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Bayesian probability

Shota Takenaka, Hiroyuki Aono
BACKGROUND: Drop foot resulting from degenerative lumbar diseases can impair activities of daily living. Therefore, predictors of recovery of this symptom have been investigated using univariate or/and multivariate analyses. However, the conclusions have been somewhat controversial. Bayesian network models, which are graphic and intuitive to the clinician, may facilitate understanding of the prognosis of drop foot resulting from degenerative lumbar diseases. QUESTIONS/PURPOSES: (1) To show a layered correlation among predictors of recovery from drop foot resulting from degenerative lumbar diseases; and (2) to develop support tools for clinical decisions to treat drop foot resulting from lumbar degenerative diseases...
December 2, 2016: Clinical Orthopaedics and related Research
Marc D Ryser, Walter T Lee, Neal E Ready, Kevin Z Leder, Jasmine Foo
High rates of local recurrence in tobacco-related head and neck squamous cell carcinoma (HNSCC) are commonly attributed to unresected fields of precancerous tissue. Because they are not easily detectable at the time of surgery without additional biopsies, there is a need for noninvasive methods to predict the extent and dynamics of these fields. Here, we developed a spatial stochastic model of tobacco-related HNSCC at the tissue level and calibrated the model using a Bayesian framework and population-level incidence data from the Surveillance, Epidemiology, and End Results (SEER) registry...
October 20, 2016: Cancer Research
Dong Li, Y B Dong, Wei Deng, Z B Shi, B Z Fu, J M Gao, T B Wang, Yan Zhou, Yi Liu, Q W Yang, X R Duan
In this article, a Bayesian tomography method using non-stationary Gaussian process for a prior has been introduced. The Bayesian formalism allows quantities which bear uncertainty to be expressed in the probabilistic form so that the uncertainty of a final solution can be fully resolved from the confidence interval of a posterior probability. Moreover, a consistency check of that solution can be performed by checking whether the misfits between predicted and measured data are reasonably within an assumed data error...
November 2016: Review of Scientific Instruments
Ilias Kappas, Spiros Vittas, Chrysoula N Pantzartzi, Elena Drosopoulou, Zacharias G Scouras
A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data...
2016: PloS One
Alex Dornburg, J Nick Fisk, Jules Tamagnan, Jeffrey P Townsend
BACKGROUND: Analyses of phylogenetic informativeness represent an important step in screening potential or existing datasets for their proclivity toward convergent or parallel evolution of molecular sites. However, while new theory has been developed from which to predict the utility of sequence data, adoption of these advances have been stymied by a lack of software enabling application of advances in theory, especially for large next-generation sequence data sets. Moreover, there are no theoretical barriers to application of the phylogenetic informativeness or the calculation of quartet internode resolution probabilities in a Bayesian setting that more robustly accounts for uncertainty, yet there is no software with which a computationally intensive Bayesian approach to experimental design could be implemented...
December 1, 2016: BMC Evolutionary Biology
L C Magalhães Silva, F Baldi, C Aboujaoude, G C Venturini, L G Albuquerque, M J R Paranhos da Costa
The aim of this study was to estimate genetic parameters for prenatal (PRE) and postnatal (POS) mortality in Nellore cattle. A total of 13 141 (PRE) and 17 818 (POS) records from Nellore females were used. PRE and POS were recorded using binary scale scores: a score of '1' was given to calves that were born alive (PRE) and those that were alive at weaning (POS), and a score of '0' was given to calves that were not alive at or around birth (PRE), as well as to those weighed at birth but not at weaning (POS)...
December 1, 2016: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
Thomas W Blythe, Andrew J Sederman, E Hugh Stitt, Andrew P E York, Lynn F Gladden
Many industrial flow processes are sensitive to changes in the rheological behaviour of process fluids, and there therefore exists a need for methods that provide online, or inline, rheological characterisation necessary for process control and optimisation over timescales of minutes or less. Nuclear magnetic resonance (NMR) offers a non-invasive technique for this application, without limitation on optical opacity. We present a Bayesian analysis approach using pulsed field gradient (PFG) NMR to enable estimation of the rheological parameters of Herschel-Bulkley fluids in a pipe flow geometry, characterised by a flow behaviour index n, yield stress τ0, and consistency factor k, by analysis of the signal in q-space...
