cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6742838
title: Additional file 1: of Antibody and cytokine response to Cystoisospora suis infections in immune-competent young pigs

description: Table S1. Hematological parameters and white blood cell counts determined on study days 1 and 29. Abbreviations: MCV, mean cell volume; MCH, mean cellular hemoglobin; MCHC, mean cellular hemoglobin concentration. Table S2. Differences in hematological parameters and white blood cell counts between groups and over time. Values of SD 1 and SD 29 were compared between uninfected animals and infected animals altogether. Additionally, differences over time were calculated for both groups. Abbreviations: x ¯ $$ \overline{\mathrm{x}} $$ , mean; σ, standard deviation. Table S3. Serum titer development over time within groups. In brackets: test statistic χ2 and degrees of freedom df according to the Friedman rank sum test. Abbreviations: SD, study day; x ¯ $$ \overline{\mathrm{x}} $$ , mean titer; σ, standard deviation. Table S4. Results (as P-values) of antibody titer comparisons between groups on each study day. Significant differences (P ≤ 0.05) are indicated in bold. Abbreviations: SD, study day; SL, Single Low; SH, Single High; TL, Trickle Low; TH, Trickle High; C, Control. Table S5. Change of cytokine mRNA expression of white blood cells over time within groups. Expression levels of study days 8, 15 and 29 of each group were compared to those of study day 1. Significant differences (P ≤ 0.05) are indicated in bold. Abbreviations: SD, study day; SL, Single Low; SH, Single High; TL, Trickle Low TH, Trickle High; C, Control. Table S6. Cytokine mRNA expression of white blood cells before infection. Expression values of study day 1 were compared between groups and resulting P-values are shown. Significant differences (P ≤ 0.05) are indicated in bold. Abbreviations: SL, Single Low; SH, Single High; TL, Trickle Low; TH, Trickle High; C, Control. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6742838.v1
title: Additional file 1: of Antibody and cytokine response to Cystoisospora suis infections in immune-competent young pigs

description: Table S1. Hematological parameters and white blood cell counts determined on study days 1 and 29. Abbreviations: MCV, mean cell volume; MCH, mean cellular hemoglobin; MCHC, mean cellular hemoglobin concentration. Table S2. Differences in hematological parameters and white blood cell counts between groups and over time. Values of SD 1 and SD 29 were compared between uninfected animals and infected animals altogether. Additionally, differences over time were calculated for both groups. Abbreviations: x ¯ $$ \overline{\mathrm{x}} $$ , mean; σ, standard deviation. Table S3. Serum titer development over time within groups. In brackets: test statistic χ2 and degrees of freedom df according to the Friedman rank sum test. Abbreviations: SD, study day; x ¯ $$ \overline{\mathrm{x}} $$ , mean titer; σ, standard deviation. Table S4. Results (as P-values) of antibody titer comparisons between groups on each study day. Significant differences (P ≤ 0.05) are indicated in bold. Abbreviations: SD, study day; SL, Single Low; SH, Single High; TL, Trickle Low; TH, Trickle High; C, Control. Table S5. Change of cytokine mRNA expression of white blood cells over time within groups. Expression levels of study days 8, 15 and 29 of each group were compared to those of study day 1. Significant differences (P ≤ 0.05) are indicated in bold. Abbreviations: SD, study day; SL, Single Low; SH, Single High; TL, Trickle Low TH, Trickle High; C, Control. Table S6. Cytokine mRNA expression of white blood cells before infection. Expression values of study day 1 were compared between groups and resulting P-values are shown. Significant differences (P ≤ 0.05) are indicated in bold. Abbreviations: SL, Single Low; SH, Single High; TL, Trickle Low; TH, Trickle High; C, Control. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6742781
title: Additional file 6 of Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

description: Table S2. Full detailed data used for the Fig.Â 4. (XLS 1690Â kb)
DOI: 10.6084/m9.figshare.6742781.v1
title: Additional file 6 of Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

description: Table S2. Full detailed data used for the Fig.Â 4. (XLS 1690Â kb)
DOI: 10.6084/m9.figshare.6742757
title: Additional file 1: of Discovery of new Toxoplasma gondii antigenic proteins using a high throughput protein microarray approach screening sera of murine model infected orally with oocysts and tissue cysts

description: Table S1. 240 exon products reactive with murine sera comprising the mouse array TG4. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.6742757.v1
title: Additional file 1: of Discovery of new Toxoplasma gondii antigenic proteins using a high throughput protein microarray approach screening sera of murine model infected orally with oocysts and tissue cysts

description: Table S1. 240 exon products reactive with murine sera comprising the mouse array TG4. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.6742745
title: Additional file 4: of Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

