cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14442249
title: Bootstrap Inference for Quantile-based Modal Regression

description: In this article, we develop uniform inference methods for the conditional mode based on quantile regression. Specifically, we propose to estimate the conditional mode by minimizing the derivative of the estimated conditional quantile function defined by smoothing the linear quantile regression estimator, and develop two bootstrap methods, a novel pivotal bootstrap and the nonparametric bootstrap, for our conditional mode estimator. Building on high-dimensional Gaussian approximation techniques, we establish the validity of simultaneous confidence rectangles constructed from the two bootstrap methods for the conditional mode. We also extend the preceding analysis to the case where the dimension of the covariate vector is increasing with the sample size. Finally, we conduct simulation experiments and a real data analysis using the U.S. wage data to demonstrate the finite sample performance of our inference method. The supplemental materials include the wage dataset, R codes and an appendix containing proofs of the main results, additional simulation results, discussion of model misspecification and quantile crossing, and additional details of the numerical implementation.
DOI: 10.6084/m9.figshare.9723674
title: Additional file 18: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S6. Chromosome locations of tandemly arrayed T. aestivum class III peroxidases. (XLS 34 kb)
DOI: 10.6084/m9.figshare.21256728.v1
title: Additional file 2 of Mucosal-associated invariant T cells predict increased acute graft-versus-host-disease incidence in patients receiving allogeneic hematopoietic stem cell transplantation

description: Additional file 2: List of differentially expressed gene in RNA-seq.
DOI: 10.6084/m9.figshare.14442249.v1
title: Bootstrap inference for quantile-based modal regression

description: In this paper, we develop uniform inference methods for the conditional mode based on quantile regression. Specifically, we propose to estimate the conditional mode by minimizing the derivative of the estimated conditional quantile function defined by smoothing the linear quantile regression estimator, and develop two bootstrap methods, a novel pivotal bootstrap and the nonparametric bootstrap, for our conditional mode estimator. Building on high-dimensional Gaussian approximation techniques, we establish the validity of simultaneous confidence rectangles constructed from the two bootstrap methods for the conditional mode. We also extend the preceding analysis to the case where the dimension of the covariate vector is increasing with the sample size. Finally, we conduct simulation experiments and a real data analysis using U.S. wage data to demonstrate the finite sample performance of our inference method. The supplemental materials include the wage dataset, R codes and an appendix containing proofs of the main results, additional simulation results, discussion of model misspecification and quantile crossing, and additional details of the numerical implementation.
DOI: 10.6084/m9.figshare.14442249.v2
title: Bootstrap Inference for Quantile-based Modal Regression

description: In this article, we develop uniform inference methods for the conditional mode based on quantile regression. Specifically, we propose to estimate the conditional mode by minimizing the derivative of the estimated conditional quantile function defined by smoothing the linear quantile regression estimator, and develop two bootstrap methods, a novel pivotal bootstrap and the nonparametric bootstrap, for our conditional mode estimator. Building on high-dimensional Gaussian approximation techniques, we establish the validity of simultaneous confidence rectangles constructed from the two bootstrap methods for the conditional mode. We also extend the preceding analysis to the case where the dimension of the covariate vector is increasing with the sample size. Finally, we conduct simulation experiments and a real data analysis using the U.S. wage data to demonstrate the finite sample performance of our inference method. The supplemental materials include the wage dataset, R codes and an appendix containing proofs of the main results, additional simulation results, discussion of model misspecification and quantile crossing, and additional details of the numerical implementation.
DOI: 10.6084/m9.figshare.9723674.v1
title: Additional file 18: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S6. Chromosome locations of tandemly arrayed T. aestivum class III peroxidases. (XLS 34 kb)
DOI: 10.6084/m9.figshare.9723668
title: Additional file 16: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S4. Collinearity events and Ka/Ks values of class III peroxidases among T. aestivum, B. distachyon and O. sativa. Sheet 1 was Ka/Ks values of collinearity events in T. aestivum class III peroxidases; sheet 2 was Ka/Ks values of collinearity events in all T. aestivum genes. Similarly, sheets 3-4 showed T. aestivum and B. distachyon. Sheets 5-6 showed T. aestivum and O. sativa. (XLS 5739 kb)
DOI: 10.6084/m9.figshare.9723662
title: Additional file 15: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S3. Chromosome locations of T. aestivum class III peroxidases. (XLS 64 kb)
DOI: 10.6084/m9.figshare.9723662.v1
title: Additional file 15: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S3. Chromosome locations of T. aestivum class III peroxidases. (XLS 64 kb)
DOI: 10.6084/m9.figshare.9723716.v1
title: Additional file 28: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S16. Primers used to clone the promoters related to predicted cis-elements. (XLS 20 kb)
DOI: 10.6084/m9.figshare.11820819
title: Additional file 1 of PlaPPISite: a comprehensive resource for plant protein-protein interaction sites

