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Abstract Background We evaluated the performance of prognostic models for predicting mortality or ICU admission in hospitalized patients with COVID-19 in the World Health Organization (WHO) Global Clinical Platform, a repository of individual-level clinical data of patients hospitalized with COVID-19, including in low- and middle-income countries (LMICs). Methods We identified eligible multivariable prognostic models for predicting overall mortality and ICU admission during hospital stay in patients with confirmed or suspected COVID-19 from a living review of COVID-19 prediction models. These models were evaluated using data contributed to the WHO Global Clinical Platform for COVID-19 from nine LMICs (Burkina Faso, Cameroon, Democratic Republic of Congo, Guinea, India, Niger, Nigeria, Zambia, and Zimbabwe). Model performance was assessed in terms of discrimination and calibration. Results Out of 144 eligible models, 140 were excluded due to a high risk of bias, predictors unavailable in LIMCs, or insufficient model description. Among 11,338 participants, the remaining models showed good discrimination for predicting in-hospital mortality (3 models), with areas under the curve (AUCs) ranging between 0.76 (95% CI 0.71–0.81) and 0.84 (95% CI 0.77–0.89). An AUC of 0.74 (95% CI 0.70–0.78) was found for predicting ICU admission risk (one model). All models showed signs of miscalibration and overfitting, with extensive heterogeneity between countries. Conclusions Among the available COVID-19 prognostic models, only a few could be validated on data collected from LMICs, mainly due to limited predictor availability. Despite their discriminative ability, selected models for mortality prediction or ICU admission showed varying and suboptimal calibration.

Abstract Most published prediction models for Coronavirus Disease 2019 (COVID-19) were poorly reported, at high risk of bias, and heterogeneous in model performance. To tackle methodological challenges faced in previous prediction studies, we investigated whether model updating and extending improves mortality prediction, using the Intensive Care Unit (ICU) as a proxy. All COVID-19 patients admitted to seven ICUs in the Euregio-Meuse Rhine during the first pandemic wave were included. The 4C Mortality and SEIMC scores were selected as promising prognostic models from an external validation study. Five predictors could be estimated based on cohort size. TRIPOD guidelines were followed and logistic regression analyses with the linear predictor, APACHE II score, and country were performed. Bootstrapping with backward selection was applied to select variables for the final model. Additionally, shrinkage was performed. Model discrimination was displayed as optimism-corrected areas under the ROC curve and calibration by calibration slopes and plots. The mortality rate of the 551 included patients was 36%. Discrimination of the 4C Mortality and SEIMC scores increased from 0.70 to 0.74 and 0.70 to 0.73 and calibration plots improved compared to the original models after updating and extending. Mortality prediction can be improved after updating and extending of promising models.

Abstract Background Wild-type and hereditary transthyretin-mediated amyloidosis (ATTRwt and ATTRv amyloidosis, respectively) are progressive, fatal diseases with a broad range of clinical presentations and multisystem effects. Despite having a higher prevalence, ATTRwt amyloidosis is less well characterized due to its non-hereditary nature, and its relatively poorer disease awareness delays diagnosis. Understanding of its natural history has evolved in recent years, but this is largely based on physician-collected data rather than patients’ reports of their own experiences. A mixed methods approach was used to evaluate how the healthcare journeys of patients with ATTRv and ATTRwt amyloidosis compare. Methods A quantitative survey was administered to US-patients diagnosed with both ATTRwt amyloidosis and ATTRv amyloidosis identified through a patient support group. Subsequent in-depth interviews with participants with ATTRwt amyloidosis were conducted. Quantitative data with related qualitative quotes from patients were produced to characterize their paths to diagnosis and the disease burden experienced. Results A total of 47 respondents completed the survey (ATTRv, n = 20 and ATTRwt, n = 27) and a total of 14 survey respondents with ATTRwt amyloidosis were interviewed. Survey results reported a high disease burden for patients with both conditions, with patients with ATTRwt amyloidosis reporting more diagnoses and procedures prior to their final diagnosis. Interviews with participants with ATTRwt amyloidosis revealed that patients face a high symptomatic burden of disease. Diagnosis was often delayed due to three key factors: (1) early signs of ATTRwt amyloidosis were often assumed to be related to old age; (2) many medical specialists working in silos were involved in participants’ diagnostic; and (3) there was a general lack of disease awareness. Early indicators such as carpal tunnel syndrome were often overlooked. Participants were typically diagnosed after the disease had progressed to include severe cardiac symptoms such as atrial fibrillation and severe shortness of breath. Sleep apnoea was also reported by a number of participants, with a considerable impact on quality of life. Conclusions Our study provides insight into the overall impact of the patient journey on their quality of life and demonstrates how increased awareness of ATTRwt amyloidosis and more coordinated engagement with physicians could reduce the time to diagnosis.

The RISMEAU project (RISques liés aux résidus de Médicaments, biocides et antibiorésistance d'origine humaine et vétérinaire sur les ressources en EAU du bassin versant de l'Arve – Risks related to residues of pharmaceuticals and biocides, and antimicrobial resistance of human and veterinary origin on the water resources of the 2083 km2 Arve catchment located in the French Alps) was implanted from 2018 to 2024 on the SIPIBEL observatory. It was devoted to the evaluation of (i) transfers of and processes related to pharmaceutical residues and biocides from both urban sludge and manure spread on fields as fertilisers, and (ii) the environmental impacts of land spreading, in particular the ecotoxicological risks and antimicrobial resistance dissemination. The methodology was based on the physico-chemical, ecotoxicological and antimicrobial resistance (AMR – assessed by molecular biology) characterisation of leachate and soil matrices samples, and focused on organic waste products application at locally representative agronomic rates. This dataset can be reused by other researchers for comparison with their own investigations on this emerging topic under different contexts and conditions, and may contribute to international reviews.The database includes in total 26,217 values, measured on 348 samples of organic waste products, soil, in situ lysimeter leachate, earthworms, plants with 3136 usual physico-chemical values, 15,469 values on pharmaceuticals and biocides concentrations, 6827 bioassay values (ecotoxicity and phytotoxicity) and 785 values of antimicrobial resistance indicators. The 348 samples have been collected from Nov. 2019 to Dec. 2022: 4 samples in 2019, 26 in 2020, 130 in 2021 and 188 in 2022. Regarding AMR, 96 assays coding for most abundant resistance genes in healthy humans, clinically relevant antibiotic resistance genes, biocide resistance genes, heavy metal genes, integrons (class I, II and III), and mobile genetic elements (transposase genes) have been carried out.

Background There is a paucity of prognostic models for COVID-19 that are usable for in-office patient assessment in general practice (GP).Objectives To develop and validate a risk prediction model for hospital admission with readily available predictors.Methods A retrospective cohort study linking GP records from 8 COVID-19 centres and 55 general practices in the Netherlands to hospital admission records. The development cohort spanned March to June 2020, the validation cohort March to June 2021. The primary outcome was hospital admission within 14 days. We used geographic leave-region-out cross-validation in the development cohort and temporal validation in the validation cohort.Results In the development cohort, 4,806 adult patients with COVID-19 consulted their GP (median age 56, 56% female); in the validation cohort 830 patients did (median age 56, 52% female). In the development and validation cohort respectively, 292 (6.1%) and 126 (15.2%) were admitted to the hospital within 14 days, respectively. A logistic regression model based on sex, smoking, symptoms, vital signs and comorbidities predicted hospital admission with a c-index of 0.84 (95% CI 0.83 to 0.86) at geographic cross-validation and 0.79 (95% CI 0.74 to 0.83) at temporal validation, and was reasonably well calibrated (intercept −0.08, 95% CI −0.98 to 0.52, slope 0.89, 95% CI 0.71 to 1.07 at geographic cross-validation and intercept 0.02, 95% CI −0.21 to 0.24, slope 0.82, 95% CI 0.64 to 1.00 at temporal validation).Conclusion We derived a risk model using readily available variables at GP assessment to predict hospital admission for COVID-19. It performed accurately across regions and waves. Further validation on cohorts with acquired immunity and newer SARS-CoV-2 variants is recommended.

