Disruption and disease: How does population management affect disease risk in wild bird populations?

Despite the ubiquity of wildlife management, from reintroductions and supplemental feeding to culling and habitat destruction, very little is known of the effects of management practices on species’ social dynamics. Species’ social structure has the potential to affect not only behaviour and evolution but also the transmission of information or disease. Understanding the effects of population management on social behaviour and organisation is a key step in understanding these species’ ecology. This thesis examines the differences between individuals’ roles in the social structure and what this means for the transmission of disease. It demonstrates how similarity in movement behaviour scales with increasing social circles, how seasonality in movement and seasonality in association rates covary as well as detailing post-cull behavioural changes. It finds that there is the potential for certain individuals (most likely non-breeding individuals) to transmit infection far and wide. It reveals the similarities in movement behaviour and body condition that birds share with their pair and social group. It emphasises the importance of autumn and winter movement in the transmission of infectious disease and it follows the short- and long-term changes in social structure and movement behaviour following a cull. Cull survivors were observed to retain a higher proportion of associations with their previous associates and moved less far in the year following the cull than in the year preceding it. This is the first application of social network analysis to quantify social structure before and after culling. The findings suggest that culling an infected population may facilitate rather than constrain the transmission of disease

Prey body size mediates the predation risk associated with being "odd"

Despite selection pressures on prey animals to maintain phenotypically homogeneous groups, variation in phenotype within animal groups is commonly observed. Although many prey animals preferentially associate with size-matched individuals, a lack of preference or a preference for nonmatching group mates is also commonly observed. We suggest that the assortative response to predation risk may be mediated by body size because larger bodied prey may be at greater risk of predation than smaller bodied prey when in a mixed group due to their greater potential profitability. We test this idea by observing attacks by three-spine sticklebacks Gasterosteus aculeatus on mixed groups of large and small Daphnia magna prey. We find that smaller Daphnia are at greatest risk when they form the majority of the group, whereas larger Daphnia are at the greatest predation risk when they form the minority. Thus, we predict that both large and small prey should benefit by association with large prey, generating a potential conflict over group membership that may lead to the mixed phenotype groups we observe in nature

Unlocking the unsustainable rice-wheat system of Indian Punjab: Assessing alternatives to crop-residue burning from a systems perspective

Crop residue burning in Indian Punjab emits particulate matter with detrimental impacts on health, climate and that threaten agricultural production. Though legal and technological barriers to residue burning exist – and alternatives considered more profitable to farmers – residue burning continues. We review black carbon (BC) emissions from residue burning in Punjab, analyse social-ecological processes driving residue burning, and rice and wheat value-chains. Our aims are to a) understand system feedbacks driving agricultural practices in Punjab; b) identify systemic effects of alternatives to residue burning and c) identify companies and financial actors investing in agricultural production in Punjab. We find feedbacks locking the system into crop residue burning. The Government of India has greatest financial leverage and risk in the current system. Corporate stakeholders have little financial incentive to enact change, but sufficient stakes in the value chains to influence change. Agricultural policy changes are necessary to reduce harmful impacts of current practices, but insufficient to bringing about sustainability. Transformative changes will require crop diversification, circular business models and green financing. Intermediating financial institutions setting sustainability conditions on loans could leverage these changes. Sustainability requires the systems perspective we provide, to reconnect production with demand and with supporting environmental conditions

Unlocking the unsustainable rice-wheat system of Indian Punjab : assessing alternatives to crop-residue burning from a systems perspective

This work was funded by Formas (Project # 2018-01824), and through the generous support of the Erling-Persson Family Foundation to the Global Economic Dynamics and the Biosphere, the Royal Swedish Academy of Sciences, Sweden.Crop residue burning in Indian Punjab emits particulate matter with detrimental impacts on health, climate and that threaten agricultural production. Though legal and technological barriers to residue burning exist – and alternatives considered more profitable to farmers – residue burning continues. We review black carbon (BC) emissions from residue burning in Punjab, analyse social-ecological processes driving residue burning, and rice and wheat value-chains. Our aims are to a) understand system feedbacks driving agricultural practices in Punjab; b) identify systemic effects of alternatives to residue burning and c) identify companies and financial actors investing in agricultural production in Punjab. We find feedbacks locking the system into crop residue burning. The Government of India has greatest financial leverage and risk in the current system. Corporate stakeholders have little financial incentive to enact change, but sufficient stakes in the value chains to influence change. Agricultural policy changes are necessary to reduce harmful impacts of current practices, but insufficient to bringing about sustainability. Transformative changes will require crop diversification, circular business models and green financing. Intermediating financial institutions setting sustainability conditions on loans could leverage these changes. Sustainability requires the systems perspective we provide, to reconnect production with demand and with supporting environmental conditions.Publisher PDFPeer reviewe

Estimating the prevalence of problem drug use from drug-related mortality data.

