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At least 1,315 records · Page 73Linked to original sources
PubMed2006

Database testing of a subcutaneous monitor with wireless alarm.

UNLABELLED: We have tested the accuracy of detection of cardiac arrest in a cardiac event recorder that has the 4x4 cm sensor implanted, the recorder external, and the two connected by wireless. Storage and transmission is activated by the patient when symptoms are present or automatically when cardiac arrest is detected, in which case the recorder sounds a loud alarm to alert bystanders. It is the automatic mode that requires database testing of accuracy. MATERIALS: We obtained an appropriate database by mapping the chest in 60 ICD patients in sinus rhythm (SR) and induced ventricular fibrillation (VF), and deriving bipolar ECGs from adjacent electrodes located where the electrodes on the subQ sensor would be. (We then implanted the device in 2 dogs and demonstrated the equivalence of ECGs recorded on the skin to subcutaneous ECGs). A blinded selection of 10 of these 60 patients, together with 14 records from the MIT/BIH database, formed a testing set; the others were available for development and training of the detection algorithm. RESULTS: In all 60 patients, ECGs from closely-spaced electrodes properly located on the chest appeared suitable for automatic VF detection. Formal testing with the 24-patient database yielded sensitivity and specificity of 100% in detecting VF. CONCLUSION: It appears a 4 cm square subcutaneous sensor with electrodes at its corners can reliably monitor cardiac activity, accurately detect the occurrence of cardiac arrest, transmit the ECG to an external receiver, and produce an alarm when a life-threatening arrhythmia is detected.

Animals↗
PubMed2005

Method of construction of a MRI-based tabular database of 3D stereotaxic co-ordinates for individual structures in the basal ganglia of Macaca mulatta.

Primate models are commonly used in Parkinson's disease research to study stereotaxic strategies that demand accurate localization of the structures in basal ganglia. We demonstrate a method to construct an extensive tabular database of 3D stereotaxic co-ordinates of various basal ganglia structures from high-quality magnetic resonance (MR) images of 47 adult female 3-5 kg rhesus monkeys. For each animal, the structures in the basal ganglia were traced as they appeared on the axial MR images. Their maximal outlines were projected in the axial plane to create a stack of images and X, Y, Z co-ordinates were calculated for margins of each structure. These co-ordinates and the outlines of the individual nuclei help delineate a "common area," which was further narrowed down to a point that represents the 'most reliable target point' (MRTP) in subthalamic nucleus, globus pallidum, caudate and putamen on both sides. Common area and MRTP represent the region that can most definitely be associated with a structure and hence the most definite target for a given structure. The goal of this study is to demonstrate the method of construction, discuss the feasibility and usefulness of such a tabular database that could potentially add to accuracy of localization while using atlas-based stereotaxy. Though use of MRI remains a standard practice and advances in imaging have made targeting for functional surgery more accurate, in developing countries that implies prohibitive costs per procedure. Population based human databases similar to the monkey database described here, when used along with less expensive imaging modalities can reduce the costs considerably as well as add to the accuracy of targeting.

Animals↗
PubMed2006

Progress in in silico functional genomics: the malaria Metabolic Pathways database.

Genomic, transcriptomic and proteomic data can be turned into biologically meaningful information if they are synthesized into processes. Such amalgamation has been done for the most virulent malaria parasite Plasmodium falciparum in the Metabolic Pathways database. The dialectics of construction of metabolic pathways and other biological processes using this database is presented here. Additional features, such as links to other databases and the incorporation of transcriptomic clocks, are elucidated. Comparison of Metabolic Pathways to other similar databases is analyzed.

Animals↗
PubMed2005

The occurrence of hormetic dose responses in the toxicological literature, the hormesis database: an overview.

