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Algorithmic approaches to clonal reconstruction in heterogeneous cell populations

Quantitative Biology 2019年第4期7卷 255-265页

作者： Wazim Mohammed Ismail etienne Nzabarushimana Haixu Tang School of Informatics Computing and EngineeringIndiana UniversityBloomingtonIN 47405-7000USA

Background:The reconstruction of clonal haplotypes and their evolutionary history in evolving populations is a common problem in both microbial evolutionary biology and cancer *** clonal theory of evolution provides a theoretical framework for modeling the evolution of ***:In this paper,we review the theoretical framework and assumptions over which the clonal reconstruction problem is *** formally define the problem and then discuss the complexity and solution space of the *** methods have been proposed to find the phylogeny that best explains the observed *** categorize these methods based on the type of input data that they use(space-resolved or time-resolved),and also based on their computational formulation as either combinatorial or *** is crucial to understand the different types of input data because each provides essential but distinct information for drastically reducing the solution space of the clonal reconstruction *** information provided by single cell sequencing or from whole genome sequencing of randomly isolated clones can also improve the accuracy of clonal *** briefly review the existing algorithms and their *** we summarize the tools that are developed for either directly solving the clonal reconstruction problem or a related computational ***:In this review,we discuss the various formulations of the problem of inferring the clonal evolutionary history from allele frequeny data,review existing algorithms and catergorize them according to their problem formulation and solution *** note that most of the available clonal inference algorithms were developed for elucidating tumor evolution whereas clonal reconstruction for unicellular genomes are less *** conclude the review by discussing more open problems such as the lack of benchmark datasets and comparison of performance between available tools.

关键词： clonal theory infinite sites assumption clonal reconstruction problem bacteria evolution tumor evolution combinatorial algorithm probabilistic algorithm

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Targeting mRNA translation aberrations:A novel approach for therapy in chronic lymphocytic leukemia

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Cancer Communications 2023年第12期43卷 1373-1376页

作者： Vanessa Klapp Jerome Paggetti Anne Largeot etienne Moussay Tumor Stroma Interactions Department of Cancer Research Luxembourg Institute of Health Luxembourg Luxembourg Faculty of Science Technology and Medicine University of Luxembourg Esch-sur-Alzette Luxembourg

1 mRNA TRANSLATION IS AFFECTED IN CHRONIC LYMPHOCYTIC LEUKEMIA(CLL)AT VARIOUS LEVELS mRNA translation dynamics enable tight regulation of protein expression and rapid stress adaptation;however,its contribution to oncogenesis is overlooked compared to genetic and epigenetic *** in mRNA translation are a common feature of cancer and are established as a therapeutic *** is growing evidence of dysregulated protein synthesis in CLL.

关键词： lymphocytic leukemia translation

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Age structure in neutral theory resolves inconsistencies related to reproductive-size threshold

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Journal of Plant Ecology 2012年第1期5卷 64-71页

作者： James Rosindell Patrick A.Jansen Rampal S.etienne Institute of Integrative and Comparative Biology Faculty of Biological SciencesUniversity of LeedsLeeds LS29JTWest YorkshireUK Institute of Bioinformatics and Evolutionary Studies University of IdahoMoscowID 83844USA Center for Tropical Forest Science Smithsonian Tropical Research InstitutePO Box 0843-03092BalboaAnconRepublic of Panama Centre of Ecosystem Studies Wageningen UniversityPO Box 476700 AA Wageningenthe Netherlands Community and Conservation Ecology Centre for Ecological and Evolutionary StudiesUniversity of GroningenPO Box 111039700 CC Groningenthe Netherlands

Aims Neutral theory consists of a suite of models that assume ecological equivalence among individual *** have been most commonly applied to tropical forest tree communities either as null models or as *** models typically only include reproductive adults;therefore,fitting to empirical tree community data requires defining a reproductive-size threshold,which for trees is usually set arbitrarily to a diameter at breast height(DBH)of 100 *** inevitable exclusion of some reproductive adults and inclusion of some saplings cause a non-random sampling bias in neutral model ***,we investigate this problem and resolve it by introducing simple age structure into a neutral *** We compared the performance and sensitivity of DBH threshold of three variants of a spatially explicit neutral model:the traditional model,a model incorporating random sampling and a model with two distinct age classes—reproductive adults and *** the age-structured model,saplings are offspring from adults that disperse according to a Gaussian dispersal kernel around the *** only extra parameter is the ratio of adults to saplings,which is not a free parameter but directly *** used species–area relationships(SARs)to explore the predicted effect of saplings on the species richness at different scales in our *** then evaluated the three model variations to find the parameters required to maintain the observed level of species richness in the 50-ha plot on Barro Colorado Island(BCI).We repeated our analysis filtering the data at different minimum tree-size thresholds in order to find the effect this threshold has on our ***,we used empirical species–individual relationships(SIRs)to test the pre-existing hypothesis that environmental filtering is the primary cause of differences between the assemblage of saplings and that of adults on *** Findings Our age-structured neutral model was characterized by SARs that

