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Objectives Informing research participants of the results of studies in which they took part is viewed as an ethical imperative. However, there is little guidance in the literature about how to do this. The Fluoxetine Or Control Under Supervision trial randomised 3127 patients with a recent acute stroke to 6 months of fluoxetine or placebo and was published in the Lancet on 5 December 2018. The trial team decided to inform the participants of the results at exactly the same time as the Lancet publication, and also whether they had been allocated fluoxetine or placebo. In this report, we describe how we informed participants of the results.Design In the 6-month and 12-month follow-up questionnaires, we invited participants to provide an email address if they wished to be informed of the results of the trial. We re-opened our trial telephone helpline between 5 December 2018 and 31 March 2019.Setting UK stroke services.Participants 3127 participants were randomised. 2847 returned 6-month follow-up forms and 2703 returned 12-month follow-up forms; the remaining participants had died (380), withdrawn consent or did not respond.Results Of those returning follow-up questionnaires, a total of 1845 email addresses were provided and a further 50 people requested results to be sent by post. Results were sent to all email and postal addresses provided; 309 emails were returned unrecognised. Seventeen people replied, of whom three called the helpline and the rest responded by email.Conclusion It is feasible to disseminate results of large trials to research participants, though only around 60% of those randomised wanted to receive the results. The system we developed was efficient and required very little resource, and could be replicated by trialists in the future.Trial registration number ISRCTN83290762; Post-results.

ABSTRACT Influenza A viruses present a major challenge for animal and human health. They circulate widely in wild waterfowl and frequently spillover into poultry, emphasizing the need for risk-based surveillance in wild birds and an understanding of the relative importance of different transmission mechanisms. We addressed this objective with a replicated (N = 6) experimental infection study in which we serially exposed eight cohorts of four naïve contact mallards to an experimentally infected mallard and a shared water pool. Viral concentration in the water was a better predictor of transmission than several direct measures of viral shedding in the focal duck. Our data provide quantification of transmission probability and its variation throughout the infectious period of an infected duck. Our findings highlight the need to consider environmental surveillance in risk-based surveillance planning and provide realistic parameters for identifying optimal control strategies using epidemiological inference. IMPORTANCE Wild birds are the natural reservoir hosts of influenza A viruses. Highly pathogenic strains of influenza A viruses pose risks to wild birds, poultry, and human health. Thus, understanding how these viruses are transmitted between birds is critical. We conducted an experiment where we experimentally infected mallards which are ducks that are commonly exposed to influenza viruses. We exposed several contact ducks to the experimentally infected duck to estimate the probability that a contact duck would become infected from either exposure to the virus shed directly from the infected duck or shared water contaminated with the virus from the infected duck. We found that environmental transmission from contaminated water best predicted the probability of transmission to naïve contact ducks, relatively low levels of virus in the water were sufficient to cause infection, and the probability of a naïve duck becoming infected varied over time.

Background: Antidepressants are a first-line treatment for depression. However, only a third of individuals experience remission after the first treatment. Common genetic variation, in part, likely regulates antidepressant response, yet the success of previous genome-wide association studies has been limited by sample size. This study performs the largest genetic analysis of prospectively assessed antidepressant response in major depressive disorder to gain insight into the underlying biology and enable out-of-sample prediction. Methods: Genome-wide analysis of remission (nremit = 1852, nnonremit = 3299) and percentage improvement (n = 5218) was performed. Single nucleotide polymorphism–based heritability was estimated using genome-wide complex trait analysis. Genetic covariance with eight mental health phenotypes was estimated using polygenic scores/AVENGEME. Out-of-sample prediction of antidepressant response polygenic scores was assessed. Gene-level association analysis was performed using MAGMA and transcriptome-wide association study. Tissue, pathway, and drug binding enrichment were estimated using MAGMA. Results: Neither genome-wide association study identified genome-wide significant associations. Single nucleotide polymorphism–based heritability was significantly different from zero for remission (h2 = 0.132, SE = 0.056) but not for percentage improvement (h2 = −0.018, SE = 0.032). Better antidepressant response was negatively associated with genetic risk for schizophrenia and positively associated with genetic propensity for educational attainment. Leave-one-out validation of antidepressant response polygenic scores demonstrated significant evidence of out-of-sample prediction, though results varied in external cohorts. Gene-based analyses identified ETV4 and DHX8 as significantly associated with antidepressant response. Conclusions: This study demonstrates that antidepressant response is influenced by common genetic variation, has a genetic overlap schizophrenia and educational attainment, and provides a useful resource for future research. Larger sample sizes are required to attain the potential of genetics for understanding and predicting antidepressant response.

Summary: Background: The initiation and cessation of opioid agonist treatment (OAT) have both been associated with elevated risk of fatal overdose. We examined risk of non-fatal overdose during OAT initiation and cessation and specifically between methadone versus buprenorphine recipients. Methods: We utilised primary care electronic health records from the Clinical Practice Research Datalink to delineate a study cohort of adults aged 18-64 who were prescribed OAT between Jan 1, 1998 and Dec 31, 2017. These records were linked to hospitalisation, mortality records and patient neighbourhood and practice-level Index of Multiple Deprivation quintiles. With inverse probability treatment weights applied and negative binomial regression models we estimated incidence rate ratios for hospital admissions among patients who experienced multiple overdoses. Findings: A total of 20898 patients were prescribed methadone or buprenorphine over 83856 person-years of follow-up. Compared with periods in treatment, patients not in treatment were 51% more likely to experience a non-fatal overdose that required hospitalisation (weighted rate ratio, wRR 1·51; 95% CI 1·42, 1·60), especially during the four weeks of OAT initiation (5·59; 5·31, 5·89) and following cessation (13·39; 12·78, 14·03). The wRR of overdose during (0·37; 0·34, 0·39) and after treatment (0·36; 0·34, 0·38) favoured buprenorphine compared to methadone. Interpretation: OAT is associated with decreased non-fatal overdose risk. Buprenorphine may act more protectively than methadone, especially during the first four weeks of treatment. Funding: National Institute for Health and Care Research (NIHR) Greater Manchester Patient Safety Translational Research Centre (PSTRC-2016-003).

Plasmodium falciparum, the causative agent of malaria, remains a global health threat as parasites continue to develop resistance to antimalarial drugs used throughout the world. Accordingly, drugs with novel modes of action are desperately required to combat malaria. P. falciparum parasites infect human red blood cells where they digest the host’s main protein constituent, hemoglobin. Leucine aminopeptidase PfA-M17 is one of several aminopeptidases that have been implicated in the last step of this digestive pathway. Here, we use both reverse genetics and a compound specifically designed to inhibit the activity of PfA-M17 to show that PfA-M17 is essential for P. falciparum survival as it provides parasites with free amino acids for growth, many of which are highly likely to originate from hemoglobin. We further show that loss of PfA-M17 results in parasites exhibiting multiple digestive vacuoles at the trophozoite stage. In contrast to other hemoglobin-degrading proteases that have overlapping redundant functions, we validate PfA-M17 as a potential novel drug target.

Process monitoring seeks to identify anomalous plant operating states so that operators can take the appropriate actions for recovery. Instrumental to process monitoring is the labeling of known operating states in historical data, so that departures from these states can be identified. This task can be challenging and time consuming as plant data is typically high dimensional and extensive. Moreover, automation of this procedure is not trivial since ground truth labels are often unavailable. In this contribution, this problem is approached as a multi-mode classification one, and an automatic framework for labeling using unsupervised Machine Learning (ML) methods is presented. The implementation was tested using data from the Tennessee Eastman Process and an industrial pyrolysis process. A total of 9 ML ensembles were included. Hyperparameters were optimized using a multi-objective evolutionary optimization algorithm. Unsupervised clustering metrics (silhouette score, Davies-Bouldin index, and Calinski-Harabasz Index) were investigated as candidates for objective functions in the optimization implementation. Results show that ensembles and hyperparameter selection can be aided by multi-objective optimization. It was found that Silhouette score and Davies-Bouldin index are strong predictions of the ensemble’s performance and can then be used to obtain good initial results for subsequent fault detection and fault diagnosis procedures.

