Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
210
datasets available to search
ShareScore release 0.9.0
Dataset results
210 results for “mediation model”
Datasets of sequences, alignments and structural models generated for the structural prediction of complexes mediated by intrinsically disordered regions.
<p>This repository contains input and ouput files used and generated for the scanning of intrinsically disordered region and the prediction of their binding sites to receptor proteins using the <a href="https://github.com/i2bc/SCAN_IDR">SCAN_IDR</a> pipeline with AlphaFold2-Multimer.</p><p>It contains two archives: </p><ol><li><a href="https://zenodo.org/api/records/10068949/draft/files/scanidr_data_repository_corr6J08.tar/content"><i><strong>scanidr_data_repository_corr6J08.tar</strong></i></a> dedicated to the analysis of a dataset of 42 protein complexes non redundant with the dataset used for AlphaFold2 training,</li><li><a href="https://zenodo.org/api/records/10068949/draft/files/923_elm_cases_repository.tar.gz/content"><i><strong>923_elm_cases_repository.tar.gz</strong></i></a> dedicated to the analysis of 923 complexes from the ELM database.</li></ol><p>These data can be used to rerun specific sections of the pipeline and scripts provided in: <a href="https://github.com/i2bc/SCAN_IDR">https://github.com/i2bc/SCAN_IDR</a></p><h4><strong>Dataset of 42 non redundant complexes</strong></h4><p>The first archive <a href="https://zenodo.org/api/records/10068949/draft/files/scanidr_data_repository_corr6J08.tar/content"><i><strong>scanidr_data_repository_corr6J08.tar</strong></i></a> contains 3 compressed directories and a README file detailing their contents :</p><ul><li>the initial raw sequence and alignment data for every chain -> DIRECTORY <strong>fasta_msa/</strong></li><li>the input and output data of every Alphafold run for every complex -> DIRECTORY <strong>af2_runs/</strong></li><li>the native reference structures -> DIRECTORY <strong>ref_capri_curated/</strong></li></ul><p>The protein-peptide complex cases have been assigned a distinct index number, from 1 to 42, consistent across the several directories of the archive. Their corresponding directories are labelled as <i><index>_<pdbcode></i>.</p><p><i>The models in this archive were generated using AlphaFold2-Multimer v2.2</i></p><h4><strong>Dataset of 923 complexes selected from the ELM database</strong></h4><p>The second archive <a href="https://zenodo.org/api/records/10068949/draft/files/923_elm_cases_repository.tar.gz/content"><i><strong>923_elm_cases_repository.tar.gz</strong></i></a> contains input and ouput files used and generated for the analysis of 923 Eukaryotic Linear Motifs (ELM) database entries.</p><p>Each ELM entry is indexed with specific integer id and is composed of a receptor and a ligand protein. </p><p>The archive contains a Table associating ELM indexes with the ELM entry information, 5 directories and a README file detailing their contents:</p><ul><li>the table describing ELM entries -> FILE <strong>Table_923ELM_uid_delimitations_info_for_archive.txt</strong></li><li>the initial raw sequence and multiple sequence alignment (MSA) data for every chain -> DIRECTORY <strong>fasta_msa/</strong></li><li>the concatenated MSA model for every ELM complex and protocol used -> DIRECTORY <strong>af2_elm_coali_inputs/</strong></li><li>the best model of every AF2 protocol for every complex according to the AF2 -> DIRECTORY <strong>af2_elm_models/</strong></li><li>the best model cut in the ligand part to select only the ELM motifs as used for the evaluation of the models -> DIRECTORY <strong>elm_cut_models/</strong></li><li>the reference structures used for the evaluation of the models -> DIRECTORY <strong>ref_capri_curated/</strong></li></ul><p><i>The models in this archive were generated using AlphaFold2-Multimer v2.3</i></p>
Supplementary Data: Global fits if simplified models for dark matter with GAMBIT II. Vector dark matter with an s-channel vector mediator
