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PubMedDate not supplied

Ultrastructural morphometric data of human spermatozoa.

A morphometric study of the volumetric parameters of human spermatozoa has been carried out, volume densities being obtained by point counting and converted to absolute volumes by employing the point-sampled intercept method. Data for the Spermatozoa from the semen of 15 recently fertile men are presented. The significance of the results is discussed in relation to results obtained by other methods and in relation to the building of a diagnostic reference database.

Humans↗
PubMed1990

PaperChase: a user-friendly program for searching the biomedical literature.

PaperChase is a computer program which provides an efficient interface to the National Library of Medicine's MEDLINE database of references to the biomedical literature. The database includes references (citations) and abstracts compiled from Index Medicus, the International Nursing Index and the Index to Dental Literature. PaperChase may be accessed using any computer terminal or personal computer with modem. No special knowledge of computers or biomedical terms is necessary. Simple menus enable the novice to search the biomedical literature without training. A command language speeds searching for the experienced user. PaperChase does not require the user to know the database's indexing terminology, called Medical Subject Headings. Everyday language may be used and PaperChase will translate, or "map", the user's search term into the required Medical Subject Heading. PaperChase monitors a search in progress and suggests additional Medical Subject Headings which can be used to broaden or narrow a search. The searcher can order a full-text photocopy of any reference found in PaperChase. Support documentation and a subscriber newsletter are provided at no charge. Trained search specialists are available to offer assistance and to answer questions.

MEDLARS↗
PubMed2026

MetaFX: feature extraction from whole-genome metagenomic sequencing data.

MOTIVATION: Microbial communities consist of thousands of microorganisms and viruses and have a tight connection with an environment, such as gut microbiota modulation of host body metabolism. However, the direct relationship between the presence of certain microorganism and the host state often remains unknown. Toolkits using reference-based approaches are limited to microbes present in databases. Reference-free methods often require enormous resources for metagenomic assembly or results in many poorly interpretable features based on k-mers. RESULTS: Here we present MetaFX-an open-source library for feature extraction from whole-genome metagenomic sequencing data and classification of groups of samples. Using a large volume of metagenomic samples deposited in databases, MetaFX compares samples grouped by metadata criteria (e.g. disease, treatment, etc.) and constructs genomic features distinct for certain types of communities. Features constructed based on statistical k-mer analysis and de Bruijn graphs partition. Those features are used in machine learning models for classification of novel samples. Extracted features can be visualized on de Bruijn graphs and annotated for providing biological insights. We demonstrate the utility of MetaFX by building classification models for 590 human gut samples with inflammatory bowel disease. Our results outperform the previous research disease prediction accuracy up to 17%, and improves classification results compared to taxonomic analysis by 9±10% on average. AVAILABILITY AND IMPLEMENTATION: MetaFX is a feature extraction toolkit applicable for metagenomic datasets analysis and samples classification. The source code, test data, and relevant information for MetaFX are freely accessible at https://github.com/ctlab/metafx under the MIT License. Alternatively, MetaFX can be obtained via http://doi.org/10.5281/zenodo.16949369.

Metagenomics↗
PubMed1992

Genome-related datasets within the E. coli Genetic Stock Center database.

The contents of the E. coli Genetic Stock Center database and the availability in electronic form of the subset of information most relevant to sequence databases are described. The database uses the long-standing Stock Center records (developed and curated by Dr B.J.Bachmann) in describing genotypes of mutant derivatives of E.coli K-12 in terms of alleles, structural mutations, mating type, and plasmids as well as the derivation, names and originators of the strain, and references. The database includes descriptions of mutations, mutation properties, genes, gene properties, and gene products, with EC number identifiers for enzymes. Sequence information is not included, but entries refer to sequence database accession numbers for sequenced regions. A gene is described as a subtype of a more general category of chromosome interval called Site. Since sites are used to describe any chromosomal interval, mapping information is associated with sites. Alleles are described as mutations of those sites and they are not primary map objects, but inherit map position information from the corresponding site description. The database design is intended to preserve richness of detail where it is known and uncertainty of measurements or information as it occurs in order to represent the stock center records as accurately as possible.

Bacterial Proteins↗
PubMed1991

Comparison and evaluation of nine bibliographic databases concerning adverse drug reactions.

