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https://www.readbyqxmd.com/read/30118523/parameter-estimation-using-randomized-phases-in-an-integrated-assessment-model-for-antarctic-krill
#1
Douglas Kinzey, George M Watters, Christian S Reiss
An integrated model assessing the status and productivity of Antarctic krill (Euphausia superba, hereafter krill) was configured to estimate different subsets of 118 potentially estimable parameters in alternative configurations. We fixed the parameters that were not estimated in any given configuration at pre-specified values. The model was fitted to over forty years of fisheries and survey data for krill in Subarea 48.1, a statistical reporting area around the Antarctic Peninsula used by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR)...
2018: PloS One
https://www.readbyqxmd.com/read/30118481/a-rad-sequencing-approach-to-genome-wide-marker-discovery-genotyping-and-phylogenetic-inference-in-a-diverse-radiation-of-primates
#2
Lina M Valencia, Amely Martins, Edgardo M Ortiz, Anthony Di Fiore
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods...
2018: PloS One
https://www.readbyqxmd.com/read/30118057/one-symbol-training-receiver-for-the-spad-based-uvlc-system
#3
Chao Wang, Hongyi Yu, Yi-Jun Zhu, Tao Wang, Yawei Ji
For the long distance single photon avalanche diode (SPAD)-based underwater visible light communication (UVLC) system, the multiple-symbol union detection scheme is presented. However, an error floor curve of the bit-to-error ratio (BER) occurs and cannot vanish even though the transmitted power approaches infinity. In this paper, to solve the problems of error floor and channel estimation in the long distance SPAD-based UVLC system, we propose the one training symbol maximum likelihood (ML) detection receiver...
July 10, 2018: Applied Optics
https://www.readbyqxmd.com/read/30115073/time-spent-on-work-related-activities-social-activities-and-time-pressure-as-intermediary-determinants-of-health-disparities-among-elderly-women-and-men-in-5-european-countries-a-structural-equation-model
#4
Nicholas Kofi Adjei, Kenisha Russell Jonsson, Tilman Brand
BACKGROUND: Psychosocial factors shape the health of older adults through complex inter-relating pathways. Besides socioeconomic factors, time use activities may explain gender inequality in self-reported health. This study investigated the role of work-related and social time use activities as determinants of health in old age. Specifically, we analysed whether the impact of stress in terms of time pressure on health mediated the relationship between work-related time use activities (i...
August 16, 2018: International Journal for Equity in Health
https://www.readbyqxmd.com/read/30112825/analysis-of-longitudinal-data-from-outcome-dependent-visit-processes-failure-of-proposed-methods-in-realistic-settings-and-potential-improvements
#5
John M Neuhaus, Charles E McCulloch, Ross D Boylan
The timing and frequency of the measurement of longitudinal outcomes in databases may be associated with the value of the outcome. Such visit processes are termed outcome dependent, and previous work showed that conducting standard analyses that ignore outcome-dependent visit times can produce highly biased estimates of the associations of covariates with outcomes. The literature contains several classes of approaches to analyze longitudinal data subject to outcome-dependent visit times, and all of these are based on simplifying assumptions about the visit process...
August 15, 2018: Statistics in Medicine
https://www.readbyqxmd.com/read/30112806/subgroup-specific-dose-finding-in-phase-i-clinical-trials-based-on-time-to-toxicity-allowing-adaptive-subgroup-combination
#6
Andrew G Chapple, Peter F Thall
A Bayesian design is presented that does precision dose finding based on time to toxicity in a phase I clinical trial with two or more patient subgroups. The design, called Sub-TITE, makes sequentially adaptive subgroup-specific decisions while possibly combining subgroups that have similar estimated dose-toxicity curves. Decisions are based on posterior quantities computed under a logistic regression model for the probability of toxicity within a fixed follow-up period, as a function of dose and subgroup. Similarly to the time-to-event continual reassessment method (TITE-CRM, Cheung and Chappell), the Sub-TITE design downweights each patient's likelihood contribution using a function of follow-up time...
August 15, 2018: Pharmaceutical Statistics
https://www.readbyqxmd.com/read/30110802/fast-bayesian-inference-of-the-multivariate-ornstein-uhlenbeck-process
#7
Rajesh Singh, Dipanjan Ghosh, R Adhikari
The multivariate Ornstein-Uhlenbeck process is used in many branches of science and engineering to describe the regression of a system to its stationary mean. Here we present an O(N) Bayesian method to estimate the drift and diffusion matrices of the process from N discrete observations of a sample path. We use exact likelihoods, expressed in terms of four sufficient statistic matrices, to derive explicit maximum a posteriori parameter estimates and their standard errors. We apply the method to the Brownian harmonic oscillator, a bivariate Ornstein-Uhlenbeck process, to jointly estimate its mass, damping, and stiffness and to provide Bayesian estimates of the correlation functions and power spectral densities...
