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Activity Report2015 / 2017

LabEx

NUMEV

www.lirmm.fr/numev

Activity Report LabEx NUMEV 2015-2017 / 2

MONTPELLIER UNIVERSITY OF EXCELLENCE (I-SITE MUSE)

The “Montpellier University of Excellence” (I-SITE project gathers the forces of 19 institutions towards a common ambition: create in Montpellier a thematic research-intensive university that will be internatio-nally recognized for its impact in the fields of agriculture, environment and health. For all its consortium members, this university strives to act as the academic partner they can establish strong ties with, and on which they can fully rely.

The vision of a planet with seemingly unlimited resources is coming to an end, and the world needs to address increasing competition for limited and finite natural resources. Continuing hu-man population growth increases the use of land to yield goods and services, resulting in substantial alteration of most ecosystems on Earth. At the same time, and in addition to their intrinsic pathologies, ageing population faces novel health problems linked to envi-ronmental issues.

MUSE intends to address three intertwined challenges: • promoting an innovative agriculture to contribute to food security and environmental quality;• fostering a transition towards an environmentally-friendly society;• improving human health in changing environments.

The agriculture, environment and health sciences are MUSE core sectors. However, as MUSE aims at a radi-cal transformation on these challenges, from a mono-thematic perspective to a more holistic approach, these sciences are fully connected to chemical, social, natural and computational and engineering sciences. The six Labexes of Montpellier are at the core of the Montpellier University of Excellence, with the unified long-term am-bition to make Montpellier one of the European capitals for health and agro-environment, a true European portal for scientific issues of the Southern countries.

“The Labex NUMEV was created in 2011 to connect hard, computational and engineering sciences with life and environment sciences. This interdisciplinary orientation is completely in line with the MUSE directions, and NUMEV reached this objective beyond our expectations. NUMEV has played a key structuring role by fostering the cooperation between its core community with three other scientific communities: agronomy, bio-health, bio-diversity. Interfaces created with these commu-nities have been very fruitful and as presented into this activity report the scientific, pedagogic, social and economic leverage effect obtained these three last years by the NUMEV teams as been truly impressive. Today NUMEV acts as one major stakeholder of the Montpellier scientific ecosys-tem and we are proud of the results achieved.“Dr. François Pierrot, University of Montpellier/CNRS, Executive Director of MUSE


CONTENTS

EXECUTIVE SUMMARY 4

RESEARCH LABORATORIES MEMBER OF NUMEV 5

OBJECTIVES AND SCIENTIFIC STRUCTURE 7

GOVERNANCE 8

ATTRACTIVINESS 10

RESEARCH TOPICS & PROJECTS 12

FLAGSHIP PROJECTS 30

SOCIO-ECONOMIC LINKS, INNOVATION AND TRANSFER 40

TRAINING AND HIGHER EDUCATION 42

SCIENTIFIC ANIMATIONS 44

PUBLICATIONS 45


The cluster of excellence LabEx NUMEV was created in 2011 in the framework of the French Program of In-vestments to the Future (“Programme d’Investissement d’Avenir“). It brings together 7 laboratories of Montpel-lier and involves 5 partners: University of Montpellier (project leader), CNRS, INRA, INRIA, SupAGRO.

In the last 10 years, Montpellier’s scientists developed true know-how in interfacing hard and computational sciences (Mathematics, Informatics, Physics, Electro-nics, Robotics, Mechanics) with Life Sciences (Biology, Medicine and Health, Environment, Bio-diversity, Agro-nomy), leading to a cross-fertilization of disciplines. In-deed, to analyze, model, understand and meet XXI cen-tury global challenges on health, demographic change and well-being, as well as food security and sustainable agriculture, require quantitative descriptions of sys-tems. Reciprocally, addressing real-life applications gives rise to new fundamental questions for our core disciplines.

For these reasons the LabEx NUMEV (Digital and Hard-ware Solutions, Environmental and Organic Life Mode-ling) aims, to unify along a common scientific strategy, the research strengths in the fields of modeling, com-putational methods, simulation and experimentation

to stimulate their interface with life and environmen-tal sciences. The representation and understanding of natural and man-made systems and their interactions, the virtualization and digitization for life sciences, and technological contributions are the main scientific am-bitions of NUMEV. The objective is also to promote long-term projects with a great potential in terms of re-search, education and/or exploitation, developing new partnerships or reinforcing existing ones between the Mathematics-Informatics-Physics-Systems community (MIPS) and Life and Environmental Sciences. Developing the Research / Education / Transfer dyna-mics, leading creativity and innovation will contribute to the main scientific, technical, and economic changes for the future.

This document can obviously not consist of an exhaus-tive report on NUMEV scientific, technological, training and transfer activities, awards and publications from 2015 to 2017. Its objective is to provide a short over-view to the reader of achievements and highlights of the LabEx during these last 3 years.

Co-directors of the LabEx NUMEV: Pr. Lionel Torres & Pr. Andrea Parmeggiani

EXECUTIVE SUMMARY

€ 8 M€ of Allocated budget45 National collaborations30 International Cooperations initiated2 to 4 invited professor each year

300 Publications (180 since 2015) including145 International journal10 patents

35 Pedagogic actions supported

2 CNRS Medals6 Nominations at the Institut Universitaire de France5 Young Researchers Occitanie Awards1 ACM Fellow1 IIAM Medal (USA)1 French INRIA Académie des sciences Grand Prize

200 Scientists concerned

35 PhD fellowships (19 defended) 43 Post-doc fellowships (14 on going)20 Master Internships each year 14 Engineers recruited (4 on going)

120 Research projects supported10 Scientific animations each year

6 on going Valorisation (SATT) projects6 Start-ups created


Institute of Electronics and Systems (IES) is a Joint Research Unit of CNRS and UM (INSIS CNRS Institute). With its 220 staff, IES is internationally recognized for its scientific and technological knowledge, in the fields of Infrared, Reliability, Sensors and Terahertz. The IES will contribute to the development of innovative solutions for the observation and analysis of physical and natu-

ral objects. Smart sensors and actuators devices and analysis observation techniques (Terahertz for instance) will be at the heart of the NUMEV project.

The Institut Montpelliérain Alex Grothedieck (IMAG) is a joint research unit UM/CNRS (INSMI CNRS Institute). The laboratory now has 80 permanent research staff, mainly teacher-resear-chers from UM and CNRS researchers. The UMR has been revitalized with nearly 30% renewal of its scientific staff, which is the lab policy. An obvious consequence is a strong presence in

the laboratory of young teacher-researchers, which is very positive for the vitality of the unit. From fundamental maths to applied maths, numerical simulation and statistics with industrial collaborations, IMAG will contribute to bring new formalized solutions to modelize (probalistic/biostatistic or formal way) complex systems into the NUMEV project.

The Laboratory Charles Coulomb (L2C) is a Physics Research Unit of the University of Mont-pellier (UM) and the National Center for Scientific Research (CNRS; principal INP, secondary INC). The Unit gathers more than one hundred researchers in physics, nearly 50 support staff, and about 80 non-permanent staff (doctoral students, post-doctoral fellows...). L2C covers a

range of topics ranging from the most mathematical theoretical physics to chemical physics / physical chemistry, from semiconductors to biophysics, with a theoretical and experimental research base on condensed matter and nanosciences. A significant part of the L2C professors and researchers currently undergo research oriented towards life sciences. Their skills in theoretical physics, nanosciences/nanotechnologies, condensed and/or soft matter, will feed the interdisciplinary research of NUMEV.

The Montpellier Laboratory of Informatics, Robotics, and Microelectronics (LIRMM) is a joint research unit of the University of Montpellier (UM) and the National Center for Scientific Research (CNRS, mainly INS2I, secondary INSIS). LIRMM research activities focus on modeling and designing various hardware and software systems (such as robots and integrated circuits),

as well as research activities on theoretical computer science (algorithmic, bioinformatics, etc.), data science and artificial intelligence. LIRMM brings together more than 425 people including University full and associate profes-sors, CNRS and INRIA junior and senior scientists, staff engineers, support and administrative staff and around 150 PhD candidates and postdoctoral fellows. The LIRMM will contribute to NUMEV on all the scientific objectives, with a wide range of expertise on IC design, mobile & communicating systems, artificial intelligence, agent-based modeling of complex systems, bio-informatics, human-machine interactions, robotics.

The Laboratory of Mechanics and Civil Engineering (LMGC) is a joint UM/CNRS research la-boratory (principal INSIS, secondary INEE). Its activities included (1) original themes arising from basic questionings (granular materials, non-smooth dynamics, tensegrity, plant biomechanics, strong thermomechanical couplings, multi-scale approaches) (2) well-established interactions

with biology through the theme of tree and wood, recently reinforced by contributions on human biomechanics; (3) actions related to environment through transports in soils (water, pollutions...); with close links with mathema-tics especially through a highly productive team on mathematic modeling in mechanics. An important expertise for the NUMEV project is centered on biomechanics and specific mechanics understanding of natural phenomen (granular, wood, soils, water).

RESEARCH LABORATORIES MEMBERS OF NUMEV


The Euromov Research Unit (EA 2991) belongs to University of Montpellier and spans over several faculties. It is a nexus for Research, Technology and Innovation in Movement Sciences,

hosts fundamental and translational science projects, a large motion capture and simulation platform, as well as startups and R&D services. The Euromov mission is the identification of movement signatures of health. The Eu-romov team includes movement and brain scientists, as well as digital health experts from Ecole des Mines d’Ales (EMA) and medical doctors from Montpellier and Nîmes academic hospitals (CHUs). EuroMov will bring to NUMEV its expertise related to Movement & Health. Euromov supervises and is strongly involved in the Master of Human Movement Sciences, the doctoral school in Human Movement Sciences (ED 463), with strong cooperation with MIPS (Mathematics-Informatic-Physic-Systems) masters and research labs.

The MISTEA research laboratory is a JRU (Joint Research Unit) bringing together (teachers-) researchers from the INRA MIA (Applied Mathematics and Informatics) department and from the Montpellier SupAgro SABP (Sciences for agri-bio-processes) department. The MISTEA challenge is to develop digital models based on observations for understanding

and decision-making in Agriculture and Environment. For this purpose, mathematics, statistics and computer science, as well as data sciences are used. The systems under study are dynamic, multi-scale and require the development of adapted tools. The development of mathematical, statistical and numerical methods for analysis and decision making for systems from agronomy and environment, with a strong emphasis on dynamical and complex systems, fits objectives of the NUMEV project.

INRIA: Inria, the French National Institute for computer science and applied mathema-tics, promotes “scientific excellence for technology transfer and society”. Graduates from the world’s top universities, Inria’s 2,600 employees rise to the challenges of digital sciences. Re-search at Inria is organised in “project teams” which bring together researchers with comple-

mentary skills to focus on specific scientific projects. With this open, agile model, Inria is able to explore original approaches with its partners in industry and academia and provide an efficient response to the multidisciplinary and application challenges of the digital transformation. Several teams of INRIA are involved into the NUMEVproject, as Camin on biomedical devices, Zenith team on scientific data, Lemon team on methods and tools for littoral and environment, Graphik for graph inferences and knowledge representation and Virtual Plants on the digital simulation and modeling of plant growth.

The PhD Graduate School for Information, Structures and Systems sciences (I2S) gathers all PhD students of the Montpellier area in fundamental sciences: mathematics, physics, compu-ter sciences, and engineering sciences. Seven attractive PhD programs are offered: Biosta-tistics, Electronics Engineering, Informatics, Mathematics, Mechanical Engineering, Physics,

Microelectronics and Robotics. The number of enrolled PhD students is closed to 400 and more than 100 are receiving a PhD diploma each year (530 over the 2013-2017 period). Mentoring of PhD students is performed by more than 600 academics and researchers, among which about 330 with an HDR, members of about 30 research laboratories and units associated with University of Montpellier, CNRS, INRA, CIRAD, INRIA, Montpellier Sup’Agro and IMT Mines d’Alès. Most of the PhD students hired by the LabEx are registered at the I2S doctoral school. I2S lies at the heart of NUMEV project: already 35% of PhD students are currently developing researches at the in-terface with the life and environment sciences. In 2011, this figure was only 13%. This notable increase is due to two main factors: the willingness of the laboratories to focus their scientific activity towards these interfaces and obviously the key role of NUMEV.


NUMEV seeks to harmonize hard and computatio-nal sciences approaches with life sciences and pave the way for emerging interdisciplinary groups with an international profile.

Major interdisciplinary challenges related to life sciences define the global NUMEV scientific objectives:

• Observing, Characterizing, Modeling systems.• Extracting and Representing data.• Developing Computational/Algorithmic Methods for large data sets.• Conceiving Computational & Mathematical Represen-tations of systems.

The expected outcomes of LabEx NUMEV projects are: (1) to increase the excellence and international visibility of research within its laboratories; (2) to ensure the excellence of education, especially at the PhD and master levels; (3) to create new synergies between communities and economic world.In order to reach these objectives, NUMEV is today or-ganized in three levels of scientific action.The first level corresponds to Generic Directions (GD): allowing the conception of methods and tools addres-sing fundamental problems arising at different domain interfaces. The second level corresponds to Integrated Projects (IP) focused on research objects with direct so-cial and economic impact (3 IP today, 4 between 2011 and 2016). The GD evolution can generate, in the me-dium or long term, novel IP based on multidisciplinary skills and aiming at meeting challenges in life and envi-ronmental sciences.

In 2016, and following the mid-term LabEx evaluation, we introduced the third level known as Flagship Pro-jetcs (FP). The aim was to select a limited number of am-bitious scientific programs focused on specific research directions. Supported with substantial funding (initial NUMEV funding, from 250 k€ to 450 k€) and meeting criteria for a strong structuring effect by a unifying in-novative research project with a long life-span, trans-formative effect to position research at national and international levels, clear and measurable impact on training, potential for leveraging or service provision, including interactions with socio-economic actors.

GENERIC DIRECTIONS (GD) PRESENTATION

GD Data, Algorithms & Computations. Representing and extracting knowledge from massive and heteroge-neous data requires different techniques. Approaches combine theoretical analyses, exact and optimal algo-rithms, heuristics, efficient implementations of algo-rithms and methods in appropriate systems, tests on large datasets (simulated and real benchmarks) and dissemination in the form of software or web based tools. GD Data, Algorithm & Computations, foster the link between scientific data and algorithms-computa-tions to offer a higher visibility to the research commu-nity.

GD Modeling offers a wide range of theoretical, simu-lation and computational approaches. It aims at pro-moting mathematical or numerical representations of the physical world in relation to applications involving living and environmental systems. Special attention is paid to plants computational modeling (roots, soil-plant interaction, growth) and microbial interaction modeling in the field of ecology and agronomy (biomass, water, food safety). This GD contributed to the launch of the Rheoblood flagship project, where an important part is about digital blood modeling.

GD Model Systems and Measurements fulfills its role in the characterization and observation of environmen-tal and life systems and strongly cooperates with GD Modeling. This GD will pursue objectives on unders-tanding mechanical systems and phenomena (wood, wheat, soil etc.) at micro or macro levels. The objective is to identify general mechanisms that govern the phy-sical behavior of living objects and the environment by overcoming the intrinsic complexity of natural objects. New directions based on Imaging (holography, Nuclear Magnetic Resonance), acoustic analysis, or Terahertz spectroscopy are within the scope of this GD.

INTEGRATED PROJECT (IP)PRESENTATION

IP Genomes. The IP Genomes will focus its activities on the genome as a complex object in relation with mul-

OBJECTIVES AND STRUCTURE


tiple activities in the Montpellier perimeter like: popu-lation genomics, spatio-temporal characterization and mechanisms of genome organization and the support of novel collaborations in new disciplines such as viral genomics. IP will explore different approaches to the study of the genome as an object and its impact in bio-technological applications via mathematical modeling, physics and bio-informatics of genomes, functional and structural genomics, informational content and evolu-tion. Methods and algorithms focus on the treatment and analysis of genomic and post-genomic big data and innovative applications with strong societal impact in biology, health, agronomy, food and environmental sciences, ecology and biodiversity.

IP Monitoring Environment. Research activities fo-cus on sensors and instrumented UAVs (Vehicles) de-dicated to the monitoring of environmental issues are widely into this IP. “Monitoring Environment“ deals in particular with fields related to the development of sen-sors and devices to detect pollutants, to quantify the impact of agricultural products on the environment (in situ measurement of particle dispersion by a photonic sensor), to study biotopes. The vectorization of sensors is also addressed through the contribution of the deve-lopment of different autonomous system such as nano-satellite-based systems, drone, and robotics systems especially for underwater exploration.

IP “Assistive and health”. This IP aims to (1) provide advanced healthcare methodologies and technological tools, based on a better understanding of patho-phy-siological knowledge, to support health professionals to quantify and measure the clinical status and/or the rehabilitation progress of patients suffering from neurological disorders (e.g., chronic or sudden brain/spinal cord injuries), towards developing effective and case-specific rehabilitation programs; (2) improve reha-bilitation in humans by modulating the peripheral and central nervous system activities; (3) investigate large-scale brain plasticity of the sensorimotor network, at both inter- and intrahemispheric levels with the help of combined neuroimaging approaches and (4) design and provide surgical gestures guidance, learning, trai-ning and evaluation with the help of advanced medical devices.

FLAGSHIP PROJECTS

RHEOBLOOD federates 10 academic, clinical or indus-trial teams whose ambition is to develop constitutive model of blood. In RheoBlood, blood is considered as a dense suspension of deformable cells. This point of view is different from the one in previous studies where aggregation is considered as the most striking process in hemo-rheology. By providing Montpellier with a nu-merical and material platforms dedicated to the study of blood rheo-physics, Rheoblood naturally contributes to the structuration of the local community. RheoBlood aims to make Montpellier a major site in hemodyna-mics and hemophysics, in terms of research, training and transfer to the clinical and industrial worlds.

ALEYIN aims to design an autonomous system (un-derwater robotics) to explore karstic environments, to understand the current resurgences, the state of wa-ter resources, to have a unique mapping of the current karstic networks and to provide a decision-making tool for public authorities. This project brings together 5 la-boratories with the scientific ambition of becoming one of the European leaders in karstic exploration. This year the first experiment in a real karstic environment has been realized providing a dynamic cartography of a ka-rst network.

GEM : Gene expression is a key mechanism to unders-tand basic biological mechanisms such as cell differen-tiation and understanding pathologies such as cancer. The transcription of DNA into RNA and the translation of RNA into proteins are both molecular and systemic. This project brings together 5 laboratories (Physics, Biology-Health, Computer Sciences and Mathematics) in order to establish a new community in Montpellier centered on modern quantitative genomics applied to medical sciences and to develop multidisciplinary trai-ning programs at the University of Montpellier.


GENERIC DIRECTIONS

Data, Algorithms and Computations Modelling Model Systems

and Measures

Observation of the Environment

Assistive and Health

Genomes

INTEGRATED PROJECTS

Syst.Phys.

Math.Info.

FLAGSHIPS

RHEOBLOODModeling blood flow

ALEYINAn underneath robotic

journey, karst exploration

GEMInformation fuelled biophysical models for the control of gene

expression

• Digital and experimental

platform for blood flow

• Rheological blood model based

on new data Modèle

• Rheologic data base

• Prospecting/préservation/

management of water resource

• Hydrological risk management,

forecasting model and decision

support

• Understanding karst dynamics,

cartography – instrumentation -

measures

• Understanding genes

expression for the emergence

of diseases (eg cancer)

• Understanding principles and

mechanisms of gene regulation

• Biophysical modeling and

genomic analysis by

bioinformatic toolsInitial budget: 410K€

Initial budget: 250K€

Initial budget: 250K€

CURRENT LABEX SCIENTIFIC ORGANISATION


The bodies that ensure governance of NUMEV LabEx are the Executive Committee, the Pedagogical and Scientific Council (PSC), the Scientific Committee (SC) and the Strategic Orientation Committee (SOC). These bodies manage the LabEx as a whole, Executive Committee is in charge of bringing resource mana-gement to the Strategic Orientation Committee.

Executive Commitee (EC): in charge of daily management, headed by NUMEV director, and co-directors, for research & innovation, training and international programs, and the project and assistant managers to follow the project life. The EC encourages the emergence of new research projects and foster cooperations from the various actions proposed by NUMEV. EC manages scientific personalities responsible for leading actions specific to NUMEV.

Pedagogical and Scientific Council (PSC): this committee is chaired by the LabEx director(s) and comprises scientists in charge to develop research actions and plan (Generic Directions and Integrated Projects coordina-tors). It is a decision making organ to monitor and coordinate the LabEx commitments. The PSC is in charge to develop and foster the link between research and training, selects research projects, manages training issues and innovation-related activities, fosters international programs.

