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https://www.readbyqxmd.com/read/28214700/uncertainty-estimation-by-bayesian-approach-in-thermochemical-conversion-of-walnut-hull-and-lignite-coal-blends
#1
Musa Buyukada
The main purpose of the present study was to incorporate the uncertainties in the thermal behavior of walnut hull (WH), lignite coal, and their various blends using Bayesian approach. First of all, thermal behavior of related materials were investigated under different temperatures, blend ratios, and heating rates. Results of ultimate and proximate analyses showed the main steps of oxidation mechanism of (co-)combustion process. Thermal degradation started with the (hemi-)cellulosic compounds and finished with lignin...
February 8, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28213474/a-bayesian-approach-for-analysis-of-whole-genome-bisulphite-sequencing-data-identifies-disease-associated-changes-in-dna-methylation
#2
Owen J L Rackham, Sarah R Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K Srivastava, Jacques Behmoaras, Petros Dellaportas, Leonardo Bottolo, Enrico Petretto
DNA methylation is a key epigenetic modification involved in gene regulation whose contribution to disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to detect differentially methylated regions (DMRs) from whole-genome bisulphite sequencing (WGBS). We also show how this approach can be leveraged to identify disease-associated changes in DNA methylation, suggesting mechanisms through which these alterations might affect disease. From a data modeling perspective, ABBA has the distinctive feature of automatically adapting to different correlation structures in CpG methylation levels across the genome whilst taking into account the distance between CpG sites as a covariate...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28213206/selected-aspects-of-prior-and-likelihood-information-for-a-bayesian-classifier-in-a-road-safety-analysis
#3
Marzena Nowakowska
The development of the Bayesian logistic regression model classifying the road accident severity is discussed. The already exploited informative priors (method of moments, maximum likelihood estimation, and two-stage Bayesian updating), along with the original idea of a Boot prior proposal, are investigated when no expert opinion has been available. In addition, two possible approaches to updating the priors, in the form of unbalanced and balanced training data sets, are presented. The obtained logistic Bayesian models are assessed on the basis of a deviance information criterion (DIC), highest probability density (HPD) intervals, and coefficients of variation estimated for the model parameters...
February 14, 2017: Accident; Analysis and Prevention
https://www.readbyqxmd.com/read/28213113/a-variational-bayesian-inference-method-for-parametric-imaging-of-pet-data
#4
M Castellaro, G Rizzo, M Tonietto, M Veronese, F E Turkheimer, M A Chappell, A Bertoldo
In dynamic Positron Emission Tomography (PET) studies, compartmental models provide the richest information on the tracer kinetics of the tissue. Inverting such models at the voxel level is however quite challenging due to the low signal-to-noise ratio of the time activity curves. In this study, we propose the use of a Variational Bayesian (VB) approach to efficiently solve this issue and thus obtain robust quantitative parametric maps. VB was adapted to the non-uniform noise distribution of PET data. Moreover, we propose a novel hierarchical scheme to define the model parameter priors directly from the images in case such information are not available from the literature, as often happens with new PET tracers...
February 14, 2017: NeuroImage
https://www.readbyqxmd.com/read/28212786/interplay-between-microbial-trait-dynamics-and-population-dynamics-revealed-by-the-combination-of-laboratory-experiment-and-computational-approaches
#5
Kenta Suzuki, Yuji Yamauchi, Takehito Yoshida
Filament formation is a common bacterial defense mechanism and possibly has a broad impact on microbial community dynamics. In order to examine the impact of filament formation on population dynamics, we developed an experimental system with a filamentous bacterium Flectobacillus sp. MWH38 and a ciliate predator Tetrahymena pyriformis. In this system, the effective defense of Flectobacillus resulted in the extinction of Tetrahymena by allowing almost no population growth. The result of a kairomone experiment suggested the existence of chemical signals for filament formation...
February 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28212045/publisher-s-note-nonparametric-bayesian-inference-of-the-microcanonical-stochastic-block-model-phys-rev-e-95-012317-2017
#6
Tiago P Peixoto
This corrects the article DOI: 10.1103/PhysRevE.95.012317.
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28211944/bayesian-response-adaptive-designs-for-basket-trials
#7
Steffen Ventz, William T Barry, Giovanni Parmigiani, Lorenzo Trippa
We develop a general class of response-adaptive Bayesian designs using hierarchical models, and provide open source software to implement them. Our work is motivated by recent master protocols in oncology, where several treatments are investigated simultaneously in one or multiple disease types, and treatment efficacy is expected to vary across biomarker-defined subpopulations. Adaptive trials such as I-SPY-2 (Barker et al., 2009) and BATTLE (Zhou et al., 2008) are special cases within our framework. We discuss the application of our adaptive scheme to two distinct research goals...
