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1,876 results for “pathology”
Raw data to "Blunting neuroinflammation with resolvin D1 prevents early pathology in a rat model of Parkinson's disease"
<p>Background: In vivo treatment of animals with anti-inflammatory and pro-resolving mediators (SPMs) could be counteracted by their limited in vivo bioavailability due to their unstable nature as lipids that can undergo oxidation or enzymatic degradation.</p> <p>Results: Thus, we performed a time course of RvD1 plasma levels over 36 hours after an initial intraperitonael injection of this lipid mediator at a concentration of 200 ng/animal. After a single injection the plasma concentration of RvD1 peaked at 1h (~360 pg/ml), stayed almost constant at 3h(~360 pg/ml), halved its levels after 6h (~180 pg/ml) and slowly returned close to the baseline after 36h (~30 pg/ml). These results indicate that RvD1 is rapidly distributed into the bloodstream and eliminated from the vascular compartment due to metabolism and/or diffusion into the blood–brain barrier.</p> <p>Conclusions: These findings are important to define route and timing of in vivo administration of SPMs in order to maintain sufficient levels to sustain biological activities both in the periphery and within the central nervous system.</p>
Data from: Phenological synchrony shapes pathology in host–parasite systems
<p>A key challenge surrounding ongoing climate shifts is to identify how they alter species interactions, including those between hosts and parasites. Because transmission often occurs during critical time windows, shifts in the phenology of either taxa can alter the likelihood of interaction or the resulting pathology. We quantified how phenological synchrony between vulnerable stages of an amphibian host (<i>Pseudacris regilla</i>) and infection by a pathogenic trematode (<i>Ribeiroia ondatrae</i>), determined infection prevalence, parasite load, and host pathology. By tracking hosts and parasite infection throughout development between low- and high-elevation regions (San Francisco Bay Area and the Southern Cascades [Mt. Lassen]), we found that when phenological synchrony was high (Bay Area), each established parasite incurred a 33% higher probability of causing severe limb malformations relative to areas with less synchrony (Mt. Lassen). As a result, hosts in the Bay Area had up to a 50% higher risk of pathology even while controlling for mean infection load. Our results indicate that host-parasite interactions and the resulting pathology were the joint product of infection load and phenological synchrony, highlighting the sensitivity of disease outcomes to forecasted shifts in climate.</p>
Models from: Exploring ensemble applications for multi-sequence myocardial pathology segmentation
<p>Trained models for the MyoPS2020 challenge http://www.sdspeople.fudan.edu.cn/zhuangxiahai/0/MyoPS20/</p> <p>As described in the publication: "Exploring ensemble applications for multi-sequence myocardial pathology segmentation"</p> <p>Source code available at: https://github.com/chfc-cmi/miccai2020-myops</p>
On Transferability of Histological Tissue Labels in Computational Pathology
<p>This Zip file contains all Convolutional Neural Network (CNN) models of HistoNet trained on ADP database introduced in</p> <p><em>Hosseini et. al. “On Transferability of Histological Tissue Labels in Computational Pathology.” Accepted in the European Conference on Computer Vision (ECCV), Glasgow, UK, August 2020 </em></p> <p>For more information on the models and how to train them, please refer to <strong>https://github.com/mahdihosseini/HistoLabelTransfer</strong></p> <p> </p>
Genome-wide association results from: Transcriptomic stratification of late-onset Alzheimer's cases reveals novel genetic modifiers of disease pathology
