cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17638/datacat.liverpool.ac.uk/2247
title: AGILE: Candidate specific trial protocol 2 (CST2): EIDD-2801 (molnupiravir) Primary Analysis

description: AGILE: Seamless Phase I/IIa Platform for the Rapid Evaluation of Candidates for COVID-19 treatment. (UoL001542B) The antiviral drug molnupiravir was licensed for treating at-risk patients with COVID-19 on the basis of data from unvaccinated adults. The randomised, placebo-controlled, double-blind, phase 2 trial (AGILE CST-2) aimed to evaluate the safety and virological efficacy of molnupiravir in vaccinated and unvaccinated individuals with COVID-19. The primary outcome was the time from randomisation to SARS-CoV-2 PCR negativity on nasopharyngeal swabs, analysed by use of a Bayesian Cox proportional hazards model for estimating the probability of a superior virological response (hazard ratio [HR]&gt;1) for molnupiravir versus placebo. This trial is registered in ClinicalTrials.gov (NCT04746183), and the ISRCTN registry (ISRCTN27106947). We undertook a dose-escalating, open-label, randomized-controlled (standard-of-care) Bayesian adaptive Phase I trial to evaluate the safety and optimal dose of molnupiravir in patients with early symptomatic infection. �-d-N4-hydroxycytidine (NHC), the parent nucleoside of molnupiravir, a COVID-19 antiviral, was quantified at SARS-CoV-2 transmission sites in 12 patients enrolled in AGILE Candidate-Specific Trial-2. Saliva, nasal, and tear NHC concentrations were 3%, 21%, and 22% that of plasma. Molnupiravir induces lethal error catastrophe in SARS-CoV-2. How this drug-induced mechanism of action might impact the emergence of resistance mutations is unclear. To investigate this, we used samples from the AGILE CST-2. We describe the pre-specified exploratory virological endpoint of CST-2, to determine the possible genomic changes in SARS-CoV-2 induced by molnupiravir treatment.
description: These data were used for the trial primary analysis detailed in the associated publications.
DOI: 10.6084/m9.figshare.14345032.v1
title: Phylogenetic position of the hemiuroid genus <i>Paraccacladium</i> Bray & Gibson, 1977 (Trematoda: Hemiuroidea) and the status of the subfamily Paraccacladiinae Bray & Gibson, 1977

description: In this study we tested the current taxonomic model of the trematode superfamily Hemiuroidea, according to which the genus <i>Paraccacladium</i> belongs to the family Accacoeliidae. We reconstructed the phylogeny of the hemiuroid Clade A using novel <i>28S rRNA</i> gene sequences of <i>Paraccacladium</i> sp., <i>Derogenes varicus</i>, <i>Progonus muelleri</i> and <i>Lampritrema miescheri</i> as well as data available in GenBank. Based on phylogenetic data, the genus <i>Paraccacladium</i> should be assigned to a separate family, the Paraccacladiidae Bray & Gibson, 1977 stat. nov. The morphological differences between the Paraccacladiidae and the Accacoeliidae are the absence of a uroproct, anteriorly directed diverticula of intestinal caeca, and the position of Mehlis’ gland, posterior or postero-lateral to the ovary. Phylogenetic analysis indicates a sister relationship between the Derogenidae and the Sclerodistomidae. It also shows that the Paraccacladiidae, on the one hand, and a group of families, the Accacoeliidae, Hirudinellidae and Syncoeliidae, on the other, share the most recent common ancestor. Our data support the hypothesis that the genus <i>Lampritrema</i> is affiliated to the Hirudinellidae. Genetic divergence between North Atlantic and North Pacific isolates of <i>D. varicus</i> was also determined.
DOI: 10.6084/m9.figshare.14345032
title: Phylogenetic position of the hemiuroid genus <i>Paraccacladium</i> Bray & Gibson, 1977 (Trematoda: Hemiuroidea) and the status of the subfamily Paraccacladiinae Bray & Gibson, 1977

