cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12328076.v1
title: GeologyNC_GSL_Line.dbf: Introduction to New Caledonia: geology, geodynamic evolution and mineral resources

description: polyline shapefile, corresponding to the geological map of Figure 1.2.
DOI: 10.6084/m9.figshare.12328067
title: GeologyNC_GSL_Line.shx: Introduction to New Caledonia: geology, geodynamic evolution and mineral resources

description: polyline shapefile, corresponding to the geological map of Figure 1.2.
DOI: 10.6084/m9.figshare.12328070.v1
title: GeologyNC_GSL_Surface.dbf: Introduction to New Caledonia: geology, geodynamic evolution and mineral resources

description: Polygon shapefile, corresponding to the geological map of Figure 1.2.
DOI: 10.6084/m9.figshare.12328067.v1
title: GeologyNC_GSL_Line.shx: Introduction to New Caledonia: geology, geodynamic evolution and mineral resources

description: polyline shapefile, corresponding to the geological map of Figure 1.2.
DOI: 10.6084/m9.figshare.12328019
title: Supplementary Material for: Short-Term Psychodynamic Psychotherapy for Functional Somatic Disorders: A Meta-Analysis of Randomized Controlled Trials

description: <b><i>Introduction:</i></b> Functional<b><i></i></b>somatic disorders (FSD) are common and costly, thereby driving the need for the development of effective brief treatment options. Short-term psychodynamic psychotherapy (STPP) is one candidate treatment method. <b><i>Objective:</i></b> To review and meta-analyze, where possible, randomized controlled trials (RCTs) of STPP for FSD. <b><i>Methods:</i></b> Following a systematic search of the literature, we performed a meta-analysis of available RCT groups to determine the effects of STPP on a range of outcomes after treatment, and medium- and long-term follow-ups. <b><i>Results:</i></b> In meta-analyses of 17 RCTs, STPP significantly outperformed minimal treatment, treatment as usual, or waiting list controls on somatic symptom measures at all time frames, with small to large magnitude effect sizes. Descriptive reviews of 5 RCTs suggest that STPP performed at least as well as other bona fide psychological therapies. Limitations of this meta-analysis include small samples of studies and possible publication bias. <b><i>Conclusions:</i></b> STPP is a valid treatment option for diverse FSD conditions resulting in somatic symptom reductions that persist over time. STPP should be included in FSD treatment guidelines.
DOI: 10.6084/m9.figshare.12327923
title: Supplementary Material for: Localization of Cell Receptor-Related Genes of SARS-CoV-2 in the Kidney through Single-Cell Transcriptome Analysis

description: <b><i>Background:</i></b> The new coronavirus (SARS-CoV-2), which has been responsible for the recent coronavirus disease 2019 (COVID-19) pandemic, uses the cell receptor angiotensin converting enzyme-2 (ACE2) for entry and the serine protease TMPRSS2 for spike (S) protein priming. Meanwhile, the presence of B<sup>0</sup>AT1 (SLC6A19) may prevent TMPRSS2 from accessing the cutting position on ACE2. Identifying the expression of these cell receptor-related genes of SARS-CoV-2 is critical for understanding the pathogenesis of SARS-CoV-2 in various tissues, especially in the kidney. <b><i>Methods:</i></b> The single-cell transcription datasets of the human cell landscape (HCL) and other relevant single-cell transcription databases were used to analyze the expression of ACE2, TMPRSS2, and SLC6A19 in various organs and tissues, but mainly in the kidney. <b><i>Results:</i></b> ACE2 was significantly expressed in the S1, S2, and S3 segments of proximal tubule (PT) cells. TMPRSS2 was widely expressed in several renal tubule populations extending from the PT cells to the collection system cell type, of which intercalated cells and the distal convoluted tubule cells showed more significant expression than PT cells. Unexpectedly, although expressed on various renal tubule populations, SLC6A19 was mainly enriched in PT cells, in line with ACE2 expression. Although alveolar-type (AT) 2 cells of the lung and intestinal epithelial cells expressed ACE2 as well as PT cells, AT 2 cells significantly expressed TMPRSS2 but not SLC6A19, while all 3 genes were significantly expressed in intestinal epithelial cells. <b><i>Conclusions:</i></b> ACE2 was widely expressed in specific cell subgroups of various human tissues, especially in intestinal epithelial cells, kidney PT cells, and also AT 2 cells of the lung. These 3 types of cells demonstrated significant differences in the distribution of the cell receptor-related genes of SARS-CoV-2, which may indicate the diversity of cell surface structures and differences in the affinity between SARS-CoV-2 and cells.
DOI: 10.6084/m9.figshare.12327986
title: Estimating and Accounting for Unobserved Covariates in High-Dimensional Correlated Data

