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At least 217 records · Page 12Linked to original sources
PubMed1996

A World Wide Web (WWW) server database engine for an organelle database, MitoDat.

We describe a simple database search engine "dbEngine" which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relationship database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.

Computer Communication Networks↗
PubMed2026

Comparative genomics reveals hidden biosynthetic diversity in Streptomyces spp. and metal-dependent regulatory features associated with untapped specialized metabolites.

The genus Streptomyces is one of the richest sources of bioactive natural products; however, a substantial proportion of its biosynthetic gene clusters (BGCs) remain cryptic and their metabolic products are unresolved. Advances in genome mining and computational prediction now enable comprehensive exploration of this hidden biosynthetic repertoire. In this study, whole-genome sequencing and comparative genomic analyses were performed on three three newly isolated Streptomyces strains to evaluate their specialized metabolic potential. Genome assemblies were annotated and systematically analyzed using antiSMASH, DeepBGC, GECCO, and PRISM to identify, cross-validate, and functionally characterize BGCs while predicting their associated secondary metabolite scaffolds. Taxonomic analyses based on Average Nucleotide Identity (ANI), phylogenomics, and BLAST identified the isolates as Streptomyces thinghirensis, Streptomyces novocaesareae, and Streptomyces griseorubens. Applying the consensus framework across the three Streptomyces genomes yielded 43 cryptic BGCs, lacking close similarity to reference BGCs in the MIBiG database, of which 26 were classified as HIGH, 10 as MEDIUM, and 7 as LOW confidence. Notably, numerous BGCs exhibited low abundance to characterized reference clusters, indicating a high potential for previously undescribed biosynthetic pathways and novel metabolite scaffolds. Comparative analyses further revealed strain-specific biosynthetic architectures together with putative metal-responsive regulatory systems; Fur, Zur, and Nur, which were frequently associated with specialized metabolite biosynthetic loci. Collectively, these findings demonstrate the effectiveness of integrated genome-mining strategies for prioritizing cryptic biosynthetic gene clusters and highlight the remarkable biosynthetic potential of newly identified Streptomyces isolates as a source of novel natural products.

comparative genomics↗
PubMed1996

Consultation-liaison psychiatry in an Australian oncology unit.

OBJECTIVE: To provide an overview of the work of a consultation-liaison (C-L) psychiatry service to an oncology unit in a university affiliated teaching hospital, with the aid of a comprehensive clinical database. METHOD: The MICROCARES prospective clinical database system was used to record data on all oncology inpatients referred to C-L psychiatry, and the hospital clinical database was used to compare referred inpatients with all oncology inpatients. RESULTS: Two hundred and seventy-one referrals were made in the 3 years from 1991 to 1993, a referral rate of 10.4%. The referred patients were younger but there was no bias in sex and marital status. The mean length of stay was twice that for all other oncology admissions, day cases excluded. The most frequent reasons for referral were coping problems, depression, terminal illness issues and anxiety. The most common psychiatric diagnoses were Systemic Family Problems (V codes, 24%), Mood Disorders (23%), Adjustment Disorders (16%) and Organic Mental Disorders (10%). Management involved family conferences in half of the patients and antidepressant medication in one-quarter. Concordance with pharmacological recommendations was 98%. Existential issues and family-centred care are discussed. CONCLUSIONS: Both individual and family-centred care is required in an oncology service; a dedicated liaison attachment offers considerable staff support. Psycho-oncology is underdeveloped in Australia compared to many overseas services; there is scope for substantial growth in preventive and supportive work.

Adaptation, Psychological↗
PubMedDate not supplied

Microcomputer database management for surgical residents.

Surgical residents must record procedures performed and may choose to keep files of photographic slides, bibliographic references, and a curriculum vitae. Four databases that store this information are produced with an inexpensive and easily obtained microcomputer software program. A surgical procedure database is modeled after the procedure list recommended by surgical boards. This list can be viewed while one enters data, thereby enabling production of accurate and complete records. In the second database, photographic slides are assigned sequence numbers and slide content is designated using both procedure codes and key words, allowing structured and personal recall of data. Data can be printed in many report formats, including that used by the boards of surgery for final submission of reports of residents' operations at the completion of residency. The bibliographic and CV databases contain highly segmented citation data. This structure enables manipulation of data to satisfy the sequence requirements of journals or institutions to which articles or CV are submitted. Database maintenance consumes a few minutes daily and requires a minimum of experience with computers. By providing ease of access to organized data, these databases enhance the potential for critical review of clinical experience by both residents and program directors.

General Surgery↗
PubMed1987

The use of a computerised database for the diagnosis of a rare neurological syndrome.

