cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5513500
title: Dataset for: Carbonic Anhydrase 2-like in the giant clam, <i>Tridacna squamosa</i>: characterization, localization, response to light, and possible role in the transport of inorganic carbon from the host to its symbionts

description: The fluted giant clam, <i>Tridacna squamosa</i>, lives in symbiosis with zooxanthellae which reside extracellularly inside a tubular system. Zooxanthellae fix inorganic carbon (C<sub>i</sub>) during insolation and donate photosynthate to the host. Carbonic anhydrases catalyze the interconversion of CO<sub>2</sub> and HCO<sub>3</sub><sup>-</sup>, of which carbonic anhydrase 2 (CA2) is the most ubiquitous and involved in many biological processes. This study aimed to clone a <i>CA2</i> homolog (<i>CA2-like</i>) from the fleshy and colorful outer mantle as well as the thin and whitish inner mantle of <i>T. squamosa</i>, to determine its cellular and subcellular localization, and to examine the effects of light exposure on its gene and protein expression levels. The cDNA coding sequence of <i>CA2-like</i> from <i>T. squamosa</i> comprised 789 bp, encoding 263 amino acids with an estimated molecular mass of 29.6 kDa. A phenogramic analysis of the deduced CA2-like sequence denoted an animal origin. CA2-like was not detectable in the shell-facing epithelium of the inner mantle adjacent to the extrapallial fluid. Hence, CA2-like is unlikely to participate directly in light-enhanced calcification. By contrast, the outer mantle, which contains the highest density of tertiary tubules and zooxanthellae, displayed high level of <i>CA2-like</i> expression, and CA2-like was localized to the tubule epithelial cells. More importantly, exposure to light induced significant increases in the protein abundance of CA2-like in the outer mantle. Hence, CA2-like could probably take part in the increased supply of inorganic carbon (C<sub>i</sub>) from the host clam to the symbiotic zooxanthellae when the latter conduct photosynthesis to fix C<sub>i</sub> during light exposure.
DOI: 10.6084/m9.figshare.5513500.v1
title: Dataset for: Carbonic Anhydrase 2-like in the giant clam, <i>Tridacna squamosa</i>: characterization, localization, response to light, and possible role in the transport of inorganic carbon from the host to its symbionts

description: The fluted giant clam, <i>Tridacna squamosa</i>, lives in symbiosis with zooxanthellae which reside extracellularly inside a tubular system. Zooxanthellae fix inorganic carbon (C<sub>i</sub>) during insolation and donate photosynthate to the host. Carbonic anhydrases catalyze the interconversion of CO<sub>2</sub> and HCO<sub>3</sub><sup>-</sup>, of which carbonic anhydrase 2 (CA2) is the most ubiquitous and involved in many biological processes. This study aimed to clone a <i>CA2</i> homolog (<i>CA2-like</i>) from the fleshy and colorful outer mantle as well as the thin and whitish inner mantle of <i>T. squamosa</i>, to determine its cellular and subcellular localization, and to examine the effects of light exposure on its gene and protein expression levels. The cDNA coding sequence of <i>CA2-like</i> from <i>T. squamosa</i> comprised 789 bp, encoding 263 amino acids with an estimated molecular mass of 29.6 kDa. A phenogramic analysis of the deduced CA2-like sequence denoted an animal origin. CA2-like was not detectable in the shell-facing epithelium of the inner mantle adjacent to the extrapallial fluid. Hence, CA2-like is unlikely to participate directly in light-enhanced calcification. By contrast, the outer mantle, which contains the highest density of tertiary tubules and zooxanthellae, displayed high level of <i>CA2-like</i> expression, and CA2-like was localized to the tubule epithelial cells. More importantly, exposure to light induced significant increases in the protein abundance of CA2-like in the outer mantle. Hence, CA2-like could probably take part in the increased supply of inorganic carbon (C<sub>i</sub>) from the host clam to the symbiotic zooxanthellae when the latter conduct photosynthesis to fix C<sub>i</sub> during light exposure.
DOI: 10.6084/m9.figshare.5513449
title: Politicians by Country from the English-language Wikipedia

