cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9768101.v10
title: Datasets, matrices and supplementary figure for QMaker

description: Pfam_datasets.zip: Pfam training and test sets which were used with QMaker.<br>Matrices-normalized.zip: Eight output matrices for LG, Pfam, Pfam-gb, Bird, Insect, Mammal, Plant, and Yeast datasets.<br>Figure S1_new.pdf: The performance of five matrices, i.e., Q.pfam, JTT, LG, WAG on five clade-specific datasets, i.e., Bird, Plant, Insect, Yeast Mammal.<br>Table S1 (Correlations).docx: Correlation values (1000x) between six new matrices and 20 existing matrices, upper half are correlations of frequencies, lower half are correlations of exchangeabilities.<br>sample_training_10alignments.zip, sample_training_10genes.zip: two small datasets and training scripts, one has 10 alignments (these alignments do not share species and are extracted from Pfam dataset, shoulf be trained with option -S), the other has 10 genes of a same species (extracting from Plant dataset, training with option -p). Each dataset will need ~30 mins training time on a 10-core machine.
DOI: 10.5281/zenodo.4173186
title: Detailed global modelling of soil organic carbon in cropland, grassland and forest soils

description: Supporting information of the paper: Morais, T.G., Teixeira, R.F.M., Domingos, T. 2019. Detailed global modelling of soil organic carbon in cropland, grassland and forest soils. PloS One. Version 2 includes raster files (.tif) for each land use class (including: Attainable SOC stock, mineralization rate, and fator K).
DOI: 10.5281/zenodo.3387664
title: Detailed global modelling of soil organic carbon in cropland, grassland and forest soils

description: Supporting information of the paper: Morais, T.G., Teixeira, R.F.M., Domingos, T. 2019. Detailed global modelling of soil organic carbon in cropland, grassland and forest soils. PloS One. Version 2 includes raster files (.tif) for each land use class (including: Attainable SOC stock, mineralization rate, and fator K).
DOI: 10.5281/zenodo.3387665
title: Detailed global modelling of soil organic carbon in cropland, grassland and forest soils

description: Supporting information of the paper: Morais, T.G., Teixeira, R.F.M., Domingos, T. 2019. Detailed global modelling of soil organic carbon in cropland, grassland and forest soils. PloS One. <strong>EDIT: Version 2 includes raster files (.tif) for each land use class (including: Attainable SOC stock, mineralization rate, and fator K). Available here: https://zenodo.org/record/4173186#.X57hYYj7SUk</strong>
DOI: 10.6084/m9.figshare.13173617.v1
title: R0198_20171127a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13173623.v1
title: R0198_20171128a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.5281/zenodo.3885771
title: Barnase-Barstar Binding Pathways

description: This is a collection of binding trajectories from the atomistic simulation of the Barnase-Barstar system presented in Protein–protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations by Saglam and Chong. There is one representative trajectory from each of the five pathways identified. The GRO file here is to be used as a "topology" file, so if your chosen MD viewer or analysis software includes the reference frame from the GRO file, be sure to delete the frame before running your analysis, etc. If you want to analyze just the first frame of a trajectory, load in the GRO/topology file, delete the frame from that file, load in the relevant XTC file and use the first frame from that. Please cite the Saglam and Chong paper if you use these data.
description: This work was supported by NSF CAREER Award MCB-0845216 and NIH 1R01GM115805-01 to LT Chong and a DAAD graduate research grant to AS Saglam. Computational resources were provided by NSF XSEDE allocation TG-MCB100109 to LT Chong, NSF CNS-1229064, and the University of Pittsburgh's Center for Research Computing.
DOI: 10.5281/zenodo.3885770
title: Barnase-Barstar Binding Pathways

description: This is a collection of binding trajectories from the atomistic simulation of the Barnase-Barstar system presented in Protein–protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations by Saglam and Chong. There is one representative trajectory from each of the five pathways identified. The GRO file here is to be used as a "topology" file, so if your chosen MD viewer or analysis software includes the reference frame from the GRO file, be sure to delete the frame before running your analysis, etc. If you want to analyze just the first frame of a trajectory, load in the GRO/topology file, delete the frame from that file, load in the relevant XTC file and use the first frame from that. Please cite the Saglam and Chong paper if you use these data.
description: This work was supported by NSF CAREER Award MCB-0845216 and NIH 1R01GM115805-01 to LT Chong and a DAAD graduate research grant to AS Saglam. Computational resources were provided by NSF XSEDE allocation TG-MCB100109 to LT Chong, NSF CNS-1229064, and the University of Pittsburgh's Center for Research Computing.
DOI: 10.6084/m9.figshare.13174514
title: 1950-1983 Projected Species Data For MaxEnt.csv

