cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1538626
title: A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment

description: Updated March 30th, 2016<br>This project contains R code to replicate the results of our modelling research on sea lice. The file, Marty_Data.csv, is a .csv conversion of data from Marty et al. (2010), DOI: 10.1073/pnas.1009573108. The file, RittenhouseEtAl_eggviability, fits a linear model to salinity and egg viability data from Johnson & Albright (1991). The file, RittenhouseEtAl_ModelDynamics.R produces figure 2 and figure 3 of our manuscript. The file, RittenhouseEtAl_SensitivityAnalysis.R, produces our sensitivity analysis results and figure 5 of our manuscript. The file, RittenhouseEtAl_SiteEnvironment, fits sinusoidal models to temperature and salinity data from British Columbia (Marty_Data.csv) and Newfoundland (not included), and finds the the 5th, 50th, and 95th percentiles of the temperature and salinity data at these two sites. The file, RittenhouseEtAl_R0t, finds R<sub>e</sub>(t) for the two sites as well as mortality rates and maturation times. The file, RittenhouseEtAl_CaseStudyFigure creates figure 4 of the main text. For legal reasons, we unfortunately can not include data from our Newfoundland case study site. As such, errors will be returned on the RittenhouseEtAl_SiteEnvironment.R and RittenhouseEtAl_CaseStudyFigure.R files. The information for the British Columbia site, as well as panels A, B, and C of figure 5 are still able to be replicated without this data. The files, RittenhouseEtAl_SiteEnvironment.R and RittenhouseEtAl.R0t.R should be run before RittenhouseEtAl_CaseStudyFigure.R. The files are meant to be placed in the same file and run in the following order and manner: rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_eggviability.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_ModelDynamics.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_SensitivityAnalysis.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_SiteEnvironment.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_R0t.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_CaseStudyFigure.R")
DOI: 10.6084/m9.figshare.1538627
title: Plant Paleopolyploidy

description: Known ancient whole genome duplications among the flowering plants and their positioning on a phylogenetic tree of flowering plant species with sequenced genomes.
DOI: 10.6084/m9.figshare.1538611
title: HiC Test dataset and script for HiFive

description: Mouse ESC HiC data produced with NcoI for chromosomes 18 and 19 from GSE35156, a bed file containing all chromosome 18 and 19 NcoI cut sites, and a shell script with commands for a complete HiC analysis from loading raw reads to producing a normalized heatmap using HiFive. Raw reads were mapped using bwa and only reads with both paired ends aligning to chromosom 18 or 19 are included in the raw files.
DOI: 10.6084/m9.figshare.1538626.v2
title: A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment

description: Updated March 30th, 2016<br>This project contains R code to replicate the results of our modelling research on sea lice. The file, Marty_Data.csv, is a .csv conversion of data from Marty et al. (2010), DOI: 10.1073/pnas.1009573108. The file, RittenhouseEtAl_eggviability, fits a linear model to salinity and egg viability data from Johnson & Albright (1991). The file, RittenhouseEtAl_ModelDynamics.R produces figure 2 and figure 3 of our manuscript. The file, RittenhouseEtAl_SensitivityAnalysis.R, produces our sensitivity analysis results and figure 5 of our manuscript. The file, RittenhouseEtAl_SiteEnvironment, fits sinusoidal models to temperature and salinity data from British Columbia (Marty_Data.csv) and Newfoundland (not included), and finds the the 5th, 50th, and 95th percentiles of the temperature and salinity data at these two sites. The file, RittenhouseEtAl_R0t, finds R<sub>e</sub>(t) for the two sites as well as mortality rates and maturation times. The file, RittenhouseEtAl_CaseStudyFigure creates figure 4 of the main text. For legal reasons, we unfortunately can not include data from our Newfoundland case study site. As such, errors will be returned on the RittenhouseEtAl_SiteEnvironment.R and RittenhouseEtAl_CaseStudyFigure.R files. The information for the British Columbia site, as well as panels A, B, and C of figure 5 are still able to be replicated without this data. The files, RittenhouseEtAl_SiteEnvironment.R and RittenhouseEtAl.R0t.R should be run before RittenhouseEtAl_CaseStudyFigure.R. The files are meant to be placed in the same file and run in the following order and manner: rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_eggviability.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_ModelDynamics.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_SensitivityAnalysis.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_SiteEnvironment.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_R0t.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_CaseStudyFigure.R")
DOI: 10.6084/m9.figshare.1538606
title: Texture analysis in gel electrophoresis images using an integrative kernel-based approach

