cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gj040/2
title: Leslie matrix strain BW25113

description: This csv file contains data of a age structured, Leslie matrix population projection model for E. coli strain BW25113. The data has been collected using a microfluidic device, called the mother machine. The discrete time steps in the Leslie matrix is one hour (note the initial data has been collected at 4 min time intervals). Age goes from birth (second column) to the last column of the matrix. Fertility rates (number of division per hour) are in the top row (first row after the header row). Survival rates are in the sub-diagonal. Final age with open age class.
DOI: 10.5061/dryad.gj040/3
title: Leslie matrix strain IAI1

description: This csv file contains data of a age structured, Leslie matrix population projection model for E. coli strain IAI1. The data has been collected using a microfluidic device, called the mother machine. The discrete time steps in the Leslie matrix is one hour (note the initial data has been collected at 4 min time intervals). Age goes from birth (second column) to the last column of the matrix. Fertility rates (number of division per hour) are in the top row (first row after the header row). Survival rates are in the sub-diagonal. Final age with open age class.
DOI: 10.5061/dryad.gj040/4
title: Leslie matrix strain MG1655

description: This csv file contains data of a age structured, Leslie matrix population projection model for E. coli strain MG1655. The data has been collected using a microfluidic device, called the mother machine. The discrete time steps in the Leslie matrix is one hour (note the initial data has been collected at 4 min time intervals). Age goes from birth (second column) to the last column of the matrix. Fertility rates (number of division per hour) are in the top row (first row after the header row). Survival rates are in the sub-diagonal. Final age with open age class.
DOI: 10.5061/dryad.gj040/5
title: Leslie matrix strain MG1655Inlag

description: This csv file contains data of a age structured, Leslie matrix population projection model for E. coli strain MG1655Inlag. The data has been collected using a microfluidic device, called the mother machine. The discrete time steps in the Leslie matrix is one hour (note the initial data has been collected at 4 min time intervals). Age goes from birth (second column) to the last column of the matrix. Fertility rates (number of division per hour) are in the top row (first row after the header row). Survival rates are in the sub-diagonal. Final age with open age class.
DOI: 10.5061/dryad.gj318/3
title: Data Files
DOI: 10.5061/dryad.j1sb5/10
title: wukalina collated trap files for Tasmanian devils

description: Each sheet within the file contains the trap locations for
the specified month of survey for respective sites.
DOI: 10.5061/dryad.j1sb5/11
title: Island wide devil spotlight counts

description: Contains spotlight count information for devils across
132 transects that are 10 km in length that have been surveyed annually since 1985.
DOI: 10.5061/dryad.j1sb5/9
title: Woolnorth collated trap files for Tasmanian devils

description: Each sheet within the file contains the trap locations for
the specified month of survey for respective sites.
DOI: 10.5061/dryad.k272c/1
title: Experiment Raw Data

description: Excel spreadsheet of raw data from the experiment. See second sheet ('metadata') for definitions of each data column.
DOI: 10.5061/dryad.k272c/2
title: R Script for Data Analysis

description: An R script file with comments to obtain the test statistics and values observed in the manuscript.
DOI: 10.5061/dryad.kd1d4/1
title: CHELSA_prec_4_land
DOI: 10.5061/dryad.kd1d4/2
title: CHELSA_prec_1_land
DOI: 10.5061/dryad.kd1d4/3
title: CHELSA_prec_2_land
DOI: 10.5061/dryad.kd1d4/4
title: CHELSA_prec_3_land
DOI: 10.5061/dryad.kd1d4/5
title: CHELSA_prec_5_land
DOI: 10.5061/dryad.p592s/1
title: Species abundance per plot
DOI: 10.5061/dryad.p592s/2
title: Physical-chemical soil variables
DOI: 10.5061/dryad.p592s/3
title: Stand age, basal area and soil PC axes
DOI: 10.5061/dryad.p592s/4
title: Species traits
DOI: 10.5061/dryad.s53ns/1
title: barre_et_al_2017 farming_practices_bats
DOI: 10.5061/dryad.s57d6/1
title: cow_lrr_files