<p>Late-Onset Alzheimer's disease (LOAD) is a common, complex genetic disorder well-known for its heterogeneous pathology. The genetic heterogeneity underlying common, complex diseases poses a major challenge for targeted therapies and the identification of novel disease-associated variants. Case-control approaches are often limited to examining a specific outcome in a group of heterogenous patients with different clinical characteristics. Here, we developed a novel approach to define relevant transcriptomic endophenotypes and stratify decedents based on molecular profiles in three independent human LOAD cohorts. By integrating post-mortem brain gene co-expression data from 2114 human samples with LOAD, we developed a novel quantitative, composite phenotype that can better account for the heterogeneity in genetic architecture underlying the disease. We used iterative weighted gene co-expression network analysis (WGCNA) to reduce data dimensionality and to isolate gene sets that are highly co-expressed within disease subtypes and represent specific molecular pathways. We then performed single variant association testing using whole genome-sequencing data for the novel composite phenotype in order to identify genetic loci that contribute to disease heterogeneity. Distinct LOAD subtypes were identified for all three study cohorts (two in ROSMAP, three in Mayo Clinic, and two in Mount Sinai Brain Bank). Single variant association analysis identified a genome-wide significant variant in <i>TMEM106B</i> (p-value < 5´10<sup>-8</sup>, rs1990620<sup><span><span>G</span></span></sup>) in the ROSMAP cohort that confers protection from the inflammatory LOAD subtype. Taken together,<b> </b>our novel approach can be used to stratify LOAD into distinct molecular subtypes based on affected disease pathways.</p>
Data from: The presubiculum links incipient amyloid and tau pathology to memory function in older persons
Objective: To identify the hippocampal subregions linking initial amyloid and tau pathology to memory performance in clinically normal older individuals, reflecting preclinical Alzheimer's disease (AD). Methods: A total of 127 individuals from the Harvard Aging Brain Study (Mean age: 76.22 years ± 6.42, 68 females (53.5%)) with a Clinical Dementia Rating score of 0, a flortaucipir tau-PET scan, a Pittsburgh Compound B amyloid-PET scan, a structural MRI scan and cognitive testing were included. From these images, we calculated neocortical, hippocampal and entorhinal amyloid pathology, entorhinal and hippocampal tau pathology and the volumes of six hippocampal subregions and total hippocampal volume. Memory was assessed with the selective reminding test. Mediation and moderation analyses modeled associations between regional markers and memory. Analyses included covariates for age, sex and education. Results: Neocortical amyloid, entorhinal tau and presubiculum volume univariately associated with memory performance. The relationship between neocortical amyloid and memory was mediated by entorhinal tau and presubiculum volume, which was modified by hippocampal amyloid burden. With other biomarkers held constant, presubiculum volume was the only marker predicting memory performance in the total sample and in individuals with elevated hippocampal amyloid burden. Conclusions: The presubiculum captures unique AD-related biological variation that is not reflected in total hippocampal volume. Presubiculum volume may be a promising marker of imminent memory problems, and can contribute to understanding the interaction between incipient AD-related pathologies and memory performance. The modulation by hippocampal amyloid suggests that amyloid is a necessary process – but not sufficient – to drive neurodegeneration in memory-related regions.
Balaeonoptera floridana pathological mandible
Partial pathological balaeonopterid whale mandible near corpus (re Pyenson et al. (2013)a; Pyenson, personal communication), Pliocene-Pleistocene Hawthorn gp. (Peace River fm.), Renz Arcadia R. Ranch locality, Peace River dredge, Arcadia, FL. Specimen may be attributed to Balaenoptera floridana. Numerous feeding traces dot the specimen, chief among them a single ~12cm long, 5mm deep groove that may be attributable to Otodus megalodon. Let's get more eyes on this! Specimen recovered and prepared by S. Clawson 7/24/2012, photogrammetrically imaged by S. Clawson 9/27/2019 using Agisoft Metashape Pro and an IPhone camera. Source: Objaverse 1.0 / Sketchfab
A series of pathological macromolecular crystallography datasets with twinning and other lattice disorders
<p>These 11 datasets were collected at the Diamond Light Source and belong to the same protein, NAL (N-acetyl neuraminic acid lyase), which crystallised in 4 different crystal forms from the same crystallisation conditions producing crystals with the same morphology. The file names, where applicable (10/11 cases), contain the corresponding PDB deposition code.</p>
Breast carcinoma histological images from the Department of Pathology, "Agios Pavlos" General Hospital of Thessaloniki, Greece
