cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11719806.v1
title: Additional file 4 of Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions

description: Additional file 4: Table S3. dCypher Results. Excel Tab Peptide Phase A is a compiled set of binding data: chromatin reader titration vs. several peptide targets. Data is presented as raw Alpha counts in duplicates at each concentration tested. Excel Tab Peptide Phase B is a compiled set of binding data: chromatin reader at optimized concentrations vs. entire 293 peptide library. Data is presented as the average and standard deviation of duplicates. Excel Tab Peptide Phase B Heatmap contains a condensed form of Peptide Phase B data displaying an average of duplicates for each chromatin reader tested and individually formatted to demonstrate binding specificity. Key: red = strong binding; blue = weak/no binding.
DOI: 10.6084/m9.figshare.11719782
title: Additional file 1 of Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions

description: Additional file 1: Table S1. PHD finger Domain Array Constructs and Map. Excel Tab PHD Proteins is a compiled list of the 123 GST-tagged proteins used for the domain array. The list contains information on the domains, UniProt accession numbers, sequence coverage, and amino acid sequence for each protein. Excel Tab Array Map represents the pattern in which each of the GST-tagged proteins has been printed for the domain microarray.
DOI: 10.6084/m9.figshare.11719782.v1
title: Additional file 1 of Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions

description: Additional file 1: Table S1. PHD finger Domain Array Constructs and Map. Excel Tab PHD Proteins is a compiled list of the 123 GST-tagged proteins used for the domain array. The list contains information on the domains, UniProt accession numbers, sequence coverage, and amino acid sequence for each protein. Excel Tab Array Map represents the pattern in which each of the GST-tagged proteins has been printed for the domain microarray.
DOI: 10.6084/m9.figshare.11719692
title: Additional file 9 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 9. List and action spectrum of all insecticides/acaricides and some other pesticides mentioned in the included articles.
DOI: 10.6084/m9.figshare.11719692.v1
title: Additional file 9 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 9. List and action spectrum of all insecticides/acaricides and some other pesticides mentioned in the included articles.
DOI: 10.6084/m9.figshare.11719689
title: Additional file 3 of Cancer-associated fibroblasts promote prostate tumor growth and progression through upregulation of cholesterol and steroid biosynthesis

description: Additional file 2. Array data mono vs co-cultures.
DOI: 10.6084/m9.figshare.11719683
title: Additional file 8 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 8. Amendatory information on (i) interventions (definitions), (ii) additional organisms, (iii) sources of production statistics, and (iv) original keywords listed by the articles’ authors.
DOI: 10.6084/m9.figshare.11719689.v1
title: Additional file 3 of Cancer-associated fibroblasts promote prostate tumor growth and progression through upregulation of cholesterol and steroid biosynthesis

description: Additional file 2. Array data mono vs co-cultures.
DOI: 10.6084/m9.figshare.11719680
title: Additional file 2 of Cancer-associated fibroblasts promote prostate tumor growth and progression through upregulation of cholesterol and steroid biosynthesis

description: Additional file 1. Array data 3D vs 2D culture.
DOI: 10.6084/m9.figshare.11719683.v1
title: Additional file 8 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 8. Amendatory information on (i) interventions (definitions), (ii) additional organisms, (iii) sources of production statistics, and (iv) original keywords listed by the articles’ authors.
DOI: 10.6084/m9.figshare.11719680.v1
title: Additional file 2 of Cancer-associated fibroblasts promote prostate tumor growth and progression through upregulation of cholesterol and steroid biosynthesis

description: Additional file 1. Array data 3D vs 2D culture.
DOI: 10.6084/m9.figshare.11719671
title: Additional file 6 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 6. List of excluded and unobtainable articles.
DOI: 10.6084/m9.figshare.11719674
title: Additional file 7 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 7. List of used code sets.
DOI: 10.6084/m9.figshare.11719671.v1
title: Additional file 6 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 6. List of excluded and unobtainable articles.
DOI: 10.6084/m9.figshare.11719674.v1
title: Additional file 7 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 7. List of used code sets.
DOI: 10.6084/m9.figshare.11719665
title: Additional file 5 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 5. List of search strings and literature sources searched.
DOI: 10.6084/m9.figshare.11719665.v1
title: Additional file 5 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 5. List of search strings and literature sources searched.
DOI: 10.6084/m9.figshare.11719662
title: Additional file 4 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 4. ROSES form for systematic map report.
DOI: 10.6084/m9.figshare.11719662.v1
title: Additional file 4 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 4. ROSES form for systematic map report.
DOI: 10.6084/m9.figshare.11719650
title: Additional file 1 of Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants

description: Additional file 1: Supplementary Details on Genomic Comparisons. Sheet 1: Complete List of Genomes Used; Sheet 2: Genome Characteristics of Sequenced Genomes; Sheet 3: COG Analysis; Sheet 4: COG Pivot Chart; Sheet 5: COG graphs; Sheet 6: COG correlation and p values; Sheet 7: AMR phenotypic profiles and breakpoints; Sheet 8: AMR genes detected; Sheet 9: Virulence Factors Raw Output; Sheet 10: Virulence Factors by Species; Sheet 11: Virulence Factors Summary; Sheet 12: Phage Detected; Sheet 13: CRISPRfinder Output; Sheet 14: CRISPRfinder Confirmed Systems; Sheet 15: CRISPRdb BLAST Results; Sheet 16: CRISPR Summary Table; Sheet 17: ICEberg Raw Results; Sheet 18: antiSMASH results; Sheet 19: Neptune Biomarker Combinations
DOI: 10.6084/m9.figshare.11719647
title: Additional file 2 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 2. List of relevant articles (Excel-Version).
DOI: 10.6084/m9.figshare.11719650.v1
title: Additional file 1 of Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants

description: Additional file 1: Supplementary Details on Genomic Comparisons. Sheet 1: Complete List of Genomes Used; Sheet 2: Genome Characteristics of Sequenced Genomes; Sheet 3: COG Analysis; Sheet 4: COG Pivot Chart; Sheet 5: COG graphs; Sheet 6: COG correlation and p values; Sheet 7: AMR phenotypic profiles and breakpoints; Sheet 8: AMR genes detected; Sheet 9: Virulence Factors Raw Output; Sheet 10: Virulence Factors by Species; Sheet 11: Virulence Factors Summary; Sheet 12: Phage Detected; Sheet 13: CRISPRfinder Output; Sheet 14: CRISPRfinder Confirmed Systems; Sheet 15: CRISPRdb BLAST Results; Sheet 16: CRISPR Summary Table; Sheet 17: ICEberg Raw Results; Sheet 18: antiSMASH results; Sheet 19: Neptune Biomarker Combinations
DOI: 10.6084/m9.figshare.11719647.v1
title: Additional file 2 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 2. List of relevant articles (Excel-Version).
DOI: 10.6084/m9.figshare.11719638
title: Additional file 1 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 1. List of relevant articles (Access-Version).
DOI: 10.6084/m9.figshare.11719638.v1
title: Additional file 1 of What evidence exists on the impact of agricultural practices in fruit orchards on biodiversity? A systematic map

description: Additional file 1. List of relevant articles (Access-Version).
DOI: 10.6084/m9.figshare.11719611
title: StimDust: A wireless millimetre-scale implantable neural stimulator with ultrasonically powered bidirectional communication: Raw data

description: Raw, pre-processed data for StimDust. "A wireless millimetre-scale implantable neural stimulator with ultrasonically powered bidirectional communication", as published in Nature Biomedical Engineering, 2020
DOI: 10.6084/m9.figshare.11719542
title: Row Data of Growth performance of Gurami Sago.doc

description: Row data of weight and length of gurami sago (<i>Osphronemus goramy</i>) strain during 0, 30, 60 and 90 days in different aquaculture system.
DOI: 10.6084/m9.figshare.11719470
title: Simulated significant wave height (3-hourly, 150a) from FIO-ESM v2.0 abrupt-4xCO2 experiment r1i1p1f1

description: Simulated significant wave height (3-hourly, 150a) from FIO-ESM v2.0 abrupt-4xCO2 experiment (CO2 abruptly quadrupled and then held constant) r1i1p1f1, which is branch from Jan 1, 301 of piControl experiment. The grid, named gx1v6, is the displaced pole (the North Pole displaced to the Greenland) grid with 1.1 degree in longitude and 0.27-0.54 degree in latitude.
DOI: 10.6084/m9.figshare.11719470.v1
title: Simulated significant wave height (3-hourly, 150a) from FIO-ESM v2.0 abrupt-4xCO2 experiment r1i1p1f1

description: Simulated significant wave height (3-hourly, 150a) from FIO-ESM v2.0 abrupt-4xCO2 experiment (CO2 abruptly quadrupled and then held constant) r1i1p1f1, which is branch from Jan 1, 301 of piControl experiment. The grid, named gx1v6, is the displaced pole (the North Pole displaced to the Greenland) grid with 1.1 degree in longitude and 0.27-0.54 degree in latitude.
DOI: 10.6084/m9.figshare.11719338
title: Tree file RAxML to order genomes in Anvi'o

