Advanced search in Research products
Research products
arrow_drop_down
Searching FieldsTerms
Any field
arrow_drop_down
includes
arrow_drop_down
Include:
The following results are related to COVID-19. Are you interested to view more results? Visit OpenAIRE - Explore.
194 Research products, page 1 of 20

  • COVID-19
  • Publications
  • Other research products
  • 2018-2022
  • Open Access
  • English
  • HAL - UPEC / UPEM
  • Aurora Universities Network
  • COVID-19

10
arrow_drop_down
Relevance
arrow_drop_down
  • Open Access English
    Authors: 
    Mathieu Bourgarel; Davies M. Pfukenyi; Vanina Boué; Loïc Talignani; Ngoni Chiweshe; Fodé Diop; Alexandre Caron; Gift Matope; Dorothée Missé; Florian Liegeois;
    Publisher: HAL CCSD
    Country: France
    Project: ANR | TIMTAMDEN (ANR-14-CE14-0029)

    Bats carry a great diversity of zoonotic viruses with a high-impact on human health and livestock. Since the emergence of new coronaviruses and paramyxoviruses in humans (e.g. Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Nipah virus), numerous studies clearly established that bats can maintain some of these viruses. Improving our understanding on the role of bats in the epidemiology of the pathogens they harbour is necessary to prevent cross-species spill over along the wild/domestic/human gradient. In this study, we screened bat faecal samples for the presence of Coronavirus and Paramyxovirus in two caves frequently visited by local people to collect manure and/or to hunt bats in Zimbabwe. We amplified partial RNA-dependent RNA polymerase genes of Alpha and Betacoronavirus together with the partial polymerase gene of Paramyxovirus. Identified coronaviruses were related to pathogenic human strains and the paramyxovirus belonged to the recently described Jeilongvirus genus. Our results highlighted the importance of monitoring virus circulation in wildlife, especially bats, in the context of intense human-wildlife interfaces in order to strengthen prevention measures among local populations and to implement sentinel surveillance in sites with high zoonotic diseases transmission potential. Highlights • Coronavirus and Paramyxovirus circulate in Hipposideros bat species in Zimbabwe. • Importance of widening viral screening in under-investigated countries • Sentinel surveillance in sites with high zoonotic transmission potential

  • Open Access English
    Authors: 
    Rania Mabrouk; Ramzi MAHMOUDI; Nihed Yousfi; Mohamed Bedoui;
    Publisher: HAL CCSD
    Country: France

    International audience; Corona-Virus Disease (COVID-19), caused by the novel Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) has been spreading rapidly worldwide causing the world to face a global health crisis. Countries are experiencing a new wave of contamination and are witnessing spikes in the disease without being able to control its spread again. This paper aims to analyze the mortality rate related to the COVID-19 pandemic infection in Tunisia and to assess the effectiveness of health control policies. Data collection for this document was stopped on October, 31 st , 2020.

  • Open Access English
    Authors: 
    Young-Jun Park; Kaitlyn D. LaCourse; Christian Cambillau; Frank DiMaio; Joseph D. Mougous; David Veesler;
    Publisher: Nature Portfolio
    Country: France
    Project: NIH | Protein structure determi... (1R01GM123089-01)

    Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although some information is available about the mechanisms of tail contraction leading to effector delivery, the detailed architecture and function of the baseplate remain unknown. Here, we report the 3.7 Å resolution cryo-electron microscopy reconstruction of an enteroaggregative Escherichia coli baseplate subcomplex assembled from TssK, TssF and TssG. The structure reveals two TssK trimers interact with a locally pseudo-3-fold symmetrical complex comprising two copies of TssF and one copy of TssG. TssF and TssG are structurally related to each other and to components of the phage T4 baseplate and of the type IV secretion system, strengthening the evolutionary relationships among these macromolecular machines. These results, together with bacterial two-hybrid assays, provide a structural framework to understand the T6SS baseplate architecture. Type VI secretion systems (T6SSs) translocate effector proteins into eukaryotic and bacterial recipient cells and are present in many Gram-negative bacteria. Here the authors present the 3.7 Å cryoEM structure of the E.coli T6SS baseplate wedge comprising TssK–TssF–TssG and propose a model for the T6SS baseplate and needle complex.

