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Microbial markers in colorectal cancer detection and/or prognosis

World Journal of Gastroenterology 2018年第22期24卷 2327-2347页

作者： romain villéger Amélie Lopès Julie Veziant Johan Gagnière Nicolas Barnich Elisabeth Billard Delphine Boucher Mathilde Bonnet Université Clermont Auvergne Research Biologics Sanofi R&D Chirurgie digestive Centre Hospitalier Universitaire Université Clermont Auvergne Institut Universitaire de Technologie de Clermont-Ferrand

Colorectal cancer(CRC) is the second leading cause of cancer worldwide. CRC is still associated with a poor prognosis among patients with advanced disease. On the contrary, due to its slow progression from detectable precancerous lesions, the prognosis for patients with early stages of CRC is encouraging. While most robust methods are invasive and costly, actual patient-friendly screening methods for CRC suffer of lack of sensitivity and specificity. Therefore, the development of sensitive, non-invasive and cost-effective methods for CRC detection and prognosis are necessary for increasing the chances of a cure. Beyond its beneficial functions for the host, increasing evidence suggests that the intestinal microbiota is a key factor associated with carcinogenesis. Many clinical studies have reported a disruption in the gut microbiota balance and an alteration in the faecal metabolome of CRC patients, suggesting the potential use of a microbialbased test as a non-invasive diagnostic and/or prognostic tool for CRC screening. This review aims to discuss the microbial signatures associated with CRC known to date, including dysbiosis and faecal metabolome alterations, andthe potential use of microbial variation markers for noninvasive early diagnosis and/or prognostic assessment of CRC and advanced adenomas. We will finally discuss the possible use of these markers as predicators for treatment response and their limitations.

关键词： Colorectal cancer microbiota F.nucleatum Colibactin-producing E.coli prognostic markers diagnostic markers dysbiosis

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Thermo-mechanical simulation of frost heave in saturated soils

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Frontiers of Structural and Civil Engineering 2023年第9期17卷 1400-1412页

作者： Saeed VOSOUGHIAN romain BALIEU Department of Civil and Architectural Engineering KTH Royal Institute of TechnologyStockholm 10044Sweden

Roads are exposed to various degradation mechanisms during their *** pavement deterioration caused by the surrounding environment is particularly severe in winter when the humidity and subfreezing temperatures *** heave-induced damage is one of the winter-related pavement *** occurs when the porewater in the soil is exposed to freezing *** study of frost heave requires conducting a multiphysics analysis,considering the thermal,mechanical,and hydraulic *** paper presents the use of a coupled thermo-mechanical approach to simulate frost heave in saturated soils.A function predicting porosity evolution is implemented to couple the thermal and mechanical field *** function indirectly considers the effect of the water seepage inside the *** frost heave scenarios with uniform and non-uniform boundary conditions are considered to demonstrate the capabilities of the *** results of the simulations indicate that the thermo-mechanical model captures various processes involved in the frost heave phenomenon,such as water fusion,porosity variation,cryogenic suction force generation,and soil *** characteristics and consequences of each process are determined and discussed ***,the results show that non-uniform thermal boundaries and presence of a culvert inside the soil result in uneven ground surface deformations.

关键词： frost heave multiphysics analysis thermo-mechanical approach saturated soils

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Color and Shape efficiency for outlier detection from automated to user evaluation

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Visual Informatics 2022年第2期6卷 25-40页

作者： Loann Giovannangeli romain Bourqui romain Giot David Auber Univ.Bordeaux CNRSBordeaux INPINRIALaBRIUMR 5800F-33400 TalenceFrance

