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36,943 results for “HUMANE”
An inflamed human alveolar model for testing the efficiency of anti-inflammatory drugs in vitro
<p>The data set accompanies the study where we developed an inflamed human alveolar epithelium model and to test the resolution<strong><em> </em></strong>lipopolysaccharide (LPS)-induced inflammation <em>in vitro</em> with a corticosteroid, methylprednisolone (MP). A specific focus of the study was in macrophage phenotype shifts in response to these stimuli.</p> <p>The data set includes:</p> <p>- Pro-inflammatory marker (interleukin (IL)-8, tumor necrosis factor α (TNFα), IL1β) secretion data, analysed via ELISA, and cell viability (analysed via lactate dehydrogenase assay) of both monocultures (human monocyte-derived macrophages) and of the multicellular human alveolar model, composed of macrophages, dendritic cells, and epithelial cells. </p> <p>- Barrier permeability data of the multicellular model, assessed via labeled-dextran permeability assay. </p> <p>All the above-stated data is joined in the file: DraslerB_Frontiers 2020_Inflammatory model. Sample codes are explained int he first tabs. </p> <p>- Pro-inflammatory marker gene expression data of the multicellular model, assessed via real time RT-qPCR. The data prepared for analysis and analysed is joined to the above-mentioned folder, whereas the direct PCR runs are joined in the file: DraslerB_Frontiers 2020_Inflammatory model_PCR runs. </p> <p>- Confocal laser scanning microscopy raw files (lsm) of the multicellular model can be opened with an open source software Fiji, based on ImageJ. </p>
Dataset do DH2020 [The Lusophone Digital Humanities and What they (we) are doing from the South: textual corpus analysis and FAIR principles to tackle Hegemony]
<p>Planilha de dados recuperados do Google Scholar utilizado na análise e apresentação da pesquisa empírica intitulada - <strong>The Lusophone Digital Humanities and What they (we) are doing from the South: textual corpus analysis and FAIR principles to tackle Hegemony </strong>- no evento <strong>DH2020 Ottawa</strong>: <a href="https://hcommons.org/deposits/item/hc:32051/">https://hcommons.org/deposits/item/hc:32051/</a></p>
Risk assessment on Glycoalkaloids in feed and food: Occurrence data in food and feed submitted to EFSA and dietary exposure assessment for humans
<p><strong>UPDATE to version 2 of this upload:</strong></p> <p>Also the raw (no data cleaning applied to it) occurrence dataset as extracted from EFSA DWH is provided <em>in csv format</em>. This dataset is compliant with EFSA SSD model and contains two additional columns documenting issues identified in the cleaning process (column: issue) and the action taken (column: action) to address the issue (e.g. delete record or update values in specific fields).</p> <p><strong>Description - Version 1</strong></p> <p><strong>Annex: Tables on GAs on occurrence data in food and feed, and dietary exposure assessment for humans</strong></p> <p>Table A.1. Dietary surveys used for the estimation of acute dietary exposure to GA</p> <p>Table A.2. Number of results and samples per food category submitted to EFSA through the continuous call for data</p> <p>Table A.3. Analytical results excluded from the final dataset used to estimate dietary exposure and the criteria applied for exclusion</p> <p>Table A.4. Occurrence of alpha-chaconine and alpha-solanine (UB mg/kg) in the samples included in the final dataset (left censored results highlighted in yellow)</p> <p>Table A.5. European Starch Association data on feed and potatoes for starch</p> <p>Table A.6. Details acute assessment across surveys (consumption days only)</p> <p>Table A.7. Comparison of exposure summary results obtained using the uniform vs the normal distribution for reduction factors</p>
Human Brain MRI Template and Myelin Atlas
<p>The structural template, quantitative myelin water imaging atlases, tissue segmentations, and regions of interest (ROIs) generated and analyzed for <em>An atlas for human brain myelin content throughout the adult life span</em></p> <p><a href="https://www.nature.com/articles/s41598-020-79540-3">https://www.nature.com/articles/s41598-020-79540-3</a></p>
Data from: The impact of human mobility networks on the global spread of COVID-19
