Find research datasets worth reusing

opencc-by-4.0Jul 2021View details →

fMRI study of experimental endotoxemia in humans

This dataset was acquired at Hannover Medical School, Hanover, Germany. The study complied with the Declaration of Helsinki, and was approved by the local ethics committee (#7427). All subjects gave written informed consent, and consent to publish their data anonimously. Using high-resolution functional magnetic resonance imaging (fMRI) we recorded brain activity in healthy male subjects undergoing experimental inflammation from intravenous endotoxin. Four fMRI runs covered key phases of the developing inflammation: pre-inflammatory baseline, onset of endotoxemia, onset of proinflammatory cytokinemia, and peak of proinflammatory cytokinemia. We informed the participants that they would either receive an endotoxin or saline injection at some point during the fMRI experiment. However, all subjects received the endotoxin with the start of the second fMRI acquisition. General exclusion criteria included a body mass index of <18 and >30 kg/m², any concurrent medical condition, history of allergies, current use of prescription and non-prescription medications, smoking, and regular high alcohol use. To exclude any inflammatory diseases that may aggravate through the HEM, each subject was interviewed and examined by a physician before being admitted to the study.   Data acquisition Experimental design [min] <ul> <li>-30 -> -10: Baseline fMRI</li> <li>-5: Baseline blood levels</li> <li>0: Endotoxin administration</li> <li>0-20: Second fMRI</li> <li>20, 30: Blood sampling</li> <li>30-50: Third fMRI</li> <li>50, 60, 70, 80: Blood sampling</li> <li>80-100: Fourth fMRI</li> <li>100, 110, 120, 180, 240, 300, 360: Blood sampling</li> </ul> Human endotoxemia model All subjects received an intravenous bolus injection of endotoxin over one minute through an intravenous catheter in an antecubital forearm vein. GMP-grade lipopolysaccharide from Escherichia coli O:113:H10:K-strain (Lot 94332B1) provided by National Institute of Health Clinical Center, Bethesda, MD, USA was prepared for human use by reconstitution with sterile water for injection, shaking for 15 minutes on a vortex shaker and final dilution. We used a dose of 1ng/kg (0,02 ml/kg) body weight. All endotoxin solutions were administered immediately after their preparation. Subjects were injected between nine and ten o’clock in the morning and discharged six to eight hours later, when their symptoms had receded, all altered physiological parameters had demonstrated consistent reduction toward baseline values, and the physical exam was normal. MRI data All MR images were acquired on a Siemens 3T MAGNETOM Skyra using a 64-channel head/neck coil. The scanning protocol consisted of the following sequences (see Sequences.ods): <ul> <li>func_i: Functional whole brain gradient-echo echo-planar images (EPI) (TR=1180 ms; TE=32 ms; 2 mm isotropic resolution; simultaneous multi-slice factor=6; partial Fourier=7/8)</li> <li>func_ref: Reference scan for motion correction and template formation; equivalent to func but without multi-band acceleration (TR=6770 ms)</li> <li>SE_pe1_pe2: Reference scans for unwarping: Two spin-echo images matched to func in distortion without multi-band acceleration; one with the same, the other one with inverted phase encoding direction.</li> <li>t1: T1-weighted magnetisation-prepared rapid acquisition gradient-echo image (MPRAGE) (TR=2400 ms; TE=2.13 ms; TI=1000 ms; 1 mm isotropic resolution; in-plane acceleration factor=2)</li> <li>t2: T2-weighted image (TR=3200 ms; TE=564 ms; 1 mm isotropic resolution; in-plane acceleration factor=2)</li> </ul> fMRI data preprocessing Our preprocessing pipleine (JPreprocessing) is optimised for the brainstem and hypothalamus by avoiding superfluous resampling steps and unnecessary smoothing. On that account, motion correction (MCFLIRT [Jenkinson et al., 2002]) and unwarping (topup [Andersson et al.,2003]) are applied in a single transformation. Afterwards, brain extraction (BET [Smith, 2002]), grand mean scaling and high pass filtering (0.005 Hz) are applied. The data are not smoothed. Two study templates were generated using Advanced Normalization Tools (ANTs [Avants et al., 2008] using antsMultivariateTemplateConstruction2.sh). The first one using the unwarped EPI reference images (func_ref); the second one using the T1-images. Physiological data The following physiological measures were acquired with an MR-compatible BIOPAC MP150 system <ul> <li>Blood pressure (systolic and dyastolic): Non-invasive continuous blood pressure of the digital artery (pulse decomposition analysis using CareTaker)</li> <li>Electrodermal activity</li> <li>Photoplethysmography</li> <li>Respiration (belt)</li> <li>Electrocardiography</li> </ul> Subject information 01    m    25 a    175 cm    70 kg 02    m    44 a    192 cm    84 kg 03    m    27 a    188 cm    85 kg 04    m    19 a    183 cm    99 kg 05    m    20 a    183 cm    90 kg 06    m    26 a    180 cm    78 kg 07    m    21 a    189 cm    80 kg Missing data <ul> <li>sub01: functional data during run3 and run4 is shorter</li> </ul>   Data structure data.csv <ul> <li>Contains blood parameters, symptom ratings, as well as blood pressure measurements for all subjects.</li> </ul> sequences.ods <ul> <li>MRI sequence parameters</li> </ul> subXX <ul> <li>acqparams.txt: Acquisition parameters needed for topup</li> <li>func_i: raw functional data</li> <li>func_ref: Reference image for motion correction and template generation</li> <li>physio.acq: Physiological measurements <ul> <li>Trigger</li> <li>Blood pressure (systolic and dyastolic)</li> <li>Electrodermal activity</li> <li>Photoplethysmogram</li> <li>Respiration</li> <li>Electrocardiogram</li> </ul> </li> <li>physio_cuts.txt: time points in the physio data that correspond to fMRI blocks (start-time end-time TR #volumes)</li> <li>SE_pe1_pe2: auxiliary image for unwarping</li> <li>slicetiming_i.txt: Slice timing information in seconds</li> <li>t1: Defaced T1-weighted image (undefaced images were used for template generation)</li> <li>t2: Defaced T1-weighted image</li> </ul> templates <ul> <li>EPI-template: Generated from unwarped func_ref images <ul> <li>Transformations for all subjects (can be applied using antsApplyTransforms)</li> <li>wb_mask</li> </ul> </li> <li>EPI-2-T1: Transformation from EPI to T1-template</li> <li>MNI-template: T1-template warped into MNI_152 <ul> <li>wb_mask</li> </ul> </li> <li>T1-template: Generated from t1 images <ul> <li>hyp_mask</li> <li>wb_mask</li> </ul> </li> <li>T1-2-MNI: Transformation from T1 to MNI_152-template</li> </ul> JPreprocessing Preprocessing pipeline

