One Health evaluation of brucellosis control in Kazakhstan

Brucellosis is one of the main livestock disease risks in Kazakhstan. It's been endemic there since 1930, accounting for over 1300 human cases per annum. The economic loss was 45 million USD in 2015 alone. Since 1952, Kazakhstan has implemented various control strategies with little success. One Health approaches have been suggested to tackle brucellosis, however, there is a lack of evidence for best practices to operationalise One Health in the literature, and methods for implementation are not established. The intention of this study was to introduce the One Health approach during the evaluation phase of the policy cycle. A two-day workshop was organized by the authors to familiarize participants with the evaluation methodology. Twenty-one specialists representing veterinary and public health sector, together with researchers, took part in this study. For two weeks following the workshop, first author conducted individual interviews with workshop participants to obtain individual scorings to assess knowledge integration capacity (One Health-ness). The evaluation results show that there is a lack of knowledge about the perceived damage caused by brucellosis to animal owners and other stakeholders. There is insufficient data available about farmers' practices, interests and motivations, and also data is missing for important transmission processes such as the amount of unsafe dairy consumption. The absence of such data illustrates the extent of the uncertainty to which decision-makers are exposed despite well-elaborated transmission models and supports the importance of co-producing solutions with participatory methods. The results suggest the need for broader involvement of stakeholders. Outputs of this study could help navigate the initial stages of One Health operationalization.

Young Adulthood Outcomes of Joint Mental Health Trajectories: A Group-Based Trajectory Model Analysis of a 13-Year Longitudinal Cohort Study

Developmental trajectories of common mental health issues such as ADHD symptoms, internalising problems, and externalising problems can often be usefully summarised in terms of a small number of 'developmental subtypes' (e.g., 'childhood onset', 'adolescent onset') that may differ in their profiles or levels of clinically meaningful variables such as etiological risk factors. However, given the strong tendency for symptoms in these domains to co-occur, it is important to consider not only developmental subtypes in each domain individually, but also the joint developmental subtypes defined by symptoms trajectories in all three domains together (e.g., 'late onset multimorbid', 'pure internalising', 'early onset multimorbid'). Previous research has illuminated the joint developmental subtypes of ADHD symptoms, internalising problems, and externalising problems that emerge from normative longitudinal data using methods such as group-based trajectory modelling, as well as predictors of membership in these developmental subtypes. However, information on the long-term outcomes of developmental subtype membership is critical to illuminate the likely nature and intensity of support needs required for individuals whose trajectories fit different developmental subtypes. We, therefore, evaluated the relations between developmental subtypes previously derived using group-based trajectory modelling in the z-proso study (n = 1620 with trajectory data at ages 7, 8, 9, 10, 11, 12, 13, 15) and early adulthood outcomes. Individuals with multimorbid trajectories but not 'pure' internalising problem elevations showed higher levels of social exclusion and delinquency at age 20. These associations held irrespective of the specific developmental course of symptoms (e.g., early versus late onset versus remitting). There was also some evidence that intimate partner violence acts as a form of heterotypic continuity for earlier externalising problems. Results underline the need for early intervention to address the pathways that lead to social exclusion and delinquency among young people with multiple co-occurring mental health issues.

Modeling and mitigating supply chain disruptions as a bilevel network flow problem

Years of globalization, outsourcing and cost cutting have increased supply chain vulnerability calling for more effective risk mitigation strategies. In our research, we analyze supply chain disruptions in a production setting. Using a bilevel optimization framework, we minimize the total production cost for a manufacturer interested in finding optimal disruption mitigation strategies. The problem constitutes a convex network flow program under a chance constraint bounding the manufacturer's regrets in disrupted scenarios. Thus, in contrast to standard bilevel optimization schemes with two decision-makers, a leader and a follower, our model searches for the optimal production plan of a manufacturer in view of a reduction in the sequence of his own scenario-specific regrets. Defined as the difference in costs of a reactive plan, which considers the disruption as unknown until it occurs, and a benchmark anticipative plan, which predicts the disruption in the beginning of the planning horizon, the regrets allow measurement of the impact of scenario-specific production strategies on the manufacturer's total cost. For an efficient solution of the problem, we employ generalized Benders decomposition and develop customized feasibility cuts. In the managerial section, we discuss the implications for the risk-adjusted production and observe that the regrets of long disruptions are reduced in our mitigation strategy at the cost of shorter disruptions, whose regrets typically stay far below the risk threshold. This allows a decrease of the production cost under rare but high-impact disruption scenarios.

Test-trace-isolate-quarantine (TTIQ) intervention strategies after symptomatic COVID-19 case identification

The test-trace-isolate-quarantine (TTIQ) strategy, where confirmed-positive pathogen carriers are isolated from the community and their recent close contacts are identified and pre-emptively quarantined, is used to break chains of transmission during a disease outbreak. The protocol is frequently followed after an individual presents with disease symptoms, at which point they will be tested for the pathogen. This TTIQ strategy, along with hygiene and social distancing measures, make up the non-pharmaceutical interventions that are utilised to suppress the ongoing COVID-19 pandemic. Here we develop a tractable mathematical model of disease transmission and the TTIQ intervention to quantify how the probability of detecting and isolating a case following symptom onset, the fraction of contacts that are identified and quarantined, and the delays inherent to these processes impact epidemic growth. In the model, the timing of disease transmission and symptom onset, as well as the frequency of asymptomatic cases, is based on empirical distributions of SARS-CoV-2 infection dynamics, while the isolation of confirmed cases and quarantine of their contacts is implemented by truncating their respective infectious periods. We find that a successful TTIQ strategy requires intensive testing: the majority of transmission is prevented by isolating symptomatic individuals and doing so in a short amount of time. Despite the lesser impact, additional contact tracing and quarantine increases the parameter space in which an epidemic is controllable and is necessary to control epidemics with a high reproductive number. TTIQ could remain an important intervention for the foreseeable future of the COVID-19 pandemic due to slow vaccine rollout and highly-transmissible variants with the potential for vaccine escape. Our results can be used to assess how TTIQ can be improved and optimised, and the methodology represents an improvement over previous quantification methods that is applicable to future epidemic scenarios.

Giving birth: A hermeneutic study of the expectations and experiences of healthy primigravid women in Switzerland

Switzerland experiences one of the highest caesarean section rates in Europe but it is unclear why and when the decision is made to perform a caesarean section. Many studies have examined from a medical and physiological point of view, but research from a women’s standpoint is lacking. Our aim was to develop a model of the emerging expectations of giving birth and the subsequent experiences of healthy primigravid women, across four cantons in Switzerland. This longitudinal study included 30 primigravidae from the German speaking, 14 from the French speaking and 14 from the Italian speaking cantons who were purposively selected. Data were collected by semi-structured interviews taking place around 22 and 36 weeks of pregnancy and six weeks and six months postnatally. Following Gadamer’s hermeneutic, which in this study comprised 5 stages, a model was developed. Four major themes emerged: Decisions, Care, Influences and Emotions. Their meandering paths and evolution demonstrate the complexity of the expectations and experiences of women becoming mothers. In this study, women’s narrated mode of birth expectations did not foretell how they gave birth and their lived experiences. A hermeneutic discontinuity arises at the 6 week postnatal interview mark. This temporary gap illustrates the bridge between women’s expectations of birth and their actual lived experiences, highlighting the importance of informed consent, parent education and ensuring women have a positive birth and immediate postnatal experiences. Other factors than women’s preferences should be considered to explain the increasing caesarean section rates.

ΔFBA-Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data

Genome-scale metabolic models (GEMs) provide a powerful framework for simulating the entire set of biochemical reactions in a cell using a constraint-based modeling strategy called flux balance analysis (FBA). FBA relies on an assumed metabolic objective for generating metabolic fluxes using GEMs. But, the most appropriate metabolic objective is not always obvious for a given condition and is likely context-specific, which often complicate the estimation of metabolic flux alterations between conditions. Here, we propose a new method, called ΔFBA (deltaFBA), that integrates differential gene expression data to evaluate directly metabolic flux differences between two conditions. Notably, ΔFBA does not require specifying the cellular objective. Rather, ΔFBA seeks to maximize the consistency and minimize inconsistency between the predicted flux differences and differential gene expression. We showcased the performance of ΔFBA through several case studies involving the prediction of metabolic alterations caused by genetic and environmental perturbations in Escherichia coli and caused by Type-2 diabetes in human muscle. Importantly, in comparison to existing methods, ΔFBA gives a more accurate prediction of flux differences.

Metabolic alterations are often used as hallmarks of observable phenotypes. In this regard, reconstructed genome-scale metabolic models (GEMs) provide a rich and computable representation of the entire set of biochemical reactions in a cell. However, the performance of analytical tools for predicting metabolic reaction rates or fluxes using GEMs is sensitive to the assumed metabolic objective that is often unknown and likely context-specific. Here, we propose a novel method called ΔFBA that combines differential gene expression data and GEMs to evaluate differences in the metabolic fluxes between two conditions (perturbation vs. control) without the need for specifying a metabolic objective. In our demonstration, ΔFBA outperformed other existing methods in predicting metabolic flux alterations.

