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PubMed1988

Computerized family practitioner committee records--a data base for general practitioners.

In the primary care environment the role of preventive medicine is assuming increasing importance and general practitioners need accurate and up-to-date information about their practice population. Computerization of family practitioner committee registers should provide a readily accessible data base from which data about groups of patients within the practice area can easily be extracted. This paper describes a study carried out in Northumberland, which set out to establish the type of information which would be of interest to general practitioners and how it could be produced.It was found that a data base holding only registration data was of limited value to general practitioners, although useful for identifying target groups for screening programmes and showing demographic trends within the practice. The doctors felt that the inclusion of medical data would make the register a far more effective resource.

Ambulatory Care Information Systems↗

PubMed2004

A common open representation of mass spectrometry data and its application to proteomics research.

A broad range of mass spectrometers are used in mass spectrometry (MS)-based proteomics research. Each type of instrument possesses a unique design, data system and performance specifications, resulting in strengths and weaknesses for different types of experiments. Unfortunately, the native binary data formats produced by each type of mass spectrometer also differ and are usually proprietary. The diverse, nontransparent nature of the data structure complicates the integration of new instruments into preexisting infrastructure, impedes the analysis, exchange, comparison and publication of results from different experiments and laboratories, and prevents the bioinformatics community from accessing data sets required for software development. Here, we introduce the 'mzXML' format, an open, generic XML (extensible markup language) representation of MS data. We have also developed an accompanying suite of supporting programs. We expect that this format will facilitate data management, interpretation and dissemination in proteomics research.

Database Management Systems↗

PubMed2005

GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections.

The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species. Data are stored in GERMINATE in a technology-independent manner, such that new technologies can be accommodated in the database as they emerge, without modification of the underlying schema. Users can access data in GERMINATE databases either via a lightweight Perl-CGI Web interface or by the more complex Genomic Diversity and Phenotype Connection software. GERMINATE is released under the GNU General Public License and is available at http://germinate.scri.sari.ac.uk/germinate/.

Computational Biology↗

PubMed2006

Megx.net--database resources for marine ecological genomics.

Marine microbial genomics and metagenomics is an emerging field in environmental research. Since the completion of the first marine bacterial genome in 2003, the number of fully sequenced marine bacteria has grown rapidly. Concurrently, marine metagenomics studies are performed on a regular basis, and the resulting number of sequences is growing exponentially. To address environmentally relevant questions like organismal adaptations to oceanic provinces and regional differences in the microbial cycling of nutrients, it is necessary to couple sequence data with geographical information and supplement them with contextual information like physical, chemical and biological data. Therefore, new specialized databases are needed to organize and standardize data storage as well as centralize data access and interpretation. We introduce Megx.net, a set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts. Megx.net includes (i) a geographic information system to systematically store and analyse marine genomic and metagenomic data in conjunction with contextual information; (ii) an environmental genome browser with fast search functionalities; (iii) a database with precomputed analyses for selected complete genomes; and (iv) a database and tool to classify metagenomic fragments based on oligonucleotide signatures. These integrative databases and webserver will help researchers to generate a better understanding of the functioning of marine ecosystems. All resources are freely accessible at http://www.megx.net.

Databases, Genetic↗

PubMed2004

Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments.

The Onto-Tools suite is composed of an annotation database and five seamlessly integrated web-accessible data mining tools: Onto-Express (OE), Onto-Compare (OC), Onto-Design (OD), Onto-Translate (OT) and Onto-Miner (OM). OM is a new tool that provides a unified access point and an application programming interface for most annotations available. Our database has been enhanced with more than 120 new commercial microarrays and annotations for Rattus norvegicus, Drosophila melanogaster and Carnorhabditis elegans. The Onto-Tools have been redesigned to provide better biological insight, improved performance and user convenience. The new features implemented in OE include support for gene names, LocusLink IDs and Gene Ontology (GO) IDs, ability to specify fold changes for the input genes, links to the KEGG pathway database and detailed output files. OC allows comparisons of the functional bias of more than 170 commercial microarrays. The latest version of OD allows the user to specify keywords if the exact GO term is not known as well as providing more details than the previous version. OE, OC and OD now have an integrated GO browser that allows the user to customize the level of abstraction for each GO category. The Onto-Tools are available online at http://vortex.cs.wayne.edu/Projects.html.

Animals↗

PubMed1992

CASSPERT--an expert system to guide choice and strategy in coronary angioplasty.

