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Nuclear Science and Techniques 2022年第3期33卷 113-125页

作者： Xiao-Wen Zhu Claude Marchand Olivier Piquet Michel Desmons IRFU CEAUniversite´Paris-Saclay91191 Gif-sur-YvetteFrance

Compact accelerator-based neutron source facilities are garnering attention and play an important and expanding role in material and engineering sciences,as well as in neutron science education and training.Neutrons are produced by bombarding a low-energy proton beam onto a beryllium or lithium target.In such an acceleratorbased neutron source,a radio frequency quadrupole(RFQ)is usually utilized to accelerate a high-intensity proton beam to a few MeV.This study mainly covers the highfrequency structure design optimizations of a 4-vane RFQ with pi-mode stabilizer loops(PISLs)and its RF stability analysis.A 176 MHz RFQ accelerator is designed to operate at a 10%duty factor and could accelerate an80 mA proton beam from 65 keV to 2.5 MeV within a length of 5.3 m.The adoption of PISLs ensures high RF stability,eases the operation of the accelerator,and implies less stringent alignment and machining tolerances.

关键词： Accelerator-based neutron source 4-vane RFQ accelerator Pi-mode stabilizer loops Perturbative analysis Electromagnetic design Multipacting simulation

Sampling via the aggregation value for data-driven manufacturing

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National Science Review 2022年第11期9卷 161-171页

作者： Xu Liu Gengxiang Chen Yingguang Li Lu Chen Qinglu Meng Charyar Mehdi-Souzani School of Mechanical and Power Engineering Nanjing Tech University College of Mechanical &Electrical Engineering Nanjing University of Aeronautics and Astronautics University Research Laboratory in Automated Production Ecole normale superieure Paris-SaclayUniversite Paris-SaclayUniversite Sorbonne Paris Nord

Data-driven modelling has shown promising potential in many industrial applications, while the expensive and time-consuming labelling of experimental and simulation data restricts its further development.Preparing a more informative but smaller dataset to reduce labelling efforts has been a vital research problem. Although existing techniques can assess the value of individual data samples, how to represent the value of a sample set remains an open problem. In this research, the aggregation value is defined using a novel representation for the value of a sample set by modelling the invisible redundant information as the overlaps of neighbouring values. The sampling problem is hence converted to the maximisation of the submodular function over the aggregation value. The comprehensive analysis of several manufacturing datasets demonstrates that the proposed method can provide sample sets with superior and stable performance compared with state-of-the-art methods. The research outcome also indicates its appealing potential to reduce labelling efforts for more data-scarcity scenarios.

关键词： data-driven modelling intelligent manufacturing data sampling data value

Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq

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Plant Communications 2023年第5期4卷 63-78页

作者： Etienne Delannoy Bastien Batardiere Ste phanie Pateyron Ludivine Soubigou-Taconnat Julien Chiquet Jean Colcombet Julien Lang Universite Paris-Saclay CNRSINRAEUniversite EvryInstitute of Plant Sciences Paris-Saclay(IPS2)91190 Gif sur YvetteFrance universite paris Cite CNRSINRAEInstitute of Plant Sciences Paris-Saclay(IPS2)91190 Gif sur YvetteFrance UMR MIA paris-saclay Universite Paris-SaclayAgroParisTechINRAE91120 PalaiseauFrance

Plant defense responses involve several biological processes that allow plants to fight against pathogenic attacks.How these different processes are orchestrated within organs and depend on specific cell types is poorly known.Here,using single-cell RNA sequencing(scRNA-seq)technology on three independent biological replicates,we identified several cell populations representing the core transcriptional responses of wild-type Arabidopsis leaves inoculated with the bacterial pathogen Pseudomonas syringae DC3000.Among these populations,we retrieved major cell types of the leaves(mesophyll,guard,epidermal,companion,and vascular S cells)with which we could associate characteristic transcriptional reprogramming and regulators,thereby specifying different cell-type responses to the pathogen.Further analyses of transcriptional dynamics,on the basis of inference of cell trajectories,indicated that the different cell types,in addition to their characteristic defense responses,can also share similar modules of gene reprogramming,uncovering a ubiquitous antagonism between immune and susceptible processes.Moreover,it appears that the defense responses of vascular S cells,epidermal cells,and mesophyll cells can evolve along two separate paths,one converging toward an identical cell fate,characterized mostly by lignification and detoxification functions.As this divergence does not correspond to the differentiation between immune and susceptible cells,we speculate that this might reflect the discrimination between cellautonomous and non-cell-autonomous responses.Altogether our data provide an upgraded framework to describe,explore,and explain the specialization and the coordination of plant cell responses upon pathogenic challenge.

