cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11328419.v5
title: zebrafish patterns simulated with stochastic length scales

description: We provide model simulations of wild-type, shady, nacre, and pfeffer zebrafish patterns generated using a modified version of the the agent-based model from "Volkening A and Sandstede B (2018) Iridophores as a source of robustness in zebrafish stripes and variability in Danio patterns. Nat. Commun. 9(3231)." These simulations were generated by choosing each length scale parameter in the model randomly per cell and per day from a normal distribution. The mean of the normal distributions was set to the default parameter value (presented in the aforementioned paper) for each parameter. We varied the standard deviation of the noise across the simulations and this information is stored in the file names. For example, WT_sigma_1 corresponds to stochastic wild type simulations with a standard deviation set to 1% the parameter means. <br>The shady patterns were generated by turning off cell birth for iridiopores; the nacre patterns were generated by turning off cell birth for melanophores; and, the pfeffer patterns were generated by turning off cell birth for xanthophores (see reference above for details). All simulations were run in MATLAB.<br>Each simulation output contains data in the form of .mat files. Within each .mat file are the cell locations of all cells across the simulation, an array that tracks the distances that the cells moved throughout the simulation, vectors containing the number of cells born/dead/present at each day of the simulation, and the x- and y-boundaries of the domain for each day of the simulations. The cell locations are stored in N X 2 X T arrays, where N is an upper bound on the total number of cells in the simulation, and T is the number of days that the simulation was run for. For example, cellsM(1:N_M,:,T) contains the x- and y-coordinates of the melanophore cells on the last day of the simulation. Similarly, cellsIl contains the cell coordinates of the loose iridophores, cellsId contains the cell coordinates of the dense iridophores, cellsXc contains the cell coordinates of the dense xanthophores, and cellsXsn contains the cell coordinates of the loose xanthophores.
DOI: 10.6084/m9.figshare.11328206
title: s pombe files

description: S pombe<br>
DOI: 10.6084/m9.figshare.11328203
title: d melanogaster files

description: D melanogaster<br>
DOI: 10.6084/m9.figshare.11328206.v1
title: s pombe files

description: S pombe<br>
DOI: 10.6084/m9.figshare.11328197
title: h sapiens files

description: H sapiens files<br>
DOI: 10.6084/m9.figshare.11328200
title: m musculus files

description: M musculus<br>
DOI: 10.6084/m9.figshare.11328203.v1
title: d melanogaster files

description: D melanogaster<br>
DOI: 10.6084/m9.figshare.11328227.v1
title: Forest soil microbes

description: Soil microbes across eastern China
DOI: 10.6084/m9.figshare.11328188
title: c elegans files

description: C elegans<br>
DOI: 10.6084/m9.figshare.11328200.v1
title: m musculus files

description: M musculus<br>
DOI: 10.6084/m9.figshare.11328197.v1
title: h sapiens file

description: H sapiens files<br>
DOI: 10.6084/m9.figshare.11328227.v2
title: Forest soil microbes

description: Soil microbes across eastern China
DOI: 10.6084/m9.figshare.11328176
title: human

description: Human
DOI: 10.6084/m9.figshare.11328227.v5
title: Forest soil microbes

description: Soil microbes across eastern China
DOI: 10.6084/m9.figshare.11328227
title: Forest soil microbes

description: Soil microbes across eastern China
DOI: 10.6084/m9.figshare.11328110
title: Table S1. Museum Specimens Information Piezogaster reclusus Bugs.docx

description: This table contains the information of collected specimens from bugs living on acacia ant-defended trees (<i>Piezogaster reclusus </i>and <i>P. chontalensis</i>), from Panama and Costa Rica. The table includes information of the collection site, sex of the animal, and museum collection. <br>
DOI: 10.6084/m9.figshare.11328110.v1
title: Table S1. Museum Specimens Information Piezogaster reclusus Bugs.docx

description: This table contains the information of collected specimens from bugs living on acacia ant-defended trees (<i>Piezogaster reclusus </i>and <i>P. chontalensis</i>), from Panama and Costa Rica. The table includes information of the collection site, sex of the animal, and museum collection. <br>
DOI: 10.6084/m9.figshare.11327981
title: Genome assembly of the yellow drum (Nibea albiflora)

