cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5336560
title: Meta-analysis of parasitism levels of the invasive ladybird, Harmonia axyridis

description: This repository provides the analysis of the parasitism data (table 3 and 4) from the following review paper : <br> Ceryngier, P., Nedvěd, O., Grez, A.A., Riddick, E.W., Roy, H.E., San Martin, G., Steenberg, T., Veselý, P., Zaviezo, T., Zúñiga-Reinoso, Á., Haelewaters, D., 2017. Predators and parasitoids of the harlequin ladybird, Harmonia axyridis, in its native range and invaded areas. Biological Invasions 1–23. doi:10.1007/s10530-017-1608-9 https://link.springer.com/article/10.1007/s10530-017-1608-9<br><br>For Dinocampus coccinellae, we used both parasitism rates determined by dissection of field collected ladybirds and emergence level of the parasitoïds (in separate analyses) and for Phalacrotophora spp. we used only the parasitism level ascertained as the proportion of field collected ladybirds pupae giving rise to the parasitoïd larvae.<br> <br>For these three dataset, we checked if we could find differences between regions (invaded or not), between species (H.axyridis vs other species) and if we could find temporal trends of parasitism levels in the invaded regions.<br><br><br>Summary of the paper : <br><br>Over the past 30 years, the harlequin ladybird Harmonia axyridis (Coleoptera: Coccinellidae) has rapidly spread in several continents and is considered an invasive alien species. The success of H. axyridis as an invader is often attributed to weak control by natural enemies. In this paper we provide an overview of current knowledge on predators and parasitoids of H. axyridis. The common feature of predators and parasitoids is that they directly kill exploited organisms. Currently available data show that H. axyridis, displaying a variety of chemical, mechanical, and microbiological anti-predator defenses, is usually avoided by predators. However, some birds and invertebrates can eat this ladybird without harmful consequences. The primary defenses of H. axyridis against parasitoids include immune response and physiological and nutritional unsuitability for parasitoid development. These defenses are probably relatively efficient against most ladybird parasitoids, but not against flies of the genus Phalacrotophora. The latter are idiobiont parasitoids and hence can evade the host's immune response. Indeed, rates of parasitism of H. axyridis by Phalacrotophora in the Palaearctic region (both in the native range in Asia and in Europe) are relatively high. While strong evidence for enemy release on the invasive populations of H. axyridis is lacking, several cases of parasitoid acquisition have been recorded in Europe, North America, and South America. We conclude that enemy release cannot be excluded as a possible mechanism contributing to the spread and increase of H. axyridis in the early stages of invasion, but adaptation of parasitoids may lead to novel associations which might offset previous effects of enemy release. However, further work is required to elucidate the population-level effects of such interactions.
DOI: 10.6084/m9.figshare.5336638.v1
title: capture targets bed file of customized short stature panel by NimbleDesign

description: capture targets bed file of customized short stature panel by NimbleDesign
DOI: 10.6084/m9.figshare.5336560.v1
title: Meta-analysis of parasitism levels of the invasive ladybird, Harmonia axyridis