<p>This dataset contains cases of breast carcinoma histological specimens received at the Department of Pathology, “Agios Pavlos” General Hospital of Thessaloniki, Greece. The dataset consists of 300 annotated images of resolution 1280x960 corresponding to 21 different patients with invasive ductal carcinoma of the breast of grades 1-3 (grouped in the corresponding folders).</p> <p>More details about the dataset are presented in the paper: </p> <p>K. Dimitropoulos, P. Barmpoutis, C. Zioga, A. Kamas, K. Patsiaoura and N. Grammalidis, "Grading of invasive breast carcinoma through Grassmannian VLAD encoding", submitted for publication to PLOS ONE, 2017.</p>
Mechanical stimulation prevents impairment of axon growth and overcompensates microtubules destabilization in cellular models of Alzheimer's disease related Tau pathology
<p>Data and metadata associated to a publication 10.3389/fmed.2025.1519628</p>
Enhanced mTORC1 signaling and protein synthesis in pathologic alpha-synuclein cellular and animal models of Parkinson's disease
<p>Pathologic alpha-synuclein plays an important role in the pathogenesis of alpha-synucleinopathies such as Parkinson's disease (PD). Disruption of proteostasis is thought to be central to pathologic alpha-synuclein (alpha-syn) toxicity; however, the molecular mechanism of this deregulation is poorly understood. Here we report that pathologic alpha-syn activates the mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) leading to enhanced mRNA translation via binding tuberous sclerosis protein (TSC) 2 and destabilizing the TSC1-TSC2 complex. Genetic and pharmacologic inhibition of mTOR and protein synthesis rescue the dopamine neuron loss, behavioral deficits, and aberrant biochemical signaling in the alpha-syn preformed fibril (PFF) and Drosophila alpha-syn transgenic models of pathologic alpha-syn induced degeneration. Our findings establish a potential molecular mechanism by which pathologic alpha-syn activates mTORC1 leading to enhanced protein synthesis and concomitant neurodegeneration in PD.</p>
Profiling of pancreatic adenocarcinoma using artificial intelligence-based integration of multi-omic and computational pathology features - Validation Data Sets
<p>Two public validation cohorts were utilized in the MT-Pilot study, the Cancer Genome Atlas (TCGA) and cohort-1 Johns Hopkins University (JHU). These datasets included DNA, RNA, clinical data, and tissue protein analytes analyzed for survival outcome prediction using AI/Machine Learning modeling. </p>
A Promising Concept for the Development of Means for the Prevention of Radiation Pathologies
<p>The problem of developing radioprotective means, capable of mitigating the effects of radiation exposure on the body, is associated not only with the danger of terrorist, military incidents or emergencies at nuclear facilities. An important area for the use of radioprotectors is space exploration, in particular, the need for crew members, protected only by a spacesuit, to enter open space. Furthermore, the solution to the problem of radiotherapy complications in oncology can also be the use of selective radioprotectors able to protect healthy tissues without reducing the effectiveness of tumor radiotherapy. An example of such approach is the use of amifostine in radiotherapy of a number of head-neck tumors.</p> <p>It is important to understand that the developed means should be well tolerated not only by healthy volunteers, but also by people of different ages, physical conditions, including the elderly and debilitated cancer patients. In particular, the adverse effects of amifostine in its effective radioprotective doses lead to a significant limitation of its clinical use.</p> <p>The solution to the problem of radioprotector safety can be the development of combinations containing several radiomodifying substances in small doses. Such compositions are capable of providing a synergistic radioprotective effect and good patient tolerance.</p> <p>Compounds capable of selectively inhibiting endothelial and inducible nitric oxide synthase (NOS) could be the base of such combinations. We have shown that NOS-inhibitors, in particular, N,S-substituted isothioureas, are highly effective in relatively safe doses. For example, the optimal radioprotective dose of one of them, T1023, with dose modifying factor (DMF) of 1.6 - 1.8, is 1/5-1/4 LD10.</p> <p>It has been shown that T1023 and its derivatives are highly effective both for parenteral and oral administration.