cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7579883.v1
title: Manhattan plots of the differential alternative splicing events and differentially expressed genes by splicing factors

description: The data show circular Manhattan overview of genome-wide alternative splicing and gene expression changes regulated by each SF.
DOI: 10.6084/m9.figshare.22767449.v1
title: Additional file 3 of Transcriptomic profiling of near-isogenic lines reveals candidate genes for a significant locus conferring metribuzin resistance in wheat

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.22767458.v1
title: Additional file 6 of Transcriptomic profiling of near-isogenic lines reveals candidate genes for a significant locus conferring metribuzin resistance in wheat

description: Supplementary Material 6
DOI: 10.5281/zenodo.5816194
title: Data for "The Geologic Impact of 16 Psyche's Surface Temperatures"

description: This repository contains the data used to create the figures in "The Geologic Impact of 16 Psyche's Surface Temperatures"
DOI: 10.5281/zenodo.5816193
title: Data for "The Geologic Impact of 16 Psyche's Surface Temperatures"

description: This repository contains the data used to create the figures in "The Geologic Impact of 16 Psyche's Surface Temperatures"
DOI: 10.25721/wr4c-3e07
title: Export multi-format du corpus "S'écrire au XIXe siècle. Une correspondance familiale" édité et publié sur lettresfamiliales.ehess.fr.
DOI: 10.5281/zenodo.5818039
title: Supplements - Apomictic fern fathers: An experimental approach to the reproductive characteristics of sexual, apomict and hybrid fern gametophytes

description: Supplementary files for the article "Apomictic fern fathers: An experimental approach to the reproductive characteristics of sexual, apomict and hybrid fern gametophytes" published in American Journal of Botany
DOI: 10.5281/zenodo.5818038
title: Supplements - Apomictic fern fathers: An experimental approach to the reproductive characteristics of sexual, apomict and hybrid fern gametophytes

description: Supplementary files for the article "Apomictic fern fathers: An experimental approach to the reproductive characteristics of sexual, apomict and hybrid fern gametophytes" published in American Journal of Botany
DOI: 10.5517/ccdc.csd.cc11x2np
title: CCDC 980302: Experimental Crystal Structure Determination

description: Related Article: Virendra Kumar, Uzra Diwan, Nidhi Tyagi, Rakesh K. Mishra, Manish Kumar Singh, K.K. Upadhyay|2022|J.Photochem.Photobiol.A:Chem.|425|113692|doi:10.1016/j.jphotochem.2021.113692
DOI: 10.5517/ccdc.csd.cc12g4k7
title: CCDC 996698: Experimental Crystal Structure Determination

description: Related Article: Virendra Kumar, Uzra Diwan, Nidhi Tyagi, Rakesh K. Mishra, Manish Kumar Singh, K.K. Upadhyay|2022|J.Photochem.Photobiol.A:Chem.|425|113692|doi:10.1016/j.jphotochem.2021.113692
DOI: 10.5517/ccdc.csd.cc11x2pq
title: CCDC 980303: Experimental Crystal Structure Determination

description: Related Article: Virendra Kumar, Uzra Diwan, Nidhi Tyagi, Rakesh K. Mishra, Manish Kumar Singh, K.K. Upadhyay|2022|J.Photochem.Photobiol.A:Chem.|425|113692|doi:10.1016/j.jphotochem.2021.113692
DOI: 10.5517/ccdc.csd.cc11yk9v
title: CCDC 981717: Experimental Crystal Structure Determination

description: Related Article: Virendra Kumar, Uzra Diwan, Nidhi Tyagi, Rakesh K. Mishra, Manish Kumar Singh, K.K. Upadhyay|2022|J.Photochem.Photobiol.A:Chem.|425|113692|doi:10.1016/j.jphotochem.2021.113692
DOI: 10.5517/ccdc.csd.cc28bc00
title: CCDC 2095321: Experimental Crystal Structure Determination

