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1. PatchProt: Hydrophobic patch prediction using protein foundation models

Author

Gogishvili, Dea, Minois-Genin, Emmanuel, van Eck, Jan, and Abeln, Sanne

Subjects
Quantitative Biology - Quantitative Methods, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

Hydrophobic patches on protein surfaces play important functional roles in protein-protein and protein-ligand interactions. Large hydrophobic surfaces are also involved in the progression of aggregation diseases. Predicting exposed hydrophobic patches from a protein sequence has been shown to be a difficult task. Fine-tuning foundation models allows for adapting a model to the specific nuances of a new task using a much smaller dataset. Additionally, multi-task deep learning offers a promising solution for addressing data gaps, simultaneously outperforming single-task methods. In this study, we harnessed a recently released leading large language model ESM-2. Efficient fine-tuning of ESM-2 was achieved by leveraging a recently developed parameter-efficient fine-tuning method. This approach enabled comprehensive training of model layers without excessive parameters and without the need to include a computationally expensive multiple sequence analysis. We explored several related tasks, at local (residue) and global (protein) levels, to improve the representation of the model. As a result, our fine-tuned ESM-2 model, PatchProt, cannot only predict hydrophobic patch areas but also outperforms existing methods at predicting primary tasks, including secondary structure and surface accessibility predictions. Importantly, our analysis shows that including related local tasks can improve predictions on more difficult global tasks. This research sets a new standard for sequence-based protein property prediction and highlights the remarkable potential of fine-tuning foundation models enriching the model representation by training over related tasks.

Published
2024

2. Thawed Gaussian wave packet dynamics: a critical assessment of three propagation schemes

Author

Ryabinkin, Ilya G., Gherib, Rami, and Genin, Scott N.

Subjects
Physics - Chemical Physics, Quantum Physics
Abstract

We assessed three schemes for propagating a variable-width (thawed) Gaussian wave packet moving under the influence of Morse or double-well potentials with parameters that are chemically representative. The most rigorous scheme is based on the time-dependent variational principle (TDVP); it leads to realistic behaviour of the center and width of a wave packet in all investigated regimes. Two other approximate schemes, Heller's and the extended semiclassical ones, demonstrate various aberrations. Heller's scheme does not properly account for various zero-point energy-related effects, is unable to predict tunneling, and more importantly, exhibits completely nonphysical unbound width oscillations. The extended semiclassical scheme, which was developed to address some of the shortcomings of the Heller counterpart, demonstrates another unphysical behaviour: self-trapping of a trajectory in both Morse and double-well potentials. We conclude that only the TDVP-based scheme is suitable for problem-free dynamical simulations. This, however, raises the question of how to utilize it efficiently in high-dimensional systems., Comment: 11 pages, 8 figures

Published
2024

3. Thawed Gaussian wavepacket dynamics with $\Delta$-machine learned potentials

Author

Gherib, Rami, Ryabinkin, Ilya G., and Genin, Scott N.

Subjects
Physics - Chemical Physics, Quantum Physics
Abstract

A method for performing variable-width (thawed) Gaussian wavepacket (GWP) variational dynamics on machine-learned potentials is presented. Instead of fitting the potential energy surface (PES), the anharmonic correction to the global harmonic approximation (GHA) is fitted using kernel ridge regression -- this is a $\Delta$-machine learning approach. The training set consists of energy differences between ab initio electronic energies and values given by the GHA. The learned potential is subsequently used to propagate a single thawed GWP using the time-dependent variational principle to compute the autocorrelation function, which provides direct access to vibronic spectra via its Fourier transform. We applied the developed method to simulate the photoelectron spectrum of ammonia and found excellent agreement between theoretical and experimental spectra. We show that fitting the anharmonic corrections requires a smaller training set as compared to fitting total electronic energies. We also demonstrate that our approach allows to reduce the dimensionality of the nuclear space used to scan the PES when constructing the training set. Thus, only the degrees of freedom associated with large amplitude motions need to be treated with $\Delta$-machine learning, which paves a way for reliable simulations of vibronic spectra of large floppy molecules., Comment: 12 pages, 3 figures

Published
2024

4. Sparse Simulation of VQE Circuits for Quantum Chemistry

Author

Steiger, Damian S., Häner, Thomas, Genin, Scott N., and Katzgraber, Helmut G.

Subjects
Quantum Physics
Abstract

The Variational Quantum Eigensolver (VQE) is a promising algorithm for future Noisy Intermediate-Scale Quantum (NISQ) devices to simulate chemical systems. In this paper, we consider the classical simulation of the iterative Qubit Coupled Cluster (iQCC) ansatz. To this end, we implement a multi-threaded sparse wave function simulator and simulate iQCC circuits with up to 80 qubits and 980 entanglers to compare our results to experimental values and previous approximate simulations. In contrast to previous iQCC simulations, e.g., for computing the emission spectra of a phosphorescent emitting material, our approach features a variational guarantee, such that the resulting energies are true upper bounds on the exact energies. Additionally, our method is two orders of magnitude more memory-efficient, because it does not store the transformed Hamiltonians. Our theoretical analysis also enables the construction of ans\"atze with a limited number of nonzero amplitudes, for which our simulator can obtain exact results. This will allow one to generate complex benchmarking instances for future NISQ quantum computers and simulators.

Published
2024

5. From the Fair Distribution of Predictions to the Fair Distribution of Social Goods: Evaluating the Impact of Fair Machine Learning on Long-Term Unemployment

Author

Zezulka, Sebastian and Genin, Konstantin

Subjects
Computer Science - Computers and Society
Abstract

Deploying an algorithmically informed policy is a significant intervention in society. Prominent methods for algorithmic fairness focus on the distribution of predictions at the time of training, rather than the distribution of social goods that arises after deploying the algorithm in a specific social context. However, requiring a "fair" distribution of predictions may undermine efforts at establishing a fair distribution of social goods. First, we argue that addressing this problem requires a notion of prospective fairness that anticipates the change in the distribution of social goods after deployment. Second, we provide formal conditions under which this change is identified from pre-deployment data. That requires accounting for different kinds of performative effects. Here, we focus on the way predictions change policy decisions and, consequently, the causally downstream distribution of social goods. Throughout, we are guided by an application from public administration: the use of algorithms to predict who among the recently unemployed will remain unemployed in the long term and to target them with labor market programs. Third, using administrative data from the Swiss public employment service, we simulate how such algorithmically informed policies would affect gender inequalities in long-term unemployment. When risk predictions are required to be "fair" according to statistical parity and equality of opportunity, targeting decisions are less effective, undermining efforts to both lower overall levels of long-term unemployment and to close the gender gap in long-term unemployment., Comment: 41 pages, 12 figures, 6 tables; substantial text overlap with arXiv:2310.08349

Published
2024
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6. Variational Bayes image restoration with compressive autoencoders

Author

Biquard, Maud, Chabert, Marie, Genin, Florence, Latry, Christophe, and Oberlin, Thomas

Subjects
Computer Science - Computer Vision and Pattern Recognition, Statistics - Machine Learning
Abstract

Regularization of inverse problems is of paramount importance in computational imaging. The ability of neural networks to learn efficient image representations has been recently exploited to design powerful data-driven regularizers. While state-of-the-art plug-and-play methods rely on an implicit regularization provided by neural denoisers, alternative Bayesian approaches consider Maximum A Posteriori (MAP) estimation in the latent space of a generative model, thus with an explicit regularization. However, state-of-the-art deep generative models require a huge amount of training data compared to denoisers. Besides, their complexity hampers the optimization involved in latent MAP derivation. In this work, we first propose to use compressive autoencoders instead. These networks, which can be seen as variational autoencoders with a flexible latent prior, are smaller and easier to train than state-of-the-art generative models. As a second contribution, we introduce the Variational Bayes Latent Estimation (VBLE) algorithm, which performs latent estimation within the framework of variational inference. Thanks to a simple yet efficient parameterization of the variational posterior, VBLE allows for fast and easy (approximate) posterior sampling.Experimental results on image datasets BSD and FFHQ demonstrate that VBLE reaches similar performance than state-of-the-art plug-and-play methods, while being able to quantify uncertainties significantly faster than other existing posterior sampling techniques.

