cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12268673.v1
title: Efficient Parameter Sampling for Markov Jump Processes

description: Markov jump processes (MJPs) are continuous-time stochastic processes widely used in a variety of applied disciplines. Inference typically proceeds via Markov chain Monte Carlo (MCMC), the state-of-the-art being a uniformization-based auxiliary variable Gibbs sampler. This was designed for situations where the process parameters are known, and Bayesian inference over unknown parameters is typically carried out by incorporating it into a larger Gibbs sampler. This strategy of sampling parameters given path, and path given parameters can result in poor Markov chain mixing. In this work, we propose a simple and efficient algorithm to address this problem. Our scheme brings Metropolis–Hastings (MH) approaches for discrete-time hidden Markov models to the continuous-time setting, resulting in a complete and clean recipe for parameter and path inference in MJPs. In our experiments, we demonstrate superior performance over Gibbs sampling, a more naïve MH algorithm, as well as another popular approach, particle MCMC. We also show our sampler inherits geometric mixing from an “ideal” sampler that is computationally much more expensive. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12844493.v1
title: Fast Search and Estimation of Bayesian Nonparametric Mixture Models Using a Classification Annealing EM Algorithm

description: Bayesian nonparametric (BNP) infinite-mixture models provide flexible and accurate density estimation, cluster analysis, and regression. However, for the posterior inference of such a model, MCMC algorithms are complex, often need to be tailor-made for different BNP priors, and are intractable for large data sets. We introduce a BNP classification annealing EM algorithm which employs importance sampling estimation. This new fast-search algorithm, for virtually any given BNP mixture model, can quickly and accurately calculate the posterior predictive density estimate (by posterior averaging) and the maximum a-posteriori clustering estimate (by simulated annealing), even for data sets containing millions of observations. The algorithm can handle a wide range of BNP priors because it primarily relies on the ability to generate prior samples. The algorithm can be fast because in each iteration, it performs a sampling step for the (missing) clustering of the data points, instead of a costly E-step; and then performs direct posterior calculations in the M-step, given the sampled (imputed) clustering. The new algorithm is illustrated and evaluated through BNP Gaussian mixture model analyses of benchmark simulated data and real data sets. MATLAB code for the new algorithm is provided in Supplementary Materials.
DOI: 10.6084/m9.figshare.12844502.v1
title: Spectrally Sparse Nonparametric Regression via Elastic Net Regularized Smoothers

description: Nonparametric regression frameworks, such as generalized additive models (GAMs) and smoothing spline analysis of variance (SSANOVA) models, extend the generalized linear model (GLM) by allowing for unknown functional relationships between an exponential family response variable and a collection of predictor variables. The unknown functional relationships are typically estimated using penalized likelihood estimation, which adds a roughness penalty to the (negative) log-likelihood function. In this article, I propose a spectral parameterization of a smoothing spline, which allows for an efficient application of Elastic Net regression to smooth and select eigenvectors of a kernel matrix. The classic (ridge regression) solution for a smoothing spline is a special case of the proposed kernel eigenvector smoothing and selection operator. Extensions for tensor product smoothers are developed for both the GAM and SSANOVA frameworks. Using simulated and real data examples, I demonstrate that the proposed approach offers practical and computational gains over typical approaches for fitting GAMs, SSANOVA models, and Elastic Net penalized GLMs. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12844520.v3
title: Model Interpretation Through Lower-Dimensional Posterior Summarization

description: Nonparametric regression models have recently surged in their power and popularity, accompanying the trend of increasing dataset size and complexity. While these models have proven their predictive ability in empirical settings, they are often difficult to interpret and do not address the underlying inferential goals of the analyst or decision maker. In this article, we propose a modular two-stage approach for creating parsimonious, interpretable summaries of complex models which allow freedom in the choice of modeling technique and the inferential target. In the first stage, a flexible model is fit which is believed to be as accurate as possible. In the second stage, lower-dimensional summaries are constructed by projecting draws from the distribution onto simpler structures. These summaries naturally come with valid Bayesian uncertainty estimates. Further, since we use the data only once to move from prior to posterior, these uncertainty estimates remain valid across multiple summaries and after iteratively refining a summary. We apply our method and demonstrate its strengths across a range of simulated and real datasets. The methods we present here are implemented in an R package available at github.com/spencerwoody/possum. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12844520.v2
title: Model Interpretation Through Lower-Dimensional Posterior Summarization

description: Nonparametric regression models have recently surged in their power and popularity, accompanying the trend of increasing dataset size and complexity. While these models have proven their predictive ability in empirical settings, they are often difficult to interpret and do not address the underlying inferential goals of the analyst or decision maker. In this article, we propose a modular two-stage approach for creating parsimonious, interpretable summaries of complex models which allow freedom in the choice of modeling technique and the inferential target. In the first stage, a flexible model is fit which is believed to be as accurate as possible. In the second stage, lower-dimensional summaries are constructed by projecting draws from the distribution onto simpler structures. These summaries naturally come with valid Bayesian uncertainty estimates. Further, since we use the data only once to move from prior to posterior, these uncertainty estimates remain valid across multiple summaries and after iteratively refining a summary. We apply our method and demonstrate its strengths across a range of simulated and real datasets. The methods we present here are implemented in an R package available at github.com/spencerwoody/possum. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12867305
title: Brain mass, body mass and population density in mammals

description: Datasets and R scripts from González-Suárez, M; Gonzalez-Voyer, A; von Hardenberg, A; Santini, L (2021) The role of brain size on mammalian population densities Journal of Animal Ecology, 90: 653– 661. DOI: 10.1111/1365-2656.13397<br>Additional details in the README.pdf file<br> SUMMARY OF FILES INCLUDED - CSV datasets: total 21 files representing · 12 csv datasets from other sources (described below) with brain and body mass data in the zip file Brain and Mass data. · Six csv datasets from other sources and compilations (described below) with population density and diet information · Two csv files (Complete_dataset_published.csv, Brain_data_compilation_published.csv) produced during this study. Details of the files and the compilation protocol are provided in the README file. - R scripts: three scripts that describe the protocols to: combine brain and body mass data (brain_data_compilation_published.Rmd), combine all sources (Joining_all_data_published.Rmd), and analyse and produce tables and figures presented in the manuscript (Data_analysesPPA_published.Rmd). <br>
DOI: 10.6084/m9.figshare.7627178
title: Microbial Communities of Low Temperature, Saline Groundwater Used for Therapeutical Purposes in North Poland

description: Knowledge on microbial community composition and ecology in highly mineralized (TDS up to 71 g l<sup>−1</sup>), cold waters (T Desulfovibrio) in the deepest waters. The most important geochemical drivers of the observed microbial community composition were TDS including Cl<sup>−</sup>, Na<sup>+</sup>, Mg<sup>2+</sup>, and NO<sub>3</sub><sup>−</sup>. Bacterial isolates belonged mostly to the genus <i>Bacillus</i>. Sequences assigned to Archaea (<i>Methanobacterium</i>) were detected only in the deepest borehole water.
DOI: 10.6084/m9.figshare.7627178.v1
title: Microbial Communities of Low Temperature, Saline Groundwater Used for Therapeutical Purposes in North Poland

description: Knowledge on microbial community composition and ecology in highly mineralized (TDS up to 71 g l<sup>−1</sup>), cold waters (T Desulfovibrio) in the deepest waters. The most important geochemical drivers of the observed microbial community composition were TDS including Cl<sup>−</sup>, Na<sup>+</sup>, Mg<sup>2+</sup>, and NO<sub>3</sub><sup>−</sup>. Bacterial isolates belonged mostly to the genus <i>Bacillus</i>. Sequences assigned to Archaea (<i>Methanobacterium</i>) were detected only in the deepest borehole water.
DOI: 10.6084/m9.figshare.7960943
title: Combined Yeast Biofilm Screening – Characterization and Validation of Yeast Related Biofilms in a Brewing Environment with Combined Cultivation and Specific Real-time PCR Screening of Selected Indicator Species