description: In this study we tested the current taxonomic model of the trematode superfamily Hemiuroidea, according to which the genus <i>Paraccacladium</i> belongs to the family Accacoeliidae. We reconstructed the phylogeny of the hemiuroid Clade A using novel <i>28S rRNA</i> gene sequences of <i>Paraccacladium</i> sp., <i>Derogenes varicus</i>, <i>Progonus muelleri</i> and <i>Lampritrema miescheri</i> as well as data available in GenBank. Based on phylogenetic data, the genus <i>Paraccacladium</i> should be assigned to a separate family, the Paraccacladiidae Bray & Gibson, 1977 stat. nov. The morphological differences between the Paraccacladiidae and the Accacoeliidae are the absence of a uroproct, anteriorly directed diverticula of intestinal caeca, and the position of Mehlis’ gland, posterior or postero-lateral to the ovary. Phylogenetic analysis indicates a sister relationship between the Derogenidae and the Sclerodistomidae. It also shows that the Paraccacladiidae, on the one hand, and a group of families, the Accacoeliidae, Hirudinellidae and Syncoeliidae, on the other, share the most recent common ancestor. Our data support the hypothesis that the genus <i>Lampritrema</i> is affiliated to the Hirudinellidae. Genetic divergence between North Atlantic and North Pacific isolates of <i>D. varicus</i> was also determined.
DOI: 10.6084/m9.figshare.14472694
title: Tier 2 above-ground biomass expansion functions for South African plantation forests

description: Carbon stocks estimated for greenhouse gas emission reporting in South African plantation forests require improvement for local relevance. We developed biomass expansion and conversion factor (BECF) models to convert enumeration data to above-ground biomass (AGB) for major genera. Local biomass data and allometric models were aggregated across major taxa and scaled to utilisable stem and non-utilisable (bark, branch, foliar) biomass on 1 735 permanent sample plots. Models were developed for each genus to estimate BECF from utilisable volume to overcome bracket stepping in the Intergovernmental Panel on Climate Change (IPCC) lookup tables. To enable more accurate biomass estimates for growers who record tree volume and bone-dry wood density, an alternative calculation was developed that capitalises on stem-wood comprising 70% to 90% of AGB at rotation age. AGB is the sum of utilisable stem and non-utilisable components. Stem mass can be calculated as the product of volume and wood density. Models to estimate non-utilisable biomass from utilisable volume were developed for each genus. Local models estimated lower hardwood biomass and marginally lower softwood biomass than IPCC estimates. Use of local estimates compared to default values result in lower carbon stock estimates and reduced fluxes using the stock change method. Developing further allometric models and BECFs at the species or hybrid level will have little value due to rapidly changing genetic deployment and current work has indicated non-significant differences between genotypes within each genus. Further work should focus on improved tree volume and wood density estimates as well as on below-ground biomass estimates.
DOI: 10.6084/m9.figshare.14472694.v1
title: Tier 2 above-ground biomass expansion functions for South African plantation forests

description: Carbon stocks estimated for greenhouse gas emission reporting in South African plantation forests require improvement for local relevance. We developed biomass expansion and conversion factor (BECF) models to convert enumeration data to above-ground biomass (AGB) for major genera. Local biomass data and allometric models were aggregated across major taxa and scaled to utilisable stem and non-utilisable (bark, branch, foliar) biomass on 1 735 permanent sample plots. Models were developed for each genus to estimate BECF from utilisable volume to overcome bracket stepping in the Intergovernmental Panel on Climate Change (IPCC) lookup tables. To enable more accurate biomass estimates for growers who record tree volume and bone-dry wood density, an alternative calculation was developed that capitalises on stem-wood comprising 70% to 90% of AGB at rotation age. AGB is the sum of utilisable stem and non-utilisable components. Stem mass can be calculated as the product of volume and wood density. Models to estimate non-utilisable biomass from utilisable volume were developed for each genus. Local models estimated lower hardwood biomass and marginally lower softwood biomass than IPCC estimates. Use of local estimates compared to default values result in lower carbon stock estimates and reduced fluxes using the stock change method. Developing further allometric models and BECFs at the species or hybrid level will have little value due to rapidly changing genetic deployment and current work has indicated non-significant differences between genotypes within each genus. Further work should focus on improved tree volume and wood density estimates as well as on below-ground biomass estimates.
DOI: 10.6084/m9.figshare.14251022
title: Dataset and code for "Improved Estimates of Preindustrial Biomass Burning Reduce the Magnitude of Aerosol Climate Forcing in the Southern Hemisphere"

description: Dataset and code for "Improved Estimates of Preindustrial Biomass Burning Reduce the Magnitude of Aerosol Climate Forcing in the Southern Hemisphere" by Liu et al., Science Advances, in press
DOI: 10.6084/m9.figshare.14251022.v1
title: Datasets for "Improved Estimates of Preindustrial Biomass Burning Reduce the Magnitude of Aerosol Climate Forcing in the Southern Hemisphere"

description: Black carbon deposition fluxes from 14 Antarctic ice cores and Bolivia Illimani ice core
DOI: 10.6084/m9.figshare.14531937
title: AZ-Fritillaria_unibracteata.gbk

