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PubMedDate not supplied

Design of a diagnostic encyclopaedia using AIDA.

Diagnostic Encyclopaedia Workstation (DEW) is the name of a digital encyclopaedia constructed to contain reference knowledge with respect to the pathology of the ovary. Comparing DEW with the common sources of reference knowledge (i.e. books) leads to the following advantages of DEW: it contains more verbal knowledge, pictures and case histories, and it offers information adjusted to the needs of the user. Based on an analysis of the structure of this reference knowledge we have chosen AIDA to develop a relational database and we use a video-disc player to contain the pictorial part of the database. The system consists of a database input version and a read-only run version. The design of the database input version is discussed. Reference knowledge for ovary pathology requires 1-3 Mbytes of memory. At present 15% of this amount is available. The design of the run version is based on an analysis of which information must necessarily be specified to the system by the user to access a desired item of information. Finally, the use of AIDA in constructing DEW is evaluated.

Computer Systems↗
PubMed1989

ERIC: a resource for researchers in nursing education.

This chapter provides information on the ERIC system of bibliographic information covering the field of education. Information on topics related to nursing and specifically to research in nursing education is presented. The number of references in these areas and in the ERIC database and the content of these references is described.

Bibliographies as Topic↗
PubMed2026

Long-read Sequences Mapped to a Complete Reference Genome Uncover Uncaptured Structural Variants across the Beta-globin Cluster in Africans with Sickle Cell Disease.

African genomes are marked by extensive complexity in the number and distribution of variants, yet remain under-represented in genetic databases and the human reference genome. This gap in representation limits the broad application of genomic medicine. Sickle cell disease (SCD) - one of the most common monogenic diseases - has its highest prevalence in Africa, and variation in disease severity has consistently been linked to the beta-globin locus, including levels of fetal hemoglobin (HbF). Modulation of HbF is central to current SCD gene therapies; however, the inherent complexity and variation at the locus in African genomes presents a challenge to translating these advances to Africa. Here, we align long-read single molecule sequences (LRS) targeted to the beta-globin region to the hg38 and T2T-CHM13v2 genome references in 40 individuals with SCD, predominantly recruited from three African countries. We demonstrate that the expanded T2T-CHM13v2 reference sequence at this locus reduces Structural Variant (SV) calls by 70% and uncovers uncaptured single nucleotide variants (SNVs). Across the cluster we report 343 SVs and 196 SNVs that have not been previously reported, including in LRS data from the All of Us project. By including African populations from ethnolinguistic groups that have not been previously surveyed we improve variant resolution and bolster evidence for observed variation. Finally, we identify a common ∼4kb insertion locus overlapping the HBB promoter among individuals with high HbF. These results demonstrate the utility of combining a comprehensive reference genome with LRS in African populations to uncover genomic variation at disease-associated loci.

SNV↗
PubMed2025

Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.

Metagenomics has become a powerful tool for studying microbial communities, allowing researchers to investigate microbial diversity within complex environmental samples. Recent advances in sequencing technology have enabled the recovery of near-complete microbial genomes directly from metagenomic samples, also known as metagenome-assembled genomes (MAGs). However, accurately characterizing these genomes remains a significant challenge due to the presence of sequencing errors, incomplete assembly, and contamination. Here we present MetaSBT, a new tool for organizing, indexing, and characterizing microbial reference genomes and MAGs. It is able to identify clusters of genomes at all seven taxonomic levels, from the kingdom all the way down to the species level, using the Sequence Bloom Tree (SBT) data structure that relies on Bloom Filters (BFs) to index massive amounts of genomes based on their k-mers composition. We have built an initial set of databases composed of over 190 thousand viral genomes from NCBI GenBank and public sources grouped into sequence consistent clusters at different taxonomic levels, making it the first software solution for the classification of viruses at different ranks, including still unknown ones. This results in the definition of over 40 thousand species clusters where ~80% do not match with any known viral species in reference databases to date. Furthermore, we show how our databases can be used as a new basis for existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. Finally, the framework is released open-source and, along with its public databases, is fully integrated into the Galaxy Platform enabling broad accessibility.

metagenome-assembled genomes↗
PubMed1992

'References'.

Explore the source record for details and available documents.

Databases, Bibliographic↗
PubMed1991

Classification and identification of bacteria by Fourier-transform infrared spectroscopy.

This study describes a computer-based technique for classifying and identifying bacterial samples using Fourier-transform infrared spectroscopy (FT-IR) patterns. Classification schemes were tested for selected series of bacterial strains and species from a variety of different genera. Dissimilarities between bacterial IR spectra were calculated using modified correlation coefficients. Dissimilarity matrices were used for cluster analysis, which yielded dendrograms broadly equated with conventional taxonomic classification schemes. Analyses were performed with selected strains of the taxa Staphylococcus, Streptococcus, Clostridium, Legionella and Escherichia coli in particular, and with a database containing 139 bacterial reference spectra. The latter covered a wide range of Gram-negative and Gram-positive bacteria. Unknown specimens could be identified when included in an established cluster analysis. Thirty-six clinical isolates of Staphylococcus aureus and 24 of Streptococcus faecalis were tested and all were assigned to the correct species cluster. It is concluded that: (1) FT-IR patterns can be used to type bacteria; (2) FT-IR provides data which can be treated such that classifications are similar and/or complementary to conventional classification schemes; and (3) FT-IR can be used as an easy and safe method for the rapid identification of clinical isolates.

Antigens, Bacterial↗
PubMed2026

National genomic projects in Asia and Africa: a review.