description: Microbial spoilage of alcohol-free and low-alcohol beers, beer-mixed beverages, and soft drinks is most commonly caused by yeast. Yeast-related biofilms are therefore a serious problem in the production of these beverages. Fast detection of developing biofilms is a key factor to prevent subsequent spoilage of the product. For fast yeast detection, a new specific medium was developed and combined with real-time polymerase chain reaction (PCR) detection of characteristic beverage spoiling yeast species. The medium is based on MYPG broth (malt extract, yeast extract, peptone, glucose broth) with resazurin as a redox indicator for cell activity. The growth and biofilm potential of representative strains of commonly present beverage spoilage yeast species was evaluated using the developed medium. A novel real-time PCR detection system for <i>Rhodotorula mucilaginosa,</i> an early biofilm colonizer, was designed and successfully validated. Two field tests of the medium in combination with real-time PCR were performed. One test showed a differentiated hygienic status on a filler, and the other test tracked the contamination source of <i>Saccharomyces cerevisiae</i> var. <i>diastaticus</i>. Biofilm relevance of the strain set was proven. The modified MYPG proved to be highly sensitive when detecting yeasts. The detection of the selected target species directly in the medium was compatible and can provide detailed hygienic profiles when combined with additional information on the target species. This provides a fast detection method for yeast-related biofilms in brewery environments, differentiated hygienic monitoring, and makes it possible to troubleshoot contamination incidents.
DOI: 10.6084/m9.figshare.7960943.v1
title: Combined Yeast Biofilm Screening – Characterization and Validation of Yeast Related Biofilms in a Brewing Environment with Combined Cultivation and Specific Real-time PCR Screening of Selected Indicator Species

description: Microbial spoilage of alcohol-free and low-alcohol beers, beer-mixed beverages, and soft drinks is most commonly caused by yeast. Yeast-related biofilms are therefore a serious problem in the production of these beverages. Fast detection of developing biofilms is a key factor to prevent subsequent spoilage of the product. For fast yeast detection, a new specific medium was developed and combined with real-time polymerase chain reaction (PCR) detection of characteristic beverage spoiling yeast species. The medium is based on MYPG broth (malt extract, yeast extract, peptone, glucose broth) with resazurin as a redox indicator for cell activity. The growth and biofilm potential of representative strains of commonly present beverage spoilage yeast species was evaluated using the developed medium. A novel real-time PCR detection system for <i>Rhodotorula mucilaginosa,</i> an early biofilm colonizer, was designed and successfully validated. Two field tests of the medium in combination with real-time PCR were performed. One test showed a differentiated hygienic status on a filler, and the other test tracked the contamination source of <i>Saccharomyces cerevisiae</i> var. <i>diastaticus</i>. Biofilm relevance of the strain set was proven. The modified MYPG proved to be highly sensitive when detecting yeasts. The detection of the selected target species directly in the medium was compatible and can provide detailed hygienic profiles when combined with additional information on the target species. This provides a fast detection method for yeast-related biofilms in brewery environments, differentiated hygienic monitoring, and makes it possible to troubleshoot contamination incidents.
DOI: 10.6084/m9.figshare.12848706
title: Tristichopterids (Sarcopterygii, Tetrapodomorpha) from the Upper Devonian tetrapod-bearing locality of Strud (Belgium, upper Famennian), with phylogenetic and paleobiogeographic considerations

description: We describe new material of the tristichopterids cf. <i>Langlieria socqueti</i> and cf. <i>Eusthenodon wangsjoi</i> and other unassignable tetrapodomorph remains from the upper Famennian locality of Strud, Belgium. Because of recent improvements in our tristichopterid knowledge, a new phylogenetic analysis is presented in addition to a paleobiogeographic analysis using the Bayesian binary Markov chain Monte Carlo (MCMC) statistical method. The origin of the whole tristichopterid clade is reconstructed with a very likely western European origin. Much of the early tristichopterid history took place in Euramerica. During the Late Devonian, tristichopterids most probably spread from Euramerica into Gondwana. The highly nested tristichopterid clade formed by <i>Cabonnichthys burnsi</i>, <i>Mandageria fairfaxi</i>, <i>E. wangsjoi</i>, <i>Edenopteron keithcrooki</i>, and <i>Hyneria lindae</i> most likely differentiated in Australia. Then dispersal events occurred from Australia to Euramerica with <i>Hyneria lindae</i> (to eastern North America) and <i>E. wangsjoi</i> (to Greenland/western Europe). The latter dispersal events, during the Famennian, are in agreement with the Great Devonian Interchange, which predicts dispersal events between Gondwana and Euramerica at this time.
DOI: 10.6084/m9.figshare.12848694.v2
title: A systematic review of the giant alligatoroid <i>Deinosuchus</i> from the Campanian of North America and its implications for the relationships at the root of Crocodylia

