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https://www.readbyqxmd.com/read/28719601/clic-a-tool-for-expanding-biological-pathways-based-on-co-expression-across-thousands-of-datasets
#1
Yang Li, Alexis A Jourdain, Sarah E Calvo, Jun S Liu, Vamsi K Mootha
In recent years, there has been a huge rise in the number of publicly available transcriptional profiling datasets. These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways. Such analyses can be very challenging, however, since biological pathways are modular and may exhibit co-expression only in specific contexts. To overcome these challenges we introduce CLIC, CLustering by Inferred Co-expression...
July 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28717987/interventions-for-refractory-trigeminal-neuralgia-a-bayesian-mixed-treatment-comparison-network-meta-analysis-of-randomized-controlled-clinical-trials
#2
Kannan Sridharan, Gowri Sivaramakrishnan
INTRODUCTION: Patients with trigeminal neuralgia (TN) are often refractory to recommended first-line agents. Due to the absence of a systematic review, we undertook a network meta-analysis to assess various interventions that can be used to manage refractory TN. METHODS: Electronic databases were searched using appropriate strategies to identify randomized controlled clinical trials in patients with refractory TN, evaluating the proportion of patients with a minimum of 50% reduction in pain or a minimum of 2 cm reduction in score in an appropriate pain scale or complete pain relief by subjective pain scales...
July 17, 2017: Clinical Drug Investigation
https://www.readbyqxmd.com/read/28716741/inferring-the-shallow-phylogeny-of-true-salamanders-salamandra-by-multiple-phylogenomic-approaches
#3
Ariel Rodríguez, James D Burgon, Mariana Lyra, Iker Irisarri, Denis Baurain, Leon Blaustein, Bayram Göcmen, Sven Künzel, Barbara Mable, Arne W Nolte, Michael Veith, Sebastian Steinfartz, Kathryn R Elmer, Hervé Philippe, Miguel Vences
The rise of high-throughput sequencing techniques provides the unprecedented opportunity to analyse controversial phylogenetic relationships in great depth, but also introduce the risk of being misinterpreted by high node support values influenced by unevenly distributed missing data or unrealistic model assumptions. Here, we use three largely independent phylogenomic data sets to reconstruct the controversial phylogeny of true salamanders of the genus Salamandra. a group of amphibians providing an intriguing model to study the evolution of aposematism and viviparity...
July 14, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28716060/nonlinear-joint-models-for-individual-dynamic-prediction-of-risk-of-death-using-hamiltonian-monte-carlo-application-to-metastatic-prostate-cancer
#4
Solène Desmée, France Mentré, Christine Veyrat-Follet, Bernard Sébastien, Jérémie Guedj
BACKGROUND: Joint models of longitudinal and time-to-event data are increasingly used to perform individual dynamic prediction of a risk of event. However the difficulty to perform inference in nonlinear models and to calculate the distribution of individual parameters has long limited this approach to linear mixed-effect models for the longitudinal part. Here we use a Bayesian algorithm and a nonlinear joint model to calculate individual dynamic predictions. We apply this approach to predict the risk of death in metastatic castration-resistant prostate cancer (mCRPC) patients with frequent Prostate-Specific Antigen (PSA) measurements...
July 17, 2017: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/28710702/bayesian-inference-for-biomarker-discovery-in-proteomics-an-analytic-solution
#5
Noura Dridi, Audrey Giremus, Jean-Francois Giovannelli, Caroline Truntzer, Melita Hadzagic, Jean-Philippe Charrier, Laurent Gerfault, Patrick Ducoroy, Bruno Lacroix, Pierre Grangeat, Pascal Roy
This paper addresses the question of biomarker discovery in proteomics. Given clinical data regarding a list of proteins for a set of individuals, the tackled problem is to extract a short subset of proteins the concentrations of which are an indicator of the biological status (healthy or pathological). In this paper, it is formulated as a specific instance of variable selection. The originality is that the proteins are not investigated one after the other but the best partition between discriminant and non-discriminant proteins is directly sought...
