cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5146357
title: Comparing Objective and Subjective Bayes Factors for the Two-Sample Comparison: The Classification Theorem in Action

description: Many Bayes factors have been proposed for comparing population means in two-sample (independent samples) studies. Recently, Wang and Liu presented an “objective” Bayes factor (BF) as an alternative to a “subjective” one presented by Gönen et al. Their report was evidently intended to show the superiority of their BF based on “undesirable behavior” of the latter. A wonderful aspect of Bayesian models is that they provide an opportunity to “lay all cards on the table.” What distinguishes the various BFs in the two-sample problem is the choice of priors (cards) for the model parameters. This article discusses desiderata of BFs that have been proposed, and proposes a new criterion to compare BFs, no matter whether subjectively or objectively determined. A BF may be preferred if it correctly classifies the data as coming from the correct model most often. The criterion is based on a famous result in classification theory to minimize the total probability of misclassification. This criterion is objective, easily verified by simulation, shows clearly the effects (positive or negative) of assuming particular priors, provides new insights into the appropriateness of BFs in general, and provides a new answer to the question, “Which BF is best?”
DOI: 10.6084/m9.figshare.5146360
title: A Bayesian Survival Analysis of a Historical Dataset: How Long Do Popes Live?

description: University courses in statistical modeling often place great emphasis on methodological theory, illustrating it only briefly by means of limited and repeatedly used standard examples. Unfortunately, this approach often fails to actively engage and motivate students in their learning process. The teaching of statistical topics such as Bayesian survival analysis can be enhanced by focusing on innovative applications. Here, we discuss the visualization and modeling of a dataset of historical events comprising the post-election survival times of popes. Inference, prediction, and model checking are performed in the Bayesian framework, with comparisons being made with the frequentist approach. Further opportunities for similar statistical investigations are outlined. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5146357.v2
title: Comparing Objective and Subjective Bayes Factors for the Two-Sample Comparison: The Classification Theorem in Action

description: Many Bayes factors have been proposed for comparing population means in two-sample (independent samples) studies. Recently, Wang and Liu presented an “objective” Bayes factor (BF) as an alternative to a “subjective” one presented by Gönen et al. Their report was evidently intended to show the superiority of their BF based on “undesirable behavior” of the latter. A wonderful aspect of Bayesian models is that they provide an opportunity to “lay all cards on the table.” What distinguishes the various BFs in the two-sample problem is the choice of priors (cards) for the model parameters. This article discusses desiderata of BFs that have been proposed, and proposes a new criterion to compare BFs, no matter whether subjectively or objectively determined. A BF may be preferred if it correctly classifies the data as coming from the correct model most often. The criterion is based on a famous result in classification theory to minimize the total probability of misclassification. This criterion is objective, easily verified by simulation, shows clearly the effects (positive or negative) of assuming particular priors, provides new insights into the appropriateness of BFs in general, and provides a new answer to the question, “Which BF is best?”
DOI: 10.6084/m9.figshare.5146357.v1
title: Comparing Objective and Subjective Bayes Factors for the Two-Sample Comparison: The Classification Theorem in Action<sup>1</sup>

description: Many Bayes factors have been proposed for comparing population means in two-sample (independent samples) studies. Recently, Wang and Liu (2015) presented an “objective” Bayes factor (BF) as an alternative to a “subjective” one presented by Gönen et al. (2005). Their report was evidently intended to show the superiority of their BF based on “undesirable behavior” of the latter. A wonderful aspect of Bayesian models is that they provide an opportunity to “lay all cards on the table.” What distinguishes the various BFs in the two-sample problem is the choice of priors (cards) for the model parameters. This article discusses desiderata of BFs that have been proposed, and proposes a new criterion to compare BFs, no matter whether subjectively or objectively determined: A BF may be preferred if it correctly classifies the data as coming from the correct model most often. The criterion is based on a famous result in classification theory to minimize the total probability of misclassification. This criterion is objective, easily verified by simulation, shows clearly the effects (positive or negative) of assuming particular priors, provides new insights into the appropriateness of BFs in general, and provides a new answer to the question, “Which BF is best?”
DOI: 10.6084/m9.figshare.5146360.v1
title: A Bayesian Survival Analysis of a Historical Dataset: How Long Do Popes Live?

