Sampling constrained probability distributions using Spherical Augmentation

Statistical models with constrained probability distributions are abundant in machine learning. Some examples include regression models with norm constraints (e.g., Lasso), probit, many copula models, and latent Dirichlet allocation (LDA). Bayesian inference involving probability distributions confined to constrained domains could be quite challenging for commonly used sampling algorithms. In this paper, we propose a novel augmentation technique that handles a wide range of constraints by mapping the constrained domain to a sphere in the augmented space. By moving freely on the surface of this sphere, sampling algorithms handle constraints implicitly and generate proposals that remain within boundaries when mapped back to the original space. Our proposed method, called {Spherical Augmentation}, provides a mathematically natural and computationally efficient framework for sampling from constrained probability distributions. We show the advantages of our method over state-of-the-art sampling algorithms, such as exact Hamiltonian Monte Carlo, using several examples including truncated Gaussian distributions, Bayesian Lasso, Bayesian bridge regression, reconstruction of quantized stationary Gaussian process, and LDA for topic modeling.Comment: 41 pages, 13 figure

Between virus correlations in the outcome of infection across host species: Evidence of virus by host species interactions

This is the final version. Available from Wiley via the DOI in this record. Virus host shifts are a major source of outbreaks and emerging infectious diseases, and predicting the outcome of novel host and virus interactions remains a key challenge for virus research. The evolutionary relationships between host species can explain variation in transmission rates, virulence, and virus community composition between hosts, but it is unclear if correlations exist between related viruses in infection traits across novel hosts. Here, we measure correlations in viral load of four Cripavirus isolates across experimental infections of 45 Drosophilidae host species. We find positive correlations between every pair of viruses tested, suggesting that some host clades show broad susceptibility and could act as reservoirs and donors for certain types of viruses. Additionally, we find evidence of virus by host species interactions, highlighting the importance of both host and virus traits in determining the outcome of virus host shifts. Of the four viruses tested here, those that were more closely related tended to be more strongly correlated, providing tentative evidence that virus evolutionary relatedness may be a useful proxy for determining the likelihood of novel virus emergence, which warrants further research.Wellcome TrustRoyal SocietyNatural Environment Research Counci

Trust and transparency in times of crisis: Results from an online survey during the first wave (April 2020) of the COVID-19 epidemic in the UK

BACKGROUND: The success of a government's COVID-19 control strategy relies on public trust and broad acceptance of response measures. We investigated public perceptions of the UK government's COVID-19 response, focusing on the relationship between trust and perceived transparency, during the first wave (April 2020) of the COVID-19 pandemic in the United Kingdom. METHODS: Anonymous survey data were collected (2020-04-06 to 2020-04-22) from 9,322 respondents, aged 20+ using an online questionnaire shared primarily through Facebook. We took an embedded-mixed-methods approach to data analysis. Missing data were imputed via multiple imputation. Binomial & multinomial logistic regression were used to detect associations between demographic characteristics and perceptions or opinions of the UK government's response to COVID-19. Structural topic modelling (STM), qualitative thematic coding of sub-sets of responses were then used to perform a thematic analysis of topics that were of interest to key demographic groups. RESULTS: Most respondents (95.1%) supported government enforcement of behaviour change. While 52.1% of respondents thought the government was making good decisions, differences were apparent across demographic groups, for example respondents from Scotland had lower odds of responding positively than respondents in London. Higher educational levels saw decreasing odds of having a positive opinion of the government response and decreasing household income associated with decreasing positive opinion. Of respondents who thought the government was not making good decisions 60% believed the economy was being prioritised over people and their health. Positive views on government decision-making were associated with positive views on government transparency about the COVID-19 response. Qualitative analysis about perceptions of government transparency highlighted five key themes: (1) the justification of opacity due to the condition of crisis, (2) generalised mistrust of politics, (3) concerns about the role of scientific evidence, (4) quality of government communication and (5) questions about political decision-making processes. CONCLUSION: Our study suggests that trust is not homogenous across communities, and that generalised mistrust, concerns about the transparent use and communication of evidence and insights into decision-making processes can affect perceptions of the government's pandemic response. We recommend targeted community engagement, tailored to the experiences of different groups and a new focus on accountability and openness around how decisions are made in the response to the UK COVID-19 pandemic

