cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12586214
title: Additional file 3 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 3: Table S2. Overrepresented function of predicted cancer-specific vulnerabilities in clinical samples.
DOI: 10.6084/m9.figshare.12586214.v1
title: Additional file 3 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 3: Table S2. Overrepresented function of predicted cancer-specific vulnerabilities in clinical samples.
DOI: 10.6084/m9.figshare.12586217
title: Additional file 4 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 4: Table S3. Common cancer-specific vulnerabilities.
DOI: 10.6084/m9.figshare.12586217.v1
title: Additional file 4 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 4: Table S3. Common cancer-specific vulnerabilities.
DOI: 10.6084/m9.figshare.12586220
title: Additional file 5 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 5: Table S4. Functional enrichment of overexpressed genes in RAN-dependent samples (CRISPR+RNAi).
DOI: 10.6084/m9.figshare.12586220.v1
title: Additional file 5 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 5: Table S4. Functional enrichment of overexpressed genes in RAN-dependent samples (CRISPR+RNAi).
DOI: 10.6084/m9.figshare.12586226
title: Additional file 6 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 6: Table S5. Bayesian network in breast cancer.
DOI: 10.6084/m9.figshare.12586226.v1
title: Additional file 6 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 6: Table S5. Bayesian network in breast cancer.
DOI: 10.6084/m9.figshare.12586211
title: Additional file 2 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 2: Table S1. Calibration parameters for deep learning.
DOI: 10.6084/m9.figshare.12586229
title: Additional file 7 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 7: Table S6. ARACNe network in breast cancer.
DOI: 10.6084/m9.figshare.12586229.v1
title: Additional file 7 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 7: Table S6. ARACNe network in breast cancer.
DOI: 10.6084/m9.figshare.12586232
title: Additional file 8 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 8: Table S7. The sequences of the sgRNAs.
DOI: 10.6084/m9.figshare.12586232.v1
title: Additional file 8 of Computational inference of cancer-specific vulnerabilities in clinical samples

description: Additional file 8: Table S7. The sequences of the sgRNAs.
DOI: 10.25625/v7htb8/klvwdv
title: final-model.pt

description: :unav
DOI: 10.25625/v7htb8/pqag00
title: final-model.pt

description: :unav
DOI: 10.6084/m9.figshare.17304840
title: Additional file 2 of Comparative transcriptome and DNA methylation analysis in temperature-sensitive genic male sterile wheat BS366

description: Additional file 2.
DOI: 10.6084/m9.figshare.17304840.v1
title: Additional file 2 of Comparative transcriptome and DNA methylation analysis in temperature-sensitive genic male sterile wheat BS366

description: Additional file 2.
DOI: 10.6084/m9.figshare.12586252
title: Additional file 6 of Robust principal component analysis for accurate outlier sample detection in RNA-Seq data

description: Additional file 6. Supplemental Table 6: List of genes validated by qRT-PCR with primer sequences, results and DEG status in each analysis strategy.
DOI: 10.6084/m9.figshare.12586252.v1
title: Additional file 6 of Robust principal component analysis for accurate outlier sample detection in RNA-Seq data

description: Additional file 6. Supplemental Table 6: List of genes validated by qRT-PCR with primer sequences, results and DEG status in each analysis strategy.
DOI: 10.4121/1f174b7b-02f9-4ab1-a5ff-36a7868a3b78
title: Pupil diameter calibration for the EyeLink 1000 Plus

description: contains the results of a calibration of the EyeLink pupil size measurements with respect to printed black circles.<br>
DOI: 10.4121/1f174b7b-02f9-4ab1-a5ff-36a7868a3b78.v1
title: Pupil diameter calibration for the EyeLink 1000 Plus

description: contains the results of a calibration of the EyeLink pupil size measurements with respect to printed black circles.<br>
DOI: 10.6084/m9.figshare.12586298.v1
title: Additional file 8 of Exosomal circSHKBP1 promotes gastric cancer progression via regulating the miR-582-3p/HUR/VEGF axis and suppressing HSP90 degradation

description: Additional file 8.
DOI: 10.6084/m9.figshare.12586298
title: Additional file 8 of Exosomal circSHKBP1 promotes gastric cancer progression via regulating the miR-582-3p/HUR/VEGF axis and suppressing HSP90 degradation

