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469 results on '"Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)"'

1. Improving logic-based Benders' algorithms for solving min-max regret problems

Author: Assunção, Lucas, Santos, Andréa Cynthia, de Noronha, Thiago Ferreira, Castro De Andrade, Rafael, Universidade Federal de Minas Gerais, Brésil, Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Equipe Réseaux d'interactions et Intelligence Collective (RI2C - LITIS), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Normandie Université (NU), and Universidade Federal do Ceará = Federal University of Ceará (UFC)
Subjects: [INFO]Computer Science [cs], [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2021

2. Analysis of a Marseillevirus Transcriptome Reveals Temporal Gene Expression Profile and Host Transcriptional Shift

Author: Rodrigo Araújo Lima Rodrigues, Amina Cherif Louazani, Agnello Picorelli, Graziele Pereira Oliveira, Francisco Pereira Lobo, Philippe Colson, Bernard La Scola, Jônatas Santos Abrahão, Laboratório de Vírus, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Instituto de Ciências Biológicas [Goiânia, Brésil] (ICB), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), and Universidade Federalde Minas Gerais
Subjects: Microbiology (medical), [SDV]Life Sciences [q-bio], lcsh:QR1-502, marseillevirus, RNA-Seq, Computational biology, Microbiology, Genome, lcsh:Microbiology, Transcriptome, 03 medical and health sciences, Transcription (biology), Gene expression, Gene, giant virus, Original Research, promoter motifs, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, biology, 030306 microbiology, Marseillevirus, biology.organism_classification, gene expression, RNA-seq, transcriptome
Abstract: Marseilleviruses comprise a family of large double-stranded DNA viruses belonging to the proposed order ``Megavirales.'' These viruses have a circular genome of similar to 370 kbp, coding hundreds of genes. Over a half of their genes are associated with AT-rich putative promoter motifs, which have been demonstrated to be important for gene regulation. However, the transcriptional profile of Marseilleviruses is currently unknown. Here we used RNA sequencing technology to get a general transcriptional profile of Marseilleviruses. Eight million 75-bp-long nucleotide sequences were robustly mapped to all 457 genes initially predicted for Marseillevirus isolate T19, the prototype strain of the family, and we were able to assemble 359 viral contigs using a genome-guided approach with stringent parameters. These reads were differentially mapped to the genes according to the replicative cycle time point from which they were obtained. Cluster analysis indicated the existence of three main temporal categories of gene expression, early, intermediate and late, which were validated by quantitative reverse transcription polymerase chain reaction assays targeting several genes. Genes belonging to different functional groups exhibited distinct expression levels throughout the infection cycle. We observed that the previously predicted promoter motif, AAATATTT, as well as new predicted motifs, were not specifically related to any of the temporal or functional classes of genes, suggesting that other components are involved in temporally regulating virus transcription. Moreover, the host transcription machinery is heavily altered, and many genes are down regulated, including those related to translation process. This study provides an overview of the transcriptional landscape of Marseilleviruses.
Published: 2020
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3. From the environment to the host: How non-azole agrochemical exposure affects the antifungal susceptibility and virulence of Cryptococcus gattii

Author: Frédérique Moyrand, Guilhem Janbon, Hellem Cristina Silva Carneiro, Ludmila Gouveia-Eufrasio, Daniel Assis Santos, Rafael Wesley Bastos, Lorena Vívien Neves de Oliveira, Gustavo José Cota de Freitas, Corinne Maufrais, Anderson Philip Nonato Santos, Departamento de Microbiologia [Minas Gerais, Brazil], Instituto de Ciencias Biologicas [Minas Gerais], Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Faculdade de Ciências Farmacêuticas de Ribeirão Preto [São Paulo], Universidade de São Paulo = University of São Paulo (USP), Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris] (IP), This study was supported by Fundação de Amparo a Pesquisa do Estado de Minas Gerais - FAPEMIG (Grants APQ-00727-16 and PPM-00061-18) and Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq (Grants 403006/2016-3 and 440010/2018-7). RWB received fellowships from CNPq and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (PDSE-CAPES-88881.131683/2016-01). DAS is a research fellow of the CNPq (Grant 302670/2017-3)., Universidade de São Paulo (USP), and Institut Pasteur [Paris]
Subjects: Antifungal Agents, 010504 meteorology & atmospheric sciences, 010501 environmental sciences, Ravuconazole, 01 natural sciences, Mice, Efflux pumps, MESH: Animals, Waste Management and Disposal, Fluconazole, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, 2. Zero hunger, chemistry.chemical_classification, MESH: Microbial Sensitivity Tests, biology, MESH: Agrochemicals, Temperature, MESH: Strobilurins / toxicity, MESH: Cryptococcus neoformans, Strobilurins, Pollution, Agrochemicals, medicine.drug, Environmental Engineering, Itraconazole, Virulence, Microbial Sensitivity Tests, Microbiology, MESH: Antifungal Agents, Minimum inhibitory concentration, Drug Resistance, Fungal, parasitic diseases, medicine, Environmental Chemistry, Animals, Humans, Cross-resistance, Cryptococcus gattii, MESH: Mice, 0105 earth and related environmental sciences, MESH: Humans, biology.organism_classification, bacterial infections and mycoses, chemistry, MESH: Cryptococcus gattii / physiology, Cryptococcus neoformans, Pyraclostrobin, Azole, MESH: Drug Resistance, Fungal / physiology
Abstract: International audience; Agrochemicals such as the non-azoles, used to improve crop productivity, poses severe undesirable effects on the environment and human health. In addition, they induce cross-resistance (CR) with clinical drugs in pathogenic fungi. However, till date emphasis has been given to the role of azoles on the induction of CR. Herein, we analyzed the effect of a non-azole agrochemical, pyraclostrobin (PCT), on the antifungal susceptibility and virulence of the human and animal pathogens Cryptococcus gattii and C. neoformans. We determined the minimum inhibitory concentration (MIC) of fluconazole (FLC), itraconazole, ravuconazole, amphotericin B, and PCT on colonies: (i) that were not exposed to PCT (non-adapted-NA-cultures), (ii) were exposed at the maximum concentration of PCT (adapted-A-cultures) and (iii) the adapted colonies after cultivation 10 times in PCT-free media (10 passages-10p-cultures). Our results showed that exposure to PCT induced both temporary and permanent CR to clinical azoles in a temperature-dependent manner. With the objective to understand the mechanism of induction of CR through non-azoles, the transcriptomes of NA and 10p cells from C. gattii R265 were analyzed. The transcriptomic analysis showed that expression of the efflux-pump genes (AFR1 and MDR1) and PCT target was higher in resistant 10p cells than that in NA. Moreover, the virulence of 10p cells was reduced as compared to NA cells in mice, as observed by the differential gene expression analysis of genes related to ion-metabolism. Additionally, we observed that FLC could not increase the survival rate of mice infected with 10p cells, confirming the occurrence of permanent CR in vivo. The findings of the present study demonstrate that the non-azole agrochemical PCT can induce permanent CR to clinical antifungals through increased expression of efflux pump genes in resistant cells and that such phenomenon also manifests in vivo.
Published: 2019
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4. The potential effect of improved provision of rabies post-exposure prophylaxis in Gavi-eligible countries: a modelling study

Author: Hampson, Katie, Ventura, Francesco, Steenson, Rachel, Mancy, Rebecca, Trotter, Caroline, Cooper, Laura, Abela-Ridder, Bernadette, Knopf, Lea, Ringenier, Moniek, Tenzin, Tenzin, Ly, Sowath, Tarantola, Arnaud, Moyengar, Ronelngar, Oussiguéré, Assandi, Bonfoh, Bassirou, Narayana, DH Ashwath, Sudarshan, Mysore Kalappa, Muturi, Matthew, Mwatondo, Athman, Wambura, Gati, Andriamandimby, Soa Fy, Baril, Laurence, Edosoa, Glenn, Traore, Abdallah, Jayme, Sarah, Kotzé, Johann, Gunesekera, Amila, Chitnis, Nakul, Hattendorf, Jan, Laager, Mirjam, Léchenne, Monique, ZINSSTAG, Jakob, Changalucha, Joel, Mtema, Zac, Lugelo, Ahmed, Lushasi, Kennedy, Yurachai, Onphirul, Metcalf, Charlotte Jessica E., Rajeev, Malavika, Blanton, Jesse, Costa, Galileu Barbosa, Sreenivasan, Nandini, Wallace, Ryan, Briggs, Deborah, Taylor, Louise, Thumbi, Samuel, Huong, Nguyen Thi Thanh, University of Glasgow, University of Cambridge [UK] (CAM), Neglected Zoonotic Diseases (NZD), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), World Health Organisation (WHO), Unité d'Épidémiologie et de Santé Publique [Phnom Penh], Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre de Recherche Agronomique de la Savane Humide, Institut Togolais de Recherche Agronomique, Unité de Virologie [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Ministère de la Santé Publique [Antananarivo, Madagascar], Laboratoire Central Vétérinaire du Mali, Partenaires INRAE, Swiss Tropical and Public Health Institute [Basel], Princeton University, Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention (CDC), Laboratório de Vírus, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Instituto de Ciências Biológicas [Goiânia, Brésil] (ICB), Global Alliance for Rabies Control [Manhattan, Kansas], Institute of Biodiversity, Animal Health & Comparative Medicine, Universiteit Gent = Ghent University [Belgium] (UGENT), National Centre for Animal Health [Bhoutan] (NCAH), Centre de Support en Santé Internationale [N'Djamena, Tchad] (CSSI), Institut de Recherche en Elevage pour le Developpement [N'Djamena, Tchad] (IRED), Centre Suisse de Recherches Scientifiques en Cote d'Ivoire [Abidjan] (CSRS-CI), Laboratoire Central Vétérinaire [Bamako, Mali], Centers for Disease Control and Prevention, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Kansas State University, Washington State University (WSU), National Institute of Hygiene and Epidemiology [Hanoi, Vietnam] (NIHE), This work is supported by a grant from WHO to the Universities of Glasgow and Cambridge. KH and RMa were supported by the Wellcome Trust (207569/Z/17/Z), with additional funding for RMa from Stuart H Leckie. The Wellcome Trust through Afrique One ASPIRE also supported MLe and several unpublished studies and the UBS Optimus Foundation supported LT and SJ. The Gavi learning agenda on rabies supported many of the unpublished studies that contributed data. The Swiss National Science Foundation supported MLa. The Institut Pasteur financed studies in Cambodia., and WHO Rabies Modelling Consortium
Subjects: MESH: Rabies virus / isolation & purification, MESH: Rabies virus / immunology, MESH: Bites and Stings / virology, MESH: World Health Organization, MESH: Cost-Benefit Analysis / methods, MESH: Dogs, MESH: Rabies / prevention & control, MESH: Rabies / epidemiology, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Post-Exposure Prophylaxis / economics, MESH: Rabies / virology, MESH: Animals, MESH: Incidence, MESH: Dog Diseases / prevention & control, MESH: Immunoglobulins / therapeutic use, ComputingMilieux_MISCELLANEOUS, MESH: Models, Economic, MESH: Humans, MESH: Rabies Vaccines / therapeutic use, MESH: Endemic Diseases / prevention & control, MESH: Child, Preschool, MESH: Post-Exposure Prophylaxis / methods, MESH: Rabies / mortality, MESH: Male, MESH: Quality-Adjusted Life Years, MESH: Rabies Vaccines / economics, MESH: Vaccination / economics, MESH: Female
Abstract: International audience; Background: Tens of thousands of people die from dog-mediated rabies annually. Deaths can be prevented through post-exposure prophylaxis for people who have been bitten, and the disease eliminated through dog vaccination. Current post-exposure prophylaxis use saves many lives, but availability remains poor in many rabies-endemic countries due to high costs, poor access, and supply.Methods: We developed epidemiological and economic models to investigate the effect of an investment in post-exposure prophylaxis by Gavi, the Vaccine Alliance. We modelled post-exposure prophylaxis use according to the status quo, with improved access using WHO-recommended intradermal vaccination, with and without rabies immunoglobulin, and with and without dog vaccination. We took the health provider perspective, including only direct costs.Findings: We predict more than 1 million deaths will occur in the 67 rabies-endemic countries considered from 2020 to 2035, under the status quo. Current post-exposure prophylaxis use prevents approximately 56 000 deaths annually. Expanded access to, and free provision of, post-exposure prophylaxis would prevent an additional 489 000 deaths between 2020 and 2035. Under this switch to efficient intradermal post-exposure prophylaxis regimens, total projected vaccine needs remain similar (about 73 million vials) yet 17·4 million more people are vaccinated, making this an extremely cost-effective method, with costs of US$635 per death averted and $33 per disability-adjusted life-years averted. Scaling up dog vaccination programmes could eliminate dog-mediated rabies over this time period; improved post-exposure prophylaxis access remains cost-effective under this scenario, especially in combination with patient risk assessments to reduce unnecessary post-exposure prophylaxis use.Interpretation: Investing in post-exposure vaccines would be an extremely cost-effective intervention that could substantially reduce disease burden and catalyse dog vaccination efforts to eliminate dog-mediated rabies.Funding: World Health Organization.
Published: 2019
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5. Plasmodium falciparum gametocyte-infected erythrocytes do not adhere to human primary erythroblasts

Author: Neveu, Gaëlle, Dupuy, Florian, Ladli, Meriem, Barbieri, Daniela, Naissant, Bernina, Richard, Cyrielle, Martins, Rafael, Lopez-Rubio, Jose-Juan, Bachmann, Anna, Verdier, Frédérique, Lavazec, Catherine, THALES, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratório de Linguagens de Programação, Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and THALES [France]
Subjects: Erythrocytes, Erythroblasts, [SDV]Life Sciences [q-bio], lcsh:R, Plasmodium falciparum, lcsh:Medicine, Antigens, Protozoan, Article, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, hemic and lymphatic diseases, Cell Adhesion, Humans, lcsh:Q, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Malaria, Falciparum, lcsh:Science, Cells, Cultured, ComputingMilieux_MISCELLANEOUS
Abstract: Plasmodium falciparum gametocytes, the sexual stages responsible for malaria parasite transmission, develop in the human bone marrow parenchyma in proximity to the erythroblastic islands. Yet, mechanisms underlying gametocytes interactions with these islands are unknown. Here, we have investigated whether gametocyte-infected erythrocytes (GIE) adhere to erythroid precursors, and whether a putative adhesion may be mediated by a mechanism similar to the adhesion of erythrocytes infected with P. falciparum asexual stages to uninfected erythrocytes. Cell-cell adhesion assays with human primary erythroblasts or erythroid cell lines revealed that immature GIE do not specifically adhere to erythroid precursors. To determine whether adhesion may be dependent on binding of STEVOR proteins to Glycophorin C on the surface of erythroid cells, we used clonal lines and transgenic parasites that overexpress specific STEVOR proteins known to bind to Glycophorin C in asexual stages. Our results indicate that GIE overexpressing STEVOR do not specifically adhere to erythroblasts, in agreement with our observation that the STEVOR adhesive domain is not exposed at the surface of GIE.
Published: 2018
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6. CXCR1/2 Antagonism Is Protective during Influenza and Post-Influenza Pneumococcal Infection