<p>This record contains the YAML files, data files, and some of the plotting scripts for: "Global fits of simplified models for dark matter with GAMBIT II. Vector dark matter with an s-channel vector mediator".</p> <p>Samples have been created using GAMBIT and figures can be reproduced with pippi. Plotting scripts (*.pip) are designed to work with either the original version of pippi 2.1 or the forked unreleased version. The provided scripts do not reproduce all the figures in the paper exactly.</p> <p>To save storage space, all samples have been compressed using <code>tar</code>. To inflate each dataset after downloading run <code>tar -zxvf <samples>.hdf5.gz</code>.</p> <p>To facilitate uploading to Zenodo, several of the data files have been thinned to only include enough points to reproduce plots.</p>
Data for: "Dynamic species distribution modeling reveals the pivotal role of human-mediated long-distance dispersal in plant invasion"
<p>All the data needed to reproduce the results and Figures of our article:</p> <p>Botella, C., Bonnet, P., Hui, C., Joly, A., & Richardson, D. M. (2022). Dynamic Species Distribution Modeling Reveals the Pivotal Role of Human-Mediated Long-Distance Dispersal in Plant Invasion. <em>Biology</em>, <em>11</em>(9), 1293. <a href="https://doi.org/10.3390/biology11091293">https://doi.org/10.3390/biology11091293</a></p> <p>Please, find the R scripts and guidelines to reproduce our results on the article's Github repository :</p> <p><a href="https://github.com/ChrisBotella/plectranthus_barbatus/tree/main">https://github.com/ChrisBotella/plectranthus_barbatus/tree/main</a></p>
Rps19 R67∆ mutation creates a model of Diamond-Blackfan anemia and reveals downstream mediators of p53 pathway.
<p>Diamond-Blackfan anemia (DBA) is a rare bone marrow failure syndrome accompanied by cardiovascular, skeletal, and urogenital abnormalities. Most of the affected individuals carry mutations in ribosomal proteins, including S19 (Rps19), a part of the 40S ribosomal subunit. We developed a transgenic model harboring deletion of conserved Arg 67 in <em>RPS19</em>, which is the site of post-translational modification by protein-arginine methyl transferase family and could show that the defect in Rps19 causes phenotype in perfect overlap with the DBA including hematologic dysfunctions, hypotrophy, intrinsic anemia, severe craniofacial, skeletal, urogenital, cardiovascular, and cerebral abnormalities leading to premature lethality during the adolescence of the mouse. This DBA mouse model exhibited activation of the Trp53 signaling pathway in hematopoietic stem cells (HSCs) leading to reduced erythroid lineage development. Competitive transplantation assays using Rps19-deficient bone marrow cells confirmed that HSCs and their progeny lineages were affected while their differentiation was rescued after inactivation of the tumor suppressor Trp53 showing that the development of the DBA phenotype significantly involves non-canonical components of the p53 signaling pathway in the etiopathogenesis of DBA with the Rps19R67∆ mutation leading to the disrupted hematopoietic hierarchy starting at the stage of short-term repopulating stem cells. The activated p53 pathway was mediated by downstream molecules Zmat3, Phlda3, and Eda2r, whose overall function in the pathology of DBA involve erythroid differentiation blockade coupled with cell proliferation and survival disruption. To conclude, the new DBA model represents a powerful tool for exploring new therapeutic options for DBA.</p>
Model Output for Eddy Mediated Mixing in the Equatorial Pacific
<p>This repository contains processed model outputs used in the "Eddy Mediated Mixing in the Equatorial Pacific" submitted manuscript. </p>
Dataset for Gelatinous zooplankton-mediated carbon flows in the global oceans: A data-driven modeling study
<p>Gridded dataset of gelatinous zooplankton (GZ) biomass (mg C m<sup>-3</sup>) and numeric density (individuals m<sup>-3</sup>), time-averaged, in a 1-degree grid. Data are separated by phyla: Cnidaria, Ctenophora, and Chordata (pelagic tunicates). Original data compiled as part of the Jellyfish Database Initiative Project (JeDI; Condon et al. 2015, doi:10.1575/1912/7191) and converted to carbon biomass units for Lucas et al. 2014.