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Finite-Size Conformational Transitions: A Unifying Concept Underlying Chromosome Dynamics

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Communications in Theoretical Physics 2014年第10期61卷 607-616页

作者： Bertrand r.Caré Pascal Carrivain Thierry Forné Jean-Marc Victor annick Lesne Laboratoire de Physique Théorique de la Matière Condensée CNRS UMR 7600UPMC University Paris 06F-75005ParisFrance CNrS gDr 3536 UPMC University Paris 06F-75005ParisFrance Institut de génétique Humaine CNRS UPR 1142 MontpellierFrance Institut de génétique Moléculaire de Montpellier CNRS UMR 5535University of MontpellierMontpellierFrance Kavli Institute for Theoretical Physics China CAS

Investigating average thermodynamic quantities is not sufficient to understand conformational transitions of a finite-size polymer. We propose that such transitions are better described in terms of the probability distribution of some finite-size order parameter, and the evolution of this distribution as a control parameter varies. We demonstrate this claim for the coil-globule transition of a linear polymer and its mapping onto a two-state model. In a biological context, polymer models delineate the physical constraints experienced by the genome at different levels of organization,from DNA to chromatin to chromosome. We apply our finite-size approach to the formation of plectonemes in a DNA segment submitted to an applied torque and the ensuing helix-coil transition that can be numerically observed, with a coexistence of the helix and coil states in a range of parameters. Polymer models are also essential to analyze recent in vivo experiments providing the frequency of pairwise contacts between genomic loci. The probability distribution of these contacts yields quantitative information on the conformational fluctuations of chromosome regions. The changes observed in the shape of the distribution when the cell type or the physiological conditions vary may reveal an epigenetic modulation of the conformational constraints experienced by the chromosomes.

关键词： coil-globule transition helix-coil transition chromosome conformational capture two-state model

SECOND-OrDEr CONVErgENCE PrOPErTIES OF TrUST-rEgION METHODS USINg INCOMPLETE CUrVATUrE INFOrMATION, WITH AN APPLICATION TO MULTIgrID OPTIMIZATION

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Journal of Computational Mathematics 2006年第6期24卷 676-692页

作者： Serge gratton annick Sartenaer Philippe L. Toint CErFACS av. G. Coriolis Toulouse France Department of Mathematics University of Namur 61 rue de Bruxelles B-5000 Namur Belgium

Convergence properties of trust-region methods for unconstrained nonconvex optimization is considered in the case where information on the objective function＇s local curvature is incomplete, in the sense that it may be restricted to a fixed set of ＂test directions＂ and may not be available at every iteration. It is shown that convergence to local ＂weak＂ minimizers can still be obtained under some additional but algorithmically realistic conditions. These theoretical results are then applied to recursive multigrid trust-region methods, which suggests a new class of algorithms with guaranteed second-order convergence properties.

关键词： Nonlinear optimization Convergence to local minimizers Multilevel problems.

Single-atom catalysts for the electrochemical reduction of carbon dioxide into hydrocarbons and oxygenates

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Carbon Energy 2024年第3期6卷 64-117页

作者： Karl Adrian gandionco Juwon Kim Lieven Bekaert annick Hubin Jongwoo Lim Department of Chemistry Seoul National UniversitySeoulRepublic of Korea research group Electrochemical and Surface Engineering(SUrF) Department of Materials and ChemistryVrije Universiteit BrusselBrusselsBelgium

The electrochemical reduction of carbon dioxide offers a sound and economically viable technology for the electrification and decarbonization of the chemical and fuel *** this technology,an electrocatalytic material and renewable energy-generated electricity drive the conversion of carbon dioxide into high-value chemicals and carbon-neutral *** the past few years,single-atom catalysts have been intensively studied as they could provide near-unity atom utilization and unique catalytic ***-atom catalysts have become one of the state-of-the-art catalyst materials for the electrochemical reduction of carbon dioxide into carbon ***,it remains a challenge for single-atom catalysts to facilitate the efficient conversion of carbon dioxide into products beyond carbon *** this review,we summarize and present important findings and critical insights from studies on the electrochemical carbon dioxide reduction reaction into hydrocarbons and oxygenates using single-atom *** is hoped that this review gives a thorough recapitulation and analysis of the science behind the catalysis of carbon dioxide into more reduced products through singleatom catalysts so that it can be a guide for future research and development on catalysts with industry-ready performance for the electrochemical reduction of carbon dioxide into high-value chemicals and carbon-neutral fuels.

