cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19613849.v1
title: Additional file 1 of Identification of two novel pathogenic variants of the NR1H4 gene in intrahepatic cholestasis of pregnancy patients

description: Additional file 1. DNA sanger sequencing electropherograms of two novel mutations (p.S145F and p.M185L) in the NR1H4 gene.
DOI: 10.6084/m9.figshare.16994225.v1
title: Additional file 1 of Natural hybridization among three Rhododendron species (Ericaceae) revealed by morphological and genomic evidence

description: Additional file 1.
DOI: 10.6084/m9.figshare.16994215.v1
title: Additional file 8 of ATRX regulates glial identity and the tumor microenvironment in IDH-mutant glioma

description: Additional file 8:. Table S7: NSC chromatin-loops annotated with genomic coordinates, ATRX-WT/KO differential anti-CTCF scCUT&Tag peaks, loop-averaged ATRX-KO/WT cell-averaged in vivo log fold-change in expression in neoplastic cells represented as a percentage of a data-driven null distribution, and the number of genes on each loop.
DOI: 10.6084/m9.figshare.19613849
title: Additional file 1 of Identification of two novel pathogenic variants of the NR1H4 gene in intrahepatic cholestasis of pregnancy patients

description: Additional file 1. DNA sanger sequencing electropherograms of two novel mutations (p.S145F and p.M185L) in the NR1H4 gene.
DOI: 10.5281/zenodo.8112246
title: mvTCR - trained models

description: The zip directory contains the trained models used in the publication "Multimodal learning to integrate single-cell T-cell receptor and transcriptome" (formerly "Integrating T-cell receptor and transcriptome for large-scale single-cell immune profiling analysis "). The full code to reproduce the results of the publication can be found at https://github.com/SchubertLab/mvTCR_reproducibility
DOI: 10.5281/zenodo.10634209
title: mvTCR - trained models

description: The zip directory contains the trained models used in the publication "Multimodal learning to integrate single-cell T-cell receptor and transcriptome" (formerly "Integrating T-cell receptor and transcriptome for large-scale single-cell immune profiling analysis "). The full code to reproduce the results of the publication can be found at https://github.com/SchubertLab/mvTCR_reproducibility
DOI: 10.5281/zenodo.7215446
title: mvTCR - trained models

description: The zip directory contains the trained models used in the publication "Multimodal learning to integrate single-cell T-cell receptor and transcriptome" (formerly "Integrating T-cell receptor and transcriptome for large-scale single-cell immune profiling analysis "). The full code to reproduce the results of the publication can be found at https://github.com/SchubertLab/mvTCR_reproducibility
DOI: 10.17028/rd.lboro.22761503.v1
title: Supplementary information files for: Covalent bonded bilayers from germanene and stanene with topological giant capacitance effects

description: Supplementary files for article Covalent bonded bilayers from germanene and stanene with topological giant capacitance effects.
The discovery of twisted bilayer graphene with tunable superconductivity has diverted great focus at the world of twisted van der Waals heterostructures. Here we propose a paradigm for bilayer materials, where covalent bonding replaces the van der Waals interaction between the layers. On the example of germanene-stanene bilayer, we show that such systems demonstrate fascinating topological properties and manifest giant capacitance effects of the order of C = 10<sup>2</sup>μ F as well as dipole-like charge densities of q = 1 − 2 × 10<sup>−4</sup>μ C cm<sup>−2</sup>, showing promise for 2D ferroelectricity. The observed unique behaviour is closely linked to transverse strain-induced buckling deformations at the bilayer/substrate interface. In alternative GeSn bilayer structures with low twist angles the strain distortions trigger rich topological defect physics. We propose that the GeSn bilayer topology may be switched locally by a substrate-strain-induced electric fields. We demonstrate an approach to fabricate covalent bilayer materials, holding vast possibilities to transform applications technologies across solar, energy and optoelectronic sectors.
DOI: 10.6084/m9.figshare.16994288
title: Additional file 1 of Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

description: Additional file 1. Summary of the datasets generated in this study.
DOI: 10.6084/m9.figshare.16994288.v1
title: Additional file 1 of Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

