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At least 1,585 records · Page 88Linked to original sources
PubMed2005

Heavy-atom Database System: a tool for the preparation of heavy-atom derivatives of protein crystals based on amino-acid sequence and crystallization conditions.

Heavy-atom Database System (HATODAS) is a WWW-based tool designed to assist the heavy-atom derivatization of proteins. The conventional procedure for the preparation of derivatives is usually a time-consuming 'trial-and-error' process. The present program provides a solution for this problem using a database of known heavy-atom derivatives. A database search suggests potential heavy-atom reagents for any target protein based on its amino-acid sequence and crystallization conditions. A mining of the database identified 93 preferred motifs for heavy-atom binding. The motifs are observed frequently at the actual heavy-atom-binding sites encountered in the process of structure determination.

Amino Acid Motifs↗
PubMed2006

Introduction and validation of an invariom database for amino-acid, peptide and protein molecules.

A database of invarioms for structural refinement of amino-acid, oligopeptide and protein molecules is presented. The spherical scattering factors of the independent atom or promolecule model are replaced by ;individual' aspherical scattering factors that take into account the chemical environment of a bonded atom. All amino acids were analysed in terms of their invariom fragments. In order to generate 73 database entries that cover this class of compounds, 37 model compounds were geometry-optimized and theoretical structure factors were calculated. Multipole refinements were then performed on these theoretical structure factors to yield the invariom database. Validation of this database on an extensive number of experimental small-molecule crystal structures of varying quality and resolution shows that invariom modelling improves various figures of merit. Differences in figures of merit between invariom and promolecule models give insight into the importance of disorder for future protein-invariom refinements. The suitability of structural data for application of invarioms can be predicted by Cruickshank's diffraction-component precision index [Cruickshank (1999), Acta Cryst. D55, 583-601].

Amino Acids↗
PubMed2001

Computerized radiographic mass detection--part II: Decision support by featured database visualization and modular neural networks.

Based on the enhanced segmentation of suspicious mass areas, further development of computer-assisted mass detection may be decomposed into three distinctive machine learning tasks: 1) construction of the featured knowledge database; 2) mapping of the classified and/or unclassified data points in the database; and 3) development of an intelligent user interface. A decision support system may then be constructed as a complementary machine observer that should enhance the radiologists performance in mass detection. We adopt a mathematical feature extraction procedure to construct the featured knowledge database from all the suspicious mass sites localized by the enhanced segmentation. The optimal mapping of the data points is then obtained by learning the generalized normal mixtures and decision boundaries, where a is developed to carry out both soft and hard clustering. A visual explanation of the decision making is further invented as a decision support, based on an interactive visualization hierarchy through the probabilistic principal component projections of the knowledge database and the localized optimal displays of the retrieved raw data. A prototype system is developed and pilot tested to demonstrate the applicability of this framework to mammographic mass detection.

Artificial Intelligence↗
PubMed2004

A wavelet-based ECG delineator: evaluation on standard databases.

In this paper, we developed and evaluated a robust single-lead electrocardiogram (ECG) delineation system based on the wavelet transform (WT). In a first step, QRS complexes are detected. Then, each QRS is delineated by detecting and identifying the peaks of the individual waves, as well as the complex onset and end. Finally, the determination of P and T wave peaks, onsets and ends is performed. We evaluated the algorithm on several manually annotated databases, such as MIT-BIH Arrhythmia, QT, European ST-T and CSE databases, developed for validation purposes. The QRS detector obtained a sensitivity of Se = 99.66% and a positive predictivity of P+ = 99.56% over the first lead of the validation databases (more than 980,000 beats), while for the well-known MIT-BIH Arrhythmia Database, Se and P+ over 99.8% were attained. As for the delineation of the ECG waves, the mean and standard deviation of the differences between the automatic and manual annotations were computed. The mean error obtained with the WT approach was found not to exceed one sampling interval, while the standard deviations were around the accepted tolerances between expert physicians, outperforming the results of other well known algorithms, especially in determining the end of T wave.

Algorithms↗
PubMed2002

The fibril_one on-line database: mutations, experimental conditions, and trends associated with amyloid fibril formation.

The association of amyloid fibril formation with a number of important diseases, and the extensive study of this process in vitro, has resulted in a large literature containing a vast amount of information about the fibril formation process. This includes mutations and experimental conditions that promote or protect against fibril formation. A database (fibril_one) was designed to hold information relating to the formation of fibrils. It was populated by extensive searches of the literature and other databases. A powerful World Wide Web query interface to the database was developed, enabling a simple and effective method to view amyloidogenic mutations associated with specific proteins. The Web interface was used to identify trends in the data. This revealed that mutations promoting fibril formation through altered folding tend to be associated with destabilization of the native fold. In particular, tendencies of mutations to disrupt the native secondary structure and packing in the hydrophobic core were discovered to be significant. Query access to the database is available freely on the World Wide Web at http://www.bioinformatics.leeds.ac.uk/group/online/fibril_one.

