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Numerical Optimization of a Walk-on-Spheres Solver for the Linear Poisson-Boltzmann Equation

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communications in computational Physics 2013年第1期13卷 195-206页

作者： Travis Mackoy robert c.Harris Jesse Johnson Michael Mascagni Marcia O.Fenley Institute of Molecular Biophysics Florida State UniversityTallahasseeFL 32306USA Department of Physics Florida State UniversityTallahasseeFL 32306USA Departments of computer Science Mathematics and Scientific ComputingFlorida State UniversityTallahasseeFL 32306USA

Stochastic walk-on-spheres(WOS)algorithms for solving the linearized Poisson-Boltzmann equation(LPBE)provide several attractive features not available in traditional deterministic solvers:Gaussian error bars can be computed easily,the algorithm is readily parallelized and requires minimal memory and multiple solvent environments can be accounted for by reweighting ***,previouslyreported computational times of these Monte carlo methods were not competitive with existing deterministic numerical *** present paper demonstrates a series of numerical optimizations that collectively make the computational time of these Monte carlo LPBE solvers competitive with deterministic *** optimization techniques used are to ensure that each atom’s contribution to the variance of the electrostatic solvation free energy is the same,to optimize the bias-generating parameters in the algorithm and to use an epsilon-approximate rather than exact nearest-neighbor search when determining the size of the next step in the Brownian motion when outside the molecule.

关键词： Poisson-Boltzmann equation walk-on-spheres solvation

Validation of the Rockall scoring system for outcomes from non-variceal upper gastrointestinal bleeding in a canadian setting

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World Journal of Gastroenterology 2006年第48期12卷 7779-7785页

作者： robert A Enns Yves M Gagnon Alan N Barkun David Armstrong Jamie c Gregor Richard N Fedorak RUGBE Investigators Group Division of Gastroenterology University of British Columbia Vancouver Canada Occam Research & consulting Inc. VancouverCanada Department of Medicine Division of Gastroenterology McGill University and the McGill UniversityHealth Center Montreal Canada Division of Gastroenterology McMaster University Medical Centre Hamilton Canada Division of Gastroenterology University of Western Ontario London Canada Division of Gastroenterology University of Alberta Edmonton Canada 不详

AIM: To validate the Rockall scoring system for predicting outcomes of rebleeding, and the need for a surgical procedure and death. METHODS: We used data extracted from the Registry of Upper Gastrointestinal Bleeding and Endoscopy including information of 1869 patients with non-variceal upper gastrointestinal bleeding treated in canadian hospitals. Risk scores were calculated and used to classify patients based on outcomes. For each outcome, we used χ2 goodness-of-fit tests to assess the degree of calibration, and built receiver operating characteristic curves and calculated the area under the curve (AUc) to evaluate the discriminative ability of the scoring system. RESULTS: For rebleeding, the χ2 goodness-of-fit test indicated an acceptable fit for the model [χ2 (8) = 12.83, P = 0.12]. For surgical procedures [χ2 (8) = 5.3, P = 0.73] and death [χ2 (8) = 3.78, P = 0.88], the tests showed solid correspondence between observed proportions and predicted probabilities. The AUc was 0.59 (95% cI: 0.55-0.62) for the outcome of rebleeding and 0.60 (95% cI: 0.54-0.67) for surgical procedures, representing apoor discriminative ability of the scoring system. For the outcome of death, the AUc was 0.73 (95% cI: 0.69-0.78), indicating an acceptable discriminative ability. cONcLUSION: The Rockall scoring system provides an acceptable tool to predict death, but performs poorly for endpoints of rebleeding and surgical procedures.

关键词： Upper gastrointestinal bleeding Nonvariceal Predictors Rockall Outcomes

Reheating and entropy perturbations in fibre inflation

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chinese Physics c 2020年第1期44卷 136-148页

作者： Bao-Min Gu robert Brandenberger Department of Physics Nanchang UniversityNanchang 330031China center for Relativistic Astrophysics and High Energy Physics Nanchang UniversityNanchang 330031China Department of Physics McGill UniversityMontr′ealQCH3A 2T8Canada

We study reheating in some one and two field realizations of fibre *** find that reheating begins with a phase of preheating in which long wavelength fluctuation modes are *** two field models there is a danger that the parametric amplification of infrared fluctuations in the second scalar field-associated with an entropy mode-might induce an instability of the curvature *** show that,at least in the models we consider,the entropy mode has a sufficiently large mass to prevent this ***,from the point of view of reheating the models we consider are well-behaved.