description: <i>Deinosuchus</i> is a lineage of giant (≥10 m) Late Cretaceous crocodylians from North America. These were the largest semiaquatic predators in their environments and are known to have fed on large vertebrates, including contemporaneous terrestrial vertebrates such as dinosaurs. Fossils have been found in units of Campanian age from northern Mexico to Montana in the west and Mississippi to New Jersey in the east. Three species have been named, and recent consensus suggests that they represent a single, widely ranging species. The authors studied newly collected material from western Texas and increased sampling from throughout North America to review species-level systematics of <i>Deinosuchus</i> and help refine its phylogenetic placement among crocodylians. <i>Deinosuchus</i> from eastern and western North America can be consistently differentiated and represent different species. A phylogenetic study is conducted including new character states. This work reinforces the identity of the ‘terror crocodile’ as an alligatoroid. Reference to the holotypes indicates that the generic name holder, <i>Deinosuchus hatcheri</i>, is extremely incomplete. As a result, the three known species of <i>Deinosuchus</i> cannot be differentiated. To ensure nomenclatural stability, the type species for <i>Deinosuchus</i> should be transferred to <i>Deinosuchus riograndensis</i>, a species known from multiple mostly complete individuals. Additionally, <i>Deinosuchus rugosus</i> is based on a holotype that is not diagnostic, and a new species, <i>Deinosuchus schwimmeri</i>, is named to encompass some specimens formerly assigned to <i>D. rugosus</i>.
DOI: 10.6084/m9.figshare.12848706.v2
title: Tristichopterids (Sarcopterygii, Tetrapodomorpha) from the Upper Devonian tetrapod-bearing locality of Strud (Belgium, upper Famennian), with phylogenetic and paleobiogeographic considerations

description: We describe new material of the tristichopterids cf. <i>Langlieria socqueti</i> and cf. <i>Eusthenodon wangsjoi</i> and other unassignable tetrapodomorph remains from the upper Famennian locality of Strud, Belgium. Because of recent improvements in our tristichopterid knowledge, a new phylogenetic analysis is presented in addition to a paleobiogeographic analysis using the Bayesian binary Markov chain Monte Carlo (MCMC) statistical method. The origin of the whole tristichopterid clade is reconstructed with a very likely western European origin. Much of the early tristichopterid history took place in Euramerica. During the Late Devonian, tristichopterids most probably spread from Euramerica into Gondwana. The highly nested tristichopterid clade formed by <i>Cabonnichthys burnsi</i>, <i>Mandageria fairfaxi</i>, <i>E. wangsjoi</i>, <i>Edenopteron keithcrooki</i>, and <i>Hyneria lindae</i> most likely differentiated in Australia. Then dispersal events occurred from Australia to Euramerica with <i>Hyneria lindae</i> (to eastern North America) and <i>E. wangsjoi</i> (to Greenland/western Europe). The latter dispersal events, during the Famennian, are in agreement with the Great Devonian Interchange, which predicts dispersal events between Gondwana and Euramerica at this time.
DOI: 10.6084/m9.figshare.12848694
title: A systematic review of the giant alligatoroid <i>Deinosuchus</i> from the Campanian of North America and its implications for the relationships at the root of Crocodylia

description: <i>Deinosuchus</i> is a lineage of giant (≥10 m) Late Cretaceous crocodylians from North America. These were the largest semiaquatic predators in their environments and are known to have fed on large vertebrates, including contemporaneous terrestrial vertebrates such as dinosaurs. Fossils have been found in units of Campanian age from northern Mexico to Montana in the west and Mississippi to New Jersey in the east. Three species have been named, and recent consensus suggests that they represent a single, widely ranging species. The authors studied newly collected material from western Texas and increased sampling from throughout North America to review species-level systematics of <i>Deinosuchus</i> and help refine its phylogenetic placement among crocodylians. <i>Deinosuchus</i> from eastern and western North America can be consistently differentiated and represent different species. A phylogenetic study is conducted including new character states. This work reinforces the identity of the ‘terror crocodile’ as an alligatoroid. Reference to the holotypes indicates that the generic name holder, <i>Deinosuchus hatcheri</i>, is extremely incomplete. As a result, the three known species of <i>Deinosuchus</i> cannot be differentiated. To ensure nomenclatural stability, the type species for <i>Deinosuchus</i> should be transferred to <i>Deinosuchus riograndensis</i>, a species known from multiple mostly complete individuals. Additionally, <i>Deinosuchus rugosus</i> is based on a holotype that is not diagnostic, and a new species, <i>Deinosuchus schwimmeri</i>, is named to encompass some specimens formerly assigned to <i>D. rugosus</i>.
DOI: 10.6084/m9.figshare.12848721
title: <i>Norisdelphis annakaensis</i>, A new Miocene delphinid from Japan