description: The “cow_lrr_files.zip” contains total signal intensity (LRR) and B allele frequency signal (BAF) data of 100 cattle samples (100 sample text files). The zip folder also includes “snp_list.txt” file which contains the information about SNP id, chromosome id and Base-pair position. Please note that the markers’ order in “snp_list.txt” file align with the order of these markers in a sample text file. For example, the first row of a sample text file displays LRR and BAF value of the first marker in “snp_list.txt” file.
DOI: 10.5061/dryad.s86sd/1
title: Plowright_et_al._2017_ELE_12829_data

description: The attached data is a subset of that used in the Ecology Letters paper. Please email the corresponding author for the full data set and metadata and to discuss how the data can be appropriately used.
DOI: 10.5061/dryad.sp5ff.2
title: Data from: Contrasting ecological roles of non-native ungulates in a novel ecosystem
DOI: 10.5061/dryad.sp5ff.2/1.2
title: Guam seedling plots

description: Survival or mortality of set of six species planted in fenced and unfenced seedling plots.
DOI: 10.5061/dryad.sp5ff.2/2.2
title: Scat germination and forest species

description: Data used to calculate proportions of seedlings of given species that germinated from collected scat and compare that information to proportion of adult trees that could have been seeding in forests from which scats were collected.
DOI: 10.5061/dryad.sp5ff.2/3.2
title: Vegetation and scat transect

description: Belt transects in forest, with counts and identification of all seedlings and adult plants and counts of pig and deer scat used for abundance indices.
DOI: 10.5061/dryad.sp5ff.2/4.2
title: Script for seedling plots

description: Code for model selection analyses and figure about seedling survival in fenced compared to unfenced plots.
DOI: 10.6084/m9.figshare.5402467
title: Ashford and St Peters Hospitals NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5402497.v2
title: Investigation of associations between exposures to pesticides and testosterone levels in Thai farmers

description: We conducted a cross-sectional study to assess the relationship between pesticide exposures and testosterone levels in 133 male Thai farmers. Urine and serum samples were collected concurrently from participants. Urine was analyzed for levels of specific and nonspecific metabolites of organophosphates (OPs), pyrethroids, select herbicides, and fungicides. Serum was analyzed for total and free testosterone. Linear regression analyses revealed significant negative relationships between total testosterone and the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) after controlling for covariates (eg, age, BMI, smoking status). Positive significant associations were found between some OP pesticides and total testosterone. Due to the small sample size and the observational nature of the study, future investigation is needed to confirm our results and to elucidate the biological mechanisms.
DOI: 10.6084/m9.figshare.5402443
title: Airedale NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5402449
title: Alder Hey Children's NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5402467.v1
title: Ashford and St Peters Hospitals NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5402428
title: 5 Boroughs Partnership NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5402449.v1
title: Alder Hey Children's NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5402497.v1
title: Investigation of Associations Between Exposures to Pesticides and Testosterone Levels in Thai Farmers

description: We conducted a cross-sectional study to assess the relationship between pesticide exposures and testosterone levels in 133 male Thai farmers. Urine and serum samples were collected concurrently from participants. Urine was analyzed for levels of specific- and non-specific metabolites of organophosphates (OPs), pyrethroids, select herbicides, and fungicides. Serum was analyzed for total and free testosterone. Linear regression analyses revealed significant negative relationships between total testosterone and the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) after controlling for covariates (e.g., age, BMI, smoking status). Positive significant associations were found between some OP pesticides and total testosterone. Due to the small sample size and the observational nature of the study, future investigation is needed to confirm our results and to elucidate the biological mechanisms.
DOI: 10.6084/m9.figshare.5402419
title: 2gether NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5402419.v1
title: 2gether NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5402428.v1
title: 5 Boroughs Partnership NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5402443.v2
title: Airedale NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5402443.v1
title: Airedale NHS Foundation Trust

description: Response to our Freedom of Information Act request received from this NHS Trust.
DOI: 10.6084/m9.figshare.5402422
title: Persistent Left Superior Vena Cava

description: Persistent Left Superior Vena Cava
DOI: 10.6084/m9.figshare.5402329
title: BTV spread in Europe and predictors - SpatialData