description: How to cite this article: Fernandez-Lozano, C. et al. Texture analysis in gel electrophoresis images using an integrative kernel-based approach. Sci. Rep. 5, 19256; doi: 10.1038/srep19256 (2015). <br>In order to generate the dataset, ten 2-DE images of different types of tissues and different experimental conditions were used. For each image out of these ten 100 regions of interest (ROI), 50 spots representing proteins and 50 representing noise (noise, background, non-protein regions) manually segmented that were selected to build a training set with 1000 samples and 274 textural features. We preprocess this dataset in order to have a standard normal distribution (a mean of zero and a standard deviation of one). The dataset is available for download at http://dx.doi.org/10.6084/m9.figshare.1368643 We calculated those features with a specialized software called Mazda. With Mazda it is only possible to define up to 16 regions of interest for each image, so there exist eight (.roi) files for each image. Please refer to Mazda user's manual for the particular instructions to load an image and (.roi) files.
DOI: 10.6084/m9.figshare.1538626.v1
title: A Model For Sea Lice (Lepeophtheirus salmonis) Dynamics In A Seasonally Changing Environment

description: This project contains R code to replicate the results of our modelling research on sea lice. The file, Marty_Data.csv, is a .csv conversion of data from Marty et al. (2010), DOI: 10.1073/pnas.1009573108. The file, RittenhouseEtAl_eggviability, fits a linear model to salinity and egg viability data from Johnson & Albright (1991). The file, RittenhouseEtAl_ModelDynamics.R produces figure 2 and figure 3 of our manuscript. The file, RittenhouseEtAl_SensitivityAnalysis.R, produces our sensitivity analysis results and figure 5 of our manuscript. The file, RittenhouseEtAl_SiteEnvironment, fits sinusoidal models to temperature and salinity data from British Columbia (Marty_Data.csv) and Newfoundland(not included), and finds the the 5th, 50th, and 95th percentiles of the temperature and salinity data at these two sites. The file, RittenhouseEtAl_R0t, finds R0(t) for the two sites as well as mortality rates and maturation times. The file, RittenhouseEtAl_CaseStudyFigure creates figure 4 of the main text. For legal reasons, we unfortunately can not include data from our Newfoundland case study site. As such, errors will be returned on the RittenhouseEtAl_SiteEnvironment.R and RittenhouseEtAl_CaseStudyFigure.R files. The information for the British Columbia site, as well as panels A, B, and C of figure 5 are still able to be replicated without this data. The files, RittenhouseEtAl_SiteEnvironment.R and RittenhouseEtAl.R0t.R should be run before RittenhouseEtAl_CaseStudyFigure.R. The files are meant to be placed in the same file and run in the following order and manner: rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_eggviability.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_ModelDynamics.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_SensitivityAnalysis.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_SiteEnvironment.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_R0t.R") rm(list = ls()) # clear workspace setwd() # Set this to folder's location source("RittenhouseEtAl_CaseStudyFigure.R")
DOI: 10.6084/m9.figshare.1538604
title: Animal plague data - US

description: These data were used in the Maxent model in the manuscript entitled "Delineating the ecologic niche of sylvan and domestic animal plague to inform its human landscape epidemiology in the western United States."
DOI: 10.6084/m9.figshare.1538606.v1
title: Texture analysis in gel electrophoresis images using an integrative kernel-based approach

description: How to cite this article: Fernandez-Lozano, C. et al. Texture analysis in gel electrophoresis images using an integrative kernel-based approach. Sci. Rep. 5, 19256; doi: 10.1038/srep19256 (2015). <br>In order to generate the dataset, ten 2-DE images of different types of tissues and different experimental conditions were used. For each image out of these ten 100 regions of interest (ROI), 50 spots representing proteins and 50 representing noise (noise, background, non-protein regions) manually segmented that were selected to build a training set with 1000 samples and 274 textural features. We preprocess this dataset in order to have a standard normal distribution (a mean of zero and a standard deviation of one). The dataset is available for download at http://dx.doi.org/10.6084/m9.figshare.1368643 We calculated those features with a specialized software called Mazda. With Mazda it is only possible to define up to 16 regions of interest for each image, so there exist eight (.roi) files for each image. Please refer to Mazda user's manual for the particular instructions to load an image and (.roi) files.
DOI: 10.6084/m9.figshare.1538611.v1
title: HiC Test dataset and script for HiFive