Coronary angioplasty is a technique widely used in the treatment of coronary artery disease. The success of coronary angioplasty depends on patient selection, the use of an appropriate technique, and to a large extent a carefully considered choice of angioplasty equipment. The authors have developed an expert system which can assist in this decision making process. CASSPERT was developed using the expert system shell 'Leonardo' running on a standard Personal Computer. The user interacts with CASSPERT to build up a detailed profile of clinical, investigational and angiographic features of the patient. This information, together with technical data stored within Leonardo's own object orientated database, is used to infer a suitable choice of equipment. To make the expert system useful in clinical practise, it was interfaced within a functional, readily accessible, data acquisition and storage environment which could be used within the day to day running of the department.

Angioplasty, Balloon, Coronary↗

PubMed2025

Sustainability in translational genomics research with undiagnosed patients: What is it, why do we need it, and how do we do it?

PURPOSE: Genomics research enrolling undiagnosed patients can provide answers for one-third of participants, and more can be diagnosed through future reanalysis. The long-term value for participants has raised questions of the sustainability of these studies, but the meaning, goals, and best practices for sustainability remain unclear. METHODS: We conducted semistructured interviews with researchers leading studies enrolling undiagnosed patients in the United States and Canada and used thematic content analysis to summarize key themes. RESULTS: Researchers lacked consensus regarding what sustainability was actually intended to sustain, variably referencing study procedures, personnel, data access, and participant recontact. However, the primary driver of sustainability was widely shared as the perceived obligation to continue to search for answers for undiagnosed participants. Proposed sustainability strategies included diversifying funding sources, developing centralized data infrastructure, and building collaborations across disciplines and institutions. Researchers also emphasized the need to address ethical concerns, to integrate research with clinical care, and for leadership from research funders to guide these efforts. CONCLUSION: Although genomics researchers perceived continued obligations to undiagnosed participants, they also lacked a shared understanding of the goals of sustainability and called for coordinated efforts to develop centralized infrastructure that integrated research and clinical care.

Humans↗

PubMed2002

User-oriented views in health care information systems.

In this paper, we present the methodology we adopted in designing and developing an object-oriented database system for the management of medical records. The designed system provides technical solutions to important requirements of most clinical information systems, such as 1) the support of tools to create and manage views on data and view schemas, offering to different users specific perspectives on data tailored to their needs; 2) the capability to handle in a suitable way the temporal aspects related to clinical information; and 3) the effective integration of multimedia data. Remote data access for authorized users is also considered. As clinical application, we describe here the prototype of a user-oriented clinical information system for the archiving and the management of multimedia and temporally oriented clinical data related to percutaneous transluminal coronary angioplasty (PTCA) patients. Suitable view schemas for various user roles (cath-lab physician, ward nurse, general practitioner) have been modeled and implemented on the basis of a detailed analysis of the considered clinical environment, carried out by an object-oriented approach.

Algorithms↗

PubMed2004

Multicentre analysis of treatment planning information: technical requirements, possible applications and a proposal.

Digital data from 3-D treatment planning computers is generally used for patient planning and then never considered again. However, such data contains enormous quantities of information regarding patient geometries, tissue outlining, treatment approaches and dose distributions. Were such data accessible from planning systems from multiple manufacturers, there would be substantial opportunities for undertaking quality assurance of radiotherapy clinical trials, prospective assessment of trial outcomes and basic treatment planning research and development. The technicalities of data exchange between planning systems are outlined, and previous attempts at producing systems capable of viewing and/or manipulating imaging and radiotherapy digital data reviewed. Development of a software system for enhancing the quality of Australasian clinical trials is proposed.

Clinical Trials as Topic↗

PubMed2006

HvrBase++: a phylogenetic database for primate species.

HvrBase++ is the improved and extended version of HvrBase. Extensions are made by adding more population-based sequence samples from all primates including humans. The current collection comprises 13,873 hypervariable region I (HVRI) sequences and 4940 hypervariable region II (HVRII) sequences. In addition, we included 1376 complete mitochondrial genomes, 205 sequences from X-chromosomal loci and 202 sequences from autosomal chromosomes 1, 8, 11 and 16. In order to reduce the introduction of erroneous data into HvrBase++, we have developed a procedure that monitors GenBank for new versions of the current data in HvrBase++ and automatically updates the collection if necessary. For the stored sequences, supplementary information such as geographic origin, population affiliation and language of the sequence donor can be retrieved. HvrBase++ is Oracle based and easily accessible by a web interface (http://www.hvrbase.org). As a new key feature, HvrBase++ provides an interactive graphical tool to easily access data from dynamically created geographical maps.