Amyloid beta-Peptides↗
PubMed2004

Database searching by flexible protein structure alignment.

We have recently developed a flexible protein structure alignment program (FATCAT) that identifies structural similarity, at the same time accounting for flexibility of protein structures. One of the most important applications of a structure alignment method is to aid in functional annotations by identifying similar structures in large structural databases. However, none of the flexible structure alignment methods were applied in this task because of a lack of significance estimation of flexible alignments. In this paper, we developed an estimate of the statistical significance of FATCAT alignment score, allowing us to use it as a database-searching tool. The results reported here show that (1) the distribution of the similarity score of FATCAT alignment between two unrelated protein structures follows the extreme value distribution (EVD), adding one more example to the current collection of EVDs of sequence and structure similarities; (2) introducing flexibility into structure comparison only slightly influences the sensitivity and specificity of identifying similar structures; and (3) the overall performance of FATCAT as a database searching tool is comparable to that of the widely used rigid-body structure comparison programs DALI and CE. Two examples illustrating the advantages of using flexible structure alignments in database searching are also presented. The conformational flexibilities that were detected in the first example may be involved with substrate specificity, and the conformational flexibilities detected in the second example may reflect the evolution of structures by block building.

Databases, Protein↗
PubMed2003

A tree-based scan statistic for database disease surveillance.

Many databases exist with which it is possible to study the relationship between health events and various potential risk factors. Among these databases, some have variables that naturally form a hierarchical tree structure, such as pharmaceutical drugs and occupations. It is of great interest to use such databases for surveillance purposes in order to detect unsuspected relationships to disease risk. We propose a tree-based scan statistic, by which the surveillance can be conducted with a minimum of prior assumptions about the group of occupations/drugs that increase risk, and which adjusts for the multiple testing inherent in the many potential combinations. The method is illustrated using data from the National Center for Health Statistics Multiple Cause of Death Database, looking at the relationship between occupation and death from silicosis.

Databases, Factual↗
PubMed1993

A comparison of doctors' practice in notifying addicts to the Home Office and reporting them to the North Western Drug Misuse Database.

Doctors have been required to notify named addict patients to the Chief Medical Officer at the Home Office since 1968, and since 1990 have been encouraged to report voluntarily all their drug misusing patients to anonymized NHS regional databases. The North Western Drug Misuse Database, set-up for research purposes in 1985, was the forerunner of these databases. Compliance by doctors from three North Western District Health Authorities with both data collection systems between 1986 and 1989 was assessed by matching the names of notified addicts with the attributors of individuals reported to the NWDMD as users of notifiable drugs. By 1989 72% of addicts notified were also reported to the NWDMD although doctors working in hospital general departments still tended only to notify them. There was no evidence that particular general practitioners consistently did not notify their addict patients while reporting them to the NWDMD. The findings suggest that it will take some time for doctors to become accustomed to reporting all their drug misusing patients to the regional databases as well as notifying to Home Office those who met the notification criteria.

Data Collection↗
PubMed2007

A database on treating drug addiction with traditional Chinese medicine.

AIMS: Traditional Chinese medicine (TCM) has been used to treat drug addiction for more than 160 years and valuable experiences have been accumulated with regard to patients' detoxification and rehabilitation. The aims of this project were (1) to establish a computerized, bilingual (Chinese-English) database on TCM for drug addiction; (2) to analyse the literature published in this field; and (3) to identify those Chinese herbs commonly used for drug addiction treatment. DESIGN: (1) Paper collection: related papers were collected through electronic databases and hand-searched materials; (2) data computerization: the Microsoft Access program and Delphi language were used as the major data management systems; (3) paper analysis: annual publications from 1989 to 2003 were classified and calculated; and (4) herbal analysis: the frequency of herbs used and herbal function categories were analysed. FINDINGS: (1) A special bilingual database that contained 340 works of professional literature, including 85 patent files on TCM for drug addiction, was established, in which more than 90% of the publications originated from mainland China; (2) the literature classification showed a significant increase in the number of publications on clinical and laboratory researches in this field over the past decade; (3) five functional categorizations of Chinese herbs and the 10 most frequently used Chinese herbs as well as three toxic herbs were identified from more than 200 herbs reported in 150 original research articles and 85 patent files. CONCLUSIONS: For the first time, the published data on TCM in the treatment of drug addiction were analysed systematically by using a new database. The results are invaluable for further laboratory and clinical studies to obtain more direct evidence.

Databases as Topic↗
PubMed2006

From information to understanding: the role of model organism databases in comparative and functional genomics.