description: This project contains data on most English-language Wikipedia articles within the category "Category:Politicians by nationality" and subcategories, along with the code used to generate that data. Both are released under the CC-BY-SA 4.0 license.<br><b>Data</b>The data was extracted via the Wikimedia API using the associated code. It is formatted as a CSV and saved as <i>page_data.csv</i> in the "data" directory. Columns are:<br>1. "country", containing the sanitised country name, extracted from the category name;2. "page", containing the unsanitised page title.3. "last_edit", containing the edit ID of the last edit to the page.<br>Country codes are inconsistent. Where possible, they have been modified to match the country names found in http://www.prb.org/DataFinder/Topic/Rankings.aspx?ind=14 - but the PRB dataset contains nations not found in Wikipedia, and vice versa.<br>The actual recursion only went 2 levels deep into the category tree: someone listed as an Antiguan politician, say, is included - someone exclusively listed as an Antiguan politician who was assassinated is not.<br><b>Code</b>The code is written in the programming language R, and heavily commented; it can be found in the "code" directory, and is split into 3 files:<br>1. <i>utils.R, </i>which contains utilities for operating the code in the other files;2. <i>retrieve.R</i>, which contains functions for retrieving the category and page data from Wikipedia;3. <i>main.R</i>, which executes the data retrieval code and performs sanitisation before writing it to file.
DOI: 10.6084/m9.figshare.5513548.v4
title: Additional data for involved analysis

description: The item contains necessary data to reproduce analytical results in the manuscript.
DOI: 10.6084/m9.figshare.5513407
title: Virtual E Dataset

description: - Virtual E Dataset<br>E dataset (3317 images) - Diagnosis predicted by CNNs (ResNet-152 + VGG-19; arithmatic mean of both outputs; training dataset: A1)<br>We created the E dataset to assess the semisupervised learning performance by conducting a Web-based image search for “tinea,” “onychomycosis,” “nail dystrophy,” “onycholysis,” and “melanonychia” in English, Korean, and Japanese on http://google.com and http://bing.com, and downloaded a total of 15,844 images. From these images, the R-CNNs created a nail dataset of 3,317 images, since we had to discard many images because of low image resolution. The CNNs (model: ResNet-152 + VGG-19; arithmetic mean of both outputs; training dataset: A1) automatically classified images generated by the R-CNNs into six classes (760 onychomycosis, 1,316 nail dystrophy, 363 onycholysis, 185 melanonychia, 424 normal, and 269 others).
DOI: 10.6084/m9.figshare.5513416
title: Robust encoding of spatial information in orbitofrontal cortex and striatum

description: Single neuron activity obtained from WCST task in OFC, VS, DS
DOI: 10.6084/m9.figshare.5513449.v1
title: Untitled Item

description: This project contains data on most English-language Wikipedia articles within the category "Category:Politicians by nationality" and subcategories, along with the code used to generate that data. Both are released under the CC-BY-SA 4.0 license.<br><b>Data</b>The data was extracted via the Wikimedia API using the associated code. It is formatted as a CSV and saved as <i>page_data.csv</i> in the "data" directory. Columns are:<br>1. "country", containing the sanitised country name, extracted from the category name;2. "page", containing the unsanitised page title.<br>Country codes are inconsistent. Where possible, they have been modified to match the country names found in http://www.prb.org/DataFinder/Topic/Rankings.aspx?ind=14 - but the PRB dataset contains nations not found in Wikipedia, and vice versa.<br>The actual recursion only went 2 levels deep into the category tree: someone listed as an Antiguan politician, say, is included - someone exclusively listed as an Antiguan politician who was assassinated is not.<br><b>Code</b>The code is written in the programming language R, and heavily commented; it can be found in the "code" directory, and is split into 3 files:<br>1. <i>utils.R, </i>which contains utilities for operating the code in the other files;2. <i>retrieve.R</i>, which contains functions for retrieving the category and page data from Wikipedia;3. <i>main.R</i>, which executes the data retrieval code and performs sanitisation before writing it to file.
DOI: 10.6084/m9.figshare.5513407.v1
title: Virtual E Dataset