description: Excel file specifying metabolites, reactions, genes contained, and databases IDs present in the iAA1259 metabolic model. (XLS 2531Â kb)
DOI: 10.6084/m9.figshare.6742745.v1
title: Additional file 4: of Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

description: Excel file specifying metabolites, reactions, genes contained, and databases IDs present in the iAA1259 metabolic model. (XLS 2531Â kb)
DOI: 10.5281/zenodo.3979452
title: Computational Implementation of "Uncoupling electrokinetic flow solutions", published in Mathematical Geosciences

description: This dataset includes Python and Mathematica scripts used to generate figures, and images used in the Mathematical Geosciences (MG) manuscript "Uncoupling Electrokinetic Flow Solutions" by Kuhlman and Malama (2020). Python scripts implementing eigenvalue uncoupling approach for differential equations governing 1D cylindrically symmetric electrokinetic flow problem (i.e., flow to a pumping well). mpmath python script (recombine-expint.py) implementing Theis "type curve" solution for an infinite domain (Figures 1-3 in MG manuscript) fipy python script (compare-via-fipy.py) and plotting script (plot_fipy_results.py) showing a finite-volume fully coupled solution for a similar finite domain for comparison against eigenvalue uncoupling approach (Figure 4 in MG manuscript). Also includes two shell scripts for driving python scripts for a variety of inputs. mathematica script (periodic-1D-steady-state-type-1.nb) for solving the algebra associated with the governing equations and plotting figures for analytical solution of periodically driven 1D solution (i.e., laboratory sinusoidal streaming potential and electroosmosis; Figures 4-9 in MG manuscript).
DOI: 10.5281/zenodo.3979451
title: Computational Implementation of "Uncoupling electrokinetic flow solutions", published in Mathematical Geosciences

description: This dataset includes Python and Mathematica scripts used to generate figures, and images used in the Mathematical Geosciences (MG) manuscript "Uncoupling Electrokinetic Flow Solutions" by Kuhlman and Malama (2020). Python scripts implementing eigenvalue uncoupling approach for differential equations governing 1D cylindrically symmetric electrokinetic flow problem (i.e., flow to a pumping well). mpmath python script (recombine-expint.py) implementing Theis "type curve" solution for an infinite domain (Figures 1-3 in MG manuscript) fipy python script (compare-via-fipy.py) and plotting script (plot_fipy_results.py) showing a finite-volume fully coupled solution for a similar finite domain for comparison against eigenvalue uncoupling approach (Figure 4 in MG manuscript). Also includes two shell scripts for driving python scripts for a variety of inputs. mathematica script (periodic-1D-steady-state-type-1.nb) for solving the algebra associated with the governing equations and plotting figures for analytical solution of periodically driven 1D solution (i.e., laboratory sinusoidal streaming potential and electroosmosis; Figures 4-9 in MG manuscript).
DOI: 10.6084/m9.figshare.6742721
title: Additional file 3: of Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

description: iAA1259 metabolic model in SBML format. (XML 4249Â kb)
DOI: 10.6084/m9.figshare.12889616
title: R0189_20170928a_videos

description: Rat 0189, skilled reaching data collected on 9/28/2017 in Leventhal laboratory by Alexandra Bova
DOI: 10.6084/m9.figshare.6742721.v1
title: Additional file 3: of Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

description: iAA1259 metabolic model in SBML format. (XML 4249Â kb)
DOI: 10.6084/m9.figshare.6742703
title: Additional file 2: of Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

description: Table S1. Biomass modifications and recalculation of ATP consumption. (XLS 81Â kb)
DOI: 10.6084/m9.figshare.6742703.v1
title: Additional file 2: of Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism

description: Table S1. Biomass modifications and recalculation of ATP consumption. (XLS 81Â kb)
DOI: 10.6084/m9.figshare.6742646
title: Additional file 5: of Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing

description: Table S4. Clonality calculations for the 69 P. vivax samples using the Fws (within-host heterozygosity) statistic and number of heterozygous calls in the core single nucleotide polymorphisms (SNPs). As expected, the majority of samples were monoclonal (97%) and only two samples (highlighted) were multiclonal based on Fwsâ â ¤â 0.95 and number of heterozygous calls greater than two times the median. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6742646.v1
title: Additional file 5: of Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing

description: Table S4. Clonality calculations for the 69 P. vivax samples using the Fws (within-host heterozygosity) statistic and number of heterozygous calls in the core single nucleotide polymorphisms (SNPs). As expected, the majority of samples were monoclonal (97%) and only two samples (highlighted) were multiclonal based on Fwsâ â ¤â 0.95 and number of heterozygous calls greater than two times the median. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6742616
title: Additional file 3: of Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing

description: Table S3. High quality single nucleotide polymorphisms in the core genome of the 69 P. vivax sequences. Samples are listed starting at column M and are labeled with the subject code followed by the day of collection. (XLSX 17419 kb)
DOI: 10.6084/m9.figshare.6742616.v1
title: Additional file 3: of Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing

description: Table S3. High quality single nucleotide polymorphisms in the core genome of the 69 P. vivax sequences. Samples are listed starting at column M and are labeled with the subject code followed by the day of collection. (XLSX 17419 kb)
DOI: 10.6084/m9.figshare.6742604
title: Additional file 2: of Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing

description: Table S2. Sequencing statistics for 69 Plasmodium vivax sequences collected in 3 villages in the Peruvian Amazon after alignment to the P. vivax reference genome. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6742604.v1
title: Additional file 2: of Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing

description: Table S2. Sequencing statistics for 69 Plasmodium vivax sequences collected in 3 villages in the Peruvian Amazon after alignment to the P. vivax reference genome. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.6742589
title: Additional file 1: of Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing

description: Table S1. Study information for 46 of the P. vivax whole genome sequences obtained from 3 villages surrounding Iquitos, Peru. Data for 23 subjects was unavailable. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6742589.v1
title: Additional file 1: of Exploration of Plasmodium vivax transmission dynamics and recurrent infections in the Peruvian Amazon using whole genome sequencing

description: Table S1. Study information for 46 of the P. vivax whole genome sequences obtained from 3 villages surrounding Iquitos, Peru. Data for 23 subjects was unavailable. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6742583
title: Additional file 2: of Potential gains in life expectancy by reducing inequality of lifespans in Denmark: an international comparison and cause-of-death analysis

description: Figure S2A and S2B. Death counts by cause-of-death group for Denmark (A) and Sweden (B). Colored-vertical lines indicate changes in ICD versions. For example, in the case of Denmark, the green vertical line indicates the change from ICD 7 to ICD 8, which was in 1969. (ZIP 269 kb)
DOI: 10.6084/m9.figshare.6742583.v1
title: Additional file 2: of Potential gains in life expectancy by reducing inequality of lifespans in Denmark: an international comparison and cause-of-death analysis

description: Figure S2A and S2B. Death counts by cause-of-death group for Denmark (A) and Sweden (B). Colored-vertical lines indicate changes in ICD versions. For example, in the case of Denmark, the green vertical line indicates the change from ICD 7 to ICD 8, which was in 1969. (ZIP 269 kb)
DOI: 10.6084/m9.figshare.6742571
title: Additional file 4 of Identification of candidate chemosensory genes in Mythimna separata by transcriptomic analysis

description: Table S3. Primers used in the qPCR analysis. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6742571.v1
title: Additional file 4 of Identification of candidate chemosensory genes in Mythimna separata by transcriptomic analysis

description: Table S3. Primers used in the qPCR analysis. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.6742547
title: Additional file 3: of Identification of candidate chemosensory genes in Mythimna separata by transcriptomic analysis

description: Comparison of chemosensory proteins identified in our study with previous work. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6742547.v1
title: Additional file 3: of Identification of candidate chemosensory genes in Mythimna separata by transcriptomic analysis

description: Comparison of chemosensory proteins identified in our study with previous work. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.6742529
title: Additional file 9: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Data extracted from the ixo files; the data are in Excel files with the endpoint analyses for all the individuals in all the three subpopulations. (ZIP 252 kb)
DOI: 10.6084/m9.figshare.6742529.v1
title: Additional file 9: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Data extracted from the ixo files; the data are in Excel files with the endpoint analyses for all the individuals in all the three subpopulations. (ZIP 252 kb)
DOI: 10.6084/m9.figshare.6742517
title: Additional file 8: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Original data. Each subfolder has two ixo files output by the Roche LightCycler480. The two files cover qPCR results for oca2 and mc1r. Subfolder names end in 1, 2, or 3, denoting which subpopulation of sperm was analyzed. (ZIP 10643 kb)
DOI: 10.6084/m9.figshare.6742517.v1
title: Additional file 8: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Original data. Each subfolder has two ixo files output by the Roche LightCycler480. The two files cover qPCR results for oca2 and mc1r. Subfolder names end in 1, 2, or 3, denoting which subpopulation of sperm was analyzed. (ZIP 10643 kb)
DOI: 10.6084/m9.figshare.6742493
title: Additional file 5: of Dipeptide repeat proteins activate a heat shock response found in C9ORF72-ALS/FTLD patients

description: Table S3. Genes significantly changes in RNA-seq analysis from ALS patients. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.6742493.v1
title: Additional file 5: of Dipeptide repeat proteins activate a heat shock response found in C9ORF72-ALS/FTLD patients