The design of efficient representations is well established as a fruitful way to explore and analyze complex or large *** these representations,data are encoded with various visual attributes depending on the needs of the representation *** make coherent design choices about visual attributes,the visual search field proposes guidelines based on the human brain’s perception of ***,information visualization representations frequently need to depict more data than the amount these guidelines have been validated ***,the information visualization community has extended these guidelines to a wider parameter *** paper contributes to this theme by extending visual search theories to an information visualization *** consider a visual search task where subjects are asked to find an unknown outlier in a grid of randomly laid out *** are defined by color and shape features for the purpose of visually encoding categorical *** experimental protocol is made of a parameters space reduction step(i.e.,sub-sampling)based on a machine learning model,and a user evaluation to validate hypotheses and measure capacity *** results show that the major difficulty factor is the number of visual attributes that are used to encode the *** redundantly encoded,the display heterogeneity has no effect on the *** encoded with one attribute,the difficulty depends on that attribute heterogeneity until its capacity limit(7 for color,5 for shape)is ***,when encoded with two attributes simultaneously,performances drop drastically even with minor heterogeneity.

关键词： Visual search Outlier detection User evaluation Deep learning Automated evaluation

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Endogenous retinal neural stem cell reprogramming for neuronal regeneration

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Neural Regeneration Research 2017年第11期12卷 1765-1767页

作者： romain Madelaine Philippe Mourrain Stanford Center for Sleep Sciences and Medicine Department of Psychiatry and Behavioral SciencesStanford University INSERM 1024 Ecole Normale SupérieureParisFrance

In humans, optic nerve injuries and associated neurodegenerative diseases are often followed by perma- nent vision loss. Consequently, an important challenge is to develop safe and effective methods to replace retinal neurons and thereby restore neuronal functions and vision. Identifying cellular and molecular mechanisms allowing to replace damaged neurons is a major goal for basic and translational research in regenerative medicine. Contrary to mammals, the zebrafish has the capacity to fully regenerate entire parts of the nervous system, including retina. This regenerative process depends on endogenous retinal neural stem cells, the Miiller glial cells. Following injury, zebrafish Miiller cells go back into cell cycle to proliferate and generate new neurons, while mammalian Mtiller cells undergo reactive gliosis. Recently, transcription factors and microRNAs have been identified to control the formation of new neurons derived from ze- brafish and mammalian Mtiller cells, indicating that cellular reprogramming can be an efficient strategy to regenerate human retinal neurons. Here we discuss recent insights into the use of endogenous neural stem cell reprogramming for neuronal regeneration, differences between zebrafish and mammalian Mtiller cells, and the need to pursue the identification and characterization of new molecular factors with an instructive and potent function in order to develop theurapeutic strategies for eye diseases.

关键词： neuronal regeneration retina Muller glial cells neural stem cell reprogramming achaete-scute homolog 1 microRNA-9 Tlx Onecut

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NetPrune:A sparklines visualization for network pruning

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Visual Informatics 2023年第2期7卷 85-99页

作者： Luc-Etienne Pommé romain Bourqui romain Giot Jason Vallet David Auber Univ.Bordeaux CNRSBordeaux INPINRIALaBRIUMR 5800F-33400 TalenceFrance

Current deep learning approaches are cutting-edge methods for solving classification *** transfer learning techniques allows applying large generic model to simple tasks whereas simpler models could be *** models raise the major problem of their memory consumption and processor usage and lead to a prohibitive ecological *** that paper,we present a novel visual analytics approach to interactively prune those networks and thus limit that *** technique leverages a novel sparkline matrix visualization technique as well as a novel local metric which evaluates the discriminatory power of a filter to guide the pruning process and make it *** assess the well-founded of our approach through two realistic case studies and a user *** both of them,the interactive refinement of the model led to a significantly smaller model having similar prediction accuracy than the original one.

