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Bayesian modeling

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https://www.readbyqxmd.com/read/28651371/sleep-and-physiological-dysregulation-a-closer-look-at-sleep-intraindividual-variability
#1
Bei Bei, Teresa E Seeman, Judith E Carroll, Joshua F Wiley
Study Objectives: Variable daily sleep (i.e., higher intraindividual variability; IIV) is associated with negative health consequences, but potential physiological mechanisms are poorly understood. This study examined the associations between sleep timing, duration, and quality IIV and physiological dysregulation, with diurnal cortisol trajectories as a proximal outcome, and allostatic load (AL) as a multi-system distal outcome. Methods: Participants are 436 adults (Mage±SD=54...
June 23, 2017: Sleep
https://www.readbyqxmd.com/read/28650962/novel-inference-models-for-estimation-of-abundance-survivorship-and-recruitment-in-mosquito-populations-using-mark-release-recapture-data
#2
Daniel Antunes Maciel Villela, Gabriela de Azambuja Garcia, Rafael Maciel-de-Freitas
BACKGROUND: Experiments involving mosquito mark-release-recapture (MRR) design are helpful to determine abundance, survival and even recruitment of mosquito populations in the field. Obstacles in mosquito MRR protocols include marking limitations due to small individual size, short lifespan, low efficiency in capturing devices such as traps, and individual removal upon capture. These limitations usually make MRR analysis restricted to only abundance estimation or a combination of abundance and survivorship, and often generate a great degree of uncertainty about the estimations...
June 26, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28650380/high-levels-of-post-migration-hiv-acquisition-within-nine-european-countries
#3
Debora Alvarez-Del Arco, Fakoya Ibidun, Christos Thomadakis, Nikos Pantazis, Giota Touloumi, Anne-Francoise Gennotte, Freke Zuure, Henrique Barros, Cornelia Staehelin, Siri Göpel, Christoph Boesecke, Tullio Prestileo, Alain Volny-Anne, Fiona Burns, Julia Del Amo
OBJECTIVE: We aimed to estimate the proportion of post-migration HIV acquisition among HIV-positive migrants in Europe. DESIGN: To reach HIV positive migrants we designed a cross sectional study performed in HIV clinics. METHODS: The study was conducted from July 2013-July 2015 in 57 clinics (9 European countries, targeting individuals over 18 years diagnosed in the preceding 5 years and born abroad. Electronic questionnaires supplemented with clinical data were completed in any of 15 languages...
June 23, 2017: AIDS
https://www.readbyqxmd.com/read/28649438/translational-learning-from-clinical-studies-predicts-drug-pharmacokinetics-across-patient-populations
#4
Markus Krauss, Ute Hofmann, Clemens Schafmayer, Svitlana Igel, Jan Schlender, Christian Mueller, Mario Brosch, Witigo von Schoenfels, Wiebke Erhart, Andreas Schuppert, Michael Block, Elke Schaeffeler, Gabriele Boehmer, Linus Goerlitz, Jan Hoecker, Joerg Lippert, Reinhold Kerb, Jochen Hampe, Lars Kuepfer, Matthias Schwab
Early indication of late-stage failure of novel candidate drugs could be facilitated by continuous integration, assessment, and transfer of knowledge acquired along pharmaceutical development programs. We here present a translational systems pharmacology workflow that combines drug cocktail probing in a specifically designed clinical study, physiologically based pharmacokinetic modeling, and Bayesian statistics to identify and transfer (patho-)physiological and drug-specific knowledge across distinct patient populations...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649436/using-approximate-bayesian-computation-to-quantify-cell-cell-adhesion-parameters-in-a-cell-migratory-process
#5
Robert J H Ross, R E Baker, Andrew Parker, M J Ford, R L Mort, C A Yates
In this work, we implement approximate Bayesian computational methods to improve the design of a wound-healing assay used to quantify cell-cell interactions. This is important as cell-cell interactions, such as adhesion and repulsion, have been shown to play a role in cell migration. Initially, we demonstrate with a model of an unrealistic experiment that we are able to identify model parameters that describe agent motility and adhesion, given we choose appropriate summary statistics for our model data. Following this, we replace our model of an unrealistic experiment with a model representative of a practically realisable experiment...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/28649336/phylogeography-of-a-widespread-small-carnivore-the-western-spotted-skunk-spilogale-gracilis-reveals-temporally-variable-signatures-of-isolation-across-western-north-america