Genome-wide association studies (GWAS) have successfully identified common variants associated with BMI. However, the stability of aggregate genetic variation influencing BMI from midlife and beyond is unknown. By analysing 165,717 men and 193,073 women from the UKBiobank, we performed BMI GWAS on six independent five-year age intervals between 40 and 72 years. We then applied genomic structural equation modeling to test competing hypotheses regarding the stability of genetic effects for BMI. LDSR genetic correlations between BMI assessed between ages 40 to 73 were all very high and ranged 0.89 to 1.00. Genomic structural equation modeling revealed that molecular genetic variance in BMI at each age interval could not be explained by the accumulation of any age-specific genetic influences or autoregressive processes. Instead, a common set of stable genetic influences appears to underpin genome-wide variation in BMI from middle to early old age in men and women alike.

BackgroundLittle is known about people who are admitted to medium secure services (MSSs) from prison, including characteristics and factors that influence clinical pathways and subsequent discharge. We recently published the first study to establish the circumstances by which MSS “prison-transfer” patients are returned to prison. Of particular concern was the finding that a quarter of prison-transfer patients were returned to prison by Responsible Medical Officers (RMOs) because they were not engaging with treatment or were deemed too “high risk” to remain detained within the services, circumstances that would be unacceptable when considering discharge via a community care pathway. It is important to further explore the characteristics of people admitted to MSSs from prison, and to investigate how these may differ for individuals who are returned to prison, as compared to those discharged into the community.Aim(a) To describe the characteristics of prison-transfers who receive an RMO directed discharge from MSSs; and (b) to compare these characteristics by discharge destination; prison return and community discharge.MethodsProspective cohort comparative study: all prison-transfer patients discharged under the instruction of their RMO over a 6-month period, from 33 NHS medium secure units across England and Wales. Data on patient demographic, clinical and legal characteristics were extracted via full patient health record review and collateral information from clinicians was also obtained. This information was used to complete The Historical, Clinical and Risk-−20 items (HCR-20v3) and The Structured Assessment of Protective Factors (SAPROF). Individuals who were returned to prison were compared with those who were discharged to the community.ResultsPersons returned to prison represented a vulnerable group at time of discharge as compared to those discharged into the community and had a significantly shorter length of stay in MSSs. Over half of those returned to prison had a length of stay of

Abstract Background Links between parental socioeconomic position during childhood and subsequent risks of developing mental disorders have rarely been examined across the diagnostic spectrum. We conducted a comprehensive analysis of parental income level, including income mobility, during childhood and risks for developing mental disorders diagnosed in secondary care in young adulthood. Methods National cohort study of persons born in Denmark 1980–2000 (N = 1,051,265). Parental income was measured during birth year and at ages 5, 10 and 15. Follow-up began from 15th birthday until mental disorder diagnosis or 31 December 2016, whichever occurred first. Hazard ratios and cumulative incidence were estimated. Results A quarter (25.2%; 95% CI 24.8–25.6%) of children born in the lowest income quintile families will have a secondary care-diagnosed mental disorder by age 37, versus 13.5% (13.2–13.9%) of those born in the highest income quintile. Longer time spent living in low-income families was associated with higher risks of developing mental disorders. Associations were strongest for substance misuse and personality disorders and weaker for mood disorders and anxiety/somatoform disorders. An exception was eating disorders, with low parental income being associated with attenuated risk. For all diagnostic categories examined except for eating disorders, downward socioeconomic mobility was linked with higher subsequent risk and upward socioeconomic mobility with lower subsequent risk of developing mental disorders. Conclusions Except for eating disorders, low parental income during childhood is associated with subsequent increased risk of mental disorders diagnosed in secondary care across the diagnostic spectrum. Early interventions to mitigate the disadvantages linked with low income, and better opportunities for upward socioeconomic mobility could reduce social and mental health inequalities.

The cell envelope of Gram-negative bacteria consists of two membranes surrounding a periplasm and peptidoglycan layer. Molecular machines spanning the cell envelope depend on spatial constraints and load-bearing forces across the cell envelope and surface. The mechanisms dictating spatial constraints across the cell envelope remain incompletely defined. In Escherichia coli, the coiled-coil lipoprotein Lpp contributes the only covalent linkage between the outer membrane and the underlying peptidoglycan layer. Using proteomics, molecular dynamics, and a synthetic lethal screen, we show that lengthening Lpp to the upper limit does not change the spatial constraint but is accommodated by other factors which thereby become essential for viability. Our findings demonstrate E. coli expressing elongated Lpp does not simply enlarge the periplasm in response, but the bacteria accommodate by a combination of tilting Lpp and reducing the amount of the covalent bridge. By genetic screening, we identified all of the genes in E. coli that become essential in order to enact this adaptation, and by quantitative proteomics discovered that very few proteins need to be up- or down-regulated in steady-state levels in order to accommodate the longer Lpp. We observed increased levels of factors determining cell stiffness, a decrease in membrane integrity, an increased membrane vesiculation and a dependance on otherwise non-essential tethers to maintain lipid transport and peptidoglycan biosynthesis. Further this has implications for understanding how spatial constraint across the envelope controls processes such as flagellum-driven motility, cellular signaling, and protein translocation

Abstract Background Suicide and non-fatal self-harm represent key patient safety events in mental healthcare services. However, additional important learning can also be derived by highlighting examples of optimal practice that help to keep patients safe. In this study, we aimed to explore clinicians’ views of what constitutes good practice in mental healthcare services in the context of suicide prevention. Methods Data were extracted from the National Confidential Inquiry into Suicide and Safety in Mental Health (NCISH) database, a consecutive case series study of suicide by people in contact with mental healthcare services. A large national sample of clinicians’ responses was analysed with a hybrid thematic analysis. Results Responses (n = 2331) were submitted by clinicians across 62 mental healthcare providers. The following five themes illustrated good practice that helps to: 1) promote safer environments, 2) develop stronger relationships with patients and families, 3) provide timely access to tailored and appropriate care, 4) facilitate seamless transitions, and 5) establish a sufficiently skilled, resourced and supported staff team. Conclusion This study highlighted clinicians’ views on key elements of good practice in mental health services. Respondents included practice specific to mental health services that focus on enhancing patient safety via prevention of self-harm and suicide. Clinicians possess important understanding of optimal practice but there are few opportunities to share such insight on a broader scale. A further challenge is to implement optimal practice into routine, daily care to improve patient safety and reduce suicide risk.

Abstract Background Antimicrobial resistance (AMR) of bacterial pathogens is an emerging public health threat. This threat extends to pets as it also compromises our ability to treat their infections. Surveillance programs in the United States have traditionally focused on collecting data from food animals, foods, and people. The Veterinary Laboratory Investigation and Response Network (Vet-LIRN), a national network of 45 veterinary diagnostic laboratories, tested the antimicrobial susceptibility of clinically relevant bacterial isolates from animals, with companion animal species represented for the first time in a monitoring program. During 2017, we systematically collected and tested 1968 isolates. To identify genetic determinants associated with AMR and the potential genetic relatedness of animal and human strains, whole genome sequencing (WGS) was performed on 192 isolates: 69 Salmonella enterica (all animal sources), 63 Escherichia coli (dogs), and 60 Staphylococcus pseudintermedius (dogs). Results We found that most Salmonella isolates (46/69, 67%) had no known resistance genes. Several isolates from both food and companion animals, however, showed genetic relatedness to isolates from humans. For pathogenic E. coli, no resistance genes were identified in 60% (38/63) of the isolates. Diverse resistance patterns were observed, and one of the isolates had predicted resistance to fluoroquinolones and cephalosporins, important antibiotics in human and veterinary medicine. For S. pseudintermedius, we observed a bimodal distribution of resistance genes, with some isolates having a diverse array of resistance mechanisms, including the mecA gene (19/60, 32%). Conclusion The findings from this study highlight the critical importance of veterinary diagnostic laboratory data as part of any national antimicrobial resistance surveillance program. The finding of some highly resistant bacteria from companion animals, and the observation of isolates related to those isolated from humans demonstrates the public health significance of incorporating companion animal data into surveillance systems. Vet-LIRN will continue to build the infrastructure to collect the data necessary to perform surveillance of resistant bacteria as part of fulfilling its mission to advance human and animal health. A One Health approach to AMR surveillance programs is crucial and must include data from humans, animals, and environmental sources to be effective.