Strategic Orientation Committee (SOC): chaired by the University of Montpellier and with representative members of each institution, the SOC role consists in reviewing the achievement and projects reported by EC and CPS, deciding strategic orientation, approving budget allocation.

Scientific Committee (SC): based on international renowned scientists and independent stakeholders and repre-sentatives of companies. It works with the CPS and SOC to analyze scientific and training orientations, to suggest developments, investigation & innovation, and international collaborations. It takes part in scientific project eva-luations.

Since 2015 the Governance scheme was reinforced by a natural link with research labs and today a direct link between Heads of research labs and the Pedagogical and Scientific Committees was established by the Executive Committee.

“NUMEV LabEx rallies the mathematics, computer sciences, physics and system com-munities with the objectives to interface hard sciences with organic life, health and environmental problems. This LabEx has strong knock-on effects beyond other na-tional initiatives and provides evidence for the original contribution to research and training of the Montpellier community. The effective participation of the system and computational science community is particularly original and this network develops new interfaces and trade-offs between, for example, physics and bioinformatics. It has successfully contributed to making new research groups emerge. In particular,

some of these groups gained strong momentum thanks to the «Étendards» projects. This LabEx, initiated in 2011, is well positioned, as evidenced by the large number of Ph.D and postdoctoral fellowships, of publications at the international level and of training activities funded in this network.“ Pr. Bertrand Fourcade, University of Joseph Fourrier, Member of LiPhy laboratory, General Chair of the Scientific Committee.

GOVERNANCE


The total initially budget allocated to the LabEx NUMEV by the PIA Program is 8 M€. 2,1 M€ budget have been allo-cated from 2011 to 2014, and 3,1 M€ from 2015 to 2017. For 2018-2021 the overall budget is scheduled and 90% is already engaged. For this three last years, most of this allocation 85% has been devoted to actions for research program actions. Flagship Projects have been initiated in 2016 and today 18% of the budget are allocated for these projects. We remind that these 3 projects are ongoing until the end of 2020, and the overall budget allocated is 1M€. Post-doc and Phd fellowship (42% of the total allocated budget) programs allow cooperations with life and science environment. To support technological platforms and engineering development associated to research projects 12% of the budget is allocated to equipment and human resources. Each year NUMEV support training actions into the scientific perimeter of the LabEx, and 9% of the budget is allocated to different actions for Master, engineers and PhD curricula. For scientific exchanges, a set of workshops, conferences, seminars are organized and 7% of the budget is allocated to these actions.

Significant co-funding

NUMEV benefits from co-funding from various sources, one important leverage effect is the co-funding PhD sche-me. From 2015 to 2017, 25 on-going PhD fellowship have been co-funded with external partners of the LabEx permitting a leverage effect on the PhD Program of 1,8 M€. On the 2015-2017 period, the overall co-funding part is estimated to 7 M€ (x2,5 compare to the 2011-2014 period). It is important to notice: the increasing part of competitive national and european projects funding, an important increases of the public institute contribution (half is the co-funding PhD Scheme) and a substantial co-funding part of the SATT AxLR, based on the success of projects launched before 2015 and the recent work done by SATT to detect projects able to generate exploitable intellectual property. For 2015-2017 period for one euro invest by the LabEx NUMEV, 2.4 € are obtained by the leverage effect.

CO-FUNDING PARTNERS 2011-2014 2015-2017OCCITANIE REGION 96 K€ 325 K€ OTHERS PIA PROGRAM 392 K€ 614 K€ COMPETITIVE NATIONAL PROJECTS (ANR, FUI etc …) 216 K€ 836 K€ PRIVATE COMPANIES 142 K€ 547 K€ PUBLIC INSTITUTE 1 595 K€ 3 500 K€ EUROPE 360 K€ 1 012 K€ VALORISATION PROJECTS FUNDED BY SaTT AxLR 200 K€ 811 K€ TOTAL 3 001 K€ 7 645 K€

BUDGET RESOURCES ALLOCATION

Co-funding scheme don’t take into account State-Region plan contract supporting large cost equipment.For instance BioNanoNMRI equipment (3M€). But the scientific justification is at the heart of the NUMEV project.

18%

22%

20%

12%

9%

7%

6%6%

Allocatedfunding2015-2017

FlagshipProgram Post-Doctoralfellowshipprogram

PhDfellowshipprogram Platformsupportequipment&humanresources

TrainingProgram Workshopandscientificanimation

ManagementCost ScientificSupportprogram

18%

22%

20%

12%

9%

7%

6%6%






18%

22%

20%

12%

9%

7%

6%6%






Allocated funding 2015-2017


PhD and Post-doc fellowships

From 2015 to 2017, 55 young researchers (PhD and Post-Doc) have been hired by the LabEx.

Young researchers focus

Jean-Charles Walter received his PhD in France in 2009 in Theoretical Physics of critical phe-nomena. During his first postdoc in KULeuven (2009-2011), Belgium, he used his background to study systems inspired from Biology like the mechanical and statistical properties of DNA. During his second postdoc in 2012 at the Lorentz Institute in Leiden, The Netherlands, he was introduced to the Physics of the genome and the organization of DNA inside the cell nucleus. In 2013 he hired as a postdoc in Montpellier at the Laboratory Charles Coulomb (L2C) to model

the dynamics of molecular motors on the cytoskeleton. Between 2014 and 2017, he benefited cofunding from the LabEx NUMEV to perform research on bacterial DNA segregation in collaboration with biologists in Toulouse and experimental biophysicists in Montpellier. He has also established and developed collaborations with theoretical physicists at Princeton University, USA, and at LMU in Munich, Germany. Together with the biophysical modeling team at L2C, he introduced the first model able to describe consistently the different phases of the bacterial DNA segregation. This work gave rise to several publications in high impact journals namely in Cell System (2015) and in Physical Review Letters (2017). He is also a partner of the LabEx NUMEV flagship project (2016-2020) «Gene Expression Modeling» in collaboration with biologists and bioinformaticians to study the two main steps of gene expression: transcription and translation. Based on this project he has been hired as permanent researcher at CNRS in 2017.

ATTRACTIVENESS

POST-DOC FIGURE BETWEEN 2015-2017

28 on going Post-Docs (11 different nationalities)

15Foreigners Post-Docs (10 different nationalities)

12 obtained their PhD in another country

8 Women / 20 Men

PHD FIGURE BETWEEN 2015-2017

27 on-going PhD (15 started between 2015-2017),

11 PhD defense

19 obtained their Master out of Montpellier

8 obtained their Master at Montpellier

13 foreigners students (10 different nationalities)

11 Women / 16 Men

National and International Attractiveness

A set of cooperations have been developed during these last years with a set of national and international ins-titutes or universities. Many cooperations have been initiated within the framework of the LabEx through diffe-rent actions as summarized in the scientific description of GD and IP. One objective to set-up attractive PhD and Post-Doc Fellowship programs attracting best national and international researchers in NUMEV laboratories. The University of Montpellier is labelised “HR Excellence in Research“ allowing to the LabEx to promote research ex-cellence and giving increased visibility and attractiveness. For PhD programs, Doctoral School is involved in the recruting process thus guaranteeing the quality of recruting process or recrutement process. For Post-Doc fel-lowhsip, young researchers are hired for a 12 to 24 months period. For instance, several Post-Doc researchers join permanent position in LabEx partner laboratories.


THO Dang Huu obtained his master degree in cybernetics in 2007 in Vietnam. He had spent 10 years in industries and academia in Vietnam and Malaysia before to join EXPLORE team of LIRMM in 2017 into the framework of the NUMEV Flagship ALEYIN project, in which karst au-tonomous systems is the main research topic. He is pursuing his PhD degree of the University of Montpellier under the supervision of Dr Lionel Lapierre. He is developing nonlinear control algorithms and optimal designs for an over-actuated karstic robot. His research interests are

nonlinear control, optimization, and control allocation for underwater robots.

Anna Dupleix graduated in 2013 from a PhD in wood sciences from Arts et Metiers ParisTech and Aalto University, Finland on the development of an InfraRed heating system embedded di-rectly on the peeling machine, a project known as the “wood kebab”. After 2 years work and stu-dy in the agricultural sector and more personally in the beekeeping field, she has come back to research with another challenge: questioning the influence of wood from the beehive material on the bee colonies. Can wood, thanks to its natural physical and chemical properties, provide

better living conditions for the colonies in terms of fight against pathogens - such as Varroa destructor (chemical interaction) and hygrothermal climate (physical interaction)? She has joined the LabEx Numev in 2016 to work on this topic in the current “bee crisis” situation. Her interdisciplinary approach combines also social sciences in order to study the traditional knowledge of beekeepers on the material of their hives. She has gathered a fruitful team of researchers and engineers working now on the development of electronics into the hive (electronic observation hive and technological innovation for automatically varroa counting). She has collaborated to the creation and the management of an experimental apiary opened to the community of researchers willing to work in cooperation and interested into bees in this scientific field.

Viviana Claveria obtained her MS Degre in 2010 from University of Santiago of Chile, and her Ph.D. in Physics in the frame of the Franco-German University Cotutelle program between Saar-land University, Germany and the University of Montpellier, France, the Optical Society of Ame-rica and the American Society. She is currently working as postdoc, on a post-doc program fellowship, at the Hemophysics group lead by Dr. Abkarian at the Center of Structural Biology (CBS), linked with the IMAG group in the framework of the Rheoblood flagship of NUMEV. She

is interested into understanding and characterizing the blood behaviour as a whole fluid under different micro-circulatory conditions. Researches are also centred on the understanding of the mechanical properties of health red blood cells at rest as complementary information. She notably uses bright field and fluorescence microscopy, pressure and flow control systems, microchips, to bring new measurement methods for blood cells.


RESEARCH TOPICS & PROJECTS


KEYWORDS: ALGORITHMS, DATA ANALYSIS, MACHINE LEARNING AND DATA MINING, DEEP LEARNING, CLAS-SIFICATION, COMPLEXITY, PARAMETER ESTIMATION, DATA FUSION, GRAPHS, UNCERTAINTIES, BIOSTATISTICS, ONTOLOGIES, PREDICTIONS.

COORDINATORS: P. PONCELET (LIRMM), B. DE SAPORTA (IMAG), N. HILGERT (MISTEA)

MAJOR RESEARCH UNITS INVOLVED: LIRMM, IMAG, MISTEA, INRIA-GRAPHIK, INRIA-ZENITH

PHD FUNDED 2015-2017: 3

MAN-MONTHS POST-DOC FUNDED 2015-2017: 36

EXAMPLES OF CROSS COOPERATION: UMR DIADE: DIVERSITE - ADAPTATION – DEVELOPPEMENT; UMR MAR-BEC: MARINE BIODIVERSITY, EXPLOITATION AND CONSERVATION; UMR ITAP: INFORMATION-TECHNOLO-GIES-ANALYSES ENVIRONNEMENTALES-PROCEDES AGRICOLES; UMR HSM: HYDROSCIENCES MONTPELLIER; UMR ISEM: INSTITUTE OF EVOLUTION SCIENCES OF MONTPELLIER; UMR BPMP: BIOCHIMIE ET PHYSIOLOGIE MOLÉCULAIRE DES PLANTES, UMR CEFE CENTRE D’ÉCOLOGIE FONCTIONNELLE ÉVOLUTIVE

EXAMPLES OF INTERNATIONAL COOPERATION: STANFORD UNIVERSITY, UNIVERSITY OF DAVIS (USA), FOOD AND AGRICULTURE ORGANIZATION (FAO) OF THE UNITED NATIONS (ITALY), UNIVERSITY OF HANOI (VIETNAM)

HIGHLIGHT: A YOUNG RESEARCHER OBTAINED A MARIE SKLODOWSKA-CURIE FELLOWSHIP WITH STANFORD UNIVERSITY – AWARD 2016 OF THE AFIA (FRENCH ASSOCIATION OF ARTIFICIAL INTELLIGENCE)

GENERAL DIRECTION “DATA, ALGORITHMS & COMPUTATIONS”

ObjectivesThis GD promotes researches that aim to extract, repre-sent and manage knowledge associated with large vo-lumes of data from environment and life sciences. The GD focuses on heterogeneous and complex data in or-der for instance to enrich them or to extract knowledge that are relevant for the decision maker. It also deals with designing algorithms to analyze complex data as well as optimizing computational methods to achieve efficiency and process large-scale data. It also takes care about applications such as recommendations that can be obtained by mining or analyzing data.

ContributionsWhen addressing complex data one of the main is-sues is to deal with heterogeneity. A key aspect for semantic interoperability in agronomy, plant sciences, nutrition and biodiversity is the use of ontologies as a common denominator to describe data, make them interoperable and turn them into structured and for-malized knowledge. One very recent and important

contribution on this topic is the AgroPortal project1 which aims at developing and supporting an internatio-nal reference ontology repository for agronomy, plant sciences, nutrition, and biodiversity. This project is also supported by the AGRO LabEx and #IC DIGITAG. This work was recognized by an award of the AFIA (Artificial Intelligence Association). It is part of a Marie Sklodows-ka-Curie fellowship for a young researcher in coopera-tion with Stanford University. Several projects from the GD have considered complex objects related to images. For instance, a research work derived a procedure to select the dependency structure of a random field that models a numeric picture with approximate Bayesian computation2. Other research works present two supervised AI machine-learning me-thods to automatically detect and recognize coral reef fishes in underwater HD videos. The first method relies on a traditional two-step approach: extraction of HOG features and use of a SVM classifier. The second me-thod is based on Deep Learning2 (Fig. 1).Complex data can also be represented as a multigraph


structure (e.g., protein-protein interaction multigraphs, where the protein pairs have direct interactions/phy-sical associations or they are co-localized); remote sensing images where objects have different associa-tions according to some indices NDVI, NDWI, VSDI, Bri-ghtness). One project has proposed a novel frequent subgraph mining approach MuGraM that extract fre-quent useful patterns that can be used for better un-derstanding the correlations embedded in the data3.Complexity is also related to the dynamic flow of data. A research work was co-funded by Phenome, the French plant phenotyping network (PIA « FPPN » ani-mated by INRA). This work is about estimation methods for functional regression models with functional res-ponse, with application to model the dependency re-lationship between random functions obtained from high throughput plant phenotyping techniques4 (Fig. 2).Classifying data is a challenging problem when data have not been labelled, i.e. unsupervised classification. Recently, the GD funded (Post-doc) studied data-clus-tering like problem in the context of phylogenetic re-construction through the approach of parameterized complexity and kernelization (Fig. 3).

Another example of data classification is about the in-ferring transcriptional gene regulatory networks from transcriptomic datasets, which is a key challenge of sys-tems biology, with potential impacts ranging from me-dicine to agronomy. There are several techniques used presently to experimentally assay transcription factors to target relationships, defining important information about real gene regulatory networks connections. These techniques include classical ChIP-seq, yeast one-hybrid, or more recently, DAP-seq or target technologies. Here, a reverse engineering approach based on mathema-tical and computer simulation has been developed to evaluate the impact that this prior knowledge on gene regulatory networks may have on training machine

learning algorithms. A GRN-simulating algorithm called FRANK for Fast Randomizing Algorithm for Network Knowledge has been developed5, which is able to (i) si-mulate very large networks (potentially containing as many genes as real eukaryotic genomes ~10^4 genes including ~10^3 TFs); (ii) simulate gene expression over-several thousands of simulated time points or system levels (see below), (iii) in a relatively short computation time (several minutes).

The complexity is not only related to the inherent data and may also appear in the model selection as in a PhD work. This thesis aims to improve suitable statistical methods or stochastic models of population genetics and to develop statistical methods adapted to

next generation sequencing data. A first contribution modifies a previous sequential importance sampling algorithm to improve the efficiency of the likelihood estimation using a resampling technique with a new resampling probability distribution depending on the pairwise composite likelihood6. The aim of the second contribution is to propose a model choice procedure between demographic models of different complexity. A penalized model choice criterion based on the

Fig. 1: Automatic detection of fish (S. Villon [C-60])

Fig. 2: High throughput phenotyping plant data (T. Manrique PhD)


comparison of observed and predicted haplotype homozygosity is developed7.

The data that has been analyzed or extracted can be used efficiently for recommending systems for instance. Several large projects now involve sizable laboratories of biologists, computer scientists, chemists and statis-ticians. In cross-discipline domains, users belonging to different communities produce various scientific mate-rials that they own, share, or endorse. In that context, it is interesting to query and recommend scientific ma-terial in the form of documents. Such documents cover various topics such as models for plant phenotyping, statistics on specific kinds of plants, or biological expe-riments. For example, the research work has proposed new efficient recommendation systems8 that have been applied in the context of Pl@ntNet. Pl@ntNet reaches an extraordinary visibility and social impact (also supported by AGRO LabEx) by proposing recogni-tion plant based on a mobile application (http://www.plantnet-project.org/page:MOBILE, more than one mil-lion of downloads). In the same way, a Post-Doc in 2016 focused on Web accessibility (contents and interaction) for people with low vision. He studied how to acquire

the user needs; the web page data that are relevant for the user; how to efficiently compute an adaptation of a web page, via meta-heuristics (genetic algorithms); and how to apply the adaptation to the web page for the end user. This work was awarded by the IFRATH2015 conference and a valorization project is planned.

References:

1 C. Jonquet, A. Toulet, E. Arnaud, S. Aubin, E. Dzalé Yeumo, V. Emonet, J. Graybeal, M.A. Laporte, M.A. Musen, V. Pesce, P. Lar-mande (2018), AgroPortal: A vocabulary and ontology repository for agronomy, Computers and Electronics in Agriculture, Volume 144, Pages 126-143.

2 S. Villon, M. Chaumont, G. Subsol, S. Villeger, T. Claverie, D. Mouillot (2016), «Coral reef fish detection and recognition in un-derwater videos by supervised machine learning: Comparison between Deep Learning and hog+svm methods», ACIVS’2016, Ad-vanced Concepts for Intelligent Vision Systems, Lecce, Italy, Octo-ber 24-27, Springer.

3 V. Ingalalli, D. Ienco and P. Poncelet (2018). «Mining frequent subgraphs in multigraphs». In Information Sciences, Vol. 451-452 pp. 50-66.

4 T. Manrique, C. Crambes and N. Hilgert (2018) Ridge regression for the functional concurrent model, Electron. J. Statist. 12 (1), 985-1018.

5 C. Carré, A. Mas, G. Krouk (2017) Reverse engineering highlights potential principles of large gene regulatory network design and learning, npj Systems Biology and Applications 3:17; www.nature.com/npjsba

6 C. Merle, R. Leblois, F. Rousset, P. Pudlo (2016), Resampling: an improvement of Important Sampling in varying population size models. Theoretical Population Biology, vol. 114, pp. 70-87

7 J. Stoehr, P. Pudlo, L. Cucala (2015) Adaptive ABC model choice and geometric summary statistics for hidden Gibbs random fields. Statistics and Computing, vol. 25 (1), pp. 129-141.

8 M. Servajean, R. Akbarinia, E. Pacitti and S. Amer-Yahia (2015) Profile Diversity for Query Processing using User Recommenda-tions. Information Systems, vol.48, pp.44-63.

Fig. 3: A constraint graph, DS tree with speciation and duplica-tion events and Species tree (M. Jones [Pdoc25])


GENERAL DIRECTION “MODELING”

KEYWORDS: MATHEMATICAL, NUMERICAL, COUPLED METHODS, REDUCED MODELS, IDENTIFICATION AND OPTIMISATION

COORDINATORS: F. JOURDAN (LMGC), J. PALMERI (L2C)

MAJOR RESEARCH UNITS INVOLVED: LIRMM, L2C, IMAG, IES, MISTEA, INRIA (EX-MODEMIC / LEMON)

PHD FUNDED 2015-2017: 4


EXAMPLES OF CROSS COOPERATION: UMR CBS: CENTRE DE BIOCHIMIE STRUCTURALE; UNIVERSITÉ DE GUYANE (LABEX CEBA); UMR BPMP: BIOCHIMIE ET PHYSIOLOGIE MOLÉCULAIRE DES PLANTES, UMR GÉOS-CIENCES MONTPELLIER, UMR AMAP: BOTANIQUE ET MODELISATION DE L’ARCHITECTURE DES PLANTES ET DES VEGETATIONS; UMR INSTITUT CHARLES GERHARDT

EXAMPLES OF INTERNATIONAL COOPERATION: UNIVERSITY OF BERKLEY (USA), ECOLE POLYTECHNIQUE FÉDÉRALE, LAUSANNE (SUISSE), UNIVERSITY OF GRATZ (AUSTRIA), UNIVERSITY OF CHILE (CHILE), SOUTHERN FEDERAL UNIVERSITY (RUSSIA)

HIGHLIGHT: JOINT WORKSHOP WITH LABEX AGRO AND CEMEB ON “MODELING AND NUMERICAL SIMULA-TIONS OF THE PLANT” (2017); GRISBI (“GROUPEMENT DE RECHERCHE INTERDISCIPLINAIRE SUR LES SYSTÈMES BIOLOGIQUES) INTERNATIONAL WORKSHOP ON “BIOPHYSICS: TODAY AND BEYOND” (WITH LABEX EPIGEN-MED, 2018).

