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34,778 results for “diseases”
Data used in the article "Cryptic disease-induced mortality may cause host extinction in an apparently-stable host-parasite system"
<p>These data files include all the capture-history matrices that were used in the article, including two matrices with the age of captured individuals (adults or juveniles) according to the definition presented in the main text. Infection intensity (zoospore equivalents per swab) is provided in separate files for all <em>Rhinoderma darwini</em>i and<em> Eupsophus contulmoensis</em> individuals that tested positive for <em>Batrachochytrium dendrobatidis</em> infection. Also, the R code used for the fully paramaterized matrix population model 1 (including figures) is provided. Other codes used to analyze our data, especifically capture-recapture models, were obtained from Kéry and Schaub 2012 (<em>Bayesian population analysis using WinBUGS. A hierarchical perspective</em>. Waltham, USA: Academic Press.)</p>
Type-II kinase inhibitors that target Parkinson's Disease-associated LRRK2
<p>This dataset includes all of the tabular data used in the tables and figures in the article. Additionally, we provide a table with key resources for data aquisition.</p> <p>Aberrant increases in kinase activity of leucine-rich repeat kinase 2 (LRRK2) are associated with Parkinson’s disease (PD). Numerous LRRK2-selective type-I kinase inhibitors have been developed and some have entered clinical trials. In this study, we present the first LRRK2-selective type-II kinase inhibitors. Targeting the inactive conformation of LRRK2 is functionally distinct from targeting the active-like conformation using type-I inhibitors. We designed these inhibitors using a combinatorial chemistry approach fusing selective LRRK2 type-I and promiscuous type-II inhibitors by iterative cycles of synthesis supported by structural biology and activity testing. Our current lead structures are selective and potent LRRK2 inhibitors. Through cellular assays, cryo-electron microscopy structural analysis, and in vitro motility assays, we show that our inhibitors stabilize the open, inactive kinase conformation. These new conformation-specific compounds will be invaluable as tools to study LRRK2’s function and regulation, and expand the potential therapeutic options for PD.</p>
Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis
<p>We performed comprehensive epigenetic profiling in immune cell samples from patients with ankylosing spondylitis and healthy controls. <br><br><em>Note: Due to Zenodo updating their maximum file limit to 100 files, version 4 </em>(v4) <em>of this archive has been split into 5 compressed archive (tar.gz) files containing all previous and additional files. <br><br></em>Version 4 of this archive (updated 03/06/2025) adds 4 files to the archive that were omitted in previous versions which have now been made available. These were: <em><br></em></p> <ul> <li>RNA_CD8_raw_counts.txt.gz</li> <li>RNA_CD8_normalised_counts.txt.gz</li> <li>RNA_CD14_raw_counts.txt.gz</li> <li>RNA_CD14_normalised_counts.txt.gz </li> </ul> <p><em>--------------------------------------------------------------------------------------------------------------------------</em></p> <p><strong>RNA-seq/ATAC-seq/ChIPm/eRNA: </strong>Raw and normalised count data for each gene or epigenetic peak in CD4+ T cells, CD8+ T cells, and CD14+ monocytes from AS patients and healthy controls. File name is in the format: "modality_cell-type_raw/normalised_counts.txt.gz". Table S2 shows which experiments were performed on which samples. </p> <p>This data can be found in the "Raw_Counts.tar.gz" and "Normalised_Counts.tar.gz" archives. </p> <p>--------------------------------------------------------------------------------------------------------------------------</p> <p><strong>ChromHMM: </strong>We used ChromHMM to integrate epigenomic data into a 14-emission state model detailing chromatin functionality in AS patients and healthy controls. ChromHMM filenames are in the format: "ChromHMM_sampleID_celltype_n.bed.gz" where n is the number of states in the ChromHMM emission model.</p> <p>This data can be found in the "ChromHMM_AS_HV.tar.gz" archive. </p> <p>--------------------------------------------------------------------------------------------------------------------------</p> <p><strong>Capture-C: </strong>We performed Capture-C to detect chromosome looping interactions between gene promoters and SNPs associated with ankylosing spondylitis. Capture-C count data are shown in the format: "CaptureC_celltype_gene_Pro/SNP_normalised.unionbdg". We used PeakY to calculate a score for each interaction. PeakY scores are given in the following format: "PeakY_AS/HV_celltype_tier_chrloc_gene_Pro/SNP.txt". gene_Pro and gene_SNP relate to the baitsets given in Table S8.</p> <p>This data can be found in the "CapC_Count_Data.tar.gz" and "PeakY_regions.tar.gz" archives. </p>