关键词： inflation preheating perturbations

Genetic variation amongst biotypes of Dactylopius tomentosus

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Insect Science 2015年第3期22卷 360-374页

作者： catherine W. Mathenge Markus Riegler G. Andrew c. Beattie robert N. Spooner-Hart Paul Holford School of Science and Health University of Western Sydney (Hawkesbury Campus) Hawkesbury Institute for the Environment University of Western Sydney Locked Bag 1797 Penrith NSW 2751 Australia

The tomentose cochineal scale insect, Dactylopius tomentosus （Lamarck）（Hemiptera： Dactylopiidae）, is an important biological control agent against invasive species of cylindropuntia （caryophyllales： cactaceae）. Recent studies have demonstrated that this scale is composed of host-affiliated biotypes with differential host specificity and fitness on particular host species. We investigated genetic variation and phylogenetic rela-tionships among D. tomentosus biotypes and provenances to examine the possibility that genetic diversity may be related to their host-use pattern, and whether their phylogenetic relationships would give insights into taxonomic relatedness of their host plants. Nucleotide sequence comparison was accomplished using sequences of the mitochondrial cytochrome c oxidase I （cOI） gene. Sequences of individuals from the same host plant within a region were identical and characterized by a unique haplotype. Individuals belonging to the same biotype but from different regions had similar haplotypes. However, haplotypes were not shared between different biotypes. Phylogenetic analysis grouped the monophyletic D. tomentosus into 3 well-resolved clades of biotypes. The phylogenetic relationships and clustering of biotypes corresponded with known taxonomic relatedness of their hosts. Two biotypes, Fulgida and Mamillata, tested positive for Wolbachia （α-Proteobacteria）, a common endosymbiont of insects. The Wolbachia sequences were serendipitously detected by using insect-specific cOI DNA barcoding primers and are most similar to Wolbachia Supergroup F strains. This study is the first molecular characterization of cochineal biotypes that, together with Wolbachia sequences, contribute to the better identification of the biotypes of cochineal insects and to the biological control of cacti using host-specific biotypes of the scale.

关键词： biotypes cylindropuntia spp. Dactylopiidae Hemiptera tomentose cochineal scale Wolbachia spp.

cyclooxygenase-2 and epithelial growth factor receptor up-regulation during progression of Barrett's esophagus to adenocarcinoma

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World Journal of Gastroenterology 2006年第6期12卷 928-934页

作者： Yan Li John M Wo Mukunda B Ray Whitney Jones Ruifeng R Su Susan Ellis robert c G Martin Division of Surgical Oncology University of Louisville School ofMedicine Louisville KY 40202 United States Division of Gastroenterology/Hepatology University of Louisville School of MedicineLouisville KY 40202 United States Department of Anatomical Pathology University of Louisville School of Medicine Louisville KY40202 United States

AIM： To investigate the expression of cyclooxygenase-2 （cOX-2） and epithelial growth factor receptor （EGFR） throughout the progression of Barrett＇s esophagus （BE）. METHODS： cOX-2 and EGFR protein expressions were detected by using immunohistochemical method. A detailed cytomorphological changes were determined. Areas of cOX-2 and EGFR expression were quantified by using computer Imaging System. RESULTS： The expressions of both cOX-2 and EGFR increased along with the progression from BE to esophagus adenocarcinoma （EAc）. A positive correlation was found between cOX-2 expression and EGFR expression. cONcLUSION： cOX-2 and EGFR may be cooperative in the stepwise progression from BE to EAc, thereby leading to carcinogenesis.

关键词： cycloxygenase -2 (cOX-2) Epithelial growth factor receptor (EGFR) Barrett's esophagus carcinogenesis

How do we define “castration” in men on androgen deprivation therapy?

