cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12623930
title: Processed Plaque-2.0 infection scores of the PCL screen, imaged and analysed at EPFL.

description: PCL compounds are indicated (name). The Plaque2.0-based infection scores of the four biological replicates of each PCL compound were averaged (mean). The Plaque2.0-based infection scores of the positive and negative controls are averaged (mean) over the 32 technical replicates, each, per plate. Each compound’s scores were normalized by the mean score of the negative control of the respective plate and indicated by Mean N_nuclei (number of nuclei based on Hoechst staining), Mean N_infected (number of GFP reporter-based infected nuclei), Mean InfIndex (ratio of numberOfInfectedNuclei to numberOfNuclei), Mean N_plaques (number of GFP reporter-based plaques) and Mean TotVirInt (total GFP reporter signal intensity). Non-toxic compounds were filtered by applying an inclusive μ- (mean of the negative control)  2σ (SD of the negative control) threshold for number of nuclei. Efficacy was filtered by applying an excluding μ-  3σ (SD of the negative control) threshold for the infection scores. The obtained scores for each infection score of each PCL compound indicated as Mean Scores N_nuclei (number of nuclei based on Hoechst staining), Scores N_Infected (number of GFP reporter-based number of infected nuclei), Scores InfIndex (ratio of numberOfInfectedNuclei to numberOfNuclei), Scores N_plaques (number of GFP reporter-based plaques) and Scores TotVirInt (total GFP reporter signal intensity). Compounds exhibiting significant toxicity to noninfected cells were excluded.
DOI: 10.6084/m9.figshare.12623936.v1
title: Static data with fundamental geographic information

description: Static data with fundamental geographic information, e.g., the road network structure and the POI distribution
DOI: 10.6084/m9.figshare.12623918
title: Raw Plaque-2.0 infection scores of the PCL screen, imaged and analysed at UZH.

description: virus indicates virus genotype, the PCL was tested against, compoundIdentifier indicates the UZH identifier for blinded testing by UZH, setPlate is the subset plate A to D and replicate refers to the replicate 1 to 4, wellRow and wellColumn indicate the well and plate indicate the screening plate sequence number. The Plaque2.0-based infection scores are numberOfNuclei reporting the number of nuclei based on Hoechst staining, numberOfInfectedNuclei refers to the number of GFP reporter-based number of infected nuclei, infectionIndex is the ratio of numberOfInfectedNuclei to numberOfNuclei, the number of GFP reporter-based plaques is given by numberOfPlaques and totalVirusIntensity indicates total GFP reporter signal intensity.
DOI: 10.6084/m9.figshare.12623921
title: Processed Plaque-2.0 infection scores of the PCL screen, imaged and analysed at UZH.

description: virus indicates virus genotype, the PCL was tested against, compoundIdentifier indicates the UZH identifier for blinded testing by UZH, PCL_ID and compoundName disclose the PCL compound identifier and name, respectively. Barcode1, Barcode2, Barcode3 and Barcode4 indicate on which screening plates, given by the screening plate sequence number defined by EPFL, the PCL compound was tested on. The PrestoBlue toxicity scoring of the compound tested in noninfected cells is given as 1 (toxic) and 0 (non-toxic) in nonInfectedToxHit. The mean Plaque2.0-based infection scores of the four biological replicates are provided by mean_numberOfNuclei (number of nuclei based on Hoechst staining), mean_numberOfInfectedNuclei (number of GFP reporter-based infected nuclei), mean_infectionIndex (ratio of numberOfInfectedNuclei to numberOfNuclei), mean_numberOfPlaques (number of GFP reporter-based plaques) and mean_totalVirusIntensity (total GFP reporter signal intensity). The infection scores of the positive and negative controls are averaged (mean) over the 32 technical replicates, each, per plate, and the mean PCL compound infection scores were normalized by the mean negative control infection score of the respective plate indicated by by mean_numberOfNucleiRel (number of nuclei based on Hoechst staining), mean_numberOfInfectedNucleiRel (number of GFP reporter-based number of infected nuclei), mean_infectionIndexRel (ratio of numberOfInfectedNuclei to numberOfNuclei), mean_numberOfPlaquesRel (number of GFP reporter-based plaques) and mean_totalVirusIntensityRel (total GFP reporter signal intensity).
DOI: 10.6084/m9.figshare.12623927.v1
title: Raw Plaque-2.0 infection scores of the PCL screen, imaged and analysed at EPFL.