December 2017: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/28706499/valence-dependent-belief-updating-computational-validation
#6
Bojana Kuzmanovic, Lionel Rigoux
People tend to update beliefs about their future outcomes in a valence-dependent way: they are likely to incorporate good news and to neglect bad news. However, belief formation is a complex process which depends not only on motivational factors such as the desire for favorable conclusions, but also on multiple cognitive variables such as prior beliefs, knowledge about personal vulnerabilities and resources, and the size of the probabilities and estimation errors. Thus, we applied computational modeling in order to test for valence-induced biases in updating while formally controlling for relevant cognitive factors...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28706157/a-bayesian-pick-the-winner-design-in-a-randomized-phase-ii-clinical-trial
#7
Dung-Tsa Chen, Po-Yu Huang, Hui-Yi Lin, Alberto A Chiappori, Dmitry I Gabrilovich, Eric B Haura, Scott J Antonia, Jhanelle E Gray
PURPOSE: Many phase II clinical trials evaluate unique experimental drugs/combinations through multi-arm design to expedite the screening process (early termination of ineffective drugs) and to identify the most effective drug (pick the winner) to warrant a phase III trial. Various statistical approaches have been developed for the pick-the-winner design but have been criticized for lack of objective comparison among the drug agents. METHODS: We developed a Bayesian pick-the-winner design by integrating a Bayesian posterior probability with Simon two-stage design in a randomized two-arm clinical trial...
July 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28702465/a-dynamic-transmission-model-to-evaluate-the-effectiveness-of-infection-control-strategies
#8
Karim Khader, Alun Thomas, W Charles Huskins, Molly Leecaster, Yue Zhang, Tom Greene, Andrew Redd, Matthew H Samore
BACKGROUND: The advancement of knowledge about control of antibiotic resistance depends on the rigorous evaluation of alternative intervention strategies. The STAR*ICU trial examined the effects of active surveillance and expanded barrier precautions on acquisition of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) in intensive care units. We report a reanalyses of the STAR*ICU trial using a Bayesian transmission modeling framework. METHODS: The data included admission and discharge times and surveillance test times and results...
2017: Open Forum Infectious Diseases
https://www.readbyqxmd.com/read/28699595/effectiveness-of-non-steroidal-anti-inflammatory-drugs-for-the-treatment-of-pain-in-knee-and-hip-osteoarthritis-a-network-meta-analysis
#9
Bruno R da Costa, Stephan Reichenbach, Noah Keller, Linda Nartey, Simon Wandel, Peter Jüni, Sven Trelle
BACKGROUND: Non-steroidal anti-inflammatory drugs (NSAIDs) are the backbone of osteoarthritis pain management. We aimed to assess the effectiveness of different preparations and doses of NSAIDs on osteoarthritis pain in a network meta-analysis. METHODS: For this network meta-analysis, we considered randomised trials comparing any of the following interventions: NSAIDs, paracetamol, or placebo, for the treatment of osteoarthritis pain. We searched the Cochrane Central Register of Controlled Trials (CENTRAL) and the reference lists of relevant articles for trials published between Jan 1, 1980, and Feb 24, 2015, with at least 100 patients per group...
July 8, 2017: Lancet
https://www.readbyqxmd.com/read/28697640/on-bayesian-simplicity-in-human-visual-perceptual-organization
#10
Peter A van der Helm
A returning idea among some Bayesians in research on human visual perceptual organization is that the surprisal of something (i.e., the negative logarithm of its probability) expresses its complexity (i.e., the length of its shortest description). Bayes' rule is a powerful modeling tool and descriptive simplicity is a rich concept, but this idea is wishful thinking at best: If true, it would unify the simplicity and likelihood principles, which reflect two traditionally opposed schools of thought on perceptual organization...