Published
2023

9. Performativity and Prospective Fairness

Author

Zezulka, Sebastian and Genin, Konstantin

Subjects
Computer Science - Computers and Society, K.4.1, K.4.2, J.4
Abstract

Deploying an algorithmically informed policy is a significant intervention in the structure of society. As is increasingly acknowledged, predictive algorithms have performative effects: using them can shift the distribution of social outcomes away from the one on which the algorithms were trained. Algorithmic fairness research is usually motivated by the worry that these performative effects will exacerbate the structural inequalities that gave rise to the training data. However, standard retrospective fairness methodologies are ill-suited to predict these effects. They impose static fairness constraints that hold after the predictive algorithm is trained, but before it is deployed and, therefore, before performative effects have had a chance to kick in. However, satisfying static fairness criteria after training is not sufficient to avoid exacerbating inequality after deployment. Addressing the fundamental worry that motivates algorithmic fairness requires explicitly comparing the change in relevant structural inequalities before and after deployment. We propose a prospective methodology for estimating this post-deployment change from pre-deployment data and knowledge about the algorithmic policy. That requires a strategy for distinguishing between, and accounting for, different kinds of performative effects. In this paper, we focus on the algorithmic effect on the causally downstream outcome variable. Throughout, we are guided by an application from public administration: the use of algorithms to (1) predict who among the recently unemployed will stay unemployed for the long term and (2) targeting them with labor market programs. We illustrate our proposal by showing how to predict whether such policies will exacerbate gender inequalities in the labor market., Comment: 15 pages, 2 figures

Published
2023

13. Efficient construction of involutory linear combinations of anti-commuting Pauli generators for large-scale iterative qubit coupled cluster calculations

Author

Ryabinkin, Ilya G., Jena, Andrew J., and Genin, Scott N.

Subjects
Quantum Physics, Physics - Chemical Physics
Abstract

We present an efficient method for construction of a fully anti-commutative set of Pauli generators (elements of the Pauli group) from a commutative set of operators that are composed exclusively from Pauli $\hat x_i$ operators (purely X generators) and sorted by an associated numerical measure, such as absolute energy gradients. Our approach uses the Gauss-Jordan elimination applied to a binary matrix that encodes the set of X generators to bring it to the reduced row echelon form, followed by the construction of an anti-commutative system in a standard basis by means of a modified Jordan-Wigner transformation and returning to the original basis. The algorithm complexity is linear in the size of the X set and quadratic in the number of qubits. The resulting anti-commutative sets are used to construct the qubit coupled cluster Ansatz with involutory linear combinations of anti-commuting Paulis (QCC-ILCAP) proposed in [J. Chem. Theory Comput. 2021, 17, 1, 66-78]. We applied the iterative qubit coupled cluster method with the QCC-ILCAP Ansatz to calculations of ground-state potential energy curves for symmetric stretching of the water molecule (36 qubits) and dissociation of N$_2$ (56 qubits).

Published
2023

14. Safety and tolerability of immune checkpoint inhibitors in people with HIV infection and cancer: insights from the national prospective real-world OncoVIHAC ANRS CO24 cohort study

Author

Olivier Lambotte, Pierre Delobel, Jean-Philippe Spano, Kevin Bihan, Dominique Costagliola, Christine Katlama, Anne-Geneviève Marcelin, Laurent Greillier, Baptiste Abbar, Armelle Lavole, Séverine Gibowski, Cathia Soulié, Lambert Assoumou, Raghiatou Baldé, Thierry Allegre, Alain Makinson, Olivia Zaegel-Faucher, Marianne Veyri, Mathilde Bertheau, Michèle Algarte Genin, and Marine Baron

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Background Immune checkpoint inhibitors (ICIs) have been a major advance in cancer management. However, we still lack prospective real-world data regarding their usage in people with HIV infection (PWH).Methods The ANRS CO24 OncoVIHAC study (NCT03354936) is an ongoing prospective observational cohort study in France of PWH with cancer treated with ICI. We assessed the incidence of grade ≥3 immune-related adverse events (irAEs). All grade ≥3 irAEs were reviewed by an event review.Results Between January 17, 2018, and December 05, 2023, 150 participants were recruited from 33 sites and 140 were included in this analysis. At the data cut-off date of December 05, 2023, the median follow-up was 9.2 months (IQR: 3.9–18.3), with a total of 126.2 person-years.Median age was 59 years (IQR: 54–64) and 111 (79.3%) were men. Median time since HIV diagnosis was 25 years (12–31), the median duration on antiretroviral (ARV) was 19.5 years (7.7–25.4), and the CD4 nadir was 117/µL (51–240). ICI regimens comprised anti-programmed cell death protein-1 (PD-1) for 111 (79.3%) participants, anti-programmed death-ligand 1 for 25 (17.9%), a combination of anti-PD-1 and anti-cytotoxic T-lymphocyte associated protein 4 for 3 (2.1%), and anti-PD-1 along with anti-vascular endothelial growth factor receptor for 1 (0.7%). The most frequent cancers were lung (n=65), head/neck (n=15), melanoma (n=12), liver (n=11) and Hodgkin’s lymphoma (n=9).During follow-up, a total of 34 grade ≥3 irAEs occurred in 20 participants, leading to an incidence rate of 26.9 per 100 person-years. The Kaplan-Meier estimates of the proportion of participants with at least one episode of grade ≥3 irAEs were 13.8% at 6 months, 15.0% at 12 months and 18.7% at 18 months. One treatment-related death due to myocarditis was reported (0.7%). Multivariable analysis of cumulative incidence showed that participants with time since HIV diagnosis >17 years (incidence rate ratio (IRR)=4.66, p=0.002), with CD4

Published
2024
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18. A Bayesian shared-frailty spatial scan statistic model for time-to-event data

Author

Frévent, Camille, Ahmed, Mohamed-Salem, Dabo-Niang, Sophie, and Genin, Michaël

Subjects
Statistics - Methodology
Abstract

Spatial scan statistics are well known and widely used methods for the detection of spatial clusters of events. In the field of spatial analysis of time-to-event data, several models of scan statistics have been proposed. However, these models do not take into account the potential intra-unit spatial correlation of individuals nor a potential correlation between spatial units. To overcome this problem, we propose here a scan statistic based on a Cox model with shared frailty that takes into account the spatial correlation between spatial units. In simulation studies, we have shown that (i) classical models of spatial scan statistics for time-to-event data fail to maintain the type I error in the presence of intra-spatial unit correlation, and (ii) our model performs well in the presence of both intra-spatial unit correlation and inter-spatial unit correlation. Our method has been applied to epidemiological data and to the detection of spatial clusters of mortality in patients with end-stage renal disease in northern France.

Published
2022

22. On the Importance of Well-Defined Thermal Correlation Functions in Simulating Vibronic Spectra

Author

Gherib, Rami, Genin, Scott N., and Ryabinkin, Ilya G.

Subjects
Physics - Chemical Physics
Abstract

Two difficulties associated with the computations of thermal vibrational correlation functions are discussed. The first one is the lack of a well-behaved expression that is valid at both high-temperature and $T \to 0$ K limits. Specifically, if the partition function and the propagator are considered separately, then thermal vibrational correlation functions may have an indeterminate form 0/0 in the limit $T \to 0$ K. This difficulty is resolved when the partition function and the propagator are jointly considered in the harmonic approximation, which allows a problematic term that emanates from the zero-point energy to be cancelled out thereby producing a thermal correlation function with a determinate form in $T \to 0$ K limit. The second difficulty is related to the multivaluedness of the vibrational correlation function. We show numerically that an improper selection of branch leads to discontinuities in the computed correlation function and an incorrect vibronic spectra. We propose a phase tracking procedure that ensures continuity of both real and imaginary parts of the correlation function to recover the correct spectra. We support our findings by simulating the UV-vis absorption spectra of pentacene at 4 K and benzene at 298 K. Both are found to be in good agreement with their experimental counterparts.

Published
2022
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23. Envelopes and Waves: Safe Multivehicle Collision Avoidance for Horizontal Non-deterministic Turns

Author

Kouskoulas, Yanni, Machado, T. J., Genin, Daniel, Schmidt, Aurora, Papusha, Ivan, and Brulé, Joshua

Subjects
Computer Science - Logic in Computer Science, Computer Science - Robotics, Mathematics - Optimization and Control, F.4.1, I.2.3, I.2.8
Abstract

We present an approach to analyzing the safety of asynchronous, independent, non-deterministic, turn-to-bearing horizontal maneuvers for two vehicles. Future turn rates, final bearings, and continuously varying ground speeds throughout the encounter are unknown but restricted to known ranges. We develop a library of formal proofs about turning kinematics, and apply the library to create a formally verified timing computation. Additionally, we create a technique that evaluates future collision possibilities that is based on waves of position possibilities and relies on the timing computation. The result either determines that the encounter will be collision-free, or computes a safe overapproximation for when and where collisions may occur., Comment: Coq proofs are at https://bitbucket.org/ykouskoulas/ottb-foundation-proofs; Accepted 08 Mar 2022 (International Journal on Software Tools for Technology Transfer)

Published
2022
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24. Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer’s disease