description: Barcode indicates the screening plate sequence number defined by EPFL and Well Position gives the well. Plaque2.0-based infection scores are numberOfNuclei reporting the number of nuclei based on Hoechst stai¬ning, numberOfInfectedNuclei refers to the number of GFP reporter-based number of infected nu¬clei, infectionIndex is the ratio of numberOfInfectedNuclei to numberOfNuclei, the GFP reporter-based number of plaques is given by numberOfPlaques and totalVirusIntensity indicates total GFP reporter signal intensity.
DOI: 10.6084/m9.figshare.12623957.v1
title: Fig 2 (panels A, B, C)

description: Dhh, Cldn5 and Zo1 mRNA expression level in CNS MECs isolated from Dhh<sup>ECKO</sup> vs Ctrl mice under resting condition.<br>
DOI: 10.6084/m9.figshare.12623918.v1
title: Raw Plaque-2.0 infection scores of the PCL screen, imaged and analysed at UZH.

description: virus indicates virus genotype, the PCL was tested against, compoundIdentifier indicates the UZH identifier for blinded testing by UZH, setPlate is the subset plate A to D and replicate refers to the replicate 1 to 4, wellRow and wellColumn indicate the well and plate indicate the screening plate sequence number. The Plaque2.0-based infection scores are numberOfNuclei reporting the number of nuclei based on Hoechst staining, numberOfInfectedNuclei refers to the number of GFP reporter-based number of infected nuclei, infectionIndex is the ratio of numberOfInfectedNuclei to numberOfNuclei, the number of GFP reporter-based plaques is given by numberOfPlaques and totalVirusIntensity indicates total GFP reporter signal intensity.
DOI: 10.6084/m9.figshare.12623921.v1
title: Processed Plaque-2.0 infection scores of the PCL screen, imaged and analysed at UZH.

description: virus indicates virus genotype, the PCL was tested against, compoundIdentifier indicates the UZH identifier for blinded testing by UZH, PCL_ID and compoundName disclose the PCL compound identifier and name, respectively. Barcode1, Barcode2, Barcode3 and Barcode4 indicate on which screening plates, given by the screening plate sequence number defined by EPFL, the PCL compound was tested on. The PrestoBlue toxicity scoring of the compound tested in noninfected cells is given as 1 (toxic) and 0 (non-toxic) in nonInfectedToxHit. The mean Plaque2.0-based infection scores of the four biological replicates are provided by mean_numberOfNuclei (number of nuclei based on Hoechst staining), mean_numberOfInfectedNuclei (number of GFP reporter-based infected nuclei), mean_infectionIndex (ratio of numberOfInfectedNuclei to numberOfNuclei), mean_numberOfPlaques (number of GFP reporter-based plaques) and mean_totalVirusIntensity (total GFP reporter signal intensity). The infection scores of the positive and negative controls are averaged (mean) over the 32 technical replicates, each, per plate, and the mean PCL compound infection scores were normalized by the mean negative control infection score of the respective plate indicated by by mean_numberOfNucleiRel (number of nuclei based on Hoechst staining), mean_numberOfInfectedNucleiRel (number of GFP reporter-based number of infected nuclei), mean_infectionIndexRel (ratio of numberOfInfectedNuclei to numberOfNuclei), mean_numberOfPlaquesRel (number of GFP reporter-based plaques) and mean_totalVirusIntensityRel (total GFP reporter signal intensity).
DOI: 10.6084/m9.figshare.12623930.v1
title: Processed Plaque-2.0 infection scores of the PCL screen, imaged and analysed at EPFL.

