cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1598247
title: Phylogeny of the Ichthyopterygia incorporating recent discoveries from South China

description: During the last decade, abundant ichthyopterygian material has been found from the Triassic of South China as well as the Upper Jurassic and Lower Cretaceous of Europe and South America, significantly expanding our knowledge of ichthyopterygian diversity through the Mesozoic. Previous phylogenetic hypotheses of the group no longer account for these extensive additions, necessitating a new phylogenetic framework for the entire Ichthyopterygia to enable evolutionary studies of the group. We present here a comprehensive phylogenetic hypothesis for Ichthyopterygia based on cladistic analysis of 163 characters coded for 59 ingroup and five outgroup taxa. The monophyly of Ichthyopterygia is strongly supported by a Bremer index value of 7. Five major groups of Ichthyopterygia during the Triassic, viz., Grippioidea, Cymbospondylidae, Mixosauridae, Shastasauridae, and Toretocnemidae, are well supported by Bremer index values between 3 and 5. Major clades that evolved in the Triassic, including Merriamosauria, Euichthyosauria, and Parvipelvia, are also robustly supported, whereas most post-Triassic clades are very weakly supported with a Bremer index value of 1, with a few exceptions, such as Thunnosauria and Ophthalmosauridae. The traditional Shastasauridae is expanded to comprise six genera but excludes <i>Callawayia</i>, which is more closely related to Parvipelvia than to Shastasauridae. ‘<i>C.</i>’ <i>wolonggangensis</i> is a shastasaurid but does not form a monophyletic clade with <i>Callawayia neoscapularis</i> or <i>Guizhouichthyosaurus tangae</i> as previously asserted. The new phylogenetic hypothesis is generally consistent with the stratigraphic occurrences of each taxon especially for the Triassic taxa. http://zoobank.org/urn:lsid:zoobank.org:pub:901B6FB6-2D80-4AE9-B017-A0226175AFDA SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Ji, C., D.-Y. Jiang, R. Motani, O. Rieppel, W.-C. Hao, and Z.-Y. Sun. 2015. Phylogeny of the Ichthyopterygia incorporating the recent discoveries from South China. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2015.1025956.
DOI: 10.6084/m9.figshare.1598247.v2
title: Phylogeny of the Ichthyopterygia incorporating recent discoveries from South China

description: During the last decade, abundant ichthyopterygian material has been found from the Triassic of South China as well as the Upper Jurassic and Lower Cretaceous of Europe and South America, significantly expanding our knowledge of ichthyopterygian diversity through the Mesozoic. Previous phylogenetic hypotheses of the group no longer account for these extensive additions, necessitating a new phylogenetic framework for the entire Ichthyopterygia to enable evolutionary studies of the group. We present here a comprehensive phylogenetic hypothesis for Ichthyopterygia based on cladistic analysis of 163 characters coded for 59 ingroup and five outgroup taxa. The monophyly of Ichthyopterygia is strongly supported by a Bremer index value of 7. Five major groups of Ichthyopterygia during the Triassic, viz., Grippioidea, Cymbospondylidae, Mixosauridae, Shastasauridae, and Toretocnemidae, are well supported by Bremer index values between 3 and 5. Major clades that evolved in the Triassic, including Merriamosauria, Euichthyosauria, and Parvipelvia, are also robustly supported, whereas most post-Triassic clades are very weakly supported with a Bremer index value of 1, with a few exceptions, such as Thunnosauria and Ophthalmosauridae. The traditional Shastasauridae is expanded to comprise six genera but excludes <i>Callawayia</i>, which is more closely related to Parvipelvia than to Shastasauridae. ‘<i>C.</i>’ <i>wolonggangensis</i> is a shastasaurid but does not form a monophyletic clade with <i>Callawayia neoscapularis</i> or <i>Guizhouichthyosaurus tangae</i> as previously asserted. The new phylogenetic hypothesis is generally consistent with the stratigraphic occurrences of each taxon especially for the Triassic taxa. http://zoobank.org/urn:lsid:zoobank.org:pub:901B6FB6-2D80-4AE9-B017-A0226175AFDA SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Ji, C., D.-Y. Jiang, R. Motani, O. Rieppel, W.-C. Hao, and Z.-Y. Sun. 2015. Phylogeny of the Ichthyopterygia incorporating the recent discoveries from South China. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2015.1025956.
DOI: 10.6084/m9.figshare.1598247.v1
title: Phylogeny of the Ichthyopterygia incorporating recent discoveries from South China

