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Background: Disfluency is a multifactorial concept that can be linked to several of the language production levels, in both typical and atypical populations. In children, the language system is still developing and few studies have explored disfluency patterns. In typical development (TD), in particular, studies have shown discrepancies according to the language being considered. In neurodevelopmental disorders, such as developmental dyslexia (DD), it is still unclear whether the pattern of disfluency is similar to TD. Aims: To analyse the type of disfluency and their evolution in French children aged 8-12 years. Also to compare the pattern of disfluency in DD and TD, and to test whether disfluencies were correlated with reading difficulties. Methods & Procedures: A total of 25 children with DD and 21 children with TD aged 8-12.6 years produced an autobiographical narrative. Seven types of disfluencies were coded: part-word repetitions; repetitions of monosyllabic words; other types of repetitions (words and phrases); filled pauses; revisions-substitutions; revisions-additions; and abandoned utterances. We compared the proportion of each disfluency in DD and TD. Spearman correlations were then performed between disfluencies, reading performance and age. Outcomes & Results: The results showed that both DD and TD children mainly produced filled pauses, repetitions of monosyllabic words and substitutions. Both groups displayed a high rate of disfluency (> 10%). No correlations with age were found. Correlations with reading performance were significant in the TD group only. Conclusions & Implications: The study showed that DD is not characterized by a specific pattern of disfluency. Additionally, disfluency rates were similar in children aged 8-12 years. In contrast to other languages, the current study suggests that French-speaking children have a high rate of disfluency. The study also suggests that disfluency should be interpreted with caution in DD, given that TD children also have a high rate of disfluency. Therefore, it seems important to adapt the pathological threshold of disfluency to the language being spoken in order to avoid an overestimation of the prevalence of these deficits in French-speaking children.

Abstract Understanding the architecture of the human deep brain is especially challenging because of the complex organization of the nuclei and fascicles that support most sensorimotor and behaviour controls. There are scant dedicated tools to explore and analyse this region. Here we took a transdisciplinary approach to build a new deep-brain MRI architecture atlas drawing on advanced clinical experience of MRI-based deep brain mapping. This new tool comprises a young-male-adult MRI template spatially normalized to the ICBM152, containing T1, inversion-recovery, and diffusion MRI datasets (in vivo acquisition), and an MRI atlas of 118 labelled deep brain structures. It is open-source and gives users high resolution image datasets to describe nuclear-based and axonal architecture, combining pioneering and recent knowledge. It is a useful addition to current 3D atlases and clinical tools.

Abstract Context While a growing body of research has been demonstrating how exposure to social and built environments relate to various health outcomes, specific pathways generally remain poorly understood. But recent technological advancements have enabled new study designs through continuous monitoring using mobile sensors and repeated questionnaires. Such geographically explicit momentary assessments (GEMA) make it possible to link momentary subjective states, behaviors, and physiological parameters to momentary environmental conditions, and can help uncover the pathways linking place to health. Despite its potential, there is currently no review of GEMA studies detailing how location data is used to measure environmental exposure, and how this in turn is linked to momentary outcomes of interest. Moreover, a lack of standard reporting of such studies hampers comparability and reproducibility. Aims The objectives of this research were twofold: 1) conduct a systematic review of GEMA studies that link momentary measurement with environmental data obtained from geolocation data, and 2) develop a STROBE extension guideline for GEMA studies. Method The review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Inclusion criteria consisted of a combination of repeated momentary measurements of a health state or behavior with GPS coordinate collection, and use of these location data to derive momentary environmental exposures. To develop the guideline, the variables extracted for the systematic review were compared to elements of the STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) and CREMAS (CRedibility of Evidence from Multiple Analyses of the Same data) checklists, to provide a new guideline for GEMA studies. An international panel of experts participated in a consultation procedure to collectively develop the proposed checklist items. Results and developed tools A total of 20 original GEMA studies were included in the review. Overall, several key pieces of information regarding the GEMA methods were either missing or reported heterogeneously. Our guideline provides a total of 27 categories (plus 4 subcategories), combining a total of 70 items. The 22 categories and 32 items from the original STROBE guideline have been integrated in our GEMA guideline. Eight categories and 6 items from the CREMAS guideline have been included to our guideline. We created one new category (namely “Consent”) and added 32 new items specific to GEMA studies. Conclusions and recommendations This study offers a systematic review and a STROBE extension guideline for the reporting of GEMA studies. The latter will serve to standardize the reporting of GEMA studies, as well as facilitate the interpretation of results and their generalizability. In short, this work will help researchers and public health professionals to make the most of this method to advance our understanding of how environments influence health.