January 1, 2017: Perception
https://www.readbyqxmd.com/read/28695620/correlated-response-in-litter-size-components-in-rabbits-selected-for-litter-size-variability
#11
M J Argente, E W Calle, M L García, A Blasco
A divergent selection experiment for the environmental variability of litter size (Ve) over seven generations was carried out in rabbits at the University Miguel Hernández of Elche. The Ve was estimated as the phenotypic variance within the female, after correcting for year-season and parity-lactation status. The aim of this study was to analyse the correlated responses to selection in litter size components. The ovulation rate (OR) and number of implanted embryos (IE) in females were measured by laparoscopy at 12 day of the second gestation...
July 11, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28692831/children-s-quantitative-bayesian-inferences-from-natural-frequencies-and-number-of-chances
#12
Stefania Pighin, Vittorio Girotto, Katya Tentori
Zhu and Gigerenzer (2006) showed that an appreciable number of Chinese children aged between 9 and 12years old made correct quantitative Bayesian inferences requiring the integration of priors and likelihoods as long as they were presented with numerical information phrased in terms of natural frequencies. In this study, we sought to replicate this finding and extend the investigation of children's Bayesian reasoning to a different numerical format (chances) and other probability questions (distributive and relative)...
July 7, 2017: Cognition
https://www.readbyqxmd.com/read/28691311/bayesian-adaptive-dose-escalation-designs-for-simultaneously-estimating-the-optimal-and-maximum-safe-dose-based-on-safety-and-efficacy
#13
Wai Yin Yeung, Bruno Reigner, Ulrich Beyer, Cheikh Diack, Daniel Sabanés Bové, Giuseppe Palermo, Thomas Jaki
The main purpose of dose-escalation trials is to identify the dose(s) that is/are safe and efficacious for further investigations in later studies. In this paper, we introduce dose-escalation designs that incorporate both the dose-limiting events and dose-limiting toxicities (DLTs) and indicative responses of efficacy into the procedure. A flexible nonparametric model is used for modelling the continuous efficacy responses while a logistic model is used for the binary DLTs. Escalation decisions are based on the combination of the probabilities of DLTs and expected efficacy through a gain function...
July 9, 2017: Pharmaceutical Statistics
https://www.readbyqxmd.com/read/28690422/detection-methods-for-stochastic-gravitational-wave-backgrounds-a-unified-treatment
#14
REVIEW
Joseph D Romano, Neil J Cornish
We review detection methods that are currently in use or have been proposed to search for a stochastic background of gravitational radiation. We consider both Bayesian and frequentist searches using ground-based and space-based laser interferometers, spacecraft Doppler tracking, and pulsar timing arrays; and we allow for anisotropy, non-Gaussianity, and non-standard polarization states. Our focus is on relevant data analysis issues, and not on the particular astrophysical or early Universe sources that might give rise to such backgrounds...
2017: Living Reviews in Relativity
https://www.readbyqxmd.com/read/28690054/fuzzy-evidential-network-and-its-application-as-medical-prognosis-and-diagnosis-models
#15
Amin Janghorbani, Mohammad Hassan Moradi
Uncertainty is one of the important facts of the medical knowledge. Medical prognosis and diagnosis, as the essential parts of medical knowledge, is affected by different aspects of uncertainty, which must be managed. In the previous studies, different theories such as Bayesian probability theory, evidence theory, and fuzzy set theory have been developed to represent and manage different aspects of uncertainty. Recently, hybrid frameworks are suggested to deal with various types of uncertainty in a single framework...