description: ABSTRACTDuring the last decade, abundant ichthyopterygian material has been found from the Triassic of South China as well as the Upper Jurassic and Lower Cretaceous of Europe and South America, significantly expanding our knowledge of ichthyopterygian diversity through the Mesozoic. Previous phylogenetic hypotheses of the group no longer account for these extensive additions, necessitating a new phylogenetic framework for the entire Ichthyopterygia to enable evolutionary studies of the group. We present here a comprehensive phylogenetic hypothesis for Ichthyopterygia based on cladistic analysis of 163 characters coded for 59 ingroup and five outgroup taxa. The monophyly of Ichthyopterygia is strongly supported by a Bremer index value of 7. Five major groups of Ichthyopterygia during the Triassic, viz., Grippioidea, Cymbospondylidae, Mixosauridae, Shastasauridae, and Toretocnemidae, are well supported by Bremer index values between 3 and 5. Major clades that evolved in the Triassic, including Merriamosauria, Euichthyosauria, and Parvipelvia, are also robustly supported, whereas most post-Triassic clades are very weakly supported with a Bremer index value of 1, with a few exceptions, such as Thunnosauria and Ophthalmosauridae. The traditional Shastasauridae is expanded to comprise six genera but excludes <i>Callawayia</i>, which is more closely related to Parvipelvia than to Shastasauridae. ‘<i>C.</i>’ <i>wolonggangensis</i> is a shastasaurid but does not form a monophyletic clade with <i>Callawayia neoscapularis</i> or <i>Guizhouichthyosaurus tangae</i> as previously asserted. The new phylogenetic hypothesis is generally consistent with the stratigraphic occurrences of each taxon especially for the Triassic taxa.http://zoobank.org/urn:lsid:zoobank.org:pub:901B6FB6-2D80-4AE9-B017-A0226175AFDASUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVPCitation for this article: Ji, C., D.-Y. Jiang, R. Motani, O. Rieppel, W.-C. Hao, and Z.-Y. Sun. 2015. Phylogeny of the Ichthyopterygia incorporating the recent discoveries from South China. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2015.1025956.
DOI: 10.6084/m9.figshare.1598241
title: Interweaving Markov Chain Monte Carlo Strategies for Efficient Estimation of Dynamic Linear Models

description: In dynamic linear models (DLMs) with unknown fixed parameters, a standard Markov chain Monte Carlo (MCMC) sampling strategy is to alternate sampling of latent states conditional on fixed parameters and sampling of fixed parameters conditional on latent states. In some regions of the parameter space, this standard data augmentation (DA) algorithm can be inefficient. To improve efficiency, we apply the interweaving strategies of Yu and Meng to DLMs. For this, we introduce three novel alternative DAs for DLMs: the scaled errors, wrongly scaled errors, and wrongly scaled disturbances. With the latent states and the less well known scaled disturbances, this yields five unique DAs to employ in MCMC algorithms. Each DA implies a unique MCMC sampling strategy and they can be combined into interweaving and alternating strategies that improve MCMC efficiency. We assess these strategies using the local level model and demonstrate that several strategies improve efficiency relative to the standard approach and the most efficient strategy interweaves the scaled errors and scaled disturbances. Supplementary materials are available online for this article.
DOI: 10.6084/m9.figshare.1598239
title: Separate Spheres Model of Gendered Inequality

description: These studies validate a scale that measures individuals' endorsement of the separate spheres ideology.
DOI: 10.6084/m9.figshare.1598246.v1
title: Enabling Interactivity on Displays of Multivariate Time Series and Longitudinal Data

