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https://www.readbyqxmd.com/read/29675600/a-probabilistic-view-on-the-deterministic-mutation-selection-equation-dynamics-equilibria-and-ancestry-via-individual-lines-of-descent
#1
Ellen Baake, Fernando Cordero, Sebastian Hummel
We reconsider the deterministic haploid mutation-selection equation with two types. This is an ordinary differential equation that describes the type distribution (forward in time) in a population of infinite size. This paper establishes ancestral (random) structures inherent in this deterministic model. In a first step, we obtain a representation of the deterministic equation's solution (and, in particular, of its equilibria) in terms of an ancestral process called the killed ancestral selection graph. This representation allows one to understand the bifurcations related to the error threshold phenomenon from a genealogical point of view...
April 19, 2018: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/29675120/supervised-multiway-factorization
#2
Eric F Lock, Gen Li
We describe a probabilistic PARAFAC/CANDECOMP (CP) factorization for multiway (i.e., tensor) data that incorporates auxiliary covariates, SupCP . SupCP generalizes the supervised singular value decomposition (SupSVD) for vector-valued observations, to allow for observations that have the form of a matrix or higher-order array. Such data are increasingly encountered in biomedical research and other fields. We use a novel likelihood-based latent variable representation of the CP factorization, in which the latent variables are informed by additional covariates...
2018: Electronic Journal of Statistics
https://www.readbyqxmd.com/read/29674983/is-there-a-conjunction-fallacy-in-legal-probabilistic-decision-making
#3
Bartosz W Wojciechowski, Emmanuel M Pothos
Classical probability theory (CPT) has represented the rational standard for decision making in human cognition. Even though CPT has provided many descriptively excellent decision models, there have also been some empirical results persistently problematic for CPT accounts. The tension between the normative prescription of CPT and human behavior is particularly acute in cases where we have higher expectations for rational decisions. One such case concerns legal decision making from legal experts, such as attorneys and prosecutors and, more so, judges...
2018: Frontiers in Psychology
https://www.readbyqxmd.com/read/29671740/spectral-reflectance-estimation-using-gaussian-processes-and-combination-kernels
#4
Ville Heikkinen
This paper explores hyperspectral reflectance factor estimation using Gaussian process regression with multispectral- and trichromatic measurements. Estimations are performed in visible- (400-700 nm) or visible-near infrared (400-980 nm) wavelength ranges using the learning-based approach, where sensor and light spectral characteristics are not required. We first construct new estimation models via Gaussian processes, show connection to previous kernel-based models, and then evaluate new models by using marginal likelihood optimization within the probabilistic interpretation...
July 2018: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/29671388/estimation-of-diffusion-constants-from-single-molecular-measurement-without-explicit-tracking
#5
Shunsuke Teraguchi, Yutaro Kumagai
BACKGROUND: Time course measurement of single molecules on a cell surface provides detailed information about the dynamics of the molecules that would otherwise be inaccessible. To extract the quantitative information, single particle tracking (SPT) is typically performed. However, trajectories extracted by SPT inevitably have linking errors when the diffusion speed of single molecules is high compared to the scale of the particle density. METHODS: To circumvent this problem, we develop an algorithm to estimate diffusion constants without relying on SPT...
April 11, 2018: BMC Systems Biology
https://www.readbyqxmd.com/read/29670344/cost-effectiveness-analysis-of-a-fixed-dose-combination-of-indacaterol-and-glycopyrronium-as-maintenance-treatment-for-copd
#6
Ming-Cheng Chan, Elise Chia-Hui Tan, Ming-Chin Yang
Objective: The aim of this study was to evaluate the cost-effectiveness of the long-acting beta-2 agonist (LABA)/long-acting muscarinic antagonist (LAMA) dual bronchodilator indacaterol/glycopyrronium (IND/GLY) as a maintenance treatment for COPD patients from the perspective of health care payer in Taiwan. Patients and methods: We adopted a patient-level simulation model, which included a cohort of COPD patients aged ≥40 years. The intervention used in the study was the treatment using IND/GLY, and comparators were tiotropium or salmeterol/fluticasone combination (SFC)...