  • Publication . Conference object . Preprint . Article . 2020
    Open Access English
    Authors: 
    Hadrien Titeux; Rachid Riad; Xuan-Nga Cao; Nicolas Hamilakis; Kris Madden; Alejandrina Cristia; Anne-Catherine Bachoud-Lévi; Emmanuel Dupoux;
    Publisher: HAL CCSD
    Country: France
    Project: ANR | ACLEW (ANR-16-DATA-0004), ANR | LangAge (ANR-17-CE28-0007), ANR | PSL (ANR-10-IDEX-0001), ANR | PRAIRIE (ANR-19-P3IA-0001), ANR | FrontCog (ANR-17-EURE-0017), ANR | MechELex (ANR-14-CE30-0003)

    International audience; We introduce Seshat, a new, simple and open-source software to efficiently manage annotations of speech corpora. The Seshat software allows users to easily customise and manage annotations of large audio corpora while ensuring compliance with the formatting and naming conventions of the annotated output files. In addition, it includes procedures for checking the content of annotations following specific rules that can be implemented in personalised parsers. Finally, we propose a double-annotation mode, for which Seshat computes automatically an associated inter-annotator agreement with the γ measure taking into account the categorisation and segmentation discrepancies.; Nous introduisons Seshat, un nouveau logiciel libre permettant d'efficacement gérer l'annotation de corpora de parole. Le logiciel Seshat permet aux utilisateurs de facilement spécifier et gérer l'annotation de corpora d'audio conséquents, tout en s'assurant que les fichiers des annotations respectent des conventions de formattage et de nommage prédéfinies. En outre, des procédures de vérification du contenu des annotations sont livrées dans Seshat, avec la possibilité d'inclure des parsers externes. Finalement, nous proposons un mode dit de "double annotation", dans lequel Seshat calcule automatiquement une mesure de la concordance inter-annotateur avec la mesure γ, qui prend en compte les différences de catégorisation et de segmentation.

  • Open Access English
    Authors: 
    Robin Ohannessian; Tu Anh Duong; Anna Odone;
    Publisher: HAL CCSD
    Country: France

    International audience; On March 11, 2020, the World Health Organization declared the coronavirus disease 2019 (COVID-19) outbreak as a pandemic, with over 720,000 cases reported in more than 203 countries as of 31 March. The response strategy included early diagnosis, patient isolation, symptomatic monitoring of contacts as well as suspected and confirmed cases, and public health quarantine. In this context, telemedicine, particularly video consultations, has been promoted and scaled up to reduce the risk of transmission, especially in the United Kingdom and the United States of America. Based on a literature review, the first conceptual framework for telemedicine implementation during outbreaks was published in 2015. An updated framework for telemedicine in the COVID-19 pandemic has been defined. This framework could be applied at a large scale to improve the national public health response. Most countries, however, lack a regulatory framework to authorize, integrate, and reimburse telemedicine services, including in emergency and outbreak situations. In this context, Italy does not include telemedicine in the essential levels of care granted to all citizens within the National Health Service, while France authorized, reimbursed, and actively promoted the use of telemedicine. Several challenges remain for the global use and integration of telemedicine into the public health response to COVID-19 and future outbreaks. All stakeholders are encouraged to address the challenges and collaborate to promote the safe and evidence-based use of telemedicine during the current pandemic and future outbreaks. For countries without integrated telemedicine in their national health care system, the COVID-19 pandemic is a call to adopt the necessary regulatory frameworks for supporting wide adoption of telemedicine.

