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https://www.readbyqxmd.com/read/29040396/survival-analysis-with-time-dependent-covariates-subject-to-missing-data-or-measurement-error-multiple-imputation-for-joint-modeling-mijm
#1
Margarita Moreno-Betancur, John B Carlin, Samuel L Brilleman, Stephanie K Tanamas, Anna Peeters, Rory Wolfe
Modern epidemiological studies collect data on time-varying individual-specific characteristics, such as body mass index and blood pressure. Incorporation of such time-dependent covariates in time-to-event models is of great interest, but raises some challenges. Of specific concern are measurement error, and the non-synchronous updating of covariates across individuals, due for example to missing data. It is well known that in the presence of either of these issues the last observation carried forward (LOCF) approach traditionally used leads to bias...
October 12, 2017: Biostatistics
https://www.readbyqxmd.com/read/29036274/a-robust-df-reml-framework-for-variance-components-estimation-in-genetic-studies
#2
V M Lourenço, P C Rodrigues, A M Pires, H-P Piepho
Motivation: In genetic association studies, linear mixed models (LMMs) are used to test for associations between phenotypes and candidate single nucleotide polymorphisms (SNPs). These same models are also used to estimate heritability, which is central not only to evolutionary biology but also to the prediction of the response to selection in plant and animal breeding, as well as the prediction of disease risk in humans. However, when one or more of the underlying assumptions are violated, the estimation of variance components may be compromised and therefore so may the estimates of heritability and any other functions of these...
July 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036114/stochastic-calculus-analysis-of-optical-time-of-flight-range-imaging-and-estimation-of-radial-motion
#3
Lee Streeter
Time-of-flight range imaging is analyzed using stochastic calculus. Through a series of interpretations and simplifications, the stochastic model leads to two methods for estimating linear radial velocity: maximum likelihood estimation on the transition probability distribution between measurements, and a new method based on analyzing the measured correlation waveform and its first derivative. The methods are tested in a simulated motion experiment from (-40)-(+40)  m/s, with data from a camera imaging an object on a translation stage...
July 1, 2017: Journal of the Optical Society of America. A, Optics, Image Science, and Vision
https://www.readbyqxmd.com/read/29034502/ghost-reduction-in-echo-planar-imaging-by-joint-reconstruction-of-images-and-line-to-line-delays-and-phase-errors
#4
Julianna D Ianni, E Brian Welch, William A Grissom
PURPOSE: To correct line-to-line delays and phase errors in echo-planar imaging (EPI). THEORY AND METHODS: EPI-trajectory auto-corrected image reconstruction (EPI-TrACR) is an iterative maximum-likelihood technique that exploits data redundancy provided by multiple receive coils between nearby lines of k-space to determine and correct line-to-line trajectory delays and phase errors that cause ghosting artifacts. EPI-TrACR was efficiently implemented using a segmented FFT and was applied to in vivo brain data acquired at 7 T across acceleration (1×-4×) and multishot factors (1-4 shots), and in a time series...
October 16, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/29032744/acoustic-simulation-of-cochlear-implant-hearing-effect-of-manipulating-various-acoustic-parameters-on-intelligibility-of-speech
#5
Saransh Jain, Vipin Ghosh P G
OBJECTIVE: Cochlear implants process the acoustic speech signal and convert it into electrical impulses. During this processing, many parameters contribute to speech perception. The available literature reviewed the effect of manipulating one or two such parameters on speech intelligibility, but multiple parameters are seldom manipulated. METHOD: Acoustic parameters, including pulse rate, number of channels, 'n of m', number of electrodes, and channel spacing, were manipulated in acoustic simulations of cochlear implant hearing and 90 different combinations were created...