A relational retrieval database has been developed compiling toxicological studies assessing the occurrence of hormetic dose responses and their quantitative characteristics. This database permits an evaluation of these studies over numerous parameters, including study design and dose-response features and physical/chemical properties of the agents. The database contains approximately 5600 dose-response relationships satisfying evaluative criteria for hormesis across over approximately 900 agents from a broadly diversified spectrum of chemical classes and physical agents. The assessment reveals that hormetic dose-response relationships occur in males and females of numerous animal models in all principal age groups as well as across species displaying a broad range of differential susceptibilities to toxic agents. The biological models are extensive, including plants, viruses, bacteria, fungi, insects, fish, birds, rodents, and primates, including humans. The spectrum of endpoints displaying hormetic dose responses is also broad being inclusive of growth, longevity, numerous metabolic parameters, disease incidences (including cancer), various performance endpoints such as cognitive functions, immune responses among others. Quantitative features of the hormetic dose response reveal that the vast majority of cases display a maximum stimulatory response less than two-fold greater than the control while the width of the stimulatory response is typically less than 100-fold in dose range immediately contiguous with the toxicological NO(A)EL. The database also contains a quantitative evaluation component that differentiates among the various dose responses concerning the strength of the evidence supporting a hormetic conclusion based on study design features, magnitude of the stimulatory response, statistical significance, and reproducibility of findings.

Animals↗
PubMed2005

Development of a biomarkers database for the National Children's Study.

The National Children's Study (NCS) is a federally-sponsored, longitudinal study of environmental influences on the health and development of children across the United States (). Current plans are to study approximately 100,000 children and their families beginning before birth up to age 21 years. To explore potential biomarkers that could be important measurements in the NCS, we compiled the relevant scientific literature to identify both routine or standardized biological markers as well as new and emerging biological markers. Although the search criteria encouraged examination of factors that influence the breadth of child health and development, attention was primarily focused on exposure, susceptibility, and outcome biomarkers associated with four important child health outcomes: autism and neurobehavioral disorders, injury, cancer, and asthma. The Biomarkers Database was designed to allow users to: (1) search the biomarker records compiled by type of marker (susceptibility, exposure or effect), sampling media (e.g., blood, urine, etc.), and specific marker name; (2) search the citations file; and (3) read the abstract evaluations relative to our search criteria. A searchable, user-friendly database of over 2000 articles was created and is publicly available at: . PubMed was the primary source of references with some additional searches of Toxline, NTIS, and other reference databases. Our initial focus was on review articles, beginning as early as 1996, supplemented with searches of the recent primary research literature from 2001 to 2003. We anticipate this database will have applicability for the NCS as well as other studies of children's environmental health.

Biomarkers↗
PubMed2006

REPDOSE: A database on repeated dose toxicity studies of commercial chemicals--A multifunctional tool.

A database for repeated dose toxicity data has been developed. Studies were selected by data quality. Review documents or risk assessments were used to get a pre-screened selection of available valid data. The structure of the chemicals should be rather simple for well defined chemical categories. The database consists of three core data sets for each chemical: (1) structural features and physico-chemical data, (2) data on study design, (3) study results. To allow consistent queries, a high degree of standardization categories and glossaries were developed for relevant parameters. At present, the database consists of 364 chemicals investigated in 1018 studies which resulted in a total of 6002 specific effects. Standard queries have been developed, which allow analyzing the influence of structural features or PC data on LOELs, target organs and effects. Furthermore, it can be used as an expert system. First queries have shown that the database is a very valuable tool.

Animals↗
PubMed2007

A comprehensive model for reproductive and developmental toxicity hazard identification: I. Development of a weight of evidence QSAR database.

A weight of evidence (WOE) reproductive and developmental toxicology (reprotox) database was constructed that is suitable for quantitative structure-activity relationship (QSAR) modeling and human hazard identification of untested chemicals. The database was derived from multiple publicly available reprotox databases and consists of more than 10,000 individual rat, mouse, or rabbit reprotox tests linked to 2134 different organic chemical structures. The reprotox data were classified into seven general classes (male reproductive toxicity, female reproductive toxicity, fetal dysmorphogenesis, functional toxicity, mortality, growth, and newborn behavioral toxicity), and 90 specific categories as defined in the source reprotox databases. Each specific category contained over 500 chemicals, but the percentage of active chemicals was low, generally only 0.1-10%. The mathematical WOE model placed greater significance on confirmatory observations from repeat experiments, chemicals with multiple findings within a category, and the categorical relatedness of the findings. Using the weighted activity scores, statistical analyses were performed for specific data sets to identify clusters of categories that were correlated, containing similar profiles of active and inactive chemicals. The analysis revealed clusters of specific categories that contained chemicals that were active in two or more mammalian species (trans-species). Such chemicals are considered to have the highest potential risk to humans. In contrast, some specific categories exhibited only single species-specific activities. Results also showed that the rat and mouse were more susceptible to dysmorphogenesis than rabbits (6.1- and 3.6-fold, respectively).