关键词： scRNA-seq plant defense responses plant immunity plant susceptibility Arabidopsis/Pseudomonas interactions biotic stress

Mucosal healing progression after acute colitis in mice

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World Journal of Gastroenterology 2019年第27期25卷 3572-3589页

作者： Sandra Vidal-Lletjós Mireille Andriamihaja Anne Blais Marta Grauso Patricia Lepage Anne-Marie Davila Claire Gaudichon Marion Leclerc Francois Blachier Annaig Lan UMR PNCA AgroParisTechINRAUniversite Paris-SaclayParis 75005France UMR MICALIS INRAUniversite Paris-SaclayJouy-en-Josas 78350France

BACKGROUND Mucosal healing has become a therapeutic goal to achieve stable remission in patients with inflammatory bowel diseases. To achieve this objective, overlapping actions of complex cellular processes, such as migration, proliferation, and differentiation, are required. These events are longitudinally and tightly controlled by numerous factors including a wide range of distinct regulatory proteins. However, the sequence of events associated with colon mucosal repair after colitis and the evolution of the luminal content characteristics during this process have been little studied.AIM To document the evolution of colon mucosal characteristics during mucosal healing using a mouse model with chemically-induced colitis.METHODS C57 BL/6 male mice were given 3.5% dextran sodium sulfate(DSS) in drinking water for 5 d. They were euthanized 2(day 7), 5(day 10), 8(day 13), and 23(day28) d after DSS removal. The colonic luminal environment and epithelial repair processes during the inflammatory flare and colitis resolution were analyzed with reference to a non-DSS treated control group, euthanized at day 0. Epithelial repair events were assessed histo-morphologically in combination with functional permeability tests, expression of key inflammatory and repairing factors, and evaluation of colon mucosa-adherent microbiota composition by 16 S rRNA sequencing.RESULTS The maximal intensity of colitis was concomitant with maximal alterations of intestinal barrier function and histological damage associated with goblet cell depletion in colon mucosa. It was recorded 2 d after termination of the DSStreatment, followed by a progressive return to values similar to those of control mice. Although signs of colitis were severe(inflammatory cell infiltrate, crypt disarray, increased permeability) and associated with colonic luminal alterations(hyperosmolarity, dysbiosis, decrease in short-chain fatty acid content), epithelial healing processes were launched early during the inflammatory flare with increased gene expression of cert

关键词： Colon luminal environment Dextran sodium sulfate-induced colitis Dysbiosis Epithelial repair Acute colitis

Recapture probability, flight morphology, and microorganisms

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Current Zoology 2018年第3期64卷 277-283页

作者： Zaid AL RUBAIEE Haider AL-MURAYATI Anders Pape MФLLER Ecologie Systematique Evolution Universite Paris-Sud CNRS AgroParisTech Universite Paris-Saclay F-91405 Orsay Cedex France

Microorganisms on and within organisms are ubiquitous and interactions with their hosts range from mutualistic over commensal, to pathogenic. We hypothesized that microorganisms might affect the ability of barn swallows to escape from potential predators, with positive associations between the abundance of microorganisms and escape ability implying mutualistic effects, while negative associations would imply antagonistic effects. We quantified escape behavior as the ability to avoid capture in a mist net and hence as a small number of recaptures. Because recapture probability may also depend on timing of reproduction and reproductive success, we also tested whether the association between recapture and microorganisms was mediated by an association between recapture and life history. We found intermediate to strong positive relationships between recapture probability and abundance of , but not abundance of other bacteria or fungi. The abundance of was associated with an advance in laying date and an increase in reproductive success. However, these effects were independent of the number of recaptures. This interpretation is supported by the fact that there was no direct correlation between laying date and reproductive success on one hand and the number of recaptures on the other. These findings have implications not only for predator-prey interactions, but also for capture-mark-recapture analyses of vital rates such as survival and dispersal.