IntroductionSeveral COVID-19 outbreaks have been reported in meat processing plants in different countries. The aim of this study was to assess the environmental and socio-economic risk factors favouring the transmission of SARS-CoV-2 in meat processing plants and to describe the prevention measures implemented.MethodsData from epidemiological investigations of COVID-19 clusters in France, the scientific literature, structured interviews and site visits were collected and summarised to investigate the main risk factors for SARS-CoV-2 infection in meat processing plants, including determinants within and outside the workplace.ResultsAn increased risk of infection was identified among workers with unfavourable socio-economic status (temporary/non-permanent workers, migrants, ethnic minorities, etc.), possibly related to community activities (house-sharing, car-sharing, social activities). Working conditions (proximity between workers) and environmental factors (low temperatures and inadequate ventilation) also appear to be important risk factors. These environmental conditions are particularly prevalent in cutting and boning plants, where the majority of reported cases are concentrated. Preventive measures applied included screening for COVID-19 symptoms, testing, wearing masks, increased hygiene and sanitation, physical and temporal distancing, control of ventilation. Certain food safety hygiene measures were compatible with protecting workers from SARS-CoV-2. The hygiene culture of agri-food workers made it easier to implement preventive measures after adaptation.ConclusionThis study made it possible to identify the environmental and socio-economic factors conducive to the transmission of SARS-CoV-2 in meat processing plants. The knowledge gained from this work was used in simulations to understand the transmission of the virus in the plants.

Peanut is a worldwide oilseed crop and the need to assess germplasm in a non-destructive manner is important for seed nutritional breeding. In this study, Near Infrared Spectroscopy (NIRS) was applied to rapidly assess germplasm variability from whole seed of 699 samples, field-collected and assembled in four genetic and environment-based sets: one set of 300 varieties of a core-collection and three sets of 133 genotypes of an interspecific population, evaluated in three environments in a large spatial scale of two countries, Mbalmayo and Bafia in Cameroon and Nioro in Senegal, under rainfed conditions. NIR elemental spectra were gathered on six subsets of seeds of each sample, after three rotation scans, with a spectral resolution of 16 cm-1 over the spectral range of 867 nm to 2530 ​nm. Spectra were then processed by principal component analysis (PCA) coupled with Partial least squares-discriminant analysis (PLS-DA). As results, a huge variability was found between varieties and genotypes for all NIR wavelength within and between environments. The magnitude of genetic variation was particularly observed at 11 relevant wavelengths such as 1723 ​nm, usually related to oil content and fatty acid composition. PCA yielded the most chemical attributes in three significant PCs (i.e., eigenvalues >10), which together captured 93% of the total variation, revealing genetic and environment structure of varieties and genotypes into four clusters, corresponding to the four samples sets. The pattern of genetic variability of the interspecific population covers, remarkably half of spectrum of the core-collection, turning out to be the largest. Interestingly, a PLS-DA model was developed and a strong accuracy of 99.6% was achieved for the four sets, aiming to classify each seed sample according to environment origin. The confusion matrix achieved for the two sets of Bafia and Nioro showed 100% of instances classified correctly with 100% at both sensitivity and specificity, confirming that their seed quality was different from each other and all other samples. Overall, NIRS chemometrics is useful to assess and distinguish seeds from different environments and highlights the value of the interspecific population and core-collection, as a source of nutritional diversity, to support the breeding efforts.