description: University courses in statistical modeling often place great emphasis on methodological theory, illustrating it only briefly by means of limited and repeatedly used standard examples. Unfortunately, this approach often fails to actively engage and motivate students in their learning process. The teaching of statistical topics such as Bayesian survival analysis can be enhanced by focusing on innovative applications. Here we discuss the visualization and modelling of a data set of historical events comprising the post–election survival times of popes. Inference, prediction and model checking are performed in the Bayesian framework, with comparisons being made with the frequentist approach. Further opportunities for similar statistical investigations are outlined.
DOI: 10.6084/m9.figshare.5146309
title: New draft item

description: Additional analyses for "Mutant Phenotypes for Thousands of Genes of Unknown Function from Diverse Bacteria". See the README.txt file for more explanation.<br><br>
DOI: 10.6084/m9.figshare.5146231
title: TFFluorescence.xls

description: Drosophila melanogaster transcription factor fluorescence measurements at nuclear cycle 14A, timeclass 6, from 35.5% to 92.5% embryo length. Includes Stat92E (dst), Bicoid (bcd), Caudal (cad), Giant (gt), Hunchback (hb), Knirps (kni), Kruppel (Kr), and Tailless (tll).
DOI: 10.6084/m9.figshare.5146309.v1
title: New draft item

description: Additional analyses for "Mutant Phenotypes for Thousands of Genes of Unknown Function from Diverse Bacteria". See the README.txt file for more explanation.<br><br>
DOI: 10.6084/m9.figshare.5146090
title: Puerto Rican Paso Fino GWAS Illumina Equine SNP70 BeadChip

description: GWAS from 24 Puerto Rican Paso Fino horses phenotyped for eye color. Illumina Equine SNP70 BeadChip.
DOI: 10.6084/m9.figshare.5146090.v1
title: Puerto Rican Paso Fino GWAS Illumina Equine SNP70 BeadChip

description: GWAS from 24 Puerto Rican Paso Fino horses phenotyped for eye color. Illumina Equine SNP70 BeadChip.
DOI: 10.6084/m9.figshare.5145826
title: Nucleophagy.cpproj

description: CellProfiler Pipeline for analyzing images
DOI: 10.6084/m9.figshare.5145832
title: SplitTile.ijm

description: ImageJ Macro for splitting tiled images
DOI: 10.6084/m9.figshare.5146096.v1
title: 48-spot smFRET-PAX measurements of dsDNA oligos

description: Measurements used in:<br>48-spot single-molecule FRET setup with periodic acceptor excitation<br>Ingargiola et al., bioRxiv (2017), doi: *to-be-issued*<br><br>Copyright (C) 2017 The Regents of the University of California
DOI: 10.6084/m9.figshare.5145817
title: 40x 0.6NA 2Manual Focus.xml

description: Nikon Microscope file with the coordinates of the 96-well plate, focus parameters, and other capture data.
DOI: 10.6084/m9.figshare.5145826.v1
title: Nucleophagy.cpproj

description: CellProfiler Pipeline for analyzing images
DOI: 10.6084/m9.figshare.5145832.v1
title: SplitTile.ijm

description: ImageJ Macro for splitting tiled images
DOI: 10.6084/m9.figshare.5145058
title: Description of <i>Turritopsoides marhei</i> sp. nov. (Hydrozoa, Anthoathecata) from the Maldives and its phylogenetic position

