cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25402/fsg.11284484.v1
title: An efficient and novel technology for the extraction of parasite genomic DNA from whole blood or culture

description: Supplemental file 1 for: An efficient and novel technology for the extraction of parasite genomic DNA from whole blood or culture Supplementary Figure 1: Plasmodium falciparumDNA from spiked whole blood determined by PfBetatubulin PCR. A and B. low volume eluate template, 1 μl C and D. high volume eluate template, 10 μl. Two extractions run per parasitaemia condition. M: 100bp marker, NTC: No template control. Percentage denotes the parasitaemia post spiking. Supplementary Figure 2: Plasmodium falciparumDNA from spiked whole blood determined by PfBetatubulin PCR. A and B. low volume eluate template, 1 μl C and D. high volume eluate template, 10 μl. Two extractions run per parasitaemia condition. M: 100bp marker, NTC: No template control. Percentage denotes the parasitaemia post spiking.
DOI: 10.6084/m9.figshare.11284352
title: S1 File. Daily microclimatic variation in study area (Caquetá, Colombia).txt

description: Daily microclimatic variation in study area (Caquetá, Colombia)
DOI: 10.6084/m9.figshare.11284352.v1
title: S1 File. Daily microclimatic variation in study area (Caquetá, Colombia).txt

description: Daily microclimatic variation in study area (Caquetá, Colombia)
DOI: 10.6084/m9.figshare.11284427.v1
title: S2 File. Daily net CO2 assimilation rate (A) in 10 rubber tree clones

description: Daily net CO<sub>2</sub> assimilation rate (<i>A</i>) in 10 rubber tree (<i>Hevea brasiliensis</i>) clones under two climatic periods at three sites in Caquetá (Colombia). <br>
DOI: 10.6084/m9.figshare.11283848
title: master_reg_2_22_19.dta

description: Banking data
DOI: 10.6084/m9.figshare.11283848.v1
title: master_reg_2_22_19.dta

description: Banking data
DOI: 10.6084/m9.figshare.11283845
title: t10master5_u.dta

description: Banking data
DOI: 10.6084/m9.figshare.11283845.v1
title: t10master5_u.dta

description: Banking data
DOI: 10.6084/m9.figshare.11283407
title: Metadata record for: Interaction data from the Copenhagen Networks Study

description: This dataset contains key characteristics about the data described in the Data Descriptor Interaction data from the Copenhagen Networks Study. <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.11283407.v2
title: Metadata record for: Interaction data from the Copenhagen Networks Study

description: This dataset contains key characteristics about the data described in the Data Descriptor Interaction data from the Copenhagen Networks Study. <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: 10.17866/rd.salford.11283299
title: Norther Voices Opera Project - Read First

description: a "how to" guide to this collection
DOI: 10.6084/m9.figshare.11283233
title: Data for "The evolving distribution of relative humidity conditional upon daily maximum temperature in a warming climate"

description: This dataset includes results data for the study "The evolving distribution of relative humidity conditional upon daily maximum temperature in a warming climate"<br>Files titled with "***_QR_RH_on_Tmax_***_group*_***.Rdata" are estimated quantiles of relative humidity conditional upon daily maximum temperatures. Where, CHI, PHX, NOLA, and NYC represent Chicago, Phoenix, New Orlean, and New York City, respectively. JUL represents July. Group1, 2, and 3 represent three different time periods: 1990-2005, 2026-2035, 2071-2080. Each file contains three variables: z is the estimated values of relative humidity at specified quantiles; q denotes the 11 selected quantiles (0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90, 0.95); tmax_sub is the evenly spaced daily maximum temperature intervals.These files are in format of .Rdata, which could be opened and processed by software R or R-studio. <br><br>The Distributions of dew point and heat wave index are converted from the conditional quantiles of relative humidity on temperature. The dew point is calculated based on the equation (4) and (5) of this study. The heat wave index is calculated based on the equation (6) of the study.
DOI: 10.6084/m9.figshare.11283407.v1
title: Metadata record for: Interaction data from the Copenhagen Networks Study

description: This dataset contains key characteristics about the data described in the Data Descriptor Interaction data from the Copenhagen Networks Study. <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.11283758.v1
title: Global Hydropower Database (GHD)

