5,159 research outputs found
Ordinal Probit Functional Regression Models with Application to Computer-Use Behavior in Rhesus Monkeys
Research in functional regression has made great strides in expanding to
non-Gaussian functional outcomes, however the exploration of ordinal functional
outcomes remains limited. Motivated by a study of computer-use behavior in
rhesus macaques (\emph{Macaca mulatta}), we introduce the Ordinal Probit
Functional Regression Model or OPFRM to perform ordinal function-on-scalar
regression. The OPFRM is flexibly formulated to allow for the choice of
different basis functions including penalized B-splines, wavelets, and
O'Sullivan splines. We demonstrate the operating characteristics of the model
in simulation using a variety of underlying covariance patterns showing the
model performs reasonably well in estimation under multiple basis functions. We
also present and compare two approaches for conducting posterior inference
showing that joint credible intervals tend to out perform point-wise credible.
Finally, in application, we determine demographic factors associated with the
monkeys' computer use over the course of a year and provide a brief analysis of
the findings
Model Selection in Variational Mixed Effects Models
Variational inference is an alternative estimation technique for Bayesian
models. Recent work shows that variational methods provide consistent
estimation via efficient, deterministic algorithms. Other tools, such as model
selection using variational AICs (VAIC) have been developed and studied for the
linear regression case. While mixed effects models have enjoyed some study in
the variational context, tools for model selection are lacking. One important
feature of model selection in mixed effects models, particularly longitudinal
models, is the selection of the random effects which in turn determine the
covariance structure for the repeatedly sampled outcome. To address this, we
derive a VAIC specifically for variational mixed effects (VME) models. We also
implement a parameter-efficient VME as part of our study which reduces any
general random effects structure down to a single subject-specific score. This
model accommodates a wide range of random effect structures including random
intercept and slope models as well as random functional effects. Our VAIC can
model and perform selection on a variety of VME models including more classic
longitudinal models as well as longitudinal scalar-on-function regression. As
we demonstrate empirically, our VAIC performs well in discriminating between
correctly and incorrectly specified random effects structures. Finally, we
illustrate the use of VAICs for VMEs on two datasets: a study of lead levels in
children and a study of diffusion tensor imaging
Bayesian Analysis of Multivariate Matched Proportions with Sparse Response
Multivariate matched proportions (MMP) data appears in a variety of contexts
including post-market surveillance of adverse events in pharmaceuticals,
disease classification, and agreement between care providers. It consists of
multiple sets of paired binary measurements taken on the same subject. While
recent work proposes non-Bayesian methods to address the complexities of MMP
data, the issue of sparse response, where no or very few "yes" responses are
recorded for one or more sets, is unaddressed. The presence of sparse response
sets results in underestimates of variance, loss of coverage, and lowered power
in existing methods. Bayesian methods have not previously been considered for
MMP data but provide a useful framework when sparse responses are present. In
particular, the Bayesian probit model provides an elegant solution to the
problem of variance underestimation. We examine three approaches built on that
model: a naive analysis with flat priors, a penalized analysis using
half-Cauchy priors on the mean model variances, and a multivariate analysis
with a Bayesian functional principal component analysis (FPCA) to model the
latent covariance. We show that the multivariate analysis performs well on MMP
data with sparse responses and outperforms existing non-Bayesian methods. In a
re-analysis of data from a study of the system of care (SOC) framework for
children with mental and behavioral disorders, we are able to provide a more
complete picture of the relationships in the data. Our analysis provides
additional insights into the functioning on the SOC that a previous univariate
analysis missed
On Non- and Weakly-Informative Priors for the Conway-Maxwell-Poisson (COM-Poisson) Distribution
Previous Bayesian evaluations of the Conway-Maxwell-Poisson (COM-Poisson)
distribution have little discussion of non- and weakly-informative priors for
the model. While only considering priors with such limited information
restricts potential analyses, these priors serve an important first step in the
modeling process and are useful when performing sensitivity analyses. We
develop and derive several weakly- and non-informative priors using both the
established conjugate prior and Jeffreys' prior. Our evaluation of each prior
involves an empirical study under varying dispersion types and sample sizes. In
general, we find the weakly informative priors tend to perform better than the
non-informative priors. We also consider several data examples for illustration
and provide code for implementation of each resulting posterior
Heads or tails: L1 insertion-associated 5' homopolymeric sequences
