cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8786837
title: Additional file 1: of Feasibility assessment of phenotyping cotton fiber maturity using infrared spectroscopy and algorithms for genotyping analyses

description: Comparisons of the observed phenotypes with the predicted phenotypes based on their DNA marker genotypes in a genetic population with various fiber maturity. Seven hundred andÂ eight F2 progeny plants were derived from a cross between wild-type (WT) upland cultivar MD52ne and immature fiber (im) mutant. Genotypes including homozygosity for the wild type (WT-homo), heterozygosity for the wild type (WT-hetro), and homozygosity for the im type (im-homo) were determined by DNA markers. The predicted WT phenotype (WT-homo and WT-hetro genotypes) and the im phenotype (im-homo genotype) were compared with the observed phenotypes based MIC values and lint percentage. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.8786840.v1
title: Additional file 2: of Feasibility assessment of phenotyping cotton fiber maturity using infrared spectroscopy and algorithms for genotyping analyses

description: Comparisons of the observed infrared maturity (MIR) and crystallinity (CIIR) with the predicted phenotypes based on their DNA marker genotypes. ATR FT-IR spectra were measured from the second set composed of 80 F2 plants with various MIC values. MIR and CIIR values were determined by algorithms and compared with the predicted phenotypes based on their DNA marker genotypes as well as the observed MIC values and lint percentage. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8786837.v1
title: Additional file 1: of Feasibility assessment of phenotyping cotton fiber maturity using infrared spectroscopy and algorithms for genotyping analyses

description: Comparisons of the observed phenotypes with the predicted phenotypes based on their DNA marker genotypes in a genetic population with various fiber maturity. Seven hundred andÂ eight F2 progeny plants were derived from a cross between wild-type (WT) upland cultivar MD52ne and immature fiber (im) mutant. Genotypes including homozygosity for the wild type (WT-homo), heterozygosity for the wild type (WT-hetro), and homozygosity for the im type (im-homo) were determined by DNA markers. The predicted WT phenotype (WT-homo and WT-hetro genotypes) and the im phenotype (im-homo genotype) were compared with the observed phenotypes based MIC values and lint percentage. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.8786774
title: Additional file 1: of Prevalence, knowledge and attitudes towards using sports supplements among young athletes

description: The survey. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8786774.v1
title: Additional file 1: of Prevalence, knowledge and attitudes towards using sports supplements among young athletes

description: The survey. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8786762
title: Additional file 3: of An in-home intervention of parent-implemented strategies to increase child vegetable intake: results from a non-randomized cluster-allocated community trial

description: Raw data used in analysis. (XLSX 1624â kb)
DOI: 10.6084/m9.figshare.8786762.v1
title: Additional file 3: of An in-home intervention of parent-implemented strategies to increase child vegetable intake: results from a non-randomized cluster-allocated community trial

description: Raw data used in analysis. (XLSX 1624â kb)
DOI: 10.6084/m9.figshare.8786753
title: Additional file 7: of Bibliometric analysis of cardiometabolic disorders studies involving NO2, PM2.5 and noise exposure

description: The data set, including references identified in the literature search and classifications. (CSV 4854 kb)
DOI: 10.6084/m9.figshare.8786753.v1
title: Additional file 7: of Bibliometric analysis of cardiometabolic disorders studies involving NO2, PM2.5 and noise exposure

description: The data set, including references identified in the literature search and classifications. (CSV 4854 kb)
DOI: 10.6084/m9.figshare.8786678
title: Additional file 3: of Under pressure: force resistance measurements in box mites (Actinotrichida, Oribatida)

description: Supporting data of the actual experiment and all supporting measurements. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.8786678.v1
title: Additional file 3: of Under pressure: force resistance measurements in box mites (Actinotrichida, Oribatida)

description: Supporting data of the actual experiment and all supporting measurements. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.8786552
title: Additional file 2: of The global impact and cost-effectiveness of a melioidosis vaccine

description: Copy of Data summary LOSR2. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8786552.v1
title: Additional file 2: of The global impact and cost-effectiveness of a melioidosis vaccine

description: Copy of Data summary LOSR2. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8786516
title: Additional file 2: of The haustorial transcriptome of the cucurbit pathogen Podosphaera xanthii reveals new insights into the biotrophy and pathogenesis of powdery mildew fungi