description: Related Article: Nikita M. Baraboshkin, Victor P. Zelenov, Mikhail E. Minyaev, Tatyana S. Pivina|2021|CrystEngComm|24|235|doi:10.1039/D1CE00977J
DOI: 10.5517/ccdc.csd.cc28bc11
title: CCDC 2095322: Experimental Crystal Structure Determination

description: Related Article: Nikita M. Baraboshkin, Victor P. Zelenov, Mikhail E. Minyaev, Tatyana S. Pivina|2021|CrystEngComm|24|235|doi:10.1039/D1CE00977J
DOI: 10.6084/m9.figshare.12084960
title: Real World experiment - Mocap

description: -- Mocap tests in .tak and .csv formats. -- Parameters.ods
DOI: 10.6084/m9.figshare.12084960.v1
title: Real World experiment - Mocap

description: -- Mocap tests in .tak and .csv formats. -- Parameters.ods
DOI: 10.6084/m9.figshare.17844233
title: DATA.CSV

description: This csv file contains the data used for the empirical example published in Jiménez-Valverde (2022). ARIDITY was derived from the CGIAR-CSI Global-Aridity and Global-PET Database (Zomer et al. 2007, 2008; http://www.cgiar-csi.org); TMIN was derived from the information provided by the Spanish Meteorological State Agency (AEMET, MITECO); occurrence data for <i>Argiope trifasciata</i> were obtained from Peña-Aguilera et al. (2019).<br>Jiménez-Valverde, A. (2022). The uniform AUC: dealing with the representativeness effect in presence-absence models. Methods Ecol. Evol. XX:xxx-xxx.<br><br>Peña-Aguilera, P., Burguillo-Madrid, L., Barve, V., Aragón, P. & Jiménez-Valverde, A. (2019). Niche segregation in Iberian <i>Argiope</i> species. J. Arachnol., 47, 37-44.<br><br>Zomer, R.J., Bossio, D.A., Trabucco, A., Yuanjie, L., Gupta, D.C. & Singh, V.P. (2007). Trees and Water: Smallholder Agroforestry on Irrigated Lands in Northern India (IWMI Research Report 122). International Water Management Institute, Colombo, Sri Lanka.<br>Zomer, R.J., Trabucco, A., Bossio, D.A. & Verchot, L.V. (2008). Climate change mitigation: a spatial analysis of global land suitability for clean development mechanism afforestation and reforestation. Agric. Ecosyst. Environ., 126, 67-80.<br>
DOI: 10.6084/m9.figshare.17844233.v1
title: DATA.CSV

description: This csv file contains the data used for the empirical example published in Jiménez-Valverde (2022). ARIDITY was derived from the CGIAR-CSI Global-Aridity and Global-PET Database (Zomer et al. 2007, 2008; http://www.cgiar-csi.org); TMIN was derived from the information provided by the Spanish Meteorological State Agency (AEMET, MITECO); occurrence data for <i>Argiope trifasciata</i> were obtained from Peña-Aguilera et al. (2019).<br>Jiménez-Valverde, A. (2022). The uniform AUC: dealing with the representativeness effect in presence-absence models. Methods Ecol. Evol. XX:xxx-xxx.<br><br>Peña-Aguilera, P., Burguillo-Madrid, L., Barve, V., Aragón, P. & Jiménez-Valverde, A. (2019). Niche segregation in Iberian <i>Argiope</i> species. J. Arachnol., 47, 37-44.<br><br>Zomer, R.J., Bossio, D.A., Trabucco, A., Yuanjie, L., Gupta, D.C. & Singh, V.P. (2007). Trees and Water: Smallholder Agroforestry on Irrigated Lands in Northern India (IWMI Research Report 122). International Water Management Institute, Colombo, Sri Lanka.<br>Zomer, R.J., Trabucco, A., Bossio, D.A. & Verchot, L.V. (2008). Climate change mitigation: a spatial analysis of global land suitability for clean development mechanism afforestation and reforestation. Agric. Ecosyst. Environ., 126, 67-80.<br>
DOI: 10.6084/m9.figshare.13634057
title: BER_data&covariates