<p>This is empirical dataset from the paper "The impact of human mobility networks on the global spread of COVID-19". Specifically, the dataset includes several files: (a) the COVID-19 network - an origin/destination matrix (i.e., "covid_network.csv"); (b) the common language network - edgelist format (i.e. "edge_list_comlang.csv"); (c) the same continent network - edgelist format (i.e., "edge_list_continent.csv"; (d) the contiguity network (i.e., "edge_list_contig.csv"); (e) the migration network - edgelist format (i.e., "edge_list_migration_in.csv"; (f) the tourism network - edgelist format (i.e., edge_list_tourism_in.csv"); (g) the list of nodes (countries) corresponding to files (b)-(e) (i.e., "nodes.csv"). Additionally, we uploaded the Rcode used in the paper (i.e. "code"), as a .pdf file format, the data source for the figures included in the paper (i.e., "covid_network_matrix.csv", "matrix_migration_out.csv", "matrix_tourism.csv" - Figure 1; "Fig_2_a_matrix_comlang.csv", Fig_2_b_matrix_contig.csv", "Fig_2_c_matrix_continent.csv" - Figure 2; "Fig_3.graphmlz - Figure 3; Fig_4.graphmlz - Figure 4) and the "global network of COVID-19 onset" (an individual-level data) (i.e., "global_covid_network.csv"). </p> <p>For details, please, see the Methods section of the paper: The impact of human mobility networks on the global spread of COVID-19 (Hancean, M.-G., Slavinec, M., Perc, M). </p> <p> </p> <p> </p> <p> </p>
Virus+ Sequence Masked Human Reference Genome (hg19)
<p>A version of the human genome (hg19) originally masked for ribosomal, plant, animal, fungal and low-entropy sequences by Brian Bushnell (<a href="https://zenodo.org/record/1208052#.X5BuTy9h3UI">Bushnell Masked Human Genome</a>) additionally masked for all possible viral sequences.</p> <p>The following commands were used to generate the additional virus sequence masked reference database:</p> <p><strong>1) Download all RefSeq and Neighbor nucleotide records:</strong></p> <p><a href="https://www.ncbi.nlm.nih.gov/nuccore/?term=Viruses[Organism]%20NOT%20cellular%20organisms[ORGN]%20NOT%20wgs[PROP]%20NOT%20gbdiv%20syn[prop]%20AND%20(srcdb_refseq[PROP]%20OR%20nuccore%20genome%20samespecies[Filter])">https://www.ncbi.nlm.nih.gov/nuccore/?term=Viruses[Organism]%20NOT%20cellular%20organisms[ORGN]%20NOT%20wgs[PROP]%20NOT%20gbdiv%20syn[prop]%20AND%20(srcdb_refseq[PROP]%20OR%20nuccore%20genome%20samespecies[Filter])</a></p> <p><strong>2) Shred the downloaded viral genomes using shred.sh from the <a href="https://jgi.doe.gov/data-and-tools/bbtools/">bbtools</a> package</strong></p> <p>shred.sh in=refseq_virus_reformated.fasta out=virus_shred.fasta.gz length=85 minlength=75 overlap=30</p> <p><strong>3) Map shredded virus sequence to the hg19-masked human genome using bbmap.sh from the <a href="https://jgi.doe.gov/data-and-tools/bbtools/">bbtools</a> package</strong></p> <p>bbmap.sh ref=hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz in=virus_shred.fasta.gz outm=map_human_all_viruses.sam minid=0.90</p> <p><strong>4) Mask virus sequenced mapped regions from the hg19-masked human genome using bbmask.sh from the <a href="https://jgi.doe.gov/data-and-tools/bbtools/">bbtools</a> package</strong></p> <p>bbmask.sh in=hg19_main_mask_ribo_animal_allplant_allfungus.fa.gz out=human_virus_masked.fasta.gz sam=map_human_all_viruses<br> .sam</p> <p><strong>5) Remove all N's to further reduce file size using <a href="https://bioinf.shenwei.me/seqkit/">seqkit</a></strong><br> seqkit -is replace -p "n" -r "" human_virus_masked.fasta.gz > human_virus_masked.fasta_Ns_removed.gz</p> <p><strong>Additional References:</strong></p> <ol> <li><a href="http://seqanswers.com/forums/showthread.php?t=42552">http://seqanswers.com/forums/showthread.php?t=42552</a> for additional information on the original masking of hg19</li> <li><a href="https://jgi.doe.gov/data-and-tools/bbtools/">bbtools</a></li> <li><a href="https://bioinf.shenwei.me/seqkit/">seqkit</a></li> <li><a href="https://www.ncbi.nlm.nih.gov/genome/viruses/">NCBI Virus Genome RefSeq</a></li> </ol>
Human Stromal Antigen 1 (STAG1) Cohesin Subunit SA-1; A Target Enabling Package
<p>Loss of function mutations in the cohesin subunit gene <a href="https://www.ncbi.nlm.nih.gov/gene/10735">STAG2</a> are common in a variety of cancers (1). These cells become dependent on the paralogous cohesin subunit <a href="https://www.ncbi.nlm.nih.gov/gene/10274">STAG1</a> (2-4). Mutants of STAG1 that disrupt the binding to the cohesin subunit <a href="https://www.ncbi.nlm.nih.gov/gene/5885">RAD21</a> cannot complement the loss of STAG2. This TEP examines the druggability of STAG1 as a synthetic lethal strategy to treat <em>stag2<sup>-</sup></em> cancers. The TEP includes crystal structures of two domains of STAG1, alone and in complex with Rad21-rderived peptides. We performed screens of a fragment library and identified small molecules bound to pockets in the two domains of STAG1. We also developed assays for binding of RAD21 peptides to STAG1, which can be used to screen for molecules that disrupt binding.</p>