Abstract Background Radio(chemo)therapy is often required in pelvic malignancies (cancer of the anus, rectum, cervix). Direct irradiation adversely affects ovarian and endometrial function, compromising the fertility of women. While ovarian transposition is an established method to move the ovaries away from the radiation field, surgical procedures to displace the uterus are investigational. This study demonstrates the surgical options for uterine displacement in relation to the radiation dose received. Methods The uterine displacement techniques were carried out sequentially in a human female cadaver to demonstrate each procedure step by step and assess the uterine positions with dosimetric CT scans in a hybrid operating room. Two treatment plans (anal and rectal cancer) were simulated on each of the four dosimetric scans (1. anatomical position, 2. uterine suspension of the round ligaments to the abdominal wall 3. ventrofixation of the uterine fundus at the umbilical level, 4. uterine transposition). Treatments were planned on Eclipse® System (Varian Medical Systems®,USA) using Volumetric Modulated Arc Therapy. Data about maximum (Dmax) and mean (Dmean) radiation dose received and the volume receiving 14 Gy (V14Gy) were collected. Results All procedures were completed without technical complications. In the rectal cancer simulation with delivery of 50 Gy to the tumor, Dmax, Dmean and V14Gy to the uterus were respectively 52,8 Gy, 34,3 Gy and 30,5cc (1), 31,8 Gy, 20,2 Gy and 22.0cc (2), 24,4 Gy, 6,8 Gy and 5,5cc (3), 1,8 Gy, 0,6 Gy and 0,0cc (4). For anal cancer, delivering 64 Gy to the tumor respectively 46,7 Gy, 34,8 Gy and 31,3cc (1), 34,3 Gy, 20,0 Gy and 21,5cc (2), 21,8 Gy, 5,9 Gy and 2,6cc (3), 1,4 Gy, 0,7 Gy and 0,0cc (4). Conclusions The feasibility of several uterine displacement procedures was safely demonstrated. Increasing distance to the radiation field requires more complex surgical interventions to minimize radiation exposure. Surgical strategy needs to be tailored to the multidisciplinary treatment plan, and uterine transposition is the most technically complex with the least dose received.

Abstract Background Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease that commonly results from a high-calorie diet and sedentary lifestyle, leading to insulin resistance and glucose homeostasis perturbation. Physical activity is recommended as one first-line treatment in T2DM, but it leads to contrasted results. We hypothesized that, instead of applying standard exercise protocols, the prescription of personalized exercise programs specifically designed to reverse the potential metabolic alterations in skeletal muscle could result in better results. Methods To test this hypothesis, we drew the metabolic signature of the fast-twitch quadriceps muscle, based on a combined unbiased NMR spectroscopy and RT-qPCR study, in several T2DM mouse models of different genetic background (129S1/SvImJ, C57Bl/6J), sex and aetiology (high-fat diet (HFD) or HFD/Streptozotocin (STZ) induction or transgenic MKR (FVB-Tg Ckm-IGF1R*K1003R)1Dlr/J) mice. Three selected mouse models with unique muscular metabolic signatures were submitted to three different swimming-based programs, designed to address each metabolic specificity. Results We found that depending on the genetic background, the sex, and the mode of T2DM induction, specific muscular adaptations occurred, including depressed glycolysis associated with elevated PDK4 expression, shift to β-oxidation, or deregulation of amino-acid homeostasis. Interestingly, dedicated swimming-based exercises designed to restore specific metabolic alterations in muscle were found optimal in improving systemic T2DM hallmarks, including a significant reduction in insulin resistance, the improvement of glucose homeostasis, and a delay in sensorimotor function alterations. Conclusion The muscle metabolism constitutes an important clue for the design of precision exercises with potential clinical implications for T2DM patients.

Potato growers worldwide have been at war for more than 150 years with an enemy whose lifecycle, genome size and architecture, infection rate, and economic impacts are the epitome of a plant pathogen. Phytophthora infestans is an oomycete that causes the notorious late blight infection in potato and tomato fields. This study explored the benefits of the multitalented plant symbiotic fungi Trichoderma spp. and their metabolites as potential biopesticides against P. infestans. Eleven strains of Trichoderma spp. were obtained from soil and tree barks and were identified using DNA sequence analysis of three molecular markers. The antagonistic potential of the strains against P. infestans was first evaluated in vitro. In dual-culture assays, P. infestans growth was significantly inhibited (53 to 95%) by different Trichoderma spp. through direct mycoparasitism, competition for space and nutrients, or antibiosis. The cell-free filtrates (CFFs) of different Trichoderma strains were obtained and characterized for anti-Phytophthora activities as well as biochemical stability. The obtained results indicated that Trichoderma CFFs were chemically stable and strongly decreased P. infestans’ mycelial growth and zoospore motility and viability. Similarly, in leaf-disk assays, Trichoderma CFFs showed significant protection against P. infestans infection. Ultraperformance liquid chromatography analysis revealed the presence of harzianic acid, iso-harzianic acid, and 6-pentyl-2H-pyran-2-one as major compounds in different Trichoderma CFFs. Furthermore, selected Trichoderma strains significantly protected potato plants against soil-mediated late blight infection. Finally, Trichoderma spp. showed high compatibility with a copper-based fungicide, especially at lower concentrations, suggesting that both protective agents could be combined in integrated pest management programs. [Graphic: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Objectives To conduct a systematic review of studies externally validating the ADNEX (Assessment of Different Neoplasias in the adnexa) model for diagnosis of ovarian cancer and to present a meta-analysis of its performance.Design Systematic review and meta-analysis of external validation studiesData sources Medline, Embase, Web of Science, Scopus, and Europe PMC, from 15 October 2014 to 15 May 2023.Eligibility criteria for selecting studies All external validation studies of the performance of ADNEX, with any study design and any study population of patients with an adnexal mass. Two independent reviewers extracted the data. Disagreements were resolved by discussion. Reporting quality of the studies was scored with the TRIPOD (Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis) reporting guideline, and methodological conduct and risk of bias with PROBAST (Prediction model Risk Of Bias Assessment Tool). Random effects meta-analysis of the area under the receiver operating characteristic curve (AUC), sensitivity and specificity at the 10% risk of malignancy threshold, and net benefit and relative utility at the 10% risk of malignancy threshold were performed.Results 47 studies (17 007 tumours) were included, with a median study sample size of 261 (range 24-4905). On average, 61% of TRIPOD items were reported. Handling of missing data, justification of sample size, and model calibration were rarely described. 91% of validations were at high risk of bias, mainly because of the unexplained exclusion of incomplete cases, small sample size, or no assessment of calibration. The summary AUC to distinguish benign from malignant tumours in patients who underwent surgery was 0.93 (95% confidence interval 0.92 to 0.94, 95% prediction interval 0.85 to 0.98) for ADNEX with the serum biomarker, cancer antigen 125 (CA125), as a predictor (9202 tumours, 43 centres, 18 countries, and 21 studies) and 0.93 (95% confidence interval 0.91 to 0.94, 95% prediction interval 0.85 to 0.98) for ADNEX without CA125 (6309 tumours, 31 centres, 13 countries, and 12 studies). The estimated probability that the model has use clinically in a new centre was 95% (with CA125) and 91% (without CA125). When restricting analysis to studies with a low risk of bias, summary AUC values were 0.93 (with CA125) and 0.91 (without CA125), and estimated probabilities that the model has use clinically were 89% (with CA125) and 87% (without CA125).Conclusions The results of the meta-analysis indicated that ADNEX performed well in distinguishing between benign and malignant tumours in populations from different countries and settings, regardless of whether the serum biomarker, CA125, was used as a predictor. A key limitation was that calibration was rarely assessed.Systematic review registration PROSPERO CRD42022373182.