Cellulose nanocrystals (CNCs) are bio-based materials able to be functionalized following different approaches, which expands their range of applications. One such approach is surface-initiated polymerization, which involves the attachment of an initiator to the CNC’s surface to initiate the growth of the polymer. This work reports the modification of CNCs using the described approach. First, a CNC-based film was prepared, on which an initiator (RAFT agent) was grafted, and then (trimethylaminoethyl methacrylate, a positively charged monomer, was polymerized using reversible addition–fragmentation chain-transfer (RAFT) polymerization. The CNC film was successfully modified and fully characterized. Different degrees of polymerization were targeted to emphasize the effect of the positively charged polymer and their chain length on the adsorption efficiency. The results showed that by increasing the chain length of the grafted polymer, up to 80% of both pollutants could be removed, with a faster adsorption of PFOS as compared to PFOA.

Abstract Studies have found a pronounced decline in male effective population sizes worldwide around 3000–5000 years ago. This bottleneck was not observed for female effective population sizes, which continued to increase over time. Until now, this remarkable genetic pattern was interpreted as the result of an ancient structuring of human populations into patrilineal groups (gathering closely related males) violently competing with each other. In this scenario, violence is responsible for the repeated extinctions of patrilineal groups, leading to a significant reduction in male effective population size. Here, we propose an alternative hypothesis by modelling a segmentary patrilineal system based on anthropological literature. We show that variance in reproductive success between patrilineal groups, combined with lineal fission (i.e., the splitting of a group into two new groups of patrilineally related individuals), can lead to a substantial reduction in the male effective population size without resorting to the violence hypothesis. Thus, a peaceful explanation involving ancient changes in social structures, linked to global changes in subsistence systems, may be sufficient to explain the reported decline in Y-chromosome diversity.

Abstract Background During the first COVID-19 pandemic wave, COVID-19-associated pulmonary aspergillosis (CAPA) has been reported in up to 11–28% of critically ill COVID-19 patients and associated with increased mortality. As new SARS-CoV-2 variants emerged, the characteristics of critically ill COVID-19 patients have evolved, particularly in the era of Omicron. The purpose of this study is to investigate the characteristics of CAPA in the era of new variants. Methods This is a prospective multicenter observational cohort study conducted in France in 36 participating intensive care units (ICU), between December 7th, 2021 and April 26th 2023. Diagnosis criteria of CAPA relied on European Confederation of Medical Mycology (ECMM)/International Society for Human & Animal Mycology (ISHAM) consensus criteria. Results 566 patients were included over the study period. The prevalence of CAPA was 5.1% [95% CI 3.4–7.3], and rose to 9.1% among patients who required invasive mechanical ventilation (IMV). Univariable analysis showed that CAPA patients were more frequently immunosuppressed and required more frequently IMV support, vasopressors and renal replacement therapy during ICU stay than non-CAPA patients. SAPS II score at ICU admission, immunosuppression, and a SARS-CoV-2 Delta variant were independently associated with CAPA in multivariable logistic regression analysis. Although CAPA was not significantly associated with day-28 mortality, patients with CAPA experienced a longer duration of mechanical ventilation and ICU stay. Conclusion This study contributes valuable insights into the prevalence, characteristics, and outcomes of CAPA in the era of Delta and Omicron variants. We report a lower prevalence of CAPA (5.1%) among critically-ill COVID-19 patients than previously reported, mainly affecting intubated-patients. Duration of mechanical ventilation and ICU stay were significantly longer in CAPA patients.

Diabetes represents a spectrum of disease in which metabolic dysfunction damages multiple organ systems including liver, kidneys and peripheral nerves1,2. Although the onset and progression of these co-morbidities are linked with insulin resistance, hyperglycaemia and dyslipidaemia3-7, aberrant non-essential amino acid (NEAA) metabolism also contributes to the pathogenesis of diabetes8-10. Serine and glycine are closely related NEAAs whose levels are consistently reduced in patients with metabolic syndrome10-14, but the mechanistic drivers and downstream consequences of this metabotype remain unclear. Low systemic serine and glycine are also emerging as a hallmark of macular and peripheral nerve disorders, correlating with impaired visual acuity and peripheral neuropathy15,16. Here we demonstrate that aberrant serine homeostasis drives serine and glycine deficiencies in diabetic mice, which can be diagnosed with a serine tolerance test that quantifies serine uptake and disposal. Mimicking these metabolic alterations in young mice by dietary serine or glycine restriction together with high fat intake markedly accelerates the onset of small fibre neuropathy while reducing adiposity. Normalization of serine by dietary supplementation and mitigation of dyslipidaemia with myriocin both alleviate neuropathy in diabetic mice, linking serine-associated peripheral neuropathy to sphingolipid metabolism. These findings identify systemic serine deficiency and dyslipidaemia as novel risk factors for peripheral neuropathy that may be exploited therapeutically.