description: Mouse ESC HiC data produced with NcoI for chromosomes 18 and 19 from GSE35156, a bed file containing all chromosome 18 and 19 NcoI cut sites, and a shell script with commands for a complete HiC analysis from loading raw reads to producing a normalized heatmap using HiFive. Raw reads were mapped using bwa and only reads with both paired ends aligning to chromosom 18 or 19 are included in the raw files.
DOI: 10.6084/m9.figshare.1538611.v3
title: HiC Test dataset and script for HiFive

description: Mouse ESC HiC data produced with NcoI for chromosomes 18 and 19 from GSE35156, a bed file containing all chromosome 18 and 19 NcoI cut sites, and a shell script with commands for a complete HiC analysis from loading raw reads to producing a normalized heatmap using HiFive. Raw reads were mapped using bwa and only reads with both paired ends aligning to chromosom 18 or 19 are included in the raw files.
DOI: 10.6084/m9.figshare.1538604.v1
title: Animal plague data - US

description: These data were used in the Maxent model in the manuscript entitled "Delineating the ecologic niche of sylvan and domestic animal plague to inform its human landscape epidemiology in the western United States."
DOI: 10.6084/m9.figshare.1538584
title: Test of accuracy of host associations from BEAST analysis

description: To test the accuracy of our predictions of current host associations we randomly selected a set of viruses with known associations, re-described their host association as ambiguous between all possible states (a greater level of uncertainty than we generally attributed to viruses in our data), and re-ran our analysis. The three viruses highlighted in red were given an incorrect host association in the analysis.
DOI: 10.6084/m9.figshare.1538611.v2
title: HiC Test dataset and script for HiFive

description: Mouse ESC HiC data produced with NcoI for chromosomes 18 and 19 from GSE35156, a bed file containing all chromosome 18 and 19 NcoI cut sites, and a shell script with commands for a complete HiC analysis from loading raw reads to producing a normalized heatmap using HiFive. Raw reads were mapped using bwa and only reads with both paired ends aligning to chromosom 18 or 19 are included in the raw files.
DOI: 10.6084/m9.figshare.1538580
title: Visualizing group data

description: The code and example data used in my blog post 'Visualising group data':https://neuroneurotic.wordpress.com/2015/09/09/visualising-group-data<br><br>Uses the data set from this study by Thorstenson et al 2015 (http://www.ncbi.nlm.nih.gov/pubmed/26307592) as an example. The original data can be found here: https://osf.io/sb58f/<br><br>This archive includes my cateye Matlab function for creating cat-eye/violin plots.
DOI: 10.6084/m9.figshare.1538581
title: britishblogs.co.uk in the UK Host Link Graph

description: Contains an expression of host-to-host links in content from the Internet Archive from the UK country code top level domain (.uk). Specifically, it contains all instances of the string 'britishblogs.co.uk', and occurs in the form: 2008|britishblogs.co.uk|peterwebster.me|24 This declares that the IA in 2008 found 24 individual archived resources in the britishblogs.co.uk domain that linked at least once to content in the peterwebster.me domain. It is derived, via a simple command line grep operation, from the UK Host Link Graph, itself derived from the JISC UK Web Domain Dataset (1996-2010) held by the British Library. (information: http://data.webarchive.org.uk/opendata/ukwa.ds.2/host-linkage/ , DOI:10.5259/ukwa.ds.2/host.linkage/1 ).
DOI: 10.6084/m9.figshare.1538566
title: Altmetrics und Rankings bei Artikel-Publikationen Für mehr Transparenz