Few evaluations and statistical comparisons of bibliographic databases have been published. As a drug information center, we were particularly interested in databases providing references on adverse drug reactions (ADRs). Ten drugs were randomly chosen from the 2000 files at our center. Nine databases were selected according to the high frequency of references concerning ADRs: eight online systems (MEDLINE, BIOSIS, TOXLINE, Iowa Drug Information System, PASCAL, EMBASE, PHARMLINE, and International Pharmaceutical Abstracts [IPA]), and one Compact Disk Read Only Memory (CD-ROM) system (Core MEDLINE). The total number of references, the number of references from 1987 to 1989, and the number of relevant references from 1987 to 1989 were analyzed using the Friedman two-way ANOVA by ranks. The overlap between databases for only one drug, carboplatin, and the quality:cost ratio were also studied. Considering the total number of references, TOXLINE and EMBASE were significantly superior to IPA, PHARMLINE, PASCAL, and Core MEDLINE. For the period 1987-1989, EMBASE was significantly superior to PASCAL, IPA, PHARMLINE, and Core MEDLINE with regard to total number of references, and significantly superior to PASCAL, Core MEDLINE, and IPA with regard to relevance. MEDLINE, TOXLINE, and EMBASE had the best quality:cost ratio. EMBASE had the slightest overlap of references, with 53 percent of the unique references on carboplatin. This comparative evaluation showed that the ability of bibliographic databases to provide information on ADRs is dependent on both the size and the quality of each database.

Databases, Bibliographic↗
PubMed1991

Algorithm for point-to-point correlation of geometrically nearly similar microscopic objects.

An algorithm is presented that compares two quasi similar images by correlating selected points on them--assuming their coordinates are available. The procedure involves translational, magnificational and rotational operations to find corresponding point pairs on the pictures. The algorithm automatically compensates for slight dissimilarities between images and constructs a reference point database for correlation during the evaluation process. Establishment of the reference point networks on the images prior to the examination is avoided.

Algorithms↗
PubMed2026

theBIGbam: compression and interactive exploration of large-scale sequencing alignments with circular mapping support.

SUMMARY: theBIGbam (github.com/bhagavadgitadu22/theBIGbam) is a genome browser and alignment viewer designed for massive metagenomic and metatranscriptomic datasets. The tool takes BAM files containing read alignments, together with genome assemblies in FASTA format or annotated genome sequences in GenBank format. Alternatively, it can start from raw FASTQ reads and generate alignments using a modified mapper that supports circular genomes, enabling seamless read mapping across genome ends. theBIGbam can compress hundreds of gigabytes of input files 10- to 100-fold into dedicated databases while retaining key per-position information, including coverage depth and recurrent mismatches, insertions, and deletions between reads and the reference. These databases can be served to a local web browser, enabling interactive exploration of any contig in any sample using DNAFeaturesViewer for genome maps and Bokeh for mapping-derived features. Contig-sample pairs available for visualization can be filtered using a range of summary metrics calculated per contig, per sample, and per contig-sample pair to guide users toward the most relevant signals. Through its interactive visualization, theBIGbam facilitates the exploration of complex datasets, while its integrated database-combining assembly features, annotated features, and mapping-derived features-provides the information needed to investigate biological hypotheses systematically. Designed to complement existing browsing tools like IGV and Anvi'o, theBIGbam is particularly suited for examining misassemblies, subpopulations, microdiversity, and contig topology in large-scale datasets. AVAILABILITY AND IMPLEMENTATION: theBIGbam is an open-source Rust/Python package that can be installed from Bioconda or PyPI. The source code and documentation are available on GitHub (github.com/bhagavadgitadu22/theBIGbam).

Software↗
PubMed2025

Mapping the oral microbiome opens links to periodontitis.

Many microbiome analysis techniques can only detect the microbes present in the reference genome database used. In this issue of Cell Host & Microbe, Cha et al. establish an improved genome database of the human oral microbiome, which they use to discover a connection between periodontitis and an enigmatic bacterial phylum.

Humans↗
PubMed1991

Medical reference filing systems.

Low priced shareware packages may be adequate for those whose main need is to index a collection of articles read in journals. Those who search the literature electronically will need a package able to import mass data. Pro-Cite is set up for bibliographic functions only, but Reference File and Notebook II can be used to index any kind of collection, with Reference File having the advantage of being memory-resident. Other reference filing databases being considered for purchase could be measured against those reviewed here.

Abstracting and Indexing↗
PubMed1988

Hazardous Substance Center: a poison center's workers right to know program.

