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Abstract By‐product mutualisms are ubiquitous yet seldom considered in models of mutualism. Most models represent conditional mutualisms that shift between mutualism and antagonism in response to shifts in costs and benefits resulting from changes in environmental quality. However, in by‐product mutualisms, benefits arise as a part of normal life processes that may be costly to produce but incur little‐to‐no additional costs in response to the interaction. Without costs associated with the interaction, they do not have antagonistic alternate states. Here, we present a conceptual model that differs from traditional conditional models in three ways: (1) partners exchange by‐product benefits, (2) interactions do not have alternate antagonistic states, and (3) tradeoffs are allowed among factors that influence environmental quality (rather than all factors that contribute to environmental quality being combined into a single gradient ranging from high to low). We applied this model to bark and ambrosia beetles (Curculionidae: Scolytinae), a diverse group that associates with fungi and that has repeatedly developed two distinct pathways to by‐product mutualism. We used independent axes for each major factor influencing environmental quality in these systems, including those that exhibit tradeoffs (tree defense and nutritional quality). For these symbioses, tradeoffs in these two factors are key to which mutualism pathway is taken.

Abstract This study aims to quantify the contribution of anthropogenic forcings on the retreat of the Argentière Glacier (European Alps). The glacier evolution is simulated over 1850–2014 following retrospective scenarios produced with the IPSL‐CM6‐LR climate model, with and without natural and anthropogenic forcings. The scenarios used to force an ice flow model are statistically downscaled, preserving the long‐term trends and the physical consistency between precipitation and temperature. Since the late 19th century, the regional aerosol cooling has partially counteracted the greenhouse gas‐induced warming, delaying the time of emergence of the anthropogenic signal. The anthropogenic signal emerged from natural variability in 1979 for temperature and surface melting, and in 2008 for the glacier mass, whereas its snout position in 2014 remains compatible with natural variability. From the total mass loss between 1850 and 2014, 66% [21%–111%] is attributed to anthropogenic activities.

On 9 December 2021, the European Commission announced its proposal for a Directive on improving working conditions in platform work—the ‘Platform Work Directive.’ The Directive’s main goals are to reduce false self-employment among persons performing platform work, to regulate algorithmic management on digital labour platforms, and to provide legal certainty for platforms. This blog post focuses on an element of the proposed Directive that has gone relatively unremarked in the scholarly and policy debates so far: the definition of ‘digital labour platform.’

ObjectivesTo evaluate extracellular vesicles levels in a cohort of SARS-CoV-2’s patients hospitalized in an intensive care unit with and without COVID-19 associated thromboembolic events.MethodsIn this study, we aim to assess endothelial and platelet membrane-derived extracellular vesicles levels in a cohort of SARS-CoV-2 patients with and without COVID-19-associated thromboembolic events who were hospitalized in an intensive care unit. Annexin-V positive extracellular vesicles levels were prospectively assessed by flow cytometry in one hundred twenty-three critically ill adults diagnosed with acute respiratory distress syndrome associated with a SARS-CoV-2 infection, ten adults diagnosed for moderate SARS-CoV-2 infection and 25 healthy volunteers.ResultsOn our critically ill patients, thirty-four patients (27.6%) had a thromboembolic event, Fifty-three (43%) died. Endothelial and platelet membrane-derived extracellular vesicles were drastically increased in SARS-CoV-2 patients hospitalized in the ICU compared to healthy volunteers. Moreover a slighty higher small/large ratio for platelets membrane-derived extracellular vesicles in patients was linked to thrombo-embolic events.ConclusionA comparison between total annexin-V positive extracellular vesicles levels in severe and moderate SARS-CoV-2 infection and healthy controls showed a significant increase in patients with severe infection and their sizes could be considered as biomarkers of SARS-CoV-2 associated thrombo-embolic events.

