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At least 19 recordsLinked to original sources
PubMed1978

Effects of adding a Medex on practice costs and productivity.

Archival data on ten rural practices employing a Medex and on ten matched controls were compared to determine changes in the volume of patients seen and changes in the practice finances before and after the employment of a Medex. There were no significant differences in the changes in patient volume; however, the practices that employed a Medex showed an increase in revenue and in net profit per physician. On the average, the net profit increased approximately $11,000 (22%) for the physicians with Medex, compared with $9,000 (21%) for the control physicians.

Costs and Cost Analysis↗
PubMed1978

Ambient temperature and the occurrence of collective violence: the "long, hot summer" revisited.

Archival data pertaining to 102 instances of serious collective violence were examined in order to study the relationship between ambient temperature and the occurrence of such events. Results indicated that the frequency of collective violence and ambient temperature were curvilinearly related. Specifically, ambient temperature was directly associated with the frequency of collective violence through the mid-80s (degrees Fahrenheit). Beyond this point, however, further increments in temperature were associated with a decreasing incidence of such events. Additional findings indicated that ambient temperature increased significantly during the 7 days preceding the outbreak of collective violence, remained stable during its occurrence, but then decreased significantly in the 3 days following its termination. Possible implications of these findings, as well as their relationship to the results of previous laboratory studies, are discussed.

Civil Disorders↗
PubMed1978

Driving offenders and the defensive driving course--an archival study.

Two hundred and seventy-five drivers who had been required by court order to attend a Defensive Driving Course (DDC) were compared on six posttreatment driving measures obtained from archival data with 275 drivers who also had had a court appearance and standard treatment. The DDC group showed greater reductions in serious and accident-promoting convictions but no greater reduction in accidents when compared with the standard treatment comparison group.

Accidents, Traffic↗
PubMed1979

Family care in a family practice group.

A fundamental claim of family medicine is that the family physician treats the "whole" family--an ideological principle that guides undergraduate and residency education. Using archival data obtained from a random sample of 500 patients in one group of family physicians, this study analyzed the extent to which this principle is carried out in practice. Physicians trained in family practice residency programs were compared with their colleagues. Family types and marital stability were also examined. Results indicate that in only 28 percent of families (excluding single person households) were all family members seen by the same family physician. This occurred despite the high preponderance and stability of traditional nuclear families in the practice. There was no significant difference in this rate between graduates and nongraduates of approved family practice residency programs.

Adolescent↗
PubMed1979

An archival system for clinical laboratory data.

A magnetic tape-based archival system that provides for generation of computer-output microfiche has been developed. Data from magnetic tapes written on a turnkey laboratory system are used as the basis for generating the archival tapes. Programmed searches of the tapes allow retrieval directly by name or test(s). Accessing the computer-output microfiche allows retrieval by name and is being used to supplant a traditional file system.

Archives↗
PubMed2025

The GSA Family in 2025: A Broadened Sharing Platform for Multi-omics and Multimodal Data.

The Genome Sequence Archive family (GSA family) provides a comprehensive suite of database resources for archiving, retrieving, and sharing multi-omics data for the global academic and industrial communities. It currently comprises four distinct database members: the Genome Sequence Archive (GSA, https://ngdc.cncb.ac.cn/gsa), the Genome Sequence Archive for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human), the Open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix), and the Open Biomedical Imaging Archive (OBIA, https://ngdc.cncb.ac.cn/obia). Compared to its 2021 version, the GSA family has expanded significantly by introducing a new repository, the OBIA, and by comprehensively upgrading the existing databases. Notable enhancements to the existing members include broadening the range of accepted data types, strengthening quality control systems, improving the data retrieval system, and refining data-sharing management mechanisms.

Humans↗
PubMed1977

The Protein Data Bank. A computer-based archival file for macromolecular structures.

The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americas), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. alpha-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.

Computers↗
PubMed2026

GICPIdb: an archival repository of multimodal data focusing on pathological images for gastrointestinal cancers.

INTRODUCTION: Deep learning (DL) shows great potential for predicting biomarkers from routine histopathological slides of gastrointestinal (GI) cancers. Yet most existing models are validated on limited patient cohorts, while pathological image annotation and molecular marker standardization demand substantial professional expertise. To address these gaps, we constructed the Gastrointestinal Cancer Pathological Image Archive (GICPIdb, gicpidb.shubuzuo.top), a dedicated database and web platform covering seven major GI cancer types. METHODS: High-quality hematoxylin and eosin (H&E)-stained whole-slide images were collected from multiple sources and uniformly processed. Image annotations were performed by board-certified pathologists following standardized protocols. GICPIdb offers five interactive web modules for data uploading, quality control, feature extraction, online annotation and AI-based prediction. Its intuitive interface supports data browsing, retrieval, visualization and downloading. RESULTS: The database houses 2,863 pathologist-annotated, uniformly processed, high-quality H&E stained images collected from 2,655 patients. Of these, 1,699 patients were sourced from The Cancer Genome Atlas (TCGA), 182 from the Clinical Proteomic Tumor Analysis Consortium (CPTAC), and 424 from China-Japan Friendship Hospital and 350 from Chifeng Municipal Hospital in Inner Mongolia, China. It also integrates data on over 50 key molecular markers (e.g., MSI, TMB) and prognostic labels related to survival, recurrence and metastasis. DISCUSSION: GICPIdb aims to promote the development of DL-driven AI tools for cancer research and clinical translation. The multi-institutional data collection and standardized annotation pipeline are expected to enhance the generalizability and reproducibility of AI-based prediction models across diverse patient populations.

deep learning↗
PubMed1979

Microbiology subsystem of a total, dedicated laboratory computer system.

