cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5024441
title: Model Choice and Diagnostics for Linear Mixed-Effects Models Using Statistics on Street Corners

description: The complexity of linear mixed-effects (LME) models means that traditional diagnostics are rendered less effective. This is due to a breakdown of asymptotic results, boundary issues, and visible patterns in residual plots that are introduced by the model fitting process. Some of these issues are well known and adjustments have been proposed. Working with LME models typically requires that the analyst keeps track of all the special circumstances that may arise. In this article, we illustrate a simpler but generally applicable approach to diagnosing LME models. We explain how to use new visual inference methods for these purposes. The approach provides a unified framework for diagnosing LME fits and for model selection. We illustrate the use of this approach on several commonly available datasets. A large-scale Amazon Turk study was used to validate the methods. R code is provided for the analyses. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5024447
title: Application of bar adsorptive microextraction to determine trace organic micro-pollutants in environmental water matrices

description: The present work proposes the application of bar adsorptive micro-extraction (BAµE) coated with an N-vinylpyrrolidone polymer (NVP) combined with micro-liquid desorption (200 µL) followed by high-performance liquid chromatography with diode array detection (BAµE(NVP)-µLD/HPLC-DAD) for the determination of trace levels of emerging organic micro-pollutants in environmental water matrices. The model compounds selected include an antibacterial/antifungal agent (triclosan), two pharmaceuticals (carbamazepine and diclofenac) and two steroid hormones (17α-ethinylestradiol and 17β-estradiol), in which the latter three were recently included in the European Union watch list of substances to be monitored in the field of water policy. Assays performed on 25 mL of ultrapure water samples spiked at the 8.0 µg L<sup>−1</sup> level yielded average recoveries ranging from 81.9 to 102.4% for the compounds studied using optimised experimental conditions. The proposed analytical methodology demonstrated suitable detection limits (0.02–0.10 µg L<sup>−1</sup>) and good linear dynamic ranges (0.1–20.0 µg L<sup>−1</sup>) with determination coefficients higher than 0.9909. Using the standard addition method (SAM), the present analytical approach was applied on environmental water matrices, including surface, sea, river and groundwaters. The proposed method proved to be a suitable and alternative sorption-based static micro-extraction technique for monitoring trace levels of organic micro-pollutants in environmental water matrices.
DOI: 10.6084/m9.figshare.5024432
title: The Self-Multiset Sampler

description: The multiset sampler has been shown to be an effective algorithm to sample from complex multimodal distributions, but the multiset sampler requires that the parameters in the target distribution can be divided into two parts: the parameters of interest and the nuisance parameters. We propose a new self-multiset sampler (SMSS), which extends the multiset sampler to distributions without nuisance parameters. We also generalize our method to distributions with unbounded or infinite support. Numerical results show that the SMSS and its generalization have a substantial advantage in sampling multimodal distributions compared to the ordinary Markov chain Monte Carlo algorithm and some popular variants. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.5024447.v1
title: Application of bar adsorptive microextraction to determine trace organic micro-pollutants in environmental water matrices

description: The present work proposes the application of bar adsorptive micro-extraction (BAµE) coated with an N-vinylpyrrolidone polymer (NVP) combined with micro-liquid desorption (200 µL) followed by high-performance liquid chromatography with diode array detection (BAµE(NVP)-µLD/HPLC-DAD) for the determination of trace levels of emerging organic micro-pollutants in environmental water matrices. The model compounds selected include an antibacterial/antifungal agent (triclosan), two pharmaceuticals (carbamazepine and diclofenac) and two steroid hormones (17α-ethinylestradiol and 17β-estradiol), in which the latter three were recently included in the European Union watch list of substances to be monitored in the field of water policy. Assays performed on 25 mL of ultrapure water samples spiked at the 8.0 µg L<sup>−1</sup> level yielded average recoveries ranging from 81.9 to 102.4% for the compounds studied using optimised experimental conditions. The proposed analytical methodology demonstrated suitable detection limits (0.02–0.10 µg L<sup>−1</sup>) and good linear dynamic ranges (0.1–20.0 µg L<sup>−1</sup>) with determination coefficients higher than 0.9909. Using the standard addition method (SAM), the present analytical approach was applied on environmental water matrices, including surface, sea, river and groundwaters. The proposed method proved to be a suitable and alternative sorption-based static micro-extraction technique for monitoring trace levels of organic micro-pollutants in environmental water matrices.
DOI: 10.6084/m9.figshare.5024450.v1
title: Supplementary Material for: An Insight into the Changes in Skin Texture and Properties following Dietary Intervention with a Nutricosmeceutical Containing a Blend of Collagen Bioactive Peptides and Antioxidants

