cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p9q1kln4
title: Giant Gartersnake (Thamnophis gigas) Prey Preference (2014)

description: This is an examination of the diet of a threatened snake, giant gartersnake (Thamnophis gigas). Prey preference, prey selection and prey availability (in the laboratory and the field) were measured to understand prey dynamics for better conservation of this snake. In the laboratory, olfactory trials were performed on neonate snakes and tongue-flicks, lounges and attacks were counted and calculated into 'tongue-flick attack scores', a measure of prey preference. Prey-choice trials were used to measure prey selection in the laboratory. In the field, we measured prey choice and prey availability to gain an understanding of prey choice in nature. These data support the following publication: Ersan, J.S., Halstead, B.J., Wildy, E.L., Casazza, M.L. and Wylie, G.D., 2020. Intrinsic Prey Preference and Selection of the Giant Gartersnake: A Threatened Predator in a Nonnative Prey-Dominated Community. Journal of Fish and Wildlife Management, 11(1), pp.164-173. https://doi.org/10.3996/062019-JFWM-051.
DOI: 10.5281/zenodo.5908612
title: Tropical extreme droughts drive long-term increase in atmospheric CO2 growth rate variability

description: This repository includes the code and the processed climate data used to examine the long-term change in atmospheric CO<sub>2</sub> growth rate. The code will generate the main figures (Figure 1, 2 and 3) in the paper - Luo, X. & Keenan, T. F. (2022) Tropical extreme droughts drive long-term increase in atmospheric CO2 growth rate variability. Nature Communications, doi: 10.1038/s41467-022-28824-5. Please refer to the "Data Availability Statement" in the paper and cite the original sources if you need to use one or more datasets published here. There are three files in the repository: 1) CGR_analysis_input.mat is the processed data in matlab format to support the study; 2) master_figures_CGR_publish_v1.m is the main matlab routine that used to generate figures; 3) supporting code is a folder that contains third-party routines to support the main routine.
DOI: 10.5281/zenodo.5908611
title: Tropical extreme droughts drive long-term increase in atmospheric CO2 growth rate variability

description: This repository includes the code and the processed climate data used to examine the long-term change in atmospheric CO<sub>2</sub> growth rate. The code will generate the main figures (Figure 1, 2 and 3) in the paper - Luo, X. & Keenan, T. F. (2022) Tropical extreme droughts drive long-term increase in atmospheric CO2 growth rate variability. Nature Communications, doi: 10.1038/s41467-022-28824-5. Please refer to the "Data Availability Statement" in the paper and cite the original sources if you need to use one or more datasets published here. There are three files in the repository: 1) CGR_analysis_input.mat is the processed data in matlab format to support the study; 2) master_figures_CGR_publish_v1.m is the main matlab routine that used to generate figures; 3) supporting code is a folder that contains third-party routines to support the main routine.
DOI: 10.5281/zenodo.6496539
title: The first annotated genome assembly of Macrophomina tecta associated with charcoal rot of sorghum

description: Raw reads of Macrophomina tecta were obtained from Nanopore, Illumina, and NextSeq (RNA). Files with information about the genome annotation, functional prediction, repeats, effectors and orthologous genes are included.
DOI: 10.5281/zenodo.6363764
title: The first annotated genome assembly of Macrophomina tecta associated with charcoal rot of sorghum

description: Raw reads of Macrophomina tecta were obtained from Nanopore, Illumina, and NextSeq (RNA). Files with information about the genome annotation, functional prediction, repeats, effectors and orthologous genes are included.
DOI: 10.5281/zenodo.6544625
title: GOES-16 simulated BTs over the Southeastern US.

description: This dataset contains simulated brightness temperatures from WRF V3.9.1.1.1 model output used in "<strong>Examining the Role of the Land Surface On Convection Using High-Resolution Model Forecasts Over the Southeastern United States</strong>", Henderson, Otkin, and Mecikalski, submitted to JGR-Atmospheres, in review.
DOI: 10.17632/3m6gs9hfsd.1
title: A diabetic milieu increases ACE2 expression and cellular susceptibility to SARS-CoV-2 infections in human kidney organoids and patient cells. Garreta et al.

description: Data S1 - Source Data file that contains all values used to generate the graphs of the paper, original western blot images and additional microscopy images.
DOI: 10.17632/xpfbp7vt8f.1
title: Assembly and annotation of the genome of a lipid accumulator strain (LAS) obtained from the biolistic genetic transformation of Aurantiochytrium limacinum strain CCAP_4062/1 

description: The deposited files include the genome sequence and annotation of an Aurantiochytrium limacinum strain CCAP_4062/1 obtained by biolistic genetic transformation called LAS (Lipid Accumulator Strain).
The following files are available:
- LAS_Assembly.fasta = Genome assembly obtained with Pacbio Sequel I long reads
- Augustus_Annotation_model_LAS.gtf = GTF file containing the gene models obtained with Augustus
- LAS_Gene_Descriptions.txt = gene descriptions obtained from the predicted proteome using the Pannzer2 Pipeline
- LAS_GO_Annotation.txt = Gene Ontology Annotation obtained from the predicted proteome using the Pannzer2 Pipeline
DOI: 10.17632/cm5vk9mmw4.1
title: Complete set of binding and functional data for 545 HCV E1E2 mutations. 

description: Complete set of binding and functional data for 545 HCV E1E2 mutations.
To understand how HCV E1E2 folds and functions on an amino acid level, we generated an alanine scan library of mutants covering E1E2, using a parental expression construct for E1E2 (HCV genotype 1a, strain H77) with a V5 tag at the E2 C-terminus, and introduced an alanine substitution at each of 545 E1E2 residues. Existing alanine residues were changed to serine. All clones (545/555 residues, 98% coverage) were individually transfected intoHEK-293T cells and tested by flow cytometry for binding to 37 different MAbs and to a soluble fragment of CD81 (CD81-LEL). Data were obtained with each E1E2 mutant for the ability to support MAb binding, CD81 LEL binding, E1E2 expression, HCVpp budding, and HCVpp infectivity in HEK293T cells expressing Claudin 1 (CLDN1). Values are expressed as % of values obtained with WT E1E2 (defined as 100%). Some of the data have been shown in a previous examination of HCV E1E2 structure (Gopal et al., 2017 PLoS Pathog); the data set here extends this original data set to additional MAbs (including E1 MAbs) and tests the infectivity of each mutant. The line between A383 and E384 indicates the E1E2 junction.
DOI: 10.17632/w3c8p5w3hn.1
title: Diet of Mesozoic toothed birds (Longipterygidae) inferred from quantitative analysis of extant avian diet proxies

description: Spreadsheets and R code used for data analysis and figure creation in the BMC Biology paper "Diet of Mesozoic toothed birds (Longipterygidae) inferred from quantitative analysis of extant avian diet proxies" (doi 10.1186/s12915-022-01294-3). Outputs from all finite element models are provided as well. A README text file is included to explain the file types included and best practices for running them to recreate our outputs.
DOI: 10.48661/fk2/7chmji
title: Autores ecuatorianos agrupados automáticamente en clusters de áreas de investigación en proyecto REDI

description: Dataset de autores agrupados automáticamente en clusters basados áreas de investigación en el proyecto REDI
DOI: 10.6084/m9.figshare.19759018
title: Growth Curve Optical Density of Sacharomyces cerevisiae wildtype, EGFP vector insertion and EGFP PolyR insertion.csv

description: Growth curve of <em>Saccharomyces cerevisiae</em> with and without plasmid insertion. The data showed : A. Growth curve of <em>Saccharomyces cerevisiae</em> without plasmid. B. Growth curve of transformant <em>Saccharomyces cerevisiae</em> with EGFP plasmid with induction medium MM (2% galactose and 1% raffinose) C. Growth curve of transformant <em>Saccharomyces cerevisiae</em> with EGFP polyarginine plasmid. D. Growth curve comparison on 48 hours and 72 hours of wildtype <em>Saccharomyces cerevisiae</em> and transformant <em>Saccharomyces cerevisiae</em> (EGFP plasmid and EGFP polyarginine plasmid).
DOI: 10.7303/syn30255033.1
title: UCSD GNPS Suspect Library
DOI: 10.6084/m9.figshare.19723189.v1
title: Directed differentiation of human pluripotent stem cells into diverse organ-specific mesenchyme of the digestive and respiratory systems.