Animals↗

PubMed2002

Moving forward: addressing the health of Asian American and Pacific Islander women.

Little is known about the health of Asian American and Pacific Islander (AAPI) women, a rapidly growing population marked by diverse sociodemographic characteristics, health needs, and access to and use of health services. This commentary provides broad recommendations for research, program development, and policy development based on the first-ever White House Initiative report on AAPIs. These recommendations address the issues of data, access, civil rights, community capacity, and the need to recognize ethnic subgroups among the AAPI population. Reflecting on the events of the past year, the recommendations provide direction for public health to address the health and well-being of AAPI women.

Asian↗

PubMed2004

Development of a model based on body composition to predict drug kinetics-1 evaluation in healthy volunteers.

A kinetic model for widely used drugs, based on body composition analysis, was developed and evaluated in young and elderly healthy individuals. Body composition was studied by body impedance analysis (BIA). Antipyrine, amlodipine, digoxin and tobramycin kinetics, liver microsomal activity enzyme (lidocaine/MEGX test), and appropriate clinical and laboratory tests were carried out. Major variables (V(d), AUC, t(1/2), C(max), Cl) for these drugs were calculated, and the possible relationships with the other clinical and biochemical data were analyzed by the Pearson's moment correlation, forecasting models being then obtained by a multiple linear regression method. Major kinetic parameters, particularly for the mixed elimination drugs (liver/renal), i.e. digoxin and amlodipine, proved to be well correlated to data collected during the study, in particular with body structure parameters. Results were less satisfactory in the case of the mainly renally handled tobramycin. Mathematical models to forecast the kinetic behaviors of the three chosen drugs, using readily accessible data, showed both in the young and the elder, as well as in the whole examined population, very satisfactory correlations in the case of digoxin (R(2) ranging from 0.89 to 0.85) and amlodipine (R(2) between 0.81 and 0.91), less satisfactory (with a wide range of R(2), from 0.65 to 0.94), in the case of tobramycin.

Adult↗

PubMed1988

A medical information relational database system (MIRDS).

A medical information relational database system (MIRDS) which is resident on a relational database machine and is accessed via microcomputers has been created for a pediatric pulmonary division of a research hospital. The power and flexibility of MIRDS has permitted the integration of clinical tasks, research interests, and laboratory functions. Procedures have been devised to assure data integrity, allow flexibility in data retrievals, produce standardized report formats, and permit data access for users with a wide range of query expertise. There are few impediments to the integration of additional clinical, research, and laboratory functions as the system evolves.

Child↗

PubMed2026

Epigenetics and In Silico Transcriptome Analysis of Pediatric Acute Myeloid Leukemia.

Pediatric acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy that accounts for about 15%-20% of childhood leukemias. Despite therapeutic advances, relapses remain common, and survival for high-risk patients is below 60%. Unlike adult AML, pediatric AML displays distinct genetic mutations, including FLT3-ITD, NPM1, KMT2A rearrangements, and core-binding factors (CBF) fusions, as well as extensive epigenetic dysregulation. Aberrant DNA methylation, histone modifications, and altered non-coding RNA expressions disrupt hematopoietic differentiation and activate oncogenic transcriptional networks. Recent advances in silico transcriptomic analysis have transformed the study of pediatric AML by integrating gene expression and epigenetic data to identify molecular drivers and regulatory networks. Computational RNA-seq pipelines and pathway analyses have highlighted key epigenetic regulators, including DNMT3A, TET2, and HDACs, as potential therapeutic targets. Multi-omics approaches combining transcriptomic, methylomic, and chromatin accessibility data are increasingly used to define biomarkers for diagnosis, prognosis, and therapeutic response. This review provides a comprehensive overview of the molecular and epigenetic landscape of pediatric AML, emphasizing the power of in silico transcriptome analysis to uncover disease mechanisms, refine patient stratification, and guide the development of precision-based epigenetic therapies aimed at improving long-term outcomes in children with AML.

Humans↗

PubMed2001

Expert systems, security and quality assurance: implications of patient records as data-space.

The concept of data-space is fruitful in trying to understand the ethical rights and duties that surround the treatment of patient records. However, it also provides a solution to three apparently unconnected problems: the construction of expert diagnostic systems, the development of an internal security element within the sphere of permitted data-access for health care professionals, and the development of a professional quality assurance mechanism. This paper presents a model of how these diverse aims may be achieved. It does so by developing the notion of the logical form of data within a data-space and by showing how the path taken by a health care professional through a profession-relative data-space can provide checks for the security, quality and appropriateness of the path itself. The result is important in that it provides an integrated method for information specialists to meet their fiduciary obligations towards the patients whose records are in their care, and towards the institutions that employ them.