  • Open Access English
    Authors: 
    Bérengère Dequéant; Quentin Pascal; Héloïse Bilbault; Elie Dagher; Maria-Laura Boschiroli; Nathalie Cordonnier; Edouard Reyes-Gomez;
    Publisher: HAL CCSD
    Country: France

    International audience; A 6-y-old neutered male ferret (Mustela putorius furo) was presented because of a 1-mo history of progressive weight loss, chronic cough, and hair loss. On clinical examination, the animal was coughing, slightly depressed, moderately hypothermic, and had bilateral epiphora. Thoracic radiography was suggestive of severe multinodular interstitial pneumonia. Abdominal ultrasound examination revealed hepatosplenomegaly and mesenteric and pancreaticoduodenal lymphadenopathy. Fine-needle aspiration of the pancreaticoduodenal lymph node, followed by routine Romanowsky and Ziehl-Neelsen stains, revealed numerous macrophages containing myriad acid-fast bacilli, leading to identification of mycobacteriosis. Autopsy and histologic examination confirmed the presence of disseminated, poorly defined, acid-fast, bacilli-rich granulomas in the pancreaticoduodenal and mesenteric lymph nodes, intestines, and lungs. Destaining of May-Grunwald/Giemsa-stained slides with alcohol, and then restaining with Ziehl-Neelsen, revealed acid-fast rods and avoided repeat tissue sampling without affecting the Ziehl-Neelsen stain quality and cytologic features. Tissue samples were submitted for a PCR assay targeting the heat shock protein gene (hsp65) and revealed 100% homology with Mycobacterium genavense. We emphasize the use of special stains and PCR for identification of this potential zoonotic agent.

  • Open Access English
    Authors: 
    Laurent Menut; Bertrand Bessagnet; Guillaume Siour; Sylvain Mailler; Romain Pennel; Arineh Cholakian;
    Publisher: The Authors. Published by Elsevier B.V.
    Country: France

    Recent studies based on observations have shown the impact of lockdown measures taken in various European countries to contain the Covid-19 pandemic on air quality. However, these studies are often limited to compare situations without and with lockdown measures, which correspond to different time periods and then under different meteorological conditions. We propose a modelling study with the WRF-CHIMERE modelling suite for March 2020, an approach allowing to compare atmospheric composition with and without lockdown measures without the biases of meteorological conditions. This study shows that the lockdown effect on atmospheric composition, in particular through massive traffic reductions, has been important for several short-lived atmospheric trace species, with a large reduction in NO2 concentrations, a lower reduction in Particulate Matter (PM) concentrations and a mitigated effect on ozone concentrations due to non-linear chemical effects. Highlights • Air pollution modelling • COVID19 epidemy • Regional modelling • Anthropogenic emissions scenario • Impact of emissions reduction Graphical abstract Unlabelled Image

  • Open Access English
    Authors: 
    El Karoui, Khalil; Hourmant, Maryvonne; Ayav, Carole; Glowacki, François; Couchoud, Cécile; Lapidus, Nathanaël;
    Publisher: HAL CCSD
    Country: France

    Background and objectivesDialysis patients have a high mortality risk after coronavirus disease 2019 (COVID-19) and an altered immunologic response to vaccines, but vaccine clinical effectiveness remains unknown in this population.Design, setting, participants, & measurementsUsing Bayesian multivariable spatiotemporal models, we estimated the association between vaccine exposure and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) severe infections (with hospital admission) in dialysis patients from simultaneous incidence in the general population. For dialysis patients, cases were reported within the French end-stage kidney disease REIN registry from March 11, 2020, to April 29, 2021, and vaccine exposure (first dose) was reported in weekly national surveys since January 2021. Cases in the general population were obtained from the national exhaustive inpatient surveillance system (SI-VIC database), and vaccination coverage (first dose) was obtained from the national surveillance system (VAC-SI database).ResultsDuring the first wave, incidence in dialysis patients was approximately proportional to the general population. However, we showed a lower relative incidence for dialysis patients during the second wave (compared with that observed in nondialysis patients), suggesting an effect of prevention measures. Moreover, from the beginning of the vaccination rollout, incidence in dialysis patients was lower compared with predictions based on the first and second waves. Adding vaccination coverages in dialysis and nondialysis patients as predictors allowed the reported cases to be fit correctly (3685 predicted cases, 95% confidence interval, 3552 to 3816, versus 3620 reported). Incidence rate ratios were 0.37 (95% confidence interval, 0.18 to 0.71) for vaccine exposure in dialysis patients and 0.50 (95% confidence interval, 0.40 to 0.61) per 10% higher in vaccination coverage in the same-age general population, meaning that vaccine exposure in dialysis patients and the general population was independently associated with lower hospitalization rate of dialysis patients.ConclusionsOur findings suggest that vaccination may yield a protective effect against severe forms of COVID-19 in dialysis patients, despite altered immunologic vaccine responses.

  • Open Access English
    Authors: 
    M. Fieux; Antoine Gavoille; Fabien Subtil; Sophie Bartier; S. Tringali;
    Publisher: HAL CCSD
    Country: France

    Abstract Background The ongoing COVID-19 pandemic has disrupted the surgical training of residents. There is a real concern that trainees will not be able to meet their training requirements. Low-fidelity surgical simulation appears to be an alternative for surgical training. The educational benefits of repeating ossiculoplasty simulations under a microscope have never been evaluated. With this study we aimed to evaluate the differences in performance scores and on a global rating scale before and after training on an ossiculoplasty simulator. Methods In this quasi-experimental, prospective, single-centre, before-after study with blinded rater evaluation, residents performed five microscopic ossiculoplasty tasks with a difficulty gradient (sliding beads onto rods, the insertion of a partial prosthesis, the insertion of a total prosthesis, and the insertion of a stapedotomy piston under microscopic or endoscopic surgery) before and after training on the same simulator. Performance scores were defined for each task, and total performance scores (score/min) were calculated. All data were collected prospectively. Results Six out of seven intermediate residents and 8/9 novices strongly agreed that the simulator was an effective training device and should be included in the ENT residency program. The mean effect of training was a significant increase in the total performance score (+ 0.52 points/min, [95 % CI, 0.40–0.64], p < 0.001), without a significant difference between novice and intermediate residents. Conclusions This preliminary study shows that techniques for middle-ear surgery can be acquired using a simulator, avoiding any risk for patients, even under lockdown measures.

  • Open Access English
    Authors: 
    Marine Gauthier; Denis Agniel; Rodolphe Thiébaut; Boris P. Hejblum;
    Publisher: HAL CCSD
    Country: France

    SummaryState-of-the-art methods for single-cell RNA sequencing (scRNA-seq) Differential Expression Analysis (DEA) often rely on strong distributional assumptions that are difficult to verify in practice. Furthermore, while the increasing complexity of clinical and biological single-cell studies calls for greater tool versatility, the majority of existing methods only tackle the comparison between two conditions. We propose a novel, distribution-free, and flexible approach to DEA for single-cell RNA-seq data. This new method, called ccdf, tests the association of each gene expression with one or many variables of interest (that can be either continuous or discrete), while potentially adjusting for additional covariates. To test such complex hypotheses, ccdf uses a conditional independence test relying on the conditional cumulative distribution function, estimated through multiple regressions. We provide the asymptotic distribution of the ccdf test statistic as well as a permutation test (when the number of observed cells is not sufficiently large). ccdf substantially expands the possibilities for scRNA-seq DEA studies: it obtains good statistical performance in various simulation scenarios considering complex experimental designs (i.e. beyond the two condition comparison), while retaining competitive performance with state-of-the-art methods in a two-condition benchmark. We apply ccdf to a large publicly available scRNA-seq dataset of 84,140 SARS-CoV-2 reactive CD8+ T cells, in order to identify the diffentially expressed genes across 3 groups of COVID-19 severity (mild, hospitalized, and ICU) while accounting for seven different cellular subpopulations.