Summary: Background: Ambient air pollution affects neurological function, but its association with schizophrenia risk is unclear. We investigated exposure to nitrogen oxides (NOX) as a whole and nitrogen dioxide (NO2) specifically, as well as PM10, and PM2·5, during childhood and subsequent schizophrenia risk. Methods: People born in Denmark from 1980 to 1984 (N=230 844), who were residing in the country on their tenth birthday, and who had two Danish-born parents were followed-up from their tenth birthday until schizophrenia diagnosis or Dec 31, 2016. Mean daily exposure to each pollutant (NO2, NOX, PM10, and PM2·5) at all of an individual's residential addresses from birth to their tenth birthday was modelled. Incidence rate ratios, cumulative incidence, and population attributable risks were calculated using survival analysis techniques. Findings: We analysed data between Aug 1, 2018, and Nov 15, 2019. Of 230 844 individuals included, 2189 cohort members were diagnosed with schizophrenia during follow-up. Higher concentrations of residential NO2 and NOX exposure during childhood were associated with subsequent elevated schizophrenia risk. People exposed to daily mean concentrations of more than 26·5 μg/m3 NO2 had a 1·62 (95% CI 1·41–1·87) times increased risk compared with people exposed to a mean daily concentration of less than 14·5 μg/m3. The absolute risks of developing schizophrenia by the age of 37 years when exposed to daily mean concentrations of more than 26·5 μg/m3 NO2 between birth and 10 years were 1·45% (95% CI 1·30–1·62%) for men and 1·03% (0·90–1·17) for women, whereas when exposed to a mean daily concentration of less than 14·5 μg/m3, the risk was 0·80% (95% CI 0·69–0·92%) for men and 0·67% (0·57–0·79) for women. Associations between exposure to PM2·5 or PM10 and schizophrenia risk were less consistent. Interpretation: If the association between air pollution and schizophrenia is causal, reducing ambient air pollution including NO2 and NOX could have a potentially considerable effect on lowering schizophrenia incidence at the population level. Further investigations are necessary to establish a causal relationship. Funding: Lundbeck Foundation, Stanley Medical Research Institute, European Research Council, NordForsk, Novo Nordisk Foundation, National Health and Medical Research Council, Danish National Research Foundation.

Descriptions of soil hydraulic properties, such as the soil moisture retention curve, θ(h), and saturated hydraulic conductivities, Ks, are a prerequisite for hydrological models. Since the measurement of Ks is expensive, it is frequently derived from statistical pedotransfer functions (PTFs). Because it is usually more difficult to describe Ks than θ(h) from pedotransfer functions, Pollacco et al. (2013) developed a physical unimodal model to compute Ks solely from hydraulic parameters derived from the Kosugi θ(h). This unimodal Ks model, which is based on a unimodal Kosugi soil pore-size distribution, was developed by combining the approach of Hagen–Poiseuille with Darcy's law and by introducing three tortuosity parameters. We report here on (1) the suitability of the Pollacco unimodal Ks model to predict Ks for a range of New Zealand soils from the New Zealand soil database (S-map) and (2) further adaptations to this model to adapt it to dual-porosity structured soils by computing the soil water flux through a continuous function of an improved bimodal pore-size distribution. The improved bimodal Ks model was tested with a New Zealand data set derived from historical measurements of Ks and θ(h) for a range of soils derived from sandstone and siltstone. The Ks data were collected using a small core size of 10 cm diameter, causing large uncertainty in replicate measurements. Predictions of Ks were further improved by distinguishing topsoils from subsoil. Nevertheless, as expected, stratifying the data with soil texture only slightly improved the predictions of the physical Ks models because the Ks model is based on pore-size distribution and the calibrated parameters were obtained within the physically feasible range. The improvements made to the unimodal Ks model by using the new bimodal Ks model are modest when compared to the unimodal model, which is explained by the poor accuracy of measured total porosity. Nevertheless, the new bimodal model provides an acceptable fit to the observed data. The study highlights the importance of improving Ks measurements with larger cores.

Abstract Background Craniosynostosis, or premature fusion of the skull sutures, is a group of disorders that can present in isolation (nonsyndromic) or be associated with other anomalies (syndromic). Delineation of syndromic craniosynostosis is confounded due to phenotypic overlap, variable expression as well as molecular heterogeneity. We report on an infant who presented at birth with multisuture synostosis, turribrachycephaly, midface hypoplasia, beaked nose, low set ears, a high palate and short squat appearing thumbs, and great toes without deviation. The additional MRI findings of choanal stenosis and a Chiari I malformation suggested a diagnosis of Pfeiffer syndrome. First tier molecular testing did not reveal a pathogenic variant. Methods Whole exome sequencing on DNA samples from the proband and her unaffected parents was utilized to delineate the variant causative for the Pfeiffer syndrome diagnosis. Results On whole exome sequencing, a de novo NM_000142.4:c.1428C>A missense variant causing a p.Ala391Glu amino acid change in FGFR3 has been identified. The p.Ala391Glu change has been predominantly identified in patients with Crouzon syndrome with acanthosis nigricans. Conclusions This finding illustrates the first reported case of a child with an overlap with Pfeiffer syndrome to have the p.Ala391Glu variant.

How multitrophic relationships between wildlife communities and their ectoparasitic vectors interact to shape the diversity of vector-borne microorganisms is poorly understood. Nested levels of dependence among microbes, vectors, and vertebrate hosts may have complicated effects on both microbial community assembly and evolution. We examined Bartonella sequences from European bats and their ectoparasites with a combination of network analysis, Bayesian phylogenetics, tip-association and cophylogeny tests, and linear regression to understand the ecological and evolutionary processes that shape parasite communities. We detected seven bat–ectoparasite–Bartonella communities that can be differentiated based on bat families and roosting patterns. Tips of the Bartonella tree were significantly clustered by host taxonomy and geography. We also found significant evidence of evolutionary congruence between bat host and Bartonella phylogenies, indicating that bacterial species have evolved to infect related bat species. Exploring these ecological and evolutionary associations further, we found that sharing of Bartonella species among bat hosts was strongly associated with host phylogenetic distance and roost sharing and less strongly with geographic range overlap. Ectoparasite sharing between hosts was strongly predicted by host phylogenetic distance, roost sharing, and geographic overlap but had no additive effect on Bartonella sharing. Finally, historical Bartonella host-switching was more frequent for closely related bats after accounting for sampling bias among bat species. This study helps to disentangle the complex ecology and evolution of Bartonella bacteria in bat species and their arthropod vectors. Our work provides insight into the important mechanisms that partition parasite communities among hosts, particularly the effect of host phylogeny and roost sharing, and could help to elucidate the evolutionary patterns of other diverse vector-borne microorganisms.

Summary: Background: Since the mid-1990s, excess mortality has increased markedly for adults aged 25–44 years in the north compared with the south of England. We examined the underlying causes of this excess mortality and the contribution of socioeconomic deprivation. Methods: Mortality data from the Office of National Statistics for adults aged 25–44 years were aggregated and compared between England's five most northern versus five most southern government office regions between Jan 1, 1981, and Dec 31, 2016. Poisson regression models, adjusted for age and sex, were used to quantify excess mortality in the north compared with the south by underlying cause of death (accidents, alcohol related, cardiovascular disease and diabetes, drug related, suicide, cancer, and other causes). The role of socioeconomic deprivation, as measured by the 2015 Index of Multiple Deprivation, in explaining the excess and regional variability was also explored. Findings: A mortality divide between the north and south appeared in the mid-1990s and rapidly expanded thereafter for deaths attributed to accidents, alcohol misuse, and drug misuse. In the 2014–16 period, the northern excess was incidence rate ratio (IRR) 1·47 (95% CI 1·39–1·54) for cardiovascular reasons, 2·09 (1·94–2·25) for alcohol misuse, and 1·60 (1·51–1·70) for drug misuse, across both men and women aged 25–44 years. National mortality rates for cardiovascular deaths declined over the study period but a longstanding gap between north and south persisted (from 33·3 [95% CI 31·8–34·8] in 1981 to 15·0 [14·0–15·9] in 2016 in the north vs from 23·5 [22·3–24·8] to 9·9 [9·2–10·5] in the south). Between 2014 and 2016, estimated excess numbers of death in the north versus the south for those aged 25–44 years were 1881 (95% CI 726–2627) for women and 3530 (2216–4511) for men. Socioeconomic deprivation explained up to two-thirds of the excess mortality in the north (IRR for northern effect reduced from 1·15 [95% CI 1·14–1·15; unadjusted] to 1·05 [1·04–1·05; adjusted for Index of Multiple Deprivation]). By 2016, in addition to the persistent north–south gap, mortality rates in London were lower than in all other regions, with IRRs ranging from IRR 1·13 (95% CI 1·12–1·15) for the East England to 1·22 (1·20–1·24) for the North East, even after adjusting for deprivation. Interpretation: Sharp relative rises in deaths from cardiovascular reasons, alcohol misuse and drug misuse in the north compared with the south seem to have created new health divisions between England's regions. This gap might be due to exacerbation of existing social and health inequalities that have been experienced for many years. These divisions might suggest increasing psychological distress, despair, and risk taking among young and middle-aged adults, particularly outside of London. Funding: Medical Research Council and Wellcome Trust.