A database which runs on an office microcomputer is being developed for the diagnosis of genetically determined neurological disorders. At present about 1100 conditions with their clinical features and 3000 references are stored in the database. We discuss a family with 3 sibs affected by a unique neurological disorder and show how the database is used. The 3 sibs, 4, 5 and 10 years old, show the same clinical course characterized by congenital cataracts, microcephaly, hypotonia, mental retardation, pyramidal signs and choreoathetoid movements starting in early childhood. The parents are first cousins of Bangladeshi origin. This condition does not appear in published report and is not listed in the database. It can therefore be concluded that the sibs have a unique autosomal recessive disorder.

Athetosis↗
PubMed1996

Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data.

While a two-dimensional electrophoresis (2-DE) database is a relatively old concept, in recent years it generated renewed interest within the 2-DE community due to two main factors: (i) The high reproducibility of the current 2-DE method allows 2-DE images to be exchanged and compared between laboratories. (ii) The recent development of faster and more powerful techniques for protein identification such as microsequencing, matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) and amino acid composition makes the production of reference protein maps and 2-DE databases cost- and time-effective. Additionally, the Internet network's current increase in popularity, combined with the rapid growth of Internet-connected laboratories, provides a straightforward means of publishing and sharing 2-DE data. While a small number of laboratories have already successfully published their data over the net, the increasing number of 2-DE database servers that are currently being set up will sooner or later require some kind of standardization. Unfortunately, standardization can be a long and cumbersome process inevitably leading to undesirable compromises. A federated database offers a simple and efficient way to publish and share 2-DE data without the need for standardization. Taking advantage of Internet protocols such as World Wide Web, they allow each laboratory to maintain their own database and to interconnect it with other similar databases through the use of active cross-references. This paper first presents guidelines for building a federated 2-DE database that may easily be followed by most laboratories. It then briefly reviews the state-of-the-art in networked 2-DE databases, and finally describes the SWISS-2DPAGE database which fully implements the concept of a federated 2-DE database.

Computer Communication Networks↗
PubMed1991

TQuery: a context-sensitive temporal query language.

Users of electronic medical databases request pertinent information by recasting their clinical questions into a formal database query language. Because the query language is the user's only access to the data, the query language must be powerful enough to enable users to express their data requirements. However, a competing need is for the query language to be restrictive enough so that queries can have unambiguous semantics and the query processor can generate correct answers. We describe a query language, called TQuery , that was designed specifically to formulate database queries that are dependent on temporal and contextual relationships. TQuery specifications express contextual constraints without the need to explicitly reference calendar dates. TQuery is the database query language used to retrieve patient data from an object-oriented electronic patient medical-record system called the temporal network (TNET). TNET and TQuery were developed to support the real-time temporal reasoning and representation needs of a LISP workstation-based medical expert system.

Databases, Factual↗
PubMed1995

Comparison of eight microcomputer dietary analysis programs with the USDA Nutrient Data Base for Standard Reference.

OBJECTIVE: To compare the general operating features and nutrient databases of eight microcomputer dietary analysis programs. DESIGN: A 3-day food record with 73 food items was entered into each program by the authors. The general operating features of the program were summarized and evaluated. The nutrient database was evaluated by comparing the nutrient analysis output with the 1993 US Department of Agriculture (USDA) Nutrient Data Base for Standard Reference (NDB), full version, release 10, for microcomputers. RESULTS: The programs varied in cost, number of foods and nutrients in the database, use of non-USDA data, and inputting of data for missing values. We also found differences in the quality of user manuals and help screens, ease of food entry and averaging of 3-day nutrient intake, speed of analyzing and printing results, quality and number of print/export options, and overall ease of learning and using the program. All but one of the programs were within 15% of the USDA NDB for energy, protein, total fat, and total carbohydrates. However, there was some difference in the number of other nutrients and food components varying more than 15% from the USDA NDB. These differences occurred because of variations in the number of food items included in each programs' database and the number of missing nutrient values in the database. APPLICATIONS: Our results demonstrate the importance of carefully choosing a microcomputer dietary analysis program that is suitable to the user's specific and predetermined needs.

Databases, Factual↗
PubMed1995

Reference materials and reference measurement systems in laboratory medicine. Harmonization of nomenclature and definitions in reference measurement systems.

