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At least 19 recordsLinked to original sources
PubMed2023

EMPIAR: the Electron Microscopy Public Image Archive.

Public archiving in structural biology is well established with the Protein Data Bank (PDB; wwPDB.org) catering for atomic models and the Electron Microscopy Data Bank (EMDB; emdb-empiar.org) for 3D reconstructions from cryo-EM experiments. Even before the recent rapid growth in cryo-EM, there was an expressed community need for a public archive of image data from cryo-EM experiments for validation, software development, testing and training. Concomitantly, the proliferation of 3D imaging techniques for cells, tissues and organisms using volume EM (vEM) and X-ray tomography (XT) led to calls from these communities to publicly archive such data as well. EMPIAR (empiar.org) was developed as a public archive for raw cryo-EM image data and for 3D reconstructions from vEM and XT experiments and now comprises over a thousand entries totalling over 2 petabytes of data. EMPIAR resources include a deposition system, entry pages, facilities to search, visualize and download datasets, and a REST API for programmatic access to entry metadata. The success of EMPIAR also poses significant challenges for the future in dealing with the very fast growth in the volume of data and in enhancing its reusability.

Imaging, Three-Dimensional↗
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↗
PubMed1978

[Experience in creating an automated pathoanatomic archive in prosection at the A. N. Bakulev Institute of Cardiovascular Surgery of the Academy of Medical Sciences of the USSR].

An information system "Automatic pathological anatomy archive" has been created in the cardiac surgery center existing 22 years. A special card has been developed for resording of the results of morphological examinations and the main information on the patient, which is filled by the dissector after autopsy. Treatment of the data contained in the information mass stipulates an urgent search of the cases according to the set of data indicated in the request, interpretation of the content of unified cards for the selected cases, calculation of per cent ratios, etc. Realization of information systems in universal computers opens wide possibilities for principally new organization of pathological archives.

Archives↗
PubMed2025

Cerebrospinal fluid microbiome revisited: no evidence of resident bacteria in archived samples.

UNLABELLED: DNA from oral bacteria has been detected in the cerebrospinal fluid (CSF) of patients with Alzheimer's disease and related dementias (AD/ADRD). We hypothesized that examination of archived CSF samples from donors with variable cognitive status would reveal evidence of a resident microbiome. 176 CSF samples harvested from community-dwelling individuals (77% between 61 and 80 years old) were analyzed; 57% originated from donors with impaired cognitive status. DNA was extracted after adding microbial spike-in controls, and libraries were prepared and sequenced on an Illumina-MiSeq platform. 16S rRNA sequences were processed, and a taxonomic classification was performed. Spike-in bacteria were consistently detected, and Streptococcus pneumoniae was found in a positive control sample from a patient with bacterial meningitis. However, very few reads mapping to other bacterial taxa were detected across samples, suggesting a negligible bacterial content consistent with occasional contamination or sequencing errors. CSF is a privileged, sterile environment that does not harbor a resident microbiome in elderly people with various morbidities, including AD/ADRD. IMPORTANCE: Recent reports have suggested that DNA from oral bacteria has been found in the cerebrospinal fluid (CSF) of patients with Alzheimer's disease and related dementias (AD/ADRD). We hypothesized that examination of archived CSF samples from donors with variable cognitive status would reveal evidence of a resident microbiome. We thus analyzed 176 CSF samples harvested from community-dwelling individuals including donors with impaired cognitive status. While our findings suggested the presence of occasional bacterial contamination, they provided no evidence of a resident microbiome. We thus conclude that the CSF is indeed a privileged, sterile environment that does not harbor a resident microbiome in elderly people with various morbidities including AD/ADRD.

Humans↗
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↗
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↗
PubMed1977

Hutchinson's Archives of Surgery revisited.

I present a bried review of Hutchinson's Archives of Surgery. I have listed most of his well-known and not-so-well-known early clinical descriptions. To this list can be added descriptions of Peutz-Jegher syndrome, lipomelanic reticulosis, telangiectatic lupus erythematosus, temporal arteritis, and recurrent herpes simplex on the thigh and buttocks. The characteristics of Hutchinson's writing are the use of catchy, descriptive terms, his use of patients' names for diseases, his belief in the effectiveness of illustrations, superb clinical observation but faulty conclusions, and a lack of humor. Seventy-two years after his death, there is still much that can be learned about clinical disease from Hutchinson.

Dermatology↗
PubMed1979

[Electron microscopic study of archival material fixed in formalin].

A method for treatment of formalin-fixed and paraffin-embedded material for electron microscope examinations is described. Archive material may be examined in the electron microscope for the elucidation of some problems concerning conditions of intercellular structures, comparative size and localization in the cells of secrete granules, myofibrillar apparatus and various inclusions.

Autopsy↗