Analysis of human humoral responses in a typhoid vaccine efficacy trial used for SIMON analysis
<p>The VAST dataset contains data from 72 individuals enrolled in the clinical study to evaluate humoral responses in a typhoid vaccine efficacy trial in a controlled human <em>Salmonella </em>Typhi infection model (see original publication: <a href="https://doi.org/10.3389/fimmu.2019.02582">https://doi.org/10.3389/fimmu.2019.02582</a>). Only day 0 (day of the challenge) log-transformed data were used in the SIMON analysis, as described in the publication (<a href="https://doi.org/10.1101/2020.08.16.252767">https://doi.org/10.1101/2020.08.16.252767</a>). Individuals were vaccinated with either a purified Vi polysaccharide (Vi-PS) vaccine (35 individuals) or the Vi tetanus toxoid conjugate (Vi-TT) vaccine (37 individuals) one month prior to oral challenge with live <em>Salmonella </em>Typhi. Out of 72 individuals, 26 developed an acute typhoid infection following the challenge.</p>
Human Pleckstrin Homology domain Interacting Protein (PHIP); A Target Enabling Package
<p>SGC Oxford has expressed, purified and crystallized the second bromodomain of PHIP as part of the probe programme. Fragment screening and X-ray crystallography identified binders, some of which optimised to uM affinity. However, molecules with probe properties were not obtained. Consequently it has been decided to put the information generated into the public domain.</p>
Human With No Lysine Kinase 3 (WNK3); A Target Enabling Package
<p>Kinases WNK1-4 regulate cation-chloride cotransporters via phosphorylation of SPAK and OSR1 and thereby control salt homeostasis, cell volume and blood pressure. Gain of function mutations in WNK kinases are found in Gordon’s hypertension syndrome suggesting the WNK pathway as a therapeutic target. WNK3 inhibition in particular has also been shown to reduce cerebral injury after Ischemic stroke. Here we present assays and crystal structures that define (i) the molecular basis for disease mutations; (ii) the multiple functional domains of WNK kinases and their protein interactions; (iii) the binding of small molecule kinase inhibitors and a potential allosteric pocket.</p>
Human Hydroxyacid Oxidase (HAO1); A Target Enabling Package
<p>This project provides the tools and data to develop small molecule inhibitors for an inherited metabolic disorder (Primary hyperoxaluria type 1) due to the defective enzyme (<a href="https://www.ncbi.nlm.nih.gov/gene/189">AGXT</a>), by targeting the enzyme (<a href="https://www.ncbi.nlm.nih.gov/gene/54363">HAO1</a>) upstream of the glyoxylate metabolic pathway to mitigate the defect (i.e. substrate reduction approach). This TEP package includes recombinant human HAO1 purification protocols, structures of the HAO1 in different states, <em>in vitro </em>assays to detect ligand/inhibitor binding (DSF, SPR) and enzyme activity (amplex red assay) of human HAO1, as well as initial chemical matters identified from crystallography-based fragment screening.</p>
Human Methylene- tetrahydrofolate reductase (MTHFR) A Target Enabling Package (TEP)
<p>The folate and methionine cycles are essential metabolic pathways for life, involved respectively in DNA synthesis and generation of the ubiquitous methyl donor S-adenosylmethionine (SAM). The enzyme 5,10-methylenetetrahydrofolate reductase (<a href="https://www.ncbi.nlm.nih.gov/gene/4524">MTHFR</a>) represents a key regulatory connection between these cycles, hence exerting a strong influence on an array of diseases. This TEP presents the first structures for any eukaryotic MTHFR, revealing a novel SAM-binding fold. The TEP provides additional mass spectrometry, activity assay and biophysical binding methods yielding mechanistic insights into how phosphorylation and allosteric binding of SAM act in concert to inhibit MTHFR activity. This work further provides the starting point for the design of tool molecules (e.g. SAM-analogues) aimed at disrupting the SAM-induced inhibition of MTHFR activity.</p> <p> </p>
2d U-net models trained to segment human placental maternal/fetal blood volumes and blood vessels from syncrotron micro-CT data along with a sample data volume.
