Find research datasets worth reusing

opencc-zeroJan 2015View details →

Supplement 1: Full list of ICD10 codes and number of gene-disease links (tab-separated-value file); Supplement 2: Mapping (tab-separated-value file)

Supplements to BioMedBridges deliverable 10.2 A prototype linking ICD10/SNOMED CT concepts to Ensembl gene identifiers: Supplement 1: Full list of ICD10 codes and number of gene-disease links: table_icd10_gene_count_descr.tsv Supplement 2: Mapping of disease terms: ICD10_to_doid.tsv

opencc-zeroApr 2024View details →

SeMRA Disease Mappings Database

Supports the analysis of the landscape of disease nomenclature resources. See instructions for reproduction and usage in the attached README.md.

opencc-by-4.0Jun 2024View details →

Dautan et al 2024 " Gut-Initiated Alpha Synuclein Fibrils Drive Parkinson's Disease Phenotypes: Temporal Mapping of non-Motor Symptoms and REM Sleep Behavior Disorder"

Parkinson’s disease (PD) is characterized by progressive motor as well as less recognized non-motor symptoms that arise often years before motor manifestation, including sleep and gastrointestinal disturbances. Despite the heavy burden on the patient’s quality of life, these non-motor manifestations are poorly understood. To elucidate the temporal dynamics of the disease, we employed a mice model involving injection of alpha-synuclein (αSyn) pre-formed fibrils (PFF) in the duodenum and antrum as a gut-brain model of Parkinsonism. Using anatomical mapping of αSyn PFF propagation and behavioral and physiological characterizations, we unveil a correlation between post-injection time the temporal dynamics of αSyn propagation and non-motor/motor manifestations of the disease. We highlight the concurrent presence of aggregates in key brain regions, expressing acetylcholine or dopamine and their functions in sleep duration, wakefulness, and particularly REM-associated atonia corresponging to REM behavioral disorder-like symptoms. This study presents a novel and in-depth exploration into the multifaceted nature of PD, unraveling the complex connections between α-synucleinopathies, gut-brain connectivity, and the emergence of non-motor phenotypes.

opencc-by-4.0Dec 2022View details →

Atrophy Pattern Maps of Alzheimer's Disease, Mild Cognitive Impairment, Parkinson's Disease, and Frontotemporal Dementia

The files contain voxel-wise t-statistics maps contrasting deformation based morphometry (DBM) measurements of Alzheimer's disease (AD), Parkinson's disease (PD), mild cognitive impairment (MCI), and fronto-temporal dementia (FTD) patients against matched normal controls. AD and MCI maps are based on ADNI data, available at: PD map is based on PPMI data, available at: FTD map is based on NIFD data, available at: For more information regarding the participants and method details, see: Dadar, Mahsa, et al. "White matter hyperintensities are associated with grey matter atrophy and cognitive decline in Alzheimer's disease and frontotemporal dementia." Neurobiology of aging 111 (2022): 54-63.

opencc-by-4.0Nov 2022View details →

Integrative in situ mapping of single-cell transcriptional states and tissue histopathology in an Alzheimer disease model

Amyloid-β plaques and neurofibrillary tau tangles are the neuropathologic hallmarks of Alzheimer’s disease (AD), but the spatiotemporal cellular responses and molecular mechanisms underlying AD pathophysiology remain poorly understood. Here we introduce STARmap PLUS to simultaneously map single-cell transcriptional states and disease marker proteins in brain tissues of AD mouse models at a voxel size of 95  95  350 nm. This high-resolution spatial transcriptomics map revealed a core-shell structure where disease-associated microglia (DAM) closely contact amyloid-β plaques, whereas disease-associated astrocyte-like cells (DAA-like) and oligodendrocyte precursor cells (OPC) are enriched in the outer shells surrounding the plaque-DAM complex. Hyperphosphorylated tau emerged mainly in excitatory neurons in the CA1 region accompanied by infiltration of oligodendrocyte subtypes into the axon bundles of hippocampal alveus. The integrative STARmap PLUS method bridges single-cell gene expression profiles with tissue histopathology at subcellular resolution, providing an unprecedented roadmap to pinpoint the molecular and cellular mechanisms of AD pathology and neurodegeneration.

opencc-by-4.0Dec 2020View details →

Disease and lesion maps - part of the Scientific opinion on the evaluation of public and animal health risks in case of a delayed post-mortem inspection in ungulates