description: data and covariates used to predict sloth bear distribution and conflict with people in central India
DOI: 10.6084/m9.figshare.13634057.v1
title: BER_data&covariates

description: data and covariates used to predict sloth bear distribution and conflict with people in central India
DOI: 10.25345/c55c5r
title: MassIVE MSV000088636 - TMT-10 labeled colon biopsies from hyperbaric oxygen therapy patients with ulcerative colitis
title: TMT-10 labeled proteome set of biopsies. 12 fractions per 10-plex
DOI: 10.5281/zenodo.5654554
title: Pallandt_etal2021_JGRBG_Decomposition_SM_Response

description: This repository provides access to an R script and supporting data files connected to the following manuscript: Pallandt M., Ahrens B., Koirala S., Lange H., Reichstein M., Schrumpf M., Zaehle S: "<em>Vertically divergent responses of SOC decomposition to soil moisture in a changing climate</em>" (accepted for publication on 27.12.2021 in the Journal of Geophysical Research - Biogeosciences). The manuscript contains an application of the DAMM model by Davidson et al. (2012), with soil moisture and soil temperature data from the CMIP5 ensemble (https://esgf-node.llnl.gov/projects/esgf-llnl/) and soil data from SoilGrids (https://soilgrids.org/). For more details, downloading the latest version, and code repository history, see https://gitlab.com/MarleenPallandt/pallandt_etal2021_jgrbg_decomposition_sm_response.
DOI: 10.5281/zenodo.5654553
title: Pallandt_etal2021_JGRBG_Decomposition_SM_Response

description: This repository provides access to an R script and supporting data files connected to the following manuscript: Pallandt M., Ahrens B., Koirala S., Lange H., Reichstein M., Schrumpf M., Zaehle S: "<em>Vertically divergent responses of SOC decomposition to soil moisture in a changing climate</em>" (accepted for publication on 27.12.2021 in the Journal of Geophysical Research - Biogeosciences). The manuscript contains an application of the DAMM model by Davidson et al. (2012), with soil moisture and soil temperature data from the CMIP5 ensemble (https://esgf-node.llnl.gov/projects/esgf-llnl/) and soil data from SoilGrids (https://soilgrids.org/). For more details, downloading the latest version, and code repository history, see https://gitlab.com/MarleenPallandt/pallandt_etal2021_jgrbg_decomposition_sm_response.
DOI: 10.6084/m9.figshare.17847539
title: Dataset: Observations from National Moth Week 2021 (Greece)

description: This dataset is from the National Moth Week 2021: Greece. <br><br><br>
DOI: 10.6084/m9.figshare.17096747
title: Functional PCA With Covariate-Dependent Mean and Covariance Structure

description: Incorporating covariates into functional principal component analysis (PCA) can substantially improve the representation efficiency of the principal components and predictive performance. However, many existing functional PCA methods do not make use of covariates, and those that do often have high computational cost or make overly simplistic assumptions that are violated in practice. In this article, we propose a new framework, called covariate-dependent functional principal component analysis (CD-FPCA), in which both the mean and covariance structure depend on covariates. We propose a corresponding estimation algorithm, which makes use of spline basis representations and roughness penalties, and is substantially more computationally efficient than competing approaches of adequate estimation and prediction accuracy. A key aspect of our work is our novel approach for modeling the covariance function and ensuring that it is symmetric positive semidefinite. We demonstrate the advantages of our methodology through a simulation study and an astronomical data analysis.
DOI: 10.6084/m9.figshare.17096747.v2
title: Functional PCA With Covariate-Dependent Mean and Covariance Structure

description: Incorporating covariates into functional principal component analysis (PCA) can substantially improve the representation efficiency of the principal components and predictive performance. However, many existing functional PCA methods do not make use of covariates, and those that do often have high computational cost or make overly simplistic assumptions that are violated in practice. In this article, we propose a new framework, called covariate-dependent functional principal component analysis (CD-FPCA), in which both the mean and covariance structure depend on covariates. We propose a corresponding estimation algorithm, which makes use of spline basis representations and roughness penalties, and is substantially more computationally efficient than competing approaches of adequate estimation and prediction accuracy. A key aspect of our work is our novel approach for modeling the covariance function and ensuring that it is symmetric positive semidefinite. We demonstrate the advantages of our methodology through a simulation study and an astronomical data analysis.
DOI: 10.6084/m9.figshare.17096747.v1
title: Functional PCA with Covariate Dependent Mean and Covariance Structure

