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Bayesian probability

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https://www.readbyqxmd.com/read/28340274/regularized-quantile-regression-applied-to-genome-enabled-prediction-of-quantitative-traits
#1
M Nascimento, F F E Silva, M D V de Resende, C D Cruz, A C C Nascimento, J M S Viana, C F Azevedo, L M A Barroso
Genomic selection (GS) is a variant of marker-assisted selection, in which genetic markers covering the whole genome predict individual genetic merits for breeding. GS increases the accuracy of breeding values (BV) prediction. Although a variety of statistical models have been proposed to estimate BV in GS, few methodologies have examined statistical challenges based on non-normal phenotypic distributions, e.g., skewed distributions. Traditional GS models estimate changes in the phenotype distribution mean, i...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28338960/organellar-genomes-from-a-%C3%A2-5-000-years-old-archaeological-maize-sample-are-closely-related-to-nb-genotype
#2
Bernardo Pérez-Zamorano, Miguel Vallebueno-Estrada, Javier Martínez González, Angel García Cook, Rafael Montiel, Jean-Philippe Vielle-Calzada, Luis Delaye
The story of how pre-Columbian civilizations developed goes hand-in-hand with the process of plant domestication by Mesoamerican inhabitants. Here we present the almost complete sequence of a mitochondrial genome and a partial chloroplast genome from an archaeological maize sample collected at the Valley of Tehuacán, México. Accelerator mass spectrometry dated the maize sample to be 5,040 to 5,300 years before present (95% probability). Phylogenetic analysis of the mitochondrial genome shows that the archaeological sample branches basal to the other Zea mays genomes, as expected...
March 17, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28334098/untangling-the-reticulate-history-of-species-complexes-and-horticultural-breeds-in-abelia-caprifoliaceae
#3
Sven Landrein, Sven Buerki, Hua-Feng Wang, James J Clarkson
Background and Aims: The genetic and morphological consequences of natural selection and selective breeding are explored in the genus Abelia . The genus consists of ornamental shrubs endemic to China, which have been bred to create attractive and diverse cultivars. Methods: DNA fingerprinting (AFLP) and DNA sequence data are used to investigate the genetic diversity among 46 accessions of Abelia (22 natural taxa and 24 horticultural breeds). In the cultivated varieties these data are used to explore taxon boundaries, hybridisation and backcrossing...
February 20, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28333493/bayesian-approaches-to-autism-towards-volatility-action-and-behavior
#4
Colin J Palmer, Rebecca P Lawson, Jakob Hohwy
Autism spectrum disorder currently lacks an explanation that bridges cognitive, computational, and neural domains. In the past 5 years, progress has been sought in this area by drawing on Bayesian probability theory to describe both social and nonsocial aspects of autism in terms of systematic differences in the processing of sensory information in the brain. The present article begins by synthesizing the existing literature in this regard, including an introduction to the topic for unfamiliar readers. The key proposal is that autism is characterized by a greater weighting of sensory information in updating probabilistic representations of the environment...
March 23, 2017: Psychological Bulletin
https://www.readbyqxmd.com/read/28328145/short-range-dispersal-maintains-a-volatile-marine-metapopulation-the-brown-alga-postelsia-palmaeformis
#5
Robert T Paine, Eric R Buhle, Simon A Levin, Peter Kareiva
The annual brown alga Postelsia palmaeformis is dependent for its survival on short-distance dispersal (SDD) where it is already established, as well as occasional long-distance colonization of novel sites. To quantify SDD, we transplanted Postelsia to sites lacking established plants within ≥10 m. The spatial distribution of the first naturally produced sporophyte generation was used to fit dispersal kernels in a hierarchical Bayesian framework. Mean dispersal distance within a year ranged from 0.16 to 0...
March 22, 2017: Ecology
https://www.readbyqxmd.com/read/28327290/bayesian-brains-without-probabilities
#6
REVIEW
Adam N Sanborn, Nick Chater
Bayesian explanations have swept through cognitive science over the past two decades, from intuitive physics and causal learning, to perception, motor control and language. Yet people flounder with even the simplest probability questions. What explains this apparent paradox? How can a supposedly Bayesian brain reason so poorly with probabilities? In this paper, we propose a direct and perhaps unexpected answer: that Bayesian brains need not represent or calculate probabilities at all and are, indeed, poorly adapted to do so...