description: We sequenced a gynogenetic yellow drum and assembled a near-complete genome. A total of 42.96 Gb of Illumina short-reads and 80.27 Gb of PacBio long-reads were generated and assembled into a 628.01 Mb genome with a contig N50 length of 4.42 Mb. Hi-C analysis resulted in the identification of 24 chromosomes with a scaffold N50 of 26.73 Mb. The mtDNA was also assembled.
DOI: 10.6084/m9.figshare.11327927
title: Tree species richness and composition in a fragmented landscape of the Brazilian lowland Atlantic Forest - Appendix

description: <b>Appendix</b> – List of tree species in seven remnants in the São João river basin, Rio de Janeiro, Brazil.<br>Tropical forests are one of the most important ecosystems and loss of biological diversity in these is a major concern. We studied seven forest remnants on the coast of Rio de Janeiro, southeastern Brazil, three medium-sized (24–63 ha) and four small (5–11 ha), to assess the influence of size, degree of disturbance and isolation on composition and diversity of the tree layer. A total of 443 species in 60 families and 185 genera were recorded, with Myrtaceae, Lauraceae and Fabaceae being the most species-rich families. The results showed areas of high α-diversity (α= 34.86–75.69) and a slightly greater decline of similarity with distance between the study areas. Remnant size not explained the variation in the species composition and we found correlation between the level of disturbance and the floristic composition. The remnants had low floristic similarity, strongly influenced by the degree of disturbance. Results suggest that disturbance influences composition and diversity and confirm the importance of including both medium-sized and small remnants in the conservation of tropical forest diversity.
DOI: 10.6084/m9.figshare.11327822
title: Supplemental Table 4 TASK-3 TAC Heart Weights

description: <b>Supplemental Table 4. TASK-3 Global KO TAC Experiment Heart Weights</b> Wild Type and TASK-3 KO mice after Transverse Aortic Constriction (TAC) underwent measurement of average Body Weight, Tibia Length, Cardiac Chamber weight (Left and Right Ventricle; Left and Right Atria) indexed to either Body Weight or Tibial Length. Statistical comparisons were made using a One-Way ANOVA with Bonferroni’s test for multiple comparisons, *p&lt;0.05 vs Wild Type Sham, †p&lt;0.05 vs Wild Type TAC, ‡p&lt;0.05 vs TASK-1 KO Sham.
DOI: 10.6084/m9.figshare.11327927.v1
title: Tree species richness and composition in a fragmented landscape of the Brazilian lowland Atlantic Forest - Appendix

description: <b>Appendix</b> – List of tree species in seven remnants in the São João river basin, Rio de Janeiro, Brazil.<br>Tropical forests are one of the most important ecosystems and loss of biological diversity in these is a major concern. We studied seven forest remnants on the coast of Rio de Janeiro, southeastern Brazil, three medium-sized (24–63 ha) and four small (5–11 ha), to assess the influence of size, degree of disturbance and isolation on composition and diversity of the tree layer. A total of 443 species in 60 families and 185 genera were recorded, with Myrtaceae, Lauraceae and Fabaceae being the most species-rich families. The results showed areas of high α-diversity (α= 34.86–75.69) and a slightly greater decline of similarity with distance between the study areas. Remnant size not explained the variation in the species composition and we found correlation between the level of disturbance and the floristic composition. The remnants had low floristic similarity, strongly influenced by the degree of disturbance. Results suggest that disturbance influences composition and diversity and confirm the importance of including both medium-sized and small remnants in the conservation of tropical forest diversity.
DOI: 10.6084/m9.figshare.11327615
title: Supplemental Table 3 TASK-3 Echo

description: <b>Supplemental Table 3. TASK-3 Serial Echocardiography after Pressure Overload (TAC) </b> Wild Type and TASK-3 KO mice after Transverse Aortic Constriction (TAC) underwent serial echocardiography measurements of Left Ventricular End Diastolic Dimension (LVEDD), End Systolic Dimension (LVESD), Septal Wall Thickness (SWT), Posterior Wall Thickness (PWT), Heart Rate (HR), LV mass, Relative Wall Thickness (RWT = PWT x 2/ LVEDD), Fraction Shortening (FS= (LVEDD-LVESD)/LVEDD X 100), mean rate corrected velocity of circumferential shortening (mVcFc= Fractional Shortening/ (Aortic Ejection Time/√60/Heart Rate)). Statistical comparison between Wild Type and TASK-1 KO were made using a non-paired two tailed t-test. *p&lt;0.05 vs Wild Type
DOI: 10.6084/m9.figshare.11327822.v1
title: Supplemental Table 4 TASK-3 TAC Heart Weights