description: Incorporating covariates into functional principal component analysis (PCA) can substantially improve the representation efficiency of the principal components and predictive performance. However, many existing functional PCA methods do not make use of covariates, and those that do often have high computational cost or make overly simplistic assumptions that are violated in practice. In this article, we propose a new framework, called Covariate Dependent Functional Principal Component Analysis (CD-FPCA), in which both the mean and covariance structure depend on covariates. We propose a corresponding estimation algorithm, which makes use of spline basis representations and roughness penalties, and is substantially more computationally efficient than competing approaches of adequate estimation and prediction accuracy. A key aspect of our work is our novel approach for modeling the covariance function and ensuring that it is symmetric positive semi-definite. We demonstrate the advantages of our methodology through a simulation study and an astronomical data analysis.
DOI: 10.6084/m9.figshare.14607730
title: Estimating pure-error from near replicates in design of experiments

description: In design of experiments, setting exact replicates of factor settings enables estimation of pure-error; a model-independent estimate of experimental error useful in communicating inherent system noise and testing model lack-of-fit. Often in practice, the factor levels for replicates are precisely measured rather than precisely set, resulting in near-replicates. This can result in inflated estimates of pure-error due to uncompensated set-point variation. In this article, we review previous strategies for estimating pure-error from near-replicates and propose a simple alternative. We derive key analytical properties and investigate them via simulation. Finally, we illustrate the new approach with an application.
DOI: 10.6084/m9.figshare.14607730.v1
title: Estimating pure-error from near replicates in design of experiments

description: In design of experiments, setting exact replicates of factor settings enables estimation of pure-error; a model-independent estimate of experimental error useful in communicating inherent system noise and testing model lack-of-fit. Often in practice, the factor levels for replicates are precisely measured rather than precisely set, resulting in near-replicates. This can result in inflated estimates of pure-error due to uncompensated set-point variation. In this article, we review previous strategies for estimating pure-error from near-replicates and propose a simple alternative. We derive key analytical properties and investigate them via simulation. Finally, we illustrate the new approach with an application.
DOI: 10.5281/zenodo.5801902
title: Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

description: Metastatic progression is the main cause of death in cancer patients, whereas the underlying genomic mechanisms driving metastasis remain largely unknown. Here, we assembled MSK-MET, a pan-cancer cohort of over 25,000 patients with metastatic diseases. By analyzing genomic and clinical data from this cohort, we identified associations between genomic alterations and patterns of metastatic dissemination across 50 tumor types. We found that chromosomal instability is strongly correlated with metastatic burden in some tumor types, including prostate adenocarcinoma, lung adenocarcinoma and HR+/HER2+ breast ductal carcinoma, but not in others, including colorectal cancer and high grade serous ovarian cancer, where copy-number alteration patterns may be established early in tumor development. We also identified somatic alterations associated with metastatic burden and specific target organs. Our data offer a valuable resource for the investigation of the biological basis for metastatic spread and highlight the complex role of chromosomal instability in cancer progression.
description: Genomic and clinical data, including metastatic events at the patient level is deposited for visualization, and download in the cBioPortal for Cancer Genomics. https://www.cbioportal.org/study/summary?id=msk_met_2021
DOI: 10.5281/zenodo.5801901
title: Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