ABSTRACT Botrytis cinerea is a necrotrophic phytopathogen able to attack more than 200 different plant species causing strong yield losses worldwide. Many synthetic fungicides have been developed to control this disease, resulting in the rise of fungicide-resistance B. cinerea strains. The aim of this study was to identify Streptomyces strains showing antagonistic activity against B. cinerea to contribute to plant protection in an environmentally friendly way. We isolated 15 Actinomycete strains from 9 different Swiss soils. The culture filtrates of three isolates showing antifungal activity inhibited spore germination and delayed mycelial growth of B. cinerea. Infection experiments showed that Arabidopsis thaliana plants were more resistant to this pathogen after leaf treatment with the Streptomyces filtrates. Bioassay-guided isolation of the active compounds revealed the presence of germicidins A and B as well as of oligomycins A, B, and E. While germicidins were mostly inactive, oligomycin B reduced the mycelial growth of B. cinerea significantly. Moreover, all three oligomycins inhibited this fungus’ spore germination, suggesting that these molecules might contribute to the Streptomyces’s ability to protect plants against infection by the broad host-pathogen Botrytis cinerea.IMPORTANCEThis study reports the isolation of new Streptomyces strains with strong plant-protective potential mediated by their production of specialized metabolites. Using the broad host range pathogenic fungus Botrytis cinerea, we demonstrate that the cell-free filtrate of selected Streptomyces isolates efficiently inhibits different developmental stages of the fungus, including mycelial growth and the epidemiologically relevant spore germination. Beyond in vitro experiments, the strains and their metabolites also efficiently protected plants against the disease caused by this pathogen. This work further identifies oligomycins as active compounds involved in the observed antifungal activity of the strains. This work shows that we can harness the natural ability of soil-borne microbes and of their metabolites to efficiently fight other microbes responsible for significant crop losses. This opens the way to the development of environmentally friendly health protection measures for crops of agronomical relevance, based on these newly isolated strains or their metabolic extracts containing oligomycins.

Abstract Background A number of recent papers have proposed methods to calculate confidence intervals and p values for net benefit used in decision curve analysis. These papers are sparse on the rationale for doing so. We aim to assess the relation between sampling variability, inference, and decision-analytic concepts. Methods and results We review the underlying theory of decision analysis. When we are forced into a decision, we should choose the option with the highest expected utility, irrespective of p values or uncertainty. This is in some distinction to traditional hypothesis testing, where a decision such as whether to reject a given hypothesis can be postponed. Application of inference for net benefit would generally be harmful. In particular, insisting that differences in net benefit be statistically significant would dramatically change the criteria by which we consider a prediction model to be of value. We argue instead that uncertainty related to sampling variation for net benefit should be thought of in terms of the value of further research. Decision analysis tells us which decision to make for now, but we may also want to know how much confidence we should have in that decision. If we are insufficiently confident that we are right, further research is warranted. Conclusion Null hypothesis testing or simple consideration of confidence intervals are of questionable value for decision curve analysis, and methods such as value of information analysis or approaches to assess the probability of benefit should be considered instead.

The increasing use of chemicals requires a better understanding of their presence and dynamics in the environment, as well as their impact on ecosystems. The aim of this study was to validate the first steps of an innovative multi-omics approach based on metabolomics and 16S metabarcoding data for analyses of the fate and impact of contaminants in Mediterranean lagoons. Semi-targeted analytical procedures for water and sediment matrices were implemented to assess chemical contamination of the lagoon: forty-six compounds were detected, 28 of which could be quantified in water (between 0.09 and 47.4 ng/L) and sediment (between 0.008 and 26.3 ng/g) samples using the UHPLC-MS/MS instrument. In addition, a non-targeted approach (UHPLC-HRMS) using four different sample preparation protocols based on solid/liquid extractions or an automated pressurized fluid extraction system (EDGE®) was carried out to determine the protocol with the best metabolome coverage, efficiency and reproducibility. Solid/liquid extraction using the solvent mixture acetonitrile/methanol (50/50) was evaluated as the best protocol. Microbial diversity in lagoon sediment was also measured after DNA extraction using five commercial extraction kits. Our study showed that the DNeasy PowerSoil Pro Qiagen kit (Promega, USA) was the most suitable for assessing microbial diversity in fresh sediment.

Abstract The Streptomyces genus is known to produce many specialized metabolites of value for medicine, but the potential of these metabolites in agronomy remains largely unexplored. In this study, we investigated three phylogenetically closely related Streptomyces strains (B5, B91, and B135) isolated from three distinct soil samples in Sudan. Despite belonging to the same species, these strains exhibited different ranges of Phytophthora infestans inhibition. The objective of this work was to identify the active compound(s) responsible for the inhibition of P. infestans and of other plant pathogens by comparing the genomes and metabolomes of the three strains which showed distinct activity patterns: B5 was the strongest inhibitor of oomycetes, B5 and B91 both inhibited most fungi and B135 was the only strain showing antibacterial activity. Our comparative genomic and metabolomic analysis identified borrelidin as the bioactive compound underlying B5's strong anti‐oomycete activity and highlighted a few other metabolites as putative candidates underlying the strains' antifungal and antibacterial activities. This study illustrates the power of comparative genomics and metabolomics on phylogenetically closely related strains of differing activities to highlight bioactive compounds that could contribute to new sustainable crop protection strategies.

Abstract Background Clinical prediction models should be validated before implementation in clinical practice. But is favorable performance at internal validation or one external validation sufficient to claim that a prediction model works well in the intended clinical context? Main body We argue to the contrary because (1) patient populations vary, (2) measurement procedures vary, and (3) populations and measurements change over time. Hence, we have to expect heterogeneity in model performance between locations and settings, and across time. It follows that prediction models are never truly validated. This does not imply that validation is not important. Rather, the current focus on developing new models should shift to a focus on more extensive, well-conducted, and well-reported validation studies of promising models. Conclusion Principled validation strategies are needed to understand and quantify heterogeneity, monitor performance over time, and update prediction models when appropriate. Such strategies will help to ensure that prediction models stay up-to-date and safe to support clinical decision-making.

