cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13278500
title: Additional file 3 of RNA sequencing analysis reveals increased expression of interferon signaling genes and dysregulation of bone metabolism affecting pathways in the whole blood of patients with osteogenesis imperfecta

description: Additional file 3. Significantly dysregulated pathways in OI patients compared to healthy controls according to MinePath tool analysis. The table includes KEGG annotation with p-values &lt;0.05.
DOI: 10.6084/m9.figshare.13278497
title: Additional file 2 of RNA sequencing analysis reveals increased expression of interferon signaling genes and dysregulation of bone metabolism affecting pathways in the whole blood of patients with osteogenesis imperfecta

description: Additional file 2. Functional profiling of the 39 DEGs according to the web-based g:GOSt tool. The table includes Reactome, KEGG and WikiPathways annotation sets with pathways’ adjusted p-values &lt;0.05.
DOI: 10.6084/m9.figshare.13278497.v1
title: Additional file 2 of RNA sequencing analysis reveals increased expression of interferon signaling genes and dysregulation of bone metabolism affecting pathways in the whole blood of patients with osteogenesis imperfecta

description: Additional file 2. Functional profiling of the 39 DEGs according to the web-based g:GOSt tool. The table includes Reactome, KEGG and WikiPathways annotation sets with pathways’ adjusted p-values &lt;0.05.
DOI: 10.5281/zenodo.4287846
title: Official Datasets for LHC Olympics 2020 Anomaly Detection Challenge

description: These are the official datasets for the LHC Olympics 2020 Anomaly Detection Challenge. Each "black box" contains 1M events meant to be representative of actual LHC data. These events may include signal(s) and the challenge consists of finding these signals using the method of your choice. <strong>We have uploaded a total of THREE black boxes to be used for the challenge. </strong> In addition, we include a background sample of 1M events meant to aid in the challenge. The background sample consists of QCD dijet events simulated using Pythia8 and Delphes 3.4.1. Be warned that both the physics and the detector modeling for this simulation may not exactly reflect the "data" in the black boxes. For both background and black box data, events are selected using a single fat-jet (R=1) trigger with pT threshold of 1.2 TeV. These events are stored as pandas dataframes saved to compressed h5 format. For each event, all reconstructed particles are assumed to be massless and are recorded in detector coordinates (pT, eta, phi). More detailed information such as particle charge is not included. Events are zero padded to constant size arrays of 700 particles. The array format is therefore (Nevents=1M, 2100). For more information, including a complete description of the challenge and an example Jupyter notebook illustrating how to read and process the events, see the official LHC Olympics 2020 webpage here. <strong>UPDATE: November 23, 2020</strong> Now that the challenge is over, we have uploaded the solutions to Black Boxes 1 and 3. They are simple ASCII files (events_LHCO2020_BlackBox1.masterkey and events_LHCO2020_BlackBox3.masterkey) where each line is the truth label -- 0 for background and 1 (and 2 in the case of BB3) for signal -- of each event in the corresponding h5 files (same ordering). For more information about the solutions, please visit the LHCO2020 webpage.
DOI: 10.21227/mx9m-a056
title: Tweets Originating from India During COVID-19 Lockdowns 1, 2, 3, 4

description: This India-specific COVID-19 tweets dataset has been developed using the large-scale Coronavirus (COVID-19) Tweets Dataset, which currently contains more than 600 million COVID-19 specific English language tweets. This dataset contains tweets originating from India during the first week of each four phases of nationwide lockdowns initiated by the Government of India. For more information on filtering keywords, please visit the primary dataset page.— Dataset usage terms : By using this dataset, you agree to (i) use the content of this dataset and the data generated from the content of this dataset for non-commercial research only, (ii) remain in compliance with Twitter's Developer Policy and (iii) cite the following paper:Lamsal, R. Design and analysis of a large-scale COVID-19 tweets dataset. Applied Intelligence (2020). https://doi.org/10.1007/s10489-020-02029-z-------------------------------------Related: Coronavirus (COVID-19) Tweets Dataset, Coronavirus (COVID-19) Geo-tagged Tweets Dataset and Coronavirus (COVID-19) Tweets Sentiment Trend (Global)-------------------------------------What's inside the dataset? The files in the dataset contain IDs of the tweets present in the Coronavirus (COVID-19) Tweets Dataset. Note: Below, (all files) means that all the files mentioned and in-between have been considered to develop the ID file, while (only even-numbered files) suggests that only the even-numbered files have been considered.Lockdown period tweets: (all files)Lockdown1.zip: March 25, 2020 - April 02, 2020; corona_tweets_08.csv to corona_tweets_14.csvLockdown2.zip: April 14, 2020 - April 21, 2020; corona_tweets_27.csv to corona_tweets_33.csvLockdown3.zip: May 01, 2020 - May 07, 2020; corona_tweets_44.csv to corona_tweets_49.csvLockdown4.zip: May 18, 2020 - May 23, 2020; corona_tweets_61.csv to corona_tweets_66.csvExtras: (all files)extras_june1_june7.zip: corona_tweets_75.csv to corona_tweets_80.csvExtras: (only even-numbered files)extras_june24_july1.zip: corona_tweets_96.csv to corona_tweets_104.csvextras_july2_july15.zip: corona_tweets_106.csv to corona_tweets_118.csvextras_july16_august4.zip: corona_tweets_120.csv to corona_tweets_138.csvextras_august5_august18.zip: corona_tweets_140.csv to corona_tweets_152.csvextras_august19_september1.zip: corona_tweets_154.csv to corona_tweets_166.csvextras_september2_september15.zip: corona_tweets_168.csv to corona_tweets_180.csv
DOI: 10.21227/vw24-ze78
title: Tweets Originating from India During COVID-19 Lockdowns 1, 2, 3, 4

description: This India-specific COVID-19 tweets dataset has been developed using the large-scale Coronavirus (COVID-19) Tweets Dataset, which currently contains more than 700 million COVID-19 specific English language tweets. This dataset contains tweets originating from India during the first week of each four phases of nationwide lockdowns initiated by the Government of India. For more information on filtering keywords, please visit the primary dataset page.— Dataset usage terms : By using this dataset, you agree to (i) use the content of this dataset and the data generated from the content of this dataset for non-commercial research only, (ii) remain in compliance with Twitter's Developer Policy and (iii) cite the following paper:Lamsal, R. Design and analysis of a large-scale COVID-19 tweets dataset. Applied Intelligence (2020). https://doi.org/10.1007/s10489-020-02029-z-------------------------------------Related: Coronavirus (COVID-19) Tweets Dataset, Coronavirus (COVID-19) Geo-tagged Tweets Dataset and Coronavirus (COVID-19) Tweets Sentiment Trend (Global)-------------------------------------What's inside the dataset? The files in the dataset contain IDs of the tweets present in the Coronavirus (COVID-19) Tweets Dataset. Note: Below, (all files) means that all the files mentioned and in-between have been considered to develop the ID file, while (only even-numbered files) suggests that only the even-numbered files have been considered.Lockdown period tweets: (all files)Lockdown1.zip: March 25, 2020 - April 02, 2020; corona_tweets_08.csv to corona_tweets_14.csvLockdown2.zip: April 14, 2020 - April 21, 2020; corona_tweets_27.csv to corona_tweets_33.csvLockdown3.zip: May 01, 2020 - May 07, 2020; corona_tweets_44.csv to corona_tweets_49.csvLockdown4.zip: May 18, 2020 - May 23, 2020; corona_tweets_61.csv to corona_tweets_66.csvExtras: (all files)extras_june1_june7.zip: corona_tweets_75.csv to corona_tweets_80.csvExtras: (only even-numbered files)extras_june24_july1.zip: corona_tweets_96.csv to corona_tweets_104.csvextras_july2_july15.zip: corona_tweets_106.csv to corona_tweets_118.csvextras_july16_august4.zip: corona_tweets_120.csv to corona_tweets_138.csvextras_august5_august18.zip: corona_tweets_140.csv to corona_tweets_152.csvextras_august19_september1.zip: corona_tweets_154.csv to corona_tweets_166.csvextras_september2_september15.zip: corona_tweets_168.csv to corona_tweets_180.csv
DOI: 10.6084/m9.figshare.13278588.v1
title: Additional file 10 of Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library

description: Additional file 10: Table S3. BAGEL scores for individual genes in individual screens.
DOI: 10.6084/m9.figshare.13278588
title: Additional file 10 of Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library

description: Additional file 10: Table S3. BAGEL scores for individual genes in individual screens.
DOI: 10.6084/m9.figshare.13279518.v1
title: Additional file 4 of Dynamic changes in chromatin accessibility, altered adipogenic gene expression, and total versus de novo fatty acid synthesis in subcutaneous adipose stem cells of normal-weight polycystic ovary syndrome (PCOS) women during adipogenesis: evidence of cellular programming

description: Additional file 4: Complete dataset of RNA-seq experiments including counts per million reads (CPM) levels for each sample at each time point and fold-change values between PCOS and control of all genes analyzed. Positive values denote greater expression in PCOS and negative values denote greater expression in controls.
DOI: 10.6084/m9.figshare.13279523.v1
title: Additional file 1 of Chd8 mutation in oligodendrocytes alters microstructure and functional connectivity in the mouse brain

description: Additional file 1: Table S1. This file contains detailed information for clusters in DTI analysis.
DOI: 10.6084/m9.figshare.13279565
title: Additional file 1 of TERT promoter mutation confers favorable prognosis regardless of 1p/19q status in adult diffuse gliomas with IDH1/2 mutations

description: Additional file 1: Table S1 Detailed information of patients registered in the present study. Table S2 Cox regression analysis for survival in 1p/19q codeleted cases (n=284). Table S3 Cox regression analysis for survival in 1p/19q intact cases (n=273).
DOI: 10.6084/m9.figshare.13279565.v1
title: Additional file 1 of TERT promoter mutation confers favorable prognosis regardless of 1p/19q status in adult diffuse gliomas with IDH1/2 mutations

description: Additional file 1: Table S1 Detailed information of patients registered in the present study. Table S2 Cox regression analysis for survival in 1p/19q codeleted cases (n=284). Table S3 Cox regression analysis for survival in 1p/19q intact cases (n=273).
DOI: 10.6084/m9.figshare.13279644
title: Additional file 1 of Menstrual product choice and uptake among young women in Zimbabwe: a pilot study

description: Additional file 1. MHH Intervention Uptake and Product Choice at First Visit. Quantitative data extracted from biometric system highlighting MHH intervention uptake and product choice during pilot period.
DOI: 10.6084/m9.figshare.13279644.v1
title: Additional file 1 of Menstrual product choice and uptake among young women in Zimbabwe: a pilot study

description: Additional file 1. MHH Intervention Uptake and Product Choice at First Visit. Quantitative data extracted from biometric system highlighting MHH intervention uptake and product choice during pilot period.
DOI: 10.6084/m9.figshare.13279586.v1
title: Additional file 1 of The association between depressive symptoms and self-rated health among university students: a cross-sectional study in France and Japan

description: Additional file 1: Table S1. Description of the study population stratified by Sex. Abbreviations; PHQ-2, the 2-item Patient Health Questionnaire; BMI, body mass index. *i-Share cohort had BMI missing values: male 49(4.0), female 257 (5.8). Description of the two cohorts, stratified by Sex, concerning PHQ-2, Self-rated heatrh, Sex, Age, Year of study, Sleep, BMI, Physical activity, Smoking and Alcohol consumption, respectively. Table S2. Univariate comparison of all variables according to PHQ-2 score in the two cohorts stratified by Sex. Abbreviations; PHQ-2, the 2-item Patient Health Questionnaire; BMI, body mass index. *i-Share cohort had BMI missing values: 221 (5.1) for [0–2] and 84 (6.5) for [3–6]; p value was calculated without missing values. Table S3. Multivariate logistic regression analysis stratified by Sex. Abbreviation; BMI, body mass index. Association between PHQ-2 and Self-rated health, stratified by Sex, adjusted for Sex, Age, Year of study, Sleep, BMI, Physical activity, Smoking and Alcohol consumption. Figure S1-1. Correlation between self-rated health and depressive symptoms, PHQ-2 score and numbers and percentages of students with elevated depressive symptoms in each of the five categories of self-rated health: i-Share cohort, Spearman correlation coefficient 0.261, P value
DOI: 10.6084/m9.figshare.13279655.v1
title: Additional file 2 of Young «oil site» of the Uzon Caldera as a habitat for unique microbial life

description: Additional file 2: Table S1. Water samples. Note: b.d.l. – below detected limit, n.d. – no data.
DOI: 10.6084/m9.figshare.13279676
title: Additional file 8 of Young «oil site» of the Uzon Caldera as a habitat for unique microbial life

description: Additional file 8: Figure S4-A, Additional file 7: Fig. S4-B. Completeness of the naphthalene degradation (А) and benzoate degradation (B) metabolic pathways for the U3.4.10 sample. Red borders indicate the proteins found in U3.4.10 sample. Visualization was made with ANDVisio program of ANDSystem ( www.bionet.sscc.ru/and/cell/#!/app/andvisio ).
DOI: 10.6084/m9.figshare.13279655
title: Additional file 2 of Young «oil site» of the Uzon Caldera as a habitat for unique microbial life

description: Additional file 2: Table S1. Water samples. Note: b.d.l. – below detected limit, n.d. – no data.
DOI: 10.6084/m9.figshare.13279676.v1
title: Additional file 8 of Young «oil site» of the Uzon Caldera as a habitat for unique microbial life

description: Additional file 8: Figure S4-A, Additional file 7: Fig. S4-B. Completeness of the naphthalene degradation (А) and benzoate degradation (B) metabolic pathways for the U3.4.10 sample. Red borders indicate the proteins found in U3.4.10 sample. Visualization was made with ANDVisio program of ANDSystem ( www.bionet.sscc.ru/and/cell/#!/app/andvisio ).
DOI: 10.6084/m9.figshare.13279725
title: Additional file 3 of Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals

description: Additional file 3. Group significance based on breed and study. Group significance test for breed by Kruskal-Wallis (GS_KW_SBP) and nonparametric t-test (GS_NPT_SBP). Group significance test for study by Kruskal-Wallis (GS_KW_Study)
DOI: 10.6084/m9.figshare.13279719.v1
title: Additional file 1 of Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals

description: Additional file 1. Sequence counts of blank sequencing control. Absolute abundance counts for blank sequencing control. Highlighted in blue are OTUs found in 100% of the experimental samples.
DOI: 10.6084/m9.figshare.13279719
title: Additional file 1 of Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals

description: Additional file 1. Sequence counts of blank sequencing control. Absolute abundance counts for blank sequencing control. Highlighted in blue are OTUs found in 100% of the experimental samples.
DOI: 10.6084/m9.figshare.13279725.v1
title: Additional file 3 of Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals

description: Additional file 3. Group significance based on breed and study. Group significance test for breed by Kruskal-Wallis (GS_KW_SBP) and nonparametric t-test (GS_NPT_SBP). Group significance test for study by Kruskal-Wallis (GS_KW_Study)
DOI: 10.6084/m9.figshare.13279755.v1
title: Additional file 13 of Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

description: Additional file 13. Results from Divergence dating analyses. Summarized are median ages and 95% HPD intervals for 8 separate sets of MCMCTREE analyses, implementing different root calibrations and calibration exclusions. Node numbers refer to Fig. 2.
DOI: 10.6084/m9.figshare.13279758
title: Additional file 14 of Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

description: Additional file 14. Ancestral state reconstructions of cynipoid life histories using a three-state model. Reconstructions were performed under the ARD-model using the rayDISC function in the R-package corHMM. Summarized here are ancestral state probabilities (ranging from 0–1) from 8 variations of analyses on the three-state model, with states 0 = parasitoid, 1 = inquiline and 2 = galler. Variations are a-i = Outgroups included, Paraulacini are coded as parasitoids, uncertain taxa coded as parasitoids; a-ii = Outgroups included, Paraulacini are coded as inquilines, uncertain taxa coded as parasitoids; b-i = Outgroups excluded, Paraulacini are coded as parasitoids, uncertain taxa coded as parasitoids; b-ii = Outgroups excluded, Paraulacini are coded as inquilines, uncertain taxa coded as parasitoids; c-i = Outgroups included, Paraulacini are coded as parasitoids, uncertain taxa coded as unknown; c-ii = Outgroups included, Paraulacini are coded as inquilines, uncertain taxa coded as unknowns; d-i = Outgroups excluded, Paraulacini are coded as parasitoids, uncertain taxa coded as unknowns; d-ii = Outgroups excluded, Paraulacini are coded as inquilines, uncertain taxa coded as unknowns. For each node, the state with the highest likelihood has been bolded.
DOI: 10.6084/m9.figshare.13279761.v1
title: Additional file 15 of Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

description: Additional file 15. Ancestral state reconstructions of cynipoid life histories using a seven-state model. Reconstructions were performed under the ER-model using the rayDISC function in the R-package corHMM. Summarized here are ancestral state probabilities (ranging from 0–1) from 8 variations of analyses on the seven-state model, with states 0 = parasitoid, 1 = inquiline and 2 = galler-Fagaceae, 3 = galler-herbs, 4 = galler-Acer, 5 = galler-Rosaceae, 6 = galler-Acacia. Variations are a-i = Outgroups included, Paraulacini are coded as parasitoids, uncertain taxa coded as parasitoids; a-ii = Outgroups included, Paraulacini are coded as inquilines, uncertain taxa coded as parasitoids; b-i = Outgroups excluded, Paraulacini are coded as parasitoids, uncertain taxa coded as parasitoids; b-ii = Outgroups excluded, Paraulacini are coded as inquilines, uncertain taxa coded as parasitoids; c-i = Outgroups included, Paraulacini are coded as parasitoids, uncertain taxa coded as unknown; c-ii = Outgroups included, Paraulacini are coded as inquilines, uncertain taxa coded as unknowns; d-i = Outgroups excluded, Paraulacini are coded as parasitoids, uncertain taxa coded as unknowns; d-ii = Outgroups excluded, Paraulacini are coded as inquilines, uncertain taxa coded as unknowns. For each node, the state with the highest likelihood has been bolded. Grey shaded fields highlight nodes with conflict or variable support between the variations of analyses.
DOI: 10.6084/m9.figshare.13279758.v1
title: Additional file 14 of Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

description: Additional file 14. Ancestral state reconstructions of cynipoid life histories using a three-state model. Reconstructions were performed under the ARD-model using the rayDISC function in the R-package corHMM. Summarized here are ancestral state probabilities (ranging from 0–1) from 8 variations of analyses on the three-state model, with states 0 = parasitoid, 1 = inquiline and 2 = galler. Variations are a-i = Outgroups included, Paraulacini are coded as parasitoids, uncertain taxa coded as parasitoids; a-ii = Outgroups included, Paraulacini are coded as inquilines, uncertain taxa coded as parasitoids; b-i = Outgroups excluded, Paraulacini are coded as parasitoids, uncertain taxa coded as parasitoids; b-ii = Outgroups excluded, Paraulacini are coded as inquilines, uncertain taxa coded as parasitoids; c-i = Outgroups included, Paraulacini are coded as parasitoids, uncertain taxa coded as unknown; c-ii = Outgroups included, Paraulacini are coded as inquilines, uncertain taxa coded as unknowns; d-i = Outgroups excluded, Paraulacini are coded as parasitoids, uncertain taxa coded as unknowns; d-ii = Outgroups excluded, Paraulacini are coded as inquilines, uncertain taxa coded as unknowns. For each node, the state with the highest likelihood has been bolded.
DOI: 10.6084/m9.figshare.13279764.v1
title: Additional file 1 of Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

description: Additional file 1. Information on specimen vouchers and collection data, as well as traits. Table listing USNMENT voucher numbers for newly sequenced taxa, collection data as available, and character states for the life history analyses. Character states are: 3-state model: 0 = parasitoids, 1 = inquilines, 2 = gallers; 7-state model: 0 = parasitoids, 1 = inquilines, 2 = gallers-Fagaceae, 3 = gallers-herbs, 4 = gallers-Acer, 5 = gallers-Rosaceae, 6 = gallers-Acacia; taxa with unspecified states were not included in dating and ancestral reconstructions; taxa with two states indicated were coded both ways in two separate analyses. n/a = not applicable, n.a. = not available; Biogeographic regions are: AFR = Afrotropical, AUS = Australasian, NEA = Nearctic, NEO = Neotropical, ORI = Oriental/Indomalayan, PAL = Palearctic.
DOI: 10.6084/m9.figshare.13279773
title: Additional file 4 of Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

description: Additional file 4. BINs defined for GC content experiments. Table listing average, minimum and maximum GC content across loci, topology estimated using unpartitioned ML analysis (for a sketch of topology A,B,C refer to Additional File 12), and support for the position of E. niger.
DOI: 10.6084/m9.figshare.13279767.v1
title: Additional file 2 of Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

description: Additional file 2. Library preparation and UCE sequence capture statistics. Table listing for each taxon included in the study the pre-library preparation DNA concentration, the total DNA input, the post-library preparation DNA concentration, the total raw read count, the total number of assembled contigs and mean length, and the number of assembled UCE contigs and their mean length, the number of UCE loci, and average GC content.
DOI: 10.6084/m9.figshare.13279755
title: Additional file 13 of Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

description: Additional file 13. Results from Divergence dating analyses. Summarized are median ages and 95% HPD intervals for 8 separate sets of MCMCTREE analyses, implementing different root calibrations and calibration exclusions. Node numbers refer to Fig. 2.
DOI: 10.6084/m9.figshare.13279776
title: Additional file 5 of Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

description: Additional file 5. Calibration points used in this study and their justification. Table outlining details for each fossil calibration used in our study.
DOI: 10.6084/m9.figshare.13279776.v1
title: Additional file 5 of Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

description: Additional file 5. Calibration points used in this study and their justification. Table outlining details for each fossil calibration used in our study.