Author

Holstege, Henne, Hulsman, Marc, Charbonnier, Camille, Grenier-Boley, Benjamin, Quenez, Olivier, Grozeva, Detelina, van Rooij, Jeroen GJ, Sims, Rebecca, Ahmad, Shahzad, Amin, Najaf, Norsworthy, Penny J, Dols-Icardo, Oriol, Hummerich, Holger, Kawalia, Amit, Amouyel, Philippe, Beecham, Gary W, Berr, Claudine, Bis, Joshua C, Boland, Anne, Bossù, Paola, Bouwman, Femke, Bras, Jose, Campion, Dominique, Cochran, J Nicholas, Daniele, Antonio, Dartigues, Jean-François, Debette, Stéphanie, Deleuze, Jean-François, Denning, Nicola, DeStefano, Anita L, Farrer, Lindsay A, Fernández, Maria Victoria, Fox, Nick C, Galimberti, Daniela, Genin, Emmanuelle, Gille, Johan JP, Le Guen, Yann, Guerreiro, Rita, Haines, Jonathan L, Holmes, Clive, Ikram, M Arfan, Ikram, M Kamran, Jansen, Iris E, Kraaij, Robert, Lathrop, Marc, Lemstra, Afina W, Lleó, Alberto, Luckcuck, Lauren, Mannens, Marcel MAM, Marshall, Rachel, Martin, Eden R, Masullo, Carlo, Mayeux, Richard, Mecocci, Patrizia, Meggy, Alun, Mol, Merel O, Morgan, Kevin, Myers, Richard M, Nacmias, Benedetta, Naj, Adam C, Napolioni, Valerio, Pasquier, Florence, Pastor, Pau, Pericak-Vance, Margaret A, Raybould, Rachel, Redon, Richard, Reinders, Marcel JT, Richard, Anne-Claire, Riedel-Heller, Steffi G, Rivadeneira, Fernando, Rousseau, Stéphane, Ryan, Natalie S, Saad, Salha, Sanchez-Juan, Pascual, Schellenberg, Gerard D, Scheltens, Philip, Schott, Jonathan M, Seripa, Davide, Seshadri, Sudha, Sie, Daoud, Sistermans, Erik A, Sorbi, Sandro, van Spaendonk, Resie, Spalletta, Gianfranco, Tesi, Niccolo’, Tijms, Betty, Uitterlinden, André G, van der Lee, Sven J, Visser, Pieter Jelle, Wagner, Michael, Wallon, David, Wang, Li-San, Zarea, Aline, Clarimon, Jordi, van Swieten, John C, Greicius, Michael D, Yokoyama, Jennifer S, Cruchaga, Carlos, Hardy, John, and Ramirez, Alfredo

Subjects
Biological Sciences, Genetics, Dementia, Alzheimer's Disease, Neurosciences, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Human Genome, Prevention, Acquired Cognitive Impairment, Neurodegenerative, Aging, Clinical Research, Biotechnology, Brain Disorders, 2.1 Biological and endogenous factors, Aetiology, Neurological, Humans, Adenosine Triphosphatases, Alzheimer Disease, ATP Binding Cassette Transporter 1, Genome-Wide Association Study, Risk Factors, Exosomes, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Alzheimer's disease (AD), the leading cause of dementia, has an estimated heritability of approximately 70%1. The genetic component of AD has been mainly assessed using genome-wide association studies, which do not capture the risk contributed by rare variants2. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individuals-16,036 AD cases and 16,522 controls. Next to variants in TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Additionally, the rare-variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential drivers of respective AD-genome-wide association study loci. Variants associated with the strongest effect on AD risk, in particular loss-of-function variants, are enriched in early-onset AD cases. Our results provide additional evidence for a major role for amyloid-β precursor protein processing, amyloid-β aggregation, lipid metabolism and microglial function in AD.

Published
2022

25. Technological convergence and innovative development of natural resource economy

Author

Agafonov Felix, Genin Anton, Kalinina Oksana, Brel Olga, and Zhironkina Olga

Subjects
Environmental sciences, GE1-350
Abstract

An integral component of the innovative development of natural resource economy is the integration of technological solutions and investments in industrial production, the expansion of national manufacturing complex in the world market with the following change in the export structure. Implementation delay of convergent technologies may lead to the loss of Russian technological identity, strengthening raw vector of long-term social and economic development. In this regard, the relevance of the study of problems and obstacles to the implementation of convergent technologies in the economy of countries which specialize in production and export of mineral resources is increasing. To start the innovative development in Russian economy it is important to restore the dominance of modern industrial complex in it. This will lead to the decrease of pre-industrial economy and will contribute to the formation of post-industrial technological layer. Therefore, convergent and technological transformation of natural resource economy is imposed with the strategic task of improving profitability, investment attractiveness and international competitiveness of industrial production.

Published
2017
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27. CHCHD10S59L/+ mouse model: Behavioral and neuropathological features of frontotemporal dementia

Author

Emmanuelle C. Genin, Pauline Pozzo di Borgo, Thomas Lorivel, Sandrine Hugues, Mélissa Farinelli, Alessandra Mauri-Crouzet, Françoise Lespinasse, Lucas Godin, Véronique Paquis-Flucklinger, and Agnès Petit-Paitel

Subjects
CHCHD10, Mitochondrion, Frontotemporal dementia, Amyotrophic lateral sclerosis, Mouse model, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

CHCHD10-related disease causes a spectrum of clinical presentations including mitochondrial myopathy, cardiomyopathy, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We generated a knock-in mouse model bearing the p.Ser59Leu (S59L) CHCHD10 variant. Chchd10S59L/+ mice have been shown to phenotypically replicate the disorders observed in patients: myopathy with mtDNA instability, cardiomyopathy and typical ALS features (protein aggregation, neuromuscular junction degeneration and spinal motor neuron loss). Here, we conducted a comprehensive behavioral, electrophysiological and neuropathological assessment of Chchd10S59L/+ mice. These animals show impaired learning and memory capacities with reduced long-term potentiation (LTP) measured at the Perforant Pathway-Dentate Gyrus (PP-DG) synapses. In the hippocampus of Chchd10S59L/+ mice, neuropathological studies show the involvement of protein aggregates, activation of the integrated stress response (ISR) and neuroinflammation in the degenerative process. These findings contribute to decipher mechanisms associated with CHCHD10 variants linking mitochondrial dysfunction and neuronal death. They also validate the Chchd10S59L/+ mice as a relevant model for FTD, which can be used for preclinical studies to test new therapeutic strategies for this devastating disease.

Published
2024
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28. Developing Intercultural Business Competence via Team Learning in Post-Pandemic Era

Author

Andrienko, ?etiana, Genin, Vlad, and Kozubska, Iryna

Abstract

To become successfully competitive in the globalised post-COVID 19 virtual business world, the engineering students, besides learning the English language for Specific Purposes as stipulated by the existing Syllabi, require purposed efforts for the formation of intercultural business communication competencies. This research, conducted successively in the USA and Ukraine combining observational and experimental methodology, aimed at studying the influence of team learning on the development of intercultural business competencies and skills highly desired and valued by employers, such as team building and teamwork, critical thinking, decision making, conflict prevention, and resolution, etc. The results were processed by combining qualitative and quantitative methods. Spanning in time from 2013 to 2020, the study proved the effectiveness of project work in learning teams for the development of intercultural competence and business communication skills. Team learning in virtual teams based on andragogical principles and methodology adapted by the authors to the needs of Ukrainian engineering students resulted in developing team building, teamwork, leadership, goal setting, planning, decision making, time management, creative and critical thinking, problem solving, conflict prevention and resolution, interpersonal and group communication and collaboration skills and competences, necessary for successful integration into the global workforce marketplace. Besides significant enhancement of intercultural business communication competencies, team learning resulted in raising Ukrainian undergraduate engineering students' motivation towards learning ESP, engagement in group and classwork, persistence towards successful graduation and gainful employment, and overall positive learning experiences.