Beech tree masting explains the inter-annual variation in the fall and spring peaks of Ixodes ricinus ticks with different time lags

BACKGROUND

The tick Ixodes ricinus is an important vector of tick-borne diseases including Lyme borreliosis. In continental Europe, the nymphal stage of I. ricinus often has a bimodal phenology with a large spring peak and a smaller fall peak. There is consensus about the origin of the spring nymphal peak, but there are two alternative hypotheses for the fall nymphal peak. In the direct development hypothesis, larvae quest as nymphs in the fall of the same year that they obtained their larval blood meal. In the developmental diapause hypothesis, larvae overwinter in the engorged state and quest as nymphs one year after they obtained their larval blood meal. These two hypotheses make different predictions about the time lags that separate the larval blood meal and the density of questing nymphs (DON) in the spring and fall.

METHODS

Inter-annual variation in seed production (masting) by deciduous trees is a time-lagged index for the density of vertebrate hosts (e.g., rodents) which provide blood meals for larval ticks. We used a long-term data set on the masting of the European beech tree and a 15-year study on the DON at 4 different elevation sites in western Switzerland to differentiate between the two alternative hypotheses for the origin of the fall nymphal peak.

RESULTS

Questing I. ricinus nymphs had a bimodal phenology at the three lower elevation sites, but a unimodal phenology at the top elevation site. At the lower elevation sites, the DON in the fall was strongly correlated with the DON in the spring of the following year. The inter-annual variation in the densities of I. ricinus nymphs in the fall and spring was best explained by a 1-year versus a 2-year time lag with the beech tree masting index. Fall nymphs had higher fat content than spring nymphs indicating that they were younger. All these observations are consistent with the direct development hypothesis for the fall peak of I. ricinus nymphs at our study site. Our study provides new insight into the complex bimodal phenology of this important disease vector.

CONCLUSIONS

Public health officials in Europe should be aware that following a strong mast year, the DON will increase 1 year later in the fall and 2 years later in the spring. Studies of I. ricinus populations with a bimodal phenology should consider that the spring and fall peak in the same calendar year represent different generations of ticks.

Short-Course Versus Long-Course Systemic Antibiotic Treatment for Uncomplicated Intravascular Catheter-Related Bloodstream Infections due to Gram-Negative Bacteria, Enterococci or Coagulase-Negative Staphylococci: A Systematic Review

INTRODUCTION

The optimal duration of systemic antimicrobial treatment for catheter-related bloodstream infections (CRBSI) is unknown. In this systematic review, we aimed to assess the efficacy of short-course treatment for CRBSI due to Gram-negative bacteria, coagulase-negative staphylococci and enterococci.

METHODS

We systematically searched the electronic bibliographic databases MEDLINE, EMBASE and Cochrane Library for studies published before February 2021. All studies that investigated the duration of adequate systemic antibiotic treatment in adult patients with uncomplicated intravascular catheter infections due to Gram-negative bacteria, coagulase-negative staphylococci or enterococci were eligible for inclusion. Studies including concomitant treatment with antibiotic lock therapy were excluded. The primary outcomes were clinical failure/cure, mortality and microbiologic-confirmed relapse.

RESULTS

Seven retrospective cohort studies and one case-cohort study met the inclusion criteria. No randomized controlled studies met inclusion criteria. The quality of the included studies was low (n = 7) to moderate (n = 1). No significant differences were observed regarding mortality and microbiological relapse between short-course and long-course systemic antibiotic treatment in patients with CRBSI due to coagulase-negative staphylococci or Gram-negative bacteria. No association was found between mortality and treatment duration in the two studies assessing enterococcal CRBSI.

CONCLUSION

The limited data available suggests that shorter systemic antibiotic treatment duration may be sufficient for uncomplicated CRBSI. Further well-designed prospective studies are needed to confirm these findings.

TRIAL REGISTRATION NUMBER

CRD42021224946 (PROSPERO).

Evaluating the accuracy of facial expressions as emotion indicators across contexts in dogs

Facial expressions potentially serve as indicators of animal emotions if they are consistently present across situations that (likely) elicit the same emotional state. In a previous study, we used the Dog Facial Action Coding System (DogFACS) to identify facial expressions in dogs associated with conditions presumably eliciting positive anticipation (expectation of a food reward) and frustration (prevention of access to the food). Our first aim here was to identify facial expressions of positive anticipation and frustration in dogs that are context-independent (and thus have potential as emotion indicators) and to distinguish them from expressions that are reward-specific (and thus might relate to a motivational state associated with the expected reward). Therefore, we tested a new sample of 28 dogs with a similar set-up designed to induce positive anticipation (positive condition) and frustration (negative condition) in two reward contexts: food and toys. The previous results were replicated: Ears adductor was associated with the positive condition and Ears flattener, Blink, Lips part, Jaw drop, and Nose lick with the negative condition. Four additional facial actions were also more common in the negative condition. All actions except the Upper lip raiser were independent of reward type. Our second aim was to assess basic measures of diagnostic accuracy for the potential emotion indicators. Ears flattener and Ears downward had relatively high sensitivity but low specificity, whereas the opposite was the case for the other negative correlates. Ears adductor had excellent specificity but low sensitivity. If the identified facial expressions were to be used individually as diagnostic indicators, none would allow consistent correct classifications of the associated emotion. Diagnostic accuracy measures are an essential feature for validity assessments of potential indicators of animal emotion.

Deep learning-assisted ultra-fast/low-dose whole-body PET/CT imaging

PURPOSE

Tendency is to moderate the injected activity and/or reduce acquisition time in PET examinations to minimize potential radiation hazards and increase patient comfort. This work aims to assess the performance of regular full-dose (FD) synthesis from fast/low-dose (LD) whole-body (WB) PET images using deep learning techniques.

METHODS

Instead of using synthetic LD scans, two separate clinical WB 18F-Fluorodeoxyglucose (18F-FDG) PET/CT studies of 100 patients were acquired: one regular FD (~ 27 min) and one fast or LD (~ 3 min) consisting of 1/8th of the standard acquisition time. A modified cycle-consistent generative adversarial network (CycleGAN) and residual neural network (ResNET) models, denoted as CGAN and RNET, respectively, were implemented to predict FD PET images. The quality of the predicted PET images was assessed by two nuclear medicine physicians. Moreover, the diagnostic quality of the predicted PET images was evaluated using a pass/fail scheme for lesion detectability task. Quantitative analysis using established metrics including standardized uptake value (SUV) bias was performed for the liver, left/right lung, brain, and 400 malignant lesions from the test and evaluation datasets.

RESULTS

CGAN scored 4.92 and 3.88 (out of 5) (adequate to good) for brain and neck + trunk, respectively. The average SUV bias calculated over normal tissues was 3.39 ± 0.71% and - 3.83 ± 1.25% for CGAN and RNET, respectively. Bland-Altman analysis reported the lowest SUV bias (0.01%) and 95% confidence interval of - 0.36, + 0.47 for CGAN compared with the reference FD images for malignant lesions.

CONCLUSION

CycleGAN is able to synthesize clinical FD WB PET images from LD images with 1/8th of standard injected activity or acquisition time. The predicted FD images present almost similar performance in terms of lesion detectability, qualitative scores, and quantification bias and variance.

Arginine-dependent immune responses

A growing body of evidence indicates that, over the course of evolution of the immune system, arginine has been selected as a node for the regulation of immune responses. An appropriate supply of arginine has long been associated with the improvement of immune responses. In addition to being a building block for protein synthesis, arginine serves as a substrate for distinct metabolic pathways that profoundly affect immune cell biology; especially macrophage, dendritic cell and T cell immunobiology. Arginine availability, synthesis, and catabolism are highly interrelated aspects of immune responses and their fine-tuning can dictate divergent pro-inflammatory or anti-inflammatory immune outcomes. Here, we review the organismal pathways of arginine metabolism in humans and rodents, as essential modulators of the availability of this semi-essential amino acid for immune cells. We subsequently review well-established and novel findings on the functional impact of arginine biosynthetic and catabolic pathways on the main immune cell lineages. Finally, as arginine has emerged as a molecule impacting on a plethora of immune functions, we integrate key notions on how the disruption or perversion of arginine metabolism is implicated in pathologies ranging from infectious diseases to autoimmunity and cancer.

Joint Family and Work Trajectories and Multidimensional Wellbeing

Informed by the life course perspective, this paper investigates whether and how employment and family trajectories are jointly associated with subjective, relational and financial wellbeing later in life. We draw on data from the Swiss Household Panel which combines biographical retrospective information on work, partnership and childbearing trajectories with 19 annual waves containing a number of wellbeing indicators as well as detailed socio-demographic and social origin information. We use sequence analysis to identify the main family and work trajectories for men and women aged 20–50 years old. We use OLS regression models to assess the association between those trajectories and their interdependency with wellbeing. Results reveal a joint association between work and family trajectories and wellbeing at older age, even net of social origin and pre-trajectory resources. For women, but not for men, the association is also not fully explained by proximate (current family and work status) determinants of wellbeing. Women’s stable full-time employment combined with traditional family trajectories yields a subjective wellbeing premium, whereas childlessness and absence of a stable partnership over the life course is associated with lower levels of financial and subjective wellbeing after 50 especially in combination with a trajectory of weak labour market involvement. Relational wellbeing is not associated with employment trajectories, and only weakly linked to family trajectories among men.