description: Additional file 1. Summary of the datasets generated in this study.
DOI: 10.6084/m9.figshare.16994294.v1
title: Additional file 3 of Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

description: Additional file 3. Summary of SIRV isoform detection results (false negatives, false positives and true positives) for the 4 methods compared (FLAMES, FLAIR, TALON and StringTie2).
DOI: 10.6084/m9.figshare.16994300
title: Additional file 5 of Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

description: Additional file 5. Table of functional clustering results from DAVID for gDTU in each sample.
DOI: 10.6084/m9.figshare.16994297
title: Additional file 4 of Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

description: Additional file 4. Table of genes with differential transcript usage (gDTU) in each sample.
DOI: 10.6084/m9.figshare.16994300.v1
title: Additional file 5 of Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

description: Additional file 5. Table of functional clustering results from DAVID for gDTU in each sample.
DOI: 10.6084/m9.figshare.16994294
title: Additional file 3 of Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

description: Additional file 3. Summary of SIRV isoform detection results (false negatives, false positives and true positives) for the 4 methods compared (FLAMES, FLAIR, TALON and StringTie2).
DOI: 10.6084/m9.figshare.16994297.v1
title: Additional file 4 of Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

description: Additional file 4. Table of genes with differential transcript usage (gDTU) in each sample.
DOI: 10.17028/rd.lboro.22761503
title: Supplementary information files for: Covalent bonded bilayers from germanene and stanene with topological giant capacitance effects

description: Supplementary files for article Covalent bonded bilayers from germanene and stanene with topological giant capacitance effects.
The discovery of twisted bilayer graphene with tunable superconductivity has diverted great focus at the world of twisted van der Waals heterostructures. Here we propose a paradigm for bilayer materials, where covalent bonding replaces the van der Waals interaction between the layers. On the example of germanene-stanene bilayer, we show that such systems demonstrate fascinating topological properties and manifest giant capacitance effects of the order of C = 10<sup>2</sup>μ F as well as dipole-like charge densities of q = 1 − 2 × 10<sup>−4</sup>μ C cm<sup>−2</sup>, showing promise for 2D ferroelectricity. The observed unique behaviour is closely linked to transverse strain-induced buckling deformations at the bilayer/substrate interface. In alternative GeSn bilayer structures with low twist angles the strain distortions trigger rich topological defect physics. We propose that the GeSn bilayer topology may be switched locally by a substrate-strain-induced electric fields. We demonstrate an approach to fabricate covalent bilayer materials, holding vast possibilities to transform applications technologies across solar, energy and optoelectronic sectors.
DOI: 10.6084/m9.figshare.19615769.v1
title: Numerical Approach for Kinematic analysis of Unit II from Folding arrays of uniform-thickness panels to compact bundles with a single degree of freedom

description: Description of the numerical approach for the kinematics of unit II.
DOI: 10.6084/m9.figshare.16994348.v1
title: Additional file 1 of Construction of a microenvironment immune gene model for predicting the prognosis of endometrial cancer

description: Additional file 1.
DOI: 10.6084/m9.figshare.16994351.v1
title: Additional file 2 of Construction of a microenvironment immune gene model for predicting the prognosis of endometrial cancer

description: Additional file 2.
DOI: 10.6084/m9.figshare.16994348
title: Additional file 1 of Construction of a microenvironment immune gene model for predicting the prognosis of endometrial cancer

description: Additional file 1.
DOI: 10.6084/m9.figshare.16994354
title: Additional file 3 of Construction of a microenvironment immune gene model for predicting the prognosis of endometrial cancer

description: Additional file 3.
DOI: 10.6084/m9.figshare.16994351
title: Additional file 2 of Construction of a microenvironment immune gene model for predicting the prognosis of endometrial cancer

description: Additional file 2.
DOI: 10.6084/m9.figshare.16994354.v1
title: Additional file 3 of Construction of a microenvironment immune gene model for predicting the prognosis of endometrial cancer