National genome projects (NGPs) are increasingly shaping precision medicine by improving representation of population-specific genetic diversity. This review compiles findings from NGPs across Asia and Africa, regions that remain underrepresented in global genomic databases despite their extensive demographic and genetic diversity. A total of 53 studies from 24 countries were identified to understand (1) the genomic approach utilized, (2) novel findings that have emerged, and (3) strategies for improving research in these regions. The NGPs implement population-based variome databases (20 NGPs), linear reference genome assemblies (8 NGPs), and graph-based pangenome assemblies (1 NGP). Novel variants ranged between 0.28% (China) and 19.6% (Iran), whereas rare variants accounted for up to 88.9% of the detected variants in the Chinese population. Each NGP documents its country's evolutionary and migration history, which impacts disease frequency and pharmacogenomic variants. Clinically, NGPs revealed strong population stratification in disease-associated and pharmacogenomic variants. For example, the GJB2 rs72474224 hearing-loss variant ranged from 13% in Vietnam and 12% in Hong Kong to 0.0894% in Turkey, while the VKORC1 rs9923231 pharmacogenomic variant reached 89.2% in Taiwan but was 20%-25% in European-related Russian subpopulations. These findings demonstrate that clinically relevant allele frequencies, pathogenicity assessments, and drug-response markers differ substantially across ancestries. This review highlights ongoing efforts and strategies to enhance the representativeness of genomic data through NGPs in Asia and Africa. We also suggest future directions for national projects, including integrating family-based studies, multi-omic data, and standardized pipelines to accelerate discovery and support the equitable implementation of precision medicine.

Humans↗
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↗
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↗
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↗
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↗
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↗
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↗
PubMed2026

Prevalence of the Predisposing Gene MBD4 for Uveal Melanoma.

IMPORTANCE: MBD4 monoallelic germline pathogenic and likely pathogenic variants have recently been identified as predisposing to uveal melanoma, a rare primary intraocular tumor, with an estimated 9.15-fold increased risk of developing the disease for pathogenic variant carriers. OBJECTIVE: To assess the risk of developing uveal melanoma for carriers of the MBD4 monoallelic germline pathogenic variant. DESIGN, SETTING, AND PARTICIPANTS: In a case series involving 896 individuals, including 319 who were previously evaluated, germline target-sequencing of MBD4 was offered to every new patient with uveal melanoma at Curie Institute from February 2021 to September 2025. Non-Finnish European participants from the Genome Aggregation Database were used as a reference population. EXPOSURE: Diagnosis of uveal melanoma genetic predisposition. MAIN OUTCOMES AND MEASURES: Prevalence of MBD4 variants. RESULTS: A total of 23 of 896 patients were identified as carrying an MBD4 germline pathogenic or likely pathogenic variant, corresponding to a relative risk of 31.44 (95% CI, 18.18-53.00) of developing uveal melanoma compared with the general population (2-sided Fisher exact test, P&#x2009;<&#x2009;.001). CONCLUSIONS AND RELEVANCE: These findings confirm that MBD4 is an important predisposing gene to uveal melanoma in the French population. This reinforces a strategy of broad patient screening given the therapeutic implications and the consequences of genetic counseling.

Humans↗
PubMed1990

To what extent do congestive heart failure patients in sinus rhythm benefit from digoxin therapy? A systematic overview and meta-analysis.

PURPOSE: To reappraise the effectiveness of digoxin for the treatment of congestive heart failure (CHF) in patients with sinus rhythm in light of data from recently published randomized controlled trials and to quantitatively assess its usefulness. STUDY IDENTIFICATION: Computerized searches of the MEDLINE database were performed, and the reference list of each retrieved article was reviewed. STUDY SELECTION: Review of more than 360 citations and the reference lists of 19 review articles and 61 potentially relevant articles revealed seven double-blind randomized controlled trials that were included in this overview. DATA EXTRACTION: Study quality was assessed and descriptive information concerning the study populations, the specific interventions, and clinically relevant outcome measurements was extracted. RESULTS OF DATA SYNTHESIS: The common odds ratio for CHF deterioration while receiving digoxin versus placebo was 0.28, with a 95% confidence interval of 0.16 to 0.49. Predictors of digoxin benefit included presence of a third heart sound and the severity and duration of CHF. CONCLUSION: Data from seven trials of high methodologic quality suggest that, on average, one out of nine patients with CHF and sinus rhythm derive a clinically important benefit from digoxin (with a 95% confidence interval of 1/33 to 1/5).

Digoxin↗
PubMed1989

Control of expression of the human glutathione S-transferase pi gene differs from its rat orthologue.

We have examined regulation of the glutathione S-transferase pi gene by transient expression assay, and find that a fragment from 8 to 99 bp upstream of the cap site promotes transcription, but there is no evidence for any enhancer activity in a further 6 kb of flanking sequence. Analysis of this sequence by reference to a primate sequence database and Southern blotting revealed that as much as 5 kb of this flanking DNA were composed of repetitive insertion elements including an Alu and a LINE 1 repeat. The promoter fragment has been sequenced (Cowell et al (1988) Biochem. J. 255, 79-83) and contains a consensus AP1 binding site; in some cases, these have been associated with transcriptional induction by phorbol esters and ras oncogenes. We measured the steady state levels of glutathione S-transferase pi mRNA in human cell lines which were known to express ras oncogenes and compared them to human cell lines which have not been identified with ras activation. There was no correlation between expression of activated ras and expression of glutathione S-transferase pi mRNA. Treatment of HeLa cells, HepG2 cells and a small cell lung carcinoma line, GLC 8, with the phorbol ester 12-O-tetradecanoylphorbol 13-acetate failed to alter the steady state levels of endogenous glutathione S-transferase pi mRNA. The differences between these results and those of similar studies on rat glutathione S-transferase subunit 7, a structural orthologue of glutathione S-transferase pi, are discussed.

Animals↗