description: <b><i>Background:</i></b> Skin aging is a multifactorial phenomenon which causes alterations in skin physiological functions and, most visibly, phenotypic changes. In particular, during the aging process, hyaluronic acid, collagen, and elastin fibers undergo structural and functional changes. <b><i>Aims:</i></b> This study aimed to give an insight into the photo-protective benefits and efficacy of an oral liquid nutricosmeceutical containing collagen bioactive peptides and antioxidants to counteract the signs of aging. <b><i>Methods:</i></b> A double-blind, randomized, placebo-controlled clinical trial was conducted by an independent esthetic clinic on 120 healthy volunteer subjects for 90 days. Subjects were divided into 2 groups: 60 subjects consumed 1 bottle (50 mL) of the nutricosmeceutical daily and the other 60 consumed 1 bottle (50 mL) of the placebo. Outcome measures were related to skin elasticity (expressed as Young's elasticity modulus) and skin architecture (histological analysis). In addition, the subjects recruited in this study underwent observational assessments through self-assessment questionnaires. <b><i>Results and Conclusions:</i></b> Overall, we demonstrated a significant increase in skin elasticity (+7.5%), <i>p</i> ≤ 0.001 and an improvement in skin texture after daily oral consumption of the nutricosmeceutical. We also obtained a positive patient feedback through the self-assessment questionnaires. Taken together these results show that this nutricosmeceutical supplement may have photo-protective effects and help improve skin health.
DOI: 10.6084/m9.figshare.5024426
title: Variational Bayes With Intractable Likelihood

description: Variational Bayes (VB) is rapidly becoming a popular tool for Bayesian inference in statistical modeling. However, the existing VB algorithms are restricted to cases where the likelihood is tractable, which precludes their use in many interesting situations such as in state--space models and in approximate Bayesian computation (ABC), where application of VB methods was previously impossible. This article extends the scope of application of VB to cases where the likelihood is intractable, but can be estimated unbiasedly. The proposed VB method therefore makes it possible to carry out Bayesian inference in many statistical applications, including state--space models and ABC. The method is generic in the sense that it can be applied to almost all statistical models without requiring too much model-based derivation, which is a drawback of many existing VB algorithms. We also show how the proposed method can be used to obtain highly accurate VB approximations of marginal posterior distributions. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.5024432.v1
title: The Self-Multiset Sampler

description: The multiset sampler has been shown to be an effective algorithm to sample from complex multimodal distributions, but the multiset sampler requires that the parameters in the target distribution can be divided into two parts: the parameters of interest and the nuisance parameters. We propose a new self-multiset sampler (SMSS), which extends the multiset sampler to distributions without nuisance parameters. We also generalize our method to distributions with unbounded or infinite support. Numerical results show that the SMSS and its generalization have a substantial advantage in sampling multimodal distributions compared to the ordinary Markov chain Monte Carlo algorithm and some popular variants. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.5024441.v2
title: Model Choice and Diagnostics for Linear Mixed-Effects Models Using Statistics on Street Corners

description: The complexity of linear mixed-effects (LME) models means that traditional diagnostics are rendered less effective. This is due to a breakdown of asymptotic results, boundary issues, and visible patterns in residual plots that are introduced by the model fitting process. Some of these issues are well known and adjustments have been proposed. Working with LME models typically requires that the analyst keeps track of all the special circumstances that may arise. In this article, we illustrate a simpler but generally applicable approach to diagnosing LME models. We explain how to use new visual inference methods for these purposes. The approach provides a unified framework for diagnosing LME fits and for model selection. We illustrate the use of this approach on several commonly available datasets. A large-scale Amazon Turk study was used to validate the methods. R code is provided for the analyses. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5024423
title: Analysis of Deviance for Hypothesis Testing in Generalized Partially Linear Models