</p> <p>These compounds provide pronounced prophylaxis of bone marrow and intestinal forms of acute radiation syndrome. Moreover, they are capable to effectively, with a DMF of 1.45, provide the prophylaxis of early and late complications in mouse and rat models of single and fractionated radiotherapy of solid tumors. It is important that the use of these compounds does not reduce the effectiveness of radiotherapy.</p> <p>The radioprotective effect of these compounds is realized by a specific molecular mechanism - by suppressing the endothelium-dependent eNOS/sGC/cGMP pathway of vascular relaxation. The mechanism of radioprotective activity of NOS inhibitors brings them with vasoactive radioprotectors - α1-adrenoreceptor agonists and 5-HT2 serotonin receptors. Therefore, their combined use is accompanied by a synergistic radioprotective effect. This opens up prospects for the creation of highly effective and safe radioprotector combinations.</p>
A formative usability study of workflow management systems in label-free digital pathology - Data and Code
<p>This repository holds the necessary data and code as well as a descriptive Readme file that was used for our publication "A formative usability study of workflow management systems in label-free digital pathology" by Markus Jelonek et al. (2022), submitted to F1000Research.</p> <p> </p> <p>Abstract:</p> <p>We present a formative usability study that investigates the usability of different<br> workflow management systems in the field of biomedical data analysis. Specifically, we study a task in the field of so-called label-free digital pathology and investigate one graphical user interface based workflow and one script-based workflow to solve the task. Our main intention is to gain first insights into the systematic study of usability in the context of biomedical image analysis, and formulate experiences and guidelines for future usability studies dealing with workflow management systems. Embedded in a specific setup dealing with label-free digital pathology, the core question behind our contribution is how usability studies for scientific workflow management can be conducted, and how they can be used systematically to improve such tools. Further, we address specific questions about the resource utilisation and management of usability studies, including the recruitment of participants as well as the design of specific workflows to be investigated.</p>
A formative usability study of workflow management systems in label-free digital pathology - Questionnaires
<p>This repository holds the necessary questionnaires, participant data, interview questions and data, as well as a descriptive Readme file that was used for our publication "A formative usability study of workflow management systems in label-free digital pathology" by Markus Jelonek et al. (2022), submitted to F1000Research.</p> <p> </p> <p>Abstract:</p> <p>We present a formative usability study that investigates the usability of different<br> workflow management systems in the field of biomedical data analysis. Specifically, we study a task in the field of so-called label-free digital pathology and investigate one graphical user interface based workflow and one script-based workflow to solve the task. Our main intention is to gain first insights into the systematic study of usability in the context of biomedical image analysis, and formulate experiences and guidelines for future usability studies dealing with workflow management systems. Embedded in a specific setup dealing with label-free digital pathology, the core question behind our contribution is how usability studies for scientific workflow management can be conducted, and how they can be used systematically to improve such tools. Further, we address specific questions about the resource utilisation and management of usability studies, including the recruitment of participants as well as the design of specific workflows to be investigated.</p>
In vivo characterization of antibodies directed against TREAT-AD target proteins in mouse model of AD pathology
<p><em>In vivo </em>characterization of antibodies directed against TREAT-AD target proteins (Moesin, CD44, Midkine, and SFRP1) in the 5xFAD mouse model</p>
1H HRMAS NMR ERETIC-CPMG dataset for survival analysis and pathological classification of gliomas
<p>This repository contains the raw ERETIC-CPMG HRMAS NMR data to reproduce the results reported in the following preprint: PiDeeL: Pathway-informed deep learning model for survival analysis and pathological classification of gliomas</p> <p>The FID spectra can be found under the FID_Samples directory. The pathological classification and survival analysis labels can be found in the Dataset_Labels.xlsx file.</p>