Background: People diagnosed with schizophrenia have a much reduced life expectancy compared to the general population, and a more than doubled risk of dying from cardiovascular disease (CVD). Existing CVD risk calculators can be used to detect people with an elevated predicted risk of CVD to inform interventions to reduce risk.Aims: This study aimed to compare four different risk calculators for 10-year predicted CVD risk in a sample of people with schizophrenia.Methods: Thirty participants with a diagnosis of schizophrenia spectrum disorders living within Greater Manchester, United Kingdom took part. Ten-year predicted cardiovascular risk scores were calculated using four different models: QRISK3, Framingham, PRIMROSE BMI, and PRIMROSE lipid. Risk estimates and classified risk categories were compared.Results: QRISK3 identified 11 (39%) as having >10% risk of a CV event within 10 years, 4 (14%) of whom exceeded 20%. The Framingham model identified 4 (14%) as exceeding 10%, none of whom exceeded 20%. PRIMROSE risk calculators identified no participants as having >10% risk of a CV event within 10 years. Pairwise concordance correlation coefficients between types of model ranged 0.22–0.77. Mean (± SD) age was 40 (± 10) years but QRISK3's mean “Heart age” was 58 (± 14) years.Conclusion: Risk calculators generate differing predicted CVD risk scores for patients with schizophrenia. Using one risk calculator might yield different recommended monitoring and treatment plans compared to another. Clinicians should therefore take into account other patient-related factors, such as patients' preferences and other underlying physical conditions when making treatment decisions.

Summary: Background: Childhood poverty is associated with elevated later risks for self-directed and externalised violence, but how risks are modified by parental socioeconomic mobility remains unclear. We investigated parental income trajectories during childhood and subsequent risks of self-harm and violent criminality in young adulthood. Methods: Using Danish national registers, we delineated a nested case-control study of Danish citizens born from Jan 1, 1982, to Dec 31, 2000, with first hospital-treated self-harm episodes and first violent crime convictions at ages 15–33 years. Each case was matched on age and gender to 25 randomly selected controls. Parental income was assessed in birth-year and at ages 5 years, 10 years, and 15 years. We considered parental age, the child's number of siblings, parental mental health, and parental education to be covariates. We estimated incidence rate ratios (IRRs) by conditional logistic regression inherently adjusted for age, gender, and calendar year; we then made additional adjustments for the covariates considered. Findings: We identified 21 267 first episodes of hospital-treated self-harm, to which we matched 531 675 controls, and 23 724 first violent crime convictions, to which we matched 593 100 controls. We observed inverse relationships between parental income and risks for the two outcomes for each of the ages parental income was measured. The longer a child lived in poorer circumstances, the higher their subsequent risks for self-harm and violent criminality, and vice versa for time spent living in affluent conditions. Associations were stronger for violent criminality than for self-harm. Compared with individuals who were born and remained in the most affluent families, all other income trajectories were associated with elevated risks for both outcomes. Those who remained in the least affluent quintile showed the highest risks for self-harm (IRR 7·2, 95% CI 6·6–7·9; 1174 [6%] cases) and for violent criminality (IRR 13·0; 95% CI 11·9–14·1; 1640 [7%] cases). The risk patterns were attenuated, but essentially persisted, after covariate adjustment. For any parental income level at birth, being upwardly mobile was associated with lower risk compared with downward mobility. Interpretation: Parental income represents a multitude of unmeasured familial sociodemographic indices. Tackling the causes of inequality and associated psychosocial and sociocultural challenges to enable upwards socioeconomic mobility could potentially reduce risks for self-directed and externalised violence. Funding: European Research Council.

Formal decision-analytic methods can be used to frame disease control problems, the first step of which is to define a clear and specific objective. We demonstrate the imperative of framing clearly-defined management objectives in finding optimal control actions for control of disease outbreaks. We illustrate an analysis that can be applied rapidly at the start of an outbreak when there are multiple stakeholders involved with potentially multiple objectives, and when there are also multiple disease models upon which to compare control actions. The output of our analysis frames subsequent discourse between policy-makers, modellers and other stakeholders, by highlighting areas of discord among different management objectives and also among different models used in the analysis. We illustrate this approach in the context of a hypothetical foot-and-mouth disease (FMD) outbreak in Cumbria, UK using outputs from five rigorously-studied simulation models of FMD spread. We present both relative rankings and relative performance of controls within each model and across a range of objectives. Results illustrate how control actions change across both the base metric used to measure management success and across the statistic used to rank control actions according to said metric. This work represents a first step towards reconciling the extensive modelling work on disease control problems with frameworks for structured decision making.

Numerical models for simulating outbreaks of infectious diseases are powerful tools for informing surveillance and control strategy decisions. However, large-scale spatially explicit models can be limited by the amount of computational resources they require, which poses a problem when multiple scenarios need to be explored to provide policy recommendations. We introduce an easily implemented method that can reduce computation time in a standard Susceptible-Exposed-Infectious-Removed (SEIR) model without introducing any further approximations or truncations. It is based on a hierarchical infection process that operates on entire groups of spatially related nodes (cells in a grid) in order to efficiently filter out large volumes of susceptible nodes that would otherwise have required expensive calculations. After the filtering of the cells, only a subset of the nodes that were originally at risk are then evaluated for actual infection. The increase in efficiency is sensitive to the exact configuration of the grid, and we describe a simple method to find an estimate of the optimal configuration of a given landscape as well as a method to partition the landscape into a grid configuration. To investigate its efficiency, we compare the introduced methods to other algorithms and evaluate computation time, focusing on simulated outbreaks of foot-and-mouth disease (FMD) on the farm population of the USA, the UK and Sweden, as well as on three randomly generated populations with varying degree of clustering. The introduced method provided up to 500 times faster calculations than pairwise computation, and consistently performed as well or better than other available methods. This enables large scale, spatially explicit simulations such as for the entire continental USA without sacrificing realism or predictive power.

Background: Development of a better understanding of subsequent pathways for individuals who experienced trauma during childhood might usefully inform clinicians and public health professionals regarding the causes of self-harm and interpersonal violence. We aimed to examine these risks during late adolescence and early adulthood among people admitted to hospital following injuries or poisonings during their childhood. Methods: This national cohort study included Danish people born between Jan 1, 1977, and Dec 31, 1997, and was linked to the National Patient Register and Psychiatric Central Research Register to identify all people exposed to hospital admissions for injuries or poisonings due to self-harm, interpersonal violence, or accidents before their 15th birthday. Linkage to these two registers and to the National Crime Register enabled ascertainment of self-harm and violent offending, respectively, as adverse outcomes at ages 15–35 years. Sex-specific incidence rate ratios (IRRs; relative risks) and cumulative incidence percentage values (absolute risks) were estimated. The confounding influence of parental socioeconomic status was also explored. Findings: 1 087 672 Danish people were included in this study. The prevalence of any trauma-related hospital admission was 10% (105 753 per 1 087 672; males: 64 454 [11%]; females: 44 299 [8%]) and for both sexes, accident was by far the most prevalent of the categories assessed (males: 59 011 [11%]; females: 40 756 [8%]). Similar patterns of increased risk for self-harm and violent criminality were observed in both sexes, although the IRRs were consistently and significantly larger in women (self-harm: IRR 1·94 [95% CI 1·85–2·02]; violent criminality: 2·16 [1·97–2·36]) than in men (self-harm: 1·61 [1·53–1·69]; violent criminality: 1·58 [1·53–1·63]). Confounding by parental socioeconomic status explained little of the increased risks observed. For young adult men, the highest absolute risk observed was for violent offending among individuals admitted to hospital for interpersonal violence injury during childhood (cumulative incidence 25·0% [95% CI 21·2–28·9]). For young adult women, absolute risk was highest for repeat self-harm among those admitted to hospital following self-harm during childhood (cumulative incidence 21·4% [95% CI 19·8–23·1]). More frequent trauma-related hospital admissions in childhood, and being admitted multiple times for more than one reason, conferred substantial risk increases among young people, with especially steep gradients of this nature observed among women. Interpretation: Trauma-related hospital admission early in life could be a useful marker for childhood distress that subsequently predicts internalised and externalised destructive behaviours among youths and young adults and might provide a timely opportunity for initiating family-oriented interventions. Funding: European Research Council.