description: <b>Supplemental Table 4. TASK-3 Global KO TAC Experiment Heart Weights</b> Wild Type and TASK-3 KO mice after Transverse Aortic Constriction (TAC) underwent measurement of average Body Weight, Tibia Length, Cardiac Chamber weight (Left and Right Ventricle; Left and Right Atria) indexed to either Body Weight or Tibial Length. Statistical comparisons were made using a One-Way ANOVA with Bonferroni’s test for multiple comparisons, *p&lt;0.05 vs Wild Type Sham, †p&lt;0.05 vs Wild Type TAC, ‡p&lt;0.05 vs TASK-1 KO Sham.
DOI: 10.6084/m9.figshare.11327201
title: Supplemental Table 1 TASK-1 Echo

description: <b>Supplemental Table 1. TASK-1 Serial Echocardiography after Pressure Overload (TAC) </b> Wild Type and TASK-1 KO mice after Transverse Aortic Constriction (TAC) underwent serial echocardiography measurements of Left Ventricular End Diastolic Dimension (LVEDD), End Systolic Dimension (LVESD), Septal Wall Thickness (SWT), Posterior Wall Thickness (PWT), Heart Rate (HR), LV mass, Relative Wall Thickness (RWT = PWT x 2/ LVEDD), Fraction Shortening (FS= (LVEDD-LVESD)/LVEDD X 100), mean rate corrected velocity of circumferential shortening (mVcFc= Fractional Shortening/ (Aortic Ejection Time/√60/Heart Rate)). Statistical comparison between Wild Type and TASK-1 KO were made using a non-paired two tailed t-test. *p&lt;0.05 vs Wild Type
DOI: 10.6084/m9.figshare.11327363
title: Supplemental Table 2 TASK-1 TAC Heart Weights

description: <b>Supplemental Table 2. TASK-1 Global KO TAC Experiment Heart Weights</b> Wild Type and TASK-1 KO mice after Transverse Aortic Constriction (TAC) underwent measurement of average Body Weight, Tibia Length, Cardiac Chamber weight (Left and Right Ventricle; Left and Right Atria) indexed to either Body Weight or Tibial Length. Statistical comparisons were made using a One-Way ANOVA with Bonferroni’s test for multiple comparisons, *p&lt;0.05 vs Wild Type Sham, †p&lt;0.05 vs Wild Type TAC, ‡p&lt;0.05 vs TASK-1 KO Sham.
DOI: 10.6084/m9.figshare.11327363.v1
title: Supplemental Table 2 TASK-1 TAC Heart Weights

description: <b>Supplemental Table 2. TASK-1 Global KO TAC Experiment Heart Weights</b> Wild Type and TASK-1 KO mice after Transverse Aortic Constriction (TAC) underwent measurement of average Body Weight, Tibia Length, Cardiac Chamber weight (Left and Right Ventricle; Left and Right Atria) indexed to either Body Weight or Tibial Length. Statistical comparisons were made using a One-Way ANOVA with Bonferroni’s test for multiple comparisons, *p&lt;0.05 vs Wild Type Sham, †p&lt;0.05 vs Wild Type TAC, ‡p&lt;0.05 vs TASK-1 KO Sham.
DOI: 10.6084/m9.figshare.11327201.v1
title: Supplemental Table 1 TASK-1 Echo

description: <b>Supplemental Table 1. TASK-1 Serial Echocardiography after Pressure Overload (TAC) </b> Wild Type and TASK-1 KO mice after Transverse Aortic Constriction (TAC) underwent serial echocardiography measurements of Left Ventricular End Diastolic Dimension (LVEDD), End Systolic Dimension (LVESD), Septal Wall Thickness (SWT), Posterior Wall Thickness (PWT), Heart Rate (HR), LV mass, Relative Wall Thickness (RWT = PWT x 2/ LVEDD), Fraction Shortening (FS= (LVEDD-LVESD)/LVEDD X 100), mean rate corrected velocity of circumferential shortening (mVcFc= Fractional Shortening/ (Aortic Ejection Time/√60/Heart Rate)). Statistical comparison between Wild Type and TASK-1 KO were made using a non-paired two tailed t-test. *p&lt;0.05 vs Wild Type
DOI: 10.6084/m9.figshare.11327615.v1
title: Supplemental Table 3 TASK-3 Echo