opencc-by-4.0Sep 2021View details →

Dataset part one to the publication "CAL-1 as Cellular Model System to Study CCR7-Guided Human Dendritic Cell Migration"

This study was supported in parts by research funding from the Swiss National Science Foundation (grant number 310030_189144), the Thurgauische Stiftung für Wissenschaft und Forschung, and the State Secretariat for Education, Research and Innovation to DFL.

opencc-by-4.0Jul 2020View details →

Data supporting "Changes in human dorsal root ganglion neuron excitability from modulating Nav 1.8 conductance are non-linear and depend on the conductances of the delayed rectifier and M-type potassium currents: a simulation study"

Data and code supporting the article "Changes in human dorsal root ganglion neuron excitability from modulating Nav 1.8 conductance are non-linear and depend on the conductances of the delayed rectifier and M-type potassium currents: a simulation study".

opencc-by-4.0Oct 2021View details →

Supplementary Material: Assessment of Environmental Pollution and Human Exposure to Pesticides by Wastewater Analysis in a Seven-Year Study in Athens, Greece

Supplementary Material

opencc-by-4.0Jul 2021View details →

Human studies carried out with pomegranate-based products (juice and extract).

Background The consumption of <a href="https://www.sciencedirect.com/topics/food-science/pomegranate">pomegranate</a> juices and extracts has long been linked to many health benefits beyond nutrition, described mainly by innumerable <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/preclinical-study">preclinical studies</a>. However, the European Food Safety Authority (EFSA) concluded in 2010 that a cause and effect relationship could not be established between the consumption of pomegranate-derived products and all the health claims presented. There are no additional EFSA opinions on health claims specifically addressed to pomegranate in the last decade. Scope and approach This review comprehensively compiles all human studies conducted on pomegranate. The aim is to discuss these studies critically to identify possible flaws and propose guidelines that might help establish a cause and effect relationship between pomegranate-derived product consumption and health. Key findings and conclusions To date, 86 human studies have evaluated the health benefits of pomegranate juices and extracts. The most promising, albeit scarce, evidence is related to blood pressure improvement. Less evidence deals with inflammation, cancer, cognitive function, physical activity, and <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/intestine-flora">gut microbiota</a> modulation (prebiotic effects). After a decade since EFSA's opinion, human evidence remains inconsistent, making it difficult to support most claimed health effects. The lack of effects and(or) data discrepancy might be attributable to design limitations, including insufficient product characterization and interindividual variability that influence pomegranate polyphenols' bioefficacy. New coordinated strategies between policy makers, research/academic institutions, and industry are needed to move forward. Therefore, this review presents a roadmap to conduct well-designed trials and cover existing gaps, which could establish a cause-effect relation between pomegranate consumption and health benefits beyond nutrition.