description: PCL compounds are indicated (name). The Plaque2.0-based infection scores of the four biological replicates of each PCL compound were averaged (mean). The Plaque2.0-based infection scores of the positive and negative controls are averaged (mean) over the 32 technical replicates, each, per plate. Each compound’s scores were normalized by the mean score of the negative control of the respective plate and indicated by Mean N_nuclei (number of nuclei based on Hoechst staining), Mean N_infected (number of GFP reporter-based infected nuclei), Mean InfIndex (ratio of numberOfInfectedNuclei to numberOfNuclei), Mean N_plaques (number of GFP reporter-based plaques) and Mean TotVirInt (total GFP reporter signal intensity). Non-toxic compounds were filtered by applying an inclusive μ- (mean of the negative control)  2σ (SD of the negative control) threshold for number of nuclei. Efficacy was filtered by applying an excluding μ-  3σ (SD of the negative control) threshold for the infection scores. The obtained scores for each infection score of each PCL compound indicated as Mean Scores N_nuclei (number of nuclei based on Hoechst staining), Scores N_Infected (number of GFP reporter-based number of infected nuclei), Scores InfIndex (ratio of numberOfInfectedNuclei to numberOfNuclei), Scores N_plaques (number of GFP reporter-based plaques) and Scores TotVirInt (total GFP reporter signal intensity). Compounds exhibiting significant toxicity to noninfected cells were excluded.
DOI: 10.6084/m9.figshare.12623900
title: covariates.xlsx

description: mixed-use indices and population density of Shenzhen (TAZ-level)
DOI: 10.6084/m9.figshare.12623906
title: PCL compounds tested in the screening procedure.

description: PCL catalogue IDs (PCL_ID), compound names (CompoundName), PubChem identifier (CompoundPubChemCID) and link (CompoundPubChemURL), the tested concentration in µM (CompoundConcentrationMicroMolar), the CAS registry number (CAS), structure according SMILES notation (CompoundSMILES), acoustic dispensing spottability (SpottabilityFlag) and group (Group) for each of the 1,280 PCL compounds and control compounds. Two compounds, Prestw-354 (Clopamide) and Prestw-410 (Amphotericine B) could not be successfully transferred via acoustic dispensing due to precipitation and were not included in the screening.
DOI: 10.6084/m9.figshare.12623912
title: PCL compounds excluded due to toxicity in uninfected cells.

description: The toxicity of the PCL compounds in absence of infection was evaluated by PrestoBlue viability assay. Compounds are indicated by their PCL catalogue ID (PCL_ID) and names (compoundName). Compounds were classified as toxic, when their normalized value for all replicates was higher than the average +3σ of the DMSO negative control for the corresponding plate. Scores and score standard deviation (scoreSD) of toxic PCL compounds are listed. The PrestoBlue raw data are available at idr0081/3-Screen/Analysis/Toxicity.xls.
DOI: 10.6084/m9.figshare.12623897
title: taz-poi-counts.xlsx

description: POI count at TAZ-level of Shenzhen
DOI: 10.6084/m9.figshare.12623912.v1
title: PCL compounds excluded due to toxicity in uninfected cells.

description: The toxicity of the PCL compounds in absence of infection was evaluated by PrestoBlue viability assay. Compounds are indicated by their PCL catalogue ID (PCL_ID) and names (compoundName). Compounds were classified as toxic, when their normalized value for all replicates was higher than the average +3σ of the DMSO negative control for the corresponding plate. Scores and score standard deviation (scoreSD) of toxic PCL compounds are listed. The PrestoBlue raw data are available at idr0081/3-Screen/Analysis/Toxicity.xls.
DOI: 10.6084/m9.figshare.12623897.v1
title: taz-poi-counts.xlsx

description: POI count at TAZ-level of Shenzhen
DOI: 10.6084/m9.figshare.12623906.v1
title: PCL compounds tested in the screening procedure.

