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The consequences of genomic architecture on ecological speciation in postglacial fishes

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Current Zoology 2013年第1期59卷 53-71页

作者： Sean m. ROGERS jonathan A. mEE Ella BOWLES Department of Biological Sciences University of Calgary 2500 University Drive NW Calgary Alberta T2N 1N4 Canada

The quest for the origin of species has entered the genomics era. Despite decades of evidence confirming the role of the environment in ecological speciation, an understanding of the genomics of ecological speciation is still in its infancy. In this review, we explore the role of genomic architecture in ecological speciation in postglacial fishes. Growing evidence for the num- ber, location, effect size, and interactions among the genes underlying population persistence, adaptive trait divergence, and re- productive isolation in these fishes reinforces the importance of considering genomic architecture in studies of ecological speci- ation. Additionally, these populations likely adapt to new freshwater environments by selection on standing genetic variation, as de novo mutations are unlikely under such recent divergence times. We hypothesize that modular genomic architectures in post- glacial fish taxa may be associated with the probability of population persistence. Empirical studies have confirmed the genic na- ture of ecological speciation, implicating surprisingly extensive linkage disequilibrium across the genome. An understanding of these genomic mosaics and how they contribute to reproductive barriers remains unclear, but migration rates and the strength of selection at these loci is predicted to influence the likelihood of population divergence. Altogether, understanding the role of ge- nomic architecture is an important component of speciation research and postglacial fishes continue to provide excellent organ- isms to test these questions, both from the perspective of variation in architectures among taxa, and with respect to the distinct environments they have colonized. However, more empirical tests of ecological speciation predictions are needed [Current Zoo- logy 59 （1）： 53-71, 2013].

关键词： Adaptation Ecological speciation Genomic architecture modularity Postglacial fishes QTL

Partial Shape matching Without Point-Wise Correspondence

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Numerical mathematics(Theory,methods and Applications) 2013年第1期6卷 223-244页

作者： jonathan Pokrass Alexander m.Bronstein michael m.Bronstein School of Electrical Engineering Tel Aviv UniversityIsrael Institute of Computational Science Faculty of InformaticsUniversitàdella Svizzera Italiana(USI)LuganoSwitzerland

Partial similarity of shapes is a challenging problem arising in many important applications in computer vision,shape analysis,and graphics,*** one has to deal with partial information and acquisition *** problem is especially hard when the underlying shapes are non-rigid and are given up to a *** matching is usually approached by computing local descriptors on a pair of shapes and then establishing a point-wise non-bijective correspondence between the two,taking into account possibly different *** this paper,we introduce an alternative correspondence-less approach to matching fragments to an entire shape undergoing a non-rigid *** use region-wise local descriptors and optimize over the integration domains on which the integral descriptors of the two parts *** problem is regularized using the mumford-Shah *** show an efficient discretization based on the Ambrosio-Tortorelli approximation generalized to triangular point clouds and meshes,and present experiments demonstrating the success of the proposed method.

关键词： Deformable shapes partial matching partial correspondence partial similarity diffusion geometry Laplace-Beltrami operator shape descriptors heat kernel signature mumford-Shah regularization

Convergence Detection in Direct Simulation monte Carlo Calculations for Steady State Flows

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Communications in Computational Physics 2011年第9期10卷 807-822页

作者： jonathan m.Burt Iain D.Boyd U.S.Air Force Research Laboratory Wright-Patterson Air Force BaseOH 45433USA Department of Aerospace Engineering University of Michigan1320 Beal AvenueAnn ArborMI 48109USA

A new criterion is presented to detect global convergence to steady state,and to identify local transient characteristics,during rarefied gas flow simulations performed using the direct simulation monte Carlo(DSmC)*** deterministic computational fluid dynamics(CFD)schemes,DSmC is generally subject to large statistical scatter in instantaneous flow property evaluations,which prevents the use of residual tracking procedures as are often employed in CFD ***,reliable prediction of the time to reach steady state is necessary for initialization of DSmC sampling *** currently used in DSmC to identify steady state convergence are usually insensitive to weak transient behavior in small regions of relatively low density or recirculating *** proposed convergence criterion is developed with the goal of properly identifying such weak transient behavior,while adding negligible computational expense and allowing simple implementation in any existing DSmC *** of the proposed technique over existing convergence detection methods are demonstrated for representative nozzle/plume expansion flow,hypersonic blunt body flow and driven cavity flow problems.