description: Additional file 1: TableS1. The PPI number distribution for the 13 plants in PlaPPISite. Table S2. The number of experimentally verified PPIs of the 13 plants. Table S3. The number of experimentally verified PPIs of six model organisms. Table S4. The GO annotation covrage for the 13 plants. Table S5. The subcellular co-localization proportion for the 13 plants. Table S6. The known mutated information associated with predicted interaction sites.
DOI: 10.6084/m9.figshare.9723668.v1
title: Additional file 16: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S4. Collinearity events and Ka/Ks values of class III peroxidases among T. aestivum, B. distachyon and O. sativa. Sheet 1 was Ka/Ks values of collinearity events in T. aestivum class III peroxidases; sheet 2 was Ka/Ks values of collinearity events in all T. aestivum genes. Similarly, sheets 3-4 showed T. aestivum and B. distachyon. Sheets 5-6 showed T. aestivum and O. sativa. (XLS 5739 kb)
DOI: 10.6084/m9.figshare.9723689
title: Additional file 21: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S9. Normalized gene expression values of 170 T. aestivum class III peroxidase genes under abiotic stress treatments. (XLS 138 kb)
DOI: 10.6084/m9.figshare.11820819.v1
title: Additional file 1 of PlaPPISite: a comprehensive resource for plant protein-protein interaction sites

description: Additional file 1: TableS1. The PPI number distribution for the 13 plants in PlaPPISite. Table S2. The number of experimentally verified PPIs of the 13 plants. Table S3. The number of experimentally verified PPIs of six model organisms. Table S4. The GO annotation covrage for the 13 plants. Table S5. The subcellular co-localization proportion for the 13 plants. Table S6. The known mutated information associated with predicted interaction sites.
DOI: 10.6084/m9.figshare.9723671
title: Additional file 17: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S5. Collinearity events and Ka/Ks values of class III peroxidases in T. aestivum subgenomes, Ae. tauschii and T. urartu. Sheet 1 was Ka/Ks values of class III peroxidase collinearity events in the T. aestivum A-subgenome and T. urartu. Similarly, sheet 2 showed the T. aestivum D-subgenome and Ae. tauschii. (XLS 58 kb)
DOI: 10.6084/m9.figshare.9723710
title: Additional file 26: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S14. Primers used in qRT-PCR analysis. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.9723677.v1
title: Additional file 19: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S7. Public wheat expression data. (XLS 48 kb)
DOI: 10.6084/m9.figshare.9723704.v1
title: Additional file 24: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S12. Normalized gene expression values of 170 T. aestivum class III peroxidase genes under biotic stress treatments. (XLS 111 kb)
DOI: 10.6084/m9.figshare.9723650.v1
title: Additional file 13: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S1. Subfamily classification of class III peroxidases in the investigated plant genomes. (XLS 168 kb)
DOI: 10.6084/m9.figshare.9723692.v1
title: Additional file 22: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S10. Differentially expressed (p&lt;0.01 and |FC|&gt;1.5) T. aestivum class III peroxidase genes under abiotic stress treatments. (XLS 47 kb)
DOI: 10.6084/m9.figshare.9723698.v1
title: Additional file 23: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S11. Putative cis-acting elements related to stress and hormone responses in TaePRXs promoters. (XLS 39 kb)
DOI: 10.5281/zenodo.3749014
title: Relocated Earthquake Catalog for Java-Indonesia (April 2009 to November 2018)

description: Relocated Earthquake Catalog for Java (April 2009 to November 2018). 

Please refer to:

Widiyantoro, S., Gunawan, E., Muhari, A., Rawlinson, N., Mori, J., Hanifa, N.R., Susilo, S., Supendi, P., Shiddiqi, H.A., Nugraha, A. D., Putra, H. E. (2020). Seismic gaps south of Java, Indonesia: Implications for megathrust earthquakes and tsunamis, Scientific Reports, 10, 15274 (2020). https://doi.org/10.1038/s41598-020-72142-z
DOI: 10.5281/zenodo.3749015
title: Relocated Earthquake Catalog for Java-Indonesia (April 2009 to November 2018)

description: Relocated Earthquake Catalog for Java (April 2009 to November 2018). 