Forest management affects seasonal source-sink dynamics in a territorial, group-living bird

The persistence of wildlife populations is under threat as a consequence of human activities, which are degrading natural ecosystems. Commercial forestry is the greatest threat to biodiversity in boreal forests. Forestry practices have degraded most available habitat, threatening the persistence of natural populations. Understanding population responses is, therefore, critical for their conservation. Population viability analyses are effective tools to predict population persistence under forestry management. However, quantifying the mechanisms driving population responses is complex as population dynamics vary temporally and spatially. Metapopulation dynamics are governed by local dynamics and spatial factors, potentially mediating the impacts of forestry e.g., through dispersal. Here, we performed a seasonal, spatially explicit population viability analysis, using long-term data from a group-living territorial bird (Siberian jay, Perisoreus infaustus). We quantified the effects of forest management on metapopulation dynamics, via forest type-specific demography and spatially explicit dispersal, and how forestry impacted the stability of metapopulation dynamics. Forestry reduced metapopulation growth and stability, through negative effects on reproduction and survival. Territories in higher quality natural forest contributed more to metapopulation dynamics than managed forests, largely through demographic processes rather than dispersal. Metapopulation dynamics in managed forest were also less resilient to disturbances and consequently, may be more vulnerable to environmental change. Seasonal differences in source-sink dynamics observed in managed forest, but not natural forests, were caused by associated seasonal differences in dispersal. As shown here, capturing seasonal source-sink dynamics allows us to predict population persistence under human disturbance and to provide targeted conservation recommendations.

Sensory modulation of gait characteristics in human locomotion: A neuromusculoskeletal modeling study

The central nervous system of humans and other animals modulates spinal cord activity to achieve several locomotion behaviors. Previous neuromechanical models investigated the modulation of human gait changing selected parameters belonging to CPGs (Central Pattern Generators) feedforward oscillatory structures or to feedback reflex circuits. CPG-based models could replicate slow and fast walking by changing only the oscillation’s properties. On the other hand, reflex-based models could achieve different behaviors through optimizations of large dimensional parameter spaces. However, they could not effectively identify individual key reflex parameters responsible for gait characteristics’ modulation. This study investigates which reflex parameters modulate the gait characteristics through neuromechanical simulations. A recently developed reflex-based model is used to perform optimizations with different target behaviors on speed, step length, and step duration to analyze the correlation between reflex parameters and their influence on these gait characteristics. We identified nine key parameters that may affect the target speed ranging from slow to fast walking (0.48 and 1.71 m/s) as well as a large range of step lengths (0.43 and 0.88 m) and step duration (0.51, 0.98 s). The findings show that specific reflexes during stance significantly affect step length regulation, mainly given by positive force feedback of the ankle plantarflexors’ group. On the other hand, stretch reflexes active during swing of iliopsoas and gluteus maximus regulate all the gait characteristics under analysis. Additionally, the results show that the hamstrings’ group’s stretch reflex during the landing phase is responsible for modulating the step length and step duration. Additional validation studies in simulations demonstrated that the modulation of identified reflexes is sufficient to regulate the investigated gait characteristics. Thus, this study provides an overview of possible reflexes involved in modulating speed, step length, and step duration of human gaits.

This study investigates the possible reflex parameters that the central nervous system could use to modulate human locomotion. Specifically, we target the modulation of three gait characteristics: speed, step length, and step duration. We utilize human locomotion simulations with a previously developed reflex-based model and perform multiple optimizations ranging targeting low to high values of the three gait characteristics investigated. From the data acquired in optimizations, we investigate which reflex parameter correlates most with the gait characteristics changes. We identified nine key reflex parameters affecting gait modulation, performed validation experiments, and verified that the optimization of key reflex parameters alone could generate modulation in the studied locomotion behaviors. Kinematics, ground reaction forces, and muscle activity obtained in simulations show similarities with past experimental studies on gait modulation. Therefore, the identified parameters could potentially be used by the nervous system to regulate locomotion behaviors in a task-dependent manner. Other circuits not modeled in this study could play a crucial role in gait modulation, and further investigations should be done in the co-optimization of feedforward and feedback circuits.

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field

BACKGROUND

Plants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of root-associated microbiotas is not well understood, especially not under realistic field conditions. Maize roots secrete benzoxazinoids (BXs), a class of indole-derived defense compounds, and thereby impact the assembly of their microbiota. Here, we investigated the broader impacts of BX exudation on root and rhizosphere microbiotas of adult maize plants grown under natural conditions at different field locations in Europe and the USA. We examined the microbiotas of BX-producing and multiple BX-defective lines in two genetic backgrounds across three soils with different properties.

RESULTS

Our analysis showed that BX secretion affected the community composition of the rhizosphere and root microbiota, with the most pronounced effects observed for root fungi. The impact of BX exudation was at least as strong as the genetic background, suggesting that BX exudation is a key trait by which maize structures its associated microbiota. BX-producing plants were not consistently enriching microbial lineages across the three field experiments. However, BX exudation consistently depleted Flavobacteriaceae and Comamonadaceae and enriched various potential plant pathogenic fungi in the roots across the different environments.

CONCLUSIONS

These findings reveal that BXs have a selective impact on root and rhizosphere microbiota composition across different conditions. Taken together, this study identifies the BX pathway as an interesting breeding target to manipulate plant-microbiome interactions. Video Abstract.

Perceived built environment, health-related quality of life and health care utilization

Previous research has shown that the built environment plays a crucial role for health-related quality of life (HRQoL) and health care utilization. But, there is limited evidence on the independence of this association from lifestyle and social environment. The objective of this cross-sectional study was to investigate these associations, independent of the social environment, physical activity and body mass index (BMI). We used data from the third follow-up of the Swiss study on Air Pollution and Lung and Heart diseases In Adults (SAPALDIA), a population based cohort with associated biobank. Covariate adjusted multiple quantile and polytomous logistic regressions were performed to test associations of variables describing the perceived built environment with HRQoL and health care utilization. Higher HRQoL and less health care utilization were associated with less reported transportation noise annoyance. Higher HRQoL was also associated with greater satisfaction with the living environment and more perceived access to greenspaces. These results were independent of the social environment (living alone and social engagement) and lifestyle (physical activity level and BMI). This study provides further evidence that the built environment should be designed to integrate living and green spaces but separate living and traffic spaces in order to improve health and wellbeing and potentially save health care costs.

Using excess deaths and testing statistics to determine COVID-19 mortalities

Factors such as varied definitions of mortality, uncertainty in disease prevalence, and biased sampling complicate the quantification of fatality during an epidemic. Regardless of the employed fatality measure, the infected population and the number of infection-caused deaths need to be consistently estimated for comparing mortality across regions. We combine historical and current mortality data, a statistical testing model, and an SIR epidemic model, to improve estimation of mortality. We find that the average excess death across the entire US from January 2020 until February 2021 is 9[Formula: see text] higher than the number of reported COVID-19 deaths. In some areas, such as New York City, the number of weekly deaths is about eight times higher than in previous years. Other countries such as Peru, Ecuador, Mexico, and Spain exhibit excess deaths significantly higher than their reported COVID-19 deaths. Conversely, we find statistically insignificant or even negative excess deaths for at least most of 2020 in places such as Germany, Denmark, and Norway.

Neurocognitive processing efficiency for discriminating human non-alarm rather than alarm scream calls

Across many species, scream calls signal the affective significance of events to other agents. Scream calls were often thought to be of generic alarming and fearful nature, to signal potential threats, with instantaneous, involuntary, and accurate recognition by perceivers. However, scream calls are more diverse in their affective signaling nature than being limited to fearfully alarming a threat, and thus the broader sociobiological relevance of various scream types is unclear. Here we used 4 different psychoacoustic, perceptual decision-making, and neuroimaging experiments in humans to demonstrate the existence of at least 6 psychoacoustically distinctive types of scream calls of both alarming and non-alarming nature, rather than there being only screams caused by fear or aggression. Second, based on perceptual and processing sensitivity measures for decision-making during scream recognition, we found that alarm screams (with some exceptions) were overall discriminated the worst, were responded to the slowest, and were associated with a lower perceptual sensitivity for their recognition compared with non-alarm screams. Third, the neural processing of alarm compared with non-alarm screams during an implicit processing task elicited only minimal neural signal and connectivity in perceivers, contrary to the frequent assumption of a threat processing bias of the primate neural system. These findings show that scream calls are more diverse in their signaling and communicative nature in humans than previously assumed, and, in contrast to a commonly observed threat processing bias in perceptual discriminations and neural processes, we found that especially non-alarm screams, and positive screams in particular, seem to have higher efficiency in speeded discriminations and the implicit neural processing of various scream types in humans.

