cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8316827.v1
title: Species trees of 571 Rhizobiaceae genomes, with a focus on 41 Pseudorhizobium and Neorhizobium, based on core genome gene concatenates

description: Genomic dataset and gene family classificationWe assembled a complete bacterial genome dataset covering all known representative of the subgroup in the alphaproteobacterial families Rhizobiaceae and (sister group) Aurantimonadaceae. This dataset comprises all 564 genomes available from the NCBI RefSeq Assembly database on the 23 Apr 2018, filtering anomalous genomes and those with a contig N50 &lt; 98kb using query: ‘(txid82115[Organism:exp] OR txid255475[Organism:exp]) AND ("latest refseq"[filter] NOT anomalous[filter]) AND ("98000"[ContigN50] : "20000000"[ContigN50])’. From this dataset we removed assembly GCF_002000045.1 (R. flavum YW14) for which we had a newer, higher quality assembly. To these we added the new genome sequences from the eight strains mentioned above, for a total of 571 genomes (dataset ‘571Rhizob’).<br>Reference species treesFrom the 571Rhizob genome dataset, we define the pseudo-core genome as genes occurring only in a single copy and present in at least 561 out of the 571 genomes (98%). The resulting pseudo-core genome gene set (thereafter referred as pCG<sub>571</sub>) includes 155 loci, which protein alignments were concatenated. This concatenated protein alignment was used to compute a reference species tree (S<sub>ML571</sub>) with RAxML (Stamatakis 2014) under the model PROTCATLGX; branch supports were estimated by generating 200 rapid bootstraps under the same parameters. From the S<sub>ML571</sub> tree, we identified the well-supported clade grouping 41 genomes including all representative of Neorhizobium spp. and Pseudorhizobium spp. and our new isolates (dataset ‘41NeoPseudo’). To gain further phylogenetic resolution in this clade of interest, we restricted the pCG<sub>571</sub> concatenated alignment to the 41 genomes of this smaller genomic dataset, which we used as input to the Phylobayes program for a more accurate (but computationally more expensive) Bayesian phylogenetic inference under the CAT-GTR+G4 model (Lartillot et al. 2007). This provided us with a robust non-ultrametric tree for the 41 genomes (S<sub>BA41</sub>). We finally used this S<sub>BA41</sub> tree as a fixed input topology for Phylobayes to infer an ultrametric tree (unitless ‘time’ tree) under the CIR clock model (Lepage et al. 2007), further referred to as T<sub>BA41</sub>.
DOI: 10.6084/m9.figshare.8316767
title: Scanning FCS images

description: All Scanning FCS images used for parameter estimation in the model
DOI: 10.6084/m9.figshare.8316770.v1
title: API 20 NE biochemical profiling of Pseudorhizobium strains

description: The commercial biochemical identification system for Gram-negative bacteria ‘Api 20 NE’ (BioMérieux) was used for an initial analysis of the biochemical capacities.
DOI: 10.6084/m9.figshare.8316767.v1
title: Scanning FCS images

description: All Scanning FCS images used for parameter estimation in the model
DOI: 10.6084/m9.figshare.8316746
title: Biolog Gen III metabolism profiling of Pseudorhizobium strains

description: High-throughput phenotyping was conducted using the GenIII microplates (Biolog, Inc., Hayward, California) for testing for growth with 94 single carbon or nitrogen nutrient sources or with inhibitors (antibiotics, salt, etc.). The GenIII phenotype data were analysed using the 'opm' R package (Vaas et al. 2013).
DOI: 10.6084/m9.figshare.8316701
title: Supplemental_Table13.csv

description: DNA methylation data was used from:<br> Li, Q. et al. Examining the causes and consequences of context-specific differential DNA methylation in maize. Plant Physiology 168, 1262–1274 (2015). http://doi.org/10.1104/pp.15.00052<br>This table was generated from methylation data summarized over 100 bp, non-overlapping tiles across the maize genome. Tissue is from 3rd leaf for five different maize inbred lines. This table includes summarized methylation quantification reported as the proportion of methylated cytosines in each feature (# methylated Cs / # total Cs) in all 3 contexts separately as well as feature coverage. The data is quantified over 5 equally spaced bins across the gene model and within each bin, 3 different genomic features are quantified (whole gene, exon and intron). Each row is a gene and each column is labeled as “Inbred Line . (Methylation Context / Coverage) . Genomic Feature . Bin Number”.
DOI: 10.6084/m9.figshare.8316701.v1
title: Supplemental_Table13.csv

