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Monte carlo

Svetlana Cherlin, Sarah E Heaps, Tom M W Nye, Richard J Boys, Tom A Williams, T Martin Embley
Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inferred as part of the analysis. Yet identifying the root position is a key component of phylogenetic inference because it provides a point of reference for polarising ancestor/descendant relationships and therefore interpreting the tree...
November 15, 2017: Molecular Biology and Evolution
Guillaume Saulière, Jérôme Dedecker, Laurie-Anne Marquet, Pierre Rochcongar, Jean-Francois Toussaint, Geoffroy Berthelot
The clinical and biological follow-up of individuals, such as the biological passport for athletes, is typically based on the individual and longitudinal monitoring of hematological or urine markers. These follow-ups aim to identify abnormal behavior by comparing the individual's biological samples to an established baseline. These comparisons may be done via different ways, but each of them requires an appropriate extra population to compute the significance levels, which is a non-trivial issue. Moreover, it is not necessarily relevant to compare the measures of a biomarker of a professional athlete to that of a reference population (even restricted to other athletes), and a reasonable alternative is to detect the abnormal values by considering only the other measurements of the same athlete...
November 15, 2017: Biostatistics
Daniel D Nelson, Yuanjie Pan, Rohan V Tikekar, Nily R Dan, N Nitin
The stability of active compounds encapsulated in nanoparticles depends on the resistance of the particles to diffusion of environmental degradation agents. In this paper, off-lattice Monte Carlo simulations are used to investigate a suspension of nanostructured lipid carriers (NLC) composed of interspaced liquid and solid lipid domains, immersed in a solution containing molecules representing oxidative or other degradation agents. The simulations examine the diffusion of the degradation agents into the nanoparticles as a function of nanoparticle size, solid domain fraction, and domain size...
November 17, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Hui Khee Looe, Bjoern Delfs, Daniela Poppinga, Ping Jiang, Dietrich Harder, Bjoern Poppe
The well-known field-size dependent overresponse in small-field photon-beam dosimetry of solid-state detectors equipped with very thin sensitive volumes, such as the PTW microDiamond, cannot be caused by the photon and electron interactions within these sensitive layers because they are only a few micrometers thick. The alternative explanation is that their overresponse is caused by the combination of two effects, the modification of the secondary electron fluence profile i) by a field size too small to warrant lateral secondary electron equilibrium and ii) by the density-dependent electron ranges in the structural detector materials placed in front of or backing the sensitive layer...
November 17, 2017: Physics in Medicine and Biology
Jesper Fonslet, Boon Quan Lee, Thuy A Tran, Mattia Siragusa, Mikael Jensen, Tibor Kibedi, Andrew E Stuchbery, Gregory W Severin
<b>Introduction:</b> <sup>135</sup>La has favorable nuclear and chemical properties for Auger-based targeted internal radiotherapy. Here we present detailed investigations of the production, emissions, imaging characteristics, and dosimetry related to <sup>135</sup>La therapy. <b>Methods and Results:</b> <sup>135</sup>La was produced by 16.5 MeV proton irradiation of metallic <sup>nat</sup>Ba on a medical cyclotron, and was isolated and purified by trap-and-release on weak cation-exchange resin...
November 17, 2017: Physics in Medicine and Biology
Kannan Sridharan, Gowri Sivaramakrishnan
AIMS: Topical growth factors accelerate wound healing in patients with diabetic foot ulcers (DFU). Due to the absence of head to head comparisons, we carried out Bayesian network meta-analysis to compare the efficacy and safety of growth factors. METHODS: Using an appropriate search strategy, randomized controlled trials on topical growth factors compared with standard of care in patients with DFU, were included. Proportion of patients with complete healing was the primary outcome...
November 17, 2017: British Journal of Clinical Pharmacology
Harshit Mishra, Subhankar Karmakar, Rakesh Kumar, Praneeth Kadambala
The handling and management of municipal solid waste (MSW) are major challenges for solid waste management in developing countries. Open dumping is still the most common waste disposal method in India. However, landfilling also causes various environmental, social, and human health impacts. The generation of heavily polluted leachate is a major concern to public health. Engineered barrier systems (EBSs) are commonly used to restrict potentially harmful wastes by preventing the leachate percolation to groundwater and overflow to surface water bodies...