description: Table S2. Full annotation of P. xanthii haustorial and epiphytic transcriptomes. Table S3. Comparison of haustorial and epiphytic GO terms performed by Venn diagram. Table S4. Non-redundant GO terms related to biological processes specific to P. xanthii haustoria obtained by REVIGO. Table S5. Top 50 expressed unigenes in P. xanthii haustoria. Table S6. Non-redundant GO terms related to biological processes of the top 50 expressed haustorial unigenes obtained by REVIGO. Table S7. Top 50 expressed ncRNAs in P. xanthii haustorial transcriptome. Table S8. Subcellular localization analysis of haustorial and epiphytic candidate secreted proteins of P. xanthii performed by DeepLoc. Table S9. Annotation of P. xanthii haustorial and epiphytic secretomes. (XLSX 5574 kb)
DOI: 10.6084/m9.figshare.8786516.v1
title: Additional file 2: of The haustorial transcriptome of the cucurbit pathogen Podosphaera xanthii reveals new insights into the biotrophy and pathogenesis of powdery mildew fungi

description: Table S2. Full annotation of P. xanthii haustorial and epiphytic transcriptomes. Table S3. Comparison of haustorial and epiphytic GO terms performed by Venn diagram. Table S4. Non-redundant GO terms related to biological processes specific to P. xanthii haustoria obtained by REVIGO. Table S5. Top 50 expressed unigenes in P. xanthii haustoria. Table S6. Non-redundant GO terms related to biological processes of the top 50 expressed haustorial unigenes obtained by REVIGO. Table S7. Top 50 expressed ncRNAs in P. xanthii haustorial transcriptome. Table S8. Subcellular localization analysis of haustorial and epiphytic candidate secreted proteins of P. xanthii performed by DeepLoc. Table S9. Annotation of P. xanthii haustorial and epiphytic secretomes. (XLSX 5574 kb)
DOI: 10.6084/m9.figshare.8786303
title: Additional file 1: of Infliximab therapy together with tyrosine kinase inhibition targets leukemic stem cells in chronic myeloid leukemia

description: Gene Set Enrichment Analysis of LSK microarray data from CML mice (SCLtTA/Bcr-Abl) vs controls (SCLtTA and wt). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8786303.v1
title: Additional file 1: of Infliximab therapy together with tyrosine kinase inhibition targets leukemic stem cells in chronic myeloid leukemia

description: Gene Set Enrichment Analysis of LSK microarray data from CML mice (SCLtTA/Bcr-Abl) vs controls (SCLtTA and wt). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.8786228
title: Bacteria with natural chemotaxis towards methanol revealed by chemotaxis fishing technique

description: Motile bacteria often exhibit chemotaxis toward favorable compounds. However, the diversity of bacteria that are attracted to a given substance is largely unknown. This study aimed to reveal the diversity of bacteria with natural chemotaxis towards methanol. We tried to enrich environmental chemotactic bacteria using a glass capillary that is half-filled with methanol solidified with agarose as a trap (“chemotaxis fishing”). The pilot experiment using methanol-chemotactic <i>Methylobacterium aquaticum</i> strain 22A enriched the cells by 46-fold. The method was then applied to bacterial suspensions from paddy water and plants. Depending on the isolation sources and the methods of motility induction, methylotrophic bacteria were enriched 1.2–330-fold. The fished isolates belong to 32 species in 18 genera, mainly containing <i>Acinetobacter, Methylobacterium</i> and <i>Pseudomonas</i> species. Our chemotaxis fishing unveiled a part of diversity of the bacteria with natural chemotaxis towards methanol. A glass capillary containing methanol was used as a trap to enrich methanol-chemotactic bacteria.
DOI: 10.6084/m9.figshare.8786228.v1
title: Bacteria with natural chemotaxis towards methanol revealed by chemotaxis fishing technique

description: Motile bacteria often exhibit chemotaxis toward favorable compounds. However, the diversity of bacteria that are attracted to a given substance is largely unknown. This study aimed to reveal the diversity of bacteria with natural chemotaxis towards methanol. We tried to enrich environmental chemotactic bacteria using a glass capillary that is half-filled with methanol solidified with agarose as a trap (“chemotaxis fishing”). The pilot experiment using methanol-chemotactic <i>Methylobacterium aquaticum</i> strain 22A enriched the cells by 46-fold. The method was then applied to bacterial suspensions from paddy water and plants. Depending on the isolation sources and the methods of motility induction, methylotrophic bacteria were enriched 1.2–330-fold. The fished isolates belong to 32 species in 18 genera, mainly containing <i>Acinetobacter, Methylobacterium</i> and <i>Pseudomonas</i> species. Our chemotaxis fishing unveiled a part of diversity of the bacteria with natural chemotaxis towards methanol. A glass capillary containing methanol was used as a trap to enrich methanol-chemotactic bacteria.
DOI: 10.6084/m9.figshare.8785985
title: Meteorology data and collected microorganisms

