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Markov condition

Narayanan Viswanath
In this study, the expected time required to eradicate HIV-1 completely was found as the conditional absorbing time in a finite state space continuous-time Markov chain model. The Markov chain has two absorbing states: one corresponds to HIV eradication and another representing the possible disaster. This method allowed us to calculate the expected eradication time by solving systems of linear equations. To overcome the challenge of huge dimension of the problem, we applied a novel stop and resume technique...
October 20, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Fuming Fang, Takahiro Shinozaki, Yasuo Horiuchi, Shingo Kuroiwa, Sadaoki Furui, Toshimitsu Musha
Eye motion-based human-machine interfaces are used to provide a means of communication for those who can move nothing but their eyes because of injury or disease. To detect eye motions, electrooculography (EOG) is used. For efficient communication, the input speed is critical. However, it is difficult for conventional EOG recognition methods to accurately recognize fast, sequentially input eye motions because adjacent eye motions influence each other. In this paper, we propose a context-dependent hidden Markov model- (HMM-) based EOG modeling approach that uses separate models for identical eye motions with different contexts...
2016: Computational Intelligence and Neuroscience
Vujica Markovic, Dragan Vukovic, Aleksandra Radosavljevic, Ivan Marjanovic
PURPOSE: To investigate the possible association between acquired ectropion uveae and blunt trauma to the eye. We present 3 cases of acquired ectropion uveae that occurred after blunt trauma to the eye. There are no previously published data on possible association of these conditions. METHODS: A retrospective review was conducted of patients with ectropion uveae and eye injury at University Eye Hospital over a 10-year period (2006-2016). We analyzed medical records and clinical findings...
October 21, 2016: European Journal of Ophthalmology
Bruno Cessac, Arnaud Le Ny, Eva Löcherbach
We initiate a mathematical analysis of hidden effects induced by binning spike trains of neurons. Assuming that the original spike train has been generated by a discrete Markov process, we show that binning generates a stochastic process that is no longer Markov but is instead a variable-length Markov chain (VLMC) with unbounded memory. We also show that the law of the binned raster is a Gibbs measure in the DLR (Dobrushin-Lanford-Ruelle) sense coined in mathematical statistical mechanics. This allows the derivation of several important consequences on statistical properties of binned spike trains...
October 20, 2016: Neural Computation
Amanda A Koepke, Ira M Longini, M Elizabeth Halloran, Jon Wakefield, Vladimir N Minin
Despite seasonal cholera outbreaks in Bangladesh, little is known about the relationship between environmental conditions and cholera cases. We seek to develop a predictive model for cholera outbreaks in Bangladesh based on environmental predictors. To do this, we estimate the contribution of environmental variables, such as water depth and water temperature, to cholera outbreaks in the context of a disease transmission model. We implement a method which simultaneously accounts for disease dynamics and environmental variables in a Susceptible-Infected-Recovered-Susceptible (SIRS) model...
June 2016: Annals of Applied Statistics
Michael Ermisch, Anna Bucsics, Patricia Vella Bonanno, Francis Arickx, Alexander Bybau, Tomasz Bochenek, Marc van de Casteele, Eduardo Diogene, Jurij Fürst, Kristina Garuolienė, Martin van der Graaff, Jolanta Gulbinovič, Alan Haycox, Jan Jones, Roberta Joppi, Ott Laius, Irene Langner, Antony P Martin, Vanda Markovic-Pekovic, Laura McCullagh, Einar Magnusson, Ellen Nilsen, Gisbert Selke, Catherine Sermet, Steven Simoens, Robert Sauermann, Ad Schuurman, Ricardo Ramos, Vera Vlahovic-Palcevski, Corinne Zara, Brian Godman
Payers are a major stakeholder in any considerations and initiatives concerning adaptive licensing of new medicinal products, also referred to as Medicines Adaptive Pathways to patients (MAPPs). Firstly, the scope and necessity of MAPPs need further scrutiny, especially with regard to the definition of unmet need. Conditional approval pathways already exist for new medicines for seriously debilitating or life-threatening diseases and only a limited number of new medicines are innovative. Secondly, MAPPs will result in new medicines on the market with limited evidence about their effectiveness and safety...