Author: Luciana P. Tavares, Cristiana C. Garcia, Marina G. Machado, Celso M. Queiroz-Junior, Adeline Barthelemy, François Trottein, Marilda M. Siqueira, Laura Brandolini, Marcello Allegretti, Alexandre M. Machado, Lirlândia P. de Sousa, Mauro M. Teixeira, Laboratóriode Imunofarmacologia [Belo Horizonte, Brazil] (Departamento de Bioquímica e Imunologia), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Instituto de Ciencias Biologicas [Belo Horizonte, Brazil] (ICB), Laboratório de Vírus Respiratórios e do Sarampo [Rio de Janeiro, Brazil], Instituto Oswaldo Cruz / Oswaldo Cruz Institute [Rio de Janeiro] (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Departamento de Análises Clínicas e Toxicológicas [Belo Horizonte, Brazil] (Faculdade de Farmácia), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Departamento de Morfologia, Instituto de Ciências Biológicas [Belo Horizonte, Brazil] (ICB), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, R&D Department [L'Aquila, Italy], Dompé Farmaceutici s.p.a. [L'Aquila, Italy], Fiocruz Minas - René Rachou Research Center / Instituto René Rachou [Belo Horizonte, Brésil], This work was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, Brazil), Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG, Brazil), the National Institute for Science and Technology in Dengue and host–pathogen interactions (INCT in dengue), Fondation Mérieuxand the Région Hauts de France and Minas Gerais state/FAPEMIG grant (FLU-MICROBIOT ASTRE 2015_11910—R16004EE)., TROTTEIN, François, Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ)
Subjects: lcsh:Immunologic diseases. Allergy, 0301 basic medicine, Secondary infection, Immunology, Inflammation, immunomodulation, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, 03 medical and health sciences, Chemokine receptor, 0302 clinical medicine, CXCR1/2, secondary infection, medicine, Immunology and Allergy, influenza A, Pathogen, [SDV.IMM.II] Life Sciences [q-bio]/Immunology/Innate immunity, Original Research, business.industry, Influenza a, medicine.disease, 3. Good health, Pneumococcal infections, 030104 developmental biology, inflammation, 030220 oncology & carcinogenesis, medicine.symptom, lcsh:RC581-607, Antagonism, business, pneumococcus
Abstract: Luciana P. Tavares and Cristiana C. Garcia have contributed equally to this work.; International audience; RATIONALE:Influenza A infections are a leading cause of morbidity and mortality worldwide especially when associated with secondary pneumococcal infections. Inflammation is important to control pathogen proliferation but may also cause tissue injury and death. CXCR1/2 are chemokine receptors relevant for the recruitment of neutrophils. We investigated the role of CXCR1/2 during influenza, pneumococcal, and post-influenza pneumococcal infections.METHODS:Mice were infected with influenza A virus (IAV) or Streptococcus pneumoniae and then treated daily with the CXCR1/2 antagonist DF2162. To study secondary pneumococcal infection, mice were infected with a sublethal inoculum of IAV then infected with S. pneumoniae 14 days later. DF2162 was given in a therapeutic schedule from days 3 to 6 after influenza infection. Lethality, weight loss, inflammation, virus/bacteria counts, and lung injury were assessed.RESULTS:CXCL1 and CXCL2 were produced at high levels during IAV infection. DF2162 treatment decreased morbidity and this was associated with decreased infiltration of neutrophils in the lungs and reduced pulmonary damage and viral titers. During S. pneumoniae infection, DF2162 treatment decreased neutrophil recruitment, pulmonary damage, and lethality rates, without affecting bacteria burden. Therapeutic treatment with DF2162 during sublethal IAV infection reduced the morbidity associated with virus infection and also decreased the magnitude of inflammation, lung damage, and number of bacteria in the blood of mice subsequently infected with S. pneumoniae.CONCLUSION:Modulation of the inflammatory response by blocking CXCR1/2 improves disease outcome during respiratory influenza and pneumococcal infections, without compromising the ability of the murine host to deal with infection. Altogether, inhibition of CXCR1/2 may be a valid therapeutic strategy for treating lung infections caused by these pathogens, especially controlling secondary bacterial infection after influenza.
Published: 2017
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7. Environmental Triazole Induces Cross-Resistance to Clinical Drugs and Affects Morphophysiology and Virulence of Cryptococcus gattii and C. neoformans

Author: Gustavo José Cota de Freitas, Marliete Carvalho Costa, Guilhem Janbon, Lorena Vívien Neves de Oliveira, Frédérique Moyrand, Gabriella Freitas Ferreira, Hellem Cristina Silva Carneiro, Thais Furtado Ferreira Magalhães, Rafael Wesley Bastos, Karen Maia Rocha, Vanessa S. D. Carvalho, Cláudia Emanuela Viana Rocha, Tatiane Alves de Paixão, Daniel Assis Santos, Departamento de Microbiologia [Minas Gerais, Brazil], Instituto de Ciencias Biologicas [Minas Gerais], Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Departamento de Patologia Geral [Minas Gerais, Brazil], Faculdade de Farmácia [Juiz de Fora, Brazil] (FF), Universidade Federal de Juiz de Fora (UFJF), Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris], This study was supported by Fundação de Amparo a Pesquisa do Estado de Minas Gerais—FAPEMIG (grant APQ-00727-16) and Conselho Nacional de Desenvolvimento Científico e Tecnológico—CNPq (grant 403006/2016-3). R.W.B. received fellowships from CNPq and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (PDSE-CAPES-88881.131683/2016-01). D.A.S. is a research fellow of the CNPq (grant 305154/2014-1)., and Institut Pasteur [Paris] (IP)
Subjects: 0301 basic medicine, Male, Antifungal Agents, MESH: Cryptococcus neoformans / physiology, Ravuconazole, chemistry.chemical_compound, pseudohyphae, agrochemical, Amphotericin B, Pharmacology (medical), MESH: Animals, Fluconazole, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, chemistry.chemical_classification, MESH: Microbial Sensitivity Tests, antifungal cross-resistance, biology, Virulence, Cryptococcosis, MESH: Cryptococcosis / microbiology, MESH: Cryptococcus neoformans / drug effects, MESH: Virulence / drug effects, 3. Good health, Infectious Diseases, MESH: Cryptococcosis / drug therapy, medicine.drug, MESH: Cryptococcus gattii / drug effects, MESH: Cryptococcus gattii / physiology, 030106 microbiology, tebuconazole, Microbial Sensitivity Tests, Microbiology, 03 medical and health sciences, MESH: Triazoles / pharmacology, MESH: Antifungal Agents / pharmacology, MESH: Mice, Inbred C57BL, Drug Resistance, Multiple, Fungal, medicine, Animals, Cryptococcus gattii, Tebuconazole, Pharmacology, Cryptococcus neoformans, MESH: Fungicides, Industrial / pharmacology, Triazoles, biology.organism_classification, medicine.disease, MESH: Cryptococcus neoformans / pathogenicity, MESH: Male, MESH: Fluconazole / pharmacology, Fungicides, Industrial, Mice, Inbred C57BL, MESH: Cryptococcus gattii / pathogenicity, chemistry, Susceptibility, MESH: Drug Resistance, Multiple, Fungal / drug effects, Azole
Abstract: Cryptococcus gattii and Cryptococcus neoformans are environmental fungi that cause cryptococcosis, which is usually treated with amphotericin B and fluconazole. However, therapeutic failure is increasing because of the emergence of resistant strains. Because these species are constantly isolated from vegetal materials and the usage of agrochemicals is growing, we postulate that pesticides could be responsible for the altered susceptibility of these fungi to clinical drugs. Therefore, we evaluated the influence of the pesticide tebuconazole on the susceptibility to clinical drugs, morphophysiology, and virulence of C. gattii and C. neoformans strains. The results showed that tebuconazole exposure caused in vitro cross-resistance (CR) between the agrochemical and clinical azoles (fluconazole, itraconazole, and ravuconazole) but not with amphotericin B. In some strains, CR was observed even after the exposure ceased. Further, tebuconazole exposure changed the morphology, including formation of pseudohyphae in C. neoformans H99, and the surface charge of the cells. Although the virulence of both species previously exposed to tebuconazole was decreased in mice, the tebuconazole-exposed colonies recovered from the lungs were more resistant to azole drugs than the nonexposed cells. This in vivo CR was confirmed when fluconazole was not able to reduce the fungal burden in the lungs of mice. The tolerance to azoles could be due to increased expression of the ERG11 gene in both species and of efflux pump genes ( AFR1 and MDR1 ) in C. neoformans . Our study data support the idea that agrochemical usage can significantly affect human pathogens present in the environment by affecting their resistance to clinical drugs.
Published: 2017
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8. Filling Knowledge Gaps for Mimivirus Entry, Uncoating, and Morphogenesis

Author: Graziele Pereira Oliveira, Cláudio A. Bonjardim, Rodrigo Araújo Lima Rodrigues, Erna Geessien Kroon, Ana Cláudia dos Santos Pereira Andrade, Ketyllen Reis Andrade, Bernard La Scola, Jônatas Santos Abrahão, Departamento de Microbiologia [Minas Gerais, Brazil], Instituto de Ciencias Biologicas [Minas Gerais], Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Imunologia das Doenças Virais [Belo Horizonte, Brésil], Fiocruz Minas - René Rachou Research Center / Instituto René Rachou [Belo Horizonte, Brésil], Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Fundação Oswaldo Cruz (FIOCRUZ), and INSB-INSB-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, fibril acquisition area, Virophages, Phagosome acidification, 030106 microbiology, Immunology, Morphogenesis, mimivirus, Biology, Virus Replication, Microbiology, Genome, Virus, 03 medical and health sciences, Viral life cycle, Virology, Viral factory, Virus Uncoating, replication cycle, Mimivirus, Acanthamoeba castellanii, electron microscopy, phagocytosis, Virus Internalization, biology.organism_classification, Cell biology, Virus-Cell Interactions, 030104 developmental biology, Insect Science, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Mimiviridae
Abstract: Since the discovery of mimivirus, its unusual structural and genomic features have raised great interest in the study of its biology; however, many aspects concerning its replication cycle remain uncertain. In this study, extensive analyses of electron microscope images, as well as biological assay results, shed light on unclear points concerning the mimivirus replication cycle. We found that treatment with cytochalasin, a phagocytosis inhibitor, negatively impacted the incorporation of mimivirus particles by Acanthamoeba castellanii , causing a negative effect on viral growth in amoeba monolayers. Treatment of amoebas with bafilomicin significantly impacted mimivirus uncoating and replication. In conjunction with microscopic analyses, these data suggest that mimiviruses indeed depend on phagocytosis for entry into amoebas, and particle uncoating (and stargate opening) appears to be dependent on phagosome acidification. In-depth analyses of particle morphogenesis suggest that the mimivirus capsids are assembled from growing lamellar structures. Despite proposals from previous studies that genome acquisition occurs before the acquisition of fibrils, our results clearly demonstrate that the genome and fibrils can be acquired simultaneously. Our data suggest the existence of a specific area surrounding the core of the viral factory where particles acquire the surface fibrils. Furthermore, we reinforce the concept that defective particles can be formed even in the absence of virophages. Our work provides new information about unexplored steps in the life cycle of mimivirus. IMPORTANCE Investigating the viral life cycle is essential to a better understanding of virus biology. The combination of biological assays and microscopic images allows a clear view of the biological features of viruses. Since the discovery of mimivirus, many studies have been conducted to characterize its replication cycle, but many knowledge gaps remain to be filled. In this study, we conducted a new examination of the replication cycle of mimivirus and provide new evidence concerning some stages of the cycle which were previously unclear, mainly entry, uncoating, and morphogenesis. Furthermore, we demonstrate that atypical virion morphologies can occur even in the absence of virophages. Our results, along with previous data, allow us to present an ultimate model for the mimivirus replication cycle.
Published: 2017
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9. Impact of human milk pasteurization on the kinetics of peptide release during in vitro dynamic term newborn digestion

Author: Amélie Deglaire, Didier Dupont, Mathieu Emily, Claire Bourlieu, Julien Jardin, Valérie Briard-Bion, Olivia Ménard, Samira de Oliveira, Science et Technologie du Lait et de l'Oeuf ( STLO ), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique ( INRA ), Departamento de Ciência da Computação [Minas Gerais] ( DCC - UFMG ), Universidade Federal de Minas Gerais [Belo Horizonte] ( UFMG ), Laboratoire de Mathématiques Appliquées Agrocampus ( LMA2 ), AGROCAMPUS OUEST, Institut de Recherche Mathématique de Rennes ( IRMAR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST-École normale supérieure - Rennes ( ENS Rennes ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National des Sciences Appliquées ( INSA ) -Université de Rennes 2 ( UR2 ), Université de Rennes ( UNIV-RENNES ) -Centre National de la Recherche Scientifique ( CNRS ), Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Laboratoire de Mathématiques Appliquées Agrocampus (LMA2), Institut de Recherche Mathématique de Rennes (IRMAR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), 'COST (European Cooperation in Science and Technology) Action FA1005 'Improving health properties of food by sharing our knowledge on the digestive process (INFOGEST).', Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest
Subjects: 0301 basic medicine, Plasmin, Proteolysis, Clinical Biochemistry, Kinetics, Pasteurization, Peptide, digestion, Biochemistry, Analytical Chemistry, law.invention, 03 medical and health sciences, law, Tandem Mass Spectrometry, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], medicine, Humans, Food science, [ MATH.MATH-ST ] Mathematics [math]/Statistics [math.ST], Peptidomics, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, chemistry.chemical_classification, 030109 nutrition & dietetics, medicine.diagnostic_test, biology, Milk, Human, Lactoferrin, Human milk, Infant, Newborn, Milk Proteins, In vitro, 030104 developmental biology, chemistry, biology.protein, Digestion, Peptides, medicine.drug, Chromatography, Liquid
Abstract: International audience; Holder pasteurization (62.5°C, 30 min) ensures sanitary quality of donor’s human milk but also denatures beneficial proteins. Understanding whether this further impacts the kinetics of peptide release during gastrointestinal digestion of human milk was the aim of the present paper. Mature raw (RHM) or pasteurized (PHM) human milk were digested (RHM, n = 2; PHM, n = 3) by an in vitro dynamic system (term stage). Label-free quantitative peptidomics was performed onmilk and digesta (ten time points). Ascending hierarchical clustering was conducted on “Pasteurization × Digestion time” interaction coefficients. Preproteolysis occurred in human milk (159 unique peptides; RHM: 91, PHM: 151), mostly on -casein (88% of the endogenous peptides). The predicted cleavage number increased with pasteurization, potentially through plasmin activation (plasmin cleavages: RHM, 53; PHM, 76). During digestion, eight clusters resumed 1054 peptides from RHM and PHM, originating for 49% of them from -casein. For seven clusters (57% of peptides), the kinetics of peptide release differed between RHM and PHM. The parent protein was significantly linked to the clustering (p-value = 1.4 E-09), with -casein and lactoferrin associated to clusters in an opposite manner. Pasteurization impacted selectively gastric and intestinal kinetics of peptide release in term newborns, which may have further nutritional consequences.
Published: 2016
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10. Runtime pointer disambiguation

Author: Fabian Gruber, Alexandros Lamprineas, Johannes Doerfert, Fernando Magno Quintão Pereira, Tobias Grosser, Péricles Alves, Fabrice Rastello, Laboratório de Linguagens de Programação (LLP), Universidade Federal de Minas Gerais, Compiler Optimization and Run-time Systems (CORSE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Grenoble (LIG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF), Compiler Design Lab [Saarbrücken], Saarland University [Saarbrücken], Scalable Parallel Computing Laboratory (SPCL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Laboratório de Linguagens de Programação, Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), ANR-11-LABX-0025,PERSYVAL-lab,Systemes et Algorithmes Pervasifs au confluent des mondes physique et numérique(2011), and Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Programming language, Computer science, 020207 software engineering, 02 engineering and technology, Parallel computing, dynamic guards, computer.software_genre, Computer Graphics and Computer-Aided Design, Alias analysis, Software quality, hybrid analysis, [INFO.INFO-PF]Computer Science [cs]/Performance [cs.PF], pointer disambiguation, 020204 information systems, Pointer (computer programming), alias analysis, 0202 electrical engineering, electronic engineering, information engineering, code cloning, loop transformations, [INFO]Computer Science [cs], Compiler, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Heuristics, computer, Software
Abstract: International audience; In order to optimize code effectively, compilers must deal with memory dependences.However, the state-of-the-art heuristics available in the literature totrack memory dependencies are inherently imprecise and computationally expensive.Consequently, the most advanced code transformations that compilers have todayare ineffective when applied on real-world programs.The goal of this paper is to solve this conundrum through the hybriddisambiguation of pointers.We provide a static analysis that generates dynamic tests to determine when twomemory locations can overlap.We then produce two versions of a loop: one that is aliasing-free - hence, easyto optimize - and another that is not.Our checks lets us safely branch to the optimizable region.We have applied these ideas on polly-llvm, a loop optimizer built on top of the llvm compilation infrastructure.Our experiments indicate that our method is precise, effective and useful: wecan disambiguate every pair of pointer in the loopintensive polybench benchmark suite.The result of this precision is code quality: the binaries that we generateare 10% faster than those that polly-llvm produces without our optimization,at the -O3 optimization level of llvm.Given the current technology to statically solve alias analysis, we believe thatour ideas are a necessary step to make modern compiler optimizations useful inpractice.
Published: 2015
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11. Modulation of the expression of mimivirus-encoded translation-related genes in response to nutrient availability during Acanthamoeba castellanii infection