Dengue virus (DENV) is a Flavivirus that causes the most prevalent arthropod-borne viral disease. Clinical manifestation of DENV infection ranges from asymptomatic to severe symptoms that can lead to death. Unfortunately, no antiviral treatments against DENV are currently available. In order to identify novel DENV inhibitors, we screened a library of 1,604 chemically diversified fragment-based compounds using DENV reporter viruses that allowed quantification of viral replication in infected cells. Following a validation screening, the two best inhibitor candidates were N-phenylpyridine-3-carboxamide (NPP3C) and 6-acetyl-1H-indazole (6A1HI). The half maximal effective concentration of NPP3C and 6A1H1 against DENV were 7.1 μM and 6.5 μM, respectively. 6A1H1 decreased infectious DENV particle production up to 1,000-fold without any cytotoxicity at the used concentrations. While 6A1HI was DENV-specific, NPP3C also inhibited the replication of other flaviviruses such as West Nile virus and Zika virus. Structure-activity relationship (SAR) studies with 151 analogues revealed key structural elements of NPP3C and 6A1HI required for their antiviral activity. Time-of-drug-addition experiments identified a postentry step as a target of these compounds. Consistently, using a DENV subgenomic replicon, we demonstrated that these compounds specifically impede the viral RNA replication step and exhibit a high genetic barrier-to-resistance. In contrast, viral RNA translation and the de novo biogenesis of DENV replication organelles were not affected. Overall, our data unveil NPP3C and 6A1H1 as novel DENV inhibitors. The information revealed by our SAR studies will help chemically optimize NPP3C and 6A1H1 in order to improve their anti-flaviviral potency and to challenge them in in vivo models.

Compositional oscillations of the gut microbiome are essential for normal peripheral circadian rhythms, both of which are disrupted in diet-induced obesity (DIO). Although time-restricted feeding (TRF) maintains circadian synchrony and protects against DIO, its impact on the dynamics of the cecal gut microbiome is modest. Thus, other regions of the gut, particularly the ileum, the nexus for incretin and bile acid signaling, may play an important role in entraining peripheral circadian rhythms. We demonstrate the effect of diet and feeding rhythms on the ileal microbiome composition and transcriptome in mice. The dynamic rhythms of ileal microbiome composition and transcriptome are dampened in DIO. TRF partially restores diurnal rhythms of the ileal microbiome and transcriptome, increases GLP-1 release, and alters the ileal bile acid pool and farnesoid X receptor (FXR) signaling, which could explain how TRF exerts its metabolic benefits. Finally, we provide a web resource for exploration of ileal microbiome and transcriptome circadian data.

Black sexually minoritized men (BSMM) are the most likely to acquire HIV in Chicago- a racially segregated city where their daily travel may confer different HIV-related risks. From survey and GPS data among participants of the Neighbourhoods and Networks Cohort Study, we examined spatial (proportion of total activity space away from home), temporal (proportion of total GPS points away from home), and motivation-specific (discordance between residential and frequented sex or socializing neighbourhoods) dimensions of mobility. To identify potential drivers of BSMM’s risk, we then examined associations between mobility and sexual behaviours known to cause HIV transmission: condomless anal sex, condomless anal sex with a casual partner, transactional sex, group sex, and sex-drug use. Multivariable logistic regression models assessed associations. Of 269 cisgender BSMM, most were 20-29 years old, identified as gay, and lowincome. On average, 96.9% (Standard Deviation: 3.7%) of participants’ activity space and 53.9% (Standard Deviation: 38.1%) of participants’ GPS points occurred outside their 800m home network buffer. After covariate adjustment, those who reported sex away from home were twice as likely to report condomless sex (Odds Ratio: 2.02, [95% Confidence Interval (CI): 1.08, 3.78]). Those who reported socializing away from home were four times more likely to have condomless sex with a casual partner (Odds Ratio: 4.16 [CI: 0.99, 29.0]). BSMM are on the move in Chicago, but only motivation-specific mobility may increase HIV transmission risk. Multidimensional investigations of mobility can inform place-based strategies for HIV service delivery.

