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PubMed1997

Using other people's data: the ins and outs of secondary data analysis.

BACKGROUND AND OBJECTIVES: A variety of types of data ranging from administrative data sets to large-scale surveys have been collected for one purpose but can be accessed and used to address new questions of relevance to primary care. For many research questions, primary data collection isn't necessary because the data already exists. Although relatively few researchers consider analyzing existing data sets, there are a variety of advantages to secondary analysis. This paper introduces the practical aspects of performing secondary analysis. We review the types of questions that can addressed, where and how to access data, and the steps involved in preparing data for analysis.

Data Collection↗
PubMed1999

Optical CDMA system using bacteriorhodopsin for optical data storage

An optical CDMA (code division multiple access) system for the optical data storage using bacteriorhodopsin (BR) is reported as an application of the BR materials. The desired signal of multiple input can be recorded and reconstructed by use of orthogonal codes. An experimental setup is proposed and demonstrated.

Journal Article↗
PubMedDate not supplied

Peripheral venous access ports: outcomes analysis in 109 patients.

PURPOSE: To perform a retrospective outcomes analysis of central venous catheters with peripheral venous access ports, with comparison to published data. METHODS: One hundred and twelve central venous catheters with peripherally placed access ports were placed under sonographic guidance in 109 patients over a 4-year period. Ports were placed for the administration of chemotherapy, hyperalimentation, long-term antibiotic therapy, gamma-globulin therapy, and frequent blood sampling. A vein in the upper arm was accessed in each case and the catheter was passed to the superior vena cava or right atrium. Povidone iodine skin preparation was used in the first 65 port insertions. A combination of Iodophor solution and povidone iodine solution was used in the last 47 port insertions. Forty patients received low-dose (1 mg) warfarin sodium beginning the day after port insertion. Three patients received higher doses of warfarin sodium for preexistent venous thrombosis. Catheter performance and complications were assessed and compared with published data. RESULTS: Access into the basilic or brachial veins was obtained in all cases. Ports remained functional for a total of 28,936 patient days. The port functioned in 50% of patients until completion of therapy, or the patient's expiration. Ports were removed prior to completion of therapy in 18% of patients. Eleven patients (9.9% of ports placed) suffered an infectious complication (0.38 per thousand catheter-days)-in nine, at the port implantation site, in two along the catheter. In all 11 instances the port was removed. Port pocket infection in the early postoperative period occurred in three patients (4.7%) receiving a Betadine prep vs two patients (4.2%) receiving a standard O.R. prep. This difference was not statistically significant (p = 0.9). Venous thrombosis occurred in three patients (6.8%) receiving warfarin sodium and in two patients (3%) not receiving warfarin sodium. This difference was not statistically significant (p = 0.6). Aspiration occlusion occurred in 13 patients (11.7%). Intracatheter urokinase was infused in eight of these patients and successfully restored catheter function in all but two instances. These complication rates are comparable to or better than those reported with chest ports. CONCLUSION: Peripheral ports for long-term central venous access placed by interventional radiologists in the interventional radiology suite are as safe and as effective as chest ports.

Adult↗
PubMedDate not supplied

Confidentiality issues for medical data miners.

The first task in any medical data mining effort is ensuring patient confidentiality. In the past, most data mining efforts ensured confidentiality by the dubious policy of withholding their raw data from colleagues and the public. A cursory review of medical informatics literature in the past decade reveals that much of what we have "learned" consists of assertions derived from confidential datasets unavailable for anyone's review. Without access to the original data, it is impossible to validate or improve upon a researcher's conclusions. Without access to research data, we are asked to accept findings as an act of faith, rather than as a scientific conclusion. This special issue of Artificial Intelligence in Medicine is devoted to medical data mining. The medical data miner has an obligation to conduct valid research in a way that protects human subjects. Today, data miners have the technical tools to merge large data collections and to distribute queries over disparate databases. In order to include patient-related data in shared databases, data miners will need methods to anonymize and deidentify data. This article reviews the human subject risks associated with medical data mining. This article also describes some of the innovative computational remedies that will permit researchers to conduct research AND share their data without risk to patient or institution.

