Capturing the time-varying drivers of an epidemic using stochastic dynamical systems

Epidemics are often modelled using non-linear dynamical systems observed through partial and noisy data. In this paper, we consider stochastic extensions in order to capture unknown influences (changing behaviors, public interventions, seasonal effects etc). These models assign diffusion processes to the time-varying parameters, and our inferential procedure is based on a suitably adjusted adaptive particle MCMC algorithm. The performance of the proposed computational methods is validated on simulated data and the adopted model is applied to the 2009 H1N1 pandemic in England. In addition to estimating the effective contact rate trajectories, the methodology is applied in real time to provide evidence in related public health decisions. Diffusion driven SEIR-type models with age structure are also introduced.Comment: 21 pages, 5 figure

Bayesian inference for partially observed stochastic differential equations driven by fractional Brownian motion

We consider continuous-time diffusion models driven by fractional Brownian motion. Observations are assumed to possess a nontrivial likelihood given the latent path. Due to the non-Markovian and high-dimensional nature of the latent path, estimating posterior expectations is computationally challenging. We present a reparameterization framework based on the Davies and Harte method for sampling stationary Gaussian processes and use it to construct a Markov chain Monte Carlo algorithm that allows computationally efficient Bayesian inference. The algorithm is based on a version of hybrid Monte Carlo simulation that delivers increased efficiency when used on the high-dimensional latent variables arising in this context. We specify the methodology on a stochastic volatility model, allowing for memory in the volatility increments through a fractional specification. The method is demonstrated on simulated data and on the S&P 500/VIX time series. In the latter case, the posterior distribution favours values of the Hurst parameter smaller than 1/2 , pointing towards medium-range dependence

Volatile compounds of some popular Mediterranean seafood species

The volatile compounds of highly commercialised fresh Mediterranean seafood species, including seven fish (sand-smelt Atherina boyeri, picarel Spicara smaris, hake Merluccius merluccius, pilchard Sardina pilchardus, bogue Boobps boops, anchovy Engraulis encrasicolus and striped-mullet Mullus barbatus), squid (Loligo vulgaris), shrimp (Parapenaeus longirostris) and mussel (Mytilus galloprovincialis), were evaluated by simultaneous steam distillation-extraction and subsequent GC-MS analysis. A total of 298 volatile compounds were detected. The mussels contained the highest total concentration of volatile compounds, while pilchard among fish species contained the highest number and concentrations of volatile compounds. Individual patterns of volatile compounds have been distinguished. The fish species when compared to the shellfish species studied, contained 6 to 30 times more 1-penten-3-ol, higher quantities of 2-ethylfuran, and 2,3-pentanedione, which was absent from the shellfish species. Pilchard is characterized by a high concentration of alcohols, shrimps by the high presence of amines and S-compounds, while mussels by high amounts of aldehydes, furans, and N-containing compounds (pyridine, pyrazines and pyrrols). The fatty acid-originating carbonyl compounds in fish seem to be related to the species’ fat content

Sutureless scleral-fixated intraocular lens: long-term outcomes

Background: The purpose of this study was to evaluate the long-term outcomes of sutureless scleral-fixated intraocular lens (SFIOL) implantation at a tertiary referral center. Methods: This retrospective observational study included 50 eyes of 43 consecutive patients who underwent sutureless SFIOL implantation by a single surgeon from January 2009 to December 2015. Indications for surgery were aphakia, dislocated intraocular lens (IOL), complicated cataract surgery (posterior capsule rupture, zonular dialysis, dropped nucleus), iris-clipped IOL with corneal decompensation, and lens with poor capsular support. Indication for surgery, visual acuity, ocular history, ocular comorbidities, intraoperative and postoperative complications, and the need for further surgery were analyzed. Results: The analysis conducted on 50 eyes from 43 patients with a mean ± standard deviation (SD) follow-up of 16.64 ± 9.34 months. Patients were 27 (63%) men and 16 (37%) women with a mean ± standard deviation (SD) age of 53.36 ± 22.45 years (range 8–90 years). Final visual acuity was 6/18 or better in 39 eyes. SFIOL was stable and well centered in 48 eyes. SFIOL dislocation was noted in 2 eyes, retinal detachment in 1 eye, and worsening of diabetic cystoid macular edema in 1 eye. Two patients with pre-existing corneal decompensation from complicated cataract surgery had worsening of their condition Conclusions: Sutureless SFIOL could be considered as a long-term option for the management of aphakia, dislocated IOL, and lens with poor capsular support. However, future studies with more subjects, longer follow-ups, and robust study design are needed to confirm the results of the present study

A Bayesian approach to estimate changes in condom use from limited human immunodeficiency virus prevalence data.