description: Genomes in the pangenome of Anvi’o were ordered based on a marker gene tree. This tree was built in PhyloSift version 1.0.1 with its updated markers database (version 4) for the alignment. We used RAxML version 8.2.10 on the CIPRES web server.
DOI: 10.6084/m9.figshare.11719338.v1
title: Tree file RAxML to order genomes in Anvi'o

description: Genomes in the pangenome of Anvi’o were ordered based on a marker gene tree. This tree was built in PhyloSift version 1.0.1 with its updated markers database (version 4) for the alignment. We used RAxML version 8.2.10 on the CIPRES web server.
DOI: 10.6084/m9.figshare.11719326
title: Amino acid alignment from PhyloSift to order genomes in Anvi'o

description: Genomes in the pangenome of Anvi’o were ordered based on a marker gene tree. This tree was built in PhyloSift version 1.0.1 with its updated markers database (version 4) for the alignment. We used RAxML version 8.2.10 on the CIPRES web server.<br>
DOI: 10.6084/m9.figshare.11719326.v1
title: Amino acid alignment from PhyloSift to order genomes in Anvi'o

description: Genomes in the pangenome of Anvi’o were ordered based on a marker gene tree. This tree was built in PhyloSift version 1.0.1 with its updated markers database (version 4) for the alignment. We used RAxML version 8.2.10 on the CIPRES web server.<br>
DOI: 10.6084/m9.figshare.11719278
title: Putative amino acid sequences involved in xenobiotics biodegradation and metabolism

description: Twenty KEGG pathways known to play a role in plant secondary metabolite degradation were searched in the eggNOG annotations of Lonepinella koalarum strain UCD-LQP1. The amino acid sequences of putative hits are deposited here. Putative genes of interest are summarized in Supplementary Table Xx in the main manuscript.
DOI: 10.6084/m9.figshare.11717895
title: Contig 9 - potential Lonepinella koalarum plasmid

description: The genome assembly of this Lonepinella koalarum strain resulted in a circular contig that was similar to plasmids in related bacterial taxa when blasted on GenBank.
DOI: 10.6084/m9.figshare.11719278.v1
title: Putative amino acid sequences involved in xenobiotics biodegradation and metabolism

description: Twenty KEGG pathways known to play a role in plant secondary metabolite degradation were searched in the eggNOG annotations of Lonepinella koalarum strain UCD-LQP1. The amino acid sequences of putative hits are deposited here. Putative genes of interest are summarized in Supplementary Table Xx in the main manuscript.
DOI: 10.6084/m9.figshare.11717862
title: Detailed results obtained in the analysis of 50 selected soil samples .xlsx

description: Dataset of ammonium lactate soluble potassium and phosphorus content of the soils of north-east Hungary region: a quantifying study for publication<br>
DOI: 10.6084/m9.figshare.11717862.v1
title: Detailed results obtained in the analysis of 50 selected soil samples .xlsx

description: Dataset of ammonium lactate soluble potassium and phosphorus content of the soils of north-east Hungary region: a quantifying study for publication<br>
DOI: 10.25376/hra.11717742
title: Healthy Hearts in Heart Transplant Data Final.xlsx

description: Results from baseline, post-intervention, and post-maintenance of a 24-32 week live-video exercise and nutrition intervention for pediatric heart transplant patients.<br>
DOI: 10.6084/m9.figshare.11717715
title: S4_Raman

description: Raman spectroscopy of Ga-intercalated as-grown and O2/He plasma-treated EG/SiC with small and large step sizes.<br>The files titled "Ga_small step_asgrown..." and "Ga_small step_plasma..." provide raw data the first two columns of maps shown in Supplemental Information Figure S4. Corresponding optical microscope images are also provided. <br>
DOI: 10.6084/m9.figshare.11717715.v1
title: S4_Raman

description: Raman spectroscopy of Ga-intercalated as-grown and O2/He plasma-treated EG/SiC with small and large step sizes.<br>The files titled "Ga_small step_asgrown..." and "Ga_small step_plasma..." provide raw data the first two columns of maps shown in Supplemental Information Figure S4. Corresponding optical microscope images are also provided. <br>
DOI: 10.6084/m9.figshare.11717709
title: S3_Auger_Ga_In