description: Metastatic progression is the main cause of death in cancer patients, whereas the underlying genomic mechanisms driving metastasis remain largely unknown. Here, we assembled MSK-MET, a pan-cancer cohort of over 25,000 patients with metastatic diseases. By analyzing genomic and clinical data from this cohort, we identified associations between genomic alterations and patterns of metastatic dissemination across 50 tumor types. We found that chromosomal instability is strongly correlated with metastatic burden in some tumor types, including prostate adenocarcinoma, lung adenocarcinoma and HR+/HER2+ breast ductal carcinoma, but not in others, including colorectal cancer and high grade serous ovarian cancer, where copy-number alteration patterns may be established early in tumor development. We also identified somatic alterations associated with metastatic burden and specific target organs. Our data offer a valuable resource for the investigation of the biological basis for metastatic spread and highlight the complex role of chromosomal instability in cancer progression.
description: Genomic and clinical data, including metastatic events at the patient level is deposited for visualization, and download in the cBioPortal for Cancer Genomics. https://www.cbioportal.org/study/summary?id=msk_met_2021
DOI: 10.5066/p94docmi
title: Estimated water surface elevations for selected monthly flow exceedance percentiles for Firesteel Creek upstream from Lake Mitchell in Davison County, South Dakota, 2021

description: The City of Mitchell, South Dakota is exploring ways to improve water quality in Firesteel Creek, which flows into Lake Mitchell. One possible way is to construct a wetland on City-owned land in the Firesteel Creek floodplain above Lake Mitchell, allowing sediment deposition and nutrient uptake by aquatic vegetation in the constructed wetland. In order for a constructed wetland to be designed, information on typical flows and water surface elevations of Firesteel Creek throughout the growing season must be considered. This data release documents datasets and procedures used to estimate that information for a study area encompassing the proposed location of the constructed wetland. Monthly duration curves of daily mean flow for April through October were developed from data collected at a streamgage located upstream on Firesteel Creek (06477500, Firesteel Creek near Mouth Vernon, SD). Drainage areas for 06477500 and the study area were determined using South Dakota's StreamStats application. A drainage area ratio adjustment was applied to the 5-, 10-, 20-, 30-, 40-, 50-, 60-, 70-, 80-, 90-, and 95-percent exceedance flows at 06477500 to estimate the corresponding exceedance flows at the study area. Global Navigation Satellite System equipment was used to collect elevation data on the Firesteel Creek channel bottom and at water surface for a set of transects through Firesteel Creek near the proposed wetland location. Elevations for portions of the transects in the floodplain were determined from the one-ninth arc-second National Elevation Dataset. Because the spillway of Lake Mitchell results in backwater conditions within the study area, transects through Lake Mitchell were also determined using the NED and an existing bathymetry map of Lake Mitchell. The data collected at transects were used to develop a hydraulic model using the Hydraulic Engineering Center's River Analysis System (HEC-RAS) software. The hydraulic model was calibrated using water surface elevation data collected during a GNSS survey and the mean streamflow determined for that day. The selected monthly exceedance flows were used as input to the model to estimate water surface elevations for transects in the study area and near the proposed wetland location.
DOI: 10.5517/ccdc.csd.cc28bc22
title: CCDC 2095323: Experimental Crystal Structure Determination

description: Related Article: Nikita M. Baraboshkin, Victor P. Zelenov, Mikhail E. Minyaev, Tatyana S. Pivina|2021|CrystEngComm|24|235|doi:10.1039/D1CE00977J
DOI: 10.5517/ccdc.csd.cc28fl2d
title: CCDC 2098423: Experimental Crystal Structure Determination

description: Related Article: Andrea Delledonne, Martina Orlandini, Paolo P. Mazzeo, Cristina Sissa, Alessia Bacchi, Francesca Terenziani, Paolo Pelagatti|2022|Phys.Chem.Chem.Phys.(PCCP)|24|1191|doi:10.1039/D1CP04438A
DOI: 10.5517/ccdc.csd.cc28fl3f
title: CCDC 2098424: Experimental Crystal Structure Determination

description: Related Article: Andrea Delledonne, Martina Orlandini, Paolo P. Mazzeo, Cristina Sissa, Alessia Bacchi, Francesca Terenziani, Paolo Pelagatti|2022|Phys.Chem.Chem.Phys.(PCCP)|24|1191|doi:10.1039/D1CP04438A
DOI: 10.5517/ccdc.csd.cc28fl4g
title: CCDC 2098425: Experimental Crystal Structure Determination