A technique for obtaining true approximations for k-center with covering constraints

There has been a recent surge of interest in incorporating fairness aspects into classical clustering problems. Two recently introduced variants of the k-Center problem in this spirit are Colorful k-Center, introduced by Bandyapadhyay, Inamdar, Pai, and Varadarajan, and lottery models, such as the Fair Robust k-Center problem introduced by Harris, Pensyl, Srinivasan, and Trinh. To address fairness aspects, these models, compared to traditional k-Center, include additional covering constraints. Prior approximation results for these models require to relax some of the normally hard constraints, like the number of centers to be opened or the involved covering constraints, and therefore, only obtain constant-factor pseudo-approximations. In this paper, we introduce a new approach to deal with such covering constraints that leads to (true) approximations, including a 4-approximation for Colorful k-Center with constantly many colors-settling an open question raised by Bandyapadhyay, Inamdar, Pai, and Varadarajan-and a 4-approximation for Fair Robust k-Center, for which the existence of a (true) constant-factor approximation was also open. We complement our results by showing that if one allows an unbounded number of colors, then Colorful k-Center admits no approximation algorithm with finite approximation guarantee, assuming that P ≠ NP . Moreover, under the Exponential Time Hypothesis, the problem is inapproximable if the number of colors grows faster than logarithmic in the size of the ground set.

Drivers of linkage disequilibrium across a species' geographic range

While linkage disequilibrium (LD) is an important parameter in genetics and evolutionary biology, the drivers of LD remain elusive. Using whole-genome sequences from across a species’ range, we assessed the impact of demographic history and mating system on LD. Both range expansion and a shift from outcrossing to selfing in North American Arabidopsis lyrata were associated with increased average genome-wide LD. Our results indicate that range expansion increases short-distance LD at the farthest range edges by about the same amount as a shift to selfing. However, the extent over which LD in genic regions unfolds was shorter for range expansion compared to selfing. Linkage among putatively neutral variants and between neutral and deleterious variants increased to a similar degree with range expansion, providing support that genome-wide LD was positively associated with mutational load. As a consequence, LD combined with mutational load may decelerate range expansions and set range limits. Finally, a small number of genes were identified as LD outliers, suggesting that they experience selection by either of the two demographic processes. These included genes involved in flowering and photoperiod for range expansion, and the self-incompatibility locus for mating system.

Nearby genomic variants are often co-inherited because of limited recombination. The extent of non-random association of alleles at different loci is called linkage disequilibrium (LD) and is commonly used in genomic analyses, for example to detect regions under selection or to determine effective population size. Here we reversed testing and addressed how demographic history may affect LD within a species. Using genomic data from more than a thousand individuals of North American Arabidopsis lyrata from across the entire species’ range, we quantified the effect of postglacial range expansion and a shift in mating system from outcrossing to selfing on LD. We show that both factors lead to increased LD, and that the maximal effect of range expansion is comparable with a shift in mating system to selfing. Heightened LD involves deleterious mutations, and therefore, LD can also serve as an indicator of mutation accumulation. Furthermore, we provide evidence that some genes experienced stronger increases in LD possibly due to selection associated with the two demographic changes. Our results provide a novel and broad view on the evolutionary factors shaping LD that may also apply to the very many species that underwent postglacial range expansion.

Managing conflicting goals through prioritization? The role of age and relative goal importance

Three studies tested the role of prioritization in solving conflict between multiple goals in different age groups. Study 1 (N = 185 young, middle-aged, older adults) stressed the importance to solve two competing tasks equally well within a short time. Older adults prioritized more than younger adults. However, contrary to our expectations, prioritization led to higher perceived conflict, more negative affect, and less control. Study 2 (N = 117 younger and older adults) found that, using a more lenient instruction, deemphasizing the importance of performing equally well on both tasks, prioritization was no longer associated with perceived goal conflict. Study 3 (N = 721 young, middle-aged, older adults) was an online study using hypothetical scenarios. This study was run to substantiate the potential mechanism underlying the differences between Study 1 and 2 and supported the hypothesized effect of the instructional strictness of pursuing two goals. Thus, when encountering conflicting goals older adults prioritize more than younger adults, but prioritization might not be optimal for solving short-term goal conflict when both conflicting goals are equally important.

Multi-scale optoacoustic molecular imaging of brain diseases

The ability to non-invasively visualize endogenous chromophores and exogenous probes and sensors across the entire rodent brain with the high spatial and temporal resolution has empowered optoacoustic imaging modalities with unprecedented capacities for interrogating the brain under physiological and diseased conditions. This has rapidly transformed optoacoustic microscopy (OAM) and multi-spectral optoacoustic tomography (MSOT) into emerging research tools to study animal models of brain diseases. In this review, we describe the principles of optoacoustic imaging and showcase recent technical advances that enable high-resolution real-time brain observations in preclinical models. In addition, advanced molecular probe designs allow for efficient visualization of pathophysiological processes playing a central role in a variety of neurodegenerative diseases, brain tumors, and stroke. We describe outstanding challenges in optoacoustic imaging methodologies and propose a future outlook.

Free Boundary Regularity for Almost Every Solution to the Signorini Problem

We investigate the regularity of the free boundary for the Signorini problem in R n + 1 . It is known that regular points are ( n - 1 ) -dimensional and C ∞ . However, even for C ∞ obstacles φ , the set of non-regular (or degenerate) points could be very large-e.g. with infinite H n - 1 measure. The only two assumptions under which a nice structure result for degenerate points has been established are when φ is analytic, and when Δ φ < 0 . However, even in these cases, the set of degenerate points is in general ( n - 1 ) -dimensional-as large as the set of regular points. In this work, we show for the first time that, "usually", the set of degenerate points is small. Namely, we prove that, given any C ∞ obstacle, for almost every solution the non-regular part of the free boundary is at most ( n - 2 ) -dimensional. This is the first result in this direction for the Signorini problem. Furthermore, we prove analogous results for the obstacle problem for the fractional Laplacian ( - Δ ) s , and for the parabolic Signorini problem. In the parabolic Signorini problem, our main result establishes that the non-regular part of the free boundary is ( n - 1 - α ∘ ) -dimensional for almost all times t, for some α ∘ > 0 . Finally, we construct some new examples of free boundaries with degenerate points.

Reassessment of the enigmatic ruminant Miocene genus Amphimoschus Bourgeois, 1873 (Mammalia, Artiodactyla, Pecora)

Amphimoschus is an extinct Eurasian ruminant genus, mostly recorded in Europe, without a close living relative and, hence, an unknown systematic position. This genus is known from around 50 localities from the late early to the middle Miocene. Two species were described during 180 years, but since their first description during the late 19^th century and early 20^th century, hardly any detailed taxonomic work has been done on the genus. Over the years, extensive collecting and excavating activities have enriched collections with more and more complete material of this still rare and enigmatic animal. Most interestingly, a number of skull remains have been unearthed and are promising in terms of providing phylogenetic information. In the present paper, we describe cranial material, the bony labyrinth, the dentition through 780 teeth and five skulls from different ontogenetic stages. We cannot find a clear morphometric distinction between the supposedly smaller and older species Amphimoschus artenensis and the supposedly younger and larger species A. ponteleviensis. Accordingly, we have no reason to retain the two species and propose, following the principle of priority (ICZN chapter 6 article 23), that only A. ponteleviensis Bourgeois, 1873 is valid. Our studies on the ontogenetic variation of Amphimoschus does reveal that the sagittal crest may increase in size and a supraorbital ridge may appear with age. Despite the abundant material, the family affiliation is still uncertain.

Mms19 promotes spindle microtubule assembly in Drosophila neural stem cells

Mitotic divisions depend on the timely assembly and proper orientation of the mitotic spindle. Malfunctioning of these processes can considerably delay mitosis, thereby compromising tissue growth and homeostasis, and leading to chromosomal instability. Loss of functional Mms19 drastically affects the growth and development of mitotic tissues in Drosophila larvae and we now demonstrate that Mms19 is an important factor that promotes spindle and astral microtubule (MT) growth, and MT stability and bundling. Mms19 function is needed for the coordination of mitotic events and for the rapid progression through mitosis that is characteristic of neural stem cells. Surprisingly, Mms19 performs its mitotic activities through two different pathways. By stimulating the mitotic kinase cascade, it triggers the localization of the MT regulatory complex TACC/Msps (Transforming Acidic Coiled Coil/Minispindles, the homolog of human ch-TOG) to the centrosome. This activity of Mms19 can be rescued by stimulating the mitotic kinase cascade. However, other aspects of the Mms19 phenotypes cannot be rescued in this way, pointing to an additional mechanism of Mms19 action. We provide evidence that Mms19 binds directly to MTs and that this stimulates MT stability and bundling.