description: Development of visceral organs such as the esophagus, lung, liver and stomach are coordinated by reciprocal signaling interactions between the embryonic endoderm and adjacent mesoderm cells in the fetal foregut. While the recent successes in recapitulating developmental signaling <em>in vitro </em>has enabled the differentiation of human pluripotent stem cells (hPSCs) into various types of organ-specific endodermal epithelium, the generation of organ-specific mesenchyme has received much less attention. This is a major limitation in ongoing efforts to engineer complex human tissue. Here, we describe a series of protocols to differentiate hPSCs into different types of organ-specific mesoderm leveraging signaling networks and new molecular markers recently elucidated from single cell transcriptomic analysis of mouse foregut organogenesis. Building on established methods, hPSC-derived lateral plate mesoderm (LPM) treated with either retinoic acid (RA) or RA and a Hedgehog (HH) agonist generates posterior or anterior foregut splanchnic mesoderm respectively (pFG-SpM or aFG-SpM) after 4 days in cultures. These are then directed into organ-specific mesenchyme lineages by the combinatorial activation or inhibition of WNT, BMP, RA or HH pathways from days 4-7 in monolayer culture. By day 7 the cultures are enriched for different types of mesoderm with distinct molecular signatures: 60~90% pure liver septum transversum/mesothelium (STM/Mesothelium), 70~80% pure liver fibroblasts (LF), and populations of ~35% respiratory mesoderm (RM), gastric mesoderm (GM), or esophageal mesoderm (EM). This protocol can be carried out by anyone with moderate experience differentiating hPSCs and provides a novel platform to study human mesoderm development and can be used to tissue engineer more complex foregut organ tissue for disease modeling and regenerative medicine.
DOI: 10.6084/m9.figshare.19593037.v1
title: Supplementary tables_4-12-22.pptx

description: Supplementary tables associated with the manuscript titled, "Strain-dependent lung transcriptomic differences in cigarette smoke and LPS models of acute lung injury (ALI) and Acute Respiratory Distress Syndrome (ARDS). The manuscript is under consideration by AJP lung cellular and molecular biology.
DOI: 10.6084/m9.figshare.19593037
title: Supplementary tables_4-12-22.pptx

description: Supplementary tables associated with the manuscript titled, "Strain-dependent lung transcriptomic differences in cigarette smoke and LPS models of acute lung injury (ALI) and Acute Respiratory Distress Syndrome (ARDS). The manuscript is under consideration by AJP lung cellular and molecular biology.
DOI: 10.5281/zenodo.6544649
title: Synapse Competition Data

description: For the Synpase competition
DOI: 10.5281/zenodo.6544648
title: Synapse Competition Data

description: For the Synpase competition
DOI: 10.25345/c5348gk9m
title: MassIVE MSV000089463 - Segal_TMT_14-3-3_APMS_BioID_interactors
title: This dataset consists of 36 raw MS files acquired on Lumos Fusion Orbitrap mass spectrometer operated in Data Dependent Acquisition mode for TMT-10plex. The files are associated with a manuscript submitted for publication by Segal et al. that determines the protein-protein and proximity interaction landscape of 14-3-3 proteins. All samples comprise either BioID or FLAG AP-MS purifications of each of the human 14-3-3 proteins (with negative controls) expressed to the same level in HEK293 Flp-In T-REx cells. Purified samples were labeled with TMT reagents, and analyzed by mass spectrometry. 32 files correspond to the BioID dataset (fractionated; MS3), and 4 files to the AP-MS dataset (non fractionated, HCD MS2). Samples were generated by Dmitri Segal and Stefan Maier and affinity purification, labeling, mass spectrometry, and data analysis were performed by Stefan Maier. Corresponding authors: Mikko Taipale (mikko.taipale@utoronto.ca) and Anne-Claude Gingras (gingras@lunenfeld.ca). Anne-Claude Gingras should be contacted for questions on this dataset.
DOI: 10.5281/zenodo.6544845
title: Artifact for "Accumulation Analysis"

description: The artifact for the paper "Accumulation Analysis", published at ECOOP 2022. It contains the data for our literature survey of papers that use typestate specifications, as well as supporting evidence for miscellaneous claims. See the file `README.md` for details.
DOI: 10.5281/zenodo.5771195
title: Artifact for "Accumulation Analysis"

description: The artifact for the paper "Accumulation Analysis", published at ECOOP 2022. It contains the data for our literature survey of papers that use typestate specifications, as well as supporting evidence for miscellaneous claims. See the file `README.md` for details.
DOI: 10.6084/m9.figshare.19759114
title: Am I Masculine Data

description: Data Extraction Searching from Database
DOI: 10.6084/m9.figshare.19759114.v1
title: Am I Masculine Data

description: Data Extraction Searching from Database
DOI: 10.5281/zenodo.6544661
title: Dataset for "Investigating multiple observations around a seismic gap during the Lushan earthquake in Sichuan, China"