ObjectivesThis GD aims at promoting mathematical or numerical representations of the physical world in relation to ap-plications involving living and environmental systems. This GD interacts naturally with the “Algorithms & Com-putations“ GD projects at the frontier between the nu-merical and physical worlds, such as image or statistical analysis, and with the «model systems and measure-ments» GD whenever models require the development of original experimental approaches for input data or validation – with applications typically in agromaterials (wheat, gluten, algae, wood...), environmental fluids, microbes and pathogens, blood, DNA, etc.

The description of complex flow within blood vessels1, together with observations on the process of Malaria parasite egress from blood cells (within the “model

systems and measurements“ GD) and their physical

modeling contributed to the integrated project “Blood

complex system”.

A working group supported since 2011 devoted to

studying of the interactions between fluids and living

matter developed a model (and associated software)

that combined the equations of hydrodynamics and

biochemical reactions (Fig. 1). A working group contri-

buted to the initial construction in 2016 of the INRIA

team “Lemon“ on Methods and tools for Litoral and

Environment, a joint IMAG and INRIA project that was

started in 2017. Two research projects were supported

through a Post-Doc, on modeling and optimization

of activated sludge bioreactors for wastewater treat-

ment2, and a PhD (starting in 2018) on hydro-ecological


modeling.F u n c t i o n i n g mechanisms are studied at all scales (which is one of the origi-nalities of the GD Modeling), from the structuring of polymer gels via catalytic reac-tions at the mole-cular level, to star-

ting projects on the radial diffusion of water in roots3, the biomechanical role of bark in tropical tree species (Postdoc, started in October 2017, jointly funded with LabEx CEBA), individual-based models of bacteria, and species interactions in microbial ecology at the scale of a population. The same can be said for environmental applications ranging from the description of hygro-po-ro-mechanical couplings in soils4 or poroelastic media5, optimization of bioreactors for wastewater treatment and improvement of desalination techniques based on thermomechanical analysis (equipment for the Dune-tec start-up), to the inverse analysis of GPS data of sur-face movements to estimate lithosphere rigidity at the continental level (Fig. 2)6.

Advanced methods to predict anisotropic elasticity of wood7 were performed on local pine species in view of

their use by designers for high added value products. A study on the impact of wooden beehives on bee health and beekeeper practice has led to a multidisciplinary project combining material science and electronics, as well as biology, agronomy, anthropology, neurology.Recently an interdisciplinary project bringing together chemists (cooperation with LabEx Chemisyst), biolo-gists, doctors and biomechanics on the reconstruction of joint cartilage by stem cell techniques was supported by the LabEx. This project, combining modelling and experimentations, has the promising objective of re-constructing functional cartilage for joints worn out by osteoarthritis7. In addition to PhDs, postdocs, projects and meetings, this GD supported several networks and interdisciplina-ry working groups: GRISBI (“Groupement de Recherche Interdisciplinaire sur les Systèmes Biologiques”) with in 2018 international workshop in Montpellier on Biophy-sical modeling with 100 attendees.In May 2017, a workshop on “Modeling and numeri-cal simulations of the Plant” was organised jointly with LabEx AGRO and CeMEB to initiate communication between local research groups from various communi-ties. Digital plant modeling and simulation is becoming a scientific and societal challenge motivated by the need to better understand the interactions between plants and their environment (soil, root) and dedicated projects will start in this direction with the objective of proposing a flagship project.

References:

1 R. Sigüenza, S. Mendez, D. Ambard, F. Dubois, F. Jourdan, R. Mo-zul, F. Nicoud (2016) Validation of an immersed thick boundary method for simulating fluid–structure interactions of deformable membranes. Journal of Computational Physics, vol. 322, pp.723-746, doi <10.1016/j.jcp.2016.06.041>

2 S. Barbier, A. Rapaport and A. Rousseau (2016) «Modelling of biological decontamination of water resource in natural envi-ronment and related feedback strategies», J. Scien. Comput., Vol. 68(3), 1267-1280.

3 Y. Boursiac, M. Velez-Cardona, M. M. Calvo-Polanco, D. Felbacq, C. Pradal, M. Lucas,and C. Godin, and C. Maurel. How does water flow through the roots, Gordon Research Conferences Salt & Wa-ter Stress in Plants, From Molecules to Crops, Switzerland, 2016.

4 F. Z. El Korchi, F. Jamin, M. El Omari, M. S. El Youssoufi (2016) Collapse phenomena during wetting in granular media. Euro-pean. Journal of Environmental and Civil Engineering, vol. 20 (10), doi <10.1080/19648189.2016.1177602>

Fig. 1: Principle of Modeling the remedia-tion of lakes using bioreactors2

Fig. 2: Adaptive and robust inversion of geodetic data at the continental scale: Model prediction of weak rigidities on the San Andreas Fault6


5 D. Boffi, M. Botti, D. A. Di Pietro (2016) A nonconforming high-or-der method for the Biot problem on general meshes. SIAM Jour-nal on Scientific Computing, Society for Industrial and Applied Mathematics, vol. 38 (3), pp. A1508-A1537.

6 S. Furst, M. Peyret, J. Chery, B. Mohammadi (2017) Lithosphere rigidity by adjoint-based inversion of interseismic GPS data, ap-plication to the Western United States. Tectonophysics in press. https://doi.org/10.1016/j.tecto.2017.03.015

6 G. Dusfour, M. Maumus , S. Le Floc’h, D. Ambard, C. Jorgensen, D. Noel, P. Cañadas Mesenchymal stem cells-derived micropellet is a relevant in vitro model for biomechanical modeling of cartilage growth 8th World Congress of Biomechanics (Dublin, IE, 2018-07-08)


GENERIC DIRECTION “MODEL SYSTEMS AND MEASUREMENT (MSM)”

KEYWORDS: WOOD, SOIL, WHEAT, CORN, MUCUS, WATER TREATMENT, COLLOIDS, HUMAN CELLS, MI-CROFLUIDIC, BIODEGRADATION, POLYMERS, NANOTUBES, RHEOLOGY, STRUCTURAL ANALYSIS, AFM, BIOMI-METIC SYSTEMS, VISOELASTICITY, MECHANICAL PROPERTIES, INSTRUMENTATION.

COORDINATORS: C. LIGOURE (L2C), D. LAUX (IES)

MAJOR RESEARCH UNITS INVOLVED: : L2C, IES, LMGC

PHD FUNDED 2015-2017: 4


EXAMPLES OF CROSS COOPERATION: UMR ITAP: INFORMATION-TECHNOLOGIES-ANALYSE ENVIRONNE-MENTAL-PROCEDES AGRICOLES; CHU MONTPELLIER/NIMES; UMR IBMM: INSTITUT DE BIOLOGIE MOLÉCU-LAIRE DE MONTPELLIER; UMR PHYSIOLOGIE ET MEDECINE EXPERIMENTALE; UR CIRAD BIOWOODEB: BIO-MASSE, BOIS, ENERGIE, BIO-PRODUITS, UMR IATE: INGENIERIE DES AGROPOLYMERES ET TECHNOLOGIES EMERGENTES

EXAMPLES OF INTERNATIONAL COOPERATION: UNIVERSITY OF BERKELEY (USA), UNIVERSITY OF MONS (BELGIQUE), UNIVERSITY NAGOYA (JAPAN)

HIGHLIGHT: VINCENT JOURDAIN (L2C) NOMINATED AT THE INSTITUT UNIVERSITAIRE DE FRANCE (IUF)

ObjectivesThe MSM L2C, LMGC and IES experimenters work around the study of systems for understanding life and environment, considering (1) Characterization of mechanical, physical and physico-chemical behavior of natural systems: (granular materials, wood, blood, human cells, wheat, water) and (2) model systems: to identify general mechanisms that govern the physical behavior of living objects and the environment by over-coming the intrinsic complexity of natural objects.

ContributionsNano Material and Instrumentation for life observation: early work focused on cancer, especially on transfer of MSC mitochondria to cancer cells through tunneling nanotubes cells and stem cells in a microfluidic circuit that allows cells to be cultured separately while guiding nanotubes in microchannels. This configuration makes it possible to separate the cell types and to locate the nanotubes in microchannels to better observe them. The first experiments were conducted with breast can-cer cell lines, but more recently have been moved to

primary brain glioma cells, which are known to have internal dendrite production machinery that is better able to produce these dendrites. Production of nano-tubes from cancer cells to stem cells in both 2D culture and microfluidic has been observed1.

Another work, using nanotube has been initiated concerning transport and detection of individual bio-molecules in a carbon nanotube. The biological na-no-channels expressed in living cells provide physiolo-gical functions exhibit remarkable efficiency in terms of ion selectivity and conductivity. A protocol for the fabrication of nanofluidic devices incorporating mono-filament carbon nanotubes has been developed2 for the discrimination of ions and small individual biomo-lecules with the aim of using nucleotides and amino acids in the fine as model compounds. This work has been also supported by the IUF nomination of V. Jour-dain (2015).


Natural Systems characterizationResearch effort has been done on ultrasonic system for viscosities measurement in a test-tube. Viscosity is a key parameter in food processing (optimization of manufacturing processes) and biomedical domain (analysis of blood and biological fluids) for example. In order to assess viscosity on a very large bandwidth at room temperature, a specific ultrasonic method has been developed for these applications: a test tube has been instrumented with several ultrasonic transducers especially designed. The viscosity range covered is now 50 mPa.s – 200 Pa.s. Up to now, results7 have been ob-tained for very small shear rates (< 1 s-1) and for very high shear rates ( > MHz). Works are going on to obtain measurement in the range kHz – MHz.

Another project concerns the variability of the ther-mo-hygro-viscoelastic properties of wood: vibratory measurements and homogenization modeling. The project: (i) Experimental measurements of vibratory properties at different humidity conditions (between 10 and 85% RH) and temperature (between 10 and 70 ° C) on a series of samples of various structure and chemical composition: the aim is to build a database of viscoelastic properties over a wide range of woody woods with various chemical compositions, thanks the optimization ( controlled humidity) of an experimental set-up of vibration measurements in flexion; (ii) suc-cessful development of analytical and numerical mo-dels of viscoelastic behavior based on homogenization methods of the double cell wall of wood.

Related link with Agronomy, a research work has been carried on assemblages of wheat prolamins3. Gluten is a network of proteins known to play a major role in

the structure of many food products thanks to its vis-coelastic properties. Composed of two main classes of proteins, gliadins and glutenins, the structure of gluten is one of the most complex of the vegetable kingdom and its understanding remains incomplete. A gluten structuring protocol was established to elucidate the physical and physico-chemical mechanisms of assem-bly of wheat prolamins. The structure of gluten gels with variable protein compositions as well as structural changes of the assemblages approaching liquid/liquid phase separation were characterized. Recent results include:-Neutron scattering characterization at very small angles (January 2017 experiments in Munich) of the size and number of H-rich regions in gluten gels according to the composition of the extracts (Glu / Gli report)- Quantitative characterization of the kinetics of liquid-li-quid phase separation of gluten gels by X-ray scattering at small angles resolved temporally (ESRF Synchrotron measurements June 2017), demonstration of a spino-dal decomposition stopped for glutenin-enriched gelsThis work is part of a valorisation detection process by SATT AxLR (valorization company).

Related to bio-health, a research work aims to study se-vere chronic bronchial diseases associated with hyper-secretion of mucus and ciliary flow failure4. The project is to study the physical, and hydrodynamic mechanisms involved in the mucociliary function of the bronchial epithelium. Important recent results include:- the micro and characterization of mucus samples cultures, at two characteristic time scales. - characterization of the mechanical properties of the different mucus layers of the epithelium by micro-rheo-logy tools on cultures.

Fig. 1: (a) Schematic representation of the microfluidic circuit for cell capture and observation of the formation of cellular nanotubes, (b) electron microscopic image of the master SU8 microfluidic circuit for co-culture. (c) Confocal microscope image of a nanotube projected from a mesenchymal stem cell (MSC) (red mitotracker staining) to a cancer cell (GSC glioma cells, green staining), mito-chondria capture by cancer cells. (d) Co-culture in microfluidic circuit of MSC cells and glioma cancer cells (GSC),


- New image and data analysis tools have been deve-loped to obtain the trajectory of each cilia and to which cell this cilia belongs.

A recent research work launched mid-2016 was a per-fect example of interaction between systems and mo-dels; Fragmentation versus biodegradation of polymers in the marine environment: a coupled study of a natu-ral system and a model system in the laboratory.The pollution of the oceans by plastic waste, macros-copic or in the form of microparticles is today a major environmental challenge. Although the mechanisms of degradation at sea are identified (UV, waves, bacteria), reliable quantitative data are currently not available to predict the fate and lifetime of a plastic in the ocean. The project proposes to understand the enzymatic erosion of a polymer of controlled morphology (Fig. 2), which has been plunged into the marine environment by following in parallel the evolution of the surface of the material by atomic force microscopy and its frag-mentation into particles by dynamic diffusion of the light. The project has two components: a direct study in the marine environment, and the study of a model system in laboratory. The stage of enzymatic degra-dation which is crucial to lead to biodegradation: has been investigated on a biodegradable polymer, PLLA (polylactic acid) over time by Atomic Force Microsco-py. The appearance over time of two different surface morphologies, depending on whether the material is amorphous or crystallized has been evidenced , and a simple enzymatic erosion model based on the pre-sence of volume defects in the material and on the well-known difference in enzymatic attack for crystalline and amorphous regions is able to qualitatively reproduce the difference in appearance of the surfaces attacked by this model. A very successful workshop with more than 150 at-tendees “Polymers and Oceans 2018”, has been held in Montpellier to bring together French-speaking scientists from different disciplines (physicochemists of polymers, biophysicists, microbiologists, oceanographers ...) on the question of the degradation of polymers in the ma-rine medium. This project was laureate of the first I-SITE MUSE research program call too.

Another project related to systems is at the interface between chemistry and physics to understand the physics and physical chemistry of particle-bubble in-teractions to boost water treatment (this project is also partially supported by the LabEx Chemisyst). This action on the experimental studies of the interaction between model micro-particles dispersed in water and an air-water interface. An experimental setup able to force micro-particles of different morphologies and electrical charges toward the interface has been deve-loped5,6. In parallel an experimental technique based on interferometry in order to track the time evolution of the position and the orientation of each particle with respect to the interface and allows to record dynamics of a particle (spheres and ellipsoids) approaching to the air/water interface and show the crucial role of the electrostatic interactions between the particle and the air/water interface. A theoretical analytical model is in current progress to interpret the experiments

References:

1 B. Nzigou Mombo, S. Gerbal-Chaloin, A. Bokus, M. Daujat-Cha-vanieu, C. Jorgensen, J.-P. Hugnot, M. L. Vignais ML. MitoCeption: Transferring Isolated Human MSC Mitochondria to Glioblastoma Stem Cells. JoVE (Journal of Visualized Experiments), no. 120, pp. e55245–e55245, Feb. 2017

2 K. Yazda, S. Tahir, T. Michel, B. Loubet, M. Manghi. Voltage-acti-vated transport of ions through single-walled carbon nanotubes. Nanoscale, Royal Society of Chemistry, 2017, 9 (33), pp.11976-11986.

3 A. Banc, M. Dahesha, M. Wolf, M.-H. Morel, L. Ramos. Model Gluten Gel. Journal of Cereal Science, Volume 75, May 2017 , Pages 175-178

4 S. Dey, G. Massiera, E. Pitard - Role of spatial heterogeneity in the collective dynamics of cilia beating in a minimal one-dimen-sional model Physical Review E: Statistical, Nonlinear, And Soft Matter Physics, vol. 97 p.012403 (2018)

5 G. Boniello, S. Villa, A. Stocco, M. In, M. Gross, C. Blanc, M. Nobili (2016) Dynamics of an ellipsoid at a fluid interface. 4th Interna-tional Soft Matter Conference, Grenoble, France, September

6 A. Stocco, M. Nobili A comparison between liquid drops and so-lid particles in partial wetting Advances In Colloid And Interface Science, vol. 247 p.223-233 (2017)

7 M. A. Mograne, J.-Y. Ferrandis, D. Laux. Ultrasonic Broadband Rheological characterization of liquids. Anglo French Physical Acoustic Conference - AFPAC. Marseille. Janvier 23-25, 2017

Fig. 2: AFM topography image of the surface of a biodegradable polymer (PLA) immersed for 6 months into the sea. The clear ob-jects on the surface correspond to the bacteria. Green arrows indicate cracks that originate in areas of local damage.


INTEGRATED PROJECT “DNA & GENOMES”

KEYWORDS: HIGH-THROUGHPUT SEQUENCING, FUNCTIONAL GENOMICS, STRUCTURAL GENOMICS, POPU-LATION GENETICS, PHYLOGENOMICS, EXOME, TRANSCRIPTOME, PROTEOME, EPIGENETICS, PHARMACOGE-NOMICS, PAN-GENOME, METAGENOME, ENVIRONMENTAL GENOMICS, MATHEMATICAL MODELING, STATIS-TICAL INFERENCE, BIOPHYSICS, BIOINFORMATICS.

COORDINATOR: F. PARDI (LIRMM)

MAJOR RESEARCH UNITS INVOLVED: LIRMM, IMAG, L2C

PHD FUNDED 2015-2017: 3


EXAMPLES OF CROSS COOPERATION: BANYULS OCEANOLOGICAL OBSERVATORY; UMR CBS: CENTRE DE BIOCHIMIE STRUCTURAL; UMR LABORATOIRE DE MICROBIOLOGIE ET GÉNÉTIQUE MOLÉCULAIRE (TOU-LOUSE); UMR ISEM: INSTITUT DES SCIENCES DE L’ÉVOLUTION DE MONTPELLIER, RESEARCH ACTIONS WITH LABEX EPINGENMED (MONTPELLIER) AND LABEX CEMEB (MONTPELLIER); INSTITUT PASTEUR (PARIS); IBC: INSTITUT DE BIOLOGIE COMPUTATIONNELLE (MONTPELLIER) EXAMPLES OF INTERNATIONAL COOPERATION: JOINT GENOME INSTITUTE (USA), UNIVERSITY OF SUSSEX (UK), UNIVERSITY OF HELSINKI (FINLAND), UNIVERSITY COLLEGE LONDON (UK), UNIVERSITY OF QUÉBEC AT MONTRÉAL (CANADA), UNIVERSITY OF BRITISH COLUMBIA

HIGHLIGHT: O. GASCUEL, AWARDED OF THE 2017 INRIA - FRENCH ACADÉMIE DES SCIENCES GRAND PRIZE; THE WORK OF M. HEBRARD (POSTDOC NUMEV) RECENTLY LED TO A PUBLICATION ON THE OPEN-ACCESS VERSION OF SCIENCE.

ObjectivesThe Integrated Project (IP) “DNA and Genome” concerns the design of novel mathematical and biophysical mo-dels to understand genetic and epigenetic processes, and algorithms for the treatment and analysis of the huge amounts of DNA data available today in all life-science domains, as well as in a number of socio-eco-nomic activities (health, environment, agriculture, food etc.). By combining biology, mathematics, bioinforma-tics and physics, this IP is strongly involved in unders-tanding the fundamental principles guiding genome organization, regulation, function and evolution. The IP “DNA and Genomes” was created in 2014, in accor-dance with the NUMEV Scientific Committee. The idea was to bridge the gap between physical and compu-

tational approaches, which are traditionally developed separately. The areas where the “DNA and Genomes” community are particularly active are: (1) comparative and functional genomics, (2) evolutionary biology, in-cluding population genetics, (3) theoretical biological physics of DNA and chromosomes, and (4) the analysis of Next Generation Sequencing data (NGS).

ContributionsThere are a number of close collaborations with biology laboratories in the Montpellier area (notably within the contours of the LabEx EpiGenMed, Cemeb and Agro). These collaborations provided innovative applications and insights into HIV-AIDS and other pathogens, bac-terial replication and the biology of micro-organisms


with a role in the carbon cycle, potentially impacting environmental sciences, the management of invasive and harmful populations, health, agriculture, and food science. In the following, we illustrate the major results and actions funded.

A post-doc was funded to work on the bioinformatics of HIV. A collaboration with the University College London was established to study the transmission of resistance mutations in the UK population, a pressing topic be-cause the spread of these mutations could render inef-ficient the current drug treatments against HIV. Using an original methodology that extends a first research work2, it was shown that a surprisingly large fraction of resistance transmissions take place among drug naïve patients (Aids publication1).