2016: Frontiers in Pharmacology
Andrea Picchianti Diamanti, Milica Markovic, Giuseppe Argento, Simonetta Giovagnoli, Alberto Ricci, Bruno Laganà, Raffaele D'Amelio
Rheumatoid arthritis (RA) is an inflammatory autoimmune disease that can present different extrarticular manifestations involving heart, lungs and kidneys. In recent years there has been a growing awareness of the central role played by the lungs in the onset and progression of RA. In particular interstitial lung disease (ILD) is a common pulmonary manifestation that may be related to the inflammatory process itself, infectious complications and to the treatments used. Management of patients with ILD/RA is still a challenge for clinicians, both synthetic [mainly methotrexate (MTX), leflunomide] and biologic immunosuppressors [mainly anti-tumor necrosis factor (TNF)α] have in fact been related to the onset or worsening of lung diseases with conflicting data...
October 12, 2016: Therapeutic Advances in Respiratory Disease
Prathiba Natesan, Ratna Nandakumar, Tom Minka, Jonathan D Rubright
This study investigated the impact of three prior distributions: matched, standard vague, and hierarchical in Bayesian estimation parameter recovery in two and one parameter models. Two Bayesian estimation methods were utilized: Markov chain Monte Carlo (MCMC) and the relatively new, Variational Bayesian (VB). Conditional (CML) and Marginal Maximum Likelihood (MML) estimates were used as baseline methods for comparison. Vague priors produced large errors or convergence issues and are not recommended. For both MCMC and VB, the hierarchical and matched priors showed the lowest root mean squared errors (RMSEs) for ability estimates; RMSEs of difficulty estimates were similar across estimation methods...
2016: Frontiers in Psychology
P M Down, A J Bradley, J E Breen, W J Browne, T Kypraios, M J Green
Importance of the dry period with respect to mastitis control is now well established although the precise interventions that reduce the risk of acquiring intramammary infections during this time are not clearly understood. There are very few intervention studies that have measured the clinical efficacy of specific mastitis interventions within a cost-effectiveness framework so there remains a large degree of uncertainty about the impact of a specific intervention and its costeffectiveness. The aim of this study was to use a Bayesian framework to investigate the cost-effectiveness of mastitis controls during the dry period...
October 1, 2016: Preventive Veterinary Medicine
Ana Amić, Bono Lučić, Višnja Stepanić, Zoran Marković, Svetlana Marković, Jasmina M Dimitrić Marković, Dragan Amić
Reaction energetics of the double (2H(+)/2e(-)), i.e., the first 1H(+)/1e(-) (catechol→ phenoxyl radical) and the second 1H(+)/1e(-) (phenoxyl radical→ quinone) free radical scavenging mechanisms of quercetin and its six colonic catecholic metabolites (caffeic acid, hydrocaffeic acid, homoprotocatechuic acid, protocatechuic acid, 4-methylcatechol, and catechol) were computationally studied using density functional theory, with the aim to estimate the antiradical potency of these molecules. We found that second hydrogen atom transfer (HAT) and second sequential proton loss electron transfer (SPLET) mechanisms are less energy demanding than the first ones indicating 2H(+)/2e(-) processes as inherent to catechol moiety...
March 1, 2017: Food Chemistry
Ahmed Soliman, Fahmi Khalifa, Ahmed Elnakib, Mohamed Abou El-Ghar, Neal Dunlap, Brian Wang, Georgy Gimel'farb, Robert Keynton, Ayman El-Baz
To accurately segment pathological and healthy lungs for reliable computer-aided disease diagnostics, a stack of chest CT scans is modeled as a sample of a spatially inhomogeneous joint 3D Markov-Gibbs random field (MGRF) of voxel-wise lung and chest CT image signals (intensities). The proposed learnable MGRF integrates two visual appearance sub models with an adaptive lung shape submodel. The first-order appearance submodel accounts for both the original CT image and its Gaussian scale space (GSS) filtered version to specify local and global signal properties, respectively...
September 12, 2016: IEEE Transactions on Medical Imaging
Elad Yom-Tov, Barbara Marino, Jennifer Pai, Dawn Harris, Michael Wolf
The Internet continues to be an important supplemental health information resource for an increasing number of U.S. adults, especially for those with a new or existing chronic condition. Here we examine how people use the Internet to learn about Type 2 diabetes and how health literacy (HL) influences this information-seeking behavior. We analyzed the searches of approximately 2 million people who queried for diabetes-related information on Microsoft's Bing search engine. The HL of searchers was imputed through a community-based HL score...