description: Additional file 8.
DOI: 10.6084/m9.figshare.12062010.v1
title: Additional file 1 of Dafachronic acid and temperature regulate canonical dauer pathways during Nippostrongylus brasiliensis infectious larvae activation

description: Additional file 1: Data S1.Nippostrongylus brasiliensis dauer homolog transcript coding sequences.
DOI: 10.6084/m9.figshare.12062016
title: Additional file 2 of Dafachronic acid and temperature regulate canonical dauer pathways during Nippostrongylus brasiliensis infectious larvae activation

description: Additional file 2: Data S2.Nippostrongylus brasiliensis dauer homolog genome annotations.
DOI: 10.6084/m9.figshare.25138532
title: Data files for Gemal <i>et al.</i> (2024)

description: Data used for the journal article by Gemal <i>et al.</i> (2024), "Reindeer grazing and soil wetness interact to drive tundra plant community structure in northern Sweden". 'Metadata.xlsx' describes the columns in each dataframe. 'site_conditions.csv' and 'plots_tidy.csv' contain the data collected in the field, and reindeer grazing durations for each plot. 'spID_list.csv' is the full species list of identified plants. 'NDVI_plots.csv', 'wetness.csv', 'soildepth.csv' and 'slope.csv' contain GIS-obtained data on the respective variables. <b>Abstract</b><br>Questions: The relative importance of abiotic versus biotic factors on structuring plant communities is debated, especially in the Arctic tundra where the harsh environment is limiting together with effects of grazing by reindeer. To understand the relative and interactive effect of abiotic(bottom-up) and biotic (top-down) factors on vegetation in the Swedish mountain tundra we ask: how do bottom-up factors and their interaction affect reindeer grazing activity and vegetation composition?<br>Location: Summer pastures of Gran reindeer herding district, in Vindelfjällen mountain tundra (northern Sweden).<br>Methods: We surveyed the composition of vascular plants, bryophytes and lichens across 34 sites (17 north-facing, 17 south-facing) along a grazing duration gradient based on data collected fromaccelerometers collared on reindeer. Data on the bottom-up factors slope, soil wetness, soil depth, primary productivity and the top-down factor grazing duration were extracted for each of our sampled plots (<i>n</i> = 102). The relative and interactive effect of all factors on vegetation composition and species richness was analysed using generalized linear models.<br>Results: Reindeer grazed for a longer time in drier than wetter sites, indicating an important interaction between grazing and soil wetness. Bottom-up factors prevailed as the dominant driver of local vegetation patterns, while grazing duration had weak effects on the vegetation. Wetter sites with longer grazing duration exhibited an increase in graminoid species, while drier sites with shorter grazing duration had more shrub and lichen species.<br>Conclusions: This study shows that soil wetness has a strong effect in structuring tundra plant communities, but also highly influences reindeer grazing intensity. Based on these results, we stress the importance to further investigate the interaction between grazing and soil wetness in order to foresee changes in the tundra vegetation; especially as plant communities might change under altered grazing regimes and future hydrological conditions as an effect of predicted climate change.
DOI: 10.6084/m9.figshare.25138532.v1
title: Data files for Gemal <i>et al.</i> (2024)