description: Meteorology and number of bacteria and fungi colonies
DOI: 10.6084/m9.figshare.8784311
title: LFP data for 8-Neuropixels recordings from Stringer et al 2019 Science

description: Companion to https://janelia.figshare.com/articles/Eight-probe_Neuropixels_recordings_during_spontaneous_behaviors/7739750<br>Each LFP file has 385 channels of int16 data at 2500Hz. They can be loaded directly into software like Neuroscope, and can be read in matlab like:<br>&gt;&gt; fid = fopen('thisfile.bin', 'r');&gt;&gt; dat = fread(fid, [385 Inf], '*int16');&gt;&gt; fclose(fid);<br><br>Note that the file may well be too large to fit into memory so you may not want to read "Inf" samples as in this example. <br>Each file has different start and end times, and there are drifts in the clocks between probes - so the timestamp files, which give the aligned timing information, must be used. The aligned timestamps are specified in a particular way: an Nx2 matrix where the first column is sample numbers and the second column is the time in seconds at which those samples occurred. Since LFP was sampled regularly, N=2, just the first and last sample. So, to get the time at which every sample occurred, use this line in matlab: <br>&gt;&gt; tsData = readNPY('...lf.timestamps.npy');&gt;&gt; allTS = interp1(tsData(:,1), tsData(:,2), tsData(1,1):tsData(2,1));<br>That's just linearly interpolating between the times given for the first and last samples.<br>An important note about data quality: The referencing was not functioning properly for several probes. The AP (i.e. high-pass filtered) data was essentially perfectly recovered using common average referencing, but this has not been assessed for the LFP data. So, please check the data quality carefully for whatever you plan to analyze, and if it looks noisy with matched noise across channels, try CAR to fix it.
DOI: 10.6084/m9.figshare.8785985.v1
title: Meteorology data and collected microorganisms

description: Meteorology and number of bacteria and fungi colonies
DOI: 10.6084/m9.figshare.8783555
title: Model + observation data used in the study: Closure of secondary basins causes channel deepening in estuaries with moderate to high friction

description: <b>Description of the data used in the study : “<i>Closure of secondary basins causes channel deepening in estuaries with moderate to high friction”</i></b> <b><i>By Abdel Nnafie, Utrecht University, Netherlands,</i></b> <b><i>Email: a.nnafie@uu.nl</i></b> <i>If any further information is required, feel free to contact me.</i><br>see Readme.docx for a description of the data set
DOI: 10.6084/m9.figshare.8775839
title: RPPA quantification from MD Anderson

description: RPPA quantification of breast cancer cell lines from MD Anderson
DOI: 10.6084/m9.figshare.8774822
title: SLC2A1 expression across different patient data

description: SLC2A1 gene expression across breast cancer samples from:TCGAMETABRICPMH PDXs<br>
DOI: 10.6084/m9.figshare.8775839.v1
title: RPPA quantification from MD Anderson

description: RPPA quantification of breast cancer cell lines from MD Anderson
DOI: 10.6084/m9.figshare.8774822.v1
title: SLC2A1 expression across different patient data

description: SLC2A1 gene expression across breast cancer samples from:TCGAMETABRICPMH PDXs<br>
DOI: 10.6084/m9.figshare.8773841
title: hallMark genesets from MSigDB

description: hallMark genesets downloaded from MSigDB
DOI: 10.6084/m9.figshare.8783555.v1
title: Model + observation data used in the study: Estuarine channel evolution in response to closure of secondary basins: Changes in channel depth

description: <b>Description of the data used in the study : “<i>Estuarine channel evolution in response to closure of secondary basins: Changes in channel depth”</i></b> <b><i>By Abdel Nnafie, Utrecht University, Netherlands,</i></b> <b><i>Email: a.nnafie@uu.nl</i></b> <i>If any further information is required, feel free to contact me.</i><br>see Readme.docx for a description of the data set
DOI: 10.6084/m9.figshare.8783555.v2
title: Model + observation data used in the study: Closure of secondary basins causes channel deepening in estuaries with moderate to high friction