July 2018: Physical Review. E
https://www.readbyqxmd.com/read/30110663/anchored-phylogenomics-unravels-the-evolution-of-spider-flies-diptera-acroceridae-and-reveals-discordance-between-nucleotides-and-amino-acids
#8
Jessica P Gillung, Shaun L Winterton, Keith M Bayless, Ziad Khouri, Marek L Borowiec, David Yeates, Lynn S Kimsey, Bernhard Misof, Seunggwan Shin, Xin Zhou, Christoph Mayer, Malte Petersen, Brian M Wiegmann
The onset of phylogenomics has contributed to the resolution of numerous challenging evolutionary questions while offering new perspectives regarding biodiversity. However, in some instances, analyses of large genomic datasets can also result in conflicting estimates of phylogeny. Here, we present the first phylogenomic scale study of a dipteran parasitoid family, built upon anchored hybrid enrichment and transcriptomic data of 240 loci of 43 ingroup acrocerid taxa. A new hypothesis for the timing of spider fly evolution is proposed, wielding recent advances in divergence time dating, including the fossilized birth-death process to show that the origin of Acroceridae is younger than previously proposed...
August 12, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/30109720/the-fear-of-needles-a-systematic-review-and-meta-analysis
#9
REVIEW
Jennifer Mclenon, Mary A M Rogers
AIMS: To evaluate the prevalence of needle fear and summarize the characteristics of individuals who exhibit this fear. BACKGROUND: Injections are among the most common medical procedures, yet fear of needles can result in avoidance of preventive measures and treatment. DESIGN: Systematic review and meta-analysis. DATA SOURCES: MEDLINE (1966-2017), Embase (1947-2017), PsycINFO (1967-2017) and CINAHL (1961-2017) were searched, with no restrictions by age, gender, race, language, or country...
August 14, 2018: Journal of Advanced Nursing
https://www.readbyqxmd.com/read/30108576/the-hiv-1-subtype-b-epidemic-in-french-guiana-and-suriname-is-driven-by-ongoing-transmissions-of-pandemic-and-non-pandemic-lineages
#10
Gonzalo Bello, Mathieu Nacher, Flavia Divino, Edith Darcissac, Daiana Mir, Vincent Lacoste
The HIV-1 subtype B epidemic in French Guiana and Suriname is characterized by the co-circulation of the globally disseminated "BPANDEMIC " lineage and of non-pandemic subtype B lineages of Caribbean origin (BCAR ). To reconstruct the spatiotemporal pattern of spread of those viral lineages circulating in these two countries, a total of 361 HIV-1 subtype B pol sequences recovered from treatment-naive adult patients from French Guiana and Suriname between 2006 and 2012 were combined with BPANDEMIC and BCAR reference sequences...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30107512/forecasting-dose-from-unobserved-times-case-study-of-transient-workers-at-a-nuclear-power-plant
#11
Kathryn McNamara, Christopher Peters, Igor Burstyn
Objectives: To evaluate the likelihood of exceeding the occupational exposure limit (OEL) for annual ionizing radiation doses among transient workers at the Hope Creek Nuclear Generating Station, and to propose a method for forecasting exposures among transient workers in general. Methods: We obtained personal dosimeter data from the Hope Creek Nuclear Generating Station for the period of January-December 2014, comprising 1955 monthly dose measurements from 498 transient workers...
August 13, 2018: Annals of Work Exposures and Health
https://www.readbyqxmd.com/read/30107001/robustness-of-individual-differences-in-temporal-interference-effects
#12
Nadine Schlichting, Ritske de Jong, Hedderik van Rijn
Magnitudes or quantities of the different dimensions that define a stimulus (e.g., space, speed or numerosity) influence the perceived duration of that stimulus, a phenomenon known as (temporal) interference effects. This complicates studying the neurobiological foundation of the perception of time, as any signatures of temporal processing are tainted by interfering dimensions. In earlier work, in which judgements on either time or numerosity were made while EEG was recorded, we used Maximum Likelihood Estimation (MLE) to estimate, for each participant separately, the influence of temporal and numerical information on making duration or numerosity judgements...
2018: PloS One
https://www.readbyqxmd.com/read/30104946/might-doctors-really-know-best-utilizing-surgeon-intuition-to-strengthen-preoperative-surgical-risk-assessment
#13
James Kohler, Natalie Glass, Nicolas O Noiseux, John J Callaghan, Benjamin J Miller
Background: Many clinical factors are known to increase an individual patient's risk of perioperative complications and hospital readmission. Several novel risk calculators have been created to predict the risk of postoperative complications for specific procedures that rely entirely on objective measurements. Our goal was to determine if surgeon intuition (an estimate of the percent likelihood of minor and major medical and surgical complications and 30-day readmission) could provide an additional source of data in the preoperative setting that may enhance the prediction of complications after surgery...
2018: Iowa Orthopaedic Journal
https://www.readbyqxmd.com/read/30104261/estimating-genetic-relatedness-in-admixed-populations
#14
Arun Sethuraman
Estimating genetic relatedness, and inbreeding coefficients is important to the fields of quantitative genetics, conservation, genome-wide association studies (GWAS), and population genetics. Traditional estimators of genetic relatedness assume an underlying model of population structure. Each individual is assigned to a population, depending on a priori assumptions about geographical location of sampling, proximity, or genetic similarity. But often, this population assignment is unknown and assumptions about assignment can lead to erroneous estimates of genetic relatedness...