description: Additional file 3.
DOI: 10.5281/zenodo.10647153
title: Input and output data for real-time maximum flood inundation modelling using machine learning

description: This dataset contains the input and output files for training, testing, and validation of the Random Forest (RF) model for real-time flood inundation modelling downstream of Bhadrachalam, India. The data folder has two subfolders, each for depth and velocity models. Each folder contains two subfolders, one containing the inputs for the RF model and the other containing the outputs of the RF model. The outputs were obtained from the 2-dimensional modelling using the LISFLOOD-FP hydrodynamic model. THe inputs of the model are topographic features elevation, topographic wetness index, multi-resolution valley bottom index, terrain ruggedness index, etc. and flood characteristics like peak flows at main and tributary rivers, duration of the event, etc. The outputs of the models are maximum flood depth and velocity for RF depth and RF velocity models.
DOI: 10.5281/zenodo.10647154
title: Input and output data for real-time maximum flood inundation modelling using machine learning

description: This dataset contains the input and output files for training, testing, and validation of the Random Forest (RF) model for real-time flood inundation modelling downstream of Bhadrachalam, India. The data folder has two subfolders, each for depth and velocity models. Each folder contains two subfolders, one containing the inputs for the RF model and the other containing the outputs of the RF model. The outputs were obtained from the 2-dimensional modelling using the LISFLOOD-FP hydrodynamic model. THe inputs of the model are topographic features elevation, topographic wetness index, multi-resolution valley bottom index, terrain ruggedness index, etc. and flood characteristics like peak flows at main and tributary rivers, duration of the event, etc. The outputs of the models are maximum flood depth and velocity for RF depth and RF velocity models.
DOI: 10.6084/m9.figshare.14897225.v1
title: Additional file 1 of Characterization of Salmonella serotypes prevalent in asymptomatic people and patients

description: Additional file 1: Supplementary Table 1. The information and antimicrobial resistance phenotype of human Salmonella isolates.
DOI: 10.6084/m9.figshare.25131778
title: Residual Permutation Procedure data file from Mesophotic corals in Hawaiʻi maintain autotrophy to survive low-light conditions

description: The .csv file used to generate Residual Permutation Procedure (RPP) stats and Hotelling's T2 stats to corroborate results.
DOI: 10.6084/m9.figshare.25131781
title: Isotopic Data Sheets from Mesophotic corals in Hawaiʻi maintain autotrophy to survive low-light conditions

description: Excel sheets organizing our isotopic data and corresponding to the SIBER, simple linear regression, and multivariable linear regressions conducted in this study.
DOI: 10.6084/m9.figshare.25131784
title: R Script for Biplot Statistics from Mesophotic corals in Hawaiʻi maintain autotrophy to survive low-light conditions

description: The annotated R script used to plot and calculate all biplot carbon and nitrogen stable isotope values and related statistics.
DOI: 10.6084/m9.figshare.25131784.v1
title: R Script for Biplot Statistics from Mesophotic corals in Hawaiʻi maintain autotrophy to survive low-light conditions

description: The annotated R script used to plot and calculate all biplot carbon and nitrogen stable isotope values and related statistics.
DOI: 10.6084/m9.figshare.25131790
title: SIBER biplot data file from Mesophotic corals in Hawaiʻi maintain autotrophy to survive low-light conditions

description: The .csv file used to generate the SIBER biplot ellipses and statistics.
DOI: 10.6084/m9.figshare.25131790.v1
title: SIBER biplot data file from Mesophotic corals in Hawaiʻi maintain autotrophy to survive low-light conditions

description: The .csv file used to generate the SIBER biplot ellipses and statistics.
DOI: 10.6084/m9.figshare.14897263
title: Additional file 2 of Clinical characteristics and genetic spectrum of 26 individuals of Chinese origin with primary ciliary dyskinesia