description: This repository provides the analysis of the parasitism data (table 3 and 4) from the following review paper : <br> Ceryngier, P., Nedvěd, O., Grez, A.A., Riddick, E.W., Roy, H.E., San Martin, G., Steenberg, T., Veselý, P., Zaviezo, T., Zúñiga-Reinoso, Á., Haelewaters, D., 2017. Predators and parasitoids of the harlequin ladybird, Harmonia axyridis, in its native range and invaded areas. Biological Invasions 1–23. doi:10.1007/s10530-017-1608-9 https://link.springer.com/article/10.1007/s10530-017-1608-9<br><br>For Dinocampus coccinellae, we used both parasitism rates determined by dissection of field collected ladybirds and emergence level of the parasitoïds (in separate analyses) and for Phalacrotophora spp. we used only the parasitism level ascertained as the proportion of field collected ladybirds pupae giving rise to the parasitoïd larvae.<br> <br>For these three dataset, we checked if we could find differences between regions (invaded or not), between species (H.axyridis vs other species) and if we could find temporal trends of parasitism levels in the invaded regions.<br><br><br>Summary of the paper : <br><br>Over the past 30 years, the harlequin ladybird Harmonia axyridis (Coleoptera: Coccinellidae) has rapidly spread in several continents and is considered an invasive alien species. The success of H. axyridis as an invader is often attributed to weak control by natural enemies. In this paper we provide an overview of current knowledge on predators and parasitoids of H. axyridis. The common feature of predators and parasitoids is that they directly kill exploited organisms. Currently available data show that H. axyridis, displaying a variety of chemical, mechanical, and microbiological anti-predator defenses, is usually avoided by predators. However, some birds and invertebrates can eat this ladybird without harmful consequences. The primary defenses of H. axyridis against parasitoids include immune response and physiological and nutritional unsuitability for parasitoid development. These defenses are probably relatively efficient against most ladybird parasitoids, but not against flies of the genus Phalacrotophora. The latter are idiobiont parasitoids and hence can evade the host's immune response. Indeed, rates of parasitism of H. axyridis by Phalacrotophora in the Palaearctic region (both in the native range in Asia and in Europe) are relatively high. While strong evidence for enemy release on the invasive populations of H. axyridis is lacking, several cases of parasitoid acquisition have been recorded in Europe, North America, and South America. We conclude that enemy release cannot be excluded as a possible mechanism contributing to the spread and increase of H. axyridis in the early stages of invasion, but adaptation of parasitoids may lead to novel associations which might offset previous effects of enemy release. However, further work is required to elucidate the population-level effects of such interactions.
DOI: 10.6084/m9.figshare.5339407.v3
title: Data from: A thermal gradient of trait similarity in North American mammals

description: The associated data files and R script are all that is required to reproduce the analyses in the manuscript "A thermal gradient of trait similarity across North America," currently in review at <i>Global Ecology and Biogeography</i>. <br>The following .csv files contain data required to reproduce the analysis, with raw unprocessed small mammal data from NEON, small mammal data that has been put through our QC code, mammal trait data compiled from different sources, and site-level environmental covariates: <b>raw_NEON_mammal_data.csv, final_NEON_mammal_data.csv, mammal_traits.csv, site_covariates.csv</b><b><br></b>The following .csv files contain metadata describing the corresponding data file: <b>final_NEON_mammal_data_meta.csv, mammal_traits_meta.csv, site_covariates_meta.csv. </b>Each file lists the data sources. Please see documentation at neonscience.org for more information on the NEON small mammal trapping data.<br>The following .R file is an R script, tested under R/3.3.3, that contains code to reproduce the analyses in the manuscript: <b>code_supplement.R</b><br>Below is the abstract:<b>Aims: </b>Temperature is widely regarded as a major driver of species richness, but the mechanisms are debated. Niche theory suggests temperature may affect richness by filtering traits and species in colder habitats while promoting specialization in warmer ones. However, tests of this theory are rare because niche dimensions are challenging to quantify along broad thermal gradients. Here, we use individual-level trait data from a long-term monitoring network spanning a large geographic extent to test niche-based theory of community assembly in small mammals.<b>Location: </b>Continental United States<b>Time period: </b>2015<b>Taxon: </b>Rodentia<b>Methods: </b>We examined variation in body size among 23 communities of North American rodents sampled across the National Ecological Observatory Network (NEON), ranging from northern hardwood forests to subtropical deserts. We quantified body size similarity among species using a metric of overlap that accounts for individual variation, and fit a structural equation model to disentangle the relationships between temperature, productivity, body size overlap, and species richness. <b>Main conclusions: </b>We document a latitudinal gradient of declining similarity in body size among species towards the tropics and overall increase in the dimensions of community-wide trait space in warmer habitats. Neither environmental temperature nor net primary productivity directly affect rodent species richness. Instead, temperature determines the community-wide niche space that species can occupy, which in turn alters richness. We suggest a latitudinal gradient of trait space expansion towards the tropics may be widespread and underlie gradients in species diversity.<br>
DOI: 10.6084/m9.figshare.5336410
title: Appendices from HCC/HCV systematic review