EFSA was requested to assess the impact on effectiveness of post-mortem inspection in terms of any change in the sensitivity of detection of animal diseases of domestic and wild ungulates listed according to Article 5 of Regulation (EC) No 2016/429 and septicaemia, pyaemia, toxaemia or viraemia, when carried out after up to 24 hours or up to 72 hours after slaughter in comparison to when it is carried out immediately after slaughter. In order to identify the main lesions associated with the target diseases, a so called “disease map” was built, with the information about the clinical forms of the diseases  (acute, subacute, chronic, or latent forms) and clinical signs, as well as potential lesions that could be observed on the respective diseased animals. The following information is indicated for each disease/condition in the disease map: <ol> <li>The susceptible animal species</li> <li>Whether there is any surveillance programme in place in the EU</li> <li>The signs associated with the disease that could be detected at ante mortem inspection;</li> <li>The lesions associated with the disease that could be detected at post mortem inspection</li> <li>The probability of detecting the disease during the PMI as normally carried out.</li> <li>Whether carcass swabbing and/or laboratory tests are normally carried out.</li> </ol> From the disease map, the list of organs to be considered at post mortem inspection and the lesions, a “lesion map” was built by connecting animal species with organs, lesions and corresponding disease. This was done to facilitate the construction of a questionnaire where, for each organ and the five types of lesions, the respondents (meat inspectors) had to provide a numerical answer about how many carcasses out of 100 with the given lesion, will be still detected after 24- or 72-h of refrigerated storage.

opencc-by-4.0May 2024View details →

High-Resolution Vector-borne Disease Infection Risk Mapping with Area-to-Point Kriging and Species Distribution Modeling - Datasets

Datasets and notebooks used in the publication High-Resolution Vector-borne Disease Infection Risk Mapping with Area-to-Point Kriging and Species Distribution Modeling

opencc-by-4.0May 2024View details →

The Potential of Deep Learning Object Detection in Citizen-Driven Snail Host Monitoring to Map Putative Disease Transmission Sites

<a name="_Hlk158802145"></a>Schistosomiasis is a neglected tropical disease caused by parasitic flukes transmitted by freshwater snails. Despite increasing efforts of mass drug administration, schistosomiasis remains a public health concern and the World Health Organization recommends complementary snail control. To address the need of broad-scale and actual snail distribution data to guide snail control, we adopted a citizen science approach and recruited citizen scientists (CS) to perform weekly snail sampling in the endemic setting in Uganda. Snails were identified, sorted and counted according to genus, photographed and uploaded for expert-led validation and feedback. However, expert validation is time-consuming and introduces a delay in verified data output. Thus, artificial intelligence could provide a solution by means of automated detection and counting of multiple snails collected from the field. Trained on approximately 2500 citizen-collected images, the resulting model can simultaneously detect and count Biomphalaria and Radix snails with average precision of 98.1% and 98.8% respectively. The object detection model also agreed with the expert’s decision averagely for 98.8% of the test images and could be ran in real-time (24.6 images per second). We conclude that the automatic and instant detection can rapidly and reliably validate data submitted by CS in the field, ultimately minimizing the expert validation efforts and thereby facilitating the mapping of putative schistosomiasis transmission sites. An extension to a mobile application could equip citizen scientists in remote areas with instant learning opportunities and expert-like identification skills, overcoming the need for on-site training and extensive expert intervention.

opencc-by-4.0May 2023View details →

Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases.

Many disease-associated variants are thought to be regulatory but are not present in existing catalogues of expression quantitative trait loci (eQTL). We hypothesise that these variants may regulate expression in specific biological contexts, such as stimulated immune cells. Here, we used human iPSC-derived macrophages to map eQTLs across 24 cellular conditions. We found that 76% of eQTLs detected in at least one stimulated condition were also found in naive cells. The percentage of response eQTLs (reQTLs) varied widely across conditions (3.7% - 28.4%), with reQTLs specific to a single condition being rare (1.11%). Despite their relative rarity, reQTLs were overrepresented (p=0.05, Fisher's exact test) among disease-colocalizing eQTLs. We nominated an additional 21.7% of disease effector genes at GWAS loci via colocalization of reQTLs, with 38.6% of these not found in the Genotype–Tissue Expression (GTEx) catalogue. Our study highlights the diversity of genetic effects on expression and demonstrates how condition-specific regulatory variation can enhance our understanding of common disease risk alleles.

opencc-by-4.0Dec 2018View details →

Sentinel-2 Optical satellite imagery for Epidemic Disease Mapping

Sentinel-2 Optical satellite imagery for Epidemic Disease Mapping

opencc-by-4.0Jun 2023View details →

Source data for paper "Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data"

Sample-paired scRNA-seq and scATAC-seq data collected from human peripheral blood mononuclear cells with Staphylococcus aureus infection. ScATAC-seq data collected from human peripheral blood mononuclear cells with COVID-19 infection.

dryad40/100

Replication data for: Mapping oak wilt disease from space using land surface phenology

Open the record for dataset details and reuse information.

publicJan 2025View details →

opencc-by-4.0Oct 2015View details →

Mouse and Human Co-expression maps and supplementary material for: "A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels"

Co-expression maps of the human and mouse species derived from microarray data for the first release of the GeneFriend tool. The two co-expression maps  have been compared in order to discern similarities and differences between the two species. The results have been described in the manuscript titled: "A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels". The supplementary material of the manuscript have also been included in this repository.

