cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25909/28266923
title: <b>Tropical fishes can benefit more from novel than familiar species interactions at their cold-range edges</b>

description: Files for peer review of <b>Tropical fishes can benefit more from novel than familiar species interactions at their cold-range edges</b> submitted to and accepted by Journal of Animal Ecology.<br>
DOI: 10.25909/28266923.v1
title: <b>Tropical fishes can benefit more from novel than familiar species interactions at their cold-range edges</b>

description: Files for peer review of <b>Tropical fishes can benefit more from novel than familiar species interactions at their cold-range edges</b> submitted to and accepted by Journal of Animal Ecology.<br>
DOI: 10.25909/28300055
title: Data for: From Wild to Domestic and The In Between? How Domestication and Feralization Changed the Morphology of Rabbits

description: R Statistical Environment analysis script and associated files accompanying the paper Sherratt et al. 2025 <i>Proceedings of the Royal Society: B, Biological Sciences</i> 10.1098/rspb.2025.1150.<b>Oryctolagus analyses.R</b> Analysis script for the study, including generating figures.<b>ory lmk coords.tps</b> x,y,z raw landmark coordinate data for 52 landmarks (including 8 semilandmarks) for 912 <i>Oryctolagus cuniculus</i> crania. Landmarks follow Kraatz and Sherratt 2016 <i>PeerJ</i> 10.7717/peerj.2453<b>classifier.csv</b> metadata for the 912 adult specimens, ID/Reg No (institution ID number), Museum Collection (where the specimen is housed), Species (all <i>Oryctolagus cuniculus</i>), Sex (where known, Male or Female), Type (group used in analyses, either domesticated, feral or wild), Locality information (Country, State, Locality), GPS data (DecimalGPA Lat, DecimalGPS Long)<b>land.pairs52.csv</b> landmark index matrix, indicating which landmarks are bilaterally paired, for analysis<b>Raw Leporidae 301spp 52lmks.tps</b> x,y,z raw landmark coordinate data for 52 landmarks (including 8 semilandmarks) for 301 specimens of Leporidae (multiple species), from Sherratt and Kraatz 2023 <i>Evolution</i> 10.1093/evolut/qpad020<b>Oryctolagus missing data.csv</b> details of the missing landmark data for each specimen, as generated by the analysis script
DOI: 10.25909/28300055.v2
title: Data for: From Wild to Domestic and The In Between? How Domestication and Feralization Changed the Morphology of Rabbits

description: R Statistical Environment analysis script and associated files accompanying the paper Sherratt et al. 2025 <i>Proceedings of the Royal Society: B, Biological Sciences</i> 10.1098/rspb.2025.1150.<b>Oryctolagus analyses.R</b> Analysis script for the study, including generating figures.<b>ory lmk coords.tps</b> x,y,z raw landmark coordinate data for 52 landmarks (including 8 semilandmarks) for 912 <i>Oryctolagus cuniculus</i> crania. Landmarks follow Kraatz and Sherratt 2016 <i>PeerJ</i> 10.7717/peerj.2453<b>classifier.csv</b> metadata for the 912 adult specimens, ID/Reg No (institution ID number), Museum Collection (where the specimen is housed), Species (all <i>Oryctolagus cuniculus</i>), Sex (where known, Male or Female), Type (group used in analyses, either domesticated, feral or wild), Locality information (Country, State, Locality), GPS data (DecimalGPA Lat, DecimalGPS Long)<b>land.pairs52.csv</b> landmark index matrix, indicating which landmarks are bilaterally paired, for analysis<b>Raw Leporidae 301spp 52lmks.tps</b> x,y,z raw landmark coordinate data for 52 landmarks (including 8 semilandmarks) for 301 specimens of Leporidae (multiple species), from Sherratt and Kraatz 2023 <i>Evolution</i> 10.1093/evolut/qpad020<b>Oryctolagus missing data.csv</b> details of the missing landmark data for each specimen, as generated by the analysis script
DOI: 10.25909/28329506
title: Supplementary Data

description: Pubmed search syntax for project.AGREE-II and AGREE-S datasheets for 20 different surgical guidelines.Bland-Altman plots of domain comparisons.<br>
DOI: 10.25909/28329506.v3
title: Supplementary Data