November 16, 2017: Environmental Science and Pollution Research International
Michio Iwaoka, Toshiki Suzuki, Yuya Shoji, Kenichi Dedachi, Taku Shimosato, Toshiya Minezaki, Hironobu Hojo, Hiroyuki Onuki, Hiroshi Hirota
Single amino acid potential (SAAP) would be a prominent factor to determine peptide conformations. To prove this hypothesis, we previously developed SAAP force field for molecular simulation of polypeptides. In this study, the force field was renovated to SAAP3D force field by applying more accurate three-dimensional main-chain parameters, instead of the original two-dimensional ones, for the amino acids having a long side-chain. To demonstrate effectiveness of the SAAP3D force field, replica-exchange Monte Carlo (REMC) simulation was performed for two benchmark short peptides, chignolin (H-GYDPETGTWG-OH) and C-peptide (CHO-AETAAAKFLRAHA-NH2)...
November 17, 2017: Journal of Computer-aided Molecular Design
Alejandro Méndez-Ardoy, Nagula Markandeya, Xuesong Li, Yu-Tang Tsai, Gilles Pecastaings, Thierry Buffeteau, Victor Maurizot, Luca Muccioli, Frédéric Castet, Ivan Huc, Dario M Bassani
Aromatic foldamers are bioinspired architectures whose potential use in materials remains largely unexplored. Here we report our investigation of vertical and horizontal charge transport over long distances in helical oligo-quinolinecarboxamide foldamers organized as single monolayers on Au or SiO2. Conductive atomic force microscopy showed that vertical conductivity is efficient and that it displays a low attenuation with foldamer length (0.06 Å(-1)). In contrast, horizontal charge transport is found to be negligible, demonstrating the strong anisotropy of foldamer monolayers...
October 1, 2017: Chemical Science
Andrés Bustamante, Juan Sotelo-Campos, Daniel G Guerra, Martin Floor, Christian M A Wilson, Carlos Bustamante, Mauricio Báez
Knots are natural topologies of chains. Yet, little is known about spontaneous knot formation in a polypeptide chain-an event that can potentially impair its folding-and about the effect of a knot on the stability and folding kinetics of a protein. Here we used optical tweezers to show that the free energy cost to form a trefoil knot in the denatured state of a polypeptide chain of 120 residues is 5.8 ± 1 kcal mol(-1). Monte Carlo dynamics of random chains predict this value, indicating that the free energy cost of knot formation is of entropic origin...
November 17, 2017: Nature Communications
Sanggyu Chong, Günther Thiele, Jihan Kim
Metal-organic frameworks are known to contain defects within their crystalline structures. Successful engineering of these defects can lead to modifications in material properties that can potentially improve the performance of many existing frameworks. Herein, we report the high-throughput computational screening of a large experimental metal-organic framework database to identify 13 frameworks that show significantly improved methane storage capacities with linker vacancy defects. The candidates are first identified by focusing on structures with methane-inaccessible pores blocked away from the main adsorption channels...
November 16, 2017: Nature Communications
Mark G Papich, Cindy Lindeman
The Clinical and Laboratory Standards Institute (CLSI) uses cephalothin as the class representative for testing veterinary isolates for susceptibility to other first-generation cephalosporins, including cephalexin. We examined replacing cephalothin with cephalexin because cephalexin is used more often clinically. Bacterial isolates were obtained from dogs and cats from a national surveillance program. CLSI testing methods were used to determine the MIC for 4 cephalosporins used in veterinary medicine. Cephalexin clinical breakpoints for canine isolates were established by using published pharmacokinetic data and Monte Carlo simulations to calculate the probability of target attainment (PTA)...
November 1, 2017: Journal of Veterinary Diagnostic Investigation
Gustavo Gustavo Mora-García, María S Ruiz-Díaz, Fabian Espitia-Almeida, Doris Gómez-Camargo
BACKGROUND: Adiponectin is a hormone secreted by adipose tissue. It regulates glycolysis and lipolysis and is involved in the pathophysiology of diabetes and related disorders. Its activity is mainly mediated by the transmembrane receptors AdipoR1 and AdipoR2, which are encoded by ADIPOR1 (1q32.1) and ADIPOR2 (12p13.33) genes, respectively. In genetic association studies, single nucleotide polymorphisms (SNPs) in or near these genes have been associated with metabolic alterations. However, these relationships are still controversial...
