keyword
MENU ▼
Read by QxMD icon Read
search

Markov condition

keyword
https://www.readbyqxmd.com/read/28096490/comprehensive-essentiality-analysis-of-the-mycobacterium-tuberculosis-genome-via-saturating-transposon-mutagenesis
#1
Michael A DeJesus, Elias R Gerrick, Weizhen Xu, Sae Woong Park, Jarukit E Long, Cara C Boutte, Eric J Rubin, Dirk Schnappinger, Sabine Ehrt, Sarah M Fortune, Christopher M Sassetti, Thomas R Ioerger
: For decades, identifying the regions of a bacterial chromosome that are necessary for viability has relied on mapping integration sites in libraries of random transposon mutants to find loci that are unable to sustain insertion. To date, these studies have analyzed subsaturated libraries, necessitating the application of statistical methods to estimate the likelihood that a gap in transposon coverage is the result of biological selection and not the stochasticity of insertion. As a result, the essentiality of many genomic features, particularly small ones, could not be reliably assessed...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28092517/transformations-based-on-continuous-piecewise-affine-velocity-fields
#2
Oren Freifeld, Soren Hauberg, Kayhan Batmanghelich, John W Fisher
We propose novel finite-dimensional spaces of well-behaved Rn → Rn transformations. The latter are obtained by (fast and highly-accurate) integration of continuous piecewise-affine velocity fields. The proposed method is simple yet highly expressive, effortlessly handles optional constraints (e.g., volume preservation and/or boundary conditions), and supports convenient modeling choices such as smoothing priors and coarse-to-fine analysis. Importantly, the proposed approach, partly due to its rapid likelihood evaluations and partly due to its other properties, facilitates tractable inference over rich transformation spaces, including using Markov-Chain Monte-Carlo methods...
January 11, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28066502/a-correlated-binary-model-for-ignorable-missing-data-application-to-rheumatoid-arthritis-clinical-data
#3
Francis Erebholo, Victor Apprey, Paul Bezandry, John Kwagyan
Incomplete data are common phenomenon in research that adopts the longitudinal design approach. If incomplete observations are present in the longitudinal data structure, ignoring it could lead to bias in statistical inference and interpretation. We adopt the disposition model and extend it to the analysis of longitudinal binary outcomes in the presence of monotone incomplete data. The response variable is modeled using a conditional logistic regression model. The nonresponse mechanism is assumed ignorable and developed as a combination of Markov's transition and logistic regression model...
April 2016: Journal of Data Science: JDS
https://www.readbyqxmd.com/read/28060703/a-dataset-and-benchmarks-for-segmentation-and-recognition-of-gestures-in-robotic-surgery
#4
Narges Ahmidi, Lingling Tao, Shahin Sefati, Yixin Gao, Colin Lea, Benjamin Bejar, Luca Zappella, Sanjeev Khudanpur, Rene Vidal, Gregory D Hager
OBJECTIVE: State-of-the-art techniques for surgical data analysis report promising results for automated skill assessment and action recognition. The contributions of many of these techniques, however, are limited to study-specific data and validation metrics, making assessment of progress across the field extremely challenging. METHODS: In this paper, we address two major problems for surgical data analysis: (1) lack of uniform shared datasets and benchmarks and (2) lack of consistent validation processes...
January 4, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28050805/electrophysiological-correlates-reflect-the-integration-of-model-based-and-model-free-decision-information
#5
Ben Eppinger, Maik Walter, Shu-Chen Li
In this study, we investigated the interplay of habitual (model-free) and goal-directed (model-based) decision processes by using a two-stage Markov decision task in combination with event-related potentials (ERPs) and computational modeling. To manipulate the demands on model-based decision making, we applied two experimental conditions with different probabilities of transitioning from the first to the second stage of the task. As we expected, when the stage transitions were more predictable, participants showed greater model-based (planning) behavior...
January 3, 2017: Cognitive, Affective & Behavioral Neuroscience
https://www.readbyqxmd.com/read/28049338/fusing-heterogeneous-data-for-the-calibration-of-molecular-dynamics-force-fields-using-hierarchical-bayesian-models
#6
Stephen Wu, Panagiotis Angelikopoulos, Gerardo Tauriello, Costas Papadimitriou, Petros Koumoutsakos
We propose a hierarchical Bayesian framework to systematically integrate heterogeneous data for the calibration of force fields in Molecular Dynamics (MD) simulations. Our approach enables the fusion of diverse experimental data sets of the physico-chemical properties of a system at different thermodynamic conditions. We demonstrate the value of this framework for the robust calibration of MD force-fields for water using experimental data of its diffusivity, radial distribution function, and density. In order to address the high computational cost associated with the hierarchical Bayesian models, we develop a novel surrogate model based on the empirical interpolation method...