Author: Erna Geessien Kroon, Lorena C. F. Silva, Felipe L. Assis, Jônatas Santos Abrahão, Bernard La Scola, Fábio P. Dornas, Ketyllen Reis Andrade, Flávio Guimarães da Fonseca, Paulo V. M. Boratto, Jonas D. Albarnaz, Gabriel Magno de Freitas Almeida, Laboratório de Vírus, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Instituto de Ciências Biológicas [Goiânia, Brésil] (ICB), Laboratório Nacional de Referencia para Doenças de Animais Aquáticos AQUACEN, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratório de Virologia Básica e Aplicada, and INSB-INSB-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), In silico, aminoacyl-tRNA synthetases, lcsh:QR1-502, translation, mimivirus, Biology, Microbiology, Genome, lcsh:Microbiology, 03 medical and health sciences, TRANSFER-RNA SYNTHETASES, Gene expression, Giant Virus, Gene, tRNA, Original Research, 030304 developmental biology, Genetics, 0303 health sciences, Mimivirus, 030306 microbiology, Translation (biology), biology.organism_classification, aminoacyl-tRNA-synthetases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, gene expression, Acanthamoeba castellanii, VIRUS
Abstract: International audience; The complexity of giant virus genomes is intriguing, especially the presence of genes encoding components of the protein translation machinery such as transfer RNAs and aminoacyl-tRNA-synthetases; these features are uncommon among other viruses. Although orthologs of these genes are codified by their hosts, one can hypothesize that having these translation-related genes might represent a gain of fitness during infection. Therefore, the aim of this study was to evaluate the expression of translation-related genes by mimivirus during infection of Acanthamoeba castellanii under different nutritional conditions. In silico analysis of amino acid usage revealed remarkable differences between the mimivirus isolates and the A. castellanii host. Relative expression analysis by quantitative PCR revealed that mimivirus was able to modulate the expression of eight viral translation-related genes according to the amoebal growth condition, with a higher induction of gene expression under starvation. Some mimivirus isolates presented differences in translation-related gene expression; notably, polymorphisms in the promoter regions correlated with these differences. Two mimivirus isolates did not encode the tryptophanyl-tRNA in their genomes, which may be linked with low conservation pressure based on amino acid usage analysis. Taken together, our data suggest that mimivirus can modulate the expression of translation-related genes in response to nutrient availability in the host cell, allowing the mimivirus to adapt to different hosts growing under different nutritional conditions.
Published: 2015

12. Thread scheduling and memory coalescing for dynamic vectorization of SPMD workloads

Author: Wagner Meira, Fernando Magno Quintão Pereira, Sylvain Collange, Teo Milanez, Renato Ferreira, Computer Science Department [Belo Horizonte] (DCC), Universidade Federal de Minas Gerais, Amdahl's Law is Forever (ALF), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-ARCHITECTURE (IRISA-D3), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Laboratório de Linguagens de Programação, Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)
Subjects: [INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR], Computer Networks and Communications, Call stack, Computer science, 02 engineering and technology, Thread (computing), Parallel computing, 01 natural sciences, Program counter, SIMD, Theoretical Computer Science, Computer Architecture, High performance, Artificial Intelligence, 0103 physical sciences, Synchronization (computer science), 0202 electrical engineering, electronic engineering, information engineering, SPMD, Execution model, 010302 applied physics, Parallelism, Computer Graphics and Computer-Aided Design, 020202 computer hardware & architecture, MMT, Hardware and Architecture, SMT, Software
Abstract: We propose a new thread synchronization heuristic called Min-SP/PC.Min-SP/PC handles function calls better than previous algorithms.Many instructions in SPMD programs are identical across threads.Many memory accesses are either uniform or affine across threads. Simultaneous Multi-Threading (SMT) is a hardware model in which different threads share the same processing unit. This model is a compromise between high parallelism and low hardware cost. Minimal Multi-Threading (MMT) is one architecture recently proposed that shares instruction decoding and execution between threads running the same program in an SMT processor, thereby generalizing the approach followed by Graphics Processing Units to general-purpose processors. In this paper we propose new ways to expose redundancies in the MMT execution model. First, we propose and evaluate a new thread reconvergence heuristic that handles function calls better than previous approaches. Our heuristic only inspects the program counter and the stack frame to reconverge threads; hence, it is amenable to efficient and inexpensive hardware implementation. Second, we demonstrate that this heuristic is able to reveal the existence of substantial regularity in inter-thread memory access patterns. We validate our results on data-parallel applications from the PARSEC and SPLASH suites. Our new reconvergence heuristic increases the throughput of our MMT model by 7%, when compared to a previous, and substantially more complex approach, due to Long et al. Moreover, it gives us an effective way to increase regularity in memory accesses. We have observed that over 70% of simultaneous memory accesses are either the same for all the threads, or are affine expressions of the thread identifier. This observation motivates the design of newly proposed hardware that benefits from regularity in inter-thread memory accesses.
Published: 2014
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13. Flexible work arrangements and household-related journeys. Who takes the lead in dual-earner heterosexual couples?

Author: Eugênia Viana Cerqueira, Benjamin Motte-Baumvol, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Théoriser et modéliser pour aménager (UMR 6049) (ThéMA), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)
Subjects: 050210 logistics & transportation, Travel behavior, Inequality, media_common.quotation_subject, 05 social sciences, 0211 other engineering and technologies, Flexible work arrangements, 021107 urban & regional planning, Transportation, [SHS.GEO]Humanities and Social Sciences/Geography, 02 engineering and technology, Dual (category theory), Sustainable transport, Travel survey, Telecommuting, Work (electrical), 0502 economics and business, Demographic economics, Business, Path analysis (statistics), Dual-earner couples, Telework, media_common
Abstract: International audience; This research provides an exploration of the relationship between flexible work arrangements (FWA), CO2 emissions, and household travel allocation among dual-earner couples. Using data from the United Kingdom National Travel Survey for the period between 2002 and 2017, we develop a path analysis approach based on SEM that allows for a comprehensive study of travel behavior and trade-off effects. Results suggest that, although the partner who benefits from FWAs tends to carry out domestic provision and maintenance activities, the allocation of tasks within the household is still asymmetrical. Results also outline that the presence of children will intensely affect the allocation of activities and household arrangements, increasing gender inequalities.
Published: 2022
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14. The Minimization of the Number of Stops Problem

Author: Deleplanque, Samuel, Marques Fernandes, Ana Luisa, Real, Luiza Bernardes, Saraiva De Camargo, Ricardo, Quilliot, Alain, Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS), Institut Pascal (IP), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-SIGMA Clermont (SIGMA Clermont)-Centre National de la Recherche Scientifique (CNRS), Universidade Federal de Minas Gerais, Brésil, Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Labex IMobS3, and SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: ILP, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], Autonomous Vehicle, Vehicle Scheduling, Reliability
Abstract: In this paper two optimum models to study the transport of passengers and goods through the VIPA (Automatic individual Public Vehicle) are proposed. The objective is to minimize the number of times the vehicles stop. Since those are autonomous vehicles (they have no driver), the operations of deceleration, acceleration, stopping, opening and closing doors and going out of the circuit to go to the station implies a loss of reliability. Therefore, minimizing the number of times the vehicles stop is crucial to ensure their fleet works efficiently. Moreover, doing this we will achieve less energy expense, the minimization of the total time and the maximization of the number of served clients.
Published: 2014

15. Divergence Analysis

Author: Diogo Sampaio, Rafael Martins de Souza, Caroline Collange, Fernando Magno Quintão Pereira, LLP, Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Pushing Architecture and Compilation for Application Performance (PACAP), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-ARCHITECTURE (IRISA-D3), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratório de Linguagens de Programação, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Amdahl's Law is Forever (ALF), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)
Subjects: scalarization, [INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR], Design, Computer science, scalarizing compiler, Static program analysis, 02 engineering and technology, Parallel computing, computer.software_genre, ACM: C.: Computer Systems Organization/C.1: PROCESSOR ARCHITECTURES/C.1.2: Multiple Data Stream Architectures (Multiprocessors)/C.1.2.7: Single-instruction-stream, multiple-data-stream processors (SIMD), ACM: D.: Software/D.3: PROGRAMMING LANGUAGES/D.3.4: Processors/D.3.4.6: Optimization, SIMD, D34 [Software]: Programming Languages General Terms: Languages, CUDA, graphics processing units, 0202 electrical engineering, electronic engineering, information engineering, Execution model, divergence analysis, [INFO.INFO-PL]Computer Science [cs]/Programming Languages [cs.PL], Programming language, 020207 software engineering, Static analysis, 020202 computer hardware & architecture, Performance Additional Key Words and Phrases: Static program analysis, Variable (computer science), Allocator, affine vector, ACM: D.: Software/D.3: PROGRAMMING LANGUAGES/D.3.4: Processors/D.3.4.1: Compilers, Compiler, register allocation, computer, Software, Algorithms, high performance
Abstract: International audience; Growing interest in graphics processing units has brought renewed attention to the Single Instruction Multiple Data (SIMD) execution model. SIMD machines give application developers tremendous computational power; however, programming them is still challenging. In particular, developers must deal with memory and control-flow divergences. These phenomena stem from a condition that we call data divergence, which occurs whenever two processing elements (PEs) see the same variable name holding different values. This article introduces divergence analysis, a static analysis that discovers data divergences. This analysis, currently deployed in an industrial quality compiler, is useful in several ways: it improves the translation of SIMD code to non-SIMD CPUs, it helps developers to manually improve their SIMD applications, and it also guides the automatic optimization of SIMD programs. We demonstrate this last point by introducing the notion of a divergence-aware register spiller. This spiller uses information from our analysis to either rematerialize or share common data between PEs. As a testimony of its effectiveness, we have tested it on a suite of 395 CUDA kernels from well-known benchmarks. The divergence-aware spiller produces GPU code that is 26.21% faster than the code produced by the register allocator used in the baseline compiler.; L'intérêt croissant pour les processeurs graphiques a amené une attention nouvelle sur le modèle d'exécution SIMD (Single Instruction Multiple Data). Les machines SIMD fournissent au développeurs d'application une grande puissance de calcul. Cependant, leur programmation reste difficile. En particulier, les développeurs doivent faire face à la divergence mémoire et la divergence de contrôle. Ces phénomènes proviennent d'une condition que nous nommons divergence de données, qui advient lorsque deux éléments de calcul (PE) voient le même nom de variable contenir des valeurs différentes. Cet article introduit l'analyse de divergence, une analyse statique qui découvre les divergences de données. Cette analyse, actuellement déployée dans un compilateur de qualité industrielle, est utile de plusieurs manières : elle améliore la traduction automatique de code SIMD pour les processeurs non SIMD, elle aide les développeurs à améliorer manuellement leus applications SIMD, et elle guide aussi l'optimisation automatique de programmes SIMD. Nous démontrons ce dernier point en introduisant la notion d'allocateur de registre sensible à la divergence. Cet allocateur utilise l'information de notre analyse pour soit rematérialiser, soit partager des données communes entre les PE. Nous l'avons testé sur une suite de 395 noyaux de calcul CUDA de benchmarks connus. L'allocateur de registre sensible à la divergence produit du code GPU qui est 26% plus rapide que le code produit par l'allocateur du compilateur de base.
Published: 2013
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16. Le problème de la minimisation des arrêts

Author: Deleplanque, Samuel, Marques, Ana Luisa, Real, Luiza Bernardes, Quilliot, Alain, Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Universidade Federal de Minas Gerais, Brésil, Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: minimisation des arrêts, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], Dial a Ride, Transport, planning
Abstract: La recherche opérationnelle (RO) a longtemps accompagné les problématiques de transport, que ce soit en ce qui concerne les tournées ou encore l'approvisionnement en matières premières des sites de production. De la modélisation à la résolution, les techniques de RO doivent s'adapter aux nouvelles évolutions technologiques. Nos travaux posent alors le problème d'une intégration d'une importante contrainte de ﬁabilité dans la supervision d'une ﬂotte de véhicules proposant un service de transport à la demande (TaD) à petite échelle. Cette ﬁabilité naît de l'essor de l'autonomie des véhicules et s'associe aux nombres d'opérations de chargement, de déchargement et d'aiguillage vers les stations liées à l'arrêt des véhicules.
Published: 2013

17. Divergence Analysis with Affine Constraints

Author: Diogo Sampaio, Sylvain Collange, Fernando Magno Quintão Pereira, Rafael Martins, Laboratório de Linguagens de Programação, Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Amdahl's Law is Forever (ALF), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-ARCHITECTURE (IRISA-D3), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)
Subjects: [INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR], Scalarization, Computer science, Compiler, GPU, CUDA, 02 engineering and technology, Parallel computing, computer.software_genre, 01 natural sciences, 0103 physical sciences, 0202 electrical engineering, electronic engineering, information engineering, 010302 applied physics, Register Allocation, [INFO.INFO-PL]Computer Science [cs]/Programming Languages [cs.PL], Static Analysis, 020207 software engineering, Program optimization, Identifier, Allocator, Shared memory, Affine transformation, computer, Register allocation
Abstract: International audience; The rising popularity of graphics processing units is bringing renewed interest in code optimization techniques for SIMD processors. Many of these optimizations rely on divergence analyses, which classify variables as uniform, if they have the same value on every thread, or divergent, if they might not. This paper introduces a new kind of divergence analysis, that is able to represent variables as affine functions of thread identifiers. We have implemented this analysis in Ocelot, an open source compiler, and use it to analyze a suite of 177 CUDA kernels from well-known benchmarks. We can mark about one fourth of all program variables as affine functions of thread identifiers. In addition to the novel divergence analysis, we also introduce the notion of a divergence aware register allocator. This allocator uses information from our analysis to either rematerialize affine variables, or to move uniform variables to shared memory. As a testimony of its effectiveness, our divergence aware allocator produces GPU code that is 29.70% faster than the code produced by Ocelot's register allocator. Divergence analysis with affine constraints is publicly available in the Ocelot compiler since June/2012.
Published: 2012
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18. Data and Instruction Uniformity in Minimal Multi-Threading

Author: Milanez, Teo, Quintão Pereira, Fernando Magno, Meira, Wagner, Ferreira, Renato, Collange, Caroline, Magno, Fernando, Pereira, Quintão, Renato, A, Computer Science Department [Belo Horizonte] (DCC), Universidade Federal de Minas Gerais, Amdahl's Law is Forever (ALF), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-ARCHITECTURE (IRISA-D3), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Laboratório de Linguagens de Programação, Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)
Subjects: 010302 applied physics, [INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR], Computer science, 02 engineering and technology, Parallel computing, Thread (computing), ComputerSystemsOrganization_PROCESSORARCHITECTURES, 01 natural sciences, 020202 computer hardware & architecture, Instruction set, Identifier, Memory address, Multithreading, 0103 physical sciences, 0202 electrical engineering, electronic engineering, information engineering, SMT placement equipment, Heuristics, Execution model
Abstract: International audience; Simultaneous Multi-Threading (SMT) is a hardware model in which different threads share the same instruction fetching unit. This model is a compromise between high parallelism and low hardware cost. Minimal Multi-Threading (MMT) is a technique recently proposed to share instructions and execution between threads in a SMT machine. In this paper we propose new ways to explore redundancies in the MMT execution model. First, we propose and evaluate a new thread reconvergence heuristics that handles function calls better than previous approaches. Second, we demonstrate the existence of substantial regularity in inter-thread memory access patterns. We validate our results on the four data-parallel applications present in the PARSEC benchmark suite. The new thread reconvergence heuristics is, on the average, 82% more efficient than MMT's original reconvergence method. Furthermore, about 69% to 87% of all the memory addresses are either the same for all the threads, or are affine expressions of the thread identifier. This observation motivates the design of newly proposed hardware that benefits from regularity in inter-thread memory accesses.
Published: 2012
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19. Divergence Analysis with Affine Constraints

Author: Sampaio, Diogo, Martins, Rafael, Quintão Pereira, Fernando Magno, Collange, Caroline, Magno, Fernando, Pereira, Quintão, Laboratório de Linguagens de Programação, Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Computer arithmetic (ARENAIRE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de l'Informatique du Parallélisme (LIP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and ENS Lyon
Subjects: [INFO.INFO-AR]Computer Science [cs]/Hardware Architecture [cs.AR], [INFO.INFO-PL]Computer Science [cs]/Programming Languages [cs.PL]
Abstract: The rise of graphics processing units in high-performance computing is bringing renewed interest in code optimization techniques that target SIMD processors. Many of these optimizations rely on divergence analyses, which classify variables as uniform, if they have the same value on every thread, or divergent, if they might not. This paper introduces a new kind of divergence analysis, that is able to represent variables as affine functions of thread identifiers. We have implemented our divergence analysis with affine constraints on top of Ocelot, an open source compiler, and use it to analyze a suite of 177 CUDA kernels from well-known benchmarks. These experiments show that our algorithm reports 4% less divergent variables than the previous state-of-the-art algorithm of Coutinho et al. Furthermore, we can mark about one fourth of all divergent variables as affine functions of thread identifiers. In addition to the novel divergence analysis, we also introduce the notion of a divergence aware register allocator. This allocator uses information from our analysis to either rematerialize affine variables, or to move uniform variables to shared memory. As a testimony of its effectiveness, our divergence aware allocator produces GPU code that is 29.70% faster than the code produced by Ocelot's register allocator.
Published: 2011