description: Rasters used to compute resistance distances for the manuscript: Jacquot, M. , Nomikou, K., Palmarini, M. , Mertens, P. and Biek, R.(2017) Bluetongue virus spread in Europe is a consequence of climatic, landscape and vertebrate host factors as revealed by phylogeographic inference. <i>Proceedings of the Royal Society of London Series B: Biological Sciences</i> <br> - Climate data are all averages over 15 years (from January 1998 to December 2012) of monthly averages from: European Centre for Medium-range Weather Forecasts http://apps.ecmwf.int/datasets/data/interim-full-mnth/ <br> - Mean and standard deviation of elevation were obtained from: Global Multi-resolution Terrain Elevation Data (GMTED 2010) from the United States Geological Survey http://eros.usgs.gov/#Find_Data/Products_and_Data_Available/GMTED2010 <br> - Low- Mid- and High-elevations rasters were derived from the mean elevation one. <br> - Livestock densities were obtained from Food and Agriculture Organisation http://www.fao.org/ag/AGAInfo/resources/en/glw/GLW_dens.html <br> - The cattle density raster was used to generate the terrestrial habitat/land cover raster (Habitat vs non habitat areas).
DOI: 10.6084/m9.figshare.5402422.v2
title: Persistent Left Superior Vena Cava

description: Persistent Left Superior Vena Cava
DOI: 10.6084/m9.figshare.5402293
title: The t<sup>6</sup>A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in <i>Streptococcus mutans</i>

description: Endoribonuclease toxins (ribotoxins) are produced by bacteria and fungi to respond to stress, eliminate non-self competitor species, or interdict virus infection. PrrC is a bacterial ribotoxin that targets and cleaves tRNA<sup>Lys</sup><sub>UUU</sub> in the anticodon loop. <i>In vitro</i> studies suggested that the post-transcriptional modification threonylcarbamoyl adenosine (t<sup>6</sup>A) is required for PrrC activity but this prediction had never been validated <i>in vivo</i>. Here, by using t<sup>6</sup>A-deficient yeast derivatives, it is shown that t<sup>6</sup>A is a positive determinant for PrrC proteins from various bacterial species. <i>Streptococcus mutans</i> is one of the few bacteria where the t<sup>6</sup>A synthesis gene <i>tsaE</i> (<i>brpB</i>) is dispensable and its genome encodes a PrrC toxin. We had previously shown using an HPLC-based assay that the <i>S. mutans tsaE</i> mutant was devoid of t<sup>6</sup>A. However, we describe here a novel and a more sensitive hybridization-based t<sup>6</sup>A detection method (compared to HPLC) that showed t<sup>6</sup>A was still present in the <i>S. mutans</i> δ<i>tsaE</i>, albeit at greatly reduced levels (93% reduced compared to WT). Moreover, mutants in two other <i>S. mutans</i> t<sup>6</sup>A synthesis genes (<i>tsaB</i> and <i>tsaC</i>) were shown to be totally devoid of the modification thus confirming its dispensability in this organism. Furthermore, analysis of t<sup>6</sup>A modification ratios and of t<sup>6</sup>A synthesis genes mRNAs levels in <i>S. mutans</i> suggest they may be regulated by growth phase.
DOI: 10.6084/m9.figshare.5402311.v1
title: Sources to variability in circulating human miRNA signatures