#6
Adam W Ferguson, Molly M McDonough, Gema I Guerra, Margaret Rheude, Jerry W Dragoo, Loren K Ammerman, Robert C Dowler
We analyzed phylogeographic patterns in the western spotted skunk, Spilogale gracilis Merriam, 1890 (Carnivora: Mephitidae) in relation to historical events associated with Pre-Pleistocene Divergence (PPD) and Quaternary climate change (QCC) using mitochondrial DNA from 97 individuals distributed across Western North America. Divergence times were generated using BEAST to estimate when isolation in putative refugia occurred. Patterns and timing of demographic expansion was performed using Bayesian skyline plot...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649328/spatiotemporal-variation-in-mechanisms-driving-regional-scale-population-dynamics-of-a-threatened-grassland-bird
#7
Danielle M Ethier, Nicola Koper, Thomas D Nudds
To achieve national population targets for migratory birds, landscape-level conservation approaches are increasingly encouraged. However, knowledge of the mechanisms that drive spatiotemporal patterns in population dynamics are needed to inform scale-variant policy development. Using hierarchical Bayesian models and variable selection, we determined by which mechanism(s), and to what extent, changes in quantity and quality of surrogate grassland habitats contributed to regional variation in population trends of an obligatory grassland bird, Bobolink (Dolichonyx oryzivorous)...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649314/hierarchical-cortical-transcriptome-disorganization-in-autism
#8
Michael V Lombardo, Eric Courchesne, Nathan E Lewis, Tiziano Pramparo
BACKGROUND: Autism spectrum disorders (ASD) are etiologically heterogeneous and complex. Functional genomics work has begun to identify a diverse array of dysregulated transcriptomic programs (e.g., synaptic, immune, cell cycle, DNA damage, WNT signaling, cortical patterning and differentiation) potentially involved in ASD brain abnormalities during childhood and adulthood. However, it remains unclear whether such diverse dysregulated pathways are independent of each other or instead reflect coordinated hierarchical systems-level pathology...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28647608/a-route-based-pathway-analysis-framework-integrating-mutation-information-and-gene-expression-data
#9
Yue Zhao, Tham H Hoang, Pujan Joshi, Seung-Hyun Hong, Charles Giardina, Dong-Guk Shin
We propose a new way of analyzing biological pathways in which the analysis combines both transcriptome data and mutation information and uses the outcome to identify "routes" of aberrant pathways potentially responsible for the etiology of disease. Each pathway route is encoded as a Bayesian Network which is initialized with a sequence of conditional probabilities which are designed to encode directionality of regulatory relationships encoded in the pathways, i.e. activation and inhibition relationships. First, we demonstrate the effectiveness of our model through simulation in which the model was able to easily separate Test samples from Control samples using fictitiously perturbed pathway routes...
June 21, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28647485/dynamic-network-model-with-continuous-valued-nodes-for-longitudinal-brain-morphometry
#10
Rong Chen, Yuanjie Zheng, Erika Nixon, Edward H Herskovits
Longitudinal brain morphometry probes time-related brain morphometric patterns. We propose a method called dynamic network modeling with continuous valued nodes to generate a dynamic brain network from continuous valued longitudinal morphometric data. The mathematical framework of this method is based on state-space modeling. We use a bootstrap-enhanced least absolute shrinkage operator to solve the network-structure generation problem. In contrast to discrete dynamic Bayesian network modeling, the proposed method enables network generation directly from continuous valued high-dimensional short sequence data, being free from any discretization process...