Microglia protect against age-associated brain pathologies - all scRNAseq datasets
<p>Zipped cellranger_matrices file contains the filtered_feature_bc_matrices and the raw_feature_bc_matrices obtained from cellranger for the young (E...), middle-aged(S...), old (...vo...) and thalamic (TH...) datasets. </p> <p> The cellinfo csv files give the metadata for each cell kept in the analysis, with a relationship between each barcode and information such as the umi counts or the cell type annotation.</p> <p>The metadata file gives information about each sample, to trace back the sample names used in cellranger to the biological samples. On other tabs it also has qc information such as the thresholds used for each sample.</p> <p>The raw fastq files and RDS files are available at GEO: GSE267545 and GEO:GSE215440 with the same metadata as here as well as the SingleCellExperiment in form of RDS objects (with information such as normalised reads and dimensional reduction embedings) available at GEO: GSE267545</p> <p>The code used to do the analysis is available in Anna-Williams GitHub and also in ZENODO: </p> <p> https://github.com/Anna-Williams/David-young (10.5281/zenodo.11199128) for the young dataset</p> <p> https://github.com/Anna-Williams/David-old (10.5281/zenodo.11199278) for the middle-aged dataset</p> <p>https://github.com/Anna-Williams/David-vold (10.5281/zenodo.11199322) for the old dataset<br>https://github.com/Anna-Williams/David-Thalamus (10.5281/zenodo.11199349) for the thalamic dataset<br>https://github.com/Anna-Williams/David-AgeIntegration (10.5281/zenodo.11199367) for the integration between the young, middle-aged and old datasets.</p> <p> </p> <p>Microglia are brain-resident macrophages that contribute to central nervous system development, maturation, and preservation. Here, we examine the consequences of lifelong absence of microglia on ageing using the Csf1rΔFIRE/ΔFIRE mouse model. In juvenile Csf1rΔFIRE/ΔFIRE mice, we show that microglia are largely dispensable for the transcriptomic maturation of other brain cell types. In contrast, with advancing age, multiple pathologies accumulate in Csf1rΔFIRE/ΔFIRE brains, astrocytes and oligodendrocyte-lineage cells become increasingly dysregulated, and white matter integrity declines, mimicking many of the pathological features of human CSF1R-related leukoencephalopathy. The thalamus is particularly sensitive to neuropathological changes in the absence of microglia, with atrophy, neuron loss, vascular disturbances, macroglial dysregulation, and severe calcifications all detected in this region. Thalamic calcification formation, which often occurs with normal ageing, is dramatically accelerated in Csf1rΔFIRE/ΔFIRE brains but can be prevented via transplantation of wild-type microglia. Our results indicate that lifelong absence of microglia results in an age-related neurodegenerative condition that can be prevented by the transplantation of healthy microglia.</p>
Data from: Aplp1 interacts with Lag3 to facilitates transmission of pathologic α-synuclein
<p>Pathologic α-synuclein (α-syn) spreads from cell-to-cell, in part, through binding to the lymphocyte-activation gene 3 (Lag3). Here we report that amyloid β precursor-like protein 1 (Aplp1) interacts with Lag3 that facilitates the binding, internalization, transmission, and toxicity of pathologic α-syn. Deletion of both Aplp1 and Lag3 eliminates the loss of dopaminergic neurons and the accompanying behavioral deficits induced by α-syn preformed fibrils (PFF). Anti-Lag3 prevents the internalization of α-syn PFF by disrupting the interaction of Aplp1 and Lag3, and blocks the neurodegeneration induced by α-syn PFF <em>in vivo</em>. The identification of Aplp1 and the interplay with Lag3 for α-syn PFF induced pathology advances our understanding of the molecular mechanism of cell-to-cell transmission of pathologic α-syn and provides additional targets for therapeutic strategies aimed at preventing neurodegeneration in Parkinson's disease and related α-synucleinopathies.</p>
Fig. 3 in Description, molecular identification and pathological lesions of Huffmanela persica sp. nov. (Nematoda: Trichosomoididae: Huffmanelinae) from the daggertooth pike conger Muraenesox cinereus
Fig. 3 (See legend on previous page.)
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.