PheKnowLator Human Disease KG Benchmarks: Instance-Inverse Relations-OWLNETS (v2.1.0 - May 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.1.0)</strong></p><p><strong>Build Type: </strong><i>Instance-Inverse Relations-OWLNETS</i></p><p><strong>Build Date: </strong>May 01, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/May-01%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Instance-Standard Relations-OWLNETS (v2.1.0 - May 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.1.0)</strong></p><p><strong>Build Type: </strong><i>Instance-Standard Relations-OWLNETS</i></p><p><strong>Build Date: </strong>May 01, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/May-01%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Instance-Standard Relations-OWL (v2.1.0 - May 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.1.0)</strong></p><p><strong>Build Type: </strong><i>Instance-Standard Relations-OWL</i></p><p><strong>Build Date: </strong>May 01, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/May-01%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Instance-Inverse Relations-OWL (v2.1.0 - May 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.1.0)</strong></p><p><strong>Build Type: </strong><i>Instance-Inverse Relations-OWL</i></p><p><strong>Build Date: </strong>May 01, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/May-01%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Class-Standard Relations-OWLNETS (v2.1.0 - May 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.1.0)</strong></p><p><strong>Build Type: </strong><i>Class-Standard Relations-OWLNETS</i></p><p><strong>Build Date: </strong>May 01, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/May-01%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Instance-Standard Relations-OWL (v2.0.0 - February 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Instance-Standard Relations-OWL</i></p><p><strong>Build Date: </strong>February 11, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/February-11%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Instance-Standard Relations-OWLNETS (v2.0.0 - February 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Class-Standard Relations-OWLNETS</i></p><p><strong>Build Date: </strong>February 11, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/February-11%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Instance-Standard Relations-OWL (v2.0.0 - January 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Instance-Standard Relations-OWL</i></p><p><strong>Build Date: </strong>January 25, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/January-25%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Class-Standard Relations-OWLNETS (v2.0.0 - February 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Class-Standard Relations-OWLNETS</i></p><p><strong>Build Date: </strong>February 11, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/February-11%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Instance-Inverse Relations-OWL (v2.0.0 - February 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Instance-Inverse Relations-OWL</i></p><p><strong>Build Date: </strong>February 11, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/February-11%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Class-Inverse Relations-OWL (v2.0.0 - February 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Class-Inverse Relations-OWL</i></p><p><strong>Build Date: </strong>February 11, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/February-11%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Class-Standard Relations-OWL (v2.0.0 - February 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Class-Standard Relations-OWL</i></p><p><strong>Build Date: </strong>February 11, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/February-11%2C-2021">here</a>.</li></ul>
PheKnowLator Human Disease KG Benchmarks: Class-Inverse Relations-OWLNETS (v2.0.0 - February 2021)
<p><strong>PKT Human Disease Knowledge Graph Benchmark Builds (v2.0.0)</strong></p><p><strong>Build Type: </strong><i>Class-InverseRelations-OWLNETS</i></p><p><strong>Build Date: </strong>February 11, 2021</p><p> </p><h3><strong>Important Build Information</strong></h3><p>The benchmarks were originally built and stored using Google Cloud Platform (GCP) resources. For details and a complete description of this process, can be found on GitHub (<a href="https://github.com/callahantiff/PheKnowLator/tree/master/builds#readme">here</a>). Note that we have developed an archive for the builds on Zenodo. While the original GCP resources contained all associated files, due to the file size upload limits associated with each archive, we have limited the uploaded files to the KGs, associated metadata, and log files. The list of resources, including their URLs, and date of download, can all be found in the associated logs.</p><p>Details on each of the files generated by the build process can be found in the file associated with this directory (<a href="https://zenodo.org/records/10065431/files/PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx?download=1">PheKnowLator_HumanDiseaseKG_Output_FileInformation.xlsx</a>).</p><p> </p><p>🚨 <strong>AVAILABLE FILES </strong>🚨 </p><ul><li>Available KG benchmark files are zipped and listed below.</li><li>For additional details on what each file contains, please see the associated Wiki page 👉 <a href="https://github.com/callahantiff/PheKnowLator/wiki/February-11%2C-2021">here</a>.</li></ul>