关键词： neutral theory age structure sampling DBH

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Experimental Study on the Flow Around Two Tandem Cylinders with Unequal Diameters

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Journal of Ocean University of China 2014年第5期13卷 761-770页

作者： GAO Yangyang etienne Stephane WANG Xikun TAN Soon Keat Ocean College Zhejiang University State Key Laboratory of Satellite Ocean Environment Dynamics Second Institute of Oceanography SOA Mechanical Engineering Department Ecole Polytechnique de Montreal Maritime Research Centre and School of Civil and Environmental Engineering Nanyang Technological University

In this paper, flow around two circular cylinders in tandem arrangement with unequal diameters has been investigated using the particle image velocimetry technique(PIV) in a water channel. The upstream to downstream diameter ratio was kept constant at d/D = 2/3, the centre-to-centre distance was varied from 1.2D to 5D and the Reynolds number was varied from 1200 to 4800. The flow characteristics were analyzed through ensemble-averaged patterns of velocity, vorticity, normalized Reynolds stress contours and streamlines. Based on ensemble-averaged and instantaneous flow fields, different flow patterns, including single-wakeshedding at small spacing ratio, bi-stable flow behavior(alternating behavior of reattachment and vortex shedding) at intermediate spacing ratio and co-shedding pattern at large spacing ratio were observed. The effects of Reynolds number and the centre-to-centre spacing ratio on flow patterns and turbulent characteristics were also investigated. It was found that the diameter ratio appears to have a certain effect on the flow patterns at intermediate spacing ratios, where the reattachment of shear layer depends on the lateral width of the wake flow in the lee of the upstream cylinder. Extensive discussion on the distributions of Reynolds stress and turbulent kinetic energy was presented.

关键词： tandem cylinders with unequal diameters PIV flow patterns Reynolds stress distribution

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Regulation of hepatic EAAT-2 glutamate transporter expression in human liver cholestasis

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World Journal of Gastroenterology 2014年第6期20卷 1554-1564页

作者： Mustapha Najimi Xavier Stéphenne Christine Sempoux etienne Sokal Université Catholique de Louvain Institut de Recherche Expérimentale et Clinique (IREC) Laboratory of Pediatric Hepatology and Cell Therapy Anatomo-pathology Cliniques Universitaires St-Luc Université Catholique de Louvain

AIM: To investigate the activity and expression of EAAT2 glutamate transporter in both in vitro and in vivo models of cholestasis.

关键词： Glutamate transport Hepatocyte Bile duct ligation Cholestasis Biliary atresia

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Fluid Flow Estimation with Multiscale Ensemble Filters Based on Motion Measurements Under Location Uncertainty

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Numerical Mathematics(Theory,Methods and Applications) 2013年第1期6卷 21-46页

作者： Sébastien Beyou Thomas Corpetti Sai Gorthi etienne Mémin INRIA/FLUMINANCE 35042 Rennes CedexFrance CNRS/LETG-Rennes-Costel Campus Villejean Place du recteur Henri Le Moal CS *** Rennes cedexFrance Indian Institute of Space Science and Technology Valiamala P.O.Thiruvananthapuram–695547Kerala India

This paper proposes a novel multi-scale fluid flow data assimilation approach,which integrates and complements the advantages of a Bayesian sequential assimilationtechnique, the Weighted Ensemble Kalman filter (WEnKF) [27]. The data assimilation proposed in this work incorporates measurement brought by an efficient multiscalestochastic formulation of the well-known Lucas-Kanade (LK) estimator. This estimatorhas the great advantage to provide uncertainties associated to the motion measurements at different scales. The proposed assimilation scheme benefits from this multiscale uncertainty information and enables to enforce a physically plausible dynamicalconsistency of the estimated motion fields along the image sequence. Experimentalevaluations are presented on synthetic and real fluid flow sequences.