Gram-negative bacteria have a highly evolved cell wall with two membranes composed of complex arrays of integral and peripheral proteins, as well as phospholipids and glycolipids. In order to sense changes in, respond to, and exploit their environmental niches, bacteria rely on structures assembled into or onto the outer membrane. Protein secretion across the cell wall is a key process in virulence and other fundamental aspects of bacterial cell biology. The final stage of protein secretion in Gram-negative bacteria, translocation across the outer membrane, is energetically challenging so sophisticated nanomachines have evolved to meet this challenge. Advances in fluorescence microscopy now allow for the direct visualization of the protein secretion process, detailing the dynamics of (i) outer membrane biogenesis and the assembly of protein secretion systems into the outer membrane, (ii) the spatial distribution of these and other membrane proteins on the bacterial cell surface, and (iii) translocation of effector proteins, toxins and enzymes by these protein secretion systems. Here we review the frontier research imaging the process of secretion, particularly new studies that are applying various modes of super-resolution microscopy.

Migratory waterfowl are often viewed as vehicles for the global spread of influenza A viruses (IAVs), with mallards (Anas platyrhynchos) implicated as particularly important reservoir hosts. The physical demands and energetic costs of migration have been shown to influence birds' body condition; poorer body condition may suppress immune function and affect the course of IAV infection. Our study evaluated the impact of body condition on immune function and viral shedding dynamics in mallards naturally exposed to an H9 IAV, and then secondarily exposed to an H4N6 IAV. Mallards were divided into three treatment groups of 10 birds per group, with each bird's body condition manipulated as a function of body weight by restricting food availability to achieve either a -10%, -20%, or control body weight class. We found that mallards exhibit moderate heterosubtypic immunity against an H4N6 IAV infection after an infection from an H9 IAV, and that body condition did not have an impact on shedding dynamics in response to a secondary exposure. Furthermore, body condition did not affect aspects of the innate and adaptive immune system, including the acute phase protein haptoglobin, heterophil/lymphocyte ratios, and antibody production. Contrary to recently proposed hypotheses and some experimental evidence, our data do not support relationships between body condition, infection and immunocompetence following a second exposure to IAV in mallards. Consequently, while annual migration may be a driver in the maintenance and spread of IAVs, the energetic demands of migration may not affect susceptibility in mallards.

A considerable amount of disease is transmitted from animals to humans and many of these zoonoses are neglected tropical diseases. As outbreaks of SARS, avian influenza and Ebola have demonstrated, however, zoonotic diseases are serious threats to global public health and are not just problems confined to remote regions. There are two fundamental, and poorly studied, stages of zoonotic disease emergence: 'spillover', i.e. transmission of pathogens from animals to humans, and 'stuttering transmission', i.e. when limited human-to-human infections occur, leading to self-limiting chains of transmission. We developed a transparent, theoretical framework, based on a generalization of Poisson processes with memory of past human infections, that unifies these stages. Once we have quantified pathogen dynamics in the reservoir, with some knowledge of the mechanism of contact, the approach provides a tool to estimate the likelihood of spillover events. Comparisons with independent agent-based models demonstrates the ability of the framework to correctly estimate the relative contributions of human-to-human vs animal transmission. As an illustrative example, we applied our model to Lassa fever, a rodent-borne, viral haemorrhagic disease common in West Africa, for which data on human outbreaks were available. The approach developed here is general and applicable to a range of zoonoses. This kind of methodology is of crucial importance for the scientific, medical and public health communities working at the interface between animal and human diseases to assess the risk associated with the disease and to plan intervention and appropriate control measures. The Lassa case study revealed important knowledge gaps, and opportunities, arising from limited knowledge of the temporal patterns in reporting, abundance of and infection prevalence in, the host reservoir.

Habitat quality plays an important role in the dynamics and stability of wildlife metapopulations. However, the benefits of high-quality habitat may be modulated by the presence of an environmentally persistent pathogen. In some cases, the presence of environmental pathogen reservoirs on high-quality habitat may lead to the creation of ecological traps, wherein host individuals preferentially colonize high-quality habitat, but are then exposed to increased infection risk and disease-induced mortality. We explored this possibility through the development of a stochastic patch occupancy model, where we varied the pathogen’s virulence, transmission rate and environmental persistence as well as the distribution of habitat quality in the host metapopulation. This model suggests that for pathogens with intermediate levels of spread, high-quality habitat can serve as an ecological trap, and can be detrimental to host persistence relative to low-quality habitat. This inversion of the relative roles of high- and low-quality habitat highlights the importance of considering the interaction between spatial structure and pathogen transmission when managing wildlife populations exposed to an environmentally persistent pathogen.

Immigrant populations in western societies have grown in their size and diversity yet evidence is incomplete for their risks of suicidality and criminal violence. We examined these correlated harmful behaviours in a national cohort.(i) Compare absolute risk between first and second generation immigrants, foreign-born adoptees and native Danes by plotting cumulative incidence curves to onset of early middle age; (ii) estimate sex-specific relative risks for these immigrant type subgroups vs. native Danes; (iii) examine effect modification by higher vs. lower socio-economic status.In a cohort of over two million persons, attempted suicides and violent crimes were investigated using data from multiple interlinked registers. We plotted sex-specific cumulative incidence curves and estimated incidence rate ratios.In the whole study cohort, 1414 people died by suicide, 46,943 attempted suicide, and 51,344 were convicted of committing a violent crime. Among all immigrant subgroups combined, compared with native Danes, relative risk of attempted suicide was greater in female immigrants (incidence rate ratio, 1.59; 95% confidence interval: CI 1.54-1.64) than in male immigrants (1.26; CI 1.20-1.32), and vice versa for relative risk of violent offending in male immigrants (2.36; CI 2.31-2.42) than in female immigrants (1.74; CI 1.62-1.87). Risk for both adverse outcomes was significantly elevated in virtually every gender-specific immigrant type subgroup examined. Violent crime risk was markedly raised in first generation immigrant males and in the Danish born male children of two immigrant parents. However, male immigrants of lower social status had lower risk of attempted suicide than their native Danish peers.Young immigrants of both first and second generation status face serious challenges and vulnerabilities that western societies need to urgently address. Relative risk patterns for these adverse outcomes vary greatly between the genders and also by socioeconomic status. This high degree of heterogeneity points to the existence of modifiable factors that are amenable to positive change and a potential for effective intervention.

The Gram-negative bacterial pathogen Klebsiella pneumoniae forms biofilms to facilitate colonization of biotic and abiotic surfaces. The formation of biofilms by K. pneumoniae requires the expression of type 3 fimbriae: elongate proteinaceous filaments extruded by a chaperone-usher system in the bacterial outer membrane. The expression of the mrkABCDF cluster that encodes this fimbrial system is strongly positively regulated by MrkH, a transcriptional activator that responds to the second messenger, c-di-GMP. In this study, we analyzed the mechanism by which the MrkH protein activates transcriptional initiation from the mrkA promoter. A mutational analysis supported by electrophoretic mobility shift assays demonstrated that a 12-bp palindromic sequence (the MrkH box) centered at -78.5 is the binding site of MrkH. Deletion of half a turn, but not a full turn, of DNA located between the MrkH box and the mrkA promoter destroyed the ability of MrkH to activate mrkA transcription. In addition, a 10-bp AT-rich sequence (the UP element) centered at -63.5 contributed significantly to MrkH-dependent mrkA transcription. In vivo analysis of rpoA mutants showed that the R265 and E273 determinants in the C-terminal domain of RNA polymerase α subunit are needed for MrkH-mediated activation of mrkA transcription. Furthermore, results from mutagenesis of the mrkH gene suggest that the N-terminal region of the protein is involved in transcriptional activation. Taken together, our results suggest that MrkH activates mrkA expression by interacting directly with RNA polymerase, to overcome the inefficient transcriptional initiation caused by the presence of defective core promoter elements.