description: Appendices A to D containing full tables and references from the systematic review: "Host genetic factors associated with hepatocellular carcinoma in patients with hepatitis C virus infection: A systematic review"
DOI: 10.6084/m9.figshare.5339407.v4
title: Data from: Among-species overlap in rodent body size distributions predicts species richness along a temperature gradient

description: The associated data files and R script are all that is required to reproduce the analyses in the manuscript "A thermal gradient of trait similarity across North America," currently in review at <i>Ecography</i>. <br>The following .csv files contain data required to reproduce the analysis, with raw unprocessed small mammal data from NEON, small mammal data that has been put through our QC code, mammal trait data compiled from different sources, and site-level environmental covariates: <b>raw_NEON_mammal_data.csv, final_NEON_mammal_data.csv, mammal_traits.csv, site_covariates.csv</b><b><br></b>The following .csv files contain metadata describing the corresponding data file: <b>final_NEON_mammal_data_meta.csv, mammal_traits_meta.csv, site_covariates_meta.csv. </b>Each file lists the data sources. Please see documentation at neonscience.org for more information on the NEON small mammal trapping data.<br>The following .R file is an R script, tested under R/3.3.3, that contains code to reproduce the analyses in the manuscript: <b>code_supplement.R</b><br>Below is the abstract:<b>Aims: </b>Temperature is widely regarded as a major driver of species richness, but the mechanisms are debated. Niche theory suggests temperature may affect richness by filtering traits and species in colder habitats while promoting specialization in warmer ones. However, tests of this theory are rare because niche dimensions are challenging to quantify along broad thermal gradients. Here, we use individual-level trait data from a long-term monitoring network spanning a large geographic extent to test niche-based theory of community assembly in small mammals.<b>Location: </b>Continental United States<b>Time period: </b>2015<b>Taxon: </b>Rodentia<b>Methods: </b>We examined variation in body size among 23 communities of North American rodents sampled across the National Ecological Observatory Network (NEON), ranging from northern hardwood forests to subtropical deserts. We quantified body size similarity among species using a metric of overlap that accounts for individual variation, and fit a structural equation model to disentangle the relationships between temperature, productivity, body size overlap, and species richness. <b>Main conclusions: </b>We document a latitudinal gradient of declining similarity in body size among species towards the tropics and overall increase in the dimensions of community-wide trait space in warmer habitats. Neither environmental temperature nor net primary productivity directly affect rodent species richness. Instead, temperature determines the community-wide niche space that species can occupy, which in turn alters richness. We suggest a latitudinal gradient of trait space expansion towards the tropics may be widespread and underlie gradients in species diversity.<br>
DOI: 10.6084/m9.figshare.5336338
title: R package for PanRTK mechanistic signaling model

description: Signaling pathway model comprised of ODEs describing receptor dimerization and activation of MAPK and PI3K pathways.Data for seven individual cell lines are linked therein.The code is written for the open-source R framework dMod (https://github.com/dkaschek/dMod).<br>The corresponding paper is available at BioRxiv (http://www.biorxiv.org/content/early/2017/05/27/142901) and in press at npj Systems Biology and Applications.<br>
DOI: 10.6084/m9.figshare.5339407.v5
title: Data from: Among-species overlap in rodent body size distributions predicts species richness along a temperature gradient