description: Rankings bei Artikel-Publikationen? Mehr Transparenz! #altmetrics zeigt sinnvolle Ansätze – mit offenen Fragen. (November 2012) In welchem Kontext und nach wessen Kriterien wird der Einfluss (Impact) wissenschaftlicher Artikel gemessen? Verschiedene alternative Initiativen setzen mit dem Stichwort #altmetrics bereits Interessantes um, damit der sogenannte Journal Impact Factor (JIF) an Einfluss verliert – zugunsten von Article level metrics (ALM). Zunächst geht es allerdings allgemein um mehr Transparenz, und an ungelösten Fragen bezüglich Rankings aller Art fehlt es auch bei #altmetrics nicht, meint Claudia Koltzenburg, die in ihrem einführenden Beitrag einige Zusammenhänge kritisch aufzeigt.
DOI: 10.6084/m9.figshare.1538566.v1
title: Altmetrics und Rankings bei Artikel-Publikationen Für mehr Transparenz

description: Rankings bei Artikel-Publikationen? Mehr Transparenz! #altmetrics zeigt sinnvolle Ansätze – mit offenen Fragen. (November 2012) In welchem Kontext und nach wessen Kriterien wird der Einfluss (Impact) wissenschaftlicher Artikel gemessen? Verschiedene alternative Initiativen setzen mit dem Stichwort #altmetrics bereits Interessantes um, damit der sogenannte Journal Impact Factor (JIF) an Einfluss verliert – zugunsten von Article level metrics (ALM). Zunächst geht es allerdings allgemein um mehr Transparenz, und an ungelösten Fragen bezüglich Rankings aller Art fehlt es auch bei #altmetrics nicht, meint Claudia Koltzenburg, die in ihrem einführenden Beitrag einige Zusammenhänge kritisch aufzeigt.
DOI: 10.6084/m9.figshare.1538160
title: Luchtafweer, folder

description: Collectie A.J.R. Nivard, oorlogsdocumentatie.
DOI: 10.6084/m9.figshare.1538580.v1
title: Visualizing group data

description: The code and example data used in my blog post 'Visualising group data':https://neuroneurotic.wordpress.com/2015/09/09/visualising-group-data<br><br>Uses the data set from this study by Thorstenson et al 2015 (http://www.ncbi.nlm.nih.gov/pubmed/26307592) as an example. The original data can be found here: https://osf.io/sb58f/<br><br>This archive includes my cateye Matlab function for creating cat-eye/violin plots.
DOI: 10.6084/m9.figshare.1538151
title: Luchtafweer, folder

description: Collectie Nivard
DOI: 10.6084/m9.figshare.1538584.v1
title: Data S3

description: To test the accuracy of our predictions of current host associations we randomly selected a set of viruses with known associations, re-described their host association as ambiguous between all possible states (a greater level of uncertainty than we generally attributed to viruses in our data), and re-ran our analysis. The three viruses highlighted in red were given an incorrect host association in the analysis.
DOI: 10.6084/m9.figshare.1538160.v1
title: Luchtafweer, folder

description: Collectie A.J.R. Nivard, oorlogsdocumentatie.
DOI: 10.6084/m9.figshare.1537556
title: Mass standardization

description: This dataset includes a picture
DOI: 10.6084/m9.figshare.1538079
title: Tumbarumba Gas Exchange

description: This dataset consists of leaf gas exchange measurements made at the Tumbarumba eddy covariance site in NSW, Australia. Measurements were made during three five-day campaigns in November 2001, February 2002, May 2002. Measurements were made on the overstorey trees (Eucalyptus delegatensis) accessed using a 20-m tall cherry picker. Each day we measured about 4 A-Ci / A-PAR curves, interspersed with spot measurements of photosynthesis and stomatal conductance at ambient light, temperature and humidity. Leaves were tagged during measurements and cut at the end of the day. Specific leaf area, leaf N and P content, and Chl content were determined.
DOI: 10.6084/m9.figshare.1538151.v1
title: Luchtafweer, folder

description: Collectie Nivard
DOI: 10.6084/m9.figshare.1537554
title: Trypanosoma cruzi and Its Soluble Antigens Induce NET Release by Stimulating Toll-Like Receptors