description: An increasing number of studies propose circulating microRNAs (miRNAs) as biomarkers for a large number of human diseases including cancer, cardiovascular diseases, neurologic pathologies and others. To further validate miRNA as biomarkers it is indispensable to understand the variability of circulating miRNAs in healthy individuals. We determined the longitudinal miRNomes of 90 serum samples from the Janus Serum Bank in Norway, which have been stored between 23 and 40 y at -25 °Celsius. We profiled 3 serum samples with microarrays for 30 individuals, each. For each individual the samples were collected with a time interval of approximately 5 y. This design allowed insights into inter-individual variability, age dependent miRNA variability and the impact of storage length and pre-processing. A significant proportion of the miRNome was affected by the age of the blood donor and a not negligible, albeit small, part of the miRNome by the storage time. A substantial part of miRNAs was differentially abundant between individuals, independent of the time when samples were collected. Stepwise filtering of the 529 miRNAs that were detected in the serum samples showed 168 miRNAs with differential abundance depending on the time point analyzed, 56 miRNAs differentially abundant between individuals, and 169 miRNAs with an abundance depending on the sampling procedure. While these groups of miRNAs contain generally interesting and biologically important miRNAs, the remaining 135 miRNAs constitute very promising biomarker candidates as they show an overall low variability between healthy individuals, a likewise overall low variability across a longer life span, and a high independence of the sampling process and the storage length.
DOI: 10.6084/m9.figshare.5402122
title: DNA methylation changes in human lung epithelia cells exposed to multi-walled carbon nanotubes

description: Humans are increasingly exposed to nanoparticles and, although many of their physiological effects have been described, the molecular mechanisms underlying them are still largely unknown. The present study aimed to determine the possible role of certain epigenetic mechanisms in the cellular response of human lung epithelial cells that are triggered by long-term exposure to titanium dioxide nanoparticles (TiO<sub>2</sub>NPs) and multi-walled carbon nanotubes (MWCNTs). The results showed that exposure to TiO<sub>2</sub>NPs had only minor effects on genome-wide DNA methylation. However, we identified 755 CpG sites showing consistent DNA hypomethylation in cells exposed to MWCNTs. These sites were mainly located at low density CpG regions and enhancers, and very frequently on the X chromosome. Our results thus suggest that long-term MWCNT exposure may have important effects on the epigenome.
DOI: 10.6084/m9.figshare.5402122.v1
title: DNA methylation changes in human lung epithelia cells exposed to multi-walled carbon nanotubes

description: Humans are increasingly exposed to nanoparticles and, although many of their physiological effects have been described, the molecular mechanisms underlying them are still largely unknown. The present study aimed to determine the possible role of certain epigenetic mechanisms in the cellular response of human lung epithelial cells that are triggered by long-term exposure to titanium dioxide nanoparticles (TiO<sub>2</sub>NPs) and multi-walled carbon nanotubes (MWCNTs). The results showed that exposure to TiO<sub>2</sub>NPs had only minor effects on genome-wide DNA methylation. However, we identified 755 CpG sites showing consistent DNA hypomethylation in cells exposed to MWCNTs. These sites were mainly located at low density CpG regions and enhancers, and very frequently on the X chromosome. Our results thus suggest that long-term MWCNT exposure may have important effects on the epigenome.
DOI: 10.6084/m9.figshare.5402329.v1
title: BTV_spread_and_predictors-SpatialData.zip

description: Rasters used to compute resistance distances for the manuscript: Jacquot, M. , Nomikou, K., Palmarini, M. , Mertens, P. and Biek, R.(2017) Bluetongue virus spread in Europe is a consequence of climatic, landscape and vertebrate host factors as revealed by phylogeographic inference. <i>Proceedings of the Royal Society of London Series B: Biological Sciences</i>, (Accepted for Publication) <br> Climate data are all averages over 15 years (from January 1998 to December 2012) of monthly averages from: European Centre for Medium-range Weather Forecasts http://apps.ecmwf.int/datasets/data/interim-full-mnth/ <br> Mean and standard deviation of elevation were obtained from: Global Multi-resolution Terrain Elevation Data (GMTED 2010) from the United States Geological Survey http://eros.usgs.gov/#Find_Data/Products_and_Data_Available/GMTED2010 <br> Low- Mid and High-elevations rasters were derived from the mean elevation one. <br> Livestock densities were obtained from Food and Agriculture Organisation http://www.fao.org/ag/AGAInfo/resources/en/glw/GLW_dens.html <br> The cattle density raster was used to generate the terrestrial habitat/land cover (Habitat vs non habitat areas).
DOI: 10.6084/m9.figshare.5402293.v2
title: The t<sup>6</sup>A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in <i>Streptococcus mutans</i>