ABSTRACT Bacterial volatile compounds have emerged as important chemical messengers between bacteria themselves as well as in their interactions with other organisms. One of the earliest examples of bioactive volatiles emitted by bacteria is hydrogen cyanide (HCN), which was long considered a mere respiratory toxin conferring competitive advantage to cyanide-producing strains. Using cyanide-deficient mutants in two Pseudomonas strains and global transcriptome analysis, we demonstrate that the impact of HCN is much more global than previously thought. We first observed that the lack of cyanogenesis (i.e., the ability to produce HCN) in emitting strains led to massive transcriptome reprogramming affecting diverse traits such as motility and biofilm formation (respectively inhibited vs promoted by HCN), or the production of siderophores, phenazines, and other antimicrobial compounds (repressed by HCN). We then exposed non-cyanogenic strains to biogenically emitted HCN from neighboring cells and observed similar transcriptome modulations and phenotypic changes, suggesting that HCN not only acts endogenously but also exogenously, remotely manipulating important traits involved in competition and virulence, e.g., siderophore production, in other organisms. Cyanogenesis in Pseudomonas has long been known to play a role in both the virulence of opportunistic pathogens and the efficient biocontrol activity of plant-beneficial strains; however, this impact was so far thought to occur solely through the inhibition of respiration. We demonstrate here new ecological roles for a small and fast-diffusing volatile compound, which opens novel avenues in our understanding of and ability to interfere with important processes taking place in pathogenic and beneficial Pseudomonas strains. IMPORTANCE Bacteria communicate by exchanging chemical signals, some of which are volatile and can remotely reach other organisms. HCN was one of the first volatiles discovered to severely impact exposed organisms by inhibiting their respiration. Using HCN-deficient mutants in two Pseudomonas strains, we demonstrate that HCN’s impact goes beyond the sole inhibition of respiration and affects both emitting and receiving bacteria in a global way, modulating their motility, biofilm formation, and production of antimicrobial compounds. Our data suggest that bacteria could use HCN not only to control their own cellular functions, but also to remotely influence the behavior of other bacteria sharing the same environment. Since HCN emission occurs in both clinically and environmentally relevant Pseudomonas, these findings are important to better understand or even modulate the expression of bacterial traits involved in both virulence of opportunistic pathogens and in biocontrol efficacy of plant-beneficial strains.

IntroductionSpinal muscular atrophy (SMA) is a fatal neurodegenerative disorder, characterized by motor neuron (MN) degeneration and severe muscular atrophy and caused by Survival of Motor Neuron (SMN) depletion. Therapies aimed at increasing SMN in patients have proven their efficiency in alleviating SMA symptoms but not for all patients. Thus, combinational therapies are warranted. Here, we investigated the involvement of NADPH oxidase 4 (NOX4) in SMA-induced spinal MN death and if the modulation of Nox4 activity could be beneficial for SMA patients.MethodsWe analysed in the spinal cord of severe type SMA-like mice before and at the disease onset, the level of oxidative stress and Nox4 expression. Then, we tested the effect of Nox4 inhibition by GKT137831/Setanaxib, a drug presently in clinical development, by intrathecal injection on MN survival and motor behaviour. Finally, we tested if GKT137831/Setanaxib could act synergistically with FDA-validated SMN-upregulating treatment (nusinersen).ResultsWe show that NOX4 is overexpressed in SMA and its inhibition by GKT137831/Setanaxib protected spinal MN from SMA-induced degeneration. These improvements were associated with a significant increase in lifespan and motor behaviour of the mice. At the molecular level, GKT137831 activated the pro-survival AKT/CREB signaling pathway, leading to an increase in SMN expression in SMA MNs. Most importantly, we found that the per os administration of GKT137831 acted synergistically with a FDA-validated SMN-upregulating treatment.ConclusionThe pharmacological inhibition of NOX4 by GKT137831/Setanaxib is neuroprotector and could represent a complementary therapeutic strategy to fight against SMA.

Abstract Background Prediction modeling studies often have methodological limitations, which may compromise model performance in new patients and settings. We aimed to examine the relation between methodological quality of model development studies and their performance at external validation. Methods We systematically searched for externally validated multivariable prediction models that predict functional outcome following moderate or severe traumatic brain injury. Risk of bias and applicability of development studies was assessed with the Prediction model Risk Of Bias Assessment Tool (PROBAST). Each model was rated for its presentation with sufficient detail to be used in practice. Model performance was described in terms of discrimination (AUC), and calibration. Delta AUC (dAUC) was calculated to quantify the percentage change in discrimination between development and validation for all models. Generalized estimation equations (GEE) were used to examine the relation between methodological quality and dAUC while controlling for clustering. Results We included 54 publications, presenting ten development studies of 18 prediction models, and 52 external validation studies, including 245 unique validations. Two development studies (four models) were found to have low risk of bias (RoB). The other eight publications (14 models) showed high or unclear RoB. The median dAUC was positive in low RoB models (dAUC 8%, [IQR − 4% to 21%]) and negative in high RoB models (dAUC − 18%, [IQR − 43% to 2%]). The GEE showed a larger average negative change in discrimination for high RoB models (− 32% (95% CI: − 48 to − 15) and unclear RoB models (− 13% (95% CI: − 16 to − 10)) compared to that seen in low RoB models. Conclusion Lower methodological quality at model development associates with poorer model performance at external validation. Our findings emphasize the importance of adherence to methodological principles and reporting guidelines in prediction modeling studies.

Background The COVID-19 pandemic required science to provide answers rapidly to combat the outbreak. Hence, the reproducibility and quality of conducting research may have been threatened, particularly regarding privacy and data protection, in varying ways around the globe. The objective was to investigate aspects of reporting informed consent and data handling as proxies for study quality conduct.Methods A systematic scoping review was performed by searching PubMed and Embase. The search was performed on November 8th, 2020. Studies with hospitalised patients diagnosed with COVID-19 over 18 years old were eligible for inclusion. With a focus on informed consent, data were extracted on the study design, prestudy protocol registration, ethical approval, data anonymisation, data sharing and data transfer as proxies for study quality. For reasons of comparison, data regarding country income level, study location and journal impact factor were also collected.Results 972 studies were included. 21.3% of studies reported informed consent, 42.6% reported waivers of consent, 31.4% did not report consent information and 4.7% mentioned other types of consent. Informed consent reporting was highest in clinical trials (94.6%) and lowest in retrospective cohort studies (15.0%). The reporting of consent versus no consent did not differ significantly by journal impact factor (p=0.159). 16.8% of studies reported a prestudy protocol registration or design. Ethical approval was described in 90.9% of studies. Information on anonymisation was provided in 17.0% of studies. In 257 multicentre studies, 1.2% reported on data sharing agreements, and none reported on Findable, Accessible, Interoperable and Reusable data principles. 1.2% reported on open data. Consent was most often reported in the Middle East (42.4%) and least often in North America (4.7%). Only one report originated from a low-income country.Discussion Informed consent and aspects of data handling and sharing were under-reported in publications concerning COVID-19 and differed between countries, which strains study quality conduct when in dire need of answers.

Introduction It is known that only a limited proportion of developed clinical prediction models (CPMs) are implemented and/or used in clinical practice. This may result in a large amount of research waste, even when considering that some CPMs may demonstrate poor performance. Cross-sectional estimates of the numbers of CPMs that have been developed, validated, evaluated for impact or utilized in practice, have been made in specific medical fields, but studies across multiple fields and studies following up the fate of CPMs are lacking.Methods and analysis We have conducted a systematic search for prediction model studies published between January 1995 and December 2020 using the Pubmed and Embase databases, applying a validated search strategy. Taking random samples for every calendar year, abstracts and articles were screened until a target of 100 CPM development studies were identified. Next, we will perform a forward citation search of the resulting CPM development article cohort to identify articles on external validation, impact assessment or implementation of those CPMs. We will also invite the authors of the development studies to complete an online survey to track implementation and clinical utilization of the CPMs.We will conduct a descriptive synthesis of the included studies, using data from the forward citation search and online survey to quantify the proportion of developed models that are validated, assessed for their impact, implemented and/or used in patient care. We will conduct time-to-event analysis using Kaplan-Meier plots.Ethics and dissemination No patient data are involved in the research. Most information will be extracted from published articles. We request written informed consent from the survey respondents. Results will be disseminated through publication in a peer-reviewed journal and presented at international conferences.OSF registration (https://osf.io/nj8s9).