description: Many high-dimensional and high-throughput biological datasets have complex sample correlation structures, which include longitudinal and multiple tissue data, as well as data with multiple treatment conditions or related individuals. These data, as well as nearly all high-throughput “omic” data, are influenced by technical and biological factors unknown to the researcher, which, if unaccounted for, can severely obfuscate estimation of and inference on the effects of interest. We therefore developed CBCV and CorrConf: provably accurate and computationally efficient methods to choose the number of and estimate latent confounding factors present in high-dimensional data with correlated or nonexchangeable residuals. We demonstrate each method’s superior performance compared to other state of the art methods by analyzing simulated multi-tissue gene expression data and identifying sex-associated DNA methylation sites in a real, longitudinal twin study. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12327929
title: Multivariate Postprocessing Methods for High-Dimensional Seasonal Weather Forecasts

description: Seasonal weather forecasts are crucial for long-term planning in many practical situations and skillful forecasts may have substantial economic and humanitarian implications. Current seasonal forecasting models require statistical postprocessing of the output to correct systematic biases and unrealistic uncertainty assessments. We propose a multivariate postprocessing approach using covariance tapering, combined with a dimension reduction step based on principal component analysis for efficient computation. Our proposed technique can correctly and efficiently handle nonstationary, non-isotropic and negatively correlated spatial error patterns, and is applicable on a global scale. Further, a moving average approach to marginal postprocessing is shown to flexibly handle trends in biases caused by global warming, and short training periods. In an application to global sea surface temperature forecasts issued by the Norwegian climate prediction model, our proposed methodology is shown to outperform known reference methods. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.12327923.v1
title: Supplementary Material for: Localization of Cell Receptor-Related Genes of SARS-CoV-2 in the Kidney through Single-Cell Transcriptome Analysis

description: <b><i>Background:</i></b> The new coronavirus (SARS-CoV-2), which has been responsible for the recent coronavirus disease 2019 (COVID-19) pandemic, uses the cell receptor angiotensin converting enzyme-2 (ACE2) for entry and the serine protease TMPRSS2 for spike (S) protein priming. Meanwhile, the presence of B<sup>0</sup>AT1 (SLC6A19) may prevent TMPRSS2 from accessing the cutting position on ACE2. Identifying the expression of these cell receptor-related genes of SARS-CoV-2 is critical for understanding the pathogenesis of SARS-CoV-2 in various tissues, especially in the kidney. <b><i>Methods:</i></b> The single-cell transcription datasets of the human cell landscape (HCL) and other relevant single-cell transcription databases were used to analyze the expression of ACE2, TMPRSS2, and SLC6A19 in various organs and tissues, but mainly in the kidney. <b><i>Results:</i></b> ACE2 was significantly expressed in the S1, S2, and S3 segments of proximal tubule (PT) cells. TMPRSS2 was widely expressed in several renal tubule populations extending from the PT cells to the collection system cell type, of which intercalated cells and the distal convoluted tubule cells showed more significant expression than PT cells. Unexpectedly, although expressed on various renal tubule populations, SLC6A19 was mainly enriched in PT cells, in line with ACE2 expression. Although alveolar-type (AT) 2 cells of the lung and intestinal epithelial cells expressed ACE2 as well as PT cells, AT 2 cells significantly expressed TMPRSS2 but not SLC6A19, while all 3 genes were significantly expressed in intestinal epithelial cells. <b><i>Conclusions:</i></b> ACE2 was widely expressed in specific cell subgroups of various human tissues, especially in intestinal epithelial cells, kidney PT cells, and also AT 2 cells of the lung. These 3 types of cells demonstrated significant differences in the distribution of the cell receptor-related genes of SARS-CoV-2, which may indicate the diversity of cell surface structures and differences in the affinity between SARS-CoV-2 and cells.
DOI: 10.6084/m9.figshare.12328019.v2
title: Supplementary Material for: Short-Term Psychodynamic Psychotherapy for Functional Somatic Disorders: A Meta-Analysis of Randomized Controlled Trials