description: Data used for the journal article by Gemal <i>et al.</i> (2024), "Reindeer grazing and soil wetness interact to drive tundra plant community structure in northern Sweden". 'Metadata.xlsx' describes the columns in each dataframe. 'site_conditions.csv' and 'plots_tidy.csv' contain the data collected in the field, and reindeer grazing durations for each plot. 'spID_list.csv' is the full species list of identified plants. 'NDVI_plots.csv', 'wetness.csv', 'soildepth.csv' and 'slope.csv' contain GIS-obtained data on the respective variables. <b>Abstract</b><br>Questions: The relative importance of abiotic versus biotic factors on structuring plant communities is debated, especially in the Arctic tundra where the harsh environment is limiting together with effects of grazing by reindeer. To understand the relative and interactive effect of abiotic(bottom-up) and biotic (top-down) factors on vegetation in the Swedish mountain tundra we ask: how do bottom-up factors and their interaction affect reindeer grazing activity and vegetation composition?<br>Location: Summer pastures of Gran reindeer herding district, in Vindelfjällen mountain tundra (northern Sweden).<br>Methods: We surveyed the composition of vascular plants, bryophytes and lichens across 34 sites (17 north-facing, 17 south-facing) along a grazing duration gradient based on data collected fromaccelerometers collared on reindeer. Data on the bottom-up factors slope, soil wetness, soil depth, primary productivity and the top-down factor grazing duration were extracted for each of our sampled plots (<i>n</i> = 102). The relative and interactive effect of all factors on vegetation composition and species richness was analysed using generalized linear models.<br>Results: Reindeer grazed for a longer time in drier than wetter sites, indicating an important interaction between grazing and soil wetness. Bottom-up factors prevailed as the dominant driver of local vegetation patterns, while grazing duration had weak effects on the vegetation. Wetter sites with longer grazing duration exhibited an increase in graminoid species, while drier sites with shorter grazing duration had more shrub and lichen species.<br>Conclusions: This study shows that soil wetness has a strong effect in structuring tundra plant communities, but also highly influences reindeer grazing intensity. Based on these results, we stress the importance to further investigate the interaction between grazing and soil wetness in order to foresee changes in the tundra vegetation; especially as plant communities might change under altered grazing regimes and future hydrological conditions as an effect of predicted climate change.
DOI: 10.6084/m9.figshare.12062010
title: Additional file 1 of Dafachronic acid and temperature regulate canonical dauer pathways during Nippostrongylus brasiliensis infectious larvae activation

description: Additional file 1: Data S1.Nippostrongylus brasiliensis dauer homolog transcript coding sequences.
DOI: 10.6084/m9.figshare.12062016.v1
title: Additional file 2 of Dafachronic acid and temperature regulate canonical dauer pathways during Nippostrongylus brasiliensis infectious larvae activation

description: Additional file 2: Data S2.Nippostrongylus brasiliensis dauer homolog genome annotations.
DOI: 10.5061/dryad.kk0n9/1
title: Specimens intercepted in Great Britain by FERA

description: Overview of Leucinodes and Neoleucinodes specimens intercepted in Great Britain by the Food and Environment Research Agency and investigated in context of this publication
DOI: 10.5061/dryad.kk0n9/2
title: Overview of barcoded specimens

description: Overview of the specimens that have been DNA barcoded for this publication, including voucher numbers, sequence accession numbers and GenSeq nomenclature
DOI: 10.5061/dryad.r8b6f/1
title: Nucleotide alignment 16S rRNA

description: Nucleotide alignment of 16S rRNA sequences used for phylogenetic inferences within Megabalanus genus
DOI: 10.5061/dryad.r8b6f/2
title: Mazo COX1 Nucleotide alignment v0.1

description: Nucleotide aligment of mitochondrial COX1 (COI) sequences from Megabalanus azoricus.
DOI: 10.5061/dryad.r8b6f/3
title: Mazo CR Nucleotide alignment v1.1

description: Nucleotide Alignment of mitochondrial control region sequences from Megabalanus azoricus
DOI: 10.5061/dryad.r8b6f/4
title: Mazo CR Nucleotide alignment Haplogroup alfa

description: Nucleotide Alignment of mitochondrial control region sequences from individuals of Megabalanus azoricus belonging to the Haplogroup alfa.
DOI: 10.5061/dryad.r8b6f/5
title: Mazo CR Nucleotide alignment Haplogroup beta

description: Nucleotide Alignment of mitochondrial control region sequences from individuals of Megabalanus azoricus belonging to the Haplogroup beta.
DOI: 10.5061/dryad.r8b6f/6
title: Mazo CR Nucleotide alignment Haplogroup gamma

description: Nucleotide Alignment of mitochondrial control region sequences from individuals of Megabalanus azoricus belonging to the Haplogroup gamma.
DOI: 10.5061/dryad.c2v56/1
title: ancient DNA of Chinese donkeys

description: Samples were collected from four archaeological sites in China. 17 samples (L1- L9 and L11-L18) were from the Yanjialiang site in Inner Mongolia, which dates to 800-600 yr BP, during the Yuan dynasty. Sample L10 was from the Jinsitai cave site in Inner Mongolia, which dates to 18,000-20,000 yr BP. L21 was from the Lantianxinjie site in Shaanxi province. The date of the sample was determined to be about 568 (+/-50) yr BP using C14 dating.
DOI: 10.5061/dryad.gf067/1
title: Data for Figure 1