description: Projected species data for time period 1950-1983
DOI: 10.6084/m9.figshare.13174514.v1
title: 1950-1983 Projected Species Data For MaxEnt.csv

description: Projected species data for time period 1950-1983
DOI: 10.6084/m9.figshare.13174517.v1
title: 1984_2016 Projected Species Data for MaxEnt.csv

description: Projected species data for 1984-2016 time period
DOI: 10.6084/m9.figshare.13174517
title: 1984_2016 Projected Species Data for MaxEnt.csv

description: Projected species data for 1984-2016 time period
DOI: 10.6084/m9.figshare.13174520
title: 1950-2016 Projected Species Data For MaxEnt.csv

description: Projected species data ready for MaxEnt model for time period 1950-2016
DOI: 10.6084/m9.figshare.13174520.v1
title: 1950-2016 Projected Species Data For MaxEnt.csv

description: Projected species data ready for MaxEnt model for time period 1950-2016
DOI: 10.6084/m9.figshare.13174544.v1
title: Species Data for All Time Periods

description: Species data formatted for MaxEnt, projected in the same study area for all 3 time periods
DOI: 10.6084/m9.figshare.13174544
title: Species Data for All Time Periods

description: Species data formatted for MaxEnt, projected in the same study area for all 3 time periods
DOI: 10.34740/kaggle/dsv/1610167
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.5519/qd.6se4ggq6
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (242 records)
DOI: 10.6084/m9.figshare.13173626.v1
title: R0198_20171130a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13173626
title: R0198_20171130a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.5519/qd.q041se5i
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (164 records)
DOI: 10.6084/m9.figshare.13174580
title: MaxEnt Output for 1950-1983

description: Results for MaxEnt model validation for 1950-1983
DOI: 10.6084/m9.figshare.13174580.v1
title: MaxEnt Output for 1950-1983

description: Results for MaxEnt model validation for 1950-1983
DOI: 10.6084/m9.figshare.13174589
title: MaxEnt Output for 1950-2016

description: Output for 1950-2016
DOI: 10.6084/m9.figshare.13174589.v1
title: MaxEnt Output for 1950-2016

description: Output for 1950-2016
DOI: 10.5281/zenodo.4173256
title: Periglacial ground movement and environmental variables in the Gaissane mountain massif, Northern Norway

description: Dataset documenting ground movement and environmental conditions at 68'590 common pixels (40 m resolution).<br> Study area: ca. 148 sqkm area in the Gaissane mountain massif, County of Troms og Finnmark, Northern Norway (70°00'N, 26°14'E).<br> <br> Ground movement associated with cryoturbation and solifluction has been detected using a distributed scatterers Synthetic Aperture Radar Interferometry (InSAR) technique based on Sentinel-1 satellite images (2015-2018).<br> Two-dimensional information (vertical and horizontal in the East-West plane) has been retrieved by combining InSAR results from ascending and descending SAR geometries.<br> The results are expressed as mean annual ground velocities (mm/yr).<br> Seven environmental variables are documenting the climatic, geomorphic, hydrological and ecological conditions at similar locations.<br> The dataset was used to perform statistical modelling using generalized linear model, generalized additive model, generalized boosting method and random forest.
description: In relation with a manuscript submitted in JGR: Earth Surface "Environmental Controls of InSAR-based Periglacial Ground Movement in a Sub-Arctic Landscape" Funding: Research Council of Norway (grant 263005) and Academy of Finland (grant 315519)
DOI: 10.6084/m9.figshare.13174598.v1
title: MaxEnt Outputs for 1984-2016

description: MaxEnt outputs for the time period 1984-2016
DOI: 10.6084/m9.figshare.13174598
title: MaxEnt Outputs for 1984-2016

description: MaxEnt outputs for the time period 1984-2016
DOI: 10.5281/zenodo.4173255
title: Periglacial ground movement and environmental variables in the Gaissane mountain massif, Northern Norway