description: Additional file 2. Table S1. Clinical features and detected mutated genes and variants of the 26 confirmed PCD patients of Chinese origin. a. The patients are listed according to different categories outlining the included patients. The first thirteen patients (patient 1, 2, 3, 4, 5, 6, 13, 18, 20, 22, 24, 25, 26) have KS (with or without ciliary ultrastructural defects), the next six patients (patient 8, 9, 10, 11, 12, 15) have ciliary ultrastructural defects without KS, and the last seven patients (patient 7, 14, 16, 17, 19, 21, 23) are patients with biallelic mutations alone (without KS or any ciliary ultrastructural defect). b. Most of the patients are too young that we did not know whether they have the infertility history or let them do the sperm test. c. If family members of a patient have a history of asthma or chronic bronchitis, the patient is determined to have a suspected PCD family history. d. For bronchiectasis, 1 means the patient has bronchiectasis in that certain location shown in CT scans, while 0 means no bronchiectasis is observed in that certain location. e. For pathogenicity prediction, SNVs in exonic regions are predicted by ACMG/AMP, indels are predicted using MutationTaster, variants in splicing regions are predicted using Human Splicing Finder. f. NA: not available, ND: not detected
DOI: 10.6084/m9.figshare.8082071
title: An efficient <i>Agrobacterium</i>-mediated soybean transformation method using green fluorescent protein as a selectable marker

description: Genetic transformation plays a vital role in gene functional study and molecular breeding of soybean. Conventional soybean transformation methods using chemical selectable markers, such as antibiotic or herbicide resistance genes, rely on the identification of positive transgenic lines at advanced developmental stages, making selection procedure labor intensive and time consuming. Utilization of a visual maker to track the transgene would avoid the uncertainty and blindness in the transformation process. In this research, we used green fluorescent protein (GFP) as the selectable marker to detect transgenics at early stages of soybean development. Positive transformants were detected recurrently during each stage of the process based on visualization of the green fluorescence signal, which help us to discard the non-transgenic ones in each stage to reduce the unnecessary experimental cost and lab space. In addition, the positive transgenic seeds can be identified before planting for early detection of transgene and obtain homozygous lines in advance. The method established in this study is also a useful reference for other plant species.
DOI: 10.25386/genetics.8081648.v1
title: Supplemental Material for Brady et al., 2019

description: Supplemental data files, supplemental figures, and supplemental info for Brady et al 2019 submission to Genetics
DOI: 10.6084/m9.figshare.19091781.v1
title: Deep historical borrowing framework to prospectively and simultaneously synthesize control information in confirmatory clinical trials with multiple endpoints

description: In current clinical trial development, historical information is receiving more attention as it provides utility beyond sample size calculation. Meta-analytic-predictive (MAP) priors and robust MAP priors have been proposed for prospectively borrowing historical data on a single endpoint. To simultaneously synthesize control information from multiple endpoints in confirmatory clinical trials, we propose to approximate posterior probabilities from a Bayesian hierarchical model and estimate critical values by deep learning to construct pre-specified strategies for hypothesis testing. This feature is important to ensure study integrity by establishing prospective decision functions before the trial conduct. Simulations are performed to show that our method properly controls family-wise error rate and preserves power as compared with a typical practice of choosing constant critical values given a subset of null space. Satisfactory performance under prior-data conflict is also demonstrated. We further illustrate our method using a case study in Immunology.
DOI: 10.6084/m9.figshare.8082005.v1
title: Chlorogenic Acid Relieved Oxidative Stress Injury in Retinal Ganglion Cells Through IncRNA-TUG1/Nrf2