description: GHD comprises 8738 hydropower plants distributed across 134 countries.
DOI: 10.17866/rd.salford.11283299.v1
title: Norther Voices Opera Project - Read First

description: a "how to" guide to this collection
DOI: 10.6084/m9.figshare.11283128
title: A multi-omics approach reveals mechanisms of nanomaterial toxicity and structure–activity relationships in alveolar macrophages

description: In respect to the high number of released nanomaterials and their highly variable properties, novel grouping approaches are required based on the effects of nanomaterials. Proper grouping calls for a combination of an experimental setup with a higher number of structurally similar nanomaterials and for employing integrated omics approaches to identify the mode of action. Here, we analyzed the effects of seven well-characterized NMs comprising different chemical compositions, sizes and chemical surface modifications on the rat alveolar macrophage cell line NR8383. The NMs were investigated at three doses ranging from 2.5 to 10 µg/cm<sup>2</sup> after 24 h incubation using an integrated multi-omics approach involving untargeted proteomics, targeted metabolomics, and src homology 2 (SH2) profiling. By using Weighted Gene Correlation Network Analysis (WGCNA) for the integrative data, we identified correlations of molecular pathways with physico-chemical properties and toxicological endpoints. The three investigated SiO2 variants induced strong alterations in all three omics approaches and were, therefore, be classified as “active.” Two organic phthalocyanines showed minor responses and Mn2O3 induced a different molecular response pattern than the other NMs. WGCNA revealed that agglomerate size and surface area as well as LDH release are among the most important parameters correlating with nanotoxicology. Moreover, we identified key drivers that can serve as representative biomarker candidates, supporting the value of multi-omics approaches to establish integrated approaches to testing and assessment (IATAs).
DOI: 10.6084/m9.figshare.11283224
title: Rattlesnake Recombination Maps

description: Recombination maps inferred using LDhelmet from whole genome resequencing data of the prairie rattlesnake (<i>Crotalus viridis</i>) and northern Pacific rattlesnake (<i>Crotalus oreganus</i>).
DOI: 10.6084/m9.figshare.11283233.v2
title: Data for "The evolving distribution of relative humidity conditional upon daily maximum temperature in a warming climate"

description: This dataset includes results data for the study "The evolving distribution of relative humidity conditional upon daily maximum temperature in a warming climate"<br>Files titled with "***_QR_RH_on_Tmax_***_group*_***.Rdata" are estimated quantiles of relative humidity conditional upon daily maximum temperatures. Where, CHI, PHX, NOLA, and NYC represent Chicago, Phoenix, New Orlean, and New York City, respectively. JUL represents July. Group1, 2, and 3 represent three different time periods: 1990-2005, 2026-2035, 2071-2080. Each file contains three variables: z is the estimated values of relative humidity at specified quantiles; q denotes the 11 selected quantiles (0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90, 0.95); tmax_sub is the evenly spaced daily maximum temperature intervals.These files are in format of .Rdata, which could be opened and processed by software R or R-studio. <br><br>The Distributions of dew point and heat wave index are converted from the conditional quantiles of relative humidity on temperature. The dew point is calculated based on the equation (4) and (5) of this study. The heat wave index is calculated based on the equation (6) of the study.
DOI: 10.6084/m9.figshare.11283128.v1
title: A multi-omics approach reveals mechanisms of nanomaterial toxicity and structure–activity relationships in alveolar macrophages