description: Genome Sequence and Characteristics of Chloroplast
DOI: 10.6084/m9.figshare.14531937.v1
title: AZ-Fritillaria_unibracteata.gbk

description: Genome Sequence and Characteristics of Chloroplast
DOI: 10.6084/m9.figshare.14531946
title: GS-Fritillaria_przewalskii.gbk

description: Genome Sequence and Characteristics of Chloroplast<br>
DOI: 10.6084/m9.figshare.14531946.v1
title: GS-Fritillaria_przewalskii.gbk

description: Genome Sequence and Characteristics of Chloroplast<br>
DOI: 10.6084/m9.figshare.14531952.v1
title: SS-Fritillaria_delavayi.gbk

description: Genome Sequence and Characteristics of Chloroplast
DOI: 10.6084/m9.figshare.14531952
title: SS-Fritillaria_delavayi.gbk

description: Genome Sequence and Characteristics of Chloroplast
DOI: 10.5281/zenodo.4735788
title: Data for paper: Comparing Measures of Centrality in Bipartite Social Networks: A Study of Drug Seeking for Opioid Analgesics

description: Data and code for paper: Comparing Measures of Centrality in Bipartite Social Networks: A Study of Drug Seeking for Opioid Analgesics
DOI: 10.6084/m9.figshare.12841139
title: The effects of diet and streptozotocin on metabolism and gut microbiota in a type 2 diabetes mellitus mouse model

description: Diabetes mellitus is a metabolic disorder disease. Diabetes models can be established using diet and/or chemical agents. However, the effects of these methods on the intestinal microbiota are poorly understood. In this study, C57BL/6 mice were fed with a high-fat or high-sucrose-fat diet (HFD/HSFD), followed by 1 or 2 injections of streptozotocin (STZ) to induce type 2 diabetes mellitus. HFD-fed mice showed more severe dyslipidemia compared to HSFD-fed mice. The abundance of Bacteroidetes decreased in HFD-fed mice compared to HSFD-fed mice. After STZ injection, all the mice developed more severe hyperglycaemia, particularly in HFD-fed mice. Although the compositions of intestinal microbiota between the diet- and STZ-induced mice were similar, STZ injection increased the abundance of <i>Ruminiclostridium</i> and <i>[Eubacterium] oxidoreducens</i> and decreased the abundance of <i>PrevotellaceaeUCG_001</i>. In summary, HFD and HSFD had different metabolic phenotypes and gut microbiota. Diets play a more vital role than STZ injection in reshaping gut microbiota.
DOI: 10.6084/m9.figshare.12841139.v1
title: The effects of diet and streptozotocin on metabolism and gut microbiota in a type 2 diabetes mellitus mouse model

description: Diabetes mellitus is a metabolic disorder disease. Diabetes models can be established using diet and/or chemical agents. However, the effects of these methods on the intestinal microbiota are poorly understood. In this study, C57BL/6 mice were fed with a high-fat or high-sucrose-fat diet (HFD/HSFD), followed by 1 or 2 injections of streptozotocin (STZ) to induce type 2 diabetes mellitus. HFD-fed mice showed more severe dyslipidemia compared to HSFD-fed mice. The abundance of Bacteroidetes decreased in HFD-fed mice compared to HSFD-fed mice. After STZ injection, all the mice developed more severe hyperglycaemia, particularly in HFD-fed mice. Although the compositions of intestinal microbiota between the diet- and STZ-induced mice were similar, STZ injection increased the abundance of <i>Ruminiclostridium</i> and <i>[Eubacterium] oxidoreducens</i> and decreased the abundance of <i>PrevotellaceaeUCG_001</i>. In summary, HFD and HSFD had different metabolic phenotypes and gut microbiota. Diets play a more vital role than STZ injection in reshaping gut microbiota.
DOI: 10.6084/m9.figshare.14531961
title: SS-Fritillaria_delavayi.gbk

description: Genome Sequence and Characteristics of Chloroplast
DOI: 10.6084/m9.figshare.14531961.v1
title: SS-Fritillaria_delavayi.gbk

description: Genome Sequence and Characteristics of Chloroplast
DOI: 10.6084/m9.figshare.14531970
title: ZH-Fritillaria_sinica.gbk

description: Genome Sequence and Characteristics of Chloroplast
DOI: 10.6084/m9.figshare.14531970.v1
title: ZH-Fritillaria_sinica.gbk

description: Genome Sequence and Characteristics of Chloroplast
DOI: 10.26182/v3gc-b786
title: Data from: Can Sexual Selection Drive The Evolution Of Sperm Cell Structure?
DOI: 10.5519/qd.r36qibd7
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (49 records)
DOI: 10.3886/e139721
title: Test Score Gaps in Higher-Order Thinking Skills: Exploring Instructional Practices to Improve the Skills and Narrow the Gaps