October 16, 2017: Cochlear Implants International
https://www.readbyqxmd.com/read/29030111/double-blind-proof-of-concept-poc-trial-of-low-field-magnetic-stimulation-lfms-augmentation-of-antidepressant-therapy-in-treatment-resistant-depression-trd
#6
Maurizio Fava, Marlene P Freeman, Martina Flynn, Bettina B Hoeppner, Richard Shelton, Dan V Iosifescu, James W Murrough, David Mischoulon, Cristina Cusin, Mark Rapaport, Boadie W Dunlop, Madhukar H Trivedi, Manish Jha, Gerard Sanacora, Gretchen Hermes, George I Papakostas
BACKGROUND: Low-Field Magnetic Stimulation (LFMS) is a novel, non-invasive, sub-threshold neuromodulation technique, shown in preliminary studies to have immediate mood elevating effects in both unipolar and bipolar depressed patients. OBJECTIVE: We aimed to assess the antidepressant augmentation effects at 48 h of LFMS administered on two consecutive days compared to sham treatment in treatment resistant depression (TRD) subjects, using the Sequential Parallel Comparison Design (SPCD)...
September 23, 2017: Brain Stimulation
https://www.readbyqxmd.com/read/29029338/to-include-or-not-to-include-the-impact-of-gene-filtering-on-species-tree-estimation-methods
#7
Erin K Molloy, Tandy Warnow
With the increasing availability of whole genome data, many species trees are being constructed from hundreds to thousands of loci. Although concatenation analysis using maximum likelihood is a standard approach for estimating species trees, it does not account for gene tree heterogeneity, which can occur due to many biological processes, such as incomplete lineage sorting. Coalescent species tree estimation methods, many of which are statistically consistent in the presence of incomplete lineage sorting, include Bayesian methods that co-estimate the gene trees and the species tree, summary methods that compute the species tree by combining estimated gene trees, and site-based methods that infer the species tree from site patterns in the alignments of different loci...
September 15, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29029264/a-general-model-for-estimating-macroevolutionary-landscapes
#8
Florian C Boucher, Vincent Démery, Elena Conti, Luke J Harmon, Josef Uyeda
The evolution of quantitative characters over long timescales is often studied using stochastic diffusion models. The current toolbox available to students of macroevolution is however limited to two main models: Brownian motion and the Ornstein-Uhlenbeck process, plus some of their extensions. Here we present a very general model for inferring the dynamics of quantitative characters evolving under both random diffusion and deterministic forces of any possible shape and strength, which can accommodate interesting evolutionary scenarios like directional trends, disruptive selection, or macroevolutionary landscapes with multiple peaks...
September 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29027967/cusp-catastrophe-regression-and-its-application-in-public-health-and-behavioral-research
#9
Ding-Geng Chen, Xinguang Chen
The cusp catastrophe model is an innovative approach for investigating a phenomenon that consists of both continuous and discrete changes in one modeling framework. However, its application to empirical health and behavior data has been hindered by the complexity in data-model fit. In this study, we reported our work in the development of a new modeling method-cusp catastrophe regression (RegCusp in short) by casting the cusp catastrophe into a statistical regression. With the RegCusp approach, unbiased model parameters can be estimated with the maximum likelihood estimation method...
October 13, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29027090/morphological-and-molecular-data-for-a-new-species-of-pomphorhynchus-monticelli-1905-acanthocephala-pomphorhynchidae-in-the-mexican-redhorse-moxostoma-austrinum-bean-cypriniformes-catostomidae-in-central-mexico
#10
Martín García-Varela, Berenit Mendoza-Garfias, Anindo Choudhury, Gerardo Pérez-Ponce de León
Pomphorhynchus purhepechus n. sp. is described from the intestine of the Mexican redhorse Moxostoma austrinum Bean (Catostomidae) in central Mexico. The new species can be distinguished from the other seven described species of Pomphorhynchus Monticelli, 1905 in the Americas by a subspherical proboscis and 14 longitudinal rows with 16-18 hooks each; the third and the fourth row of hooks are alternately longest. Sequences of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene and the large subunit (LSU) rDNA (including the domains D2-D3) were used to corroborate the morphological distinction between the new species and Pomphorhynchus bulbocolli Linkins in Van Cleave, 1919, a species widely distributed in several freshwater fish species across Canada, USA, and Mexico...
