cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5284423.v1
title: Dataset for: Spatio-temporal multivariate mixture models for Bayesian model selection in disease mapping

description: It is often the case that researchers wish to simultaneously explore the behavior of multiple diseases while accounting for potential spatial and/or temporal correlation. In this paper, we propose a flexible class of multivariate spatio-temporal mixture models to fill this role. Further, these models offer flexibility with the potential for model selection as well as the ability to accommodate lifestyle, socio-economic, and physical environmental variables with spatial, temporal, or both structures. Here, we explore the capability of this approach via a large scale simulation study and examine a real data example. The results which are focused on four model variants suggest that all models possess the ability to recover simulation ground truth and display improved model fit over two baseline Knorr-Held spatio-temporal interaction model variants in a real data application.
DOI: 10.6084/m9.figshare.5284378
title: Prostate_Cancer_onc607_Data.xls

description: Exosomes may play a role in the disparity between african american and white american prostate cancer incidence and aggression.
DOI: 10.6084/m9.figshare.5284417.v1
title: Dataset for: Influence Diagnostics in Spatial Models with Censored Response

description: Environmental data are often spatially correlated and sometimes include observations below or above detection limits (i.e., censored values reported as less or more than a level of detection). Existing research mainly concentrate on parameter estimation using Gibbs sampling, and most researches conducted from a frequentist perspective in spatial censored models are elusive. In this paper, we propose an exact estimation procedure to obtain the maximum likelihood estimates of the fixed effects and variance components, using a stochastic approximation of the EM (SAEM) algorithm (Delyon et al., 1999). This approach permits estimation of the parameters of spatial linear models when censoring is present in an easy and fast way. As a byproduct, predictions of unobservable values of the response variable are possible. Motivated by this algorithm, we develop local and global influence measures on the basis of the conditional expectation of the complete-data log-likelihood function which eliminates the complexity associated with the approach of Cook (1977, 1986) for spatial censored models. Some useful perturbation schemes are discussed. The newly developed method is illustrated using data from a dioxin contaminated site in Missouri that contain left-censored data as well as a dataset related to depths of a geological horizon that contains both left- and right-censored observations. In addition, a simulation study is presented that, explores the accuracy of the proposed measures in detecting influential observations under different perturbation schemes. The methodology addressed in this paper is implemented in the R package CensSpatial.
DOI: 10.6084/m9.figshare.5284354
title: dfs.xlsx

description: Sample of 800 subjects for the validation of italian version of DFS2 by jackson
DOI: 10.6084/m9.figshare.5284237
title: result: Alzheimer's Publication Data from 2012-2015

description: result is a list of all Alzheimer's Publications that belong to a journal that published in the Alzheimer's sphere at least 30 times in the 2012-2017 window.<br>
DOI: 10.6084/m9.figshare.5284228
title: Journal Data

description: This dataset includes journal specific information aggregated from the mydata dataset including the journal specific delta values for all 114 journals in consideration.
DOI: 10.6084/m9.figshare.5284270
title: result: Alzheimer's Publication data merged with Altmetric information

description: result is a dataset that contains mydata's publication information merged with a separate altmetric database containing the specific altmetric component values. It is used to generate density plots and track altmetric composition over time.
DOI: 10.6084/m9.figshare.5284237.v2
title: result: Alzheimer's Publication Data from 2012-2015

description: result is a list of all Alzheimer's Publications that belong to a journal that published in the Alzheimer's sphere at least 30 times in the 2012-2017 window.<br>
DOI: 10.6084/m9.figshare.5284225
title: An Ecosystem-Based Approach to Evaluating Impacts and Management of Invasive Lionfish

description: Species invasions in marine ecosystems pose a threat to native fish communities and can disrupt the food webs that support valuable commercial and recreational fisheries. In the Gulf of Mexico, densities of invasive Indo-Pacific Lionfish, <i>Pterois volitans</i> and <i>P. miles</i>, are among the highest in their invaded range. In a workshop setting held over a 2-week period, we adapted an existing trophic dynamic model of the West Florida Shelf, located in the eastern Gulf of Mexico, to simulate the lionfish (both species) invasion and community effects over a range of harvest scenarios for both lionfish and native predators. Our results suggest small increases in lionfish harvest can reduce peak biomass by up to 25% and also that reduced harvest of native reef fish predators can lead to lower lionfish densities. This model can help managers identify target harvest and benefits of a lionfish fishery and inform the assessment and management of valuable reef fish fisheries.
DOI: 10.6084/m9.figshare.5284228.v1
title: Journal Data

