cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4265075
title: ESM_Tables.xlsx Extra Supplementary tables for Farrell et al._Next Gen Pop Gen from Next Gen Pop Gen: implementing a high-throughput approach to population genetics in boarfish (<i>Capros aper</i>)

description: The recently developed approach for microsatellite genotyping by sequencing (GBS) using individual combinatorial barcoding was further improved and used to assess the genetic population structure of boarfish (<i>Capros aper</i>) across the species' range. Microsatellite loci were developed <i>de novo</i> and genotyped by next-generation sequencing. Genetic analyses of the samples indicated that boarfish can be subdivided into at least seven biological units (populations) across the species' range. Furthermore, the recent apparent increase in abundance in the northeast Atlantic is better explained by demographic changes within this area than by influx from southern or insular populations. This study clearly shows that the microsatellite GBS approach is a generic, cost-effective, rapid and powerful method suitable for full-scale population genetic studies—a crucial element for assessment, sustainable management and conservation of valuable biological resources.
DOI: 10.6084/m9.figshare.4265075.v1
title: ESM_Tables.xlsx Extra Supplementary tables for Farrell et al._Next Gen Pop Gen from Next Gen Pop Gen: implementing a high-throughput approach to population genetics in boarfish (<i>Capros aper</i>)

description: The recently developed approach for microsatellite genotyping by sequencing (GBS) using individual combinatorial barcoding was further improved and used to assess the genetic population structure of boarfish (<i>Capros aper</i>) across the species' range. Microsatellite loci were developed <i>de novo</i> and genotyped by next-generation sequencing. Genetic analyses of the samples indicated that boarfish can be subdivided into at least seven biological units (populations) across the species' range. Furthermore, the recent apparent increase in abundance in the northeast Atlantic is better explained by demographic changes within this area than by influx from southern or insular populations. This study clearly shows that the microsatellite GBS approach is a generic, cost-effective, rapid and powerful method suitable for full-scale population genetic studies—a crucial element for assessment, sustainable management and conservation of valuable biological resources.
DOI: 10.6084/m9.figshare.4265072
title: Measurements used in morphometric analyses from Dietary adaptions in the ultrastructure of dinosaur dentine

description: Teeth are key to understanding the feeding ecology of both extant and extinct vertebrates. Recent studies have highlighted the previously unrecognized complexity of dinosaur dentitions and how specific tooth tissues and tooth shapes differ between taxa with different diets. However, it is unknown how the ultrastructure of these tooth tissues contributes to the differences in feeding style between taxa. In this study, we use third harmonic generation microscopy and scanning electron microscopy to examine the ultrastructure of the dentine in herbivorous and carnivorous dinosaurs to understand how the structure of this tissue contributes to the overall utility of the tooth. Morphometric analyses of dentinal tubule diameter, density and branching rates reveal a strong signal for dietary preferences, with herbivorous saurischian and ornithischian dinosaurs consistently having higher dentinal tubule density than their carnivorous relatives. We hypothesize that this relates to the hardness of the dentine, where herbivorous taxa have dentine that is more resistant to breakage and wear at the dentine–enamel junction than carnivorous taxa. This study advocates the detailed study of dentine and the use of advanced microscopy techniques to understand the evolution of dentition and feeding ecology in extinct vertebrates.
DOI: 10.6084/m9.figshare.4265072.v1
title: Measurements used in morphometric analyses from Dietary adaptions in the ultrastructure of dinosaur dentine

description: Teeth are key to understanding the feeding ecology of both extant and extinct vertebrates. Recent studies have highlighted the previously unrecognized complexity of dinosaur dentitions and how specific tooth tissues and tooth shapes differ between taxa with different diets. However, it is unknown how the ultrastructure of these tooth tissues contributes to the differences in feeding style between taxa. In this study, we use third harmonic generation microscopy and scanning electron microscopy to examine the ultrastructure of the dentine in herbivorous and carnivorous dinosaurs to understand how the structure of this tissue contributes to the overall utility of the tooth. Morphometric analyses of dentinal tubule diameter, density and branching rates reveal a strong signal for dietary preferences, with herbivorous saurischian and ornithischian dinosaurs consistently having higher dentinal tubule density than their carnivorous relatives. We hypothesize that this relates to the hardness of the dentine, where herbivorous taxa have dentine that is more resistant to breakage and wear at the dentine–enamel junction than carnivorous taxa. This study advocates the detailed study of dentine and the use of advanced microscopy techniques to understand the evolution of dentition and feeding ecology in extinct vertebrates.
DOI: 10.6084/m9.figshare.4265030
title: nPES data.zip