description: - Virtual dataset<br>E - Web dataset (3317 images) - Diagnosis predicted by CNNs (ResNet-152 + VGG-19; arithmatic mean of both outputs; training dataset: A1)<br>We created the E dataset to assess the semisupervised learning performance by conducting a Web-based image search for “tinea,” “onychomycosis,” “nail dystrophy,” “onycholysis,” and “melanonychia” in English, Korean, and Japanese on http://google.com and http://bing.com, and downloaded a total of 15,844 images. From these images, the R-CNNs created a nail dataset of 3,317 images, since we had to discard many images because of low image resolution. The CNNs (model: ResNet-152 + VGG-19; arithmetic mean of both outputs; training dataset: A1) automatically classified images generated by the R-CNNs into six classes (760 onychomycosis, 1,316 nail dystrophy, 363 onycholysis, 185 melanonychia, 424 normal, and 269 others).
DOI: 10.6084/m9.figshare.5513401
title: Dataset for: Considerations for Analysis of Time-to-Event Outcomes Measured with Error: Bias and Correction with SIMEX

description: For time-to-event outcomes, a rich literature exists on the bias introduced by covariate measurement error in regression models, such as the Cox model, and methods of analysis to address this bias. By comparison, less attention has been given to understanding the impact or addressing errors in the failure time outcome. For many diseases, the timing of an event of interest (such as progression-free survival or time to AIDS progression) can be difficult to assess or reliant on self-report and therefore prone to measurement error. For linear models, it is well known that random errors in the outcome variable do not bias regression estimates. With non-linear models, however, even random error or misclassification can introduce bias into estimated parameters. We compare the performance of two common regression models, the Cox and Weibull models, in the setting of measurement error in the failure time outcome. We introduce an extension of the SIMEX method to correct for bias in hazard ratio estimates from the Cox model and discuss other analysis options to address measurement error in the response. A formula to estimate the bias induced into the hazard ratio by classical measurement error in the event time for a log-linear survival model is presented. Detailed numerical studies are presented to examine the performance of the proposed SIMEX method under varying levels and parametric forms of the error in the outcome. We further illustrate the method with observational data on HIV outcomes from the Vanderbilt Comprehensive Care Clinic.
DOI: 10.6084/m9.figshare.5513401.v1
title: Dataset for: Considerations for Analysis of Time-to-Event Outcomes Measured with Error: Bias and Correction with SIMEX

description: For time-to-event outcomes, a rich literature exists on the bias introduced by covariate measurement error in regression models, such as the Cox model, and methods of analysis to address this bias. By comparison, less attention has been given to understanding the impact or addressing errors in the failure time outcome. For many diseases, the timing of an event of interest (such as progression-free survival or time to AIDS progression) can be difficult to assess or reliant on self-report and therefore prone to measurement error. For linear models, it is well known that random errors in the outcome variable do not bias regression estimates. With non-linear models, however, even random error or misclassification can introduce bias into estimated parameters. We compare the performance of two common regression models, the Cox and Weibull models, in the setting of measurement error in the failure time outcome. We introduce an extension of the SIMEX method to correct for bias in hazard ratio estimates from the Cox model and discuss other analysis options to address measurement error in the response. A formula to estimate the bias induced into the hazard ratio by classical measurement error in the event time for a log-linear survival model is presented. Detailed numerical studies are presented to examine the performance of the proposed SIMEX method under varying levels and parametric forms of the error in the outcome. We further illustrate the method with observational data on HIV outcomes from the Vanderbilt Comprehensive Care Clinic.
DOI: 10.6084/m9.figshare.5513449.v2
title: Politicians by Country from the English-language Wikipedia

description: This project contains data on most English-language Wikipedia articles within the category "Category:Politicians by nationality" and subcategories, along with the code used to generate that data. Both are released under the CC-BY-SA 4.0 license.<br><b>Data</b>The data was extracted via the Wikimedia API using the associated code. It is formatted as a CSV and saved as <i>page_data.csv</i> in the "data" directory. Columns are:<br>1. "country", containing the sanitised country name, extracted from the category name;2. "page", containing the unsanitised page title.<br>Country codes are inconsistent. Where possible, they have been modified to match the country names found in http://www.prb.org/DataFinder/Topic/Rankings.aspx?ind=14 - but the PRB dataset contains nations not found in Wikipedia, and vice versa.<br>The actual recursion only went 2 levels deep into the category tree: someone listed as an Antiguan politician, say, is included - someone exclusively listed as an Antiguan politician who was assassinated is not.<br><b>Code</b>The code is written in the programming language R, and heavily commented; it can be found in the "code" directory, and is split into 3 files:<br>1. <i>utils.R, </i>which contains utilities for operating the code in the other files;2. <i>retrieve.R</i>, which contains functions for retrieving the category and page data from Wikipedia;3. <i>main.R</i>, which executes the data retrieval code and performs sanitisation before writing it to file.
DOI: 10.6084/m9.figshare.5513224
title: bBSSR and BSSR-only original data