Agricultural landscapes are multifunctional and closely connected to the much wider food system. In our review, we explore three specific aspects of modelling approaches for agricultural landscape assessments: (a) how multifunctionality is commonly analysed to support decision-making for sustainable agricultural land management; (b) how the modelling approaches relate to the wider food systems; and (c) how gaps in the existing modelling approaches might be addressed. For this, we identified key elements of agricultural landscape assessments, including ecosystem services (ESS) provided, driving factors, and linkages between crop and livestock production, and to the wider food system. We reviewed 238 publications with respect to these elements. While biodiversity and the ESS ‘water conditions’ and ‘atmospheric composition/conditions’ are widely covered, they are rarely used in combination. Other ESS, such as ‘pest and disease control’, are largely missing. Our results further indicate strong differences between individual approaches regarding model parameterisation and consideration of abiotic, biotic, and management driving factors. Our analysis also shows that the interconnectedness of crop and livestock production is rarely considered and that return flows from the food system are not considered. Furthermore, impacts from the production of external inputs and off-site effects are not considered. Consequently, existing models might overlook trade-offs and synergies between landscape functions. Failure to consider variations in relevant driving factors and food system linkages likely results in studying incorrect levers for change and failing to show decision-makers the full scope of available action. We thus suggest adopting more encompassing modelling approaches to ensure coverage of the full scope of potential actions, whilst hedging against overly costly data requirements by, e.g. employing well-designed sensitivity analyses. In this way, the most relevant components and thus the most important leverage points for interventions can be identified.

In the mostly pristine Congo Basin, agricultural land-use change has intensified in recent years. One potential and understudied consequence of this deforestation and conversion to agriculture is the mobilization and loss of organic matter from soils to rivers as dissolved organic matter. Here, we quantify and characterize dissolved organic matter sampled from 19 catchments of varying deforestation extent near Lake Kivu over a two-week period during the wet season. Dissolved organic carbon from deforested, agriculturally-dominated catchments was older (14C age: ~1.5kyr) and more biolabile than from pristine forest catchments. Ultrahigh-resolution mass spectrometry revealed that this aged organic matter from deforested catchments was energy-rich and chemodiverse, with higher proportions of nitrogen- and sulfur-containing formulae. Given the molecular composition and biolability, we suggest that organic matter from deforested landscapes is preferentially respired upon disturbance, resulting in elevated in-stream concentrations of carbon dioxide. We estimate that while deforestation reduces the overall flux of dissolved organic carbon by ~56%, it does not significantly change the yield of biolabile dissolved organic carbon. Ultimately, the exposure of deeper soil horizons through deforestation and agricultural expansion releases old, previously stable, and biolabile soil organic carbon into the modern carbon cycle via the aquatic pathway.

Soil nitrogen isotopic composition is used to drive the IsoTONE model, which is constrained with measurements of tropospheric nitrous oxide isotopic composition. The model results reveal causes of rising mean global nitrous oxide emission factor.

BackgroundMutation of the IL2RG gene results in a form of severe combined immune deficiency (SCID-X1), which has been treated successfully with hematopoietic stem cell gene therapy. SCID-X1 gene therapy results in reconstitution of the previously lacking T cell compartment, allowing analysis of the roles of T cell immunity in humans by comparing before and after gene correction.MethodsHere we interrogate T cell reconstitution using four forms of high throughput analysis. (1) Estimation of the numbers of transduced progenitor cells by monitoring unique positions of integration of the therapeutic gene transfer vector. (2) Estimation of T cell population structure by sequencing of the recombined T cell receptor (TCR) beta locus. (3) Metagenomic analysis of microbial populations in oropharyngeal, nasopharyngeal, and gut samples. (4) Metagenomic analysis of viral populations in gut samples.ResultsComparison of progenitor and mature T cell populations allowed estimation of a minimum number of cell divisions needed to generate the observed populations. Analysis of microbial populations showed the effects of immune reconstitution, including normalization of gut microbiota and clearance of viral infections. Metagenomic analysis revealed enrichment of genes for antibiotic resistance in gene-corrected subjects relative to healthy controls, likely a result of higher healthcare exposure.ConclusionsThis multi-omic approach enables the characterization of multiple effects of SCID-X1 gene therapy, including T cell repertoire reconstitution, estimation of numbers of cell divisions between progenitors and daughter T cells, normalization of the microbiome, clearance of microbial pathogens, and modulations in antibiotic resistance gene levels. Together, these results quantify several aspects of the long-term efficacy of gene therapy for SCID-X1. This study includes data from ClinicalTrials.gov numbers NCT01410019, NCT01175239, and NCT01129544.