Computer Security↗
PubMed2003

GIMS: an integrated data storage and analysis environment for genomic and functional data.

Effective analyses in functional genomics require access to many kinds of biological data. For example, the analysis of upregulated genes in a microarray experiment might be aided by information concerning protein interactions or proteins' cellular locations. However, such information is often stored in different formats at different sites, in ways that may not be amenable to integrated analysis. The Genome Information Management System (GIMS) is an object database that integrates genomic data with data on the transcriptome, protein-protein interactions, metabolic pathways and annotations, such as gene ontology terms and identifiers. The resulting system supports the running of analyses over this integrated data resource, and provides comprehensive facilities for handling and interrelating the results of these analyses. GIMS has been used to store Saccharomyces cerevisiae data, and we demonstrate how the integrated storage of diverse types of data can be beneficial for analysis, using combinations of complex queries. As an example, we describe how GIMS has been used to analyse a collection of aryl alcohol dehydrogenase gene deletion mutants. The GIMS database can be accessed remotely using a Java application that can be downloaded from http://img.cs.man.ac.uk/gims.

Computational Biology↗
PubMed2001

Continuous quality assessment; development of a simple computer based model for audit.

OBJECTIVE: Accurate assessment of quality of care is a fundamental first step in the process of quality improvement. The vast amount of data generated in a hospital mandates some form of computerization for management of information. We describe a locally developed simple computer based program to access relevant information from a hospital patient management network. The objective was to reduce the amount of manual work involved for busy clinicians attempting to audit quality of care. METHODS: A single surgical procedure, Laparoscopic Cholecystectomy was chosen. Quality indicators were identified by literature review as conversion rate from laparoscopic to open cholecystectomy and length of hospital stay (LOS). A simple query was developed to extract the required information from hospital database. Commercially available spreadsheet software (Microsoft Excel) was used to calculate the rates. Outliers were defined as LOS more than 1 standard deviation from the mean. The second part of the study involved a manual review of case notes to validate the program and determine the causes for deviation from the mean. RESULTS: The program was able to access and process data as planned. In a one-year period from March 1997 to February 1998, two hundred and thirty one laparoscopic cholecystectomies were attempted. Twenty-three were converted to open procedures given a conversion rate of 9.96%. On manual review of case notes no false positives or false negatives were found. The reasons for conversion were similar to those described in the literature. The mean length of stay for laparoscopic cholecystectomy was 3.39 days and 7.17 days for converted cases. The commonest reason for delay in discharge was noted to be non-availability of elective operating time. CONCLUSION: We have successfully developed and used a simple computer based program to access information stored in hospital patient management systems. Quality of care indicators identified from literature were used as standards. Outliers with respect to these were reviewed in detail to identify causes for deviation. The program was validated by manual review.

Computer Simulation↗
PubMed1994

Accessing the Columbia Clinical Repository.

The Columbia Clinical Repository is the foundation of the Clinical Information System at the Columbia Presbyterian Medical Center (CPMC). The Repository is implemented as a relational database on an IBM mainframe, using a generic design that employs a small number of tables. Client applications on remote platforms send and receive data through Database Access Modules (DAMs), which support the HL7 protocol, while applications on the mainframe manipulate data through DAMs supporting a locally defined "query template". Implementation using static (compiled) SQL is compared to dynamic (ad hoc) SQL in terms of efficiency and flexibility.

Clinical Laboratory Information Systems↗
PubMed2000

Biochemical screening for Down syndrome: patients' perception of risk.

