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1. A counterexample to a Brenti-Carnevale conjecture

Author

Chapelier-Laget, Nathan and Fromentin, Jean

Subjects
Mathematics - Combinatorics
Abstract

Recently, F. Brenti put a preprint on the arXiv with several interesting open problems on Coxeter groups and unimodality. In this note, we refute one of these conjectures with a counterexample and provide supporting data related to it. This work serves as an initial step toward further exploration of the topic.

Published
2024

2. Fast construction of self-avoiding polygons and efficient evaluation of closed walk fractions on the square lattice

Author

Fromentin, Jean, Giscard, Pierre-Louis, and Hosten, Yohan

Subjects
Mathematics - Combinatorics
Abstract

We build upon a recent theoretical breakthrough by employing novel algorithms to accurately compute the fractions $F_p$ of all closed walks on the infinite square lattice whose the last erased loop corresponds is any one of the $762, 207, 869, 373$ self-avoiding polygons $p$ of length at most 38. Prior to this work, only 6 values of $F_p$ had been calculated in the literature. The main computational engine uses efficient algorithms for both the construction of self-avoiding polygons and the precise evaluation of the lattice Green's function. Based on our results, we propose two conjectures: one regarding the asymptotic behavior of sums of $F_p$, and another concerning the value of $F_p$ when $p$ is a large square. We provide strong theoretical arguments supporting the second conjecture. Furthermore, the algorithms we introduce are not limited to the square lattice and can, in principle, be extended to any vertex-transitive infinite lattice. In establishing this extension, we resolve two open questions related to the triangular lattice Green's function.

Published
2024

3. A verification of Wilf's conjecture up to genus 100

Author

Delgado, Manuel, Eliahou, Shalom, and Fromentin, Jean

Subjects
Mathematics - Group Theory
Abstract

For a numerical semigroup $S \subseteq \mathbb{N}$, let $m,e,c,g$ denote its multiplicity, embedding dimension, conductor and genus, respectively. Wilf's conjecture (1978) states that $e(c-g) \ge c$. As of 2023, Wilf's conjecture has been verified by computer up to genus $g \le 66$. In this paper, we extend the verification of Wilf's conjecture up to genus $g \le 100$. This is achieved by combining three main ingredients: (1) a theorem in 2020 settling Wilf's conjecture in the case $e \ge m/3$, (2) an efficient trimming of the tree $\mathcal{T}$ of numerical groups identifying and cutting out irrelevant subtrees, and (3) the implementation of a fast parallelized algorithm to construct the tree $\mathcal{T}$ up to a given genus. We further push the verification of Wilf's conjecture up to genus $120$ in the particular case where $m$ divides $c$. Finally, we unlock three previously unknown values of the number $n_g$ of numerical semigroups of genus $g$, namely for $g=73,74,75$.

Published
2023

4. A reaction mechanism for oxygen plasmas

Author

Dias, Tiago C, Fromentin, Chloé, Alves, Luís L, Tejero-del-Caz, Antonio, Silva, Tiago, and Guerra, Vasco

Subjects
Physics - Plasma Physics
Abstract

This work presents a reaction mechanism for oxygen plasmas, i.e. a set of reactions and corresponding rate coefficients that are validated against benchmark experiments. The kinetic scheme is validated in a DC glow discharge for gas pressures of 0.2-10 Torr and currents of 10-40 mA, using the 0D LisbOn KInetics (LoKI) simulation tool and available experimental data. The comparison comprises not only the densities of the main species in the discharge - $\mathrm{O_2(X^3\Sigma_g^-)}$, $\mathrm{O_2(a^1\Delta_g)}$, $\mathrm{O_2(b^1\Sigma_g^+)}$ and $\mathrm{O(^3P)}$ - but also the self-consistent calculation of the reduced electric field and the gas temperature. The main processes involved in the creation and destruction of these species are identified. Moreover, the results show that the oxygen atoms play a dominant role in gas heating, via recombination at the wall and quenching of $\mathrm{O_2(X^3\Sigma_g^-,v)}$ vibrations and $\mathrm{O_2}$ electronically-excited states. It is argued that the development and validation of kinetic schemes for plasma chemistry should adopt a paradigm based on the comparison against standard validation tests, as it is done in electron swarm validation of cross sections.

Published
2023

6. Validation of non-equilibrium kinetics in CO2-N2 plasmas

Author

Fromentin, C., Silva, T., Dias, T. C., Baratte, E., Guaitella, O., and Guerra, V.