Abnormalities, Drug-Induced↗
PubMed1997

Database and quick methods of assessing typical dietary fiber intakes using data for 228 commonly consumed foods.

To promote assessment of dietary fiber intakes in clinical settings, we established two objectives for this study: to provide a detailed database in grams per serving of fiber content and polymer composition for most fiber sources in the US diet, and to develop a quick method for estimating total fiber intakes. Data for 342 foods were condensed to 228 foods by combining similar foods. The comprehensive database developed includes pectin, hemicelluloses, and beta-glucan contents of the soluble and insoluble fractions of fiber and the cellulose and Klason lignin contents of the insoluble fiber. Three fourths of the 228 foods contained 2.0 g fiber per serving or less; only 10% contained more than 3.0 g per serving. The quick method consists of multiplying the number of servings in each food group by the mean total dietary fiber content of foods in that group: 1.5 g for fruits (n = 43), 1.5 g for vegetables (n = 68), 1.0 g for refined grains (n = 80), and 2.5 g for whole grains (n = 13). Actual fiber values from the database should be used in the quick method if foodstuffs concentrated from grains, legumes, and nuts and seeds are consumed. Sample menus demonstrate that quick assessment of total fiber intake yielded results similar to the sum of individual values from the database.

Databases, Factual↗
PubMed1999

Using database information in your clinical practice.

BACKGROUND: Clinical database information is in wide demand, but it is not always used to its full potential. Clinicians must learn to be the experts and to assert leadership in the use of their own data. METHODS: Clinical databases provide unique perspectives on the full process of care for a heterogeneous population of patients. They focus beyond individual providers, to their interaction within a complex system of care. Exploring questions that arise from this data can identify system issues, which are invisible to individual practitioners or specialties using other traditional review methods. RESULTS: Clinical database information helped our hospital staff identify problems in their approach to a small subset of high risk coronary bypass patients. Multiple system changes resulted in a dramatic reduction in mortality. Collateral impact on all care reduced overall mortality from 4.5% to below 2%. CONCLUSIONS: The greatest opportunities for improvement in patient care often lie in the areas where specialties or teams interface, eg, in overlapping or transferring care. The whole system of care for each patient must be optimized, not just the individual specialty components. Clinical database information provides a way to evaluate and improve the overall process and results of the broader system of patient care.

Coronary Artery Bypass↗
PubMed2004

Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags.

The RIKEN expression array database (READ) provides comprehensive gene expression data for the mouse, which were obtained as relative values from microarray double-staining experiments with E17.5 mRNA as common reference. To assign absolute expression values for mouse transcripts within READ, we applied the E17.5 reference sample to CAGE (cap analysis of gene expression) and expressed sequence tag (EST) high-throughput tag sequencing. Newly assigned values within the READ database were validated by comparison to expression data from serial analysis of gene expression, CAGE and EST experiments. These experiments confirmed the great significance of the absolute expression values within the improved READ database. The new Absolute READ database on absolute expression data is available under.

Animals↗
PubMed2002

Automated storage of gas chromatography-mass spectrometry data in a relational database to facilitate compound screening and identification.

This paper describes a database containing massspectra from gas chromatography-mass spectrometry(GC-MS) measurements as a tool for easy screening for multiple compounds. In this way additional compounds can be reported from the same run together with routine pesticide monitoring with little effort. The relevant analytical data from the GC-MS measurements are transferred automatically to a database. Search algorithms in the database, containing the US EPA and Dutch NEN GC-MS identification criteria as standard settings, are used to identify compounds in the data. Screening of samples analysed in our laboratory show the ubiquitous presence of--up until now in monitoring largely overlooked--compounds in surface waters in The Netherlands. Most frequently found compounds include TAED (complexing agent), 2-methyl quinoline (industrial solvent), atrazin and desethylatrazin (pesticide and degradation product), caffeine (human consumption), surfinol-104 (anti foaming agent), HHCB (Galaxolide) and AHTN (Tonalide; fragrances). The database can also be used to quickly search a large number of datafiles for rare contaminants. This way, some interesting compounds such as pentoxifilin (a pharmaceutical) and Irgarol 1051 (an antifouling compound) were found.