2018: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/29669002/tractography-verified-by-intraoperative-magnetic-resonance-imaging-and-subcortical-stimulation-during-tumor-resection-near-the-corticospinal-tract
#7
Timo Münnich, Jan Klein, Elke Hattingen, Anika Noack, Eva Herrmann, Volker Seifert, Christian Senft, Marie-Therese Forster
BACKGROUND: Tractography is a popular tool for visualizing the corticospinal tract (CST). However, results may be influenced by numerous variables, eg, the selection of seeding regions of interests (ROIs) or the chosen tracking algorithm. OBJECTIVE: To compare different variable sets by correlating tractography results with intraoperative subcortical stimulation of the CST, correcting intraoperative brain shift by the use of intraoperative MRI. METHODS: Seeding ROIs were created by means of motor cortex segmentation, functional MRI (fMRI), and navigated transcranial magnetic stimulation (nTMS)...
April 14, 2018: Operative Neurosurgery (Hagerstown, Md.)
https://www.readbyqxmd.com/read/29667538/evaluation-of-gas-well-setback-policy-in-the-marcellus-shale-region-of-pennsylvania-in-relation-to-emissions-of-fine-particulate-matter
#8
Zoya Banan, Jeremy M Gernand
Implication The Marcellus shale gas is known as a significant source of criteria pollutants and studies show that the current setback distance in Pennsylvania is not adequate to protect the residents from exceeding the established limits. Even an effective setback distance to meet the annual exposure limit may not be adequate to meet the daily limit. The probability of exceeding the annual limit increases with number of wells per site. We use a probabilistic dispersion model to introduce a technical basis to select appropriate setback distances...
April 18, 2018: Journal of the Air & Waste Management Association
https://www.readbyqxmd.com/read/29666255/digitizing-omics-profiles-by-divergence-from-a-baseline
#9
Wikum Dinalankara, Qian Ke, Yiran Xu, Lanlan Ji, Nicole Pagane, Anching Lien, Tejasvi Matam, Elana J Fertig, Nathan D Price, Laurent Younes, Luigi Marchionni, Donald Geman
Data collected from omics technologies have revealed pervasive heterogeneity and stochasticity of molecular states within and between phenotypes. A prominent example of such heterogeneity occurs between genome-wide mRNA, microRNA, and methylation profiles from one individual tumor to another, even within a cancer subtype. However, current methods in bioinformatics, such as detecting differentially expressed genes or CpG sites, are population-based and therefore do not effectively model intersample diversity...
April 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29665803/plasmodium-vivax-and-plasmodium-falciparum-infection-dynamics-re-infections-recrudescences-and-relapses
#10
Michael T White, Stephan Karl, Cristian Koepfli, Rhea J Longley, Natalie E Hofmann, Rahel Wampfler, Ingrid Felger, Tom Smith, Wang Nguitragool, Jetsumon Sattabongkot, Leanne Robinson, Azra Ghani, Ivo Mueller
BACKGROUND: In malaria endemic populations, complex patterns of Plasmodium vivax and Plasmodium falciparum blood-stage infection dynamics may be observed. Genotyping samples from longitudinal cohort studies for merozoite surface protein (msp) variants increases the information available in the data, allowing multiple infecting parasite clones in a single individual to be identified. msp genotyped samples from two longitudinal cohorts in Papua New Guinea (PNG) and Thailand were analysed using a statistical model where the times of acquisition and clearance of each clone in every individual were estimated using a process of data augmentation...
April 17, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29660877/probabilistic-modelling-and-uncertainty-analysis-of-flux-and-water-balance-changes-in-a-regional-aquifer-system-due-to-coal-seam-gas-development
#11
J Sreekanth, Tao Cui, Trevor Pickett, David Rassam, Mat Gilfedder, Damian Barrett
Large scale development of coal seam gas (CSG) is occurring in many sedimentary basins around the world including Australia, where commercial production of CSG has started in the Surat and Bowen basins. CSG development often involves extraction of large volumes of water that results in depressurising aquifers that overlie and/or underlie the coal seams thus perturbing their flow regimes. This can potentially impact regional aquifer systems that are used for many purposes such as irrigation, and stock and domestic water...