description: In this study, we develop nonparametric analysis of deviance tools for generalized partially linear models based on local polynomial fitting. Assuming a canonical link, we propose expressions for both local and global analysis of deviance, which admit an additivity property that reduces to analysis of variance decompositions in the Gaussian case. Chi-square tests based on integrated likelihood functions are proposed to formally test whether the nonparametric term is significant. Simulation results are shown to illustrate the proposed chi-square tests and to compare them with an existing procedure based on penalized splines. The methodology is applied to German Bundesbank Federal Reserve data.
DOI: 10.6084/m9.figshare.5024441.v1
title: Model Choice and Diagnostics for Linear Mixed-Effects Models Using Statistics on Street Corners

description: The complexity of linear mixed-effects (LME) models means that traditional diagnostics are rendered less effective. This is due to a breakdown of asymptotic results, boundary issues, and visible patterns in residual plots that are introduced by the model fitting process. Some of these issues are well known and adjustments have been proposed. Working with LME models typically requires that the analyst keeps track of all the special circumstances that may arise. In this article, we illustrate a simpler but generally applicable approach to diagnosing LME models. We explain how to use new visual inference methods for these purposes. The approach provides a unified framework for diagnosing LME fits and for model selection. We illustrate the use of this approach on several commonly available datasets. A large-scale Amazon Turk study was used to validate the methods. R code is provided for the analyses. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5024426.v1
title: Variational Bayes with Intractable Likelihood

description: Variational Bayes (VB) is rapidly becoming a popular tool for Bayesian inference in statistical modeling. However, the existing VB algorithms are restricted to cases where the likelihood is tractable, which precludes their use in many interesting situations such as in state space models and in approximate Bayesian computation (ABC), where application of VB methods was previously impossible. This paper extends the scope of application of VB to cases where the likelihood is intractable, but can be estimated unbiasedly. The proposed VB method therefore makes it possible to carry out Bayesian inference in many statistical applications, including state space models and ABC. The method is generic in the sense that it can be applied to almost all statistical models without requiring too much model-based derivation, which is a drawback of many existing VB algorithms. We also show how the proposed method can be used to obtain highly accurate VB approximations of marginal posterior distributions.
DOI: 10.6084/m9.figshare.5024423.v2
title: Analysis of Deviance for Hypothesis Testing in Generalized Partially Linear Models

description: In this study, we develop nonparametric analysis of deviance tools for generalized partially linear models based on local polynomial fitting. Assuming a canonical link, we propose expressions for both local and global analysis of deviance, which admit an additivity property that reduces to analysis of variance decompositions in the Gaussian case. Chi-square tests based on integrated likelihood functions are proposed to formally test whether the nonparametric term is significant. Simulation results are shown to illustrate the proposed chi-square tests and to compare them with an existing procedure based on penalized splines. The methodology is applied to German Bundesbank Federal Reserve data.
DOI: 10.6084/m9.figshare.5024423.v1
title: Analysis of Deviance for Hypothesis Testing in Generalized Partially Linear Models

description: In this study, we develop nonparametric analysis of deviance tools for generalized partially linear models based on local polynomial fitting. Assuming a canonical link, we propose expressions for both local and global analysis of deviance, which admit an additivity property that reduces to analysis of variance decompositions in the Gaussian case. Chi-square tests based on integrated likelihood functions are proposed to formally test whether the nonparametric term is significant. Simulation results are shown to illustrate the proposed chi-square tests and to compare them with an existing procedure based on penalized splines. The methodology is applied to German Bundesbank Federal Reserve data.
DOI: 10.6084/m9.figshare.5024396
title: Mitochondrial DNA heteroplasmy in cardiac tissue from individuals with and without coronary artery disease