description: PCL catalogue IDs (PCL_ID), compound names (CompoundName), PubChem identifier (CompoundPubChemCID) and link (CompoundPubChemURL), the tested concentration in µM (CompoundConcentrationMicroMolar), the CAS registry number (CAS), structure according SMILES notation (CompoundSMILES), acoustic dispensing spottability (SpottabilityFlag) and group (Group) for each of the 1,280 PCL compounds and control compounds. Two compounds, Prestw-354 (Clopamide) and Prestw-410 (Amphotericine B) could not be successfully transferred via acoustic dispensing due to precipitation and were not included in the screening.
DOI: 10.6084/m9.figshare.12623876
title: Fig 1 (panels F, G, H, I, J)

description: Dhh, Icam1, Vcam1, Cldn5, Zo1 mRNA expression level in enriched neurovascular fractions from EAE MOG induced C57BL/6 mice vs C57BL/6 mice treated with placebo.
DOI: 10.6084/m9.figshare.12623900.v2
title: covariates.xlsx

description: mixed-use indices and population density of Shenzhen (TAZ-level)
DOI: 10.6084/m9.figshare.12623873
title: Fig 1 (panels C, D, E).pzfx

description: DHH, ICAM1, VCAM1 mRNA expression level in HBMECs treated with Il1b vs Ctrl.<br>
DOI: 10.6084/m9.figshare.12623876.v1
title: Fig 1 (panels F, G, H, I, J)

description: Dhh, Icam1, Vcam1, Cldn5, Zo1 mRNA expression level in enriched neurovascular fractions from EAE MOG induced C57BL/6 mice vs C57BL/6 mice treated with placebo.
DOI: 10.6084/m9.figshare.12623900.v1
title: covariates.xlsx

description: mixed-use indices and population density of Shenzhen (TAZ-level)
DOI: 10.6084/m9.figshare.12623873.v1
title: Fig 1 (panels C, D, E).pzfx

description: DHH, ICAM1, VCAM1 mRNA expression level in HBMECs treated with Il1b vs Ctrl.<br>
DOI: 10.6084/m9.figshare.12623780
title: hazard prediction test

description: this dataset was associated with the paper entitled development and validity of a hazard prediction test for Chinese drivers<br>
DOI: 10.6084/m9.figshare.12623780.v1
title: hazard prediction test

description: this dataset was associated with the paper entitled development and validity of a hazard prediction test for Chinese drivers<br>
DOI: 10.6084/m9.figshare.12623756
title: Full_data_MA.xlsx

description: Data for wildlife crossing structures meta analysis
DOI: 10.6084/m9.figshare.12623747
title: Dataset of "Acceptance and knowledge of evolutionary theory among third-year university students in Spain"

description: Dataset from paper "Acceptance and knowledge of evolutionary theory among third-year university students in Spain". 'Sex' (1=Man; 2=Woman; 3=Other). 'Level' represents the educational attainment of each participant (1=Bachelor; 2=Degree; 3=PhD). 'Preuniversity' represents the academic itinerary followed by each student (1=Sciences; 2=Technology; 3=Humanities; 4=Social Sciences; 5=Arts). 'University' (1=Vigo; 2=Autónoma de Madrid; 3=Alicante; 4=Sevilla; 6=Granada; 7=Valencia; 8=Complutense de Madrid; 11=Salamanca; 13=Santiago de Compostela; 14=Baleares; 33=Erasmus). 'Faculty' (1=Chemistry; 2=History; 3=Philology; 4=Biology). 'Religion' (0=No religion; 1=Religious Attendant). 'Complete' (0=Incomplete Data; 1=Complete Data). 'indexkee' represents KEE scores. 'MATE_facts' represents 'Facts' construct scores within the MATE test. 'MATE_credibility represents 'Credibility' construct scores within the MATE test.
DOI: 10.6084/m9.figshare.12623651
title: Supplementary Material for: Roles of Thyroid Hormones, Mast Cells, and Inflammatory Mediators in the Initiation and Progression of Autoimmune Thyroid Diseases