description: data for figures in nPES manuscript
DOI: 10.6084/m9.figshare.4265027
title: Supplementary Material for: Modulation of Microbiota-Gut-Brain Axis by Berberine Resulting in Improved Metabolic Status in High-Fat Diet-Fed Rats

description: <i>Objective: </i>To investigate whether or not berberine could improve metabolic status of high-fat-fed rats through modulation of microbiota-gut-brain axis. <i>Methods:</i>Berberine was administered on high-fat-fed Sprague-Dawley rats. Brain-gut hormones were detected, and changes of gut microbiota were analyzed by 16S rRNA gene sequencing. <i>Results:</i> Berberine could reduce weight gain and lipolysis in the high-fat diet-fed group. Moreover, trends of ameliorated insulin resistance and decreased endogenous glucose production were observed. In addition, the microbiota-gut-brain axis was found to be modulated, including structural and diversity changes of microbiota, elevated serum glucagon-like peptide-1 and neuropeptide Y level, decreased orexin A level, up-regulated glucagon-like peptide-1 receptor mRNA level as well as ultra-structural improvement of the hypothalamus. <i>Conclusion:</i> Taken together, our findings suggest that berberine improved metabolic disorders induced by high-fat diet through modulation of the microbiota-gut-brain axis.
DOI: 10.6084/m9.figshare.4265030.v1
title: nPES data.zip

description: data for figures in nPES manuscript
DOI: 10.6084/m9.figshare.4264973
title: Wikipedia Talk Corpus

description: We provide a corpus of discussion comments from English Wikipedia talk pages. Comments are grouped into different files by year. Comments are generated by computing diffs over the full revision history and extracting the content added for each revision. See our wiki for documentation of the schema and our research paper for documentation on the data collection and processing methodology.
DOI: 10.6084/m9.figshare.4264988
title: SIMENZKIN biochemistry seminar.xlsx

description: SIMENZKIN is a data table file (Excel and ods) programmed to simulate enzymatic metabolic reactions using the Michaelis-Menten formalism. Is optimized for being used in a practical module for a enzymology class together with the problem attached.
DOI: 10.6084/m9.figshare.4264973.v1
title: Wikipedia Talk Corpus

description: We provide a corpus of discussion comments from English Wikipedia talk pages. Comments are grouped into different files by year. Comments are generated by computing diffs over the full revision history and extracting the content added for each revision. See our wiki for documentation of the schema and our research paper for documentation on the data collection and processing methodology.
DOI: 10.6084/m9.figshare.4264973.v2
title: Wikipedia Talk Corpus

description: We provide a corpus of discussion comments from English Wikipedia talk pages. Comments are grouped into different files by year. Comments are generated by computing diffs over the full revision history and extracting the content added for each revision. See our wiki for documentation of the schema and our research paper for documentation on the data collection and processing methodology.
DOI: 10.6084/m9.figshare.4264688
title: Judgment No. 72A/1947 against Colonel Shoichi IKEDA for 15 years’ imprisonment (rendered 30 March 1948)

description: An annotated translation of Judgment No. 72A/1947 of the Batavian War Crimes Tribunal against Colonel Shoichi IKEDA for 15 years’ imprisonment (rendered 30 March 1948). <br>This translation was performed by members of the community as organised by Danny Friedman via the http://koreadutchindiesproject.blogspot.com in 2007, and verified, standardised, and annotated by Nina H. B. Jørgensen, Danny Friedman, and Alainna Therese Wrigley as a part of the Batavian War Crimes Tribunal Project at the Chinese University of Hong Kong Centre for Rights and Justice in 2012-3. <br>These translations are made available to the public for research use and are included with scans of the Dutch original judgment as prepared by the Project.
DOI: 10.6084/m9.figshare.4264685
title: Judgment No. 72/1947 against 12 Japanese officers and civilians (rendered 14 February 1948)