description: In respect to the high number of released nanomaterials and their highly variable properties, novel grouping approaches are required based on the effects of nanomaterials. Proper grouping calls for a combination of an experimental setup with a higher number of structurally similar nanomaterials and for employing integrated omics approaches to identify the mode of action. Here, we analyzed the effects of seven well-characterized NMs comprising different chemical compositions, sizes and chemical surface modifications on the rat alveolar macrophage cell line NR8383. The NMs were investigated at three doses ranging from 2.5 to 10 µg/cm<sup>2</sup> after 24 h incubation using an integrated multi-omics approach involving untargeted proteomics, targeted metabolomics, and src homology 2 (SH2) profiling. By using Weighted Gene Correlation Network Analysis (WGCNA) for the integrative data, we identified correlations of molecular pathways with physico-chemical properties and toxicological endpoints. The three investigated SiO2 variants induced strong alterations in all three omics approaches and were, therefore, be classified as “active.” Two organic phthalocyanines showed minor responses and Mn2O3 induced a different molecular response pattern than the other NMs. WGCNA revealed that agglomerate size and surface area as well as LDH release are among the most important parameters correlating with nanotoxicology. Moreover, we identified key drivers that can serve as representative biomarker candidates, supporting the value of multi-omics approaches to establish integrated approaches to testing and assessment (IATAs).
DOI: 10.6084/m9.figshare.11283233.v1
title: The evolving distribution of relative humidity conditional upon daily maximum temperature in a warming climate

description: This dataset includes results data for the study "The evolving distribution of relative humidity conditional upon daily maximum temperature in a warming climate". <br>Files titled with "QR_RH_on_Tmax_***_group*_***.Rdata" are estimated quantiles of relative humidity conditional upon daily maximum temperatures. Where, JUN, JUL, AUG represents months: June, July, August, respectively. Group1, 2, and 3 represent three different time periods: 1990-2005, 2026-2035, 2071-2080. CHI, PHX, NOLA, and NYC represent Chicago, Phoenix, New Orlean, and New York City, respectively. Each file contains three variables: z is the estimated values of relative humidity at specified quantiles; q denotes the 11 selected quantiles (0.05, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90, 0.95); tmax_sub is the evenly spaced daily maximum temperature intervals.These files are in format of .Rdata, which could be opened and processed by software R or R-studio. <br><br>The Distributions of dew point and heat wave index are converted from the conditional quantiles of relative humidity on temperature. The dew point is calculated based on the equation 4 and 5 of this study. The heat wave index is calculated based on the empirical equation developed by Rothfusz (1990).
DOI: 10.6084/m9.figshare.11283044
title: Hydraulic potential energy model for hydropower operation in mixed reservoir system

description: Medium- and short-term operation data<br>
DOI: 10.6084/m9.figshare.11283038
title: Tissue factor in ulcerative colitis, with and without concomitant primary sclerosing cholangitis

description: <b>Background:</b> Ulcerative colitis (UC) in patients with the severe disease primary sclerosing cholangitis (PSC) constitutes a distinct clinical phenotype (PSC-UC) with a high incidence of colorectal cancer. Today, PSC-UC diagnosis is built on clinical observations only. Tissue factor (TF) has a potential use in UC diagnostics, and also in colorectal cancer prognostication. Here we evaluate TF expression in an inflammatory bowel disease (IBD) cohort, with special focus on differences between UC and PSC-UC patients. <b>Materials and methods:</b> Colonic biopsies from UC (<i>n</i> = 23), PSC (<i>n</i> = 24), and healthy controls (<i>n</i> = 11) were stained for TF by immunohistochemistry. Mononuclear cell contribution to TF expression was verified using flow cytometry. <b>Results:</b> TF was distributed at three distinct colonic locations: in subepithelial pericryptal sheath cells, in mononuclear cells, and in the intestinal stroma. In contrast to UC—where inflammation was accompanied with TF up-regulation—PSC-UC activity remained low during inflammation. Stromal TF positivity was found exclusively in ongoing inflammation. <b>Conclusion:</b> Our study provides additional support for a divergent pathogenesis in PSC-UC, with an inflammatory environment that differs from classical UC. Stromal TF emerges as a new marker of colonic inflammation.
DOI: 10.6084/m9.figshare.11283038.v1
title: Tissue factor in ulcerative colitis, with and without concomitant primary sclerosing cholangitis