description: Table S3. Genes significantly changes in RNA-seq analysis from ALS patients. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.6742472
title: Additional file 5: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Excel workbooks that were used for the simulation experiments. Each file has an overview sheet that details the analysis structure. (XLSM 291 kb)
DOI: 10.6084/m9.figshare.6742472.v1
title: Additional file 5: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Excel workbooks that were used for the simulation experiments. Each file has an overview sheet that details the analysis structure. (XLSM 291 kb)
DOI: 10.6084/m9.figshare.6742451
title: Additional file 4: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Excel workbooks that were used for the simulation experiments. Each file has an overview sheet that details the analysis structure. (XLSM 589 kb)
DOI: 10.6084/m9.figshare.6742451.v1
title: Additional file 4: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Excel workbooks that were used for the simulation experiments. Each file has an overview sheet that details the analysis structure. (XLSM 589 kb)
DOI: 10.6084/m9.figshare.6742439
title: Additional file 9: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

description: Table S7. Summary table for count values of sQTLs and eeQTLs in white blood and milk cells. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6742439.v1
title: Additional file 9: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

description: Table S7. Summary table for count values of sQTLs and eeQTLs in white blood and milk cells. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6742430
title: Additional file 9: of Identification and validation of single-sample breast cancer radiosensitivity gene expression predictors

description: Table S2. Patient characteristics per cohort, estrogen receptor status and radiotherapy status. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.6742430.v1
title: Additional file 9: of Identification and validation of single-sample breast cancer radiosensitivity gene expression predictors

description: Table S2. Patient characteristics per cohort, estrogen receptor status and radiotherapy status. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.6742421
title: Additional file 8: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

description: Table S6. Summary of significant cis splicing sQTLs (within 1Â Mb distance to the exon). (XLSX 14902 kb)
DOI: 10.6084/m9.figshare.6742424
title: Additional file 2: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Excel workbook which enumerates the phenotypes and numbers of sperm, as single cells or clusters of cells in untreated and dye-treated samples. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6742421.v1
title: Additional file 8: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

description: Table S6. Summary of significant cis splicing sQTLs (within 1Â Mb distance to the exon). (XLSX 14902 kb)
DOI: 10.6084/m9.figshare.6742424.v1
title: Additional file 2: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Excel workbook which enumerates the phenotypes and numbers of sperm, as single cells or clusters of cells in untreated and dye-treated samples. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6742400
title: Additional file 7: of Identification and validation of single-sample breast cancer radiosensitivity gene expression predictors

description: Table S4. Univariable and multivariable Cox -models for the ER+ tumors including variables of “Give RT” vs “No RT” and “Give more treatment”, radiotherapy, and the interaction term between the prediction variable and RT. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.6742397
title: Additional file 7: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

description: Table S5. Genes that display significant differential splicing between breeds. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.6742400.v1
title: Additional file 7: of Identification and validation of single-sample breast cancer radiosensitivity gene expression predictors

description: Table S4. Univariable and multivariable Cox -models for the ER+ tumors including variables of “Give RT” vs “No RT” and “Give more treatment”, radiotherapy, and the interaction term between the prediction variable and RT. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.6742397.v1
title: Additional file 7: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

description: Table S5. Genes that display significant differential splicing between breeds. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.6742394
title: Additional file 12: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Excel file with 10 worksheets documenting the statistical analyses of the relative allelic contents of the wells for each subpopulation. Worksheets 2, 5, and 8 contain the data on allelic proportions for the three subpopulations. Worksheets 3, 6, and 9 convert the relative allelic concentrations of the two loci into designations of HOM or HET for each well. These worksheets are interactive; change the integer in the yellow box and read out tallies of HOM and HET in the green boxes (maximum integer valueâ =â 30). Worksheets 4, 7, and 10 contain the results of the analyses for the three subpopulations. Worksheet 11 compares results for the three subpopulations and also for subpopulations 2 and 3, combined. (XLSX 801 kb)
DOI: 10.6084/m9.figshare.6742394.v1
title: Additional file 12: of Unique sperm haplotypes are associated with phenotypically different sperm subpopulations in Astyanax fish

description: Excel file with 10 worksheets documenting the statistical analyses of the relative allelic contents of the wells for each subpopulation. Worksheets 2, 5, and 8 contain the data on allelic proportions for the three subpopulations. Worksheets 3, 6, and 9 convert the relative allelic concentrations of the two loci into designations of HOM or HET for each well. These worksheets are interactive; change the integer in the yellow box and read out tallies of HOM and HET in the green boxes (maximum integer valueâ =â 30). Worksheets 4, 7, and 10 contain the results of the analyses for the three subpopulations. Worksheet 11 compares results for the three subpopulations and also for subpopulations 2 and 3, combined. (XLSX 801 kb)