February 17, 2017: Biometrics
https://www.readbyqxmd.com/read/28209373/cost-utility-of-first-line-disease-modifying-treatments-for-relapsing-remitting-multiple-sclerosis
#8
Erkki Soini, Jaana Joutseno, Marja-Liisa Sumelahti
PURPOSE: This study evaluated the cost-effectiveness of first-line treatments of relapsing-remitting multiple sclerosis (RRMS) (dimethyl fumarate [DMF] 240 mg PO BID, teriflunomide 14 mg once daily, glatiramer acetate 20 mg SC once daily, interferon [IFN]-β1a 44 µg TIW, IFN-β1b 250 µg EOD, and IFN-β1a 30 µg IM QW) and best supportive care (BSC) in the health care payer setting in Finland. METHODS: The primary outcome was the modeled incremental cost-effectiveness ratio (ICER; €/quality-adjusted life-year [QALY] gained, 3%/y discounting)...
February 13, 2017: Clinical Therapeutics
https://www.readbyqxmd.com/read/28209135/marv-a-tool-for-genome-wide-multi-phenotype-analysis-of-rare-variants
#9
Marika Kaakinen, Reedik Mägi, Krista Fischer, Jani Heikkinen, Marjo-Riitta Järvelin, Andrew P Morris, Inga Prokopenko
BACKGROUND: Genome-wide association studies have enabled identification of thousands of loci for hundreds of traits. Yet, for most human traits a substantial part of the estimated heritability is unexplained. This and recent advances in technology to produce high-dimensional data cost-effectively have led to method development beyond standard common variant analysis, including single-phenotype rare variant and multi-phenotype common variant analysis, with the latter increasing power for locus discovery and providing suggestions of pleiotropic effects...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28209119/plastome-phylogeny-and-early-diversification-of-brassicaceae
#10
Xinyi Guo, Jianquan Liu, Guoqian Hao, Lei Zhang, Kangshan Mao, Xiaojuan Wang, Dan Zhang, Tao Ma, Quanjun Hu, Ihsan A Al-Shehbaz, Marcus A Koch
BACKGROUND: The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. RESULTS: Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28208453/nonparametric-bayesian-inference-of-the-microcanonical-stochastic-block-model
#11
Tiago P Peixoto
A principled approach to characterize the hidden structure of networks is to formulate generative models and then infer their parameters from data. When the desired structure is composed of modules or "communities," a suitable choice for this task is the stochastic block model (SBM), where nodes are divided into groups, and the placement of edges is conditioned on the group memberships. Here, we present a nonparametric Bayesian method to infer the modular structure of empirical networks, including the number of modules and their hierarchical organization...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208229/comparing-the-performance-of-propensity-score-methods-in-healthcare-database-studies-with-rare-outcomes
#12
Jessica M Franklin, Wesley Eddings, Peter C Austin, Elizabeth A Stuart, Sebastian Schneeweiss
Nonrandomized studies of treatments from electronic healthcare databases are critical for producing the evidence necessary to making informed treatment decisions, but often rely on comparing rates of events observed in a small number of patients. In addition, studies constructed from electronic healthcare databases, for example, administrative claims data, often adjust for many, possibly hundreds, of potential confounders. Despite the importance of maximizing efficiency when there are many confounders and few observed outcome events, there has been relatively little research on the relative performance of different propensity score methods in this context...
February 16, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28208147/perspectives-on-speech-timing-coupled-oscillator-modeling-of-polish-and-finnish
#13
Zofia Malisz, Michael O'Dell, Tommi Nieminen, Petra Wagner
This stud y was ai med at analyzing empirical duration data for Polish spoken at different tempos using an updated version of the Coupled Oscillator Model of speech timing and rhythm variability (O'Dell and Nieminen, 1999, 2009). We use Bayesian inference on parameters relating to speech rate to investigate how tempo affects timing in Polish. The model parameters found are then compared with parameters obtained for equivalent material in Finnish to shed light on which of the effects represent general speech rate mechanisms and which are specific to Polish...