description: <b>Background:</b> Ulcerative colitis (UC) in patients with the severe disease primary sclerosing cholangitis (PSC) constitutes a distinct clinical phenotype (PSC-UC) with a high incidence of colorectal cancer. Today, PSC-UC diagnosis is built on clinical observations only. Tissue factor (TF) has a potential use in UC diagnostics, and also in colorectal cancer prognostication. Here we evaluate TF expression in an inflammatory bowel disease (IBD) cohort, with special focus on differences between UC and PSC-UC patients. <b>Materials and methods:</b> Colonic biopsies from UC (<i>n</i> = 23), PSC (<i>n</i> = 24), and healthy controls (<i>n</i> = 11) were stained for TF by immunohistochemistry. Mononuclear cell contribution to TF expression was verified using flow cytometry. <b>Results:</b> TF was distributed at three distinct colonic locations: in subepithelial pericryptal sheath cells, in mononuclear cells, and in the intestinal stroma. In contrast to UC—where inflammation was accompanied with TF up-regulation—PSC-UC activity remained low during inflammation. Stromal TF positivity was found exclusively in ongoing inflammation. <b>Conclusion:</b> Our study provides additional support for a divergent pathogenesis in PSC-UC, with an inflammatory environment that differs from classical UC. Stromal TF emerges as a new marker of colonic inflammation.
DOI: 10.6084/m9.figshare.11283044.v1
title: Hydropower operation data in mixed reservoir system

description: Medium- and short-term operation data<br>
DOI: 10.6084/m9.figshare.11282684
title: DataLad-101

description: This is a test: how well does my dataset publish?<br>
DOI: 10.6084/m9.figshare.11282684.v1
title: DataLad-101

description: This is a test: how well does my dataset publish?<br>
DOI: 10.6084/m9.figshare.11282294
title: Supplementary Material for: Comparison of a Novel Homogeneous Cyclic Amp Assay and a Luciferase Assay for Measuring Stimulating Thyrotropin-Receptor Autoantibodies

description: <b><i>Objective:</i></b> Stimulating thyrotropin-receptor antibodies (TSAb) cause Graves’ disease (GD). We tested a novel homogeneous fluorescent 3′,5′ cyclic adenine monophosphate (cAMP) assay for the detection of TSAb in a bioassay. <b><i>Methods:</i></b> Chinese hamster ovary (CHO) cell lines expressing either a chimeric (MC4) or wild-type (WT) TSH-R were incubated with the adenyl cyclase activator forskolin, a human TSAb monoclonal antibody (M22), and with sera from GD patients. Intracellular cAMP levels were measured using a Bridge-It® cAMP assay, and the results were compared with a luciferase-based bioassay. <b><i>Results:</i></b> Both cell lines were stimulated with forskolin concentrations (0.006–200 µM) in a dose-dependent manner. The linear range in the MC4 and WT cells was 0.8–25 and 3.1–50 µM, respectively. Levels of cAMP and luciferase in forskolin-treated MC4 and WT cells were positively correlated (<i>r</i> = 0.91 and 0.84, both <i>p</i> &lt; 0.001). The 50% maximum stimulatory concentration of forskolin was more than 16-fold higher for the CHO-WT cells than the CHO-MC4 cells in the cAMP assay and 4-fold higher in the luciferase assay. Incubation of both cell lines with M22 (0.006–50 ng/mL) resulted in a dose-dependent increase in cAMP levels with linear ranges for the MC4 and WT cells of 0.8–12.5 and 0.2–3.125 ng/mL, respectively. Comparison of cAMP and luciferase levels in M22-treated MC4 and WT cells also showed a positive correlation (<i>r</i> = 0.88, <i>p</i> &lt; 0.001 and 0.75, <i>p</i> = 0.002). A positive correlation was also noted when using patient samples (<i>r</i> = 0.96, <i>p</i> &lt; 0.001) that were all TSH-R-Ab binding assay positive. <b><i>Conclusion:</i></b> The novel, rapid, simple-to-perform cAMP assay provides TSAb-mediated stimulatory results comparable to a luciferase-based bioassay.
DOI: 10.6084/m9.figshare.11282165
title: Sample colletion from Temporal isolation between sympatric host plants cascades across multiple trophic levels of host-associated insects

