cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25550/3c-4g62
title: RNA-seq, ChIP-seq and ATAC-seq analysis of human fetal tissue

description: Repository for RNA-seq, ChIP-seq and ATAC-seq datasets for human craniofacial tissues. Human embryonic face tissue was received as de-identified, frozen samples from the Human Developmental Biology Resource (Newcastle University, UK). Primary data from the following embryonic samples were generated for this study: post conception weeks 7 and 8 whole face samples comprising three samples at Carnegie stage (CS)18, one sample CS 19, two samples at CS22 and one sample at CS23. Pre-print currently available at [https://doi.org/10.1101/2023.06.26.546603](https://doi.org/10.1101/2023.06.26.546603) This dataset contains 27 restricted-access human data files and 36 publicly available files. To gain access to the protected data in the dataset, you must first go through the [process outlined here](/odocs/data-guidelines/). To access the 36 publicly available files, scroll down to the Process Data section below. The manifest file listing the all 27 protected data files contained in the dataset and their corresponding checksums can be found below in the [Supplementary Files section](https://www.facebase.org/id/3K-PWVC).
DOI: 10.25550/3p-4vsa
title: Dental Score

description: In this project we examined the relationship between oral health and cardiovascular disease by performing a detailed oral/ periodontal examination on a sample of 553 adults from the greater Pittsburgh region who were already participating in the Heart Score Study - which was gathering longitudinal information on their cardiovascular health. In addition, we obtained DNA from these individuals to search for genetic variants that contribute to both oral and cardiovascular health. The ultimate goal of this research project is to use the data from this study to begin to dissect the genetic mechanisms by which periodontal disease and cardiovascular disease are connected.
DOI: 10.25550/3b-y34g
title: Cell Type and Tissue-specific Enhancers in Craniofacial Development

description: The genetic basis of craniofacial birth defects and general variation in human facial shape remains poorly understood. Distant-acting transcriptional enhancers are a major category of non-coding genome function and have been shown to control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic location and cell type-specific in vivo activities of all craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combined transcriptome, histone modification, and chromatin accessibility profiling from different stages of human craniofacial development with single-cell analyses of the developing mouse face to create a comprehensive catalogue of the regulatory landscape of facial development at tissue- and single cell-resolution. In total, we identified approximately 14,000 enhancers across seven developmental stages from weeks 4 through 8 of human embryonic face development. To annotate the cell type specificity of human-mouse conserved enhancers, we performed single-cell RNA-seq and single-nucleus ATAC-seq of mouse craniofacial tissues from embryonic days e11.5 to e15.5. By integrating across these data sets, we identify major cell populations of the developing face and annotate over 16,000 candidate enhancers by their cell type-specific epigenomic profile. Using retrospective analysis of known craniofacial enhancers in combination with single cell-resolved transgenic reporter assays, we show the value of these data for the prediction of in vivo cell type specificity. Taken together, our data provide a critical resource for genetic and developmental studies of human craniofacial development.
DOI: 10.7910/dvn/p4osda
title: Replication Data for: Assessing the effects of user accountability in contracting out

description: Dataset for the paper titled "Assessing the effects of user accountability in contracting out" on JPART
DOI: 10.5281/zenodo.8179302
title: Data from "Connecting large-scale meteorological patterns to extratropical cyclones in CMIP6 climate models using self-organizing maps"

description: The following files were used as data and analysis in the article "Connecting large-scale meteorological patterns to extratropical cyclones in CMIP6 climate models using self-organizing maps" (https://doi.org/10.1029/2022EF003211). In the study, we applied self-organizing maps (SOMs) as an automated machine-learning approach to characterize the large-scale meteorological patterns (LSMP) and associated frequency and intensity of discrete extratropical cyclone (ETC) events over the northeastern U.S. The dominant patterns of geopotential height variability are identified through SOM analysis of five reanalysis products during 1980 - 2019. ETC events are tracked using TempestExtremes and are integrated with SOMs to classify the accumulated cyclone activity associated with each pattern. We then evaluate the skill of CMIP6 historical experiments in simulating the LSMP and ETC events identified in the SOM. Please see the published paper for more details. Here we have archived: - data pre-processing scripts - code to run the self-organizing map analysis - code to calculate the SOM and ETC statistics - composites of 500-hPa geopotential height for each dataset as organized by the SOM - ETC tracking script and tracking output for each dataset - SOM output for each dataset
description: Gore and Zarzycki were supported by the Regional and Global Modeling and Analysis (RGMA) program area of the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research as part of the multi-program, collaborative Integrated Coastal Modeling (ICoM) project. Additional funding for Zarzycki to develop ETC datasets over the United States came from NOAA MAPP award NA19OAR4310288 ``Future changes in the frequency of winter snowstorms and their impact on snowfall and snow water equivalent.'' The authors acknowledge the World Climate Research Program, which, through its Working Group on Coupled Modeling, coordinated and promoted CMIP6. We thank the climate modeling groups for producing and making available their model output, the Earth System Grid Federation (ESGF) for archiving the data and providing access, and the multiple funding agencies who support CMIP6 and ESGF. We thank the Copernicus Climate Data Store for providing access to ERA5 reanalysis, as well as the Research Data Archive at the NCAR Computation and Information Systems Laboratory (CISL) for making JRA-55, CFSR, and 20CRv3 reanalyses available. We also thank the Modeling and Assimilation Data and Information Services Center (MDISC), managed by the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC), for providing access to MERRA2 reanalysis. We acknowledge the developers of the TempestExtremes software, available at https://github.com/ClimateGlobalChange/tempestextremes, as well as the developers of the somtoolbox software package, available at http://www.cis.hut.fi/somtoolbox/.
DOI: 10.6084/m9.figshare.24085830
title: <b>Genome-wide patterns of homoeologous gene flow in allotetraploid coffee</b>