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.

Summary: Interorganelle contact sites regulate lipid metabolism, organelle dynamics and positioning, as well as apoptosis and autophagy. Here, we present a proximity ligation assay (PLA) protocol for measuring the association of two organelles in fixed cells. We describe steps for primary cell culture, primary cell transfection, and the assay itself. We then detail procedures for manual and image J-based analysis of PLA foci. This protocol optimizes the use of assay products and improves the identification of PLA foci labeling actual contact sites.For complete details on the use and execution of this protocol, please refer to Ilamathi et al. (2023).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

RESUMO A espectroscopia no infravermelho próximo (NIR) é uma técnica para caracterização de materiais. Os espectros no NIR são utilizados para estabelecer modelos preditivos que permitem a caracterização da madeira em grande escala e o relativo baixo custo. O presente estudo teve por objetivo ajustar calibrações baseadas nos espectros e nas estimativas do ângulo das microfibrilas (AMF) de celulose na parede secundária obtidas por difração de raios X. Foi possível desenvolver regressões para predição desta característica da parede celular por meio da espectroscopia no NIR. O coeficiente de determinação da regressão linear entre os valores obtidos por difração de raios X e os preditos pelo modelo NIR para angulo microfibrilar foi de 0,75 e as estimativas apresentam um erro de predição de ±1,31 graus. A partir dessa calibração, foi possível estimar essa característica da fibra da madeira de Eucalyptus em grandes amostragens com base unicamente na informação espectral, que pode ser facilmente e rapidamente obtida.

This article presents an overall examination of how small temperature fluctuations affect P-wave velocity (Vp) measurements and their uncertainties in concrete using embedded piezoelectric transducers. This study highlights the fabrication of custom transducers tailored for long-term concrete monitoring. Accurate and reliable estimation of ultrasonic wave velocities is challenging, since they can be impacted by multiple experimental and environmental factors. In this work, a reliable methodology incorporating correction models is introduced for the quantification of uncertainties in ultrasonic absolute and relative velocity measurements. The study identifies significant influence quantities and suggests uncertainty estimation laws, enhancing measurement accuracy. Determining the onset time of the signal is very time-consuming if the onset is picked manually. After testing various methods to pinpoint the onset time, we selected the Akaike Information Criterion (AIC) due to its ability to produce sufficiently reliable results. Then, signal correlation was used to determine the influence of temperature (20 °C to 40 °C) on Vp in different concrete samples. This technique proved effective in evaluating velocity changes, revealing a persistent velocity decrease with temperature increases for various concrete compositions. The study demonstrated the capability of ultrasonic measurements to detect small variations in the state of concrete under the influence of environmental variables like temperature, underlining the importance of incorporating all influencing factors.

The chemical bath deposition (CBD) process enables the deposition of ZnO nanowires (NWs) on various substrates with customizable morphology. However, the hydrogen-rich CBD environment introduces numerous hydrogen-related defects, unintentionally doping the ZnO NWs and increasing their electrical conductivity. The oxygen-based plasma treatment can modify the nature and amount of these defects, potentially tailoring the ZnO NW properties for specific applications. This study examines the impact of the average ion energy on the formation of oxygen vacancies (VO) and hydrogen-related defects in ZnO NWs exposed to low-pressure oxygen plasma. Using X-ray photoelectron spectroscopy (XPS), 5 K cathodoluminescence (5K CL), and Raman spectroscopy, a comprehensive understanding of the effect of the oxygen ion energy on the formation of defects and defect complexes was established. A series of associative and dissociative reactions indicated that controlling plasma process parameters, particularly ion energy, is crucial. The XPS data suggested that increasing the ion energy could enhance Fermi level pinning by increasing the amount of VO and favoring the hydroxyl group adsorption, expanding the depletion region of charge carriers. The 5K CL and Raman spectroscopy further demonstrated the potential to adjust the ZnO NW physical properties by varying the oxygen ion energy, affecting various donor- and acceptor-type defect complexes. This study highlights the ability to tune the ZnO NW properties at low temperature by modifying plasma process parameters, offering new possibilities for a wide variety of nanoscale engineering devices fabricated on flexible and/or transparent substrates.