description: "MsCatalog.csv" includes the catalog used in the paper. "gnss2013" includes the daily horizontal surface displacement (E and N components) in the South China Block frame in 2013. “2013.tar.gz” includes the Empirical Green's functions (EGF) of all 208 station pairs in 2013, Sichuan, which were derived from the continuous seismic waveforms (ambient noise).
DOI: 10.5281/zenodo.6540992
title: Dataset for "Investigating multiple observations around a seismic gap during the Lushan earthquake in Sichuan, China"

description: "MsCatalog.csv" includes the catalog used in the paper. "gnss2013" includes the daily horizontal surface displacement (E and N components) in the South China Block frame in 2013. “2013.tar.gz” includes the Empirical Green's functions (EGF) of all 208 station pairs in 2013, Sichuan, which were derived from the continuous seismic waveforms (ambient noise).
DOI: 10.6084/m9.figshare.19753906
title: SPMP hybrid MAGs

description: MAGs (high, near complete and medium quality) from the 109 Singaporean gut metagenome project SPMP.
DOI: 10.6084/m9.figshare.19753906.v2
title: SPMP hybrid MAGs

description: MAGs (high, near complete and medium quality) from the 109 Singaporean gut metagenome project SPMP.
DOI: 10.6084/m9.figshare.19753906.v1
title: SPMP hybrid polished MAGs

description: MAGs (high, near complete and medium quality) from the 109 Singaporean gut metagenome project SPMP.
DOI: 10.6084/m9.figshare.19759120
title: electronic nose characteristics of apples infected with different fungi

description: This dataset mainly contains data collected from apples infected with different fungi and fresh apples using an electronic nose, The electronic nose contains 8 sensors, and sensor No. 1 and sensor No. 5 use the same sensor to eliminate outliers in the data，If the difference between the 150-300s of the two sensors was greater than 1.2mg/L, the specimen will then be considered anomalous and removed, and the data for removing outlier samples using this method is stored in 'Data/sensors_eliminate' file. The "Fuji" apples selected in this dataset came from apple plantations in Gansu Province, China. 160 ripe apples were selected and randomly divided into 4 groups, 40 apples in each group, namely Group A, Group B, Group C and Group D; The fungi inoculated in the middle apples were Aspergillus niger, Penicillium expansum and Penicillium crustosum. The apple samples were pretreated with 75% alcohol on a sterile bench and dried at room temperature. Then, four holes were punched in four directions of each apple of the three groups A, B, and C with the inoculator. Sample apples were inoculated with 7-day-old molds through drilled loops, and the holes were covered with sterile film. The mold-inoculated apples were then placed in a 1000ml beaker, sealed with plastic wrap, and then placed in a 25°C constant temperature incubator for 5 days. Before the test, the apple samples were taken out of the incubator and placed for 30 minutes. To eliminate the influence of residual gas on the experimental results, electronic nose was cleaned with inert gas before using. Setting electronic nose parameters: cleaning time 500s, collection time 350s, sampling interval 1s, injection flow 150ml/min, the raw data store in 'Data/raw_data' file. Then Matlab is used to preprocess the raw data，The first is to smooth and filter the data, and use 3-point smoothing, 5-point smoothing, 7-point smoothing, 9-point smoothing and 11-point smoothing to smooth and filter the data after removing abnormal samples. The smoothed filtered data is stored in ‘Data/smoothed_data’ file. The second is feature extraction, we take the integral value, variance value, average differential value, maximum gradient value, relatively stable average value and energy value of the response curve of each sensor for 30-300s as the characteristic information of electronic nose. However, the value of 7NE/H2S-1000 and VOC-300 sensors is always 0 during the whole acquisition process, so this dataset only store the data measured by 6 sensors except 7NE/H2S-1000 and VOC-300, which stores in 'Data/feature_parameters_data' file, The second is to use Mahalanobis distance to propose abnormal samples in the data again, and the eliminated data is stored in ‘Data/Data/eliminate_anomalous_data‘ file. Finally, principal component analysis, factor analysis and linear discriminant analysis are used to reduce the dimension of the above data, and the data after dimension reduction is stored in ‘Data/dimensionality_reduction_data' file.
DOI: 10.6084/m9.figshare.14524983
title: Pesticide and obesity

description: Dataset for study for pesticide exposure and obesity among Thai farmer.<br>
DOI: 10.6084/m9.figshare.14524983.v1
title: Pesticide and obesity

description: Dataset for study for pesticide exposure and obesity among Thai farmer.<br>
DOI: 10.6084/m9.figshare.19731889.v1
title: VulnerabilityModel.zip