</p> <p>Cnidarian additions to this dataset include records from the northern California Current (Brodeur et al., 2014) and Gulf of Mexico (Robinson et al., 2015). Chordata additions include salps from the Bermuda Atlantic Time Series (BATS; Stone & Steinberg, 2014), Western Antarctic Peninsula (WAP; Steinberg et al., 2015), and Southern Ocean, from KRILLBASE (Atkinson et al., 2017). Note that we excluded the KRILLBASE records from the WAP region that to prevent double-counting. See Methods in Luo et al. (2020) for details on biometric conversions to carbon biomass.</p> <p>Data were averaged by time (season, then year), and then within each 1-degree grid cell.</p> <p> </p> <p> </p> <p>Code for the model using this dataset is available at: <a href="https://github.com/jessluo/gz_biogeochem_pub">https://github.com/jessluo/gz_biogeochem_pub</a></p> <p> </p> <p><strong>Luo, Jessica Y.</strong>, Condon, R. H., Stock, C. A., Duarte, C. M., Lucas, C. H., Pitt, K. A., & Cowen, R. K. (2020). Gelatinous zooplankton‐mediated carbon flows in the global oceans: A data‐driven modeling study. <em>Global Biogeochemical Cycles</em>, 34, e2020GB006704. <a href="https://doi.org/10.1029/2020GB006704">https://doi.org/10.1029/2020GB006704</a></p>
Simulation models from: Can CRISPR-mediated gene drive work in pest and beneficial haplodiploid species?
<p>Gene drives based on CRISPR/Cas9 have the potential to reduce the enormous harm inflicted by crop pests and insect vectors of human disease, as well as to bolster valued species. In contrast with extensive empirical and theoretical studies in diploid organisms, little is known about CRISPR gene drive in haplodiploids, despite their immense global impacts as pollinators, pests, natural enemies of pests, and invasive species in native habitats. Here we analyze mathematical models demonstrating that, in principle, CRISPR homing gene drive can work in haplodiploids, as well as at sex-linked loci in diploids. However, relative to diploids, conditions favoring the spread of alleles deleterious to haplodiploid pests by CRISPR gene drive are narrower, the spread is slower, and resistance to the drive evolves faster. By contrast, the spread of alleles that impose little fitness cost or boost fitness was not greatly hindered in haplodiploids relative to diploids. Therefore, altering traits to minimize damage caused by harmful haplodiploids, such as interfering with transmission of plant pathogens, may be more likely to succeed than control efforts based on introducing traits that reduce pest fitness. Enhancing fitness of beneficial haplodiploids with CRISPR gene drive is also promising.</p>
Data from: Climate-mediated hybrid zone movement revealed with genomics, museum collection and simulation modeling
Climate-mediated changes in hybridization will dramatically alter the genetic diversity, adaptive capacity and evolutionary trajectory of interbreeding species. Our ability to predict the consequences of such changes will be key to future conservation and management decisions. Here we tested through simulations how recent warming (over a 32-year period) is affecting the geographic extent of a climate-mediated developmental threshold implicated in maintaining a butterfly hybrid zone (Papilio glaucus and Papilio canadensis; Lepidoptera: Papilionidae). These simulations predict a 68 km shift of this hybrid zone. To empirically test this prediction, we assessed genetic and phenotypic changes using contemporary and museum collections and document a 40 km northward shift of this hybrid zone. Interactions between the two species appear relatively unchanged during hybrid zone movement. We found no change in the frequency of hybridization and regions of the genome that experience little to no introgression moved largely in concert with the shifting hybrid zone. Model predictions based on climate scenarios predict this hybrid zone will continue to move northward, but with substantial spatial heterogeneity in the velocity (55-144 km/1°C), shape, and contiguity of movement. Our findings suggest that the presence of non-climatic barriers (e.g., genetic incompatibilities) and/or non-linear responses to climatic gradients may preserve species boundaries as the species shift. Further, we show that variation in the "geography" of hybrid zone movement could result in evolutionary responses that differ for geographically distinct populations spanning hybrid zones and thus have implications for the conservation and management of genetic diversity.