关键词： electrocatalysis electrochemical CO_(2)reduction hydrocarbons oxygenates single-atom catalysts

Experimental reconstructions of 3D atomic structures from electron microscopy images using a Bayesian genetic algorithm

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npj Computational Materials 2022年第1期8卷 2076-2083页

作者： annick De Backer Sandra Van Aert Christel Faes Ece Arslan Irmak Peter DNellist Lewys Jones EMAT University of AntwerpGroenenborgerlaan 1712020AntwerpBelgium NANOlab Center of Excellence University of AntwerpGroenenborgerlaan 1712020AntwerpBelgium I-BioStat Data Science InstituteHasselt UniversityHasseltBelgium Department of Materials University of OxfordParks RoadOX13PHOxfordUK Advanced Microscopy Laboratory Centre for Research on Adaptive Nanostructures and Nanodevices(CRANN)Dublin 2Ireland School of Physics Trinity College DublinThe University of DublinDublin 2Ireland

We introduce a Bayesian genetic algorithm for reconstructing atomic models of monotype crystalline nanoparticles from a single projection using Z-contrast *** number of atoms in a projected atomic column obtained from annular dark field scanning transmission electron microscopy images serves as an input for the initial three-dimensional *** algorithm minimizes the energy of the structure while utilizing a priori information about the finite precision of the atom-counting results and neighbor-mass *** results show promising prospects for obtaining reliable reconstructions of beam-sensitive nanoparticles during dynamical processes from images acquired with sufficiently low incident electron doses.

关键词： algorithm atomic utilizing

Efficacy and safety profile of LCr35 complete freeze-dried culture in irritable bowel syndrome:A randomized,double-blind study

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World Journal of gastroenterology 2012年第17期18卷 2067-2075页

作者： Michel Dapoigny Thierry Piche Philippe Ducrotte Bernard Lunaud Jean-Michel Cardot annick Bernalier-Donadille Médecine Digestive Centre Hospitalier Universitaire(CHU) Estaing CHU Clermont-FerrandClermont UniversitéInserm UMR 76663001 F-Clermont-FerrandFrance Department of gastroenterology and Inserm 576 Hpital de l'Archet 206202 NiceCedex 3France Department of Hepatogastroenterology and Nutrition Hpital Charles NicolleInserm UMR 107376031 RouenCedexFrance Department of gastroenterology Centre République63000 Clermont-FerrandFrance Biopharmacy Department Faculty of Pharmacy63000 Clermont-FerrandFrance Ur454 Microbiology Division Institut National de la Recherche AgronomiqueResearch Centre of Clermont-Ferrand-Theix63122 Saint Genès-ChampanelleFrance

AIM:To assess the effects and safety of Lactobacillus casei rhamnosus LCr35 complete freeze-dried culture(LCr35) in patients suffering from irritable bowel syndrome(IBS).METHODS:A randomized,double-blind pilot study was performed in 50 patients complaining of IBS symptoms complying with romeⅢ*** were allocated to receive either LCr35(n = 25) at a minimum daily dose of 6 × 108 colony forming units or placebo(n = 25) for 4 *** inclusion,after treatment and 2 wk later,patients completed the IBS severity *** from baseline in the IBS severity score at the end of treatment was the primary efficacy *** were compared between groups in the whole population and in IBS subtypes(IBS with predominance of constipation,IBS with predominance of diarrhoea,mixed IBS,unsubtyped IBS).The presence of lactobacillus casei rhamnosus in stools was investigated at inclusion and at the end of *** gastrointestinal quality of life questionnaire and the hospital anxiety and depression(HAD) scale were also ***:Both groups were balanced for baseline *** 85% of patients,stool analyses showed that lactobacillus casei rhamnosus able to survive in the digestive *** the whole population,improvements in the IBS severity score did not differ significantly between treatments with a 25% decrease after 4-wk treatment,and a 15% decrease from baseline 2 wk later in both *** IBS subgroups,statistical analysis could not be performed due to small sample size,but a clinical response in favour of LCr35 was observed in IBS patients with predominance of diarrhoea:no change in the symptom severity score was seen with the placebo after 4 wk treatment,whereas a clinically relevant decrease occurred with LCr35(-37% vs-3%).Furthermore,in spite of an increase in symptom intensity,the IBS severity score was maintained below the baseline value 2 wk later with LCr35(-19% from baseline),whilst a slight 5% increase from baseline was observ