description: Data in this fileset are those used in the PLOS ONE publication "A snapshot of translational research funded by the National Institutes of Health (NIH): A case study using behavioral and social science research awards and Clinical and Translational Science Awards funded publications." The article can be accessed here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196545<br><br>Original bBSSR and BSSR-only award and publication data downloaded from NIH Reporter (https://projectreporter.nih.gov/reporter.cfm). Data files used by R scripts in publication.<br>* bBSSR award data (7 csv files in total): "bBSSR [2008-2014] NIH reporter 7 August 2017"<br>* bBSSR publication data (6 csv files in total): "Publications from NIH Reporter batch [1-6]"<br>* BSSR award data (10 csv files in total): "BSSR [2008-2014, part 1/2] NIH reporter 16/17 August 2017"<br><br>* BSSR publication data (13 csv files in total): "BSSR publications batch [1-13] 17 August 2017"<br><br>* "Foward citation data for analysis": list of forward citation PMIDs retrieved from Scopus for a select subset of bBSSR publications<br>* Citation data for bBSSR and BSSR-only publications retrieved from the NIH iCite database (https://icite.od.nih.gov/analysis): "NIH iCite batch [1-40]"<br>* "List of CTSA PMIDs from Surkis et al 2016": publications and associated PMIDs that are linked to CTSA awards; data retrieved from Surkis et al 2016 (reference below)<br>ReferenceSurkis, A., Hogle, J.A., DiazGranados, D., Hunt, J.D., Mazmanian, P.E., Connors, E., Westaby, K., Whipple, E.C., Adamus, T., Mueller, M., and Aphinyanaphongs, Y. 2016. “Classifying publications from the clinical and translational science award program along the translational research spectrum: a machine learning approach.” <i>Journal of Translational Medicine</i> 14: 235. DOI: 10.1186/s12967-016-0992-8.
DOI: 10.6084/m9.figshare.5513374
title: Dataset for: Temperature-dependent body size effects determine population responses to climate warming

description: Current understanding of animal population responses to rising temperatures is based on the assumption that biological rates such as metabolism, which governs fundamental ecological processes, scale independently with body size and temperature, despite empirical evidence for interactive effects. Here we investigate the consequences of interactive temperature- and size-scaling of vital rates for the dynamics of populations experiencing warming using a stage-structured consumer-resource model. We show that interactive scaling alters population and stage-specific responses to rising temperatures, such that warming can induce shifts in population regulation and stage-structure, influence community structure and govern population responses to mortality. Analyzing experimental data for 20 fish species, we found size-temperature interactions in intraspecific scaling of metabolic rate to be common. Given the evidence for size-temperature interactions and the ubiquity of size structure in animal populations, we argue that accounting for size-specific temperature effects is pivotal for understanding how warming affects animal populations and communities.
DOI: 10.6084/m9.figshare.5513374.v1
title: Dataset for: Temperature-dependent body size effects determine population responses to climate warming

description: Current understanding of animal population responses to rising temperatures is based on the assumption that biological rates such as metabolism, which governs fundamental ecological processes, scale independently with body size and temperature, despite empirical evidence for interactive effects. Here we investigate the consequences of interactive temperature- and size-scaling of vital rates for the dynamics of populations experiencing warming using a stage-structured consumer-resource model. We show that interactive scaling alters population and stage-specific responses to rising temperatures, such that warming can induce shifts in population regulation and stage-structure, influence community structure and govern population responses to mortality. Analyzing experimental data for 20 fish species, we found size-temperature interactions in intraspecific scaling of metabolic rate to be common. Given the evidence for size-temperature interactions and the ubiquity of size structure in animal populations, we argue that accounting for size-specific temperature effects is pivotal for understanding how warming affects animal populations and communities.
DOI: 10.6084/m9.figshare.5513170
title: R scripts