Identification of a small molecule Tim-3 inhibitor to potentiate T cell-mediated antitumor immunotherapy in preclinical models
<p><span>T cell immunoglobulin and mucin-containing molecule 3 (Tim-3), expressed in dysfunctional and exhausted T cells, has been widely acknowledged as a promising immune checkpoint target for tumor immunotherapy. Here, using a strategy combining virtual and functional screening, we identified a compound named ML-T7 that targets the FG-CC' cleft of Tim-3, a highly conserved binding site of </span><span>phosphatidylserine</span><span> (PtdSer) and carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1). ML-T7 enhanced the survival and antitumor activity of </span><span>primary CD8<sup>+</sup> cytotoxic T lymphocytes (CTLs) and human chimeric antigen receptor (CAR) T cells and reduced their exhaustion </span><span>in vitro and in vivo</span><span>. In addition, ML-T7 promoted NK cells' killing activity and DC antigen-presenting capacity, consistent with the reported activity of Tim-3.</span><span> Notably, ML-T7 strengthened DCs' functions through both Tim-3 and Tim-4, consistent with the hypothesis that Tim-4 contains a similar FG-CC' loop. Intraperitoneal dosing of ML-T7 showed comparable tumor inhibitory effects to Tim-3 blocking antibody. ML-T7 reduced syngeneic tumor progression in both wildtype and Tim-3 humanized mice and alleviated the immunosuppressive microenvironment. Furthermore, combined ML-T7 and anti-PD-1 therapy had greater therapeutic efficacy than monotherapy in mice, supporting further development of ML-T7 for tumor immunotherapy. Our study demonstrates a potential small molecule for selectively blocking Tim-3 and warrants further study.</span></p>
Hematopoietic Tumors in a Mouse Model of X-linked Chronic Granulomatous Disease after Lentiviral Vector-Mediated Gene Therapy
<p>Chronic granulomatous disease (CGD) is a rare inherited disorder due to loss-of-function mutations in genes encoding the NADPH oxidase subunits. Hematopoietic stem and progenitor cell (HSPC) gene therapy (GT) using regulated lentiviral vectors (LVs) has emerged as a promising therapeutic option for CGD patients. We performed non-clinical Good Laboratory Practice (GLP) and laboratory-grade studies to assess the safety and genotoxicity of LV targeting myeloid specific Gp91phox expression in X-linked chronic granulomatous disease (XCGD) mice. We found persistence of gene-corrected cells for up to 1 year, restoration of Gp91phox expression and NADPH oxidase activity in XCGD phagocytes, and reduced tissue inflammation after LV-mediated HSPC GT.<br> Although most of the mice showed no hematological or biochemical toxicity, a small subset of XCGD GT mice developed<br> T cell lymphoblastic lymphoma (2.94%) and myeloid leukemia (5.88%). No hematological malignancies were identified in C57BL/6 mice transplanted with transduced XCGD HSPCs. Integration pattern analysis revealed an oligoclonal composition with rare dominant clones harboring vector insertions near oncogenes in mice with tumors. Collectively, our data support the long-term efficacy of LV-mediated HSPC GT in XCGD mice and provide a safety warning because the chronic inflammatory XCGD background may contribute to oncogenesis.</p>
DYRK1a inhibitor mediated rescue of Drosophila models of Alzheimer's disease-Down Syndrome phenotypes
<p>Alzheimer's disease (AD) is the most common neurodegenerative disease which is becoming increasingly prevalent due to ageing populations resulting in huge social, economic, and health costs to the community. Despite the pathological processing of genes such as Amyloid Precursor Protein (APP) into Amyloid-b and Microtubule Associated Protein Tau (MAPT) gene, into hyperphosphorylated Tau tangles being known for decades, there remains no treatments to halt disease progression. One population with increased risk of AD are people with Down syndrome (DS), who have a 90% lifetime incidence of AD, due to trisomy of human chromosome 21 (HSA21) resulting in three copies of APP and other AD-associated genes, such as DYRK1A (Dual