Reliability of clinical laboratory results is obtained through quality assurance in both their production and transmission. The former involves a reference measurement system of reference materials and reference measurement procedures with metrological and statistical verification of results. The latter requires that sender and receiver have access to a common terminology. Thus, two data banks are required. A plurilingual systematic vocabulary related to the reference measurement system, giving concepts with terms and definitions concerning measurement standards, reference measurement procedures, internal quality control, external quality assessment, probability and statistics-mainly based on existing authoritative publications. The material should be processed by standard scientific terminological procedure and offered to pertinent organizations and specialists for comment before finalization and authorization. A multilingual collection of systematic names for properties examined by the branches of Laboratory Medicine, such as clinical chemistry, clinical immunology, clinical microbiology, clinical pharmacology, haematology and blood banking, and histochemistry and cytology. The database should function as a reference to consultation and as a link in the transmission of data between local laboratory "dialects". This should be based on the ongoing comprehensive IUPAC/IFCC project for forming names in collaboration with relevant scientific organisations and area specialists. The relational data base including "run-time" software would be accessed by e-mail (gopher or other storage medium).

Chemistry, Clinical↗
PubMed1988

A two-dimensional electrophoresis study of phosphorylation and dephosphorylation of chromaffin cell proteins in response to a secretory stimulus.

Phosphorylated proteins of bovine chromaffin cells, radioactively labeled with [32P]orthophosphate, have been analyzed by two-dimensional polyacrylamide gel electrophoresis and autoradiography. Complex two-dimensional electrophoretograms were studied with the aid of computer-assisted image analysis (CAIA). A database map of 32P-labeled proteins was constructed; approximately 500 polypeptides have been detected, numbered, and characterized according to the intensity of labeling, molecular weight, and isoelectric point. The database was constructed from cells kept in resting conditions or stimulated with 59 mM K+ in 2.5 mM Ca2+ or in 0 Ca2+ solution. These manipulations caused statistically significant changes in the degree of phosphorylation of 20 proteins; they were classified as Ca2+-dependent substrates for the phosphorylation or dephosphorylation processes. These changes were also shown in cells stimulated in the presence of the Ca2+ channel activator Bay K 8644. New proteins that show as much as a fivefold increase in their phosphorylation state during cell stimulation have been located with this methodology, as well as many others that had not previously been detected with conventional methods. These experiments provide the first CAIA database of chromaffin cell phosphoproteins; the map constructed with these data will allow the location of specific phosphoproteins and serve as a reference for future ongoing studies. The database will continue to grow to identify more proteins and to facilitate the comparison of complex patterns obtained in different laboratories for normal and transformed pheochromocytoma PC12 cells.

Adrenal Medulla↗
PubMed1997

Liaison psychiatry in an HIV/AIDS unit.

OBJECTIVE: To provide an overview of the work of a liaison psychiatry service to an HIV/AIDS inpatient unit, and particularly to examine the identification of mood and related disorders by referring doctors. METHOD: The MICRO-CARES prospective clinical database system was used to obtain data on all patients referred to the HIV/AIDS consultation-liaison psychiatry service in an infectious diseases hospital in Melbourne. RESULTS: Three hundred and ninety-two inpatient referrals were made in the 2 years from 1993-1995: a referral rate of 16.7%. The most frequent reasons for referral were evaluation of coping problems (42%), assessment of possible depression (31%), and assessment of psychotropic medication (24.5%). The most common psychiatric diagnoses were mood disorders (36.5%), psychoactive substance use disorders (22.7%) and organic mental disorders (18.1%). Overall concordance of recognition of depression by the referring doctor and diagnosis of depression by the consultant psychiatrist was 79%; 20% false positive rate, 23% false negative rate. CONCLUSIONS: Psychiatric comorbidity is common in patients with HIV/AIDS. Reasons for referral vary from those seen in other inpatient settings. Previously noted problems such as the misdiagnosis of psychiatric disorder and the mislabelling of the syndrome recognised by psychiatrists as depression were noted here.

Acquired Immunodeficiency Syndrome↗
PubMed1996

Consultation-liaison psychiatry in an obstetric service.

OBJECTIVE: The aim of this paper is to provide an overview of the work of a consultation-liaison (C-L) psychiatry service to an obstetric inpatient unit in a university affiliated teaching hospital, with the aid of a comprehensive clinical database. METHOD: The MICRO-CARES clinical database system was used for prospective recording of data on all obstetric inpatients referred to the C-L psychiatry service and the hospital clinical database was used to compare referred inpatients with all obstetric inpatients. RESULTS: Ninety patients were referred in 3 years, a referral rate of 1.2% of obstetric admissions. There was no bias in referral on age, but there were significantly more unmarried patients in the referred group (p < 0.001). Referred patients had a significantly prolonged length of stay: a mean of 9 days for referred patients, with 6 days for all obstetric patients (p < 0.001). The most frequent reasons for referral were: coping problems, depression, anxiety/fear and past history of major psychiatric illness. The most common DMS-III-R psychiatric diagnoses were: Personality Disorders (19%), Mood Disorders (17%), Schizophrenic Disorders (15%) and Adjustment Disorders (13%). At least one confirmed diagnosis was made in 77% of patients, but 42% of diagnoses remained differential. There were significantly more patients with diseases of the nervous system, endocrine and circulatory disorders in the referred group (p < 0.001). Recommendations of psychosocial interventions predominated over psychopharmacological interventions, and concordance with these was 97% and 98%, respectively. Issues in the relationship of obstetrics and psychiatric C-L services are discussed and future directions indicated. CONCLUSIONS: The referral rate was low compared with other specialty units. This is probably due to factors inherent in obstetric practice. A wide spectrum of psychiatric disorders was referred, including a higher than expected number of women with postpartum psychotic disorders, the majority of whom were managed successfully in the obstetric ward. There is a need for increased liaison with obstetric and community services and for collaborative research, with a particular emphasis on the prevention of psychiatric morbidity associated with pregnancy.

