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13,587
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ShareScore release 0.9.0
Dataset results
13,587 results for “specification”
The specific interactions of Bcl9/Bcl9L with b-catenin and Pygopus promote breast cancer growth, invasion and metastasis
GEO Series GSE182404. Mus musculus. 27 samples. Type: Expression profiling by high throughput sequencing.
Lineage-Specific Chromatin Signatures Reveal a Master Lipid Switch in Microalgae
GEO Series GSE59629. Chlamydomonas reinhardtii. 112 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Context-specific regulation of BMAL1 target genes during the circadian cycle in mammals
GEO Series GSE61775. Mus musculus. 58 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis; Expression profiling by high throughput sequencing.
Fate specification of GFAP-negative primitive neural stem cells and their progeny at clonal resolution
GEO Series GSE206844. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
The methylation level alterations from cardiac-specific NPRA-deficient mice.
GEO Series GSE181039. Mus musculus. 20 samples. Type: Methylation profiling by array.
Genome wide SOX4 specific binding sites in BT549 human TNBC cells
GEO Series GSE144012. Homo sapiens. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Functions of the Mediator subunit Med31 in Candida albicans support a role in shaping species-specific gene expression.
GEO Series GSE31632. Candida albicans. 4 samples. Type: Expression profiling by array.
Specific pre-plasma cell states and local proliferation at the dark zone – medulla interface characterize germinal center-derived plasma cell differentiation in lymph node (Figure 4 and Figure 5)
GEO Series GSE275124. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Partial dataset related to the article: "Fibrosis Rescue Improves Cardiac Function in Dystrophin-Deficient Mice and Duchenne Patient-Specific Cardiomyocytes by Immunoproteasome Modulation".
<p>This record contains raw data related to the article: "Fibrosis Rescue Improves Cardiac Function in Dystrophin-Deficient Mice and Duchenne Patient-Specific Cardiomyocytes by Immunoproteasome Modulation".</p> <p>Abstract</p> <p>Patients affected by Duchenne muscular dystrophy (DMD) develop a progressive dilated cardiomyopathy<br> characterized by inflammatory cell infiltration, necrosis, and cardiac fibrosis. Standard<br> treatments consider the use of b-blockers and angiotensin-converting enzyme inhibitors that are<br> symptomatic and unspecific toward DMD disease. Medications that target DMD cardiac fibrosis are<br> in the early stages of development. We found immunoproteasome dysregulation in affected hearts<br> of mdx mice (murine animal model of DMD) and cardiomyocytes derived from induced pluripotent<br> stem cells of patients with DMD. Interestingly, immunoproteasome inhibition ameliorated cardiomyopathy<br> in mdx mice and reduced the development of cardiac fibrosis. Establishing the<br> immunoproteasome inhibitionedependent cardioprotective role suggests the possibility of modulating<br> the immunoproteasome as new and clinically relevant treatment to rescue dilated cardiomyopathy<br> in patients with DMD.</p>
Link to dataset related to article "FOXA2 controls the cis-regulatory networks of pancreatic cancer cells in a differentiation grade-specific manner."
<p>Differentiation of normal and tumor cells is controlled by regulatory networks enforced by lineage-determining transcription factors (TFs). Among them, TFs such as FOXA1/2 bind naïve chromatin and induce its accessibility, thus establishing new gene regulatory networks. Pancreatic ductal adenocarcinoma (PDAC) is characterized by the coexistence of well- and poorly differentiated cells at all stages of disease. How the transcriptional networks determining such massive cellular heterogeneity are established remains to be determined. We found that FOXA2, a TF controlling pancreas specification, broadly contributed to the cis-regulatory networks of PDACs. Despite being expressed in both well- and poorly differentiated PDAC cells, FOXA2 displayed extensively different genomic distributions and controlled distinct gene expression programs. Grade-specific functions of FOXA2 depended on its partnership with TFs whose expression varied depending on the differentiation grade. These data suggest that FOXA2 contributes to the regulatory networks of heterogeneous PDAC cells via interactions with alternative partner TFs.</p>
Dataset related to article "Donor-Specific Anti-HLA Antibodies in Haploidentical Stem Cell Transplantation with Post-Transplantation Cyclophosphamide: Risk of Graft Failure, Poor Graft Function, and Impact on Outcomes."
<p>The presence of donor-specific anti-HLA antibodies (DSA) is associated with a 10-fold increased risk of graft failure in haploidentical stem cell transplantation (haplo-SCT). Consensus guidelines from the European Society for Blood and Marrow Transplantation set a mean fluorescence intensity (MFI) >1000 as a cutoff for DSA positivity. In the absence of an alternative donor, it is recommended that patients undergo desensitization therapy, especially with high DSA levels (>5000 MFI). The aim of this study was to analyze the impact of DSA on risk of graft failure and poor graft function, as well as on major outcomes in a consecutive cohort of patients who were systematically screened for DSA before haplo-SCT. A total of 141 consecutive patients were candidates for unmanipulated haplo-SCT with post-transplantation cyclophosphamide (PT-Cy) at our center between January 2012 and January 2018, and 135 were analyzed for the presence of HLA antibodies. Of these 134 patients underwent haplo-SCT. HLA antibodies were detected in 40 patients, including 19 with DSA and 21 without DSA. Ten of the 19 patients with DSA underwent transplantation using that donor, whereas 2 underwent a desensitization program before transplantation. Only 2 patients experienced primary graft failure (1.4 %), both of whom were without DSA. Twenty patients developed a poor graft function (15%). The 3-year overall survival (OS), 3-year progression-free survival (PFS), and 1-year nonrelapse mortality (NRM) were analyzed according to the presence or absence of DSA. No statistically significant difference was found. No impact of the presence of DSA on the risk of developing graft failure and poor graft function was revealed. Major outcomes of transplantation were analyzed separately in patients with poor graft function and those with good graft function. The 3-year OS, 3-year PFS, and 1-year NRM in good graft function and poor graft function populations were 62% versus 20% (P < .0001), 53% versus 20% (P < .0001), and 12% versus 40% (P = .009), respectively. The presence of low-level DSA in the absence of desensitization did not correlate with the risk of developing graft failure and poor graft function. Patients who experienced poor graft function had worse outcomes than patients with good graft function.</p>
Data sets for Perspective: SARS-CoV-2's potential mechanism of regulating cellular responses through depletion of specific host miRNAs
<p>Using a bioinformatic analysis of human miRNA potential interactions with the SARS-CoV-2’s genome, we examined the potential miRNA target sites in 7 coronavirus genomes that include SARS-CoV-2, MERS-CoV, SARS-CoV, and 4 non-pathogenic coronaviruses. (<strong>Data Set 1</strong>).</p> <p><em>Our approach was to examine and compare 3 pathogenic and 4 non-pathogenic strains of HCoVs. The HCoVs' RNA genomes of pathogenic strains were SARS-CoV-2 (NC_045512.2), SARS-CoV (NC_004718.3), MERS-CoV (NC_019843.3). The non-pathogenic strains were HCoV-OC43 (KU131570.1), HCoV-229E (NC_002645.1), HCoV-HKU1 (KF686346.1), and HCoV-NL63 (NC_005831.2). These coronaviruses were tested against the set of 896 confident mature human miRNA sequences that were obtained from the miRBbase v2.21 using the RNA22 v2 microRNA target discovery tool web-server. In order to reduce the false discovery rate of the MTS predictions, the most strict parameters were applied to the default computation workflow using a specificity of 92% versus a sensitivity of 22%.</em></p> <p><em>In <strong>Data set 2</strong>, using the miRDIP database with only top 1% of the most probable targets considered, we analyzed the potential targets of miRNA that could be bound to either the pathogenic, the non-pathogenic or both groups of HCoVs. </em></p> <p>In <strong>Data set 3</strong>, using miRNAFold webserver we identified 10 pre-miRNA sequences in the <em>SARS-CoV-2</em> RNA sequence that could potentially enter the human RNAi pathway.</p> <p>The graphical summary of our working hypothesis is provided in the<strong> graphical abstract</strong>.</p> <p> </p> <p> </p>
Reconstruction of hippocampus CA1 stratum radiatum, interneuron-specific 1
<p>title : Reconstruction of hippocampus CA1 cell morphologies</p> <p>specimen : Rattus norvegicus</p> <p>sex : male</p> <p>weight : 100-200 g</p> <p>This neuron was recorded and filled with biocytin in a 450-500 µm thick coronal slice of adult rat hippocampus, using sharp electrodes (for methods see PMID: 11807843). The fixed slice was resectioned at 50-60 µm and the cell reconstructed with Neurolucida using a 100x oil immersion objective.</p>
Lookup Tables and Code for "Impact of Scene-Specific Enhancement Spectra on Matched Filter Greenhouse Gas Retrievals from Imaging Spectroscopy"
<p>Lookup Tables and Code for <a href="https://doi.org/10.1016/j.rse.2021.112574">"Impact of Scene-Specific Enhancement Spectra on Matched Filter Greenhouse Gas Retrievals from Imaging Spectroscopy"</a></p><p>The <a href="https://hive.utah.edu/concern/datasets/9w0323039?locale=en">original dataset link</a> is broken, so I uploaded it here for personal use.</p>
Artifact of "How Effective are Large Language Models in Generating Software Specifications?"