description: Neutrophils release fibrous traps of DNA, histones, and granule proteins known as neutrophil extracellular traps (NETs), which contribute to microbicidal killing and have been implicated in autoimmunity. The role of NET formation in the host response to nonbacterial pathogens is not well-understood. In this study, we investigated the release of NETs by human neutrophils upon their interaction with Trypanosoma cruzi (Y strain) parasites. Our results showed that human neutrophils stimulated by T. cruzi generate NETs composed of DNA, histones, and elastase. The release occurred in a dose-, time-, and reactive oxygen species-dependent manner to decrease trypomastigote and increase amastigote numbers of the parasites without affecting their viability. NET release was decreased upon blocking with antibodies against Toll-like receptors 2 and 4. In addition, living parasites were not mandatory in the release of NETs induced by T. cruzi, as the same results were obtained when molecules from its soluble extract were tested. Our results increase the understanding of the stimulation of NETs by parasites, particularly T. cruzi. We suggest that contact of T. cruzi with NETs during Chagas’s disease can limit infection by affecting the infectivity/pathogenicity of the parasite.
DOI: 10.6084/m9.figshare.1537501
title: Maize and Sorghum Genesets

description: This dataset consists of a set of bed files describing the positions of syntenic and nonsyntenic genes in maize, as well as aggregate counts for these two gene classes in sliding windows of either 5 MB (step size = 1 MB) or 1 MB (step size = 1 MB, no overlap). Two additional bed files describe the predicted orthologous locations of sorghum genes within the two subgenomes of maize. One attempts to predict the location for each sorghum gene in each maize subgenome (33,032*2=66,064) and succeeds in predicting locations in 59,384 cases. The second file only considers genes syntenically conserved between sorghum and setaria as a method of eliminating the influence of recent gene insertion hotspots within the sorghum genome. This file is recommended for most applications. A product of the Schnable Lab@UNL
DOI: 10.6084/m9.figshare.1537554.v1
title: Trypanosoma cruzi and Its Soluble Antigens Induce NET Release by Stimulating Toll-Like Receptors

description: Neutrophils release fibrous traps of DNA, histones, and granule proteins known as neutrophil extracellular traps (NETs), which contribute to microbicidal killing and have been implicated in autoimmunity. The role of NET formation in the host response to nonbacterial pathogens is not well-understood. In this study, we investigated the release of NETs by human neutrophils upon their interaction with Trypanosoma cruzi (Y strain) parasites. Our results showed that human neutrophils stimulated by T. cruzi generate NETs composed of DNA, histones, and elastase. The release occurred in a dose-, time-, and reactive oxygen species-dependent manner to decrease trypomastigote and increase amastigote numbers of the parasites without affecting their viability. NET release was decreased upon blocking with antibodies against Toll-like receptors 2 and 4. In addition, living parasites were not mandatory in the release of NETs induced by T. cruzi, as the same results were obtained when molecules from its soluble extract were tested. Our results increase the understanding of the stimulation of NETs by parasites, particularly T. cruzi. We suggest that contact of T. cruzi with NETs during Chagas’s disease can limit infection by affecting the infectivity/pathogenicity of the parasite.
DOI: 10.6084/m9.figshare.1537556.v1
title: Data from: Lombardi et al_PLoS ONE_Mass standardization_Oxygen Comsumption_Oyster Physiology

description: This dataset includes the raw data used for standardizing oxygen consumption of two oyster species and age classes, through various mass-standardization techniques as used in the article by Lombardi et al. PLoS ONE.
DOI: 10.6084/m9.figshare.1537461
title: Data for AMS Short Course on Open Source Radar Software

description: Data used to support the teaching of the AMS Radar Short course. NOTE: Not for research purposes, please go to the original providers (NOAA and ARM DOE) to download data so the use and metrics can be captured
DOI: 10.6084/m9.figshare.1537556.v2
title: Data from: Lombardi et al_PLoS ONE_Mass standardization_Oxygen Consumption_Oyster Physiology

description: This dataset includes the raw data (not mass-corrected) used for standardizing oxygen consumption of two oyster species and age classes using sealed chambers filled with water of salinity 15 and 25°C. The log values of oyster mass (in grams) and respiration (µl 02 h-1) are provided in the data files. These data were used to understand the impacts of different mass-standardization techniques as is presented in Lombardi et al. PLoS ONE.
DOI: 10.6084/m9.figshare.1537556.v4
title: Mass standardization

description: This dataset includes a picture
DOI: 10.6084/m9.figshare.1537461.v1
title: Data for AMS Short Course on Open Source Radar Software

description: Data used to support the teaching of the AMS Radar Short course. NOTE: Not for research purposes, please go to the original providers (NOAA and ARM DOE) to download data so the use and metrics can be captured