Networks are rarely completely observed and prediction of unobserved edges is an important problem, especially in disease spread modeling where networks are used to represent the pattern of contacts. We focus on a partially observed cattle movement network in the U.S. and present a method for scaling up to a full network based on bayesian inference, with the aim of informing epidemic disease spread models in the United States. The observed network is a 10% state stratified sample of Interstate Certificates of Veterinary Inspection that are required for interstate movement; describing approximately 20,000 movements from 47 of the contiguous states, with origins and destinations aggregated at the county level. We address how to scale up the 10% sample and predict unobserved intrastate movements based on observed movement distances. Edge prediction based on a distance kernel is not straightforward because the probability of movement does not always decline monotonically with distance due to underlying industry infrastructure. Hence, we propose a spatially explicit model where the probability of movement depends on distance, number of premises per county and historical imports of animals. Our model performs well in recapturing overall metrics of the observed network at the node level (U.S. counties), including degree centrality and betweenness; and performs better compared to randomized networks. Kernel generated movement networks also recapture observed global network metrics, including network size, transitivity, reciprocity, and assortativity better than randomized networks. In addition, predicted movements are similar to observed when aggregated at the state level (a broader geographic level relevant for policy) and are concentrated around states where key infrastructures, such as feedlots, are common. We conclude that the method generally performs well in predicting both coarse geographical patterns and network structure and is a promising method to generate full networks that incorporate the uncertainty of sampled and unobserved contacts.

Integrating evidence from multiple domains is useful in prioritizing disease candidate genes for subsequent testing. We ranked all known human genes (n=3819) under linkage peaks in the Irish Study of High-Density Schizophrenia Families using three different evidence domains: 1) a meta-analysis of microarray gene expression results using the Stanley Brain collection, 2) a schizophrenia protein-protein interaction network, and 3) a systematic literature search. Each gene was assigned a domain-specific p-value and ranked after evaluating the evidence within each domain. For comparison to this ranking process, a large-scale candidate gene hypothesis was also tested by including genes with Gene Ontology terms related to neurodevelopment. Subsequently, genotypes of 3725 SNPs in 167 genes from a custom Illumina iSelect array were used to evaluate the top ranked vs. hypothesis selected genes. Seventy-three genes were both highly ranked and involved in neurodevelopment (category 1) while 42 and 52 genes were exclusive to neurodevelopment (category 2) or highly ranked (category 3), respectively. The most significant associations were observed in genes PRKG1, PRKCE, and CNTN4 but no individual SNPs were significant after correction for multiple testing. Comparison of the approaches showed an excess of significant tests using the hypothesis-driven neurodevelopment category. Random selection of similar sized genes from two independent genome-wide association studies (GWAS) of schizophrenia showed the excess was unlikely by chance. In a further meta-analysis of three GWAS datasets, four candidate SNPs reached nominal significance. Although gene ranking using integrated sources of prior information did not enrich for significant results in the current experiment, gene selection using an a priori hypothesis (neurodevelopment) was superior to random selection. As such, further development of gene ranking strategies using more carefully selected sources of information is warranted.

An ability to forecast the prevalence of specific subtypes of avian influenza viruses (AIV) in live-bird markets would facilitate greatly the implementation of preventative measures designed to minimize poultry losses and human exposure. The minimum requirement for developing predictive quantitative tools is surveillance data of AIV prevalence sampled frequently over several years. Recently, a 4-year time series of monthly sampling of hemagglutinin subtypes 1-13 in ducks, chickens and quail in live-bird markets in southern China has become available. We used these data to investigate whether a simple statistical model, based solely on historical data (variables such as the number of positive samples in host X of subtype Y time t months ago), could accurately predict prevalence of H5 and H9 subtypes in chickens. We also examined the role of ducks and quail in predicting prevalence in chickens within the market setting because between-species transmission is thought to occur within markets but has not been measured. Our best statistical models performed remarkably well at predicting future prevalence (pseudo-R(2) = 0.57 for H9 and 0.49 for H5), especially considering the multi-host, multi-subtype nature of AIVs. We did not find prevalence of H5/H9 in ducks or quail to be predictors of prevalence in chickens within the Chinese markets. Our results suggest surveillance protocols that could enable more accurate and timely predictive statistical models. We also discuss which data should be collected to allow the development of mechanistic models.

The Mediterranean Sea provides habitat for globally threatened cetaceans. The Hellenic Trench is an Important Marine Mammal Area, providing core habitat for sperm whales Physeter macrocephalus and Cuvier’s beaked whales Ziphius cavirostris. Surveys have characterized distributions of these species in near-shore areas (

There is an unmet need to monitor human and natural environments for substances that are intentionally or unintentionally introduced. A long-sought goal is to adapt plants to sense and respond to specific substances for use as environmental monitors. Computationally re-designed periplasmic binding proteins (PBPs) provide a means to design highly sensitive and specific ligand sensing capabilities in receptors. Input from these proteins can be linked to gene expression through histidine kinase (HK) mediated signaling. Components of HK signaling systems are evolutionarily conserved between bacteria and plants. We previously reported that in response to cytokinin-mediated HK activation in plants, the bacterial response regulator PhoB translocates to the nucleus and activates transcription. Also, we previously described a plant visual response system, the de-greening circuit, a threshold sensitive reporter system that produces a visual response which is remotely detectable and quantifiable.We describe assembly and function of a complete synthetic signal transduction pathway in plants that links input from computationally re-designed PBPs to a visual response. To sense extracellular ligands, we targeted the computational re-designed PBPs to the apoplast. PBPs bind the ligand and develop affinity for the extracellular domain of a chemotactic protein, Trg. We experimentally developed Trg fusions proteins, which bind the ligand-PBP complex, and activate intracellular PhoR, the HK cognate of PhoB. We then adapted Trg-PhoR fusions for function in plants showing that in the presence of an external ligand PhoB translocates to the nucleus and activates transcription. We linked this input to the de-greening circuit creating a detector plant.Our system is modular and PBPs can theoretically be designed to bind most small molecules. Hence our system, with improvements, may allow plants to serve as a simple and inexpensive means to monitor human surroundings for substances such as pollutants, explosives, or chemical agents.

Individuals with schizophrenia tend to be heavy smokers and are at high risk for tobacco dependence. However, the nature of the comorbidity is not entirely clear. We previously reported evidence for association of schizophrenia with SNPs and SNP haplotypes in a region of chromosome 5q containing the SPEC2, PDZ-GEF2 and ACSL6 genes. In this current study, analysis of the control subjects of the Molecular Genetics of Schizophrenia (MGS) sample showed similar pattern of association with number of cigarettes smoked per day (numCIG) for the same region. To further test if this locus is associated with tobacco smoking as measured by numCIG and FTND, we conducted replication and meta-analysis in 12 independent samples (n>16,000) for two markers in ACSL6 reported in our previous schizophrenia study. In the meta-analysis of the replication samples, we found that rs667437 and rs477084 were significantly associated with numCIG (p = 0.00038 and 0.00136 respectively) but not with FTND scores. We then used in vitro and in vivo techniques to test if nicotine exposure influences the expression of ACSL6 in brain. Primary cortical culture studies showed that chronic (5-day) exposure to nicotine stimulated ACSL6 mRNA expression. Fourteen days of nicotine administration via osmotic mini pump also increased ACSL6 protein levels in the prefrontal cortex and hippocampus of mice. These increases were suppressed by injection of the nicotinic receptor antagonist mecamylamine, suggesting that elevated expression of ACSL6 requires nicotinic receptor activation. These findings suggest that variations in the ACSL6 gene may contribute to the quantity of cigarettes smoked. The independent associations of this locus with schizophrenia and with numCIG in non-schizophrenic subjects suggest that this locus may be a common liability to both conditions.

Host populations for the plague bacterium, Yersinia pestis, are highly variable in their response to plague ranging from near deterministic extinction (i.e., epizootic dynamics) to a low probability of extinction despite persistent infection (i.e., enzootic dynamics). Much of the work to understand this variability has focused on specific host characteristics, such as population size and resistance, and their role in determining plague dynamics. Here, however, we advance the idea that the relative importance of alternative transmission routes may vary causing shifts from epizootic to enzootic dynamics. We present a model that incorporates host and flea ecology with multiple transmission hypotheses to study how transmission shifts determine population responses to plague. Our results suggest enzootic persistence relies on infection of an off-host flea reservoir and epizootics rely on transiently maintained flea infection loads through repeated infectious feeds by fleas. In either case, early-phase transmission by fleas (i.e., transmission immediately following an infected blood meal) has been observed in laboratory studies, and we show that it is capable of driving plague dynamics at the population level. Sensitivity analysis of model parameters revealed that host characteristics (e.g., population size and resistance) vary in importance depending on transmission dynamics, suggesting that host ecology may scale differently through different transmission routes enabling prediction of population responses in a more robust way than using either host characteristics or transmission shifts alone.

The responses of the reindeer lichens (Cladina stellaris, C. rangiferina, and C. mitis) to logging and fire were compared in lichen-rich forest stands in northwestern Ontario. In the summer of 1992, reindeer lichen cover, in total and by species, was visually estimated and detailed notes were taken on reindeer lichen conditions, modes of reproduction, and substrate use on 34 undisturbed, burned, or logged sites. While virtually no reindeer lichens survived forest fire, much of the reindeer lichen cover remained after logging. Reindeer lichen cover increased with time since fire. Total reindeer lichen cover was not correlated with time since logging. Fragment growth was found to be an important mode of reproduction on logged sites, and occurred with greater frequency on logged sites than on burned sites. Colonization of organic substrates by reindeer lichens was observed on both logged and burned sites.

Few studies have examined the genetic population structure of vector-borne microparasites in wildlife, making it unclear how much these systems can reveal about the movement of their associated hosts. This study examined the complex host–vector–microbe interactions in a system of bats, wingless ectoparasitic bat flies (Nycteribiidae), vector-borne microparasitic bacteria (Bartonella) and bacterial endosymbionts of flies (Enterobacterales) across an island chain in the Gulf of Guinea, West Africa. Limited population structure was found in bat flies and Enterobacterales symbionts compared to that of their hosts. Significant isolation by distance was observed in the dissimilarity of Bartonella communities detected in flies from sampled populations of Eidolon helvum bats. These patterns indicate that, while genetic dispersal of bats between islands is limited, some non-reproductive movements may lead to the dispersal of ectoparasites and associated microbes. This study deepens our knowledge of the phylogeography of African fruit bats, their ectoparasites and associated bacteria. The results presented could inform models of pathogen transmission in these bat populations and increase our theoretical understanding of community ecology in host–microbe systems.

New antimalarial drug candidates that act via novel mechanisms are urgently needed to combat malaria drug resistance. Here, we describe the multi-omic chemical validation of Plasmodium M1 alanyl metalloaminopeptidase as an attractive drug target using the selective inhibitor, MIPS2673. MIPS2673 demonstrated potent inhibition of recombinant Plasmodium falciparum (PfA-M1) and Plasmodium vivax (PvA-M1) M1 metalloaminopeptidases, with selectivity over other Plasmodium and human aminopeptidases, and displayed excellent in vitro antimalarial activity with no significant host cytotoxicity. Orthogonal label-free chemoproteomic methods based on thermal stability and limited proteolysis of whole parasite lysates revealed that MIPS2673 solely targets PfA-M1 in parasites, with limited proteolysis also enabling estimation of the binding site on PfA-M1 to within ~5 Å of that determined by X-ray crystallography. Finally, functional investigation by untargeted metabolomics demonstrated that MIPS2673 inhibits the key role of PfA-M1 in haemoglobin digestion. Combined, our unbiased multi-omic target deconvolution methods confirmed the on-target activity of MIPS2673, and validated selective inhibition of M1 alanyl metalloaminopeptidase as a promising antimalarial strategy.

ABSTRACTThis paper assesses the relationship between economic resilience in English regions and the allocation of the UK government’s Community Renewal Fund (CRF). The CRF is part of the government’s ‘Levelling Up’ agenda to address place-based inequalities. Economic resilience is measured using a composite index comprising productivity, skills, unemployment, population density and household income. Data were obtained for the five indicators at local authority (LA) level in England. Regional resilience scores were produced by calculating the weighted mean score of the constituent LAs. Regional resilience values were used to generate an ‘expected share’ funding allocation, which was compared with the actual allocation using differences and correlation. Regional resilience scores ranged from 28.5 (North East) to 66.6 (London). A total of £125.56 million was allocated in the first round of the CRF. All regions in the North received less than their expected share allocation of the CRF, with the least resilient region in England (North East) receiving £13.4 million less. The South West received £9.9 million more than their expected share. All regions in the North of England received less than their expected share allocation of the CRF. There was no significant correlation between resilience values and CRF allocations (r = −0.16, p = 0.68). The current method for CRF allocation may therefore widen existing inequalities rather than ‘level up’.

Introduction: Genetic factors impact alcohol consumption and use disorder (AUD), with large-scale genome-wide association studies (GWAS) identifying numerous associated variants. Aggregate genetic methods in combination with important environmental factors (e.g., interpersonal trauma [IPT]) can be applied to expand our understanding of the ways by which genetic and environmental variables work together to influence alcohol consumption and disordered use. The present study aimed to detail the relationships between genome-wide polygenic scores (PGS) for alcohol phenotypes (i.e., alcohol consumption and AUD status) and IPT exposure as well as the interaction between them across ancestry.Methods: Data were drawn from the Spit for Science (S4S) study, a US college student population, where participants reported on IPT exposure prior to college and alcohol consumption and problems during college (N = 9,006; ancestry: 21.3% African [AFR], 12.5% Admixed Americas [AMR], 9.6% East Asian [EAS], 48.1% European [EUR], 8.6% South Asian [SAS]). Two trans-ancestry PGS were constructed, one for alcohol consumption and another for AUD, using large-scale GWAS summary statistics from multiple ancestries weighted using PRS-CSx. Regression models were applied to test for the presence of associations between alcohol-PGS and IPT main and interaction effects.Results: In the meta-analysis across ancestry groups, IPT exposure and PGS were significantly associated with alcohol consumption (βIPT = 0.31, PIPT = 0.0002; βPGS = 0.09, PPGS = 0.004) and AUD (ORIPT = 1.12, PIPT = 3.5 × 10−8; ORPGS = 1.02, PPGS = 0.002). No statistically significant interactions were detected between IPT and sex nor between IPT and PGS. When inspecting ancestry specific results, the alcohol consumption-PGS and AUD-PGS were only statistically significant in the EUR ancestry group (βPGS = 0.09, PPGS = 0.04; ORPGS = 1.02, PPGS = 0.022, respectively).Discussion: IPT exposure prior to college was strongly associated with alcohol outcomes in this college-age sample, which could be used as a preventative measure to identify students at high risk for problematic alcohol use. Additionally, results add to developing evidence of polygenic score association in meta-analyzed samples, highlighting the importance of continued efforts to increase ancestral representation in genetic studies and inclusive analytic approaches to increase the generalizability of results from genetic association studies.

Hybrid immunity (vaccination + natural infection) to SARS-CoV-2 provides superior protection to re-infection. We performed immune profiling studies during breakthrough infections in mRNA-vaccinated hamsters to evaluate hybrid immunity induction. The mRNA vaccine, BNT162b2, was dosed to induce binding antibody titers against ancestral spike, but inefficient serum virus neutralization of ancestral SARS-CoV-2 or variants of concern (VoCs). Vaccination reduced morbidity and controlled lung virus titers for ancestral virus and Alpha but allowed breakthrough infections in Beta, Delta and Mu-challenged hamsters. Vaccination primed for T cell responses that were boosted by infection. Infection back-boosted neutralizing antibody responses against ancestral virus and VoCs. Hybrid immunity resulted in more cross-reactive sera, reflected by smaller antigenic cartography distances. Transcriptomics post-infection reflects both vaccination status and disease course and suggests a role for interstitial macrophages in vaccine-mediated protection. Therefore, protection by vaccination, even in the absence of high titers of neutralizing antibodies in the serum, correlates with recall of broadly reactive B- and T-cell responses.

