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Data-driven modeling based on machine learning (ML) is showing enormous potential for weather forecasting. Rapid progress has been made with impressive results for some applications. The uptake of ML methods could be a game changer for the incremental progress in traditional numerical weather prediction (NWP) known as the "quiet revolution" of weather forecasting. The computational cost of running a forecast with standard NWP systems greatly hinders the improvements that can be made by increasing model resolution and ensemble sizes. An emerging new generation of ML models, developed using high-quality reanalysis datasets like ERA5 for training, allows forecasts that require much lower computational costs and that are highly competitive in terms of accuracy. Here, we compare for the first time ML-generated forecasts with standard NWP-based forecasts in an operational-like context, initialized from the same initial conditions. Focusing on deterministic forecasts, we apply common forecast verification tools to assess to what extent a data-driven forecast produced with one of the recently developed ML models (PanguWeather) matches the quality and attributes of a forecast from one of the leading global NWP systems (the ECMWF IFS). The results are very promising, with comparable accuracy for both global metrics and extreme events, when verified against both the operational IFS analysis and synoptic observations. Overly smooth forecasts, increasing bias with forecast lead time, and poor performance in predicting tropical cyclone intensity are identified as current drawbacks of ML-based forecasts. A new NWP paradigm is emerging relying on inference from ML models and state-of-the-art analysis and reanalysis datasets for forecast initialization and model training. SIGNIFICANCE STATEMENT: We compare the traditional approach of generating weather forecasts with a new approach based on machine learning (ML). The traditional approach is based on resolving physical equations with numerical methods and can be quite expensive to run on supercomputers. ML models are trained on a very large dataset that combines observations and physically based models to derive our best estimate of the state of the atmosphere hour after hour, over the past decades. In this work, we assess the forecast performance with statistical tools and a focus on extreme events. Our results suggest that ML models, which are much less expensive to run than standard methods, could have a promising future in numerical weather prediction. Our study also points out weaknesses and limitations that would require further investigations and future ML model improvements. KEYWORDS: Forecast verification/skill; Operational forecasting; Machine learning, 1. Introduction Numerical weather prediction (NWP) is the dominant approach for weather forecasting. A weather forecast is the result of the numerical integration of partial differential equations starting from the [...]

Abstract Background Pervasive translation is a widespread phenomenon that plays a critical role in the emergence of novel microproteins, but the diversity of translation patterns contributing to their generation remains unclear. Based on 54 ribosome profiling (Ribo-Seq) datasets, we investigated the yeast Ribo-Seq landscape using a representation framework that allows the comprehensive inventory and classification of the entire diversity of Ribo-Seq signals, including non-canonical ones. Results We show that if coding regions occupy specific areas of the Ribo-Seq landscape, noncoding regions encompass a wide diversity of Ribo-Seq signals and, conversely, populate the entire landscape. Our results show that pervasive translation can, nevertheless, be associated with high specificity, with 1055 noncoding ORFs exhibiting canonical Ribo-Seq signals. Using mass spectrometry under standard conditions or proteasome inhibition with an in-house analysis protocol, we report 239 microproteins originating from noncoding ORFs that display canonical but also non-canonical Ribo-Seq signals. Each condition yields dozens of additional microprotein candidates with comparable translation properties, suggesting a larger population of volatile microproteins that are challenging to detect. Our findings suggest that non-canonical translation signals may harbor valuable information and underscore the significance of considering them in proteogenomic studies. Finally, we show that the translation outcome of a noncoding ORF is primarily determined by the initiating codon and the codon distribution in its two alternative frames, rather than features indicative of functionality. Conclusion Our results enable us to propose a topology of a species’ Ribo-Seq landscape, opening the way to comparative analyses of this translation landscape under different conditions.