April 12, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29660688/implementation-and-validation-of-an-improved-allele-specific-stutter-filtering-method-for-electropherogram-interpretation
#12
Tim Kalafut, Curt Schuerman, Joel Sutton, Tom Faris, Luigi Armogida, Jo-Anne Bright, John Buckleton, Duncan Taylor
Modern probabilistic genotyping (PG) software is capable of modeling stutter as part of the profile weighting statistic. This allows for peaks in stutter positions to be considered as allelic or stutter or both. However, prior to running any sample through a PG calculator, the examiner must first interpret the sample, considering such things as artifacts and number of contributors (NOC or N). Stutter can play a major role both during the assignment of the number of contributors, and the assessment of inclusion and exclusion...
March 31, 2018: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29658779/fully-closed-loop-multiple-model-probabilistic-predictive-controller-artificial-pancreas-performance-in-adolescents-and-adults-in-a-supervised-hotel-setting
#13
Gregory P Forlenza, Faye M Cameron, Trang T Ly, David Lam, Daniel P Howsmon, Nihat Baysal, Georgia Kulina, Laurel Messer, Paula Clinton, Camilla Levister, Stephen D Patek, Carol J Levy, R Paul Wadwa, David M Maahs, B Wayne Bequette, Bruce A Buckingham
BACKGROUND: Initial Food and Drug Administration-approved artificial pancreas (AP) systems will be hybrid closed-loop systems that require prandial meal announcements and will not eliminate the burden of premeal insulin dosing. Multiple model probabilistic predictive control (MMPPC) is a fully closed-loop system that uses probabilistic estimation of meals to allow for automated meal detection. In this study, we describe the safety and performance of the MMPPC system with announced and unannounced meals in a supervised hotel setting...
April 16, 2018: Diabetes Technology & Therapeutics
https://www.readbyqxmd.com/read/29658401/probabilistic-risk-assessment-of-gold-nanoparticles-after-intravenous-administration-by-integrating-in-vitro-and-in-vivo-toxicity-with-physiologically-based-pharmacokinetic-modeling
#14
Yi-Hsien Cheng, Jim E Riviere, Nancy A Monteiro-Riviere, Zhoumeng Lin
This study aimed to conduct an integrated and probabilistic risk assessment of gold nanoparticles (AuNPs) based on recently published in vitro and in vivo toxicity studies coupled to a physiologically based pharmacokinetic (PBPK) model. Dose-response relationships were characterized based on cell viability assays in various human cell types. A previously well-validated human PBPK model for AuNPs was applied to quantify internal concentrations in liver, kidney, skin, and venous plasma. By applying a Bayesian-based probabilistic risk assessment approach incorporating Monte Carlo simulation, probable human cell death fractions were characterized...
April 14, 2018: Nanotoxicology
https://www.readbyqxmd.com/read/29657808/hypothesized-diprotomeric-enzyme-complex-supported-by-stochastic-modelling-of-palytoxin-induced-na-k-pump-channels
#15
Gabriel D Vilallonga, Antônio-Carlos G de Almeida, Kelison T Ribeiro, Sergio V A Campos, Antônio M Rodrigues
The sodium-potassium pump (Na+ /K+ pump) is crucial for cell physiology. Despite great advances in the understanding of this ionic pumping system, its mechanism is not completely understood. We propose the use of a statistical model checker to investigate palytoxin (PTX)-induced Na+ /K+ pump channels. We modelled a system of reactions representing transitions between the conformational substates of the channel with parameters, concentrations of the substates and reaction rates extracted from simulations reported in the literature, based on electrophysiological recordings in a whole-cell configuration...