Database Management Systems↗
PubMed1996

Utility of the National Cooperative Growth Study database for safety reporting.

The National Cooperative Growth Study (NCGS) maintains the largest database in the world, collecting information on patients with growth disorders treated with growth hormone (GH). More than 24,000 children have been monitored during its first decade (1985 through 1995). The database provides unique opportunities to learn about effectiveness of GH therapy in a real-world context. Its size also makes it possible to investigate rare adverse reactions, which is not reasonable in a randomized controlled trial (RCT). The frequency of adverse experiences reported in an observational study like the NCGS is lower than in an RCT, because the investigators in an observational study typically do not report events that they believe are clearly unrelated to the study drug. Nevertheless the NCGS has greatly facilitated collecting adverse-event data; approximately 75% of all adverse-event reports for GH received by the manufacturer are through NCGS data-collection forms. The NCGS has thus amassed a repository of GH safety data that is unparalleled. Furthermore, in contrast to an RCT, the NCGS database reflects real-world experience with long-term GH therapy in North America. Although the advantages of an observational study such as the NCGS must be recognized, such a study does differ from an RCT in important ways. For example, because the NCGS protocol allows customized patient treatment and individualization of GH therapy, it may be difficult to use the database to address questions (e. g., estimation of dose-response relationships, true incidence of adverse events) that require RCT designs.

Adverse Drug Reaction Reporting Systems↗
PubMed2001

Transgenic and knockout databases: behavioral profiles of mouse mutants.

Genetically engineered strains of mice, modified by transgenesis or gene targeting ("knockouts") are being generated at an impressive rate and used, among other areas, as premiere research tools in deciphering the genetic basis of behavior. As behavioral phenotyping strategies continue to evolve, characterization of these "designer" mice will provide models to evaluate the efficacy of new pharmacological and gene therapy treatments in human hereditary diseases. Reported behavioral profiles include aberrant social, reproductive, and parental behaviors, learning and memory deficits, feeding disorders, aggression, anxiety-related behaviors, pain/analgesia, and altered responses to antidepressants, antipsychotics, ethanol, and psychostimulant drugs of abuse. The Induced Mutant Resource (IMR) at The Jackson Laboratory (TJL, Bar Harbor, ME, USA) imports, cryopreserves, develops, maintains, and distributes biomedically important stocks of transgenic and targeted mutant mice to the research community. Information on neurological/behavioral strains--including behavioral performance, husbandry requirements, strain availability, and genetic typing protocols--is provided through the IMR database (http://www.jax.org/resources/documents/imr/). A catalog of available strains is readily accessible via the JAX Mice website at http://jaxmice.jax.org/index.shtml. In addition, TJL is now host to TBASE (http://tbase.jax.org/), a comprehensive, public-domain database with primary emphasis on mouse knockouts. TBASE contains an exhaustive list of knockout-related citations and provides an extensive phenotypic characterization of numerous behavioral mutants that is extracted directly from the literature. Present efforts to merge the two resources into a novel, schematically enhanced database, provisionally named Transgenic and Targeted Mutation Database (TTMD), will be briefly discussed.

Animals↗
PubMed2000

Computer databases for the sentinel lymph node program.

At the University of California San Francisco Comprehensive Cancer Center, a computer database system was created using the FileMaker Pro database program. The system allows the clinical team to bring together data from all aspects of a multidisciplinary effort toward improving daily clinical management, for research, and ultimately, for the clinical standard of care for melanoma patients. With modest objectives during the initiation of the database, its adaptability has allowed it to become an integral link in all the efforts of the melanoma program. For the future, tapping into the immense potential of the Internet has begun to organize multicenter efforts. Through nationwide collaboration, the Sentinel Lymph Node Working Group will be able to follow, on a larger scale, the successes of the FileMaker pro database at the UCSF Comprehensive Cancer Center.