October 12, 2017: Systematic Parasitology
https://www.readbyqxmd.com/read/29026853/molecular-characterization-and-phylogenetic-congruence-of-hydropsyche-sciligra-tricoptera-hydropsychidae-using-mitochondrial-and-nuclear-markers
#11
Naseh Maleki-Ravasan, Abbas Bahrami, Hassan Vatandoost, Mansoureh Shayeghi, Mona Koosha, Mohammad Ali Oshaghi
BACKGROUND: Caddisflies have significant roles in freshwater ecosystems. Morphological identification is the major impediment in accurate species identification of Hydropsychids. Mitochondrial and nuclear markers are suitable for molecular systematics of these group of arthropods. METHODS: Trichopteran specimens of Lavasan District in northeastern Tehran, Iran were collected in 2012, and described using the morphological and molecular characters of mitochondrial cytochrome c oxidase subunit I (mt-COI) and three expansion fragments of large subunit (LSU) nuclear ribosomal DNA (28S rDNA) D1, D2, and D3...
March 2017: Journal of Arthropod-borne Diseases
https://www.readbyqxmd.com/read/29026168/gene-losses-and-partial-deletion-of-small-single-copy-regions-of-the-chloroplast-genomes-of-two-hemiparasitic-taxillus-species
#12
Ying Li, Jian-Guo Zhou, Xin-Lian Chen, Ying-Xian Cui, Zhi-Chao Xu, Yong-Hua Li, Jing-Yuan Song, Bao-Zhong Duan, Hui Yao
Numerous variations are known to occur in the chloroplast genomes of parasitic plants. We determined the complete chloroplast genome sequences of two hemiparasitic species, Taxillus chinensis and T. sutchuenensis, using Illumina and PacBio sequencing technologies. These species are the first members of the family Loranthaceae to be sequenced. The complete chloroplast genomes of T. chinensis and T. sutchuenensis comprise circular 121,363 and 122,562 bp-long molecules with quadripartite structures, respectively...
October 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29024264/deutetrabenazine-for-tardive-dyskinesia-a-systematic-review-of-the-efficacy-and-safety-profile-for-this-newly-approved-novel-medication-what-is-the-number-needed-to-treat-number-needed-to-harm-and-likelihood-to-be-helped-or-harmed
#13
REVIEW
Leslie Citrome
OBJECTIVE: Deutetrabenazine is a deuterated formulation of tetrabenazine. The aim of this systematic review is to describe the efficacy, tolerability and safety of deutetrabenazine for the treatment of tardive dyskinesia (TD). DATA SOURCES: The pivotal registration trials were accessed by querying http://www.ncbi.nlm.nih.gov/pubmed/ and http://www.clinicaltrials.gov, for the search terms 'deutetrabenazine' OR 'SD-809', and by also querying the EMBASE (Elsevier) commercial database for clinical poster abstracts, and by asking the manufacturer for copies of posters presented at congresses...
October 12, 2017: International Journal of Clinical Practice
https://www.readbyqxmd.com/read/29023970/phenotype-validation-in-electronic-health-records-based-genetic-association-studies
#14
Lu Wang, Scott M Damrauer, Hong Zhang, Alan X Zhang, Rui Xiao, Jason H Moore, Jinbo Chen
The linkage between electronic health records (EHRs) and genotype data makes it plausible to study the genetic susceptibility of a wide range of disease phenotypes. Despite that EHR-derived phenotype data are subjected to misclassification, it has been shown useful for discovering susceptible genes, particularly in the setting of phenome-wide association studies (PheWAS). It is essential to characterize discovered associations using gold standard phenotype data by chart review. In this work, we propose a genotype stratified case-control sampling strategy to select subjects for phenotype validation...
October 11, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/29023547/correction-can-quartet-analyses-combining-maximum-likelihood-estimation-and-hennigian-logic-overcome-long-branch-attraction-in-phylogenomic-sequence-data
#15
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pone.0183393.].