specificity tyrosine-phosphorylation-regulated kinase 1A) overexpression. This suggests that blocking DYRK1A might have therapeutic potential. However, it is still not clear to what extent DYRK1A overexpression by itself leads to AD-like phenotypes and how these compare to Tau and Amyloid-b mediated pathology. Likewise, it is still not known how effective a DYRK1A antagonist may be at preventing or improving any Tau, Amyloid-b and DYRK1a mediated phenotype. To address these outstanding questions, we characterised Drosophila models with targeted overexpression of human Tau, human Amyloid-b or the fly orthologue of DYRK1A, called minibrain (mnb). We found targeted overexpression of these AD-associated genes caused degeneration of photoreceptor neurons, shortened lifespan, as well as causing loss of locomotor performance, sleep, and memory. Treatment with the experimental DYRK1A inhibitor PST-001 decreased pathological phosphorylation of human Tau (at serine (S) 262). PST-001 reduced degeneration caused by human Tau, Amyloid-b or mnb lengthening lifespan as well as improving locomotion, sleep and memory loss caused by expression of these AD and DS genes. This demonstrated PST-001 effectiveness as a potential new therapeutic targeting AD and DS pathology.</p>
New Zealand native forest plant cover data for Popovic et al. MEE (2019), Untangling direct species associations from indirect mediator species effects with graphical models.
<p>Forest cover measurements were collected at 1246 native forest sites that form part of a network of permanent 20 x 20 m plots spread throughout New Zealand. A total of 1831 plant species were present in these plots, with the most common being herbs, graminoids, ferns, shrubs and trees. Plant cover (in ordinal categories) was assessed for each species in several tiers at different heights. The cover data we analysed (<em>NZ_native_forest_cover.csv) </em>were the maximum cover recorded over all the tiers at the 964 sites identified as native forests, containing 1311 species with at least one presence. <em>NZ_native_forest_species.csv</em> contains species data including species name, exotic/native, and plant type (tree, shrub, etc.), corresponding to the plant species in the columns of <em>NZ_native_forest_cover.csv</em>.</p> <p>We acknowledge the use of data drawn from the Natural Forest plot data collected between January 2002 and March 2007 by the LUCAS programme for the Ministry for the Environment, New Zealand.</p> <p> </p>
A model-based approach to characterize enzyme-mediated response to antibiotic treatments: towards a model-guided classification
<p>This dataset, taken together with the scripts at <a href="https://gitlab.inria.fr/Public/InBio/esbl-escape">https://gitlab.inria.fr/Public/InBio/esbl-escape</a>, allows one to reproduce the analyses and figures of the article "A model-based approach to characterize enzyme-mediated response to antibiotic treatments: towards a model-guided classification".</p>
Supplementary Data: Global fits of vector-mediated s-channel simplified models for scalar and fermionic dark matter with GAMBIT
<p>This record contains the YAML files, data files, and some of the plotting scripts for: "Global fits of vector-mediated s-channel simplified models for scalar and fermionic dark matter with GAMBIT". The paper can be found at https://arxiv.org/abs/2209.13266.</p> <p>Samples have been created using GAMBIT and figures can be reproduced with pippi.</p>
Antagonism of CGRP Receptor: Central and Peripheral Mechanisms and Mediators in an Animal Model of Chronic Migraine