description: <i>Turritopsoides marhei</i>, a new species of the hydrozoan family Oceaniidae, is described from the Maldives. This species can be distinguished from the only other member of the genus by the presence of more branched colonies, branches not being adnate to pedicels, longer pedicels, larger nematocysts, nematocyst-rich nematophore-like outgrowths from pedicels, smaller male gonophores, and a different geographic distribution. This finding represents the first record of the genus outside the type locality of its type species, in Belize. Molecular phylogenetic analyses show that, as expected, <i>T. marhei</i> belongs to the clade Filifera IV. However, the phylogenetic hypothesis based on both mitochondrial and nuclear DNA sequences reveals that most of the families of this group are polyphyletic, including Oceaniidae, and suggests that the morphological characters used to discriminate among filiferan families need to be revised thoroughly. http://zoobank.org/urn:lsid:zoobank.org:pub:CE901E0D-B125-4A87-BB97-8020C0658B5D
DOI: 10.6084/m9.figshare.5145058.v1
title: Description of <i>Turritopsoides marhei</i> sp. nov. (Hydrozoa, Anthoathecata) from the Maldives and its phylogenetic position

description: <i>Turritopsoides marhei</i>, a new species of the hydrozoan family Oceaniidae, is described from the Maldives. This species can be distinguished from the only other member of the genus by the presence of more branched colonies, branches not being adnate to pedicels, longer pedicels, larger nematocysts, nematocyst-rich nematophore-like outgrowths from pedicels, smaller male gonophores, and a different geographic distribution. This finding represents the first record of the genus outside the type locality of its type species, in Belize. Molecular phylogenetic analyses show that, as expected, <i>T. marhei</i> belongs to the clade Filifera IV. However, the phylogenetic hypothesis based on both mitochondrial and nuclear DNA sequences reveals that most of the families of this group are polyphyletic, including Oceaniidae, and suggests that the morphological characters used to discriminate among filiferan families need to be revised thoroughly. http://zoobank.org/urn:lsid:zoobank.org:pub:CE901E0D-B125-4A87-BB97-8020C0658B5D
DOI: 10.6084/m9.figshare.5145817.v1
title: 40x 0.6NA 2Manual Focus.xml

description: Nikon Microscope file with the coordinates of the 96-well plate, focus parameters, and other capture data.
DOI: 10.6084/m9.figshare.5146096.v2
title: 48-spot smFRET-PAX measurements of dsDNA oligos

description: Measurements used in:<br>48-spot single-molecule FRET setup with periodic acceptor excitation<br>Ingargiola et al., bioRxiv (2017), doi: 10.1101/156182<br><br>Copyright (C) 2017 The Regents of the University of California
DOI: 10.6084/m9.figshare.5145052
title: Final_Dataset_Combined

description: Analysis data in 6 worksheets.
DOI: 10.6084/m9.figshare.5146096.v4
title: 48-spot smFRET-PAX measurements of dsDNA oligos

description: The measurement data files in this repository have been used in the following publications:<br><i>48-spot single-molecule FRET setup with periodic acceptor excitation.</i><br>Ingargiola et al., bioRxiv (2017), doi: https://doi.org/10.1101/156182<br><i>Optical crosstalk in SPAD arrays for high-throughput single-molecule fluorescence spectroscopy.</i> Ingargiola et al., bioRxiv (2017), doi: https://doi.org/10.1101/207118<br><br><br>Copyright (C) 2017 The Regents of the University of California
DOI: 10.6084/m9.figshare.5146096.v3
title: 48-spot smFRET-PAX measurements of dsDNA oligos

description: Measurements used in:<br>48-spot single-molecule FRET setup with periodic acceptor excitation<br>Ingargiola et al., bioRxiv (2017), doi: 10.1101/156182<br><br>Copyright (C) 2017 The Regents of the University of California
DOI: 10.6084/m9.figshare.5144329
title: The cosmopolitan-parochial divide: changing patterns of party and electoral competition in the Netherlands and beyond