description: <b>Supplemental Table 3. TASK-3 Serial Echocardiography after Pressure Overload (TAC) </b> Wild Type and TASK-3 KO mice after Transverse Aortic Constriction (TAC) underwent serial echocardiography measurements of Left Ventricular End Diastolic Dimension (LVEDD), End Systolic Dimension (LVESD), Septal Wall Thickness (SWT), Posterior Wall Thickness (PWT), Heart Rate (HR), LV mass, Relative Wall Thickness (RWT = PWT x 2/ LVEDD), Fraction Shortening (FS= (LVEDD-LVESD)/LVEDD X 100), mean rate corrected velocity of circumferential shortening (mVcFc= Fractional Shortening/ (Aortic Ejection Time/√60/Heart Rate)). Statistical comparison between Wild Type and TASK-1 KO were made using a non-paired two tailed t-test. *p&lt;0.05 vs Wild Type
DOI: 10.6084/m9.figshare.11324024
title: Results_Cuyapo, SJC and Talavera.xlsx

description: The data tagged as results are statistical analysis from raw data on morphometry of Bactrocera dorsalis reared-out from isofemales. Measurements were compared statistically by offspring of one female, by sex and by geographic location.
DOI: 10.6084/m9.figshare.11324024.v1
title: Results_Cuyapo, SJC and Talavera.xlsx

description: The data tagged as results are statistical analysis from raw data on morphometry of Bactrocera dorsalis reared-out from isofemales. Measurements were compared statistically by offspring of one female, by sex and by geographic location.
DOI: 10.6084/m9.figshare.11323976
title: Data for "Invasive plants facilitated by socioeconomic change harbor vectors of scrub typhus and spotted fever"

description: Original data set for "Invasive plants facilitated by socioeconomic change harbor vectors of scrub typhus and spotted fever" published in PLoS Neglected Tropical Diseases
DOI: 10.6084/m9.figshare.11323976.v1
title: Data for "Invasive plants facilitated by socioeconomic change harbor vectors of scrub typhus and spotted fever"

description: Original data set for "Invasive plants facilitated by socioeconomic change harbor vectors of scrub typhus and spotted fever" published in PLoS Neglected Tropical Diseases
DOI: 10.6084/m9.figshare.11323838
title: Default simulations of zebrafish patterns

description: We provide model simulations of wild-type, shady, nacre, and pfeffer zebrafish patterns generated using the agent-based model from "Volkening A and Sandstede B (2018) Iridophores as a source of robustness in zebrafish stripes and variability in Danio patterns. Nat. Commun. 9(3231)." These simulations were generated under the default parameter regime presented in the paper. The shady patterns were generated by turning off cell birth for iridiopores; the nacre patterns were generated by turning off cell birth for melanophores; and, the pfeffer patterns were generated by turning off cell birth for xanthophores (see reference above for details). All simulations were run in MATLAB. <br>Each simulation output contains data in the form of .mat files. Within each .mat file are the cell locations of all cells across the simulation, an array that tracks the distances that the cells moved throughout the simulation, vectors containing the number of cells born/dead/present at each day of the simulation, and the x- and y-boundaries of the domain for each day of the simulations. The cell locations are stored in N X 2 X T arrays, where N is an upper bound on the total number of cells in the simulation, and T is the number of days that the simulation was run for. For example, cellsM(N_M:,:,T) contains the x- and y-coordinates of the melanophore cells on the last day of the simulation. Similarly, cellsIl contains the cell coordinates of the loose iridophores, cellsId contains the cell coordinates of the dense iridophores, cellsXc contains the cell coordinates of the dense xanthophores, and cellsXsn contains the cell coordinates of the loose xanthophores. <br><br><br>
DOI: 10.6084/m9.figshare.11323724
title: Metadata record for: PGxCorpus, a manually annotated corpus for pharmacogenomics

description: This dataset contains key characteristics about the data described in the Data Descriptor PGxCorpus, a manually annotated corpus for pharmacogenomics. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11323724.v2
title: Metadata record for: PGxCorpus, a manually annotated corpus for pharmacogenomics

description: This dataset contains key characteristics about the data described in the Data Descriptor PGxCorpus, a manually annotated corpus for pharmacogenomics. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.11323724.v1
title: Metadata record for: PGxCorpus, a manually annotated corpus for pharmacogenomics

description: This dataset contains key characteristics about the data described in the Data Descriptor PGxCorpus, a manually annotated corpus for pharmacogenomics. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.11323559
title: LOGITECH 2 CAMERAS DATA PUPIL ALONE_1.sav

description: The pupil sizes observed from the different thresholds of corneal pain stratified by modality and sex.<br>
DOI: 10.6084/m9.figshare.11323538
title: Supplementary Material for: Allergic Rhinitis to Weed Pollen in Germany: Dominance by Plantain, Rising Prevalence, and Polysensitization Rates over 20 Years

description: <b><i>Background:</i></b> In contrast to the 3 major aeroallergens tree pollen, grass pollen, and house dust mites, allergic rhinitis caused by herbal pollen has received comparatively little attention in recent clinical studies. Since various weeds flower during summer until fall, allergic rhinitis to weeds may be underdiagnosed and/or mistakenly diagnosed as grass pollen allergy. <b><i>Objective:</i></b> To investigate (i) the currently most frequent weed allergy between mugwort, ragweed, plantain, chamomile, nettle, and oilseed rape and (ii) time trends in prevalence of sensitization to weed pollen in the middle of Germany over the last 20 years. <b><i>Methods:</i></b> This study, the largest of its kind to date, monocentrically evaluated the prick test results of a total of 6,220 patients with suspected RCA over a period of 20 years (1998–2017). <b><i>Results:</i></b> In the study cohort, sensitization rates to plantain almost doubled from 26.6% in the decade 1998–2007 to 50.5% in 2008–2017. Identical increases were observed for ragweed, while sensitization rates for mugwort stayed largely unchanged. The most prominent increase in positive skin prick tests to plantain and ragweed pollen was mainly observed in younger patients. Further, we identified a trend toward polysensitization, currently dominated by plantain and ragweed. Sensitization to weed pollen was found to be highly associated with additional sensitizations to grass and/or birch pollen. <b><i>Conclusion:</i></b> Plantain is currently the best choice to screen rhinitis patients for weed allergy which identifies 86% of all weed-sensitized individuals, at least in Germany. Over the last 20 years, we demonstrate a significant rise in the total number of weed pollen sensitization as well as increases in polysensitization, predominantly in younger patients.
DOI: 10.6084/m9.figshare.11323538.v1
title: Supplementary Material for: Allergic Rhinitis to Weed Pollen in Germany: Dominance by Plantain, Rising Prevalence, and Polysensitization Rates over 20 Years

description: <b><i>Background:</i></b> In contrast to the 3 major aeroallergens tree pollen, grass pollen, and house dust mites, allergic rhinitis caused by herbal pollen has received comparatively little attention in recent clinical studies. Since various weeds flower during summer until fall, allergic rhinitis to weeds may be underdiagnosed and/or mistakenly diagnosed as grass pollen allergy. <b><i>Objective:</i></b> To investigate (i) the currently most frequent weed allergy between mugwort, ragweed, plantain, chamomile, nettle, and oilseed rape and (ii) time trends in prevalence of sensitization to weed pollen in the middle of Germany over the last 20 years. <b><i>Methods:</i></b> This study, the largest of its kind to date, monocentrically evaluated the prick test results of a total of 6,220 patients with suspected RCA over a period of 20 years (1998–2017). <b><i>Results:</i></b> In the study cohort, sensitization rates to plantain almost doubled from 26.6% in the decade 1998–2007 to 50.5% in 2008–2017. Identical increases were observed for ragweed, while sensitization rates for mugwort stayed largely unchanged. The most prominent increase in positive skin prick tests to plantain and ragweed pollen was mainly observed in younger patients. Further, we identified a trend toward polysensitization, currently dominated by plantain and ragweed. Sensitization to weed pollen was found to be highly associated with additional sensitizations to grass and/or birch pollen. <b><i>Conclusion:</i></b> Plantain is currently the best choice to screen rhinitis patients for weed allergy which identifies 86% of all weed-sensitized individuals, at least in Germany. Over the last 20 years, we demonstrate a significant rise in the total number of weed pollen sensitization as well as increases in polysensitization, predominantly in younger patients.
DOI: 10.6084/m9.figshare.11323463
title: Supp_material_Merdithetal_Frontiers.zip

description: Supplementary Material for:<br>Merdith AS, Atkins SE and Tetley MG (2019) Tectonic Controls on Carbon and Serpentinite Storage in Subducted Upper Oceanic Lithosphere for the Past 320 Ma. Front. Earth Sci. 7:332. doi: 10.3389/feart.2019.00332<br>