description: R scripts in this fileset are those used in the PLOS ONE publication "A snapshot of translational research funded by the National Institutes of Health (NIH): A case study using behavioral and social science research awards and Clinical and Translational Science Awards funded publications." The article can be accessed here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0196545<br><br>This consists of all R scripts used for data cleaning, data manipulation, and statistical analysis used in the publication.<br>There are eleven files in total:<br>1. "Step1a.bBSSR.format.grants.and.publications.data.R" combines all bBSSR 2008-2014 grant award data and associated publications downloaded from NIH Reporter. 2. "Step1b.BSSR.format.grants.and.publications.data.R" combines all BSSR-only 2008-2014 grant award data and associated publications downloaded from NIH Reporter. 3. "Step2a.bBSSR.get.pubdates.transl.and.all.grants.R" queries PubMed and downloads associated bBSSR publication data.4. "Step2b.BSSR.get.pubdates.transl.and.all.grants.R" queries PubMed and downloads associated BSSR-only publication data.<br>5. "Step3.summary.stats.R" performs summary statistics6. "Step4.time.to.first.publication.R" performs time to first publication analysis.7. "Step5.time.to.citation.analysis.R" performs time to first citation and time to overall citation analyses.8. "Step6.combine.NIH.iCite.data.R" combines NIH iCite citation data.9. "Step7.iCite.data.analysis.R" performs citation analysis on combined iCite data.10. "Step8.MeSH.descriptors.R" queries PubMed and pulls down all MeSH descriptors for all publications11. "Step9.CTSA.publications.R" compares the percent of translational publications among bBSSR, BSSR-only, and CTSA publications.
DOI: 10.6084/m9.figshare.5513173
title: Data used in "Currents and mixing in the San Lorenzo overflow: Northern Gulf of California".

description: Data used in the paper "Currents and mixing in the San Lorenzo overflow: Northern Gulf of California" by Froylan Rosas-Villegas, Manuel López and Julio Candela.<br>(Submitted to JGR Oceans July 5th, 2017)<br><br>
DOI: 10.6084/m9.figshare.5513449.v3
title: Politicians by Country from the English-language Wikipedia

description: This project contains data on most English-language Wikipedia articles within the category "Category:Politicians by nationality" and subcategories, along with the code used to generate that data. Both are released under the CC-BY-SA 4.0 license.<br><b>Data</b>The data was extracted via the Wikimedia API using the associated code. It is formatted as a CSV and saved as <i>page_data.csv</i> in the "data" directory. Columns are:<br>1. "country", containing the sanitised country name, extracted from the category name;2. "page", containing the unsanitised page title.3. "last_edit", containing the edit ID of the last edit to the page.<br>Country codes are inconsistent. Where possible, they have been modified to match the country names found in http://www.prb.org/DataFinder/Topic/Rankings.aspx?ind=14 - but the PRB dataset contains nations not found in Wikipedia, and vice versa.<br>The actual recursion only went 2 levels deep into the category tree: someone listed as an Antiguan politician, say, is included - someone exclusively listed as an Antiguan politician who was assassinated is not.<br><b>Code</b>The code is written in the programming language R, and heavily commented; it can be found in the "code" directory, and is split into 3 files:<br>1. <i>utils.R, </i>which contains utilities for operating the code in the other files;2. <i>retrieve.R</i>, which contains functions for retrieving the category and page data from Wikipedia;3. <i>main.R</i>, which executes the data retrieval code and performs sanitisation before writing it to file.
DOI: 10.6084/m9.figshare.5513173.v1
title: Data used in "Currents and mixing in the San Lorenzo overflow: Northern Gulf of California".

description: Data used in the paper "Currents and mixing in the San Lorenzo overflow: Northern Gulf of California" by Froylan Rosas-Villegas, Manuel López and Julio Candela.<br>(Submitted to JGR Oceans July 5th, 2017)<br><br>
DOI: 10.6084/m9.figshare.5513104
title: Altmetric data on journal articles with "altmetrics" in the title or abstract, October 18 2017

description: This is the full 220 item dataset from exported from Altmetric Explorer on October 18, 2017. It includes items where "altmetrics" appears in journal articles' titles or abstracts. Of the 220 items in this dataset, only 215 have online attention in the sources tracked by Altmetric.<br>The top 50 articles in this dataset (by Altmetric Attention Score) will profiled in the Open Access Week 2017 blogpost, "The top altmetrics research is impressively Open Access!" on the Altmetric blog.