description: Recent election outcomes in Europe and beyond reflect a growing scepticism of open borders among the public. From the Brexit vote in the United Kingdom to the election of Donald Trump in the United States, rhetoric that is critical of the organizations facilitating policy co-operation and learning across borders as well as international trade and migration is popular among a growing segment of the electorate. Are these recent developments part of a larger trend of party and electoral change? By focusing on changing patterns in party and electoral competition in the Netherlands, this article suggests that they are. Relying on expert and voter data, it argues that party and electoral politics in the Netherlands are increasingly characterized by both an economic left–right as well as a cosmopolitan–parochial divide. While the former relates to issues of state intervention into the economy, the second refers to stances on European integration, migration and national control in international affairs. This cosmopolitan–parochial divide has become largely independent of the economic left–right dimension, and influences people’s voting decisions independently of their left–right views. Interestingly, the cosmopolitan–parochial divide in the Netherlands should not necessarily be understood as a cultural backlash, but rather seems a reflection of increased economic insecurity. Although the evidence stems from the Dutch case, I suggest that the cosmopolitan–parochial divide is a useful lens through which we can understand political change in Europe more generally.
DOI: 10.6084/m9.figshare.5144320
title: Modeling Heterogeneity in Healthcare Utilization Using Massive Medical Claims Data

description: We introduce a modeling approach for characterizing heterogeneity in healthcare utilization using massive medical claims data. We first translate the medical claims observed for a large study population and across five years into individual-level discrete events of care called <i>utilization sequences</i>. We model the utilization sequences using an exponential proportional hazards mixture model to capture heterogeneous behaviors in patients’ healthcare utilization. The objective is to cluster patients according to their longitudinal utilization behaviors and to determine the main drivers of variation in healthcare utilization while controlling for the demographic, geographic, and health characteristics of the patients. Due to the computational infeasibility of fitting a parametric proportional hazards model for high-dimensional, large-sample size data we use an iterative one-step procedure to estimate the model parameters and impute the cluster membership. The approach is used to draw inferences on utilization behaviors of children in the Medicaid system with persistent asthma across six states. We conclude with policy implications for targeted interventions to improve adherence to recommended care practices for pediatric asthma. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5144329.v1
title: The cosmopolitan-parochial divide: changing patterns of party and electoral competition in the Netherlands and beyond

description: Recent election outcomes in Europe and beyond reflect a growing scepticism of open borders among the public. From the Brexit vote in the United Kingdom to the election of Donald Trump in the United States, rhetoric that is critical of the organizations facilitating policy co-operation and learning across borders as well as international trade and migration is popular among a growing segment of the electorate. Are these recent developments part of a larger trend of party and electoral change? By focusing on changing patterns in party and electoral competition in the Netherlands, this article suggests that they are. Relying on expert and voter data, it argues that party and electoral politics in the Netherlands are increasingly characterized by both an economic left–right as well as a cosmopolitan–parochial divide. While the former relates to issues of state intervention into the economy, the second refers to stances on European integration, migration and national control in international affairs. This cosmopolitan–parochial divide has become largely independent of the economic left–right dimension, and influences people’s voting decisions independently of their left–right views. Interestingly, the cosmopolitan–parochial divide in the Netherlands should not necessarily be understood as a cultural backlash, but rather seems a reflection of increased economic insecurity. Although the evidence stems from the Dutch case, I suggest that the cosmopolitan–parochial divide is a useful lens through which we can understand political change in Europe more generally.
DOI: 10.6084/m9.figshare.5144320.v1
title: Modeling Heterogeneity in Healthcare Utilization Using Massive Medical Claims Data