Advanced search in Research products
Research products
arrow_drop_down
Searching FieldsTerms
Any field
arrow_drop_down
includes
arrow_drop_down
Include:
The following results are related to COVID-19. Are you interested to view more results? Visit OpenAIRE - Explore.
194 Research products, page 1 of 20
  • Open Access English
    Authors: 
    Mathieu Bourgarel; Davies M. Pfukenyi; Vanina Boué; Loïc Talignani; Ngoni Chiweshe; Fodé Diop; Alexandre Caron; Gift Matope; Dorothée Missé; Florian Liegeois;
    Publisher: HAL CCSD
    Country: France
    Project: ANR | TIMTAMDEN (ANR-14-CE14-0029)

    Bats carry a great diversity of zoonotic viruses with a high-impact on human health and livestock. Since the emergence of new coronaviruses and paramyxoviruses in humans (e.g. Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Nipah virus), numerous studies clearly established that bats can maintain some of these viruses. Improving our understanding on the role of bats in the epidemiology of the pathogens they harbour is necessary to prevent cross-species spill over along the wild/domestic/human gradient. In this study, we screened bat faecal samples for the presence of Coronavirus and Paramyxovirus in two caves frequently visited by local people to collect manure and/or to hunt bats in Zimbabwe. We amplified partial RNA-dependent RNA polymerase genes of Alpha and Betacoronavirus together with the partial polymerase gene of Paramyxovirus. Identified coronaviruses were related to pathogenic human strains and the paramyxovirus belonged to the recently described Jeilongvirus genus. Our results highlighted the importance of monitoring virus circulation in wildlife, especially bats, in the context of intense human-wildlife interfaces in order to strengthen prevention measures among local populations and to implement sentinel surveillance in sites with high zoonotic diseases transmission potential. Highlights • Coronavirus and Paramyxovirus circulate in Hipposideros bat species in Zimbabwe. • Importance of widening viral screening in under-investigated countries • Sentinel surveillance in sites with high zoonotic transmission potential

  • Open Access English
    Authors: 
    Rania Mabrouk; Ramzi MAHMOUDI; Nihed Yousfi; Mohamed Bedoui;
    Publisher: HAL CCSD
    Country: France

    International audience; Corona-Virus Disease (COVID-19), caused by the novel Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) has been spreading rapidly worldwide causing the world to face a global health crisis. Countries are experiencing a new wave of contamination and are witnessing spikes in the disease without being able to control its spread again. This paper aims to analyze the mortality rate related to the COVID-19 pandemic infection in Tunisia and to assess the effectiveness of health control policies. Data collection for this document was stopped on October, 31 st , 2020.

  • Open Access English
    Authors: 
    Young-Jun Park; Kaitlyn D. LaCourse; Christian Cambillau; Frank DiMaio; Joseph D. Mougous; David Veesler;
    Publisher: Nature Portfolio
    Country: France
    Project: NIH | Protein structure determi... (1R01GM123089-01)

    Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although some information is available about the mechanisms of tail contraction leading to effector delivery, the detailed architecture and function of the baseplate remain unknown. Here, we report the 3.7 Å resolution cryo-electron microscopy reconstruction of an enteroaggregative Escherichia coli baseplate subcomplex assembled from TssK, TssF and TssG. The structure reveals two TssK trimers interact with a locally pseudo-3-fold symmetrical complex comprising two copies of TssF and one copy of TssG. TssF and TssG are structurally related to each other and to components of the phage T4 baseplate and of the type IV secretion system, strengthening the evolutionary relationships among these macromolecular machines. These results, together with bacterial two-hybrid assays, provide a structural framework to understand the T6SS baseplate architecture. Type VI secretion systems (T6SSs) translocate effector proteins into eukaryotic and bacterial recipient cells and are present in many Gram-negative bacteria. Here the authors present the 3.7 Å cryoEM structure of the E.coli T6SS baseplate wedge comprising TssK–TssF–TssG and propose a model for the T6SS baseplate and needle complex.