In a collaboration with the Banyuls oceanological ob-servatory and the Joint Genome Institute in the USA, the work of Maxime Hebrard (Post-doc) on the genome of the smallest known alga, O. tauri3 recently led to im-portant discoveries on the biology of these pico-algae, showing their sexual reproduction and an intriguing link between genome structure and viral immunity4. This work is an interesting example of how bioinfor-matic analyses can help shed light on the biology of an organism, especially when direct observation is proble-matic.

Several projects have been carried out in collaboration with the “Algorithms & Computations”, notably the PhD Theses of Coralie Merle in population genetics5 and of Manuel Binet on phylogenomics6. Another research work who showed that 3D proximity between genomic regions may play an important role in the structural evolution of genomes7. This finding may help the re-construction of the evolutionary rearrangement scena-rios linking two genomes, and opens the way to a num-ber of biologically-relevant algorithmic problems.

With the “Modeling”, a leveraging action has been fun-ded to initiate activities in Physical Genomics, with the active participation of the Montpellier biophysics com-munity: two post-docs were funded to support the collaboration of the L2C with the CBS (Montpellier, M. Nollmann) and the LMGM (Toulouse, J.-Y. Bouet) on the physics of active DNA segregation and positioning in bacteria. Physical modeling allows to describe, quan-titatively and within a unique framework, the experi-mental results for the partition complex coming from both high throughout sequencing data (ChIP-sequen-

cing) on protein-DNA interactions and quantitative su-per-resolution microscopy experiments8, see Figure 1. Very recent modeling results also reveal that a non-li-near physics approach leads to a coherent description of the dynamics of DNA (partition complex) segregation and stable positioning before cell division in bacteria, a mechanism that has until now resisted full understan-ding9.

Fig 1: The predictions of three different biophysical models are confronted with the ChIP-sequencing data giving the density of the protein ParB (making up the DNA-protein partition complex) along the DNA chain, starting from the specific parS binding site. The Stochastic Binding model (green curve) developed in (Cell Systems 2015 [RI46]) agrees best with the data.

Together with INSERM, CNRS, LabEx EpiGenMed, Pole BioMED Rabelais, the IP funded a Joint International Meeting “Biophysics across Scales 2015” of the “Interna-tional Physics of Living Systems” network (GDRI IPoLS, created by CNRS-NSF with major worldwide universi-ties) and the local GRISBi network with a focus on regu-latory mechanisms of the genome.

The Mathematical and Computational Evolutionary Bio-logy conferences, supported by NUMEV, continued from 2014 to 2017, with the latest edition entitled «Methods for Integrative Evolutionary Biology: various sources of data, various scales of evolution». This conference, which has become a reference, attracts annually a nu-mber of world famous researchers working on these essential questions.

Several scientists with NUMEV funding visited Mont-pellier for long time periods, including Anne Bergeron,


Professor of bioinformatics in Montreal, working on gene rearrangements (notably in viruses), for 3 months in 2015, a collaboration that led to a publication10.

References

1 R. Mourad, F. Chevennet, D. T. Dunn, E. Fearnhill, V. Delpech, D. Asboe, O. Gascuel, S. Hue. (2015) A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK. AIDS, vol. 29(15), pp.1917-25, doi: 10.1097/QAD.0000000000000768.

2 F. Chevenet, M. Jung, M. Peeters, T. De Oliveira, O. Gascuel (2013) Searching for Virus Phylotypes. Bioinformatics, 29 (5), pp. 561-570

3 R. Blanc-Mathieu, B. Verhelst, E. Derelle, S. Rombauts, F.-Y. Bou-get, I. Carré, A. Château, A. Eyre-Walker, N. Grimsley, H. Moreau, B. Piégu, E. Rivals, W. Schackwitz, Y. Van de Peer, G. Piganeau (2014) An improved genome of the model marine alga Ostreococ-cus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics. Vol. 15 (1103), doi: 10.1186/1471-2164-15-1103 2014

4 R. Blanc-Mathieu, M. Krasovec, M. Hebrard, S. Yau, E. Des-granges, J. Martin, W. Schackwitz, A. Kuo, G. Salin, C. Donnadieu, Y. Desdevises (2017). Population genomics of picophytoplankton unveils novel chromosome hypervariability. Science Advances 1;3(7):e1700239.

5 C. Merle, R. Leblois, F. Rousset, P. Pudlo (2016), Resampling: an improvement of Important Sampling in varying population size models. Theoretical Population Biology, vol. 114, pp. 70-87

6 M. Binet, O. Gascuel, C. Scornavacca, E. Douzery, F. Pardi (2016) Fast and accurate branch lengths estimation for phylogenomic trees, BMC Bioinformatics, BioMed Central, 17 (23), doi: <10.1186/s12859-015-0821-8>

7 S. Pulicani, P. Simonaitis, E. Rivals, K. M. Swenson (2017). Rear-rangement scenarios guided by chromatin structure. In RECOMB International Workshop on Comparative Genomics (pp. 141-155). Springer

8 A. Sanchez, D. I. Cattoni, J.-C. Walter, J. Rech, A. Parmeggiani, M. Nollmann, J.-Y. Bouet. (2015) Stochastic Self-Assembly of ParB Proteins Builds the Bacterial DNA Segregation Apparatus. Cell Systems Vol. 1 (2), p. 163–173, doi: 10.1016/j.cels.2015.07.013.

9 J.C. Walter, J. Dorignac, V. Lorman, J. Rech, J.-Y. Bouet, M. Noll-mann, J. Palmeri, A. Parmeggiani, F. Geniet (2017). Surfing on protein waves: proteophoresis as a mechanism for bacterial ge-nome partitioning. Physical Review Letters, 119(2), 028101

10 S. Bérard, A. Château, N. Pompidor, P. Guertin, A. Bergeron, K. M. Swenson (2016) Aligning the unalignable: bacteriophage whole genome alignments. BMC Bioinformatics, BioMed Central, 17 (1), pp. 1-13, doi<10.1186/s12859-015-0869-5>


INTEGRATED PROJECT “ASSISTIVE AND HEALTH”

KEYWORDS: LEARNING, MOVEMENT, NEUROPLASTICITY, REHABILITATION, SURGICAL ROBOTICS, ELECTRI-CAL STIMULATION, SENSORY MOTOR SIGNATURES, HEALTH

COORDINATORS: S. PERREY (EUROMOV), N. ZEMITI (LIRMM)

MAJOR RESEARCH UNITS INVOLVED: LIRMM, EUROMOV, L2C, LMGC, CAMIN INRIA TEAM

PHD FUNDED 2015-2017: 3


EXAMPLES OF CROSS COOPERATION: CHU MONTPELLIER AND NÎMES; MONTPELLIER-NÎMES MEDICAL SCHOOL; IMT MINES ALÈS; UMR PHYSIOLOGIE ET MEDECINE EXPERIMENTALE; INSTITUT DE NEUROSCIENCES DE MONTPELLIER

EXAMPLES OF INTERNATIONAL COOPERATION: UNIVERSITY OF SOUTHERN CALIFORNIA (USA), UNIVERSITY OF MONTREAL (CAN), WASHINGTON UNIVERSITY (USA)

HIGHLIGHT: NEUROINNOV, SPIN-OFF UNDER CREATION, ILAB2017 AWARD - BRAIN TOPOGRAPHY’S EDITOR’S CHOICE AWARD 20176

ObjectivesThe Integrated Project “Assistive and Health” since end 2016 targets to (1) provide advanced healthcare me-thodologies and technological tools to support health professionals to quantify and measure objectively the movement, the clinical status and/or the rehabilitation progress of patients suffering from neurological disor-ders (e.g., chronic or sudden brain/spinal cord injuries), towards developing effective and case-specific rehabi-litation programmes; (2) investigate large-scale brain plasticity of the sensorimotor network, at both inter- and intra-hemispheric levels with the help of combined neuroimaging methods and computer modeling ap-proaches; (3) design and provide surgical gestures gui-dance, learning, training and evaluation with the help of advanced medical devices.

ContributionsDuring the last years, several projects have been car-ried out in collaboration mainly with the CHU of Nîmes and Montpellier. One PhD work defended last 2017 funded by the IP proposed a new animal model of di-rect spinal stimulation on bladder and bowel functions facilitated by an innovative powerful stimulation device enabling real time modulation of stimulation parame-

ters1. This study showed, for the first time, that epispi-nal stimulation causes significant detrusor and rectal responses (Fig. 1) in pigs and allows considering further studies with the objective of treating urinary and rectal disorders in spinal cord injury patients.

Fig. 1. Bladder and rectum pressure profiles recorded while stimulating with the needle electrode. During this stimulation session, stool evacuation was induced causing the expulsion of the rectal balloon — this expulsion is manifesting itself by a decrease in the recorded rectal pressure before the end of the stimulation

Thereafter, one can cite a second current granted PhD work aiming to evaluate subtle subcortical changes on resting state level with new tools based on functional magnetic resonance imaging (fMRI) and electroence-


phalography (EEG) techniques before and subsequent to wide-awake surgery for brain diffuse low-grade glio-ma2. It is expected that the complementarity of these modalities (spatial resolution with fMRI vs. temporal with EEG) makes it possible to identify and quantify the phenomena of plasticity in the whole brain over time. Another PhD work supported recently by the IP aims to propose new approaches to functional electrical sti-mulation for lower limb movement assistance using a theoretical framework and an embedded network of generic sensors – actuators (Fig. 2) in Parkinson’s di-sease, hemiplegia or paraplegia. A preliminary study showed a positive global effect on gait and freezing of gait episodes occurrence (decrease of 12%) in subjects with Parkinson’s disease by a somatosensory cueing based on sensitive electrical stimulation3.

Fig. 2. The subject is equipped with an inertial measurement unit (a) and a programmable stimulator (b) wirelessly connected through a PC.

One collaborative project (LIRMM-EuroMov) was also funded within the IP through an equipment combining near-infrared spectroscopy (NIRS) and EEG neuroima-ging techniques to guide multi-electrode transcranial electrical stimulation to modulate cortical excitability/activation at the cortical ‘motor hotspot’ in healthy hu-mans. A proof-of-concept study4 has provided evidence to confirm that functional NIRS neuroimaging can be used to provide a hemodynamic correlate of the ano-dal high-density transcranial direct current stimulation electric field in humans. This finding can be used to pro-vide information about the brain-tissue effects of the electrical stimulation when measured in a resting-state during and/or after interventions in humans.The IP funded also a post doc (L. Van Dokkum5; L2C) to work on the dynamic perspective of the brain functions from the functional integration of distributed networks. By confronting anatomical disconnectivity with functio-nal connectivity of resting-state networks and task per-formance on a semantic language task, this research program was able to highlight continuous plasticity with shifting activity to the edges of the tumor/cavitas.

It is important to note that the IP supports and pro-motes scientific meetings, for instance in September 2017 to increase the interaction between neurophysio-

logists, engineers, mathematicians and clinicians: the 7th joint workshop on new technologies for computer/robot-assisted surgery and the annual scientific mee-ting of the “Institut Fédératif de Recherche sur le Handi-cap” on new technologies for restoring movement and provide assistive.Regarding training related to research activities, a Re-search Engineer has been funded and recruited for 12 months (12/2017 to 11/2018) to support and take in charge the equipment/platforms of the medical ro-botics group of LIRMM located since October 2017 at the new Montpellier-Nîmes Medical School which inte-grates an innovative “Learning and Simulation Medical Training and Research Center” and an “Experimental Surgery Lab.”. The vocation of this training center, especially through the medical and surgical robotics equipment and plat-forms of LIRMM, is to train the doctors and the sur-geons for the practice of the medical robotics gesture and for the new computer and robot-assisted medical and surgical technologies.

References

1 T. Guiho, C. Delleci, C. Azevedo-Coste, C. Fattal, D. Guiraud, J. R.Vignes, L. Bauchet (2018). Impact of direct epispinal stimulation on bladder and bowel functions in pigs: A feasibility study. Neu-rourol Urodyn, 37(1):138-147. doi: 10.1002/nau.23325

2 A. Boyer, J. Deverdun, H. Duffau, E. Le Bars, F. Molino, N. Men-jot de Champfleur, F. Bonnetblanc (2016). Longitudinal Changes in Cerebellar and Thalamic Spontaneous Neuronal Activity After Wide-Awake Surgery of Brain Tumors: a Resting-State fMRI Study. Cerebellum, 4: 51-65. doi: 10.1007/s12311-015-0709-1

3 B. Sijobert, C. Azevedo, D. Andreu, C. Verna, C. Geny (2017). Ef-fects of Sensitive Electrical Stimulation-Based Somatosensory Cueing in Parkinson’s Disease Gait and Freezing of Gait Assess-ment. Artif Organs., 41(11):E222-E232. doi: 10.1111/aor.13059

4 M. Muthalib, P. Besson, J. Rothwell, S. Perrey (2017). Focal He-modynamic Responses in the Stimulated Hemisphere during High-Definition Transcranial Direct Current Stimulation. Neuro-modulation, doi:10.1111/ner.12632.

5 L. E. H. Van Dokkum, E. Le Bars, D. Mottet, A. Bonafé, N. Menjot de Champfleur, I. Laffont (2018). Modified Brain Activations of the Nondamaged Hemisphere During Ipsilesional Upper-Limb Mo-vement in Persons With Initial Severe Motor Deficits Poststroke. Neurorehabilitation and Neural Repair, 32 (1): 34-45.

6 M. Muthalib, S. Perrey, A. Galka, O. Granert, S. Wolff, U. Heute, G. Deuschl, J. Raethjen, M. Muthuraman (2016). Effective connec-tivity of cortical sensorimotor networks during finger movement tasks: A simultaneous fNIRS, fMRI, EEG study. Brain Topography 29(5):645-660, doi: 10.1007/s10548-016-0507-1


INTEGRATED PROJECT “MONITORING OF THE ENVIRONMENT”

KEYWORDS: SENSORS (OPTICS, LASER, TERAHERTZ, ACOUSTICS, THERMAL, …); SYSTEMS; EMBEDDED ELEC-TRONICS; SIGNAL PROCESSING; SMART SYSTEMS; ROBOTICS; INTEGRATION / MULTIMODAL MEASUREMENTS; MULTISENSOR SYSTEMS; SENSOR NETWORKS/VEHICLES NETWORKS; VISION; MINIATURISATION; SENSOR FOR VECTOR; IOT; IOEVERYTHING; UNITED MODELS; MODULARITY.

COORDINATORS: E. LE CLÉZIO (IES), S. DRUON (LIRMM)

MAJOR RESEARCH UNITS INVOLVED: IES, LIRMM, L2C

PHD FUNDED 2015-2017: 3


EXAMPLES OF CROSS COOPERATION: IFREMER; UMR ITAP: INFORMATION-TECHNOLOGIES-ANALYSE ENVI-RONNEMENTALE-PROCEDES AGRICOLES; UMR MARBEC: MARINE BIODIVERSITY EXPLOITATION AND CONSER-VATION; UMR HYDROSCIENCES MONTPELLIER; RESEARCH ACTIONS WITH LABEX CEMEB

EXAMPLES OF INTERNATIONAL COOPERATION: STANFORD UNIVERSITY (USA), UNIVERSITY OF BUENOS AIRES (ARGENTINE), UNIVERSITY OF BOLOGNA (ITALY), UNIVERSITY OF BELGRADE (SERBIA)

HIGHLIGHT: 2 PATENTS RELATED TO SENSOR DEVELOPMENTS, 2 PROJECTS CURRENTLY VALORISED BY THE SATT AXLR COMPANY (TATITAG, CUBESAT-IOT)

ObjectivesThe IP Observation of the Environment has initially been designed to link, in the framework of the NUMEV Community, research actions dealing with the design of sensors and their deployment with the goal to collect and analyze environmental data.Indeed, in the last two years, research activities cente-red on sensors and instrumented UAVs dedicated to the monitoring of environmental issues have been wi-dely supported by NUMEV.

ContributionsCurrently, the integrated project is structured in two parts: The first one is focused on the development and implementation of new sensors in specific environ-mental situations. The second one concerns the de-ployment and the moving of these sensors.

New sensors for monitoring environment: since the beginning of the project, several actions have been ini-tiated, addressing the development of new sensors for environmental measurements. The selected projects on sensors deal in particular with fields related to the development of sensors and devices to detect pollu-tants, to quantify the impact of agricultural products on the environment (in situ measurement of particle dis-persion by a photonic sensor), to study biotopes (contri-butions of wood material to the activity and health of bee colonies), or to develop robotics dedicated to the collection of underwater biological samples (Figure 1).A recent advance concerns in-vivo sensors to identi-fied environment parameters. Another project, PhD cofunded with IFREMER, is running concerning in situ recording of fish physiological status information. For the first time, it will be possible to evaluate the physio-


logical state of the fish in its natural environment, for example by measuring the spatial and temporal varia-tions of its fat content, which is representative of the environment. Several external factors can thus be mea-sured/deduced. For that Specifics Embedded Tags on Mediterranean tunas has been developed and used on real environment1,2. This started with NUMEV in 2014 is now part of IFREMER Flagship POPSTAR3.A second example is a project aiming to the develop-ment of a laser sensor technology, dedicated to the control of vortex beams to create high performance bio-sensors4,5. It has been supported through the fun-ding of a post-doctoral position. The objective was to control the physical properties of a semiconductor laser cavity, based on III-V semiconductor VCSEL and photo-nic crystals nanotechnologies, to build a compact cohe-rent laser source with a stable and controllable orbital angular momentum, termed Optical Vortex. This laser, via the exchange of angular momentum, is able to inte-ract with matter to allow the deployment of new novel technologies in mechanical control (optical tweezers) and measurements (velocimetry Doppler) at the level of single molecules of biological relevance. A company, named INNOPTICS, currently works on the sensor integration to allow industrial applications such as velocimetry measurements dedicated to droplet control at the output of spreading nozzles to limit pest risk.

This IP has been also strongly structured around re-search projects dealing with the deployment of sensors to study our environment. The “Monitoring Environ-ment” IP also enabled the creation of a momentum in Montpellier in the field of underwater exploration. A project developing an adapted UUV with a specific ma-nipulator arm of the latest generation to collect fragile biological samples6 on the deep seabed has been also recently granted with IFREMER and a cooperation with Stanford is ongoing concerning this activity.

The highlight of this dynamic appeared in 2016 with the emergence and the funding of the ALEYIN Flagship Project. It aims to the design of an autonomous system (underwater robotics, figure 2) for the exploration of karst environments7. Through the understanding of the resurgences, the estimation of the state of the water resources, and the development of a precise cartogra-

phy, its major challenge concerns the development of a decision-making tool for the public authorities. This project brings together 4 laboratories with the scien-tific ambition to create a global center of expertise in karst exploration. ALEYIN’s initial budget is € 250,000, financed by NUMEV’s flagship projects.

Fig 2: a. Underwater robotic exploration;

b. Cartography of a karst structure.

The vectorization of sensors is also addressed through the contribution of the development of satellite-based radiocommunication systems8 (Robusta-3A, Figure 3) or the analysis of functional data at geographical posi-tions. For this reason, the LabEx is proud to contribute to the Space Center of the University of Montpellier and two nanosatellites were launched in 2017 (one from In-dia and another one from Russia) with the ultimate goal to use nanosatellite to observe no accessible biodiversity zone.

Fig 1: UUV with manipulator arm to collect biological samples


Fig 3: Robusta-3A Nanosatellite project

The structuring character of the IP is clearly visible through the number of partners involved in the diffe-rent projects. Within the NUMEV community, this IP has been able to LMGC and IES, LIRMM and IES or L2C and IES forces on specific multidisciplinary research projects. In addition, external collaborators to MIPS, scientific references of the environment community, are multiple. In particular, IFREMER, IRD, INRA, IRSTEA can be noted.

The IP has also contributed the diffusion of the knowledge in the Environment or Living fields through the funding of scientific events as the International Conference “Biomedical and Photonics” organized at Montpellier (La Grande-Motte) or “Biologging workshop” common with the LabEx CEMEB in 2016. In terms of training, the IP participated with the axis Modeling in the funding of stays in Montpellier of a Tunisian doctoral student on a topic dealing with the mathematical analysis of a model of anaerobic digestion and contributed to the funding of training periods for Master students. This IP also ini-tiated Hackathon students like contest, especially Hy-drocontest9, an international student contest dealing with embedded sensors on race ship.