Intro: As a nouveau approach for active surveillance of Acute Flaccid Paralysis (AFP) in Cameroon, community-based surveillance (CBS) of AFP has been implemented in security challenged settings in Far North Region of Cameroon since 2015. This article displays the contribution of CBS to AFP surveillance over the years in the areas of intervention. Methods: This transverse study analyzed the performance of CBS of AFP from 2015 to June 2022 in 10 conflict hit health districts in the Far North region of Cameroon. The 10 health districts were enrolled progressively from 2015-2022. A data capture sheet was used to extract data from the national database, cleaned and analyzed using excel_365. The indicators measured included AFP case notification, stool adequacy and annualized non-polio AFP (ANPAFP) rate. Findings: Over 458 AFP cases were notified between 2015-June 2022, with 234 (51%) by CHW and 224 (49%) by health personnel compared to 252 cases notified between 2003-2014 by health personnel. The proportion of cases notified by CHWs increased from 15% in 2015 to over 80% in 2022. The mean age of notified cases was 4.1±3.9. Stool adequacy rate was 87.7% (87.4% Female and 86.1% Male) throughout the period. The ANPAFP rate per 100,000 under-15 children improved from averagely 2.4 per 100000 between 2003-2014 to over 11.6 per 100000 between 2015-2022. During the period of analysis, the last wild poliovirus was seen between 2013-2014 (health personnel), however, four circulating Vaccine Derived Poliovirus Type 2 (cVDPV2) cases were detected in 2021 by CHWs in the zones of intervention. Conclusion: The results above show the enormous contribution of CBS of AFP over the years with a great improvement of the measured indictors over time. Close supervision and monitoring of activities of community health workers in AFP surveillance improved detection and notification of cases over the years.

Intro: Disease outbreaks, in insecurity settings grow rapidly due to weakened public health systems. In such areas, Community-Based Surveillance (CBS) can contribute to strengthen Acute Flaccid Paralysis (AFP) surveillance. Since 2015, Chad implements CBS in Batha and Hadjer-Lamis provinces but its performance is less documented. We aimed to describe the CBS contribution in the detection, notification and investigation of AFP cases. Methods: It's a cross-sectional study that included all AFP cases reported by surveillance system from week-1, 2012 to week-22, 2022. We reviewed the national database to extract data and performed a descriptive analysis. To assess CBS's contribution, we calculated proportions and compared the Non- polio AFP rate (NPAFP-R), district reporting, notification and investigation timelines and stool samples quality over two periods: before CBS, 2012-2014 (P1) and during CBS, 2015-2022 (P2). Findings: During P1, the overall NPAFP-R per 100,000 under 15 boys and girls were 5.2 and 5.8 in 2012 respectively, 6.0/3.1 in 2014. In P2, it was 5.9/5.4 in 2015, 11.2/9.2 in 2019 and 19.0/16.1 in 2022. During P2, CBS reported 97.2% (341/351) and 98.1%(259/264) of male and female cases. Silent districts represented 33.3%(3/9) in P1 and 0.0%(0/13) since 2018 in P2. The cases with two stool samples collected within 14 days in females ranged from 85.7%(42/49) in P1 to 86.2%(299/347) in P2 while it was respectively 89.6%(60/67) and 91.0% (437/480) in males. The samples received to the laboratory in good condition in females were 87.8%(43/49) in P1 and 93.7%(325/347) in P2 while it was respectively 79.1%(53/67) and 91.1%(442/480) in males. The proportion of cases notified within 7 days after paralysis onset in males and females was respectively 59.7%(40/67) versus 59.6%(286/480) and 63.3%(31/49) versus 57.1%(198/347). Conclusion: CBS in insecurity areas contributed to increase surveillance's sensitivity and sample quality. However, the notification timeline doesn't reflect its reactivity. Training, supervision and monitoring could further improve performance.