<p>Abstract</p> <p>Background</p> <p>L1s are one of the most successful autonomous mobile elements in primate genomes. These elements comprise as much as 17% of primate genomes with the majority of insertions occurring via target primed reverse transcription (TPRT). Twin priming, a variant of TPRT, can result in unusual DNA sequence architecture. These insertions appear to be inverted, truncated L1s flanked by target site duplications.</p> <p>Results</p> <p>We report on loci with sequence architecture consistent with variants of the twin priming mechanism and introduce dual priming, a mechanism that could generate similar sequence characteristics. These insertions take the form of truncated L1s with hallmarks of classical TPRT insertions but having a poly(T) simple repeat at the 5' end of the insertion. We identified loci using computational analyses of the human, chimpanzee, orangutan, rhesus macaque and marmoset genomes. Insertion site characteristics for all putative loci were experimentally verified.</p> <p>Conclusions</p> <p>The 39 loci that passed our computational and experimental screens probably represent inversion-deletion events which resulted in a 5' inverted poly(A) tail. Based on our observations of these loci and their local sequence properties, we conclude that they most probably represent twin priming events with unusually short non-inverted portions. We postulate that dual priming could, theoretically, produce the same patterns. The resulting homopolymeric stretches associated with these insertion events may promote genomic instability and create potential target sites for future retrotransposition events.</p
Variability and Proper Motion of X-ray Knots in the Jet of Centaurus A
Accepted to ApJ, 14 pages, 8 figures, 2 tablesWe report results from Chandra observations analyzed for evidence of variability and proper motion in the X-ray jet of Centaurus A. Using data spanning 15 yr, collective proper motion of 11.3 ± 3.3 mas yr -1 , or 0.68 ± 0.20c, is detected for the fainter X-ray knots and other substructure present within the jet. The three brightest knots (AX1A, AX1C, and BX2) are found to be stationary to an upper limit of . Brightness variations up to 27% are detected for several X-ray knots in the jet. For the fading knots, BX2 and AX1C, the changes in spectral slope expected to accompany synchrotron cooling are not found, ruling it out and placing upper limits of ≃80 μG for each of their magnetic field strengths. Adiabatic expansion can account for the observed decreases in brightness. Constraints on models for the origin of the knots are established. Jet plasma overrunning an obstacle is favored as the generator of stationary knots, while moving knots are likely produced either by internal differences in jet speed or the late stages of jet interaction with nebular or cloud material.Peer reviewe
Stability transitions for axisymmetric relative equilibria of Euclidean symmetric Hamiltonian systems
In the presence of noncompact symmetry, the stability of relative equilibria
under momentum-preserving perturbations does not generally imply robust
stability under momentum-changing perturbations. For axisymmetric relative
equilibria of Hamiltonian systems with Euclidean symmetry, we investigate
different mechanisms of stability: stability by energy-momentum confinement,
KAM, and Nekhoroshev stability, and we explain the transitions between these.
We apply our results to the Kirchhoff model for the motion of an axisymmetric
underwater vehicle, and we numerically study dissipation induced instability of
KAM stable relative equilibria for this system.Comment: Minor revisions. Typographical errors correcte
A comprehensive fate map by intracellular injection of identified blastomeres in the marine polychaete Capitella teleta
<p>Abstract</p> <p>Background</p> <p>The polychaete annelid <it>Capitella teleta </it>(formerly <it>Capitella </it>sp. I) develops by spiral cleavage and has been the focus of several recent developmental studies aided by a fully sequenced genome. Fate mapping in polychaetes has lagged behind other spiralian taxa, because of technical limitations.</p> <p>Results</p> <p>To generate a modern fate map for <it>C. teleta</it>, we injected 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate (DiI) into individual identified blastomeres through fourth-quartet micromere formation. Confocal laser scanning microscopy at single-cell resolution was used to characterize blastomere fates during larval stages. Our results corroborate previous observations from classic studies, and show a number of similarities with other spiralian fate maps, including unique and stereotypic fates for individual blastomeres, presence of four discrete body domains arising from the A, B, C and D cell quadrants, generation of anterior ectoderm from first quartet micromeres, and contributions to trunk ectoderm and ventral nerve cord by the 2d somatoblast. Of particular interest are several instances in which the <it>C. teleta </it>fate map deviates from other spiralian fate maps. For example, we identified four to seven distinct origins of mesoderm, all ectomesodermal. In addition, the left and right mesodermal bands arise from 3d and 3c, respectively, whereas 4d generates a small number of trunk muscle cells, the primordial germ cells and the anus. We identified a complex set of blastomere contributions to the posterior gut in <it>C. teleta</it>, which establishes the most complete map of posterior gut territories to date.</p> <p>Conclusions</p> <p>Our detailed cellular descriptions reveal previously underappreciated complexity in the ontogenetic contributions to several spiralian larval tissues, including the mesoderm, nervous system and gut. The formation of the mesodermal bands by 3c and 3d is in stark contrast to other spiralians, in which 4d generates the mesodermal bands. The results of this study provide a framework for future phylogenetic comparisons and functional analyses of cell-fate specification.</p
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