The dengue virus (DENV) causes the most prevalent arthropod-borne viral disease worldwide. While its incidence is increasing in many countries, there is no approved antiviral therapy currently available. In infected cells, the DENV induces extensive morphological alterations of the endoplasmic reticulum (ER) to generate viral replication organelles (vRO), which include convoluted membranes (CM) and vesicle packets (VP) hosting viral RNA replication. The viral non-structural protein NS4B localizes to vROs and is absolutely required for viral replication through poorly defined mechanisms, which might involve cellular protein partners. Previous interactomic studies identified the ATPase valosin-containing protein (VCP) as a DENV NS4B-interacting host factor in infected cells. Using both pharmacological and dominant-negative inhibition approaches, we show, in this study, that VCP ATPase activity is required for efficient DENV replication. VCP associates with NS4B when expressed in the absence of other viral proteins while in infected cells, both proteins colocalize within large DENV-induced cytoplasmic structures previously demonstrated to be CMs. Consistently, VCP inhibition dramatically reduces the abundance of DENV CMs in infected cells. Most importantly, using a recently reported replication-independent plasmid-based vRO induction system, we show that de novo VP biogenesis is dependent on VCP ATPase activity. Overall, our data demonstrate that VCP ATPase activity is required for vRO morphogenesis and/or stability. Considering that VCP was shown to be required for the replication of other flaviviruses, our results argue that VCP is a pan-flaviviral host dependency factor. Given that new generation VCP-targeting drugs are currently evaluated in clinical trials for cancer treatment, VCP may constitute an attractive broad-spectrum antiviral target in drug repurposing approaches.

Abstract Background Despite current broad natural and vaccine-induced protection, a substantial number of patients infected with emerging SARS-CoV-2 variants (e.g., BF.7 and BQ.1.1) still experience severe COVID-19. Real-life studies investigating the impact of these variants on clinical outcomes of severe cases are currently not available. We performed a prospective multicenter observational cohort study. Adult patients with acute respiratory failure admitted between December 7, 2021 and December 15, 2022, in one of the 20 participating intensive care units (17 from the Greater Paris area and 3 from the North of France) were eligible for inclusion if they had SARS-CoV-2 infection confirmed by a positive reverse transcriptase-polymerase chain reaction (RT-PCR). Full-length SARS-CoV-2 genomes from all included patients were sequenced by means of next-generation sequencing. The primary endpoint of the study was day-28 mortality. Results The study included 158 patients infected with three groups of Omicron sublineages, including (i) BA.2 variants and their early sublineages referred as “BA.2” (n = 50), (ii) early BA.4 and BA.5 sublineages (including BA.5.1 and BA.5.2, n = 61) referred as “BA.4/BA.5”, and (iii) recent emerging BA.5 sublineages (including BQ.1, BQ.1.1, BF.7, BE.1 and CE.1, n = 47) referred as “BQ.1.1”. The clinical phenotype of BQ1.1-infected patients compared to earlier BA.2 and BA.4/BA.5 sublineages, showed more frequent obesity and less frequent immunosuppression. There was no significant difference between Omicron sublineage groups regarding the severity of the disease at ICU admission, need for organ failure support during ICU stay, nor day 28 mortality (21.7%, n = 10/47 in BQ.1.1 group vs 26.7%, n = 16/61 in BA.4/BA.5 vs 22.0%, n = 11/50 in BA.2, p = 0.791). No significant relationship was found between any SARS-CoV-2 substitution and/or deletion on the one hand and survival on the other hand over hospital follow-up. Conclusions Critically-ill patients with Omicron BQ.1.1 infection showed a different clinical phenotype than other patients infected with earlier Omicron sublineage but no day-28 mortality difference.