description: Description: columns in csv file contain data as follows: ecotype - lineage of Ostreococccus. Initial plasticity - plasticity as measured at t0. Response - fitness response as measured at t400. for calculation see main manuscript and SI. whichresp - indicates whether response was measured in ancestral or selection environment. sdini and sdresp are standard deviations for plasticity at t0 and fitness response at t400 respectively. Here, they are pooled for 3 biological and 3 technical replicates. clade - clade A,B,C,D based on ITS sequences. year and culturing for year of isolation and culturing method at the Roscoff culture collection respectively. wherefrom: sampling depth as factor. Pst0 and growtht0 - are photosynthesis and growth rates at t0 (foldchange PS and foldchangegrowth are foldchanges thereof). Figure legend: (a–d) Lineages with higher ancestral plasticity evolve more. Direct and correlated responses to selection plotted as a function of plasticity in oxygen evolution rates before evolution (ancestral plasticity). For all panels (a–d), different shapes represent mean values for each lineages ± 1 s.e. For each lineage n = 3. Dashed line indicates no response to selection. Panel (a) (selection in FH, assay at 1000 ppm CO2): ancestral plasticity in FH evolved lineages predicts up to 47% of the evolutionary response (F2,13 = 210.67, p &lt; 0.001). FH populations evolve slow growth in response to high pCO2. Panel (b) (selection in SH, assay at 1000 ppm CO2): with no selection for plasticity, a linear relationship using ancestral plasticity as the only explaining variable is not statistically significant (p = 0.63). Still, most lineages evolve lower growth rates (range from −0.31 to −0.08, mean −0.15 ± 0.12). Panel (c) (selection in FH, assay at 430 ppm CO2): ancestral plasticity is a significant nonlinear predictor of the correlated response to selection (F2,13 = 563.38, p &lt; 0.0001). Lineages from FH increased their growth rate at ambient pCO2 the most when their ancestral plasticity was high (increase in growth of 0.12–0.30, mean 0.19 ± 0.05). Panel (d) (selection in SH, assay at 430 ppm CO2): lineages selected in SH had a negative correlated response, and the relationship between ancestral plasticity and the correlated response to selection was significant (F2,13 = 22.28, p &lt; 0.01), though best described by a nonlinear fit (p-values and r2 reported on the panels are for linear regression).
DOI: 10.5061/dryad.gf067/2
title: Data for Figure 2

description: Columns in data file contain - evoplas (evolved plasticity), iniplas (initial plasticity), as well as - evoplassd and - iniplassd (standard deviations pooled here for three biological and three technical replicates). clade - A,B,C,D - clade as found by ITS sequences.
DOI: 10.5061/dryad.gf067/3
title: data for Figure 3

description: Data in columns is organised as follows: growthdif - foldchange difference of growth rate in selection environment compared to control environment. selected assay - selection environment and assay environment, e.g. 1000fluc 1000ppm lineages have been selected at fluctuating 1000ppm CO2 (FH in main manuscript) and were measured at 1000ppm CO2 (mean ppm in their selection environment). ecotype - lineage of Ostreococcus . forwhat - trait considered. Here, growth rate. hl - high or low pCO2. ls - long term or short term response.
DOI: 10.5061/dryad.742gv/1
title: simulation data and code

description: (1) The codes and relevant files for simulation studies can also be downloaded at     http://www4.stat.ncsu.edu/~tzeng/Data/Genetics2014.GxE.binary/   (2) Code for simulations:    • "simulation_code.sas" is the SAS code to perform the simulation, including data generation and analyses    • "glmm_em_sim.sas" is the SAS macro to calculate the estimates of the variance component and covariate coefficients    • "COSI_geno.zip" is the zipped version of "COSI_geno.csv", which contains the 10K haplotypes of 100 rare loci generated from COSI. From COSI_geno.csv, we randomly drew two haplotypes with replacement to form a subject’s genotype.(3) One replication of the simulated data (1500 subjects):     • "simu.dataset1.Y.E.txt" contains the trait variable and the environmental variable    • "simu.dataset1.geno.txt" contains the simulated genotypes
DOI: 10.5061/dryad.rv109/1
title: Marshall et al 2014 - EE - experiment agonism data

description: Please see ReadMe file.
DOI: 10.5061/dryad.rv109/2
title: Marshall et al 2014 - EE - natural agonism data

description: Please see ReadMe file.
DOI: 10.5061/dryad.rv109/3
title: Marshall et al 2014 - EE - experiment intake rate data