Published
2021

29. Impact of vaccination with third generation modified vaccinia Ankara and sexual behaviour on mpox incidence in men who have sex with men: analysis among participants of the ANRS-174 DOXYVAC trial

Author

Ghosn, Jade, Assoumou, Lambert, Ouattara, Moussa, Rubenstein, Emma, Pialoux, Gilles, Katlama, Christine, Surgers, Laure, Duvivier, Claudine, Pavie, Juliette, Viard, Jean-Paul, Algarte-Genin, Michèle, Gibowski, Severine, Ollivier, Manon, Costagliola, Dominique, and Molina, Jean-Michel

Published
2024
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30. Doxycycline prophylaxis and meningococcal group B vaccine to prevent bacterial sexually transmitted infections in France (ANRS 174 DOXYVAC): a multicentre, open-label, randomised trial with a 2 × 2 factorial design

Author

Aslan, Alexandre, Pintado, Claire, Delaugerre, Constance, Ponscarme, Diane, Dalle, Eve, Chas, Julie, Siguier, Martin, Palich, Romain, Valentin, Marc-Antoine, Yazdanpanah, Yazdan, Lacombe, Karine, Viard, Jean-Paul, Lourenco, Jeremy, Rachline, Anne, Detruchis, Pierre, Diemer, Myriam, Azemar, Laurene, Landowski, Stephanie, Ometsguine, Philippe, Buisson, Martin, Feliho, Philip, Bachelard, Antoine, Phung, Bao, Rioux, Christophe, Proux, Caroline, Le Gac, Sylvie, Schneider, Luminita, Charmak, Aziza, Ktorza, Nadine, Seang, Sophie, Orriere, Thibaut, Sellem, Baptiste, Palacios, Christia, Mebarki, Soraya, Molina, Jean-Michel, Bercot, Beatrice, Assoumou, Lambert, Rubenstein, Emma, Algarte-Genin, Michele, Pialoux, Gilles, Katlama, Christine, Surgers, Laure, Bébéar, Cécile, Dupin, Nicolas, Ouattara, Moussa, Slama, Laurence, Pavie, Juliette, Duvivier, Claudine, Loze, Benedicte, Goldwirt, Lauriane, Gibowski, Severine, Ollivier, Manon, Ghosn, Jade, and Costagliola, Dominique

Published
2024
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35. The Ralstonia Research Community Rejects the Proposal to Classify Phylotype I Ralstonia into the New Species Ralstonia nicotianae

Author

Tiffany Lowe-Power, Parul Sharma, Poliane Alfenas-Zerbini, Belén Álvarez, Mohammad Arif, Caroline Baroukh, Ana Maria Bocsanczy, Elena G. Biosca, José A. Castillo, Gilles Cellier, Teresa Coutinho, André Drenth, Ville-Petri Friman, Stephane Genin, Alice Guidot, Yasufumi Hikichi, Qi Huang, Anjali Iyer-Pascuzzi, Kenji Kai, Yann Pecrix, Stephane Poussier, Jane D. Ray, Maurício Rossato, Rebecca Schomer, Maria Inés Siri, Boris A. Vinatzer, and Caitilyn Allen

Subjects
bacterial wilt disease, Ralstonia phylotypes, Ralstonia pseudosolanacearum, Ralstonia solanacearum, Ralstonia syzygii, taxonomy, Plant culture, SB1-1110, Botany, QK1-989
Abstract

The Ralstonia solanacearum species complex is a group of globally important plant pathogens. Bacteria in this very large and genetically diverse group all colonize the xylem elements of angiosperm plants and cause high-impact wilting diseases of many crops. Because they threaten economic and food security, several R. solanacearum species complex subgroups are strictly regulated as quarantine pests. Biologically meaningful and consistent nomenclature is essential for organisms that have major economic and regulatory importance, such as plant-pathogenic Ralstonia. There are currently three species of Ralstonia wilt pathogens: R. pseudosolanacearum (corresponding to two phylogenetic groups that are described in the literature as phylotypes I and III), R. solanacearum (phylotypes IIA, IIB, and IIC), and R. syzygii (phylotype IV, containing three subspecies: subsp. syzygii, subsp. celebensis, and subsp. indonesiensis). A recent paper proposed reclassifying phylotype I as a new species named “Ralstonia nicotianae.” The purpose of this commentary is to register our objection to the taxon “Ralstonia nicotianae.” [Figure: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Published
2023
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36. 3G R&D: R&D for the Next Generation of Ground-based Gravitational-wave Detectors

Author

McClelland, David, Lueck, Harald, Adhikari, Rana, Ando, Masaki, Billingsley, GariLynn, Cagnoli, Geppo, Evans, Matt, Fejer, Martin, Freise, Andreas, Fulda, Paul, Genin, Eric, González, Gabriela, Harms, Jan, Hild, Stefan, Losurdo, Giovanni, Martin, Ian, Prabhakar, Anil, Reid, Stuart, Ricci, Fulvio, Robertson, Norna, Brand, Jo van den, Willke, Benno, Zucker, Michael, Bertolini, Alessandro, Danilishin, Stefan, Fidecaro, Francesco, Gemme, Gianluca, Hammond, Giles, Lough, James, Majorana, Ettore, Massaki, Ando, Smith, Joshua, Vocca, Helios, Venkateswara, Krishna, Ward, Robert L., Yamamoto, Kazuhiro, Punturo, Michele, Reitze, David, Couvares, Peter, Katsanevas, Stavros, Kajita, Takaaki, Kalogera, Vicky, Rowan, Sheila, Sanders, Gary, Sathyaprakash, B. S., and Shoemaker, David

Subjects
General Relativity and Quantum Cosmology
Abstract

To deliver on the promise of next generation gravitational-wave observatories, a sustained and coordinated detector research and development program is required. This report examines in detail the wide range of nearer- and longer-term detector R&D programs needed for next generation GW detectors commensurate with the key science targets presented in "The Next Generation Global Gravitational Wave Observatory: The Science Book", including considerations of site selection and large-scale vacuum infrastructure. The report makes a series of detailed recommendations on the needed advances in detector technology and the timescales needed to achieve those advances. It also identifies areas where larger-scale globally coordinated R&D efforts will be critical to ensuring success while minimizing costs. This report is the third in a six part series of reports by the GWIC 3G Subcommittee: i) Expanding the Reach of Gravitational Wave Observatories to the Edge of the Universe, ii) The Next Generation Global Gravitational Wave Observatory: The Science Book, iii) 3G R&D: R&D for the Next Generation of Ground-based Gravitational Wave Detectors (this report), iv) Gravitational Wave Data Analysis: Computing Challenges in the 3G Era, v) Future Ground-based Gravitational-wave Observatories: Synergies with Other Scientific Communities, and vi) An Exploration of Possible Governance Models for the Future Global Gravitational-Wave Observatory Network., Comment: 81 pages, 12 figures

Published
2021

37. Estimating Phosphorescent Emission Energies in Ir(III) Complexes using Large-Scale Quantum Computing Simulations

Author

Genin, Scott N., Ryabinkin, Ilya G., Paisley, Nathan R., Whelan, Sarah O., Helander, Michael G., and Hudson, Zachary M.

Subjects
Quantum Physics, Physics - Chemical Physics
Abstract

Quantum chemistry simulations that accurately predict the properties of materials are among the most highly anticipated applications of quantum computing. It is widely believed that simulations running on quantum computers will allow for higher accuracy, but there has not yet been a convincing demonstration that quantum methods are competitive with existing classical methods at scale. Here we apply the iterative qubit coupled cluster (iQCC) method on classical hardware to the calculation of the $T_1 \to S_0$ transition energies in nine phosphorescent iridium complexes, to determine if quantum simulations have any advantage over traditional computing methods. Phosphorescent iridium complexes are integral to the widespread commercialization of organic light-emitting diode (OLED) technology, yet accurate computational prediction of their emission energies remains a challenge. Our simulations would require a gate-based quantum computer with a minimum of 72 fully-connected and error-corrected logical qubits. Since such devices do not yet exist, we demonstrate the iQCC quantum method using a special purpose quantum simulator on classical hardware. The results are compared to a selection of common density-functional theory (DFT) functionals (B3LYP, CAM-B3LYP, LC-wHPBE), ab initio methods (HF and MP2), and experimental data. The iQCC quantum method is found to match the accuracy of the fine-tuned DFT functionals, has a better Pearson correlation coefficient, and still has considerable potential for systematic improvement. Based on these results, we anticipate that the iQCC quantum method will have the required accuracy to design organometallic complexes when deployed on emerging quantum hardware., Comment: Supplementary is added

Published
2021
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40. Emotional Intelligence and Acquisition of English Language Oral Communication Skills

Author

Andrienko, ?etiana, Chumak, Nataliia, and Genin, Vlad

Abstract

Studying the factors of successful acquisition of ESL speaking skills in Ukrainian adult learners, the authors focused on the correlation between emotional intelligence and development of oral communication skills, and, on the other hand, on the growth of these indicators as a result of purposeful inclusion of content-related emotions into activities aimed at the development of speaking and listening skills. Theoretically based on the ideas of emotional intelligence as an important factor in human interaction and guided by the hypothesis that content-related emotions intensify emotional involvement and have a positive influence on the acquisition of oral communication skills, the researchers applied Mayer-Salovey-Caruso Emotional Intelligence Test and the English Language Oral Communication Skills Test developed by the authors, to measure the key oral communication skills indicators against a 100 point scale. Experimental teaching of 124 undergraduate students of International Relations during September 2018-May 2019 proved a beneficial influence of including emotions in the learning activities on the acquisition of ESL oral communication skills, as well as on student motivation and overall quality of student experiences. Significant increments in Emotional Intelligence and ESL oral communication skills in the experimental group compared to insignificant growth of the same indicators in the Reference group allow to establish a positive correlation between the growth of emotional intelligence and acquisition of the ESL speaking skills pursuant to inclusion of content-related emotions into the ESL learning in Ukrainian students.