IntroductionConverging evidence suggests that urban living is associated with an increased likelihood of developing mental health and sleep problems. Although these aspects have been investigated in separate streams of research, stress, autonomic reactivity and circadian misalignment can be hypothesized to play a prominent role in the causal pathways underlining the complex relationship between the urban environment and these two health dimensions. This study aims at quantifying the momentary impact of environmental stressors on increased autonomic reactivity and circadian rhythm, and thereby on mood and anxiety symptoms and sleep quality in the context of everyday urban living.MethodThe present article reports the protocol for a feasibility study that aims at assessing the daily environmental and mobility exposures of 40 participants from the urban area of Jerusalem over 7 days. Every participant will carry a set of wearable sensors while being tracked through space and time with GPS receivers. Skin conductance and heart rate variability will be tracked to monitor participants' stress responses and autonomic reactivity, whereas electroencephalographic signal will be used for sleep quality tracking. Light exposure, actigraphy and skin temperature will be used for ambulatory circadian monitoring. Geographically explicit ecological momentary assessment (GEMA) will be used to assess participants' perception of the environment, mood and anxiety symptoms, sleep quality and vitality. For each outcome variable (sleep quality and mental health), hierarchical mixed models including random effects at the individual level will be used. In a separate analysis, to control for potential unobserved individual-level confounders, a fixed effect at the individual level will be specified for case-crossover analyses (comparing each participant to oneself).ConclusionRecent developments in wearable sensing methods, as employed in our study or with even more advanced methods reviewed in the Discussion, make it possible to gather information on the functioning of neuro-endocrine and circadian systems in a real-world context as a way to investigate the complex interactions between environmental exposures, behavior and health. Our work aims to provide evidence on the health effects of urban stressors and circadian disruptors to inspire potential interventions, municipal policies and urban planning schemes aimed at addressing those factors.

ObjectivesAs sex between men is a major route of human immunodeficiency virus (HIV) infection in most western countries, restrictive deferral rules for blood donation have largely been implemented regarding men having sex with men (MSM). Here, we sought here to assign unreported HIV risk factors in blood donors (BDs) and reevaluated the MSM-associated fraction of HIV transfusion residual risk (%RRMSM ).MethodsWe applied a genetic distance-based approach to infer an HIV transmission network for 384 HIV sequences from French BDs and 1337 HIV sequences from individuals with known risk factors (ANRS PRIMO primary HIV infection cohort). We validated the possibility of assigning a risk factor according to clustering using assortative mixing. Finally, we recalculated the %RRMSM .ResultsA total of 81 of 284 (28.5%) male and 5 of 100 (5%) female BDs belonged to a cluster; 72 (88.9%) of the 81 male BDs belonged to MSM clusters. After cluster correction, 8 of 67 (11.9%), 4 of 21 (19.0%), and 19 of 88 (21.6%) HIV-positive (HIV+) male BDs with heterosexual, other, or unknown risk factors could be reclassified as MSM, accounting for 10.9% of the total HIV+ male BDs. Overall, 139 of 284 HIV+ male donors (48.9%) could be considered MSM between 2000 and 2016 in France. Between 2005 and 2016, the %RRMSM increase varied from 0 to 19%, without differing significantly from the %RRMSM before reclassification.ConclusionNetwork inference can be used to complement declaration data on risk factors for HIV infection in BDs. This approach, complementary to behavioral studies, is a valuable tool to evaluate the effect of changes in deferral criteria on BD compliance.

Procedural learning has been mainly tested through motor sequence learning tasks in children with neurodevelopmental disorders, especially with isolated Developmental Coordination Disorder (DCD) and Reading Disorder (RD). Studies on motor adaptation are scarcer and more controversial. This study aimed to compare the performance of children with isolated and associated DCD and RD in a graphomotor adaptation task. In total, 23 children with RD, 16 children with DCD, 19 children with DCD-RD, and 21 typically developing (TD) children wrote trigrams both in the conventional (from left to right) and opposite (from right to left) writing directions. The results show that movement speed and accuracy were more impacted by the adaptation condition (opposite writing direction) in children with neurodevelopmental disorders than TD children. Our results also reveal that children with RD have less difficulty adapting their movement than children with DCD. Children with DCD-RD had the most difficulty, and analysis of their performance suggests a cumulative effect of the two neurodevelopmental disorders in motor adaptation.

We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or ‘unidentifiable bovid’ from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments.