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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↗

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 ≥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.↗

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↗

PubMed1991

Body dysmorphic disorder: the distress of imagined ugliness.

OBJECTIVE: Body dysmorphic disorder, a preoccupation with an imagined defect in physical appearance, has a rich tradition in European psychiatry but has been largely neglected in the United States. Because this little-known disorder is probably more common than is generally realized and can have profound consequences, the author reviews its history, clinical features, and possible relationship to other psychiatric disorders. DATA COLLECTION: Data sources consisted of the MEDLINE database and relevant references in articles obtained from this search. Of 145 articles and books obtained, 100 were selected for inclusion in this review on the basis of how closely they conformed to the concept of body dysmorphic disorder as defined in DSM-III-R and how substantially they contributed to an understanding of the disorder's history, clinical features, or nosologic status. FINDINGS: Body dysmorphic disorder has been colorfully described in the European literature for more than a century. Although its concerns might sound trivial, this disorder can lead to social isolation (including being housebound), occupational dysfunction, unnecessary cosmetic surgery, and suicide. The most commonly associated psychiatric disorder appears to be depression. Although a definitive treatment does not exist, preliminary evidence suggests that serotonergic antidepressant medications may be useful. Whether body dysmorphic disorder is related to other psychiatric disorders, such as psychosis, mood disorder, social phobia, or obsessive-compulsive disorder, is unclear at this time. CONCLUSIONS: More research on the nosology, clinical features, and treatment response of body dysmorphic disorder is important, given the distress and impairment this often secret disorder can cause.

Antidepressive Agents↗

PubMed1991

The study of cancer in minorities.

Data inventories provide a concise reference base for researchers. The authors created a set of reference volumes listing databases used for studying cancer in New Jersey minorities. The process followed can be adapted for other disease outcomes or other regions.

Data Collection↗

PubMed2026

The Role of Small Segmental Duplications in Generating Identical Isoforms Through Alternative Splicing Sites.

Alternative splicing plays a crucial role in expanding proteomic diversity but can also generate identical isoforms under certain conditions. While mutually exclusive splicing of tandem exons has occasionally been reported to produce identical isoforms, the extent to which other splicing events contribute to this phenomenon remains unclear. In this study, we demonstrate that alternative 5' and 3' splice site selection can also lead to the formation of identical isoforms, providing an additional type of splicing event for functional redundancy in transcriptomes. To address this, we analyzed reference genome annotations from 15 plant species, including Arabidopsis thaliana and wheat (Triticum aestivum), obtained from the RefSeq database. Identical isoforms were computationally defined as transcripts with distinct exon-intron structures but identical coding sequences. Our analysis reveals that the majority of alternative 5' and 3' fragments originate from small segmental duplications, suggesting that sequence repetition within gene regions facilitates the emergence of such splicing patterns. We also observed differences in the annotated 5' UTRs of some identical isoforms. However, since the alternative splicing sites themselves were not located within UTRs, these differences may reflect annotation uncertainty rather than genuine AS-derived variation. Given that UTR predictions in reference databases are not always precise, such observations should be interpreted cautiously. Expression analysis using an isoform-specific k-mer approach confirmed that identical isoforms can be differentially regulated. These findings suggest that, beyond expanding protein diversity, alternative splicing can also generate redundant isoforms that are differentially expressed at the RNA level, indicating potential regulatory roles. By elucidating the structural and regulatory factors contributing to the formation and retention of identical isoforms, our study provides new insights into the evolutionary and functional significance of alternative splicing in plants.

Alternative Splicing↗

PubMed2024

Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.

Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.

User-Computer Interface↗

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↗