关键词： monte Carlo methods particle methods direct simulation monte Carlo

Cardiorespiratory fitness and cancer in women:A prospective pilot study

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Journal of Sport and Health Science 2019年第5期8卷 457-462页

作者： Baruch Vainshelboim Ricardo m.Lima jonathan myers master of Cancer Care Program School of Health SciencesSaint Francis UniversityLorettoPA 15940USA Cardiology Division Veterans Affairs Palo Alto Health Care System/Stanford UniversityPalo AltoCA 94304USA Faculty of Physical Education University of BrasiliaBrasilia 70910-900Brazil

Purpose:To assess the association between cardiorespiratory fitness(CRF)and the incidence and mortality from cancer in women,and to evaluate the potential public health implications for cancer ***:maximal exercise testing was performed in a pilot cohort of 184 women(59.3 ± 15.2 years)who were followed for 12.0 ± 6.9 *** hazard models adjusted for established cancer risk factors and accounting for competing events were analyzed for all-type cancer incidence and mortality from ***-attributable risks and exposure impact number were determined for low CRF(metabolic equivalents(mETs))as a risk ***:During the follow-up,11.4% of the participants were diagnosed with cancer and 3.2% died from *** was inversely and independently associated with cancer *** every 1-metabolic equivalent increase in CRF,there was a 20% decrease in the risk of cancer incidence(hazard ratio(HR)= 0.80,95% confidence interval(CI):0.69-0.92;p=0.001)and a 26% reduction in risk of cancer mortality(HR = 0.74,95%CI:0.61-0.90;p=0.002).The population-attributable risks of low CRF were 11.6% and 14% for incidence and mortality of cancer,respectively,and the respective exposure impact numbers were 8 and ***:Greater CRF was independently associated with a lower risk of incidence and mortality from cancer in *** for low CRF as a cancer risk factor and referring unfit individuals to a supervised exercise program could be a public health strategy for cancer prevention in middle-age women.

关键词： Exercise capacity Exercise testing Fitness Public health

Celiac plexus neurolysis in the management of unresectable pancreatic cancer:When and how?

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World Journal of Gastroenterology 2014年第9期20卷 2186-2192页

作者： jonathan m Wyse Yen-I Chen Anand V Sahai Division of Gastroenterology Jewish General Hospital McGill University Montreal H3T 1E2 QuebecCanada mcGill University Health Center mcGill University Montreal H3A 1A1 Quebec Canada Division of Gastroenterology Hopital Saint Luc Centre Hospitaliér de l’Universite de Montréal Montreal H2X 1P1 Quebec Canada

Pancreatic cancer is the second most common abdominal cancer in North America with an estimated 20%resectability at diagnosis,and overall 5-year survival of 5%.Pain is common in pancreatic cancer patients with 70%-80%suffering substantial *** plexus neurolysis(CPN)is a technique that can potentially improve pain control in pancreatic cancer while preventing further escalation of opioid *** is performed by injecting absolute alcohol into the celiac plexus neural network of *** review sets out to explore the current status of CPN in non-resectable pancreatic *** will examine:(1)the efficacy and safety of percutaneous-CPN and endoscopic ultrasound guided-CPN;(2)specific technique modifications including bilateral(vs central)injections and celiac ganglia neurolysis;and(3)the issue of CPN timing,early at pancreatic cancer diagnosis vs traditional late use as salvage therapy.

关键词： Celiac plexus neurolysis Endoscopic ultrasound Pancreatic cancer Pain Opioid Gastrointestinal endoscopy

Long-term changes in biological soil crust cover and composition

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Ecological Processes 2013年第1期2卷 54-63页

作者： Eva Dettweiler-Robinson Jeanne m Ponzetti jonathan D Bakker Department of Biology University of New MexicoMSC0320201 University of New MexicoAlbuquerqueNM 98131U.S.A. 2914 Central St.SE OlympiaWA 98501U.S.A. School of Environmental and Forest Sciences University of WashingtonBox 354115SeattleWA98195-4115U.S.A.

Introduction:Communities change over time due to disturbances,variations in climate,and species *** soil crust communities are important because they contribute to erosion control and nutrient *** types may respond differently to changes in environmental conditions:single-celled organisms and bryophytes quickly recover after a disturbance,while lichens are slow growing and dominate favorable *** change in crusts has seldom been assessed using repeated *** this study,we hypothesized that changes in crust composition were related to disturbance,topographic position,and invasive ***:We monitored permanent plots in the Columbia Basin in 1999 and 2010 and compared changes in crust composition,cover,richness,and turnover with predictor variables of herbivore exclosure,elevation,heat load index,time since fire,presence of an invasive grass,and change in cover of the invasive ***:Bryophytes were cosmopolitan with high *** lichens did not change *** taxa differed by monitoring *** and total crust cover declined,and there was lower turnover outside of herbivore *** cover did not change *** that burned recently had high *** in taxon richness was correlated with presence of an invasive grass in *** in cover of the invasive grass was positively related to proportional loss and negatively related to ***:Composition and turnover metrics differed significantly over 11 years,though cover was more stable between *** study can be a baseline for assessing change in crust composition due to anthropogenic influences.