July 6, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28688460/chronometric-investigations-of-the-middle-to-upper-paleolithic-transition-in-the-zagros-mountains-using-ams-radiocarbon-dating-and-bayesian-age-modelling
#16
Lorena Becerra-Valdivia, Katerina Douka, Daniel Comeskey, Behrouz Bazgir, Nicholas J Conard, Curtis W Marean, Andreu Ollé, Marcel Otte, Laxmi Tumung, Mohsen Zeidi, Thomas F G Higham
The Middle to Upper Paleolithic transition is often linked with a bio-cultural shift involving the dispersal of modern humans outside of Africa, the concomitant replacement of Neanderthals across Eurasia, and the emergence of new technological traditions. The Zagros Mountains region assumes importance in discussions concerning this period as its geographic location is central to all pertinent hominin migration areas, pointing to both east and west. As such, establishing a reliable chronology in the Zagros Mountains is crucial to our understanding of these biological and cultural developments...
August 2017: Journal of Human Evolution
https://www.readbyqxmd.com/read/28687922/was-kaposi-s-sarcoma-associated-herpesvirus-introduced-into-china-via-the-ancient-silk-road-an-evolutionary-perspective
#17
Zhenqiu Liu, Qiwen Fang, Jialu Zuo, Veenu Minhas, Charles Wood, Na He, Tiejun Zhang
Kaposi's sarcoma-associated herpesvirus (KSHV) has become widely dispersed worldwide since it was first reported in 1994, but the seroprevalence of KSHV varies geographically. KSHV is relatively ubiquitous in Mediterranean areas and the Xinjiang Uygur Autonomous Region, China. The origin of KSHV has long been puzzling. In the present study, we collected and analysed 154 KSHV ORF-K1 sequences obtained from samples originating from Xinjiang, Italy, Greece, Iran and southern Siberia using Bayesian evolutionary analysis in BEAST to test the hypothesis that KSHV was introduced into Xinjiang via the ancient Silk Road...
July 7, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28686651/a-preliminary-approach-to-quantifying-the-overall-environmental-risks-posed-by-development-projects-during-environmental-impact-assessment
#18
Sam Nicol, Iadine Chadès
Environmental impact assessment (EIA) is used globally to manage the impacts of development projects on the environment, so there is an imperative to demonstrate that it can effectively identify risky projects. However, despite the widespread use of quantitative predictive risk models in areas such as toxicology, ecosystem modelling and water quality, the use of predictive risk tools to assess the overall expected environmental impacts of major construction and development proposals is comparatively rare. A risk-based approach has many potential advantages, including improved prediction and attribution of cause and effect; sensitivity analysis; continual learning; and optimal resource allocation...
2017: PloS One
https://www.readbyqxmd.com/read/28684720/developing-a-hierarchical-model-for-the-spatial-analysis-of-pm10-pollution-extremes-in-the-mexico-city-metropolitan-area
#19
Alejandro Ivan Aguirre-Salado, Humberto Vaquera-Huerta, Carlos Arturo Aguirre-Salado, Silvia Reyes-Mora, Ana Delia Olvera-Cervantes, Guillermo Arturo Lancho-Romero, Carlos Soubervielle-Montalvo
We implemented a spatial model for analysing PM 10 maxima across the Mexico City metropolitan area during the period 1995-2016. We assumed that these maxima follow a non-identical generalized extreme value (GEV) distribution and modeled the trend by introducing multivariate smoothing spline functions into the probability GEV distribution. A flexible, three-stage hierarchical Bayesian approach was developed to analyse the distribution of the PM 10 maxima in space and time. We evaluated the statistical model's performance by using a simulation study...
July 6, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28682091/a-quantum-probability-framework-for-human-probabilistic-inference
#20
Jennifer S Trueblood, James M Yearsley, Emmanuel M Pothos
There is considerable variety in human inference (e.g., a doctor inferring the presence of a disease, a juror inferring the guilt of a defendant, or someone inferring future weight loss based on diet and exercise). As such, people display a wide range of behaviors when making inference judgments. Sometimes, people's judgments appear Bayesian (i.e., normative), but in other cases, judgments deviate from the normative prescription of classical probability theory. How can we combine both Bayesian and non-Bayesian influences in a principled way? We propose a unified explanation of human inference using quantum probability theory...
July 6, 2017: Journal of Experimental Psychology. General
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