Sex-dependent influence of endogenous estrogen in pulmonary hypertension

Rationale: The incidence of pulmonary arterial hypertension (PAH) is greater in women suggesting estrogens may play a role in the disease pathogenesis. Experimentally, in males exogenously administered estrogen can protect against PH; however in models that display female susceptibility estrogens may play a causative role. Objectives: To clarify the influence of endogenous estrogen and gender in PH and assess the therapeutic potential of a clinically available aromatase inhibitor. Methods: We interrogated the effect of reduced endogenous estrogen in males and females using the aromatase inhibitor, anastrozole, in two models of PH; the hypoxic mouse and Sugen 5416/hypoxic rat. We also determined the effects of gender on pulmonary expression of aromatase in these models and in lungs from PAH patients. Results: Anastrozole attenuated PH in both models studied, but only in females. To verify this effect was due to reduced estrogenic activity we confirmed that in hypoxic mice inhibition of estrogen receptor alpha also has a therapeutic effect specifically in females. Female rodent lung displays increased aromatase and decreased BMPR2 and Id1 expression compared to male. Anastrozole treatment reversed the impaired BMPR2 pathway in females. Increased aromatase expression was also detected in female human pulmonary artery smooth muscle cells compared to male. Conclusions: The unique phenotype of female pulmonary arteries facilitates the therapeutic effects of anastrozole in experimental PH confirming a role for endogenous estrogen in the disease pathogenesis in females and suggests aromatase inhibitors may have therapeutic potential

Child deaths due to injury in the four UK countries: a time trends study from 1980 to 2010

Injuries are an increasingly important cause of death in children worldwide, yet injury mortality is highly preventable. Determining patterns and trends in child injury mortality can identify groups at particularly high risk. We compare trends in child deaths due to injury in four UK countries, between 1980 and 2010

HEXACO Personality Factors and their Associations with Facebook use and Facebook Network Characteristics

Personality factors affect the properties of 'offline' social networks, but how they are associated with the structural properties of online networks is still unclear. We investigated how the six HEXACO personality factors (Honesty-Humility, Emotionality, Extraversion, Agreeableness, Conscientiousness and Openness to Experience) relate to Facebook use and three objectively measured Facebook network characteristics - network size, density, and number of clusters. Participants (n = 107, mean age = 20.6, 66% female) extracted their Facebook networks using the GetNet app, completed the 60-item HEXACO questionnaire and the Facebook Usage Questionnaire. Users high in Openness to Experience spent less time on Facebook. Extraversion was positively associated with network size (number of Facebook Friends). These findings suggest that some personality factors are associated with Facebook use and the size of Facebook networks, and that personality is an important influence on both online and offline sociality

Effects of preservation by ethanol on <scp>δ¹³C</scp> and <scp>δ¹⁵N</scp> of three tissues of the critically endangered <scp>European</scp> eel <i>Anguilla anguilla</i>

The temporal effects of ethanol preservation on the δ13C and δ15N values of tissues excised from European eel Anguilla anguilla were assessed. Preservation significantly enriched 13C values of fin and mucus but not dorsal muscle. The 13C enrichment occurred in the initial 15 days of preservation and was independent of initial eel mass. Tissue preservation effects on δ15N values were negligible. These tissue-specific isotopic shifts should be considered when ethanol-preserved eel samples are used

Diet of the South African large-spotted genet Genetta tigrina (Carnivora, Viverridae) in a coastal dune forest

We studied seasonal variations in the diet of the large-spotted genet Genetta tigrina Schreber, 1776 in the coastal dune forest of the Dwesa Nature Reserve, Eastern Cape Province, South Africa. The food items with the highest relative percentage occurrence were Coleoptera, Orthoptera and Mammalia. However, by volume they ate mostly grass then followed by Coleoptera and Orthoptera. Main prey items originated from the litter layer or low lying bushes, such as arachnids, insects, myriapods, and most mammals. The latter included ten rodent (main staple: Dendromus sp.), two golden mole and two shrew species, from 10–100 g mass. They were represented dependent on species density, but switching between seasons and habitats occupied. Birds appeared under-represented in the diet for a semi-arboreal carnivore, although this correlates with data from other studies. Remains of birds in the diet, however, peaked during winter and spring probably as a result of the main nesting period in spring. There were some variation in diet between habitats (riparian, forest and beach) and seasons. Our results show the South African large-spotted genet to have an opportunistic, generalist diet.NERC, Eastern Cape Parks, NRF, CI