description: We investigated the vulnerability of Chinese forests to fires during the period 2001-2020 by integrating automatic machine learning with fire disturbance data and satellite products. The proposed methodology is purely data-driven and therefore reproducible, applicable at large scales, and in line with the measurement/reporting/verification process of UNFCCC. Results of this study have been submitted to the journal Ecology. Part of pre-processed data, codes of vulnerability models developed in the afore-mentioned work are made publicly available here and briefly described to facilitate reproducibility and applicability.
DOI: 10.6084/m9.figshare.19731889.v2
title: VulnerabilityModel.zip

description: We investigated the vulnerability of Chinese forests to fires during the period 2001-2020 by integrating automatic machine learning with fire disturbance data and satellite products. The proposed methodology is purely data-driven and therefore reproducible, applicable at large scales, and in line with the measurement/reporting/verification process of UNFCCC. Results of this study have been submitted to the journal Ecology. Part of pre-processed data, codes of vulnerability models developed in the afore-mentioned work are made publicly available here and briefly described to facilitate reproducibility and applicability.
DOI: 10.18139/nndc.xundl/1860326
title: Experimental Unevaluated Nuclear Data List (XUNDL)

description: Contains nuclear structure and decay data from published articles. Data include nuclear level properties, such as energy, half-life, decay modes, spin and parity, as well as energy and intensity for radiation types such as gammas, alphas, betas and neutrons. For articles published in Physical Review C and the European Physical Journal, compilation takes place during the article submission process. Data from approximately 250 articles are added per year. All the compilation effort is supported by the US Nuclear Data Program and coordinated by the National Nuclear Data Center at Brookhaven National Laboratory, which is also responsible for its web dissemination.
DOI: 10.13139/ornlnccs/1866593
title: OpenMDlr Dataset

description: Protein structure dataset created with OpenMDlr. Restraints applied to fold proteins into native-like conformations were obtained from a variety of methods; results from these different restraint sets are contained in respective subdirectories.
DOI: 10.5281/zenodo.6489354
title: Stimulation of medial amygdala GABA neurons with kinetically different channelrhodopsins yields opposite behavioral outcomes

description: This dataset continues the dataset accessible by doi 10.5281/zenodo.4311847. The latter also contains all the relevant metadata description.
description: This work was supported by Swiss National Science Foundation (SNSF) National Competence Center for Research Synapsy, Synaptic Bases of Mental Disease Project #28 to Ralf Schneggenburger. Image acquisition was done at the Bioimaging and Optics Platform (BIOP) of École Polytechnique Fédérale de Lausanne (EPFL).
DOI: 10.5281/zenodo.6489353
title: Stimulation of medial amygdala GABA neurons with kinetically different channelrhodopsins yields opposite behavioral outcomes

description: This dataset continues the dataset accessible by doi 10.5281/zenodo.4311847. The latter also contains all the relevant metadata description.
description: This work was supported by Swiss National Science Foundation (SNSF) National Competence Center for Research Synapsy, Synaptic Bases of Mental Disease Project #28 to Ralf Schneggenburger. Image acquisition was done at the Bioimaging and Optics Platform (BIOP) of École Polytechnique Fédérale de Lausanne (EPFL).
DOI: 10.6084/m9.figshare.19759228
title: Supplementary file 1

description: Supplementary file 1
DOI: 10.6084/m9.figshare.19759228.v1
title: Supplementary file 1

description: Supplementary file 1
DOI: 10.25912/rdf_1652410027274
title: Determinants of Food Security Among People from Refugee Backgrounds Resettled in High-Income Countries: A Systematic Review and Thematic Synthesis
DOI: 10.5281/zenodo.6544897
title: Code of "Inclusion of flood diversion canal operation in the H08 hydrological model with a case study from the Chao Phraya River basin: model development and validation"

description: Code used to prepare a paper entitled "Inclusion of flood diversion canal operation in the H08 hydrological model with a case study from the Chao Phraya River basin: model development and validation" which was submitted to Hydrology and Earth System Sciences.
DOI: 10.5281/zenodo.6544896
title: Code of "Inclusion of flood diversion canal operation in the H08 hydrological model with a case study from the Chao Phraya River basin: model development and validation"

description: Code used to prepare a paper entitled "Inclusion of flood diversion canal operation in the H08 hydrological model with a case study from the Chao Phraya River basin: model development and validation" which was submitted to Hydrology and Earth System Sciences.
DOI: 10.18112/openneuro.ds004064.v1.0.0
title: Queensland Twin IMaging (QTIM)
DOI: 10.34740/kaggle/dsv/3625295
title: BBC News