关键词： Explainable pruning Guided Fine-tuning Visualization Deep learning

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Simple experimental procedures to distinguish photothermal from hot-carrier processes in plasmonics

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Light(Science & Applications) 2020年第1期9卷 974-989页

作者： Guillaume Baffou Ivan Bordacchini Andrea Baldi romain Quidant Institut Fresnel CNRSAix Marseille UniversityCentrale MarseilleMarseilleFrance ICFO-Institut de Ciencies Fotoniques The Barcelona Institute of Science and Technology08860CastelldefelsBarcelonaSpain DIFFER-Dutch Institute for Fundamental Energy Research De Zaale 205612 AJ EindhovenThe Netherlands Vrije Universiteit Amsterdam De Boelelaan 10811081 HV AmsterdamThe Netherlands ICREA-Institucio Catalana de Recerca i Estudis Avancats 08010 BarcelonaSpain Nanophotonic Systems Laboratory Department of Mechanical and Process EngineeringETH Zurich8092ZurichSwitzerland

Light absorption and scattering of plasmonic metal nanoparticles can lead to non-equilibrium charge carriers,intense electromagnetic near-fields,and heat generation,with promising applications in a vast range of fields,from chemical and physical sensing to nanomedicine and photocatalysis for the sustainable production of fuels and *** the relative contribution of thermal and non-thermal contributions in plasmon-driven processes is,however,*** temperature measurements are technically challenging,and macroscale experiments are often characterized by collective heating effects,which tend to make the actual temperature increase *** work is intended to help the reader experimentally detect and quantify photothermal effects in plasmon-driven chemical reactions,to discriminate their contribution from that due to photochemical processes and to cast a critical eye on the current *** this aim,we review,and in some cases propose,seven simple experimental procedures that do not require the use of complex or expensive thermal microscopy *** proposed procedures are adaptable to a wide range of experiments and fields of research where photothermal effects need to be assessed,such as plasmonic-assisted chemistry,heterogeneous catalysis,photovoltaics,biosensing,and enhanced molecular spectroscopy.

关键词： collective photochemical intense

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Thermogravimetric analysis and kinetic modeling of the co-pyrolysis of a bituminous coal and poplar wood

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Chinese Journal of Chemical Engineering 2023年第6期58卷 53-68页

作者： Wei Wang romain Lemaire Ammar Bensakhria Denis Luart Department of Mechanical Engineering École de technologie supérieureMontrealQuebec H3C 1K3Canada Universitéde Technologie de Compiègne Centre de recherche de RoyallieuEA 4297-TIMRBP2052960205 CompiègneFrance École Supérieure de Chimie Organique et Minérale 1 Rue du Réseau Jean-Marie Buckmaster60200 CompiègneFrance

The co-pyrolysis of coal and biomass has proven to be a promising route to produce liquid and gaseous fuels as well as specific value-added chemicals while contributing to mitigating CO_(2) *** interactions between the co-processed feedstocks,however,need to be elucidated to support the development of such a thermochemical conversion *** this context,the present work covers the kinetic analysis of the co-pyrolysis of a bituminous coal with poplar *** this research,biomass was blended with coal at two different mass ratios(10%(mass)and 20%(mass)).Thermogravimetric analyses were carried out with pure and blended samples at four heating rates(5,10,15 and 30℃·min^(-1)).A direct comparison of experimental and theoretical results(based on a simple additivity rule)failed to yield a clear-cut conclusion regarding the existence of synergistic *** analyses have therefore been achieved using two model-free methods(the Ozawa-Flynn-Wall and Kissinger-Akahira-Sunose models)to estimate the rate constant parameters related to the pyrolysis process.A significant decrease of the activation energy has thus been observed when adding wood to coal(activation energies associated with the blend containing 20%(mass)of biomass being even lower than those estimated for pure wood at low conversion degrees).This trend was attributed to the possible presence of synergies whose related mechanisms are *** rate constant parameters derived by means of the two tested models were finally used to simulate the evolution of the conversion degree of each sample as a function of the temperature,thus leading to a satisfying agreement between measured and simulated data.

