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Abstract Purpose The aim of the study was to identify settings associated with SARS-CoV-2 transmission throughout the COVID-19 pandemic in France. Methods Cases with recent SARS-CoV-2 infection were matched with controls (4:1 ratio) on age, sex, region, population size, and calendar week. Odds ratios for SARS-CoV-2 infection were estimated for nine periods in models adjusting for socio-demographic characteristics, health status, COVID-19 vaccine, and past infection. Results Between October 27, 2020 and October 2, 2022, 175,688 cases were matched with 43,922 controls. An increased risk of infection was documented throughout the study for open-space offices compared to offices without open space (OR range across the nine periods: 1.12 to 1.57) and long-distance trains (1.25 to 1.88), and during most of the study for convenience stores (OR range in the periods with increased risk: 1.15 to 1.44), take-away delivery (1.07 to 1.28), car-pooling with relatives (1.09 to 1.68), taxis (1.08 to 1.89), airplanes (1.20 to 1.78), concerts (1.31 to 2.09) and night-clubs (1.45 to 2.95). No increase in transmission was associated with short-distance shared transport, car-pooling booked over platforms, markets, supermarkets and malls, hairdressers, museums, movie theatres, outdoor sports, and swimming pools. The increased risk of infection in bars and restaurants was no longer present in restaurants after reopening in June 2021. It persisted in bars only among those aged under 40 years. Conclusion Closed settings in which people are less likely to wear masks were most affected by SARS-CoV-2 transmission and should be the focus of air quality improvement. ClinicalTrials.gov (03/09/2022) NCT04607941.

Abstract Background Seed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays. Results Intermediate wheatgrass seeds harvested from four field sites in Europe over three consecutive years were dominated by Proteobacteria (88%), followed by Firmicutes (10%). Pantoea was the most abundant genus and Pantoea agglomerans was identified as the only core taxon present in all samples. While bacterial diversity and species richness were similar across all accessions, the relative abundance varied especially in terms of low abundant and rare taxa. Seeds from four different breeding cycles (TLI C3, C5, C704, C801) showed significant differences in bacterial community composition and abundance. We found a decrease in the relative abundance of the functional genes nirK and nifH as well as a drop in bacterial diversity and richness. This was associated with a loss of amplicon sequence variants (ASVs) in Actinobacteria, Alphaproteobacteria, and Bacilli, which could be partially compensated in offspring seeds, which have been cultivated at a new site. Interestingly, only a subset assigned to potentially beneficial bacteria, e.g. Pantoea, Kosakonia, and Pseudomonas, was transmitted to the next plant generation or shared with offspring seeds. Conclusion Overall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs.

Abstract Background We aimed to study the source of infection for recently SARS-CoV-2-infected individuals from October 2020 to August 2022 in France. Methods Participants from the nationwide ComCor case–control study who reported recent SARS-CoV-2 infection were asked to document the source and circumstances of their infection through an online questionnaire. Multivariable logistic regression was used to identify the factors associated with not identifying any source of infection. Results Among 584,846 adults with a recent SARS-CoV-2 infection in France, 46.9% identified the source of infection and an additional 22.6% suspected an event during which they might have become infected. Known and suspected sources of infection were household members (30.8%), extended family (15.6%), work colleagues (15.0%), friends (11.0%), and possibly multiple/other sources (27.6%). When the source of infection was known, was not a household member, and involved a unique contact (n = 69,788), characteristics associated with transmission events were indoors settings (91.6%), prolonged (> 15 min) encounters (50.5%), symptomatic source case (64.9%), and neither the source of infection nor the participant wearing a mask (82.2%). Male gender, older age, lower education, living alone, using public transportation, attending places of public recreation (bars, restaurants, nightclubs), public gatherings, and cultural events, and practicing indoor sports were all independently associated with not knowing the source of infection. Conclusion Two-thirds of infections were attributed to interactions with close relatives, friends, or work colleagues. Extra-household indoor encounters without masks were commonly reported and represented avoidable circumstances of infection. Trial registration ClinicalTrials.gov registration number: NCT04607941.