Workers Right To Know (WRTK) legislation has been enacted in several states. It is landmark advocacy legislation for employees and communities who may be exposed to hazardous chemicals, but it is also a complex and costly problem for business, industry, and nonprofit organizations. The Hazardous Substance Center (HSC), a division of the Pittsburgh Poison Center, was created to develop and implement programs to enable the business community to comply with the requirements of WRTK legislation. Specifically, the HSC provides the client with a 24-hour toxicology resource which objectively assists employees in the interpretation of the health-related effects information on material safety data sheets (MSDS) and assists them and medical professionals in the management of acute and chronic exposures. A variety of online databases and reference materials are utilized to respond to these inquiries. Each case is documented using the AAPCC Report Form. Data is analyzed to identify trends which can be used to assist the client in complying with the educational component. The HSC also provides a labeling program to the client to identify and classify hazardous substances. The service is provided for an annual contractual fee and creates an additional source of poison center revenue.

Humans↗
PubMed1989

Review of Papyrus bibliographic database software.

Papyrus is an inexpensive bibliographic database which provides some features not found in other similar packages. Its flexibility in handling references of many types and formats, its capacity for integration with manuscripts prepared with word processors, its capacity for importing references from national databases and its ability to perform microcosmic literature searches are attractive features. Because Papyrus has tackled a complex task, mastery of the intricacies of the program may present a substantial challenge to novice computer users. Although the manipulation of an existing customized bibliographic database would seem to be attractive for any researcher or author who prepares manuscripts for publication, the optimal use of the program also requires an extensive commitment of time and labor for the initial entry of all pertinent references into the database. While this could be accomplished gradually in conjunction with the preparation of individual manuscripts, the creation of a complete file of references could require hundreds of hours of labor. Individual authors, as well as larger research groups, should be prepared for this type of commitment before acquiring the Papyrus system.

Bibliographies as Topic↗
PubMedDate not supplied

Wheat gliadin: digital imaging and database construction using a 4-band reference system of agarose isoelectric focusing patterns.

An isoelectric focusing method using thin-layer agarose gel has been developed for wheat gliadin. Using flat-bed units with a third electrode, up to 72 samples per gel may be analyzed. Advantages over traditional acid polyacrylamide gel electrophoresis methodology include: faster run times, nontoxic media, and greater sample capacity. The method is suitable for fingerprinting or purity testing of wheat varieties. Using digital images captured by a flat-bed scanner, a 4-band reference system using isoelectric points was devised. Software enables separated bands to be assigned pI values based upon reference tracks. Precision of assigned isoelectric points is shown to be on the order of 0.02 pH units. Captured images may be stored in a computer database and compared to unknown patterns to enable an identification. Parameters for a match with a stored pattern may be adjusted for pI interval required for a match, and number of best matches.

Databases, Factual↗
PubMed2026

Performance of MALDI-TOF MS for human Capnocytophaga identification verified by whole-genome sequencing.

OBJECTIVE: This study aims to evaluate the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for species identification of human Capnocytophaga and to confirm results by whole-genome sequencing. METHODS: Six reference strains, representing human Capnocytophaga species and one taxon, and a total of 126 clinical strains, selected based on their biochemical profiles from a large collection of preliminarily identified Capnocytophaga isolates, were analyzed. RESULTS: Of those, 125 strains (94%) were identified at least at the genus level (log score variation of 1.7-1.999), while 52 strains (39%) were identified at the species level with a cut-off score of &#x2265;2.0. Eight strains (6%) remained unidentified with a log score of <1.69. C. leadbetteri and Capnocytophaga genospecies AHN8471 strains were accurately identified at the genus level. Minor identification errors were observed in three cases: C. leadbetteri (n=1), C. ochracea (n=2), and Capnocytophaga genospecies AHN8471 (n=38). MALDI-TOF MS was unable to distinguish between C. sputigena and Capnocytophaga genospecies AHN8471 at the species level but clustered them together in the Main Spectra Profile (MSP) dendrogram. CONCLUSIONS: MALDI-TOF MS shows promise as a diagnostic tool for identifying human Capnocytophaga species when correct taxonomy and sufficient reference strains are available in the database. Based on the close phenotypic, ribosomal, and genotypic structures, we propose to establish the term "C. sputigena group" encompassing C. sputigena, Capnocytophaga genospecies AHN8471, and other related Capnocytophaga variants. Nevertheless, updating and expanding the MALDI-TOF MS reference database is essential to improve identification accuracy.

