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Bayesian probability

Peter A Nigrovic, Timothy Beukelman, George Tomlinson, Brian M Feldman, Laura E Schanberg, Yukiko Kimura
BACKGROUND: Systemic juvenile idiopathic arthritis is a rare febrile arthritis of childhood characterized by a potentially severe course, including prolonged glucocorticoid exposure, growth failure, destructive arthritis, and life-threatening macrophage activation syndrome. Early cytokine-blocking biologic therapy may improve long-term outcomes, although some systemic juvenile idiopathic arthritis patients respond well to non-biologic treatment, leaving optimal management undefined. Consequently, treatment of new-onset systemic juvenile idiopathic arthritis by expert clinicians varies widely...
March 1, 2018: Clinical Trials: Journal of the Society for Clinical Trials
Oleg Kovalevskiy, Robert A Nicholls, Fei Long, Azzurra Carlon, Garib N Murshudov
Refinement is a process that involves bringing into agreement the structural model, available prior knowledge and experimental data. To achieve this, the refinement procedure optimizes a posterior conditional probability distribution of model parameters, including atomic coordinates, atomic displacement parameters (B factors), scale factors, parameters of the solvent model and twin fractions in the case of twinned crystals, given observed data such as observed amplitudes or intensities of structure factors...
March 1, 2018: Acta Crystallographica. Section D, Structural Biology
Remco R Bouckaert, Claire Bowern, Quentin D Atkinson
It remains a mystery how Pama-Nyungan, the world's largest hunter-gatherer language family, came to dominate the Australian continent. Some argue that social or technological advantages allowed rapid language replacement from the Gulf Plains region during the mid-Holocene. Others have proposed expansions from refugia linked to climatic changes after the last ice age or, more controversially, during the initial colonization of Australia. Here, we combine basic vocabulary data from 306 Pama-Nyungan languages with Bayesian phylogeographic methods to explicitly model the expansion of the family across Australia and test between these origin scenarios...
March 12, 2018: Nature Ecology & Evolution
Seth Jonas, Kassandra Fronczyk, Lucas M Pratt
An extreme space weather event has the potential to disrupt or damage infrastructure systems and technologies that many societies rely on for economic and social well-being. Space weather events occur regularly, but extreme events are less frequent, with a small number of historical examples over the last 160 years. During the past decade, published works have (1) examined the physical characteristics of the extreme historical events and (2) discussed the probability or return rate of select extreme geomagnetic disturbances, including the 1859 Carrington event...
March 12, 2018: Risk Analysis: An Official Publication of the Society for Risk Analysis
Elizabeth Krachey, Kert Viele, Philip C Spinella, Marie E Steiner, Nicole D Zantek, Roger J Lewis
BACKGROUND: Storage of platelets at 4°C compared to 22°C may increase both hemostatic activity and storage duration; however, the maximum duration of cold storage is unknown. We report the design of an innovative, prospective, randomized, Bayesian adaptive, "duration-finding" clinical trial to evaluate the efficacy and maximum duration of storage of platelets at 4°C. METHODS: Patients undergoing cardiac surgery and requiring platelet transfusions will be enrolled...
March 8, 2018: Journal of Trauma and Acute Care Surgery
Georgios A Kotsakis, Qinshu Lian, Andreas L Ioannou, Bryan S Michalowicz, Mike John, Haitao Chu
BACKGROUND: A wide selection of Interdental Oral Hygiene (IOH) aids is available to consumers. Recommendations for selection are, however, limited by the lack of direct comparisons in available studies. We aimed to assess the comparative efficacy of IOH aids using Bayesian Network Meta-Analysis (BNMA). METHODS: Two independent reviewers performed a systematic literature review of randomized clinical trials assessing IOH aids, based on a focused question. Gingival inflammation (Gingival Index (GI), Bleeding-on-probing (BOP)) was the primary outcome and plaque and probing depth were secondary outcomes A random-effects arm-based BNMA model was run for each outcome; posterior medians and 95% credible-intervals (CIs) summarized marginal distributions of parameters...
February 19, 2018: Journal of Periodontology
Fattaneh Jabbari, Joseph Ramsey, Peter Spirtes, Gregory Cooper
Discovering causal structure from observational data in the presence of latent variables remains an active research area. Constraint-based causal discovery algorithms are relatively efficient at discovering such causal models from data using independence tests. Typically, however, they derive and output only one such model. In contrast, Bayesian methods can generate and probabilistically score multiple models, outputting the most probable one; however, they are often computationally infeasible to apply when modeling latent variables...