BACKGROUND AND AIMS: Indirect estimation methods are required for estimating the size of populations where only a proportion of individuals are observed directly, such as problem drug users (PDUs). Capture-recapture and multiplier methods are widely used, but have been criticized as subject to bias. We propose a new approach to estimating prevalence of PDU from numbers of fatal drug-related poisonings (fDRPs) using linked databases, addressing the key limitations of simplistic 'mortality multipliers'. METHODS: Our approach requires linkage of data on a large cohort of known PDUs to mortality registers and summary information concerning additional fDRPs observed outside this cohort. We model fDRP rates among the cohort and assume that rates in unobserved PDUs are equal to rates in the cohort during periods out of treatment. Prevalence is estimated in a Bayesian statistical framework, in which we simultaneously fit regression models to fDRP rates and prevalence, allowing both to vary by demographic factors and the former also by treatment status. RESULTS: We report a case study analysis, estimating the prevalence of opioid dependence in England in 2008/09, by gender, age group and geographical region. Overall prevalence was estimated as 0.82% (95% credible interval = 0.74-0.94%) of 15-64-year-olds, which is similar to a published estimate based on capture-recapture analysis. CONCLUSIONS: Our modelling approach estimates prevalence from drug-related mortality data, while addressing the main limitations of simplistic multipliers. This offers an alternative approach for the common situation where available data sources do not meet the strong assumptions required for valid capture-recapture estimation. In a case study analysis, prevalence estimates based on our approach were surprisingly similar to existing capture-recapture estimates but, we argue, are based on a much more objective and justifiable modelling approach

Factors associated with early menarche: results from the French Health Behaviour in School-aged Children (HBSC) study

<p>Abstract</p> <p>Background</p> <p>Puberty is a transition period making physiological development a challenge adolescents have to face. Early pubertal development could be associated with higher risks of poor health. Our objective was to examine risk behaviours, physical and psychological determinants associated with early menarche (<11 years).</p> <p>Methods</p> <p>Early menarche was assessed in the Health Behaviour in School-aged Children French cross-sectional survey. Data were collected in 2006 by anonymous self-reported standardized questionnaire from a nationally representative sample of 1072 15 years old girls in school classrooms. Family environment, school experience, physical and psychological factors, risk behaviours (substance use and sexual initiation) were recorded. Logistic regression models were applied (analysing for crude and adjusted relationships between early menarche and risk behaviours controlled for family context).</p> <p>Results</p> <p>Median age at menarche was 13.0 years; 57 girls (5.3%) were early-matured. Controlled for familial environment, early menarche was associated with having had more than two life-drunkenness episodes (adjusted OR = 2.5 [1.3-4.6]), early sexual initiation (adjusted OR = 2.8 [1.3-6.0]) and overweight (adjusted OR = 7.3 [3.6-14.9]).</p> <p>Conclusion</p> <p>Early-maturing girls may affiliate with older adolescents, hence engage in risk behaviours linked to their appearance rather than their maturity level. Factors associated with early menarche highlight the need to focus attention on early-matured girls to prevent further health problems linked to risk behaviours.</p

Early Category-Specific Cortical Activation Revealed by Visual Stimulus Inversion

Visual categorization may already start within the first 100-ms after stimulus onset, in contrast with the long-held view that during this early stage all complex stimuli are processed equally and that category-specific cortical activation occurs only at later stages. The neural basis of this proposed early stage of high-level analysis is however poorly understood. To address this question we used magnetoencephalography and anatomically-constrained distributed source modeling to monitor brain activity with millisecond-resolution while subjects performed an orientation task on the upright and upside-down presented images of three different stimulus categories: faces, houses and bodies. Significant inversion effects were found for all three stimulus categories between 70–100-ms after picture onset with a highly category-specific cortical distribution. Differential responses between upright and inverted faces were found in well-established face-selective areas of the inferior occipital cortex and right fusiform gyrus. In addition, early category-specific inversion effects were found well beyond visual areas. Our results provide the first direct evidence that category-specific processing in high-level category-sensitive cortical areas already takes place within the first 100-ms of visual processing, significantly earlier than previously thought, and suggests the existence of fast category-specific neocortical routes in the human brain

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) Salmonella Typhi in sub-Saharan Africa. Here we present a phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolated between 2008-2015 in 11 sub-Saharan African countries, in context of the 2,057 global S. Typhi genomic framework. Despite the broad genetic diversity, the majority of organisms (225/249; 90%) belong to only three genotypes, 4.3.1 (H58) (99/249; 40%), 3.1.1 (97/249; 39%), and 2.3.2 (29/249; 12%). Genotypes 4.3.1 and 3.1.1 are confined within East and West Africa, respectively. MDR phenotype is found in over 50% of organisms restricted within these dominant genotypes. High incidences of MDR S. Typhi are calculated in locations with a high burden of typhoid, specifically in children aged <15 years. Antimicrobial stewardship, MDR surveillance, and the introduction of typhoid conjugate vaccines will be critical for the control of MDR typhoid in Africa

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant