cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12789692
title: Supplementary Material for: Neuroendocrine Tumor Omic Gene Cluster Analysis Amplifies the Prognostic Accuracy of the NETest

description: <b><i>Background:</i></b> The NETest is a multigene assay comprising 51 circulating neuroendocrine tumor (NET)-specific transcripts. The quotient of the 51-gene assay is based upon an ensemble of machine learning algorithms. Eight cancer hallmarks or “omes” (apoptome, epigenome, growth factor signalome, metabolome, proliferome, plurome, secretome, SSTRome) represent 29 genes. The NETest is an accurate diagnostic (&gt;90%) test, but its prognostic utility has not been assessed. In this study, we describe the expansion of the NETest omic cluster components and demonstrate that integration amplifies NETest prognostic accuracy. <b><i>Methods:</i></b> Group 1: <i>n</i> = 222; including stable disease (SD, <i>n</i> = 146), progressive disease (PD, <i>n</i> = 76), and controls (<i>n</i> = 139). Group 2: NET Registry NCT02270567; <i>n</i> = 88; prospective samples (SD, <i>n</i> = 54; PD, <i>n</i> = 34) with up to 24 months follow-up. We used PubMed literature review, interactomic analysis, nonparametric testing, Kaplan-Meier survival curves, and χ<sup>2</sup> analyses to inform and define the prognostic significance of NET genomic “hallmarks.” <b><i>Results:</i></b> 2020 analyses: In-depth analyses of 47 ­NETest genes identified a further six omes: fibrosome, inflammasome, metastasome, NEDome, neurome, and TFome. Group 1 analysis: Twelve omes, excluding the inflammasome and apoptome, were significantly (<i>p</i> &lt; 0.05, 2.1- to 8.2-fold) elevated compared to controls. In the PD group, seven omes (proliferome, NEDome, epigenome, SSTRome, neurome, metastasome, and fibrosome) were elevated (both expression levels and fold change &gt;2) versus SD. Group 2 analysis: All these seven omes were upregulated. In PD, they were significantly more elevated (<i>p</i> &lt; 0.02) than in SD. The septet omic expression exhibited a 69% prognostic accuracy. The NETest alone was 70.5% accurate. A low NETest (≤40) integrated with epigenome/metastasome levels was an accurate prognostic for PD (90%). A high NETest (&gt;40) including the fibrosome/NEDome predicted PD development within 3 months (100%). Using decision tree analysis to integrate the four omes (epigenome, metastasome, fibrosome, and NEDome) with the NETest score generated an overall prognostic accuracy of 93%. <b><i>Conclusions:</i></b> Examination of NETest omic gene cluster analysis identified five additional clinically relevant cancer hallmarks. Identification of seven omic clusters (septet) provides a molecular pathological signature of disease progression. The integration of the quartet (epigenome, fibrosome, metastasome, NEDome) and the NETest score yielded a 93% accuracy in the prediction of future disease status.
DOI: 10.6084/m9.figshare.12789812.v1
title: Supplemental File 5. Discharge and Follow-up Care Dataset

description: Survey results from the Pediatric Discharge and Follow-up Care study.
DOI: 10.6084/m9.figshare.12789692.v1
title: Supplementary Material for: Neuroendocrine Tumor Omic Gene Cluster Analysis Amplifies the Prognostic Accuracy of the NETest

description: <b><i>Background:</i></b> The NETest is a multigene assay comprising 51 circulating neuroendocrine tumor (NET)-specific transcripts. The quotient of the 51-gene assay is based upon an ensemble of machine learning algorithms. Eight cancer hallmarks or “omes” (apoptome, epigenome, growth factor signalome, metabolome, proliferome, plurome, secretome, SSTRome) represent 29 genes. The NETest is an accurate diagnostic (&gt;90%) test, but its prognostic utility has not been assessed. In this study, we describe the expansion of the NETest omic cluster components and demonstrate that integration amplifies NETest prognostic accuracy. <b><i>Methods:</i></b> Group 1: <i>n</i> = 222; including stable disease (SD, <i>n</i> = 146), progressive disease (PD, <i>n</i> = 76), and controls (<i>n</i> = 139). Group 2: NET Registry NCT02270567; <i>n</i> = 88; prospective samples (SD, <i>n</i> = 54; PD, <i>n</i> = 34) with up to 24 months follow-up. We used PubMed literature review, interactomic analysis, nonparametric testing, Kaplan-Meier survival curves, and χ<sup>2</sup> analyses to inform and define the prognostic significance of NET genomic “hallmarks.” <b><i>Results:</i></b> 2020 analyses: In-depth analyses of 47 ­NETest genes identified a further six omes: fibrosome, inflammasome, metastasome, NEDome, neurome, and TFome. Group 1 analysis: Twelve omes, excluding the inflammasome and apoptome, were significantly (<i>p</i> &lt; 0.05, 2.1- to 8.2-fold) elevated compared to controls. In the PD group, seven omes (proliferome, NEDome, epigenome, SSTRome, neurome, metastasome, and fibrosome) were elevated (both expression levels and fold change &gt;2) versus SD. Group 2 analysis: All these seven omes were upregulated. In PD, they were significantly more elevated (<i>p</i> &lt; 0.02) than in SD. The septet omic expression exhibited a 69% prognostic accuracy. The NETest alone was 70.5% accurate. A low NETest (≤40) integrated with epigenome/metastasome levels was an accurate prognostic for PD (90%). A high NETest (&gt;40) including the fibrosome/NEDome predicted PD development within 3 months (100%). Using decision tree analysis to integrate the four omes (epigenome, metastasome, fibrosome, and NEDome) with the NETest score generated an overall prognostic accuracy of 93%. <b><i>Conclusions:</i></b> Examination of NETest omic gene cluster analysis identified five additional clinically relevant cancer hallmarks. Identification of seven omic clusters (septet) provides a molecular pathological signature of disease progression. The integration of the quartet (epigenome, fibrosome, metastasome, NEDome) and the NETest score yielded a 93% accuracy in the prediction of future disease status.
DOI: 10.6084/m9.figshare.12789632
title: Data_Spillover

description: The dataset can be used to study spillover effects from future champion. The variable superstar is a dummy which equals either team has played against the future champion in its last match.<br>
DOI: 10.6084/m9.figshare.12789578
title: Supplementary Material for: Mobility Impairment in Patients New to Dialysis

description: <b><i>Background:</i></b> Impaired mobility is associated with functional dependence, frailty, and mortality in prevalent patients undergoing dialysis. We investigated risk factors for mobility impairment, (poor gait speed) in patients incident to dialysis, and changes in gait speed over time in a 2-year longitudinal study. <b><i>Methods:</i></b> One hundred eighty-three patients enrolled within 6 months of dialysis initiation were followed up 6, 12, and 24 months later. Grip strength, health-related quality of life, and comorbidities were assessed at baseline. Outcomes were (a) baseline gait speed and (b) change in gait speed over time. Gait speed was assessed by 4-meter walk. Multivariate linear regression was used to identify risk factors for low gait speed at baseline. For longitudinal analyses, linear mixed effects modeling with gait speed modeled over time was used as the outcome. <b><i>Results:</i></b> Participants were 54.7 ± 12.8 years old, 52.5% men, 73.9% black with mean dialysis vintage of 100.1 ± 46.9 days and median gait speed 0.78 (0.64–0.094) m/s. Lower health utility and grip strength, diabetic nephropathy, and walking aids were associated with lower baseline gait speed. Loss of 0.1 m/s gait speed occurred in 24% of subjects at 1 year. In multivariate mixed effects models, only age, walking aid use, lower health utility, and lower handgrip strength were significantly associated with gait speed loss. <b><i>Conclusions:</i></b> In our cohort of incident dialysis patients, overall gait speed is very low and 54.2% of the subjects continue to lose gait speed over 2 years. Older age, lower handgrip strength, and quality of life are risk factors for slowness. Patients at highest risk of poor gait speed can be identified at dialysis initiation to allow targeted implementation of therapeutic options.
DOI: 10.6084/m9.figshare.12789632.v1
title: Data_Spillover

description: The dataset can be used to study spillover effects from future champion. The variable superstar is a dummy which equals either team has played against the future champion in its last match.<br>
DOI: 10.6084/m9.figshare.12789356
title: DATA: Not all words are equally acquired: Transitional probabilities and instructions affect the electrophysiological correlates of statistical learning

description: Behavioral and Electrophisiological (for N1, N250, and N400 components, in three ROI of 9 electrodes) data
DOI: 10.6084/m9.figshare.12789302
title: Dataset_Spillover.csv

description: This dataset can be used to study spillover effects in European football. The variable superstar is a dummy which is one if either team has played against the future champion in its last match.<br>
DOI: 10.6084/m9.figshare.12789308
title: Safer sex work guidelines

description: A collection of five English-language 'safer sex work' guidelines published by community-based sex work organizations in relation to COVID-19, as compiled in July 2020. These were used to undertake a content analysis describing different recommendations, as published in the journal 'Sexual Health' in August 2020. <br><b>Article reference: </b>Callander D, Meunier E, DeVea R, Grov C, Donovan B, Minichiello V, Duncan, DT. Sex workers are returning to work and require enhanced support in the face of COVID-19: Results from a longitudinal analysis of online sex work activity and a content analysis of safer sex work guidelines. <i>Sexual Health</i>, 2020; online first. <br><b><br></b><b>Files included:</b><i>Organization name shortened (Location) [Reference]</i><br><i><br></i>1) Butterfly (Canada) [8]2) Berufsverband Sexarbeit (Germany) [9]3) COYOTE (USA) [10]4) Scarlet Alliance (Australia) [11]5) Vital Strategies (International) [12]
DOI: 10.6084/m9.figshare.12789356.v1
title: DATA: Not all words are equally acquired: Transitional probabilities and instructions affect the electrophysiological correlates of statistical learning

description: Behavioral and Electrophisiological (for N1, N250, and N400 components, in three ROI of 9 electrodes) data
DOI: 10.6084/m9.figshare.12789302.v1
title: Dataset_Thiem.csv

description: This dataset can be used to study spillover effects in European football. The variable superstar is a dummy which is one if either team has played against the future champion in its last match.<br>
DOI: 10.6084/m9.figshare.12789278
title: Supplementary Information for the "High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing" article

description: Supplementary Information for the "High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing" article. Data contains results from Nanopore targeted sequencing analysis of 142 TRs using VNTRTyper and Tandem-genotypes.
DOI: 10.6084/m9.figshare.12789278.v1
title: Supplementary Information for the "High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing" article

description: Supplementary Information for the "High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing" article. Data contains results from Nanopore targeted sequencing analysis of 142 TRs using VNTRTyper and Tandem-genotypes.
DOI: 10.6084/m9.figshare.12789200
title: Data for paper: Status Does Not Predict Stress: Women in an Egalitarian Hunter-Gatherer Society

description: Data for replicating the analysis in the paper "Status Does Not Predict Stress: Women in an Egalitarian Hunter-Gatherer Society".<br>To protect the anonymity of health data from the Hadza people collected by Piotr Fedurek, we provide a simulated dataset of two domains of social status and hair cortisol concentration generated using the R package synthpop (Nowok et al. 2016). <br><br>Nowok, B., Raab, G. M., & Dibben, C. (2016). synthpop: Bespoke creation of synthetic data in R. <i>J Stat Softw</i>, <i>74</i>(11), 1-26.<br>
DOI: 10.6084/m9.figshare.12789200.v1
title: Data for paper: Status Does Not Predict Stress: Women in an Egalitarian Hunter-Gatherer Society

description: Data for replicating the analysis in the paper "Status Does Not Predict Stress: Women in an Egalitarian Hunter-Gatherer Society".<br>To protect the anonymity of health data from the Hadza people collected by Piotr Fedurek, we provide a simulated dataset of two domains of social status and hair cortisol concentration generated using the R package synthpop (Nowok et al. 2016). <br><br>Nowok, B., Raab, G. M., & Dibben, C. (2016). synthpop: Bespoke creation of synthetic data in R. <i>J Stat Softw</i>, <i>74</i>(11), 1-26.<br>
DOI: 10.6084/m9.figshare.12789161
title: Calculating 95% Confidence Intervals for Hazard Ratios from No, you go first: phenotype and social context affect house sparrow neophobia

description: 95% confidence intervals were manually calculated in Excel for hazard ratios of Cox Proportional Hazard models.
DOI: 10.6084/m9.figshare.12789161.v1
title: Calculating 95% Confidence Intervals for Hazard Ratios from No, you go first: phenotype and social context affect house sparrow neophobia

description: 95% confidence intervals were manually calculated in Excel for hazard ratios of Cox Proportional Hazard models.
DOI: 10.6084/m9.figshare.12789152
title: Greater rhea vocal activity database

description: Raw data employed for graphs and data analyses.<br>
DOI: 10.6084/m9.figshare.12789143
title: agz7 dataset

description: AGZ7—a calculated organic chemistry building-block dictionary based on the AMON approach [Huang and von Lilienfeld,Nature Chemistry(2020)]. AGZ7records Cartesian coordinates of compositional and constitutional isomers, as well as properties for∼140k small organicmolecules obtained by systematically fragmenting all molecules of Zinc and the majority of GDB17 into smaller entities,saturating with hydrogens, and containing no more than 7 heavy atoms (excluding hydrogen atoms). AGZ7 cover the elements{H, B, C, N, O, F, Si, P, S, Cl, Br, Sn and I} and includes optimized geometries, total energy and its decomposition, Mullikenatomic charges, dipole moment vectors, quadrupole tensors, electronic spatial extent, eigenvalues of all occupied orbitals,LUMO, gap, isotropic polarizability, harmonic frequencies, reduced masses, force constants, IR intensity, normal coordinates,rotational constants, zero-point energy, internal energy, enthalpy, entropy, free energy, and heat capacity (all at ambientconditions) using B3LYP/cc-pVTZ.
DOI: 10.6084/m9.figshare.12789143.v1
title: agz7 dataset

description: AGZ7—a calculated organic chemistry building-block dictionary based on the AMON approach [Huang and von Lilienfeld,Nature Chemistry(2020)]. AGZ7records Cartesian coordinates of compositional and constitutional isomers, as well as properties for∼140k small organicmolecules obtained by systematically fragmenting all molecules of Zinc and the majority of GDB17 into smaller entities,saturating with hydrogens, and containing no more than 7 heavy atoms (excluding hydrogen atoms). AGZ7 cover the elements{H, B, C, N, O, F, Si, P, S, Cl, Br, Sn and I} and includes optimized geometries, total energy and its decomposition, Mullikenatomic charges, dipole moment vectors, quadrupole tensors, electronic spatial extent, eigenvalues of all occupied orbitals,LUMO, gap, isotropic polarizability, harmonic frequencies, reduced masses, force constants, IR intensity, normal coordinates,rotational constants, zero-point energy, internal energy, enthalpy, entropy, free energy, and heat capacity (all at ambientconditions) using B3LYP/cc-pVTZ.
DOI: 10.6084/m9.figshare.12789152.v1
title: Greater rhea vocal activity database

description: Raw data employed for graphs and data analyses.<br>
DOI: 10.6084/m9.figshare.12789113
title: Supplementary Material for: Comparison of the Safety Profiles of 3 Different Hymenoptera Venom Immunotherapy Protocols: A Retrospective 2-Center Study of 143 Patients

description: <b><i>Introduction:</i></b> Venom immunotherapy (VIT) is highly effective and the treatment of choice for patients with a history of systemic anaphylactic reactions to a Hymenoptera sting. It has been assumed that VIT protocols with a rapid dose increase during the induction phase are associated with a higher frequency of systemic reactions (SR); however, study data addressing this issue are conflicting. <b><i>Objective:</i></b> The aim of this study was to compare the safety of 3 different Hymenoptera VIT protocols (half-day ultra-rush, 3-day rush, 3-week cluster). <b><i>Methods:</i></b> This retrospective 2-center study included 143 Hymenoptera venom-allergic patients, who underwent 147 VIT procedures during the years 2015–2018. Twenty cluster, 75 rush, and 52 ultra-rush VIT protocols were performed with honeybee (54 protocols) and wasp (93 protocols) venom. All documented side effects were classified into large local and SR (Ring and Messmer classification). <b><i>Results:</i></b> SR were observed during 11 (7.5%) VIT procedures and did not exceed severity grade II. SR occurred more frequently in cluster compared to accelerated protocols. This result was observed for both honeybee (cluster: 25%, rush: 8.7%, and ultra-rush: 15.8%) and wasp VIT (cluster: 12.5%, rush: 0%, and ultra-rush: 6.1%), though the differences were statistically significant only in the wasp VIT subgroup. Honeybee venom elicited more SR than wasp venom (14.8 and 3.2%, respectively, <i>p</i> = 0.01). The risk for SR did not depend on age, sex, concomitant antihypertensive medication, hypertryptasemia, or severity of the index sting reaction. <b><i>Conclusion:</i></b> Accelerated VIT protocols, namely, rush and ultra-rush protocols are safe therapeutic options for Hymenoptera venom-allergic patients and displayed fewer SR than cluster VIT protocols in our study.
DOI: 10.17028/rd.lboro.12789110
title: Supplementary information files for Probing the enhanced methanol electrooxidation mechanism on platinum-metal oxide catalyst

description: Supplementary information files for Probing the enhanced methanol electrooxidation mechanism on platinum-metal oxide catalyst<br>Pt-metal oxide nanocomposites are classified as an alternative promising catalyst besides Pt-Ru nanoalloys for electrochemical methanol oxidation reaction (MOR), and yet the relevant enhancement mechanism for MOR remains largely elusive in terms of catalyst functions and reaction pathways. Herein, interface-rich Pt-SnO2 nanoflakes supported on reduced graphene oxide have been prepared and employed as a model catalyst for such a study. X-ray photoelectron spectroscopy and X-ray absorption spectroscopy measurements reveal significant electronic structure modification on Pt in contact with SnO2, concomitant with enhanced MOR. In-situ surface enhanced infrared absorption spectroscopy and on-line differential electrochemical mass spectrometry measurements indicate that the non-CO pathway is selectively enhanced on Pt-SnO2 compared to the CO pathway which prevails on Pt. DFT calculations reinforce that this electronic structure manipulation favors the non-CO reaction pathway on Pt-SnO2.<br>
DOI: 10.6084/m9.figshare.12789068
title: Personalized Cancer Therapy Prioritization Based on Driver Alteration Co-occurrence Patterns

description: This compressed folder contains a cytoscape session for each treatment with all the driver co-occurrence networks generated from whole exome sequencing (WES), IMPACT410 (IM) and Foundation Medicine (FM) gene panels. This information complements the information provided as Additional File 1: Table S2.
DOI: 10.6084/m9.figshare.12789068.v1
title: Personalized Cancer Therapy Prioritization Based on Driver Alteration Co-occurrence Patterns

description: This compressed folder contains a cytoscape session for each treatment with all the driver co-occurrence networks generated from whole exome sequencing (WES), IMPACT410 (IM) and Foundation Medicine (FM) gene panels. This information complements the information provided as Additional File 1: Table S2.
DOI: 10.6084/m9.figshare.12788941
title: Additional file 4 of Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells

description: Additional file 4: Table S3. Gene ontology analysis of differentially expressed genes from Stag1−/−, Stag2−/−, or Stag2−/− siStag1 mESCs. Lists of the top 30 GO-terms for both up- and down-regulated genes in the four gene classes (common, Stag1−/− specific, Stag2−/− specific, and redundant).
DOI: 10.6084/m9.figshare.12788938
title: Additional file 3 of Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells

description: Additional file 3: Table S2. Differentially expressed genes for all depletion conditions compared to wild-type siGLO. Full lists of differentially expressed genes for the four conditions used in RNA-seq analysis in this study, all compared to wild-type siGLO (Stag1−/− siGLO, wild-type siStag1, Stag2−/− siGLO, and Stag2−/− siStag1).
DOI: 10.6084/m9.figshare.12788941.v1
title: Additional file 4 of Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells

description: Additional file 4: Table S3. Gene ontology analysis of differentially expressed genes from Stag1−/−, Stag2−/−, or Stag2−/− siStag1 mESCs. Lists of the top 30 GO-terms for both up- and down-regulated genes in the four gene classes (common, Stag1−/− specific, Stag2−/− specific, and redundant).
DOI: 10.6084/m9.figshare.12788938.v1
title: Additional file 3 of Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells

description: Additional file 3: Table S2. Differentially expressed genes for all depletion conditions compared to wild-type siGLO. Full lists of differentially expressed genes for the four conditions used in RNA-seq analysis in this study, all compared to wild-type siGLO (Stag1−/− siGLO, wild-type siStag1, Stag2−/− siGLO, and Stag2−/− siStag1).
DOI: 10.6084/m9.figshare.12788914
title: Additional file 4 of ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

description: Additional file 4: Table S3. ContamLD, ContamMix, and ANGSD Estimates. Excel spreadsheet providing ContamLD, ContamMix, and ANGSD estimates from ancient male individuals with meta-data of the ancient individuals also included.
DOI: 10.6084/m9.figshare.12788917
title: Additional file 5 of ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

description: Additional file 5: Table S4. Simulation with Damaged Contaminated Reads. Excel spreadsheet providing ContamLD estimates for a simulation where the damaged reads of the contaminant individual were also included in the contamination.
DOI: 10.6084/m9.figshare.12788908
title: Additional file 2 of ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

description: Additional file 2: Table S1. Ancient Individual Meta-Data. Excel spreadsheet detailing information about the ancient individuals analyzed.
DOI: 10.6084/m9.figshare.12788911
title: Additional file 3 of ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

description: Additional file 3: Table S2. ContamLD and ANGSD Estimates. Excel spreadsheet providing ContamLD and ANGSD estimates from simulations of ancient individuals with meta-data of the ancient individuals also included.
DOI: 10.6084/m9.figshare.12788911.v1
title: Additional file 3 of ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

description: Additional file 3: Table S2. ContamLD and ANGSD Estimates. Excel spreadsheet providing ContamLD and ANGSD estimates from simulations of ancient individuals with meta-data of the ancient individuals also included.