Subjects
Physics - Plasma Physics
Abstract

This work explores the effect of N2 addition on CO2 dissociation and on the vibrational kinetics of CO2 and CO under various non-equilibrium plasma conditions. A self-consistent kinetic model, previously validated for pure CO2 and CO2-O2 discharges, is further extended by adding the kinetics of N2. The vibrational kinetics considered include levels up to v = 10 for CO, v = 59 for N2 and up to v1 = 2 and v2 = v3 = 5, respectively for the symmetric stretch, bending and asymmetric stretch modes of CO2, and account for electron-impact excitation and de-excitation (e-V), vibration-to-translation (V-T) and vibration-to-vibration energy exchange (V-V) processes. The kinetic scheme is validated by comparing the model predictions with recent experimental data measured in a DC glow discharge operating in pure CO2 and in CO2-N2 mixtures, at pressures in the range 0.6 - 4 Torr (80.00 - 533.33 Pa) and a current of 50 mA. The experimental results show a higher vibrational temperature of the different modes of CO2 and CO and an increased dissociation fraction of CO2, that can reach values as high as 70%, when N2 is added to the plasma. On the one hand, the simulations suggest that the former effect is the result of the CO2-N2 and CO-N2 V-V transfers and the reduction of quenching due to the decrease of atomic oxygen concentration; on the other hand, the dilution of CO2 and dissociation products, CO and O2, reduces the importance of back reactions and contributes to the higher CO2 dissociation fraction with increased N2 content in the mixture, while the N2(B3Pg) electronically excited state further enhances the CO2 dissociation.

Published
2023
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9. Benchmarking between fluid and global models for low-pressure oxygen DC glow discharges

Author

Viegas, Pedro, Dias, Tiago Cunha, Fromentin, Chloé, Chukalovsky, Alexander, Mankelevich, Yuri, Proshina, Olga, Rakhimova, Tatyana, Guerra, Vasco, and Voloshin, Dmitry

Subjects
Physics - Plasma Physics, Physics - Computational Physics
Abstract

This work focuses on the benchmarking between a zero-dimensional (0D) global model (LoKI) and a one-dimensional (1D) radial fluid model for the positive column of oxygen DC glow discharges in a tube of 1 cm inner radius at pressures between 0.5 Torr and 10 Torr. The data used in the two models are the same, so that the difference between the models is reduced to dimensionality. A good agreement is found between the two models on the main discharge parameters, with relative differences below 5%. The agreement on species average number densities, charged and neutral, is slightly worse, with relative differences increasing with pressure from 11% at 0.5 Torr to 57% at 10 Torr. The success of the 0D global model in describing these plasmas through volume averaged quantities decreases with pressure, due to pressure-driven narrowing of radial profiles. Hence, in the studied conditions, we recommend the use of volume-averaged models only in the pressure range up to 10 Torr., Comment: 31 pages, 11 figures

Published
2022
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10. Study of vibrational kinetics of CO2 and CO in CO2-O2 plasmas under non-equilibrium conditions

Author

Fromentin, C., Silva, T., Dias, T. C., Morillo-Candas, A. S., Biondo, O., Guaitella, O., and Guerra, V.

Subjects
Physics - Plasma Physics
Abstract

This work explores the effect of O2 addition on CO2 dissociation and on the vibrational kinetics of CO2 and CO under various non-equilibrium plasma conditions. A self-consistent model, previously validated for pure CO2 discharges, is further extended by adding the vibrational kinetics of CO, including electron impact excitation and de-excitation (e-V), vibration-to-translation relaxation (V-T) and vibration-to-vibration energy exchange (V-V) processes. The vibrational kinetics considered include levels up to v = 10 for CO and up to v1=2 and v2=v3=5, respectively for the symmetric stretch, bending and asymmetric stretch modes of CO2, and accounts for e-V, V-T in collisions between CO, CO2 and O2 molecules and O atoms and V-V processes involving all possible transfers involving CO2 and CO molecules. The kinetic scheme is validated by comparing the model predictions with recent experimental data measured in a DC glow discharge, operating at pressures in the range 0.4 - 5 Torr (53.33 - 666.66 Pa). The experimental results show a lower vibrational temperature of the different modes of CO2 and a decreased dissociation fraction of CO2 when O2 is added to the plasma but an increase of the vibrational temperature of CO. On the one hand, the simulations suggest that the former effect is the result of the stronger V-T energy-transfer collisions with O atoms which leads to an increase of the relaxation of the CO2 vibrational modes; On the other hand, the back reactions with O2 contribute to the lower CO2 dissociation fraction with increased O2 content in the mixture., Comment: 34 pages 15 figures

Published
2022
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16. Realizable cycle structures in digraphs

Author

Fromentin, J., Giscard, P. -L, and Karaboghossian, T.