description: Auger electron spectroscopy maps of Ga and In-intercalated O2/He plasma treated EG/SiC. C, Si, O, In, and Ga are mapped. Two samples are mapped: 181016A_Ga (Ga-intercalated) and 181104_In (In-intercalated). <br>
DOI: 10.6084/m9.figshare.11717691
title: S2_XPS_air stable

description: X-ray photoelectron spectroscopy measurements of a Ga-intercalated O2/He plasma treated EG/SiC sample after synthesis, and over 8 months later.
DOI: 10.6084/m9.figshare.11717691.v1
title: S2_XPS_air stable

description: X-ray photoelectron spectroscopy measurements of a Ga-intercalated O2/He plasma treated EG/SiC sample after synthesis, and over 8 months later.
DOI: 10.6084/m9.figshare.11717676
title: Data breast cancer study.xlsx

description: Cost of illness study estimating the household treatment cost of breast cancer in a tertiary health facility.
DOI: 10.6084/m9.figshare.11717670
title: S1_XPS

description: X-ray photoelectron spectroscopy data acquired for epitaxial graphene on silicon carbide intercalated with Ga, In, or Sn.<br>"All Elements_O2HeEG_annealed at intercalation conditions" contains spectra for a sample of epitaxial graphene on silicon carbide (EG/SiC) that was exposed to a 50W O2/He plasma for 60s and subsequently annealed at 800C, 300 Torr for 30 minutes under 50 sccm Ar. <br>"All Elements_O2HeEG_SiC_HOPG_AsGrownEG_HydrogEG_GaIntO2HeEG_GaIntAsGrownEG" contains spectra for the following samples: O2/He plasma treated EG/SiC, bare SiC, highly ordered pyrolytic graphite (HOPG), as-grown EG/SiC, hydrogenated (or hydrogen intercalated) EG/SiC, Ga-intercalated, O2/He plasma treated EG/SiC, and Ga-intercalated as-grown EG/SiC. This file contains C 1s, O 1s, Si 2p, Ga 3d, and survey spectra.<br>"C1sEGGaInt" contains C 1s spectra for O2/He plasma treated EG/SiC, bare SiC, highly ordered pyrolytic graphite (HOPG), as-grown EG/SiC, hydrogenated (or hydrogen intercalated) EG/SiC, Ga-intercalated, O2/He plasma treated EG/SiC, and Ga-intercalated as-grown EG/SiC.<br>"Ga3dGaInt" contains Ga 3d spectra for Ga-intercalated, O2/He plasma treated EG/SiC, Ga-intercalated as-grown EG/SiC.<br>"InSnInterc" contains O 1s, Si 2p ,C 1s, Sn 3d and In 3d spectra for Sn and In-intercalated, O2/He plasma treated EG/SiC.<br>"O1s_GaIntO2HeEG_GaIntAsGrownEG_Hinterc" contains O 1s spectra for Ga-intercalated, O2/He plasma treated EG/SiC, Ga-intercalated as-grown EG/SiC.<br>"Si2pO2HeEGAsG" contains Si 2p spectra for O2/He plasma treated EG/SiC, as-grown EG/SiC, hydrogenated (or hydrogen intercalated) EG/SiC, Ga-intercalated, O2/He plasma treated EG/SiC, and Ga-intercalated as-grown EG/SiC.
DOI: 10.6084/m9.figshare.11717361
title: Community rescue in experimental phytoplankton communities facing severe herbicide pollution

description: Data for:<br><br>Fugère V, Hébert MP, Costa NB, Xu CCY, Barrett RDH, Beisner BE, Bell G, Fussmann GF, Shapiro BJ, Yargeau V, Gonzalez A. (2020) Community rescue in experimental phytoplankton communities facing severe herbicide pollution.<br><br>Abstract: Community rescue occurs when ecological or evolutionary processes restore positive growth in a highly stressful environment that was lethal to the community in its ancestral form, thus averting biomass collapse in a deteriorating environment. Laboratory evidence suggests that community rescue is most likely in high-biomass communities that have previously experienced moderate doses of sublethal stress. We assessed this result under more natural conditions, in a mesocosm experiment with phytoplankton communities exposed to the ubiquitous herbicide glyphosate. We tested whether community biomass and prior herbicide exposure would facilitate community rescue after severe contamination. We found that prior exposure to glyphosate was a very strong predictor of the rescue outcome while high community biomass was not. Furthermore, although glyphosate had negative effects on diversity, it did not influence community composition significantly, suggesting a modest role for genus sorting in this rescue process. Our results expand the scope of community rescue theory to complex ecosystems and confirm that prior stress exposure is a key predictor of rescue.
DOI: 10.6084/m9.figshare.11717355
title: Specialization for rapid excitation in fast squid tentacle muscle involves action potentials absent in slow arm muscle