description: Two well-preserved delphinid crania have been recovered from the Haraichi Formation, Annaka Group, Gunma Prefecture, Japan (earliest late Miocene, Tortonian; 11.29–11.25 Ma). The specimens represent a new genus and species of delphinid, <i>Norisdelphis annakaensis</i>. The new species is characterized by transversely narrow and anteroposteriorly elongated external bony nares, and a wider proximal extremity of the left premaxilla. Phylogenetic analysis suggests that <i>Norisdelphis</i> is the most basal member of the Delphinidae. The previous oldest known described delphinid, <i>Eodelphinus kabatensis</i>, is from the upper Miocene (ca. 9 Ma), and other reliably dated and described fossil delphinids are no older than Pliocene; thus, <i>N. annakaensis</i> is the oldest convincingly dated and well-diagnosed fossil delphinid species yet described. <i>Norisdelphis annakaensis</i> expands the geological range of the family Delphinidae.
DOI: 10.6084/m9.figshare.12848721.v2
title: <i>Norisdelphis annakaensis</i>, A new Miocene delphinid from Japan

description: Two well-preserved delphinid crania have been recovered from the Haraichi Formation, Annaka Group, Gunma Prefecture, Japan (earliest late Miocene, Tortonian; 11.29–11.25 Ma). The specimens represent a new genus and species of delphinid, <i>Norisdelphis annakaensis</i>. The new species is characterized by transversely narrow and anteroposteriorly elongated external bony nares, and a wider proximal extremity of the left premaxilla. Phylogenetic analysis suggests that <i>Norisdelphis</i> is the most basal member of the Delphinidae. The previous oldest known described delphinid, <i>Eodelphinus kabatensis</i>, is from the upper Miocene (ca. 9 Ma), and other reliably dated and described fossil delphinids are no older than Pliocene; thus, <i>N. annakaensis</i> is the oldest convincingly dated and well-diagnosed fossil delphinid species yet described. <i>Norisdelphis annakaensis</i> expands the geological range of the family Delphinidae.
DOI: 10.6084/m9.figshare.12848706.v1
title: Tristichopterids (Sarcopterygii, Tetrapodomorpha) from the Upper Devonian tetrapod-bearing locality of Strud (Belgium, upper Famennian), with phylogenetic and paleobiogeographic considerations

description: We describe new material of the tristichopterids cf. <i>Langlieria socqueti</i> and cf. <i>Eusthenodon wangsjoi</i> and other unassignable tetrapodomorph remains from the upper Famennian locality of Strud, Belgium. Because of recent improvements in our tristichopterid knowledge, a new phylogenetic analysis is presented in addition to a paleobiogeographic analysis using the Bayesian binary Markov chain Monte Carlo (MCMC) statistical method. The origin of the whole tristichopterid clade is reconstructed with a very likely western European origin. Much of the early tristichopterid history took place in Euramerica. During the Late Devonian, tristichopterids most probably spread from Euramerica into Gondwana. The highly nested tristichopterid clade formed by <i>Cabonnichthys burnsi</i>, <i>Mandageria fairfaxi</i>, <i>E. wangsjoi</i>, <i>Edenopteron keithcrooki</i>, and <i>Hyneria lindae</i> most likely differentiated in Australia. Then dispersal events occurred from Australia to Euramerica with <i>Hyneria lindae</i> (to eastern North America) and <i>E. wangsjoi</i> (to Greenland/western Europe). The latter dispersal events, during the Famennian, are in agreement with the Great Devonian Interchange, which predicts dispersal events between Gondwana and Euramerica at this time.