description: Please see ReadMe file.
DOI: 10.5061/dryad.rv109/4
title: Marshall et al 2014 - EE - natural intake rate data

description: Please see ReadMe file.
DOI: 10.5061/dryad.rv109/5
title: Marshall et al 2014 - EE - experiment patch residency time data

description: Please see ReadMe file.
DOI: 10.5061/dryad.4337n/1
title: MdPME sequence alignment

description: The HMM profile of the Pectinesterase proteins (PF01095) was downloaded from the Pfam database (http://pfam.sanger.ac.uk), and used as a query to search the translated Apple genome (http://www.rosaceae.org/) using the HMMER 3.0 program with default parameters (hmmer.org). All sequences collected were checked using the NCBI conserved domain database [65]. Protein coding genes without a complete pectinesterase domain (EC 3.1.1.11) or with extra and incoherent domain were discarded from further analyses. Multiple protein sequence alignments were performed with the online MUSCLE tool (http://www.ebi.ac.uk/Tools/msa/muscle/).
DOI: 10.5061/dryad.4337n/2
title: Phylogenic trees of Malus domestica PMEs

description: The HMM profile of the Pectinesterase proteins (PF01095) was downloaded from the Pfam database (http://pfam.sanger.ac.uk), and used as a query to search the translated Apple genome (http://www.rosaceae.org/) using the HMMER 3.0 program with default parameters (hmmer.org). All sequences collected were checked using the NCBI conserved domain database [65]. Protein coding genes without a complete pectinesterase domain (EC 3.1.1.11) or with extra and incoherent domain were discarded from further analyses. Multiple protein sequence alignments were performed with the online MUSCLE tool (http://www.ebi.ac.uk/Tools/msa/muscle/). Phylogenetic analysis was carried out by the neighbor-joining method using MEGA 5 software [66] using a p-distance model and pairwise deletion for missing data treatment; 1,000 replicates were used for bootstrap analysis.
DOI: 10.5061/dryad.fb41s/1
title: Demographics_participants
DOI: 10.5061/dryad.fb41s/2
title: MRI_Exam_card_flash
DOI: 10.5061/dryad.fb41s/3
title: MRI_Exam_card_mp2rage_slab
DOI: 10.5061/dryad.fb41s/4
title: MRI_Exam_card_mp2rage_whole_brain
DOI: 10.5061/dryad.fb41s/5
title: flash_young

description: The flash scans of the young participants.
DOI: 10.5061/dryad.rv109/6
title: Marshall et al 2014 - EE - natural patch residency time data

description: Please see ReadMe file.
DOI: 10.5061/dryad.fb41s/10
title: mp2rage_whole_brain_middle

description: The mp2rage whole brain scans of the middle aged participants.
DOI: 10.5061/dryad.fb41s/11
title: flash_elderly

description: The flash scans of the elderly participants.
DOI: 10.5061/dryad.fb41s/12
title: mp2rage_slab_elderly

description: The mp2rage slab scans of the elderly participants.
DOI: 10.5061/dryad.fb41s/6
title: mp2rage_slab_young

description: The mp2rage slab scans for the young participants.
DOI: 10.5061/dryad.fb41s/7
title: mp2rage_whole_brain_young

description: The mp2rage whole brain scans for the young participants.
DOI: 10.5061/dryad.fb41s/8
title: flash_middle

description: The flash scans of the middle aged participants
DOI: 10.5061/dryad.fb41s/9
title: mp2rage_slab_middle

description: The mp2rage slab scans of the middle aged participants.
DOI: 10.5061/dryad.7dn7m/1
title: Ablattaria_Data

description: Distribution data on Ablattaria Reitter (Coleoptera: Silphidae)
DOI: 10.5061/dryad.7dn7m/2
title: Ablattaria_Data

description: Distribution data of Ablattaria Reitter (Coleoptera: Silphidae), Excel table
DOI: 10.5061/dryad.fb41s/13
title: mp2rage_whole_brain_elderly

description: The mp2rage whole brain scans of the elderly participants.
DOI: 10.5061/dryad.fb41s/14
title: readme
DOI: 10.5061/dryad.sb175.1
title: Data from: Environmental harshness is positively correlated with intraspecific divergence in mammals and birds
DOI: 10.5061/dryad.sb175.2
title: Data from: Environmental harshness is positively correlated with intraspecific divergence in mammals and birds