Abstract In semiconductors, the identification of doping atomic elements allowing to encode a qubit within spin states is of intense interest for quantum technologies. In transition metal dichalcogenides semiconductors, the strong spin-orbit coupling produces locked spin-valley states with expected long coherence time. Here we study the substitutional Bromine BrTe dopant in 2H-MoTe2. Electron spin resonance measurements show that this dopant carries a spin with long-lived nanoseconds coherence time. Using scanning tunneling spectroscopy, we find that the hydrogenic wavefunctions associated with the dopant levels have characteristics spatial modulations that result from their hybridization to the Q-valleys of the conduction band. From a Fourier analysis of the conductance maps, we find that the amplitude and phase of the Fourier components change with energy according to the different irreducible representations of the impurity-site point-group symmetry. These results demonstrate that a dopant can inherit the locked spin-valley properties of the semiconductor and so exhibit long spin-coherence time.

Abstract Non-technical summary Agriculture has been dominated by annual plants, such as all cereals and oilseeds, since the very beginning of civilization over 10,000 years ago. Annual plants are planted and uprooted every year which results in severe disturbance of the soil and disrupts ecosystem services. Science has shown that it is possible to domesticate completely new perennial grain crops, i.e. planted once and harvested year after year. Such crops would solve many of the problems of agriculture, but their development and uptake would be at odds with the current agricultural technology industry. Technical summary Agriculture is arguably the most environmentally destructive innovation in human history. A root cause is the reliance on annual crops requiring uprooting and restarting every season. Most environmental predicaments of agriculture can be attributed to the use of annuals, as well as many social, political, and economic ones. Advances in domestication and breeding of novel perennial grain crops have demonstrated the possibility of a future agricultural shift from annual to perennial crops. Such a change could have many advantages over the current agricultural systems which are to over 80% based on annual crops mainly grown in monocultures. We analyze and review the prospects for such scientific advances to be adopted and scaled to a level where it is pertinent to talk about a perennial revolution. We follow the logic of E.O. Wright's approach of Envisioning Real Utopias by discussing the desirability, viability, and achievability of such a transition. Proceeding from Lakatos' theory of science and Lukes' three dimensions of power, we discuss the obstacles to such a transition. We apply a transition theory lens to formulate four reasons of optimism that a perennial revolution could be imminent within 3–5 decades and conclude with an invitation for research.

Summary: Background: We aimed to assess the settings and activities associated with SARS-CoV-2 infection in the context of B.1.617.2 (Delta) variant circulation in France, as well as the protection against symptomatic Delta infection. Methods: In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 23 May and 13 August 2021. Controls were non-infected adults from a national representative panel matched to cases by age, sex, region, population density and calendar week. Participants completed an online questionnaire and multivariable logistic regression analysis was used to determine the association between acute SARS-CoV-2 infection and recent activity-related exposures, past history of SARS-CoV-2 infection, and COVID-19 vaccination. Findings: We did not find any differences in the settings and activities associated with Delta versus non-Delta infections and grouped them for subsequent analyses. In multivariable analysis involving 12634 cases (8644 Delta and 3990 non-Delta) and 5560 controls, we found individuals under 40 years and attending bars (aOR:1.9; 95%CI:1.6-2.2) or parties (aOR:3.4; 95%CI:2.8-4.2) to be at increased risk of infection. In those aged 40 years and older, having children attend daycare (aOR:1.9; 95%CI:1.1-3.3), kindergarten (aOR:1.6; 95%CI:1.2-2.1), primary school (aOR:1.4; 95%CI:1.2-1.6) or middle school (aOR:1.3; 95%CI:1.2-1.6) were associated with increased risk of infection. We found strong protection against symptomatic Delta infection for those with prior infection whether it was recent (2-6 months) (95%; 95%CI:90-97) or associated with one dose (85%; 95%CI:78-90) or two doses of mRNA vaccine (96%; 95%CI:87-99). For those without past infection, protection was lower with two doses of mRNA vaccine (67%; 95%CI:63-71). Interpretation: In line with other observational studies, we find reduced vaccine effectiveness against symptomatic Delta infections. The settings and activities at increased risk of infection indicate where efforts to reinforce individual and public health measures need to be concentrated.