description: <b><i>Introduction:</i></b> Functional<b><i></i></b>somatic disorders (FSD) are common and costly, thereby driving the need for the development of effective brief treatment options. Short-term psychodynamic psychotherapy (STPP) is one candidate treatment method. <b><i>Objective:</i></b> To review and meta-analyze, where possible, randomized controlled trials (RCTs) of STPP for FSD. <b><i>Methods:</i></b> Following a systematic search of the literature, we performed a meta-analysis of available RCT groups to determine the effects of STPP on a range of outcomes after treatment, and medium- and long-term follow-ups. <b><i>Results:</i></b> In meta-analyses of 17 RCTs, STPP significantly outperformed minimal treatment, treatment as usual, or waiting list controls on somatic symptom measures at all time frames, with small to large magnitude effect sizes. Descriptive reviews of 5 RCTs suggest that STPP performed at least as well as other bona fide psychological therapies. Limitations of this meta-analysis include small samples of studies and possible publication bias. <b><i>Conclusions:</i></b> STPP is a valid treatment option for diverse FSD conditions resulting in somatic symptom reductions that persist over time. STPP should be included in FSD treatment guidelines.
DOI: 10.6084/m9.figshare.12327986.v2
title: Estimating and Accounting for Unobserved Covariates in High-Dimensional Correlated Data

description: Many high-dimensional and high-throughput biological datasets have complex sample correlation structures, which include longitudinal and multiple tissue data, as well as data with multiple treatment conditions or related individuals. These data, as well as nearly all high-throughput “omic” data, are influenced by technical and biological factors unknown to the researcher, which, if unaccounted for, can severely obfuscate estimation of and inference on the effects of interest. We therefore developed CBCV and CorrConf: provably accurate and computationally efficient methods to choose the number of and estimate latent confounding factors present in high-dimensional data with correlated or nonexchangeable residuals. We demonstrate each method’s superior performance compared to other state of the art methods by analyzing simulated multi-tissue gene expression data and identifying sex-associated DNA methylation sites in a real, longitudinal twin study. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12328019.v1
title: Supplementary Material for: Short-Term Psychodynamic Psychotherapy for Functional Somatic Disorders: A Meta-Analysis of Randomized Controlled Trials

description: <b><i>Introduction:</i></b> Functional<b><i></i></b>somatic disorders (FSD) are common and costly, thereby driving the need for the development of effective brief treatment options. Short-term psychodynamic psychotherapy (STPP) is one candidate treatment method. <b><i>Objective:</i></b> To review and meta-analyze, where possible, randomized controlled trials (RCTs) of STPP for FSD. <b><i>Methods:</i></b> Following a systematic search of the literature, we performed a meta-analysis of available RCT groups to determine the effects of STPP on a range of outcomes after treatment, and medium- and long-term follow-ups. <b><i>Results:</i></b> In meta-analyses of 17 RCTs, STPP significantly outperformed minimal treatment, treatment as usual, or waiting list controls on somatic symptom measures at all time frames, with small to large magnitude effect sizes. Descriptive reviews of 5 RCTs suggest that STPP performed at least as well as other bona fide psychological therapies. Limitations of this meta-analysis include small samples of studies and possible publication bias. <b><i>Conclusions:</i></b> STPP is a valid treatment option for diverse FSD conditions resulting in somatic symptom reductions that persist over time. STPP should be included in FSD treatment guidelines.
DOI: 10.6084/m9.figshare.12327929.v2
title: Multivariate Postprocessing Methods for High-Dimensional Seasonal Weather Forecasts

description: Seasonal weather forecasts are crucial for long-term planning in many practical situations and skillful forecasts may have substantial economic and humanitarian implications. Current seasonal forecasting models require statistical postprocessing of the output to correct systematic biases and unrealistic uncertainty assessments. We propose a multivariate postprocessing approach using covariance tapering, combined with a dimension reduction step based on principal component analysis for efficient computation. Our proposed technique can correctly and efficiently handle nonstationary, non-isotropic and negatively correlated spatial error patterns, and is applicable on a global scale. Further, a moving average approach to marginal postprocessing is shown to flexibly handle trends in biases caused by global warming, and short training periods. In an application to global sea surface temperature forecasts issued by the Norwegian climate prediction model, our proposed methodology is shown to outperform known reference methods. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.12327899
title: Supplementary Material for: Predictors of Augmented Renal Clearance in a Heterogeneous ICU Population as Defined by Creatinine and Cystatin C