Aftercare↗
PubMed1998

Database tools for integrating and searching membrane property data correlated with neuronal morphology.

A critical problem in neuroscience is the lack of database tools for integrating neuronal property data. We report here the development of a combined object oriented-relational database (NeuronDB, http://senselab.med.yale.edu/neurondb) that meets these needs by providing tools for integrating data within neurons and comparing data across neurons. It focuses on three types of neuronal properties voltage-gated channels, neurotransmitter receptors, and neurotransmitters. The data are organized in relation to different regions of neurons as represented in canonical forms; using simple canonical models of complex cells as a vehicle for indexing information permits the database to be searchable across different neurons. Using these multidimensional search tools, users can locate specific properties in specific regions of a neuron; obtain integrated summaries of all properties within a region; and carry out searches to compare properties across equivalent compartments in different neurons. These tools thus permit searches of the multidimensional neuron property space equivalent to homology searches of sequence databases. NeuronDB is accessible over the Internet; it provides immediate links to citation indexes and abstracts supporting the deposited data, and annotations that indicate the state of acceptance of the data. Users are encouraged to contribute data. The ability to input the data from NeuronDB directly to NEURON and GENESIS is being developed. As a shared Web resource, NeuronDB should enhance the efforts of neuroscientists and neuronal modellers to analyze and compare the functional operations of different types of neurons.

Automation↗
PubMed2000

PPMdb: a plant plasma membrane database.

PPMdb is a proteome database dedicated to proteins from plant plasma membranes. It provides comprehensive two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) maps, partial amino acid sequences and expression data. All this information is gathered and structured in a relational database, after being analyzed and annotated. PPMdb includes active links to related biological databases (EMBL, GenBank, GenPep, and SWISS-PROT and TrEMBL) as well as to MEDLINE abstracts. Information on specific protein spots can be displayed by clicking on the 2-D maps. In addition, users can query the database by accession number, protein name, pI and MW, and cellular location. Access to PPMdb is available at the following URL: http://sphinx.rug. ac.be:8080.

Amino Acid Sequence↗
PubMedDate not supplied

VIR.II: a new interface with the antibody sequences in the Kabat database.

The Kabat database is the source of information par excellence on antibody sequences. In 1995, we developed an interface with the Kabat database, called VIR. VIR has been very useful in conducting studies aiming to find structure-function relationships in antibodies. Here we report a new version adapted to the World Wide Web, called VIR.II. VIR.II allows searches by type of chain (V(H) or V(L)), by species, and by specificity. The species are selected using a pulldown menu, whereas the specificities can be selected from a list containing the unique specificities reported in the Kabat database. These facilities avoid mistakes and redundancies in the searches. Another feature, and probably the most important one, is that VIR.II introduces a classification of specificities in terms of the chemical and biochemical nature of the antigen, like anti-protein, anti-peptide, anti-hapten, etc. This classification has been useful in discovering patterns in the antigen-binding site of antibodies that correlate with the type of antigen the antibody interacts with. To illustrate this, while showing the capabilities of VIR.II, we analyze all the murine anti-peptide and anti-protein antibody sequences compiled as of July, 2000 in the Kabat database.

Amino Acid Sequence↗
PubMed2003

Development of a centralized inland marine hazardous materials response database.

The state of the practice for obtaining chemical reference at a typical hazardous materials transportation accident scene is to consult multiple printed references. This often leads to confusion. This paper describes the design and development of a centralized response database. This is accomplished by identifying the most commonly used emergency response databases for all modes of transportation, developing relationships between the data, and building intuitive interfaces that allow for rapid information retrieval. The tool is subsequently applied to a previous accident to demonstrate the value-added from its availability in a response scenario. By combining all datasets in one application, data redundancy, errors and lags between updates of the data sets can be reduced. The linkages between the database and supporting files enables the data to be easily updated. While the database is designed to aid response to marine transportation accidents, the tool could also be applied to other modes of transportation. Moreover, facility and vessel operators could benefit from having a comprehensive chemical source accessible in case of release or human contact with the material. Finally, the inclusion of commodity flow information enables decision makers to prepare for high risk commodities.

Accidents, Occupational↗