Transmissible cancers and the evolution of sex under the Red Queen hypothesis

The predominance of sexual reproduction in eukaryotes remains paradoxical in evolutionary theory. Of the hypotheses proposed to resolve this paradox, the 'Red Queen hypothesis' emphasises the potential of antagonistic interactions to cause fluctuating selection, which favours the evolution and maintenance of sex. Whereas empirical and theoretical developments have focused on host-parasite interactions, the premises of the Red Queen theory apply equally well to any type of antagonistic interactions. Recently, it has been suggested that early multicellular organisms with basic anticancer defences were presumably plagued by antagonistic interactions with transmissible cancers and that this could have played a pivotal role in the evolution of sex. Here, we dissect this argument using a population genetic model. One fundamental aspect distinguishing transmissible cancers from other parasites is the continual production of cancerous cell lines from hosts' own tissues. We show that this influx dampens fluctuating selection and therefore makes the evolution of sex more difficult than in standard Red Queen models. Although coevolutionary cycling can remain sufficient to select for sex under some parameter regions of our model, we show that the size of those regions shrinks once we account for epidemiological constraints. Altogether, our results suggest that horizontal transmission of cancerous cells is unlikely to cause fluctuating selection favouring sexual reproduction. Nonetheless, we confirm that vertical transmission of cancerous cells can promote the evolution of sex through a separate mechanism, known as similarity selection, that does not depend on coevolutionary fluctuations.

Ruelle Zeta Function from Field Theory

We propose a field-theoretic interpretation of Ruelle zeta function and show how it can be seen as the partition function for BF theory when an unusual gauge-fixing condition on contact manifolds is imposed. This suggests an alternative rephrasing of a conjecture due to Fried on the equivalence between Ruelle zeta function and analytic torsion, in terms of homotopies of Lagrangian submanifolds.

Switch to second-line versus continued first-line antiretroviral therapy for patients with low-level HIV-1 viremia: An open-label randomized controlled trial in Lesotho

BACKGROUND

Current World Health Organization (WHO) antiretroviral therapy (ART) guidelines define virologic failure as two consecutive viral load (VL) measurements ≥1,000 copies/mL, triggering empiric switch to next-line ART. This trial assessed if patients with sustained low-level HIV-1 viremia on first-line ART benefit from a switch to second-line treatment.

METHODS AND FINDINGS

This multicenter, parallel-group, open-label, superiority, randomized controlled trial enrolled patients on first-line ART containing non-nucleoside reverse transcriptase inhibitors (NNRTI) with two consecutive VLs ≥100 copies/mL, with the second VL between 100-999 copies/mL, from eight clinics in Lesotho. Consenting participants were randomly assigned (1:1), stratified by facility, demographic group, and baseline VL, to either switch to second-line ART (switch group) or continued first-line ART (control group; WHO guidelines). The primary endpoint was viral suppression (<50 copies/mL) at 36 weeks. Analyses were by intention to treat, using logistic regression models, adjusted for demographic group and baseline VL. Between August 1, 2017, and August 7, 2019, 137 individuals were screened, of whom 80 were eligible and randomly assigned to switch (n = 40) or control group (n = 40). The majority of participants were female (54 [68%]) with a median age of 42 y (interquartile range [IQR] 35-51), taking tenofovir disoproxil fumarate/lamivudine/efavirenz (49 [61%]) and on ART for a median of 5.9 y (IQR 3.3-8.6). At 36 weeks, 22/40 (55%) participants in the switch versus 10/40 (25%) in the control group achieved viral suppression (adjusted difference 29%, 95% CI 8%-50%, p = 0.009). The switch group had significantly higher probability of viral suppression across different VL thresholds (<20, <100, <200, <400, and <600 copies/mL) but not for <1,000 copies/mL. Thirty-four (85%) participants in switch group and 21 (53%) in control group experienced at least one adverse event (AE) (p = 0.002). No hospitalization or death or other serious adverse events were observed. Study limitations include a follow-up period too short to observe differences in clinical outcomes, missing values in CD4 cell counts due to national stockout of reagents during the study, and limited generalizability of findings to other than NNRTI-based first-line ART regimens.

CONCLUSIONS

In this study, switching to second-line ART among patients with sustained low-level HIV-1 viremia resulted in a higher proportion of participants with viral suppression. These results endorse lowering the threshold for virologic failure in future WHO guidelines.

TRIAL REGISTRATION

The trial is registered at ClinicalTrials.gov, NCT03088241.

Climate and tree seed production predict the abundance of the European Lyme disease vector over a 15-year period

BACKGROUND

To predict the risk of tick-borne disease, it is critical to understand the ecological factors that determine the abundance of ticks. In Europe, the sheep tick (Ixodes ricinus) transmits a number of important diseases including Lyme borreliosis. The aim of this long-term study was to determine the abiotic and biotic factors driving the annual abundance of I. ricinus at a location in Switzerland where Lyme borreliosis is endemic.

METHODS

Over a 15-year period (2004 to 2018), we monitored the abundance of I. ricinus ticks on a monthly basis at three different elevations on Chaumont Mountain in Neuchâtel, Switzerland. We collected climate variables in the field and from nearby weather stations. We obtained data on beech tree seed production from the literature, as the abundance of Ixodes nymphs can increase dramatically two years after a masting event. We used AIC-based model selection to determine which ecological variables drive annual variation in tick density.

RESULTS

We found that elevation site, year, seed production by beech trees two years prior, and mean annual relative humidity together explained 73.2% of the variation in our annual estimates of nymph density. According to the parameter estimates of our models, (i) the annual density of nymphs almost doubled over the 15-year study period, (ii) changing the beech tree seed production index from very poor mast (1) to full mast (5) increased the abundance of nymphs by 86.2% two years later, and (iii) increasing the field-collected mean annual relative humidity from 50.0 to 75.0% decreased the abundance of nymphs by 46.4% in the same year. Climate variables collected in the field were better predictors of tick abundance than those from nearby weather stations indicating the importance of the microhabitat.

CONCLUSIONS

From a public health perspective, the increase in nymph abundance is likely to have increased the risk of tick-borne disease in this region of Switzerland. Public health officials in Europe should be aware that seed production by deciduous trees is a critical driver of the abundance of I. ricinus, and hence the risk of tick-borne disease.

Separation and recovery of exotic radiolanthanides from irradiated tantalum targets for half-life measurements

The current knowledge of the half-lives (T_1/2) of several radiolanthanides is either affected by a high uncertainty or is still awaiting confirmation. The scientific information deriving from this imprecise T_1/2 data has a significant impact on a variety of research fields, e.g., astrophysics, fundamental nuclear sciences, and nuclear energy and safety. The main reason for these shortcomings in the nuclear databases is the limited availability of suitable sample material together with the difficulties in performing accurate activity measurements with low uncertainties. In reaction to the urgent need to improve the current nuclear databases, the long-term project “ERAWAST” (Exotic Radionuclides from Accelerator Waste for Science and Technology) was launched at Paul Scherrer Institute (PSI). In this context, we present a wet radiochemical separation procedure for the extraction and purification of dysprosium (Dy), terbium (Tb), gadolinium (Gd), and samarium (Sm) fractions from highly radioactive tantalum specimens, in order to obtain ¹⁵⁴Dy, ^157-158Tb, ^148,150Gd, and ¹⁴⁶Sm samples, needed for T_1/2 determination studies. Ion-exchange chromatography was successfully applied for the separation of individual lanthanides. All separations were conducted in aqueous phase. The separation process was monitored via γ-spectrometry using suitable radioactive tracers. Both the purity and the quantification of the desired radiolanthanides were assessed by inductively coupled plasma mass spectrometry. Test experiments revealed that, prior to the Dy, Tb, Gd, and Sm separation, the removal of hafnium, lutetium, and barium from the irradiated tantalum material was necessary to minimize the overall dose rate exposure (in the mSv/h range), as well to obtain pure lanthanide fractions. With the herein proposed separation method, exotic ¹⁵⁴Dy, ^157-158Tb, ^148,150Gd, and ¹⁴⁶Sm radionuclides were obtained in sufficient amounts and purity for the preparation of samples for envisaged half-life measurements. During the separation process, fractions containing holmium, europium, and promethium radionuclides were collected and stored for further use.

Estimation of SARS-CoV-2 mortality during the early stages of an epidemic: A modeling study in Hubei, China, and six regions in Europe

BACKGROUND

As of 16 May 2020, more than 4.5 million cases and more than 300,000 deaths from disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported. Reliable estimates of mortality from SARS-CoV-2 infection are essential for understanding clinical prognosis, planning healthcare capacity, and epidemic forecasting. The case-fatality ratio (CFR), calculated from total numbers of reported cases and reported deaths, is the most commonly reported metric, but it can be a misleading measure of overall mortality. The objectives of this study were to (1) simulate the transmission dynamics of SARS-CoV-2 using publicly available surveillance data and (2) infer estimates of SARS-CoV-2 mortality adjusted for biases and examine the CFR, the symptomatic case-fatality ratio (sCFR), and the infection-fatality ratio (IFR) in different geographic locations.