description: An annotated translation of Judgment No. 72/1947 of the Batavian War Crimes Tribunal against 12 Japanese officers and civilians (rendered 14 February 1948). The officers are understood to be Shoichi IKEDA, Hiromu MITSUHASHI, Keiji OKADA, Ohiomatsu KAWAMURA, Kuizo MURAKAMI, Shiro NAKASHIMA, Eiichi ISHIDA, Taranosuke SAI, Iwao FURUYA, Shinji SHIMODA, Yukio MORIMOTO, Kenjiro TSUTAKI. <br>This translation was created by members of the community as organised by Danny Friedmann via the http://koreadutchindiesproject.blogspot.com in 2007, and verified, standardised, and annotated by Nina H. B. Jørgensen, Danny Friedmann, and Alainna Therese Wrigley as a part of the Batavian War Crimes Tribunal Project at the Chinese University of Hong Kong Centre for Rights and Justice in 2012-3. <br>These translations are made available to the public for research use and are included with scans of the Dutch original judgment as prepared by the Project.
DOI: 10.6084/m9.figshare.4264682
title: Judgment No. 40/1946 against Washio AWOCHI for 10 years’ imprisonment (rendered 25 October 1946)

description: An annotated translation of Judgment No. 40/1946 of the Batavian War Crimes Tribunal against Washio AWOCHI for 10 years’ imprisonment (rendered 25 October 1946)<br>This translation was created by members of the community as organised by Danny Friedmann via the http://koreadutchindiesproject.blogspot.com in 2007, and verified, standardised, and annotated by Nina H. B. Jørgensen, Danny Friedmann, and Alainna Therese Wrigley as a part of the Batavian War Crimes Tribunal Project at the Chinese University of Hong Kong Centre for Rights and Justice in 2012-3. <br>These translations are made available to the public for research use and are included with scans of the Dutch original judgment as prepared by the Project.
DOI: 10.6084/m9.figshare.4264685.v1
title: Judgment No. 72/1947 against 12 Japanese officers and civilians (rendered 14 February 1948)

description: An annotated translation of Judgment No. 72/1947 of the Batavian War Crimes Tribunal against 12 Japanese officers and civilians (rendered 14 February 1948). The officers are understood to be Shoichi IKEDA, Hiromu MITSUHASHI, Keiji OKADA, Ohiomatsu KAWAMURA, Kuizo MURAKAMI, Shiro NAKASHIMA, Eiichi ISHIDA, Taranosuke SAI, Iwao FURUYA, Shinji SHIMODA, Yukio MORIMOTO, Kenjiro TSUTAKI. <br>This translation was created by members of the community as organised by Danny Friedmann via the http://koreadutchindiesproject.blogspot.com in 2007, and verified, standardised, and annotated by Nina H. B. Jørgensen, Danny Friedmann, and Alainna Therese Wrigley as a part of the Batavian War Crimes Tribunal Project at the Chinese University of Hong Kong Centre for Rights and Justice in 2012-3. <br>These translations are made available to the public for research use and are included with scans of the Dutch original judgment as prepared by the Project.
DOI: 10.6084/m9.figshare.4264541
title: 20Deg EDM Bearing Experimental Test Data

description: Measured vibration of a defective bearing with an EDM defect on the outer raceway of the bearing. Entry and exit slope of 20 degrees and 9.7mm long with an appiled load of 2.5-10kN and a shaft speed of 5-12.5Hz.
DOI: 10.6084/m9.figshare.4264541.v1
title: 20Deg EDM Bearing Experimental Test Data

description: Measured vibration of a defective bearing with an EDM defect on the outer raceway of the bearing. Entry and exit slope of 20 degrees and 9.7mm long with an appiled load of 2.5-10kN and a shaft speed of 5-12.5Hz.
DOI: 10.17608/k6.auckland.4264520
title: Data Files - TCoA-IIIA Primary Schools

description: The SPSS data file containing all data collected from the TCoA-IIIA questionnaire administered in 2001 for primary schools. <br>The AMOS data file is the confirmatory factor analysis input for the primary school TCoA-IIIA data set. <br>Results were published in:Brown, G. T. L. (2006). Teachers’ conceptions of assessment: Validation of an abridged instrument. <i>Psychological Reports, 99</i>(1)<i>, </i>166-170<i>. </i>doi: 10.2466/pr0.99.1.166-170
DOI: 10.6084/m9.figshare.4264499
title: Micromonas polaris CCMP2099 evolution experiments