Published
2020

43. Effects of flow speed and prey density on the rate and efficiency of prey capture in zooplanktivorous coral-reef fishes

Author

Amatzia Genin, Svetlana Rickel, Margarita Zarubin, and Moshe Kiflawi

Subjects
zooplankton, predation, foraging, site-attached, movement, Red Sea, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

Holling’s classical functional response model describes the mechanistic foundations of the relationships between predation rate and prey density. As such, the model is pertinent to predators that actively search for prey, but not to stationary predators in which additional factors, such as flow speed, determine the rates of prey encounter. The main objective of this study was to measure the rates and corresponding efficiencies of zooplanktivory among different common species of coral-reef fishes under a wide range of prey densities and current speeds. All our experiments were carried out in a flume with different combinations of flow speeds (3-28.5 cm/s) and prey densities (210 - 1050 prey m-3). Nauplii of Artemia salina were used as prey. Despite major differences in the taxonomic origin of the studied species, their morphologies, and the types of shelters they use, the foraging performances of the fish, their predation rates, and the way those rates were affected by prey density and flow speed were surprisingly similar. Under a fixed prey density, capture rates did not change much as function of flow speed. Under conditions of equal prey flux, predation rates were always higher under conditions of high density and weaker flow than under lower density and faster flow. A sharp decline in capture efficiency with increasing flow speed was explained by a corresponding narrowing of the fish’s body orientation relative to the flow. In other words, with increasing flow speed, the fish gradually became more-narrowly oriented head-on onto the flow, exhibiting a decrease in the frequency of body turns (“maneuverability”). These trends, especially the reduced maneuverability under strong currents, can explain our findings that predation rates did not increase when the flow, hence prey flux, increased. Inter-specific differences in predation rates and efficiencies, however small, agree well with observed differences in the type of habitats the different species occupy.

Published
2024
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44. Zooplanktivory in garden eels: benefits and shortcomings of being 'anchored' compared with other coral-reef fish

Author

Alexandra Khrizman, Irena Kolesnikov, Dmitri Churilov, and Amatzia Genin

Subjects
foraging, movement, flow, prey density, Red Sea, niche, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

Garden eels are elongated zooplanktivorous fish that live in colonies on sandy bottoms, often adjacent to coral reefs. Each eel digs its own burrow, from which it partially emerges to forage on drifting zooplankton while being “anchored” with its tail inside the burrow. Feeding rates and foraging movements were examined in the garden eel Gorgasia sillneri and compared with corresponding measurements carried out as part of this study and by (Genin et al.)1 with 3 species of “free”, site-attached coral-reef fish. Feeding rates by the garden eels were substantially lower than those of the free fish. In the eels, those rates monotonically increased with increasing current speed up to ~20 cm/s, whereas in the free fish maximum rates were observed under moderate flows. A nearly linear increase in feeding rate as function of prey density was observed in both the garden eels and the free fish. However, the slope of that increase in the eels was over an order of magnitude more gradual than that reported for the free fish. The different functional responses of the two fish groups appear to be related to their morphology and maneuverability capabilities. Being elongated, anchored in a burrow and able to modulate body posture according to the flow speed allow the eels high feeding rates under strong currents. The tradeoff, compared with free fish, include limited maneuverability, slower swimming, and smaller foraging volume, rendering the eels’ functional response less efficient to increasing prey density. This cost appears to be compensated by the eels’ ability to occupy sandy, shelter-less bottoms, which in some locations are immensely more abundant than coral-covered rocks, where most planktivorous free fish live.

Published
2024
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45. Immunomodulators for immunocompromised patients hospitalized for COVID-19: a meta-analysis of randomized controlled trialsResearch in context