description: Endoribonuclease toxins (ribotoxins) are produced by bacteria and fungi to respond to stress, eliminate non-self competitor species, or interdict virus infection. PrrC is a bacterial ribotoxin that targets and cleaves tRNA<sup>Lys</sup><sub>UUU</sub> in the anticodon loop. <i>In vitro</i> studies suggested that the post-transcriptional modification threonylcarbamoyl adenosine (t<sup>6</sup>A) is required for PrrC activity but this prediction had never been validated <i>in vivo</i>. Here, by using t<sup>6</sup>A-deficient yeast derivatives, it is shown that t<sup>6</sup>A is a positive determinant for PrrC proteins from various bacterial species. <i>Streptococcus mutans</i> is one of the few bacteria where the t<sup>6</sup>A synthesis gene <i>tsaE</i> (<i>brpB</i>) is dispensable and its genome encodes a PrrC toxin. We had previously shown using an HPLC-based assay that the <i>S. mutans tsaE</i> mutant was devoid of t<sup>6</sup>A. However, we describe here a novel and a more sensitive hybridization-based t<sup>6</sup>A detection method (compared to HPLC) that showed t<sup>6</sup>A was still present in the <i>S. mutans</i> δ<i>tsaE</i>, albeit at greatly reduced levels (93% reduced compared to WT). Moreover, mutants in two other <i>S. mutans</i> t<sup>6</sup>A synthesis genes (<i>tsaB</i> and <i>tsaC</i>) were shown to be totally devoid of the modification thus confirming its dispensability in this organism. Furthermore, analysis of t<sup>6</sup>A modification ratios and of t<sup>6</sup>A synthesis genes mRNAs levels in <i>S. mutans</i> suggest they may be regulated by growth phase.
DOI: 10.6084/m9.figshare.5402329.v3
title: BTV spread in Europe and predictors - SpatialData

description: Rasters used to compute resistance distances for the manuscript: Jacquot, M. , Nomikou, K., Palmarini, M. , Mertens, P. and Biek, R.(2017) Bluetongue virus spread in Europe is a consequence of climatic, landscape and vertebrate host factors as revealed by phylogeographic inference. <i>Proceedings of the Royal Society of London Series B: Biological Sciences</i> <br> - Climate data are all averages over 15 years (from January 1998 to December 2012) of monthly averages from: European Centre for Medium-range Weather Forecasts http://apps.ecmwf.int/datasets/data/interim-full-mnth/ <br> - Mean and standard deviation of elevation were obtained from: Global Multi-resolution Terrain Elevation Data (GMTED 2010) from the United States Geological Survey http://eros.usgs.gov/#Find_Data/Products_and_Data_Available/GMTED2010 <br> - Low- Mid- and High-elevations rasters were derived from the mean elevation one. <br> - Livestock densities were obtained from Food and Agriculture Organisation http://www.fao.org/ag/AGAInfo/resources/en/glw/GLW_dens.html <br> - The cattle density raster was used to generate the terrestrial habitat/land cover raster (Habitat vs non habitat areas).
DOI: 10.6084/m9.figshare.5402110
title: Mapping the history of botanical collectors: spatial patterns, diversity, and uniqueness through time

description: This study examines changing spatial patterns of botanical collections over a 400 year time frame, focussing on the collections at the Natural History Museum (BM) in comparison with global patterns. The Plant Collector Resource Database, which contains 68,000 collector records was used to generate 250,667 unique collector × country × date records. We observe an exponential increase in the number of collectors over time. The activities of collectors were investigated in 50-year time-slices from 1650–2000. We specifically considered the geographic scope of collections (i.e., countries in which collections were made), the depth of collections (i.e., the number of collectors per country) and the uniqueness of collections (i.e., the proportion not duplicated in other herbaria). Uniqueness was highest for the earliest time-slice. Collector activity is shown to be strongly influenced by extrinsic factors such as the development of trade and empire, which allowed for collections to expand in scope and depth, and conflicts, which reduced collecting activity. A striking finding concerns the uniqueness of collections through time. The considerable unique element of the collections in herbaria highlighted by this study provides a strong motivation for digitization efforts to ensure that collections are accessible to address key questions in systematics, biogeography, and ecology.