description: <b>Description of the data used in the study : “<i>Closure of secondary basins causes channel deepening in estuaries with moderate to high friction”</i></b> <b><i>By Abdel Nnafie, Utrecht University, Netherlands,</i></b> <b><i>Email: a.nnafie@uu.nl</i></b> <i>If any further information is required, feel free to contact me.</i><br>see Readme.docx for a description of the data set
DOI: 10.6084/m9.figshare.8755259
title: As plantas comestíveis no Brasil dos séculos XVI e XVII  segundo relatos de época

description: <b>Apêndice 1 -</b> Plantas alimentícias do Brasil nos séculos XVI e XVII<br>
DOI: 10.6084/m9.figshare.8765492
title: As plantas comestíveis no Brasil dos séculos XVI e XVII segundo relatos de época

description: <b>Apêndice 1 -</b> Plantas alimentícias do Brasil nos séculos XVI e XVII
DOI: 10.6084/m9.figshare.8766389
title: Sensitivity index for phytoplankton

description: Analysis results and visualization for RNAseq-based index of the effect of oil and oil-dispersant treatments on natural communities of eukaryotic phytoplankton from the Gulf of Mexico.<br>See Finkel et al (2020) for more.<br>Files provided here:<br>1) Supplementary Figure 1. Krona visualizations of community composition under the four treatments determined by KrakenUniq using the PR2 18S database. Two files, one for counts using full-length 18S sequences and one using the V4 region only.<br>2) Supplementary Table 1. Full table of KrakenUniq counts (not normalized) and transcripts per million (TPM, normalized) for each replicate and treatment, with one row per taxon. Taxonomy information from PR2 database. Two files, one for counts using full-length 18S sequences and one using the V4 region only.<br>
DOI: 10.6084/m9.figshare.8783555.v4
title: Model + observation data used in the study: Closure of secondary basins causes channel deepening in estuaries with moderate to high friction

description: <b>Description of the data used in the study : “<i>Closure of secondary basins causes channel deepening in estuaries with moderate to high friction”</i></b> <b><i>By Abdel Nnafie, Utrecht University, Netherlands,</i></b> <b><i>Email: a.nnafie@uu.nl</i></b> <i>If any further information is required, feel free to contact me.</i><br>see Readme.docx for a description of the data set
DOI: 10.6084/m9.figshare.8766389.v1
title: Sensitivity index for phytoplankton

description: Analysis results and visualization for RNAseq-based index of the effect of oil and oil-dispersant treatments on natural communities of eukaryotic phytoplankton from the Gulf of Mexico.<br>See Finkel et al (2020) for more.<br>Files provided here:<br>1) Supplementary Figure 1. Krona visualizations of community composition under the four treatments determined by KrakenUniq using the PR2 18S database. Two files, one for counts using full-length 18S sequences and one using the V4 region only.<br>2) Supplementary Table 1. Full table of KrakenUniq counts (not normalized) and transcripts per million (TPM, normalized) for each replicate and treatment, with one row per taxon. Taxonomy information from PR2 database. Two files, one for counts using full-length 18S sequences and one using the V4 region only.<br>
DOI: 10.6084/m9.figshare.8783555.v3
title: Model + observation data used in the study: Closure of secondary basins causes channel deepening in estuaries with moderate to high friction

description: <b>Description of the data used in the study : “<i>Closure of secondary basins causes channel deepening in estuaries with moderate to high friction”</i></b> <b><i>By Abdel Nnafie, Utrecht University, Netherlands,</i></b> <b><i>Email: a.nnafie@uu.nl</i></b> <i>If any further information is required, feel free to contact me.</i><br>see Readme.docx for a description of the data set
DOI: 10.6084/m9.figshare.8731400
title: processed images

description: These are 100 32x32 processed images and are ready to feed into the reconstruction algorithm.
DOI: 10.6084/m9.figshare.8731400.v1
title: processed images

description: These are 100 32x32 processed images and are ready to feed into the reconstruction algorithm.
DOI: 10.6084/m9.figshare.8721455
title: Table S8

description: Datafile of the LD (r<sup>2</sup>) for all pairs of markers, by morph
DOI: 10.6084/m9.figshare.8719784
title: Table S5