December 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28047797/su-g-iep4-03-cone-beam-x-ray-luminescence-computed-tomography-based-on-generalized-gaussian-markov-random-field
#7
G Zhang, L Xing
PURPOSE: Cone beam X-ray luminescence computed tomography (CB-XLCT), which aims to achieve molecular and functional imaging by X-rays, has recently been proposed as a new imaging modality. However, the inverse problem of CB-XLCT is seriously ill-conditioned, hindering us to achieve good image quality. In this work, a novel reconstruction method based on Bayesian theory is proposed to tackle this problem METHODS: Bayesian theory provides a natural framework for utilizing various kinds of available prior information to improve the reconstruction image quality...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28047608/su-d-brb-05-quantum-learning-for-knowledge-based-response-adaptive-radiotherapy
#8
I El Naqa, R Ten
PURPOSE: There is tremendous excitement in radiotherapy about applying data-driven methods to develop personalized clinical decisions for real-time response-based adaptation. However, classical statistical learning methods lack in terms of efficiency and ability to predict outcomes under conditions of uncertainty and incomplete information. Therefore, we are investigating physics-inspired machine learning approaches by utilizing quantum principles for developing a robust framework to dynamically adapt treatments to individual patient's characteristics and optimize outcomes...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28039616/a-cost-effectiveness-analysis-of-nintedanib-in-idiopathic-pulmonary-fibrosis-in-the-uk
#9
C Rinciog, M Watkins, S Chang, T M Maher, C LeReun, D Esser, A Diamantopoulos
BACKGROUND: International guidelines recommend nintedanib (OFEV(®)) as an option for the treatment of idiopathic pulmonary fibrosis (IPF). OBJECTIVE: The objective of this study was to assess the cost effectiveness of nintedanib versus pirfenidone, N-acetylcysteine and best supportive care (BSC) for the treatment of IPF from a UK payer's perspective. METHODS: A Markov model was designed to capture the changes in the condition of adults with IPF...
December 31, 2016: PharmacoEconomics
https://www.readbyqxmd.com/read/28027614/decision-modelling-in-donation-after-circulatory-death-dcd-liver-transplantation
#10
K A McLean, J Camilleri-Brennan, S R Knight, T Drake, R Ots, C A Shaw, S J Wigmore, E M Harrison
INTRODUCTION: Donation after circulatory death (DCD) liver allografts are increasingly used for transplantation. However, the post-transplantation clinical and quality of life outcomes of DCD recipients are traditionally considered to be inferior compared with donation after brain death (DBD) allograft recipients. Decision making for such marginal organs can be difficult. This study investigated the optimal decision to accept or decline a DCD liver allograft for a patient based on their current health...
December 27, 2016: Liver Transplantation
https://www.readbyqxmd.com/read/28018185/life-and-understanding-the-origins-of-understanding-in-self-organizing-nervous-systems
#11
REVIEW
Yan M Yufik, Karl Friston
This article is motivated by a formulation of biotic self-organization in Friston (2013), where the emergence of "life" in coupled material entities (e.g., macromolecules) was predicated on bounded subsets that maintain a degree of statistical independence from the rest of the network. Boundary elements in such systems constitute a Markov blanket; separating the internal states of a system from its surrounding states. In this article, we ask whether Markov blankets operate in the nervous system and underlie the development of intelligence, enabling a progression from the ability to sense the environment to the ability to understand it...
2016: Frontiers in Systems Neuroscience
https://www.readbyqxmd.com/read/28013336/hybrid-markov-chain-models-of-s-i-r-disease-dynamics
#12
Nicolas P Rebuli, N G Bean, J V Ross
Deterministic epidemic models are attractive due to their compact nature, allowing substantial complexity with computational efficiency. This partly explains their dominance in epidemic modelling. However, the small numbers of infectious individuals at early and late stages of an epidemic, in combination with the stochastic nature of transmission and recovery events, are critically important to understanding disease dynamics. This motivates the use of a stochastic model, with continuous-time Markov chains being a popular choice...
December 24, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28011233/septic-shock-prediction-for-icu-patients-via-coupled-hmm-walking-on-sequential-contrast-patterns
#13
Shameek Ghosh, Jinyan Li, Longbing Cao, Kotagiri Ramamohanarao
BACKGROUND AND OBJECTIVE: Critical care patient events like sepsis or septic shock in intensive care units (ICUs) are dangerous complications which can cause multiple organ failures and eventual death. Preventive prediction of such events will allow clinicians to stage effective interventions for averting these critical complications. METHODS: It is widely understood that physiological conditions of patients on variables such as blood pressure and heart rate are suggestive to gradual changes over a certain period of time, prior to the occurrence of a septic shock...
December 20, 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/27982083/netdiff-bayesian-model-selection-for-differential-gene-regulatory-network-inference
#14
Thomas Thorne
Differential networks allow us to better understand the changes in cellular processes that are exhibited in conditions of interest, identifying variations in gene regulation or protein interaction between, for example, cases and controls, or in response to external stimuli. Here we present a novel methodology for the inference of differential gene regulatory networks from gene expression microarray data. Specifically we apply a Bayesian model selection approach to compare models of conserved and varying network structure, and use Gaussian graphical models to represent the network structures...