METHOD AND FINDINGS

We developed an age-stratified susceptible-exposed-infected-removed (SEIR) compartmental model describing the dynamics of transmission and mortality during the SARS-CoV-2 epidemic. Our model accounts for two biases: preferential ascertainment of severe cases and right-censoring of mortality. We fitted the transmission model to surveillance data from Hubei Province, China, and applied the same model to six regions in Europe: Austria, Bavaria (Germany), Baden-Württemberg (Germany), Lombardy (Italy), Spain, and Switzerland. In Hubei, the baseline estimates were as follows: CFR 2.4% (95% credible interval [CrI] 2.1%-2.8%), sCFR 3.7% (3.2%-4.2%), and IFR 2.9% (2.4%-3.5%). Estimated measures of mortality changed over time. Across the six locations in Europe, estimates of CFR varied widely. Estimates of sCFR and IFR, adjusted for bias, were more similar to each other but still showed some degree of heterogeneity. Estimates of IFR ranged from 0.5% (95% CrI 0.4%-0.6%) in Switzerland to 1.4% (1.1%-1.6%) in Lombardy, Italy. In all locations, mortality increased with age. Among individuals 80 years or older, estimates of the IFR suggest that the proportion of all those infected with SARS-CoV-2 who will die ranges from 20% (95% CrI 16%-26%) in Switzerland to 34% (95% CrI 28%-40%) in Spain. A limitation of the model is that count data by date of onset are required, and these are not available in all countries.

CONCLUSIONS

We propose a comprehensive solution to the estimation of SARS-Cov-2 mortality from surveillance data during outbreaks. The CFR is not a good predictor of overall mortality from SARS-CoV-2 and should not be used for evaluation of policy or comparison across settings. Geographic differences in IFR suggest that a single IFR should not be applied to all settings to estimate the total size of the SARS-CoV-2 epidemic in different countries. The sCFR and IFR, adjusted for right-censoring and preferential ascertainment of severe cases, are measures that can be used to improve and monitor clinical and public health strategies to reduce the deaths from SARS-CoV-2 infection.

Comparative RNA-Seq analyses of Drosophila plasmatocytes reveal gene specific signatures in response to clean injury and septic injury

Drosophila melanogaster's blood cells (hemocytes) play essential roles in wound healing and are involved in clearing microbial infections. Here, we report the transcriptional changes of larval plasmatocytes after clean injury or infection with the Gram-negative bacterium Escherichia coli or the Gram-positive bacterium Staphylococcus aureus compared to hemocytes recovered from unchallenged larvae via RNA-Sequencing. This study reveals 676 differentially expressed genes (DEGs) in hemocytes from clean injury samples compared to unchallenged samples, and 235 and 184 DEGs in E. coli and S. aureus samples respectively compared to clean injury samples. The clean injury samples showed enriched DEGs for immunity, clotting, cytoskeleton, cell migration, hemocyte differentiation, and indicated a metabolic reprogramming to aerobic glycolysis, a well-defined metabolic adaptation observed in mammalian macrophages. Microbial infections trigger significant transcription of immune genes, with significant differences between the E. coli and S. aureus samples suggesting that hemocytes have the ability to engage various programs upon infection. Collectively, our data bring new insights on Drosophila hemocyte function and open the route to post-genomic functional analysis of the cellular immune response.

Overlapping functions and protein-protein interactions of LRR-extensins in Arabidopsis

Plant cell growth requires the coordinated expansion of the protoplast and the cell wall, which is controlled by an elaborate system of cell wall integrity (CWI) sensors linking the different cellular compartments. LRR-eXtensins (LRXs) are cell wall-attached extracellular regulators of cell wall formation and high-affinity binding sites for RALF (Rapid ALkalinization Factor) peptide hormones that trigger diverse physiological processes related to cell growth. LRXs function in CWI sensing and in the case of LRX4 of Arabidopsis thaliana, this activity was shown to involve interaction with the transmembrane CatharanthusroseusReceptor-Like Kinase1-Like (CrRLK1L) protein FERONIA (FER). Here, we demonstrate that binding of RALF1 and FER is common to most tested LRXs of vegetative tissue, including LRX1, the main LRX protein of root hairs. Consequently, an lrx1-lrx5 quintuple mutant line develops shoot and root phenotypes reminiscent of the fer-4 knock-out mutant. The previously observed membrane-association of LRXs, however, is FER-independent, suggesting that LRXs bind not only FER but also other membrane-localized proteins to establish a physical link between intra- and extracellular compartments. Despite evolutionary diversification of various LRX proteins, overexpression of several chimeric LRX constructs causes cross-complementation of lrx mutants, indicative of comparable functions among members of this protein family. Suppressors of the pollen-growth defects induced by mutations in the CrRLK1Ls ANXUR1/2 also alleviate lrx1 lrx2-induced mutant root hair phenotypes. This suggests functional similarity of LRX-CrRLK1L signaling processes in very different cell types and indicates that LRX proteins are components of conserved processes regulating cell growth.

Cell growth in plants requires the coordinated enlargement of the cell and the surrounding cell wall, which is regulated by an elaborate system of cell wall integrity sensors, proteins involved in the exchange of information between the cell and the cell wall. In Arabidopsis thaliana, LRR-extensins (LRXs) are localized in the cell wall and bind RALF peptides, hormones that regulate cell growth-related processes. LRX4 also binds the plasma membrane-localized protein FERONIA (FER), thereby establishing a link between the cell and the cell wall. Here, we show that membrane association of LRX4 is not dependent on FER, suggesting that LRX4 binds other, so far unknown proteins. The LRR domain of several LRXs can bind to FER, consistent with the observation that mutations in multiple LRX genes are required to recapitulate a fer knock-out phenotype. Our results support the notion that LRX-FER interactions are key to proper cell growth.

CINeMA: An approach for assessing confidence in the results of a network meta-analysis

BACKGROUND

The evaluation of the credibility of results from a meta-analysis has become an important part of the evidence synthesis process. We present a methodological framework to evaluate confidence in the results from network meta-analyses, Confidence in Network Meta-Analysis (CINeMA), when multiple interventions are compared.

METHODOLOGY

CINeMA considers 6 domains: (i) within-study bias, (ii) reporting bias, (iii) indirectness, (iv) imprecision, (v) heterogeneity, and (vi) incoherence. Key to judgments about within-study bias and indirectness is the percentage contribution matrix, which shows how much information each study contributes to the results from network meta-analysis. The contribution matrix can easily be computed using a freely available web application. In evaluating imprecision, heterogeneity, and incoherence, we consider the impact of these components of variability in forming clinical decisions.

CONCLUSIONS

Via 3 examples, we show that CINeMA improves transparency and avoids the selective use of evidence when forming judgments, thus limiting subjectivity in the process. CINeMA is easy to apply even in large and complicated networks.

Harmonic tropical morphisms and approximation

Harmonic amoebas are generalisations of amoebas of algebraic curves immersed in complex tori. Introduced by Krichever in 2014, the consideration of such objects suggests to enlarge the scope of tropical geometry. In the present paper, we introduce the notion of harmonic morphisms from tropical curves to affine spaces and show how these morphisms can be systematically described as limits of families of harmonic amoeba maps on Riemann surfaces. It extends previous results about approximation of tropical curves in affine spaces and provides a different point of view on Mikhalkin's approximation Theorem for regular phase-tropical morphisms, as stated e.g. by Mikhalkin in 2006. The results presented here follow from the study of imaginary normalised differentials on families of punctured Riemann surfaces and suggest interesting connections with compactifications of moduli spaces.

A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici

BACKGROUND

The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures.

RESULTS

Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species.

CONCLUSIONS

Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.

The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter

Bacterial growth and division require regulated synthesis of the macromolecules used to expand and replicate components of the cell. Transcription of housekeeping genes required for metabolic homeostasis and cell proliferation is guided by the sigma factor σ70. The conserved CarD-like transcriptional regulator, CdnL, associates with promoter regions where σ70 localizes and stabilizes the open promoter complex. However, the contributions of CdnL to metabolic homeostasis and bacterial physiology are not well understood. Here, we show that Caulobacter crescentus cells lacking CdnL have severe morphological and growth defects. Specifically, ΔcdnL cells grow slowly in both rich and defined media, and are wider, more curved, and have shorter stalks than WT cells. These defects arise from transcriptional downregulation of most major classes of biosynthetic genes, leading to significant decreases in the levels of critical metabolites, including pyruvate, α-ketoglutarate, ATP, NAD+, UDP-N-acetyl-glucosamine, lipid II, and purine and pyrimidine precursors. Notably, we find that ΔcdnL cells are glutamate auxotrophs, and ΔcdnL is synthetic lethal with other genetic perturbations that limit glutamate synthesis and lipid II production. Our findings implicate CdnL as a direct and indirect regulator of genes required for metabolic homeostasis that impacts morphogenesis through availability of lipid II and other metabolites.