关键词： Irritable bowel syndrome Lactobacillus casei rhamnosus Probiotics Symptom severity score

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聚焦离子束在金属研究中的应用

冶金分析 2012年第7期32卷 7-11页

作者： XHOFFEr Chris DHONT annick WILLEMS annick 阿塞洛米塔尔研究工业有限公司

由于聚焦离子束(Focused Ion Beam,简称FIB)显微镜的最新运用,材料科学得以迅速发展。钢铁行业中,聚焦离子束技术不仅可以不断将涂料和钝化层变薄,而且特别适用于多相或成分混杂的和/或多孔材料的透射电子显微镜(Transmission Electron ... 详细信息

由于聚焦离子束(Focused Ion Beam,简称FIB)显微镜的最新运用,材料科学得以迅速发展。钢铁行业中,聚焦离子束技术不仅可以不断将涂料和钝化层变薄,而且特别适用于多相或成分混杂的和/或多孔材料的透射电子显微镜(Transmission Electron Microscope,简称TEM)薄片制备。四年前,在ArcelorMittal gent设备上安装了三重束聚焦离子束仪器。随后利用该仪器对大量的各种各样的材料进行筛选和/或处理,以进一步进行TEM分析。FIB技术成功运用于图层、基体和界面研究领域。比如:1)图层应用:厚度均匀性、缺损性及腐蚀研究;2)衬底分析:裂纹扩展、晶界及晶粒取向;3)界面分析:金属间(化合的)相、扩散和偏聚,外延研究。由于FIB仪器的高成本性以及配套需要的专业操作技能,毫无疑问局限了其在钢铁研究中的日常应用。不过,仍然可以从聚焦离子束制备样品的独特方式中获得许多经济效益,比如更短的样品制备时间、对抽样区域的选择性,当然还有人为因素的影响极其有限。因此,通常情况下,FIB样品制备成为唯一一种可以用于制备透射电子显微镜薄片的途径。FIB同TEM的联用分析技术开启了一个化学的、微结构和晶体信息的新世界,这种新领域将在以下研究中得以体现:1)锌-铝-镁涂层的共晶相表征;2)富铬钝化层的缺损学研究;3)耐候钢的结构组成;4)无锌涂层的微结构:铝/镁显示为纳米晶体状的铝镁多相结构。

关键词：聚焦离子束透射电子显微镜截面涂层

ribavirin:Past,present and future

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World Journal of Hepatology 2016年第2期8卷 123-130页

作者： Véronique Loustaud-ratti Marilyne Debette-gratien Jérémie Jacques Sophie Alain Pierre Marquet DenisSautereau annick rousseau Paul Carrier Fédération Hépatologie CHU Dupuytren87042 LimogesFrance Service d’Hépatogastroentérologie CHU Limoges87042 LimogesFrance U850 INSErM Universitéde LimogesCHU Limoges87042 LimogesFrance Service de Bactériologie Virologie CHU Limoges87042 LimogesFrance U1092 INSErM Universitéde LimogesCHU Limoges87042 LimogesFrance Service de Pharmacologie CHU Limoges87042 LimogesFrance

Before the advent of direct acting antiviral agents(DAAs) ribavirin, associated to pegylated-interferon played a crucial role in the treatment of chronic hepatitis C, preventing relapses and breakthroughs. In the present era of new potent DAAs, a place is still devoted to the drug. ribavirin associated with sofosbuvir alone is efficient in the treatment of most cases of g2 infected patients. All options currently available for the last difficult-to-treat cirrhotic g3 patients contain ribavirin. reducing treatment duration to 12 wk in g1 or g4 cirrhotic compensated patients is feasible thanks to ribavirin. retreating patients with acquired anti NS5 A resistance-associated variants using ribavirin-based strategies could be useful. The addition of ribavirin with DAAs combinations however, leads to more frequent but mild adverse events especially in cirrhotic patients. Preliminary data with interferon-free second generation DAAs combinations without ribavirin suggest that future of the drug is jeopardized even in difficult-totreat patients: The optimization of ribavirin dosage according to an early monitoring of blood levels has been suggested to be relevant in double therapy with peginterferon or sofosbuvir but not with very potent combinations of more than two DAAs.