March 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29655947/co-occurrence-of-medical-conditions-exposing-patterns-through-probabilistic-topic-modeling-of-snomed-codes
#16
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
Patients associated with multiple co-occurring health conditions often face aggravated complications and less favorable outcomes. Co-occurring conditions are especially prevalent among individuals suffering from kidney disease, an increasingly widespread condition affecting 13% of the general population in the US. This study aims to identify and characterize patterns of co-occurring medical conditions in patients employing a probabilistic framework. Specifically, we apply topic modeling in a non-traditional way to find associations across SNOMED-CT codes assigned and recorded in the EHRs of >13,000 patients diagnosed with kidney disease...
April 12, 2018: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29653395/learning-physical-parameters-from-dynamic-scenes
#17
Tomer D Ullman, Andreas Stuhlmüller, Noah D Goodman, Joshua B Tenenbaum
Humans acquire their most basic physical concepts early in development, and continue to enrich and expand their intuitive physics throughout life as they are exposed to more and varied dynamical environments. We introduce a hierarchical Bayesian framework to explain how people can learn physical parameters at multiple levels. In contrast to previous Bayesian models of theory acquisition (Tenenbaum, Kemp, Griffiths, & Goodman, 2011), we work with more expressive probabilistic program representations suitable for learning the forces and properties that govern how objects interact in dynamic scenes unfolding over time...
April 10, 2018: Cognitive Psychology
https://www.readbyqxmd.com/read/29652581/a-learning-framework-for-winner-take-all-networks-with-stochastic-synapses
#18
Hesham Mostafa, Gert Cauwenberghs
Many recent generative models make use of neural networks to transform the probability distribution of a simple low-dimensional noise process into the complex distribution of the data. This raises the question of whether biological networks operate along similar principles to implement a probabilistic model of the environment through transformations of intrinsic noise processes. The intrinsic neural and synaptic noise processes in biological networks, however, are quite different from the noise processes used in current abstract generative networks...
April 13, 2018: Neural Computation
https://www.readbyqxmd.com/read/29652101/switching-from-sitagliptin-to-liraglutide-to-manage-patients-with-type-2-diabetes-in-the-uk-a-long-term-cost-effectiveness-analysis
#19
Anthony H Barnett, Simon Arnoldini, Barnaby Hunt, Gowri Subramanian, Christina Stentoft Hoxer
AIMS: The recent LIRA-SWITCH trial showed that switching from sitagliptin 100 mg to liraglutide 1.8 mg led to statistically significant and clinically relevant improvements in glycated haemoglobin (HbA1c ) and body mass index (BMI). Based on these findings, the aim of the present study was to assess the long-term cost-effectiveness of switching from sitagliptin to liraglutide in patients with type 2 diabetes in the UK. MATERIALS AND METHODS: The IQVIA CORE Diabetes Model Version 8...
April 13, 2018: Diabetes, Obesity & Metabolism
https://www.readbyqxmd.com/read/29651791/a-discrete-event-simulation-model-to-assess-the-economic-value-of-a-hypothetical-pharmacogenomics-test-for-statin-induced-myopathy-in-patients-initiating-a-statin-in-secondary-cardiovascular-prevention
#20
Dominic Mitchell, Jason R Guertin, Anick Dubois, Marie-Pierre Dubé, Jean-Claude Tardif, Ange Christelle Iliza, Fiorella Fanton-Aita, Alexis Matteau, Jacques LeLorier
BACKGROUND: Statin (HMG-CoA reductase inhibitor) therapy is the mainstay dyslipidemia treatment and reduces the risk of a cardiovascular (CV) event (CVE) by up to 35%. However, adherence to statin therapy is poor. One reason patients discontinue statin therapy is musculoskeletal pain and the associated risk of rhabdomyolysis. Research is ongoing to develop a pharmacogenomics (PGx) test for statin-induced myopathy as an alternative to the current diagnosis method, which relies on creatine kinase levels...
April 12, 2018: Molecular Diagnosis & Therapy
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