description: The cellular environment associated with coronary artery disease (CAD) can lead to mitochondrial DNA (mtDNA) damage. Mitochondrial variants in some copies of mtDNA (heteroplasmy) and mtDNA content are potential genetic biomarkers for CAD-associated disease states. Massively parallel sequencing and qRT-PCR techniques were used to measure heteroplasmic variants and mtDNA content in heart samples from donors with (<i>n</i> = 8) and without (<i>n</i> = 7) documented CAD. Both groups showed increased numbers of heteroplasmic mtDNA variants in the control region (CR) (<i>p</i> p = .043), an 87.50% increase in the number of heteroplasmic mtDNA deletions (<i>p</i> = .12), and a 48.76% increase in the number of heteroplasmic mtDNA single nucleotide variants (<i>p</i> = .029). These data suggest potential trends towards higher cardiac mtDNA heteroplasmy levels in heart samples from donors with CAD.
DOI: 10.6084/m9.figshare.5024396.v1
title: Mitochondrial DNA heteroplasmy in cardiac tissue from individuals with and without coronary artery disease

description: The cellular environment associated with coronary artery disease (CAD) can lead to mitochondrial DNA (mtDNA) damage. Mitochondrial variants in some copies of mtDNA (heteroplasmy) and mtDNA content are potential genetic biomarkers for CAD-associated disease states. Massively parallel sequencing and qRT-PCR techniques were used to measure heteroplasmic variants and mtDNA content in heart samples from donors with (<i>n</i> = 8) and without (<i>n</i> = 7) documented CAD. Both groups showed increased numbers of heteroplasmic mtDNA variants in the control region (CR) (<i>p</i> p = .043), an 87.50% increase in the number of heteroplasmic mtDNA deletions (<i>p</i> = .12), and a 48.76% increase in the number of heteroplasmic mtDNA single nucleotide variants (<i>p</i> = .029). These data suggest potential trends towards higher cardiac mtDNA heteroplasmy levels in heart samples from donors with CAD.
DOI: 10.6084/m9.figshare.5024363
title: A genetic study on subtropical <i>Anadenanthera colubrina</i> (Vell.) Brenan var. <i>cebil</i> (Griseb.) Altschul tree from Northwestern Argentina

description: <i>Anadenanthera colubrina</i> (Vell.) Brenan var. <i>cebil</i> (Griseb.) Altschul is a tree species in South America important for its cultural, economic, and medicinal uses. In addition, it represents a trace in memory of the forests that have decreased over the years and for this reason it is not only interesting to study but also important to preserve the tree species for future generations. In this paper, we have characterized the genetic diversity of four populations. We collected seeds from four different sites: San Bernardo (B), El Cebilar (C), Metán (M), and El Gallinato (G) in Salta Province, North Argentina. We then compared the intergenic transcribed sequences of ribosomal DNA, a known genetic molecular marker. Our previous results, obtained through the morphological and genetic analysis of only four individuals (one for each zone), have showed that the individuals from B and M sites were more similar to each other as well as the individuals from G and C sites. In this paper, a larger number of individuals (25) were characterized and their phylogenetic relationships were computed. The results confirmed the previously found similarities.
DOI: 10.6084/m9.figshare.5024366
title: Cost-effectiveness analysis of rivaroxaban for treatment and secondary prevention of venous thromboembolism in the Netherlands