description: Related Article: Andrea Delledonne, Martina Orlandini, Paolo P. Mazzeo, Cristina Sissa, Alessia Bacchi, Francesca Terenziani, Paolo Pelagatti|2022|Phys.Chem.Chem.Phys.(PCCP)|24|1191|doi:10.1039/D1CP04438A
DOI: 10.5517/ccdc.csd.cc28fl5h
title: CCDC 2098426: Experimental Crystal Structure Determination

description: Related Article: Andrea Delledonne, Martina Orlandini, Paolo P. Mazzeo, Cristina Sissa, Alessia Bacchi, Francesca Terenziani, Paolo Pelagatti|2022|Phys.Chem.Chem.Phys.(PCCP)|24|1191|doi:10.1039/D1CP04438A
DOI: 10.5517/ccdc.csd.cc28fl6j
title: CCDC 2098427: Experimental Crystal Structure Determination

description: Related Article: Andrea Delledonne, Martina Orlandini, Paolo P. Mazzeo, Cristina Sissa, Alessia Bacchi, Francesca Terenziani, Paolo Pelagatti|2022|Phys.Chem.Chem.Phys.(PCCP)|24|1191|doi:10.1039/D1CP04438A
DOI: 10.5517/ccdc.csd.cc28gg5d
title: CCDC 2099263: Experimental Crystal Structure Determination

description: Related Article: Rui Wang, Wei Zhang, Ying Tang, Ze-Hui Qi, Yuan-Hui Yu, Hong-Bo Tan, Dian-Yong Tang, Zhi-Gang Xu, Zhong-Zhu Chen|2021|New J.Chem.|46|592|doi:10.1039/D1NJ04233E
DOI: 10.5517/ccdc.csd.cc28ggcl
title: CCDC 2099269: Experimental Crystal Structure Determination

description: Related Article: Rui Wang, Wei Zhang, Ying Tang, Ze-Hui Qi, Yuan-Hui Yu, Hong-Bo Tan, Dian-Yong Tang, Zhi-Gang Xu, Zhong-Zhu Chen|2021|New J.Chem.|46|592|doi:10.1039/D1NJ04233E
DOI: 10.5517/ccdc.csd.cc28gggp
title: CCDC 2099272: Experimental Crystal Structure Determination

description: Related Article: Rui Wang, Wei Zhang, Ying Tang, Ze-Hui Qi, Yuan-Hui Yu, Hong-Bo Tan, Dian-Yong Tang, Zhi-Gang Xu, Zhong-Zhu Chen|2021|New J.Chem.|46|592|doi:10.1039/D1NJ04233E
DOI: 10.5281/zenodo.5818065
title: Time dependence of advection-diffusion coupling for nanoparticle ensembles

description: Data appearing in the figures of the article DOI:10.1103/PhysRevFluids.6.064201.
DOI: 10.5281/zenodo.5818064
title: Time dependence of advection-diffusion coupling for nanoparticle ensembles

description: Data appearing in the figures of the article DOI:10.1103/PhysRevFluids.6.064201.
DOI: 10.15480/336.3946
title: Partice Image Velocimetry (PIV) Measurements of the Velocity Field Behind the Truncated Cylinder

description: Three-dimensional, two-cameras particle image velocimetry snapshots of the velocity field behind the truncated cylinder at two horizontal sections (T,M). Instantaneous snapshots of the velocity field are saved in *.npy format which is a binary format, provided by NumPy Python library. Naming convention: TC25-8-SP-T - Truncated cylinder 25cm, 8m/s inflow velocity, Stereo PIV (SP), T - top section
DOI: 10.5281/zenodo.5818333
title: Artifacts for Prioritizing Test Scripts for the Testing of Memory Bloat in Web Applications

description: Artifacts for the paper "Prioritizing Test Scripts for the Testing of Memory Bloat in Web Applications", including the source code, links to the subject web apps, the test scripts, and the execution records.