References:

1 S. David-Grignot, A. Lamlih, M. Moez Belhaj, V. Kerzérho, F. Azaïs, F. Soulier, P. Freitas, T. Rouyer, S. Bonhommeau, S. Bernard. On-chip Generation of Sine-wave Summing Digital Signals: an Ana-lytic Study Considering Implementation Constraints. Journal of Electronic Testing, Springer Verlag, 2018, (10.1007/s10836-018-5710-4)

2 A. Lamlih, V. Kerzérho, S. Bernard, F. Soulier, M. Comte, M. Re-novell, T. Rouyer, S. Bonhommeau (2017) Mixed-level Simulation Tool for Design Optimization of Electrical Impedance Spectros-copy Systems. 10th International Workshop on Impedance Spec-troscopy, Chemnitz, Germany, September 26-29

3 https://www.lirmm.fr/actualites/un-beau-projet-merlin-lance-par-l-ifremer-en-collaboration-directe-avec-le-lirmm

4 M. Sellahi, M. Myara, G. Beaudoin, I. Sagnes, A. Garnache (2015) Highly coherent modeless broadband semiconductor laser. Op-tics Letters, vol. 40 (18), p. 4301, doi: 10.1364/OL.40.004301.

5 M. Seghilani, M. Myara, I. Sagnes, B. Chomet, R. Bendoula, A. Gar-nache (2015) Self-mixing in low noise semiconductor vortex laser: detection of rotational Doppler shift in backscattered light. Optics Letters, 40 (24), pp.5778-5781, doi.org/10.1364/OL.40.005778

6 F. Leborne, V. Creuze, A. Chemori and L. Brignone Dynamic Modeling and Identification of an Heterogeneously Actuated Un-derwater Manipulator Arm ICRA 2018, IEEE International Confe-rence on Robotics and Automation, Brisbane, Australia, 21-25 May 2018.

7 S. Louis, K. Godary-Dejean, L. Lapierre, T. Claverie, S. Villéger. Formal Method for Mission Controller Generation of a Mobile Ro-bot. SpringerLink. TAROS: Towards Autonomous Robotic Systems, Jul 2017, University of Surrey, Guildford, United Kingdom. Sprin-gerLink, 18th Towards Autonomous Robotic Systems (TAROS) Conference, LNCS (10454), pp.586-600, 2017, Towards Autono-mous Robotic Systems.

8 F. Giamarchi, G. Gervois, L. Dusseau, J.R.Vaillé, X. Laurand, S. Hesse “Robusta 1B: Return of Experience from the Energy Power System In-Flight Telemetry” Accepté au Small Satellite Services and Systems Symposium 2018, Sorrento, Italie, 28 mai-2 juin 2018

9 http://www.midilibre.fr/2017/09/05/le-bateau-du-futur-concu-a-montpellier-pret-a-decoller,1556224.php

10 A. Garnache-Creuillot, M. Myara, I. Sagnes, G. Beaudoin, L. Fer-rieres, V. Lecocq, S. DENET Vertical external cavity surface emit-ting laser devices allowing high coherence, high power and largetunability, PCT/EP2015/061341, 2015

11 A. Garnache-Creuillot, M. Myara, I. Sagnes, L. Le Gratiet, M. Sel-lahi, M. Seghilani, P. Lalanne, Laser device with a beam carrying controlled orbital angular momentum, patent, H01S5/14; H01S5/183; H01S5/10, 2016


FLAGSHIPPROJECTS


The RHEOBLOOD project will initiate the crossover from blood rheology to blood rheophysics, so that he-modynamics ceases to be a descriptive science and be-comes indeed predictive. Rheophysics is used to stress that rheology is not sufficient and has to be completed by detailed microstructure description under flow. This is all the more necessary that the tremendous deve-lopment of microfluidics now enables to design new biomedical devices for diagnosis and bio-engineering in general. One can mention systems to detect pa-thological cell, perform cell sorting, cell enrichment or phase separation. As such devices feature geometrical complexities that have never been studied before, a framework to predict blood flow in arbitrary geometries would represent a huge step further for medical appli-cations. Currently, the development of such devices is only performed through a time and money-consuming trial and error approach.

The long-term objective is thus to provide the com-munity with a validated constitutive model for blood. RHEOBLOOD will focus on the study of blood as a sus-pension of deformable cells. This point of view is diffe-rent from many studies, where aggregation is consi-dered as the most striking process in hemorheology, which is indeed the case for low shear rates (< 1 s-1,

typically). In contrast, RHEOBLOOD will focus on pre-dicting shear-thinning due to deformability and hete-rogeneous distribution of cells in complex geometries, which is one of the most important phenomena in mi-crocirculation and microfluidic devices, especially at moderate to high shear rates.

RHEOBLOOD gathers 10 local academic, industrial and clinical groups with the ambition to take up the challenge of developing a constitutive model for blood. By providing Montpellier with a numerical and material platform dedicated to the study of blood rheophysics, RHEOBLOOD naturally contributes to the structura-tion of the local community. This scientific project goes hand in hand with a strategy aiming at making Mont-pellier a major site for the knowledge of blood flows, in terms of research, training and technology transfer

LABS: IMAG, IES, LMGC, L2C

LEADERS: F. NICOUD (IMAG), S. MENDEZ (IMAG), M. ABKARIAN (CBS)

STARTED MID 2016

PARTNERS: CHU, CBS (CENTRE DE BIOCHIMIE STRUCTURALE), IGF (INSTITUT DE GENOMIQUE FONCTION-NELLE), SYS2DIAG (MEDICAL DIAGNOSTIC), LIBM (LABORATOIRE INTERUNIVERSITAIRE DE BIOLOGIE ET DE LA MOTRICITE), HORIBA MEDICAL

TRAINING: POLYTECH MECHANICAL ENGINEERING AND INTERACTIVE DESIGN, MASTER OF MECHANICS, MASTER OF PHYSICS, MASTER SCIENCES AND NUMERICS FOR HEALTH

BUDGET: 410 K€ FUNDED BY NUMEV

LEVERAGE EFFECTS: SIMULATION LICENSE TRANSFER TO HORIBA MEDICAL, 3 CIFRE PHD STUDENTS FUNDED (HORIBA MEDICAL – SIM&CURE – ALARA EXPERTISE), 1 RESEARCH ENGINEER FUNDED BY SIM&CURE, 1 PHD STUDENT FUNDED BY THE GLOBULE RESEARCH PROJECT SELECTED AFTER THE FIRST MUSE CALL

INTERNATIONAL COOPERATIONS: ETH ZURICH (PR. KOUMOUTSAKOS – UNCERTAINTY QUANTIFICATION IN BLOOD FLOWS - ON GOING); PENNSTATE UNIVERSITY (PR. MANNING – THROMBUS MODELING - EXPECTED)

RHEOBLOOD FLAGSHIP PROJECT


to the industry and the clinical practice. The early re-sults obtained during the preparation and first year of RHEOBLOOD constitute the basis of an application for the next ERC Consolidator Grant; RHEOBLOOD is clearly seen here as a first step of an ambitious pro-ject for the community. Taking advantage of the unique potential of Montpellier regarding blood studies, an International School on hemophysics was organized in May 2018 at Genopolys (https://hemphys.sciencesconf.org/). Open to PhD students, researchers and engineers worldwide, this was the first edition of a biannual event that will gather in Montpellier world-class researchers in the field, thus promoting the international visibility, attractiveness and structuration of the site. The general idea of the creation of the Montpellier Blood Institute which would gather clinicians, biologists and engineers able to address issues as challenging as designing ar-tificial blood or new diagnosis and biomedical devices has emerged from discussions within the consortium. More than 100 researchers/engineers disseminated in 12 laboratories, 5 clinical groups and 8 companies from the Montpellier area were identified as potential parti-cipants. A working group led by Horiba Medical is now organizing further discussions.

Few publications related to this project:

L. Lanotte, J. Mauer, S. Mendez, D. Fedosov, J.-M. Fromen-tal, V. Claveria, F. Nicoud, G. Gompper and M. Abkarian (2016) Red cells dynamic morphologies govern blood shear thinning under microcirculatory flow conditions. Procee-dings of the National Academy of Sciences of the United States of America, Vol. 113(47), pages 13289-13294, Doi: 10.1073/pnas.1608074113

R. Méndez Rojano, S. Mendez, F. Nicoud (2018) Introducing the pro-coagulant contact system in the numerical assess-ment of device-related thrombosis. Biomech Model Mecha-nobiol, First online , doi.org/10.1007/s10237-017-0994-3

J. Sigüenza, S. Mendez & F. Nicoud (2017) How should the optical tweezers experiment be used to characterize the red blood cell membrane mechanics? Biomechanics and Modeling in Mechanobiology, Vol. 16(5), pp. 1645-165, doi: 10.1007/s10237-017-0910-x

L. Lanotte, D. Laux, B. Charlot, and M. Abkarian (2017) Role of red cells and plasma composition on blood ses-sile droplet evaporation. Physical Review E 96, 053114, doi.org/10.1103/PhysRevE.96.053114


The ALEYIN proposal aims at conceiving, designing and engineering an intelligent and practical robotic system (i.e. Sensors System with Controlled Mobility) to ex-plore/inspect underwater confined environment. As generic case studies, the project focuses on karst ex-ploration and hydraulic galleries inspections.Karst generally comprises a network of underground natural conduits, resulting from the dissolution of so-luble rocks, limestone, dolomite and gypsum, which may drain groundwater on a large scale. In karst aqui-fers, which supply drinking water to millions of people worldwide, these conduits correspond to preferential groundwater flow paths. In karst area, the access to the groundwater resource is generally constrained by the knowledge of the underneath conduit network since wells drilled into karst aquifers for water supply must intersect these conduits. In such areas, it is thus of ma-jor importance to get information about the geometry of theses preferential flow paths. This is a major and urgent issue for public authorities involved in prospec-tion, protection and management of the groundwater resource in karst regions. Assessing the geometry of flow paths network in karst, which constrain the dy-namics of groundwater and transport processes, is an ambitious scientific objective that requires field infor-mation, which may be difficult to acquire. Cave divers are heroic, but face physiological limitations.The use of a robotic solution may induce a significant evolution, in its capacity to go further and deeper in the karst maze. This requires an interdisciplinary scientific

journey where hydrogeologists, mathematicians, elec-tronic and control scientists share the same objective. This transdisciplinary posture is necessary to achieve the ALEYIN’s objectives. Moreover, the confined and chaotic conditions impose to keep the expert in the sys-tem’s decision loop during the exploration phase. He is indeed the best to decide on the system’s global and opportunistic objectives. This requires a communica-tion link capable of streaming the current data acqui-sition, acoustic, or visual if turbidity allows. In the un-derwater environment, where wireless communication has very poor quality (bandwidth, latency), an umbilical cable is mandatory. Nevertheless, this cable is a heavy burden that is not admissible for the way back. Hence, the system has to be able to get rid of its cable, and return back autonomously. This question of varying au-tonomy is one of the exciting scientific issues on which the ALEYIN project proposes to progress. As it will be exposed in the sequel, ALEYIN presents a true and com-plete challenge, in terms of interdisciplinary academic research, engineering and socio-economical impacts, while structuring the skills of laboratories of the Uni-versity of Montpellier. ALEYIN contributes to the struc-turation of the local community on environmental is-sues, consistently with the «protection and sustainable management of natural resources ». Initially setup with local and national actors, ALEYIN is contributing to the international visibility of Montpellier, since it stimulates the interest of many international actors from hydro-geology and robotic fields. Moreover, several laborato-

LABS: LIRMM, IES, IMAG

STARTED MID 2016

PARTNERS: HSM (HYDROSCIENCES MONTPELLIER), EDF, HSM, GM, EDF, PLONGEESOUT, BRGM

TRAINING INTERACTIONS: MASTER EEA-FDS, POLYTECH MONTPELLIER (MEA, M&I)

BUDGET: 250K€ FUNDED BY NUMEV

LEVERAGE EFFECTS: PHD CO-FUNDED AND SUPPORT OF THE OCCITANIE REGION , CREATION OF A START-UP (REEDS), FUNDING FROM THE BEZIERS METROPOLE

INTERNATIONAL COOPERATIONS: ON GOING EUROPEAN PROJECT SUBMISSION WITH IST-LISBON (PORTU-GAL), GERONE UNIVERSITY (SPAIN)

ALEYIN FLAGSHIP PROJECT


ries are already interested and the project could gather actors from Spain, Italy, Portugal, Switzerland and Ser-bia, creating an effective opportunity to build a Euro-pean network on this urgent societal and worldwide issue, notably through PRIMA H2020 program.

Example of publications related to this project:

B. Ropars, L. Lapierre, A. Lasbouygues, D. Andreu and R. Zapata (2018) Redundant Actuation System of an Un-derwater Vehicle. Ocean engineering, vol 151, March 2018, Pages 276-289

B. Ropars, A. Lasbouygues, L. Lapierre and D. Andreu, Thruster’s Dead-zones Compensation for the Actuation Sys-tem of an Underwater Vehicle, ECC’15 Linz, Austria, 2015

R. Hmida, A. Ben Abdelali, F. Comby, L. Lapierre, A. Mtibaa and R. Zapata, (2016) Hardware implementation and vali-dation of a 3D underwater shape reconstruction algorithm using a stereo-catadioptric system, MDPI Applied Science Journal, vol. 6 (9) pp. 247, http://www.mdpi.com/2076-3417/6/9/247


The way a cell controls how genes are activated to produce RNA and proteins relies on a complex pro-cess called gene expression. It involves several levels of control, the two major ones being the transcription from DNA into RNA and the translation from RNA into proteins. Gene expression is a key to understanding cell differentiation and plays an important role in diseases like cancer. GEM aims to (1) propose innovative syner-gistic methods combining bioinformatics, biophysics and biology, and (2) structure the community around these research axes, which are widely studied locally by life sciences research teams.The GEM project started in January 2017 and was not based on an initially existing tri-disciplinary interaction. NUMEV acted as a catalyst to start this original project at the national level.

The dynamics of ribosome behavior during translation is a key element in gene expression, but it is a complex issue. Three research topics are under study:1. The difference in ribosome flux between the initia-tion phase, which results in a relative «slowing down» of the ribosomes, and the elongation phase of of trans-lation (we speak of processivity rates along the RNA)2. The influence of the nucleotide and di-nucleotide composition on the jump rates of ribosomes.3. Finally, the influence of the cellular reservoir limits in

the tRNA populations that are necessary for decoding mRNA codons by tRNA.For these three questions about translation, we looked into the Totally Asymmetric Simple Exclusion Process (TASEP) models, the availability of data that allows us to use these models, and the possibilities for controlling results. For questions 1 and 3, we identified, retrieved and per-formed the bioinformatics analysis of published data for yeast (a unicellular eukaryote).In addition, we continued studies on the relationships between genomic rearrangements and chromatin contact points that influence transcription and thus the level of gene activation. This work led to the develop-ment of distance calculation algorithms that take into account chromatin contact cards that are experimen-tally established2,3.Another research step was to use bioinformatics tools to explore interactive Ribo-Seq data. Ribo-seq is the type of high-throughput sequencing that can be used to study translation. All fragments covered by ribosomes on the RNAs being translated are isolated, captured, and sequenced. Thus, short sequences of ribosome-co-vered mRNA portions are obtained irrespective of mRNA in the entire cell sample subjected to sequen-cing. Bioinformatic analysis allow us to identify the po-sition of ribosomes on mRNA sequences or genes. We

LABS: LIRMM, L2C, IMAG

LEADERS: E. RIVALS (LIRMM), J. PALMERI (L2C)

STARTED JANUARY 2017

PARTNERS: UMR INSTITUT DE GÉNÉTIQUE HUMAIN, UMR INSTITUT DE GÉNÉTIQUE MOLÉCULAIRE DE MONT-PELLIER, COMPUTATIONAL BIOLOGY INSTITUTE

TRAINING INTERACTIONS: MASTER OF PHYSIC “PHYSIQUE INGÉNIERIE DU VIVANT”, MASTER OF INFORMATIC “BIOINFORMATIQUE, CONNASSANCES, DONNÉES”

BUDGET: 250K€ FUNDED BY NUMEV

LEVERAGE EFFECTS: RECRUITMENT OF A CR CNRS (L2C, BIOPHYSICS), POSTDOC POSITION FUNDED BY INS-TITUTE OF COMPUTATIONAL BIOLOGY, PHD FELLOWSHIP FROM DOCTORAL SCHOOL OF BIOLOGY (CBS2)

INTERNATIONAL COOPERATIONS: PRINCETON UNIVERSITY, LMU MUNICH

GEM FLAGSHIP PROJECT


can then explore the variation of the ribosome profile along the mRNAs across different conditions or expe-riments. However, interactive tools to verify, explore, and interpret these data are missing. For this reason, we develop a bioinformatics tool facilitating the biolo-gist/biophysicist’s exploration of these data through an interactive visualization interface; it should interest a growing community and find its usefulness in both re-search and teaching.Concerning biophysics models, we proposed a mode-ling of translation based on the TASEP model. After a thorough study of the literature and extensive discus-sions between partners, we focused on homogeneous and inhomogeneous TASEP models. The inhomoge-neous TASEP model can be used to account for the inhomogeneity of codon-dependent mRNA ribosome elongation rates related to the abundance of the cor-responding tRNAs.

Fig. 1: TASEP model for ribosome elongation on mRNA.

Thanks to the Ribo-seq technique, the study of the co-don dependent ribosome speed has become possible. However, there is a major obstacle in the way of suc-cessful modeling: Ribo-seq data give access to the local density of ribosomes along the mRNA, but no theoreti-cal method has yet made it possible to reliably obtain ribosome speeds as a function of the density. We pro-pose to resolve this issue.1. We first used mean-field methods developed by (Shaw et al., 2004) to obtain ribosome speeds. Before applying these methods to biological data, we did a test on data from numerical simulations (Monte Carlo) for which densities and speeds are known. The results are unsatisfactory in some cases, inciting us to develop a method to account for correlation effects between neighboring ribosome sites, which are neglected in the mean field approach.2. We have worked with bioinformaticians to identify a set of Ribo-seq experimental results that could serve

as a «test case» and the analysis of these data is un-derway.To address such complex issues, the collaboration between the five involved academic partner laborato-ries (LIRMM, L2C, IGMM, IGF, IMAG) will strongly struc-ture the local community. The dynamic GEM community that is being established is projected to be the core of a major effort in integrative genomics centered in Mont-pellier. A better understanding of gene expression lets us foresee a wide spectrum of applications in medicine and biotechnology, including its role in certain diseases, especially cancer. The results of this project should the-refore interest other groups (for instance Heidelberg, Munich and especially Princeton University, following the visit of Prof. N. Wingreen in April 2017) and foster new collaborations, including opportunities for techno-logy transfer to industry and hospitals.

Example of Publications related to this project:

1 C. Bessière, M. Taha, F. Petitprez, J. Vandel, J.-M. Marin, L. Bréhélin, S. Lèbre, C.-H. Lecellier. Probing instructions for expression regulation in gene nucleotide compositions. PLoS Comput Biol. 2018 Jan2 ;14(1):e1005921. 2018

2 S. Pulicani, P. Simonaitis, E. Rivals, K. M. Swenson. Rear-rangement Scenarios Guided by Chromatin Structure. RE-COMB-CG LNCS vol 10562 p. 141-155, 2017.

3 P. Simonaitis, K. M. Swenson. Finding Local Genome Rear-rangements. Proc. WABI, LIPIcs Schloss Dagstuhl - Leib-niz-Zentrum fuer Informatik, vol. 88, 24:1-24:13, 2017.

4 J.-C. Walter et al., Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome, New J. Phys. 20,035002 (2018).


SOCIO-ECONOMIC LINKS, INNOVATION AND TRANSFER

TRAINING AND HIGHER EDUCATION

SCIENTIFIC ANIMATIONS

PUBLICATIONS


The socio-economic links between NUMEV members and the socio-economic sphere are strongly anchored. An important work has been done since 2015 to foste-ring socio-economic cooperations.

Since mid-2015 we highlighted valorization and techno-logy transfer collaborating with the Acceleration Com-pany Technology Transfer (SATT-AxLR, specific call for projects in 2016) to identify and encourage the trans-fer of innovations (technologies, products, know-how, technological platforms):

• Starting end of 2016 an analysis on the upgrading valorization potential of 20 NUMEV projects, resulting in a maturation process instruction for 5 of them.

• Fostering cooperations with the economic world through common workshops and working groups (Elec-tronics and Environment Days 2015 with the presence of a dozen of companies or Data 2016 seminars co-built with industrial players, )

• Creating a Club of Partners (CoP) in 2017. It provides a co-working research space and promotes research activities of NUMEV.

• 4 Companies creation (on-going or acted) have co-funded research actions with the LabEx since 2015

• 5 Patents since 2015, 1 Software deposit

• 5 On-going selected projects accompanied by the SATT AxLR for an overall funding of 0,8 M€

CUBESAT project (2016) - Wi-reless communication system between connected objects and a nanosatellite, application to envi-ronment monitoring.