description: <b>Background:</b> Until recently, standard treatment of venous thromboembolism (VTE) concerned a combination of short-term low-molecular-weight heparin (LMWH) and long-term vitamin-K antagonist (VKA). Risk of bleeding and the requirement for regular anticoagulation monitoring are, however, limiting their use. Rivaroxaban is a novel oral anticoagulant associated with a significantly lower risk of major bleeds (hazard ratio = 0.54, 95% confidence interval = 0.37–0.79) compared to LMWH/VKA therapy, and does not require regular anticoagulation monitoring. <b>Aims:</b> To evaluate the health economic consequences of treating acute VTE patients with rivaroxaban compared to treatment with LMWH/VKA, viewed from the Dutch societal perspective. <b>Methods:</b> A life-time Markov model was populated with the findings of the EINSTEIN phase III clinical trial to analyze cost-effectiveness of rivaroxaban therapy in treatment and prevention of VTE from a Dutch societal perspective. Primary model outcomes were total and incremental quality-adjusted life years (QALYs), as well as life expectancy and costs. <b>Results:</b> Over a patient’s lifetime, rivaroxaban was shown to be dominant, with health gains of 0.047 QALYs and cost savings of €304 compared to LMWH/VKA therapy. Dominance was robustly present in all sensitivity analyses. Major drivers of the differences between the two treatment arms were related to anticoagulation monitoring (medical costs, travel costs, and loss of productivity) and the occurrence of major bleeds. <b>Conclusion:</b> Rivaroxaban treatment of patients with venous thromboembolism results in health gains and cost savings compared to LMWH/VKA therapy. This conclusion holds for the Dutch setting, both for the societal perspective, as well as the healthcare perspective.
DOI: 10.6084/m9.figshare.5024363.v1
title: A genetic study on subtropical <i>Anadenanthera colubrina</i> (Vell.) Brenan var. <i>cebil</i> (Griseb.) Altschul tree from Northwestern Argentina

description: <i>Anadenanthera colubrina</i> (Vell.) Brenan var. <i>cebil</i> (Griseb.) Altschul is a tree species in South America important for its cultural, economic, and medicinal uses. In addition, it represents a trace in memory of the forests that have decreased over the years and for this reason it is not only interesting to study but also important to preserve the tree species for future generations. In this paper, we have characterized the genetic diversity of four populations. We collected seeds from four different sites: San Bernardo (B), El Cebilar (C), Metán (M), and El Gallinato (G) in Salta Province, North Argentina. We then compared the intergenic transcribed sequences of ribosomal DNA, a known genetic molecular marker. Our previous results, obtained through the morphological and genetic analysis of only four individuals (one for each zone), have showed that the individuals from B and M sites were more similar to each other as well as the individuals from G and C sites. In this paper, a larger number of individuals (25) were characterized and their phylogenetic relationships were computed. The results confirmed the previously found similarities.
DOI: 10.6084/m9.figshare.5024366.v1
title: Cost-effectiveness analysis of rivaroxaban for treatment and secondary prevention of venous thromboembolism in the Netherlands

description: <b>Background:</b> Until recently, standard treatment of venous thromboembolism (VTE) concerned a combination of short-term low-molecular-weight heparin (LMWH) and long-term vitamin-K antagonist (VKA). Risk of bleeding and the requirement for regular anticoagulation monitoring are, however, limiting their use. Rivaroxaban is a novel oral anticoagulant associated with a significantly lower risk of major bleeds (hazard ratio = 0.54, 95% confidence interval = 0.37–0.79) compared to LMWH/VKA therapy, and does not require regular anticoagulation monitoring. <b>Aims:</b> To evaluate the health economic consequences of treating acute VTE patients with rivaroxaban compared to treatment with LMWH/VKA, viewed from the Dutch societal perspective. <b>Methods:</b> A life-time Markov model was populated with the findings of the EINSTEIN phase III clinical trial to analyze cost-effectiveness of rivaroxaban therapy in treatment and prevention of VTE from a Dutch societal perspective. Primary model outcomes were total and incremental quality-adjusted life years (QALYs), as well as life expectancy and costs. <b>Results:</b> Over a patient’s lifetime, rivaroxaban was shown to be dominant, with health gains of 0.047 QALYs and cost savings of €304 compared to LMWH/VKA therapy. Dominance was robustly present in all sensitivity analyses. Major drivers of the differences between the two treatment arms were related to anticoagulation monitoring (medical costs, travel costs, and loss of productivity) and the occurrence of major bleeds. <b>Conclusion:</b> Rivaroxaban treatment of patients with venous thromboembolism results in health gains and cost savings compared to LMWH/VKA therapy. This conclusion holds for the Dutch setting, both for the societal perspective, as well as the healthcare perspective.
DOI: 10.6084/m9.figshare.5023592
title: ESM 1 from Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?

description: <b>GPS locations of lionfish abundance survey locations around Utila, Honduras</b>.