Integrating information from historical data into mechanistic models for influenza forecasting.

Seasonal influenza causes significant annual morbidity and mortality worldwide. In France, it is estimated that, on average, 2 million individuals consult their GP for influenza-like-illness (ILI) every year. Traditionally, mathematical models used for epidemic forecasting can either include parameters capturing the infection process (mechanistic or compartmental models) or rely on time series analysis approaches that do not make mechanistic assumptions (statistical or phenomenological models).

Comparing the Performance of Three Models Incorporating Weather Data to Forecast Dengue Epidemics in Reunion Island, 2018-2019.

We developed mathematical models to analyze a large dengue virus (DENV) epidemic in Reunion Island in 2018-2019. Our models captured major drivers of uncertainty including the complex relationship between climate and DENV transmission, temperature trends, and underreporting. Early assessment correctly concluded that persistence of DENV transmission during the austral winter 2018 was likely and that the second epidemic wave would be larger than the first one.

Impact of palmiped farm density on the resilience of the poultry sector to highly pathogenic avian influenza H5N8 in France.

We analysed the interplay between palmiped farm density and the vulnerability of the poultry production system to highly pathogenic avian influenza (HPAI) H5N8. To do so, we used a spatially-explicit transmission model, which was calibrated to reproduce the observed spatio-temporal distribution of outbreaks in France during the 2016-2017 epidemic of HPAI. Six scenarios were investigated, in which the density of palmiped farms was decreased in the municipalities with the highest palmiped farm density.

An ensemble model based on early predictors to forecast COVID-19 health care demand in France.

Short-term forecasting of the COVID-19 pandemic is required to facilitate the planning of COVID-19 health care demand in hospitals. Here, we evaluate the performance of 12 individual models and 19 predictors to anticipate French COVID-19-related health care needs from September 7, 2020, to March 6, 2021. We then build an ensemble model by combining the individual forecasts and retrospectively test this model from March 7, 2021, to July 6, 2021.

Impact of BNT162b2 Vaccination and Isolation on SARS-CoV-2 Transmission in Israeli Households: An Observational Study.

Several studies have characterized the effectiveness of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. However, estimates of their impact on transmissibility remain limited. Here, we evaluated the impact of isolation and vaccination (7 days after the second dose) on SARS-CoV-2 transmission within Israeli households.

Impact of booster vaccination on the control of COVID-19 Delta wave in the context of waning immunity: application to France in the winter 2021/22.

Europe has experienced a large COVID-19 wave caused by the Delta variant in winter 2021/22. Using mathematical models applied to Metropolitan France, we find that boosters administered to ≥ 65, ≥ 50 or ≥ 18 year-olds may reduce the hospitalisation peak by 25%, 36% and 43% respectively, with a delay of 5 months between second and third dose. A 10% reduction in transmission rates might further reduce it by 41%, indicating that even small increases in protective behaviours may be critical to mitigate the wave.

Benefits and risks associated with different uses of the COVID-19 vaccine Vaxzevria: a modelling study, France, May to September 2021.

Thrombosis with thrombocytopenia (TTS) has been identified as a rare adverse event following COVID-19 vaccination with Vaxzevria. We modelled the benefits and risks of Vaxzevria distribution from May to September 2021 in metropolitan France where other vaccines are available, considering French hospitalisation data and European data on TTS. Across different scenarios, benefits of Vaxzevria distribution in people 55 years and older exceeded the risk of death from COVID-19.

Neonatal susceptibility to meningitis results from the immaturity of epithelial barriers and gut microbiota.

Neonates are highly susceptible to bacterial meningitis as compared to children and adults. Group B streptococcus (GBS) is a major cause of neonatal meningitis. Neonatal meningitis can result from GBS intestinal colonization and translocation across the intestinal barrier (IB).

Evaluating the impact of curfews and other measures on SARS-CoV-2 transmission in French Guiana.

While general lockdowns have proven effective to control SARS-CoV-2 epidemics, they come with enormous costs for society. It is therefore essential to identify control strategies with lower social and economic impact. Here, we report and evaluate the control strategy implemented during a large SARS-CoV-2 epidemic in June-July 2020 in French Guiana that relied on curfews, targeted lockdowns, and other measures.

Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021.

The emergence of SARS-CoV-2 variant 20I/501Y.V1 (VOC-202012/1 or GR/501Y.V1) is concerning given its increased transmissibility.

Estimating the burden of SARS-CoV-2 in France.

France has been heavily affected by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic and went into lockdown on 17 March 2020. Using models applied to hospital and death data, we estimate the impact of the lockdown and current population immunity. We find that 2.

Assessing Zika Virus Transmission Within Households During an Outbreak in Martinique, 2015-2016.