OBJECTIVES: To determine the utility of the triple test in routine clinical practice and in addition to the document, the acceptability of a cut-off of 1:250 for invasive testing. DESIGN: Retrospective analysis of data from screening and invasive testing for Down syndrome over a 5-year period in Hull Maternity Hospital. Computer-based records were accessed and individual data drawn from case notes were analyzed. RESULTS: 14827 (78%) of all patients opted for the triple test. A positive result (1:250 or greater) was found in 586 (4%). Fifteen percent of this group refused further testing with amniocentesis. 0.08% requested amniocentesis despite a negative triple test result. Of the screened pregnancies the triple test and selective invasive testing identified nine out of 15 (60%) of Down syndrome cases. CONCLUSION: Sixty percent of Down syndrome pregnancies were identified with a 4% invasive testing rate. Fifteen percent of women who had a positive test did not agree with the cut-off of 1:250 and therefore declined invasive testing. Invasive procedure complication rates do not equate with patients' perception of Down syndrome.

Amniocentesis↗
PubMedDate not supplied

Emerging communication technologies in emergency medical services.

Advances in communication technologies are changing the face of emergency medical services (EMS). Two communication technologies in particular--cellular-enhanced 9-1-1 service and automatic crash notification (ACN)--will have a considerable impact on EMS. Although enhanced 9-1-1 service from land-line phones is now available in nearly every EMS system across the country, enhanced 9-1-1 service from cell phones currently does not exist. With more and more emergency calls made from cell phones, the implementation of this service is a clear priority. Automatic crash notification, a quickly emerging technology, can potentially provide EMS systems with invaluable data within seconds of when a collision occurs. However, many issues with regard to ACN systems need to be addressed, including liability concerns, access to ACN data, ability of drivers to understand the ACN system, and ACN system architecture. The potential interfaces between ACN systems and EMS systems create significant opportunities to enhance EMS resource management and care of patients involved in motor vehicle crashes. With both cellular-enhanced 9-1-1 and ACN in their infancy, EMS physicians and administrators have a valuable opportunity to provide leadership in the development of these services.

Accidents, Traffic↗
PubMed2004

GeneXplorer: an interactive web application for microarray data visualization and analysis.

BACKGROUND: When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures within the paper, can be browsed. We set out to create a CGI application containing many of the features of some of the existing standalone software for the visualization of clustered microarray data. RESULTS: We present GeneXplorer, a web application for interactive microarray data visualization and analysis in a web environment. GeneXplorer allows users to browse a microarray dataset in an intuitive fashion. It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. It provides radar and zoom views of the data, allows display of the nearest neighbors to a gene expression vector based on their Pearson correlations and provides the ability to search gene annotation fields. CONCLUSIONS: The software is released under the permissive MIT Open Source license, and the complete documentation and the entire source code are freely available for download from CPAN http://search.cpan.org/dist/Microarray-GeneXplorer/.

Computer Graphics↗
PubMedDate not supplied

Intraspinal use of morphine.

OBJECTIVE: To compare the different sterility standards and the cost issues involved when choosing an opioid product for intraspinal administration. DATA SOURCES: Literature accessed through MEDLINE and other Internet search engines (September 2002-April 2003) was evaluated. Key search terms included epidural/intrathecal, opioids, sterility, and compounding. DATA SYNTHESIS: Intraspinal use is prevalent in the area of pain management. Product selection is of utmost importance when administering through the intraspinal route. An evaluation of guidelines on sterility and a cost comparison were conducted. CONCLUSIONS: The preservative-free commercially available products that are indicated for intrathecal/epidural use are the best alternative due to proper outside testing and stringent quality assurance. The generic morphine preservative-free product may also be considered if proper steps are taken to ensure that the final product is diluted properly.

Analgesics, Opioid↗
PubMed1985

A minicomputer approach to consultation-liaison data basing: Pedagog-Admin-CLINFO.

Minicomputer systems have been designed for researchers who have no prior computer experience and, therefore, require no computer training, that is, programming knowledge. Such systems allow immediate access to the data, their retrieval, reduction, and analysis, and the retention of direct control over the data base by the researcher. In addition, CLINFO offers a wide range of calculations and statistical procedures. The three-dimensional, time-oriented data-base format of CLINFO allows for a longitudinal study of a particular variable, and its repeated measure over time in the same patient. This system has been adapted for use in the consultation-liaison setting to provide pedagogic, research, and administrative functions from a field-tested data base.