Summary: Background: No study has compared the virological and immunological status of young people with perinatally-acquired HIV infection (P-HIV) with that of people with HIV adulthood (A-HIV) having a similar duration of infection. Methods: 5 French cohorts of P-HIV and A-HIV patients with a known date of HIV-infection and receiving antiretroviral treatment (ART), were used to compare the following proportions of: virological failure (VF) defined as plasma HIV RNA ≥ 50 copies/mL, CD4 cell percentages and CD4:CD8 ratios, at the time of the most recent visit since 2012. The analysis was stratified on time since infection, and multivariate models were adjusted for demographics and treatment history. Findings: 310 P-HIV were compared to 1515 A-HIV (median current ages 20.9 [IQR:14.4–25.5] and 45.9 [IQR:37.9–53.5] respectively). VF at the time of the most recent evaluation was significantly higher among P-HIV (22.6%, 69/306) than A-HIV (3.3%, 50/1514); p ≤ 0.0001. The risk of VF was particularly high among the youngest children (2–5 years), adolescents (13–17 years) and young adults (18–24 years), compared to A-HIV with a similar duration of infection: adjusted Odds-Ratio (aOR) 7.0 [95% CI: 1.7; 30.0], 11.4 [4.2; 31.2] and 3.3 [1.0; 10.8] respectively. The level of CD4 cell percentages did not differ between P-HIV and A-HIV. P-HIV aged 6–12 and 13–17 were more likely than A-HIV to have a CD4:CD8 ratio ≥ 1: 84.1% vs. 58.8% (aOR = 3.5 [1.5; 8.3]), and 60.9% vs. 54.7% (aOR = 1.9 [0.9; 4.2]) respectively. Interpretation: P-HIV were at a higher risk of VF than A-HIV with a similar duration of infection, even after adjusting for treatment history, whereas they were not at a higher risk of immunological impairment. Exposure to viral replication among young patients living with HIV since birth or a very early age, probably because of lower adherence, could have an impact on health, raising major concerns about the selection of resistance mutations and the risk of HIV transmission. Funding: Inserm - ANRS MIE.

The drivers of the HIV epidemic, the viruses, the opportunistic infections, the attitudes and the resources allocated to the fight against HIV/AIDS, vary substantially across countries. French Guiana, at the crossroads between Amazonian South America and the Caribbean, constitutes a singular context with poor populations and rich country health funding, which has allowed researchers to gather lots of information on the particulars of our epidemic. We aimed to focus on the little known story of forty years of HIV research in French Guiana and emphasize how local research intertwined with public health action has yielded continuous progress, despite the difficult social conditions of the affected population. We searched Web of Science and associated local experts who worked through much of the epidemic in selecting the most meaningful products of local research for clinical and public health outcomes in French Guiana. Research tools and facilities included, from 1991 onwards, the HIV hospital cohort and the HIV-histoplasmosis cohort. Ad hoc studies funded by the ANRS or the European Regional Development fund shed light on vulnerable groups. The cumulative impact of prospective routine collection and focused efforts has yielded a breadth of knowledge, allowing for informed decisions and the adaptation of prevention, testing and care in French Guiana. After this overview, we emphasize that the close integration of research and public health was crucial in adapting interventions to the singular context of French Guiana.

Abstract Background In French Guiana (population 294,000) the prevalence of type 2 diabetes (10%) and of HIV(1.1%) are very high. Our objective was to determine the prevalence of diabetes and its complications in a HIV cohort. Materials and methods We enrolled HIV-infected persons followed in Cayenne, Kourou, and Saint Laurent du Maroni hospitals between January 1, 1992 and December 31, 2021 in the French Hospital Database for HIV (FHDH) a national database compiling data from all French regions. Results There was no difference of diabetes prevalence between men (8.2%) and women (8.8%), P = 0.4. Patients with diabetes were older (56 years ± 13.4) than those without diabetes (44.7 years ± 13.6) and prevalence increased with age. The proportion of persons with diabetes was greater among virologically suppressed persons (10%) than those with a detectable viral load under antiretroviral treatment (5.8%). Persons with diabetes had substantially greater CD4 counts at diagnosis than persons without diabetes. The majority of macro and microvascular complications were observed in people with diabetes. Persons with diabetes and HIV were significantly less likely to have had AIDS (1.6 versus 2.2 per 100 person-years, respectively). Overall, 374 persons living with HIV of 4167 had died (9%) the proportion of persons with diabetes among the dead was greater than those who did not die 11.7% versus 8.1%, respectively, p = 0.017. However, persons with diabetes were older and hence died older, 62.3 years (SD = 1.9) for deceased persons with diabetes versus 50.4 years (SD = 0.8), P