Background: We aimed to assess the effectiveness of two doses of mRNA COVID-19 vaccines against COVID-19 with the original virus and other lineages circulating in France. Methods: In this nationwide case-control study, cases were SARS-CoV-2 infected adults with onset of symptoms between 14 February and 3 May 2021. Controls were non-infected adults from a national representative panel matched to cases by age, sex, region, population density and calendar week. Participants completed an online questionnaire on recent activity-related exposures and vaccination history. Information about the infecting virus was based on a screening RT-PCR for either B.1.1.7 or B.1.351/P.1 variants. Findings: Included in our analysis were 7 288 adults infected with the original SARS-CoV-2 virus, 31 313 with the B.1.1.7 lineage, 2 550 with B.1.351/P1 lineages, and 3 644 controls. In multivariable analysis, the vaccine effectiveness (95% confidence interval) seven days after the second dose of mRNA vaccine was estimated at 88% (81-92), 86% (81-90) and 77% (63-86) against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively. Recent (2 to 6 months) history of virologically confirmed SARS-CoV-2 infection was found to be 83% (76-88), 88% (85-91) and 83% (71-90) protective against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively; and more distant (> 6 months) infections were 76% (54-87), 84% (75-90), and 74% (41-89) protective against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively. Interpretation: In real-life settings, two doses of mRNA vaccines proved to be effective against COVID-19 with the original virus, B.1.1.7 lineage and B.1.351/P.1 lineages. Funding: Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance “Tous unis contre le virus”).

Summary: Background: We aimed to assess the role of different setting and activities in acquiring SARS-CoV-2 infection. Methods: In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 27 October and 30 November 2020. Controls were individuals from the Ipsos market research database matched to cases by age, sex, region, population density and time period. Participants completed an online questionnaire on recent activity-related exposures. Findings: Among 3426 cases and 1713 controls, in multivariable analysis, we found an increased risk of infection associated with any additional person living in the household (adjusted-OR: 1•16; 95%CI: 1•11-1•21); having children attending day-care (aOR: 1•31; 95%CI: 1•02-1•62), kindergarten (aOR: 1•27; 95%CI: 1•09-1•45), middle school (aOR: 1•30; 95%CI: 1•15-1•47), or high school (aOR: 1•18; 95%CI: 1•05-1•34); with attending professional (aOR: 1•15; 95%CI: 1•04-1•26) or private gatherings (aOR: 1•57; 95%CI: 1•45-1•71); and with having frequented bars and restaurants (aOR: 1•95; 95%CI: 1•76-2•15), or having practiced indoor sports activities (aOR: 1•36; 95%CI: 1•15-1•62). We found no increase in risk associated with frequenting shops, cultural or religious gatherings, or with transportation, except for carpooling (aOR: 1•47; 95%CI: 1•28-1•69). Teleworking was associated with decreased risk of infection (aOR: 0•65; 95%CI: 0•56-0•75). Interpretation: Places and activities during which infection prevention and control measures may be difficult to fully enforce were those with increased risk of infection. Children attending day-care, kindergarten, middle and high schools, but not primary schools, were potential sources of infection for the household. Funding: Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance” Tous unis contre le virus”).

How quantum size effects affect superconductivity has been predicted, but it has never been verified. Here, Vlaicet al. report superconducting parity effect as a function of lead nanocrystal volume, unambiguously validating the Anderson criterion.