September 2017: Machine Learning and Knowledge Discovery in Databases: European Conference, ECML PKDD: Proceedings
Alexander Feckler, Matthew Low, Jochen P Zubrod, Mirco Bundschuh
Bayesian methods and frequentist confidence intervals are proposed as an alternative approach in ecotoxicology emphasizing effect sizes and associated (un)certainties to judge the biological relevance of effects instead of basing decisions on p-values. These approaches show advantages over null hypothesis significance testing. In particular, Bayesian methods revealed more potential than frequentist counterparts, as the posterior distribution and its credible intervals can be directly interpreted as the probability of effect sizes...
March 6, 2018: Environmental Toxicology and Chemistry
Jeferson Carneiro, Iracilda Sampaio, José de Sousa E Silva-Júnior, Izeni Farias, Tomas Hrbek, Alcides Pissinatti, Ronylson Silva, Antônio Martins-Junior, Jean Boubli, Stephen Francis Ferrari, Horacio Schneider
The titi monkeys belong to a genus of New World primates endemic to South America, which were recently reclassified in three genera (Cheracebus, Plecturocebus and Callicebus). The genus Callicebus, which currently includes five species, is endemic to eastern Brazil, occurring in the Caatinga, Savanna, and Atlantic Forest biomes. In the present study, we investigated the validity of these species and inferred their phylogenetic relationships, divergence times, and biogeographic patterns based on the molecular analysis of a concatenated sequence of 11 mitochondrial and nuclear DNA markers, derived from 13 specimens...
March 2, 2018: Molecular Phylogenetics and Evolution
Ryo Tamura, Koji Hukushima
An efficient method for finding a better maximizer of computationally extensive probability distributions is proposed on the basis of a Bayesian optimization technique. A key idea of the proposed method is to use extreme values of acquisition functions by Gaussian processes for the next training phase, which should be located near a local maximum or a global maximum of the probability distribution. Our Bayesian optimization technique is applied to the posterior distribution in the effective physical model estimation, which is a computationally extensive probability distribution...
2018: PloS One
Bhornsawan Thanathornwong
Objectives: In this study, a clinical decision support system was developed to help general practitioners assess the need for orthodontic treatment in patients with permanent dentition. Methods: We chose a Bayesian network (BN) as the underlying model for assessing the need for orthodontic treatment. One thousand permanent dentition patient data sets chosen from a hospital record system were prepared in which one data element represented one participant with information for all variables and their stated need for orthodontic treatment...
January 2018: Healthcare Informatics Research
Michelle E Miller, Victoria M Allen, Jo-Ann K Brock
OBJECTIVE: Fetal echogenic bowel (echogenic bowel) is associated with cystic fibrosis (CF), with a reported incidence ranging from 1% to 13%. Prenatal testing for CF in the setting of echogenic bowel can be done by screening parental or fetal samples for pathogenic CFTR variants. If only one pathogenic variant is identified, sequencing of the CFTR gene can be undertaken, to identify a second pathogenic variant not covered in the standard screening panel. Full gene sequencing, however, also introduces the potential to identify variants of uncertain significance (VUSs) that can create counselling challenges and cause parental anxiety...
March 1, 2018: Journal of Obstetrics and Gynaecology Canada: JOGC, Journal D'obstétrique et Gynécologie du Canada: JOGC
Eric M Maiese, Claire Ainsworth, Jean-Gabriel Le Moine, Outi Ahdesmäki, Judith Bell, Emma Hawe
PURPOSE: New therapies, including daratumumab plus lenalidomide plus dexamethasone (DRd) and daratumumab plus bortezomib plus dexamethasone (DVd), have recently been approved in the United States for patients with multiple myeloma (MM) who have received at least 1 prior line of therapy. However, few treatments have been compared in head-to-head clinical trials to determine the most efficacious therapy. In an update of the POLLUX (Phase 3 Study Comparing DRd Versus Rd in Subjects with Relapsed or Refractory Multiple Myeloma [RRMM]) trial, median progression-free survival (PFS) for DRd was not reached; the hazard ratio compared with Rd was 0...
February 27, 2018: Clinical Therapeutics
V Schetinin, L Jakaite, W Krzanowski
INTRODUCTION: For making reliable decisions, practitioners need to estimate uncertainties that exist in data and decision models. In this paper we analyse uncertainties of predicting survival probability for patients in trauma care. The existing prediction methodology employs logistic regression modelling of Trauma and Injury Severity Score (TRISS), which is based on theoretical assumptions. These assumptions limit the capability of TRISS methodology to provide accurate and reliable predictions...
April 2018: International Journal of Medical Informatics
Moh A Alkhamis, Carmina Gallardo, Cristina Jurado, Alejandro Soler, Marisa Arias, José M Sánchez-Vizcaíno
African swine fever (ASF) is a complex infectious disease of swine that constitutes devastating impacts on animal health and the world economy. Here, we investigated the evolutionary epidemiology of ASF virus (ASFV) in Eurasia and Africa using the concatenated gene sequences of the viral protein 72 and the central variable region of isolates collected between 1960 and 2015. We used Bayesian phylodynamic models to reconstruct the evolutionary history of the virus, to identify virus population demographics and to quantify dispersal patterns between host species...
2018: PloS One
Dietrich Doll, F Bosche, A Hauser, P Moersdorf, I Sinicina, J Grunwald, F Reckel, M M Luedi
PURPOSE: Hair in the pilonidal sinus is not growing within the sinus cavity, as hair follicles are not present there. Not few pilonidal patients do not have intergluteal hair, which is said to be the causative agent of folliculitis and pilonidal genesis. So, what is the real source of the hair forming the typical pilonidal hair nest? METHODS: A trifold approach was used: First, axial hair strength testing of pilonidal hair and body hair harvested from head, lower back (glabella sacralis), and cranial third of intergluteal fold...
February 28, 2018: International Journal of Colorectal Disease
Jaime S Ide, Sanja Nedic, Kin F Wong, Shmuel L Strey, Elizabeth A Lawson, Bradford C Dickerson, Lawrence L Wald, Giancarlo La Camera, L R Mujica-Parodi
Oxytocin (OT) is an endogenous neuropeptide that, while originally thought to promote trust, has more recently been found to be context-dependent. Here we extend experimental paradigms previously restricted to de novo decision-to-trust, to a more realistic environment in which social relationships evolve in response to iterative feedback over twenty interactions. In a randomized, double blind, placebo-controlled within-subject/crossover experiment of human adult males, we investigated the effects of a single dose of intranasal OT (40 IU) on Bayesian expectation updating and reinforcement learning within a social context, with associated brain circuit dynamics...
February 24, 2018: NeuroImage
Azam Korhani Kangi, Abbas Bahrampour
Introduction and purpose: In recent years the use of neural networks without any premises for investigation of prognosis in analyzing survival data has increased. Artificial neural networks (ANN) use small processors with a continuous network to solve problems inspired by the human brain. Bayesian neural networks (BNN) constitute a neural-based approach to modeling and non-linearization of complex issues using special algorithms and statistical methods. Gastric cancer incidence is the first and third ranking for men and women in Iran, respectively...
February 26, 2018: Asian Pacific Journal of Cancer Prevention: APJCP
Elisabete F Dias, Norbert Kilian, Luís Silva, Hanno Schaefer, Mark Carine, Paula J Rudall, Arnoldo Santos-Guerra, Mónica Moura
The phylogenetic relationships and phylogeography of two relatively rare Macaronesian Lactuca species, Lactuca watsoniana (Azores) and L. palmensis (Canary Islands), were, until this date, unclear. Karyological information of the Azorean species was also unknown. For this study, a chromosome count was performed and L. watsoniana showed 2n = 34. A phylogenetic approach was used to clarify the relationships of the Azorean endemic L. watsoniana and the La Palma endemic L. palmensis within the subtribe Lactucinae...
February 24, 2018: Biochemical Genetics
A Toumazi, E Comets, C Alberti, T Friede, F Lentz, N Stallard, S Zohar, M Ursino
BACKGROUND AND OBJECTIVE: Dose-finding, aiming at finding the maximum tolerated dose, and pharmacokinetics studies are the first in human studies in the development process of a new pharmacological treatment. In the literature, to date only few attempts have been made to combine pharmacokinetics and dose-finding and to our knowledge no software implementation is generally available. In previous papers, we proposed several Bayesian adaptive pharmacokinetics-based dose-finding designs in small populations...
April 2018: Computer Methods and Programs in Biomedicine
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