Adaptation, Psychological↗
PubMed1992

Comparison of six microcomputer dietary analysis systems with the USDA Nutrient Data Base for Standard Reference.

We compared the general operating features and nutrient databases of six microcomputer dietary analysis systems. A 3-day food record with 73 food items was entered into each program; nutrient averages were compared with the US Department of Agriculture Nutrient Data Base for Standard Reference (USDA NDB), full version, release 9, for microcomputers. The six programs were found to vary widely in cost, number of foods and nutrients in the database, use of non-USDA data and imputation of data for missing values, number of print/export options, time to analyze the 3-day food record, and overall ease of use. Although all of the microcomputer dietary analysis systems were within 7% of the USDA NDB for energy, protein, total fat, and total carbohydrates, the proportion of other nutrients varying more than 15% from the USDA NDB varied considerably between programs. Variance among programs for 3-day food record nutrient values occurred because of differences in the number of food items included in the database (leading to varying degrees of substitution), the recency of the nutrient data (whether or not the most recent USDA releases had been incorporated), and the number of missing values (the degree to which non-USDA sources or estimated calculations were used to fill in the blanks from the USDA standard). Our results demonstrate that it is important for each dietitian to carefully choose a microcomputer dietary analysis system that is suitable to specific and predetermined needs.

Databases, Factual↗
PubMedDate not supplied

Challenges of high throughput screening against cell surface receptors.

Excessive or inappropriate activation of cell surface receptors can mediate the development of disease. Receptors, therefore, are a focus for drug discovery activities. Empirical screening is important in the search for novel compounds acting as receptors. Technical developments and the application of molecular biology have facilitated access to receptors of interest and have provided efficient screening methods capable of very high throughput. Reliability in high throughput screening requires the use of appropriate methodology, good screen design and effective validation and quality control processes. Validation should aim to establish that the basic experimental design is sound. In developing software to handle high throughput screening data, a fundamental requirement is to provide performance monitoring and error trapping facilities. Additional requirements are automatic data capture from instruments, on-line data reduction and analysis and transfer of results to central databases. As data volumes increase through effective high throughput screening, conventional interrogation methods become less appropriate and are being augmented by newer computing techniques referred to as knowledge mapping or database mining. Targeting cell surface receptors has been very successful as an approach to drug discovery. If the challenges of high throughput empirical screening are addressed effectively, cell surface receptors will provide new opportunities for improved therapy in the coming years.

Animals↗
PubMed1996

Does the normal contralateral wrist provide the best reference for X-ray film measurements of the pathologic wrist?

This study compares in normal subjects the variability of wrist x-ray film measurements between the right and left sides with the variability of the distribution of those measurements within the population. Additional purposes were to evaluate possible differences of these measurements according to sex, age, side, and hand dominance. The variability when comparing both sides was found to be statistically less for the carpal height, radiolunate, scapholunate, and capitolunate angles than within the whole group of subjects, and for those measurements, there was a high correlation (r > .88) between the right and left sides. In addition, the carpal height and the carporadial ratios were lower and the capitolunate angle was higher in women than in men. There was also a significant decrease of the scapholunate angle in older individuals. The clinical implication of these findings is that in unilateral wrist diseases, the normal wrist should be used to provide the reference values of the carpal height and of the carpal angles on profile x-ray films. However, for the radial inclination and palmar tilt of the distal radius and for the ulnar variance, the normal side does not provide a better reference than normal values obtained from databases.

Adult↗
PubMed1991

Structure prediction and modelling.

Protein structure prediction from sequence remains a major goal in molecular biology. The methods described in this review concentrate on deriving structural information through the detection of similarities between a test sequence and a database of known structures. Such methods are often referred to as knowledge-based strategies reflecting the use of a structural database in the analyses. The past year has seen considerable advances in both the development of automated procedures and their application to protein sequences of outstanding biological interest.

Algorithms↗