关键词： Data assimilation stochastic filter particle filters fluid motion estimation

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Itinerary-Dependent Degradation Analysis of a Lithium-Ion Battery Cell for E-Bike Applications in Rwanda

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Energy Engineering 2024年第11期121卷 3121-3131页

作者： Aimable Ngendahayo AdriàJunyent-Ferré JoanMarc Rodriguez Bernuz etienne Ntagwirumugara African Center of Excellence in Energy for Sustainable Development College of Science and TechnologyUniversity of RwandaKigaliP.O.Box 3900Rwanda Department of Electrical and Electronic Engineering Imperial College LondonLondonSW72BXUK Departament d’Enginyeria Elèctrica Universitat Politècnica de CatalunyaBarcelona08034Spain

There are obstacles to the widespread use of small electric vehicles(EVs)in Rwanda,including concerns regarding the battery range and ***-ion batteries(LIBs)play an important role in ***,their performance declines over time because of several *** optimize battery management systems and extend the range of EVs in Rwanda,it is essential to understand the influence of the driving profiles on lithium-ion battery *** study analyzed the degradation patterns of a lithium-ion battery cell that propels an E-bike using various real-world E-bike driving cycles that represent Rwandan driving conditions under deep discharge(>80%).By being aware of these variables,battery failure can be slowed and improved battery performance can be achieved to promote the transition to cleaner transportation in Rwanda for the productive use of *** analyzed parameters that affect battery performance are temperature,driving cycles,and state of *** was found that the higher the temperature,the higher was the rate of *** the other hand,the EVs that operate in the region with higher elevation(hilly region)combined with a flat surface where the riders use their physical forces to propel the E-bike and their batteries lose their capacity rapidly compared to those operating in regions where the energy from the lithium-ion battery assists for the entire *** draining the battery to 10%and charging it to 90%of its initial capacity,the capacity fading decreased by 5%.

关键词： Degradation driving cycle E-bike state of charge lithium manganese oxide

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Pigs receiving daily tailored diets using precision-feeding techniques have different threonine requirements than pigs fed in conventional phase-feeding systems

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Journal of Animal Science and Biotechnology 2019年第3期10卷 719-735页

作者： Aline Remus Luciano Hauschild etienne Corrent Marie-Pierre Letourneau-Montminy Candido Pomar Sherbrooke Research and Development Centre Agriculture and Agri-Food CanadaSherbrookeQuebec J1M 0C8Canada Departement des sciences animales Universite LavalQuebec CityQuebec G1V 0A6Canada School of Agricultural and Veterinary Studies(FCAV) Department of Animal ScienceUniversity of Sao Paulo State (UNESP)JaboticabalSao Paulo 14883-108Brazil Ajinomoto Animal Nutrition Europe Paris Cedex 17 F-75817France

Background: There is large variation in amino acids requirements among pigs,hence feeding pigs individually with daily tailored diets or in groups with a single feed may require different levels of ***,the response to different threonine levels(70%,85%,100%,115%,and 130% of the ideal threonine:lysine protein ratio of 0.65) was studied in growing pigs raised in a conventional group phase-feeding(GPF) system or fed individually using individual precision-feeding(IPF) *** a 21-day trial,110 barrows(25 ± 0.80 kg body weight) were housed in the same room and fed using electronic *** pigs per treatment were slaughtered at the end of the ***: Threonine intake increased linearly for the IPF and GPF pigs(P < 0.05).Lysine intake was similar across the *** daily gain,gain:feed ratio,and protein deposition were affected linearly by threonine level(P < 0.05)in both feeding *** deposition in the GPF pigs was maximized at 150 g/d and a 0.65 threonine:lysine ratio,whereas protein deposition increased linearly in the IPF *** Met and serine levels were 11 and 7% higher,respectively,in the IPF pigs than in the GPF pigs(P < 0.05).Dietary threonine increased(P < 0.05)threonine concentration in the longissimus dorsi in a quadratic manner in the IPF pigs,whereas there was no effect in the GPF *** dorsi collagen decreased as dietary threonine increased in the IPF and GPF pigs(P < 0.10).Carcass muscle crude protein was 2% higher in the GPF pigs than in the IPF pigs(P < 0.05).Conclusions: Individual pigs are able to modulate growth and the composition of growth according to threonine *** average amino acid ratio value that is currently used for GPF cannot be used for IPF.