Microbes communicate with each other using a wide array of chemical compounds, including volatile organic compounds (VOCs). Usually, such volatile-mediated interactions are studied by growing two different microbes in a shared, confined environment and by subsequently collecting and analyzing the emitted VOCs by gas chromatography. This procedure has several drawbacks, including artificial volatile overaccumulation and potential oxygen limitation, as well as the impossibility to assign a producer to the compounds newly emitted during the interaction. To address these challenges, we have developed a novel system specifically designed to analyze volatile-mediated interactions allowing for sequential unidirectional exposure of a “receiver” microorganism to the VOCs of an “emitter” microorganism. Using hermetically sealed systems connected to an air compressor, a constant unidirectional airflow could be generated, driving emitted volatiles to be absorbed by a collection charcoal filter. Thus, our developed system avoids artificial overaccumulation of volatile compounds and lack of oxygen in the headspace and enables the univocal assignment of VOCs to their producers. As a proof of concept, we used this newly developed experimental setup to characterize the reaction of plant growth-promoting and biocontrol fungus (Trichoderma simmonsii) to the perception of VOCs emitted by two plant pathogens, namely Botrytis cinerea and Fusarium oxysporum. Our results show that the perception of each pathogen's volatilome triggered a specific response, resulting in significant changes in the VOCs emitted by Trichoderma. Trichoderma's volatilome modulation was overall stronger when exposed to the VOCs from Fusarium than to the VOCs from Botrytis, which correlated with increased siderophore production when co-incubated with this fungus. Our newly developed method will not only help to better understand volatile-mediated interactions in microbes but also to identify new molecules of interest that are induced by VOC exposure, as well as the putative-inducing signals themselves.

The function of the aminotransferase Aat (GenBank Protein WP_159211138) from Pediococcus acidilactici FAM 18098 was studied in vivo. For this purpose, the gene was replaced with an erythromycin resistance gene using the temperature-sensitive Escherichia coli-Pediococcus shuttle plasmid pSET4T_Δaat. The knockout was verified by PCR and genome sequencing. Subsequently, the differences between the metabolism of the knockout and of the wild-type strain were investigated by determining the free amino acids and organic acids in culture supernatants. It was found that the knockout mutant no longer synthesized 3-phenyllactic acid (PLA) and 4-hydroxyphenyllactic acid (HPLA). Additionally, the mutant strain no longer catabolized phenylalanine. Metabolic pathway analysis using the KEGG database indicate that P. acidilactici cannot synthesize α-ketoglutarate that is a predominant amino-group acceptor in many transamination reactions. To study the transfer of the amino group of phenylalanine, the wild-type strain was incubated with [15N] phenylalanine. Mass spectrometry showed that during fermentation, [15N] alanine was formed, indicating that pyruvic acid is an amino group acceptor in P. acidilactici. The present study shows that Aat plays a crucial role in PLA/HPLA biosynthesis and pyruvic acid is an amino acceptor in transamination reactions in P. acidilactici.

Abstract Background Non-dystrophic myotonias (NDMs) comprise muscle chloride and sodium channelopathies due to genetic defects of the CLCN1- and SCN4A-channels. No licensed antimyotonic treatment has been available until approval of mexiletine (NaMuscla®) for adult patients by the EMA in December 2018. This Delphi panel aimed to understand how outcomes of the pivotal phase III Mexiletine study (MYOMEX) translate to real world practice and investigate health resource use, quality of life and the natural history of NDM to support economic modelling and facilitate patient access. Methods Nine clinical experts in treating NDM took part in a two-round Delphi panel. Their knowledge of NDM and previous use of mexiletine as an off-label treatment prior to NaMuscla’s approval ensured they could provide both qualitative context and quantitative estimates to support economic modelling comparing mexiletine (NaMuscla) to best supportive care. Consensus in four key areas was sought: healthcare resource utilization (HRU), treatment with mexiletine (NaMuscla), patient quality of life (QoL), and the natural history of disease. Concept questions were also asked, considering perceptions on the feasibility of mapping the validated Individualized Neuromuscular Quality of Life (INQoL) instrument to the generic EQ-5D™, and the potential impact on caregiver QoL. Results Consensus was achieved for key questions including the average long-term dosage of mexiletine (NaMuscla) in practice, the criteria for eligibility of myotonia treatment, the clinical importance of QoL outcomes in MYOMEX, the higher proportion of patients with increased QoL, and the reduction in the need for mental health resources for patients receiving mexiletine (NaMuscla). While consensus was not achieved for other questions, the results demonstrated that most experts felt mexiletine (NaMuscla) reduced the need for HRU and was expected to improve QoL. The QoL mapping exercise suggested that it is feasible to map domains of INQoL to EQ-5D. Points of interest for future research were identified, including that mexiletine (NaMuscla) may slow the annual decrease in QoL of patients over their lifetime, and a significant negative impact on QoL for some caregivers. Conclusions This project successfully provided data from an informed group of clinical experts, complementing the currently available clinical trial data for mexiletine (NaMuscla) to support patient access decisions.

BAFF (B cell activation factor of the TNF family/B lymphocyte stimulator, BLyS) and APRIL (a proliferation-inducing ligand) are targeted by atacicept, a decoy receptor consisting of the extracellular domain of TACI (transmembrane activator and calcium-modulator and cyclophilin (CAML) interactor) fused to the Fc portion of human IgG1. The purpose of the study was to characterize free and ligand-bound atacicept in humans. Total and active atacicept in serum of healthy volunteers receiving a single dose of subcutaneous atacicept or in patients treated weekly for one year were measured by ELISA, Western blot, or cell-based assays. Pharmacokinetics of free and bound atacicept were predicted based on total atacicept ELISA results. Persistence of complexes of purified atacicept bound to recombinant ligands was also monitored in mice. Results show that unbound or active atacicept in human serum exceeded 0.1 µg/ml for one week post administration, or throughout a 1-year treatment with weekly administrations. After a single administration of atacicept, endogenous BAFF bound to atacicept was detected after 8 h then increased about 100-fold within 2 to 4 weeks. Endogenous heteromers of BAFF and APRIL bound to atacicept also accumulated, but atacicept-APRIL complexes were not detected. In mice receiving intravenous injections of purified complexes pre-formed in vitro, atacicept-BAFF persisted longer (more than a week) than atacicept-APRIL (less than a day). Thus, only biologically inactive BAFF and BAFF-APRIL heteromers accumulate on atacicept in vivo. The measure of active atacicept provides further support for the once-weekly dosing regimen implemented in the clinical development of atacicept.

Plants are densely colonized by diverse microbial communities. These microbes, which provide important benefit to their host supporting its growth and health, interact with each other and with their host plant by exchanging chemical signals, among which volatile organic compounds (VOCs). This review presents some of our current research lines in the field of microbial VOCs, including their bioactivities on both plants and plant pathogens, and the abiotic and biotic factors influencing their emission. Understanding how VOCs emission is regulated in plant-associated microbes is one of the major challenges for both fundamental and translational aspects of this research field.