关键词：微生物概率形态学飞行相互作用食肉动物对抗效果调查结果

Experimental manipulation of size and shape of tail spots and sexual selection in barn swallows

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Current Zoology 2017年第5期63卷 569-572页

作者： Anders P. MOLLER Ecologie Systematique Evolution CNRS Universite Paris-Sud AgroParisTech Universite Paris-Saclay 0rsayF-91400 France

Barn swallows Hirundo rustica have white spots on their tail feathers, and they have been hypothe-sized to be a handicap because white spots are prone to feather breakage, ectoparasites are dispro-portionately common in white spots, and size of white spots increases with tail length. Here I testfor attractiveness of narrow and long tail spots by manipulation of their shape while using com-plete painting of spots and an absence of treatment as a control. Female barn swallows are knownto differentially invest in reproduction when mated to attractive males. Spot manipulation tookplace during laying of the first clutch, and there were no effects of treatment on clutch size or broodsize of first or second broods. In contrast, the incidence of second clutches and the total number ofeggs and fledglings produced during the breeding season was larger in males with painting of theside of tail spots rather than painting of the tip of spots, painting of entire spots, or no treatment.These findings are consistent with the hypothesis that it is the shape rather than the size of tailspots that affects differential reproductive effort by female barn swallows.

关键词： Hirundo rustica, reliable signals, shape of tail spots, tail spots.

Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima

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Synthetic and Systems Biotechnology 2022年第2期7卷 791-801页

作者： Paul Soudier Daniel Rodriguez Pinzon Tristan Reif-Trauttmansdorff Hassan Hijazi Maeva Cherriere Catia Goncalves Pereira Doriane Blaise Maxime Pispisa Angelyne Saint-Julien William Hamlet Melissa Nguevo Eva Gomes Sophia Belkhelfa Anna Niarakis Manish Kushwaha Ioana Grigoras Evry paris-saclay 2020 iGEM team France Universite Paris-Saclay INRAEAgroParisTechMicalis Institute78352Jouy-en-JosasFrance Universite Paris-Saclay Univ EvryLaboratoire Europeen de Recherche pour la Polyarthrite Rhumatoïde-GenhotelEvryFrance Universite Paris-Saclay Univ EvryCNRSCEAGenomique MetaboliqueEvryFrance DNA Script Le Kremlin-BicetreFrance SYNMIKRO Center of Synthetic Microbiology MarburgGermany universite Grenoble Alpes CEAInsermEDyP-BGEGrenobleFrance National Institute of Industrial Property(INPI) CourbevoieFrance

Nucleic acid sensing is a 3 decades old but still challenging area of application for different biological sub-domains,from pathogen detection to single cell transcriptomics analysis.The many applications of nucleic acid detection and identification are mostly carried out by PCR techniques,sequencing,and their derivatives used at large scale.However,these methods’limitations on speed,cost,complexity and specificity have motivated the development of innovative detection methods among which nucleic acid biosensing technologies seem promising.Toehold switches are a particular class of RNA sensing devices relying on a conformational switch of secondary structure induced by the pairing of the detected trigger RNA with a de novo designed synthetic sensing mRNA molecule.Here we describe a streamlined methodology enabling the development of such a sensor for the RNA-mediated detection of an endangered plant species in a cell-free reaction system.We applied this methodology to help identify the rosewood Dalbergia maritima,a highly trafficked wood,whose protection is limited by the capacity of the authorities to distinguish protected logs from other unprotected but related species.The streamlined pipeline presented in this work is a versatile framework enabling cheap and rapid development of new sensors for custom RNA detection.

关键词： Toehold switch Riboregulator Biosensor Rosewood

Fashion and out of fashion:appearance and disappearance of a novel nest building innovation

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Avian Research 2017年第2期8卷 71-75页

作者： Anders P.Møller Ecologie Systematique Evolution Universite Paris‑SudCNRSAgroParisTechUniversite Paris‑Saclay91405 Orsay CedexFrance

Background:Nests are composed of and built with different materials that are handled in specific ways. These mate?rials must initially have been used de novo before commonly being incorporated into nests. Plastic and plastic bags were invented in the 1950s, and they are widely distributed in the environment. Birds started picking up plastic from plastic used to cover farm produce such as silage, potatoes, beets and other crops for use in their nests in the 1960s.Methods:I recorded the frequency of such plastic use by the Blackbird(Turdus merula) in nests in Denmark, starting in 1966, followed by a peak in use in the 1970s and a subsequent decline.Results:Nests with plastic were initially built earlier in the season than those without plastic, indicating an associa?tion between innovation and early reproduction. Plastic use was subsequently selected against because nests with plastic suffered from higher rates of predation than nests without plastic, probably because nests with plastic were easier to locate. However, the elevated risk of nest predation only applied to outdoor nests, but not to nests inside buildings, probably because visually searching nest predators such as corvids do not enter buildings.Conclusions:These findings show that the dynamics of nest material use depend on the benefits of innovation and the fitness costs of nest predation.