Intro: Insecurity in Tillaberi region in Niger is a threat to the poliomyelitis eradication achievement due to weakened public health systems. Community- Based Surveillance (CBS) is implemented since June 2017 to strengthen Acute Flaccid Paralysis (AFP) surveillance but its performance is not yet assed. The purpose is to describe the CBS's usefulness, acceptability, representativeness and reactivity in Tillaberi region. Methods: This is a cross sectional study that included all AFP cases notified by surveillance system from January 2014 to July 2022. “CDC-Atlanta Guidelines 2003” were used to assess the studied attributes. We performed descriptive analysis using defined variables presented in proportions, median, interquartile range (IQR) and sex ratio. Usefulness: Non Polio AFP Rate (NPAFP-R) before CBS (2014) and during CBS (2022). Acceptability: percentage of stool samples collected within 14 days after paralysis onset and received to the laboratory in good condition. Representativeness: true AFP cases, AFP cases age group and their distribution in place and time. Reactivity: timeline between paralysis onset and the stool samples reception at the national laboratory. Findings: The NPAFP-R per 100,000 under 15 children ranged from 1.9 in 2014 to 26.1 in 2022. The percentage of AFP cases with two stool samples collected within 14 days after paralysis onset and received at the laboratory in good condition was 73.4%(122/166). True AFP cases represented 97.6%(166/170), belonged to under 15 age group, were from all CBS implementing districts and were notified every year of CBS implementation. Male to female sex ratio was 1.27(93/73). The median timeline between the paralysis onset and stool samples reception at the laboratory was 21 days, IQR (16-31). Conclusion: CBS was useful, representative, less acceptable and not reactive. Stakeholders capacity building, monitoring and appropriate means for samples transportation from the collection site to the national laboratory could improve its acceptability and reactivity.

IntroductionIn north-western France, Salmonella enterica susp. enterica serovar Mbandaka (S. Mbandaka) is most frequently isolated from bovine and dairy samples. While this serovar most often results in asymptomatic carriage, for a number of years it has caused episodes of abortions, which have serious economic consequences for the sector. Interestingly, this serovar is also isolated from Gallus gallus in the same geographic zone. Despite its prevalence in bovines in north-western France, S. Mbandaka has not been broadly studied at the genomic level, and its prevalence and host adaptation are still not fully understood.MethodsIn this study, we analyzed the genomic diversity of 304 strains of S. Mbandaka isolated from the bovine and poultry sectors in this area over a period of 5 years. A phylogenetic analysis was carried out and two approaches were followed to identify conserved genes and mutations related to host associations. The first approach targeted the genes compiled in the MEGARESv2, Resfinder, VFDB and SPI databases. Plasmid and phage contents were also investigated. The second approach refers to an in-house algorithm developed for this study that computes sensitivity, specificity, and accuracy of accessory genes and core variants according to predefined genomes groups.Results and discussionAll the analyzed strains belong to the multi-locus sequence type profile ST413, and the phylogenomic analysis revealed main clustering by host (bovine and poultry), emphasizing the circulation of 12 different major clones, of which seven circulate in poultry and five in the bovine sector in France and a likely food production chain adaptation of these clones. All strains present resistance determinants including heavy metals and biocides that could explain the ability of this serovar to survive and persist in the environment, within herds, and in food processing plants. To explore the wild animal contribution to the spread of this serovar in north-western France, we retrieved S. Mbandaka genomes isolated from wild birds from EnteroBase and included them in the phylogenomic analysis together with our collection. Lastly, screening of accessory genes and major variants allowed us to identify conserved specific mutations characteristic of each major cluster. These mutations could be used to design useful probes for food safety surveillance.

T-cell receptors (TCRs) are formed by stochastic gene rearrangements, theoretically generating >1019 sequences. They are selected during thymopoiesis, which releases a repertoire of about 108 unique TCRs per individual. How evolution shaped a process that produces TCRs that can effectively handle a countless and evolving set of infectious agents is a central question of immunology. The paradigm is that a diverse enough repertoire of TCRs should always provide a proper, though rare, specificity for any given need. Expansion of such rare T cells would provide enough fighters for an effective immune response and enough antigen-experienced cells for memory. We show here that human thymopoiesis releases a large population of clustered CD8+ T cells harboring α/β paired TCRs that (i) have high generation probabilities and (ii) a preferential usage of some V and J genes, (iii) which CDR3 are shared between individuals, and (iv) can each bind and be activated by multiple unrelated viral peptides, notably from EBV, CMV, and influenza. These polyspecific T cells may represent a first line of defense that is mobilized in response to infections before a more specific response subsequently ensures viral elimination. Our results support an evolutionary selection of polyspecific α/β TCRs for broad antiviral responses and heterologous immunity.