description: The associated data files and R script are all that is required to reproduce the analyses in the manuscript "A thermal gradient of trait similarity across North America," currently in review at <i>Ecography</i>. <br>The following .csv files contain data required to reproduce the analysis, with raw unprocessed small mammal data from NEON, small mammal data that has been put through our QC code, mammal trait data compiled from different sources, and site-level environmental covariates: <b>raw_NEON_mammal_data.csv, final_NEON_mammal_data.csv, mammal_traits.csv, site_covariates.csv</b><b><br></b>The following .csv files contain metadata describing the corresponding data file: <b>final_NEON_mammal_data_meta.csv, mammal_traits_meta.csv, site_covariates_meta.csv. </b>Each file lists the data sources. Please see documentation at neonscience.org for more information on the NEON small mammal trapping data.<br>The following .R file is an R script, tested under R/3.3.3, that contains code to reproduce the analyses in the manuscript: <b>code_supplement.R</b><br>Below is the abstract:<b>Aims: </b>Temperature is widely regarded as a major driver of species richness, but the mechanisms are debated. Niche theory suggests temperature may affect richness by filtering traits and species in colder habitats while promoting specialization in warmer ones. However, tests of this theory are rare because niche dimensions are challenging to quantify along broad thermal gradients. Here, we use individual-level trait data from a long-term monitoring network spanning a large geographic extent to test niche-based theory of community assembly in small mammals.<b>Location: </b>Continental United States<b>Time period: </b>2015<b>Taxon: </b>Rodentia<b>Methods: </b>We examined variation in body size among 23 communities of North American rodents sampled across the National Ecological Observatory Network (NEON), ranging from northern hardwood forests to subtropical deserts. We quantified body size similarity among species using a metric of overlap that accounts for individual variation, and fit a structural equation model to disentangle the relationships between temperature, productivity, body size overlap, and species richness. <b>Main conclusions: </b>We document a latitudinal gradient of declining similarity in body size among species towards the tropics and overall increase in the dimensions of community-wide trait space in warmer habitats. Neither environmental temperature nor net primary productivity directly affect rodent species richness. Instead, temperature determines the community-wide niche space that species can occupy, which in turn alters richness. We suggest a latitudinal gradient of trait space expansion towards the tropics may be widespread and underlie gradients in species diversity.<br>
DOI: 10.6084/m9.figshare.5336338.v1
title: R package for PanRTK mechanistic signaling model

description: Signaling pathway model comprised of ODEs describing receptor dimerization and activation of MAPK and PI3K pathways.Data for seven individual cell lines are linked therein.The code is written for the open-source R framework dMod (https://github.com/dkaschek/dMod).<br>The corresponding paper is available at BioRxiv (http://www.biorxiv.org/content/early/2017/05/27/142901) and in press at npj Systems Biology and Applications.<br>
DOI: 10.6084/m9.figshare.5339407.v6
title: Data from: Among-species overlap in rodent body size distributions predicts species richness along a temperature gradient

description: The associated data files and R script are all that is required to reproduce the analyses in the manuscript "A thermal gradient of trait similarity across North America," published in <i>Ecography</i>: https://onlinelibrary.wiley.com/doi/10.1111/ecog.03641<br>The following .csv files contain data required to reproduce the analysis, with raw unprocessed small mammal data from NEON, small mammal data that has been put through our QC code, mammal trait data compiled from different sources, and site-level environmental covariates: <b>raw_NEON_mammal_data.csv, final_NEON_mammal_data.csv, mammal_traits.csv, site_covariates.csv</b><b><br></b>The following .csv files contain metadata describing the corresponding data file: <b>final_NEON_mammal_data_meta.csv, mammal_traits_meta.csv, site_covariates_meta.csv. </b>Each file lists the data sources. Please see documentation at neonscience.org for more information on the NEON small mammal trapping data.<br>The following .R file is an R script, tested under R/3.3.3, that contains code to reproduce the analyses in the manuscript: <b>code_supplement.R</b><br>Below is the abstract:Temperature is widely regarded as a major driver of species richness, but the mechanisms are debated. Niche theory suggests temperature may affect richness by filtering traits and species in colder habitats while promoting specialization in warmer ones. However, tests of this theory are rare because niche dimensions are challenging to quantify along broad thermal gradients. Here, we use individual-level trait data from a long-term monitoring network spanning a large geographic extent to test niche-based theory of community assembly in small mammals.<b> </b>We examined variation in body size among 23 communities of North American rodents sampled across the National Ecological Observatory Network (NEON), ranging from northern hardwood forests to subtropical deserts. We quantified body size similarity among species using a metric of overlap that accounts for individual variation, and fit a structural equation model to disentangle the relationships between temperature, productivity, body size overlap, and species richness. We document a latitudinal gradient of declining similarity in body size among species towards the tropics and overall increase in the dimensions of community-wide trait space in warmer habitats. Neither environmental temperature nor net primary productivity directly affect rodent species richness. Instead, temperature determines the community-wide niche space that species can occupy, which in turn alters richness. We suggest a latitudinal gradient of trait space expansion towards the tropics may be widespread and underlie gradients in species diversity.
DOI: 10.6084/m9.figshare.5336056
title: FACE