IntroductionIn a context of high HIV prevalence, poor pregnancy follow-up, frequent poverty, preeclampsia, and preterm delivery, we aimed to describe the characteristics and outcomes of pregnancies among women living with HIV in French Guiana.MethodsA retrospective cohort study was conducted on HIV-infected pregnancies enrolled between January 1st 1992 to 31st July 2022. Overall, there were 1,774 pregnancies in 881 women living with HIV.ResultsFor 75.1% of pregnancies, the HIV diagnosis was already known before pregnancy and in 67.6% of women, HIV follow-up predated pregnancy. Nearly half of women, 49.6%, only had one pregnancy since having been diagnosed with HIV. Although most women received antiretroviral therapy during pregnancy, for those with the available information we found only 48.5% had an undetectable viral load at delivery. Overall, 15.3% of pregnancies ended with an abortion. There were a total of 110 newborns infected with HIV representing an overall transmission rate of 6.2% (110/1,771). Between 1993 and 2002, the transmission rate was 34%, between 2003 and 2012 it was 1.3%, and between 2013 and 2022 it was 0.7%. Overall, in Cayenne, since 2008, 106 of 581 HIV–infected pregnancies (18.2%) with available information were premature before 37 weeks of pregnancy; of these, 33 (5.7%) were very preterm deliveries and 73 (13.3%) were late preterm deliveries. Over time, in Cayenne, preterm delivery declined significantly.ConclusionsThe present study emphasizes that, despite spectacular progress in reducing mother to child transmission, pregnancy outcomes among women living with HIV are still preoccupying with high incidence of preterm delivery and low birth weight. Teasing out what fraction is linked to HIV and what fraction is linked to social precariousness and poor follow-up was not possible in this study. Despite the high incidence of very preterm delivery recent progress suggests that coordination efforts to improve follow-up may also have improved obstetrical outcomes.

Sudden sensorineural hearing loss (SSNHL), a rare audiological condition that accounts for 1% of all cases of sensorineural hearing loss, can cause permanent hearing damage. Soon after the launch of global COVID-19 vaccination campaigns, the World Health Organization released a signal detection about SSNHL cases following administration of various COVID-19 vaccines. Post-marketing studies have been conducted in different countries using either pharmacovigilance or medico-administrative databases to investigate SSNHL as a potential adverse effect of COVID-19 vaccines. Here, we examine the advantages and limitations of each type of post-marketing study available. While pharmacoepidemiological studies highlight the potential association between drug exposure and the event, pharmacovigilance approaches enable causality assessment. The latter objective can only be achieved if an expert evaluation is provided using internationally validated diagnostic criteria. For a rare adverse event such as SSNHL, case information and quantification of hearing loss are mandatory for assessing seriousness, severity, delay onset, differential diagnoses, corrective treatment, recovery, as well as functional sequelae. Appropriate methodology should be adopted depending on whether the target objective is to assess a global or individual risk.

BackgroundThe World Health Organization recently described sudden sensorineural hearing loss (SSNHL) as a possible adverse effect of COVID-19 vaccines. Recent discordant pharmacoepidemiologic studies invite robust clinical investigations of SSNHL after COVID-19 messenger RNA (mRNA) vaccines. This postmarketing surveillance study, overseen by French public health authorities, is the first to clinically document postvaccination SSNHL and examine the role of potential risk factors. ObjectiveThis nationwide study aimed to assess the relationship between SSNHL and exposure to mRNA COVID-19 vaccines and estimate the reporting rate (Rr) of SSNHL after mRNA vaccination per 1 million doses (primary outcome). MethodsWe performed a retrospective review of all suspected cases of SSNHL after mRNA COVID-19 vaccination spontaneously reported in France between January 2021 and February 2022 based on a comprehensive medical evaluation, including the evaluation of patient medical history, side and range of hearing loss, and hearing recovery outcomes after a minimum period of 3 months. The quantification of hearing loss and assessment of hearing recovery outcomes were performed according to a grading system modified from the Siegel criteria. A cutoff of 21 days was used for the delay onset of SSNHL. The primary outcome was estimated using the total number of doses of each vaccine administered during the study period in France as the denominator. ResultsFrom 400 extracted cases for tozinameran and elasomeran, 345 (86.3%) spontaneous reports were selected. After reviewing complementary data, 49.6% (171/345) of documented cases of SSNHL were identified. Of these, 83% (142/171) of SSNHL cases occurred after tozinameran vaccination: Rr=1.45/1,000,000 injections; no difference for the rank of injections; complete recovery in 22.5% (32/142) of cases; median delay onset before day 21=4 days (median age 51, IQR 13-83 years); and no effects of sex. A total of 16.9% (29/171) of SSNHL cases occurred after elasomeran vaccination: Rr=1.67/1,000,000 injections; rank effect in favor of the first injection (P=.03); complete recovery in 24% (7/29) of cases; median delay onset before day 21=8 days (median age 47, IQR 33-81 years); and no effects of sex. Autoimmune, cardiovascular, or audiovestibular risk factors were present in approximately 29.8% (51/171) of the cases. SSNHL was more often unilateral than bilateral for both mRNA vaccines (P