description: Temporal data is information measured in the context of time. This contextual structure provides components that need to be explored to understand the data and that can form the basis of interactions applied to the plots. In multivariate time series we expect to see temporal dependence, long term and seasonal trends and cross-correlations. In longitudinal data we also expect within and between subject dependence. Time series and longitudinal data, although analyzed differently, are often plotted using similar displays. We provide a taxonomy of interactions on plots that can enable exploring temporal components of these data types, and describe how to build these interactions using data transformations. Because temporal data is often accompanied other types of data we also describe how to link the temporal plots with other displays of data. The ideas are conceptualized into a data pipeline for temporal data, and implemented into the R package <b>cranvas</b>. This package provides many different types of interactive graphics that can be used together to explore data or diagnose a model fit.
DOI: 10.6084/m9.figshare.1598241.v2
title: Interweaving Markov Chain Monte Carlo Strategies for Efficient Estimation of Dynamic Linear Models

description: In dynamic linear models (DLMs) with unknown fixed parameters, a standard Markov chain Monte Carlo (MCMC) sampling strategy is to alternate sampling of latent states conditional on fixed parameters and sampling of fixed parameters conditional on latent states. In some regions of the parameter space, this standard data augmentation (DA) algorithm can be inefficient. To improve efficiency, we apply the interweaving strategies of Yu and Meng to DLMs. For this, we introduce three novel alternative DAs for DLMs: the scaled errors, wrongly scaled errors, and wrongly scaled disturbances. With the latent states and the less well known scaled disturbances, this yields five unique DAs to employ in MCMC algorithms. Each DA implies a unique MCMC sampling strategy and they can be combined into interweaving and alternating strategies that improve MCMC efficiency. We assess these strategies using the local level model and demonstrate that several strategies improve efficiency relative to the standard approach and the most efficient strategy interweaves the scaled errors and scaled disturbances. Supplementary materials are available online for this article.
DOI: 10.6084/m9.figshare.1598241.v1
title: Interweaving Markov Chain Monte Carlo Strategies for Efficient Estimation of Dynamic Linear Models

description: In dynamic linear models (DLMs) with unknown fixed parameters, a standard Markov chain Monte Carlo (MCMC) sampling strategy is to alternate sampling of latent states conditional on fixed parameters and sampling of fixed parameters conditional on latent states. In some regions of the parameter space, this standard data augmentation (DA) algorithm can be inefficient. To improve efficiency, we apply the interweaving strategies of Yu and Meng (2011) to DLMs. For this, we introduce three novel alternative DAs for DLMs: the scaled errors, wrongly-scaled errors, and wrongly-scaled disturbances. With the latent states and the less well known scaled disturbances, this yields five unique DAs to employ in MCMC algorithms. Each DA implies a unique MCMC sampling strategy and they can be combined into interweaving and alternating strategies that improve MCMC efficiency. We assess these strategies using the local level model and demonstrate that several strategies improve efficiency relative to the standard approach and the most efficient strategy interweaves the scaled errors and scaled disturbances. Supplementary materials are available for this article online.
DOI: 10.6084/m9.figshare.1598220
title: Seagrass Microbiome

description: This fileset includes data for several projects that fall under the umbrella of the Seagrass Microbiome Project. See seagrassmicrobiome.org for more details. Each project file contains processed 16SrRNA sequence data (in FASTA format) as well as a corresponding metadata file. As we analyze these data, we will add data analysis information, including an ipython notebook, and all of the text, data, and figures associated with the published manuscript. The raw sequence data is available via NCBI, and the Genbank Accession numbers can be found in the README.odt file included here. Please feel free to contact me for any additional information.
DOI: 10.6084/m9.figshare.1598220.v1
title: Seagrass Microbiome

description: This fileset includes data for several projects that fall under the umbrella of the Seagrass Microbiome Project. See seagrassmicrobiome.org for more details. Each project file contains processed 16SrRNA sequence data (in FASTA format) as well as a corresponding metadata file. As we analyze these data, we will add data analysis information, including an ipython notebook, and all of the text, data, and figures associated with the published manuscript. The raw sequence data is available via NCBI, and the Genbank Accession numbers can be found in the README.odt file included here. Please feel free to contact me for any additional information.
DOI: 10.6084/m9.figshare.1598222.v1
title: Defining the Relationships Among Retinal Function, Layer Thickness and Visual Behavior During Oxidative Stress-Induced Retinal Degeneration

description: <i>Purpose</i>: The purpose of this study was to identify how changes in retinal structure and function correlate with visual deficits during increasing amounts of retinal degeneration.<i>Materials and methods</i>: Retinal degeneration was induced in adult mice by subretinal injections of paraquat (PQ) (0.2–1 mM). Retinal anatomy and photoreceptor layer thickness were quantified by histology and optical coherence tomography (OCT), retinal function was measured using electroretinography (ERG), and visual behavior were measured by optokinetic tracking, at 1 to 3 week post-injury.<i>Results</i>: Photoreceptor layer structure, function and visual behavior declined at a linear rate over time following PQ-induced degeneration, with the correlations between outcome measures being lowest at mild injury levels and increasing with injury severity. Overall reductions in visual acuity were highly correlated with declines in retinal thickness (<i>r</i><sup>2</sup> = 0.78) and function (<i>r</i><sup>2</sup> = 0.67) and retinal thickness correlated with photoreceptor function (<i>r</i><sup>2</sup> = 0.72). ERG a-wave scotopic amplitudes showed a stronger correspondence to retinal structure and visual behavior than b-waves.<i>Conclusions</i>: Measurements of photoreceptor loss at the structural and functional levels showed good correspondence with degeneration-associated changes in visual behavior after oxidative stress injury. The results provide new insight about the relative kinetics of measurements of retinal degeneration induced by oxidative stress, which could guide the choice of optimal outcome measurements for other retinal diseases.
DOI: 10.6084/m9.figshare.1598222.v2
title: Defining the Relationships Among Retinal Function, Layer Thickness and Visual Behavior During Oxidative Stress-Induced Retinal Degeneration

description: <i>Purpose</i>: The purpose of this study was to identify how changes in retinal structure and function correlate with visual deficits during increasing amounts of retinal degeneration.<i>Materials and methods</i>: Retinal degeneration was induced in adult mice by subretinal injections of paraquat (PQ) (0.2–1 mM). Retinal anatomy and photoreceptor layer thickness were quantified by histology and optical coherence tomography (OCT), retinal function was measured using electroretinography (ERG), and visual behavior were measured by optokinetic tracking, at 1 to 3 week post-injury.<i>Results</i>: Photoreceptor layer structure, function and visual behavior declined at a linear rate over time following PQ-induced degeneration, with the correlations between outcome measures being lowest at mild injury levels and increasing with injury severity. Overall reductions in visual acuity were highly correlated with declines in retinal thickness (<i>r</i><sup>2</sup> = 0.78) and function (<i>r</i><sup>2</sup> = 0.67) and retinal thickness correlated with photoreceptor function (<i>r</i><sup>2</sup> = 0.72). ERG a-wave scotopic amplitudes showed a stronger correspondence to retinal structure and visual behavior than b-waves.<i>Conclusions</i>: Measurements of photoreceptor loss at the structural and functional levels showed good correspondence with degeneration-associated changes in visual behavior after oxidative stress injury. The results provide new insight about the relative kinetics of measurements of retinal degeneration induced by oxidative stress, which could guide the choice of optimal outcome measurements for other retinal diseases.
DOI: 10.5066/p9y7k5cd
title: Molecular and morphological data to resolve species boundaries in the critically imperiled freshwater mussel species, Fusconaia mitchelli