Inhibition of Parkinson's Disease-related LRRK2 by type-I and type-II kinase inhibitors: activity and structures
<p>Mutations in Leucine Rich Repeat Kinase 2 (LRRK2) are a common cause of familial Parkinson’s Disease (PD), and a risk factor for the sporadic form. Increased kinase activity has been shown in both familial and sporadic PD patients. This has made LRRK2 kinase inhibitors a major focus of drug development efforts in PD. Although significant progress has been made in understanding the structural biology of LRRK2, there are no available structures of LRRK2 inhibitor complexes. To this end, we solved cryo-EM structures of LRRK2, wild-type and PD-linked mutants, bound to the LRRK2-specific type-I inhibitor MLi-2 and the broad-spectrum type-II inhibitor GZD-824. Our structures revealed LRRK2’s kinase in the active-like state, stabilized by type-I inhibitor interactions, and an inactive DYG-out type-II inhibitor complex. The structures also showed how inhibitor-induced conformational changes are affected by the N-terminal half of LRRK2. The structural models provide a template for the rational development of LRRK2 kinase inhibitors covering both canonical inhibitor binding modes.</p>
Raw dataset and additional data for article "Nonmotor symptoms associated with progressive loss of dopaminergic neurons in a mouse model of Parkinson's disease"
<p>Dataset from the project investigating the presence of nonmotor symptoms of Parkinson's disease in a mouse model of progressive loss of dopaminergic neurons (namely,TIF-IADATCreERT2 strain). Mice were tested for executive and cognitive functions (males: Operant Sensation Seeking test, OSS; females: Probabilistic Reversal Learning Task in Intellicages), olfactory acuity (males: buried food test), saccharin preference (males and females), and motor performance (males and females: test using CatWalk apparatus).</p><p>The dataset includes files used to perform statistical analyses but their names may vary from the ones used in the scripts. For the purpose of recreating our analyses, please refer to the GitHub page, where both scripts and input data file names (in 'Raw data files' section) are compliant: https://github.com/annaradli/tif-pd-behavior.</p><p><strong>Description of files:</strong></p><p><i>Raw data files:</i></p><ul><li>animals_info.csv - animals data: genotype, sex, age, Intellicage tag identifier</li><li>catwalk_run_statistics_all_females.csv - data recorded in CatWalk apparatus for females</li><li>catwalk_run_statistics_all_males.csv - data recorded in CatWalk apparatus for males</li><li>females_weight_raw_data_revised.csv - females' body weight (revised for containing Polish words)</li><li>intellicage_raw_data.csv - data recorded in IntelliCage exported to .csv format</li><li>intellicage_raw_data_R.RData - data recorded in IntelliCage in .RData format</li><li>males_weight_raw_data.csv - males' body weight</li><li>olfactory_time_digging_raw_data.csv - time to start digging at the right place in the buried food test</li><li>olfactory_time_retrieve_raw_data.csv- time to retrieve cracker in the buried food test</li><li>oss_raw_data.csv - data recorded in the OSS test</li><li>saccharin_preference_males_raw_data.csv - saccharin preference test results for males</li><li>snvta_cells_count.csv - number of TH+ cells in SN and VTA in male mice (3+3) 14 weeks after tamoxifen treatment</li></ul><p><i>Additional data files:</i></p><ul><li>all_anova.xlsx - summary of two-way ANOVAs of all behavioral tests and weight measurements for males and females</li><li>catwalk_complete.xlsx - CatWalk complete dataset with datapoints</li><li>catwalk_correlation_between_paws.xlsx - correlation coefficients of CatWalk parameters between the left and right paws</li><li>catwalk_reduced.xlsx - CatWalk parameters used in linear regression model reduction of data</li><li>intelli.xlsx - IntelliCage data summarized in bins</li><li>oss.xlsx - operant sensation-seeking data</li></ul><p>v2 contains the corrected 'animals_info.csv' file without an unnecessary column.</p><p>v3 has a revised version of file containing females' weight measurements and also added a file with midbrain cell counts</p><p>v4 has a whole section of 'Additional data files' added</p>
Figure 2. Box-plot head centroid size. A. Rhodnius prolixus instars. B in Head geometric morphometrics of two Chagas disease vectors from Venezuela
Figure 2. Box-plot head centroid size. A. Rhodnius prolixus instars. B. Triatoma maculata instars. Abbreviation: I—First instar; II— Second instar; III—Third instar; IV—Fourth instar; V—Fifth instar; F—Adult female; M—Adult male.
Figure 4. Canonical Variates Analysis head conformation diagram for 136 in Head geometric morphometrics of two Chagas disease vectors from Venezuela
Figure 4. Canonical Variates Analysis head conformation diagram for 136 Triatoma maculata specimens and thin-plate deformation grids. A. V instar–Adults. B. I instar–Adults. C. II instar–III instar.
ScienceDex guides
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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.