description: DNA methylation data was used from:<br> Li, Q. et al. Examining the causes and consequences of context-specific differential DNA methylation in maize. Plant Physiology 168, 1262–1274 (2015). http://doi.org/10.1104/pp.15.00052<br>This table was generated from methylation data summarized over 100 bp, non-overlapping tiles across the maize genome. Tissue is from 3rd leaf for five different maize inbred lines. This table includes summarized methylation quantification reported as the proportion of methylated cytosines in each feature (# methylated Cs / # total Cs) in all 3 contexts separately as well as feature coverage. The data is quantified over 5 equally spaced bins across the gene model and within each bin, 3 different genomic features are quantified (whole gene, exon and intron). Each row is a gene and each column is labeled as “Inbred Line . (Methylation Context / Coverage) . Genomic Feature . Bin Number”.
DOI: 10.6084/m9.figshare.8316515
title: Wainwright et al 2019 OECO

description: Environmental, survival, biomass, inflorescence response data.
DOI: 10.6084/m9.figshare.8316512
title: Supplementary Table 1

description: Differentially regulated bacteria after 4 weeks of supplementation with UCC118 by order and taxonomic group.
DOI: 10.6084/m9.figshare.8316515.v1
title: Wainwright et al 2019 OECO

description: Environmental, survival, biomass, inflorescence response data.
DOI: 10.6084/m9.figshare.8316512.v1
title: Supplementary Table 1

description: Differentially regulated bacteria after 4 weeks of supplementation with UCC118 by order and taxonomic group.
DOI: 10.6084/m9.figshare.8316383
title: Fatty acid profiling of Pseudorhizobium strains

description: Fatty acid profilesFatty acid methyl esters were obtained as previously described (Kämpfer & Kroppenstedt 1996) and separated by using a gas chromatograph (model 6890 N; Agilent Technologies). Peaks were automatically computed and assigned using the Microbial Identification software package (MIDI), TSBA40 method, Sherlock version 6.1. The dendrogram was created with Sherlock Version 6.1. <br>Polar lipids and respiratory lipoquinonesPolar lipids and respiratory lipoquinones were extracted from 100 mg freeze-dried cells and separated by two dimensional silica gel thin layer chromatography by the identification service of the DSMZ as previously described (Hahnke et al. 2012).
DOI: 10.6084/m9.figshare.8316383.v1
title: Fatty acid profiling of Pseudorhizobium strains

description: Fatty acid profilesFatty acid methyl esters were obtained as previously described (Kämpfer & Kroppenstedt 1996) and separated by using a gas chromatograph (model 6890 N; Agilent Technologies). Peaks were automatically computed and assigned using the Microbial Identification software package (MIDI), TSBA40 method, Sherlock version 6.1. The dendrogram was created with Sherlock Version 6.1. <br>Polar lipids and respiratory lipoquinonesPolar lipids and respiratory lipoquinones were extracted from 100 mg freeze-dried cells and separated by two dimensional silica gel thin layer chromatography by the identification service of the DSMZ as previously described (Hahnke et al. 2012).
DOI: 10.6084/m9.figshare.8315417
title: Data from Suraci et al. 2019. Ecology Letters

description: All datasets used in:<br>Suraci et al. 2019. Fear of humans as apex predators has landscape-scale impacts from mountain lions to mice. Ecology Letters. <br>See included README.txt file for full details.
DOI: 10.6084/m9.figshare.8314226
title: TCX2:TCX2-YFP tracking images

description: Images used to track TCX2:TCX2-YFP expression in the stem cells
DOI: 10.6084/m9.figshare.8314217
title: CYCB1;1:CYCB1;1-GFP tracking images

description: Images used for tracking CYCB1;1:CYCB1;1-GFP expression in WT and tcx2 mutant roots
DOI: 10.6084/m9.figshare.8314226.v1
title: TCX2:TCX2-YFP tracking images