description: We report the growth rate of a single strain of the Arctic prasinophyte Micromonas polaris CCMP2099 measured in the lab over long-duration experiments (170-340 generations).<br>There are five treatments (2°C, 6°C, 13°C, 13°C high light, 13°C periodic nitrate depletion) with 6 replicate lines per treatment. Growth rates are estimated at each culture transfer (semi-continuous cultures). <br>See Benner et al (2020) Limnology and Oceanography: Letters for more information.
DOI: 10.6084/m9.figshare.4264394
title: Survey questions - Textbooks- cost and access - University of Otago Student Survey 2016

description: Questions from a student survey on Textbooks - cost and access, University of Otago, 2015.<br>Provided in Word format for general reuse. Also provided in QSF format for those with access to Qualtrics software, which was used to design and run the survey. This format allows you to import the survey, including all skip logic and formatting.
DOI: 10.6084/m9.figshare.4264271
title: Estimating the Effects of Environmental Variables and Gear Type on the Detection and Occupancy of Large-River Fishes in a Standardized Sampling Program Using Multiseason Bayesian Mixture Models

description: Sampling in non-wadeable rivers presents methodological challenges for monitoring fish species. Changing environmental conditions may affect the ability to accurately capture species (i.e., detection) and consequently may lead to inappropriate inferences on occupancy rates. We used hierarchical Bayesian multiseason mixture models to estimate occupancy and detection of 41 of 52 fish species in the Kankakee River, Illinois, by using data from a standardized monitoring program. Fish were sampled with AC boat electrofishing and shoreline seining over 7 years. Some centrarchids (e.g., Smallmouth Bass <i>Micropterus dolomieu</i>) were efficiently sampled by boat electrofishing, whereas most other species had low detection probabilities. Moderate changes in environmental conditions, such as water velocity and temperature, produced moderate changes in detection and occupancy. Generally, when species had high detection probabilities, changes in environmental conditions produced relatively small changes in the estimated detection probabilities. Our results also suggested that some sport fishes collected from rivers with only moderate environmental fluctuations are unlikely to produce strongly biased estimates of detection and occupancy among years. However, many species had detection probabilities that were low, imprecisely estimated, or both. Overall, we demonstrate that long-term fisheries monitoring can effectively detect some species at levels that are often relevant for management, but assessments of species with lower and more uncertain detection probabilities may not provide adequate information for management decisions. We recommend the use of sampling designs that allow the estimation of both detection and occupancy. Received November 19, 2015; accepted June 21, 2016 Published online November 28, 2016
DOI: 10.6084/m9.figshare.4264271.v1
title: Estimating the Effects of Environmental Variables and Gear Type on the Detection and Occupancy of Large-River Fishes in a Standardized Sampling Program Using Multiseason Bayesian Mixture Models

description: Sampling in non-wadeable rivers presents methodological challenges for monitoring fish species. Changing environmental conditions may affect the ability to accurately capture species (i.e., detection) and consequently may lead to inappropriate inferences on occupancy rates. We used hierarchical Bayesian multiseason mixture models to estimate occupancy and detection of 41 of 52 fish species in the Kankakee River, Illinois, by using data from a standardized monitoring program. Fish were sampled with AC boat electrofishing and shoreline seining over 7 years. Some centrarchids (e.g., Smallmouth Bass <i>Micropterus dolomieu</i>) were efficiently sampled by boat electrofishing, whereas most other species had low detection probabilities. Moderate changes in environmental conditions, such as water velocity and temperature, produced moderate changes in detection and occupancy. Generally, when species had high detection probabilities, changes in environmental conditions produced relatively small changes in the estimated detection probabilities. Our results also suggested that some sport fishes collected from rivers with only moderate environmental fluctuations are unlikely to produce strongly biased estimates of detection and occupancy among years. However, many species had detection probabilities that were low, imprecisely estimated, or both. Overall, we demonstrate that long-term fisheries monitoring can effectively detect some species at levels that are often relevant for management, but assessments of species with lower and more uncertain detection probabilities may not provide adequate information for management decisions. We recommend the use of sampling designs that allow the estimation of both detection and occupancy. Received November 19, 2015; accepted June 21, 2016 Published online November 28, 2016
DOI: 10.6084/m9.figshare.4264265
title: Multi-Criteria Decision Analysis for Recreational Trout Fisheries in British Columbia, Canada: A Bayesian Network Implementation