Subjects
Mathematics - Combinatorics, Mathematics - Group Theory
Abstract

Simple cycles on a digraph form a trace monoid under the rule that two such cycles commute if and only if they are vertex disjoint. This rule describes the spatial configuration of simple cycles on the digraph. Cartier and Foata have showed that all combinatorial properties of closed walks are dictated by this trace monoid. We find that most graph properties can be lost while maintaining the monoidal structure of simple cycles and thus cannot be inferred from it, including vertex-transitivity, regularity, planarity, Hamiltonicity, graph spectra, degree distribution and more. Conversely we find that even allowing for multidigraphs, many configurations of simple cycles are not possible at all. The problem of determining whether a given configuration of simple cycles is realizable is highly non-trivial. We show at least that it is decidable and equivalent to the existence of integer solutions to systems of polynomial equations.

Published
2021
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17. The bacterial species profiles of the lingual and salivary microbiota differ with basic tastes sensitivity in human

Author

Hélène Licandro, Caroline Truntzer, Sébastien Fromentin, Christian Morabito, Benoit Quinquis, Nicolas Pons, Christophe Martin, Hervé M. Blottière, and Eric Neyraud

Subjects
Medicine, Science
Abstract

Abstract Taste perception is crucial and impairments, which can be linked to pathologies, can lead to eating disorders. It is triggered by taste compounds stimulating receptors located on the tongue. However, the tongue is covered by a film containing saliva and microorganisms suspected to modulate the taste receptor environment. The present study aimed to elucidate the links between taste sensitivity (sweetness, sourness, bitterness, saltiness, umami) and the salivary as well as the tongue microbiota using shotgun metagenomics. 109 bacterial species were correlated with at least one taste. Interestingly, when a species was correlated with at least two tastes, the correlations were unidirectional, indicating a putative global implication. Some Streptococcus, SR1 and Rickenellaceae species correlated with five tastes. When comparing both ecosystems, saliva appears to be a better taste predictor than tongue. This work shows the implication of the oral microbiota in taste and exhibits specificities depending on the ecosystem considered.

Published
2023
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19. The HIV-1 proviral landscape reveals Nef contributes to HIV-1 persistence in effector memory CD4+ T-cells

Author

Duette, Gabriel, Hiener, Bonnie, Morgan, Hannah, Mazur, Fernando G, Mathivanan, Vennila, Horsburgh, Bethany A, Fisher, Katie, Tong, Orion, Lee, Eunok, Ahn, Haelee, Shaik, Ansari, Fromentin, Rémi, Hoh, Rebecca, Bacchus-Souffan, Charline, Nasr, Najla, Cunningham, Anthony, Hunt, Peter W, Chomont, Nicolas, Turville, Stuart G, Deeks, Steven G, Kelleher, Anthony D, Schlub, Timothy E, and Palmer, Sarah

Subjects
HIV/AIDS, Infectious Diseases, Clinical Research, Aetiology, 2.1 Biological and endogenous factors, Infection, CD4-Positive T-Lymphocytes, DNA, Viral, HIV Infections, HIV-1, Humans, Proviruses, Viral Load, nef Gene Products, Human Immunodeficiency Virus, AIDS/HIV, Adaptive immunity, Infectious disease, Molecular genetics, T cells, Medical and Health Sciences, Immunology
Abstract

Despite long-term antiretroviral therapy (ART), HIV-1 persists within a reservoir of CD4+ T cells that contribute to viral rebound if treatment is interrupted. Identifying the cellular populations that contribute to the HIV-1 reservoir and understanding the mechanisms of viral persistence are necessary to achieve an effective cure. In this regard, through Full-Length Individual Proviral Sequencing, we observed that the HIV-1 proviral landscape was different and changed with time on ART across naive and memory CD4+ T cell subsets isolated from 24 participants. We found that the proportion of genetically intact HIV-1 proviruses was higher and persisted over time in effector memory CD4+ T cells when compared with naive, central, and transitional memory CD4+ T cells. Interestingly, we found that escape mutations remained stable over time within effector memory T cells during therapy. Finally, we provided evidence that Nef plays a role in the persistence of genetically intact HIV-1. These findings posit effector memory T cells as a key component of the HIV-1 reservoir and suggest Nef as an attractive therapeutic target.