December 2016: Trends in Cognitive Sciences
https://www.readbyqxmd.com/read/28326596/systematic-review-with-network-meta-analysis-comparative-efficacy-and-tolerability-of-different-intravenous-iron-formulations-for-the-treatment-of-iron-deficiency-anaemia-in-patients-with-inflammatory-bowel-disease
#7
REVIEW
A Aksan, H Işık, H H Radeke, A Dignass, J Stein
BACKGROUND: Iron deficiency anaemia (IDA) is a common complication of inflammatory bowel disease (IBD) associated with reduced quality of life and increased hospitalisation rates. While the best way of treating IDA in IBD patients is not clearly established, current European guidelines recommend intravenous iron therapy in IBD patients with severe anaemia or intolerance to oral iron compounds. AIM: To compare the efficacy and tolerability of different intravenous iron formulations used to treat IDA in IBD patients in a systematic review and Bayesian network meta-analysis (NMA), PROSPERO registration number: 42016046565...
March 21, 2017: Alimentary Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28324148/comparative-efficacy-and-tolerability-of-sarilumab-150-and-200%C3%A2-mg-in-patients-with-active-rheumatoid-arthritis-a%C3%A2-bayesian-network-meta-analysis-of-randomized-controlled-trials
#8
S-C Bae, Y H Lee
OBJECTIVE: This study aimed to assess the relative efficacy and tolerability of every other week (q2w) dosing of sarilumab 150 and 200 mg in patients with active rheumatoid arthritis (RA). METHODS: In this network meta-analysis, randomized controlled trials (RCTs) examining the efficacy and tolerability of sarilumab in patients with active RA were included. A Bayesian network meta-analysis was conducted to combine the direct and indirect evidence from the RCTs...
March 21, 2017: Zeitschrift Für Rheumatologie
https://www.readbyqxmd.com/read/28323512/evaluating-the-costs-of-glycemic-response-with-canagliflozin-versus-dapagliflozin-and-empagliflozin-as-add-on-to-metformin-in-patients-with-type-2-diabetes-mellitus-in-the-united-arab-emirates
#9
Agata Schubert, Anders T Buchholt, Antoine C El Khoury, Ahmed Kamal, Vanessa Taieb
OBJECTIVE: This study evaluates the cost of achieving glycemic control with 3 sodium glucose co-transporter 2 (SGLT2) inhibitors, canagliflozin, dapagliflozin, and empagliflozin, in patients with type 2 diabetes mellitus (T2DM) from the payer perspective in the United Arab Emirates (UAE). METHODS: A systematic literature review identified randomized controlled trials of antihyperglycemic agents as add-on to metformin in patients with T2DM of 26 ± 4 weeks in duration, published by 10 September 2014...
March 21, 2017: Current Medical Research and Opinion
https://www.readbyqxmd.com/read/28320526/assessment-and-risk-modeling-of-airborne-enteric-viruses-emitted-from-wastewater-reused-for-irrigation
#10
D Courault, I Albert, S Perelle, A Fraisse, P Renault, A Salemkour, P Amato
Reclamation of wastewater (WW) for irrigation, after treatment represents a challenge that could alleviate pressure on water resources and address the increasing demand for agriculture. However, the risks to human health must be assessed, particularly those related to human enteric viruses that resist standard treatments in most wastewater treatment plants (WWTP). The risks associated with exposure to viral bioaerosols near WWTP and near agricultural plots irrigated with WW are poorly documented. The objectives of this study were to 1) better characterize human enteric viruses found in bioaerosols near a "standard WWTP" and over fields irrigated with treated WW and 2) propose a numeric model to assess the health risk to populations located close to the irrigated areas, with particular attention to norovirus, which is responsible for most viral gastroenteritis in France...
