Fast Predictive Image Registration

We present a method to predict image deformations based on patch-wise image appearance. Specifically, we design a patch-based deep encoder-decoder network which learns the pixel/voxel-wise mapping between image appearance and registration parameters. Our approach can predict general deformation parameterizations, however, we focus on the large deformation diffeomorphic metric mapping (LDDMM) registration model. By predicting the LDDMM momentum-parameterization we retain the desirable theoretical properties of LDDMM, while reducing computation time by orders of magnitude: combined with patch pruning, we achieve a 1500x/66x speed up compared to GPU-based optimization for 2D/3D image registration. Our approach has better prediction accuracy than predicting deformation or velocity fields and results in diffeomorphic transformations. Additionally, we create a Bayesian probabilistic version of our network, which allows evaluation of deformation field uncertainty through Monte Carlo sampling using dropout at test time. We show that deformation uncertainty highlights areas of ambiguous deformations. We test our method on the OASIS brain image dataset in 2D and 3D

Threshold photoelectron photoion coincidence spectroscopy of trichloroethene and tetrachloroethene

The threshold photoelectron, the threshold photoelectron photoion coincidence and ion breakdown spectra of trichloroethene and tetrachloroethene have been recorded from 9 – 22 eV. Comparisons with the equivalent data for the three dichloroethene molecules and theoretical calculations highlight the nature of the orbitals involved during photoionisation in this energy range. The ground electronic state of C$_2$HCl$_3^+$ (C$_2$Cl$_4^+$) is bound, with excited valence states dissociating to C$_2$HCl$_2^+$ (C$_2$Cl$_3^+$) and C$_2$HCl$^+$ (C$_2$Cl$_2^+$). Appearance energies suggest that C$_2$HCl$^+$ forms from C$_2$HCl$_3^+$ by loss of two chlorine atoms, whereas C$_2$Cl$_2^+$ forms from C$_2$Cl$_4^+$ by loss of a Cl$_2$ molecule. The translational kinetic energy release into C$_2$HCl$_2^+$ (C$_2$Cl$_3^+$) + Cl is determined as a function of energy. In both cases, the fraction of the available energy released into translational energy of the two products decreases as the photon energy increases

Historical processes and contemporary anthropogenic activities influence genetic population dynamics of Nassau grouper (Epinephelus striatus) within The Bahamas

This is the final version of the article. Available from Frontiers Media via the DOI in this record.Severe declines of endangered Nassau grouper (Epinephelus striatus) across The Bahamas and Caribbean have spurred efforts to improve their fisheries management and population conservation. The Bahamas is reported to hold the majority of fish spawning aggregations for Nassau grouper, however, the status and genetic population structure of fish within the country is largely unknown, presenting a major knowledge gap for their sustainable management. Between August 2014-February 2017, 464 individual Nassau grouper sampled from The Bahamas were genotyped using 15 polymorphic microsatellite loci to establish measures of population structure, genetic diversity and effective population size (N e ). Nassau grouper were characterized by mostly high levels of genetic diversity, but we found no evidence for geographic population structure. Microsatellite analyses revealed weak, but significant genetic differentiation of Nassau grouper throughout the Bahamian archipelago (Global FST 0.00236, p = 0.0001). Temporal analyses of changes in N e over the last 1,000 generations provide evidence in support of a pronounced historic decline in Bahamian Nassau grouper that appears to pre-date anthropogenic fishing activities. M-ratio results corroborate significant reductions in N e throughout The Bahamas, with evidence for population bottlenecks in three islands and an active fish spawning aggregation along with apparent signs of inbreeding at two islands. Current estimates of N e for Nassau grouper are considerably lower compared with historic levels. These findings represent important new contributions to our understanding of the evolutionary history, demographics and genetic connectivity of this endangered species, which are of critical importance for advancing their sustainable management.Molecular research was financially supported by the University of Exeter and research cruises were funded by the John G. Shedd Aquarium. Partial funding for KS was provided by the Shirley Oakes Butler Charitable Trust, Rotary Club of East Nassau and a private donation by I. de la Rocha