20. Perception of rainwater harvesting in public buildings: Comparison between two case studies in France and in Brazil

Author: Seidl , Martin, de Gouvello , Bernard, Nascimento , Nilo de Oliveira, laboratoire Eau, Environnement et Systèmes Urbains (LEESU), AgroParisTech-Université Paris-Est Marne-la-Vallée (UPEM)-École des Ponts ParisTech (ENPC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Brelot, Elodie, laboratoire Eau, Environnement et Systèmes Urbains ( LEESU ), AgroParisTech-Université Paris-Est Marne-la-Vallée ( UPEM ) -École des Ponts ParisTech ( ENPC ) -Université Paris-Est Créteil Val-de-Marne - Paris 12 ( UPEC UP12 ), Universidade Federal de Minas Gerais [Belo Horizonte] ( UFMG ), Service irevues, irevues, Bordignon, Frédérique, and Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)
Subjects: [SDE] Environmental Sciences, Contrôle à la source, [SDE.IE]Environmental Sciences/Environmental Engineering, Reuse, [ SDE ] Environmental Sciences, Récupération des eaux pluviales, Source control, Réutilisation, [SDE]Environmental Sciences, Bâtiment, Building, [SDE.IE] Environmental Sciences/Environmental Engineering, Stormwater harvesting, ComputingMilieux_MISCELLANEOUS
Abstract: Colloque avec actes et comité de lecture. Internationale.; International audience
Published: 2010

21. Incomplete tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis: is it still a virus?

Author: Eric Chabrière, David C. Lamb, Didier Raoult, Sarah Aherfi, Anthony Levasseur, Bernard La Scola, Lucile Pinault, Jônatas Santos Abrahão, Jean-Pierre Baudoin, Philippe Colson, Djamal Brahim Belhaouari, Philippe Decloquement, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Swansea University, and Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille)
Subjects: Citric Acid Cycle, Genome, Viral, medicine.disease_cause, 7. Clean energy, Microbiology, Virus, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Giant Virus, Electrochemical gradient, Gene, Escherichia coli, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, Mimivirus, biology, Pandoravirus, 030306 microbiology, DNA Viruses, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Citric acid cycle, Biochemistry, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Protons, Mimiviridae
Abstract: The discovery of Acanthamoeba polyphaga Mimivirus, the first isolated giant virus of amoeba, challenged the historical hallmarks defining a virus. Giant virion sizes are known to reach up to 2.3 µm, making them visible by optical microscopy. Their large genome sizes of up to 2.5 Mb can encode proteins involved in the translation apparatus. We have investigated possible energy production in Pandoravirus massiliensis. Mitochondrial membrane markers allowed for the detection of a membrane potential in purified virions and this was enhanced by a regulator of the tricarboxylic acid cycle but abolished by the use of a depolarizing agent. Bioinformatics was employed to identify enzymes involved in virion proton gradient generation and this approach revealed that eight putative P. massiliensis proteins exhibited low sequence identities with known cellular enzymes involved in the universal tricarboxylic acid cycle. Further, all eight viral genes were transcribed during replication. The product of one of these genes, ORF132, was cloned and expressed in Escherichia coli, and shown to function as an isocitrate dehydrogenase, a key enzyme of the tricarboxylic acid cycle. Our findings show for the first time that a membrane potential can exist in Pandoraviruses, and this may be related to tricarboxylic acid cycle. The presence of a proton gradient in P. massiliensis makes this virus a form of life for which it is legitimate to ask the question “what is a virus?”.
Published: 2021
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22. Resonance Raman enhancement by the intralayer and interlayer electron–phonon processes in twisted bilayer graphene

Author: Thierry Michel, Marcus V. O. Moutinho, G. S. N. Eliel, Po-Wen Chiu, Rafael N. Gontijo, Matthieu Paillet, Ariete Righi, Marcos A. Pimenta, Pedro Venezuela, Universidade Federal do Rio de Janeiro (UFRJ), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Laboratoire Charles Coulomb (L2C), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), National Tsing Hua University [Hsinchu] (NTHU), and Universidade Federal Fluminense [Rio de Janeiro] (UFF)
Subjects: Photon, Materials science, Electronic properties and materials, Phonon, Superlattice, Science, 02 engineering and technology, 01 natural sciences, Resonance (particle physics), Article, law.invention, symbols.namesake, law, Condensed Matter::Superconductivity, 0103 physical sciences, 010306 general physics, [PHYS.COND.CM-MSQHE]Physics [physics]/Condensed Matter [cond-mat]/Mesoscopic Systems and Quantum Hall Effect [cond-mat.mes-hall], Multidisciplinary, Condensed matter physics, Graphene, 021001 nanoscience & nanotechnology, Brillouin zone, Optical properties and devices, symbols, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Medicine, Condensed Matter::Strongly Correlated Electrons, 0210 nano-technology, Raman spectroscopy, Bilayer graphene
Abstract: Twisted bilayer graphene is a fascinating system due to the possibility of tuning the electronic and optical properties by controlling the twisting angle $$\theta$$ θ between the layers. The coupling between the Dirac cones of the two graphene layers gives rise to van Hove singularities (vHs) in the density of electronic states, whose energies vary with $$\theta$$ θ . Raman spectroscopy is a fundamental tool to study twisted bilayer graphene (TBG) systems since the Raman response is hugely enhanced when the photons are in resonance with transition between vHs and new peaks appear in the Raman spectra due to phonons within the interior of the Brillouin zone of graphene that are activated by the Moiré superlattice. It was recently shown that these new peaks can be activated by the intralayer and the interlayer electron–phonon processes. In this work we study how each one of these processes enhances the intensities of the peaks coming from the acoustic and optical phonon branches of graphene. Resonance Raman measurements, performed in many different TBG samples with $$\theta$$ θ between $$4^{\circ }$$ 4 ∘ and $$16^{\circ }$$ 16 ∘ and using several different laser excitation energies in the near-infrared (NIR) and visible ranges (1.39–2.71 eV), reveal the distinct enhancement of the different phonons of graphene by the intralayer and interlayer processes. Experimental results are nicely explained by theoretical calculations of the double-resonance Raman intensity in graphene by imposing the momentum conservation rules for the intralayer and the interlayer electron–phonon resonant conditions in TBGs. Our results show that the resonant enhancement of the Raman response in all cases is affected by the quantum interference effect and the symmetry requirements of the double resonance Raman process in graphene.
Published: 2021
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23. Learning to dance: A graph convolutional adversarial network to generate realistic dance motions from audio

Author: Renato Martins, Erickson R. Nascimento, João Pedro Moreira Ferreira, José Fernandes Bezerra Neto, Thiago M. Coutinho, Rafael Alves de Azevedo, Thiago L. Gomes, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Intelligence artificielle et algorithmes efficaces pour la robotique autonome (ACENTAURI), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Signal, Images et Systèmes (Laboratoire I3S - SIS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: FOS: Computer and information sciences, Sound (cs.SD), Dance, Adversarial network, Computer science, Computer Vision and Pattern Recognition (cs.CV), media_common.quotation_subject, Automatic identification and data capture, Computer Science - Computer Vision and Pattern Recognition, 02 engineering and technology, Machine learning, computer.software_genre, Computer Science - Sound, Computer Science - Graphics, Audio and Speech Processing (eess.AS), Perception, FOS: Electrical engineering, electronic engineering, information engineering, 0202 electrical engineering, electronic engineering, information engineering, media_common, business.industry, General Engineering, [INFO.INFO-CV]Computer Science [cs]/Computer Vision and Pattern Recognition [cs.CV], 020207 software engineering, Human motion, Computer Graphics and Computer-Aided Design, Graphics (cs.GR), Human-Computer Interaction, Manifold structure, Graph (abstract data type), 020201 artificial intelligence & image processing, Artificial intelligence, business, computer, Generative grammar, Electrical Engineering and Systems Science - Audio and Speech Processing
Abstract: Synthesizing human motion through learning techniques is becoming an increasingly popular approach to alleviating the requirement of new data capture to produce animations. Learning to move naturally from music, i.e., to dance, is one of the more complex motions humans often perform effortlessly. Each dance movement is unique, yet such movements maintain the core characteristics of the dance style. Most approaches addressing this problem with classical convolutional and recursive neural models undergo training and variability issues due to the non-Euclidean geometry of the motion manifold structure.In this paper, we design a novel method based on graph convolutional networks to tackle the problem of automatic dance generation from audio information. Our method uses an adversarial learning scheme conditioned on the input music audios to create natural motions preserving the key movements of different music styles. We evaluate our method with three quantitative metrics of generative methods and a user study. The results suggest that the proposed GCN model outperforms the state-of-the-art dance generation method conditioned on music in different experiments. Moreover, our graph-convolutional approach is simpler, easier to be trained, and capable of generating more realistic motion styles regarding qualitative and different quantitative metrics. It also presented a visual movement perceptual quality comparable to real motion data., Comment: Accepted at the Elsevier Computers & Graphics (C&G) 2020
Published: 2021
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24. Yaravirus: A novel 80-nm virus infecting Acanthamoeba castellanii

Author: Saïd Azza, Jean-Pierre Baudoin, Philippe Decloquement, Talita Bastos Machado, Anthony Levasseur, Eric Chabrière, Frederik Schulz, Thomas Klose, Philippe Colson, Paulo V. M. Boratto, Ana Cláudia dos Santos Pereira Andrade, Jônatas Santos Abrahão, Bernard La Scola, Graziele Pereira Oliveira, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Universidade Federal de Minas Gerais, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Department of Biological Sciences [Lafayette IN], Purdue University [West Lafayette], DOE Joint Genome Institute [Walnut Creek], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Laboratório de Vírus, and Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)-Instituto de Ciências Biológicas [Goiânia, Brésil] (ICB)
Subjects: [SDV]Life Sciences [q-bio], Genome, Viral, Biology, Proteomics, Genome, Virus, Viral Proteins, Yaravirus, 03 medical and health sciences, chemistry.chemical_compound, Phylogenetics, capsid, Genetics, 2.2 Factors relating to the physical environment, Viral, Aetiology, Gene, Phylogeny, 030304 developmental biology, Acanthamoeba castellanii, metagenomics, 0303 health sciences, Multidisciplinary, 030306 microbiology, Human Genome, DNA Viruses, ORFan, Genome project, Biological Sciences, chemistry, Metagenomics, NCLDV, Infection, DNA
Abstract: Here we report the discovery of Yaravirus, a lineage of amoebal virus with a puzzling origin and evolution. Yaravirus presents 80-nm-sized particles and a 44,924-bp dsDNA genome encoding for 74 predicted proteins. Yaravirus genome annotation showed that none of its genes matched with sequences of known organ-isms at the nucleotide level; at the amino acid level, six predicted proteins had distant matches in the nr database. Complimentary prediction of three-dimensional structures indicated possible func-tion of 17 proteins in total. Furthermore, we were not able to retrieve viral genomes closely related to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe. The Yaravirus genome also contained six types of tRNAs that did not match commonly used codons. Proteomics revealed that Yaravirus particles contain 26 viral proteins, one of which potentially represent-ing a divergent major capsid protein (MCP) with a predicted double jelly-roll domain. Structure-guided phylogeny of MCP suggests that Yaravirus groups together with the MCPs of Pleurochrysis endemic viruses. Yaravirus expands our knowledge of the diversity of DNA viruses. The phylogenetic distance between Yaravirus and all other viruses highlights our still preliminary assessment of the genomic diversity of eukaryotic viruses, reinforcing the need for the isolation of new viruses of protists.
Published: 2020
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25. Reducing the Vertex Cover Number via Edge Contractions

Author: Lima, Paloma T., dos Santos, Vinicius F., Sau, Ignasi, Souza, Uéverton S., Tale, Prafullkumar, IT University of Copenhagen (ITU), Departamento de Ciência da Computação [Minas Gerais] (DCC - UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Algorithmes, Graphes et Combinatoire (ALGCO), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Instituto de Computação [Niteroi-Rio de Janeiro] (IC-UFF), Universidade Federal Fluminense [Rio de Janeiro] (UFF), Helmholtz Center for Information Security [Saarbrücken] (CISPA), CAPES-PRINT Institutional Internationalization Program, process 88887.371209/ 2019-00, ANR-16-CE40-0028,DE-MO-GRAPH,Décomposition de Modèles Graphiques(2016), ANR-17-CE23-0010,ESIGMA,Efficacité et structure pour les applications de la fouille de graphes(2017), ANR-20-CE48-0008,ELIT,Un Parcours par les Limites de l'Efficacité(2020), ANR-20-CE92-0027,UTMA,Théories Unifiantes dans les Algorithmes Multivarieés(2020), European Project: 714704,CUTACOMBS, European Project: 725978,SYSTEMATICGRAPH(2017), Szeider, Stefan, Ganian, Robert, Silva, Alexandra, Universidade Federal de Minas Gerais = Federal University of Minas Gerais [Belo Horizonte, Brazil] (UFMG), and Vinicius F. dos Santos: Grant APQ-01707-21 Minas Gerais Research Support Foundation (FAPEMIG) and Grant 312069/2021-9 National Council for Scientific and Technological Development (CNPq).Ignasi Sau: CAPES-PRINT Institutional Internationalization Program, process 88887.371209/ 2019-00, and projects DEMOGRAPH (ANR-16-CE40-0028), ESIGMA (ANR-17-CE23-0010), ELIT (ANR-20-CE48-0008-01), and UTMA (ANR-20-CE92-0027).Uéverton S. Souza: This research has received funding from Rio de Janeiro Research Support Foundation (FAPERJ) under grant agreement E-26/201.344/2021, National Council for Scientific and Technological Development (CNPq) under grant agreement 309832/2020-9, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation pro- gramme under grant agreement CUTACOMBS (No. 714704).
Subjects: FOS: Computer and information sciences, General Computer Science, Blocker problems, Computer Networks and Communications, Applied Mathematics, G.2.2, F.2.2, Computational Complexity (cs.CC), vertex cover, Theoretical Computer Science, Computer Science - Computational Complexity, 05C15, Computational Theory and Mathematics, edge contraction, Computer Science - Data Structures and Algorithms, FOS: Mathematics, Theory of computation → Parameterized complexity and exact algorithms, Mathematics - Combinatorics, Data Structures and Algorithms (cs.DS), [INFO]Computer Science [cs], Combinatorics (math.CO), [MATH]Mathematics [math], phrases Blocker problems, parameterized complexity
Abstract: The CONTRACTION(vc) problem takes as input a graph $G$ on $n$ vertices and two integers $k$ and $d$, and asks whether one can contract at most $k$ edges to reduce the size of a minimum vertex cover of $G$ by at least $d$. Recently, Lima et al. [JCSS 2021] proved, among other results, that unlike most of the so-called blocker problems, CONTRACTION(vc) admits an XP algorithm running in time $f(d) \cdot n^{O(d)}$. They left open the question of whether this problem is FPT under this parameterization. In this article, we continue this line of research and prove the following results: 1. CONTRACTION(vc) is W[1]-hard parameterized by $k + d$. Moreover, unless the ETH fails, the problem does not admit an algorithm running in time $f(k + d) \cdot n^{o(k + d)}$ for any function $f$. In particular, this answers the open question stated in Lima et al. [JCSS 2021] in the negative. 2. It is NP-hard to decide whether an instance $(G, k, d)$ of CONTRACTION(vc) is a yes-instance even when $k = d$, hence enhancing our understanding of the classical complexity of the problem. 3. CONTRACTION(vc) can be solved in time $2^{O(d)} \cdot n^{k - d + O(1)}$. This XP algorithm improves the one of Lima et al. [JCSS 2021], which uses Courcelle's theorem as a subroutine and hence, the $f(d)$-factor in the running time is non-explicit and probably very large. On the other hard, it shows that when $k=d$, the problem is FPT parameterized by $d$ (or by $k$)., 35 pages, 5 figures
Published: 2022
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26. The dairy probiotic bacterium Propionibacterium freudenreichii against colitis and mucositis: a key role of the surface layer protein SlpB