Evaluation of large-scale intervention programmes against human immunodeficiency virus (HIV) is becoming increasingly important, but impact estimates frequently hinge on knowledge of changes in behaviour such as the frequency of condom use over time, or other self-reported behaviour changes, for which we generally have limited or potentially biased data. We employ a Bayesian inference methodology that incorporates an HIV transmission dynamics model to estimate condom use time trends from HIV prevalence data. Estimation is implemented via particle Markov chain Monte Carlo methods, applied for the first time in this context. The preliminary choice of the formulation for the time varying parameter reflecting the proportion of condom use is critical in the context studied, because of the very limited amount of condom use and HIV data available. We consider various novel formulations to explore the trajectory of condom use over time, based on diffusion-driven trajectories and smooth sigmoid curves. Numerical simulations indicate that informative results can be obtained regarding the amplitude of the increase in condom use during an intervention, with good levels of sensitivity and specificity performance in effectively detecting changes. The application of this method to a real life problem demonstrates how it can help in evaluating HIV interventions based on a small number of prevalence estimates, and it opens the way to similar applications in different contexts

Effect of deprivation and ethnicity on primary macula-on retinal detachment repair success rate and clinical outcomes:A study of 568 patients

Purpose Socio-economic deprivation and ethnic variation have been frequently linked to poorer health outcomes. We collected a large series of primary macula-on rhegmatogenous retinal detachment (RRD) cases and analysed the effect of socio-economic deprivation and ethnicity on both six-month retinal re-detachment rate and visual outcomes. Materials and methods Retrospective consecutive case series of 568 patients attending Birmingham and Midlands Eye Centre from January 2017–2020. Multiple Indices of Deprivation (IMD) deciles were used for deprivation status and split to two groups: IMD-A (Decile 1–5) and IMD-B (Decile 6–10). The two largest subgroups of ethnicities were compared, White and South Asians (SA). Results We report an overall retinal re-detachment rate of 8.5%. IMD-A re-detached significantly more than IMD-B (11.2% vs 6.0% respectively, p = 0.034). No statistical significance was found between White and SA re-detachment rate (9.1% and 5.6% respectively, p = 0.604). SA median age significantly lower at 49 years (IQR: 37–61) compared to White patients at 57 years (IQR: 50–65) (p = Conclusion We demonstrated an increased retinal re-detachment rate in our more deprived patients according to IMD and a younger cohort of SA compared to White ethnicity. Further prospective studies are required to demonstrate the link between socio-economic deprivation and surgical success

Bayesian epidemic models for spatially aggregated count data

Epidemic data often possess certain characteristics, such as the presence of many zeros, the spatial nature of the disease spread mechanism, environmental noise, serial correlation and dependence on time varying factors. This paper addresses these issues via suitable Bayesian modelling. In doing so we utilise a general class of stochastic regression models appropriate for spatio-temporal count data with an excess number of zeros. The developed regression framework does incorporate serial correlation and time varying covariates through an Ornstein Uhlenbeck process formulation. In addition, we explore the effect of different priors, including default options and variations of mixtures of g-priors. The effect of different distance kernels for the epidemic model component is investigated. We proceed by developing branching process-based methods for testing scenarios for disease control, thus linking traditional epidemiological models with stochastic epidemic processes, useful in policy-focused decision making. The approach is illustrated with an application to a sheep pox dataset from the Evros region, Greece

Identification of novel filament-forming proteins in Saccharomyces cerevisiae and Drosophila melanogaster

A screen for GFP-tagged yeast proteins that can assemble into visible structures reveals four new filamentous structures in the cytoplasm formed by metabolic enzymes and translation factors

A Time Purified Separated Antiproton Beam At The AGS

Physic