关键词： Fashion Indoor breeding Innovation Nest predation Turdus merula

Integrating Functional Status Information into Knowledge Graphs to Support Self-Health Management

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Data Intelligence 2023年第3期5卷 636-662页

作者： Mauro Dragoni Tania Bailoni Ivan Donadello Jean-Claude Martin Helena Lindgren Fondazione Bruno Kessler TrentoItaly Free University of Bolzano BolzanoItaly LISN-CNRS Universite Paris SaclayParisFrance Umea University UmeaSweden

Functional Status Information(FSI)describes physical and mental wellness at the whole-person level.It includes information on activity performance,social role participation,and environmental and personal factors that affect the well-being and quality of life.Collecting and analyzing this information is critical to address the needs for caring for an aging global population,and to provide effective care for individuals with chronic conditions,multi-morbidity,and disability.Personal knowledge graphs(PKGs)represent a suitable way for meaning in a complete and structured way all information related to people's FSI and reasoning over them to build tailored coaching solutions supporting them in daily life for conducting a healthy living.In this paper,we present the development process related to the creation of a PKG by starting from the HeLis ontology in order to enable the design of an Al-enabled system with the aim of increasing,within people,the self-awareness of their own functional status.In particular,we focus on the three modules extending the HeLis ontology aiming to represent(i)enablers and(ii)barriers playing potential roles in improving(or deteriorating)own functional status and(iii)arguments driving the FSI collection process.Finally,we show how these modules have been instantiated into real-world scenarios.

关键词： Knowledge Graph Personal Healthcare Functional Status Enablers Barriers Arguments

Distinctive and complementary roles of E2F transcription factors during plant replication stress responses

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Molecular Plant 2023年第8期16卷 1269-1282页

作者： Maherun Nisa Thomas Eekhout Clara Bergis Jose-Antonio Pedroza-Garcia Xiaoning He Christelle Mazubert Ilse Vercauteren Toon Cools Rim Brik-Chaouche Jeannine Drouin-Wahbi Layla Chmaiss David Latrasse Catherine Bergounioux Klaas Vandepoele Moussa Benhamed Lieven De Veylder Cécile Raynaud Universite Paris-Saclay CNRSINRAEUniversite EvryInstitute of Plant Sciences Paris-Saclay(IPS2)91190 Gif-sur-YvetteFrance universite de paris Cite CNRSINRAEInstitute of Plant Sciences Paris-Saclay(IPS2)91190 Gif-sur-YvetteFrance Department of Plant Biotechnology and Bioinformatics Ghent University9052 GhentBelgium Center for Plant Systems Biology VIB9052 GhentBelgium Present address:Plant Molecular and Cellular Biology Laboratory Salk Institute for Biological StudiesLa JollaCA 92037USA

Survival of living organisms is fully dependent on their maintenance of genome integrity,being permanently threatened by replication stress in proliferating cells.Although the plant DNA damage response(DDR)regulator SOG1 has been demonstrated to cope with replication defects,accumulating evidence points to other pathways functioning independent of SOG1.Here,we report the roles of the Arabidopsis E2FA and EF2B transcription factors,two well-characterized regulators of DNA replication,in plant response to replication stress.Through a combination of reverse genetics and chromatin immunoprecipitation approaches,we show that E2FA and E2FB share many target genes with SOG1,providing evidence for their involvement in the DDR.Analysis of double-and triple-mutant combinations revealed that E2FB,rather than E2FA,plays the most prominent role in sustaining plant growth in the presence of replication defects,either operating antagonistically or synergistically with SOG1.Conversely,SOG1 aids in overcoming the replication defects of E2FA/E2FB-deficient plants.Collectively,our data reveal a complex transcriptional network controlling the replication stress response in which E2Fs and SOG1 act as key regulatory factors.

关键词： replication stress E2F SOG1 cell cycle Arabidopsis