关键词： Amino acid body composition Dose-response Ideal protein profile Lysine Threonine

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Production performance and plasma metabolite concentrations of broiler chickens fed low crude protein diets differing in Thr and Gly

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Animal Nutrition 2021年第2期7卷 472-480页

作者： Laura Star Sophie Tesseraud Marije van Tol Ilaria Minussi etienne Corrent William Lambert Schothorst Feed Research Meerkoetenweg 268218 NA Lelystadthe Netherlands INRAE BOAUniversitéde Tours37380 NouzillyFrance Orffa Additives B.V. Vierlinghstraat 514251 LC Werkendamthe Netherlands Ajinomoto Animal Nutrition Europe 32 rue Guersant75017 ParisFrance

The aim of the study was to test the interaction between Thr and Gly in low crude protein(CP)diets in 7 to 28 d broilers on production performance and plasma metabolites.A total of 2,040 broilers were allocated to 17 treatments.A positive control(PC)diet(20.5%CP)was formulated to be adequate in dietary Thr and Gly.A negative control(NC)diet(18.5%CP,deficient in Thr and Gly)was supplemented with crystalline L-Thr and Gly to obtain a 4 Thr×4 Gly *** Thr was tested at an apparent faecal digestibility(AFD)Thr-to-Lys ratio,which was 55%,58%,61%or 64%,and dietary Gly was tested at an AFD(Gly+Ser)-to-Lys ratio,which was 135%,142%,149%or 156%.Plasma samples were collected at 28 *** low CP diet,formulated at 64%Thr and 156%Gly,resulted in a higher body weight gain(BWG)(P<0.01)and similar feed conversion ratio(FCR)as the high CP treatment(PC).FCR was improved(P<0.001)by L-Thr *** response to dietary Thr was significant for feed intake(FI),BWG and FCR(P<0.01).A near-significant interaction for Thr×Gly was observed for FI and BWG(Plinear=0.091 and P=0.074,respectively).Gly did not affect production *** interaction between Thr×Gly on plasma free AA level was observed(P<0.05).Free AA concentration in plasma linearly decreased with increase in AFD Thr-to-Lys ratio,and increased with increase in AFD(Gly+Ser)-to-Lys *** uric acid concentration was higher in PC than in all of the other diets,and plasma triglyceride concentration was decreased by L-Thr supplementation,but not by *** conclusion,Gly was not limiting for growth at low dietary CP level unless Thr was deficient,showing that adequate amounts of Thr in broiler diets can overcome marginal supply of Gly and Ser and allow reduction of dietary CP from 20.5%to 18.5%for broilers from 7 to 28 d of age.

关键词： Broiler Threonine Glycine Low protein Performance Plasma metabolite

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Non-Value-Added Tax to improve market fairness and quality

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Financial Innovation 2022年第1期8卷 523-552页

作者： Iryna Veryzhenko Arthur Jonath etienne Harb Conservatoire National des Arts et Métiers ParisFrance Profit and Entropy Portola ValleyCAUSA ESSCA School of Management AngersFrance

The promotion of both market fairness and efficiency has long been a goal of securities market regulators *** digital disruption and abusive trading behaviors,such as the GameStop mania,prompt regulatory *** is unclear how this“democratization”of trading power affects market fairness as economies cope with pandemic-driven shifts in basic *** speculation and market manipulation undermine the quality of financial markets in the sense that they cause volatil-ity and increase the pain of bubble and crash ***,they weaken public confidence in financial markets to fulfill their roles in proper capital allocation to irrigate the real economy and generate value for *** previous studies have mostly focused on market efficiency,our study proposes a tool to improve market fairness,even under periods of *** encourage value generation and improve market quality,we advance a graduated Non-Value-Added Tax that we implement in an agent-based model that can realistically capture the properties of real-world financial markets.A profitable transaction is taxed at a higher rate if it does not enhance the efficiency measured by deviation from *** an agent locks in profit not supported by fundamentals but driven by trend-following strategies,the generated profit is taxed at various rates under the Non-Value-Added Tax *** existing financial transaction taxes,the non-value-added tax is levied on profit rather than on price or *** show that the proposed tax encourages profitable trades that add value to the market and discourages valueless *** significantly curtails volatility and prevents the occurrence of extreme market events,such as bubbles and crashes.

关键词： Market fairness Financial transaction tax Non-Value-Added Tax High-frequency trading Bubbles and crashes Efficiency

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