March 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28320477/risk-prediction-model-for-knee-pain-in-the-nottingham-community-a-bayesian-modelling-approach
#11
G S Fernandes, A Bhattacharya, D F McWilliams, S L Ingham, M Doherty, W Zhang
BACKGROUND: Twenty-five percent of the British population over the age of 50 years experiences knee pain. Knee pain can limit physical ability and cause distress and bears significant socioeconomic costs. The objectives of this study were to develop and validate the first risk prediction model for incident knee pain in the Nottingham community and validate this internally within the Nottingham cohort and externally within the Osteoarthritis Initiative (OAI) cohort. METHODS: A total of 1822 participants from the Nottingham community who were at risk for knee pain were followed for 12 years...
March 20, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28319254/a-bayesian-subgroup-analysis-using-collections-of-anova-models
#12
Jinzhong Liu, Siva Sivaganesan, Purushottam W Laud, Peter Müller
We develop a Bayesian approach to subgroup analysis using ANOVA models with multiple covariates, extending an earlier work. We assume a two-arm clinical trial with normally distributed response variable. We also assume that the covariates for subgroup finding are categorical and are a priori specified, and parsimonious easy-to-interpret subgroups are preferable. We represent the subgroups of interest by a collection of models and use a model selection approach to finding subgroups with heterogeneous effects...
March 20, 2017: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/28318286/asking-better-questions-how-presentation-formats-influence-information-search
#13
Charley M Wu, Björn Meder, Flavia Filimon, Jonathan D Nelson
While the influence of presentation formats have been widely studied in Bayesian reasoning tasks, we present the first systematic investigation of how presentation formats influence information search decisions. Four experiments were conducted across different probabilistic environments, where subjects (N = 2,858) chose between 2 possible search queries, each with binary probabilistic outcomes, with the goal of maximizing classification accuracy. We studied 14 different numerical and visual formats for presenting information about the search environment, constructed across 6 design features that have been prominently related to improvements in Bayesian reasoning accuracy (natural frequencies, posteriors, complement, spatial extent, countability, and part-to-whole information)...
March 20, 2017: Journal of Experimental Psychology. Learning, Memory, and Cognition
https://www.readbyqxmd.com/read/28314157/bayesian-updating-in-a-fault-tree-model-for-shipwreck-risk-assessment
#14
H Landquist, L Rosén, A Lindhe, T Norberg, I-M Hassellöv
Shipwrecks containing oil and other hazardous substances have been deteriorating on the seabeds of the world for many years and are threatening to pollute the marine environment. The status of the wrecks and the potential volume of harmful substances present in the wrecks are affected by a multitude of uncertainties. Each shipwreck poses a unique threat, the nature of which is determined by the structural status of the wreck and possible damage resulting from hazardous activities that could potentially cause a discharge...
March 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28304237/cervical-disc-arthroplasty-with-the-prestige-lp-disc-versus-anterior-cervical-discectomy-and-fusion-at-2-levels-results-of-a-prospective-multicenter-randomized-controlled-clinical-trial-at-24-months
#15
Matthew F Gornet, Todd H Lanman, J Kenneth Burkus, Scott D Hodges, Jeffrey R McConnell, Randall F Dryer, Anne G Copay, Hui Nian, Frank E Harrell
OBJECTIVE The authors compared the efficacy and safety of arthroplasty using the Prestige LP cervical disc with those of anterior cervical discectomy and fusion (ACDF) for the treatment of degenerative disc disease (DDD) at 2 adjacent levels. METHODS Patients from 30 investigational sites were randomized to 1 of 2 groups: investigational patients (209) underwent arthroplasty using a Prestige LP artificial disc, and control patients (188) underwent ACDF with a cortical ring allograft and anterior cervical plate...