Author

Ilias I. Siempos, Andre C. Kalil, Drifa Belhadi, Viviane Cordeiro Veiga, Alexandre Biasi Cavalcanti, Westyn Branch-Elliman, Eleni Papoutsi, Konstantinos Gkirgkiris, Nikoleta A. Xixi, Anastasia Kotanidou, Olivier Hermine, Raphaël Porcher, Xavier Mariette, Philippe Ravaud, Serge Bureau, Maxime Dougados, Matthieu Resche-Rigon, Pierre-Louis Tharaux, Annick Tibi, Elie Azoulay, Jacques Cadranel, Joseph Emmerich, Muriel Fartoukh, Bertrand Guidet, Marc Humbert, Karine Lacombe, Matthieu Mahevas, Frédéric Pene, Valerie Pourchet-Martinez, Frédéric Schlemmer, Yazdan Yazdanpanah, Gabriel Baron, Elodie Perrodeau, Damien Vanhoye, Cécile Kedzia, Lauren Demerville, Anne Gysembergh-Houal, Alexandre Bourgoin, Nabil Raked, Lakhdar Mameri, Claire Montlahuc, Lucie Biard, St.phanie Alary, Samir Hamiria, Thinhinane Bariz, Hala Semri, Dhiaa Meriem Hai, Moustafa Benafla, Mohamed Belloul, Pernelle Vauboin, Saskia Flamand, Claire Pacheco, Anouk Walter-Petrich, Emilia Stan, Souad Benarab, Corine Nyanou, Robin Charreteur, Céline Dupre, Kévin Cardet, Blandine Lehmann, Kamyl Baghli, Claire Madelaine, Eric D'Ortenzio, Oriane Puéchal, Caroline Semaille, Laurent Savale, Anatole Harrois, Samy Figueiredo, Jacques Duranteau, Nadia Anguel, Arthur Pavot, Xavier Monnet, Christian Richard, Jean-Louis Teboul, Philippe Durand, Pierre Tissieres, Mitja Jevnikar, David Montani, Stephan Pavy, Gaétane Nocturne, Samuel Bitoun, Nicolas Noel, Olivier Lambotte, Lelia Escaut, Stephane Jauréguiberry, Elodie Baudry, Christiane Verny, Edouard Lefevre, Mohamad Zaidan, Domitille Molinari, Gaël Leprun, Alain Fourreau, Laurent Cylly, Lamiae Grimaldi, Myriam Virlouvet, Ramdane Meftali, Soléne Fabre, Marion Licois, Asmaa Mamoune, Yacine Boudali, Clotilde Le Tiec, Céline Verstuyft, Anne-Marie Roques, Sophie Georgin-Lavialle, Patricia Senet, Gilles Pialoux, Angele Soria, Antoine Parrot, Helene François, Nathalie Rozensztajn, Emmanuelle Blin, Pascaline Choinier, Juliette Camuset, Jean-Simon Rech, Antony Canellas, Camille Rolland-Debord, Nadege Lemarié, Nicolas Belaube, Marine Nadal, Martin Siguier, Camille Petit-Hoang, Julie Chas, Elodie Drouet, Matthieu Lemoine, Audrey Phibel, Lucie Aunay, Eliane Bertrand, Sylviane Ravato, Marie Vayssettes, Anne Adda, Celine Wilpotte, Pélagie Thibaut, Julie Fillon, Isabelle Debrix, Soraya Fellahi, Jean-Philippe Bastard, Guillaume Lefévre, Jacques-Eric Gottenberg, Yves Hansmann, Frédéric Blanc, Sophie Ohlmann-Caillard, Vincent Castelain, Emmanuel Chatelus, Eva Chatron, Olivier Collange, François Danion, Frédéric De Blay, Pierre Diemunsch, Sophie Diemunsch, Renaud Felten, Bernard Goichot, Valentin Greigert, Aurelien Guffroy, Bob Heger, Charlotte Kaeuffer, Loic Kassegne, Anne Sophie Korganow, Pierrick Le Borgne, Nicolas Lefebvre, Paul-Michel Mertes, Eric Noll, Mathieu Oberlin, Vincent Poindron, Julien Pottecher, Yvon Ruch, François Weill, Nicolas Meyer, Emmanuel Andres, Eric Demonsant, Hakim Tayebi, Gabriel Nisand, Stéphane Brin, Cédric Sublon, Guillaume Becker, Anne Hutt, Tristan Martin, Sophie Bayer, Catherine Metzger, Arsene Mekinian, Noémie Abisror, Amir Adedjouma, Diane Bollens, Marion Bonneton, Nathalie Bourcicaux, Anne Bourrier, Maria Chauchard Thibault Chiarabiani, Doroth.e Chopin, Jonathan Cohen, Ines Devred, Bruno Donadille, Olivier Fain, Geoffrey Hariri, Vincent Jachiet, Patrick Ingliz, Marc Garnier, Marc Gatfosse, Etienne Ghrenassia, Delphine Gobert, Jessica Krause le Garrec, Cecilia Landman, Jean Remy Lavillegrand, Benedicte Lefebvre, Thibault Mahevas, Sandie Mazerand, Jean Luc Meynard, Marjolaine Morgand, Zineb Ouaz.ne, Jerome Pacanowski, S.bastien Riviere, Philippe Seksik, Harry Sokol, Heithem Soliman, Nadia Valin, Thomas Urbina, Chloé McAvoy, Maria Pereira Miranda, Gladys Aratus, Laurence Berard, Tabassome Simon, Anne Daguenel Nguyen, Elise Girault, Cl.mentine Mayala-Kanda, Marie Antignac, Céline Leplay, Jean-Benoit Arlet, Jean-Luc Diehl, Florence Bellenfant, Anne Blanchard, Alexandre Buffet, Bernard Cholley, Antoine Fayol, Edouard Flamarion, Anne Godier, Thomas Gorget, Sophie-Rym Hamada, Caroline Hauw-Berlemont, Jean-Sébastien Hulot, David Lebeaux, Marine Livrozet, Adrien Michon, Arthur Neuschwander, Marie-Aude Pennet, Benjamin Planquette, Brigitte Ranque, Olivier Sanchez, Geoffroy Volle, Sandrine Briois, Mathias Cornic, Virginie Elisee, Jesuthasan Denis, Juliette Djadi-Prat, Pauline Jouany, Ramon Junquera, Mickael Henriques, Amina Kebir, Isabelle Lehir, Jeanne Meunier, Florence Patin, Val.rie Paquet, Anne Tréhan, Véronique Vigna, Brigitte Sabatier, Damien Bergerot, Charléne Jouve, Camille Knosp, Olivia Lenoir, Nassim Mahtal, Léa Resmini, Xavier Lescure, Jade Ghosn, Antoine Bachelard, Anne Rachline, Valentina Isernia, Bao-chau, Phung, Dorothée Vallois, Aurelie Sautereau, Catherine Neukrich, Antoine Dossier, Raphaël Borie, Bruno Crestani, Gregory Ducrocq, Philippe Gabriel Steg, Philippe Dieude, Thomas Papo, Estelle Marcault, Marhaba Chaudhry, Charléne Da Silveira, Annabelle Metois, Ismahan Mahenni, Meriam Meziani, Cyndie Nilusmas, Sylvie Le Gac, Awa Ndiaye, Fran.oise Louni, Malikhone Chansombat, Zelie Julia, Solaya Chalal, Lynda Chalal, Laura Kramer, Jeniffer Le Grand, Kafif Ouifiya, Valentine Piquard, Sarah Tubiana, Yann Nguyen, Vasco Honsel, Emmanuel Weiss, Anais Codorniu, Virginie Zarrouk, Victoire de Lastours, Matthieu Uzzan, Naura Gamany, Agathe Claveirole, Alexandre Navid, Tiffanie Fouque, Yonathan Cohen, Maya Lupo, Constance Gilles, Roza Rahli, Zeina Louis, David Boutboul, Lionel Galicier, Yaël Amara, Gabrielle Archer, Amira Benattia, Anne Bergeron, Louise Bondeelle, Nathalie de Castro, Melissa Clément, Michaël Darmon, Blandine Denis, Clairelyne Dupin, Elsa Feredj, Delphine Feyeux, Adrien Joseph, Etienne Lenglin, Pierre Le Guen, Geoffroy Liégeon, Gwenaël Lorillon, Asma Mabrouki, Eric Mariotte, Grégoire Martin de Frémont, Adrien Mirouse, Jean-Michel Molina, Régis Peffault de Latour, Eric Oksenhendler, Julien Saussereau, Abdellatif Tazi, Jean-Jacques Tudesq, Lara Zafrani, Isabelle Brindele, Emmanuelle Bugnet, Karine Celli Lebras, Julien Chabert, Lamia Djaghout, Catherine Fauvaux, Anne Lise Jegu, Ewa Kozakiewicz, Martine Meunier, Marie-Thérèse Tremorin, Claire Davoine, Isabelle Madelaine, Sophie Caillat-Zucman, Constance Delaugerre, Florence Morin, Damien Sène, Ruxandra Burlacu, Benjamin Chousterman, Bruno Mégarbanne, Pascal Richette, Jean-Pierre Riveline, Aline Frazier, Eric Vicaut, Laure Berton, Tassadit Hadjam, Miguel Alejandro Vazquez-Ibarra, Clément Jourdaine, Olivia Tran, Véronique Jouis, Aude Jacob, Julie Smati, Stéphane Renaud, Claire Pernin, Lydia Suarez, Luca Semerano, Sébastien Abad, Ruben B. nainous, Nicolas Bonnet, Celine Comparon, Yves Cohen, Hugues Cordel, Robin Dhote, Nathalie Dournon, Boris Duchemann, Nathan Ebstein, Thomas Gille, Benedicte Giroux-Leprieur, Jeanne Goupil de Bouille, Hilario Nunes, Johanna Oziel, Dominique Roulot, Lucile Sese, ClaireTantet, Yurdagul Uzunhan, Coralie Bloch-Queyrat, Vincent Levy, Fadhila Messani, Mohammed Rahaoui, Myléne Petit, Sabrina Brahmi, Vanessa Rathoin, Marthe Rigal, Nathalie Costedoat-Chalumeau, Liem Binh Luong, Zakaria Ait Hamou, Sarah Benghanem, Philippe Blanche, Nicolas Carlier, Benjamin Chaigne, Remy Gauzit, Hassan Joumaa, Mathieu Jozwiak, Marie Lachétre, Hélène Lafoeste, Odie Launay, Paul Legendre, Jonathan Marey, Caroline Morbieu, Lola-Jade Palmieri, Tali-Anne Szwebel, Hendy Abdoul, Alexandra Bruneau, Audrey Beclin-Clabaux, Charly Larrieu, Pierre Montanari, Eric Dufour, Ada Clarke, Catherine Le Bourlout, Nathalie Marin, Nathalie Menage, Samira Saleh-Mghir, Mamadou Salif Cisse, Kahina Cheref, Corinne Guerin, Jérémie Zerbit, Marc Michel, Sébastien Gallien, Etienne Crickx, Benjamin Le Vavasseur, Emmanuelle Kempf, Karim Jaffal, William Vindrios, Julie Oniszczuk, Constance Guillaud, Pascal Lim, Elena Fois, Giovanna Melica, Marie Matignon, Maud Jalabert, Jean-Daniel Lelièvre, David Schmitz, Marion Bourhis, Sylia Belazouz, Laetitia Languille, Caroline Boucle, Nelly Cita, Agnés Didier, Fahem Froura, Katia Ledudal, Thiziri Sadaoui, Alaki Thiemele, Delphine Le Febvre De Bailly, Muriel Carvhalo Verlinde, Julien Mayaux, Patrice Cacoub, David Saadoun, Mathieu Vautier, Héléne Bugaut, Olivier Benveniste, Yves Allenbach, Gaëlle Leroux, Aude Rigolet, Perrine Guillaume-Jugnot, Fanny Domont, Anne Claire Desbois, Chloé Comarmond, Nicolas Champtiaux, Segolene Toquet, Amine Ghembaza, Matheus Vieira, Georgina Maalouf, Goncalo Boleto, Yasmina Ferfar, Jean-Christophe Corvol, C.line Louapre, Sara Sambin, Louise-Laure Mariani, Carine Karachi, Florence Tubach, Candice Estellat, Linda Gimeno, Karine Martin, Aicha Bah, Vixra Keo, Sabrine Ouamri, Yasmine Messaoudi, Nessima Yelles, Pierre Faye, Sebastien Cavelot, Cecile Larcheveque, Laurence Annonay, Jaouad Benhida, Aida Zahrate-Ghoul, Soumeya Hammal, Ridha Belilita, Fanny Charbonnier, Claire Aguilar, Fanny Alby-Laurent, Carole