<p>We release the artifact of paper "How Effective are Large Language Models in Generating Software Specifications?" For more details, please refer to the readme.md in the folder.</p>
Dataset related to article " Mapping region-specific seizure-like patterns in the in vitro isolated guinea pig brain"
<p><strong>Raw data and statistical analysis of the experiments of the paper. they describe the typical and specific seizure-like activity recorded in the isolated guinea pig brains after application of the two proconvulsant bicuculline and 4-aminopyridine.</strong></p>
Data set of "Context-sensitive Requirements Search in Natural Language Specifications"
<p>We use this data set for the evaluation of our Context-sensitive Requirements Search approach. It contains three files and 15 searches.</p> <p> </p> <p><strong>Attribution</strong></p> <p>The foundation of this data set is PURE:<br> A. Ferrari, G. O. Spagnolo, and S. Gnesi. <em>PURE: a Dataset of Public Requirements Documents</em>. Version 1.0. Sept. 2018.<br> Available at: <a href="https://doi.org/10.5281/zenodo.1414117">https://doi.org/10.5281/zenodo.1414117</a></p> <p>The original data is licensed under <a href="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</a></p> <p> </p> <p><strong>Annotations</strong></p> <ul> <li>Each of the provided files contains annotations that we created with Label Studio for the corresponding file of the PURE data set.</li> <li>These annotations depict the search results of Plain Keyword Search (PKS) and the corresponding gold standard.</li> <li>The following is an example of an annotation in the .json file:</li> </ul> <pre><code class="language-json">{ "id": "UnaxUjB6oY", "meta": { "text": ["0"] }, "type": "labels", "value": { "end": "/text()[2]", "text": "speed", "start": "/text()[2]", "labels": ["speed: train speed profile"], "endOffset": 364, "startOffset": 359, "globalOffsets": { "end": 1403, "start": 1398 } }, "origin": "manual", "to_name": "text", "from_name": "ner" },</code></pre> <p> </p> <p><strong>Important Json attributes to consider</strong></p> <p><strong>Meta</strong></p> <p>We encode the relevance of each result in its metadata.</p> <p><em>Example:</em></p> <pre><code class="language-json">"meta": { "text": ["0"] },</code></pre> <ul> <li>1 = relevant for this search and found by PKS</li> <li>0 = irrelevant for this search but found by PKS</li> <li>-1 = relevant for this search and not found by PKS</li> </ul> <p> </p> <p><strong>Labels</strong></p> <p>This element is the search identifier we use in Label Studio. It corresponds to the table in the thesis that describes each search in detail.</p> <p><em>Example:</em></p> <pre><code class="language-json">"labels": ["speed: train speed profile"],</code></pre> <p> </p> <p><strong>GlobalOffsets</strong></p> <p>"globalOffsets" describes the position of a label in the text.</p> <p><em>Example:</em></p> <pre><code class="language-json">"globalOffsets": { "end": 1403, "start": 1398 }</code></pre> <p> </p>
Dataset related to article "COMPARISON ON WELL-BEING, ENGAGEMENT AND PERCEIVED SCHOOL CLIMATE IN SECONDARY SCHOOL STUDENTS WITH LEARNING DIFFICULTIES AND SPECIFIC LEARNING DISORDERS: AN EXPLORATORY STUDY"
<p>xls. file with of all variables analyzed in the study: gender, groups, socio-economic background, engagement scale, school climate scale, items of Big Five Inventory questionnaire and items Comprehensive Inventory of Thriving.</p> <p> </p>
Longitudinal humoral analysis in RSV-infected infants points to pre-existing strain-specific G and evolving cross-reactive F antibodies against RSV
<p>dataset for "Longitudinal humoral analysis in RSV-infected infants points to pre-existing strain-specific G and evolving cross-reactive F antibodies against RSV"</p>
Specification and Verification for Unrestricted Algebraic Effects and Handling
<p>This repository serves for the artifact evaluation for the ICFP24 (#95) submission: Specification and Verification for Unrestricted Algebraic Effects and Handling. </p> <p>To get started, please check out the <a href="../api/records/11363460/draft/files/README.md/content" target="_blank" rel="noopener noreferrer">README.md</a> file. </p> <p> </p> <p> </p>
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.