description: <b>Premise</b>: Allopolyploidy – a hybridization-induced whole-genome duplication event – has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. with their homoeolog in allopolyploids varies across taxa, and methods to detect homoeologous gene flow (HGF) are needed to understand how HGF has shaped polyploid lineages.<b>Methods</b>: The ABBA/BABA test represents a classic method for detecting introgression between closely related species, but here we used it to characterize the extent and direction of HGF in allotetraploid <i>Coffea arabica</i>. <b>Results</b>: We found that homoeologous conversion is abundant in the <i>C. arabica</i> genome, with both subgenomes serving as donors and recipients of HGF. We also found that HGF is highly maternally biased in plastid-targeted – but not mitochondrial-targeted – genes, as would be expected if plastid-nuclear incompatibilities exist between the two parent species.<b>Discussion:</b> Together our analyses provide a simple framework for detecting HGF and new evidence consistent with selection favoring overwriting of paternally derived alleles by maternally derived alleles to ameliorate plastid-nuclear incompatibilities. Natural selection therefore appears to shape the direction and intensity of HGF in allopolyploid coffee, indicating that cytoplasmic inheritance has long-term consequences for polyploid lineages.
DOI: 10.15468/6pr73g
title: Malagasy Scoliidae recorded by PREP as flower visitors

description: "Malagasy Scoliidae recorded by PREP as flower visitors" reports the Scoliidae specimens recorded and collected by members of the project team and kept at the Museum of Evolution - EBC - Uppsala University but reported here as observation data. Duplicates of these specimens are deposited at the PBZT - Antananarivo. The data was digitized By B. Pettersson. There where verbatimCoordinates is provided the geographic location was directly acquired with a GPS, there where, otherwise, the coordinates were inferred from google map (googlemap) or google map and of aquaitance of the area (Google+). The data set contain 164 records grouped into 18 species belonging to ten (10) genera and 18 species. PREP stands for Plant Reproductive Ecology Project and was a joint project between a Swedish team from the Department of Systematic Botany - Uppsala University and a Malagasy team from the Department of Plant Biology and Ecology (DBEV) - Faculty of Science - Antananarivo University and the National Centre for Environmental Research (CNRE). This project was aiming to documenting Malagasy plants and pollinators relationship.
DOI: 10.5281/zenodo.8320369
title: Vocal data in the Dioula language related to the numbers 1, 2, 3, and 4

description: The dataset we have compiled for our research on "Setting up a speech recognition model for under-resourced languages" consists of audio recordings of Dioula speakers pronouncing the numbers 1, 2, 3, and 4. These recordings were collected under various conditions, featuring variability in speakers, accents, and environmental contexts. The data has been categorized into four distinct classes, each corresponding to one of the numbers (1, 2, 3, or 4), enabling the training and evaluation of a machine learning-based speech recognition model.
DOI: 10.5517/ccdc.csd.cc2gkgzh
title: CCDC 2280917: Experimental Crystal Structure Determination

description: Related Article: Hang Li, Na Li, Jinghao Wu, Tianyang Yu, Ran Zhang, Li-Ping Xu, Hao Wei|2023|J.Am.Chem.Soc.|145|17570|doi:10.1021/jacs.3c07640
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gt77s
title: CCDC 2288365: Experimental Crystal Structure Determination

description: Related Article: Arnold L. Rheingold and Phil Baran|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gt78t
title: CCDC 2288366: Experimental Crystal Structure Determination