Since 2015, Zika virus (ZIKV) has caused large epidemics in the Americas. Households are natural targets for control interventions, but quantification of the contribution of household transmission to overall spread is needed to guide policy. We developed a modeling framework to evaluate this contribution and key epidemic features of the ZIKV epidemic in Martinique in 2015-2016 from the joint analysis of a household transmission study (n = 68 households), a study among symptomatic pregnant women (n = 281), and seroprevalence surveys of blood donors (n = 457).

Highly pathogenic avian influenza H5N8 in south-west France 2016-2017: A modeling study of control strategies.

In the winter 2016-2017 the largest epidemic of highly pathogenic avian influenza (HPAI) ever recorded in the European Union spread to all 28 member states. France was hit particularly hard and reported a total of 484 infected premises (IPs) by March 2017. We developed a mathematical model to analyze the spatiotemporal evolution of the epidemic and evaluate the impact of control strategies.

Real-Time Assessment of Health-Care Requirements During the Zika Virus Epidemic in Martinique.

The spread of Zika virus in the Americas has been associated with a surge in Guillain-Barré syndrome (GBS) cases. Given the severity of GBS, territories affected by Zika virus need to plan health-care resources to manage GBS patients. To inform such planning in Martinique, we analyzed Zika virus surveillance and GBS data from Martinique in real time with a modeling framework that captured dynamics of the Zika virus epidemic, the risk of GBS in Zika virus-infected persons, and the clinical management of GBS cases.

Seroepidemiology of Human Enterovirus 71 Infection among Children, Cambodia.

Enterovirus 71 is reported to have emerged in Cambodia in 2012; at least 54 children with severe encephalitis died during that outbreak. We used serum samples collected during 2000-2011 to show that the virus had been widespread in the country for at least a decade before the 2012 outbreak.

Use of Viremia to Evaluate the Baseline Case Fatality Ratio of Ebola Virus Disease and Inform Treatment Studies: A Retrospective Cohort Study.

Background: The case fatality ratio (CFR) of Ebola virus disease (EVD) can vary over time and space for reasons that are not fully understood. This makes it difficult to define the baseline CFRs needed to evaluate treatments in the absence of randomized controls. Here, we investigate whether viremia in EVD patients may be used to evaluate baseline EVD CFRs.

Photoelastic coupling in gallium arsenide optomechanical disk resonators.

We analyze the magnitude of the radiation pressure and electrostrictive stresses exerted by light confined inside GaAs semiconductor WGM optomechanical disk resonators, through analytical and numerical means, and find the electrostrictive stress to be of prime importance. We investigate the geometric and photoelastic optomechanical coupling resulting respectively from the deformation of the disk boundary and from the strain-induced refractive index changes in the material, for various mechanical modes of the disks. Photoelastic optomechanical coupling is shown to be a predominant coupling mechanism for certain disk dimensions and mechanical modes, leading to total coupling gom and g(0) reaching respectively 3 THz/nm and 4 MHz.

ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm.

AlGaAs microdisk cavities for second-harmonic generation.

We report on the design, the fabrication, and the optical characterization of AlGaAs microdisks suspended on a GaAs pedestal, conceived for second-harmonic generation with a pump in the third telecom window. We discuss the results concerning the linear characterization of whispering gallery modes at fundamental and second-harmonic wavelengths, an essential step prior to the investigation of quasi-phase-matched processes in this type of microcavity.

Nearly-degenerate three-wave mixing at 1.55 μm in oxidized AlGaAs waveguides.

We report on continuous-wave sum and difference frequency generation in selectively oxidized AlGaAs waveguides designed for degenerate spontaneous parametric down-conversion at 1.55 μm. Sum frequency generation with two pumps around this wavelength is observed with a conversion efficiency η = 1080%W-1cm-2.

Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress.

Accurate prediction of the 3-D structure of small molecules is essential in order to understand their physical, chemical, and biological properties, including how they interact with other molecules. Here, we survey the field of high-throughput methods for 3-D structure prediction and set up new target specifications for the next generation of methods. We then introduce COSMOS, a novel data-driven prediction method that utilizes libraries of fragment and torsion angle parameters.

Integrated terahertz source based on three-wave mixing of whispering-gallery modes.

We propose an integrated terahertz emitter operating at room temperature between 2.4 and 6 THz. Based on difference-frequency generation in a triply resonant Au/AlAs/GaAs/AlAs/Au microcylinder, this nonlinear source is pumped by two near-IR whispering-gallery modes that are excited by InAs quantum dots embedded in the resonator.

Difference frequency generation in GaAs microdisks.

Semiconductor-based whispering-gallery-mode microcavities are very promising for nonlinear optics applications, thanks to the high optical quality factors attainable with today's technology. We propose to exploit this advantage to generate cw light through phase-matched difference frequency generation in a triply resonant GaAs microdisk. A proper choice of the microdisk radius and thickness allows one to select the generated wavelength in the band of 2.