Author: Jan, Gwénaël, Foligné, Benoît, Rosa Do Carmo, Fillipe Luiz, Rodovalho, Vinícius, Rabah, Houem, Gaucher, Floriane, Azevedo, Vasco, Guédon, Eric, Giboulot, Anne, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institute for Translational Research in Inflammation - U 1286 (INFINITE (Ex-Liric)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), and Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)
Subjects: Inflammation, Mucositis, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Vesicle, Gut, Colitis, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology
Abstract: International audience; IntroductionGut inflammation constitutes a growing health concern in developed countries. It may consist in spontaneous ailments of the gut, involving both the host immune system and microbiota, such as IBD, including ulcerative colitis and Crohn’s disease. It may be caused by a medical treatment, such as mucositis induced by cancer chemotherapy and/or radiotherapy. It coincides with a dysbiosis including a lack of anti-inflammatory bacteria. As an example, propionibacteria are lacking in the microbiota of newborns that develop necrotizing enterocolitis.Methods Dairy propionibacteria strains were tested in vitro on human PBMCs with respect to their ability to induce immunomodulatory cytokines. Selected strains were then tested in vitro with respect to their ability to protect mice from TNBS-induced colitis, from DSS-induced colitis, and from 5FU-induced mucositis.ResultsWe thus focused on the immunomodulatory properties of GRAS propionibacteria. Selected strains of Propionibacterium freudenreichii induced the regulatory IL-10 cytokine in human immune cells (Foligné et al., 2010, 2013), depending on surface proteins (Le Marechal et al., 2015). Mutation of the slpB gene suppressed this immunomodulatory effect and the resulting slpB mutant induced a rather proinflammatory response (Deutsch et al., 2017). Consumption of wild-type P. freudenreichii protected from colitis induced by both TNBS and by DSS. It alleviated severity of symptoms, modulated local and systemic inflammation, as well as colonic oxidative stress and epithelial cell damages (Plé et al., 2015, 2016; Rabah et al., 2020). Accordingly, consumption of Lactococcus lactis NCDO 2118 harboring pXIES-SEC:slpB and expressing the propionibacterial SlpB reduced severity of colitis, lowered weight loss, disease activity index, shortening of the colon length, and histopathological score, compared with mice treated with L. lactis NCDO 2118 wild-type strain (Belo et al., 2021).In the context of mucositis induced by the chemotherapy 5-FU, P. freudenreichii prevented weight loss, reduced inflammation and consequently intestinal damages. It regulated key markers, including Claudin-1 and IL-17a genes, as well as IL-12 and IL-1β cytokines levels (Cordeiro et al., 2018). Mutant strain slpB displayed opposite regulatory effect on cld1 expression and on IL-12 levels, and failed to afford protection towards 5-FU-mucositis (do Carmo et al., 2019).P. freudenreichii was further shown to produce extracellular vesicles (EVs), which mimic the immunomodulatory features of propionibacteria in vitro by modulating NF-κB transcription factor activity and IL-8 release in cultured human intestinal epithelial cells (Rodovalho et al., 2020). Proteomic analysis revealed presence of SlpB in these EVs.DiscussionThis work emphasizes the importance of SlpB in P. freudenreichii ability to reduce both mucositis and colitis inflammation. It opens perspectives for the development of probiotic products aimed at decreasing side effects of chemotherapy and at helping treatment of colitis, thanks to GRAS bacteria.
Published: 2022

27. Altération hydrothermale des monazites-(Ce) des pegmatites du district de Santa Maria de Itabira (Minas Gerais, Brésil)

Author: Bilal , Essaïd, Marciano , Vitoria, Fuzikawa , Kazuo, Fernando Riffel , Bruno, Nalini Jr. , Hermínio Arias, Lourdes Fernandes , Maria, Nasraoui , Mohamed, Centre Sciences des Processus Industriels et Naturels (SPIN-ENSMSE), École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Département Géochimie, environnement, écoulement, réacteurs industriels et cristallisation (GENERIC-ENSMSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-SPIN, Laboratoire Magmas et Volcans (LMV-ENSMSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-SPIN-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Magmas et Volcans (LMV), Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Institut de Recherche pour le Développement et la société-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Observatoire de Physique du Globe de Clermont-Ferrand (OPGC), Institut national des sciences de l'Univers (INSU - CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Institut de Recherche pour le Développement et la société-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Observatoire de Physique du Globe de Clermont-Ferrand (OPGC), Institut national des sciences de l'Univers (INSU - CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Centro de Desenvolvimento de Tecnologia Nuclear, Minas Gerais, Comissão National de Energia Nuclear (CNEN), CBMM (Companhia Brasileira de Metalurgia e Mineraçào ), CBMM, Institut Geociências, Universidade Federale de Minas Gerais (Brézil), Centro de Desenvolvimento de Tecnologia Nuclear, Centre Sciences des Processus Industriels et Naturels ( SPIN-ENSMSE ), École des Mines de Saint-Étienne ( Mines Saint-Étienne MSE ), Institut Mines-Télécom [Paris]-Institut Mines-Télécom [Paris], Département Géochimie, environnement, écoulement, réacteurs industriels et cristallisation ( GENERIC-ENSMSE ), Institut Mines-Télécom [Paris]-Institut Mines-Télécom [Paris]-SPIN, Laboratoire Magmas et Volcans ( LMV-ENSMSE ), Institut Mines-Télécom [Paris]-Institut Mines-Télécom [Paris]-SPIN-Centre National de la Recherche Scientifique ( CNRS ) -Laboratoire Magmas et Volcans ( LMV ), Institut national des sciences de l'Univers ( INSU - CNRS ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Institut de Recherche pour le Développement et la société-Université Clermont Auvergne ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université Jean Monnet [Saint-Étienne] ( UJM ) -Institut de Recherche pour le Développement et la société-Université Clermont Auvergne ( UCA ), Institut Geociências, Universidade Federale de Minas Gerais, Département de géologie, Comissão National de Energia Nuclear ( CNEN ), Universidade Federal de Minas Gerais [Belo Horizonte] ( UFMG ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut de Recherche pour le Développement et la société-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Observatoire de Physique du Globe de Clermont-Ferrand (OPGC), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet [Saint-Étienne] (UJM)-Institut de Recherche pour le Développement et la société-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Observatoire de Physique du Globe de Clermont-Ferrand (OPGC), and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut national des sciences de l'Univers (INSU - CNRS)
Subjects: Xenotime, Albitization, Huttonite, Monazite-(Ce), [ SPI.GPROC ] Engineering Sciences [physics]/Chemical and Process Engineering, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Cheralite, Brazil, Pegmatite
Abstract: International audience; Monazite-(Ce) is found in granitic pegmatites in the Santa Maria de Itabira pegmatite district (Minas Gerais, Brazil). During the magmatic stage, monazite-(Ce) seems to have had higher contents of cheralite and huttonite in the solid solution. The Th content in primary monazite-(Ce) is high and characteristic for each pegmatite body. During the late stage (albitization), the mean LREE content in the altered zone is slightly higher and Th content is very low. The accessory mineral assemblages changed; huttonite and cheralite crystallize together with Th-poor and La-rich monazite-(Ce) at the border of altered crystals. Nd/Sm and U/Pb ratios are also changed during the hydrothermal stage.; Les monazites-(Ce) ont été collectées dans cinq corps pegmatitiques du district de Santa Maria de Itabira (Minas Gerais, Brésil). Les monazites-(Ce) primaires sont riches en thorium et présentent en solution solide de la chéralite et de la huttonite. Une albitisation tardive affecte les pegmatites ; durant ce stade hydrothermal, les monazites-(Ce) s'enrichissent en terres rares légères et s'appauvrissent en thorium. Huttonite et chéralite cristallisent dans les microfissures des monazites-(Ce). Les rapports Sm/Nd et U/Pb varient également au cours de l'altération hydrothermale
Published: 1998
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28. Higher Category Theory and Hilbert's Sixth Problem

Author: Ximenes Martins, Yuri, Biezuner, Rodney Josué, and Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG)
Subjects: [PHYS.HTHE]Physics [physics]/High Energy Physics - Theory [hep-th], [MATH.MATH-MP]Mathematics [math]/Mathematical Physics [math-ph], [MATH.MATH-DG]Mathematics [math]/Differential Geometry [math.DG], Mathematics::Category Theory, [MATH.MATH-AT]Mathematics [math]/Algebraic Topology [math.AT], [MATH.MATH-KT]Mathematics [math]/K-Theory and Homology [math.KT], [PHYS.GRQC]Physics [physics]/General Relativity and Quantum Cosmology [gr-qc], [MATH.MATH-CT]Mathematics [math]/Category Theory [math.CT]
Abstract: In 1900 David Hilbert published his famous list of 23 problems. The sixth of them-the axiomatization of Physics-remains partially unsolved. In this work we will give a gentle introduction and a brief review to one of the most recent and formal approaches to this problem, based on synthetic higher categorical languages. This approach, developed by Baez, Schreiber, Sati, Fiorenza, Freed, Lurie and many others, provides a formalization to the notion of classical field theory in terms of twisted differential cohomologies in cohesive (∞, 1)-topos. Furthermore, following the Atiyah-Witten functorial style of topological quantum field theories, it provides a nonperturbative quantization for classical field theories whose underlying cohomology satisfies orientability and duality conditions. We follow a pedagogical and almost non-technical style trying to minimize the mathematical prerequisites. No categorical background is required.
Published: 2021

29. pH-sensitive doxorubicin-tocopherol succinate prodrug encapsulated in docosahexaenoic acid-based nanostructured lipid carriers: An effective strategy to improve pharmacokinetics and reduce toxic effects

Author: Marina Mol Sena Andrade, André Luís Branco de Barros, Renata Salgado Fernandes, Christian Fernandes, Lucas Antônio Miranda Ferreira, Eduardo Burgarelli Lages, Sylvain Richard, Renata Barbosa de Oliveira, Nitchawat Paiyabhroma, Geovanni Dantas Cassali, Pierre Sicard, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), BioCampus (BCM), MORNET, Dominique, Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), BioCampus Montpellier (BCM), and Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Amide, [SDV]Life Sciences [q-bio], alpha-Tocopherol, 02 engineering and technology, Pharmacology, Ventricular Function, Left, Mice, polycyclic compounds, Prodrugs, Cytotoxicity, 0303 health sciences, Drug Carriers, Mice, Inbred BALB C, Antibiotics, Antineoplastic, Chemistry, General Medicine, Prodrug, Hydrogen-Ion Concentration, 021001 nanoscience & nanotechnology, Lipids, Hydrazone, 3. Good health, [SDV] Life Sciences [q-bio], Long QT Syndrome, Nanomedicine, 0210 nano-technology, medicine.drug, Docosahexaenoic Acids, Ion-pairing, Drug Compounding, Breast Neoplasms, RM1-950, macromolecular substances, 03 medical and health sciences, Pharmacokinetics, In vivo, Cell Line, Tumor, medicine, Animals, Humans, Doxorubicin, 030304 developmental biology, organic chemicals, Hydrazones, technology, industry, and agriculture, In vitro, Nanostructures, carbohydrates (lipids), Drug Liberation, Therapeutics. Pharmacology, Nanocarriers, Antitumor activity, Neoplasm Transplantation, Conjugate
Abstract: International audience; Side effects often limit the use of doxorubicin (DOX) in cancer treatment. We have recently developed a nanostructured lipid carrier (NLC) formulation for synergistic chemotherapy, encapsulating DOX and the anticancer adjuvants docosahexaenoic acid (DHA) and α-tocopherol succinate (TS). Hydrophobic ion-pairing with TS allowed a high DOX entrapment in the nanocarrier. In this work, we investigated the pharmacokinetics of this formulation after intravenous administration in mice. The first data obtained led us to propose synthesizing covalent DOX-TS conjugates to increase DOX retention in the NLC. We successfully conjugated DOX to TS via an amide or hydrazone bond. In vitro studies in 4T1 tumor cells indicated low cytotoxicity of the amide derivative, while the hydrazone conjugate was effective in killing cancer cells. We encapsulated the hydrazone derivative in a DHA-based nanocarrier (DOX-hyd-TS/NLC), which had reduced particle size and high drug encapsulation efficiency. The pH-sensitive hydrazone bond allowed controlled DOX release from the NLC, with increased drug release at acidic conditions. In vivo studies revealed that DOX-hyd-TS/NLC had a better pharmacokinetic profile than free DOX and attenuated the short-term cardiotoxic effects caused by DOX, such as QT prolongation and impaired left ventricular systolic function. Moreover, this formulation showed excellent therapeutic performance by reducing tumor growth in 4T1 tumor-bearing mice and decreasing DOX-induced toxicity to the heart and liver, demonstrated by hematologic, biochemical, and histologic analyses. These results indicate that DOX-hyd-TS/NLC may be a promising nanocarrier for breast cancer treatment.
Published: 2021
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30. Extracting Deformation-Aware Local Features by Learning to Deform

Author: Potje, Guilherme, Martins, Renato, Cadar, Felipe, Nascimento, Erickson R., Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Equipe VIBOT - VIsion pour la roBOTique [ImViA EA7535 - ERL CNRS 6000] (VIBOT), Centre National de la Recherche Scientifique (CNRS)-Imagerie et Vision Artificielle [Dijon] (ImViA), Université de Bourgogne (UB)-Université de Bourgogne (UB), and Martins, Renato
Subjects: FOS: Computer and information sciences, Computer Science - Machine Learning, [INFO.INFO-CV] Computer Science [cs]/Computer Vision and Pattern Recognition [cs.CV], Computer Vision and Pattern Recognition (cs.CV), Computer Science::Computer Vision and Pattern Recognition, ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, Computer Science - Computer Vision and Pattern Recognition, [INFO.INFO-CV]Computer Science [cs]/Computer Vision and Pattern Recognition [cs.CV], Machine Learning (cs.LG), ComputingMethodologies_COMPUTERGRAPHICS
Abstract: Despite the advances in extracting local features achieved by handcrafted and learning-based descriptors, they are still limited by the lack of invariance to non-rigid transformations. In this paper, we present a new approach to compute features from still images that are robust to non-rigid deformations to circumvent the problem of matching deformable surfaces and objects. Our deformation-aware local descriptor, named DEAL, leverages a polar sampling and a spatial transformer warping to provide invariance to rotation, scale, and image deformations. We train the model architecture end-to-end by applying isometric non-rigid deformations to objects in a simulated environment as guidance to provide highly discriminative local features. The experiments show that our method outperforms state-of-the-art handcrafted, learning-based image, and RGB-D descriptors in different datasets with both real and realistic synthetic deformable objects in still images. The source code and trained model of the descriptor are publicly available at https://www.verlab.dcc.ufmg.br/descriptors/neurips2021., To appear in Proceedings of the Thirty-fifth Annual Conference on Neural Information Processing Systems (NeurIPS) 2021
Published: 2021

31. Ultra slim and small UHF RFID tag design for mounting on curved surfaces

Author: Carlos David Morales Peña, Diogo Batista de Oliveira, Elson J. Silva, Maurício Weber Benjó da Silva, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), and Fluminense Federal University [Niterói]
Subjects: Computer science, Frequency band, business.industry, Acoustics, chemistry.chemical_element, 020206 networking & telecommunications, 02 engineering and technology, Substrate (printing), Input impedance, 03 medical and health sciences, [SPI.ELEC]Engineering Sciences [physics]/Electromagnetism, 0302 clinical medicine, chemistry, Ultra high frequency, Hardware_GENERAL, 0202 electrical engineering, electronic engineering, information engineering, Radio-frequency identification, Electrical and Electronic Engineering, Reflection coefficient, Antenna (radio), Tin, business, 030217 neurology & neurosurgery
Abstract: International audience; This paper proposes a UHF flexible passive tag antenna for Radio Frequency Identification (RFID) which operates at 902-928 MHz frequency band. As main contribution, we design an electrically small and slim tag antenna by using a flexible commercial substrate. The small antenna has dimensions of 13 mm × 28 mm × 0.35 mm. The geometry of the tag antenna was optimized, using a Genetic Algorithm, to maximize its read range. The antenna performance was evaluated on flat and curve surfaces, by means of simulations of input impedance, reflection coefficient, gain and read range. Measurements of reflection coefficient were also developed. Results prove that the tag antenna can be wrapped on cylindrical surfaces with read ranges above one meter, suitable for applications related to industrial asset management, access control and identification of small objects such as hardware tools, tin cans, spray bottles and tin PET cylindrical containers.
Published: 2021
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32. Reversible Photo-Induced Phase Segregation and Origin of Long Carrier Lifetime in Mixed-Halide Perovskite Films