description: This dataset includes journal specific information aggregated from the mydata dataset including the journal specific delta values for all 114 journals in consideration.
DOI: 10.6084/m9.figshare.5284237.v1
title: mydata: Alzheimer's Publication Data from 2012-2015

description: mydata is a list of all Alzheimer's Publications that belong to a journal that published in the Alzheimer's sphere at least 30 times in the 2012-2015 window.<br>
DOI: 10.6084/m9.figshare.5284270.v2
title: result: Alzheimer's Publication data merged with Altmetric information

description: result is a dataset that contains mydata's publication information merged with a separate altmetric database containing the specific altmetric component values. It is used to generate density plots and track altmetric composition over time.
DOI: 10.6084/m9.figshare.5284222
title: On Estimation of the Hazard Function From Population-Based Case–Control Studies

description: The population-based case–control study design has been widely used for studying the etiology of chronic diseases. It is well established that the Cox proportional hazards model can be adapted to the case–control study and hazard ratios can be estimated by (conditional) logistic regression model with time as either a matched set or a covariate. However, the baseline hazard function, a critical component in absolute risk assessment, is unidentifiable, because the ratio of cases and controls is controlled by the investigators and does not reflect the true disease incidence rate in the population. In this article, we propose a simple and innovative approach, which makes use of routinely collected family history information, to estimate the baseline hazard function for any logistic regression model that is fit to the risk factor data collected on cases and controls. We establish that the proposed baseline hazard function estimator is consistent and asymptotically normal and show via simulation that it performs well in finite samples. We illustrate the proposed method by a population-based case–control study of prostate cancer where the association of various risk factors is assessed and the family history information is used to estimate the baseline hazard function. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5284225.v1
title: An Ecosystem-Based Approach to Evaluating Impacts and Management of Invasive Lionfish

description: Species invasions in marine ecosystems pose a threat to native fish communities and can disrupt the food webs that support valuable commercial and recreational fisheries. In the Gulf of Mexico, densities of invasive Indo-Pacific Lionfish, <i>Pterois volitans</i> and <i>P. miles</i>, are among the highest in their invaded range. In a workshop setting held over a 2-week period, we adapted an existing trophic dynamic model of the West Florida Shelf, located in the eastern Gulf of Mexico, to simulate the lionfish (both species) invasion and community effects over a range of harvest scenarios for both lionfish and native predators. Our results suggest small increases in lionfish harvest can reduce peak biomass by up to 25% and also that reduced harvest of native reef fish predators can lead to lower lionfish densities. This model can help managers identify target harvest and benefits of a lionfish fishery and inform the assessment and management of valuable reef fish fisheries.
DOI: 10.6084/m9.figshare.5284270.v1
title: result: Alzheimer's Publication data merged with Altmetric information

description: result is a dataset that contains mydata's publication information merged with a separate altmetric database containing the specific altmetric component values. It is used to generate density plots and track altmetric composition over time.
DOI: 10.6084/m9.figshare.5284144
title: Evolution of the growth hormone, prolactin, prolactin 2 and somatolactin family [DATASET]

description: Phylogenetic analyses and chromosomal data for the growth hormone (<i>GH</i>), prolactin (<i>PRL</i>), prolactin 2 (<i>PRL2</i>) and somatolactin (<i>SL</i>) gene family, as well as 31 neighboring gene families in paralogous chromosome blocks.<br><br>Supporting data for manuscript GCE_2017_309 submitted to <i>General and Comparative Endocrinology</i>.<br><br>Sequence alignment files are in FASTA format. Phylogenetic tree files are in PHYLIP/Newick format.<br>Phylogenetic trees were made using the IQ-TREE program (http://www.iqtree.org/), supported by Ultra-Fast Bootstrap (UFBoot) and approximate Likelihood Ratio Test (aLRT).
DOI: 10.6084/m9.figshare.5284144.v1
title: Evolution of the growth hormone, prolactin, prolactin 2 and somatolactin family [DATASET]