description: <b><i>Introduction:</i></b> The incidence of augmented renal clearance (ARC) in the intensive care unit (ICU) is highly variable, and identification of these patients remains challenging. <b><i>Objective:</i></b> The objective of this study was to define the incidence of ARC in a cohort of critically ill adults, using serum Cr and cystatin C, and to identify factors associated with its development. <b><i>Methods:</i></b> This is a retrospective cohort study of critically ill patients without stage 2 or 3 acute kidney injury with both serum Cr and cystatin C available. The incidence of ARC was defined as a Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI)<sub>Cr-cystatin C</sub>-estimated glomerular filtration rate &gt;130 mL/min. A multivariable logistic regression model using a penalized Lasso method was fit to identify independent predictors of ARC. <b><i>Results:</i></b> Among the 368 patients included in the study, indication for ICU admission was nonoperative in 55% of patients, and 9% of patients were admitted for major trauma. The overall incidence of ARC was low at 4.1%. In a multivariable logistic regression model, Charlson comorbidity index, major trauma, intracerebral hemorrhage, age, and Sequential Organ Failure Assessment score were found to predict ARC. <b><i>Conclusion:</i></b> The incidence of ARC in this study was low, but prediction models identified several factors for early identification of patients with risk factors for or who develop ARC, particularly in a cohort with a low baseline risk of ARC. These factors could be used to help identify patients who may develop ARC.
DOI: 10.6084/m9.figshare.12327893
title: Dataset for Fig 5

description: Chronic stimulation of hM3Dq in microglia prevents LPS-induced sickness behavior.
DOI: 10.6084/m9.figshare.12327899.v1
title: Supplementary Material for: Predictors of Augmented Renal Clearance in a Heterogeneous ICU Population as Defined by Creatinine and Cystatin C

description: <b><i>Introduction:</i></b> The incidence of augmented renal clearance (ARC) in the intensive care unit (ICU) is highly variable, and identification of these patients remains challenging. <b><i>Objective:</i></b> The objective of this study was to define the incidence of ARC in a cohort of critically ill adults, using serum Cr and cystatin C, and to identify factors associated with its development. <b><i>Methods:</i></b> This is a retrospective cohort study of critically ill patients without stage 2 or 3 acute kidney injury with both serum Cr and cystatin C available. The incidence of ARC was defined as a Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI)<sub>Cr-cystatin C</sub>-estimated glomerular filtration rate &gt;130 mL/min. A multivariable logistic regression model using a penalized Lasso method was fit to identify independent predictors of ARC. <b><i>Results:</i></b> Among the 368 patients included in the study, indication for ICU admission was nonoperative in 55% of patients, and 9% of patients were admitted for major trauma. The overall incidence of ARC was low at 4.1%. In a multivariable logistic regression model, Charlson comorbidity index, major trauma, intracerebral hemorrhage, age, and Sequential Organ Failure Assessment score were found to predict ARC. <b><i>Conclusion:</i></b> The incidence of ARC in this study was low, but prediction models identified several factors for early identification of patients with risk factors for or who develop ARC, particularly in a cohort with a low baseline risk of ARC. These factors could be used to help identify patients who may develop ARC.
DOI: 10.6084/m9.figshare.12327872
title: Dataset for Fig 2

description: Microglia from CX3CR1CreER-hM3Dq(+/-) mice express functional hM3Dq upon tamoxifen treatment.<br>
DOI: 10.6084/m9.figshare.12327887
title: Dataset for Fig 3

description: Acute microglial hM3Dq activation by CNO increases cytokine expression in the brain.
DOI: 10.6084/m9.figshare.12327890
title: Dataset for Fig 4

description: Chronic microglial hM3Dq activation by CNO attenuates LPS-induced increase of pro-inflammatory cytokines in the brain.
DOI: 10.6084/m9.figshare.12327872.v1
title: Dataset for Fig 2

description: Microglia from CX3CR1CreER-hM3Dq(+/-) mice express functional hM3Dq upon tamoxifen treatment.<br>
DOI: 10.6084/m9.figshare.12327887.v1
title: Dataset for Fig 3

description: Acute microglial hM3Dq activation by CNO increases cytokine expression in the brain.
DOI: 10.6084/m9.figshare.12327767
title: Data supplements for ASD meta-analysis