November 10, 2016: Journal of Magnetic Resonance
James S Sedinger, Amanda W VanDellen, Alan G Leach, Thomas V Riecke
Lack 18:125-128 (1967) proposed that clutch size in precocial species was regulated by nutrients available to females during breeding. Drent and Daan 68:225-252 (1980) proposed the individual optimization hypothesis, whereby individual state determines the optimal combination of breeding date and clutch size. Neither hypothesis accounts for variation in nutrients among females at the end of egg laying, strong right truncations in clutch size distributions, or the fact that many species with precocial young are determinate layers...
November 28, 2016: Oecologia
Othman Soufan, Wail Ba-Alawi, Moataz Afeef, Magbubah Essack, Panos Kalnis, Vladimir B Bajic
BACKGROUND: Mining high-throughput screening (HTS) assays is key for enhancing decisions in the area of drug repositioning and drug discovery. However, many challenges are encountered in the process of developing suitable and accurate methods for extracting useful information from these assays. Virtual screening and a wide variety of databases, methods and solutions proposed to-date, did not completely overcome these challenges. This study is based on a multi-label classification (MLC) technique for modeling correlations between several HTS assays, meaning that a single prediction represents a subset of assigned correlated labels instead of one label...
2016: Journal of Cheminformatics
Greg A Breed, Emily A Golson, M Tim Tinker
The home-range concept is central in animal ecology and behavior, and numerous mechanistic models have been developed to understand home range formation and maintenance. These mechanistic models usually assume a single, contiguous home range. Here we describe and implement a simple home-range model that can accommodate multiple home-range centers, form complex shapes, allow discontinuities in use patterns, and infer how external and internal variables affect movement and use patterns. The model assumes individuals associate with two or more home-range centers and move among them with some estimable probability...
October 6, 2016: Ecology
Shuai Zhao, Yunhai Tong, Zitian Wang, Shaohua Tan
In the stock market, return reversal occurs when investors sell overbought stocks and buy oversold stocks, reversing the stocks' price trends. In this paper, we develop a new method to identify key drivers of return reversal by incorporating a comprehensive set of factors derived from different economic theories into one unified dynamical Bayesian factor graph. We then use the model to depict factor relationships and their dynamics, from which we make some interesting discoveries about the mechanism behind return reversals...
2016: PloS One
Toon Haer, W J Wouter Botzen, Hans de Moel, Jeroen C J H Aerts
Recent studies showed that climate change and socioeconomic trends are expected to increase flood risks in many regions. However, in these studies, human behavior is commonly assumed to be constant, which neglects interaction and feedback loops between human and environmental systems. This neglect of human adaptation leads to a misrepresentation of flood risk. This article presents an agent-based model that incorporates human decision making in flood risk analysis. In particular, household investments in loss-reducing measures are examined under three economic decision models: (1) expected utility theory, which is the traditional economic model of rational agents; (2) prospect theory, which takes account of bounded rationality; and (3) a prospect theory model, which accounts for changing risk perceptions and social interactions through a process of Bayesian updating...
November 28, 2016: Risk Analysis: An Official Publication of the Society for Risk Analysis
Shinjo Yada, Chikuma Hamada
Treatment during cancer clinical trials sometimes involves the combination of multiple drugs. In addition, in recent years there has been a trend toward phase I/II trials in which a phase I and a phase II trial are combined into a single trial to accelerate drug development. Methods for the seamless combination of phases I and II parts are currently under investigation. In the phase II part, adaptive randomization on the basis of patient efficacy outcomes allocates more patients to the dose combinations considered to have higher efficacy...