description: Images used to track TCX2:TCX2-YFP expression in the stem cells
DOI: 10.6084/m9.figshare.8314154
title: tcx2 mutant crosses

description: Images of all crosses performed on the tcx2 mutant
DOI: 10.6084/m9.figshare.8314151
title: Phenotyping

description: All images used for phenotyping
DOI: 10.6084/m9.figshare.8314154.v1
title: tcx2 mutant crosses

description: Images of all crosses performed on the tcx2 mutant
DOI: 10.6084/m9.figshare.8314151.v1
title: Phenotyping

description: All images used for phenotyping
DOI: 10.6084/m9.figshare.8314004
title: Data from The loud scratch: a newly identified gesture of Sumatran orangutan mothers in the wild

description: The communicative function of primates' self-directed behaviours like scratching has gained increasing attention in recent years, but their intentional use is still debated. Here, we addressed this issue by exploring the communicative function of ‘loud scratches’ in wild Sumatran orangutans. Building on previous studies in chimpanzees, we examined the prediction that audio-visual loud scratches are used communicatively in mother–infant travel coordination. Specifically, we examined whether individual, social and scratch features affected the use of pre-move scratches, markers of intentional signal use and approach responses. We analysed a total of 1457 scratching bouts, produced by 17 individuals (including four mothers and their dependent offspring) observed during 305 h of focal follows. Overall, we found that scratching bouts preceded departure mainly when these were produced by mothers and showed features of exaggeration. If the scratching individual was a mother, associates were more likely to be visually attentive during pre-move scratches than in other contexts. Approach or follow responses to scratches by individuals in association were predicted by context, the relationship with the scratcher (i.e. offspring) and the associate's attentional state. We conclude that orangutan mothers use loud scratches as communicative strategies to coordinate joint travel with their infants.
DOI: 10.6084/m9.figshare.8314004.v1
title: Data from The loud scratch: a newly identified gesture of Sumatran orangutan mothers in the wild

description: The communicative function of primates' self-directed behaviours like scratching has gained increasing attention in recent years, but their intentional use is still debated. Here, we addressed this issue by exploring the communicative function of ‘loud scratches’ in wild Sumatran orangutans. Building on previous studies in chimpanzees, we examined the prediction that audio-visual loud scratches are used communicatively in mother–infant travel coordination. Specifically, we examined whether individual, social and scratch features affected the use of pre-move scratches, markers of intentional signal use and approach responses. We analysed a total of 1457 scratching bouts, produced by 17 individuals (including four mothers and their dependent offspring) observed during 305 h of focal follows. Overall, we found that scratching bouts preceded departure mainly when these were produced by mothers and showed features of exaggeration. If the scratching individual was a mother, associates were more likely to be visually attentive during pre-move scratches than in other contexts. Approach or follow responses to scratches by individuals in association were predicted by context, the relationship with the scratcher (i.e. offspring) and the associate's attentional state. We conclude that orangutan mothers use loud scratches as communicative strategies to coordinate joint travel with their infants.
DOI: 10.6084/m9.figshare.8313869
title: The gambler’s fallacy in problem and non-problem gamblers

description: dataset of the study "The gambler’s fallacy in problem and non-problem gamblers" - Matarazzo et al.<br>
DOI: 10.6084/m9.figshare.8313794
title: Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata

description: The tangerine pathotype of the ascomycete fungus Alternaria alternata is the causal agent of citrus brown spot, which can result in significant losses of both yield and marketability for tangerines worldwide. A conditionally dispensable chromosome (CDC), which harbors the host-selective ACT toxin gene cluster, is required for tangerine pathogenicity of A. alternata. To understand the genetic makeup and evolution of the tangerine pathotype CDC, we isolated and sequenced the CDCs of the A. alternata Z7 strain and analyzed the function and evolution of their genes.
DOI: 10.6084/m9.figshare.8313782
title: Survey on Understanding Experiments and Research Practices for Reproducibility: Material and Results