description: Objective: To discover the possible underlying mechanism of Chlorogenic acid (CGA) in protecting against oxidative stress injury in glaucoma. Methods: LncRNA TUG1 and Nrf2 expressions were detected by qRT-PCR and Western blot. Retinal ganglion cell (RGC) viability and apoptosis were measured by MTT and flow cytometry, respectively. Reactive oxygen species (ROS) level was determined by reactive oxygen species assay kit. The interaction between lncRNA TUG1 and Nrf2 was confirmed by RNA pull-down and RIP assay. Results: IPL thickness and lncRNA TUG1 expression were significantly decreased in glaucoma mice model, and CGA treatment increased IPL thickness and lncRNA TUG1 expression. <i>In vitro</i> H2O2-induced RGCs, RGC viability was significantly decreased, and ROS level and cell apoptosis were significantly increased. CGA up-regulated lncRNA TUG1 and Nrf2 expressions, decreased cell apoptosis and ROS production in RGCs, and increased RGCs viability. We further verified the interaction between lncRNA TUG1 and Nrf2, and proved Nrf2 was positively regulated by lncRNA TUG1. We found CGA promoted Nrf2 expression through lncRNA-TUG1, and further verified CGA protected RGCs from oxidative stress through regulating lncRNA TUG1/Nrf2. <i>In vivo</i> experiments showed TUG1 knockdown abrogated therapeutic effect of CGA on glaucoma. Conclusion: CGA increased RGC viability and decreased ROS level and RGC apoptosis after oxidative stress injury through lncRNA TUG1/Nrf2 pathway, which protected against glaucoma.
DOI: 10.6084/m9.figshare.8082014.v1
title: Establishing the relationship between urban land-cover configuration and night time land-surface temperature using spatial regression

description: Studies suggest that urban form can influence microclimate regulation. Remote sensing studies have contributed to these findings through analysis of high-resolution land cover maps, landscape ecology metrics, and thermal imagery. Collectively, these have been referred to as land cover configuration studies. There are three objectives to this study. The first is to assess the relationship between nighttime land surface temperatures (LST) and land cover configuration and composition. The second objective is to outline a comprehensive methodology that includes ordinary least squares (OLS), spatial regression, variable selection, and multicollinearity analysis. Our last objective is to test three hypotheses about the relationship between LST and land cover, which can briefly be described as: 1) the importance of land-use regimes in modeling LST from land cover composition and configuration variables; 2) the strength of the correlation between LST and roads, buildings, and vegetation; and 3) the improved quality of models using landscape metrics in modeling the relationship between LST and land cover. Based on 16 different models (8 OLS, 8 spatial regression) we could confirm the above hypotheses, but we found that the configuration of buildings, roads, and vegetation have a complex relationship with LST. Our interpretation of this complexity, combined with the strength of composition variables, is that parsimonious models, for now, are more useful to urban planners because they are more generalizable. Finally, spatial regression models of land cover configuration and LST demonstrated an improvement over non-spatial linear models (OLS). Spatial regression models reduced heteroskedasticity and clusters of residuals, and tempered coefficients, suggesting that the OLS models could be biased. OLS models were still found to be a valuable tool for exploratory analysis.
DOI: 10.6084/m9.figshare.8082014.v2
title: Establishing the relationship between urban land-cover configuration and night time land-surface temperature using spatial regression

description: Studies suggest that urban form can influence microclimate regulation. Remote sensing studies have contributed to these findings through analysis of high-resolution land cover maps, landscape ecology metrics, and thermal imagery. Collectively, these have been referred to as land cover configuration studies. There are three objectives to this study. The first is to assess the relationship between nighttime land surface temperatures (LST) and land cover configuration and composition. The second objective is to outline a comprehensive methodology that includes ordinary least squares (OLS), spatial regression, variable selection, and multicollinearity analysis. Our last objective is to test three hypotheses about the relationship between LST and land cover, which can briefly be described as: 1) the importance of land-use regimes in modeling LST from land cover composition and configuration variables; 2) the strength of the correlation between LST and roads, buildings, and vegetation; and 3) the improved quality of models using landscape metrics in modeling the relationship between LST and land cover. Based on 16 different models (8 OLS, 8 spatial regression) we could confirm the above hypotheses, but we found that the configuration of buildings, roads, and vegetation have a complex relationship with LST. Our interpretation of this complexity, combined with the strength of composition variables, is that parsimonious models, for now, are more useful to urban planners because they are more generalizable. Finally, spatial regression models of land cover configuration and LST demonstrated an improvement over non-spatial linear models (OLS). Spatial regression models reduced heteroskedasticity and clusters of residuals, and tempered coefficients, suggesting that the OLS models could be biased. OLS models were still found to be a valuable tool for exploratory analysis.