opencc-by-4.0Apr 2024View details →

Improved multi-ancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk

sushie.molqtl.weights.tar.gz contains ancestry-specific eQTL and pQTL weights trained on mRNA and protein levels measured in American European, American African, and American Hispanic ancestries from TOPMed-MESA and GENOA studies. Column “a1” is the counting allele. mesa.*.fusion.tar.gz contains the weights in FUSION format. sushie_real_data_results.tar.gz contains all the real data analyzed in the sushie project. sushie_sim_data_results.tar.gz contains all the sim data analyzed in the sushie project. sushie_analysis_codes.tar.gz contains all the codes and scripts to generate and analyze these data.

opencc-by-4.0Dec 2023View details →

Voxel-wise maps for the paper: Longitudinal associations of magnetic susceptibility with clinical severity in Parkinson's disease

This upload contains voxel-wise group level QSM data, and statistical maps for group level results associated with the paper: Longitudinal associations of magnetic susceptibility with clinical severity in Parkinson's disease. The assocaited code for reproducing these statistical maps can be found here: <a href="https://github.com/gecthomas/QSM_PD_longitudinal">gecthomas/QSM_PD_longitudinal (github.com)</a>

dryad36/100

Complex feline disease mapping using a dense genotyping array

The current feline genotyping array of 63k single nucleotide polymorphisms has proven its utility within breeds, and its use has led to the identification of variants associated with Mendelian traits in purebred cats. However, compared to single gene disorders, association studies of complex diseases, especially with the inclusion of random bred cats with relatively low linkage disequilibrium, require a denser genotyping array and an increased sample size to provide statistically significant associations. Here, we undertook a multi-breed study of 1,122 cats, most of which were admitted and phenotyped for nine common complex feline diseases at the Cornell University Hospital for Animals. Using a proprietary 340k single nucleotide polymorphism mapping array, we identified significant genome-wide associations with hyperthyroidism, diabetes mellitus, and eosinophilic keratoconjunctivitis. These results provide genomic locations for variant discovery and candidate gene screening for these important complex feline diseases, which are relevant not only to feline health, but also to the development of disease models for comparative studies.

opencc-zeroApr 2022View details →

opencc-by-4.0Jun 2022View details →

Other supporting data for our manuscript "Mapping the Single Cell Transcriptomic Response of Murine Diabetic Kidney Disease to Therapies"

Other supplementary data for our paper "Mapping the Single Cell Transcriptomic Response of Murine Diabetic Kidney Disease to Therapies"

dryad36/100

Large scale eDNA monitoring of multiple aquatic pathogens as a tool to provide risk maps for wildlife diseases

Multiple parasites and pathogens cause disease in aquatic wildlife and in aquaculture species, generating a need for monitoring and management. Conventional disease monitoring methods involve laborious, costly and invasive capture and examination of host species, and require specialised expertise for every host and pathogen of interest. These restrictions could be alleviated by using pathogen detection techniques based on environmental DNA that provide simultaneous surveys of multiple aquatic pathogens across different host taxa. This would also be valuable for approaches employing parasite diversity as bioindicators of ecosystem disturbance, which suffer from similar restrictions. Here, we tested the potential for simultaneous detection of four wildlife pathogens in water samples from 280, mainly riverine, sites across Switzerland. We targeted the crayfish pathogen Aphanomyces astaci, the amphibian pathogen Batrachochytrium dendrobatidis, and the fish pathogens Saprolegnia parasitica and Tetracapsuloides bryosalmonae. The eDNA detection showed a widespread distribution of A. astaci, S. parasitica and T. bryosalmonae, although A. astaci and T. bryosalmonae were not detected in some alpine river catchments. B. dendrobatidis was detected only rarely, which was expected since the sampling did not target amphibian breeding sites. Co-detection rates were higher in rivers than in lakes, likely reflecting the habitat preferences and distributions of the host species. We discuss the advantages and limitations of eDNA-based pathogen monitoring and list a set of recommendations for managers. Our study illustrates how eDNA-based techniques can monitor several pathogen species concurrently, thus facilitating more comprehensive disease monitoring schemes. Combined with metabarcoding approaches in the future, eDNA based sampling and detection can facilitate the incorporation of parasite and pathogen occurrence and diversity as an indicator for aquatic ecosystem health, and for revealing the hidden biodiversity and structure of parasite communities.

opencc-zeroSep 2022View details →

opencc-by-4.0Jun 2024View details →

White matter hyperintensity maps in aging and neurodegenerative diseases

<div>The files contain voxel-wise white matter hyperintensity (WMH) maps for 11 different neurodegenerative disease cohorts from the Canadian Consortium on Neurodegeneration in Aging (CCNA) COMPASS-ND dataset in the MNI-ICBM152-2009c space.</div> <div> </div> <div>For more information regarding the participants and method details, see: </div> <div>Dadar, M., Mahmoud, S., Zhernovaia, M., Camicioli, R., Maranzano, J., Duchesne, S., & CCNA Group. (2022). White matter hyperintensity distribution differences in aging and neurodegenerative disease cohorts. NeuroImage: Clinical, 36, 103204.</div>