description: Genetic polymorphisms studied in the population sample of Arctic charr.<br><b>Transcript_ID:</b> Name of the transcript from the Trinity assembly<b>Variant:</b> Name of variant.<b>Gene:</b> Short name of gene.<b>Gene_name:</b> Long name of gene.<b>Start:</b> Position of polymorphism within contig.<b>Ref:</b> Base(s) of the reference allele.<b>Alt:</b> Base(s) of the alternative allele.<b>Outg:</b> Base(s) in the salmonid outgroup.<b>Chr_NCBI_id:</b> Sequence identifier for chromosome or scaffold in genome.<b>Chr:</b> Name of chromosome.<b>Chr_position:</b> Position mapped to in chromosome.<b>Effect:</b> Which effect does the mutation have on the gene, 3’- and 5’ UTR indicate mutations in those regions, synonymousdo not change the reading frame but mutations that do so are coded as transitions from one amino acid to another (single letter a.a. code)<b>Marker_ID:</b> Abbreviated ID of each marker.<b>Sequence:</b> The sequence used to design the KASP assay, the polymorphism are marked by e.g. [A/T].
DOI: 10.6084/m9.figshare.8721317
title: Table S6

description: Datafile of the genotypes for the 22 markers scored in the population samples from the four sympatric charr morphs (coded by bases, missing data indicated by “NA”).
DOI: 10.6084/m9.figshare.8721317.v1
title: Table S6

description: Datafile of the genotypes for the 22 markers scored in the population samples from the four sympatric charr morphs (coded by bases, missing data indicated by “NA”).
DOI: 10.6084/m9.figshare.8721455.v1
title: Table S8

description: Datafile of the LD (r<sup>2</sup>) for all pairs of markers, by morph
DOI: 10.6084/m9.figshare.8719784.v1
title: Table S5

description: Genetic polymorphisms studied in the population sample of Arctic charr.<br><b>Transcript_ID:</b> Name of the transcript from the Trinity assembly<b>Variant:</b> Name of variant.<b>Gene:</b> Short name of gene.<b>Gene_name:</b> Long name of gene.<b>Start:</b> Position of polymorphism within contig.<b>Ref:</b> Base(s) of the reference allele.<b>Alt:</b> Base(s) of the alternative allele.<b>Outg:</b> Base(s) in the salmonid outgroup.<b>Chr_NCBI_id:</b> Sequence identifier for chromosome or scaffold in genome.<b>Chr:</b> Name of chromosome.<b>Chr_position:</b> Position mapped to in chromosome.<b>Effect:</b> Which effect does the mutation have on the gene, 3’- and 5’ UTR indicate mutations in those regions, synonymousdo not change the reading frame but mutations that do so are coded as transitions from one amino acid to another (single letter a.a. code)<b>Marker_ID:</b> Abbreviated ID of each marker.<b>Sequence:</b> The sequence used to design the KASP assay, the polymorphism are marked by e.g. [A/T].
DOI: 10.6084/m9.figshare.8718695
title: Table S2

description: VCF-file with the final set of variants after all filtering steps.
DOI: 10.6084/m9.figshare.8718695.v1
title: Table S2

description: VCF-file with the final set of variants after all filtering steps.
DOI: 10.6084/m9.figshare.8705888
title: Table S1

description: Tab-delimited text file with the position, alleles, alternative frequencies within morphs, F-statistics between morphs and samples and predicted effect of the variant on protein composition for all the variants after the final filtering step.<br><b>id: </b>Identifier for each variant from 1 to 19,252<b>transcript_id: </b>Name of the transcript from the Trinity assembly.<b>start:</b> Start position of polymorphism within contig.<b>end: </b>End position of polymorphism within contig.<b>ref: </b>Base(s) of the reference allele.<b>alt: </b>Base(s) of the alternative allele.<b>var_pos: </b>Position of polymorphism within contig.<b>NCBI_id: </b>Sequence identifier for chromosome or scaffold in genome.<b>Chr:</b> Name of chromosome.<b>Chr_pos:</b> Position mapped to in chromosome.<b>Freq_LB:</b> Frequency of alternative allele within the LB morph.<b>Freq_PL:</b> Frequency of alternative allele within the PL morph.<b>Freq_SB:</b> Frequency of alternative allele within the SB morph.<b>Fst:</b> Estimate of F ST between morphs.<b>Fpt:</b> Estimate of F P T or variation among samples (pools). See methods for further explanation.<b>effect:</b> Which effect does the mutation have on the gene, 3’- and 5’ UTR indicate mutations in those regions, synonymousdo not change the reading frame but mutations that do so are coded as transitions from one amino acid to another (single letter a.a. code)<b>gene_name:</b> Gene name based on SalmonBase annotation.