Please refer to:

Widiyantoro, S., Gunawan, E., Muhari, A., Rawlinson, N., Mori, J., Hanifa, N.R., Susilo, S., Supendi, P., Shiddiqi, H.A., Nugraha, A. D., Putra, H. E. (2020). Seismic gaps south of Java, Indonesia: Implications for megathrust earthquakes and tsunamis, Scientific Reports, 10, 15274 (2020). https://doi.org/10.1038/s41598-020-72142-z
DOI: 10.6084/m9.figshare.21256728
title: Additional file 2 of Mucosal-associated invariant T cells predict increased acute graft-versus-host-disease incidence in patients receiving allogeneic hematopoietic stem cell transplantation

description: Additional file 2: List of differentially expressed gene in RNA-seq.
DOI: 10.6084/m9.figshare.9723707.v1
title: Additional file 25: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S13. Differentially expressed (p&lt;0.01 and |FC|&gt;1.5) T. aestivum class III peroxidase genes under biotic stress treatments. (XLS 38 kb)
DOI: 10.6084/m9.figshare.9723683.v1
title: Additional file 20: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S8. Normalized gene expression values of 170 T. aestivum class III peroxidase genes in different tissues. (XLS 72 kb)
DOI: 10.6084/m9.figshare.9723710.v1
title: Additional file 26: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S14. Primers used in qRT-PCR analysis. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.9723713
title: Additional file 27: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S15. Primers of TaePRXs used for subcellular localization. (XLS 20 kb)
DOI: 10.6084/m9.figshare.9723716
title: Additional file 28: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S16. Primers used to clone the promoters related to predicted cis-elements. (XLS 20 kb)
DOI: 10.6084/m9.figshare.9723713.v1
title: Additional file 27: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S15. Primers of TaePRXs used for subcellular localization. (XLS 20 kb)
DOI: 10.6084/m9.figshare.19160880.v1
title: Characteristics and outcomes of COVID-19 patients with and without asthma from the United States, South Korea, and Europe

description: <b>Objective:</b> Large international comparisons describing the clinical characteristics of patients with COVID-19 are limited. The aim of the study was to perform a large-scale descriptive characterization of COVID-19 patients with asthma. <b>Methods:</b> We included nine databases contributing data from January to June 2020 from the US, South Korea (KR), Spain, UK and the Netherlands. We defined two cohorts of COVID-19 patients (‘diagnosed’ and ‘hospitalized’) based on COVID-19 disease codes. We followed patients from COVID-19 index date to 30 days or death. We performed descriptive analysis and reported the frequency of characteristics and outcomes in people with asthma defined by codes and prescriptions. <b>Results:</b> The diagnosed and hospitalized cohorts contained 666,933 and 159,552 COVID-19 patients respectively. Exacerbation in people with asthma was recorded in 1.6–8.6% of patients at presentation. Asthma prevalence ranged from 6.2% (95% CI 5.7–6.8) to 18.5% (95% CI 18.2–18.8) in the diagnosed cohort and 5.2% (95% CI 4.0–6.8) to 20.5% (95% CI 18.6–22.6) in the hospitalized cohort. Asthma patients with COVID-19 had high prevalence of comorbidity including hypertension, heart disease, diabetes and obesity. Mortality ranged from 2.1% (95% CI 1.8–2.4) to 16.9% (95% CI 13.8–20.5) and similar or lower compared to COVID-19 patients without asthma. Acute respiratory distress syndrome occurred in 15–30% of hospitalized COVID-19 asthma patients. <b>Conclusion:</b> The prevalence of asthma among COVID-19 patients varies internationally. Asthma patients with COVID-19 have high comorbidity. The prevalence of asthma exacerbation at presentation was low. Whilst mortality was similar among COVID-19 patients with and without asthma, this could be confounded by differences in clinical characteristics. Further research could help identify high-risk asthma patients.KEY MESSAGESAsthma prevalence in COVID-19 patients varied internationally (5.2–20.5%).The prevalence of asthma exacerbation at presentation with COVID-19 in diagnosed and hospitalized patients was low.Comorbidities were common in COVID-19 patients with asthma. KEY MESSAGES Asthma prevalence in COVID-19 patients varied internationally (5.2–20.5%).The prevalence of asthma exacerbation at presentation with COVID-19 in diagnosed and hospitalized patients was low.Comorbidities were common in COVID-19 patients with asthma. Supplemental data for this article is available online at https://doi.org/10.1080/02770903.2021.2025392 .
DOI: 10.6084/m9.figshare.21256840.v1
title: Additional file 1 of Identification of molecular subtypes based on inflammatory response in lower-grade glioma

description: Additional file 1. The clinical information of LGG patients obtained from TCGA, CGGA, and GEO database.
DOI: 10.6084/m9.figshare.9723683
title: Additional file 20: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S8. Normalized gene expression values of 170 T. aestivum class III peroxidase genes in different tissues. (XLS 72 kb)
DOI: 10.6084/m9.figshare.9723704
title: Additional file 24: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S12. Normalized gene expression values of 170 T. aestivum class III peroxidase genes under biotic stress treatments. (XLS 111 kb)
DOI: 10.6084/m9.figshare.9723707
title: Additional file 25: of Genome-wide and evolutionary analysis of the class III peroxidase gene family in wheat and Aegilops tauschii reveals that some members are involved in stress responses