description: Data are raw electrophysiological traces abtained in whole-cell patch recordings in voltage- and current-clamp mode. Format is Axon Binary File that must be read with Clampfit software available free on line. Metadata file is excel format.<br>
DOI: 10.6084/m9.figshare.11717361.v1
title: Community rescue in experimental phytoplankton communities facing severe herbicide pollution

description: Data for:<br><br>Fugère V, Hébert MP, Costa NB, Xu CCY, Barrett RDH, Beisner BE, Bell G, Fussmann GF, Shapiro BJ, Yargeau V, Gonzalez A. (2020) Community rescue in experimental phytoplankton communities facing severe herbicide pollution.<br><br>Abstract: Community rescue occurs when ecological or evolutionary processes restore positive growth in a highly stressful environment that was lethal to the community in its ancestral form, thus averting biomass collapse in a deteriorating environment. Laboratory evidence suggests that community rescue is most likely in high-biomass communities that have previously experienced moderate doses of sublethal stress. We assessed this result under more natural conditions, in a mesocosm experiment with phytoplankton communities exposed to the ubiquitous herbicide glyphosate. We tested whether community biomass and prior herbicide exposure would facilitate community rescue after severe contamination. We found that prior exposure to glyphosate was a very strong predictor of the rescue outcome while high community biomass was not. Furthermore, although glyphosate had negative effects on diversity, it did not influence community composition significantly, suggesting a modest role for genus sorting in this rescue process. Our results expand the scope of community rescue theory to complex ecosystems and confirm that prior stress exposure is a key predictor of rescue.
DOI: 10.6084/m9.figshare.11714532
title: KCML: a machine-learning framework for inference of multi-scale gene functions from genetic perturbation screens

description: Top predictions of KCML based on three genetic perturbation datasets.
DOI: 10.6084/m9.figshare.11714400.v1
title: Concomitant experimental co-infection by Plasmodium berghei NK65 and Ascaris suum downregulates immunological responses and impairs lung function

description: Ascariasis and malaria are highly prevalent parasitic diseases in tropical regions and often overlap in endemic areas, contributing to high morbidity and mortality rates in areas with poor sanitary conditions. Several studies aiming to correlate the effects of <i>Ascaris</i> infections with malaria have contradictory and inconclusive results. In this context, we investigated parasitological and immunopathological aspects of the lung in the experimental concomitant co-infection of <i>Plasmodium berghei</i> NK65 and <i>Ascaris suum</i> during larval ascariasis. The most important findings related to <i>P. berghei Nk65 and A. suum</i> co-infection results in downregulation of Th1, Th2, Th17 and Treg responses and alteration of larvae migration in the lungs associated with decrease of larvae recovered in the lung parenchyma and increase of larvae recovered in the airways, which reflected in the severe morbidity and mortality of the animals, associated with impaired lung function. Taken together, our results suggest that the presence of both parasites contribute to the compromised host immune response. The low immunological responsiveness and the loss of lung function of the co-infected animals are evidence of an advanced sepsis-like process, resulting in the early death of the animals.
DOI: 10.6084/m9.figshare.11710440
title: slab symmetry, p = 1e5, w = 1e-4

description: slab symmetry, p = 1e5, w = 1e-4
DOI: 10.6084/m9.figshare.11710440.v1
title: slab symmetry, p = 1e5, w = 1e-4

description: slab symmetry, p = 1e5, w = 1e-4
DOI: 10.6084/m9.figshare.11710320
title: (replaced) Table S3 fault energy, grain size calcs.xlsx

description: none
DOI: 10.6084/m9.figshare.11710425
title: books

description: Books
DOI: 10.6084/m9.figshare.11710320.v1
title: Table S3 fault energy, grain size calcs.xlsx

description: none
DOI: 10.6084/m9.figshare.11710425.v1
title: books

description: Books
DOI: 10.6084/m9.figshare.11710290
title: Dataset from Calcified gill filaments increase respiratory function in fishes

description: All data analyzed in the manuscript.
DOI: 10.6084/m9.figshare.11710425.v3
title: books

description: Books
DOI: 10.6084/m9.figshare.11710425.v2
title: books

description: Books