description: <b><i>Background:</i></b> Interrelation between thyrocytes and immunocytes has been established. However, the roles of mast cells and thyroid hormones in the triggering mechanism of thyroid autoimmune processes have been insufficiently investigated. This study evaluated the role of thyroid hormones and mast cells in the mechanisms of losing tolerance to thyroid autoantigens. <b><i>Materials and Methods:</i></b> Two groups of patients were studied: patients with Graves’ disease and patients with nodular euthyroid goiter. Wistar rats with induced exogenous hypothyroidism, thyrotoxicosis, and thyrotoxicosis in parallel with administration of interleukin-2 were used. The levels of hormones, autoantibodies, and cytokines in the serum and thyroid tissue were analyzed through the enzyme-linked immunosorbent assay. Morphological verification was performed through the immune-histochemical method with antibodies against tryptase and CD86. Transmission electron microscopy and laser confocal microscopy were used. <b><i>Results:</i></b> In both Graves’ disease and induced thyrotoxicosis, we detected a significant increase in the levels of interferon-γ, active interfollicular infiltration and degranulation of mast cells, and the intrathyroid overexpression of CD86. Complex analysis of the rat’s thyroid morphofunctional state and systemic and local levels of cytokines in induced thyrotoxicosis and hypothyroidism demonstrated an increase of intrathyroid degranulation of mast cells and a drastic disruption of IFNγ/IL10 balance. <b><i>Conclusions:</i></b> When exposed to excessive amounts of thyroid hormones, an inflammatory response is triggered in the thyroid gland, and mast cells overexpress costimulating CD86 in the thyroid. This finding confirms their possible involvement in auto­antigen presentation. Significant increase in the levels of interferon-γ shows a determining influence of cytokine on the progression of the pathological process.
DOI: 10.6084/m9.figshare.12623552
title: Supplementary Material for: The Protein Translocation Defect of MCT8<sup>L291R</sup> Is Rescued by Sodium Phenylbutyrate

description: <b><i>Introduction:</i></b> The monocarboxylate transporter 8 (MCT8; SLC16A2) is a specific transporter for thyroid hormones. MCT8 deficiency, formerly known as the Allan-Herndon-Dudley syndrome, is a rare genetic disease that leads to neurological impairments and muscle weakness. Current experimental treatment options rely on thyromimetic agonists that do not depend on MCT8 for cellular uptake. Another approach comes from studies with the chemical chaperone sodium phenylbutyrate (NaPB), which was able to stabilize MCT8 mutants having protein folding defects in vitro. In addition, NaPB is known as a compound that assists with plasma membrane translocation. <b><i>Objective:</i></b> The pathogenic MCT8<sup>L291R</sup> leads to the same severe neurological impairments found for other MCT8-deficient patients but, unexpectedly, lacks alterations in plasma 3,3′,5-triiodothyronine (T<sub>3</sub>) levels. Here we tried to unravel the underlying mechanism of MCT8 deficiency and tested whether the pathogenic MCT8<sup>L291R</sup> mutant responds to NaPB treatment. Therefore, we overexpressed the mutant in Madin-Darby canine kidney cells in the human choriocarcinoma cell line JEG1 and in COS7 cells of African green monkey origin. <b><i>Results:</i></b> In our recent study we describe that the MCT8<sup>L291R</sup> mutation most likely leads to a translocation defect. The pathogenic mutant is not located at the plasma membrane, but shows overlapping expression with a marker protein of the lysosome. Mutation of the corresponding amino acid in murine Mct8 (Mct8<sup>L223R</sup>) displays a similar effect on cell surface expression and transport function as seen before for MCT8<sup>L291R</sup>. NaPB was able to correct the translocation defect of MCT8<sup>L291R</sup>/Mct8<sup>L223R</sup> and restored protein function by increasing T<sub>3</sub> transport activity. Furthermore, we detected enhanced mRNA levels of wild-type and mutant <i>MCT8/Mct8</i> after NaPB treatment. The increase in mRNA levels could be an explanation for the positive effect on protein expression and function detected for wild-type MCT8. <b><i>Conclusion:</i></b> NaPB is not only suitable for the treatment of mutations leading to misfolding and protein degradation, but also for a mutant wrongly sorted inside a cell which is otherwise functional.
DOI: 10.6084/m9.figshare.12623501
title: Data for "Evidence of unprecedented rise in growth synchrony from global tree ring records"