description: Phylogenetic analyses and chromosomal data for the growth hormone (<i>GH</i>), prolactin (<i>PRL</i>), prolactin 2 (<i>PRL2</i>) and somatolactin (<i>SL</i>) gene family, as well as 31 neighboring gene families in paralogous chromosome blocks.<br><br>Supporting data for manuscript GCE_2017_309 submitted to <i>General and Comparative Endocrinology</i>.<br><br>Sequence alignment files are in FASTA format. Phylogenetic tree files are in PHYLIP/Newick format.<br>Phylogenetic trees were made using the IQ-TREE program (http://www.iqtree.org/), supported by Ultra-Fast Bootstrap (UFBoot) and approximate Likelihood Ratio Test (aLRT).
DOI: 10.6084/m9.figshare.5284222.v2
title: On Estimation of the Hazard Function From Population-Based Case–Control Studies

description: The population-based case–control study design has been widely used for studying the etiology of chronic diseases. It is well established that the Cox proportional hazards model can be adapted to the case–control study and hazard ratios can be estimated by (conditional) logistic regression model with time as either a matched set or a covariate. However, the baseline hazard function, a critical component in absolute risk assessment, is unidentifiable, because the ratio of cases and controls is controlled by the investigators and does not reflect the true disease incidence rate in the population. In this article, we propose a simple and innovative approach, which makes use of routinely collected family history information, to estimate the baseline hazard function for any logistic regression model that is fit to the risk factor data collected on cases and controls. We establish that the proposed baseline hazard function estimator is consistent and asymptotically normal and show via simulation that it performs well in finite samples. We illustrate the proposed method by a population-based case–control study of prostate cancer where the association of various risk factors is assessed and the family history information is used to estimate the baseline hazard function. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5284222.v1
title: On Estimation of the Hazard Function from Population-based Case-Control Studies

description: The population-based case-control study design has been widely used for studying the etiology of chronic diseases. It is well established that the Cox proportional hazards model can be adapted to the case-control study and hazard ratios can be estimated by (conditional) logistic regression model with time as either a matched set or a covariate (Prentice and Breslow, 1978). However, the baseline hazard function, a critical component in absolute risk assessment, is unidentifiable, because the ratio of cases and controls is controlled by the investigators and does not reflect the true disease incidence rate in the population. In this paper we propose a simple and innovative approach, which makes use of routinely collected family history information, to estimate the baseline hazard function for any logistic regression model that is fit to the risk factor data collected on cases and controls. We establish that the proposed baseline hazard function estimator is consistent and asymptotically normal and show via simulation that it performs well in finite samples. We illustrate the proposed method by a population-based case-control study of prostate cancer where the association of various risk factors is assessed and the family history information is used to estimate the baseline hazard function.
DOI: 10.6084/m9.figshare.5281891
title: A method for analysing small samples of floral pollen for free and protein-bound amino acids

description: Data for manuscript on the analysis of small pollen samples published in Methods in Ecology and Evolution
DOI: 10.6084/m9.figshare.5281900
title: Streptococcus pneumoniae serotype 19A: worldwide epidemiology

description: <b>Introduction</b>: <i>Streptococcus pneumoniae</i> causes mucosal and invasive diseases with high morbidity and mortality. Introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) into routine infant immunization programs worldwide resulted in serotype 19A becoming a leading cause of the remaining pneumococcal disease burden in vaccinated and nonvaccinated individuals. This article reviews the impact of the latest generation PCVs (10-valent PCV, PCV10, and 13-valent PCV, PCV13) on serotype 19A. <b>Areas covered</b>: This article covers immune responses elicited by PCV7, PCV10 and PCV13 against serotype 19A and their impact on nasopharyngeal (NP) carriage and disease in vaccinated and unvaccinated populations using data from surveillance systems, randomized controlled trials, and observational studies. <b>Expert commentary</b>: As expected from a PCV containing serotype 19A, PCV13 elicits significantly higher functional immune responses against serotype 19A than PCV7 and PCV10. Higher responses are likely to be linked to both direct impact in vaccinated populations and reductions in 19A NP carriage in children, thus inducing herd protection and reducing 19A invasive pneumococcal disease (IPD) in nonvaccinated children and adults. In contrast, PCV7 and PCV10 have shown mixed evidence of direct short-lived cross-protection and little to no impact on 19A carriage, resulting in continued transmission and disease.
DOI: 10.6084/m9.figshare.5281891.v1
title: A method for analysing small samples of floral pollen for free and protein-bound amino acids