description: detect
DOI: 10.6084/m9.figshare.5336026
title: Tsanov Data 2017 B

description: 1) Temporal photostimulation in BLA of rats injected with AVV-CaMKIIa-hChR2(H134R)-eYFP-WPRE-hGH<br><br>2) Spatial optostimulation in BLA of rats injected with AVV-CaMKIIa-hChR2(H134R)-eYFP-WPRE-hGH<br><br>3) Hippocampal local field potential in beta range from rectangular-shaped linear track before and after exposure to TMT.<br><br>4) Single-unit recordings of place cells from rectangular-shaped linear track before and after exposure to TMT.<br><br><br>
DOI: 10.6084/m9.figshare.5335999
title: APC data collected by Jisc 2013-2016

description: This data is collected by Jisc yearly. It has been cleaned using Open Refine. <br><br>The individual files are available on Figshare: https://figshare.com/search?q=:tag: article processing charges<br><br>For detailed information and analysis see: http://nbviewer.jupyter.org/github/kshamash/Article-processing-charges/blob/master/Autogenerate APC report.ipynb<br><br>The code and data are available on Github: https://github.com/kshamash/Article-processing-charges<br><br><br><br>
DOI: 10.6084/m9.figshare.5335999.v1
title: APC data collected by Jisc 2013-2016

description: This data is collected by Jisc yearly. It has been cleaned using Open Refine. <br><br>The individual files are available on Figshare: https://figshare.com/search?q=:tag: article processing charges<br><br>For detailed information and analysis see: http://nbviewer.jupyter.org/github/kshamash/Article-processing-charges/blob/master/Autogenerate APC report.ipynb<br><br>The code and data are available on Github: https://github.com/kshamash/Article-processing-charges<br><br><br><br>
DOI: 10.6084/m9.figshare.5335945
title: Supplementary Material for: Cancer Genomic Resources and Present Needs in the Latin American Region

description: In Latin America (LA), cancer is the second leading cause of death, and little is known about the capacities and needs for the development of research in the field of cancer genomics. In order to evaluate the current capacity for and development of cancer genomics in LA, we collected the available information on genomics, including the number of next-generation sequencing (NGS) platforms, the number of cancer research institutions and research groups, publications in the last 10 years, educational programs, and related national cancer control policies. Currently, there are 221 NGS platforms and 118 research groups in LA developing cancer genomics projects. A total of 272 articles in the field of cancer genetics/genomics were published by authors affiliated to Latin American institutions. Educational programs in genomics are scarce, almost exclusive of graduate programs, and only few are concerning cancer. Only 14 countries have national cancer control plans, but all of them consider secondary prevention strategies for early diagnosis, opportune treatment, and decreasing mortality, where genomic analyses could be implemented. Despite recent advances in introducing knowledge about cancer genomics and its application to LA, the region lacks development of integrated genomic research projects, improved use of NGS platforms, implementation of associated educational programs, and health policies that could have an impact on cancer care.