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Bayesian probability

Ethan O Romero-Severson, Ingo Bulla, Nick Hengartner, Inês Bártolo, Ana Abecasis, José M Azevedo-Pereira, Nuno Taveira, Thomas Leitner
Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods and the reconstruction of epidemiologic histories. To infer who-infected-whom and to compute the probability of alternative transmission scenarios, while explicitly taking phylogenetic uncertainty into account, we created an Approximate Bayesian Computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity...
September 14, 2017: Genetics
Brett K Hayes, Jeremy Ngo, Guy E Hawkins, Ben R Newell
Three studies reexamined the claim that clarifying the causal origin of key statistics can increase normative performance on Bayesian problems involving judgment under uncertainty. Experiments 1 and 2 found that causal explanation did not increase the rate of normative solutions. However, certain types of causal explanation did lead to a reduction in the magnitude of errors in probability estimation. This effect was most pronounced when problem statistics were expressed in percentage formats. Experiment 3 used process-tracing methods to examine the impact of causal explanation of false positives on solution strategies...
September 13, 2017: Memory & Cognition
G T Fosgate, B Motimele, A Ganswindt, P C Irons
Accurate diagnosis of pregnancy is an essential component of an effective reproductive management plan for dairy cattle. Indirect methods of pregnancy detection can be performed soon after breeding and offer an advantage over traditional direct methods in not requiring an experienced veterinarian and having potential for automation. The objective of this study was to estimate the sensitivity and specificity of pregnancy-associated glycoprotein (PAG) detection ELISA and transrectal ultrasound (TRUS) in dairy cows of South Africa using a Bayesian latent class approach...
September 15, 2017: Preventive Veterinary Medicine
Francesco Bartolucci, Alessio Farcomeni, Luisa Scaccia
We propose a nonparametric item response theory model for dichotomously-scored items in a Bayesian framework. The model is based on a latent class (LC) formulation, and it is multidimensional, with dimensions corresponding to a partition of the items in homogenous groups that are specified on the basis of inequality constraints among the conditional success probabilities given the latent class. Moreover, an innovative system of prior distributions is proposed following the encompassing approach, in which the largest model is the unconstrained LC model...
September 12, 2017: Psychometrika
Weitao Chen, Zaixuan Zhong, Wei Dai, Qi Fan, Shunping He
BACKGROUND: Species with broad distributions frequently divide into multiple genetic forms and may therefore be viewed as "cryptic species". Here, we used the mitochondrial cytochrome b (Cytb) and 12 nuclear DNA loci to investigate phylogeographic structures of the sharpbelly (Hemiculter leucisculus) in rivers in southern China and explored how the geological and climatic factors have shaped the genetic diversity and evolutionary history of this species. RESULTS: Our mitochondrial phylogenetic analysis identified three major lineages (lineages A, B, and C)...
September 12, 2017: BMC Evolutionary Biology
Diego Ortega-Del Vecchyo, Daniel Piñero, Lev Jardón-Barbolla, Joost van Heerwaarden
BACKGROUND: Homoplasy affects demographic inference estimates. This effect has been recognized and corrective methods have been developed. However, no studies so far have defined what homoplasy metrics best describe the effects on demographic inference, or have attempted to estimate such metrics in real data. Here we study how homoplasy in chloroplast microsatellites (cpSSR) affects inference of population expansion time. cpSSRs are popular markers for inferring historical demography in plants due to their high mutation rate and limited recombination...
September 11, 2017: BMC Evolutionary Biology
Conor G McAloon, Michael L Doherty, Paul Whyte, Simon J More, Luke O'Grady, Lorna Citer, Martin J Green
Control of paratuberculosis is challenging due to the relatively poor performance of diagnostic tests, a prolonged incubation period, and protracted environmental survival. Prioritization of herd-level interventions is not possible because putative risk factors are often not supported by risk factor studies. The objective for this study was to investigate the relative importance of risk factors for an increased probability of herd paratuberculosis infection. Risk assessment data, comprehensive animal purchase history, and diagnostic test data were available for 936 Irish dairy herds...