description: Data for manuscript on the analysis of small pollen samples published in Methods in Ecology and Evolution
DOI: 10.6084/m9.figshare.5281870
title: Characterization of the piRNA pathway during development of the sea anemone <i>Nematostella vectensis</i>

description: PIWI-interacting RNAs (piRNAs) and associated proteins comprise a conserved pathway for silencing transposons in metazoan germlines. piRNA pathway components are also expressed in multipotent somatic stem cells in various organisms. piRNA functions have been extensively explored in bilaterian model systems, however, comprehensive studies in non-bilaterian phyla remain limited. Here we investigate the piRNA pathway during the development of <i>Nematostella vectensis</i>, a well-established model system belonging to Cnidaria, the sister group to Bilateria. To date, no population of somatic stem cells has been identified in this organism, despite its long life-span and regenerative capacities that require a constant cell-renewal. We show that <i>Nematostella</i> piRNA pathway components are broadly expressed in early developmental stages, while piRNAs themselves show differential expression, suggesting specific developmental roles of distinct piRNA families. In adults, piRNA associated proteins are enriched in the germline but also expressed in somatic cells, indicating putative stem cell properties. Furthermore, we provide experimental evidence that <i>Nematostella</i> piRNAs cleave transposable elements as well as protein-coding genes. Our results demonstrate that somatic expression of piRNA associated proteins as well as the roles of piRNAs in transposon repression and gene regulation are likely ancestral features that evolved before the split between Cnidaria and Bilateria.
DOI: 10.6084/m9.figshare.5281900.v2
title: Streptococcus pneumoniae serotype 19A: worldwide epidemiology

description: <b>Introduction</b>: <i>Streptococcus pneumoniae</i> causes mucosal and invasive diseases with high morbidity and mortality. Introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) into routine infant immunization programs worldwide resulted in serotype 19A becoming a leading cause of the remaining pneumococcal disease burden in vaccinated and nonvaccinated individuals. This article reviews the impact of the latest generation PCVs (10-valent PCV, PCV10, and 13-valent PCV, PCV13) on serotype 19A. <b>Areas covered</b>: This article covers immune responses elicited by PCV7, PCV10 and PCV13 against serotype 19A and their impact on nasopharyngeal (NP) carriage and disease in vaccinated and unvaccinated populations using data from surveillance systems, randomized controlled trials, and observational studies. <b>Expert commentary</b>: As expected from a PCV containing serotype 19A, PCV13 elicits significantly higher functional immune responses against serotype 19A than PCV7 and PCV10. Higher responses are likely to be linked to both direct impact in vaccinated populations and reductions in 19A NP carriage in children, thus inducing herd protection and reducing 19A invasive pneumococcal disease (IPD) in nonvaccinated children and adults. In contrast, PCV7 and PCV10 have shown mixed evidence of direct short-lived cross-protection and little to no impact on 19A carriage, resulting in continued transmission and disease.
DOI: 10.6084/m9.figshare.5281831
title: Glutathione oxidation in response to intracellular H<sub>2</sub>O<sub>2</sub>: Key but overlapping roles for dehydroascorbate reductases