description: <b>Data includes:</b>-itrdb-v713-cleaned-rwl_no_subfolders: ITRDB raw rwl data-ages.csv: age structure of ITRDB data, calculated from tree ring series-GlobalTemperatureAnomaly:Time series of global temperature data-ITRDB_prec_updated.csv and ITRDB_prec_updated2.csv: total annual precipitation for each ITRDB location-ITRDB_temp_updated: mean annual temperatuer for each ITRDB location-metadata_itrdb_final: metadata associated with each ITRDB location-nitrogen_nhx_timeseries.csv and nitrogen_noy_timeseries.csv: time series of nitrogen deposition for each ITRDB location.-standardized series.csv: standardized growth series for each ITRDB location.-standardized series.with.spl.csv: low-frequency spline standardized series for each ITRDB location
DOI: 10.6084/m9.figshare.12623492
title: Annex 5_script

description: Script for the analysis of the paper 'Evidence of unprecedented rise in growth synchrony from global tree ring records'<br>
DOI: 10.6084/m9.figshare.12623234
title: Additional file 6 of Cumulative inactivated vaccine exposure and allergy development among children: a birth cohort from Japan

description: Additional file 6: Table S7. Prevalence for RQ3
DOI: 10.6084/m9.figshare.12623231
title: Additional file 5 of Cumulative inactivated vaccine exposure and allergy development among children: a birth cohort from Japan

description: Additional file 5: Table S6. Prevalence for RQ2
DOI: 10.6084/m9.figshare.12623231.v1
title: Additional file 5 of Cumulative inactivated vaccine exposure and allergy development among children: a birth cohort from Japan

description: Additional file 5: Table S6. Prevalence for RQ2
DOI: 10.6084/m9.figshare.12623234.v1
title: Additional file 6 of Cumulative inactivated vaccine exposure and allergy development among children: a birth cohort from Japan

description: Additional file 6: Table S7. Prevalence for RQ3
DOI: 10.6084/m9.figshare.12623228
title: Additional file 4 of Cumulative inactivated vaccine exposure and allergy development among children: a birth cohort from Japan

description: Additional file 4: Table S5. Prevalence for RQ1
DOI: 10.6084/m9.figshare.12623228.v1
title: Additional file 4 of Cumulative inactivated vaccine exposure and allergy development among children: a birth cohort from Japan

description: Additional file 4: Table S5. Prevalence for RQ1
DOI: 10.5281/zenodo.3866686
title: Additional materials for the AD appendix

description: Self-generated input parameters for the GT5D software using 1440, 2880, and 5760 computing nodes.
DOI: 10.6084/m9.figshare.12623175
title: Additional file 1 of Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter

description: Additional file 1. Hierarchical classification of taxonomic entities found from metagenomic sequencing in the study.
DOI: 10.6084/m9.figshare.12623175.v1
title: Additional file 1 of Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter

description: Additional file 1. Hierarchical classification of taxonomic entities found from metagenomic sequencing in the study.
DOI: 10.5281/zenodo.3866685
title: Additional materials for the AD appendix

description: Self-generated input parameters for the GT5D software using 1440, 2880, and 5760 computing nodes.
DOI: 10.6084/m9.figshare.12623162
title: Additional file 1 of Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach

description: Additional file 1. Origin and Accession # of recently emerged SARS coronaviruses and viral RdRps.
DOI: 10.6084/m9.figshare.12623162.v1
title: Additional file 1 of Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach

description: Additional file 1. Origin and Accession # of recently emerged SARS coronaviruses and viral RdRps.