Published
2022

20. Is the Syracuse falling time bounded by 12?

Author

Eliahou, Shalom, Fromentin, Jean, and Simonetto, Rénald

Subjects
Mathematics - Number Theory, 11A25
Abstract

Let $T \colon \mathbb{N} \to \mathbb{N}$ denote the $3x+1$ function, where $T(n)=n/2$ if $n$ is even, $T(n)=(3n+1)/2$ if $n$ is odd. As an accelerated version of $T$, we define a jump at $n \ge 1$ by jp$(n) = T^{(\ell)}(n)$, where $\ell$ is the number of digits of $n$ in base 2. We present computational and heuristic evidence leading to surprising conjectures. The boldest one, inspired by the study of $2^{\ell}-1$ for $\ell \le 500000$, states that for any $n \ge 2^{500}$, at most four jumps starting from $n$ are needed to fall below $n$, a strong form of the Collatz conjecture., Comment: 17 pages, 3 figures. Augmented version, with updated conjectures based on greatly extended computations

Published
2021

21. Pembrolizumab induces HIV latency reversal in people living with HIV and cancer on antiretroviral therapy

Author

Uldrick, Thomas S, Adams, Scott V, Fromentin, Remi, Roche, Michael, Fling, Steven P, Gonçalves, Priscila H, Lurain, Kathryn, Ramaswami, Ramya, Wang, Chia-Ching Jackie, Gorelick, Robert J, Welker, Jorden L, O'Donoghue, Liz, Choudhary, Harleen, Lifson, Jeffrey D, Rasmussen, Thomas A, Rhodes, Ajantha, Tumpach, Carolin, Yarchoan, Robert, Maldarelli, Frank, Cheever, Martin A, Sékaly, Rafick, Chomont, Nicolas, Deeks, Steven G, and Lewin, Sharon R

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Infectious Diseases, Genetics, Cancer, HIV/AIDS, 2.2 Factors relating to the physical environment, Aetiology, Infection, Antibodies, Monoclonal, Humanized, CD4-Positive T-Lymphocytes, HIV Infections, HIV-1, Humans, Neoplasms, Phylogeny, Programmed Cell Death 1 Receptor, RNA, Virus Latency, Biological Sciences, Medical and Health Sciences, Medical biotechnology, Biomedical engineering
Abstract

In people living with HIV (PLWH) on antiretroviral therapy (ART), virus persists in a latent form where there is minimal transcription or protein expression. Latently infected cells are a major barrier to curing HIV. Increasing HIV transcription and viral production in latently infected cells could facilitate immune recognition and reduce the pool of infected cells that persist on ART. Given that programmed cell death protein 1 (PD-1) expressing CD4+ T cells are preferentially infected with HIV in PLWH on ART, we aimed to determine whether administration of antibodies targeting PD-1 would reverse HIV latency in vivo. We therefore evaluated the impact of intravenous administration of pembrolizumab every 3 weeks on HIV latency in 32 PLWH and cancer on ART. After the first infusion of anti-PD-1, we observed a median 1.32-fold increase in unspliced HIV RNA and 1.61-fold increase in unspliced RNA:DNA ratio in sorted blood CD4+ T cells compared to baseline. We also observed a 1.65-fold increase in plasma HIV RNA. The frequency of CD4+ T cells with inducible virus evaluated using the tat/rev limiting dilution assay was higher after 6 cycles compared to baseline. Phylogenetic analyses of HIV env sequences in a participant who developed low concentrations of HIV viremia after 6 cycles of pembrolizumab did not demonstrate clonal expansion of HIV-infected cells. These data are consistent with anti-PD-1 being able to reverse HIV latency in vivo and support the rationale for combining anti-PD-1 with other interventions to reduce the HIV reservoir.