description: Glutathione is a pivotal molecule in oxidative stress, during which it is potentially oxidized by several pathways linked to H<sub>2</sub>O<sub>2</sub> detoxification. We have investigated the response and functional importance of 3 potential routes for glutathione oxidation pathways mediated by glutathione S-transferases (GST), glutaredoxin-dependent peroxiredoxins (PRXII), and dehydroascorbate reductases (DHAR) in Arabidopsis during oxidative stress. Loss-of-function <i>gstU8, gstU24, gstF8, prxIIE</i> and <i>prxIIF</i> mutants as well as double <i>gstU8 gstU24, gstU8 gstF8, gstU24 gstF8, prxIIE prxIIF</i> mutants were obtained. No mutant lines showed marked changes in their phenotype and glutathione profiles in comparison to the wild-type plants in either optimal conditions or oxidative stress triggered by catalase inhibition. By contrast, multiple loss of DHAR functions markedly decreased glutathione oxidation triggered by catalase deficiency. To assess whether this effect was mediated directly by loss of DHAR enzyme activity, or more indirectly by upregulation of other enzymes involved in glutathione and ascorbate recycling, we measured expression of glutathione reductase (GR) and expression and activity of monodehydroascorbate reductases (MDHAR). No evidence was obtained that either GRs or MDHARs were upregulated in plants lacking DHAR function. Hence, interplay between different DHARs appears to be necessary to couple ascorbate and glutathione pools and to allow glutathione-related signaling during enhanced H<sub>2</sub>O<sub>2</sub> metabolism.
DOI: 10.6084/m9.figshare.5281870.v1
title: Characterization of the piRNA pathway during development of the sea anemone <i>Nematostella vectensis</i>

description: PIWI-interacting RNAs (piRNAs) and associated proteins comprise a conserved pathway for silencing transposons in metazoan germlines. piRNA pathway components are also expressed in multipotent somatic stem cells in various organisms. piRNA functions have been extensively explored in bilaterian model systems, however, comprehensive studies in non-bilaterian phyla remain limited. Here we investigate the piRNA pathway during the development of <i>Nematostella vectensis</i>, a well-established model system belonging to Cnidaria, the sister group to Bilateria. To date, no population of somatic stem cells has been identified in this organism, despite its long life-span and regenerative capacities that require a constant cell-renewal. We show that <i>Nematostella</i> piRNA pathway components are broadly expressed in early developmental stages, while piRNAs themselves show differential expression, suggesting specific developmental roles of distinct piRNA families. In adults, piRNA associated proteins are enriched in the germline but also expressed in somatic cells, indicating putative stem cell properties. Furthermore, we provide experimental evidence that <i>Nematostella</i> piRNAs cleave transposable elements as well as protein-coding genes. Our results demonstrate that somatic expression of piRNA associated proteins as well as the roles of piRNAs in transposon repression and gene regulation are likely ancestral features that evolved before the split between Cnidaria and Bilateria.
DOI: 10.6084/m9.figshare.5281831.v2
title: Glutathione oxidation in response to intracellular H<sub>2</sub>O<sub>2</sub>: Key but overlapping roles for dehydroascorbate reductases

description: Glutathione is a pivotal molecule in oxidative stress, during which it is potentially oxidized by several pathways linked to H<sub>2</sub>O<sub>2</sub> detoxification. We have investigated the response and functional importance of 3 potential routes for glutathione oxidation pathways mediated by glutathione S-transferases (GST), glutaredoxin-dependent peroxiredoxins (PRXII), and dehydroascorbate reductases (DHAR) in Arabidopsis during oxidative stress. Loss-of-function <i>gstU8, gstU24, gstF8, prxIIE</i> and <i>prxIIF</i> mutants as well as double <i>gstU8 gstU24, gstU8 gstF8, gstU24 gstF8, prxIIE prxIIF</i> mutants were obtained. No mutant lines showed marked changes in their phenotype and glutathione profiles in comparison to the wild-type plants in either optimal conditions or oxidative stress triggered by catalase inhibition. By contrast, multiple loss of DHAR functions markedly decreased glutathione oxidation triggered by catalase deficiency. To assess whether this effect was mediated directly by loss of DHAR enzyme activity, or more indirectly by upregulation of other enzymes involved in glutathione and ascorbate recycling, we measured expression of glutathione reductase (GR) and expression and activity of monodehydroascorbate reductases (MDHAR). No evidence was obtained that either GRs or MDHARs were upregulated in plants lacking DHAR function. Hence, interplay between different DHARs appears to be necessary to couple ascorbate and glutathione pools and to allow glutathione-related signaling during enhanced H<sub>2</sub>O<sub>2</sub> metabolism.