Computers↗
PubMedDate not supplied

The importance of outcome data in brain injury rehabilitation.

Rehabilitation nurses, rehabilitation clients and their families, and healthcare funders easily can obtain brochures about or tours of agencies that provide rehabilitation services to people with brain injuries. Less accessible are outcome data from these agencies, data that should be as readily available as the tours and the brochures--and that reveal far more about the agencies. In this article, the authors describe the system developed by a private, comprehensive postacute service provider for collecting, analyzing, and using the outcome data of its discharged clients. The importance of outcome data for funders, families, and facilities is stressed, and the article provides examples of how to use the data for decision making and program development.

Adult↗
PubMed2006

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.

Proteomics is a key field of modern biomolecular research, with many small and large scale efforts producing a wealth of proteomics data. However, the vast majority of this data is never exploited to its full potential. Even in publicly funded projects, often the raw data generated in a specific context is analysed, conclusions are drawn and published, but little attention is paid to systematic documentation, archiving, and public access to the data supporting the scientific results. It is often difficult to validate the results stated in a particular publication, and even simple global questions like "In which cellular contexts has my protein of interest been observed?" can currently not be answered with realistic effort, due to a lack of standardised reporting and collection of proteomics data. The Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organisation (HUPO), defines community standards for data representation in proteomics to facilitate systematic data capture, comparison, exchange and verification. In this article we provide an overview of PSI organisational structure, activities, and current results, as well as ways to get involved in the broad-based, open PSI process.

Databases, Protein↗
PubMed1994

A Saccharomyces cerevisiae gene encoding a potential adenine phosphoribosyltransferase.

The nucleotide sequence of a Saccharomyces cerevisiae gene encoding a potential adenine phosphoribosyltransferase (APRT) has been determined. The protein encoded by this gene shows a high degree of similarity with APRTs from a variety of other species. The S. cerevisiae gene, named APT2, has been mapped to chromosome IV. The sequence has been deposited in the GenBank data library under Accession Number L14434.

Adenine Phosphoribosyltransferase↗
PubMed2000

Antibiotic prophylaxis in intensive care units: meta-analyses versus clinical practice.

OBJECTIVE: At least 7 meta-analyses (MA) have been published since 1991 on the effectiveness of antibiotic prophylaxis in Intensive care units (ICU) patients, but controversy still remains about the overall effectiveness and risk-benefits profile of the treatment. This paper aims to summarise available data on effectiveness and discuss reasons why the controversy is still open and possible directions for future research. DESIGN: Review of available published MA on the effectiveness of various regimens of antibiotic prophylaxis with particular emphasis on the results of the individual patient data analysis published in 1998. SETTING: MA or randomised control trials (RCTs), published and unpublished, conducted anywhere in the world. PATIENTS AND PARTICIPANTS: Unselected adult ICU populations included in studies, published and unpublished, comparing different forms of antibiotic prophylaxis. MAIN OUTCOME MEASURE: Respiratory tract infections (RTIs) - however defined in individual studies - and total mortality. DATA SOURCES: General information from the 7 MAs published between 1991 and 1999 and detailed information from the MA published in the British Medical Journal in 1998 that reported data on 5727 patients enrolled in 33 RCTs; access to individual patients data could be obtained from 25 of 33 RCTs and allowed a confirmatory individual patient MA on 4343 patients. RESULTS: Pooled estimates from 16 RCTs (including 3361 patients) testing the effect of the topical and systemic antibiotic combination indicates a significant reduction of both RTIs (OR=0.35, 95% CI=0.29-0.41) and total mortality (OR=0.80, 95% CI=0.69-0.93). Five and 23 patients need to be treated to prevent one infection and one death, respectively, using this treatment. Pooled data from the 17 RCTs (including 2366 patients) testing the effect of a regimen based on topical antimicrobials indicated a statistically significant reduction in RTIs (OR=0.57, 95% CI=0.46-0.69) but not in total mortality (OR=1.01; 95% CI=0.84-1.22). Individual patient data analyses confirmed these results. CONCLUSIONS: After over 30 RCTs and seven MAs, there is strong evidence that antibiotic prophylaxis can reduce both RTIs and total mortality in ICUs patients in a statistically and clinically significant way. Concerns about the possible occurrence of antimicrobial resistance are not supported by available data but cannot, at the same time, be ruled out due to methodologic inadequacies of the studies carried out so far. Whether new trials are needed, and how they should be designed to answer the question of the potential for antibiotic resistance following widespread use of the treatment, are now the main issues to be settled. Convening an international panel of clinical experts and methodologists could be appropriate, in order to explore the best way to resolve the controversy that seems to be preventing the widespread use of a treatment that the best analysis of available data now indicates is effective.