September 6, 2017: Journal of Dairy Science
Daniel J Friedman, Sana M Al-Khatib, Emily P Zeitler, JooYoon Han, Gust H Bardy, Jeanne E Poole, J Thomas Bigger, Alfred E Buxton, Arthur J Moss, Kerry L Lee, Richard Steinman, Paul Dorian, Riccardo Cappato, Alan H Kadish, Peter J Kudenchuk, Daniel B Mark, Lurdes Y T Inoue, Gillian D Sanders
BACKGROUND: Primary prevention implantable cardioverter defibrillator (ICD) reduce all-cause mortality by reducing sudden cardiac death. There are conflicting data regarding whether patients with more advanced heart failure derive ICD benefit owing to the competing risk of nonsudden death. METHODS: We performed a patient-level meta-analysis of New York Heart Association (NYHA) class II/III heart failure patients (left ventricular ejection fraction ≤35%) from 4 primary prevention ICD trials (MADIT-I, MADIT-II, DEFINITE, SCD-HeFT)...
September 2017: American Heart Journal
Caitlyn Meinzer, Renee Martin, Jose I Suarez
BACKGROUND: In phase II trials, the most efficacious dose is usually not known. Moreover, given limited resources, it is difficult to robustly identify a dose while also testing for a signal of efficacy that would support a phase III trial. Recent designs have sought to be more efficient by exploring multiple doses through the use of adaptive strategies. However, the added flexibility may potentially increase the risk of making incorrect assumptions and reduce the total amount of information available across the dose range as a function of imbalanced sample size...
September 8, 2017: Trials
Billy Amzal, Shuai Fu, Jie Meng, Johanna Lister, Helene Karcher
BACKGROUND: Relative effect of therapies indicated for the treatment of advanced renal cell carcinoma (aRCC) after failure of first line treatment is currently not known. The objective of the present study is to evaluate progression-free survival (PFS) and overall survival (OS) of cabozantinib compared to everolimus, nivolumab, axitinib, sorafenib, and best supportive care (BSC) in aRCC patients who progressed after previous VEGFR tyrosine-kinase inhibitor (TKI) treatment. METHODOLOGY & FINDINGS: Systematic literature search identified 5 studies for inclusion in this analysis...
2017: PloS One
Hu Li, John M Leavengood, Eric G Chapman, Daniel Burkhardt, Fan Song, Pei Jiang, Jinpeng Liu, Xuguo Zhou, Wanzhi Cai
Hemiptera, the largest non-holometabolous order of insects, represents approximately 7% of metazoan diversity. With extraordinary life histories and highly specialized morphological adaptations, hemipterans have exploited diverse habitats and food sources through approximately 300 Myr of evolution. To elucidate the phylogeny and evolutionary history of Hemiptera, we carried out the most comprehensive mitogenomics analysis on the richest taxon sampling to date covering all the suborders and infraorders, including 34 newly sequenced and 94 published mitogenomes...
September 13, 2017: Proceedings. Biological Sciences
Long-Long Cong, Zhi-Qiang Cai, Peng Guo, Chen Chen, De-Chun Liu, Wen-Zhi Li, Lin Wang, Yaling Zhao, Shu-Bin Si, Zhi-Min Geng
BACKGROUND AND OBJECTIVES: To determine whether radical resection can benefit patients with advanced gallbladder adenocarcinoma using a Bayesian network (BN) with clinical data. METHODS: In total, 362 patients who had undergone surgical treatment of gallbladder adenocarcinoma at a tertiary institute were evaluated to establish two BN models using a tree-augmented naïve Bayes algorithm. We then chose 250 patients with T3-4N0-2M0 stage gallbladder adenocarcinoma to test the posterior probability after the surgical type was taken into account...
September 6, 2017: Journal of Surgical Oncology
Remco Bouckaert, Brenna C Simons, Henrik Krarup, T Max Friesen, Carla Osiowy
BACKGROUND: Indigenous populations of the circumpolar Arctic are considered to be endemically infected (>2% prevalence) with hepatitis B virus (HBV), with subgenotype B5 (formerly B6) unique to these populations. The distinctive properties of HBV/B5, including high nucleotide diversity yet no significant liver disease, suggest virus adaptation through long-term host-pathogen association. METHODS: To investigate the origin and evolutionary spread of HBV/B5 into the circumpolar Arctic, fifty-seven partial and full genome sequences from Alaska, Canada and Greenland, having known location and sampling dates spanning 40 years, were phylogeographically investigated by Bayesian analysis (BEAST 2) using a reversible-jump-based substitution model and a clock rate estimated at 4...