<p>This dataset contains a 512 x 512 x 512 pixel volume taken from an imaging dataset of human placental tissue collected at Diamond Light Source Manchester Imaging Branchline, I13-2 on visits MG23941 and MG22562 using in-line high-resolution synchrotron-sourced phase contrast micro-computed X-ray tomography. This data is saved in HDF5 format with a uint8 datatype. Alongside this are two 2d binary U-net models that have been trained to segment this data. One model segments the data into regions of maternal/fetal blood volume, the other segments the blood vessels. Both models were trained using the fastai python package, which utilises the pytorch library. These models were used to segment the data in our paper "A massively multi-scale approach to characterising tissue architecture by synchrotron micro-CT applied to the human placenta" which can be found at <a href="https://www.biorxiv.org/content/10.1101/2020.12.07.411462v1">https://www.biorxiv.org/content/10.1101/2020.12.07.411462v1</a>. The code used for training the U-net models and for predicting the segmentation of the data volume can be found at <a href="https://github.com/DiamondLightSource/placental-segmentation-2dunet">https://github.com/DiamondLightSource/placental-segmentation-2dunet</a> and is published at <a href="https://doi.org/10.5281/zenodo.4252562">https://doi.org/10.5281/zenodo.4252562</a> </p>
Human T-box transcription factor T (Brachyury); A Target Enabling Package
<p>Chordoma is a rare cancer occurring along the spinal cord (OMIM: <a href="https://www.omim.org/entry/215400">215400</a>). Chordoma is derived from an embryonic tissue, the notochord, and over-expresses the embryonic transcription factor T-box transcription factor T, the homologue of mouse Brachyury. Chordomas are “genomicaly silent” cancers that do not carry an extensive mutation load. Recent studies indicate that expression of TBXT is essential for persistence and growth of chordoma cells. As TBXT is not expressed in any post-embryonic tissues, it could be an excellent target for treatment of chordoma. The long-term aim of this project is to test whether TBXT can be targeted with small molecules with sufficient affinity and specificity to be therapeutically useful. In this TEP we have determined crystal structures of the DNA-binding domain (DBD) of TBXT with and without cognate DNA oligonucleotides. The DNA-free protein crystals were used in a high-throughput fragment screen to identify 29 fragments bound in 6 clusters. The crystal structures of the bound fragments provide starting points for development of stronger binders which could be used to disrupt TBXT activity or to induce the degradation of the protein through a Proteolysis-targeting chimeric molecule (PROTAC) approach.</p>
Body measurements of human adults, with repeated readings
<p>This data file contains body measurements of participants of a course in morphometrics. The data are entirely anonymized and the compliance for publication of the data in the present form was obtained from each person.</p> <p>The participants were asked to measure themselves twice at intervals of one or two days, which resulted in reading a and reading b. The following measurements were taken (in mm):</p> <p>arm.l -> arm length<br> bod.h -> total body height<br> foo.l -> foot length<br> hea.c -> head circumference<br> leg.l -> leg length</p> <p>The dataset may be considered for demonstration of measurement error.</p>
Human TMEM16K (ANO10); A Target Enabling Package
<p>There are ten members of the TMEM16/Anoctamin family of proteins in mammals. Although the first members of this family to be discovered, TMEM16A and TMEM16B, have a calcium-regulated chloride channel function, subsequently other members of the family, such as TMEM16F, were found to have lipid scramblase activity combined with non-selective ion channel activity. TMEM16K was a relatively understudied member of the family despite the observation that mutations in TMEM16K have been linked to the genetic disease autosomal recessive spinocerebellar ataxia Type 10 (Also known as SCAR10 or ARCA3). SCAR10 is a late-onset neurodegenerative disorder which causes marked atrophy of the cerebellum with consequential deterioration in limb co-ordination, speech and eye movement. We have solved several structures of human TMEM16K through X-ray crystallography and cryo-EM capturing both active and