ObjectivesTo assess practices of French psychiatrists regarding their management of children and adolescents with suicidal behaviors, focusing on the use of a separation protocol in which the youths are separated from their relatives.MethodsIn 2017, we conducted an online cross-sectional survey of French psychiatrists caring for children and adolescents. Participants were asked to describe their practice of a separation protocol in children and adolescents admitted for suicidal behavior. Our main analysis followed a descriptive approach. We also explored whether participant characteristics were associated with the use of a separation protocol.ResultsThe response rate was 218/2403 (9,1%); 57.9 % of respondents worked in a University hospital, and 60% of respondents reported routinely hospitalizing children. A separation protocol was set up by 91.1% of survey participants (systematically 39.6%, on a case-by-case basis 51.5%). The mean age from which a separation protocol was indicated was above 11 years; 64% of participants reported a separation period of ≤ 48 h. The most common (87%) criterion cited for establishing a separation period was family relationship difficulties. The most common (80.9%) reason to justify the use of a separation protocol was to allow a better clinical assessment. Exploratory analyses did not identify any participant characteristics associated with the use of a separation protocol (p > 0.2 for all).ConclusionThe use of a separation protocol in children and adolescents admitted for suicidal behavior is a widespread practice in France, despite the deprivation of liberty it implies. This raises the question of the relevance and usefulness of such a practice.

Deficiency of ectodysplasin A1 (EDA1) due to variants of the gene EDA causes X-linked hypohidrotic ectodermal dysplasia (XLHED), a rare genetic condition characterized by abnormal development of ectodermal structures. XLHED is defined by the triad of hypotrichosis, hypo- or anhidrosis, and hypo- or anodontia. Anhidrosis may lead to life-threatening hyperthermia. A definite genetic diagnosis is, thus, important for the patients’ management and amenability to a novel prenatal treatment option. Here, we describe five familial EDA variants segregating with the disease in three families, for which different prediction tools yielded discordant results with respect to their significance. Functional properties in vitro and levels of circulating serum EDA were compared with phenotypic data on skin, hair, eyes, teeth, and sweat glands. EDA1-Gly176Val, although associated with relevant hypohidrosis, still bound to the EDA receptor (EDAR). Subjects with EDA1-Pro389LeufsX27, -Ter392GlnfsX30, -Ser125Cys, and an EDA1 splice variant (c.924+7A > G) showed complete absence of pilocarpine-induced sweating. EDA1-Pro389LeufsX27 was incapable of binding to EDAR and undetectable in serum. EDA1-Ter392GlnfsX30, produced in much lower amounts than wild-type EDA1, could still bind to EDAR, and so did EDA1-Ser125Cys that was, however, undetectable in serum. The EDA splice variant c.924+7A > G resulted experimentally in a mix of wild-type EDA1 and EDA molecules truncated in the middle of the receptor-binding domain, with reduced EDA serum concentration. Thus, in vitro assays reflected the clinical phenotype in two of these difficult cases, but underestimated it in three others. Absence of circulating EDA seems to predict the full-blown phenotype of XLHED, while residual EDA levels may also be found in anhidrotic patients. This indicates that unborn subjects carrying variants of uncertain significance could benefit from an upcoming prenatal medical treatment even if circulating EDA levels or tests in vitro suggest residual EDA1 activity.

Soil microorganisms play crucial roles in soil fertility, e.g., through decomposing organic matter, cycling nutrients or through beneficial interactions with plants. Actinomycetes are a major component of soil inhabitants; they are prolific producers of specialized metabolites, among which many antibiotics. Here we report the isolation and characterization of 175 Actinomycetes from rhizosphere and bulk soil samples collected in 18 locations in Sudan. We evaluated the strains’ metabolic potential for plant protection by testing their ability to inhibit the mycelial growth of the oomycete Phytophthora infestans, which is one of the most devastating plant pathogens worldwide. Most strains significantly reduced the oomycete’s growth in direct confrontational in vitro assays. A significant proportion of the tested strains (15%) were able to inhibit P. infestans to more than 80%, 23% to 50%–80%, while the remaining 62% had inhibition percentages lesser than 50%. Different morphologies of P. infestans mycelial growth and sporangia formation were observed upon co-inoculation with some of the Actinomycetes isolates, such as the production of fewer, thinner hyphae without sporangia leading to a faint growth morphology, or on the contrary, of clusters of thick-walled hyphae leading to a bushy, or “frozen” morphology. These morphologies were caused by strains differing in activity levels but phylogenetically closely related with each other. To evaluate whether the isolated Actinomycetes could also inhibit the pathogen’s growth in planta, the most active strains were tested for their ability to restrict disease progress in leaf disc and full plant assays. Five of the active strains showed highly significant protection of potato leaves against the pathogen in leaf disc assays, as well as substantial reduction of disease progress in full plants assays. Using cell-free filtrates instead of the bacterial spores also led to full protection against disease on leaf discs, which highlights the strong crop protective potential of the secreted metabolites that could be applied as leaf spray. This study demonstrates the strong anti-oomycete activity of soil- and rhizosphere-borne Actinomycetes and highlights their significant potential for the development of sustainable solutions based on either cell suspensions or cell-free filtrates to safeguard potatoes from their most damaging pathogen.

Abstract During cheese ripening, the bacterial strain Pediococcus acidilactici FAM18098 produces the non-proteinogenic amino acid, α-aminobutyrate (AABA). The metabolic processes that lead to the biosynthesis of this compound are unknown. In this study, 10 P. acidilactici, including FAM18098 and nine Pediococcus pentosaceus strains, were screened for their ability to produce AABA. All P. acidilactici strains produced AABA, whereas the P. pentosaceus strains did not. The genomes of the pediococcal strains were sequenced and searched for genes encoding aminotransferases to test the hypothesis that AABA could result from the transamination of α-ketobutyrate. A GenBank and KEGG database search revealed the presence of a species-specific aminotransferase in P. acidilactici. The gene was cloned and its gene product was produced as a His-tagged fusion protein in Escherichia coli to determine the substrate specificity of this enzyme. The purified recombinant protein showed aminotransferase activity at pH 5.5. It catalyzed the transfer of the amino group from leucine, methionine, AABA, alanine, cysteine, and phenylalanine to the amino group acceptor α-ketoglutarate. Αlpha-ketobutyrate could replace α-ketoglutarate as an amino group acceptor. In this case, AABA was produced at significantly higher levels than glutamate. The results of this study show that P. acidilactici possesses a novel aminotransferase that might play a role in cheese biochemistry and has the potential to be used in biotechnological processes for the production of AABA.

The Bellecombe pilot site – SIPIBEL – was created in 2010 in order to study the characterisation, treatability and impacts of hospital effluents in an urban wastewater treatment plant. This pilot site is composed of: i) the Alpes Léman hospital (CHAL), opened in February 2012, ii) the Bellecombe wastewater treatment plant, with two separate treatment lines allowing to fully separate the hospital wastewater and the urban wastewater, and iii) the Arve River as the receiving water body and a tributary of the Rhône River and the Geneva aquifer. The database includes in total 48 439 values measured on 961 samples (raw and treated hospital and urban wastewater, activated sludge in aeration tanks, dried sludge after dewatering, river and groundwater, and a few additional campaigns in aerobic and anaerobic sewers) with 44 455 physico-chemistry values (including 15 pharmaceuticals and 14 related transformation products, biocides compounds, metals, organic micropollutants), 2 193 bioassay values (ecotoxicity), 1 679 microbiology values (including microorganisms and antibioresistance indicators) and 112 hydrobiology values.