description: Dataset documenting ground movement and environmental conditions at 68'590 common pixels (40 m resolution).<br> Study area: ca. 148 sqkm area in the Gaissane mountain massif, County of Troms og Finnmark, Northern Norway (70°00'N, 26°14'E).<br> <br> Ground movement associated with cryoturbation and solifluction has been detected using a distributed scatterers Synthetic Aperture Radar Interferometry (InSAR) technique based on Sentinel-1 satellite images (2015-2018).<br> Two-dimensional information (vertical and horizontal in the East-West plane) has been retrieved by combining InSAR results from ascending and descending SAR geometries.<br> The results are expressed as mean annual ground velocities (mm/yr).<br> Seven environmental variables are documenting the climatic, geomorphic, hydrological and ecological conditions at similar locations.<br> The dataset was used to perform statistical modelling using generalized linear model, generalized additive model, generalized boosting method and random forest.
description: In relation with a manuscript submitted in JGR: Earth Surface "Environmental Controls of InSAR-based Periglacial Ground Movement in a Sub-Arctic Landscape" Funding: Research Council of Norway (grant 263005) and Academy of Finland (grant 315519)
DOI: 10.6084/m9.figshare.13174553.v1
title: R0198_20171129a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13174553
title: R0198_20171129a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.5281/zenodo.4173468
title: Social cues of a robot and cognitive control

description: The data presented here are reported in Ciardo & Wykowska 2020 submitted to Jornal of Cognition. <br> Please refer to that paper for context and method. We intend to upload the raw data shortly, which until then will be available upon request. The file includes Correct mean reaction times.
DOI: 10.5281/zenodo.4173467
title: Social cues of a robot and cognitive control

description: The data presented here are reported in Ciardo & Wykowska 2020 submitted to Jornal of Cognition. <br> Please refer to that paper for context and method. We intend to upload the raw data shortly, which until then will be available upon request. The file includes Correct mean reaction times.
DOI: 10.5281/zenodo.4173635
title: The critical role of MetR/MetB/MetC/MetX in cysteine and methionine metabolism, fungal development and virulence of Alternaria alternata

description: Methionine is a unique sulfur-containing amino acid, which plays an important role in biological protein synthesis and various cellular processes. Here, we characterize the biological functions of <em>AaMetB</em>, <em>AaMetC</em>, and <em>AaMetX</em> in the tangerine pathotype of <em>Alternaria alternata</em>. Morphological analysis showed that mutants lacking <em>AaMetB</em>, <em>AaMetC</em>, or <em>AaMetX</em> resulted in less aerial hypha and fewer conidia in artificial media. The virulence assays revealed that <em>AaMetB</em>, <em>AaMetC</em>, and <em>AaMetX </em>are required for full virulence. The defects of <em></em><em>MetB</em>, <em></em><em>MetC</em>, and <em></em><em>MetX</em> in vegetative growth, conidiation and virulence can be restored by exogenous methionine and homocysteine, indicating that <em>AaMetB</em>, <em>AaMetC</em>, and <em>AaMetX </em>are required for methionine biosynthesis. The defects of <em></em><em>MetR </em>in vegetative growth and virulence can be restored by exogenous cysteine, indicating that <em>AaMetR</em> is essential for cysteine biosynthesis. The oxidant sensitivity assay showed that only <em></em><em>MetR</em> is sensitivity to H<sub>2</sub>O<sub>2</sub> and many ROS-generating compounds, which indicates that <em>AaMetR</em> is essential for oxidative tolerance. Interestingly, indoor bioassays of these mutants on fungicides showed that only the <em></em><em>MetR </em>mutants<em> </em>are susceptive to chlorothalonil, which can interact with the cysteine of glyceraldehyde-3-phosphate dehydrogenase. Comparative transcriptome analysis showed that the inactivation of <em>MetB</em>, <em>MetC</em>, <em>MetX</em>, or <em>MetR</em> significantly affected the expression of many genes related to methionine metabolism. Moreover, the inactivation of Aa<em>MetR</em> significantly affected the expression of many genes related to glutathione metabolism, which is required for ROS tolerance. In conclusion, our study provides genetic evidence to define the critical roles of <em>AaMetB</em>, <em>AaMetC</em>, <em>AaMetX</em>, and <em>AaMetR</em> in the metabolism of cysteine and methionine, fungal development and virulence of <em>Alternaria alternata.</em>
DOI: 10.5281/zenodo.4173634
title: The critical role of MetR/MetB/MetC/MetX in cysteine and methionine metabolism, fungal development and virulence of Alternaria alternata

description: Methionine is a unique sulfur-containing amino acid, which plays an important role in biological protein synthesis and various cellular processes. Here, we characterize the biological functions of <em>AaMetB</em>, <em>AaMetC</em>, and <em>AaMetX</em> in the tangerine pathotype of <em>Alternaria alternata</em>. Morphological analysis showed that mutants lacking <em>AaMetB</em>, <em>AaMetC</em>, or <em>AaMetX</em> resulted in less aerial hypha and fewer conidia in artificial media. The virulence assays revealed that <em>AaMetB</em>, <em>AaMetC</em>, and <em>AaMetX </em>are required for full virulence. The defects of <em></em><em>MetB</em>, <em></em><em>MetC</em>, and <em></em><em>MetX</em> in vegetative growth, conidiation and virulence can be restored by exogenous methionine and homocysteine, indicating that <em>AaMetB</em>, <em>AaMetC</em>, and <em>AaMetX </em>are required for methionine biosynthesis. The defects of <em></em><em>MetR </em>in vegetative growth and virulence can be restored by exogenous cysteine, indicating that <em>AaMetR</em> is essential for cysteine biosynthesis. The oxidant sensitivity assay showed that only <em></em><em>MetR</em> is sensitivity to H<sub>2</sub>O<sub>2</sub> and many ROS-generating compounds, which indicates that <em>AaMetR</em> is essential for oxidative tolerance. Interestingly, indoor bioassays of these mutants on fungicides showed that only the <em></em><em>MetR </em>mutants<em> </em>are susceptive to chlorothalonil, which can interact with the cysteine of glyceraldehyde-3-phosphate dehydrogenase. Comparative transcriptome analysis showed that the inactivation of <em>MetB</em>, <em>MetC</em>, <em>MetX</em>, or <em>MetR</em> significantly affected the expression of many genes related to methionine metabolism. Moreover, the inactivation of Aa<em>MetR</em> significantly affected the expression of many genes related to glutathione metabolism, which is required for ROS tolerance. In conclusion, our study provides genetic evidence to define the critical roles of <em>AaMetB</em>, <em>AaMetC</em>, <em>AaMetX</em>, and <em>AaMetR</em> in the metabolism of cysteine and methionine, fungal development and virulence of <em>Alternaria alternata.</em>
DOI: 10.6084/m9.figshare.13173629
title: R0198_20171201a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.21227/t2c7-ym90
title: TestModel 1

description: test model using sklearn KNNImpute
DOI: 10.6084/m9.figshare.13174442
title: R0198_20171203a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13173629.v1
title: R0198_20171201a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13174445
title: R0198_20171204a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13174445.v1
title: R0198_20171204a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13168370
title: 2020 01 03 Field Notes

description: Field notes including image and/or video records.<br>NOTE: Owing to size restrictions on figshare the final segment of the GoPro recording will be archived in the VID00028 Analysis item.
DOI: 10.6084/m9.figshare.13168370.v2
title: 2020 01 03 Field Notes

description: Field notes including image and/or video records.<br>NOTE: Owing to size restrictions on figshare the final segment of the GoPro recording will be archived in the VID00028 Analysis item.
DOI: 10.6084/m9.figshare.13168370.v1
title: 2020 01 03 Field Notes

description: Field notes including image and/or video records.<br>NOTE: Owing to size restrictions on figshare the final segment of the GoPro recording will be archived in the VID00028 Analysis item.
DOI: 10.6084/m9.figshare.13174448
title: R0198_20171205a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13174448.v1
title: R0198_20171205a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13174451
title: R0198_20171206a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13174451.v1
title: R0198_20171206a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13174442.v1
title: R0198_20171203a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.13048337
title: BrC Observation and Model for United States

description: This is a newly developed dataset from the Interagency Monitoring of PROtected Visual Environments (IMPROVE) observation network, combined with a 3-D chemical transport model (CTM), to evaluate the spatial and temporal variability of brown carbon (BrC) in the United States.
DOI: 10.6084/m9.figshare.13174454
title: R0198_20171207a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.25345/c5d779
title: MassIVE MSV000086395 - In-depth site-specific analysis of N-glycoproteome in human cerebrospinal fluid (CSF) and glycosylation landscape changes in Alzheimer's disease (AD)
title: In the present study, a comparative in-depth N-glycoproteomics analysis was conducted for CSF samples from healthy control and AD patients, which yielded a comparable N-glycoproteome coverage but a distinct expression pattern constitutes of different categories of glycoforms, particularly decreased fucosylation.
DOI: 10.6084/m9.figshare.13174454.v1
title: R0198_20171207a_videos