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Asian Journal of Andrology 2020年第5期22卷 441-446页

作者： Sarin Itty robert H Getzenberg Dr.Kiran c.Patel college of Allopathic Medicine Nova Southeastern UniversityFort LauderdaleFL33328USA

Androgen deprivation therapy(ADT)is the mainstay for the treatment of advanced prostate *** the clinical evolution from surgical orchiectomy,we have typically used ADT and orchiectomy to be synonymous terms for *** goal of this study is to determine if,in contemporary medical practice,surgical and chemical castration provide for similar levels of diminishment of total and free ***,what approaches should be used to most accurately measure testosterone levels in men with advanced prostate cancer and what cutoff values,for example for total testosterone 50 ng dl-1 or 20 ng dl-1,should be *** available in the literature have been analyzed and compiled to address these ***,evidence is provided that free testosterone,the biologically active component,should be utilized to provide clinically relevant state of castration.

关键词： androgen androgen deprivation therapy castration free testosterone testosterone

Bacillus amyloliquefaciens cEcT 5940 improves performance and gut function in broilers fed different levels of protein and/or under necrotic enteritis challenge

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Animal Nutrition 2021年第1期7卷 185-197页

作者： Kosar Gharib-Naseri Juliano c.P.Dorigam Kiran Doranalli Natalie Morgan robert A.Swick Mingan choct Shu-Biao Wu School of Environmental and Rural Science University of New EnglandArmidaleNSW 2351Australia Evonik Nutrition&care GmbH Rodenbacher Chaussee 463457 Hanau-WolfgangGermany University of New England Armidale 2351Australia

Two studies were conducted to investigate the effect of Bacillus amyloliquefaciens cEcr 5940(BA)as a probiotic on growth performance,amino acid digestibility and bacteria population in broiler chickens under a subclinical necrotic enteritis(NE)challenge and/or fed diets with different levels of crude protein(cP).Both studies consisted of a 2×2 factorial arrangement of treatments with 480 Ross 308 mix-sexed broiler *** study 1,treatments included 1)NE challenge(+/),and 2)BA(1.0×106 cFU/g of feed)supplementation(+/-).In study 2,all birds were under NE challenge,and treatments were 1)cP level(Standard/Reduced[2%less than standard])and 2)BA(1.0×106 cFU/g of feed)supplementation(+/-).After inducing NE infection,blood samples were taken on d 16 for uric acid evaluation,and cecal samples were collected for bacterial *** both studies,ileal digesta was collected on d 35 for nutrient digestibility *** study 1,the NE challenge reduced body weight gain(BWG),supressed feed conversion ratio(FcR)and serum uric acid levels(Pcreased BWG(Pced FcR(P=0.043)across dietary treatments,regardless of ***(P=0.030)and Ruminococcus(P=0.029)genomic DNA copy numbers and concentration of butyrate(P=0.017)were higher in birds fed the diets supplemented with *** study 2,reduced protein(RcP)diets decreased BWG(P=0.010)and uric acid levels in serum(PcR(P=0.005)and increased Ruminococcus numbers(P=0.018)and butyrate concentration(P=0.033)in the ceca,regardless of dietary cP ***,addition of BA reduced clostridium perfringens numbers only in birds fed with RcP diets(P=0.039).At d 35,BA sup-plemented diets showed higher apparent ileal digestibility of cystine(P=0.013),valine(P=0.020),and lysine(P=0.014).In conclusion,this study suggests positive effects of BA supplementation in broiler diets via modulating gut microflora and improving nutrient upta

关键词： Bacillus amyloliquefaciens Necrotic enteritis Growth performance Reduced protein diet Bacteria population Gut function

A tunable diode laser absorption spectrometer for formaldehyde atmospheric measurements validated by simulation chamber instrumentation

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Journal of Environmental Sciences 2012年第1期24卷 22-33页