Published
2022

23. Rivaroxaban vs Vitamin K Antagonist in Patients With Atrial Fibrillation and Advanced Chronic Kidney Disease

Author

Laetitia, Albano, Catherine, Albert, Joachim, Alexandre, Ayham, Al-Zoebi, Cedric, Annweiler, Johann, Auer, Sanjeet, Balgobin, Joachim, Beige, Ahmed, Berami, Jean-Baptiste, Berneau, Patrick, Biggar, Ralf, Birkemeyer, Christina, Bondke, Renate, Bonin-Schnabel, Hendrik, Bonnemeier, Marc, Bouiller, Anne-Sophie, Boureau, Johannes, Brachmann, Jörg, Brosche, Sebastien, Caudmont, Guillaume, Cayla, Vianney, Charpy, Joel, Constans, Jean-Baptiste, Dally, Guillaume, De Geeter, Fédéric, Debelle, Eric, Decoulx, Nicolas, Delarche, Georg, Delle Karth, Pascal, Delsart, Michael, Derndorfer, Laurent, Desprets, Jean-Guillaume, Dillinger, Camille, Dubart, Katrin, Eberhard, Sabine, Eichinger-Hasenauer, Volker, Eissing, Christiane, Erley, Jean-Baptiste, Esteve, Emile, Ferrari, Virginie, Fossey-Diaz, Stéphane, Fromentin, Karim, Gallouj, Estelle, Gandjbakhch, Anne-Sophie, Garnier, Laure, Gilis, Bertrand, Gondouin, Franziska, Grundmann, Isabelle, Gueffet, Sebastian, Haaß, Didier, Haguenhauer, Thierry, Hannedouche, Georg, Häusler Karl, Gerd-Ulrich, Heinz, Philipp, Herold, Klaus, Hertting, Etienne, Hoffer, Joachim, Hoyer, Burkhard, Hügl, Sybille, Jänsch, Georges, Jean-Louis, Michael, Jeserich, Werner, Jung, Samuel, Kassis, Bernd-Thomas, Kellner, Marcus, Ketteler, Thomas, Kielstein Jan, René, Koning, Fabian, Krämer, Jean-Marie, Krzesinski, Ulrich, Lammers, Jean-Marie, Lefebvre, Eric, Legrand, Matthias, Leschke, Bernhard-Paul, Lodde, Christian, Maalouli, Christian, Mahnkopf, Sebastien, Mailliez, Jacques, Mansourati, Eloi, Marijon, Christian, Meyer, Detlev, Moll, Gilles, Montalescot, Serge, Motte, Vincent, Mouquet, Krassen, Nedeltchev, Anna, Neykova, Jörg, Nothroff, Raphael, Poyet, Roland, Prondzinsky, Ursula, Rauch-Kröhnert, Frank, Richard, Werner, Rieker, Andrea, Rocco, Thomas, Rostock, Daniel, Scherr, Axel, Schlitt, Hans, Schmidt-Gürtler, Norbert, Schön, Johannes, Schwab, Carsten, Schwencke, Peter, Schwimmbeck, G, Schwinger Robert H., Andreas, Schwittay, Igor, Sibon, Ulrike, Spengler, Alexander, Stadelmann, Clemens, Steinwender, Reinhard, Stöhring, Jean-Claude, Stolear, Guillaume, Taldir, Jean-Michel, Tartière, Serge, Treille, Pierre, Tremolieres, Zead, Tubail, Xavier, Warling, Morgane, Wetzstein, Adrian, Zaman, Claudia, Zemmrich, Kreutz, Reinhold, Deray, Gilbert, Floege, Jürgen, Gwechenberger, Marianne, Hahn, Kai, Luft, Andreas R., Persson, Pontus, Axthelm, Christoph, Beer, Juerg Hans, Bergler-Klein, Jutta, Lellouche, Nicolas, Taggeselle, Jens, Coleman, Craig I., and Beyer-Westendorf, Jan

Published
2024
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24. Experiments on growth series of braid groups

Author

Fromentin, Jean

Subjects
Mathematics - Combinatorics, Mathematics - Group Theory
Abstract

We introduce an algorithmic framework to investigate spherical and geodesic growth series of braid groups relatively to the Artin's or Birman-Ko-Lee's generators. We present our experimentations in the case of three and four strands and conjecture rational expressions for the spherical growth series with respect to the Birman-Ko-Lee's generators.

Published
2020

29. Meta-analysis of CO2 conversion, energy efficiency, and other performance data of plasma-catalysis reactors with the open access PIONEER database

Author

Salden, Antoine, Budde, Maik, Garcia-Soto, Carolina A., Biondo, Omar, Barauna, Jairo, Faedda, Marzia, Musig, Beatrice, Fromentin, Chloé, Nguyen-Quang, Minh, Philpott, Harry, Hasrack, Golshid, Aceto, Domenico, Cai, Yuxiang, Jury, Federico Azzolina, Bogaerts, Annemie, Da Costa, Patrick, Engeln, Richard, Gálvez, María Elena, Gans, Timo, Garcia, Tomas, Guerra, Vasco, Henriques, Carlos, Motak, Monika, Navarro, Maria Victoria, Parvulescu, Vasile I., Van Rooij, Gerard, Samojeden, Bogdan, Sobota, Ana, Tosi, Paolo, Tu, Xin, and Guaitella, Olivier

Published
2023
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34. Gapsets of small multiplicity

Author

Eliahou, Shalom and Fromentin, Jean

Subjects
Mathematics - Group Theory
Abstract

A gapset is the complement of a numerical semigroup in N. In this paper, we characterize all gapsets of multiplicity m $\le$ 4. As a corollary, we provide a new simpler proof that the number of gapsets of genus g and fixed multiplicity m $\le$ 4 is a nondecreasing function of g., Comment: arXiv admin note: text overlap with arXiv:1811.10295

Published
2019

35. High levels of genetically intact HIV in HLA-DR+ memory T cells indicates their value for reservoir studies.

Author

Horsburgh, Bethany A, Lee, Eunok, Hiener, Bonnie, Eden, John-Sebastian, Schlub, Timothy E, von Stockenstrom, Susanne, Odevall, Lina, Milush, Jeffrey M, Liegler, Teri, Sinclair, Elizabeth, Hoh, Rebecca, Boritz, Eli A, Douek, Daniel C, Fromentin, Remi, Chomont, Nicolas, Deeks, Steven G, Hecht, Frederick M, and Palmer, Sarah