Somites are transitory metameric structures at the basis of the axial organization of vertebrate musculoskeletal system. During evolution, somites appear in the chordate phylum and compartmentalize mainly into the dermomyotome, the myotome, and the sclerotome in vertebrates. In this review, we summarized the existing literature about somite compartmentalization in Xenopus and compared it with other anamniote and amniote vertebrates. We also present and discuss a model that describes the evolutionary history of somite compartmentalization from ancestral chordates to amniote vertebrates. We propose that the ancestral organization of chordate somite, subdivided into a lateral compartment of multipotent somitic cells (MSCs) and a medial primitive myotome, evolves through two major transitions. From ancestral chordates to vertebrates, the cell potency of MSCs may have evolved and gave rise to all new vertebrate compartments, i.e., the dermomyome, its hypaxial region, and the sclerotome. From anamniote to amniote vertebrates, the lateral MSC territory may expand to the whole somite at the expense of primitive myotome and may probably facilitate sclerotome formation. We propose that successive modifications of the cell potency of some type of embryonic progenitors could be one of major processes of the vertebrate evolution.

Abstract Background The assessment of calibration performance of risk prediction models based on regression or more flexible machine learning algorithms receives little attention. Main text Herein, we argue that this needs to change immediately because poorly calibrated algorithms can be misleading and potentially harmful for clinical decision-making. We summarize how to avoid poor calibration at algorithm development and how to assess calibration at algorithm validation, emphasizing balance between model complexity and the available sample size. At external validation, calibration curves require sufficiently large samples. Algorithm updating should be considered for appropriate support of clinical practice. Conclusion Efforts are required to avoid poor calibration when developing prediction models, to evaluate calibration when validating models, and to update models when indicated. The ultimate aim is to optimize the utility of predictive analytics for shared decision-making and patient counseling.

Abstract Plant diseases are a major cause for yield losses and new strategies to control them without harming the environment are urgently needed. Plant-associated bacteria contribute to their host’s health in diverse ways, among which the emission of disease-inhibiting volatile organic compounds (VOCs). We have previously reported that VOCs emitted by potato-associated bacteria caused strong in vitro growth inhibition of the late blight causing agent Phytophthora infestans. This work focuses on sulfur-containing VOCs (sVOCs) and demonstrates the high in planta protective potential of S-methyl methane thiosulfonate (MMTS), which fully prevented late blight disease in potato leaves and plantlets without phytotoxic effects, in contrast to other sVOCs. Short exposure times were sufficient to protect plants against infection. We further showed that MMTS’s protective activity was not mediated by the plant immune system but lied in its anti-oomycete activity. Using quantitative proteomics, we determined that different sVOCs caused specific proteome changes in P. infestans, indicating perturbations in sulfur metabolism, protein translation and redox balance. This work brings new perspectives for plant protection against the devastating Irish Famine pathogen, while opening new research avenues on the role of sVOCs in the interaction between plants and their microbiome.

Abstract Background Clinical prediction models are useful in estimating a patient’s risk of having a certain disease or experiencing an event in the future based on their current characteristics. Defining an appropriate risk threshold to recommend intervention is a key challenge in bringing a risk prediction model to clinical application; such risk thresholds are often defined in an ad hoc way. This is problematic because tacitly assumed costs of false positive and false negative classifications may not be clinically sensible. For example, when choosing the risk threshold that maximizes the proportion of patients correctly classified, false positives and false negatives are assumed equally costly. Furthermore, small to moderate sample sizes may lead to unstable optimal thresholds, which requires a particularly cautious interpretation of results. Main text We discuss how three common myths about risk thresholds often lead to inappropriate risk stratification of patients. First, we point out the contexts of counseling and shared decision-making in which a continuous risk estimate is more useful than risk stratification. Second, we argue that threshold selection should reflect the consequences of the decisions made following risk stratification. Third, we emphasize that there is usually no universally optimal threshold but rather that a plausible risk threshold depends on the clinical context. Consequently, we recommend to present results for multiple risk thresholds when developing or validating a prediction model. Conclusion Bearing in mind these three considerations can avoid inappropriate allocation (and non-allocation) of interventions. Using discriminating and well-calibrated models will generate better clinical outcomes if context-dependent thresholds are used.

Volatile organic compounds (VOCs) play an important role in the communication among organisms, including plants, beneficial or pathogenic microbes, and pests. In vitro, we observed that the growth of seven out of eight Basidiomycete species tested was inhibited by the VOCs of the biocontrol agent Pseudomonas protegens strain CHA0. In the Ascomycota phylum, only some species were sensitive (e.g., Sclerotinia sclerotiorum, Botrytis cinerea, etc.) but others were resistant (e.g., Fusarium oxysporum f. sp. cubense, Verticillium dahliae, etc.). We further discovered that CHA0 as well as other ten beneficial or phytopathogenic bacterial strains were all able to inhibit Heterobasidion abietinum, which was used in this research as a model species. Moreover, such an inhibition occurred only when bacteria grew on media containing digested proteins like peptone or tryptone (e.g., Luria-Bertani agar or LBA). Also, the inhibition co-occurred with a pH increase of the agar medium where the fungus grew. Therefore, biogenic ammonia originating from protein degradation by bacteria was hypothesized to play a major role in fungus inhibition. Indeed, when tested as a synthetic compound, it was highly toxic to H. abietinum (effective concentration 50% or EC50 = 1.18 M; minimum inhibitory concentration or MIC = 2.14 M). Using gas chromatography coupled to mass spectrometry (GC/MS), eight VOCs were found specifically emitted by CHA0 grown on LBA compared to the bacterium grown on potato dextrose agar (PDA). Among them, two compounds were even more toxic than ammonia against H. abietinum: dimethyl trisulfide had EC50 = 0.02 M and MIC = 0.2 M, and 2-ethylhexanol had EC50 = 0.33 M and MIC = 0.77 M. The fungus growth inhibition was the result of severe cellular and sub-cellular alterations of hyphae occurring as early as 15 min of exposure to VOCs, as evidenced by transmission and scanning electron microscopy observations. Transcriptome reprogramming of H. abietinum induced by CHA0’s VOCs pointed out that detrimental effects occurred on ribosomes and protein synthesis while the cells tried to react by activating defense mechanisms, which required a lot of energy diverted from the growth and development (fitness cost).

Bacterial volatiles play important roles in mediating beneficial interactions between plants and their associated microbiota. Despite their relevance, bacterial volatiles are mostly studied under laboratory conditions, although these strongly differ from the natural environment bacteria encounter when colonizing plant roots or shoots. In this work, we ask the question whether plant-associated bacteria also emit bioactive volatiles when growing on plant leaves rather than on artificial media. Using four potato-associated Pseudomonas, we demonstrate that potato leaves offer sufficient nutrients for the four strains to grow and emit volatiles, among which 1-undecene and Sulfur compounds have previously demonstrated the ability to inhibit the development of the oomycete Phytophthora infestans, the causative agent of potato late blight. Our results bring the proof of concept that bacterial volatiles with known plant health-promoting properties can be emitted on the surface of leaves and warrant further studies to test the bacterial emission of bioactive volatiles in greenhouse and field-grown plants.

B cell activation factor of the TNF family (BAFF/BLyS), an essential B cell survival factor of which circulating levels are elevated in several autoimmune disorders, is targeted in the clinic for the treatment of systemic lupus erythematosus (SLE). The soluble form of BAFF can exist as 3-mer, or as 60-mer that results from the ordered assembly of twenty 3-mers and that can be obtained from naturally cleaved membrane-bound BAFF or made as a recombinant protein. However, which forms of soluble BAFF exist and act in humans is unclear. In this study, BAFF 3-mer and 60-mer in biological fluids were characterized for size, activity and response to specific stimulators or inhibitors of BAFF. Human cerebrospinal fluids (CSF) from patients with multiple sclerosis and adult human sera contained exclusively BAFF 3-mer in these assays, also when BAFF concentrations were moderately SLE or highly (BAFFR-deficient individual) increased. Human sera, but not CSF, contained a high molecular weight, saturable activity that dissociated preformed recombinant BAFF 60-mer into 3-mer. This activity was lower in cord blood. Cord blood displayed BAFF levels 10-fold higher than in adults and consistently contained a fair proportion of active high molecular weight BAFF able to dissociate into 3-mer but not endowed with all properties of recombinant BAFF 60-mer. If BAFF 60-mer is produced in humans, it is dissociated, or at least attenuated in the circulation.