  • Publication . Conference object . Preprint . Article . 2020
    Open Access English
    Authors: 
    Hadrien Titeux; Rachid Riad; Xuan-Nga Cao; Nicolas Hamilakis; Kris Madden; Alejandrina Cristia; Anne-Catherine Bachoud-Lévi; Emmanuel Dupoux;
    Publisher: HAL CCSD
    Country: France
    Project: ANR | ACLEW (ANR-16-DATA-0004), ANR | LangAge (ANR-17-CE28-0007), ANR | PSL (ANR-10-IDEX-0001), ANR | PRAIRIE (ANR-19-P3IA-0001), ANR | FrontCog (ANR-17-EURE-0017), ANR | MechELex (ANR-14-CE30-0003)

    International audience; We introduce Seshat, a new, simple and open-source software to efficiently manage annotations of speech corpora. The Seshat software allows users to easily customise and manage annotations of large audio corpora while ensuring compliance with the formatting and naming conventions of the annotated output files. In addition, it includes procedures for checking the content of annotations following specific rules that can be implemented in personalised parsers. Finally, we propose a double-annotation mode, for which Seshat computes automatically an associated inter-annotator agreement with the γ measure taking into account the categorisation and segmentation discrepancies.; Nous introduisons Seshat, un nouveau logiciel libre permettant d'efficacement gérer l'annotation de corpora de parole. Le logiciel Seshat permet aux utilisateurs de facilement spécifier et gérer l'annotation de corpora d'audio conséquents, tout en s'assurant que les fichiers des annotations respectent des conventions de formattage et de nommage prédéfinies. En outre, des procédures de vérification du contenu des annotations sont livrées dans Seshat, avec la possibilité d'inclure des parsers externes. Finalement, nous proposons un mode dit de "double annotation", dans lequel Seshat calcule automatiquement une mesure de la concordance inter-annotateur avec la mesure γ, qui prend en compte les différences de catégorisation et de segmentation.

  • Open Access English
    Authors: 
    Robin Ohannessian; Tu Anh Duong; Anna Odone;
    Publisher: HAL CCSD
    Country: France

    International audience; On March 11, 2020, the World Health Organization declared the coronavirus disease 2019 (COVID-19) outbreak as a pandemic, with over 720,000 cases reported in more than 203 countries as of 31 March. The response strategy included early diagnosis, patient isolation, symptomatic monitoring of contacts as well as suspected and confirmed cases, and public health quarantine. In this context, telemedicine, particularly video consultations, has been promoted and scaled up to reduce the risk of transmission, especially in the United Kingdom and the United States of America. Based on a literature review, the first conceptual framework for telemedicine implementation during outbreaks was published in 2015. An updated framework for telemedicine in the COVID-19 pandemic has been defined. This framework could be applied at a large scale to improve the national public health response. Most countries, however, lack a regulatory framework to authorize, integrate, and reimburse telemedicine services, including in emergency and outbreak situations. In this context, Italy does not include telemedicine in the essential levels of care granted to all citizens within the National Health Service, while France authorized, reimbursed, and actively promoted the use of telemedicine. Several challenges remain for the global use and integration of telemedicine into the public health response to COVID-19 and future outbreaks. All stakeholders are encouraged to address the challenges and collaborate to promote the safe and evidence-based use of telemedicine during the current pandemic and future outbreaks. For countries without integrated telemedicine in their national health care system, the COVID-19 pandemic is a call to adopt the necessary regulatory frameworks for supporting wide adoption of telemedicine.