description: Related Article: Arnold L. Rheingold and Phil Baran|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gv1lz
title: CCDC 2289151: Experimental Crystal Structure Determination

description: Related Article: Arnold L. Rheingold and Phil Baran|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gv1m0
title: CCDC 2289152: Experimental Crystal Structure Determination

description: Related Article: Arnold L. Rheingold and Phil Baran|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gv1n1
title: CCDC 2289153: Experimental Crystal Structure Determination

description: Related Article: Arnold L. Rheingold and Phil Baran|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gv1p2
title: CCDC 2289154: Experimental Crystal Structure Determination

description: Related Article: Arnold L. Rheingold and Phil Baran|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gv4p5
title: CCDC 2289247: Experimental Crystal Structure Determination

description: Related Article: Constantin G. Daniliuc, Vasily Kotov, Roland Fröhlich, Gerhard Erker|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gvmfd
title: CCDC 2289704: Experimental Crystal Structure Determination

description: Related Article: Arnold L. Rheingold|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gvr03
title: CCDC 2289815: Experimental Crystal Structure Determination

description: Related Article: Constantin G. Daniliuc, Martin Niehues, Roland Fröhlich, Gerhard Erker|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fz8k8
title: CCDC 2263420: Experimental Crystal Structure Determination

description: Related Article: Ming Kang, Bohong Gao, Shimin Zhang, Pengfei Hao, Gaopeng Li, Junju Shen, Yunlong Fu|2023|Dalton Trans.|52|12030|doi:10.1039/D3DT01662E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7448381
title: Fragmentomic analysis of cfDNA from LFS

description: Processed data files for reproducing figures from the publication "Cell-free DNA from germline <em>TP53</em> mutation carriers reflect cancer-like fragmentation patterns"
DOI: 10.5281/zenodo.7448380
title: Fragmentomic analysis of cfDNA from LFS

description: Processed data files for reproducing figures from the publication "Cell-free DNA from germline <em>TP53</em> mutation carriers reflect cancer-like fragmentation patterns"
DOI: 10.6084/m9.figshare.24085797
title: Yield files for "Optimal Cllimate Intervention Scenarios for Crop Production Vary by Nation".

description: Ensemble average yield files for "Optimal Cllimate Intervention Scenarios for Crop Production Vary by Nation" processed from CLM5crop output. Refer to README.txt file for details.
DOI: 10.5281/zenodo.8320109
title: Somatic reads mapped to HGAP4 CP genome (this study); and somatic CL reads mapped to CL genome (Arimoto et al, 2019)

description: Somatic reads mapped to HGAP4 CP genome (this study); and somatic CL reads mapped to CL genome (Arimoto et al, 2019)
DOI: 10.5281/zenodo.8320108
title: Somatic reads mapped to HGAP4 CP genome (this study); and somatic CL reads mapped to CL genome (Arimoto et al, 2019)

description: Somatic reads mapped to HGAP4 CP genome (this study); and somatic CL reads mapped to CL genome (Arimoto et al, 2019)
DOI: 10.5281/zenodo.8320420
title: V2.4-Abaqus2022+IntelFortran2021-128X128X128-element-C3D8-SVDinversion=0-success

description: V2.4-Abaqus2022+IntelFortran2021-128X128X128-element-C3D8-SVDinversion=0-success
DOI: 10.5281/zenodo.8320419
title: V2.4-Abaqus2022+IntelFortran2021-128X128X128-element-C3D8-SVDinversion=0-success

description: V2.4-Abaqus2022+IntelFortran2021-128X128X128-element-C3D8-SVDinversion=0-success
DOI: 10.6084/m9.figshare.22012682
title: Data associated with Distribution and Substrate Frequency of Teloschistes chrysophthalmus (L.) Th. Fr. in Iowa, USA

description: These are data collected by James Colbert assessing the distribution of the lichen Teloschistes chrysophthalmus. This data set includes general population assessments for different areas throughout Iowa, including the host tree species and its condition.
DOI: 10.6084/m9.figshare.22012682.v1
title: Data associated with Distribution and Substrate Frequency of Teloschistes chrysophthalmus (L.) Th. Fr. in Iowa, USA

description: These are data collected by James Colbert assessing the distribution of the lichen Teloschistes chrysophthalmus. This data set includes general population assessments for different areas throughout Iowa, including the host tree species and its condition.
DOI: 10.6084/m9.figshare.24085914
title: panSeq_pst9

description: <b>Puccinia striiformis f. sp. tritici</b>
DOI: 10.57841/casdc.0002068
title: 两种水基摩擦改性剂对轮轨黏着和损伤性能的影响
DOI: 10.5281/zenodo.8320433
title: Carbon storage and carbon-equivalent albedo impact for US forests, by age and forest type

description: These tables document estimates of carbon storage (Mg/ha +/- Standard Error) and carbon-equivalent albedo impacts (same units) of US forests by age and forest type (Healey et al., in review). Carbon estimates are derived from field measurements made by the USDA Forest Service on approximately 125,000 forested field plots (Domke et al., 2022). Soil organic carbon is omitted from these estimates, but all other above- and below-ground pools are included. Albedo impacts (time-dependent emissions equivalent, TDEE; Bright et al., 2016) were developed by applying atmospheric kernels (Bright and O'Halloran) to a new Landsat blue sky albedo product for the Landsat archive (Erb et al., 2022), as described by Healey et al. (in review). Standard error is supplied for each age/forest type bin for carbon storage, but upper and lower standard error bounds are specified for TDEE because log transformation creates an asymmetrical uncertainty envelope. Bright, Bogren, Bernier, Astrup, (2016). Carbon-equivalent metrics for albedo changes in land management contexts: Relevance of the time dimension. <em>Ecol. Appl.</em> 26, 1868–1880 Bright, R. M., & O'Halloran, T. L. (2019). Developing a monthly radiative kernel for surface albedo change from satellite climatologies of Earth's shortwave radiation budget: CACK v1. 0. <em>Geoscientific Model Development, </em>12(9), 3975-3990. Domke, Walters, Nowak, Greenfield, Smith, Nichols, Ogle, Coulston, Wirth (2022). Greenhouse Gas Emissions and Removals From Forest Land, Woodlands, Urban Trees, and Harvested Wood Products in the United States, 1990–2020. (US Dept. Ag. For. Service, Madison, WI; https://doi.org/10.2737/FS-RU-382). Erb, Li, Sun, Paynter, Wang, & Schaaf, (2022). Evaluation of the Landsat-8 Albedo Product across the Circumpolar Domain. <em>Remote Sensing</em>, <em>14</em>(21), 5320. Healey, Yang, Erb, Bright, Domke, Frescino, Schaaf, (in review) New satellite observations expose albedo dynamics offsetting half of carbon storage benefits in US forests.
DOI: 10.5281/zenodo.8320432
title: Carbon storage and carbon-equivalent albedo impact for US forests, by age and forest type

description: These tables document estimates of carbon storage (Mg/ha +/- Standard Error) and carbon-equivalent albedo impacts (same units) of US forests by age and forest type (Healey et al., in review). Carbon estimates are derived from field measurements made by the USDA Forest Service on approximately 125,000 forested field plots (Domke et al., 2022). Soil organic carbon is omitted from these estimates, but all other above- and below-ground pools are included. Albedo impacts (time-dependent emissions equivalent, TDEE; Bright et al., 2016) were developed by applying atmospheric kernels (Bright and O'Halloran) to a new Landsat blue sky albedo product for the Landsat archive (Erb et al., 2022), as described by Healey et al. (in review). Standard error is supplied for each age/forest type bin for carbon storage, but upper and lower standard error bounds are specified for TDEE because log transformation creates an asymmetrical uncertainty envelope. Bright, Bogren, Bernier, Astrup, (2016). Carbon-equivalent metrics for albedo changes in land management contexts: Relevance of the time dimension. <em>Ecol. Appl.</em> 26, 1868–1880 Bright, R. M., & O'Halloran, T. L. (2019). Developing a monthly radiative kernel for surface albedo change from satellite climatologies of Earth's shortwave radiation budget: CACK v1. 0. <em>Geoscientific Model Development, </em>12(9), 3975-3990. Domke, Walters, Nowak, Greenfield, Smith, Nichols, Ogle, Coulston, Wirth (2022). Greenhouse Gas Emissions and Removals From Forest Land, Woodlands, Urban Trees, and Harvested Wood Products in the United States, 1990–2020. (US Dept. Ag. For. Service, Madison, WI; https://doi.org/10.2737/FS-RU-382). Erb, Li, Sun, Paynter, Wang, & Schaaf, (2022). Evaluation of the Landsat-8 Albedo Product across the Circumpolar Domain. <em>Remote Sensing</em>, <em>14</em>(21), 5320. Healey, Yang, Erb, Bright, Domke, Frescino, Schaaf, (in review) New satellite observations expose albedo dynamics offsetting half of carbon storage benefits in US forests.
DOI: 10.57841/casdc.0002069
title: 添加Ag2Nb4O11的NiAl基复合材料的高温摩擦学性能及高温润滑机理研究