The computer system used by the Microbiology Service of the Clinical Pathology Department, Clinical Center, National Institutes of Health is discussed. This microbiology subsystem is a part of a dedicated on-line laboratory computer system used by the entire department. The laboratory computer is connected on-line to a hospital computer which provides patient admission, transfer, and discharge data. Mark sense worksheets and cathode ray tube terminals are used for result entry and correction. Cumulative patient reports are printed. Results for both active and completed accessions can be easily retrieved on cathode ray terminals in the laboratory. All laboratory data are archived on magnetic tape from which a research data base and microfiched laboratory records are generated. The manner in which the system is integrated in the routine operation of the microbiology laboratory is emphasized. In addition, some of the costs, benefits, liabilities, and pitfalls associated with the introduction of the computer in the laboratory are reviewed. Finally, we have presented our concept of some of the future enhancements to our present system and some of the directions in which any future microbiology system might develop.

Computers↗
PubMed2026

MetagenomicKG: a knowledge graph for metagenomic applications.

MOTIVATION: The sheer volume and variety of genomic content within microbial communities makes metagenomics a field rich in biomedical knowledge. To traverse these complex communities and their vast unknowns, metagenomic studies often depend on distinct reference databases, such as the Genome Taxonomy Database (GTDB), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), for various analytical purposes. These databases are crucial for the genetic and functional annotation of microbial communities. Nevertheless, the inconsistent nomenclature or identifiers of these databases present challenges for effective integration, representation, and utilization. Knowledge graphs (KGs) offer an appropriate solution by organizing biological entities from different databases to standardized identifiers, allowing their interrelations to be captured into a cohesive network regardless of the naming conventions used in each source. The graph structure not only facilitates the unveiling of hidden patterns but also enriches our biological understanding with deeper insights. Despite KGs having shown potential in various biomedical fields, their application in metagenomics remains underexplored. RESULTS: We present MetagenomicKG, a novel knowledge graph specifically tailored for metagenomic analysis. MetagenomicKG integrates taxonomic, functional, and pathogenesis-related information on the human microbiome sourced from various databases, and further connects these with existing biomedical KGs to expand the biological network. Through various case studies involving the human microbiome, we demonstrate its utility in enabling hypothesis generation regarding the relationships between microbes and diseases, generating sample-specific graph embeddings, and providing robust pathogen prediction. CODE AVAILABILITY: The source code and technical details for constructing the MetagenomicKG and reproducing all analyses are available on GitHub at https://github.com/KoslickiLab/MetagenomicKG. The data used in this manuscript, including the pre-built files and use case input data, are archived on Zenodo with DOI: 10.5281/zenodo.17546861.

Metagenomics↗
PubMed2026

Embryophyte-wide detection of natural Agrobacterium-mediated horizontal gene transfer reveals an ancient role for mini T-DNAs.

Agrobacterium transfers DNA into plant cells, leading to tumors, hairy roots (HR), and natural genetically modified organisms (nGMOs). Transferred DNAs (T-DNAs) from agrobacteria and T-DNA-derived cellular T-DNAs (cT-DNAs) from nGMOs vary considerably and may carry up to 15 different genes. Among these, opine synthase (ops) genes encode the synthesis of opines used as nutrients by the agrobacteria. Earlier studies predicted large numbers of naturally transformed plant species, but only few have been identified and studied so far. We therefore developed a general method to detect cT-DNAs in all publicly available whole genome sequences (WGS) and Sequence Read Archive (SRA) data from land plants. To avoid false positives, we only retained DNA sequences coding for T-DNA proteins. A total of 2614 nGMO species were identified, most are eudicots. However, cT-DNAs were also found in 82 mosses and 75 ferns, showing that Agrobacterium can also generate natural transformants among the early land plants. Analysis of 149 cT-DNA maps revealed different types of T-DNAs. Most notably, these included small T-DNAs (mini T-DNAs) with a single opine synthase gene. Mini T-DNAs are not expected to induce tumors or HRs. The predominance of mini cT-DNAs in mosses and ferns, and the presence of more complex cT-DNAs in spermatophytes, indicate that mini T-DNAs represent the earliest types of T-DNA. Our study also detected unusual T-DNA integration patterns, with multiple copies spread out over several hundreds of kilobases.

DNA, Bacterial↗
PubMed1978

Archival storage of clinical laboratory data.

This paper describes a data-base system for the maintenance of cumulative clinical data. A unique aspect of this data base is its ability dynamically to alter its two-level format to create an alternative three-level hierarchical structure in order to optimize retrieval efficiency. The relative advantages of these two types of data-base structures are discussed and examples of their use in clinical resrarch are presented.

Chemistry, Clinical↗