Initial NUMEV Funding: 12 man-months engineer granted to consolidate the pre-maturation project (before AxLR funding)

RARE project (2015) - Identifi-cation and tracking of cell popu-lations of interest in predictive medicine using static learning me-

thods applied to flow cytometry data.Initial NUMEV funding: PhD Grant

DIVINS project (2016) - Innova-tive implantable medical device for endovascular treatment of ce-rebral aneurysms.

Initial NUMEV funding: 12 man.months Post-doc Grant

Magnetic Gas Sensor project (2015): Implementation of an ultra high-performance hybrid sensor, operating at room tempe-rature and combining magnetic

sensivity and bistability of spin transition material on a nanometric scale («gas sensor» nanomaterials). Initial NUMEV funding: Equipment

TatiTAG project (2016): The goal is to prove the concept of a device based on the IES technology (po-rous alumina sensor on paper) that can detect bacteria instan-

taneously. Initial NUMEV funding: 15 Man-months Engineer

SOCIO-ECONOMIC LINKS, INNOVATION AND TRANSFER


Start-ups

NUMEV accompanied also a set of mix research-companies’ projects, supporting research funds associated to foster the companies-research projects and valorization of the research activities.

SIM&CURE companies - Created end 2015 - 8 employees - Sim & Cure’s objective is to de-velop and commercialize software suites, Sim & Size, to secure endovascular cerebral aneu-rysm treatment. Initial NUMEV contribution: 12 Man-months Post-Doc grant.

REEDS companies - In the process of being created - REEDS aims to enhance the technolo-gies and know-how of the ALEYIN project (carried by the LIRMM) to propose a robotic service for collecting (and analyzing) environmental and structural data in underwater environments confined to Companies in the hydroelectric and water management sectors.Initial NUMEV contribution – PhD grant and Research Engineer

NEUROINNOV companies - In the process of being created - NEURINNOV, taught and supported by the INRIA valorisation cell, offers specific technology and expertise in Europe around the development of implantable neuroprostheses.Initial NUMEV contribution: Clinical trials funded by NUMEV

TatiTAG companies - In the process of being created - The TatiTag project aims to develop a diagnostic tool based on a multiplexed, rapid and single-use colorimetric biosensor. This device meets the needs for real-time detection and simultaneously in specific samples (body fluids), application to «connected plaster».Initial NUMEV Contribution – valorization engineer.

REEDS

NUMEV – Club of Partners

The NUMEV Club of Partners has been created beginning of 2017 to foster cooperations between researchers/students and companies. It provides a co-working research space with companies and promotes research acti-vities of NUMEV.


Highlight 1 : Learning and Simulation Medical Trai-ning and Research Center

The New Montpellier-Nimes Medical School (NMMS) in-tegrates an innovative “Learning and Simulation Medi-cal Training and Research Center” and an “Experimen-tal Surgery Lab.”.The strategic localization of NMMS at the Arnaud-de-Villeneuve and the Lapeyronie Hospital Campus, where most of the surgical or and the surgical equipment (daVinci Robot, imaging platforms, …) are located, offers the best practical/applicative, learning,

and research envi-ronment for medi-cal students and re-searchers. Namely, this structure offers a dedicated space to medical and surgical robotics, simulation for training, learning

and research, experimental surgery, and offices for young researchers including master and PhD students. This configuration has been well maturated from the beginning of its design between the NMMS and the LIRMM. Equipment and platforms (teleoperated surgi-cal robot, ultrasound machine, daVinci simulator, 3D endoscopic platform, navigation platforms, …), owned by the LIRMM, have been funded by the LR Region, the CNRS, Montpellier University, and the Equipex Robotex (medical robotics node). LabEx NUMEV contributes to support this unique platform with the grant of Guil-laume Aiche, engineer dedicated to this platform to promote pedagogic actions and links between NMMS and LIRMM.

Highlight 2 : Connected Hive

Superbeelive is an observation hive combining both live broadcasting of a superorganism behaviour (at the indi-vidual scale – the bee - and at the bee colony scale) and

TRAINING AND HIGHER EDUCATIONNUMEV performed actions allowing to reinforce the continuum between MS and PhD, training and research. A strong link is established with the Information, Structures and Systems Graduate School of the University of Montpellier. I2S gathers all PhD students of the Montpellier area in fundamental sciences: mathematics, physics, computer science, and engineering sciences. It has roughly 350 PhD students, among 30% are involved into the scientific perimeter of the LabEx NUMEV. Several Master (Biostatistic, Science and Digital for Health, Electronic, Mechanics) of the Faculty Science of the University of Montpellier benefited of NUMEV support for learning ac-tions. LabEx also support several pedagogic actions with the Polytech Montpellier engineering school (Graduate Engineering School of the University of Montpellier) especially in Electronics, Computer Sciences, and Mechanics. Of course all these actions are intended to be cross-functional between components of the University and in connection with the NUMEV scientific scope. Also pedagogic actions are ongoing with Montpellier SupAgro (and the Convergence Institute #DIGITAG), with Science and Technique of Physical and Sport Activities faculty and with the New Medical school of Montpellier/Nimes. 306 man months internships grant (over the three last years), inclu-ding internships allowing students to complete their final training in one of the local Hospitals with surgeon, have been allocated to train master students to research actions. Since 2015 an overall budget of 0.3M€ have been allocated to training and higher education.

• 1 Doctoral module programs each year• 20 Internships Master program supported each year • Scientific dissemination program with PhD to valorise the scientific culture of the LabEx for college and high school students• 4 specific interdisciplinary Master projects program each year• 2 to 3 summer schools each year• Strong link with the I2S PhD Graduate School • 3 pedagogic engineers support


measurements of several physical parameters (tem-perature, humi-dity) thanks to a specially designed device based on the introduction of an electronic card

in-between the wax comb. Two video cameras recor-ding the comb on both sides will give us the required information about the changes in the behaviour of the colony. Originally, the device enables us to understand the link between the superorganism behaviour and the external physical parameters. Developing Superbeelive has gathered students from IUT Béziers around the sensors development and the broadcasting. The collec-ted data (video and measurements) are designed to be available for both scientists and a larger audience inclu-ding teachers, students. Hives installed at the CNRS De-legation of Montpellier are used as pedagogical support for visiting for middle and high schools of the region.

Highlight 3 : Scientific and technical culture

NUMEV is supporting a pedagogic action (leads by Pr. Nicolas Saby, IMAG) on the scientific and technical culture alongside schools and highschool. 6 NUMEV PhD students are each year involved into this action to promote and to share their scientific knowledge. Several one-week internships with classroom are or-ganized hosting more than 100 high school students. These internships are an opportunity to show through the scientific actions implemented by NUMEV, with the support of PhD students and researchers, the different topics addressed by NUMEV, what are the scientific re-searches, the big challenges and methods, techniques and concepts developed for associated to NUMEV.

Highlight 4 : Surgical Robotics Summer School, 2017

Robotics enables surgery to be less invasive and/or to enhance the performance of the surgeon. In minimally invasive surgery (MIS) for instance, robotics can improve the dexterity of conventional instruments, which is restricted by the insertion ports, by adding intra-cavity degrees of freedom. It can also provide the surgeon with augmented visual and haptic inputs. In open surgery, robotics makes it possible to use in real time pre-operative and per-operative image data to improve precision and reproducibility when cutting, drilling, milling bones, to locate accurately and remove tumours. In both cases, as in other surgical specialities, robotics allows the surgeon to perform more precise, reproducible and dextrous motion. It is also a promising solution to minimize his/her fatigue and to restrict his/her exposition to radiation. For the patient, robotics surgery may result in less risk, pain and discomfort, as well as a shorter recovery time. These benefits explain the increasing research efforts made all over the world since the early 90’s. Surgical robotics requires great skills in many engineering fields as the integration of robots in the operating room is technically difficult. It induces new problems such as safety, man-machine cooperation, real time sensing and processing, mechanical design, force and vision-based control. However, it is very promising as a mean to improve conventional surgical procedures, for example in neurosurgery and orthopedics, as well as providing innovative new ones in micro-surgery, image-guided therapy, MIS and Natural Orifice Transluminal Endoscopic Surgery (NOTES).The courses are addressed to PhD students, post-docs and researchers already involved in the area or inte-rested by the new challenges of such an emerging area interconnecting technology and surgery. This summer school was jointly organized with CAMI LabEx.

TRAINING AND HIGHER EDUCATION


Highlight 1 : Workshop «Modeling and digital simu-lation of plants», May 2017

The wokshop «Mo-deling and digi-tal simulation of plants» was orga-nised by three La-bEx of Montpellier, NUMEV, AGRO and CEMEB hosting 100 attendees.

Many teams from the Montpellier site are engaged in research related to this theme, and interactions already exist between the actors of the three LabEx. The aim of these days was to these exchanges, within the framework of a site policy aimed at (1) improving the visibility of research and training activities, and (2) pro-moting collaborations between communities carrying complementary disciplinary visions to facilitate the emergence of scientific issues and innovative techno-logical challenges.

The thematic field covers all approaches aimed at des-cribing and explaining the behaviour of plants in a digi-tal way or by using digital tools, hence the title «Mode-ling and Numerical Simulation of Plants». Experimental approaches associated with a modeling objective were discussed. Particular interest was given to research questions that provoke multidisciplinary interactions between several actors of the site.

Highlight 2 : NUMEV Scientific Days, Novembre 2017

The sixth scientific days of NUMEV, which took place on November 13th and 14th, was an opportunity to give

an overview on the research projects. More than 200 at-tendees were pre-sent and with 60 posters, 14 oral presentations and 2 invited presenta-tions, these scienti-fic days were a real success and a great opportunity to have exchange with all the partners of the LabEx. It is also the oppotunity to have the vision of the NUMEV’s Scientific Council on the scientific actions of the LabEx, and to trace strategic orientations with the Steering Committee of the LabEx.

Highlight 3 : University of Montpellier/LabEx NU-MEV - UETSC international workshop

University of Electronic Science and Technology of Chi-na (Chengdu) is a national key university directly under the Ministry of Education of China. To foster scientific cooperations, we organize in December the first Uni-versity of Montpelllier - LabEx NUMEV/UESTC scienti-fic exchanges to better understand structurations and reserches driven by both especially on bio-informa-tics and bio-medical applications. Training actions are also scheduled and a discussion on common Master program started. A new workshop was organized at Chengdu in May 2018 to define the actions plan of the cooperation.

SCIENTIFIC ANIMATIONSScientific animations (workshops, conferences, seminars) are scheduled regularly to develop further and foster cooperation between scientific communities. The role of these scientific animations is to propose national and international workshop, seminar, conferences to enhance the interface between core research activities and life and environment sciences and should benefit to all the scientists (comprising Ms and PhD). A dedicated budget of 0.25 M€ have been allocated to these scientific animations since 2015, and 34 events have been organized.

• 9 International scientific conferences• 15 National scientific workshops• 10 Site scientific animations to foster interdisciplinary actions


PUBLICATIONS


Based on Scimago(1) the quality of the NUMEV publications between 2015 and 2017 have been evaluated in 3 quartile – Giving the overall quality impact of publications. Mainly publications in journal citing ex-plicitly NUMEV are in majority in the Q1 quartile confirming the high ranking of publications of NUMEV.

Publications facts 2015-2017:

• 79 peer-reviewed international journal • 99 Peer-reviewed international conference• 30 invited into international or national conferences or seminars• 5 Patents and 1 enrolled software (licence used by an industrial partner)

Based on the publications analysis:• 65% of the publications are co-authored with research laboratories/institute centered on life and environment sciences • 25% of the publications are co-authored with international institute

Few examples of high ranking publications research impact:

• Research work on molecular transport in carbon nanotubes (Biophysical Journal79) led to an IUF nomination.• A study on physical modeling of protein-cell interactions58 was published in PNAS journal.• Digital modeling to understand blood rheology was proposed50 and noticed by CNRS as a new gap to understand fluidic properties of blood.• Bacterial genome segregation and Phys. Rev. Lett.27 was decrypted via modeling, super resolution microscopy and high throughput sequencing methods.• Antiretroviral-naive activities in the field of genomics and HIV-positive individuals was detected and published into the AIDS journal72.• An international consortium3 has characterized the genetic diversity of a natural population of the green mi-croalga, Ostreococcus tauri (Chlorophyte) sampled in the Gulf of Lion. This paper serves as press release on well recognized Phys site (https://phys.org/news/2017-10-natural-algal-population-environmental-affect.html) and noticed by the CNRS (http://www.cnrs.fr/insb/recherche/parutions/articles2017/g-piganeau.html).• Research collaboration done with Pr. H. Duffaut (2012 Herbert Olivecrona Award and Grand Prize of the Natio-nal Academy of surgery) on the waking surgery of brain tumor37.• Contribution on the Microglia/Monocytes Alterations after Spinal Cord Injury based on Magnetic Resonance Imagery22.

(1)The SCImago Journal & Country Rank is a publicly available portal that includes the journals and country scientific indicators deve-loped from the information contained in the Scopus® database (Elsevier B.V.) - http://www.scimagojr.com - In general publications ranked into Q1 have an average impact factor greater than 1.8.

PUBLICATIONS

69%

23%

8%

Journalsclassification(SCIMAGO/SCOPUS)

Q1 Q2 indexedQ3orQ4


2015-2017 list of publications

PATENTS:

1. C. Vernay, R. Goyal, L. Ramos, C. Ligoure, J.-C. Castaing, Agricultural adjuvant compositions of oil/surfactant/salt emulsions and methods for use. International Patent, PCT/EP2014/051963, /

2. B. Sorli, A. Vena, B. Mamadou, T. Rabe Ralam, biocap-teurs multiplex.s par code-barres 2d dynamiques pour une d.tection en temps r.el et simultan.e de bact.ries pathog.nes responsables des infections nosocomiales. FR1656702, 2016

3. A. Garnache-creuillot, M. Myara, I. Sagnes, L. Le Gratiet, M. Sellahi, M. Seghilani, P. Lalanne laser device with a beam carrying controlled orbital angular momentum, international, H01S5/14; H01S5/183; H01S5/10, 2016

4. A. Garnache-Creuillot, M. Myara, I. Sagnes, G. Beaudoin, L. Ferrieres, V. Lecocq, S. DENET Vertical external cavity surface emitting laser devices allowing high coherence, high power and large tunability, PCT/EP2015/061341, 2015

5. F. Terki, A. Bousseksou micromagnetometry detection system and method for detecting magnetic signatures of magnetic materials. IN254DEN2015, international G01R33/12, 2015

ENROLLED SOFTWARE:

1. S. Mendez, F. Nicoud, Logiciel YALES2BIO (2014) IDDN.FR.001.070034.000.S.A.2014.000.31235, http://www.math.univ-montp2.fr/~yales2bio/

International peer-reviewed journals

2017

1. A. Banc, M. Dahesh, M. Wolf, M.-H. Morel, L. Ramos (2017) Model Gluten gels. Journal of Cereal Science, vol. 75, pp. 175-178, doi.org/10.1016/j.jcs.2017.04.005

2. S. L. Berrahou, P. Buche, J. Dibie, M. Roche (2017) Xart: Discovery of correlated arguments of n-ary relations in text. Expert Systems with Applications, vol. 73, pp. 115-124, doi: 10.1016/j.eswa.2016.12.028

3. R. Blanc-Mathieu, M. Krasovec, M. Hébrard, S. Yau, E. Desgranges, J. Martin, W. Schackwitz, A. Kuo, G. Salin, C. Don-nadieu, Y. Desdevises, S. Sanchez-Ferandin, H. Moreau, E. Rivals, I. Grigoriev, N. Grimsley, A. Eyre-Walker, G. Piganeau (2017) Population genomics of picophytoplankton unveils novel chromosome hypervariability. Science Advances, vol 3 (7), e1700239, doi: 10.1126/sciadv.1700239

4. M. Botti, D. A. Di Pietro, P. Sochala (2017) A Hybrid High-Order method for nonlinear elasticity. SIAM Journal on Numerical Analysis, vol. 55 (6), pp. 2687-2717, https://doi.org/10.1137/16M1105943

5. M. Botti and R. Riedlbeck (2017) Equilibrated stress tensor reconstruction and a posteriori error estimation for nonli-near elasticity. hal-01618593v1

6. C. Carré, A. Mas, G. Krouk (2017) Reverse engineering highlights potential principles of large gene regulatory network design and learning, npj Systems Biology and Appli-cations, vol. 3 (17), doi:10.1038/s41540-017-0019-y

7. M. Crespo Moya, B. Ivorra, A. M. Ramos (2017) Asymptotic stability of a coupled advection-diffusion-reaction system ari-sing in bioreactor processes. Electronic Journal of Differential Equations, Vol.194, pp. 1-26.

8. M. Crespo, B. Ivorra, A. M. Ramos, A. Rapaport (2017) Mo-deling and optimization of activated sludge bioreactors for wastewater treatment taking into account spatial inhomoge-neities, Journal of Process Control, vol. 54, pp. 118-128, doi.org/10.1016/j.jprocont.2017.03.009

9. M. Crespo, A. Majumdar, A. M. Ramos, I. M. Griffiths (2017) Solution landscapes in nematic microfluidics. Physica D: Nonlinear Phenomena, vol. 351-352, pp. 1-13, https://doi.org/10.1016/j.physd.2017.04.004

10. L. E. H. van Dokkum, E. Le Bars, D. Mottet, A. Bonafé, N. Menjot de Champfleur, I. Laffont (2017) Modified Brain Activations of the Nondamaged Hemisphere During Ipsile-sional Upper-Limb Movement in Persons With Initial Severe Motor Deficits Poststroke Show less. Neurorehabilitation and Neural Repair, vol.32 (1), pp. 34-35

11. L. E. H. van Dokkum, D. Mottet, I. Laffont, A. Bonafé, N. Menjot de Champfleur, J. Froger, E. Le Bars, (2017). Kinema-tics in the brain: unmasking motor control strategies? Experi-mental brain research. Vol. 235 (9) https://www.ncbi.nlm.nih.gov/pubmed/28573311

12. S. Furst, M. Peyret, J. Chéry, B. Mohammadi (2017) Li-thosphere rigidity by adjoint-based inversion of interseismic GPS data, application to the Western United States, Tecto-nophysics Special Issue: Solid Earth Processes, in press, doi.org/10.1016/j.tecto.2017.03.015

13. M. Gross (2017) Selection of the tagged photons by off axis heterodyne holography in ultrasound-modulated optical tomography. Applied Optics, vol. 56, pp. 1846-185414. V. Hugouvieux and W. Kob (2017) Structuring polymer gels via catalytic reactions. Soft Matter, vol.13 (46), pp. 8706-8746, DOI: 10.1039/c7sm01814b

15. E. Krichen, J. Harmand, M. Torrijos, J. J. Godon, N. Ber-net, A. Rapaport (2017) High biomass density promotes density-dependent microbial growth rate. Biochemical Engineering Journal, Vol. 130, pp 66-75, DOI: 10.1016/j.bej.2017.11.017

16. L. Lanotte, D. Laux, B. Charlot, and M. Abkarian (2017) Role of red cells and plasma composition on blood sessile droplet evaporation. Physical Review E 96, 053114, doi.org/10.1103/PhysRevE.96.053114


17. L. Lanotte, D. Laux, B. Charlot and M. Abkarian (2017) Interconnected role of red cells and plasma on the evapo-ration of blood sessile drops. Physical Review E 96, 053114, DOI: 10.1103/PhysRevE.96.053114

18. S. Louis, K. Godary-Dejean, L. Lapierre, T. Claverie, S. Villé-ger (2017) Formal Method for Mission Controller Generation of a Mobile Robot. Proceedings of the 18th Towards Auto-nomous Robotic Systems (TAROS) Springer edition Yang, G., Fallah, S., Jin, Y., Lekakou, C. (Eds.), pp.586- 600, Guildford, United Kingdom, July 19-21. https://hal-lirmm.ccsd.cnrs.fr/lirmm-01589007/document

19. D. Mottet, L. van Dokkum, J. Froger, A. Gouaich, I. Laffont (2017) Trajectory formation principles are the same after mild or moderate stroke. PLOS ONE. 12, e0173674, https://doi.org/10.1371/journal.pone.0173674

20. M. Muthalib, P. Besson, J. Rothwell, S. Perrey (2017) Focal Hemodynamic Responses in the Stimulated Hemisphere Du-ring High-Definition Transcranial Direct Current Stimulation. Neuromodulation. https://doi.org/10.1111/ner.12632

21. H. Noristani, H. Boukhadaoudi, G. Saint-Martin, P. Auzer, R. Sidi-Boulenouar, N. Lonjon, E. Alibert, N. Tricaud, C. Go-ze-Bac, C. Coillot, F. Perrin (2017) A Combination of Ex Vivo Diffusion MRI and Multiphoton to Study Microglia/Mono-cytes Alterations after Spinal Cord Injury. Frontiers in Aging Neuroscience, vol. 9 (230), doi: 10.3389/fnagi.2017.00230.