2017: PloS One
https://www.readbyqxmd.com/read/29023077/spermatogenic-and-phylo-molecular-characterizations-of-isolated-fasciola-spp-from-cattle-north-west-iran
#16
Soheila Rouhani, Saber Raeghi, Adel Spotin
BACKGROUND AND OBJECTIVE: Fascioliasis is economically important to the livestock industry that caused with Fasciola hepatica and Fasciola gigantica. The objective of this study was to identify these two species F. hepatica and F. gigantica by using nuclear and mitochondrial markers (ITS1, ND1 and CO1) and have been employed to analyze intraspecific phylogenetic relations of Fasciola spp. MATERIALS AND METHODS: Approximately 150 Fasciola specimens were collected, then stained with haematoxylin-carmine dye and observed under an optical microscope to examine for the existence of sperm...
2017: Pakistan Journal of Biological Sciences: PJBS
https://www.readbyqxmd.com/read/29022730/integration-of-serial-sensory-information-in-haptic-perception-of-softness
#17
Anna Metzger, Alexandra Lezkan, Knut Drewing
Redundant estimates of an environmental property derived simultaneously from different senses or cues are typically integrated according to the maximum likelihood estimation model (MLE): Sensory estimates are weighted according to their reliabilities, maximizing the percept's reliability. Mechanisms underlying the integration of sequentially derived estimates from one sense are less clear. Here we investigate the integration of serially sampled redundant information in softness perception. We developed a method to manipulate haptically perceived softness of silicone rubber stimuli during bare-finger exploration...
October 12, 2017: Journal of Experimental Psychology. Human Perception and Performance
https://www.readbyqxmd.com/read/29022153/practical-considerations-when-analyzing-discrete-survival-times-using-the-grouped-relative-risk-model
#18
Rachel MacKay Altman, Andrew Henrey
The grouped relative risk model (GRRM) is a popular semi-parametric model for analyzing discrete survival time data. The maximum likelihood estimators (MLEs) of the regression coefficients in this model are often asymptotically efficient relative to those based on a more restrictive, parametric model. However, in settings with a small number of sampling units, the usual properties of the MLEs are not assured. In this paper, we discuss computational issues that can arise when fitting a GRRM to small samples, and describe conditions under which the MLEs can be ill-behaved...
October 11, 2017: Lifetime Data Analysis
https://www.readbyqxmd.com/read/29021432/prediction-of-disseminated-intravascular-coagulation-by-liver-function-tests-in-patients-with-japanese-spotted-fever
#19
Yuichi Miyashima, Masaya Iwamuro, Michihiko Shibata, Yoshio Miyabe, Yoshinari Kawai, Masanobu Kaihara, Takehide Mitogawa, Masaru Harada
Objective Cases of Japanese spotted fever (JSF) are sometimes complicated by disseminated intravascular coagulation (DIC) with an abnormal liver function, resulting in unfavorable outcomes. The aim of the present study was to clarify the correlation between liver function test results and DIC scores. Methods Twenty patients diagnosed with JSF between April 2010 and April 2014 were enrolled. Age, gender, disturbance of consciousness, body temperature, pulse rate, presence of diffuse erythema, eschar and swelling of lymph nodes, laboratory test results at the time of initial presentation such as blood cell count, C-reactive protein, liver function, renal function and blood coagulation and fibrinolysis, maximum Japanese Association for Acute Medicine (JAAM) DIC score during the course of JSF, treatment and the prognosis were retrospectively reviewed...
October 11, 2017: Internal Medicine
https://www.readbyqxmd.com/read/29021179/bayesian-and-likelihood-phylogenetic-reconstructions-of-morphological-traits-are-not-discordant-when-taking-uncertainty-into-consideration-a-comment-on-puttick-et%C3%A2-al
#20
Joseph W Brown, Caroline Parins-Fukuchi, Gregory W Stull, Oscar M Vargas, Stephen A Smith
Puttick et al. (2017 Proc. R. Soc. B284, 20162290 (doi:10.1098/rspb.2016.2290)) performed a simulation study to compare accuracy among methods of inferring phylogeny from discrete morphological characters. They report that a Bayesian implementation of the Mk model (Lewis 2001 Syst. Biol.50, 913-925 (doi:10.1080/106351501753462876)) was most accurate (but with low resolution), while a maximum-likelihood (ML) implementation of the same model was least accurate. They conclude by strongly advocating that Bayesian implementations of the Mk model should be the default method of analysis for such data...
October 11, 2017: Proceedings. Biological Sciences
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