description: Table S13. Differentially expressed (p&lt;0.01 and |FC|&gt;1.5) T. aestivum class III peroxidase genes under biotic stress treatments. (XLS 38 kb)
DOI: 10.6084/m9.figshare.9723743.v1
title: Additional file 1: of Roles of the SPL gene family and miR156 in the salt stress responses of tamarisk (Tamarix chinensis)

description: Table S1. Source and sequences of SPLs for the phylogenetic analysis. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.9723743
title: Additional file 1: of Roles of the SPL gene family and miR156 in the salt stress responses of tamarisk (Tamarix chinensis)

description: Table S1. Source and sequences of SPLs for the phylogenetic analysis. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.9723749
title: Additional file 2: of Roles of the SPL gene family and miR156 in the salt stress responses of tamarisk (Tamarix chinensis)

description: Table S2. Primers for qRT-PCR. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.9723749.v1
title: Additional file 2: of Roles of the SPL gene family and miR156 in the salt stress responses of tamarisk (Tamarix chinensis)

description: Table S2. Primers for qRT-PCR. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.19160880
title: Characteristics and outcomes of COVID-19 patients with and without asthma from the United States, South Korea, and Europe

description: <b>Objective:</b> Large international comparisons describing the clinical characteristics of patients with COVID-19 are limited. The aim of the study was to perform a large-scale descriptive characterization of COVID-19 patients with asthma. <b>Methods:</b> We included nine databases contributing data from January to June 2020 from the US, South Korea (KR), Spain, UK and the Netherlands. We defined two cohorts of COVID-19 patients (‘diagnosed’ and ‘hospitalized’) based on COVID-19 disease codes. We followed patients from COVID-19 index date to 30 days or death. We performed descriptive analysis and reported the frequency of characteristics and outcomes in people with asthma defined by codes and prescriptions. <b>Results:</b> The diagnosed and hospitalized cohorts contained 666,933 and 159,552 COVID-19 patients respectively. Exacerbation in people with asthma was recorded in 1.6–8.6% of patients at presentation. Asthma prevalence ranged from 6.2% (95% CI 5.7–6.8) to 18.5% (95% CI 18.2–18.8) in the diagnosed cohort and 5.2% (95% CI 4.0–6.8) to 20.5% (95% CI 18.6–22.6) in the hospitalized cohort. Asthma patients with COVID-19 had high prevalence of comorbidity including hypertension, heart disease, diabetes and obesity. Mortality ranged from 2.1% (95% CI 1.8–2.4) to 16.9% (95% CI 13.8–20.5) and similar or lower compared to COVID-19 patients without asthma. Acute respiratory distress syndrome occurred in 15–30% of hospitalized COVID-19 asthma patients. <b>Conclusion:</b> The prevalence of asthma among COVID-19 patients varies internationally. Asthma patients with COVID-19 have high comorbidity. The prevalence of asthma exacerbation at presentation was low. Whilst mortality was similar among COVID-19 patients with and without asthma, this could be confounded by differences in clinical characteristics. Further research could help identify high-risk asthma patients.KEY MESSAGESAsthma prevalence in COVID-19 patients varied internationally (5.2–20.5%).The prevalence of asthma exacerbation at presentation with COVID-19 in diagnosed and hospitalized patients was low.Comorbidities were common in COVID-19 patients with asthma. KEY MESSAGES Asthma prevalence in COVID-19 patients varied internationally (5.2–20.5%).The prevalence of asthma exacerbation at presentation with COVID-19 in diagnosed and hospitalized patients was low.Comorbidities were common in COVID-19 patients with asthma. Supplemental data for this article is available online at https://doi.org/10.1080/02770903.2021.2025392 .
DOI: 10.6084/m9.figshare.21256854
title: Additional file 1 of Inconsistency analysis between metagenomic next-generation sequencing results of cerebrospinal fluid and clinical diagnosis with suspected central nervous system infection

description: Additional file 1: The results of next generation sequencing of cerebrospinal fluid.
DOI: 10.6084/m9.figshare.14966267
title: Additional file 8 of Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

description: Additional file 8. Expression values (RPKM) of 163 bovine samples in 60 tissue types.
DOI: 10.6084/m9.figshare.14966267.v1
title: Additional file 8 of Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

description: Additional file 8. Expression values (RPKM) of 163 bovine samples in 60 tissue types.