July 2017: Review of Diabetic Studies: RDS
Jenny H Kang, Quang A Le
BACKGROUND: Bariatric surgery has proved to be an effective strategy in treating obesity. However, randomized controlled trials (RCTs) of 3 most common bariatric surgery procedures, Roux-en-Y gastric bypass (RYGB), sleeve gastrectomy (SG), and laparoscopic adjustable gastric band (LAGB), reported inconsistent results. We performed a systematic review and network meta-analysis to synthesize evidence of effectiveness of the 3 common bariatric procedures from relevant RCTs. METHODS: The present study was a systematic review and network meta-analysis of RCTs...
November 2017: Medicine (Baltimore)
Bing Li, Steven M Abel
The adsorption of polymers onto fluid membranes is a problem of fundamental interest in biology and soft materials, in part because the flexibility of membranes can lead to nontrivial coupling between polymer and membrane configurations. Here, we use Monte Carlo computer simulations to study the adsorption of a semiflexible polymer onto a fluid membrane vesicle. Polymer adsorption can significantly impact both the vesicle and polymer shapes, and we identify distinct classes of configurations that emerge as a function of polymer persistence length, membrane bending rigidity, adsorption strength, and vesicle size...
November 16, 2017: Soft Matter
I Levin, V Krayzman, G Cibin, M G Tucker, M Eremenko, K Chapman, R L Paul
Perovskite potassium sodium niobates, K1-xNaxNbO3, are promising lead-free piezoelectrics. Their dielectric and piezoelectric characteristics peak near x = 0.5, but the reasons for such property enhancement remain unclear. We addressed this uncertainty by analyzing changes in the local and average structures across the x = 0.5 composition, which have been determined using simultaneous Reverse Monte Carlo fitting of neutron and X-ray total-scattering data, potassium EXAFS, and diffuse-scattering patterns in electron diffraction...
November 15, 2017: Scientific Reports
Masataka Yamauchi, Hisashi Okumura
We developed a two-dimensional replica-permutation molecular dynamics method in the isothermal-isobaric ensemble. The replica-permutation method is a better alternative to the replica-exchange method. It was originally developed in the canonical ensemble. This method employs the Suwa-Todo algorithm, instead of the Metropolis algorithm, to perform permutations of temperatures and pressures among more than two replicas so that the rejection ratio can be minimized. We showed that the isothermal-isobaric replica-permutation method performs better sampling efficiency than the isothermal-isobaric replica-exchange method and infinite swapping method...
November 14, 2017: Journal of Chemical Physics
Z Jiang, Z Dou, W L Song, J Xu, Z Y Wu
Objective: To compare results of different methods: in organizing HIV viral load (VL) data with missing values mechanism. Methods We used software SPSS 17.0 to simulate complete and missing data with different missing value mechanism from HIV viral loading data collected from MSM in 16 cities in China in 2013. Maximum Likelihood Methods Using the Expectation and Maximization Algorithm (EM), regressive method, mean imputation, delete method, and Markov Chain Monte Carlo (MCMC) were used to supplement missing data respectively...
November 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
Jacqueline A R Shea, Eric Neuscamman
We demonstrate that a broad class of excited state variational principles is not size consistent. In light of this difficulty, we develop and test an approach to excited state optimization that transforms between variational principles in order to achieve state selectivity, size consistency, and compatibility with quantum Monte Carlo. To complement our formal analysis, we provide numerical examples that confirm these properties and demonstrate how they contribute to a more black box approach to excited states in quantum Monte Carlo...
November 15, 2017: Journal of Chemical Theory and Computation
Charles V Schwab, Gretchen A Mosher, Saxon J Ryan
Keeping workers safe is a continuing challenge in agricultural production. Risk assessment methodologies have been used widely in other industries to better understand systems and enhance decision making, yet their use in production agriculture has been limited. This article describes the considerations and the approach taken to measure the difference in worker injury risks between two agricultural production systems. A model was developed specifically for the comparison of worker injury risk between corn and biofuel switchgrass production systems...
July 31, 2017: Journal of Agricultural Safety and Health
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