opencc-by-4.0Dec 2022View details →

Test-Retest Reliability of the Human Connectome: An OPM-MEG study

OPM-MEG data was acquired during naturalistic viewing of a 600s clip from the film "Dog Day Afternoon". Two sets of MEG data were acquired in each of the 10 scanned subjects. Defaced, T1 weighted MRIs are available for each subject and OPM sensor locations and orientations are given relative to subject anatomy to allow for source reconstruction. An example of MATLAB code used to analyse these data can be found on <a href="https://github.com/LukasRier/Rier2022_OPM_connectome_test-retest">GitHub</a>, which includes all code used to produce the results described in "Test-Retest Reliability of the Human Connectome: An OPM-MEG study" (<a href="https://biorxiv.org/cgi/content/short/2022.12.21.521184v1">biorxiv.org/cgi/content/short/2022.12.21.521184v1</a>) ______________________________________________________________ Updates: v1.0.1 Added missing meshes and AAL source location files v1.1.0 Added video file used in the experiment

opencc-by-4.0May 2023View details →

Input data for the case study reported in "DREAM: an R package for druggability evaluation of human complex diseases".

The data included in this record constituted the input for the case study reported in the manuscript "DREAM: an R package for druggability evaluation of human complex diseases", by Antonio Federico, Michele Fratello, Alisa Pavel, Lena Möbus, Giusy del Giudice, Angela Serra, Dario Greco. The data derive from transcriptomics experiments executed on lesional skin from atopic dermatitis patients and unaffected skin counterparts. The data consists of two files in ".txt" format reporting gene expression data in tabular format, where on the rows are reported genes and on the columns are reported samples. The data is an aggregated and batch-corrected collection of datasets originally downloaded by Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/). The file "GE_Mic_AD_Pamr_MAARS.txt" reports gene expression estimates of lesional skin of atopic dermatitis patients, while the file "GE_Mic_AD_Pamr_nl_MAARS.txt" reports gene expression estimates of non-lesional skin of atopic dermatitis patients.

opencc-by-4.0Jan 2023View details →

Fig. 2. A in A large-scale study on the seroprevalence of Toxoplasma gondii infection in humans in Iran

Fig. 2. A GIS map of IgM seroprevalence of Toxoplasma gondii (Nicolle et Manceaux, 1908) in different provinces of Iran, during 2015–2020 (ND – no data).

opencc-by-4.0Jan 2023View details →

Fig. 3. A in A large-scale study on the seroprevalence of Toxoplasma gondii infection in humans in Iran

Fig. 3. A GIS map of IgG seroprevalence of Toxoplasma gondii (Nicolle et Manceaux, 1908) in different provinces of Iran, during 2015–2020.

opencc-by-4.0Jan 2023View details →

Fig. 1 in A large-scale study on the seroprevalence of Toxoplasma gondii infection in humans in Iran

Fig. 1. The seroprevalence plot of Toxoplasma gondii (Nicolle et Manceaux, 1908) in Iran in different age groups (m-month; y-year).