description: <br>In this project, I explored test score gaps in higher-order thinking skills between White and non-White students and between low- and high-SES students using TIMSS 2015 assessment data for 8th grade students in the United States. I also explored instructional practices that are associated with the test scores.<br>
DOI: 10.3886/e139721v1
title: Test Score Gaps in Higher-Order Thinking Skills: Exploring Instructional Practices to Improve the Skills and Narrow the Gaps

description: <br>In this project, I explored test score gaps in higher-order thinking skills between White and non-White students and between low- and high-SES students using TIMSS 2015 assessment data for 8th grade students in the United States. I also explored instructional practices that are associated with the test scores.<br>
DOI: 10.5281/zenodo.4735794
title: Tool and Dataset for Tracking the Adoption of Classes in JavaScript Software from 2015 to 2020

description: Tool and Dataset for Tracking the Adoption of Classes in JavaScript Software from 2015 to 2020 JavaScript is the most popular language on GitHub with over 18% of pull requests and over 40% of pushes on GitHub containing JavaScript in the beginning of 2021. In 2015, user definable classes were added to JavaScript as many developers were using other techniques to create classes. This major change to a very popular programming language has not been rigorously studied. In this paper we provide an overview of how developers have integrated these new classes. We created a tool that would detect both these legacy classes as well as the new classes and used it on mined NPM packages as well as general GitHub repositories. While many projects did not use ES6 classes, many also did not use any form of class either. Projects that used classes tended to have more new classes than legacy classes though there are still several projects that still have legacy classes.
DOI: 10.5281/zenodo.4735793
title: Tool and Dataset for Tracking the Adoption of Classes in JavaScript Software from 2015 to 2020

description: Tool and Dataset for Tracking the Adoption of Classes in JavaScript Software from 2015 to 2020 JavaScript is the most popular language on GitHub with over 18% of pull requests and over 40% of pushes on GitHub containing JavaScript in the beginning of 2021. In 2015, user definable classes were added to JavaScript as many developers were using other techniques to create classes. This major change to a very popular programming language has not been rigorously studied. In this paper we provide an overview of how developers have integrated these new classes. We created a tool that would detect both these legacy classes as well as the new classes and used it on mined NPM packages as well as general GitHub repositories. While many projects did not use ES6 classes, many also did not use any form of class either. Projects that used classes tended to have more new classes than legacy classes though there are still several projects that still have legacy classes.
DOI: 10.6084/m9.figshare.14531979
title: Distribution and dimethylsulfoniopropionate degradation of dimethylsulfoniopropionate-consuming bacteria in the Yellow Sea and East China Sea.xlsx

description: Description of sampling stations and variations in some parameters (temperature, salinity, density, Chl a concentration, and DMSP-consuming bacteria abundance) in situ in the Yellow Sea and East China Sea in the summer of 2013 and the growth of bacteria and DMSP degradation in lab experiments.
DOI: 10.6084/m9.figshare.14531979.v1
title: Distribution and dimethylsulfoniopropionate degradation of dimethylsulfoniopropionate-consuming bacteria in the Yellow Sea and East China Sea.xlsx

description: Description of sampling stations and variations in some parameters (temperature, salinity, density, Chl a concentration, and DMSP-consuming bacteria abundance) in situ in the Yellow Sea and East China Sea in the summer of 2013 and the growth of bacteria and DMSP degradation in lab experiments.
DOI: 10.6084/m9.figshare.14407616
title: NIPS data

description: NIPS results
DOI: 10.3886/e119726
title: Data and Code for: Impacts of Private Prison Contracting on Inmate Time Served and Recidivism

description: This is the replication kit for "Impacts of Private Prison Contracting on Inmate Time Served and Recidivism."<br><br>
description: All adult male inmates in Mississippi from April 1996 through July 2013 with sentences between 1 and 11 years.<br>.
description: <br>Data were obtained through a Freedom of Information Act to the Mississippi Department of Corrections; the data request file is in the folder.<br>
DOI: 10.3886/e119726v3
title: Data and Code for: Impacts of Private Prison Contracting on Inmate Time Served and Recidivism

description: This is the replication kit for "Impacts of Private Prison Contracting on Inmate Time Served and Recidivism."<br><br>
description: All adult male inmates in Mississippi from April 1996 through July 2013 with sentences between 1 and 11 years.<br>.
description: <br>Data were obtained through a Freedom of Information Act to the Mississippi Department of Corrections; the data request file is in the folder.<br>
DOI: 10.5519/qd.6xlv28g4
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (43 records)
DOI: 10.6084/m9.figshare.14532090
title: for_NN-A71271C

description: source data
DOI: 10.5519/qd.7j9ohtss
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (40 records)
DOI: 10.21948/1774178
title: DuraMAT HV+ and UV-LID Damp Heat Experiment

description: Optical maps and data for coupon samples
DOI: 10.21948/1774180
title: PVQAT TG5 Study 2 Coupon Size Experiment

description: Optical maps and data for coupon samples
DOI: 10.5439/1774952
title: AWARE Shortwave Spectroradiometer Data

description: Shortwave spectral irradiance was measured at the West Antarctic Ice Sheet (WAIS) Divide Ice Camp as part of the ARM West Antarctic Radiation Experiment (AWARE). A Panalytical (Inc.) FieldSpec Pro Jr spectroradiometer belonging to Scripps Oceanography recorded downwelling spectral irradiance every minute covering the wavelength interval 350-2200 nm . Spectral resolution is 3 nm (10 nm) for wavelengths shorter (longer) than 1000 nm. Temporal coverage is nearly continuous between 8 December 2015 and 18 January 2016, with a few minutes of data missing during each day for data backup and optical collector hygiene. Spectral irradiances, particularly in the near infrared, are sensitive to cloud optical depth, thermodynamic phase, and effective particle size.
DOI: 10.6084/m9.figshare.14532098
title: list of comparative neck lengths from A new pelomedusoid turtle, <i>Sahonachelys mailakavava</i>, from the Late Cretaceous of Madagascar provides evidence for convergent evolution of specialized suction feeding among pleurodires

description: A list of comparative neck lengths
DOI: 10.6084/m9.figshare.14532098.v1
title: list of comparative neck lengths from A new pelomedusoid turtle, <i>Sahonachelys mailakavava</i>, from the Late Cretaceous of Madagascar provides evidence for convergent evolution of specialized suction feeding among pleurodires

description: A list of comparative neck lengths
DOI: 10.6084/m9.figshare.14532107
title: character taxon matrix from A new pelomedusoid turtle, <i>Sahonachelys mailakavava</i>, from the Late Cretaceous of Madagascar provides evidence for convergent evolution of specialized suction feeding among pleurodires

description: Character taxon matrix used in study
DOI: 10.6084/m9.figshare.14532107.v1
title: character taxon matrix from A new pelomedusoid turtle, <i>Sahonachelys mailakavava</i>, from the Late Cretaceous of Madagascar provides evidence for convergent evolution of specialized suction feeding among pleurodires

description: Character taxon matrix used in study
DOI: 10.6084/m9.figshare.14532125.v1
title: Additional file 1 of Known HIV status among adolescent women attending antenatal care services in Eswatini, Ethiopia and Mozambique

description: Additional file 1: Dataset.
DOI: 10.6084/m9.figshare.14532125
title: Additional file 1 of Known HIV status among adolescent women attending antenatal care services in Eswatini, Ethiopia and Mozambique

description: Additional file 1: Dataset.
DOI: 10.6084/m9.figshare.14532150
title: Additional file 2 of Involving elderly research participants in the co-design of a future multi-generational cohort study

description: Additional file 2. Telephone Questionnaire. Version Comparison - A comparison of the versions of the telephone questionnaire used.
DOI: 10.6084/m9.figshare.14532156
title: Additional file 3 of Involving elderly research participants in the co-design of a future multi-generational cohort study

description: Additional file 3. Quantitative results - A summary of the quantitative results.
DOI: 10.6084/m9.figshare.14532150.v1
title: Additional file 2 of Involving elderly research participants in the co-design of a future multi-generational cohort study

description: Additional file 2. Telephone Questionnaire. Version Comparison - A comparison of the versions of the telephone questionnaire used.
DOI: 10.6084/m9.figshare.14532156.v1
title: Additional file 3 of Involving elderly research participants in the co-design of a future multi-generational cohort study

description: Additional file 3. Quantitative results - A summary of the quantitative results.
DOI: 10.6084/m9.figshare.14532239
title: Additional file 4 of Genetic analysis using targeted next-generation sequencing of sporadic Chinese patients with idiopathic dilated cardiomyopathy

description: Additional file 4: Table S2. List of all detected variants of DCM related genes.
DOI: 10.6084/m9.figshare.14532239.v1
title: Additional file 4 of Genetic analysis using targeted next-generation sequencing of sporadic Chinese patients with idiopathic dilated cardiomyopathy

description: Additional file 4: Table S2. List of all detected variants of DCM related genes.