and monitor compliance. Personnel policies must be updated to reflect the responsibilities and liabilities of the electronic environment. Practice efficiencies and access to clinical data must be balanced by individual responsibility and accountability for privileged patient information.

Computer Security↗

Helpseeking and access to mental health treatment for obsessive-compulsive disorder.

OBJECTIVE: To identify predictors of helpseeking and use of mental health treatment for obsessive-compulsive disorder (OCD) using the behavioral model of health service use. METHOD: Data were drawn from the 1996 National Anxiety Disorders Screening Day. Participants (n=14 860) completed screening measures providing information about demographics, mental disorders, helpseeking, and treatment experiences for OCD. RESULTS: Previous use of mental health treatment was associated with comorbid panic disorder [odds ratio (OR)=1.6 (1.3-1.98)], while minority racial status [OR=0.7 (0.5-0.9)] emerged as a barrier to receiving care among individuals with OCD. Among those who had never received mental health care, comorbid panic disorder [OR=2.0 (1.5-2.8)], post-traumatic stress disorder [OR=1.7 (1.3-2.4)], and suicidal ideation [OR=1.7 (1.2-2.3)] increased readiness to seek treatment while being employed [OR=0.7 (0.5-0.9)], and feeling one could handle the problem on his/her own [OR=0.5 (0.3-0.7)] decreased readiness to seek help for the first time. CONCLUSION: These data suggest that access to treatment for OCD may not be equally accessible to all in need by revealing non-disease related factors (e.g. race, health beliefs) that have a significant impact on decisions to seek and use mental health treatment.

Adult↗

An anthropometric survey of Indian schoolchildren aged 3-5 years.

Kindergartens of age group 3-5 years, a distinct and small subgroup of Indian schoolchildren, need special emphasis on human factors. The paper presents the results of an anthropometric survey conducted on schoolchildren. These data, previously lacking in India, can be of benefit for the designers of kindergartens. A set of 81 different body dimensions was taken from a sample of 198 children of age group 3-4 years and 4.1-5 years. Simple anthropometric techniques were used to collect the data. Statistical analyses of the data have been presented in a tabular form for designers as well as for non-technical users. It is emphasized that such data have to be developed at the national level, including every ethnic group, or on a regional basis. Designers, manufacturers and importers of goods should have access to these data.

Journal Article↗

Automatic acquisition interfaces for computed radiography, CT, MR, US, and laser scanner.

Existing radiological imaging devices such as computed radiography (CR), computed tomography (CT), magnetic resonance imaging (MR), and ultrasound (US) systems generally do not have a direct digital interface to an external computer. Thus, special developments are necessary for their integration into a Picture Archiving and Communication System (PACS). The interface architecture and software models for performing automatic data acquisition from these devices as well as a CR plate scanner and a laser film digitizer are discussed based on their networking capabilities and the accessibility of internal data structures. The design approaches and operation efficiencies vary drastically depending on whether additional modules are needed, and whether the acquisition is performed on-line or off-line. In addition to the image data link, a complete acquisition interface includes polling of text patient information, image reformatting to the UCLA standard, and communication to the archival database.

Diagnostic Imaging↗