June 21, 2017: NeuroImage
https://www.readbyqxmd.com/read/28647337/comparison-of-bayesian-regression-models-and-partial-least-squares-regression-for-the-development-of-infrared-prediction-equations
#11
V Bonfatti, F Tiezzi, F Miglior, P Carnier
The objective of this study was to compare the prediction accuracy of 92 infrared prediction equations obtained by different statistical approaches. The predicted traits included fatty acid composition (n = 1,040); detailed protein composition (n = 1,137); lactoferrin (n = 558); pH and coagulation properties (n = 1,296); curd yield and composition obtained by a micro-cheese making procedure (n = 1,177); and Ca, P, Mg, and K contents (n = 689). The statistical methods used to develop the prediction equations were partial least squares regression (PLSR), Bayesian ridge regression, Bayes A, Bayes B, Bayes C, and Bayesian least absolute shrinkage and selection operator...
June 21, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28647334/test-characteristics-of-milk-amyloid-a-elisa-somatic-cell-count-and-bacteriological-culture-for-detection-of-intramammary-pathogens-that-cause-subclinical-mastitis
#12
S Jaeger, F Virchow, P R Torgerson, M Bischoff, B Biner, S Hartnack, S R Rüegg
Bovine mastitis is an important disease in the dairy industry, causing economic losses as a result of withheld milk and treatment costs. Several studies have suggested milk amyloid A (MAA) as a promising biomarker in the diagnosis of mastitis. In the absence of a gold standard for diagnosis of subclinical mastitis, we estimated the diagnostic test accuracy of a commercial MAA-ELISA, somatic cell count (SCC), and bacteriological culture using Bayesian latent class modeling. We divided intramammary infections into 2 classes: those caused by major pathogens (e...
June 21, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28645697/clinical-high-resolution-mapping-of-the-proteoglycan-bound-water-fraction-in-articular-cartilage-of-the-human-knee-joint
#13
Mustapha Bouhrara, David A Reiter, Kyle W Sexton, Christopher M Bergeron, Linda M Zukley, Richard G Spencer
PURPOSE: We applied a recently introduced method to achieve clinically-feasible in-vivo mapping of the proteoglycan water fraction (PgWF) of human knee cartilage with improved spatial resolution and stability as compared to existing methods. MATERIAL AND METHODS: Multicomponent driven equilibrium single-pulse observation of T1 and T2 (mcDESPOT) datasets were acquired from the knees of two healthy young subjects and one older subject with previous knee injury. Each dataset was processed using Bayesian Monte Carlo (BMC) analysis incorporating a two-component tissue model...
June 20, 2017: Magnetic Resonance Imaging
https://www.readbyqxmd.com/read/28645443/once-or-twice-daily-non-vitamin-k-antagonist-oral-anticoagulants-in-asian-patients-with-atrial-fibrillation-a%C3%A2-meta-analysis-of-randomized-controlled-trials
#14
Kang-Ling Wang, Chun-Chih Chiu, Doreen Su-Yin Tan, Chun-Yi Lin, En-Yu Lai, Shinya Goto, Robert P Giugliano, Chern-En Chiang
BACKGROUND/PURPOSE: Non-vitamin K antagonist oral anticoagulants (NOACs) have a half-life of around 12 h. We aimed to clarify if there was any effect modification by dosing (once- or twice-daily) regimens in Asian patients. METHODS: Phase III randomized controlled trials of NOACs compared with warfarin in Asian patients with atrial fibrillation (AF) were identified and extracted from PubMed, CENTRAL, and CINAHL databases through November 2016. Outcomes were pooled by dosing regimens with the Mantel-Haenszel fixed-effects model...
June 20, 2017: Journal of the Formosan Medical Association, Taiwan Yi Zhi
https://www.readbyqxmd.com/read/28645318/detecting-consistent-patterns-of-directional-adaptation-using-differential-selection-codon-models
#15
Sahar Parto, Nicolas Lartillot
BACKGROUND: Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors...