description: We introduce a modeling approach for characterizing heterogeneity in healthcare utilization using massive medical claims data. We first translate the medical claims observed for a large study population and across five years into individual-level discrete events of care called <i>utilization sequences</i>. We model the utilization sequences using an exponential proportional hazards mixture model to capture heterogeneous behaviors in patients’ healthcare utilization. The objective is to cluster patients according to their longitudinal utilization behaviors and to determine the main drivers of variation in healthcare utilization while controlling for the demographic, geographic, and health characteristics of the patients. Due to the computational infeasibility of fitting a parametric proportional hazards model for high-dimensional, large-sample size data we use an iterative one-step procedure to estimate the model parameters and impute the cluster membership. The approach is used to draw inferences on utilization behaviors of children in the Medicaid system with persistent asthma across six states. We conclude with policy implications for targeted interventions to improve adherence to recommended care practices for pediatric asthma. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5144299
title: Functional Feature Construction for Individualized Treatment Regimes

description: Evidence-based personalized medicine formalizes treatment selection as an individualized treatment regime that maps up-to-date patient information into the space of possible treatments. Available patient information may include static features such race, gender, family history, genetic and genomic information, as well as longitudinal information including the emergence of comorbidities, waxing and waning of symptoms, side-effect burden, and adherence. Dynamic information measured at multiple time points before treatment assignment should be included as input to the treatment regime. However, subject longitudinal measurements are typically sparse, irregularly spaced, noisy, and vary in number across subjects. Existing estimators for treatment regimes require equal information be measured on each subject and thus standard practice is to summarize longitudinal subject information into a scalar, ad hoc summary during data preprocessing. This reduction of the longitudinal information to a scalar feature precedes estimation of a treatment regime and is therefore not informed by subject outcomes, treatments, or covariates. Furthermore, we show that this reduction requires more stringent causal assumptions for consistent estimation than are necessary. We propose a data-driven method for constructing maximally prescriptive yet interpretable features that can be used with standard methods for estimating optimal treatment regimes. In our proposed framework, we treat the subject longitudinal information as a realization of a stochastic process observed with error at discrete time points. Functionals of this latent process are then combined with outcome models to estimate an optimal treatment regime. The proposed methodology requires weaker causal assumptions than <i>Q</i>-learning with an ad hoc scalar summary and is consistent for the optimal treatment regime. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5144308
title: BNP-Seq: Bayesian Nonparametric Differential Expression Analysis of Sequencing Count Data

description: We perform differential expression analysis of high-throughput sequencing count data under a Bayesian nonparametric framework, removing sophisticated ad hoc pre-processing steps commonly required in existing algorithms. We propose to use the gamma (beta) negative binomial process, which takes into account different sequencing depths using sample-specific negative binomial probability (dispersion) parameters, to detect differentially expressed genes by comparing the posterior distributions of gene-specific negative binomial dispersion (probability) parameters. These model parameters are inferred by borrowing statistical strength across both the genes and samples. Extensive experiments on both simulated and real-world RNA sequencing count data show that the proposed differential expression analysis algorithms clearly outperform previously proposed ones in terms of the areas under both the receiver operating characteristic and precision-recall curves. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5144275
title: False Discovery Rate Smoothing

description: We present false discovery rate (FDR) smoothing, an empirical-Bayes method for exploiting spatial structure in large multiple-testing problems. FDR smoothing automatically finds spatially localized regions of significant test statistics. It then relaxes the threshold of statistical significance within these regions, and tightens it elsewhere, in a manner that controls the overall false discovery rate at a given level. This results in increased power and cleaner spatial separation of signals from noise. The approach requires solving a nonstandard high-dimensional optimization problem, for which an efficient augmented-Lagrangian algorithm is presented. In simulation studies, FDR smoothing exhibits state-of-the-art performance at modest computational cost. In particular, it is shown to be far more robust than existing methods for spatially dependent multiple testing. We also apply the method to a dataset from an fMRI experiment on spatial working memory, where it detects patterns that are much more biologically plausible than those detected by standard FDR-controlling methods. All code for FDR smoothing is publicly available in Python and R (<i>https://github.com/tansey/smoothfdr</i>). Supplementary materials for this article are available online.