Outer membrane proteins (OMPs) are essential components of the outer membrane of Gram-negative bacteria. In terms of protein targeting and assembly, the current dogma holds that a ‘β-signal’ imprinted in the final β-strand of the OMP engages the β-barrel assembly machinery (BAM) complex to initiate membrane insertion and assembly of the OMP into the outer membrane. Here, we revealed an additional rule that signals equivalent to the β-signal are repeated in other, internal β-strands within bacterial OMPs, by peptidomimetic and mutational analysis. The internal signal is needed to promote the efficiency of the assembly reaction of these OMPs. BamD, an essential subunit of the BAM complex, recognizes the internal signal and the β-signal, arranging several β-strands and partial folding for rapid OMP assembly. The internal signal-BamD ordering system is not essential for bacterial viability but is necessary to retain the integrity of the outer membrane against antibiotics and other environmental insults.

Apicomplexan parasites that reside within a parasitophorous vacuole harbor a conserved pore-forming protein that enables small-molecule transfer across the parasitophorous vacuole membrane (PVM). In Plasmodium parasites that cause malaria, this nutrient pore is formed by EXP2 which can complement the function of GRA17, an orthologous protein in Toxoplasma gondii. EXP2, however, has an additional function in Plasmodium parasites, serving also as the pore-forming component of the protein export machinery PTEX. To examine how EXP2 can play this additional role, transgenes that encoded truncations of EXP2, GRA17, hybrid GRA17-EXP2, or EXP2 under the transcriptional control of different promoters were expressed in EXP2 knockdown parasites to determine which could complement EXP2 function. This revealed that EXP2 is a unique pore-forming protein, and its protein export role in P. falciparum cannot be complemented by T. gondii GRA17. This was despite the addition of the EXP2 assembly strand and part of the linker helix to GRA17, which are regions necessary for the interaction of EXP2 with the other core PTEX components. This indicates that the body region of EXP2 plays a critical role in PTEX assembly and/or that the absence of other T. gondii GRA proteins in P. falciparum leads to its reduced efficiency of insertion into the PVM and complementation potential. Altering the timing and abundance of EXP2 expression did not affect protein export but affected parasite viability, indicating that the unique transcriptional profile of EXP2 when compared to other PTEX components enables it to serve an additional role in nutrient exchange.

Abstract Angular limb deformity (ALD) affects many species of livestock and companion animals. The mechanisms of ALD development are not well understood, but previous research suggests the involvement of genetic risk factors. A case-control genome-wide association study (GWAS) was conducted with 40 ALD-affected and 302 unaffected Rambouillet rams and 40,945 single nucleotide polymorphisms (SNPs). Forelimbs of 6 ALD-affected rams were examined and diagnosed with osteochondrosis. Genome-wide or chromosome-wide significant SNPs were positioned exonic, intronic or within the 3′UTR of genes TSPAN18, NRG3 and NOVA2, respectively. These genes have previously described roles related to angiogenesis and osteoblast, osteoclast and chondrocyte proliferation and differentiation, which suggests the possibility for their involvement in the pathogenesis of osteochondrosis. Functional consequences of SNPs were evaluated through transcription factor binding site analysis, which predicted binding sites for transcription factors of known importance to bone growth, including SOX6, SOX9 and RUNX2. The identification of genetic risk factors for ALD may help to improve animal welfare and production in Rambouillet, a breed known to be at risk for ALD development. This study proposes genes TSPAN18, NRG3 and NOVA2 as targets for further research towards understanding the etiology of ALD in Rambouillet sheep.

IntroductionControl of zoonosis can benefit from geo-referenced procedures. Focusing on brucellosis, here the ability of two methods to distinguish disease dissemination patterns and promote cost-effective interventions was compared.MethodGeographical data on bovine, ovine and human brucellosis reported in the country of Georgia between 2014 and 2019 were investigated with (i) the Hot Spot (HS) analysis and (ii) a bio-geographical (BG) alternative.ResultsMore than one fourth of all sites reported cases affecting two or more species. While ruminant cases displayed different patterns over time, most human cases described similar geo-temporal features, which were associated with the route used by migrant shepherds. Other human cases showed heterogeneous patterns. The BG approach identified small areas with a case density twice as high as the HS method. The BG method also identified, in 2018, a 2.6–2.99 higher case density in zoonotic (human and non-human) sites than in non-zoonotic sites (which only reported cases affecting a single species) –a finding that, if corroborated, could support cost-effective policy-making.DiscussionThree dissemination hypotheses were supported by the data: (i) human cases induced by sheep-related contacts; (ii) human cases probably mediated by contaminated milk or meat; and (iii) cattle and sheep that infected one another. This proof-of-concept provided a preliminary validation for a method that may support cost-effective interventions oriented to control zoonoses. To expand these findings, additional studies on zoonosis-related decision-making are recommended.

Estimation and correlation of the Hildebrand solubility parameter (δ) of polymers and small molecules is a common practice in membrane material science and is accomplished by experimental and numerical routes. In this paper, we revisit, update, and compare both routes to enhance the accuracy in the determination of δ. Best practices for the experimental determination of polymer solubility parameters are provided, and the viability of Dynamic Light Scattering (DLS) was demonstrated as an alternative to conventional time- and material-consuming techniques, such as Ubbelohde viscometry and swelling measurements. Glassy and rubbery polymers, including high fractional free volume (FFV) microporous polymers such as PIM-1 and poly(1-trimethylsilyl-1-propyne) (PTMSP), are among the samples included in this study with great relevance to membrane science. In an attempt to enhance the accuracy of numerical estimate of polymer solubility parameters via the group contribution method, we provide updated group contribution parameters, along with their uncertainty, according to the technique recently reported by Smith et al. These updated group contribution parameters result in a mean absolute relative error of 9.0% in predicting the solubility parameter on a test set of 40 polymers, which is on par with the average 10% error reported previously. We also show, using machine learning techniques, that augmenting the group contribution model with extra parameters or non-linear relationships does not improve its accuracy. Results of the updated group contribution technique and dynamic light scattering measurements were compared to experimental viscometry on four test polymers, and the difference between the three techniques is compared.

Introduction: The availability of large-scale biobanks linking genetic data, rich phenotypes, and biological measures is a powerful opportunity for scientific discovery. However, real-world collections frequently have extensive missingness. While missing data prediction is possible, performance is significantly impaired by block-wise missingness inherent to many biobanks.Methods: To address this, we developed Missingness Adapted Group-wise Informed Clustered (MAGIC)-LASSO which performs hierarchical clustering of variables based on missingness followed by sequential Group LASSO within clusters. Variables are pre-filtered for missingness and balance between training and target sets with final models built using stepwise inclusion of features ranked by completeness. This research has been conducted using the UK Biobank (n > 500 k) to predict unmeasured Alcohol Use Disorders Identification Test (AUDIT) scores.Results: The phenotypic correlation between measured and predicted total score was 0.67 while genetic correlations between independent subjects was high >0.86.Discussion: Phenotypic and genetic correlations in real data application, as well as simulations, demonstrate the method has significant accuracy and utility for increasing power for genetic loci discovery.

Antibiotic resistance is driven by selection, but the degree to which a bacterial strain’s evolutionary history shapes the mechanism and strength of resistance remains an open question. Here, we reconstruct the genetic and evolutionary mechanisms of carbapenem resistance in a clinical isolate of Klebsiella quasipneumoniae. A combination of short- and long-read sequencing, machine learning, and genetic and enzymatic analyses established that this carbapenem-resistant strain carries no carbapenemase-encoding genes. Genetic reconstruction of the resistance phenotype confirmed that two distinct genetic loci are necessary in order for the strain to acquire carbapenem resistance. Experimental evolution of the carbapenem-resistant strains in growth conditions without the antibiotic revealed that both loci confer a significant cost and are readily lost by de novo mutations resulting in the rapid evolution of a carbapenem-sensitive phenotype. To explain how carbapenem resistance evolves via multiple, low-fitness single-locus intermediates, we hypothesised that one of these loci had previously conferred adaptation to another antibiotic. Fitness assays in a range of drug concentrations show how selection in the antibiotic ceftazidime can select for one gene (blaDHA-1) potentiating the evolution of carbapenem resistance by a single mutation in a second gene (ompK36). These results show how a patient’s treatment history might shape the evolution of antibiotic resistance and could explain the genetic basis of carbapenem-resistance found in many enteric-pathogens.