Data integration is key to functional and comparative genomics because integration allows diverse data types to be evaluated in new contexts. To achieve data integration in a scalable and sensible way, semantic standards are needed, both for naming things (standardized nomenclatures, use of key words) and also for knowledge representation. The Mouse Genome Informatics database and other model organism databases help to close the gap between information and understanding of biological processes because these resources enforce well-defined nomenclature and knowledge representation standards. Model organism databases have a critical role to play in ensuring that diverse kinds of data, especially genome-scale data sets and information, remain useful to the biological community in the long-term. The efforts of model organism database groups ensure not only that organism-specific data are integrated, curated and accessible but also that the information is structured in such a way that comparison of biological knowledge across model organisms is facilitated.

Animals↗
PubMed2007

The European internet-based patient and research database for primary immunodeficiencies: results 2004-06.

Because primary immunodeficiencies (PID) are rare diseases, transnational studies are essential to maximize the scientific outcome and lead to improved diagnosis and therapy. Immunologists in Europe have united to determine the prevalence of PID in Europe and to establish and evaluate harmonized guidelines for the diagnosis and treatment of PID as well as to improve the awareness of PID in Europe. In order to achieve this aim we have developed an internet-based database for clinical and research data on patients with PID. This database forms the platform for studies of demographics, the development of new diagnostic and therapeutic strategies and the identification of novel disease-associated genes. The database is completely secure, while providing access to researchers via a standard browser using password and encrypted log-in sessions and conforms to all European and national ethics and data protection guidelines. So far 2386 patients have been documented by 35 documenting centres in 20 countries. Common variable immunodeficiency (CVID) is the most common entity, accounting for almost 30% of all entries. First statistical analyses on the quality of life of patients show the advantages of immunoglobulin replacement therapy, at the same time revealing a mean diagnostic delay of over 4 years. First studies on specific questions on selected PID are now under way. The platform of this database can be used for any type of medical condition.

Adolescent↗
PubMed1997

Development of a dietary supplement database.

Data describing the composition of dietary supplements are not readily available to the public health community. As a result, intake from dietary supplements is generally not considered in most dietary surveys and, hence, little is known about the significance of supplement intake in relation to total diet or disease risk. To enable a more comprehensive analysis of dietary data, a database of the composition of various dietary supplements has been compiled. Active ingredients of all dietary supplements sold in Australia are included in the Australian Register of Therapeutic Goods (ARTG), maintained by the Therapeutic Goods Administration. Products included in the database were restricted to those vitamin, mineral and other supplements identified in dietary data collected from studies conducted in southeast Queensland and New South Wales (850 supplements). Conversion factors from ingredients compounds to active elements were compiled from standard sources. No account has been made for bioavailability, consistent with current practice for food composition databases. The database can be queried by ARTG identification number, brand, product title, or a variety of other fields. Expected future developments include development of standard formulations for use when supplements are incompletely specified, and expansion of products included for more widespread use.

Australia↗
PubMed2004

The sumatriptan/naratriptan aggregated patient (SNAP) database: aggregation, validation and application.

Pooled data from multiple clinical trials can provide information for medical decision-making that typically cannot be derived from a single clinical trial. By increasing the sample size beyond that achievable in a single clinical trial, pooling individual-patient data from multiple trials provides additional statistical power to detect possible effects of study medication, confers the ability to detect rare outcomes, and facilitates evaluation of effects among subsets of patients. Data from pharmaceutical company-sponsored clinical trials lend themselves to data-pooling, meta-analysis, and data mining initiatives. Pharmaceutical company-sponsored clinical trials are arguably among the most rigorously designed and conducted of studies involving human subjects as a result of multidisciplinary collaboration involving clinical, academic and/or governmental investigators as well as the input and review of medical institutional bodies and regulatory authorities. This paper describes the aggregation, validation and initial analysis of data from the sumatriptan/naratriptan aggregate patient (SNAP) database, which to date comprises pooled individual-patient data from 128 clinical trials conducted from 1987 to 1998 with the migraine medications sumatriptan and naratriptan. With an extremely large sample size (>28000 migraineurs, >140000 treated migraine attacks), the SNAP database allows exploration of questions about migraine and the efficacy and safety of migraine medications that cannot be answered in single clinical trials enrolling smaller numbers of patients. Besides providing the adequate sample size to address specific questions, the SNAP database allows for subgroup analyses that are not possible in individual trial analyses due to small sample size. The SNAP database exemplifies how the wealth of data from pharmaceutical company-sponsored clinical trials can be re-used to continue to provide benefit.

Clinical Trials as Topic↗
PubMed1991

Gene maps and location databases.

A location database is defined in linear space by a vector of genetic and physical locations for each locus, which may be ordered by virtual sorting on composite location. This contrasts with an interval database defined in metric space, for which location must be inferred by list-processing from numbered intervals which are assigned different ordinals in different tables and overlap other intervals in many ways. A location database has been used for all well-studied experimental organisms. Principles for a human genome database may be derived from this experience.