Modifiable factors associated with depression and anxiety in multiple sclerosis

Objectives: Modifiable lifestyle factors are implicated in multiple sclerosis (MS) symptoms but their role in mood is unclear. This study aimed to investigate associations between lifestyle and depression and anxiety in Australian participants with MS.Materials and Methods: Self-reported data from the Australian Multiple Sclerosis Longitudinal Study included the Hospital Anxiety and Depression Scale (HADS) and lifestyle measurements from 1500 participants. SNAP score (range 0-5) was the sum of non-smoking, sufficient fruit/vegetable intake, non-hazardous alcohol consumption, sufficient physical activity and healthy BMI. Analyses by log-binomial and linear regression were adjusted for confounding.Results: Symptoms of depression and anxiety were prevalent in 27% and 40%, respectively; 20% had both. Mean SNAP score was 2.7/5; only 3% met all healthy lifestyle recommendations. Only 10% reported adequate fruit/vegetable intake, and 22% reported a combination of unhealthy BMI, inadequate physical activity and inadequate nutrition. A healthier SNAP score was associated with lower depression prevalence (adjusted prevalence ratio 0.83 [95% CI 0.75, 0.92] per unit increase) and depression severity (adjusted β-0.44 [95% CI -0.64, -0.24]), but not with anxiety.Conclusions: Modifiable lifestyle factors are associated with lower frequency and severity of depression, but not anxiety, in Australian people with multiple sclerosis. The associations between a healthier SNAP score and lower depression are likely bi-directional. SNAP risk factor prevalence and co-occurrence, especially inadequate nutrition and low physical activity, were high among Australians with MS

Probing energy transfer in an ensemble of silicon nanocrystals

Time-resolved photoluminescence measurements of silicon nanocrystals formed by ion implantation of silicon into silicon dioxide reveal multi-exponential luminescence decays. Three discrete time components are apparent in the rise and decay data, which we associate with different classes of nanocrystals. The values of decay time are remarkably constant with emission energy, but the relative contributions of the three components vary strongly across the luminescence band. In keeping with the quantum confinement model for luminescence, we assign emission at high energies to small nanocrystals and that at low energies to large nanocrystals. By deconvolving the decay data over the full emission band, it is possible to study the migration of excitation from smaller (luminescence donor) to larger (luminescence acceptor) nanocrystals. We propose a model of diffusion of excitation between neighboring nanocrystals, with long lifetime emission being from the largest nanocrystal in the local neighborhood. Our data also allow us to study the saturation of acceptor nanocrystals, effectively switching off excitation transfer, and Auger recombination in non-interacting nanocrystals. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3622151

Cluster randomised trials in the medical literature: two bibliometric surveys

Background: Several reviews of published cluster randomised trials have reported that about half did not take clustering into account in the analysis, which was thus incorrect and potentially misleading. In this paper I ask whether cluster randomised trials are increasing in both number and quality of reporting. Methods: Computer search for papers on cluster randomised trials since 1980, hand search of trial reports published in selected volumes of the British Medical Journal over 20 years. Results: There has been a large increase in the numbers of methodological papers and of trial reports using the term 'cluster random' in recent years, with about equal numbers of each type of paper. The British Medical Journal contained more such reports than any other journal. In this journal there was a corresponding increase over time in the number of trials where subjects were randomised in clusters. In 2003 all reports showed awareness of the need to allow for clustering in the analysis. In 1993 and before clustering was ignored in most such trials. Conclusion: Cluster trials are becoming more frequent and reporting is of higher quality. Perhaps statistician pressure works

Are different groups of patients with stroke more likely to be excluded from the new UK general medical services contract? A cross-sectional retrospective analysis of a large primary care population