August 13, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/30103662/modeling-clustered-binary-data-with-excess-zero-clusters
#15
John Kwagyan, Victor Apprey
We establish a zero-inflated (random-effects) logistic-Gaussian model for clustered binary data in which members of clusters in one latent class have a zero response with probability one, and members of clusters in a second latent class yield correlated outcomes. Response probabilities in terms of random-effects models are formulated, and maximum marginal likelihood estimation procedures based on Gaussian quadrature are developed. Application to esophageal cancer data in Chinese families is presented.
September 2018: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/30101507/individual-participant-data-meta-analysis-of-continuous-outcomes-a-comparison-of-approaches-for-specifying-and-estimating-one-stage-models
#16
Amardeep Legha, Richard D Riley, Joie Ensor, Kym I E Snell, Tim P Morris, Danielle L Burke
One-stage individual participant data meta-analysis models should account for within-trial clustering, but it is currently debated how to do this. For continuous outcomes modeled using a linear regression framework, two competing approaches are a stratified intercept or a random intercept. The stratified approach involves estimating a separate intercept term for each trial, whereas the random intercept approach assumes that trial intercepts are drawn from a normal distribution. Here, through an extensive simulation study for continuous outcomes, we evaluate the impact of using the stratified and random intercept approaches on statistical properties of the summary treatment effect estimate...
August 13, 2018: Statistics in Medicine
https://www.readbyqxmd.com/read/30101483/bagged-one-to-one-matching-for-efficient-and-robust-treatment-effect-estimation
#17
Lauren R Samuels, Robert A Greevy
Observational studies present challenges due to bias from imbalance in baseline confounders. One-to-one matching (OOM), a popular cohort-construction technique for observational studies, reduces bias and provides a compelling basis for inference but generally leads to at least some loss of efficiency due to the exclusion of potentially informative subjects. We introduce the bagged one-to-one matching (BOOM) estimator, which combines the bias-reducing properties of OOM with the variance-reducing properties of bootstrap aggregation (bagging)...
August 12, 2018: Statistics in Medicine
https://www.readbyqxmd.com/read/30099533/a-maximum-likelihood-approach-to-estimating-the-insertion-frequencies-of-transposable-elements-from-population-sequencing-data
#18
Xiaoqian Jiang, Haixu Tang, Wazim Mohammed Ismail, Michael Lynch
Transposable elements (TEs) contribute to a large fraction of the expansion of many eukaryotic genomes due to the capability of TEs duplicating themselves through transposition. A first step to understanding the roles of TEs in a eukaryotic genome is to characterize the population-wide variation of TE insertions in the species. Here, we present a maximum-likelihood (ML) method for estimating allele frequencies and detecting selection on TE insertions in a diploid population, based on the genotypes at TE insertion sites detected in multiple individuals sampled from the population using paired-end (PE) sequencing reads...
August 7, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/30098031/internal-radiation-dose-estimation-using-multiple-d-shuttle-dosimeters-for-positron-emission-tomography-pet-a-validation-study-using-nema-body-phantom
#19
Islam Md Shahidul, Shoichi Watanuki, Manabu Tashiro, Hiroshi Watabe
PURPOSE: Internal radiation dosimetry plays an important role in ensuring the safe use of positron emission tomography (PET) technology and is a legal requirement in most countries. We propose a new technique to estimate the internal radiation dose in PET studies by means of multiple D-shuttle dosimeters attached on the body surface of the patient. METHODS: Radioactivity in a source organ was estimated iteratively using measurements from multiple D-shuttle dosimeters with a maximum-likelihood expectation-maximization (MLEM) algorithm with dose response from a source to a D-shuttle dosimeter computed by Monte Carlo simulation...
August 11, 2018: Medical Physics
https://www.readbyqxmd.com/read/30096068/transmission-dynamics-among-participants-initiating-anti-retroviral-therapy-upon-diagnosis-of-early-acute-hiv-1-infection-in-thailand
#20
Eugène Kroon, Phuc T Pham, Sunee Sirivichayakul, Rapee Trichavaroj, Donn J Colby, Suteeraporn Pinyakorn, Nittaya Phanuphak, Eric Sanders-Buell, Frits Van Griensven, Gustavo H Kijak, Jerome H Kim, Nelson L Michael, Merlin L Robb, Jintanat Ananworanich, Mark S De Souza, Sodsai Tovanabutra
OBJECTIVE: To assess transmission characteristics in a predominantly men who have sex with men (MSM) cohort initiating anti-retroviral therapy (ART) immediately following diagnosis of acute HIV-1infection (AHI). METHODS: A longitudinal study (2009-2017) was performed in participants with AHI (n = 439) attending a single clinic in Bangkok. Plasma samples obtained prior to ART were used to obtain HIV-1 pol sequences and combined with clinical and epidemiologic data to assess transmission dynamics (cluster formation and size) using phylogenetic analysis...
August 8, 2018: AIDS
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