description: Rat 0198, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.7910/dvn/pnssxg
title: Simulation Datasets for 'Noncompensatory MIRT for Passage-Based Tests'

description: Simulation datasets used for 'Noncompensatory MIRT for Passage-Based Tests'. Datasets are generated either under the bifactor model or passage-based noncompensatory model (PB-NM). Two simulation conditions are considered: the number of respondents (1000 and 2500) and the number of items per passage (4, 6, and 9). Ten datasets are generated for each condition.
DOI: 10.6084/m9.figshare.13140422.v1
title: Data files

description: "GMP_allsamples_mapfile_forR.txt" = Metadata<br>"seqtab_wTax_mctoolsr.txt" = ESV table<br>"tax_final.txt" = Sequences and taxonomy of ESVs<br>"euks_ESVs_blastn_wTax_top10_reassgn.txt" = Reassigned taxonomy of eukaryotic ESVs by blastn search<br>"GallingInsectsMicrobiome_Rcode_24Oct2020.R" = R code for all analyses of the ESV table, excluding stats on alpha diversity (see next)<br><br>"Alpha_diversity_analysis.docx" = Word doc of R markdown file - statistical analysis of alpha diversity<br>"demultiplexed_sequences_R1.zip" = demultiplexed reads (read 1); not processed/filtered<br>"demultiplexed_sequences_R2.zip" = demultiplexed reads (read 2); not processed/filtered
DOI: 10.6084/m9.figshare.13140422
title: Data files

description: "GMP_allsamples_mapfile_forR.txt" = Metadata<br>"seqtab_wTax_mctoolsr.txt" = ESV table<br>"tax_final.txt" = Sequences and taxonomy of ESVs<br>"euks_ESVs_blastn_wTax_top10_reassgn.txt" = Reassigned taxonomy of eukaryotic ESVs by blastn search<br>"GallingInsectsMicrobiome_Rcode_24Oct2020.R" = R code for all analyses of the ESV table, excluding stats on alpha diversity (see next)<br><br>"Alpha_diversity_analysis.docx" = Word doc of R markdown file - statistical analysis of alpha diversity<br>"demultiplexed_sequences_R1.zip" = demultiplexed reads (read 1); not processed/filtered<br>"demultiplexed_sequences_R2.zip" = demultiplexed reads (read 2); not processed/filtered
DOI: 10.25919/5f9f2fe1cc45f
title: Parkes observations for project P1054 semester 2020APRS_11

description: With this proposal we ask time to begin a follow-up campaign of potential new discoveries from the TRAPUM (TRAnsients and PUlsars with Meerkat) survey, which is due to start in January 2020. About 10 new pulsars are expected to be found during the first semester of operations, in targeted pointings towards supernova remnants, pulsar wind nebulae and Fermi unidentified point sources. Timing observations have an essential role in exploiting the full potential of any pulsar discovery, allowing the precise measurement of rotational, astrometric and orbital parameters which, in turn, give us powerful tools to improve our understanding of the physics in extreme environments as well as of the population of neutron stars as a whole. The UWL receiver of the Parkes telescope is a sensitive, versatile instrument that will allow us to successfully time the bright-end of TRAPUM discoveries. We here request (up to) 2-hr long monthly observations of any new TRAPUM pulsar with a flux density at 1.4 GHz above $\sim 60 \mu$Jy.
DOI: 10.25919/5f9f2fe1cc482
title: Parkes observations for project P1067 semester 2020APRS_05

description: The Parkes Ultra-wide-bandwidth receiver enables, for the first time with the Parkes telescope, a commensal high time and high frequency resolution survey. We will observe Baade's window in which we are guaranteed detections of pulsars and spectral lines. Our science drivers are diverse and range from understanding scattering, to detecting new pulsars, to searching for galaxies in the zone of avoidance, probing the globular cluster at the centre of the window and studying OH circumstellar masers and CO-dark molecular gas. The observing strategy and processing software developed for this survey will be applicable to all future Parkes surveys with the wide-band receiver or cyrogenically-cooled phased array feed.