The use of the perennial grain intermediate wheatgrass (Thinopyrum intermedium (Host) Barkworth & D.R. Dewey) may have the potential to sustain soil health and fertility through the development of an extensive root system. However, references are scarce to demonstrate its potential influence in a context of a limited perennial grain growth phase, integrated into annual grain crops succession. This study aims at determining how early a perennial crop rooting system differs from that of an annual crop through root development and root traits and microbial indicators. Our results indicate that the two-year-old intermediate wheatgrass promotes a denser and deeper rooting system with proportionally more root biomass and length deeper in the soil profile. From the first growing season, the perennial grain demonstrated a suite of root traits typical of a more resource-conservative strategy, and more belowground-oriented resource allocation. Soil fungal biomass indicators were enhanced. Arbuscular mycorrhizal fungi (AMF) indicators were notably found to be improved at 1 m depth during the second growing season. This study provides evidence that grain-based agriculture can benefit from the potential of deeper and long-lived root systems of intermediate wheatgrass to manage soils. The periodic use of a short-term perennial phase in the crop rotation has the potential to improve soil functioning in the long term.

A departmental musculoskeletal disorder (MSD) prevention project was begun in 2003 on the initiative of the Anjou inter-company medical service and the Regional action for the improvement of working conditions in the Pays de Loire to respond to companies’ difficulties in establishing effective and ongoing projects. It brought together 6 volunteer companies in a commitment to a 5-year agreement.The institutional prevention actors provide, in a multi-disciplinary approach, a project methodology and the opportunity for exchanges and feedback between the companies. This accompanying action focused on the creation of working groups led by private consultants to consider situations that could lead to musculoskeletal disorders and to share decisions for change.After the project had been conducted in a bovine slaughterhouse for 3 years, an adaptation process is now being carried out. The evaluations are revealing human, organizational and technical changes. This experiment questions the role of institutional actors and the interest of the link between external actors and actors inside the company.

Parasitological diagnosis, using staned smears, culture and pathological examination of biopsy, was studied in 146 patients infected with mucocutaneous leishmaniasis, in Bolivia and Peru. The most efficient parasite detecting technique appeared to be the smear examination in cutaneous lesions (33 % positive) and the pathology in case of mucous lesions (28 % positive). In both, cutaneous and mucous lesions, the parasites were found most frequently in old lesions.Diagnósticoparasitolôgico, usando esfregaço, cultura e exame anatomopatológico de biópsia, foi estudado em 146pacientes infectados com leishmaniose mucocutânea, na Bolívia e Peru. A mais eficiente técnica de detectar parasitas parece ser o exame de esfregaço para lesões cutâneas (33% de positividade) e anatomopatológico para lesões de mucosas (28% de positividade). Em ambas lesões, cutânea e mucosa, parasitas foram mais frequentemente encontrados em velhas lesões.

Parasitological diagnosis, using staned smears, culture and pathological examination of biopsy, was studied in 146 patients infected with mucocutaneous leishmaniasis, in Bolivia and Peru. The most efficient parasite detecting technique appeared to be the smear examination in cutaneous lesions (33 % positive) and the pathology in case of mucous lesions (28 % positive). In both, cutaneous and mucous lesions, the parasites were found most frequently in old lesions.

Organic farming is increasingly recognized as a prototype for sustainable agriculture. Its guidelines ban the use of artificial fertilizers. However, organic farms may import nutrients from conventional farming through material exchanges. In this study, we aimed at estimating the magnitude of these flows through the quantification of nitrogen, phosphorus and potassium inflows from conventional farming to organic farming. Material inflows and outflows were collected for two cropping years on 63 farms. The farms were located in three French agricultural districts distributed over a gradient of farming activity defined by both the stocking rate and the ratio of the farm area under arable crops. Our results showed that on average, inflows from conventional farming were 23%, 73% and 53% for nitrogen, phosphorus and potassium, respectively. These inflows were strongly determined by the farm production systems. However, for farms similar in terms of production systems, the inflows also depended on the local context, such as the proximity of organic livestock farms: the reliance of organic farming on conventional farming was lower in mixed than in specialized districts. These results highlight the necessity to quantify the contribution of nutrient inflows from conventional farming when assessing organic farming and development scenarios.