  • Open Access English
    Authors: 
    Bérengère Dequéant; Quentin Pascal; Héloïse Bilbault; Elie Dagher; Maria-Laura Boschiroli; Nathalie Cordonnier; Edouard Reyes-Gomez;
    Publisher: HAL CCSD
    Country: France

    International audience; A 6-y-old neutered male ferret (Mustela putorius furo) was presented because of a 1-mo history of progressive weight loss, chronic cough, and hair loss. On clinical examination, the animal was coughing, slightly depressed, moderately hypothermic, and had bilateral epiphora. Thoracic radiography was suggestive of severe multinodular interstitial pneumonia. Abdominal ultrasound examination revealed hepatosplenomegaly and mesenteric and pancreaticoduodenal lymphadenopathy. Fine-needle aspiration of the pancreaticoduodenal lymph node, followed by routine Romanowsky and Ziehl-Neelsen stains, revealed numerous macrophages containing myriad acid-fast bacilli, leading to identification of mycobacteriosis. Autopsy and histologic examination confirmed the presence of disseminated, poorly defined, acid-fast, bacilli-rich granulomas in the pancreaticoduodenal and mesenteric lymph nodes, intestines, and lungs. Destaining of May-Grunwald/Giemsa-stained slides with alcohol, and then restaining with Ziehl-Neelsen, revealed acid-fast rods and avoided repeat tissue sampling without affecting the Ziehl-Neelsen stain quality and cytologic features. Tissue samples were submitted for a PCR assay targeting the heat shock protein gene (hsp65) and revealed 100% homology with Mycobacterium genavense. We emphasize the use of special stains and PCR for identification of this potential zoonotic agent.

  • Open Access English
    Authors: 
    Laurent Menut; Bertrand Bessagnet; Guillaume Siour; Sylvain Mailler; Romain Pennel; Arineh Cholakian;
    Publisher: The Authors. Published by Elsevier B.V.
    Country: France

    Recent studies based on observations have shown the impact of lockdown measures taken in various European countries to contain the Covid-19 pandemic on air quality. However, these studies are often limited to compare situations without and with lockdown measures, which correspond to different time periods and then under different meteorological conditions. We propose a modelling study with the WRF-CHIMERE modelling suite for March 2020, an approach allowing to compare atmospheric composition with and without lockdown measures without the biases of meteorological conditions. This study shows that the lockdown effect on atmospheric composition, in particular through massive traffic reductions, has been important for several short-lived atmospheric trace species, with a large reduction in NO2 concentrations, a lower reduction in Particulate Matter (PM) concentrations and a mitigated effect on ozone concentrations due to non-linear chemical effects. Highlights • Air pollution modelling • COVID19 epidemy • Regional modelling • Anthropogenic emissions scenario • Impact of emissions reduction Graphical abstract Unlabelled Image

  • Open Access English
    Authors: 
    El Karoui, Khalil; Hourmant, Maryvonne; Ayav, Carole; Glowacki, François; Couchoud, Cécile; Lapidus, Nathanaël;
    Publisher: HAL CCSD
    Country: France

    Background and objectivesDialysis patients have a high mortality risk after coronavirus disease 2019 (COVID-19) and an altered immunologic response to vaccines, but vaccine clinical effectiveness remains unknown in this population.Design, setting, participants, & measurementsUsing Bayesian multivariable spatiotemporal models, we estimated the association between vaccine exposure and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) severe infections (with hospital admission) in dialysis patients from simultaneous incidence in the general population. For dialysis patients, cases were reported within the French end-stage kidney disease REIN registry from March 11, 2020, to April 29, 2021, and vaccine exposure (first dose) was reported in weekly national surveys since January 2021. Cases in the general population were obtained from the national exhaustive inpatient surveillance system (SI-VIC database), and vaccination coverage (first dose) was obtained from the national surveillance system (VAC-SI database).ResultsDuring the first wave, incidence in dialysis patients was approximately proportional to the general population. However, we showed a lower relative incidence for dialysis patients during the second wave (compared with that observed in nondialysis patients), suggesting an effect of prevention measures. Moreover, from the beginning of the vaccination rollout, incidence in dialysis patients was lower compared with predictions based on the first and second waves. Adding vaccination coverages in dialysis and nondialysis patients as predictors allowed the reported cases to be fit correctly (3685 predicted cases, 95% confidence interval, 3552 to 3816, versus 3620 reported). Incidence rate ratios were 0.37 (95% confidence interval, 0.18 to 0.71) for vaccine exposure in dialysis patients and 0.50 (95% confidence interval, 0.40 to 0.61) per 10% higher in vaccination coverage in the same-age general population, meaning that vaccine exposure in dialysis patients and the general population was independently associated with lower hospitalization rate of dialysis patients.ConclusionsOur findings suggest that vaccination may yield a protective effect against severe forms of COVID-19 in dialysis patients, despite altered immunologic vaccine responses.