Computer Security↗

PubMed2006

Accessibility of cysteine residues substituted into the cytoplasmic regions of the alpha-factor receptor identifies the intracellular residues that are available for G protein interaction.

The yeast alpha-factor pheromone receptor (Ste2) belongs to the family of G protein-coupled receptors (GPCRs) that contain seven transmembrane domains. To define the residues that are accessible to the cytoplasmic G protein, Cys scanning mutagenesis was carried out in which each of the residues that span the intracellular loops and the cytoplasmic end of transmembrane domain 7 was substituted with Cys. The 90 different Cys-substituted residues were then assayed for reactivity with MTSEA-biotin [[2-[(biotinoyl)amino]ethyl]methanethiosulfonate], which reacts with solvent-accessible sulfhydryl groups. As part of these studies we show that adding free Cys to stop the MTSEA-biotin reactions has potential pitfalls in that Cys can rapidly undergo disulfide exchange with the biotinylated receptor proteins at pH >or=7. The central regions of the intracellular loops of Ste2 were all highly accessible to MTSEA-biotin. Residues near the ends of the loops typically exhibited a drop in the level of reactivity over a consecutive series of residues that was inferred to be the membrane boundary. Interestingly, these boundary residues were enriched in hydrophobic residues, suggesting that they may form a hydrophobic pocket for interaction with the G protein. Comparison with accessibility data from a previous study of the extracellular side of Ste2 indicates that the transmembrane domains vary in length, consistent with some transmembrane domains being tilted relative to the plane of the membrane as they are in rhodopsin. Altogether, these results define the residues that are accessible to the G protein and provide an important structural framework for the interpretation of the role of Ste2 residues that function in G protein activation.

Amino Acid Sequence↗

PubMed2002

Can high quality overcome consumer resistance to restricted provider access? Evidence from a health plan choice experiment.

OBJECTIVE: To investigate the impact of quality information on the willingness of consumers to enroll in health plans that restrict provider access. DATA SOURCES AND SETTING: A survey administered to respondents between the ages of 25 and 64 in the West Los Angeles area with private health insurance. STUDY DESIGN: An experimental approach is used to measure the effect of variation in provider network features and information about the quality of network physicians on hypothetical plan choices. Conditional logit models are used to analyze the experimental choice data. Next, choice model parameter estimates are used to simulate the impact of changes in plan features on the market shares of competing health plans and to calculate the quality level required to make consumers indifferent to changes in provider access. PRINCIPAL FINDINGS: The presence of quality information reduced the importance of provider network features in plan choices as hypothesized. However, there were not statistically meaningful differences by type of quality measure (i.e., consumer assessed versus expert assessed). The results imply that large quality differences are required to make consumers indifferent to changes in provider access. The impact of quality on plan choices depended more on the particular measure and less on the type of measure. Quality ratings based on the proportion of survey respondents "extremely satisfied with results of care" had the greatest impact on plan choice while the proportion of network doctors "affiliated with university medical centers" had the least. Other consumer and expert assessed measures had more comparable effects. CONCLUSIONS: Overall the results provide empirical evidence that consumers are willing to trade high quality for restrictions on provider access. This willingness to trade implies that relatively small plans that place restrictions on provider access can successfully compete against less restrictive plans when they can demonstrate high quality. However, the results of this study suggest that in many cases, the level of quality required for consumers to accept access restrictions may be so high as to be unattainable. The results provide empirical support for the current focus of decision support efforts on consumer assessed quality measures. At the same time, however, the results suggest that consumers would also value quality measures based on expert assessments. This finding is relevant given the lack of comparative quality information based on expert judgment and research suggesting that consumers have apprehensions about their ability to meaningfully interpret performance-based quality measures.

Adult↗

PubMed1992

Homicides in Auckland, New Zealand. A 14-year study.

In the 14-year period from 1976 to 1989, there have been 174 homicide victims in the Auckland colonial area. Data accessed from autopsy and police reports show that victims of marital conflict, family dispute, and arguments developing between nonmarried couples made up the largest proportion of homicide cases. Stabbing and assault with a blunt weapon were the most common causes of death. The data also show that homicide is relatively uncommon in Auckland in comparison with other cities of similar size.

Adolescent↗