description: This dataset contains the results from the survey 'Understanding Experiments and Research Practices for Reproducibility' conducted in the context of DFG CRC/TRR ReceptorLight. This survey was conducted as part of the dissertation of Sheeba Samuel. The purpose of this study was to gain a better understanding of what is needed to achieve reproducibility of experiments in science. The online survey consisted of 26 questions grouped in 6 sections. The six sections are: (1) Privacy policy, (2) Research context of the participant, (3) Reproducibility, (4) Measures to ensure reproducibility, (5) Important factors to understand a scientific experiment to enable reproducibility and (6) Experiment Workflow/Research Practices. The survey was completely anonymous. The survey was made available online on 24th January 2019. Out of 150 respondents, 101 responses were considered eligible for the analysis of the results. This dataset contains the survey questionnaire with the results. The results contain the raw and processed data along with the graphs for each question.<br>
DOI: 10.6084/m9.figshare.8313782.v1
title: Survey on Understanding Experiments and Research Practices for Reproducibility: Material and Results

description: This dataset contains the results from the survey 'Understanding Experiments and Research Practices for Reproducibility' conducted in the context of DFG CRC/TRR ReceptorLight. This survey was conducted as part of the dissertation of Sheeba Samuel. The purpose of this study was to gain a better understanding of what is needed to achieve reproducibility of experiments in science. The online survey consisted of 26 questions grouped in 6 sections. The six sections are: (1) Privacy policy, (2) Research context of the participant, (3) Reproducibility, (4) Measures to ensure reproducibility, (5) Important factors to understand a scientific experiment to enable reproducibility and (6) Experiment Workflow/Research Practices. The survey was completely anonymous. The survey was made available online on 24th January 2019. Out of 150 respondents, 101 responses were considered eligible for the analysis of the results. This dataset contains the survey questionnaire with the results. The results contain the raw and processed data along with the graphs for each question.<br>
DOI: 10.6084/m9.figshare.8313656
title: Naegleria fowleri ATCC 30894 Braker1 predicted Proteins

description: BRAKER1 predicted proteins of Naegleria fowleri ATCC 30894<br>
DOI: 10.6084/m9.figshare.8313641
title: Data for "Age-dependent plasticity in reproductive investment, regeneration capacity and survival in a partially clonal animal"

description: This is the dataset containing asexual and sexual reproduction measurements, head regeneration rate, survival and cell composition (reproductive and stem cell number) data for the manuscript entitled “Age-dependent plasticity in reproductive investment, regeneration capacity and survival in a partially clonal animal” by Sebestyén, Miklós, Iván & Tökölyi (2019)<br>
DOI: 10.6084/m9.figshare.8313641.v1
title: Data for "Age-dependent plasticity in reproductive investment, regeneration capacity and survival in a partially clonal animal"

description: This is the dataset containing asexual and sexual reproduction measurements, head regeneration rate, survival and cell composition (reproductive and stem cell number) data for the manuscript entitled “Age-dependent plasticity in reproductive investment, regeneration capacity and survival in a partially clonal animal” by Sebestyén, Miklós, Iván & Tökölyi (2019)<br>
DOI: 10.6084/m9.figshare.8313620
title: Passengers and Drivers reading while driving

description: This dataset is a naturalistic data collection that used the GPS, accelerometer, gyroscope and magnetometer sensors of a smartphone to collect this data while a driver or a passenger reading text on the phone. All data were collected while the car was moving, ie the stationary data was discarded. The data collection began in June 2018 and ended in December 2018. During this period, the 18 participants made 58 trips to collect data. All participants collected data assuming the role of driver and passenger. During our data collection, each participant created at least two files per category. In total, 58 files were created, 36 files containing sensory data instances collected while drivers read text messages and 22 files containing sensory data instances collected while passengers read text messages. The experiment participants had the autonomy to decide the appropriate time to read a text message. The only prerequisites established were: * To read the text message only when the car is in motion.* To read the text message by holding the smartphone with one or both hands. The number of messages collected on a trip was different among participants. Distance traveled and traffic conditions were two important factors that influenced the number of data collected on each trip. The amount of travel was also different among participants. In this case, because it was a voluntary data collection, a participant had the autonomy to decide how many trips he would like to make. Each dataset file represents a trip made by a volunteer. The BEGIN and END tags delimit the beginning and end of each data collection that corresponds to the reading of a message. TimestampGPS_latGPS_longGPS_altacc_xacc_yacc_zgyro_xgyro_ygyro_zmag_xmag_ymag_z
DOI: 10.6084/m9.figshare.8313656.v1
title: N. fowleri predicted proteins annotated