March 17, 2017: Journal of Neurosurgery. Spine
https://www.readbyqxmd.com/read/28304219/surgical-or-transcatheter-aortic-valve-replacement-in-intermediate-risk-patients
#16
Michael J Reardon, Nicolas M Van Mieghem, Jeffrey J Popma, Neal S Kleiman, Lars Søndergaard, Mubashir Mumtaz, David H Adams, G Michael Deeb, Brijeshwar Maini, Hemal Gada, Stanley Chetcuti, Thomas Gleason, John Heiser, Rüdiger Lange, William Merhi, Jae K Oh, Peter S Olsen, Nicolo Piazza, Mathew Williams, Stephan Windecker, Steven J Yakubov, Eberhard Grube, Raj Makkar, Joon S Lee, John Conte, Eric Vang, Hang Nguyen, Yanping Chang, Andrew S Mugglin, Patrick W J C Serruys, Arie P Kappetein
Background Although transcatheter aortic-valve replacement (TAVR) is an accepted alternative to surgery in patients with severe aortic stenosis who are at high surgical risk, less is known about comparative outcomes among patients with aortic stenosis who are at intermediate surgical risk. Methods We evaluated the clinical outcomes in intermediate-risk patients with severe, symptomatic aortic stenosis in a randomized trial comparing TAVR (performed with the use of a self-expanding prosthesis) with surgical aortic-valve replacement...
March 17, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28296781/efficacy-and-safety-of-medical-therapy-for-low-bone-mineral-density-in-patients-with-crohn-disease-a-systematic-review-with-network-meta-analysis
#17
Xiaojing Zhao, Changcheng Zhou, Han Chen, Jingjing Ma, Yunjuan Zhu, Peixue Wang, Yi Zhang, Haiqin Ma, Hongjie Zhang
BACKGROUND: Low bone mineral density (BMD) is a frequent complication of inflammatory bowel disease (IBD), particularly in patients with Crohn disease (CD). The aim of our study is to determine the efficacy and safety of different drugs used to treat low BMD in patients with CD. METHODS: PUBMED/MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials were searched for eligible studies. A random-effects model within a Bayesian framework was applied to compare treatment effects as standardized mean difference (SMD) with their corresponding 95% credible interval (CrI), while odds ratio (OR) was applied to compare adverse events with 95% CrI...
March 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28295526/pharmacological-treatments-in-asthma-affected-horses-a-pair-wise-and-network-meta-analysis
#18
L Calzetta, P Roncada, D di Cave, L Bonizzi, A Urbani, E Pistocchini, P Rogliani, M G Matera
BACKGROUND: Equine asthma is a disease characterised by reversible airflow obstruction, bronchial hyperresponsiveness and airway inflammation following exposure of susceptible horses to specific airborne agents. Although clinical remission can be achieved in a low-airborne dust environment, repeated exacerbations may lead to irreversible airway remodelling. The available data on the pharmacotherapy of equine asthma results from several small studies, and no head-to-head clinical trials have been conducted among the available medications...
March 10, 2017: Equine Veterinary Journal
https://www.readbyqxmd.com/read/28289888/value-based-decision-making-battery-a-bayesian-adaptive-approach-to-assess-impulsive-and-risky-behavior
#19
Shakoor Pooseh, Nadine Bernhardt, Alvaro Guevara, Quentin J M Huys, Michael N Smolka
Using simple mathematical models of choice behavior, we present a Bayesian adaptive algorithm to assess measures of impulsive and risky decision making. Practically, these measures are characterized by discounting rates and are used to classify individuals or population groups, to distinguish unhealthy behavior, and to predict developmental courses. However, a constant demand for improved tools to assess these constructs remains unanswered. The algorithm is based on trial-by-trial observations. At each step, a choice is made between immediate (certain) and delayed (risky) options...
March 13, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28289380/variation-in-event-related-potentials-by-state-transitions
#20
Hiroshi Higashi, Tetsuto Minami, Shigeki Nakauchi
The probability of an event's occurrence affects event-related potentials (ERPs) on electroencephalograms. The relation between probability and potentials has been discussed by using a quantity called surprise that represents the self-information that humans receive from the event. Previous studies have estimated surprise based on the probability distribution in a stationary state. Our hypothesis is that state transitions also play an important role in the estimation of surprise. In this study, we compare the effects of surprise on the ERPs based on two models that generate an event sequence: a model of a stationary state and a model with state transitions...
2017: Frontiers in Human Neuroscience
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