Peer reviewedPublisher PD

Prevalence of Allergic Disorders among Primary School-Aged Children in Madinah, Saudi Arabia: Two-Stage Cross-Sectional Survey

There are limited data on the epidemiology of allergic disorders in Saudi Arabia. Such data are needed for, amongst other things, helping to plan service provision at a time when there is considerable investment taking place in national healthcare development. We sought to estimate the prevalence of atopic eczema, allergic rhinitis and asthma in primary school children in Madinah, Saudi Arabia.We conducted a two-stage cross-sectional survey of schoolchildren in Madinah. Children were recruited from 38 randomly selected schools. Questionnaires were sent to the parents of all 6,139 6-8 year old children in these schools. These parental-completed questionnaires incorporated questions from the International Study of Asthma and Allergies in Childhood (ISAAC), which had previously been validated for use in Arab populations. We undertook descriptive analyses, using the Generalized Estimating Equation (GEE) to calculate 95% confidence intervals. The overall response rate was 85.9% (n = 5,188), 84.6% for girls and 86.2% for boys, respectively. Overall, parents reported symptoms suggestive of a history of eczema in 10.3% (95%CI 9.4, 11.4), rhinitis in 24.2% (95%CI 22.3, 26.2) and asthma in 23.6% (95%CI 21.3, 26.0) of children. Overall, 41.7% (95%CI 39.1, 44.4) of children had symptoms suggestive of at least one allergic disorder, with a substantial minority manifesting symptoms indicative of co-morbid allergic disease. Comparison of these symptom-based prevalence estimates with reports of clinician-diagnosed disease suggested that the majority of children with eczema and asthma had been diagnosed, but only a minority (17.4%) of children had been diagnosed with rhinitis. International comparisons indicated that children in Madinah have amongst the highest prevalence of allergic problems in the world.Symptoms indicative of allergic disease are very common in primary school-aged children in Madinah, Saudi Arabia, with figures comparable to the highest risk regions in the world

Informing the public health response to COVID-19: a systematic review of risk factors for disease, severity, and mortality

BACKGROUND: Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) has challenged public health agencies globally. In order to effectively target government responses, it is critical to identify the individuals most at risk of coronavirus disease-19 (COVID-19), developing severe clinical signs, and mortality. We undertook a systematic review of the literature to present the current status of scientific knowledge in these areas and describe the need for unified global approaches, moving forwards, as well as lessons learnt for future pandemics. METHODS: Medline, Embase and Global Health were searched to the end of April 2020, as well as the Web of Science. Search terms were specific to the SARS-CoV-2 virus and COVID-19. Comparative studies of risk factors from any setting, population group and in any language were included. Titles, abstracts and full texts were screened by two reviewers and extracted in duplicate into a standardised form. Data were extracted on risk factors for COVID-19 disease, severe disease, or death and were narratively and descriptively synthesised. RESULTS: One thousand two hundred and thirty-eight papers were identified post-deduplication. Thirty-three met our inclusion criteria, of which 26 were from China. Six assessed the risk of contracting the disease, 20 the risk of having severe disease and ten the risk of dying. Age, gender and co-morbidities were commonly assessed as risk factors. The weight of evidence showed increasing age to be associated with severe disease and mortality, and general comorbidities with mortality. Only seven studies presented multivariable analyses and power was generally limited. A wide range of definitions were used for disease severity. CONCLUSIONS: The volume of literature generated in the short time since the appearance of SARS-CoV-2 has been considerable. Many studies have sought to document the risk factors for COVID-19 disease, disease severity and mortality; age was the only risk factor based on robust studies and with a consistent body of evidence. Mechanistic studies are required to understand why age is such an important risk factor. At the start of pandemics, large, standardised, studies that use multivariable analyses are urgently needed so that the populations most at risk can be rapidly protected. REGISTRATION: This review was registered on PROSPERO as CRD42020177714