Are dialects socially learned in marmoset monkeys? Evidence from translocation experiments

The acoustic properties of vocalizations in common marmosets differ between populations. These differences may be the result of social vocal learning, but they can also result from environmental or genetic differences between populations. We performed translocation experiments to separately quantify the influence of a change in the physical environment (experiment 1), and a change in the social environment (experiment 2) on the acoustic properties of calls from individual captive common marmosets. If population differences were due to genetic differences, we expected no change in the vocalizations of the translocated marmosets. If differences were due to environmental factors, we expected vocalizations to permanently change contingent with environmental changes. If social learning was involved, we expected that the vocalizations of animals translocated to a new population with a different dialect would become more similar to the new population. In experiment 1, we translocated marmosets to a different physical environment without changing the social composition of the groups or their neighbours. Immediately after the translocation to the new facility, one out of three call types showed a significant change in call structure, but 5-6 weeks later, the calls were no longer different from before the translocation. Thus, the novel physical environment did not induce long lasting changes in the vocalizations of the marmosets. In experiment 2, we translocated marmosets to a new population with a different dialect. Importantly, our previous work had shown that these two populations differed significantly in vocalization structure. The translocated marmosets were still housed in their original social group, but after translocation they were surrounded by the vocalizations from neighbouring groups of the new population. The vocal distance between the translocated individuals and the new population decreased for two out of three call types over 16 weeks. Thus, even without direct social contact or interaction, the vocalizations of the translocated animals converged towards the new population, indicating that common marmosets can modify their calls due to acoustic input from conspecifics alone, via crowd vocal learning. To our knowledge, this is the first study able to distinguish between different explanations for vocal dialects as well as to show crowd vocal learning in a primate species.

Predictors of Return to Work 12 Months After Solid Organ Transplantation: Results from the Swiss Transplant Cohort Study

Background Return to work with or after a chronic disease is not a very well understood process, influenced by a variety of personal, professional, societal and medical factors. The aim of this study is to identify predictors for return to work 12 months after a solid organ transplant applying a bio-psycho-social model. Methods This study is based on patients included in the Swiss Transplant Cohort Study, a national prospective multicentre cohort, who underwent a first solid organ transplant (kidney, liver, heart, lung). Bio-psycho-social factors were tested and predictors of return to work identified using logistic regression models. Results Among the 636 patients included in the study, 49.8% (317) were employed 12 months post-transplant. The major predictor for returning to work 12 months posttransplant was pre-transplant employment status (OR 10.8). Accordingly, the population was stratified in employed and not employed pre-transplant groups. Age, self-perceived health (6 months post-transplant) and the transplanted organ were significantly associated with post-transplant employment status in both groups. Return to work was influenced by education, depression (6 month post-transplant) and waiting time in the employed pre-transplant group and by invalidity pension in the not employed pre-transplant group. Conclusion Employment status pre-transplant being highly associated with employment status post-transplant, the process promoting return to work should be started well before surgery. Biomedical, psychological and social factors must be taken into account to promote return to work in transplanted patients.

Conformal Invariance of Boundary Touching Loops of FK Ising Model

In this article we show the convergence of a loop ensemble of interfaces in the FK Ising model at criticality, as the lattice mesh tends to zero, to a unique conformally invariant scaling limit. The discrete loop ensemble is described by a canonical tree glued from the interfaces, which then is shown to converge to a tree of branching SLEs. The loop ensemble contains unboundedly many loops and hence our result describes the joint law of infinitely many loops in terms of SLE type processes, and the result gives the full scaling limit of the FK Ising model in the sense of random geometry of the interfaces. Some other results in this article are convergence of the exploration process of the loop ensemble (or the branch of the exploration tree) to SLE ( κ , κ - 6 ) , κ = 16 / 3 , and convergence of a generalization of this process for 4 marked points to SLE [ κ , Z ] , κ = 16 / 3 , where Z refers to a partition function. The latter SLE process is a process that can't be written as a SLE ( κ , ρ 1 , ρ 2 , … ) process, which are the most commonly considered generalizations of SLEs.

Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles

BACKGROUND

The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant eaters among its approximately 315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing.

RESULTS

We explore the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representative of the two most species-rich beetle suborders. We contrast the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We find gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant feeding, we identify families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There is notable support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes.

CONCLUSIONS

Our explicit modeling of the evolution of gene repertoires across 18 species identifies putative adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant feeding in general, in driving beetle diversification.

Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

BACKGROUND

An orthologous group (OG) comprises a set of orthologous and paralogous genes that share a last common ancestor (LCA). OGs are defined with respect to a chosen taxonomic level, which delimits the position of the LCA in time to a specified speciation event. A hierarchy of OGs expands on this notion, connecting more general OGs, distant in time, to more recent, fine-grained OGs, thereby spanning multiple levels of the tree of life. Large scale inference of OG hierarchies with independently computed taxonomic levels can suffer from inconsistencies between successive levels, such as the position in time of a duplication event. This can be due to confounding genetic signal or algorithmic limitations. Importantly, inconsistencies limit the potential use of OGs for functional annotation and third-party applications.

RESULTS

Here we present a new methodology to ensure hierarchical consistency of OGs across taxonomic levels. To resolve an inconsistency, we subsample the protein space of the OG members and perform gene tree-species tree reconciliation for each sampling. Differently from previous approaches, by subsampling the protein space, we avoid the notoriously difficult task of accurately building and reconciling very large phylogenies. We implement the method into a high-throughput pipeline and apply it to the eggNOG database. We use independent protein domain definitions to validate its performance.

CONCLUSION

The presented consistency pipeline shows that, contrary to previous limitations, tree reconciliation can be a useful instrument for the construction of OG hierarchies. The key lies in the combination of sampling smaller trees and aggregating their reconciliations for robustness. Results show comparable or greater performance to previous pipelines. The code is available on Github at: https://github.com/meringlab/og_consistency_pipeline .

Correlates of social role and conflict severity in wild vervet monkey agonistic screams

Screams are acoustically distinct, high-pitched and high-amplitude calls, produced by many social species. Despite a wide range of production contexts, screams are characterised by an acoustic structure that appears to serve in altering the behaviour of targeted receivers during agonistic encounters. In chimpanzees, this can be achieved by callers producing acoustic variants that correlate with their identity, social role, relationship with the targeted recipient, the composition of the audience and the nature of the event. Although vervet monkeys (Chlorocebus pygerythrus) have been studied for decades, not much is known about their agonistic screams. Here, we examined agonistic screams produced by wild vervet monkeys to investigate the degree to which caller identity, social role and conflict severity affected call structure. We found that screams were both individually distinctive and dependent of the agonistic events. In particular, victim screams were longer and higher-pitched than aggressor screams, while screams produced in severe conflicts (chases, physical contact) had higher entropy than those in mild conflicts. We discuss these findings in terms of their evolutionary significance and suggest that acoustic variation might serve to reduce the aggression level of opponents, while simultaneously attracting potential helpers.

Contextual influence on confidence judgments in human reinforcement learning

The ability to correctly estimate the probability of one’s choices being correct is fundamental to optimally re-evaluate previous choices or to arbitrate between different decision strategies. Experimental evidence nonetheless suggests that this metacognitive process—confidence judgment- is susceptible to numerous biases. Here, we investigate the effect of outcome valence (gains or losses) on confidence while participants learned stimulus-outcome associations by trial-and-error. In two experiments, participants were more confident in their choices when learning to seek gains compared to avoiding losses, despite equal difficulty and performance between those two contexts. Computational modelling revealed that this bias is driven by the context-value, a dynamically updated estimate of the average expected-value of choice options, necessary to explain equal performance in the gain and loss domain. The biasing effect of context-value on confidence, revealed here for the first time in a reinforcement-learning context, is therefore domain-general, with likely important functional consequences. We show that one such consequence emerges in volatile environments, where the (in)flexibility of individuals’ learning strategies differs when outcomes are framed as gains or losses. Despite apparent similar behavior- profound asymmetries might therefore exist between learning to avoid losses and learning to seek gains.

In order to arbitrate between different decision strategies, as well as to inform future choices, a decision maker needs to estimate the probability of her choices being correct as precisely as possible. Surprisingly, this metacognitive operation, known as confidence judgment, has not been systematically investigated in the context of simple instrumental-learning tasks. Here, we assessed how confident individuals are in their choices when learning stimulus-outcome associations by trial-and-errors to maximize gains or to minimize losses. In two experiments, we show that individuals are more confident in their choices when learning to seek gains compared to avoiding losses, despite equal difficulty and performance between those two contexts. To simultaneously account for this pattern of choices and confidence judgments, we propose that individuals learn context-values, which approximate the average expected-value of choice options. We finally show that, in volatile environments, the biasing effect of context-value on confidence induces difference in learning flexibility when outcomes are framed as gains or losses.

Detection of Plasmodium falciparum infected Anopheles gambiae using near-infrared spectroscopy

BACKGROUND

Large-scale surveillance of mosquito populations is crucial to assess the intensity of vector-borne disease transmission and the impact of control interventions. However, there is a lack of accurate, cost-effective and high-throughput tools for mass-screening of vectors.