description: Pubmed search syntax for project.AGREE-II and AGREE-S datasheets for 20 different surgical guidelines.Bland-Altman plots of domain comparisons.<br>
DOI: 10.25909/28366961
title: <b>Estimates vary but credible evidence points to gigaton-scale climate change mitigation potential of biochar</b>_Supplementary information_COMMSENV-24-2669A.docx

description: This is the supplementary document for an article entitled "<b>Estimates vary but credible evidence points to gigaton-scale climate change mitigation potential of biochar</b>" which has been accepted by Communications Earth & Environment.
DOI: 10.25909/28366961.v3
title: <b>Estimates vary but credible evidence points to gigaton-scale climate change mitigation potential of biochar</b>_Supplementary information_COMMSENV-24-2669A.docx

description: This is the supplementary document for an article entitled "<b>Estimates vary but credible evidence points to gigaton-scale climate change mitigation potential of biochar</b>" which has been accepted by Communications Earth & Environment.
DOI: 10.25909/28385819
title: <b>Range-extending fish become competitive dominants under ocean warming but not heatwaves or acidification</b>

description: Ocean warming is driving species range-extensions into cooler regions. The direct physiological influence of warming on species performance can accelerate such extensions into novel ecosystems, however, indirect effects of invader–resident interactions in cooler regions may counter these positive effects. Here we examined the foraging performance and densities of competing warm-water and cool-water fishes across a latitudinal temperature gradient spanning 1,500 km from tropical to temperate reefs subjected to rapid ocean warming in the southern hemisphere, and across natural analogues of temperate, tropicalized and acidified reef localities in the northern hemisphere, and during a severe marine heatwave at a temperate reef. While current levels of ocean warming have allowed the warm-water fish to extend their ranges into temperate ecosystems at both hemispheres, their foraging performance was reduced at both the cold- and warm-temperate reefs compared to the (sub)tropical reefs. However, at the (warmer) tropicalized reef the warm-water fish had higher foraging performance and maintained densities, even under extreme pH reduction, compared to the temperate reef. In contrast, the cool-water species struggled at the warmer tropicalized and extreme reefs with reduced foraging performance and lower population densities compared to temperate reef. Contrastingly, the severe heatwave experienced at the temperate reef did not alter the foraging behaviours of either species. We suggest that ocean warming boosts the foraging performance of the range-extending warm-water fish and impairs that of their cool-water competitor at temperate reefs, irrespective of acidification and heatwaves, leading to a shift in dominance hierarchies on temperate reefs. We conclude that warming-driven increases in foraging performance of the warm-water species may alleviate foraging limitations and enhance its establishment at its leading range edges under climate change, to the detriment of its cool-water competitors.
DOI: 10.25909/28385819.v1
title: <b>Range-extending fish become competitive dominants under ocean warming but not heatwaves or acidification</b>

description: Ocean warming is driving species range-extensions into cooler regions. The direct physiological influence of warming on species performance can accelerate such extensions into novel ecosystems, however, indirect effects of invader–resident interactions in cooler regions may counter these positive effects. Here we examined the foraging performance and densities of competing warm-water and cool-water fishes across a latitudinal temperature gradient spanning 1,500 km from tropical to temperate reefs subjected to rapid ocean warming in the southern hemisphere, and across natural analogues of temperate, tropicalized and acidified reef localities in the northern hemisphere, and during a severe marine heatwave at a temperate reef. While current levels of ocean warming have allowed the warm-water fish to extend their ranges into temperate ecosystems at both hemispheres, their foraging performance was reduced at both the cold- and warm-temperate reefs compared to the (sub)tropical reefs. However, at the (warmer) tropicalized reef the warm-water fish had higher foraging performance and maintained densities, even under extreme pH reduction, compared to the temperate reef. In contrast, the cool-water species struggled at the warmer tropicalized and extreme reefs with reduced foraging performance and lower population densities compared to temperate reef. Contrastingly, the severe heatwave experienced at the temperate reef did not alter the foraging behaviours of either species. We suggest that ocean warming boosts the foraging performance of the range-extending warm-water fish and impairs that of their cool-water competitor at temperate reefs, irrespective of acidification and heatwaves, leading to a shift in dominance hierarchies on temperate reefs. We conclude that warming-driven increases in foraging performance of the warm-water species may alleviate foraging limitations and enhance its establishment at its leading range edges under climate change, to the detriment of its cool-water competitors.
DOI: 10.25909/28406780
title: A ternary switch model governing ERalpha ligand binding domain conformation

description: Data associated with the manuscript "A ternary switch model governing ERalpha ligand binding domain conformation" by McDougal, Pederick et al. (2025).
DOI: 10.25909/28406780.v1
title: A ternary switch model governing ERalpha ligand binding domain conformation

description: Data associated with the manuscript "A ternary switch model governing ERalpha ligand binding domain conformation" by McDougal, Pederick et al. (2025).
DOI: 10.25909/28605821
title: BLCM Canine Heartworm POC and MKT

description: Dataset, likelihood functions and R scripts used for the analysis of canine heartworm diagnostic test accuracy
DOI: 10.25909/28605821.v4
title: BLCM Canine Heartworm POC and MKT

description: Dataset, likelihood functions and R scripts used for the analysis of canine heartworm diagnostic test accuracy
DOI: 10.25909/28746674
title: Supplementary Table S1

description: <b>Table S1.</b><b> </b>Rhaphidophorid specimens included in the present study and their associated collection and institution metadata. GenBank accessions of DNA sequences are coloured by whether they were generated here (black) or retrieved from existing studies (grey).
DOI: 10.25909/28746674.v1
title: Supplementary Table S1

description: <b>Table S1.</b><b> </b>Rhaphidophorid specimens included in the present study and their associated collection and institution metadata. GenBank accessions of DNA sequences are coloured by whether they were generated here (black) or retrieved from existing studies (grey).
DOI: 10.25909/28783223
title: <b>Graph-Theoretical Formulation of Gradually Varied Flow in Open Channel Networks - MATLAB Code</b>

description: Gradually varied flow frequently occurs in various open channel networks, including irrigation systems, canal networks, river systems, stormwater networks, and sewer systems. This paper presents a novel method to formulate this problem using graph theory. The characteristics and topology of an arbitrary channel network can first be defined using matrix and vector formats. The governing equations for all nodes and channel sections are then elegantly integrated using these matrices and vectors. A compact formulation comprising just two matrix equations is obtained to represent the gradually varied flow in an open channel network. Compared with traditional methods, this new approach eliminates the need to list separate equations for different types of nodes and to sequentially formulate equations for each channel. As a result, it provides a generalized process for modelling any channel network. The method also treats internal nodes as inflow/outflow boundaries, enabling more flexible applications—such as modelling complex drainage systems with manholes receiving runoff. Validation of the proposed method is demonstrated by comparing results from various channel networks with those obtained using traditional approaches.
DOI: 10.25909/28783223.v2
title: <b>Graph-Theoretical Formulation of Gradually Varied Flow in Open Channel Networks - MATLAB Code</b>

description: Gradually varied flow frequently occurs in various open channel networks, including irrigation systems, canal networks, river systems, stormwater networks, and sewer systems. This paper presents a novel method to formulate this problem using graph theory. The characteristics and topology of an arbitrary channel network can first be defined using matrix and vector formats. The governing equations for all nodes and channel sections are then elegantly integrated using these matrices and vectors. A compact formulation comprising just two matrix equations is obtained to represent the gradually varied flow in an open channel network. Compared with traditional methods, this new approach eliminates the need to list separate equations for different types of nodes and to sequentially formulate equations for each channel. As a result, it provides a generalized process for modelling any channel network. The method also treats internal nodes as inflow/outflow boundaries, enabling more flexible applications—such as modelling complex drainage systems with manholes receiving runoff. Validation of the proposed method is demonstrated by comparing results from various channel networks with those obtained using traditional approaches.
DOI: 10.25909/28801508
title: Supplementary File S1

description: <b>File S1.</b> Molecular matrix, in NEXUS format, used as input for maximum likelihood and Bayesian phylogenetic analysis. Partitions are specified in the character block at the end of the file.
DOI: 10.25909/28801508.v1
title: Supplementary File S1

description: <b>File S1.</b> Molecular matrix, in NEXUS format, used as input for maximum likelihood and Bayesian phylogenetic analysis. Partitions are specified in the character block at the end of the file.
DOI: 10.25909/28801562
title: Supplementary File S2

description: <b>File S2.</b> Raw .tree file from the maximum likelihood phylogenetic analysis conducted with IQ-TREE.
DOI: 10.25909/28801562.v1
title: Supplementary File S2

description: <b>File S2.</b> Raw .tree file from the maximum likelihood phylogenetic analysis conducted with IQ-TREE.
DOI: 10.25909/28801589
title: Supplementary File S3

description: <b>File S3.</b> Raw .tree file from the time-calibrated Bayesian phylogenetic analysis conducted with BEAST2.
DOI: 10.25909/28801589.v1
title: Supplementary File S3

description: <b>File S3.</b> Raw .tree file from the time-calibrated Bayesian phylogenetic analysis conducted with BEAST2.
DOI: 10.25909/28852628
title: Active Learning at Scale: Investigating the Benefits of Peer Instruction in Undergraduate Mathematics

description: Active learning strategies have been widely recognised for their effectiveness in tertiary education, yet their implementation at scale, particularly in large first-year mathematics courses, presents considerable challenges. A common method for actively engaging students in large classes is through online quizzes, which may include structured peer instruction. In this study, we investigate the effect of having students answer quiz-style questions during class both with and without peer discussion in a first-year large mathematics course (<i>N</i> = 550). We also investigate the short- and long-term effects of each protocol. Our findings indicate that peer instruction enhances student performance in mathematics in the following ways: First, when the responses to questions were measured before and after peer instruction the proportion of questions answered correctly increased by 0.2; second, when correct responses were compared to similar questions the following week the proportion correct increased by 0.34 (compared to 0.07 for the control); finally, when measured at the end of the semester the proportion of questions answered correctly increased by 0.42 (compared to 0.2 for the control). These results align with and build upon previous research on the benefits of peer instruction, indicating a potential long-term association with student knowledge retention of mathematical concepts. This suggests that peer discussion may do more than momentarily improve accuracy—it could also contribute to more durable learning.
DOI: 10.25909/28852628.v1
title: Active Learning at Scale: Investigating the Benefits of Peer Instruction in Undergraduate Mathematics

description: Active learning strategies have been widely recognised for their effectiveness in tertiary education, yet their implementation at scale, particularly in large first-year mathematics courses, presents considerable challenges. A common method for actively engaging students in large classes is through online quizzes, which may include structured peer instruction. In this study, we investigate the effect of having students answer quiz-style questions during class both with and without peer discussion in a first-year large mathematics course (<i>N</i> = 550). We also investigate the short- and long-term effects of each protocol. Our findings indicate that peer instruction enhances student performance in mathematics in the following ways: First, when the responses to questions were measured before and after peer instruction the proportion of questions answered correctly increased by 0.2; second, when correct responses were compared to similar questions the following week the proportion correct increased by 0.34 (compared to 0.07 for the control); finally, when measured at the end of the semester the proportion of questions answered correctly increased by 0.42 (compared to 0.2 for the control). These results align with and build upon previous research on the benefits of peer instruction, indicating a potential long-term association with student knowledge retention of mathematical concepts. This suggests that peer discussion may do more than momentarily improve accuracy—it could also contribute to more durable learning.
DOI: 10.25909/28869953
title: Initial gRNA testing in WT cells

description: NGS data files
DOI: 10.25909/28869953.v4
title: Initial gRNA testing in WT cells

description: NGS data files
DOI: 10.25909/28870022
title: gRNA testing in NR2E3 cell model

description: NGS data files
DOI: 10.25909/28870022.v1
title: gRNA testing in NR2E3 cell model

description: NGS data files
DOI: 10.25909/28870055
title: mRHO/hRHO-P23H-RFPt sorted photoreceptors (AAV treated)

description: NGS data files
DOI: 10.25909/28870055.v1
title: mRHO/hRHO-P23H-RFPt sorted photoreceptors (AAV treated)

description: NGS data files
DOI: 10.25909/28870121
title: PCOC in vitro testing

description: NGS data files
DOI: 10.25909/28870121.v1
title: PCOC in vitro testing

description: NGS data files
DOI: 10.25909/28870337
title: AAV in vitro test

description: NGS data files
DOI: 10.25909/28870337.v1
title: AAV in vitro test

description: NGS data files
DOI: 10.25909/28870367
title: gRNA testing in RHO cell model

description: NGS data files
DOI: 10.25909/28870367.v1
title: gRNA testing in RHO cell model

description: NGS data files
DOI: 10.25909/28916588
title: Identification of waterbird research priorities for the Coorong, Lower Lakes and Murray Mouth

description: This project identified and prioritised scientific research to inform management of the CLLMM region to support the viability of migratory and non-migratory waterbird populations under climate change. Firstly, we reviewed the global scientific literature to identify key threats posed to waterbirds by a changing climate along with documenting examples of direct relevance to the CLLMM region. Secondly, with the long history of CLLMM-focused waterbird research in mind, we engaged with a range of stakeholders to identify key knowledge gaps and information needs pertaining to waterbirds in the region. Through this process, we refined a set of proposed waterbird research projects and identified and developed new research projects to address these gaps and needs. Finally, we evaluated these projects based on: (1) the importance of the research for informing future management of the CLLMM, particularly under a changing climate; (2) the ability of the research to lead to improvements in the viability of threatened waterbird species; and (3) the significance of the project to stakeholders, and the project’s ability to engage community actively or passively in the research.Eight key research projects were developed and/or refined through the consultation process: (1) waterbird telemetry (i.e. GPS tracking) to document waterbird habitat selection and movement at a range of scales; (2) DNA-based monitoring of waterbird food resources, diets, and pathogen load; (3) waterbird condition monitoring through community science; (4) targeted conservation modelling for key waterbird species to inform climate preparedness and restoration actions; (5) identifying water management scenarios to support colonial nesting waterbirds in the Lower Lakes; (6) quantifying human disturbance of beach-nesting and migratory shorebirds; (7) identifying sites of shorebird congregation immediately prior to the northerly migration; and (8) control-impact studies to understand the benefits of wetland restoration for waterbirds. Based on evaluation against the three prioritisation criteria, all projects were supported to some degree, with particularly high rankings for waterbird telemetry and targeted conservation modelling projects for key threatened, migratory or culturally important waterbird species.
DOI: 10.25909/28916588.v1
title: Identification of waterbird research priorities for the Coorong, Lower Lakes and Murray Mouth

description: This project identified and prioritised scientific research to inform management of the CLLMM region to support the viability of migratory and non-migratory waterbird populations under climate change. Firstly, we reviewed the global scientific literature to identify key threats posed to waterbirds by a changing climate along with documenting examples of direct relevance to the CLLMM region. Secondly, with the long history of CLLMM-focused waterbird research in mind, we engaged with a range of stakeholders to identify key knowledge gaps and information needs pertaining to waterbirds in the region. Through this process, we refined a set of proposed waterbird research projects and identified and developed new research projects to address these gaps and needs. Finally, we evaluated these projects based on: (1) the importance of the research for informing future management of the CLLMM, particularly under a changing climate; (2) the ability of the research to lead to improvements in the viability of threatened waterbird species; and (3) the significance of the project to stakeholders, and the project’s ability to engage community actively or passively in the research.Eight key research projects were developed and/or refined through the consultation process: (1) waterbird telemetry (i.e. GPS tracking) to document waterbird habitat selection and movement at a range of scales; (2) DNA-based monitoring of waterbird food resources, diets, and pathogen load; (3) waterbird condition monitoring through community science; (4) targeted conservation modelling for key waterbird species to inform climate preparedness and restoration actions; (5) identifying water management scenarios to support colonial nesting waterbirds in the Lower Lakes; (6) quantifying human disturbance of beach-nesting and migratory shorebirds; (7) identifying sites of shorebird congregation immediately prior to the northerly migration; and (8) control-impact studies to understand the benefits of wetland restoration for waterbirds. Based on evaluation against the three prioritisation criteria, all projects were supported to some degree, with particularly high rankings for waterbird telemetry and targeted conservation modelling projects for key threatened, migratory or culturally important waterbird species.