22. B. Nzigou Mombo, S. Gerbal-Chaloin, A. Bokus, M. Dau-jat-Chavanieu, C. Jorgensen, J.-P. Hugnot, M.-L. Vignais (2017) MitoCeption: Transferring Isolated Human MSC Mitochon-dria to Glioblastoma Stem Cells. Journal of Visualized Experi-ments, vol. 120, pp. e55245–e55245http://dx.doi.org/10.3791/55245

23. J. Sigüenza, S. Mendez, F. Nicoud (2017) How should the optical tweezers experiment be used to characterize the red blood cell membrane mechanics? Biomechanics and Modeling in Mechanobiology, Vol. 16(5), pp. 1645-165, doi: 10.1007/s10237-017-0910-x

24. J. Sigüenza, D. Pott, S. Mendez, S. Sonntag, T. Kaufmann, U. Steinseifer, F. Nicoud (in press) Fluid-structure interaction of a pulsatile flow with an aortic valve model: a combined experimental and numerical study. International Journal for Numerical Methods in Biomedical Engineering. Accepted for publication Nov. 2017.

25. A. Stocco and M. Nobili (2017) A comparison between liquid drops and solid particles in partial wetting. Advances In Colloid And Interface Science, vol. 247 p.223-233. https://doi.org/10.1016/j.cis.2017.06.014

26. J.-C. Walter, J. Dorignac, V. Lorman, J. Rech, J.-Y. Bouet, M. Nollmann, J. Palmeri, A. Parmeggiani, F. Geniet (2017) Sur-fing on protein waves: proteophoresis as a mechanism for bacterial genome partitioning. Physical Review Letter vol.119 (028101), https://doi.org/10.1103/PhysRevLett.119.028101

27. X. Wang, M. In, C. Blanc, A. Würger M. Nobili, A. Stocco (2017) Janus Colloids Actively Rotating on the Surface of Wa-ter. Langmuir, vol. 33 p.13766 - 13773. https://pubs.acs.org/doi/10.1021/acs.langmuir.7b02353

28. K. Yazda, S. Tahir, T. Michel, B. Loubet, M. Manghi, J. Bentin, F. Picaud, J. Palmeri, F. Henn, V. Jourdain (2017) Voltage-activated transport of ions through single-walled car-bon nanotubes. Nanoscale, Royal Society of Chemistry, vol. 9 (33), pp.11976-11986

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29. A. Ar, M. Muthalib, S. Perrey, A. Galka, O. Granert, S. Wolff, U. Heute, G. Deuschl, J. Raethjen, M. Muthuraman (2016) Effective Connectivity of Cortical Sensorimotor Networks During Finger Movement Tasks: A Simultaneous fNIRS, fMRI, EEG Study. Brain Topogr., vol. 29 (5), pp. 645-660, doi: 10.1007/s10548-016-0507-1

30. A. Banc, C. Charbonneau, M. Dahesh, M.-S. Appavou, Z. Fu, M.-H. Morel, L. Ramos (2016) Small angle neutron scat-tering contrast variation reveals heterogeneities of interac-tions in protein gels. Soft Matter, vol. 12, pp. 5340-5352, doi: 10.1039/C6SM00710D

31. S. Barbier, A. Rapaport, A. Rousseau (2016) Modelling of biological decontamination of a water resource in natural environment and related feedback strategies. Journal of Scientific computing, Springer Verlag, vol. 68 (3), pp.1267--1280 doi 10.1007/s10915-016-0178-9

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33. P. Besson, S. Perrey, W.-P. Teo, M. Muthalib (2016) Com-mentary: Cumulative effects of anodal and priming cathodal tDCS on pegboard test performance and motor cortical excitability. Front Human Neuroscience, vol. 10 (70), doi: 10.3389/fnhum.2016.00070

34. M. Binet, O. Gascuel, C. Scornavacca, E. J.-P. Douzery, F. Pardi (2016) Fast and accurate branch lengths estimation for phylogenomic trees, BMC Bioinformatics, BioMed Central, 17 (23), doi: <10.1186/s12859-015-0821-8>

35. D. Boffi, M. Botti, D. A. Di Pietro (2016) A nonconforming high-order method for the Biot problem on general meshes. SIAM Journal on Scientific Computing, Society for Industrial and Applied Mathematics, vol. 38 (3), pp. A1508-A1537. https://doi.org/10.1137/15M1025505

36. A. Boyer, J. Deverdun, H. Duffau, E. Le Bars, F. Molino, N. Menjot de Champfleur, F. Bonnetblanc (2016) Longitu-dinal Changes in Cerebellar and Thalamic Spontaneous Neuronal Activity After Wide-Awake Surgery of Brain Tu-


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37. V. Claveria, O. Aouane, M. Thiebaud, M. Abkarian, G. Coupier, C. Misbah, T. John, C. Wagner (2016) Cluster of red blood cells in microcapillary flow: hydrodynamic versus macromolecule induced interaction. Soft Matter, vol. 12, pp. 8235-8245, doi : 10.1039/c6sm01165a

38. C. Coillot, R. Sidi-Boulenouar, E. Nativel, M. Zanca, E. Alibert, M. Cardoso, G. Saint-Martin, H. Noristani, N. Lonjon, M. Lecorre, F. Perrin, C. Goze-Bac (2016) Signal Modeling of an MRI ribbon solenoid coil dedicated to spinal cord injury investigations. Journal of Sensors Sensor Systems, vol. 5, pp. 137–145, https://doi.org/10.5194/jsss-5-137-2016

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40. L. van Dokkum, E. Le Bars, D. Mottet, A. Bonafé, N. Men-jot de Champfleur, I. Laffont (2016) Modified brain activa-tions in the non-damaged hemisphere during movements of the «supposed to be healthy» upper-limb. Annals of Physical Rehabilitation Medicine., vol. 59 Supplement p.68, https://doi.org/10.1016/j.rehab.2016.07.157.

41. D. Donnarumma, A. Brodoline, D. Alexandre, and M. Gross (2016) 4d holographic microscopy of zebrash larvae microcirculation. Optic Express 24(3), pp. 26887-26900, doi.org/10.1364/OE.24.026887

42. D. Donnarumma, A. Brodoline, D. Alexandre, and M. Gross (2016), Blood flow imaging in zebrafish by laser dop-pler digital holography. Microscopy Research and Technique, doi: 10.1002/jemt.22678

43. T. Guiho, C. A. Coste, C. Delleci, J.-P. Chenu, J. R. Vignes, L. Bauchet, D. Guiraud (2016). An intermediate animal model of spinal cord stimulation. European Journal of Translational Myology, vol. 26 (2), p. 6034, doi: 10.4081/ejtm.2016.6034.

44. K. Heinze, A. M. Kiszonas, J. C. Murray, C. F. Morris, V. Lullien-Pellerin (2016) Puroindoline genes introduced into durum wheat reduce milling energy and change milling behavior similar to soft common wheats. Journal of Ce-real Science, vol.71, pp. 183-189, https://doi.org/10.1016/j.jcs.2016.08.016

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48. L. Lanotte, J. Mauer, S. Mendez, D. Fedosov, J-M. Fro-mental, V. Claveria, F. Nicoud, G. Gompper and M. Abkarian (2016) Red cells dynamic morphologies govern blood shear thinning under microcirculatory flow conditions. Proceedings of the National Academy of Sciences of the United States of America, Vol. 113(47), pages 13289-13294, https://doi.org/10.1073/pnas.1608074113

49. Y. Le Bras, O. Collin, C. Monjeaud, V. Lacroix, É. Rivals, C. Lemaitre, V. Miele, G. Sacomoto, C. Marchet, B. Cazaux, A. El Aabidine, L. Salmela, S. Alves-Carvalho, A. Andrieux, R. Uricaru, P. Peterlongo (2016) Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads. GigaScience, BioMed Central, vol. 5 (1), https://doi.org/10.1186/s13742-015-0105-2

50. H. al Mehedi, J. Ravaux, K. Yazda, T. Michel, S. Tahir, M. Odorico, R. Podor, V. Jourdain (2016) Increased chemi-cal reactivity of single-walled carbon nanotubes on oxide substrates: In situ imaging and effect of electron and laser irradiations. Nano Research, vol. 9 (2), pp. 517-529, doi: <10.1007/s12274-015-0933-5>

51. C. Merle, R. Leblois, F. Rousset, P. Pudlo (2016), Resam-pling: an improvement of Important Sampling in varying population size models. Theoretical Population Biology, vol. 114, pp. 70-87, http://dx.doi.org/10.1016/j.tpb.2016.09.002

52. L. Ramos, M. Dahesh, A. Banc, A. Duri, M.-H. Morel (2016) Spontaneous gelation of wheat gluten proteins in a food grade solvent, Food Hydrocolloids, vol. 52, pp. 1–10, https://doi.org/10.1016/j.foodhyd.2015.06.014

53. M. de Saint Vincent, M. Abkarian, H. Tabuteau (2016) Dynamics of colloid accumulation under flow over porous obstacles. Soft Matter, vol. 12, pp. 1041–1050, DOI: 10.1039/C5SM01952D

54. M. S. Seghilani, M. Myara, M. Sellahi, L. LeGratiet, I. Sagnes, G. Beaudoin, P. Lalanne, A. Garnache (2016) Vor-tex Laser based on III-V semiconductor metasurface: direct generation of coherent Laguerre-Gauss modes carrying controlled orbital angular momentum. Scientific Reports Na-ture Publishing Group, vol. 6 (38156); doi: 10.1038/srep38156

55. J. Sigüenza, S. Mendez, D. Ambard, F. Dubois, F. Jourdan, R. Mozul, F. Nicoud (2016) Validation of an immersed thick boundary method for simulating fluid–structure interac-tions of deformable membranes. Journal of Computational Physics, vol. 322, pp.723-746, https://doi.org/10.1016/j.jcp.2016.06.041


56. M. Simunovic, E. Evergreen, I. Golushko, C. Prévost, H.-F. Renard, L. Johannes, H. T. McMahon, V. Lorman, G. A. Voth, P. Bassereau (2016) How curvature-generating proteins build scaffolds on membrane nanotubes. Proceedings of the National Academy of Sciences of the United States of Ame-rica, vol. 113 (40), pp. 11226-11231, https://doi.org/10.1073/pnas.1606943113

57. M. Sood, P. Besson, M. Muthalib, U. Jindal, S. Perrey, A. Dutta, M. Hayashibe (2016) NIRS-EEG joint imaging during transcranial direct current stimulation: online parame-ter estimation with an autoregressive model. Journal of Neuroscience Methods, vol. 274, pp. 71-80, https://doi.org/10.1016/j.jneumeth.2016.09.008

58. W.-P. Teo, M. Muthalib, S. Yamin, A. M. Hendy, K. Bramstedt, E. Kotsopoulos, S. Perrey, H. Ayaz (2016) Does a Combination of Virtual Reality, Neuromodulation and Neuroimaging Provide a Comprehensive Platform for Neurorehabilitation? A Narrative Review of the Literature Front Human Neuroscience, vol. 10 (284), doi: 10.3389/fn-hum.2016.00284

59. X. Wang, M. In, C. Blanc, P. Malgaretti, M. Nobili, A. Stocco (2016) Wetting and orientation of catalytic Janus colloids at the surface of water. Faraday Discussions, vol. 191 p.305-324. https://doi.org/10.1039/c6fd00025h

60. K. Yazda, S. Roman, S. Tahir, F. Henn V. Jourdain (2016) Fabrication of Microfluidic Devices for the study of Ion transport through Single-Walled Carbon Nanotubes. MRS Advances, vol. 1 (28), pp. 2085-2090, https://doi.org/10.1557/adv.2016.380

61. K. Yazda, S. Tahir, T. Michel, F. Henn, V. Jourdain (2016) Evidence of selective cation transport through sub-2 nm single-walled carbon nanotubes. MRS Advances, Available on CJO, doi: 10.1557/adv.2016.323, Published online

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65. J. Dupire, M. Abkarian, A. Viallat (2015) A simple model to understand the effect of membrane shear elasticity and stress-free shape on the motion of red blood cells in shear flow. Soft Matter, vol.11 (42), pp.8372-8382, doi: 10.1039/C5SM01952D

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67. E. Loiseau, G. Massiera, S. Mendez, P. Aguilar-Marti-nez, M. Abkarian (2015) Microfluidic Study of Enhanced Deposition of Sickle Cells at Acute Corners. Biophysical Journal, vol. 108, pp. 2623–2632. https://doi.org/10.1016/j.bpj.2015.04.018

68. R. Mourad, F. Chevennet, D. T. Dunn, E. Fearnhill, V. Delpech, D. Asboe, O. Gascuel, S. Hue. (2015) A phylo-type-based analysis highlights the role of drug-naive HIV-po-sitive individuals in the transmission of antiretroviral resis-tance in the UK. AIDS, vol. 29(15), pp.1917-25, doi: 10.1097/QAD.0000000000000768.

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International peer-reviewed Conferences

2017

1. M. Abkarian, O. Albarran Arriagada, G. Massiera, C. Clau-det, A. Callan Jones, V. Lorman, C. Braun-Breton (2017) Spon-taneous curvature and membrane curling for malaria-infec-ted erythrocytes, DPG of the Condensed Matter, Dresden, Germany, March 19-24

2. M. Abkarian, G. Massiera, M. Roques, A. Callan-Jones (2017) Spontaneous Curvature & Membrane Curling for Malaria-Infected Erythrocytes. DPG Spring Meeting, Dresden, Germany, March 19-24

3. J. Barés, Y. Zhao, M. Renouf, K. Dierichs, R. Behringer (2017) Structure of hexapod 3D packings: understanding the global stability from the local organization Powders and Grains, Montpellier, July 3-7

4. J. Barés, S. Mora, J.-Y. Delenne, T. Fourcaud (2017) Experi-mental observations of root growth in a controlled photoe-lastic granular material, EPJ Web of conferences 140, 14008, Powders and Grains 2017 – 8th International Conference on Micromechanics on Granular Media, Montpellier, France, July 3-7

5. M. Botti, D. A. Di Pietro, P. Sochala (2017) A Noncon-forming High-Order Method for Nonlinear Poroelasticity. In: Cancès C., Omnes P. (eds) Finite Volumes for Complex Applications VIII - Hyperbolic, Elliptic and Parabolic Problems. FVCA 2017. Springer Proceedings in Mathematics & Statistics,

vol 200. Springer, Cham, https://doi.org/10.1007/978-3-319-57394-6_56

6. J.-Y. Bouet (2017) ParABS-mediated bacterial DNA segrega-tion: partition complexes self-assemble dynamically and are positioned within the nucleoid. Gordon Research Confe-rence: chromosome dynamics, Lucca, Italy, May 21-26

7. F. Z. El Korchi, F. Jamin, M. S. El Youssoufi (2017) Col-lapse of granular media subjected to wetting. EPJ Web of Conferences 140, 05011, Powders and Grains 2017 – 8th International Conference on Micromechanics on Granular Media, Montpellier, France, July 3-7, https://doi.org/10.1051/epjconf/201714010010

8. S. Furst, K. Anderson, J. Chéry, B. Mohammadi, M. Peyret (2017) Comment fusionner plusieurs types de données géodésiques pour modéliser la source d’une déflation du Ki-lauea ? Colloque G2 2017 Géodésie - Rhéologie, Nice, France Nov. 13-15

9. S. Furst, J. Chéry, B. Mohammadi, M. Peyret, D. Dubucq, A. Jacques, P. Marchina (2017) Reservoirs characterization using inversion of a combine set of geodetic data, from salt to unconventional exploitation, 79th EAGE Conference & Exhibition, Paris, France, June 12-15

10. K. Heinze, O. Arnould, J.-Y. Delenne, V. Lullien-Pellerin, M. Ramonda, M. George (2017) Quantification of the Effect of Surface Slope on Mechanical Measurements by Contact-Re-sonance AFM, Forum des Microscopies à Sonde Locale, Juvignac, France, March 20-24

11. K. Heinze, X. Frank, V. Lullien-Pellerin, M. George, F. Radjai, J.-Y. Delenne (2017) Numerical modeling of the tensile strength of a biological granular aggregate: Effect of the particle size distribution. EPJ Web of conferences 140, 08013, Powders and Grains 2017 – 8th International Conference on Micromechanics on Granular Media, Montpellier, Fance, July 3

12. M. Joannides and O. Salles (2017) Moment closure for a metapopulation model with cooperative patches MAMERN VII. 7th International Conference on Approximation Methods and Numerical Modelling in Environment and Natural Re-sources, Oujda, Morocco, May 17-20

13. W. Kob (2017) Gel-formation via catalytic reactions: In-sight from computer simulations. Dynamics of self-organiza-tion: from colloids to biomaterials, Barcelona, Spain, Dec. 4

14. Kob W. and Hugouvieux V. (2017). Computer simulations of gel-formation via catalytic reactions. Correlation and Disorder in Classical and Quantum Systems, Bangalore, India May 29-June 2

15. A. Lamlih, V. Kerzérho, S. Bernard, F. Soulier, M. Comte, M. Renovell, T. Rouyer, S. Bonhommeau (2017) Mixed-level


Simulation Tool for Design Optimization of Electrical Impe-dance Spectroscopy Systems. 10th International Workshop on Impedance Spectroscopy, Chemnitz, Germany, Sep-tember 26-29

16. L. Lanotte, J. Mauer, S. Mendez, D. Fedosov, J.-M. Fromen-tal, V. Claveria, F. Nicoud, G. Gompper, M. Abkarian (2017) A new look at blood shear-thinning. DPG Spring Meeting, Dresden, Germany, March 19-24

17. D. Lapeine, F. Pascal, J.-Y. Ferrandis, D. Laux, P. Combette (2017) Development and improvement of acoustic sensors for the detection of pollutants in aquatic environments, I2M-CT 2017, Turin, Italy, May 22-25

18. A. Lasbouygues, S. Louis, B. Ropars, L. Rossi, H. Jourde, H. Delas, P. Balordi, R. Bouchard, R. Dighouth, M. Dugrenot M., Jacquemin E., Vasseur F., Lapierre L., Andreu D. (2017) Robotic mapping of a karst aquifer, IFAC WC 2017, Toulouse, France, July 9-14

19. J. Mauer, L. Lanotte, S. Mendez, V. Claveria, F. Nicoud, M. Abkarian, G. Gompper, D. Fedosov (2017) Intricate dynamics and morphology of red blood cells under physiological flow conditions. DPG Spring Meeting, Dresden, Germany, March 19-24

20. R. Méndez Rojano, S. Mendez, F. Nicoud (2017) A CFD model to predict the initiation of thrombosis in blood contac-ting medical devices. Proceeding of the 5th International Conference on Computational and Mathematical Biomedical Engineering (CMBE2017) P. Nithiarasu, A. M. Robertson (Eds.) ISSN 2227-9385, vol.1 pp. 86-89, Pittsburgh, PA, USA, April 10–12

21. S. Mendez, L. Lanotte, M. Abkarian, F. Nicoud (2017) Red blood cells in high shear and strain rates: how numerical simulation can contribute. DPG Spring Meeting, Dresden, Germany, March 19-24

22. S. Mendez, L. Lanotte, M. Abkarian, F. Nicoud (2017) Red blood cells in high shear and strain rates: how numerical simulation can contribute. DPG Spring Meeting, Dresden, Germany, March 19-24

23. S. Mora, T.-L. Vu, J. Baré, S. Nezamabadi (2017) Highly deformed grain: from the Hertz contact limitation to a new strain field description in 2D, EPJ Web of Conferences 140, 05011, Powders and Grains 2017 – 8th International Confe-rence on Micromechanics on Granular Media, Montpellier, France, July 3-7

24. M. A. Mograne, J.-Y. Ferrandis, D. Laux. (2017) Ultrasonic Broadband Rheological characterization of liquids. Anglo French Physical Acoustic Conference – AFPAC. Marseille, France, Jan. 23-25

25. S. Pulicani, P. Simonaitis, É. Rivals, K. M. Swenson, (2017) Rearrangement scenarios guided by chromatin structure. In Poceedings of the RECOMB 15th International Workshop on Comparative Genomics, pp. 141-155, Barcelona, Spain, Oct. 4-6. Springer, doi: http://dx.doi.org/10.1101/137323

26. P. Simonaitis and K. M. Swenson (2017) Finding Local Genome Rearrangements. 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Editors: Russell Schwartz and Knut Reinert; Article No. 24; pp. 1-13

27. R. Sidi-Boulenouar, O. Yzebe, C. Coillot, E. Alibert, E. Nativel, R. Jelinek, F. Gatineau, J.-L. Verdeil, Gilles Vercambre, N. Bertin, C. Goze-Bac (2017) Real-Time dynamical monito-ring plants status in normal and stress conditions: from Low Fields NMR in laboratory to compact NMR in planta. Eurolax, Olsztyn, Poland

28. R. Sidi-Boulenouar, O. Yzebe, C. Coillot, E. Alibert, E. Nativel, R. Jelinek, F. Gatineau, J.-L. Verdeil, G. Vercambre, N. Bertin, C. Goze-Bac (2017) Real-Time dynamical monitoring plants status in normal and stress conditions: from Low Fields NMR in laboratory to compact NMR in planta. ESMR-MB, Barcelona

29. V. Sorichetti, V. Hugouvieux, W. Kob (2017) Structure and Dynamics of a Polymer Nanocomposite. Gordon Research Conference (Soft Matter Physics) Colby-Sawyer College New London, USA, Aug. 13-18

30. S. Villa, A. Stocco, C. Blanc, M. Nobil (2017) Dynamics of a colloidal Particle near a Gas-Liquid Interface. Complex Mo-tion in Fluids Summer School, Cambridge, Sept. 24-29

31. S. Villa, A. Stocco, C. Blanc, M. Nobili (2017) Dynamics of a colloidal Particle near a Gas-Liquid Interface. 10th Liquid Matter Conference, Lubiana, July 17-21

32. T.L. Vu, S. Nezamabadi, J. Bares, S. Mora (2017) Analy-sis of dense packing of highly deformed grains, EPJ Web of Conferences 140, 15031

2016

33. J. Bares, S. Mora, J-Y. Delenne, T. Fourcaud (2016) Expe-rimental observation of root growth in a controlled photoe-lastic granular material. American Physical Society Meeting, Baltimore, Maryland, USA, March 14-18

34. S. L. Berrahou, P. Buche, J. Dibie, M. Roche (2016) Xart system: discovering and extracting correlated arguments of n-ary relations from text. 6th International Conference on Web Intelligence, Mining and Semantics, Nîmes, France, June 13-15

35. G. Boniello, S. Villa S., A. Stocco, M. In, M. Gross, C. Blanc, M. Nobili (2016) Dynamics of an ellipsoid at a fluid interface.