October 2016: Journal of Health Communication
Kiyoshi Ezawa
BACKGROUND: Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a method to reliably calculate the occurrence probabilities of sequence alignments via evolutionary processes on an entire sequence. Previously, we presented a perturbative formulation that facilitates the ab initio calculation of alignment probabilities under a continuous-time Markov model, which describes the stochastic evolution of an entire sequence via indels with quite general rate parameters...
September 27, 2016: BMC Bioinformatics
Degui Li, Runze Li
In this paper, we study the local polynomial composite quantile regression (CQR) smoothing method for the nonlinear and nonparametric models under the Harris recurrent Markov chain framework. The local polynomial CQR regression method is a robust alternative to the widely-used local polynomial method, and has been well studied in stationary time series. In this paper, we relax the stationarity restriction on the model, and allow that the regressors are generated by a general Harris recurrent Markov process which includes both the stationary (positive recurrent) and nonstationary (null recurrent) cases...
September 2016: Journal of Econometrics
Aisha Khattak, Ernest I Mandel, Matthew R Reynolds, David M Charytan
BACKGROUND: Percutaneous coronary intervention (PCI) use is low in the setting of stable symptomatic angina in individuals with advanced chronic kidney disease (CKD) despite high cardiovascular risk in this population, and PCI is frequently deferred out of concern for precipitating dialysis therapy. Whether this is appropriate is uncertain, and patient-centered data comparing the relative risks and benefits of continued medical therapy versus PCI in patients with advanced CKD and stable angina are scarce...
September 16, 2016: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
Kiyoshi Ezawa
BACKGROUND: Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a stochastic evolutionary model that enables us to reliably calculate the probability of the sequence evolution through indel processes. Recently, indel probabilistic models are mostly based on either hidden Markov models (HMMs) or transducer theories, both of which give the indel component of the probability of a given sequence alignment as a product of either probabilities of column-to-column transitions or block-wise contributions along the alignment...
August 11, 2016: BMC Bioinformatics
Krishan M Rai, Sandi W Thu, Vimal K Balasubramanian, Christopher J Cobos, Tesfaye Disasa, Venugopal Mendu
Biomass based alternative fuels offer a solution to the world's ever-increasing energy demand. With the ability to produce high biomass in marginal lands with low inputs, sorghum has a great potential to meet second-generation biofuel needs. Despite the sorghum crop importance in biofuel and fodder industry, there is no comprehensive information available on the cell wall related genes and gene families (biosynthetic and modification). It is important to identify the cell wall related genes to understand the cell wall biosynthetic process as well as to facilitate biomass manipulation...
2016: Frontiers in Plant Science
Thomas Speck
We study the linear response in systems driven away from thermal equilibrium into a nonequilibrium steady state with nonvanishing entropy production rate. A simple derivation of a general response formula is presented under the condition that the generating function describes a transformation that (to lowest order) preserves normalization and thus describes a physical stochastic process. For Markov processes we explicitly construct the conjugate quantities and discuss their relation with known response formulas...
August 2016: Physical Review. E
Marc Box, Matt W Jones, Nick Whiteley
We present a hidden Markov model that describes variation in an animal's position associated with varying levels of activity in action potential spike trains of individual place cell neurons. The model incorporates a coarse-graining of position, which we find to be a more parsimonious description of the system than other models. We use a sequential Monte Carlo algorithm for Bayesian inference of model parameters, including the state space dimension, and we explain how to estimate position from spike train observations (decoding)...
September 13, 2016: Journal of Computational Neuroscience
Xiao Wang, Jinghua Gu, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan
MOTIVATION: The advent of high-throughput DNA methylation profiling techniques has enabled the possibility of accurate identification of differentially methylated genes for cancer research. The large number of measured loci facilitates whole genome methylation study, yet posing great challenges for differential methylation detection due to the high variability in tumor samples. RESULTS: We have developed a novel probabilistic approach, DM-BLD, to detect differentially methylated genes based on a Bayesian framework...
September 11, 2016: Bioinformatics
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