Author: Bernard Geffroy, Douglas R. Miquita, Olivier Plantevin, Minjin Kim, Subodh K. Gautam, Jean-Eric Bourée, Laboratoire de Physique des Solides (LPS), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), Laboratoire de physique des interfaces et des couches minces [Palaiseau] (LPICM), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Centro de Microscopia, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire Innovation en Chimie des Surfaces et NanoSciences (LICSEN UMR 3685), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and ANR-16-CE05-0019,PERSIL,Cellules solaires tandem Perovskite-Silicium nanocristallin(2016)
Subjects: Photoluminescence, Materials science, Band gap, FOS: Physical sciences, 02 engineering and technology, Applied Physics (physics.app-ph), 010402 general chemistry, 7. Clean energy, 01 natural sciences, [SPI.MAT]Engineering Sciences [physics]/Materials, Biomaterials, [SPI]Engineering Sciences [physics], Phase segregation, Phase (matter), Electrochemistry, [CHIM.CRIS]Chemical Sciences/Cristallography, Hybrid perovskite, Perovskite (structure), [PHYS]Physics [physics], Condensed Matter - Materials Science, business.industry, Materials Science (cond-mat.mtrl-sci), Carrier lifetime, Triple-cation mixed-halide perovskite, [CHIM.MATE]Chemical Sciences/Material chemistry, Physics - Applied Physics, Exciton-phonon coupling, 021001 nanoscience & nanotechnology, Condensed Matter Physics, Long carrier lifetime, 0104 chemical sciences, Electronic, Optical and Magnetic Materials, Photoexcitation, Semiconductor, Chemical physics, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Charge carrier, 0210 nano-technology, business
Abstract: International audience; Mixed-halide based hybrid perovskite semiconductors have attracted tremendous attention as a promising candidate for high efficient photovoltaic and light-emitting devices. However, these advanced perovskite materials may undergo phase segregation under light illumination due to halide ion migration, affecting their optoelectronic properties. Here, we report photo-excitation induced phase segregation in triple-cation mixed-halide perovskite films that yields to red-shift in photoluminescence response. We demonstrate that photo-excitation induced halide ion migration leads to the formation of smaller-bandgap iodide-rich and larger-bandgap bromide-rich domains in the perovskite film, where the phase segregation rate is found to follow the excitation power-density as a power law. Results confirm that charge carrier lifetime increases with redshift in photoluminescence due to the trapping of photo-excited carriers in the segregated smaller-bandgap iodide-rich domains. Interestingly, we found that these photo-induced changes are fully reversible and thermally activated when the excitation power is turned off. A significant difference in activation energies for halide ion migration is observed during phase segregation and recovery process under darkness. Additionally, we have investigated the emission linewidth broadening as a function of temperature which is governed by the exciton-optical phonon coupling. The mechanism of photo-induced phase segregation is interpreted based on excitonphonon coupling strength in both mixed and demixed (segregated) states of perovskite film.
Published: 2021
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33. N-doped carbon nanotubes grown on red mud residue: Hybrid nanocomposites for technological applications

Author: João Paulo de Mesquita, Roberta V. Ferreira, Amanda R. Martins, Aline A. S. Oliveira, Flávia C.C. Moura, Philippe Serp, Igor Cunha, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Centro Federal de Educação Tecnológica de Minas Gerais (CEFET-MG), Laboratoire de chimie de coordination (LCC), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Universidade Federal dos Vales do Jequitinhonha e Mucuri = Federal University of Jequitinhonha and Mucuri Vallays (UFJMV)
Subjects: Materials science, 02 engineering and technology, Carbon nanotube, 010402 general chemistry, Environmental catalysis, 01 natural sciences, Catalysis, law.invention, Organic contaminants, symbols.namesake, Adsorption, law, Oxidation, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Thermal analysis, Red mud, Nanocomposite, N-Doped carbon nanotubes, General Chemistry, 021001 nanoscience & nanotechnology, 0104 chemical sciences, Chemical engineering, Elemental analysis, symbols, 0210 nano-technology, Raman spectroscopy, BET theory
Abstract: International audience; N-doped carbon nanotubes were grown on the surface of red mud residue to produce hybrid nanocomposites. The structure, composition and amphiphilic properties of the resulting nanocomposites were characterized in detail by physicochemical means such as elemental analysis, thermal analysis, Raman spectroscopy, electron microscopies, BET surface area and Mössbauer spectroscopy. Nanocomposites with different nitrogen contents were obtained. Studies on adsorption of emerging contaminants and catalysis of oxidation reactions by these nanocomposites have shown to be very promising, especially due to nitrogen content and structural defects. It was observed that composites containing carbon nanotubes doped with nitrogen present greater wettability and affinity for polar molecules and due to this fact can be easier dispersed in liquid systems and interact better with organic contaminants in water.
Published: 2020
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34. Chimeric Protein–Protein Interface Inhibitors Allow Efficient Inhibition of Type III Secretion Machinery and Pseudomonas aeruginosa Virulence

Author: Rossimiriam Pereira de Freitas, Yung-Sing Wong, Aline Thomas, Sophie Plé, Younes Bouzidi, Antoine Fortuné, Caroline Barette, Flaviane Francisco Hilário, Ina Attrée, Marie-Odile Fauvarque, Tuan-Dung Ngo, Eric Faudry, Pathogenèse bactérienne et réponses cellulaires (PBRC), Biologie du Cancer et de l'Infection (BCI ), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de pharmacochimie moléculaire (DPM ), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Genetics and Chemogenomics (GenChem), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Universidade Federal de Ouro Preto (UFOP), Associations 'Vaincre la mucoviscidose' and 'Gregory Lemarchand', AVIESAN T3SS (ANR PRP1.4), GIS-IBiSA and ChemBioFrance, Froggy platform of the CIMENT infrastructure (https://ciment.ujf-grenoble.fr), which is supported by the Rhône-Alpes region (GRANT CPER07_13 CIRA), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-15-CE11-0018,HemoPseudo,Pneumonie hémorragique à Pseudomonas aeruginosa : étude de nouvelles stratégies de virulence(2015), ANR-11-LABX-0003,ARCANE,Grenoble, une chimie bio-motivée(2011), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-10-LABX-0056,OSUG@2020,Innovative strategies for observing and modelling natural systems(2010), ANR-10-EQPX-0029,EQUIP@MESO,Equipement d'excellence de calcul intensif de Mesocentres coordonnés - Tremplin vers le calcul petaflopique et l'exascale(2010), Faudry, Eric, Grenoble Alliance for Integrated Structural Cell Biology - - GRAL2010 - ANR-10-LABX-0049 - LABX - VALID, Pneumonie hémorragique à Pseudomonas aeruginosa : étude de nouvelles stratégies de virulence - - HemoPseudo2015 - ANR-15-CE11-0018 - AAPG2015 - VALID, Grenoble, une chimie bio-motivée - - ARCANE2011 - ANR-11-LABX-0003 - LABX - VALID, CBH-EUR-GS - - CBH-EUR-GS2017 - ANR-17-EURE-0003 - EURE - VALID, Innovative strategies for observing and modelling natural systems - - OSUG@20202010 - ANR-10-LABX-0056 - LABX - VALID, Equipements d'excellence - Equipement d'excellence de calcul intensif de Mesocentres coordonnés - Tremplin vers le calcul petaflopique et l'exascale - - EQUIP@MESO2010 - ANR-10-EQPX-0029 - EQPX - VALID, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Protein subunit, 030106 microbiology, Virulence, hybrid molecules, medicine.disease_cause, Type three secretion system, Microbiology, 03 medical and health sciences, medicine, antivirulence, Secretion, biology, protein−protein interface inhibitors, Chemistry, Toxin, Pseudomonas aeruginosa, bacterial resistance, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Fusion protein, Type III secretion system, 030104 developmental biology, Infectious Diseases, click chemistry, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Bacteria
Abstract: International audience; Pseudomonas aeruginosa (P. aeruginosa) is an opportunistic pathogen naturally resistant to many common antibiotics and acquires new resistance traits at an alarming pace. Targeting the bacterial virulence factors by an antivirulence strategy, therefore, represents a promising alternative approach besides antibiotic therapy. The Type III secretion system (T3SS) of P. aeruginosa is one of its main virulence factors. It consists of more than 20 proteins building a complex syringe-like machinery enabling the injection of toxin into host cells. Previous works showed that disrupting interactions between components of this machinery efficiently lowers the bacterial virulence. Using automated target-based screening of commercial and in-house libraries of small molecules, we identified compounds inhibiting the protein-protein interaction between PscE and PscG, the two cognate chaperones of the needle subunit PscF of P. aeruginosa T3SS. Two hits were selected and assembled using Split/Mix/Click chemistry to build larger hybrid analogues. Their efficacy and toxicity were evaluated using phenotypic analysis including automated microscopy and image analysis. Two nontoxic hybrid leads specifically inhibited the T3SS and reduced the ex vivo cytotoxicity of bacteria and their virulence in Galleria mellonella.
Published: 2019
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35. An axiomatization of information flow measures

Author: Konstantinos Chatzikokolakis, Catuscia Palamidessi, Carroll Morgan, Mário S. Alvim, Geoffrey Smith, Annabelle McIver, Department of Computer Science [Minas Gerais], Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), National and Kapodistrian University of Athens (NKUA), National ICT Australia [Sydney] (NICTA), Concurrency, Mobility and Transactions (COMETE), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Florida International University [Miami] (FIU), Macquarie University, Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: Mathematical optimization, General Computer Science, Computer science, Hardware_PERFORMANCEANDRELIABILITY, 0102 computer and information sciences, 02 engineering and technology, Information theory, 01 natural sciences, Theoretical Computer Science, [INFO.INFO-CR]Computer Science [cs]/Cryptography and Security [cs.CR], Hardware_GENERAL, Hardware_INTEGRATEDCIRCUITS, 0202 electrical engineering, electronic engineering, information engineering, Information flow (information theory), Leakage (economics), Axiom, information theory, information flow, Hardware_MEMORYSTRUCTURES, axioms, g-vulnerability, [INFO.INFO-LO]Computer Science [cs]/Logic in Computer Science [cs.LO], confidentiality, Information sensitivity, 010201 computation theory & mathematics, Information leakage, 020201 artificial intelligence & image processing, Completeness (statistics)
Abstract: International audience; Quantitative information flow aims to assess and control the leakage of sensitive information by computer systems. A key insight in this area is that no single leakage measure is appropriate in all operational scenarios; as a result, many leakage measures have been proposed, with many different properties. To clarify this complex situation, this paper studies information leakage axiomatically, showing important dependencies among different axioms. It also establishes a completeness result about the g-leakage family, showing that any leakage measure satisfying certain intuitively-reasonable properties can be expressed as a g-leakage.
Published: 2019
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36. « Les enfants veulent jouer au football, pas être exploités! » Coupe du monde de football 2014 et implications sur le tourisme sexuel infantile dans la ville d’accueil de Recife, Brésil

Author: Dominique Charrier, Barbara Evrard, César Teixeira Castilho, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Centre d’études des transformations des activités physiques et sportives (CETAPS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche Interdisciplinaire Homme et Société (IRIHS), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Laboratoire de Recherche en Sciences Humaines (Lares-Las), Université de Rennes 2 (UR2), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: [SHS.SOCIO]Humanities and Social Sciences/Sociology, child sex tourism, Sociology and Political Science, 2014 World Cup, 05 social sciences, Public policy, politique de prévention, [SHS.SCIPO]Humanities and Social Sciences/Political science, Political science, 0502 economics and business, tourisme sexuel infantile, Coupe du monde 2014, preventive public policy, human activities, Humanities, 050203 business & management, 050212 sport, leisure & tourism, Tourism
Abstract: International audience; This study aims to analyze the issue of child sex tourism and its correlations with sports mega-events taking into consideration the implementation of preventive public policy in the host city of Recife – located in Northeast Brazil – in the context of the FIFA Football World Cup in 2014. Through a qualitative approach – interviews, observations, and photographs – this theme will be analyzed while taking into account the social aspects and the implications of excluded sectors of society in the organization of so-called mega-events. Although in the short term, the results obtained in the analyzed projects have been satisfactory, in the long run, effective social and educational measures must be prioritized to improve the situation of the actors involved. The topic of child sex tourism remains marginal in the context of sports mega-events, particularly in countries where social inequality persists.; Cette étude examine la question du tourisme sexuel infantile et ses corrélations avec les grands événements sportifs en prenant en considération la mise en œuvre d’une politique publique préventive dans la ville d’accueil de Recife, au Brésil, dans le cadre de la Coupe du monde de football 2014. Par le biais d’une approche qualitative – entretiens, observations et photographies – ce thème est exposé en mettant l’accent sur les aspects sociaux et la participation des groupes exclus des événements sportifs. Bien que, à court terme, les résultats des projets soient satisfaisants, à long terme, des mesures socio-éducatives effectives doivent être priorisées pour améliorer la situation des acteurs impliqués. Dans le cadre des grands événements sportifs, la thématique sur le tourisme sexuel infantile demeure marginale, en particulier dans les pays où l’inégalité sociale perdure.
Published: 2019
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37. Transient hillslope erosion in slow evolution landscapes

Author: Vincent Godard, Aster Team, André Augusto Rodrigues Salgado, Lionel Siame, Jules Fleury, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), and Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)
Subjects: landscape evolution, 010504 meteorology & atmospheric sciences, Pleistocene, Geography, Planning and Development, Inversion (geology), 010502 geochemistry & geophysics, cosmogenic nuclides, 01 natural sciences, hillslopes, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Earth and Planetary Sciences (miscellaneous), [SDU.STU.GM]Sciences of the Universe [physics]/Earth Sciences/Geomorphology, Cosmogenic nuclide, Geomorphology, 0105 earth and related environmental sciences, Earth-Surface Processes, [SDU.STU.TE]Sciences of the Universe [physics]/Earth Sciences/Tectonics, 15. Life on land, high-resolution topography, erosion, Tectonics, Denudation, 13. Climate action, Erosion, Quaternary, Sediment transport, Geology
Abstract: International audience; Transient evolution and adjustment to changing tectonic and climatic boundary conditions is an essential attribute of landscapes, and characterizing transient behavior is a key to understanding their dynamics and history. Developing new approaches to detect such transience has been explored by various methods, in particular to identify landscape response to Late Cenozoic and Quaternary climatic changes. Such studies have often focused on regions of high relief and/or active tectonic activity where interferences between tectonic and climatic signals might complicate the interpretation of the observations. We investigated the case of the hillslopes of the Serra do Cipó quartzitic range in SE Brazil in order to detect and quantify transience in a tectonically quiescent landscape over 100-ka timescales. We determined hilltop curvature from a high-resolution digital surface model derived from Pléiades imagery and measured cosmogenic nuclide (10Be and 26Al) concentrations at these hilltop sites. We compare both observations with predictions of hillslope diffusion theory, observing a distinctive signature of an acceleration of denudation. We performed a joint inversion of topographic and isotopic data to retrieve an evolution of the hillslope sediment transport coefficient through time. The timing of the increase in denudation cannot be unequivocally associated with a single climatic event but is consistent with important, climatically modulated fluctuations in precipitation and erosion in this area during the Middle and Late Pleistocene.
Published: 2021
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38. On estimating the predictability of human mobility: the role of routine

Author: Teixeira, Douglas, Almeida, Jussara, Carneiro Viana, Aline, Federal University of Minas Gerais (UFMG), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), inTeRnet BEyond the usual (TRiBE ), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), L'institution a financé les frais de publication pour que cet article soit en libre accès, and Universidade Federal de Minas Gerais = Federal University of Minas Gerais [Belo Horizonte, Brazil] (UFMG)
Subjects: [INFO.INFO-IU]Computer Science [cs]/Ubiquitous Computing, [INFO.INFO-MC]Computer Science [cs]/Mobile Computing, Human mobility, Entropy, Computer applications to medicine. Medical informatics, R858-859.7, Predictability, Mobility metrics
Abstract: International audience; Given the difficulties in predicting human behavior, one may wish to establish bounds on our ability to accurately perform such predictions. In the case of mobility-related behavior, there exists a fundamental technique to estimate the predictability of an individual’s mobility, as expressed in a given dataset. Although useful in several scenarios, this technique focused on human mobility as a monolithic entity, which poses challenges to understanding different types of behavior that may be hard to predict. In this paper, we propose to study predictability in terms of two components of human mobility: routine and novelty, where routine is related to preferential returns, and novelty is related to exploration. Viewing one’s mobility in terms of these two components allows us to identify important patterns about the predictability of one’s mobility. Additionally, we argue that mobility behavior in the novelty component is hard to predict if we rely on the history of visited locations (as the predictability technique does), and therefore we here focus on analyzing what affects the predictability of one’s routine. To that end, we propose a technique that allows us to (i) quantify the effect of novelty on predictability, and (ii) gauge how much one’s routine deviates from a reference routine that is completely predictable, therefore estimating the amount of hard-to-predict behavior in one’s routine. Finally, we rely on previously proposed metrics, as well as a newly proposed one, to understand what affects the predictability of a person’s routine. Our experiments show that our metrics are able to capture most of the variability in one’s routine (adjusted $R^{2}$ R 2 of up to 84.9% and 96.0% on a GPS and CDR datasets, respectively), and that routine behavior can be largely explained by three types of patterns: (i) stationary patterns, in which a person stays in her current location for a given time period, (ii) regular visits, in which people visit a few preferred locations with occasional visits to other places, and (iii) diversity of trajectories, in which people change the order in which they visit certain locations.
Published: 2021
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39. Environmental Plasticity of the RNA Content of Staphylococcus aureus Extracellular Vesicles

Author: Silva Rosa da Luz, Brenda, Nicolas, Aurélie, Chabelskaya, Svetlana, de Rezende Rodovalho, Vinicius, Le Loir, Yves, Ariston de Carvalho Azevedo, Vasco, Felden, Brice, Guédon, Eric, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), BRM [Bacterial Regulatory RNAs and Medicine] UMR_S 1230, University of Rennes, Inserm, Société Française de Microbiologie, Giboulot, Anne, AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Cellular and Molecular Genetics Laboratory, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Bacterial Regulatory RNAs and Medicine (BRM UMR 1230), University of Rennes, ARN régulateurs bactériens et médecine (BRM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), and 88887.179897/2018-00
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, small regulatory RNA, RNAIII, vancomycin, virulence factors, host-pathogen interaction, Microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, bacterial extracellular vesicle, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, RsaC, staphylococcuss aureus, RNA-Seq, extracellular vesicle, membrane vesicle, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Original Research
Abstract: International audience; The roles of bacterial extracellular vesicles (EVs) in cell-to-cell signaling are progressively being unraveled. These membranous spheres released by many living cells carry various macromolecules, some of which influence host-pathogen interactions. Bacterial EVs contain RNA, which may serve in communicating with their infected hosts. Staphylococcus aureus, an opportunistic human and animal pathogen, produces EVs whose RNA content is still poorly characterized. Here, we investigated in depth the RNA content of S. aureus EVs. A high-throughput RNA sequencing approach identified RNAs in EVs produced by the clinical S. aureus strain HG003 under different environmental conditions: early- and late-stationary growth phases, and presence or absence of a sublethal vancomycin concentration. On average, sequences corresponding to 78.0% of the annotated transcripts in HG003 genome were identified in HG003 EVs. However, only ~5% of them were highly covered by reads (≥90% coverage) indicating that a large fraction of EV RNAs, notably mRNAs and sRNAs, were fragmented in EVs. According to growth conditions, from 86 to 273 highly covered RNAs were identified into the EVs. They corresponded to 286 unique RNAs, including 220 mRNAs. They coded for numerous virulence-associated factors (hld encoded by the multifunctional sRNA RNAIII, agrBCD, psmβ1, sbi, spa, and isaB), ribosomal proteins, transcriptional regulators, and metabolic enzymes. Twenty-eight sRNAs were also detected, including bona fide RsaC. The presence of 22 RNAs within HG003 EVs was confirmed by reverse transcription quantitative PCR (RT-qPCR) experiments. Several of these 286 RNAs were shown to belong to the same transcriptional units in S. aureus. Both nature and abundance of the EV RNAs were dramatically affected depending on the growth phase and the presence of vancomycin, whereas much less variations were found in the pool of cellular RNAs of the parent cells. Moreover, the RNA abundance pattern differed between EVs and EV-producing cells according to the growth conditions. Altogether, our findings show that the environment shapes the RNA cargo of the S. aureus EVs. Although the composition of EVs is impacted by the physiological state of the producing cells, our findings suggest a selective packaging of RNAs into EVs, as proposed for EV protein cargo. Our study shedds light to the possible roles of potentially functional RNAs in S. aureus EVs, notably in host-pathogen interactions.
Published: 2021
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40. Assembling immunomodulatory strains of Propionibacterium freudenreichii, Lactobacillus delbrueckii and Streptococcus thermophilus to produce an anti-inflammatory Emmental cheese

Author: Rosa Do Carmo, Fillipe Luiz, de Oliveira Carvalho, Rodrigo Dias, da Silva, Sara Heloisa, Oliveira, Emiliano Rosa, Cara, Denise Carmona, Faria, Ana Maria Caetano, Rabah, Houem, Luiz, Fillipe, Do Carmo, Rosa, Dias, Rodrigo, Carvalho, Oliveira, Fernandes Cordeiro, Bárbara, Heloisa da Silva, Sara, Oliveira, Emiliano, Lemos, Luisa, Cara, Denise, Caetano Faria, Ana, Garric, Gilles, Harel-Oger, Marielle, Le Loir, Yves, Azevedo, Vasco, Bouguen, Guillaume, Foligne, Benoit, Jan, Gwénaël, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), I.M. Sechenov First Moscow State Medical University (Sechenov University), Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Pôle Agronomique Ouest, Régions Bretagne et Pays de la Loire F-35 042 Rennes, Nutrition, Métabolismes et Cancer (NuMeCan), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute for Translational Research in Inflammation - U 1286 (INFINITE (Ex-Liric)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Departamento de Genética, Ecologia e evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte Minas Gerais CP 486 CEP 31270-901 , Brazil, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Giboulot, Anne
Subjects: colitis, Inflammatory Bowel Disease, food and beverages, immunomodulation, cheese, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, inflammation, Propionibacteria, Emmental, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, intestine, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, probiotic
Abstract: International audience; Introduction and Aims. Inflammatory Bowel Diseases (IBD), including Ulcerative Colitis (UC), coincide with alterations in the gut microbiota. Consumption of immunomodulatory strains of probiotic bacteria may induce or prolong remission in UC patients. Fermented foods, including cheeses, constitute major vectors for bacteria consumption. New evidences revealed anti-inflammatory effects of selected strains within the species P.freudenreichii, S.thermophilus and L.delbrueckii. We thus hypothesized that consumption of a functional cheese, fermented by selected strains of these three species, may exert a positive effect on IBD.Methods. Strains of each bacterial species were screened based on the ability to induce regulatory IL-10 in human immune PBMC cells, or to downregulate nuclear factor kappa B (NF-κB) activation in a cultured HT-29 human intestinal epithelial cell line. We then investigated the effect of monostrain experimental cheese. We further investigated the impact two-strains experimental cheese. Finally, we produced in industrial conditions an Emmental cheese using one selected strain of each of the three species, i.e. P. freudenreichii CIRM-BIA 129 in combination with Lactobacillus delbrueckii CNRZ327 and Streptococcus thermophilus LMD-9. Consumption of all cheeses was investigated with respect to prevention of chemically induced colitis in mice.Results. Consumption of the experimental cheeses, or of the industrial Emmental, reduced the severity of subsequent chemically induced colitis, weight loss, disease activity index and histological score, in mice. Furtherrmore, consumption of the Emmental cheese, in a preventive way, reduced small bowel Immunoglobulin A (IgA) secretion, restored occludin gene expression and prevented induction of Tumor Necrosis Factor α (TNFα), Interferon γ (IFNγ) and Interleukin-17 (IL-17).Conclusion. Assembling immunomodulatory strains of both lactic acid and propionic acid starter bacteria leads to an anti-inflammatory Emmental cheese, as revealed in vivo. This opens new perspectives for the development of functional fermented food products for personalised nutrition in the context of IBD.
Published: 2021

41. Alethe: Towards a Generic SMT Proof Format (extended abstract)

Author: Pascal Fontaine, Hans-Jörg Schurr, Haniel Barbosa, Mathias Fleury, Modeling and Verification of Distributed Algorithms and Systems (VERIDIS), Department of Formal Methods (LORIA - FM), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Max-Planck-Institut für Informatik (MPII), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Proof-oriented development of computer-based systems (MOSEL), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria), Johannes Kepler University Linz [Linz] (JKU), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Université de Liège, European Project: 713999,H2020,Matryoshka(2017), Max-Planck-Institut für Informatik (MPII), Max-Planck-Gesellschaft-Max-Planck-Gesellschaft-Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Formal Methods (LORIA - FM), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), and Johannes Kepler Universität Linz - Johannes Kepler University Linz [Autriche] (JKU)
Subjects: FOS: Computer and information sciences, Computer Science - Logic in Computer Science, I.2.3, Computer science, Programming language, Multiple applications, [INFO.INFO-LO]Computer Science [cs]/Logic in Computer Science [cs.LO], 020207 software engineering, 02 engineering and technology, Mathematical proof, computer.software_genre, Logic in Computer Science (cs.LO), 03 medical and health sciences, 0302 clinical medicine, 030220 oncology & carcinogenesis, Satisfiability modulo theories, 0202 electrical engineering, electronic engineering, information engineering, computer
Abstract: The first iteration of the proof format used by the SMT solver veriT was presented ten years ago at the first PxTP workshop. Since then the format has matured. veriT proofs are used within multiple applications, and other solvers generate proofs in the same format. We would now like to gather feedback from the community to guide future developments. Towards this, we review the history of the format, present our pragmatic approach to develop the format, and also discuss problems that might arise when other solvers use the format., In Proceedings PxTP 2021, arXiv:2107.01544
Published: 2021
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42. Lyophilized Symbiotic Mitigates Mucositis Induced by 5-Fluorouracil

Author: Bruna Savassi, Bárbara F. Cordeiro, Sara H. Silva, Emiliano R. Oliveira, Giovanna Belo, Alessandra Gomes Figueiroa, Maria Izabel Alves Queiroz, Ana Maria Caetano Faria, Juliana Alves, Tales Fernando da Silva, Gabriela Munis Campos, Erick A. Esmerino, Ramon S. Rocha, Monica Q. Freitas, Marcia C. Silva, Adriano G. Cruz, Kátia Duarte Vital, Simone O.A. Fernandes, Valbert N. Cardoso, Leonardo Borges Acurcio, Gwénaël Jan, Yves Le Loir, Alfonso Gala-Garcia, Fillipe Luiz R. do Carmo, Vasco Azevedo, Instituto de Ciencias Biologicas [Minas Gerais], Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Departamento de Patologia e Clínica Veterinária, Faculdade de Veterinária, Fluminense Federal University, Departamento de Alimentos, Ciência e Tecnologia Do Rio de Janeiro (IFRJ), Instituto Federal de Educação, Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais (UFMG), Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Faculdade de Odontologia, Universidade Federal da Bahia (UFBA)
Subjects: Pharmacology, 0303 health sciences, food and beverages, RM1-950, chemotherapy, 3. Good health, 03 medical and health sciences, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 0302 clinical medicine, 030220 oncology & carcinogenesis, prebiotic, immunomodulant effects, Pharmacology (medical), symbiotic, Therapeutics. Pharmacology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, probiotic, 030304 developmental biology, Original Research
Abstract: Mucositis is an adverse effect of cancer chemotherapies using 5-Fluorouracil (5-FU). It is characterized by mucosal inflammation, pain, diarrhea, and weight loss. Some studies reported promising healing effects of probiotic strains, when associated with prebiotics, as adjuvant treatment of mucositis. We developed a lyophilized symbiotic product, containing skimmed milk, supplemented with whey protein isolate (WPI) and with fructooligosaccharides (FOS), and fermented by Lactobacillus casei BL23, Lactiplantibacillus plantarum B7, and Lacticaseibacillus rhamnosus B1. In a mice 5-FU mucositis model, this symbiotic lyophilized formulation was able to reduce weight loss and intestinal permeability. This last was determined in vivo by quantifying blood radioactivity after oral administration of 99mTc-DTPA. Finally, histological damages caused by 5-FU-induced mucositis were monitored. Consumption of the symbiotic formulation caused a reduced score of inflammation in the duodenum, ileum, and colon. In addition, it decreased levels of pro-inflammatory cytokines IL-1β, IL-6, IL-17, and TNF-α in the mice ileum. The symbiotic product developed in this work thus represents a promising adjuvant treatment of mucositis.
Published: 2021
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43. Geochronology of monazite related to REE, Nb-Ta and U-Th bearing minerals from Mesoproterozoic anorogenic magmatism in the E-Colombian Amazonian Craton: links to mantle plume activity in the Columbia (Nuna) supercontinent

Author: Alexandre de Oliveira Chaves, Marc Poujol, Jose Alejandro Franco Victoria, Heinrich A. Horn, Thomas Cramer, Universidad Nacional de Colombia [Bogotà] (UNAL), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Universidad Nacional de Colombia Hermes 35441, 35441, Universidade Federal de Minas Gerais, Funds CTeI of the Sistema General de Regalias, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: 010506 paleontology, Outcrop, Geochemistry, 010502 geochemistry & geophysics, 01 natural sciences, Supercontinent, Mantle plume, Geologic time scale, U-Pb and EPMA geochronology, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, monazite, Pegmatite, 0105 earth and related environmental sciences, Earth-Surface Processes, geography, geography.geographical_feature_category, Geology, 15. Life on land, Craton, Monazite, anorogenic magmatism, Columbia (Nuna) supercontinent, Geochronology, mantle plume, [SDU.STU.MI]Sciences of the Universe [physics]/Earth Sciences/Mineralogy
Abstract: International audience; U-Th-Pb geochronology of REE-bearing minerals such as monazite and other phosphates has become a precise tool to date mineralization events through geological time. In the E-Colombian Guainía department, from 3 colluvial sites over western Guiana Shield Mesoproterozoic rocks Nb-Ta, U-Th and REE bearing minerals probably of pegmatitic origin were sampled including up-to-0.5 cm long monazite crystals. The monazite pan concentrate samples from sites near to the indigenous communities of Barranquilla, San Jose and Chorro Bocón (Espina hills) along the Cuyari, Guainía, and Inírida rivers respectively, were analyzed geochemically and geochronologically using LA-ICP-MS and EPMA. The monazites obtained from the 3 sites are rather similar among each another and of approximate composition Ce0.44La0.16Nd0.16Sm004Y0.03Gd0.02Dy0.01Pr0.05Th0.08Pb0.01Ca0.05Si0.05P0.91O3.94. Their EPMA and LA-ICP-MS ages suggest at least two mineralization events, a first one between 1528 and 1523 Ma in the Barranquilla and San Jose sites, related to rapakivi granites outcropping along the Cuyarí River and the Tabaquen rapakivi granite near the Guainía River, both emplaced ~1545 Ma ago. The second mineralization event from 1390-1343 Ma recorded in the Espina-hills is in the age range of the Matraca and Danta rapakivi granites that crystalized between 1400 and 1340 Ma ago. These different anorogenic rapakivi granites were emplaced between 1550 and 1300 Ma into Mesoproterozoic basement rocks and were probably caused by intra-plate processes associated with mantle plume activity within the Columbia (Nuna) supercontinent.
Published: 2021
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44. Global homogenization of the structure and function in the soil microbiome of urban greenspaces