description: Phenological differences between host plants can promote temporal isolation among host-associated populations of insects with life cycles tightly coupled to plant phenology. Divergence in the timing of spring budbreak between two sympatric sister oak species has been shown to promote temporal isolation between host plants and their host-associated populations of a cynipid gall wasp. Here, we examined the generality of this mechanism by testing the hypothesis of cascading temporal isolation for five additional gall-formers and three natural enemy species associated with these same oak species. The timing of adult emergence from galls differed significantly between host-associated populations for all nine species and parallels the direction of the phenological differences between host plants. Differences in emergence timing can reduce gene flow between host-associated populations by diminishing mating opportunities and/or reducing the fitness of immigrants due to differences in the availability of ephemeral resources. Our study suggests that cascading temporal isolation could be a powerful ‘biodiversity generator’ across multiple trophic levels in tightly coupled plant–insect systems.
DOI: 10.6084/m9.figshare.11282066
title: Plant mesophyll cell shapes of Théroux-Rancourt, Voggeneder, Tholen

description: Plant cells extracted from microCT scans of spongy and palisade cells of several angiosperm species analyzed in the commentary on Harwood et al. (2019, doi:10.1111/nph.16219) by Théroux-Rancourt, Voggeneder, and Tholen.<br>Images are compressed 8-bit binary tif stacks of cells and mathematical objects. ImageJ metadata includes resolution/scale of the scan. A scale was also associated to the mathematical objects to make their volume and surface area in a similar range to the plant cells, though of no biological significance.<br>Species included in this dataset, with mesophyll cell types in parenthesis:<i>Diplotaxis tenuifolia</i> (palisade)<br><i>Glycine max </i>(spongy and palisade)<br><i>Hedera helix</i> (spongy and palisade)<br><i>Nicotiana tabacum </i>(spongy and palisade)<br><i>Populus maximowiczi x P. nigra</i> (lower spongy, upper spongy, palisade)<br><i>Quercus robur </i>(spongy and palisade)<i>Crassula ovata</i> (spongy)<br>Mathematical objects are:<i>Sphere of 498 pixels radius</i><i>Capsule</i><br><br>If you use this dataset, please cite the associated publication:Théroux‐Rancourt, G., Voggeneder, K. and Tholen, D. (2019), Shape matters: the pitfalls of analyzing mesophyll anatomy. New Phytologist. doi:10.1111/nph.16360
DOI: 10.6084/m9.figshare.11282159
title: Emergence time dataset from Temporal isolation between sympatric host plants cascades across multiple trophic levels of host-associated insects

description: Phenological differences between host plants can promote temporal isolation among host-associated populations of insects with life cycles tightly coupled to plant phenology. Divergence in the timing of spring budbreak between two sympatric sister oak species has been shown to promote temporal isolation between host plants and their host-associated populations of a cynipid gall wasp. Here, we examined the generality of this mechanism by testing the hypothesis of cascading temporal isolation for five additional gall-formers and three natural enemy species associated with these same oak species. The timing of adult emergence from galls differed significantly between host-associated populations for all nine species and parallels the direction of the phenological differences between host plants. Differences in emergence timing can reduce gene flow between host-associated populations by diminishing mating opportunities and/or reducing the fitness of immigrants due to differences in the availability of ephemeral resources. Our study suggests that cascading temporal isolation could be a powerful ‘biodiversity generator’ across multiple trophic levels in tightly coupled plant–insect systems.
DOI: 10.6084/m9.figshare.11282165.v1
title: Sample colletion from Temporal isolation between sympatric host plants cascades across multiple trophic levels of host-associated insects

description: Phenological differences between host plants can promote temporal isolation among host-associated populations of insects with life cycles tightly coupled to plant phenology. Divergence in the timing of spring budbreak between two sympatric sister oak species has been shown to promote temporal isolation between host plants and their host-associated populations of a cynipid gall wasp. Here, we examined the generality of this mechanism by testing the hypothesis of cascading temporal isolation for five additional gall-formers and three natural enemy species associated with these same oak species. The timing of adult emergence from galls differed significantly between host-associated populations for all nine species and parallels the direction of the phenological differences between host plants. Differences in emergence timing can reduce gene flow between host-associated populations by diminishing mating opportunities and/or reducing the fitness of immigrants due to differences in the availability of ephemeral resources. Our study suggests that cascading temporal isolation could be a powerful ‘biodiversity generator’ across multiple trophic levels in tightly coupled plant–insect systems.