description: BRAKER1 predicted proteins of Naegleria fowleri ATCC 30894<br>
DOI: 10.6084/m9.figshare.8313620.v1
title: Passengers and Drivers reading while driving

description: This dataset is a naturalistic data collection that used the GPS, accelerometer, gyroscope and magnetometer sensors of a smartphone to collect this data while a driver or a passenger reading text on the phone. All data were collected while the car was moving, ie the stationary data was discarded. The data collection began in June 2018 and ended in December 2018. During this period, the 18 participants made 58 trips to collect data. All participants collected data assuming the role of driver and passenger. During our data collection, each participant created at least two files per category. In total, 58 files were created, 36 files containing sensory data instances collected while drivers read text messages and 22 files containing sensory data instances collected while passengers read text messages. The experiment participants had the autonomy to decide the appropriate time to read a text message. The only prerequisites established were: * To read the text message only when the car is in motion.* To read the text message by holding the smartphone with one or both hands. The number of messages collected on a trip was different among participants. Distance traveled and traffic conditions were two important factors that influenced the number of data collected on each trip. The amount of travel was also different among participants. In this case, because it was a voluntary data collection, a participant had the autonomy to decide how many trips he would like to make. Each dataset file represents a trip made by a volunteer. The BEGIN and END tags delimit the beginning and end of each data collection that corresponds to the reading of a message. TimestampGPS_latGPS_longGPS_altacc_xacc_yacc_zgyro_xgyro_ygyro_zmag_xmag_ymag_z
DOI: 10.6084/m9.figshare.8313656.v2
title: Naegleria fowleri ATCC 30894 Braker1 predicted Proteins

description: BRAKER1 predicted proteins of Naegleria fowleri ATCC 30894<br>
DOI: 10.6084/m9.figshare.8313605
title: ACASS Motion Capture Data (N = 396)

description: This database accompanies the rticle "Introducing ACASS: An Annotated Character Animation Stimulus Set for Controlled (e)Motion Perception Studies" (doi.org/10.3389/frobt.2019.00094).<br>It contains 396 FBX-files and one text-file (TXT-file) explaining the structure of the filenames.<br><br>Please refer to the original article for further information.<br>
DOI: 10.6084/m9.figshare.8313569
title: raw-data.zip

description: The files names such as:<br><br>expXX_HH are the raw data from isolated trials, the numbers XX are the number of the experience and HH is the humidity of the shelter being recorded (40 = Dry shelter and 90 = Wet shelter).<br><br>
DOI: 10.6084/m9.figshare.8313554
title: Geographic, hydrological, and climatic significance of rock glaciers in the Great Basin, USA

description: We present the first comprehensive inventory and analysis of rock glaciers in the hydrographic Great Basin (GB), United States, documenting 842 features (mean 9.9 ha; range 0.1–201 ha) across thirty-two mountain ranges. These encompassed 8° latitude (from 36.5°N to 44.3°N) and 11° longitude (from −110.7°W to −121.4°W), and composed 83.1 km<sup>2</sup>, or 1.1 percent, of the cumulative area above the lowest rock glacier elevation. Forty-five percent of the features were mapped as intact (containing ice) and occurred across sixteen mountain ranges. Rock glaciers conservatively contained cumulative water volume of 0.8924 km<sup>3</sup>. We also mapped 237 persistent ice fields from thirteen GB ranges. Ice-field water equivalent was 0.0653 km<sup>3</sup>; rock glaciers contributed 93 percent of the total water volume (rock glacier:icefield ratio, 14:1). Rock glaciers occurred on northerly aspects at high elevations (mean, 3,196 m) and had a mean annual air temperature of 1.7°C (range, 1.3–3.3°C). Contributions of water from rock-glacier springs and groundwater have not been included in GB hydrologic assessments, nor have rock glaciers been evaluated for their roles in supporting cold-adapted aquatic fauna and promoting vegetation communities and habitat for alpine terrestrial species. Rock glaciers provide hydrologic and ecologic refugia previously unrecognized in the GB with respect to warming future climates.