Summary: Background: Adult T-cell leukemia/lymphoma (ATL), one of the most aggressive cancers in the world, occurs in 5% of the 10 million people living with HTLV-1 worldwide. French Guiana, a French overseas territory in South America, is one of the highest endemic areas of HTLV-1 worldwide. Here, we describe the demographic and clinical characteristics and outcome of ATL in this area. Methods: We retrospectively collected data from all patients diagnosed between 2009 and 2019. Patients were distributed according to Shimoyama's classification. Prognostic factors were explored through univariate analysis. Findings: Over the 10-year study period, 41 patients with a median age of 54 years at diagnosis were identified, among whom 56% were women. Sixteen (39%) patients were Maroons, a cultural group descendant of the runaway enslaved Africans from former Dutch Guiana. Among the study population, 23 (56%) had an acute type, 14 (34%) a lymphoma type, and one and one chronic and primary cutaneous tumour, respectively. First-lines of treatment included either chemotherapy or Zidovudine combined with pegylated interferon alpha. The 4-year overall survival was 11.4% for the entire population with 0% and 11% for lymphoma and acute forms, respectively. The median progression-free survival was 93 and 115 days for the acute and lymphoma groups (p = 0.37), respectively. Among the twenty-nine patients who died, 8 (28%) died of toxicity, 7 (24%) died of disease progression and the cause of death remained unknown in 14 (48%) patients. Due to the overall poor prognosis, no significant prognostic factors could be identified. Interpretation: This study provides real-life data from ATL patients in French Guiana, a remote territory in a middle-income region. Patients, mostly Maroons, presented with a younger age and the prognosis was worse than expected compared to Japanese patients. Funding: None.

Abstract Soil contamination pattern due to industrial activities often leads to high concentrations of potentially toxic elements (PTE) decreasing with depth. This spatial heterogeneity of the soil contamination may have significant consequences on the soil properties and soil living communities. We evaluated the effects of both surface and solum soil contamination heterogeneity on Coronilla juncea L. (Fabaceae) functional traits in field conditions and the phytostabilization potential of this species. Plant and soil samples were collected on 3 sites along a PTE contamination gradient. The correlations between PTE concentration in plant and soil samples at 2 depths, physico-chemical properties of soil, plant biomass and soil microbial activity were tested. Field measurements highlight a decreasing PTE concentration with soil depth in addition to an important surface heterogeneity of As, Cu, Pb, Sb and Zn soil concentrations. Root PTE concentrations in C. juncea did not follow soil PTE concentrations. Concentrations of PTE in the root parts were higher than those of the aerial parts. Low PTE translocation and root symbioses with microorganisms suggest that this native plant species may play a role as engineer species with positive implications for the phytostabilization of Mediterranean PTE contaminated soils and their ecological restoration.

Introduction Immunotherapies, such as immune checkpoint inhibitors and chimeric antigen receptor T-cell therapy, have significantly improved the clinical outcomes of various malignancies. However, they also cause immune-related adverse events (irAEs) that can be challenging to predict, prevent and treat. Although they likely interact with health-related quality of life (HRQoL), most existing evidence on this topic has come from clinical trials with eligibility criteria that may not accurately reflect real-world settings. The QUALITOP project will study HRQoL in relation to irAEs and its determinants in a real-world study of patients treated with immunotherapy.Methods and analysis This international, observational, multicentre study takes place in France, the Netherlands, Portugal and Spain. We aim to include about 1800 adult patients with cancer treated with immunotherapy in a specifically recruited prospective cohort, and to additionally obtain data from historical real-world databases (ie, databiobanks) and medical administrative registries (ie, national cancer registries) in which relevant data regarding other adult patients with cancer treated with immunotherapy has already been stored. In the prospective cohort, clinical health status, HRQoL and psychosocial well-being will be monitored until 18 months after treatment initiation through questionnaires (at baseline and 3, 6, 12 and 18 months thereafter), and by data extraction from electronic patient files. Using advanced statistical methods, including causal inference methods, artificial intelligence algorithms and simulation modelling, we will use data from the QUALITOP cohort to improve the understanding of the complex relationships among treatment regimens, patient characteristics, irAEs and HRQoL.Ethics and dissemination All aspects of the QUALITOP project will be conducted in accordance with the Declaration of Helsinki and with ethical approval from a suitable local ethics committee, and all patients will provide signed informed consent. In addition to standard dissemination efforts in the scientific literature, the data and outcomes will contribute to a smart digital platform and medical data lake. These will (1) help increase knowledge about the impact of immunotherapy, (2) facilitate improved interactions between patients, clinicians and the general population and (3) contribute to personalised medicine.Trial registration number NCT05626764.