关键词： Co-pyrolysis Coal Wood Kinetics Synergistic effects

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Slow and steady wins the race: contrasted phylogeographic signatures in two Alpine amphibians

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Integrative Zoology 2022年第1期17卷 181-190页

作者： Christophe DUFRESNES Nicolas RODRIGUES romain SAVARY LASER College of Biology and EnvironmentNanjing Forestry UniversityNanjingChina Department of Ecology&Evolution University of LausanneLausanneSwitzerland Laboratory for Biological Geochemistry School of ArchitectureCivil and Environmental EngineeringEcole Polytechnique Fédérale de Lausanne(EPFL)LausanneSwitzerland

A deeper phylogeographic structure is expected for slow-dispersing habitat specialists compared to widespread adaptable species,especially in topographically complex *** tested this classic assumption by comparing the genomic(RAD-sequencing)phylogeographies of 2 amphibians inhabiting the Swiss Alps:the mobile,cosmopolitan common frog(Rana temporaria)against the stationary,mountain endemic Alpine salamander(Salamandra atra).Our results ran opposite of predictions:the frog displayed significantly higher genetic divergences and lower within-population variation compared to the *** implies a prominent role for their distinctive glacial histories in shaping intraspecific diversity and structure:diversification and recolonization from several circum-Alpine micro-refugia for the frog versus a single refugium for the salamander,potentially combined with better population connectivity and *** striking differences emphasize the great variability of phylogeographic responses to the Quaternary glaciations,hence the complexity to predict general patterns of genetic diversity at the regional scale,and the forces that underlie them.

关键词： Alps comparative phylogeography dispersal RAD-sequencing Rana temporaria Salamandra atra

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Volumetric Vector-Based Representation for Indirect Illumination Caching

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Journal of Computer Science & Technology 2010年第5期25卷 925-932页

作者： romain Pacanowski Xavier Granier Christophe Schlick Pierre Poulin CEA-CESTA BP2 Le Barp33114France ACM INRIA Bordeaux Sud-Ouest/LaBRI-Bordeaux University Talence33405France State Key Lab of CAD&CG Zhejiang University LIGUM Dept.I.R.O.Universite de MontrealMontreal QCH3C 3J7Canada

This paper introduces a caching technique based on a volumetric representation that captures low-frequency indirect *** structure is intended for efficient storage and manipulation of *** is based on a 3D grid that stores a fixed set of irradiance *** preprocessing,this representation can be built using almost any existing global illumination *** rendering,the indirect illumination within a voxel is interpolated from its associated irradiance vectors,and is used as additional local light *** with other techniques,the 3D vector-based representation of our technique offers increased robustness against local geometric variations of a *** thus demonstrate that it may be employed as an efficient and high-quality caching data structure for bidirectional rendering techniques such as particle tracing or photon mapping.

关键词： caching for global illumination photon mapping particle tracing

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Hybrid Cellular Automaton-Parabolic Thick Needle model for equiaxed dendritic solidification

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Journal of Materials Science & Technology 2022年第29期124卷 26-40页

作者： romain Fleurisson Oriane Senninger Gildas Guillemot Charles-André Gandin MINES ParisTech PSL Research UniversityCEMEF UMR CNRS 7635CS1020706904 Sophia AntipolisFrance

A hybrid Cellular Automaton(CA)-Parabolic Thick Needle(PTN)model is developed for the simulation of an equiaxed dendritic *** is implemented by solving conservation equations with the Finite Element(FE)method at two *** the scale of the microstructure,dendritic branches are approximated by a network of *** solute field is computed in the liquid using a FE mesh with minimum size smaller than the diffusion length ahead of the dendrite tips,giving access to a detailed description of each dendrite tip growth velocity as well as solutal interactions between *** the simulation domain scale,volume averaged heat and solute transfers are solved on a coarser FE *** average volumetric fraction of phases is deduced from a field giving the fraction of dendritic microstructure together with a microsegregation *** the PTN themselves grow on CA cells,the dendrite tip growth velocity is transferred to the vertices of the polygon associated to the CA growth ***,the field giving the fraction of dendritic microstructure is deduced from the fraction of CA cells part of the mushy zone,which include cells containing PTN *** of the new multiple scale CAPTN model include solutal interaction between dendrite branches together with long range transfer of heat and solute mass,together with the role of latent heat release on equiaxed solidification.

关键词： Solidification Dendrite growth law Multiscale Finite element method

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