关键词： ribavirin Hepatitis C Peginterferon Directacting antiviral agents

Anti-hepatitis C virus drugs and kidney

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World Journal of Hepatology 2016年第32期8卷 1343-1353页

作者： Paul Carrier Marie Essig Marilyne Debette-gratien Denis Sautereau annick rousseau Pierre Marquet Jérémie Jacques Véronique Loustaud-ratti U850 INSErM Université de Limoges Service d’Hépato-gastroentérologie CHU Limoges

Hepatitis C virus(HCV) mainly targets the liver but can also induce extrahepatic manifestations. The kidney may be impacted via an immune mediated mechanism or a cytopathic effect. HCV patients are clearly at a greater risk of chronic kidney disease(CKD) than uninfected patients are, and the presence of CKD increases mortality. Interferon-based therapies and ribavirin are difficult to manage and are poorly effective in endstage renal disease and hemodialysis. These patients should be given priority treatment with new direct anti-viral agents(DAAs) while avoiding peginterferon and ribavirin. The first results were convincing. To aid in the correct use of these drugs in patients with renal insufficiency, their pharmacokinetic properties and potential renal toxicity must be known. The renal toxicity of these new drugs was not a safety signal in clinical trials, and the drugs are generally efficient in these frail populations. These drugs are usually well tolerated, but recent cohort studies have demonstrated that these new regimens may be associated with renal side effects, especially when using sofosbuvir combinations. HCV, renal diseases and comorbidities are intimately linked. The close monitoring of renal function is required, particularly for at-risk patients(transplanted, HIV-coinfected, CKD, hypertensive or diabetic patients). New DAA regimens, which will soon be approved, will probably change the landscape.

关键词： Nephrotoxicity Hepatitis C Direct anti-viral agents Kidney End-stage renal disease

Correlation between in vitro and in vivo immunomodulatory properties of lactic acid bacteria

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World Journal of gastroenterology 2007年第2期13卷 236-243页

作者： Benoit Foligne Sophie Nutten Corinne grangette Véronique Dennin Denise goudercourt Sabine Poiret Joelle Dewulf Dominique Brassart annick Mercenier Bruno Pot Bactéries Lactiques and Immunité des Muqueuses Institut Pasteur de Lille France Bactéries Lactiques and Immunité des Muqueuses Institut Pasteur de Lille France Nestlé Research Center Nutrition and Health Department Lausanne Switzerland Danisco France Culture Division France Nestlé Nutrition Vevey Switzerland

AIM： To investigate the correlation between in vitro and in vivo immunomodulation potential of the probiotic strain and its ability to prevent experimental colitis in mice. METHODS： In vitro immunomodulation was assessed by measuring interleukJn （IL）-12p70, IL-10, tumor necrosis factor alpha （TNFα） and interferon 7 （IFNγ） release by human peripheral blood mononuclear cells （PBMCs） after 24 h stimulation with 13 live bacterial strains. A murine model of acute TNBS-colitis was next used to evaluate the prophylactic protective capacity of the same set of strains. rESULTS： A strain-specific in vivo protection was observed. The strains displaying an in vitro potential to induce higher levels of the anti-inflammatory cytokine IL-10 and lower levels of the inflammatory cytokine IL-12, offered the best protection in the in vivo colitis model. In contrast, strains leading to a low IL-10/IU12 cytokine ratio could not significantly attenuate colitis symptoms, CONCLUSION：These results show that we could predict the in vivo protective capacity of the studied lactic acid bacteria （LAB） based on the cytokine profile we established in vitro. The PBHC-based assay we used may thus serve as a useful primary indicator to narrow down the number of candidate strains to be tested in murine models for their anti-inflammatory potential.

关键词： Inflammatory bowel disease Probiotics Cytokines Peripheral blood mononuclear cells Trinitrobenzene sulfonate-induced colitis