Author: Pankaj Trivedi, Javier Gutiérrez Illán, Sebastián Abades, Alberto L. Teixido, Thulani P. Makhalanyane, Hang-Wei Hu, Miguel Berdugo, Felipe Bastida, Blessing Sokoya, Xiaobing Zhou, Eli Zaady, Ana Maria Rey, Jun-Tao Wang, Brajesh K. Singh, Christina Siebe, Fernando D. Alfaro, José L. Moreno, Alexandra Rodríguez, Tine Grebenc, Jorge Durán, Manuel Delgado-Baquerizo, Tina Unuk Nahberger, Concha Cano-Díaz, Jianyong Wang, José Luis Blanco-Pastor, Jay Prakash Verma, Leho Tedersoo, Noah Fierer, Xin-Quan Zhou, David J. Eldridge, Ji-Zheng He, Adebola R. Bamigboye, César Plaza, Yu-Rong Liu, Gabriel Felipe Peñaloza-Bojacá, Ling Wang, Universidad Pablo de Olavide [Sevilla] (UPO), University of New South Wales [Sydney] (UNSW), Huazhong Agricultural University, University of Colorado [Boulder], Western Sydney University, University of Melbourne, Fujian Normal University [Fujian], Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Obafemi Awolowo University (OAU), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidad Rey Juan Carlos [Madrid] (URJC), Washington State University (WSU), University of Pretoria [South Africa], Universidad Autónoma de la Ciudad de México (UACM), Colorado State University [Fort Collins] (CSU), Gilat Research Center, Banaras Hindu University [Varanasi] (BHU), Northeast Normal University, Slovenian Forestry Institute, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Universidade Federal de Mato Grosso (UFMT), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Universidade de Coimbra [Coimbra], Xinjiang Institute of Ecology and Geography [Urumqi] (XIEG), Chinese Academy of Sciences [Beijing] (CAS), Universidad Mayor [Santiago de Chile], University of Tartu, Fundación BBVA, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), National Science Foundation (US), Estonian Science Foundation, Alexander von Humboldt Foundation, Australian Research Council, Fondo Nacional de Desarrollo Científico y Tecnológico (Chile), European Commission, Consejo Superior de Investigaciones Científicas (España), Fundación Séneca, National Research Foundation (South Africa), Slovenian Research Agency, Fundação para a Ciência e a Tecnologia (Portugal), Ministério da Ciência, Tecnologia e Ensino Superior (Portugal), and Science and Engineering Research Board (India)
Subjects: 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Nutrient cycle, funkcionalna pestrost, Environmental Studies, 030106 microbiology, Biodiversity, soil biodiversity, biodiverziteta tal, 03 medical and health sciences, 11. Sustainability, urban soils, Ecosystem, Microbiome, Research Articles, Multidisciplinary, Ecology, SciAdv r-articles, 15. Life on land, functional diversity, urbana tla, 030104 developmental biology, Geography, structural diversity, 13. Climate action, strukturna pestrost, Greenhouse gas, Soil water, Species richness, Urban ecosystem, udc:630*114, Research Article
Abstract: The structure and function of the soil microbiome of urban greenspaces remain largely undetermined. We conducted a global field survey in urban greenspaces and neighboring natural ecosystems across 56 cities from six continents, and found that urban soils are important hotspots for soil bacterial, protist and functional gene diversity, but support highly homogenized microbial communities worldwide. Urban greenspaces had a greater proportion of fast-growing bacteria, algae, amoebae, and fungal pathogens, but a lower proportion of ectomycorrhizal fungi than natural ecosystems. These urban ecosystems also showed higher proportions of genes associated with human pathogens, greenhouse gas emissions, faster nutrient cycling, and more intense abiotic stress than natural environments. City affluence, management practices, and climate were fundamental drivers of urban soil communities. Our work paves the way toward a more comprehensive global-scale perspective on urban greenspaces, which is integral to managing the health of these ecosystems and the well-being of human populations., M.D.-B. and this project were supported by a 2019 Leonardo Grant for Researchers and Cultural Creators, BBVA Foundation (URBANFUN) and by the BES grant agreement no. LRB17\1019 (MUSGONET). M.D.-B. is also supported by a Ramón y Cajal grant from the Spanish Ministry of Science and Innovation (RYC2018-025483-I). N.F. was supported by grants from the U.S. National Science Foundation (DEB1556090 and DEB1542653). L.T. acknowledges support from Norway-Baltic collaboration grant EMP442 and Estonian Science Foundation grant PRG632. B.K.S. acknowledges a research award by the Humboldt Foundation and funding from the Australian Research Council (DP190103714). F.A. is supported by ANID FONDECYT 11180538 and 1170995. S.A. is funded by ANID FONDECYT 1170995 and ANID ANILLO ACT192027. F.B. and J.L.M. acknowledge support from the Spanish Ministry and FEDER funds for the project AGL2017-85755-R, the i-LINK+ 2018 (LINKA20069) from CSIC, as well as funds from “Fundación Séneca” from Murcia Province (19896/GERM/15). C.P. acknowledges support from the Spanish State Plan for Scientific and Technical Research and Innovation (2013–2016), award reference AGL2016-75762-R (AEI/FEDER, UE). M.B. acknowledges support from a Juan de la Cierva Formación grant from the Spanish Ministry of Economy and Competitiveness (FJCI-2018-036520-I). T.P.M. would like to acknowledge contributions from the National Research Foundation of South Africa and cities involved in the South African survey. Slovenian coauthors were supported by the research project J4-1766 “Methodology approaches in genome-based diversity and ecological plasticity study of truffles from their natural distribution areas” and the Research Program in Forest Biology, Ecology, and Technology (P4-0107) of the Slovenian Research Agency. J.D. and A. Rey acknowledge support from the FCT (IF/00950/2014 and SFRH/BDP/108913/2015, respectively), as well as from the MCTES, FSE, UE, and the CFE (UIDB/04004/2020) research unit financed by FCT/MCTES through national funds (PIDDAC). J.P.V. acknowledges financial support from SERB (Science and Engineering Research Board) (EEQ/2017/000775) India. J.-Z.H. and H.-W.H. are financially supported by Australian Research Council (DP170101628).
Published: 2021
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45. How relevant are in vitro culture models for study of tick-pathogen interactions?

Author: Sara Moutailler, Lygia Decker, Cristiano Salata, Erich Zweygarth, Lesley Bell-Sakyi, Houssam Attoui, Universita degli Studi di Padova, Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Pretoria [South Africa], Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), University of Liverpool, École nationale vétérinaire d'Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, and École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], 030231 tropical medicine, 030106 microbiology, Review, Computational biology, virus, Tick, Organ culture, Microbiology, 03 medical and health sciences, Biosafety, organ culture, protozoa, 0302 clinical medicine, Ticks, tick-borne, In vivo, parasitic diseases, Animals, Humans, bacteria, Pathogen, tick cell lines, biology, Animal health, Transmission (medicine), Public Health, Environmental and Occupational Health, General Medicine, biology.organism_classification, bacterial infections and mycoses, In vitro, 3. Good health, Infectious Diseases, Tick-Borne Diseases, in vitro model, Parasitology
Abstract: Although tick-borne infectious diseases threaten human and animal health worldwide, with constantly increasing incidence, little knowledge is available regarding vector-pathogen interactions and pathogen transmission. In vivo laboratory study of these subjects using live, intact ticks is expensive, labor-intensive, and challenging from the points of view of biosafety and ethics. Several in vitro models have been developed, including over 70 continuous cell lines derived from multiple tick species and a variety of tick organ culture systems, facilitating many research activities. However, some limitations have to be considered in the translation of the results from the in vitro environment to the in vivo situation of live, intact ticks, and vertebrate hosts. In this review, we describe the available in vitro models and selected results from their application to the study of tick-borne viruses, bacteria, and protozoa, where possible comparing these results to studies in live, intact ticks. Finally, we highlight the strengths and weaknesses of in vitro tick culture models and their essential role in tick-borne pathogen research.
Published: 2021
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46. Nanomedicine in Oncocardiology: Contribution and Perspectives of Preclinical Studies

Author: Gabriel Silva Marques Borges, Eduardo Burgarelli Lages, Pierre Sicard, Lucas Antônio Miranda Ferreira, Sylvain Richard, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), BioCampus Montpellier (BCM), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Duchange, Nathalie, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and BioCampus (BCM)
Subjects: 0301 basic medicine, medicine.medical_specialty, Mini Review, [SDV]Life Sciences [q-bio], Population, nanoformulations, cardiotoxicity, Context (language use), photoacoustic, Scientific field, Cardiovascular Medicine, 030204 cardiovascular system & hematology, non-invasive imaging, 03 medical and health sciences, 0302 clinical medicine, Medicine, Diseases of the circulatory (Cardiovascular) system, education, Intensive care medicine, education.field_of_study, Potential impact, Cardiotoxicity, business.industry, small animals, Cancer, echography, medicine.disease, 3. Good health, [SDV] Life Sciences [q-bio], anticancer drugs, 030104 developmental biology, RC666-701, Nanomedicine, Nanocarriers, Cardiology and Cardiovascular Medicine, business
Abstract: International audience; Cancer and cardiovascular diseases are the leading causes of death and morbidity worldwide. Strikingly, cardiovascular disorders are more common and more severe in cancer patients than in the general population, increasing incidence rates. In this context, it is vital to consider the anticancer efficacy of a treatment and the devastating heart complications it could potentially cause. Oncocardiology has emerged as a promising medical and scientific field addressing these aspects from different angles. Interestingly, nanomedicine appears to have great promise in reducing the cardiotoxicity of anticancer drugs, maintaining or even enhancing their efficacy. Several studies have shown the benefits of nanocarriers, although with some flaws when considering the concept of oncocardiology. Herein, we discuss how preclinical studies should be designed as closely as possible to clinical protocols, considering various parameters intrinsic to the animal models used and the experimental protocols. The sex and age of the animals, the size and location of the tumors, the doses of the nanoformulations administered, and the acute vs. the long-term effects of treatments are essential aspects. We also discuss the perspectives offered by non-invasive imaging techniques to simultaneously assess both the anticancer effects of treatment and its potential impact on the heart. The overall objective is to accelerate the development and validation of nanoformulations through high-quality preclinical studies reproducing the clinical conditions.
Published: 2021
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47. A new genus and new species of macronyssid mite (Mesostigmata: Gamasina: Macronyssidae) from Brazilian caves including molecular data and key for genera occurring in Brazil

Author: Gomes-Almeida, Brenda, Pepato, Almir, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), and Tyumen State University
Subjects: 0106 biological sciences, Arthropoda, Aacriformes, Zoology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Acariformes, 01 natural sciences, Ectoparasitic mites, key, Cave, Genus, Arachnida, parasitic diseases, Animalia, Acari, Taxonomy, geography, geography.geographical_feature_category, biology, Seta, Biodiversity, biology.organism_classification, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 010602 entomology, Macronyssidae, Dermanyssoidea, Insect Science, Mesostigmata, Integrative taxonomy, Key (lock)
Abstract: A new genus and a new species of macronyssid mites is described based on material collected from caves in Minas Gerais state, Southeastern Brazil, and additional occurrences from caves in Rio de Janeiro (Southeast) and Pará (Eastern Amazon region). The new genus may be distinguished from other Macronyssidae genera by the combination of sternal shield with a distinct X-shaped area; sternal shield bearing three pairs of setae and two pairs of pores; sternal gland absent; anterior spur on coxa II lacking; adults with dorsal shield entire and j and J series complete; adults and protonymphs with setae J5 minute; males with strong-pores on dorsal shield and peritrema short extending from posterior margin of coxae II to the anterior margin of coxae IV. A key for genera occurring in Brazil is provided, as well sequences from the mitochondrial large subunit of ribosome (16S)., Acarologia, 61, 501-526
Published: 2021
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48. Distinct Roles of Hemocytes at Different Stages of Infection by Dengue and Zika Viruses in Aedes aegypti Mosquitoes

Author: Thiago H. J. F. Leite, Álvaro G. A. Ferreira, Jean-Luc Imler, João T. Marques, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Fiocruz Minas - René Rachou Research Center / Instituto René Rachou [Belo Horizonte, Brésil], Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Modèles Insectes de l'Immunité Innée (M3I), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ANR-11-EQPX-0022,I2MC,Insectarium pour l'Infectiologie Moléculaire et Cellulaire(2011), and ANR-10-LABX-0036,NetRNA,Network of regulatory RNAs across kingdoms and dynamical responses to biotic and abiotic stresses.(2010)
Subjects: 0301 basic medicine, Cellular immunity, viruses, Immunology, Mosquito Vectors, Aedes aegypti, cellular immunity, Biology, Dengue virus, medicine.disease_cause, Dengue fever, Zika virus, vector mosquitoes, 03 medical and health sciences, 0302 clinical medicine, Phagocytosis, Aedes, medicine, Animals, Immunology and Allergy, Vector (molecular biology), Original Research, Phagocytes, Innate immune system, dengue virus, fungi, macrophage-like cells, virus diseases, Midgut, biochemical phenomena, metabolism, and nutrition, RC581-607, biology.organism_classification, medicine.disease, Virology, 3. Good health, hemocytes, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, Female, Immunologic diseases. Allergy, 030217 neurology & neurosurgery
Abstract: Aedes aegypti mosquitoes are vectors for arboviruses of medical importance such as dengue (DENV) and Zika (ZIKV) viruses. Different innate immune pathways contribute to the control of arboviruses in the mosquito vector including RNA interference, Toll and Jak-STAT pathways. However, the role of cellular responses mediated by circulating macrophage-like cells known as hemocytes remains unclear. Here we show that hemocytes are recruited to the midgut of Ae. aegypti mosquitoes in response to DENV or ZIKV. Blockade of the phagocytic function of hemocytes using latex beads induced increased accumulation of hemocytes in the midgut and a reduction in virus infection levels in this organ. In contrast, inhibition of phagocytosis by hemocytes led to increased systemic dissemination and replication of DENV and ZIKV. Hence, our work reveals a dual role for hemocytes in Ae. aegypti mosquitoes, whereby phagocytosis is not required to control viral infection in the midgut but is essential to restrict systemic dissemination. Further understanding of the mechanism behind this duality could help the design of vector-based strategies to prevent transmission of arboviruses.
Published: 2021
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49. Revealing challenges in human mobility predictability

Author: Teixeira, Douglas, Carneiro Viana, Aline, Almeida, Jussara Marques, Alvim, Mário S., Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), inTeRnet BEyond the usual (TRiBE ), Inria Saclay - Ile de France, and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: entropy estimators, contextual information, [INFO.INFO-MC]Computer Science [cs]/Mobile Computing, predictability, human mobility
Abstract: International audience; Predicting mobility-related behavior is an important yet challenging task. On one hand, factors such as one's routine or preferences for a few favorite locations may help in predicting their mobility. On the other hand, several contextual factors, such as variations in individual preferences, weather, traffic, or even a person's social contacts, can affect mobility patterns and make its modeling significantly more challenging. A fundamental approach to study mobility-related behavior is to assess how predictable such behavior is, deriving theoretical limits on the accuracy that a prediction model can achieve given a specific dataset. This approach focuses on the inherent nature and fundamental patterns of human behavior captured in that dataset, filtering out factors that depend on the specificities of the prediction method adopted. However, the current state-of-the-art method to estimate predictability in human mobility suffers from two major limitations: low interpretability, and hardness to incorporate external factors which are known to help mobility prediction (i.e., contextual information). In this article, we revisit this state-of-the-art method, aiming at tackling these limitations. Specifically, we conduct a thorough analysis of how this widely used method works by looking into two different metrics that are easier to understand and, at the same time, capture reasonably well the effects of the original technique. We evaluate these metrics in the context of two different mobility prediction tasks, notably next-cell and next-place prediction, which have different degrees of difficulty. Additionally, we propose alternative strategies to incorporate different types of contextual information into the existing technique. Our evaluation of these strategies offer quantitative measures of the impact of adding context to the predictability estimate, revealing the challenges associated with doing so in practical scenarios.
Published: 2021
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50. Online Scheduling with Time Windows of Agricultural Robots

Author: Mateus Vilela Souza, Bruno Bachelet, Thiago Noronha, Loïc Yon, Christophe Duhamel, Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Clermont Auvergne (UCA)-Université Clermont Auvergne (UCA), Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU), Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)-Institut national polytechnique Clermont Auvergne (INP Clermont Auvergne), Université Le Havre Normandie (ULH), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA), and Bachelet, Bruno
Subjects: [INFO.INFO-RO] Computer Science [cs]/Operations Research [cs.RO], energy management, time window, online scheduling, [INFO.INFO-RO]Computer Science [cs]/Operations Research [cs.RO], autonomous robot
Abstract: International audience; The advances in agricultural robotics bring autonomous robots to work in farms. Farm Management Information Systems (FMIS) are sophisticated and complex systems to support production management in farms. They need to integrate software for the scheduling of a fleet of such robots. As agricultural systems are by nature subject to unpredictable events, it seems necessary to provide a solution for online scheduling. After the description of the problem, which is to schedule tasks for the robots in order to fulfill demands for agricultural activities, we propose an online approach based on solving a Mixed Integer Linear Programming (MILP) problem at each step, meaning each time the FMIS is requested to adjust or complete the schedule.
Published: 2021

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