<p>This dataset includes the findings obtained in the study aimed at investigating in more depth the interplay between the neuropeptide CGRP and the inflammatory mediators within the mechanisms of neuronal sensitization in an animal model of chronic migraine, using olcegepant as a pharmacological probe. Male Sprague-Dawley rats were exposed to nitroglycerin (NTG, 10 mg/kg, i.p.) or NTG vehicle and treated with the CGRP receptor antagonist olcegepant (1 or 2 mg/kg, i.p.) or vehicle (1 ml/kg, i.p.) 1h before the orofacial formalin test. Additionally, sets of rats received NTG (5 mg/kg, i.p.) or vehicle (equivalent volume) co-administered with olcegepant (2 mg/kg i.p.) or its vehicle every other day over a 9-day period. Twenty-four hours after the last injection of NTG (or vehicle), a first set of rats underwent the orofacial formalin test. In a second set, we evaluated the gene expression of CGRP and gene and protein expression of pro-inflammatory cytokines in specific areas involved in migraine pain. We also assessed the CGRP and cytokine levels in serum.</p> <p>The in vivo and ex vivo assessments were:</p> <p>1) Pain-related behavior in the orofacial formalin test: the face rubbing was measured counting the seconds the animal spent grooming the injected area (upper lip, lateral to the nose) with the ipsilateral forepaw or hindpaw 0–6 min (Phase I) or 12–45 min (Phase II) after formalin injection (50 µl, s.c.). The observation time was divided into 15 blocks of 3 min each.</p> <p>2) mRNA expression levels: CGRP, tumor necrosis factor-alpha (TNF-alpha), interleukin-1beta (IL-1beta), transient receptor potential ankyrin 1 (TRPA1) in cervical spinal cord (CSC), medulla-pons and trigeminal ganglia (TGs). mRNA levels were measured by rt-PCR. The same RNA was used for miRNAs (Mir-34a-5p, Mir-382-5p, Mir-155-5p) extraction in the same areas. All samples were assayed in triplicate and gene expression levels were calculated according to 2−∆∆Ct = 2− (∆Ct gene − ∆Ct housekeeping gene) formula by using Ct (cycle threshold) values.</p> <p>3) Pro-inflammatory cytokines in medulla-pons, CSC and TGs were evaluated using ELISA procedure. CGRP, TNF-alpha and IL-1beta serum levels were measured using commercial ELISA kits.</p> <p>Results in brief</p> <p>Olcegepant attenuated nitroglycerin-induced trigeminal hyperalgesia in the second phase of the orofacial formalin test. Interestingly, it also reduced gene expression and protein levels of CGRP, pro-inflammatory cytokines, inflammatory-associated miRNAs (miR-155-5p, miR-382-5p and miR-34a-5p) and TRPA1 channels in medulla-pons area, cervical spinal cord and trigeminal ganglia. Similarly, olcegepant reduced the NTG-induced increase of CGRP and inflammatory.</p>
Data on the Model of Loneliness and Smartphone Use Intensity as a Mediator of Self-Control, Emotion Regulation, and Spiritual Meaningfulness in Nomophobia
<p><em>The data collection was conducted in June-July 2022, with 355 participants completing the scales provided through offline paper-pencil surveys in the classroom. The research data was collected from three cities, namely Palembang, Jambi, and Yogyakarta, and consisted of junior high school and high school students, as well as university students. The university student participants were recruited from Ahmad Dahlan University, Jambi University, and Charitas Musi Catholic University. The participants completed the Nomophobia NMP-Q scale (Yildirim & Correia, 2015), the R-UCLA Loneliness Scale (Russell et al., 1980), self-control (Tangney, Baumeister & Boone, 2004), The Difficulties in Emotion Regulation Scale (DERS; Gratz & Roemer, 2004), and Spiritual Meaningfulness which was developed based on the theory of Pargament (2007). All the questionnaires for data collection were in the Indonesian version.</em></p>
Data from: Multi-omic analyses identify molecular targets of Chd7 that mediate CHARGE syndrome model phenotypes
Open the record for dataset details and reuse information.
Data from: Climate-mediated hybrid zone movement revealed with genomics, museum collection and simulation modeling
Open the record for dataset details and reuse information.
Development of an efficient CRISPR-mediated genome editing platform in the diploid-polyploid model system Tragopogon (Asteraceae)
Open the record for dataset details and reuse information.
Identification of a small molecule Tim-3 inhibitor to potentiate T cell-mediated antitumor immunotherapy in preclinical models
Open the record for dataset details and reuse information.
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.