关键词： Biological soil crust Columbia basin Composition change Taxa turnover rate Fire Bromus tectorum Livestock exclosure

molecular phenotypes of colorectal cancer and potential clinical applications

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Gastroenterology Report 2015年第4期3卷 269-276,I0001页

作者： jonathan m.Kocarnik Stacey Shiovitz Amanda I.Phipps Public Health Sciences Division Fred Hutchinson Cancer Research CenterSeattleWAUSA Epidemiology Department University of WashingtonSeattleWAUSA Clinical Research Division Fred Hutchinson Cancer Research CenterSeattleWAUSA Department of medicine Division of Medical OncologyUniversity of WashingtonSeattleWAUSA

Colorectal cancer(CRC)is a heterogeneous disease,arising from many possible etiological *** heterogeneity can have important implications for CRC prognosis and clinical *** studies of CRC risk and prognosis—as well as clinical trials for the treatment of CRC—must therefore be sensitive to the molecular phenotype of colorectal tumors in patients under *** this review,we describe four tumor markers that have been widely studied as reflections of CRC heterogeneity:(i)microsatellite instability(mSI)or DNA mismatch repair(mmR)deficiency,(ii)the CpG island methylator phenotype(CImP),and somatic mutations in(iii)BRAF and(iv)*** tumor markers have been used to better characterize CRC epidemiology and,increasingly,may be used to guide clinical *** beyond these traditional tumor markers,we also briefly review some more novel markers likely to be of clinical ***,recognizing that none of these individual tumor markers are isolated attributes but,rather,a reflection of broader tumor phenotypes,we review some of the hypothesized etiological pathways of CRC development and their associated clinical differences.

关键词： colorectal cancer microsatellite instability CpG island methylator phenotype KRAS BRAF treatment epidemiology

ACCELERATED OPTImIZATION WITH ORTHOGONALITY CONSTRAINTS

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Journal of Computational mathematics 2021年第2期39卷 207-226页

作者： jonathan W.Siegel Department of mathematics Pennsylvania State UniversityUniversity ParkPAUSA

We develop a generalization of Nesterov’s accelerated gradient descent method which is designed to deal with orthogonality *** demonstrate the effectiveness of our method,we perform numerical experiments which demonstrate that the number of iterations scales with the square root of the condition number,and also compare with existing state-of-the-art quasi-Newton methods on the Stiefel *** experiments show that our method outperforms existing state-of-the-art quasi-Newton methods on some large,ill-conditioned problems.

关键词： Riemannian optimization Stiefel manifold Accelerated gradient descent Eigenvector problems Electronic structure calculations

A holistic approach to improving safety for battery energy storage systems

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Journal of Energy Chemistry 2024年第5期92卷 422-439页

作者： James Close jonathan E.Barnard Y.m.John Chew Semali Perera Department of Chemical Engineering Centre for DigitalManufacturing&DesignUniversity of BathBath BA27AYUK iomosaic International Limited 16-18 Queen SquareBath BA12HNUK

The integration of battery energy storage systems(BESS)throughout our energy chain poses concerns regarding safety,especially since batteries have high energy density and numerous BESS failure events have *** spread adoption will only increase the prevalence of these failure events unless there is a step change in the management and design of *** understand the causes of failure,the main challenges of BESS safety are *** consequences and failure events are discussed,including specific focus on the chain of events causing thermal runaway,and a case study of a BESS explosion in Surprise Arizona is *** on the technology and past events,a paradigm shift is required to improve BESS *** this review,a holistic approach is *** combines currently adopted approaches including battery cell testing,lumped cell mathematical modelling,and calorimetry,alongside additional measures taken to ensure BESS safety including the requirement for computational fluid dynamics and kinetic modelling,assessment of installation level testing of the full BESS system and not simply a single cell battery test,hazard and layers of protection analysis,gas chromatography,and composition *** holistic approach proposed in this study aims to address challenges of BESS safety and form the basis of a paradigm shift in the safety management and design of these systems.

关键词： Energy storagesystems Process safety Battery safety Thermal safety