Capnocytophaga spp.↗
PubMed1985

Electronic databases.

Electronic databases corresponding to most of the world's currently published literature and many other types of information are publicly available through online systems. Scientific databases that give references for publications are numerous and widely used; scientific numeric databases that are open to the public are far fewer and less used. Online retrieval systems are becoming easier to use as a result of the introduction of artificial intelligence techniques and user-friendly front ends and gateways. Issues related to electronic databases include public-private sector competition, transborder data flow, copyright, downloading, and the changing roles in database generation and processing.

Bibliographies as Topic↗
PubMed2026

GRNContext: an interactive web platform for contextualized gene regulatory networks visualization across human cancers.

SUMMARY: While current Gene Regulatory Network (GRN) databases provide comprehensive reference maps of potential interactions between transcription factors and target genes, they do not specify which regulatory interactions are active within specific biological contexts. This limitation is particularly critical in cancer, where transcriptional programs are inherently tissue-specific. To address this gap, we developed GRNContext, an interactive web platform designed for the visualization, exploration, and comparative analysis of gene regulatory networks contextualized across 33 cancer types from The Cancer Genome Atlas (TCGA). Our approach uses the TFLink human reference GRN as a starting point and integrates TCGA transcriptomic profiles to infer cancer-specific regulatory activity. Regulatory relevance was assessed using complementary machine learning and statistical methods, which were unified into a consensus score to prioritize and filter the most relevant candidate regulators for each target gene. By providing both curated context-specific GRNs and a user-friendly platform, GRNContext constitutes a comprehensive and accessible resource that supports mechanistic investigations, hypothesis generation, and translational research focused on transcriptional regulation in cancer. AVAILABILITY AND IMPLEMENTATION: GRNContext is supported by all major browsers and freely available on the web at https://apps.cienciavida.org/grncontext. It is implemented as a client-server web application featuring a FastAPI backend and a React frontend utilizing Cytoscape.js for interactive network visualization, all containerized via Docker for cross-platform compatibility.

Humans↗
PubMed2026

Management of Soft Tissue and Visceral Leiomyosarcomas.

IMPORTANCE: Leiomyosarcoma is a rare and heterogeneous malignant mesenchymal neoplasm associated with substantial morbidity and mortality. Given recent advances in biologic understanding and the complexity of leiomyosarcoma, a consensus-driven approach is needed to harmonize management and address remaining clinical and research gaps. OBJECTIVE: To provide an evidence-based synthesis of current diagnostic and therapeutic approaches for leiomyosarcoma by an international panel of physicians, researchers, and patient advocates, focusing on site-specific management, systemic therapy strategies, and key areas of clinical uncertainty, while identifying unmet needs and research priorities. EVIDENCE REVIEW: This review is based on a comprehensive evaluation of the literature, including clinical trials, observational studies, and international consensus guidelines. Sources were identified through MEDLINE (via PubMed) and Embase database searches and reference screening, then supplemented by multidisciplinary expert consensus. Emphasis was placed on studies informing diagnosis, surgical management, radiotherapy, and systemic therapy in leiomyosarcoma. FINDINGS: The rarity and heterogeneity of leiomyosarcoma poses substantial challenges in its management. In localized disease, complete surgical resection remains the cornerstone of treatment, with evidence supporting the use of site-specific perioperative treatment strategies. Prospective data supporting neoadjuvant or adjuvant chemotherapy are lacking, and the role of radiotherapy differs across anatomic disease sites and institutions. In advanced disease, multiple systemic therapies demonstrate activity, including anthracycline-based and gemcitabine-based combinations, trabectedin, and tyrosine kinase inhibitors, although optimal sequencing after first-line therapy remains undefined. Emerging data suggest potential benefit from treatment continuation strategies and selected use of local therapies in oligometastatic settings. Molecular heterogeneity is increasingly recognized but has not yet translated into routine clinical implementation, and integration of molecular profiling into diagnostic pathways for predictive and therapeutic insights remains an unmet need. CONCLUSIONS AND RELEVANCE: This international consensus addresses the diagnosis and management of leiomyosarcoma. Management requires a multidisciplinary, site-specific approach informed by limited but evolving evidence. Key uncertainties persist, particularly regarding perioperative therapy, optimal sequencing and combination of systemic treatments, and integration of molecular data. Continued international collaboration and leiomyosarcoma-specific clinical trials are needed to refine treatment strategies and improve patient outcomes.

Journal Article↗