2017: PeerJ
Arthur Jochems, Timo M Deist, Issam El Naqa, Marc Kessler, Chuck Mayo, Jackson Reeves, Shruti Jolly, Martha Matuszak, Randall Ten Haken, Johan van Soest, Cary Oberije, Corinne Faivre-Finn, Gareth Price, Dirk de Ruysscher, Philippe Lambin, Andre Dekker
PURPOSE: Tools for survival prediction for non-small cell lung cancer (NSCLC) patients treated with chemoradiation or radiation therapy are of limited quality. In this work, we developed a predictive model of survival at 2 years. The model is based on a large volume of historical patient data and serves as a proof of concept to demonstrate the distributed learning approach. METHODS AND MATERIALS: Clinical data from 698 lung cancer patients, treated with curative intent with chemoradiation or radiation therapy alone, were collected and stored at 2 different cancer institutes (559 patients at Maastro clinic (Netherlands) and 139 at Michigan university [United States])...
October 1, 2017: International Journal of Radiation Oncology, Biology, Physics
Joe Collis, Michael R Hill, James R Nicol, Philip J Paine, Jonathan A Coulter
We propose a Bayesian hierarchical model applicable to the calibration of the linear-quadratic model of radiation dose-response. Experimental data used in model calibration were taken from a clonogenic survival assay conducted on human breast cancer cells (MDA-MB-231) across a range of radiation doses (0-6Gy). Employing Markov-chain Monte Carlo methods, we calibrated the proposed Bayesian hierarchical model, computed posterior distributions for the model parameters and survival fraction dose-response probability densities...
September 1, 2017: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
Mariana Gómez-Schiavon, Liang-Fu Chen, Anne E West, Nicolas E Buchler
Single-molecule RNA fluorescence in situ hybridization (smFISH) provides unparalleled resolution in the measurement of the abundance and localization of nascent and mature RNA transcripts in fixed, single cells. We developed a computational pipeline (BayFish) to infer the kinetic parameters of gene expression from smFISH data at multiple time points after gene induction. Given an underlying model of gene expression, BayFish uses a Monte Carlo method to estimate the Bayesian posterior probability of the model parameters and quantify the parameter uncertainty given the observed smFISH data...
September 4, 2017: Genome Biology
Yash Pershad, Siddharth Govindan, Amy K Hara, Mitesh J Borad, Tanios Bekaii-Saab, Alex Wallace, Hassan Albadawi, Rahmi Oklu
Genotype, particularly Ras status, greatly affects prognosis and treatment of liver metastasis in colon cancer patients. This pilot aimed to apply word frequency analysis and a naive Bayes classifier on radiology reports to extract distinguishing imaging descriptors of wild-type colon cancer patients and those with v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations. In this institutional-review-board-approved study, we compiled a SNaPshot mutation analysis dataset from 457 colon adenocarcinoma patients...
September 2, 2017: Diagnostics
Mourad Tighiouart, Galen Cook- Wiens, André Rogatko
We present a Bayesian adaptive design for dose finding in cancer phase I clinical trials. The goal is to estimate the maximum tolerated dose (MTD) after possible modification of the dose range during the trial. Parametric models are used to describe the relationship between the dose and the probability of dose limiting toxicity (DLT). We investigate model reparameterization in terms of the probabilities of DLT at the minimum and maximum available doses at the start of the trial. Trial design proceeds using escalation with overdose control (EWOC), where at each stage of the trial, we seek the dose of the agent such that the posterior probability of exceeding the MTD of this agent is bounded by a feasibility bound...
August 31, 2017: Journal of Biopharmaceutical Statistics
Peter Vďačný, Ľubomír Rajter, Shahed Uddin Ahmed Shazib, Seok Won Jang, Mann Kyoon Shin
Ciliates are a suitable microbial model to investigate trait-dependent diversification because of their comparatively complex morphology and high diversity. We examined the impact of seven intrinsic traits on speciation, extinction, and net-diversification of rhynchostomatians, a group of comparatively large, predatory ciliates with proboscis carrying a dorsal brush (sensoric structure) and toxicysts (organelles used to kill the prey). Bayesian estimates under the binary-state speciation and extinction model indicate that two types of extrusomes and two-rowed dorsal brush raise diversification through decreasing extinction...
August 30, 2017: Scientific Reports
Chengcheng Xu, Jie Bao, Pan Liu, Wei Wang
This study aimed to investigate the contributing factors to serious casualty crashes in China. Crashes with deaths greater than 10 people are defined as serious casualty crashes in China. The serious casualty crash data were collected from 2009 to 2014. The random forest analysis was first conducted to select the candidate variables that affect the risks of serious casualty crashes. The Bayesian random parameters accelerated failure time (AFT) model was then developed to link the probability of the serious casualty crash with road geometric conditions, pavement conditions, environmental characteristics, collision characteristics, vehicle conditions, and driver characteristics...
August 30, 2017: International Journal of Injury Control and Safety Promotion
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