December 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27978814/switchfinder-a-novel-method-and-query-facility-for-discovering-dynamic-gene-expression-patterns
#15
Svetlana Bulashevska, Colin Priest, Daniel Speicher, Jörg Zimmermann, Frank Westermann, Armin B Cremers
BACKGROUND: Biological systems and processes are highly dynamic. To gain insights into their functioning time-resolved measurements are necessary. Time-resolved gene expression data captures temporal behaviour of the genes genome-wide under various biological conditions: in response to stimuli, during cell cycle, differentiation or developmental programs. Dissecting dynamic gene expression patterns from this data may shed light on the functioning of the gene regulatory system. The present approach facilitates this discovery...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27975196/economic-studies-in-motor-neurone-disease-a-systematic-methodological-review
#16
REVIEW
Alan Moore, Carolyn A Young, Dyfrig A Hughes
BACKGROUND: Motor neurone disease (MND) is a devastating condition which greatly diminishes patients' quality of life and limits life expectancy. Health technology appraisals of future interventions in MND need robust data on costs and utilities. Existing economic evaluations have been noted to be limited and fraught with challenges. OBJECTIVE: The aim of this study was to identify and critique methodological aspects of all published economic evaluations, cost studies, and utility studies in MND...
December 14, 2016: PharmacoEconomics
https://www.readbyqxmd.com/read/27967072/synchronization-of-coupled-noisy-oscillators-coarse-graining-from-continuous-to-discrete-phases
#17
Daniel Escaff, Alexandre Rosas, Raúl Toral, Katja Lindenberg
The theoretical description of synchronization phenomena often relies on coupled units of continuous time noisy Markov chains with a small number of states in each unit. It is frequently assumed, either explicitly or implicitly, that coupled discrete-state noisy Markov units can be used to model mathematically more complex coupled noisy continuous phase oscillators. In this work we explore conditions that justify this assumption by coarse graining continuous phase units. In particular, we determine the minimum number of states necessary to justify this correspondence for Kuramoto-like oscillators...
November 2016: Physical Review. E
https://www.readbyqxmd.com/read/27929354/differences-in-mrsa-prevalence-and-resistance-patterns-in-a-tertiary-center-before-and-after-joining-an-international-program-for-surveillance-of-antimicrobial-resistance
#18
Olivera Djuric, Snezana Jovanovic, Branka Stosovic, Tanja Tosic, Milica Jovanovic, Naomi Nartey, Jovana Todorovic, Ljiljana Markovic-Denic
Methicillin-resistant Staphylococcus aureus (MRSA) emerged as one of the most important causes of hospital-acquired bloodstream infections (BSIs), especially the multidrug resistant clones. The aim of the present study was to compare prevalence and resistance patterns of MRSA bacteremia in the major tertiary-care academic and referral center in Serbia before and after implementing an active antimicrobial resistance (AMR) surveillance. Laboratory-based before-after study was conducted during a two-year period (January 2012 to December 2013) in Clinical Centre of Serbia...
December 8, 2016: Acta Microbiologica et Immunologica Hungarica
https://www.readbyqxmd.com/read/27908084/a-robust-automatic-birdsong-phrase-classification-a-template-based-approach
#19
Kantapon Kaewtip, Abeer Alwan, Colm O'Reilly, Charles E Taylor
Automatic phrase detection systems of bird sounds are useful in several applications as they reduce the need for manual annotations. However, birdphrase detection is challenging due to limited training data and background noise. Limited data occur because of limited recordings or the existence of rare phrases. Background noise interference occurs because of the intrinsic nature of the recording environment such as wind or other animals. This paper presents a different approach to birdsong phrase classification using template-based techniques suitable even for limited training data and noisy environments...
November 2016: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/27906962/population-density-climate-variables-and-poverty-synergistically-structure-spatial-risk-in-urban-malaria-in-india
#20
Mauricio Santos-Vega, Menno J Bouma, Vijay Kohli, Mercedes Pascual
BACKGROUND: The world is rapidly becoming urban with the global population living in cities projected to double by 2050. This increase in urbanization poses new challenges for the spread and control of communicable diseases such as malaria. In particular, urban environments create highly heterogeneous socio-economic and environmental conditions that can affect the transmission of vector-borne diseases dependent on human water storage and waste water management. Interestingly India, as opposed to Africa, harbors a mosquito vector, Anopheles stephensi, which thrives in the man-made environments of cities and acts as the vector for both Plasmodium vivax and Plasmodium falciparum, making the malaria problem a truly urban phenomenon...
December 2016: PLoS Neglected Tropical Diseases
keyword
keyword
84616
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"