4th International Soft Matter Conference, Grenoble, France, September 12

36. Y. Boursiac, A. M. Velez-Cardona, M. M. Calvo-Polanco, D. Felbacq, C. Pradal, M. Lucas, C. Godin, C. Maurel (2016) How does water flow through the roots. Gordon Research Conferences “Salt & Water Stress in Plants, From Molecules to Crops”, Les Diablerets, Switzerland, May

37. A. Boyer, J. Deverdun, H. Duffau, E. Le Bars, F. Molino, N. Menjot de Champfleur, F. Bonnetblanc (2016). Longitudinal Changes in Cerebellar and Thalamic Spontaneous Neuro-nal Activity After Wide-Awake Surgery of Brain Tumors: a Resting-State fMRI Study. Cerebellum, vol. 4, pp. 51-65. doi: 10.1007/s12311-015-0709-1

38. A. Brodoline, D. Donnarumma, D. Alexandre, M. Gross (2016,). 4D Holographic Reconstruction of] Embryonic Blood Flow by Greedy Algorithm. Digital Holography and Three-Di-mensional, Optical Society of America, Heidelberg, Germany, July 25-28

39. J. Dibie, P. Buche, M. Roche, S. L. Berrahou (2016) Xart system: discovering and extracting correlated arguments of n-ary relations from text. Proceedings of the 6th Interna-tional Conference on Web Intelligence, Mining and Seman-tics, WIMS, Nimes, France, June 13-15, pp.8:1-8:12, doi: 10.1145/2912845.2912855

40. S. Furst, M. Peyret, J. Chéry, B. Mohammadi (2016) Use of interseismic GPS data: a novel way to evaluate the lithos-phere rigidity variations. European Geosciences Union Gene-ral, Vienna, Austria, April 17-22

41. M. Gross, D. Donnarumma, A. Brodoline (2016). New developments in ultrasound-modulated optical tomography made by heterodyne holography. Digital Holography and Three-Dimensional Imaging, Optical Society of America, Hei-delberg, Germany, July 25-28

42. M. Gross, N. Verrier, D. Felbacq, L. Depreater, (2016). Studying Open Channels by Digital Holography. Digital Ho-lography and Three-Dimensional Imaging, Optical Society of America, Heidelberg, Germany, July 25-28

43. V. Hugouvieux and W. Kob (2016). Cluster Phase in en-zyme-induced Gelation of Polymers. 4th International Soft Matter Conference (ISMC2016), Grenoble, France, September 12-16

44. K. Heinze, J-Y. Delenne, M. George, V. Lullien-Pellerin (2016) The Wheat Grain as a Cemented Granular Mate-rial: Nanoscale Investigation of its Mechanical Properties, NANOSTRUC 2016 International Conference on Structural Nano Composites. Aberdeen, United Kingdom, Sept. 12-15

45. V. Hugouvieux and W. Kob (2016). Structuring of polymer gels via catalytic reactions. 3rd International Conference

on Bioinspired and Biobased Chemistry & Materials, Nice, France, October 16-19

46. V. Ingalalli, D. Ienco, P, Poncelet (2016) SuMGra: Que-rying Multigraphs via Efficient Indexing. Proceedings of 27th International Conference on Database and Expert Systems Applications (DEXA 2016), Porto, Portugal, September 5-8, pp. 387-401.

47. V. Ingalalli, D. Ienco, P. Poncelet, S. Villata (2016) Querying RDF Data Using A Multigraph-based Approach. Proceedings of 19th International Conference on Extending Database Technology (EDBT 2016), Bordeaux, France, March 15-18, pp. 245-256.

48. P. Jaiswal; R. Hoehndorf. ICBO: International Conference on Biomedical Ontologies, Aug 2016, Corvallis, OR, United States. 7th International Conference on Biomedical Ontolo-gies, 2016, Demo Session.

49. C. Jonquet, E. Dzalé-Yeumo, E. Arnaud, P. Larmande, A. Toulet, M.-A. Laporte (2016) AgroPortal: A Proposition for Ontology-Based Services in the Agronomic Domain. Inter-national Plant & Animal Genome 24th Meeting, San Diego, California, United States, January 9 - 13

50. C. Jonquet, A. Toulet, E. Arnaud, S. Aubin, E. Dzalé Yeumo Kaboré, V. Emonet, J. Graybeal, M. A. Musen, C. Pommier, P. Larmande (2016) Reusing the NCBO BioPortal Technology for Agronomy to Build AgroPortal. International Conference on Biological Ontology and BioCreative, Corvallis, Oregon, USA, August 1 - 4

51. C. Jonquet, A. Toulet, E. Arnaud, S. Aubin, E. Dzal ́e Yeumo Kaboré, V. Emonet, V. Pesce, P. Larmande (2016) AgroPortal: an open repository of ontologies and vocabularies for agri-culture and nutrition data. Open Data Research Symposium on Agriculture and Nutrition, New York, New Jersey, USA, September 15-16

52. D. Lapeine, J.-Y. Ferrandis, F. Pascal, P. Combette (2016) Study and optimization of screen-printed PZT transducers for acoustic applications, ICD2016, Montpellier, France, July 3-7

53. D. Lapeine, D. Laux, J.-Y. Ferrandis, F. Pascal, P. Combette (2016) Development and integration of screen printed trans-ducers for the detection of pollutants in aquatic environ-ments, poster in Symposium of DTIP 2016, Budapest, France, May 30-June 2

54. F. Leborne (2016) Coordinated Control of Two Robotic Arms for Underwater Manipulation of Deformable Biological Specimens. International conference MOQESM 2016, Quanti-tative Monitoring of Underwater Environment, Brest, France, Oct. 11-12.

55. F. Leborne (2016) Coordinated Control of Two Robotic


Arms for Underwater Manipulation of Deformable Biological Specimens – MOSQUEM 2016, Toulon, France

56. T. Manrique, C. Crambes, N. hilgert (2016) Estimation in the functional convolution model - 22nd International Confe-rence on Computational Statistics (COMPSTAT), Oviedo, Spain, August 23-26

57. H. al Mehedi, R. Podor, J. Ravaux, T. Michel, S. Tahir, K. Yazda, M. Odorico, V. Jourdain (2016) In situ High Tempe-rature ESEM study of carbon nanotubes reactivity under oxidative conditions. Proceedings of the 16th European Microscopy Congress, Lyon, France, August 28 - September 2, doi: 10.1002/9783527808465.EMC2016.5756

58. V. Muravyev, L. Dusseau, M. Balague (2016) Light Solar Panels design for Cubesat, in proc. Small Satellites Services and Systems. 2016, Valetta, Malte, may 30 - June 3.

59. T. Raberalam, M. Balde, S. Hantova, A. Vena, H. Marchan-din, B. Sorli (2016) Feasibility of capacitive aptasensor on paper to detect pathogenic bacteria responsible for nosoco-mial infections. BIOSENSORS 2016, Gothenburg, Sweden, May 25-27

60. R. Sidi-Boulenouar, O. Yzebe, E. Nativel, C. Coillot, J.-L. Verdeil, F. Gatineau, E. Alibert, N. Bertin, C. Goze-Bac (2016) Dynamical monitoring of water status in plant: from low field NMR in laboratory to compact NMR in planta, workshop KACST, Riyadh, Saudi Arabia, April 2

61. R. Sidi-Boulenouar, O. Yzebe, E. Nativel, C. Coillot, J.-L. Verdeil, F. Gatineau, E. Alibert, N. Bertin, C. Goze-Bac (2016) Dynamical monitoring of water status in plant: low field NMR investigations, GERM2016, Lisbon, Portugal, April 19-23

62. S. Villa, A. Stocco, C. Blanc et M. Nobili (2016) Dynamics of a colloidal Ellipsoid near a Gas-Liquid Interface. SoftComp Conference, Ancona, Italy, June 6-9

63. S. Villon, M. Chaumont, G. Subsol, S. Villeger, T. Claverie, D. Mouillot (2016) Coral reef fish detection and recognition in underwater videos by supervised machine learning: Com-parison between Deep Learning and hog+svm methods. Proceedings of the 17th International conference, ACIVS 2016, Advanced Concepts for Intelligent Vision Systems, Lecce, Italy, Oct. 24-27, published by Springer, Blanc-Talon, J., Distante, C., Philips, W., Popescu, D., Scheunders, P. (Eds.), in the Lecture Notes in Computer Science series 12pp.

64. N. Verrier, M. Gross, D. Donnarumma, D. Alexandre, G. Tessier (2016). Digital Holographic Microscopy With High Numerical Aperture: Wide z Range Reconstruction. Digital Holography and Three-Dimensional Imaging, Optical Society of America, Heidelberg, Germany, July 25-28.

65. S. Villon, M. Chaumont, G. Subsol, S. Villéger, T. Claverie, D. Mouillot (2016) Coral reef fish detection and recognition in underwater videos by supervised machine learning: Compa-

rison between Deep Learning and HOG+SVM methods. Ad-vanced Concepts for Intelligent Vision Systems, Proceedings of the 17th International Conference, ACIVS 2016, Lecce, Italy, October 24-27, 12 pages, published by Springer in the Lecture Notes in Computer Science series.

66. K. Yazda, S. Tahir, T. Michel, J.-B. Thibaud, F. Henn, V. Jourdain (2016) Ionic and Molecular Transport Inside Carbon Nanotubes: Towards the Detection of Individual Biomole-cules. Biophysical Journal, Biophysical Society 60st Annual Meeting, 110 (3_1), pp. 503A-503A, Los Angeles, California, USA, February 27-March 2

2015

67. D. Alexandre, G. Lutfalla, M. Gross (2015) Holographic imaging of Zebrafish embryo blood flow with dually oriented illumination beams. Digital Holography and 3-D Imaging Meeting, OSA Technical Digest, Shanghai, China, May 24-28

68. A. Banc (2015) Spontaneous gelation of wheat gluten proteins in a food grade solvent. 7th International Sympo-sium on Food Rheology and Structure. Zurich, Switzerland, June 7-11

69. A. Banc, C. Charbonneau, M.-H. Morel, L. Ramos (2015) SANS study of a gluten protein gel: Why are SAXS and SANS profiles different? 6th European Conference on Neutron Scattering (ECNS 2015), Zaragoza, Spain, August 30 – Sep-tember 4

70. P Besson, M Muthalib, S Perrey (2015) Time course of cortical sensorimotor network hemodynamics using fNIRS: a preliminary study of the effects of anodal transcranial direct current stimulation. 7th International IEEE EMBS Conference on Neural Engineering, Montpellier, France, April 22 - 24

71. M. Binet, O. Gascuel, C. Scornavacca, E. Douzery F. Pardi (2015) Fast and accurate branch lengths estimation for phy-logenomic trees. Evolution, Guaruja (Brésil), June 26-30

72. M. Binet, O. Gascuel, C. Scornavacca, E. Douzery, F. Pardi (2015) Fast and accurate branch lengths estimation for phy-logenomic trees. Mathematical and Computational Evolutio-nary Biology, Îles de Porquerolles, France, June 21-25

73. Y. Bonavero, M. Huchard, and M. Meynard (2015) Recon-ciling user and designer preferences in adapting web pages for people with low vision: Comparing NSGA-II and NSGA-III evolutionary algorithms. Proceedings of the 12th Web for All Conference (W4A), Florence, Italy, May 18-20

74. Y. Boursiac, D. Felbacq, Polanco (2015) Role of apoplastic barriers in root hydraulics. Plant Apoplastic Diffusion Bar-riers. PaDiBA meeting, Nantes, France, September 2-4

75. Y. Boursiac, D. Felbacq, C. Maurel, C. Pradal, M. Lucas, C. Godin (2015) Building a root hydraulic architecture with a keyboard and pipettes. Workshop in plant modelling, Mont-pellier, France, April 9-10


76.M. Botti and D. Di Pietro (2015) Workshop Polytopal Element Methods in Mathematics and Engineering, Georgia Tech, Atlanta (USA), October 26 - 28

77. A. Burgers, P. Langbour, C. Montero, M. Vinches, R. Marchal, B. Thibaut (2015) Influence of growth parameters on mountain pine wood properties. European Mechanics Society (EUROMECH) Colloquium 556, Theoretical, numerical, and experimental analyses in wood mechanics, Dresden, Deutschland, Mai 27-29

78. C. Crambes, N. Hilgert, T. Manrique and A. Mas (2015) Ridge Regression for the Functional Concurrent Model. 60th World Statistic Congress ISI, Rio de Janero, Brazil, July 26-30

79. C. Crambes, N. Hilgert, T. Manrique (2015) Estimation in functional convolution model. Workshop on Biosciences, Medicine, and novel Non-Parametric Methods, Graz, Austria, July 12-15

80. F. Z. El Korchi, F. Jamin, E.K. Lakhal, M. El Omari, M. S. El Youssoufi (2015) Comportement hydromécanique des milieux granulaires fins au cours de l’imbibition. 1e Congrès International sur les Ingénieries Civile, Actes du CMEEE. , Mé-canique et Electrique pour l’Energie, Marrakech, Maroc, Nov. 16-19〈hal-01412438〈

81. T. Guiho, O. Rossel, G. Souquet, H. Alfredo, L. Laporte, C. Azevedo Coste, D. Andreu, D. Guiraud (2015) Toward complex multipolar selective neural stimulation. 7th Interna-tional IEEE/EMBS Conference on, Montpellier, France, April 22-24, pp.569-572, doi: 10.1109/NER.2015.7146686

82. V. Ingalalli, D. Ienco, P. Poncelet (2015) SuMGRA: On Querying Large Graphs with Multiple Relationships. Actes de la 31ème Conférence Bases de Données Avancées, Île de Porquerolles, France, September 29 – October 2

83. W. Kob and W., V. Hugouvieux (2015). Computer simula-tions of gel-formation via catalytic reactions. FisMat 2015 the Italian National Conference on Condensed Matter Physics, Palermo, Italy September 28-October 2

84. D. Lapeine, D. Laux, J.-Y. Ferrandis, F. Pascal, P. Combette (2015) Développement de capteurs acoustiques pour la dé-tection de polluants en milieu aquatique. Journées Electro-nique et Environnement, Montpellier, France, Oct. 26-27

85. D. Lapeine, F. Very, D. Laux, J- Y. Ferrandis, B. Charlot, F. Pascal, A. Giani, P. Combette (2015) Elaboration and Charac-terization of acoustic sensors for detection of pollutants in aquatic environment. Design, Test, Integration and Packa-ging (DTIP), Montpellier, France, April 27-30

86. A. Lasbouygues, B. Ropars, R. Passama, D. Andreu, L. Lapierre (2015) Atoms Based Control of Mobile Robots with Hardware-In-the-Loop Validation. International Conference on Intelligent Robots and Systems, Hamburg, Germany, Sep-tember 28- October 2

87. S. Le Floc’h, D. Ambard, A. Baldit, P. Kouyoumdjian, P. Cañadas and F. Cherblanc (2015) Residual Stress in Pig In-tervertebral Discs. 21st Congress of the European Society of Biomechanics, Lisbon, Portugal, July 2

88. V. L. Lorman and S. B. Rochal (2016) Group Theory Me-thods in Virology: Landau Density Wave Approach. Applica-tion + Practical Conceptualization + Mathematics

89. S. Mendez, C. Chnafa, E. Gibaud, J. Sigüenza, V. Moureau, F. Nicoud (2014) YALES2BIO: a Computational Fluid Dyna-mics Software Dedicated to the Prediction of Blood Flows in Biomedical Devices. In Proceedings of the 5th International Conference on the Development of Biomedical Engineering in Vietnam, Ho Chi Minh City, VIETNAM, June 16-18. Publi-shed in IFMBE Proceedings Series, Vol. 46, pages 7-10, 2015.

90. L. Ramos (2015) Novel gels from gluten proteins. 10th Annual European Rheology Conference. Nantes, France, April 14-17

91. L. Ramos (2015) Novel gels from wheat gluten proteins. 6th International symposium on delivery of Functionality in complex food systems, Paris, France, July 14-17

92. B. Ropars, A. Lasbouygues, L. Lapierre and D. Andreu (2015) Thruster’s Dead-zones Compensation for the Actua-tion System of an Underwater Vehicle, ECC 15, Linz, Austria, July 15

93. M.S. Seghilani, M. Myara, S. Balle-Monjo, I. Sagnes, G. Beaudoin and A. Garnache (2015) Laser generation of cohe-rent photon state carrying Spin- Angular- Momentum with handedness control using electronic spin transfer. Procee-ding of the 3rd European Workshop VeCSELs, Montpellier, France, November 17-19

94. M. Servajean, E. Pacitti, M. Liroz-Gistau, S. Amer-Yahia and A. El Abbadi (2015) Exploiting Diversification in Gos-sip-Based Recommendation. International conference on Data Management in Cloud, Grid and P2P Systems (GLOBE), September 2-4, München, Deutschland, 12p.

95. B. Ropars, A. Lasbouygues, L. Lapierre and D. Andreu (2015) Thruster’s Dead-Zones Compensation for the actua-tion System of an Underwater Vehicle, European Control Conference (ECC), Linz, Austria, July 15-17

96. A. Vicet, Q. Gaimard, A. Larrue, L. Cerutti, T. Nguyenba, M. Triki, Y. Rouillard, O Gauthier-Lafaye, R. Teissier, E. Tournie (2017) New Index-Coupled Distributed-Feedback Gasb-Based Lasers Diodes: In The 2 To 3µm Wavelength Range, Applica-tions To Spectroscopy. International workshop on opportu-nities and challenges in mid-infrared laser-based gas sensing MIRS3NS, Würzburg, Germany, March 5-7

97. J.-C. Walter and G. T. Barkema (2015) An introduction to Monte Carlo methods, Proceedings of the 13th Internatio-


nal Summer School on Fundamental Problems in Statistical Physics, Physica A: Statistical Mechanics and its Applications Vol. 418, pp. 78–87, Leuven, Belgium, June 16-29. https://doi.org/10.1016/j.physa.2014.06.014

98. F. Y. Wang, A. Sallaberry, K. Klein, M. Takatsuka, M. Roche (2015) SentiCompass: Interactive visualization for exploring and comparing the sentiments of time varying twitter data. Proceedings of the 8th IEEE Pacific Visualization Symposium, Hangzhou, China, April 14-17, pp. 129-133

99. F. Y. Wang, A. Sallaberry, M. Roche (2015) RNAD Sequen-Lens for visualizing RNA secondary structures. 5th IEEE Symposium on Biological Data Visualization, Dublin, Ireland, July 10-11

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