Burger, Clara Campos-Vega, Nathalie Chavarot, Benjamin Fournier, Claire Rouzaud, Damien Vimpére, Caroline Elie, Prissile Bakouboula, Laure Choupeaux, Sophie Granville, Elodie Issorat, Christine Broissand, Marie-Alexandra Alyanakian, Guillaume Geri, Nawal Derridj, Naima Sguiouar, Hakim Meddah, Mourad Djadel, Héléne Chambrin-Lauvray, Jean-Charles Duclos-vallée, Faouzi Saliba, Sophie-Caroline Sacleux, Ilias Kounis, Sonia Tamazirt, Eric Rudant, Jean-Marie Michot, Annabelle Stoclin, Emeline Colomba, Fanny Pommeret, Christophe Willekens, Rosa Da Silva, Valérie Dejean, Yasmina Mekid, Ines Ben-Mabrouk, Florence Netzer, Caroline Pradon, Laurence Drouard, Valérie Camara-Clayette, Alexandre Morel, Gilles Garcia, Abolfazl Mohebbi, Férial Berbour, Mélanie Dehais, Anne-Lise Pouliquen, Alison Klasen, Loren Soyez-Herkert, Jonathan London, Younes Keroumi, Emmanuelle Guillot, Guillaume Grailles, Younes El amine, Fanny Defrancq, Hanane Fodil, Chaouki Bouras, Dominique Dautel, Nicolas Gambier, Thierno Dieye, Boris Bienvenu, Victor Lancon, Laurence Lecomte, Kristina Beziriganyan, Belkacem Asselate, Laure Allanic, Elena Kiouris, Marie-Héléne Legros, Christine Lemagner, Pascal Martel, Vincent Provitolo, Félix Ackermann, Mathilde Le Marchand, Aurélie Chan Hew Wai, Dimitri Fremont, Elisabeth Coupez, Mireille Adda, Frédéric Duée, Lise Bernard, Antoine Gros, Estelle Henry, Claire Courtin, Anne Pattyn, Pierre-Grégoire Guinot, Marc Bardou, Agnes Maurer, Julie Jambon, Amélie Cransac, Corinne Pernot, Bruno Mourvillier, Eric Marquis, Philippe Benoit, Damien Roux, Coralie Gernez, Cécile Yelnik, Julien Poissy, Mandy Nizard, Fanette Denies, Helene Gros, Jean-Jacques Mourad, Emmanuelle Sacco, Sophie Renet, F. Ader, Y. Yazdanpanah, F. Mentre, N. Peiffer-Smadja, F.X. Lescure, J. Poissy, L. Bouadma, J.F. Timsit, B. Lina, F. Morfin-Sherpa, M. Bouscambert, A. Gaymard, G. Peytavin, L. Abel, J. Guedj, C. Andrejak, C. Burdet, C. Laouenan, D. Belhadi, A. Dupont, T. Alfaiate, B. Basli, A. Chair, S. Laribi, J. Level, M. Schneider, M.C. Tellier, A. Dechanet, D. Costagliola, B. Terrier, M. Ohana, S. Couffin-Cadiergues, H. Esperou, C. Delmas, J. Saillard, C. Fougerou, L. Moinot, L. Wittkop, C. Cagnot, S. Le Mestre, D. Lebrasseur-Longuet, V. Petrov-Sanchez, A. Diallo, N. Mercier, V. Icard, B. Leveau, S. Tubiana, B. Hamze, A. Gelley, M. Noret, E. D’Ortenzio, O. Puechal, C. Semaille, T. Welte, J.A. Paiva, M. Halanova, M.P. Kieny, E. Balssa, C. Birkle, S. Gibowski, E. Landry, A. Le Goff, L. Moachon, C. Moins, L. Wadouachi, C. Paul, A. Levier, D. Bougon, F. Djossou, L. Epelboin, J. Dellamonica, C.H. Marquette, C. Robert, S. Gibot, E. Senneville, V. Jean-Michel, Y. Zerbib, C. Chirouze, A. Boyer, C. Cazanave, D. Gruson, D. Malvy, P. Andreu, J.P. Quenot, N. Terzi, K. Faure, C. Chabartier, V. Le Moing, K. Klouche, T. Ferry, F, Valour, B. Gaborit, E. Canet, P. Le Turnier, D. Boutoille, F. Bani-Sadr, F. Benezit, M. Revest, C. Cameli, A. Caro, MJ Ngo Um Tegue, Y. Le Tulzo, B. Laviolle, F. Laine, G. Thiery, F. Meziani, Y. Hansmann, W. Oulehri, C. Tacquard, F. Vardon-Bounes, B. Riu-Poulenc, M. Murris-Espin, L. Bernard, D. Garot, O. Hinschberger, M. Martinot, C. Bruel, B. Pilmis, O. Bouchaud, P. Loubet, C. Roger, X. Monnet, S. Figueiredo, V. Godard, J.P. Mira, M. Lachatre, S. Kerneis, J. Aboab, N. Sayre, F. Crockett, D. Lebeaux, A. Buffet, J.L. Diehl, A. Fayol, J.S. Hulot, M. Livrozet, A Mekontso- Dessap, C. Ficko, F. Stefan, J. Le Pavec, J. Mayaux, H. Ait-Oufella, J.M. Molina, G. Pialoux, M. Fartoukh, J. Textoris, M. Brossard, A. Essat, E. Netzer, Y. Riault, M. Ghislain, L. Beniguel, M. Genin, L. Gouichiche, C. Betard, L. Belkhir, A. Altdorfer, V Fraipont Centro, S. Braz, JM Ferreira Ribeiro, R Roncon Alburqueque, M. Berna, M. Alexandre, B. Lamprecht, A. Egle, R. Greil, M. Joannidis, Thomas F. Patterson, Philip O. Ponce, Barbara S. Taylor, Jan E. Patterson, Jason E. Bowling, Heta Javeri, LuAnn Larson, Angela Hewlett, Aneesh K. Mehta, Nadine G. Rouphael, Youssef Saklawi, Nicholas Scanlon, Jessica J. Traenkner, Ronald P. Trible, Jr., Emmanuel B. Walter, Noel Ivey, Thomas L. Holland, Guillermo M. Ruiz-Palacios, Alfredo Ponce de León, Sandra Rajme, Lanny Hsieh, Alpesh N. Amin, Miki Watanabe, Helen S. Lee, Susan Kline, Joanne Billings, Brooke Noren, Hyun Kim, Tyler D. Bold, Victor Tapson, Jonathan Grein, Fayyaz Sutterwala, Nicole Iovine, Lars K. Beattie, Rebecca Murray Wakeman, Matthew Shaw, Mamta K. Jain, Satish Mocherla, Jessica Meisner, Amneris Luque, Daniel A. Sweeney, Constance A. Benson, Farhana Ali, Robert L. Atmar, Hana M. El Sahly, Jennifer Whitaker, Ann R. Falsey, Angela R. Branche, Cheryl Rozario, Justino Regalado Pineda, José Arturo Martinez-Orozco, David Chien Lye, Sean WX. Ong, Po Ying Chia, Barnaby E. Young, Uriel Sandkovsky, Mezgebe Berhe, Clinton Haley, Emma Dishner, Valeria D. Cantos, Colleen F. Kelley, Paulina A. Rebolledo Esteinou, Sheetal Kandiah, Sarah B. Doernberg, Pierre-Cedric B. Crouch, Hannah Jang, Anne F. Luetkemeyer, Jay Dwyer, Stuart H. Cohen, George R. Thompson, 3rd, Hien H. Nguyen, Robert W. Finberg, Jennifer P. Wang, Juan Perez-Velazquez, Mireya Wessolossky, Patrick E.H. Jackson, Taison D. Bell, Miranda J. West, Babafemi Taiwo, Karen Krueger, Johnny Perez, Triniece Pearson, Catharine I. Paules, Kathleen G. Julian, Danish Ahmad, Alexander G. Hajduczok, Henry Arguinchona, Christa Arguinchona, Nathaniel Erdmann, Paul Goepfert, Neera Ahuja, Maria G. Frank, David Wyles, Heather Young, Myoung-don Oh, Wan Beom Park, Chang Kyung Kang, Vincent Marconi, Abeer Moanna, Sushma Cribbs, Telisha Harrison, Eu Suk Kim, Jongtak Jung, Kyoung-Ho Song, Hong Bin Kim, Seow Yen Tan, Humaira Shafi, MF Jaime Chien, Raymond KC. Fong, Daniel D. Murray, Jens Lundgren, Henrik Nielsen, Tomas Jensen, Barry S. Zingman, Robert Grossberg, Paul F. Riska, Otto O. Yang, Jenny Ahn, Rubi Arias, Rekha R. Rapaka, Naomi Hauser, James D. Campbell, William R. Short, Pablo Tebas, Jillian T. Baron, Susan L.F. McLellan, Lucas S. Blanton, Justin B. Seashore, C. Buddy Creech, Todd W. Rice, Shannon Walker, Isaac P. Thomsen, Diego Lopez de Castilla, Jason W. Van Winkle, Francis X. Riedo, Surinder Kaur Pada, Alvin DY. Wang, Li Lin, Michelle Harkins, Gregory Mertz, Nestor Sosa, Louis Yi Ann Chai, Paul Anantharajah Tambyah, Sai Meng Tham, Sophia Archuleta, Gabriel Yan, David A. Lindholm, Ana Elizabeth Markelz, Katrin Mende, Richard Mularski, Elizabeth Hohmann, Mariam Torres-Soto, Nikolaus Jilg, Ryan C. Maves, Gregory C. Utz, Sarah L. George, Daniel F. Hoft, James D. Brien, Roger Paredes, Lourdes Mateu, Cora Loste, Princy Kumar, Sarah Thornton, Sharmila Mohanraj, Noreen A. Hynes, Lauren M. Sauer, Christopher J. Colombo, Christina Schofield, Rhonda E. Colombo, Susan E. Chambers, Richard M. Novak, Andrea Wendrow, Samir K. Gupta, Tida Lee, Tahaniyat Lalani, Mark Holodniy, Aarthi Chary, Nikhil Huprikar, Anuradha Ganesan, Norio Ohmagari, Ayako Mikami, D. Ashley Price, Christopher J.A. Duncan, Kerry Dierberg, Henry J. Neumann, Stephanie N. Taylor, Alisha Lacour, Najy Masri, Edwin Swiatlo, Kyle Widmer, James D. Neaton, Mary Bessesen, David S. Stephens, Timothy H. Burgess, Timothy M. Uyeki, Robert Walker, G. Lynn Marks, Anu Osinusi, Huyen Cao, Anabela Cardoso, Stephanie de Bono, Douglas E. Schlichting, Kevin K. Chung, Jennifer L. Ferreira, Michelle Green, Mat Makowski, Michael R. Wierzbicki, Tom M. Conrad, Jill Ann El-Khorazaty, Heather Hill, Tyler Bonnett, Nikki Gettinger, Theresa Engel, Teri Lewis, Jing Wang, John H. Beigel, Kay M. Tomashek, Varduhi Ghazaryan, Tatiana Beresnev, Seema Nayak, Lori E. Dodd, Walla Dempsey, Effie Nomicos, Marina Lee, Rhonda Pikaart-Tautges, Mohamed Elsafy, Robert Jurao, Hyung Koo, Michael Proschan, Tammy Yokum, Janice Arega, Ruth Florese, Jocelyn D. Voell, Richard Davey, Ruth C. Serrano, Zanthia Wiley, Varun K. Phadke, Paul A. Goepfert, Carlos A. Gomez, Theresa A. Sofarelli, Laura Certain, Hannah N. Imlay, Cameron R. Wolfe, Emily R. Ko, John J. Engemann, Nora Bautista Felix, Claire R. Wan, Sammy T. Elmor, Laurel R. Bristow, Michelle S. Harkins, Nicole M. Iovine, Marie-Carmelle Elie-Turenne, Victor F. Tapson, Pyoeng Gyun Choe, Richard A. Mularski, Kevin S. Rhie, Rezhan H. Hussein, Dilek Ince, Patricia L. Winokur, Jin Takasaki, Sho Saito, Kimberly McConnell, PharmD, David L. Wyles, Ellen Sarcone, Kevin A. Grimes, Katherine Perez, Charles Janak, Jennifer A. Whitaker, Paulina A. Rebolledo, John Gharbin, Allison A. Lambert, Diego F. Zea, Emma Bainbridge, David C. Hostler, Jordanna M. Hostler, Brian T. Shahan, Evelyn Ling, Minjoung Go, Fleesie A. Hubbard, Melony Chakrabarty, Maryrose Laguio-Vila, Edward E. Walsh, Faheem Guirgis, Vincent C. Marconi, Christian Madar, Scott A. Borgetti, Corri Levine, Joy Nock, Keith Candiotti, Julia Rozman, Fernando Dangond, Yann Hyvert, Andrea Seitzinger, Kaitlyn Cross, Stephanie Pettibone, Seema U. Nayak, and Gregory A. Deye

Subjects
Acute respiratory distress syndrome, Acute hypoxemic respiratory failure, Pneumonia, Critically ill, Cancer, Medicine (General), R5-920
Abstract

Summary: Background: Although immunomodulators have established benefit against the new coronavirus disease (COVID-19) in general, it is uncertain whether such agents improve outcomes without increasing the risk of secondary infections in the specific subgroup of previously immunocompromised patients. We assessed the effect of immunomodulators on outcomes of immunocompromised patients hospitalized for COVID-19. Methods: The protocol was prospectively registered with PROSPERO (CRD42022335397). MEDLINE, Cochrane Central Register of Controlled Trials and references of relevant articles were searched up to 01-06-2022. Authors of potentially eligible randomized controlled trials were contacted to provide data on immunocompromised patients randomized to immunomodulators vs control (i.e., placebo or standard-of-care). Findings: Eleven randomized controlled trials involving 397 immunocompromised patients hospitalized for COVID-19 were included. Ten trials had low risk of bias. There was no difference between immunocompromised patients randomized to immunomodulators vs control regarding mortality [30/182 (16.5%) vs 41/215 (19.1%); RR 0.93, 95% CI 0.61–1.41; p = 0.74], secondary infections (RR 1.00, 95% CI 0.64–1.58; p = 0.99) and change in World Health Organization ordinal scale from baseline to day 15 (weighed mean difference 0.27, 95% CI -0.09–0.63; p = 0.15). In subgroup analyses including only patients with hematologic malignancy, only trials with low risk of bias, only trials administering IL-6 inhibitors, or only trials administering immunosuppressants, there was no difference between comparators regarding mortality. Interpretation: Immunomodulators, compared to control, were not associated with harmful or beneficial outcomes, including mortality, secondary infections, and change in ordinal scale, when administered to immunocompromised patients hospitalized for COVID-19. Funding: Hellenic Foundation for Research and Innovation.

Published
2024
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48. Immunomodulators for immunocompromised patients hospitalized for COVID-19: a meta-analysis of randomized controlled trials

Author

Hermine, Olivier, Mariette, Xavier, Ravaud, Philippe, Bureau, Serge, Dougados, Maxime, Resche-Rigon, Matthieu, Tharaux, Pierre-Louis, Tibi, Annick, Azoulay, Elie, Cadranel, Jacques, Emmerich, Joseph, Fartoukh, Muriel, Guidet, Bertrand, Humbert, Marc, Lacombe, Karine, Mahevas, Matthieu, Pene, Frédéric, Porcher, Raphaël, Pourchet-Martinez, Valerie, Schlemmer, Frédéric, Yazdanpanah, Yazdan, Baron, Gabriel, Perrodeau, Elodie, Vanhoye, Damien, Kedzia, Cécile, Demerville, Lauren, Gysembergh-Houal, Anne, Bourgoin, Alexandre, Raked, Nabil, Mameri, Lakhdar, Montlahuc, Claire, Biard, Lucie, Alary, St.phanie, Hamiria, Samir, Bariz, Thinhinane, Semri, Hala, Hai, Dhiaa Meriem, Benafla, Moustafa, Belloul, Mohamed, Vauboin, Pernelle, Flamand, Saskia, Pacheco, Claire, Walter-Petrich, Anouk, Stan, Emilia, Benarab, Souad, Nyanou, Corine, Charreteur, Robin, Dupre, Céline, Cardet, Kévin, Lehmann, Blandine, Baghli, Kamyl, Madelaine, Claire, D'Ortenzio, Eric, Puéchal, Oriane, Semaille, Caroline, Savale, Laurent, Harrois, Anatole, Figueiredo, Samy, Duranteau, Jacques, Anguel, Nadia, Pavot, Arthur, Monnet, Xavier, Richard, Christian, Teboul, Jean-Louis, Durand, Philippe, Tissieres, Pierre, Jevnikar, Mitja, Montani, David, Pavy, Stephan, Nocturne, Gaétane, Bitoun, Samuel, Noel, Nicolas, Lambotte, Olivier, Escaut, Lelia, Jauréguiberry, Stephane, Baudry, Elodie, Verny, Christiane, Lefevre, Edouard, Zaidan, Mohamad, Molinari, Domitille, Leprun, Gaël, Fourreau, Alain, Cylly, Laurent, Grimaldi, Lamiae, Virlouvet, Myriam, Meftali, Ramdane, Fabre, Soléne, Licois, Marion, Mamoune, Asmaa, Boudali, Yacine, Le Tiec, Clotilde, Verstuyft, Céline, Roques, Anne-Marie, Georgin-Lavialle, Sophie, Senet, Patricia, Pialoux, Gilles, Soria, Angele, Parrot, Antoine, François, Helene, Rozensztajn, Nathalie, Blin, Emmanuelle, Choinier, Pascaline, Camuset, Juliette, Rech, Jean-Simon, Canellas, Antony, Rolland-Debord, Camille, Lemarié, Nadege, Belaube, Nicolas, Nadal, Marine, Siguier, Martin, Petit-Hoang, Camille, 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2024
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