opencc-by-4.0Sep 2023View details →

ProteinCartography v0.4 analyses for sample of most-studied human proteins

Results from running the ProteinCartography pipeline (v0.4) using analyses on 25 proteins sampled from the most-studied human proteins listed in <a href="https://onlinelibrary.wiley.com/doi/10.1002/pro.4038">Liu and Buck, 2021</a>. The proteins included are listed in the table below. The results for each analysis are provided as individually-zipped folders, with the name of the file reflective of the protein name. To download all of the analyses in one folder, you can download the "25humanprotein_analysis.zip" file. <table> <tbody> <tr> <td> UniProt ID </td> <td> Protein name </td> <td> Protein symbol (in figures) </td> </tr> <tr> <td> Q9UM73 </td> <td> ALK tyrosine kinase receptor </td> <td> ALK </td> </tr> <tr> <td> Q96RI1 </td> <td> Bile acid receptor </td> <td> NR1H4 </td> </tr> <tr> <td> P43235 </td> <td> Cathepsin K </td> <td> CATK </td> </tr> <tr> <td> P08603 </td> <td> Complement factor H </td> <td> CFAH </td> </tr> <tr> <td> P00374 </td> <td> Dihydrofolate reductase </td> <td> DYR </td> </tr> <tr> <td> P98170 </td> <td> E3 ubiquitin-protein ligase XIAP </td> <td> XIAP </td> </tr> <tr> <td> P49841 </td> <td> Glycogen synthase kinase-3 beta </td> <td> GSK3B </td> </tr> <tr> <td> P01112 </td> <td> GTPase HRas </td> <td> RASH </td> </tr> <tr> <td> P68871 </td> <td> Hemoglobin subunit beta </td> <td> HBB </td> </tr> <tr> <td> P04439 </td> <td> HLA class I histocompatibility antigen, A alpha chain </td> <td> HLAA </td> </tr> <tr> <td> P01834 </td> <td> Immunoglobulin kappa constant </td> <td> IGKC </td> </tr> <tr> <td> P14174 </td> <td> Macrophage migration inhibitory factor </td> <td> MIF </td> </tr> <tr> <td> P53779 </td> <td> Mitogen-activated protein kinase 10 </td> <td> MK10 </td> </tr> <tr> <td> Q15596 </td> <td> Nuclear receptor coactivator 2 </td> <td> NCOA2 </td> </tr> <tr> <td> Q99497 </td> <td> Parkinson disease protein 7 </td> <td> PARK7 </td> </tr> <tr> <td> P62937 </td> <td> Peptidyl-prolyl cis-trans isomerase A </td> <td> PPIA </td> </tr> <tr> <td> Q13451 </td> <td> Peptidyl-prolyl cis-trans isomerase FKBP5 </td> <td> FKBP5 </td> </tr> <tr> <td> P27986 </td> <td> Phosphatidylinositol 3-kinase regulatory subunit alpha </td> <td> P85A </td> </tr> <tr> <td> O75530 </td> <td> Polycomb protein EED </td> <td> EED </td> </tr> <tr> <td> P28074 </td> <td> Proteasome subunit beta type-5 </td> <td> PSB5 </td> </tr> <tr> <td> P19793 </td> <td> Retinoic acid receptor RXR-alpha </td> <td> RXRA </td> </tr> <tr> <td> P50120 </td> <td> Retinol-binding protein 2 </td> <td> RET2 </td> </tr> <tr> <td> P00441 </td> <td> Superoxide dismutase [Ccu-Zn] </td> <td> SODC </td> </tr> <tr> <td> Q93009 </td> <td> Ubiquitin carboxyl-terminal hydrolase 7 </td> <td> UPB7 </td> </tr> <tr> <td> P40337 </td> <td> von Hippel -&sbquo;ÄìLindau disease tumor suppressor </td> <td> VHL </td> </tr> </tbody> </table> A TSV file, "most_studied_human_proteins.tsv", is included for use with the analysis notebook ("pub/most_studied_human_proteins.ipynb") found in our <a href="https://github.com/Arcadia-Science/ProteinCartography">GitHub repository</a> for the Arcadia Science Pub "<a href="https://doi.org/10.57844/arcadia-a5a6-1068">ProteinCartography: Comparing proteins with structure-based maps for interactive exploration</a>". The notebook produces the outputs, "sampled_proteins.tsv", and. "most_studied_human_proteins_analysis.tsv", which are used by the analysis notebook ("pub/cluster_quality_human_proteins.ipynb"), which uses the contents of this deposition.

A Study to Learn if Recombinant Human Parathyroid Hormone [rhPTH(1-84)] Can Improve Symptoms and Metabolic Control in Adults With Hypoparathyroidism (BALANCE)

ClinicalTrials.gov study NCT03324880. IPD Sharing: YES. Countries: 13. Publications: 1.

Study of Tecovirimat for Human Mpox Virus

ClinicalTrials.gov study NCT05534984. IPD Sharing: YES. Countries: 6. Publications: 1.

Phase I/II Study of U3-1402 in Subjects With Human Epidermal Growth Factor Receptor 3 (HER3) Positive Metastatic Breast Cancer

ClinicalTrials.gov study NCT02980341. IPD Sharing: YES. Countries: 2. Publications: 1.

FOCUS: A Phase I/II First in Human Study to Evaluate the Safety and Efficacy of GT005 Administered in Subjects With Dry AMD

ClinicalTrials.gov study NCT03846193. IPD Sharing: YES. Countries: 2. Publications: 1.

A Open-label Study Investigating the Safety and Tolerability of NPSP558, a Recombinant Human Parathyroid Hormone (rhPTH [1-84]), for the Treatment of Adults With Hypoparathyroidism - A Clinical Extens

ClinicalTrials.gov study NCT01297309. IPD Sharing: YES. Countries: 1. Publications: 5.

A Study of Extended Use of Recombinant Human Parathyroid Hormone (rhPTH(1-84)) in Hypoparathyroidism

ClinicalTrials.gov study NCT02910466. IPD Sharing: YES. Countries: 1. Publications: 4.