Administration, Topical↗
PubMed2005

Thoracic and cardiovascular surgery in Japan during 2003: annual report by The Japanese Association for Thoracic Surgery.

The Japanese Association for Thoracic Surgery has conducted annual surveys of thoracic surgery to reveal the statistics of the number of procedures according to the operative category throughout the country since 1986. Here we have summarized the results from our annual survey of thoracic surgery performed during 2003. The incidence of hospital mortality was added to this survey to determine the nationwide status that could be useful not only for surgeons to compare their work with that of others, but also for the association to gain a better understanding of present problems as well as future prospects. Thirty-day mortality (sometimes termed operative mortality) is death within 30 days of operation regardless of the patient's geographic location. Thirty-day mortality includes death within 30 days of operation even though the patient is discharged from the hospital within 30 days of operation. Hospital mortality is death within any time interval after operation if the patient is not discharged from the hospital. Hospital-to-hospital transfer is not considered discharge; transfer to a nursing home or a rehabilitation unit is considered hospital discharge unless the patient subsequently dies of complications of the operation (the definitions of terms are based on the published guidelines of the Society of Thoracic Surgeons and the American Association for Thoracic Surgery (Edmunds LH, et al. Ann Thorac Surg 1996; 62: 932-5)). Thoracic surgery was classified into three categories as cardiovascular, general thoracic and esophageal surgery, and the pertinent data were examined and analyzed in each group. Access to the computerized data is offered to all members of this association. We honor and value your continued kind support.

Cardiovascular Surgical Procedures↗
PubMed2005

Teaching evidence-based public health to public health practitioners.

PURPOSE: The purpose of the Evidence Based Public Health (EBPH) course is to train public health practitioners to utilize a comprehensive approach for program development and evaluation from a scientific perspective, including principles of scientific reasoning and systematic uses of data and information systems. The increasing technical sophistication of public health problems and approaches emphasizes the importance for an evidence-based approach to developing policy and interventions. METHODS: The training methods used highlight the linkages between data systems and program/policy initiatives. Participants learn to access and interpret existing data systems and methods of using data to impact specific policies or decision-makers. From 1992 through mid-2004 the EBPH course was offered a total of 20 times, in Missouri, nationally and internationally. In March 2002, the workshop was taped and pressed into a 16-CD set that public health workers can use as a self-teaching program in their own homes and offices. The group exercises from the classroom workshop have been adapted into individual self-guided applications, and background readings are included in the set. RESULTS: Compiled results of course evaluations indicate average ratings for course satisfaction ranging from 8.50 to 10.00 on a scale from 1 to 10. Satisfaction with course instructors ranged between 8.00 and 10.00 on the same scale. Ninety-four to ninety-six per cent of participants reported that they would use the course in their day-to-day work. Qualitative comments from participants at the time of and after the course show that the material is applied in a variety of ways. CONCLUSIONS: The EBPH course is making a valuable contribution in strengthening the application of scientific methods to public health practice. To expand the offerings of this training, a train-the-trainer component for the EBPH course is being developed, to be made available in 2005.

Curriculum↗