METHODS

A total of 750 Anopheles gambiae (Keele strain) mosquitoes were fed Plasmodium falciparum NF54 gametocytes through standard membrane feeding assay (SMFA) and afterwards maintained in insectary conditions to allow for oocyst (8 days) and sporozoite development (14 days). Thereupon, each mosquito was scanned using near infra-red spectroscopy (NIRS) and processed by quantitative polymerase chain reaction (qPCR) to determine the presence of infection and infection load. The spectra collected were randomly assigned to either a training dataset, used to develop calibrations for predicting oocyst- or sporozoite-infection through partial least square regressions (PLS); or to a test dataset, used for validating the calibration's prediction accuracy.

RESULTS

NIRS detected oocyst- and sporozoite-stage P. falciparum infections with 88% and 95% accuracy, respectively. This study demonstrates proof-of-concept that NIRS is capable of rapidly identifying laboratory strains of human malaria infection in African mosquito vectors.

CONCLUSIONS

Accurate, low-cost, reagent-free screening of mosquito populations enabled by NIRS could revolutionize surveillance and elimination strategies for the most important human malaria parasite in its primary African vector species. Further research is needed to evaluate how the method performs in the field following adjustments in the training datasets to include data from wild-caught infected and uninfected mosquitoes.

Miro-dependent mitochondrial pool of CENP-F and its farnesylated C-terminal domain are dispensable for normal development in mice

CENP-F is a large, microtubule-binding protein that regulates multiple cellular processes including chromosome segregation and mitochondrial trafficking at cytokinesis. This multiplicity of functions is mediated through the binding of various partners, like Bub1 at the kinetochore and Miro at mitochondria. Due to the multifunctionality of CENP-F, the cellular phenotypes observed upon its depletion are difficult to interpret and there is a need to genetically separate its different functions by preventing binding to selected partners. Here we engineer a CENP-F point-mutant that is deficient in Miro binding and thus is unable to localize to mitochondria, but retains other localizations. We introduce this mutation in cultured human cells using CRISPR/Cas9 system and show it causes a defect in mitochondrial spreading similar to that observed upon Miro depletion. We further create a mouse model carrying this CENP-F variant, as well as truncated CENP-F mutants lacking the farnesylated C-terminus of the protein. Importantly, one of these truncations leads to ~80% downregulation of CENP-F expression. We observe that, despite the phenotypes apparent in cultured cells, mutant mice develop normally. Taken together, these mice will serve as important models to study CENP-F biology at organismal level. In addition, because truncations of CENP-F in humans cause a lethal disease termed Strømme syndrome, they might also be relevant disease models.

CENP-F is a poorly characterized multifunctional regulator of metazoan cell division involved in chromosome segregation and mitochondrial dynamics. The physiological importance of CENP-F in both of these processes is not firmly established and numerous conflicting reports exist regarding its function in mitosis. Here we set out to investigate the function of CENP-F in vivo by CRISPR-mediated mutagenesis in mice where we specifically disrupt different domains of CENP-F important for mitosis and mitochondrial regulation. Surprisingly, contrasting to reported phenotypes in cultured cells, mutant animals display no obvious phenotypes. This argues against CENP-F being a major player in mammalian cell division and suggest context-specific roles of this protein. Importantly, in humans, truncations of CENP-F as small as 20 amino acids have recently emerged as a cause of human disease termed Strømme syndrome. Truncations in these mice might yield information relevant to the understanding of this disease and biology of CENP-F.

Within-country migration and obesity dynamics: analysis of 94,783 women from the Peruvian demographic and health surveys

BACKGROUND

Rural-to-urban migration is associated with increased obesity, yet it remains unknown whether this association exist, and to what extent, with other types of internal migration.

METHODS

We conducted a secondary analysis of the Peruvian Demographic and Health Surveys (2005 to 2012) on data collected from women aged 15-49 years. Participants were classified as rural stayers, urban stayers, rural-to-urban migrants, intra-rural migrants, intra-urban migrants, and urban-to-rural migrants. Marginal effects from a logit regression model were used to assess the probabilities of being and becoming obese given both the length of time in current place of residence and women's migration status.

RESULTS

Analysis of cross-sectional survey data generated between 2005 and 2012. Data from 94,783 participants was analyzed. Intra-urban migrants and rural-to-urban migrants had the highest rates of obesity (21% in 2012). A steady increase in obesity is observed across all migration statuses. Relative to rural non-migrants, participants exposed to urban environments had greater odds, two- to three-fold higher, of obesity. The intra-rural migrant group also shows higher odds relative to rural stayers (42% higher obesity odds). The length of exposure to urban settings shows a steady effect over time.

CONCLUSION

Both exposure to urban environments and migration are associated with higher odds of obesity. Expanding the characterization of within-country migration dynamics provides a better insight into the relationship between duration of exposure to urban settings and obesity.

A longitudinal investigation of the factors associated with increased RISk of playing-related musculoskeletal disorders in MUsic students (RISMUS): a study protocol

BACKGROUND

The achievement and improvement of skills in musical techniques to reach the highest levels of performance may expose music students to a wide range of playing-related musculoskeletal disorders (PRMDs). In order to establish effective solutions for PRMDs and to develop future preventive measures, it is fundamental to firstly identify the main risk factors that play a significant role in the development of musculoskeletal conditions and symptoms. The aim of the study is to identify those factors associated with increased risk of PRMDs among music students. A further goal is to characterise this population and describe the clinical features of PRMDs, as well as to determine the evolving course of PRMDs in music students during their training.

METHODS

One hundred and ninety schools have been invited to participate in this study, sixty of which have already confirmed officially their support for the investigation's recruitment procedures, by means of a subsequent distribution of the link to a web-based questionnaire to their student groups (total potential student numbers available: n = 12,000 [based on ~ 200 students per school on average, and 60 volunteering schools]; expected number of students: n = 3000 [based on a 25% response rate from the 12,000 students attending the 60 volunteering schools]). The web-based questionnaire includes questions about any PRMD that students have experienced during their training, and different potential risk factors (i.e. lifestyle and physical activity, practice habits, behaviour toward prevention and health history, level of stress, perfectionism, fatigue and disability). Overall recurrence or new onsets of PRMDs will be assessed at 6 and 12 months after the first data collection to investigate and record the development of new incidents within a period of a year and to enable characterisation of the nature and the evolving course of PRMDs.

DISCUSSION

To the best of our knowledge, no other longitudinal studies on risk factors for PRMDs among music students have been conducted so far. Therefore, this study can be considered as an opportunity to begin filling the gaps within current research in this field and to generate new knowledge within musical contexts in education and employment.

TRIAL REGISTRATION

ClinicalTrials.gov ( NCT03622190 ), registration date 09/08/2018.

PIKfyve/Fab1 is required for efficient V-ATPase and hydrolase delivery to phagosomes, phagosomal killing, and restriction of Legionella infection

By engulfing potentially harmful microbes, professional phagocytes are continually at risk from intracellular pathogens. To avoid becoming infected, the host must kill pathogens in the phagosome before they can escape or establish a survival niche. Here, we analyse the role of the phosphoinositide (PI) 5-kinase PIKfyve in phagosome maturation and killing, using the amoeba and model phagocyte Dictyostelium discoideum. PIKfyve plays important but poorly understood roles in vesicular trafficking by catalysing formation of the lipids phosphatidylinositol (3,5)-bisphosphate (PI(3,5)2) and phosphatidylinositol-5-phosphate (PI(5)P). Here we show that its activity is essential during early phagosome maturation in Dictyostelium. Disruption of PIKfyve inhibited delivery of both the vacuolar V-ATPase and proteases, dramatically reducing the ability of cells to acidify newly formed phagosomes and digest their contents. Consequently, PIKfyve- cells were unable to generate an effective antimicrobial environment and efficiently kill captured bacteria. Moreover, we demonstrate that cells lacking PIKfyve are more susceptible to infection by the intracellular pathogen Legionella pneumophila. We conclude that PIKfyve-catalysed phosphoinositide production plays a crucial and general role in ensuring early phagosomal maturation, protecting host cells from diverse pathogenic microbes.

Numerical investigation of the mixed-mode failure of snow

The failure of a weak snow layer underlying a cohesive slab is the primary step in the release process of a dry snow slab avalanche. The complex and heterogeneous microstructure of snow limits our understanding of failure initiation inside the weak layer, especially under mixed-mode shear-compression loading. Further complication arises from the dependence of snow strength on the loading rate induced by the balance between bond breaking and bond formation (sintering) during the failure process. Here, we use the discrete element method to investigate the influence of mixed-mode loading and fast sintering on the failure of a weak layer generated using cohesive ballistic deposition. Both fast and slow loading simulations resulted in a mixed-mode failure envelope in good agreement with laboratory experiments. We show that the number of broken bonds at failure and the weak layer strength significantly decreases with increasing loading angle, regardless of the loading rate. While the influence of loading rate appears negligible in shear-dominant loading (for loading angles above 30 ∘ ), simulations suggest a significant increase in the weak layer strength at low loading angles and low loading rates, characteristic of natural avalanches, due to the presence of an active sintering mechanism.