PurposeThe border between the State of Amapa, Brazil, and French Guiana is mostly primary forest. In the Oyapock basin, socioeconomic circumstances have fueled sex work, gold mining and the circulation of sexually transmitted infections. Given the lack of comprehensive data on this border area, we describe the different sexually transmitted infections along the Brazil/French Guiana border and the testing and care activity.MethodsWe conducted a review of the available scientific and technical literature on sexually transmitted infections in this complex border area. Temporal trends were graphed and for Human Immunodeficiency Virus (HIV) we estimated incidence using the European Center for prevention and Disease Control modeling tool.ResultsUntil 2019, 26 of the 46 HIV-infected patients followed and treated in Saint Georges de l'Oyapock were residing on the Brazilian side in Oiapoque. Virological suppression was only achieved for 75% of treated patients; but dropped to 62% during the COVID-19 epidemic. In 2019, cooperation efforts allowed HIV care in Oiapoque, resulting in the transfer of Brazilian patients previously followed on the French side and a substantial increase in the number of patients followed in Oiapoque. The average yearly HIV serological testing activity at the health center in Saint Georges was 16 tests per 100 inhabitants per year; in Camopi it was 12.2 per 100 inhabitants. Modeling estimated the number of persons living with HIV around 170 persons, corresponding to a prevalence of 0.54% and about 40 undiagnosed infections. The model also suggested that there were about 12 new infections per year in Saint Georges and Oiapoque, representing an HIV incidence rate of 3.8 cases per 10,000 per year. HPV prevalence in Saint Georges ranges between 25 and 30% and between 35 and 40% in Camopi. Testing activity for other sexually transmitted infections markedly increased in the past 5 years; the introduction of PCR for chlamydiasis and gonorrhea also had a substantial impact on the number of diagnoses.ConclusionsThe ongoing cooperation between multiple partners on both sides of the border has led to remarkable progress in primary prevention, in testing efforts, in treatment and retention on both sides of the border. In a region with intense health professional turnover, nurturing cooperation and providing accurate assessments of the burden of sexually transmitted infections is essential to tackle a problem that is shared on both sides of the border.

PurposeThe Maroni basin –delineating the border between Suriname and French Guiana— presents sociocultural, geographical and economic circumstances that have been conducive to the circulation of sexually transmitted infections and to delays in diagnosis and care. Given the scarcity of published data, we aimed to describe different sexually transmitted infections along the Maroni and to gain a broader understanding of the epidemiologic situation.MethodsWe conducted a scoping review of the efforts to approach the problem of sexually transmitted infections in this complex border area. Temporal trends were plotted and crude numbers were divided by local population numbers.ResultsFor HIV, despite increasing testing efforts, most patients still present at the advanced HIV stage (median CD4 count at diagnosis is < 20 per mm3), and 25% of patients in Saint Laurent du Maroni were lost to follow-up within 6 years. However, progress on both sides has led to a decline in AIDS cases and mortality. Despite a rapid increase in the 1990’s along the Maroni, the current HIV prevalence seemed lower (0.52%) in the rural villages than in coastal urban centers (> 1%). High risk HPV infection prevalence among women reaches 23.3%. The incidence of gonorrhea was 4.2 per 1,000 population aged 15-59. For chlamydiasis it was 3.4 per 1,000 population aged 15-59. For syphilis, the incidence was 2.5 per 1,000 population aged 15-59. Gonorrhea, chlamydiasis, hepatitis B detection increased over time with greater testing efforts and new diagnostic tests. Since the COVID-19 epidemic, congenital syphilis has dramatically increased in Saint Laurent du Maroni reaching 808 per 100,000 live births.ConclusionSexually transmitted infections seemed more prevalent in Saint Laurent du Maroni –the sole urban center—than in the remote villages along the Maroni. The syndromic approach and the heterogeneity of diagnostic platforms presumably overlook most infections in the region. Therefore, a concerted approach and a shared diagnostic upgrade with molecular diagnosis and rapid diagnostic tests seem necessary to reduce the burden of sexually transmitted infections on both sides of the Maroni. Congenital syphilis resulting from COVID-19 disruption of health services requires urgent attention.