description: One of the key challenges in recreational fisheries management is to provide a rational basis for decisions in the face of conflicting objectives, such as improving angling opportunities, maintaining satisfaction across a diverse fishing client base, controlling costs, and conserving wild populations. We developed a multi-criteria decision analysis approach for managing recreational trout fisheries (e.g., Rainbow Trout <i>Oncorhynchus mykiss</i>). The approach was implemented in a Bayesian decision network. The decision support tool, called “Stock-Optim,” provides a user-friendly interface for predicting fishery performance from alternate stocking prescriptions. The tool integrates survey information on angler typology and satisfaction with previously developed models for fish biology and fishery dynamics to more fully consider the biological and social outcomes of management decisions. Specifically, the tool evaluated alternative stocking options given three performance criteria: angler effort, angler satisfaction, and the cost of the stocking program. Predicted effort was highest for fish that were released in the size range of 8–20 g and at stocking densities of 200–500 fish/ha. Effort maximization at these rates and sizes is a result of compromise between the conflicting preferences of Rainbow Trout enthusiasts and occasional anglers toward fish size and harvest. Furthermore, lowering the stocking program’s costs will lead to lower stocking rates and thereby favor the enthusiasts. Currently, stocking levels in British Columbia are lower than levels that would maximize effort and are most consistent with a policy of maximizing satisfaction for Rainbow Trout enthusiasts and minimizing costs. Stock-Optim will allow managers to compare predicted outcomes from the current and alternative regimes with stated lake-specific or region-specific management objectives and regional averages and thereby more closely meet these objectives in the future. Lastly, the model was validated by comparing predicted effort with observed effort in stocked lakes. Received February 1, 2016; accepted July 14, 2016 Published online November 28, 2016
DOI: 10.6084/m9.figshare.4264265.v1
title: Multi-Criteria Decision Analysis for Recreational Trout Fisheries in British Columbia, Canada: A Bayesian Network Implementation

description: One of the key challenges in recreational fisheries management is to provide a rational basis for decisions in the face of conflicting objectives, such as improving angling opportunities, maintaining satisfaction across a diverse fishing client base, controlling costs, and conserving wild populations. We developed a multi-criteria decision analysis approach for managing recreational trout fisheries (e.g., Rainbow Trout <i>Oncorhynchus mykiss</i>). The approach was implemented in a Bayesian decision network. The decision support tool, called “Stock-Optim,” provides a user-friendly interface for predicting fishery performance from alternate stocking prescriptions. The tool integrates survey information on angler typology and satisfaction with previously developed models for fish biology and fishery dynamics to more fully consider the biological and social outcomes of management decisions. Specifically, the tool evaluated alternative stocking options given three performance criteria: angler effort, angler satisfaction, and the cost of the stocking program. Predicted effort was highest for fish that were released in the size range of 8–20 g and at stocking densities of 200–500 fish/ha. Effort maximization at these rates and sizes is a result of compromise between the conflicting preferences of Rainbow Trout enthusiasts and occasional anglers toward fish size and harvest. Furthermore, lowering the stocking program’s costs will lead to lower stocking rates and thereby favor the enthusiasts. Currently, stocking levels in British Columbia are lower than levels that would maximize effort and are most consistent with a policy of maximizing satisfaction for Rainbow Trout enthusiasts and minimizing costs. Stock-Optim will allow managers to compare predicted outcomes from the current and alternative regimes with stated lake-specific or region-specific management objectives and regional averages and thereby more closely meet these objectives in the future. Lastly, the model was validated by comparing predicted effort with observed effort in stocked lakes. Received February 1, 2016; accepted July 14, 2016 Published online November 28, 2016
DOI: 10.6084/m9.figshare.4264214
title: Learning from Data to Design Functional Materials without Inversion Symmetry (CIF files)

description: DFT optimized CIF files for the 19 compounds <br>
DOI: 10.6084/m9.figshare.4264217
title: Data from "The Emergent Worm: Dynamic Cellular Differentiation in the Caenorhabditis elegans embryogenesis"

description: Data from the manuscript "The Emergent Worm: Dynamic Cellular Differentiation in the Caenorhabditis elegans embryogenesis".<br>Contributors of primary data include Nikhil Bhatla (Worm Web.org), Dr. Stephen Larson (OpenWorm), and Mark Watts (OpenWorm)