inactive conformational states. Through collaborations, we have investigated TMEM16K’s function and location in cells. We were able to show that TMEM16K acts as a lipid scramblase with non-selective ion channel activity that is sensitive to both Ca<sup>2+</sup> and lipid chain lengths. We also showed that TMEM16K mainly resides in the endoplasmic reticulum where it may be regulated by the ER’s unique lipid profile. Our highest resolution cryo-EM structure for TMEM16K allowed us to identify a bound lipid in the cavity behind the groove that transports the lipid headgroups and this lipid binding site may represent an allosteric modulator site, providing a direction for the design of binders which could modulate TMEM16K activity in cells.</p>
Human Dolichyl-Phosphate Alpha-N-Acetyl glucosaminyl transferase (DPAGT1); A Target Enabling Package
<p>The ER integral membrane enzyme dolichyl-phosphate alpha-N-acetyl glucosaminyl phosphotransferase (DPAGT1) catalyses the first step in the synthesis of the oligosaccharide-P-P-dolichol unit which provides the glycans structure for N-glycosylation of proteins. Mutations in DPAGT1 cause two muscle weakness conditions, limb-girdle congenital myasthenic syndrome (CMS) and congenital disorder of glycosylation type 1j (CDG1j). DPAGT1 overexpression has also been implicated in oral cancer. We have produced and solved structures of this integral membrane enzyme, DPAGT1 with the V264G mutation found in a patient with CMS, and complexes with a 50 nM inhibitor, tunicamycin. We have developed enzymatic activity and thermostability assays which have allowed us to assess the activity and stability of DPAGT1 mutants and the effect of small molecules. There are > 20 DPAGT1 associated missense variants in patients with CMS and CDG1j. We have mapped these mutations to the structure, and we will used the assays described here to assess how the activity and stability of DPAGT1 is affected by these missense variants.</p>
Human Hyperpolarization Activated Cyclic Nucleotide Gated Ion Channel 4 (HCN4); A Target Enabling Package
<p>HCN4 is one of four hyperpolarisation activated cyclic nucleotide gated ion channels. It is responsible for the pacemaker or funny (If) current in the heart and is required for maintenance of a stable heartbeat. Mutations in HCN4 lead to a number of arrhythmias. HCN4 is the target for the angina drug ivabradine, which reduces HCN4 activity. However, ivabradine is non-selective, affecting all of the four HCN channels. HCN4 is a close homologue of HCN2, which is a target for neuropathic and inflammatory pain treatment. We have solved the structure of HCN4 both in complex with cyclic AMP and without nucleotide. Comparison of our HCN4 structure with that of the related HCN1 channel (86% identity) allows us to suggest ways to design selectivity for small molecule inhibitors between these closely related channels. </p>
Human TWIK-related Acid-Sensitive K+ Channel 1 (TASK1): A Target Enabling Package
<p>The TWIK related acid-sensitive K<sup>+</sup> channel 1 (<a href="https://www.ncbi.nlm.nih.gov/gene/3777">TASK-1</a>) belongs to the family of two-pore domain potassium (K<sub>2P</sub>) channels. It regulates resting membrane potential and is expressed in cardiomyocytes, neurons and vascular smooth muscle cells. Loss of function mutations in TASK-1 lead to primary pulmonary hypertension type 4 (PPH4) which is often fatal in mid-life (1). We have produced TASK-1 and determined structures of this protein alone and in complex with two highly potent inhibitors, BAY 1000493 and BAY 2341237, with EC<sub>50</sub> values of 9.5 nM and 7.6 nM, respectively. We have used a two-electrode voltage clamp assay to measure the effect of mutations in TASK-1 and the effect of inhibitors. The native structure of TASK-1 also allowed us to map the six known disease mutations leading to PPH4.</p>
What do studies in wild mammals tell us about human emerging viral diseases in Mexico? database
<p>The database used in the article "<strong>What do studies in wild mammals tell us about human emerging viral diseases in Mexico?</strong>". It contains all available records of viral zoonotic and potential zoonotic species in Mexican wild mammals.</p> <p>The first file is a .csv file and the second one is .xls</p>
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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.