November 28, 2016: Pharmaceutical Statistics
F Paternostre, Y P Charles, E A Sauleau, J-P Steib
BACKGROUND: In the normal adult spine, a link between thoracolumbar and cervical sagittal alignment exists, suggesting adaptive cervical positional changes allowing horizontal gaze. In patients with thoracic hyperkyphosis, cervical adaptation to sagittal global alignment might be different from healthy individuals. However, this relationship has not clearly been reported in hyperkyphotic deformity. PURPOSE: The purpose of this study was to identify cervical sagittal alignment types observed on radiographs in young adults with thoracic hyperkyphosis...
November 23, 2016: Orthopaedics & Traumatology, Surgery & Research: OTSR
Weijian Si, Liwei Wang, Zhiyu Qu
The cardinalized probability hypothesis density (CPHD) filter is an alternative approximation to the full multi-target Bayesian filter for tracking multiple targets. However, although the joint propagation of the posterior intensity and cardinality distribution in its recursion allows more reliable estimates of the target number than the PHD filter, the CPHD filter suffers from the spooky effect where there exists arbitrary PHD mass shifting in the presence of missed detections. To address this issue in the Gaussian mixture (GM) implementation of the CPHD filter, this paper presents an improved GM-CPHD filter, which incorporates a weight redistribution scheme into the filtering process to modify the updated weights of the Gaussian components when missed detections occur...
November 23, 2016: Sensors
Laila Cochon, Jeffrey Smith, Amado Alejandro Baez
OBJECTIVE: The objective of our study was to assess the diagnostic quality of low-dose computed tomography (CT) when compared to ultrasound (US) in diagnosis of urolithiasis using STONE score as a predictor of pre-test probability and the Bayesian statistical model to calculate post-test probabilities (POST) for both diagnostic tests. METHODS: STONE score was used to form risk groups to obtain pre-test probabilities. Likelihood ratios (LR) were calculated from external data for low-dose CT and US...
November 25, 2016: Emergency Radiology
Guido Carvajal, David J Roser, Scott A Sisson, Alexandra Keegan, Stuart J Khan
Chlorine disinfection of biologically treated wastewater is practiced in many locations prior to environmental discharge or beneficial reuse. The effectiveness of chlorine disinfection processes may be influenced by several factors, such as pH, temperature, ionic strength, organic carbon concentration, and suspended solids. We investigated the use of Bayesian multilayer perceptron (BMLP) models as efficient and practical tools for compiling and analysing free chlorine and monochloramine virus disinfection performance as a multivariate problem...
November 3, 2016: Water Research
Evan J Livesey, David J Livesey
The Stop Signal Task (SST), a commonly used measure of response inhibition, uses standard psychophysical methods to gain an estimate of the time needed to withhold a prepotent response. Under some circumstances, conventional forms of the SST are impractical to use because of the large number of trials necessary to gain a reliable estimate of the speed of inhibition. Here we applied to the SST an adaptive method for estimating psychometric parameters that can find reliable threshold estimates over a relatively small number of trials...
2016: PloS One
D P Anderson, P McMurtrie, K-A Edge, P W J Baxter, A E Byrom
Successful pest-mammal eradications from remote islands have resulted in important biodiversity benefits. Near-shore islands can also serve as refuges for native biota but require ongoing effort to maintain low-pest or pest-free status. Three management options are available in the presence of reinvasion risk: (1) control-to-zero density, in which immigration may occur but reinvaders are removed; (2) sustained population suppression (to relatively low numbers); or (3) no action. Biodiversity benefits can result from options one and two...
December 2016: Ecological Applications: a Publication of the Ecological Society of America
Luis F Iglesias-Martinez, Walter Kolch, Tapesh Santra
Reconstructing gene regulatory networks (GRNs) from gene expression data is a challenging problem. Existing GRN reconstruction algorithms can be broadly divided into model-free and model-based methods. Typically, model-free methods have high accuracy but are computation intensive whereas model-based methods are fast but less accurate. We propose Bayesian Gene Regulation Model Inference (BGRMI), a model-based method for inferring GRNs from time-course gene expression data. BGRMI uses a Bayesian framework to calculate the probability of different models of GRNs and a heuristic search strategy to scan the model space efficiently...
November 23, 2016: Scientific Reports
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