February 23, 2017: Phonetica
https://www.readbyqxmd.com/read/28207523/pharmacological-and-psychotherapeutic-interventions-for-management-of-poststroke-depression-a-bayesian-network-meta-analysis-of-randomized-controlled-trials
#14
Xuejun Sun, Linghui Deng, Shi Qiu, Xiang Tu, Deren Wang, Ming Liu
INTRODUCTION: Poststroke depression (PSD) constitutes an important complication of stroke, leading to great disability as well as increased mortality. Since which treatment for PSD should be preferred are still matters of controversy, we are aiming to compare and rank these pharmacological and nonpharmacological interventions. METHODS AND ANALYSIS: We will employ a network meta-analysis to incorporate both direct and indirect evidence from relevant trials. We will search PubMed, the Cochrane Library Central Register of Controlled Trials, Embase, and the reference lists of relevant articles for randomized controlled trials (RCT) of different PSD treatment strategies...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28207413/combinatorial-mixtures-of-multiparameter-distributions-an-application-to-bivariate-data
#15
Valeria Edefonti, Giovanni Parmigiani
Abstract: We introduce combinatorial mixtures - a flexible class of models for inference on mixture distributions whose components have multidimensional parameters. The key idea is to allow each element of the component-specific parameter vectors to be shared by a subset of other components. This approach allows for mixtures that range from very flexible to very parsimonious and unifies inference on component-specific parameters with inference on the number of components. We develop Bayesian inference and computational approaches for this class of distributions, and illustrate them in an application...
February 16, 2017: International Journal of Biostatistics
https://www.readbyqxmd.com/read/28207283/modeling-information-content-via-dirichlet-multinomial-regression-analysis
#16
Alberto Ferrari
Shannon entropy is being increasingly used in biomedical research as an index of complexity and information content in sequences of symbols, e.g. languages, amino acid sequences, DNA methylation patterns and animal vocalizations. Yet, distributional properties of information entropy as a random variable have seldom been the object of study, leading to researchers mainly using linear models or simulation-based analytical approach to assess differences in information content, when entropy is measured repeatedly in different experimental conditions...
February 16, 2017: Multivariate Behavioral Research
https://www.readbyqxmd.com/read/28204986/validation-workflow-for-a-clinical-bayesian-network-model-in-multidisciplinary-decision-making-in-head-and-neck-oncology-treatment
#17
Mario A Cypko, Matthaeus Stoehr, Marcin Kozniewski, Marek J Druzdzel, Andreas Dietz, Leonard Berliner, Heinz U Lemke
PURPOSE: Oncological treatment is being increasingly complex, and therefore, decision making in multidisciplinary teams is becoming the key activity in the clinical pathways. The increased complexity is related to the number and variability of possible treatment decisions that may be relevant to a patient. In this paper, we describe validation of a multidisciplinary cancer treatment decision in the clinical domain of head and neck oncology. METHOD: Probabilistic graphical models and corresponding inference algorithms, in the form of Bayesian networks, can support complex decision-making processes by providing a mathematically reproducible and transparent advice...
February 15, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28202809/mammal-body-size-evolution-in-north-america-and-europe-over-20-myr-similar-trends-generated-by-different-processes
#18
Shan Huang, Jussi T Eronen, Christine M Janis, Juha J Saarinen, Daniele Silvestro, Susanne A Fritz
Because body size interacts with many fundamental biological properties of a species, body size evolution can be an essential component of the generation and maintenance of biodiversity. Here we investigate how body size evolution can be linked to the clade-specific diversification dynamics in different geographical regions. We analyse an extensive body size dataset of Neogene large herbivores (covering approx. 50% of the 970 species in the orders Artiodactyla and Perissodactyla) in Europe and North America in a Bayesian framework...
February 22, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28202004/a-phase-ii-study-to-evaluate-ly2603618-in-combination-with-gemcitabine-in-pancreatic-cancer-patients
#19
Berta Laquente, Jose Lopez-Martin, Donald Richards, Gerald Illerhaus, David Z Chang, George Kim, Philip Stella, Dirk Richel, Cezary Szcylik, Stefano Cascinu, G L Frassineti, Tudor Ciuleanu, Karla Hurt, Scott Hynes, Ji Lin, Aimee Bence Lin, Daniel Von Hoff, Emiliano Calvo
BACKGROUND: The aim of this study was to determine whether checkpoint kinase 1 inihibitor (CHK1), LY2603618, and gemcitabine prolong overall survival (OS) compared to gemcitabine alone in patients with unresectable pancreatic cancer. METHODS: Patients with Stage II-IV locally advanced or metastatic pancreatic cancer were randomized (2:1) to either 230 mg of LY2603618/1000 mg/m(2) gemcitabine combined or 1000 mg/m(2) gemcitabine alone. OS was assessed using both a Bayesian augment control model and traditional frequentist analysis for inference...
February 15, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28199454/a-bayesian-observer-model-of-drug-craving
#20
Xiaosi Gu, Francesca Filbey
No abstract text is available yet for this article.
February 15, 2017: JAMA Psychiatry
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