  • Open Access English
    Authors: 
    M. Fieux; Antoine Gavoille; Fabien Subtil; Sophie Bartier; S. Tringali;
    Publisher: HAL CCSD
    Country: France

    Abstract Background The ongoing COVID-19 pandemic has disrupted the surgical training of residents. There is a real concern that trainees will not be able to meet their training requirements. Low-fidelity surgical simulation appears to be an alternative for surgical training. The educational benefits of repeating ossiculoplasty simulations under a microscope have never been evaluated. With this study we aimed to evaluate the differences in performance scores and on a global rating scale before and after training on an ossiculoplasty simulator. Methods In this quasi-experimental, prospective, single-centre, before-after study with blinded rater evaluation, residents performed five microscopic ossiculoplasty tasks with a difficulty gradient (sliding beads onto rods, the insertion of a partial prosthesis, the insertion of a total prosthesis, and the insertion of a stapedotomy piston under microscopic or endoscopic surgery) before and after training on the same simulator. Performance scores were defined for each task, and total performance scores (score/min) were calculated. All data were collected prospectively. Results Six out of seven intermediate residents and 8/9 novices strongly agreed that the simulator was an effective training device and should be included in the ENT residency program. The mean effect of training was a significant increase in the total performance score (+ 0.52 points/min, [95 % CI, 0.40–0.64], p < 0.001), without a significant difference between novice and intermediate residents. Conclusions This preliminary study shows that techniques for middle-ear surgery can be acquired using a simulator, avoiding any risk for patients, even under lockdown measures.

  • Open Access English
    Authors: 
    Marine Gauthier; Denis Agniel; Rodolphe Thiébaut; Boris P. Hejblum;
    Publisher: HAL CCSD
    Country: France

    SummaryState-of-the-art methods for single-cell RNA sequencing (scRNA-seq) Differential Expression Analysis (DEA) often rely on strong distributional assumptions that are difficult to verify in practice. Furthermore, while the increasing complexity of clinical and biological single-cell studies calls for greater tool versatility, the majority of existing methods only tackle the comparison between two conditions. We propose a novel, distribution-free, and flexible approach to DEA for single-cell RNA-seq data. This new method, called ccdf, tests the association of each gene expression with one or many variables of interest (that can be either continuous or discrete), while potentially adjusting for additional covariates. To test such complex hypotheses, ccdf uses a conditional independence test relying on the conditional cumulative distribution function, estimated through multiple regressions. We provide the asymptotic distribution of the ccdf test statistic as well as a permutation test (when the number of observed cells is not sufficiently large). ccdf substantially expands the possibilities for scRNA-seq DEA studies: it obtains good statistical performance in various simulation scenarios considering complex experimental designs (i.e. beyond the two condition comparison), while retaining competitive performance with state-of-the-art methods in a two-condition benchmark. We apply ccdf to a large publicly available scRNA-seq dataset of 84,140 SARS-CoV-2 reactive CD8+ T cells, in order to identify the diffentially expressed genes across 3 groups of COVID-19 severity (mild, hospitalized, and ICU) while accounting for seven different cellular subpopulations.