Animals↗
PubMed2005

UNITE: a database providing web-based methods for the molecular identification of ectomycorrhizal fungi.

Identification of ectomycorrhizal (ECM) fungi is often achieved through comparisons of ribosomal DNA internal transcribed spacer (ITS) sequences with accessioned sequences deposited in public databases. A major problem encountered is that annotation of the sequences in these databases is not always complete or trustworthy. In order to overcome this deficiency, we report on UNITE, an open-access database. UNITE comprises well annotated fungal ITS sequences from well defined herbarium specimens that include full herbarium reference identification data, collector/source and ecological data. At present UNITE contains 758 ITS sequences from 455 species and 67 genera of ECM fungi. UNITE can be searched by taxon name, via sequence similarity using blastn, and via phylogenetic sequence identification using galaxie. Following implementation, galaxie performs a phylogenetic analysis of the query sequence after alignment either to pre-existing generic alignments, or to matches retrieved from a blast search on the UNITE data. It should be noted that the current version of UNITE is dedicated to the reliable identification of ECM fungi. The UNITE database is accessible through the URL http://unite.zbi.ee

DNA, Ribosomal Spacer↗
PubMed2000

Developing a database to describe the practice patterns of adult nurse practitioner students.

PURPOSE: To describe the practice patterns of adult nurse practitioner students using a database composed of core health data elements and standardized nursing language. DESIGN: Descriptive study of 3,733 patient visits documented by 19 adult nurse practitioner students in the academic year 1996-1997. METHODS: A database was designed for documenting the full scope of practice of adult nurse practitioner students by use of core health data elements and the standardized nursing languages of NANDA and NIC. Nurse practitioner students used the database to document every clinical encounter during their final clinical year of study. Most visits occurred in ambulatory care settings in a midwestern American city. FINDINGS: Based on the American Medical Association's Evaluation/Management coding system, data indicated that 50% of visits were classified as problem focused, while 31.9% were expanded, 10% were detailed, and 8.1% were comprehensive. The most frequently occurring NANDA diagnoses were pain, health-seeking behavior, altered health maintenance, and knowledge deficit. The most frequently reported nursing intervention classifications (NIC) were patient education, drug management, information management, and risk management. CONCLUSIONS: Using standardized nursing language to describe clinical encounters made visible the complex clinical decision-making patterns of adult nurse practitioner students. Systematic use of a database designed for documenting the full scope of practice of nurse practitioner students showed the applicability of standardized nursing language to advanced practice nursing contexts.

Adult↗
PubMed1995

Using an encounter form to develop a clinical database for documenting nurse practitioner primary care.

A clinical database will enable nurse practitioners to document and improve characteristics of their practices. This information is vital if nurse practitioners expect to achieve success in the changing U.S. health care system. This article describes the process of creating an encounter form and a related clinical database. Changes made in a family practice clinic that were derived from using a clinical database are presented. Additional uses for a clinical database, such as quality assurance, clinical evaluation, and clinical research, are discussed.

Database Management Systems↗
PubMed2025

EucaMOD: a comprehensive multi-omics database for functional genomics research and molecular breeding of fast-growing eucalyptus trees.

Eucalyptus, one of the most widely planted plantation tree species globally, is primarily found in tropical and subtropical regions and contributes significantly to economic and social benefits. With advances in sequencing technologies, there is an increasing demand for the systematic analysis of multi-omics data among Eucalyptus species to enhance genetic breeding efforts. Although several early genomic databases have been established for eucalyptus, they have not been updated in a timely manner and lack recent multi-omics data, rendering them insufficient for current research needs. To address this gap, we developed the eucalyptus multi-omics database (EucaMOD, http://eucalyptusggd.net/eucamod), a comprehensive resource for cross-omics studies. In this study, we functionally annotated 45 eucalyptus genomes and structurally annotated 15, conducting comparative genomics and pan-proteomics analyses across all genomes. Additionally, we analyzed eucalyptus transcriptome, epigenome, and variome data through standardized workflows, enabling the in-depth mining and reanalysis of multi-omics datasets. EucaMOD is the most comprehensive multi-omics database for eucalyptus to date and includes data from 45 genomes (39 species), 870 mRNA-seq samples, 17 miRNA-seq samples, 52 epigenomic datasets (histone modifications and transcription factor binding), and genetic variation data from 1219 samples. To support functional genomics and molecular breeding research, the database is organized into the following 11 modules: Home, Species, Genomics, Comparative genomics, Pan-proteomics, Transcriptomics, Epigenetics, Variomics, Tools, Download, and Help. EucaMOD also offers online analysis tools for data mining, providing free public services to aid eucalyptus gene function and genetic engineering studies.

Eucalyptus↗