June 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28645116/the-additive-effects-of-the-tm6sf2-e167k-and-pnpla3-i148m-polymorphisms-on-lipid-metabolism
#16
Lizhen Chen, Shuixian Du, Linlin Lu, Zhonghua Lin, Wenwen Jin, Doudou Hu, Xiangjun Jiang, Yongning Xin, Shiying Xuan
There is a genetic susceptibility for nonalcoholic fatty liver disease (NAFLD). To examine the role of genetic factors in the disease, a Bayesian analysis was performed to model gene relationships in NAFLD pathogenesis. The Bayesian analysis indicated a potential gene interaction between the TM6SF2 and PNPLA3 genes. Next, to explore the underlying mechanism at the cellular level, we evaluated the additive effects between the TM6SF2 E167K and PNPLA3 I148M polymorphisms on lipid metabolism. Hepa 1-6 cells were transfected with a control vector or with overexpression vectors for TM6SF2/PNPLA3-wild type, TM6SF2-mutant type, PNPLA3-mutant type, or TM6SF2/PNPLA3-mutant type...
June 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28644882/a-spatially-explicit-risk-assessment-approach-cetaceans-and-marine-traffic-in-the-pelagos-sanctuary-mediterranean-sea
#17
Maria Grazia Pennino, Antonella Arcangeli, Vinícius Prado Fonseca, Ilaria Campana, Graham J Pierce, Andrea Rotta, Jose Maria Bellido
Spatially explicit risk assessment is an essential component of Marine Spatial Planning (MSP), which provides a comprehensive framework for managing multiple uses of the marine environment, minimizing environmental impacts and conflicts among users. In this study, we assessed the risk of the exposure to high intensity vessel traffic areas for the three most abundant cetacean species (Stenella coeruleoalba, Tursiops truncatus and Balaenoptera physalus) in the southern area of the Pelagos Sanctuary, which is the only pelagic Marine Protected Area (MPA) for marine mammals in the Mediterranean Sea...
2017: PloS One
https://www.readbyqxmd.com/read/28644546/-18-f-fluoromisonidazole-uptake-in-advanced-stage-non-small-cell-lung-cancer-a-voxel-by-voxel-pet-kinetics-study
#18
Daniel R McGowan, Ruth E Macpherson, Sara L Hackett, Dan Liu, Fergus V Gleeson, W Gillies McKenna, Geoff S Higgins, John D Fenwick
PURPOSE: To determine the relative abilities of compartment models to describe time-courses of 18F-fluoromisonidazole (FMISO) uptake in tumor voxels of patients with non-small cell lung cancer (NSCLC) imaged using dynamic positron emission tomography. Also to use fits of the best-performing model to investigate changes in fitted rate-constants with distance from the tumor edge. METHODS: Reversible and irreversible two- and three-tissue compartment models were fitted to 24,662 individual voxel time activity curves (TACs) obtained from tumors in 9 patients, each imaged twice...
June 23, 2017: Medical Physics
https://www.readbyqxmd.com/read/28644419/context-relevant-prediction-model-for-copd-domain-using-bayesian-belief-network
#19
Hamid Mcheick, Lokman Saleh, Hicham Ajami, Hafedh Mili
In the last three decades, researchers have examined extensively how context-aware systems can assist people, specifically those suffering from incurable diseases, to help them cope with their medical illness. Over the years, a huge number of studies on Chronic Obstructive Pulmonary Disease (COPD) have been published. However, how to derive relevant attributes and early detection of COPD exacerbations remains a challenge. In this research work, we will use an efficient algorithm to select relevant attributes where there is no proper approach in this domain...
June 23, 2017: Sensors
https://www.readbyqxmd.com/read/28642595/3d-bayesian-cluster-analysis-of-super-resolution-data-reveals-lat-recruitment-to-the-t-cell-synapse
#20
Juliette Griffié, Leigh Shlomovich, David J Williamson, Michael Shannon, Jesse Aaron, Satya Khuon, Garth L Burn, Lies Boelen, Ruby Peters, Andrew P Cope, Edward A K Cohen, Patrick Rubin-Delanchy, Dylan M Owen
Single-molecule localisation microscopy (SMLM) allows the localisation of fluorophores with a precision of 10-30 nm, revealing the cell's nanoscale architecture at the molecular level. Recently, SMLM has been extended to 3D, providing a unique insight into cellular machinery. Although cluster analysis techniques have been developed for 2D SMLM data sets, few have been applied to 3D. This lack of quantification tools can be explained by the relative novelty of imaging techniques such as interferometric photo-activated localisation microscopy (iPALM)...
June 22, 2017: Scientific Reports
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