description: These html files (which can be viewed in a browser) contain a report of the meta-analytic outcomes associated with the article "Social Orienting and Social Seeking Behaviors in ASD. A Meta Analysis Involving 6140 Participants" (in preparation).<br>Included are: <br>1. The raw data submitted to the model2. Global model properties.3. Assessment of bias.3. Main effect summaries4. Two way interactions.
DOI: 10.6084/m9.figshare.12327680
title: Emotion lexicons for JD reviews in Chinese

description: The data set provides two emotion lexicons that manually labeled by three well-instructed coders to calculate the emotion polarity of JD reviews in Chinese. Specifically, the negative lexicon (jd_negative_terms.txt) contains 1, 589 unique negative terms and the positive lexicon (jd_positive_terms.txt) contains 1135 unique positive terms.<br>Please cite the following paper: <br>Di Weng and Jichang Zhao. Positive emotions help rank negative reviews in e-commerce. arXiv:2005.09837, 2020.<br>Any issues please feel free to contact jichang@buaa.edu.cn for more information.
DOI: 10.6084/m9.figshare.12327680.v1
title: Emotion lexicons for JD reviews in Chinese

description: The data set provides two emotion lexicons that manually labeled by three well-instructed coders to calculate the emotion polarity of JD reviews in Chinese. Specifically, the negative lexicon (jd_negative_terms.txt) contains 1, 589 unique negative terms and the positive lexicon (jd_positive_terms.txt) contains 1135 unique positive terms.<br>Please cite the following paper: <br>Di Weng and Jichang Zhao. Positive emotions help rank negative reviews in e-commerce. arXiv:2005.09837, 2020.<br>Any issues please feel free to contact jichang@buaa.edu.cn for more information.
DOI: 10.6084/m9.figshare.12327602
title: genome fasta sequence and annotation files

description: cultivated alfalfa genome sequence, CDS sequence, protein sequence and gff files.
DOI: 10.6084/m9.figshare.12327596
title: Discerning Solution Concepts for Discrete Games

description: The empirical analysis of discrete complete-information games has relied on behavioral restrictions in the form of solution concepts, such as Nash equilibrium. Choosing the right solution concept is crucial not just for the identification of payoff parameters, but also for the validity and informativeness of counterfactual exercises and policy implications. We say that a solution concept is discernible if it is possible to determine whether it generated the observed data on the players’ behavior and covariates. We propose a set of conditions that make it possible to discern solution concepts. In particular, our conditions are sufficient to tell whether the players’ choices emerged from Nash equilibria. We can also discriminate between rationalizable behavior, maxmin behavior, and collusive behavior. Finally, we identify the correlation structure of unobserved shocks in our model using a novel approach.
DOI: 10.15131/shef.data.12327560
title: Data and figures related to publication: Investigation of a novel AlZnN semiconductor alloy

description: The data provided here is related to the publication:<br>"Investigation of a novel AlZnN semiconductor alloy"<br>Materials Letters: X (2020); https://doi.org/10.1016/j.mlblux.2020.100052<br><br>The study reported in this paper was funded by the EPSRC (Fund code EP/M507611/1) and Johson Matthey PLC. The financial support by these parties is highly appreciated.<br><br>The data required to reproduce each figure panel is provided in different text files. Columns are separated by a space character. The first line in each column describes the dataset. The complete figures are also included as .tif files.<br><br>With the added context of the paper, it should be easy to reproduce the figures.<br><br><b>Figure 1:</b> (a) Zn and Al peaks in EDS spectra, (b) AlN fraction plotted against the Zn<sub>3</sub>N<sub>2</sub> fraction, and (c) GIXRD measurements of samples ZN and AZN-1 to AZN-4. The dashed line in (b) indicates the stoichiometric ratio of Al<sub>2x</sub>Zn<sub>3(1-x)</sub>N<sub>2</sub>.<br><b><br>Figure 2:</b> (a) Extinction coefficient and (b) refractive index of AlZnN films obtained from ellipsometry measurements. (c) Cody plot analysis used to measure the optical bandgap of AlZnN films.<br><br><b>Figure 3:</b> (a) Optical bandgap, (b) refractive index, (c) resistivity, and (d) carrier concentration of different AlZnN films. The star (☆) in (a) shows the intrinsic bandgap of Zn<sub>3</sub>N<sub>2</sub> as reported by Kumagai <i>et al</i>.<sup>3</sup> The dashed lines are intended as guides to the eye.<br>