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Immunization, Sexually Transmitted Infections, Infectious Diseases, HIV/AIDS, Genetics, Human Genome, 2.1 Biological and endogenous factors, Infection, Adult, Anti-HIV Agents, CD4-Positive T-Lymphocytes, DNA, Viral, Female, HIV Infections, HIV-1, HLA-DR Antigens, Humans, Immunologic Memory, Male, Sequence Analysis, DNA, Sequence Analysis, RNA, full-length sequencing, genetically intact HIV, HIV reservoir, HLA-DR plus memory cells, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Virology, Biomedical and clinical sciences, Health sciences
Abstract

ObjectiveThe contribution of HLA-DR+ memory CD4 T cells to the HIV reservoir during prolonged antiretroviral therapy is unclear as these cells are commonly excluded when assessing for replication-competent HIV. To address this issue, we examined the distribution of genetically intact HIV DNA within HLA-DR- and HLA-DR+ memory CD4 T cells and the RNA transcriptional profile of these cells during antiretroviral therapy.Design/methodsFull-length DNA sequencing was used to examine the HIV DNA landscape within HLA-DR+ and HLA-DR- memory CD4 T cells. RNA quantification and sequencing was used to interrogate the relationship between HLA-DR status and HIV RNA transcription.ResultsHLA-DR+ CD4 T cells contained a high frequency of genetically intact HIV genomes, contributing over half of the genetically intact viral sequences to the reservoir. Expansions of genetically identical sequences were identified in all T-cell subsets, indicating that cellular proliferation maintains genetically intact and defective viral DNA during therapy. Intracellular HIV RNA levels in HLA-DR+ and HLA-DR- T cells were not statistically different by either long terminal repeat quantitative PCR quantification or single-genome RNA sequencing of the p6-RT region.ConclusionThe high proportion of intact viral DNA sequences in the proliferative HLA-DR+ subset suggests they are critical in maintaining HIV infection during effective therapy. As such, these cells should be included in any immune intervention targeting HIV during effective therapy.

Published
2020

36. Human Immunodeficiency Virus (HIV)–Infected CCR6+ Rectal CD4+ T Cells and HIV Persistence On Antiretroviral Therapy

Author

Anderson, Jenny L, Khoury, Gabriela, Fromentin, Rémi, Solomon, Ajantha, Chomont, Nicolas, Sinclair, Elizabeth, Milush, Jeffrey M, Hartogensis, Wendy, Bacchetti, Peter, Roche, Michael, Tumpach, Carolin, Gartner, Matthew, Pitman, Matthew C, Epling, Christine Lorrie, Hoh, Rebecca, Hecht, Frederick M, Somsouk, Ma, Cameron, Paul U, Deeks, Steven G, and Lewin, Sharon R

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Infectious Diseases, HIV/AIDS, Clinical Research, Sexually Transmitted Infections, Infection, Anti-Retroviral Agents, CD4-Positive T-Lymphocytes, Chemokines, DNA, Viral, Female, HIV, HIV Infections, Humans, Lymph Nodes, Male, Middle Aged, Polymerase Chain Reaction, RNA, Viral, Receptors, CCR6, Rectum, HIV reservoir, latency, persistence, chemokine receptor, CCR6, CXCR3, chemokines, rectal tissue, lymph node, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundIdentifying where human immunodeficiency virus (HIV) persists in people living with HIV and receiving antiretroviral therapy is critical to develop cure strategies. We assessed the relationship of HIV persistence to expression of chemokine receptors and their chemokines in blood (n = 48) and in rectal (n = 20) and lymph node (LN; n = 8) tissue collected from people living with HIV who were receiving suppressive antiretroviral therapy.MethodsCell-associated integrated HIV DNA, unspliced HIV RNA, and chemokine messenger RNA were quantified by quantitative polymerase chain reaction. Chemokine receptor expression on CD4+ T cells was determined using flow cytometry.ResultsIntegrated HIV DNA levels in CD4+ T cells, CCR6+CXCR3+ memory CD4+ T-cell frequency, and CCL20 expression (ligand for CCR6) were highest in rectal tissue, where HIV-infected CCR6+ T cells accounted for nearly all infected cells (median, 89.7%). Conversely in LN tissue, CCR6+ T cells were infrequent, and there was a statistically significant association of cell-associated HIV DNA and RNA with CCL19, CCL21, and CXCL13 chemokines.ConclusionsHIV-infected CCR6+ CD4+ T cells accounted for the majority of infected cells in rectal tissue. The different relationships between HIV persistence and T-cell subsets and chemokines in rectal and LN tissue suggest that different tissue-specific strategies may be required to eliminate HIV persistence and that assessment of biomarkers for HIV persistence may not be generalizable between blood and other tissues.

Published
2020

37. Alteration of Gut Microbiome in Patients With Schizophrenia Indicates Links Between Bacterial Tyrosine Biosynthesis and Cognitive Dysfunction

Author

Florence Thirion, Helene Speyer, Tue Haldor Hansen, Trine Nielsen, Yong Fan, Emmanuelle Le Chatelier, Sébastien Fromentin, Magali Berland, Florian Plaza Oñate, Nicolas Pons, Nathalie Galleron, Florence Levenez, Lajos Markó, Till Birkner, Torben Jørgensen, Sofia K. Forslund, Henrik Vestergaard, Torben Hansen, Merete Nordentoft, Ole Mors, Michael E. Benros, Oluf Pedersen, and Stanislav D. Ehrlich

Subjects
Case-control study, Cognition, Gut microbiome, Metagenomics, Schizophrenia, Tyrosine biosynthesis, Psychiatry, RC435-571
Abstract

Background: Schizophrenia (SCZ) is a heterogeneous neuropsychiatric disorder for which current treatment has insufficient efficacy and severe adverse effects. The modifiable gut microbiome might be a potential target for intervention to improve neurobiological functions through the gut-microbiome-brain axis. Methods: In this case-control study, gut microbiota of 132 patients with SCZ and increased waist circumference were compared with gut microbiota of two age- and sex-matched control groups, composed of 132 healthy individuals and 132 individuals with metabolic syndrome. Shotgun sequencing was used to characterize fecal samples at the taxonomic and functional levels. Cognition of the patients with SCZ was evaluated using the Brief Assessment of Cognition instrument. Results: SCZ gut microbiota differed significantly from those of healthy control subjects and individuals with metabolic syndrome in terms of richness and global composition. SCZ gut microbiota were notably enriched in Flavonifractor plautii, Collinsella aerofaciens, Bilophila wadsworthia, and Sellimonas intestinalis, while depleted in Faecalibacterium prausnitzii, Ruminococcus lactaris, Ruminococcus bicirculans, and Veillonella rogosae. Functional potential of the gut microbiota accounted for 11% of cognition variability. In particular, the bacterial functional module for synthesizing tyrosine, a precursor for dopamine, was in SCZ cases positively associated with cognitive score (ρ = 0.34, q ≤ .1). Conclusions: Overall, this study shows that the gut microbiome of patients with SCZ differs greatly from that of healthy control subjects or individuals with metabolic syndrome. Cognitive function of patients with SCZ is associated with the potential for gut bacterial biosynthesis of tyrosine, a precursor for dopamine, suggesting that gut microbiota might be an intervention target for alleviation of cognitive dysfunction in SCZ.

Published
2023
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38. Phenotypic characterization of single CD4+ T cells harboring genetically intact and inducible HIV genomes

Author

Caroline Dufour, Corentin Richard, Marion Pardons, Marta Massanella, Antoine Ackaoui, Ben Murrell, Bertrand Routy, Réjean Thomas, Jean-Pierre Routy, Rémi Fromentin, and Nicolas Chomont

Subjects
Science
Abstract

Some HIV-infected cells persist during antiretroviral therapies (ART) but their phenotype is less clear. Dufour et al. show that HIV-infected cells that persist in people receiving ART are phenotypically diverse and that CD4+ T cells expressing the integrin VLA-4 are highly enriched in replication-competent HIV.

Published
2023
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40. Microbially Produced Imidazole Propionate Is Associated With Heart Failure and Mortality

Author

Alves, Renato, Amouyal, Chloe, Andersson Galijatovic, Ehm Astrid, Andreelli, Fabrizio, Barthelemy, Olivier, Bastard, Jean-Philippe, Batisse, Jean-Paul, Berland, Magalie, Bittar, Randa, Blüher, Matthias, Bork, Peer, Bourron, Olivier, Camus, Mickael, Cassuto, Dominique, Ciangura, Cecile, Coelho, Luis Pedro, Collet, Jean-Philippe, Dumas, Marc-Emmanuel, Ehrlich, S. Dusko, Engelbrechtsen, Line, Fezeu, Leopold, Forslund, Sofia, Fromentin, Sebastien, Galan, Pilar, Giral, Philippe, Gøtze, Jens Peter, Hansen, Torben, Hansen, Tue H., Hartemann, Agnes, Hartmann, Bolette, Hercberg, Serge, Holmes, Bridget, Holst, Jens Juul, Hornbak, Malene, Hoyles, Lesley, Hulot, Jean-Sebastien, Jaqueminet, Sophie, Kerneis, Mathieu, Khemis, Jean, Kozlowski, Ruby, Pedersen, Helle Krogh, Kuhn, Michael, Mannerås-Holm, Louise, Marko, Lajos, Martinez-Gili Robin Massey, Laura, Maziers, Nicolas, Medina-Stamminger, Jonathan, Moitinho-Silva, Lucas, Montalescot, Gilles, Moutel, Sandrine, Neves, Ana Luisa, Olanipekun, Michael, Oppert, Jean-Michel, Poitou, Christine, Pousset, Francoise, Pouzoulet, Laurence, Rouault, Christine, Silvain, Johanne, Vestergaard, Henrik, Molinaro, Antonio, Nemet, Ina, Bel Lassen, Pierre, Chakaroun, Rima, Nielsen, Trine, Aron-Wisnewsky, Judith, Bergh, Per-Olof, Li, Lin, Henricsson, Marcus, Køber, Lars, Isnard, Richard, Helft, Gerard, Stumvoll, Michael, Pedersen, Oluf, Smith, J. Gustav, Tang, W.H. Wilson, Clément, Karine, Hazen, Stanley L., and Bäckhed, Fredrik

Published
2023
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41. Status, challenges and pathways to the sustainable use of wild species

Author

Fromentin, Jean-Marc, Emery, Marla R., Donaldson, John, Balachander, Ganesan, Barron, Elizabeth S., Chaudhary, Ram P., Danner, Marie-Claire, Gasalla, Maria A., Hallosserie, Agnès, Halmy, Marwa, Hicks, Christina, Kieling, Daniel, Park, Mi Sun, Parlee, Brenda, Rice, Jack, Ticktin, Tamara, and Tittensor, Derek

Published
2023
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47. Alteration of Gut Microbiome in Patients With Schizophrenia Indicates Links Between Bacterial Tyrosine Biosynthesis and Cognitive Dysfunction

Author

Thirion, Florence, Speyer, Helene, Hansen, Tue Haldor, Nielsen, Trine, Fan, Yong, Le Chatelier, Emmanuelle, Fromentin, Sébastien, Berland, Magali, Plaza Oñate, Florian, Pons, Nicolas, Galleron, Nathalie, Levenez, Florence, Markó, Lajos, Birkner, Till, Jørgensen, Torben, Forslund, Sofia K., Vestergaard, Henrik, Hansen, Torben, Nordentoft, Merete, Mors, Ole, Benros, Michael E., Pedersen, Oluf, and Ehrlich, Stanislav D.

Published
2023
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48. Offre territoriale de soins en imagerie gériatrique

Author

Meyblum, E., David, J.-P., Argoud, D., Villez, M., Davy, C., Fromentin, I., Broussier, A., Sevcik, B., Laurent, M., Rabier, P., Benattar, E., Dang-Tran, K.-D., Clément, O., Gageanu, C., Amoretti, N., Milliner, M., Pommier, R., Drape, J.-L., Bouchez, E., Chevallier, A., Villain, C., and Luciani, A.

Published
2023
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50. Near full-length HIV sequencing in multiple tissues collected postmortem reveals shared clonal expansions across distinct reservoirs during ART

Author

Caroline Dufour, Maria Julia Ruiz, Amélie Pagliuzza, Corentin Richard, Aniqa Shahid, Rémi Fromentin, Rosalie Ponte, Amélie Cattin, Tomas Raul Wiche Salinas, Syim Salahuddin, Teslin Sandstrom, Stephanie Burke Schinkel, Cecilia T. Costiniuk, Mohammad-Ali Jenabian, Petronela Ancuta, Jean-Pierre Routy, Éric A. Cohen, Zabrina L. Brumme, Christopher Power, Jonathan B. Angel, and Nicolas Chomont

Subjects
CP: Microbiology, Biology (General), QH301-705.5
Abstract

Summary: HIV persists in tissues during antiretroviral therapy (ART), but the relative contribution of different anatomical compartments to the viral reservoir in humans remains unknown. We performed an extensive characterization of HIV reservoirs in two men who donated their bodies to HIV cure research and who had been on suppressive ART for years. HIV DNA is detected in all tissues, with large variations across anatomical compartments and between participants. Intact HIV genomes represent 2% and 25% of all proviruses in the two participants and are mainly detected in secondary lymphoid organs, with the spleen and mediastinal lymph nodes harboring intact viral genomes in both individuals. Multiple copies of identical HIV genomes are found in all tissues, indicating that clonal expansions are common in anatomical sites. The majority (>85%) of these expanded clones are shared across multiple tissues. These findings suggest that infected cells expand, migrate, and possibly circulate between anatomical sites.

Published
2023
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