作者： V.catoire F.Bernard Y.Mbarki A.Mellouki G.Eyglunent V.Daёle c.robert Laboratoire de Physique et chimie de l'Environnement et de l'Espace (LPc2E) CNRS-Universit d'Orlans (UMR 6115)Observatoire des Sciences de l'Univers en rgion Centre (OSUC)3A Avenue de la Recherche Scientifique45071 Orlans Cedex 2France Institut de combustion ArothermiqueRactivit et Environnement (ICARE)CNRS (UPR 3021)Observatoire des Sciences de l'Univers en rgion Centre (OSUC)1C Avenue de la Recherche Scientifique45071 Orlans Cedex 2France

A tunable diode laser absorption spectrometer （TDLAS） for formaldehyde atmospheric measurements has been set up and validated through comparison experiments with a Fourier transform infrared spectrometer （FT-IR） in a simulation *** was generated in situ in the chamber from reaction of ethene with *** HcHO ro-vibrational line intensities （at 2909.71,2912.09 and 2914.46 cm-1） possibly used by TDLAS were calibrated by FT-IR spectra simultaneously recorded in the 1600–3200 cm-1 domain during ethene ozonolysis,enabling the on-line deduction of the varying concentration for HcHO in *** experimental line intensities values inferred confirmed the calculated ones from the updated HITRAN *** addition,the feasibility of stratospheric in situ HcHO measurements using the 2912.09 cm-1 line was *** TDLAS performances were also assessed,leading to a 2σ detection limit of 88 ppt in volume mixing ratio with a response time of 60 sec at 30 Torr and 294 K for 112 m optical *** part of this work,the room-temperature rate constant of this reaction and the HcHO formation yield were found to be in excellent agreement with the compiled literature data.

关键词： formaldehyde ethene ozonolysis in situ measurements stratosphere simulation chamber TDLAS FT-IR

Are eavesdroppers multimodal？ Sensory exploitation of floral signals by a non-native cockroach Blatta orientalis

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current Zoology 2011年第2期57卷 162-174页

作者： Rodrigo c. VERGARA Alejandra TORRES-ARANEDA Diego A. VILLAGRA robert A. RAGUSO Mary T. K. ARROYO cristian A. VILLAGRA Instituto de Ecologfa y Biodiversidad IEB Universidad de Chile Santiago Chile centro de Recursos Naturales y Medio Ambiente Departamento de Qufmica Facultad de Ciencias Universidad de Tarapaca Arica Chile Department of Neurobiology and Behavior Cornell University Ithaca NY 14853 USA Instituto de Entomologfa Universidad Metropolitana de Ciencias de la Educacion Casilla 147 SantiagoChile

The study of multi-modal communication has only recently been extended to innate and learned interactions between flowers and their animal visitors, and usually only to pollinators. Here we studied the relevance of floral scent and visual display of a night blooming, putatively hawkmoth-pollinated plant Oenothera acaulis （Onagraceae） in the attraction of non-native cockroaches Blatta orientalis （Blattodea： Blattidae）, which function as facultative floral larcenists in coastal habitats of central chile. We experimentally decoupled visual （corolla） and olfactory （fragrance） stimuli by presenting paper corollas and green mesh bags, with or without a freshly-picked natural flower inside. We then contrasted the behavioral responses of roaches in these treatments with those to the natural combination of traits in actual flowers and their respective control treatments, measuring the roaches＇ frequency of first visits, mean and total residence time spent in each treatment. The roaches primarily used olfactory cues when approaching O. acaulis flowers at two biologically relevant spatial scales. In addition, the presence of conspecific roaches had a strong influence on recruitment to the experimental arena, increasing the statistical differences among treatments. Our results suggest a primacy of floral fragrance over visual stimuli in the foraging responses of B. orientalis. Olfactory cues were necessary and sufficient to attract the roaches, and the visual cues presented in our manipulations only marginally increased their attraction within a 20 cm diameter of the stimulus. The full spectrum of floral visitation behavior was not elicited by the artificial flowers, suggesting the need for additional tactile or contact chemosensory stimuli not provided by paper. Although the nitrogenous scent compounds that we found in O. acaulis flowers are almost exclusively found in hawkmoth-pollinated flowers, the attractiveness of these compounds to a non-native, facultative flower-visiti

关键词： Flower fragrance corolla visual display Larcenists Night-blooming plants