Real-time imaging of bacterial virulence factor dynamics is hampered by the limited number of fluorescent tools suitable for tagging secreted effectors. Here, we demonstrated that the fluorogenic reporter FAST could be used to tag secreted proteins, and we implemented it to monitor infection dynamics in epithelial cells exposed to the human pathogen Listeria monocytogenes (Lm). By tracking individual FAST-labelled vacuoles after Lm internalisation into cells, we unveiled the heterogeneity of residence time inside entry vacuoles. Although half of the bacterial population escaped within 13 minutes after entry, 12% of bacteria remained entrapped over an hour inside long term vacuoles, and sometimes much longer, regardless of the secretion of the pore-forming toxin listeriolysin O (LLO). We imaged LLO-FAST in these long-term vacuoles, and showed that LLO enabled Lm to proliferate inside these compartments, reminiscent of what had been previously observed for Spacious Listeria-containing phagosomes (SLAPs). Unexpectedly, inside epithelial SLAP-like vacuoles (eSLAPs), Lm proliferated as fast as in the host cytosol. eSLAPs thus constitute an alternative replication niche in epithelial cells that might promote the colonization of host tissues.

BackgroundThe number of migrant youth traveling without parents continues to rise in Europe and North America. Some of t hem leave their home countries on their own and find themselves in a new country, separated from their family and cut off from their cultural roots. Besides those who leave to study, work, and pursue a better life, others are escaping war-torn countries. They need adequate social, educational, and therapeutic spaces, where they can feel entitled to speak. Social workers often ask about how they can understand these young people better so that they can provide them with better care (cope with their trauma and suspicion, deal with the cultural distance between the adolescents and their social workers, etc).AimAt Cochin Hospital in Paris, we led a participative action-research program to transmit cultural competence to social workers who provide care for these youth. The aim was to develop an approach to help these young migrants to share their representations about themselves and to train these social workers to encourage this sharing in a culturally sensitive manner.MethodsThis study used a qualitative method that mixed narrative and transcultural approaches. Two researchers met each youth and social worker with an interpreter-cultural mediator three times (once a month) to assess changes in their relationships during the study. The youth were asked to bring three items of their choice, representing their past, present, and future. They could use their imagination and creativity. We also used the circle test described by Cottle for this purpose. We used a phenomenological approach to analyze the interviews.Results and DiscussionThis study included 29 young people from 13 different countries and 29 social workers. A transcultural approach appears to be a useful framework for reactivating their identity construction process. It promotes the emergence of cultural representations and takes their experiences before, during, and after migration into account. We assisted them in developing their ability to produce a thorough narrative of their bicultural adolescences and simultaneously helped their social workers to develop their cultural competence.ConclusionTogether, a transcultural approach and methods stimulating the production of narrative are relevant ways to help children to describe their representations of themselves, especially those who have learned to protect themselves by remaining silent. This protocol could be useful for both preventive action and therapy for psychotrauma.

Wastewaters (WW) are important sources for the dissemination of antimicrobial resistance (AMR) into the environment. Hospital WW (HWW) contain higher loads of micro-pollutants and AMR markers than urban WW (UWW). Little is known about the long-term dynamics of H and U WW and the impact of their joined treatment on the general burden of AMR. Here, we characterized the resistome, microbiota and eco-exposome signature of 126 H and U WW samples treated separately for three years, and then mixed, over one year. Multi-variate analysis and machine learning revealed a robust signature for each WW with no significant variation over time before mixing, and once mixed, both WW closely resembled Urban signatures. We demonstrated a significant impact of pharmaceuticals and surfactants on the resistome and microbiota of H and U WW. Our results present considerable targets for AMR related risk assessment of WW.

For plants, the advantages of associating with beneficial bacteria include plant growth promotion, reduction of abiotic and biotic stresses and enhanced protection against various pests and diseases. Beneficial bacteria rightly equipped for successful plant colonization and showing antagonistic activity toward plant pathogens seem to be actively recruited by plants. To gain more insights into the genetic determinants responsible for plant colonization and antagonistic activities, we first sequenced and de novo assembled the complete genomes of nine Pseudomonas strains that had exhibited varying antagonistic potential against the notorious oomycete Phytophthora infestans, placed them into the phylogenomic context of known Pseudomonas biocontrol strains and carried out a comparative genomic analysis to define core, accessory (i.e., genes found in two or more, but not all strains) and unique genes. Next, we assessed the colonizing abilities of these strains and used bioassays to characterize their inhibitory effects against different stages of P. infestans’ lifecycle. The phenotype data were then correlated with genotype information, assessing over three hundred genes encoding known factors for plant colonization and antimicrobial activity as well as secondary metabolite biosynthesis clusters predicted by antiSMASH. All strains harbored genes required for successful plant colonization but also distinct arsenals of antimicrobial compounds. We identified genes coding for phenazine, hydrogen cyanide, 2-hexyl, 5-propyl resorcinol and pyrrolnitrin synthesis, as well as various siderophores, pyocins and type VI secretion systems. Additionally, the comparative genomic analysis revealed about a hundred accessory genes putatively involved in anti-Phytophthora activity, including a type II secretion system (T2SS), several peptidases and a toxin. Transcriptomic studies and mutagenesis are needed to further investigate the putative involvement of the novel candidate genes and to identify the various mechanisms involved in the inhibition of P. infestans by different Pseudomonas strains.

Salinity stress is a major challenge to agricultural productivity and global food security in light of a dramatic increase of human population and climate change. Plant growth promoting bacteria can be used as an additional solution to traditional crop breeding and genetic engineering. In the present work, the induction of plant salt tolerance by the desert plant endophyte Cronobacter sp. JZ38 was examined on the model plant Arabidopsis thaliana using different inoculation methods. JZ38 promoted plant growth under salinity stress via contact and emission of volatile compounds. Based on the 16S rRNA and whole genome phylogenetic analysis, fatty acid analysis and phenotypic identification, JZ38 was identified as Cronobacter muytjensii and clearly separated and differentiated from the pathogenic C. sakazakii. Full genome sequencing showed that JZ38 is composed of one chromosome and two plasmids. Bioinformatic analysis and bioassays revealed that JZ38 can grow under a range of abiotic stresses. JZ38 interaction with plants is correlated with an extensive set of genes involved in chemotaxis and motility. The presence of genes for plant nutrient acquisition and phytohormone production could explain the ability of JZ38 to colonize plants and sustain plant growth under stress conditions. Gas chromatography–mass spectrometry analysis of volatiles produced by JZ38 revealed the emission of indole and different sulfur volatile compounds that may play a role in contactless plant growth promotion and antagonistic activity against pathogenic microbes. Indeed, JZ38 was able to inhibit the growth of two strains of the phytopathogenic oomycete Phytophthora infestans via volatile emission. Genetic, transcriptomic and metabolomics analyses, combined with more in vitro assays will provide a better understanding the highlighted genes’ involvement in JZ38’s functional potential and its interaction with plants. Nevertheless, these results provide insight into the bioactivity of C. muytjensii JZ38 as a multi-stress tolerance promoting bacterium with a potential use in agriculture.