description: We generated multilocus DNA sequence data and traditional morphometric measurements to evaluate species boundaries in Fusconaia mitchelli. We sequenced three loci: the protein-coding mitochondrial DNA genes cytochrome oxidase subunit 1 and NADH dehydrogenase 1, and the nuclear ribosomal internal transcribed spacer 1. We also took three measurements, maximum length, maximum width, and maximum height, of mussel shells for morphometric analysis.
DOI: 10.6084/m9.figshare.1598200
title: Datasets: Mining chemical activity status from high-throughput screening assays

description: High-throughput screening (HTS) experiments provide a valuable resource that reports biological activity of numerous chemical compounds relative to their molecular targets. Building computational models that accurately predict such activity status (active vs. inactive) in specific assays is a challenging task given the large volume of data and frequently small proportion of active compounds relative to the inactive ones. We developed a method, DRAMOTE, to predict activity status of chemical compounds in HTP activity assays. For a class of HTP assays, our method achieves considerably better results than the current state-of-the-art-solutions. We achieved this by modification of a minority oversampling technique. To demonstrate that DRAMOTE is performing better than the other methods, we performed a comprehensive comparison analysis with several other methods and evaluated them on data from 11 PubChem assays through 1,350 experiments that involved approximately 500,000 interactions between chemicals and their target proteins. As an example of potential use, we applied DRAMOTE to develop robust models for predicting FDA approved drugs that have high probability to interact with the thyroid stimulating hormone receptor (TSHR) in humans. Our findings are further partially and indirectly supported by 3D docking results and literature information. The results based on approximately 500,000 interactions suggest that DRAMOTE has performed the best and that it can be used for developing robust virtual screening models. The datasets and implementation of all solutions are available as a MATLAB toolbox online at www.cbrc.kaust.edu.sa/dramote
DOI: 10.6084/m9.figshare.1598200.v1
title: Datasets: Mining chemical activity status from high-throughput screening assays

description: High-throughput screening (HTS) experiments provide a valuable resource that reports biological activity of numerous chemical compounds relative to their molecular targets. Building computational models that accurately predict such activity status (active vs. inactive) in specific assays is a challenging task given the large volume of data and frequently small proportion of active compounds relative to the inactive ones. We developed a method, DRAMOTE, to predict activity status of chemical compounds in HTP activity assays. For a class of HTP assays, our method achieves considerably better results than the current state-of-the-art-solutions. We achieved this by modification of a minority oversampling technique. To demonstrate that DRAMOTE is performing better than the other methods, we performed a comprehensive comparison analysis with several other methods and evaluated them on data from 11 PubChem assays through 1,350 experiments that involved approximately 500,000 interactions between chemicals and their target proteins. As an example of potential use, we applied DRAMOTE to develop robust models for predicting FDA approved drugs that have high probability to interact with the thyroid stimulating hormone receptor (TSHR) in humans. Our findings are further partially and indirectly supported by 3D docking results and literature information. The results based on approximately 500,000 interactions suggest that DRAMOTE has performed the best and that it can be used for developing robust virtual screening models. The datasets and implementation of all solutions are available as a MATLAB toolbox online at www.cbrc.kaust.edu.sa/dramote
DOI: 10.6084/m9.figshare.1598196
title: Mining chemical activity status from high-throughput screening assays

description: This is the set of labels indicating active and inactive cases (i.e. binary classification problem) corresponding to the databench set.
DOI: 10.6084/m9.figshare.1598196.v1
title: Mining chemical activity status from high-throughput screening assays

description: This is the set of labels indicating active and inactive cases (i.e. binary classification problem) corresponding to the databench set.
DOI: 10.6084/m9.figshare.1598138
title: Cannabis Liberalization and Adolescent Cannabis Use: A Cross-national Study in 38 Countries_Appendix

description: Supplementary tables for paper "Cannabis Liberalization and Adolescent Cannabis Use: A Cross-national Study in 38 Countries" by Shi. Y et al.
DOI: 10.6084/m9.figshare.1598176
title: Gaussian Job Archive for C6H16NO5(1+)

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1598176.v1
title: Gaussian Job Archive for C6H16NO5(1+)

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.