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

What determines patient satisfaction with surgery? A prospective cohort study of 4709 patients following total joint replacement

Objectives To investigate the factors which influence patient satisfaction with surgical services and to explore the relationship between overall satisfaction, satisfaction with specific facets of outcome and measured clinical outcomes (patient reported outcome measures (PROMs)). \ud \ud \ud Design Prospective cohort study. \ud \ud \ud Setting Single National Health Service (NHS) teaching hospital. \ud \ud \ud Participants 4709 individuals undergoing primary lower limb joint replacement over a 4-year period (January 2006–December 2010). \ud \ud \ud Main outcome measures Overall patient satisfaction, clinical outcomes as measured by PROMs (Oxford Hip or Knee Score, SF-12), satisfaction with five specific aspects of surgical outcome, attitudes towards further surgery, length of hospital stay. \ud \ud \ud Results Overall patient satisfaction was predicted by: (1) meeting preoperative expectations (OR 2.62 (95% CI 2.24 to 3.07)), (2) satisfaction with pain relief (2.40 (2.00 to 2.87)), (3) satisfaction with the hospital experience (1.7 (1.45 to 1.91)), (4) 12 months (1.08 (1.05 to 1.10)) and (5) preoperative (0.95 (0.93 to 0.97)) Oxford scores. These five factors contributed to a model able to correctly predict 97% of the variation in overall patient satisfaction response. The factors having greatest effect were the degree to which patient expectations were met and satisfaction with pain relief; the Oxford scores carried little weight in the algorithm. Various factors previously reported to influence clinical outcomes such as age, gender, comorbidities and length of postoperative hospital stay did not help explain variation in overall patient satisfaction. \ud \ud \ud Conclusions Three factors broadly determine the patient's overall satisfaction following lower limb joint arthroplasty; meeting preoperative expectations, achieving satisfactory pain relief, and a satisfactory hospital experience. Pain relief and expectations are managed by clinical teams; however, a fractured access to surgical services impacts on the patient's hospital experience which may reduce overall satisfaction. In the absence of complications, how we deliver healthcare may be of key importance along with the specifics of what we deliver, which has clear implications for units providing surgical services

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

Mixed integer programming in production planning with backlogging and setup carryover : modeling and algorithms

This paper proposes a mixed integer programming formulation for modeling the capacitated multi-level lot sizing problem with both backlogging and setup carryover. Based on the model formulation, a progressive time-oriented decomposition heuristic framework is then proposed, where improvement and construction heuristics are effectively combined, therefore efficiently avoiding the weaknesses associated with the one-time decisions made by other classical time-oriented decomposition algorithms. Computational results show that the proposed optimization framework provides competitive solutions within a reasonable time

Risk factors for exacerbations and pneumonia in patients with chronic obstructive pulmonary disease: a pooled analysis.

BACKGROUND: Patients with chronic obstructive pulmonary disease (COPD) are at risk of exacerbations and pneumonia; how the risk factors interact is unclear. METHODS: This post-hoc, pooled analysis included studies of COPD patients treated with inhaled corticosteroid (ICS)/long-acting β2 agonist (LABA) combinations and comparator arms of ICS, LABA, and/or placebo. Backward elimination via Cox's proportional hazards regression modelling evaluated which combination of risk factors best predicts time to first (a) pneumonia, and (b) moderate/severe COPD exacerbation. RESULTS: Five studies contributed: NCT01009463, NCT01017952, NCT00144911, NCT00115492, and NCT00268216. Low body mass index (BMI), exacerbation history, worsening lung function (Global Initiative for Chronic Obstructive Lung Disease [GOLD] stage), and ICS treatment were identified as factors increasing pneumonia risk. BMI was the only pneumonia risk factor influenced by ICS treatment, with ICS further increasing risk for those with BMI <25 kg/m2. The modelled probability of pneumonia varied between 3 and 12% during the first year. Higher exacerbation risk was associated with a history of exacerbations, poorer lung function (GOLD stage), female sex and absence of ICS treatment. The influence of the other exacerbation risk factors was not modified by ICS treatment. Modelled probabilities of an exacerbation varied between 31 and 82% during the first year. CONCLUSIONS: The probability of an exacerbation was considerably higher than for pneumonia. ICS reduced exacerbations but did not influence the effect of risks associated with prior exacerbation history, GOLD stage, or female sex. The only identified risk factor for ICS-induced pneumonia was BMI <25 kg/m2. Analyses of this type may help the development of COPD risk equations

Asymmetric triplex metallohelices with high and selective activity against cancer cells

Small cationic amphiphilic α-helical peptides are emerging as agents for the treatment of cancer and infection, but they are costly and display unfavourable pharmacokinetics. Helical coordination complexes may offer a three-dimensional scaffold for the synthesis of mimetic architectures. However, the high symmetry and modest functionality of current systems offer little scope to tailor the structure to interact with specific biomolecular targets, or to create libraries for phenotypic screens. Here, we report the highly stereoselective asymmetric self-assembly of very stable, functionalized metallohelices. Their anti-parallel head-to-head-to-tail ‘triplex’ strand arrangement creates an amphipathic functional topology akin to that of the active sub-units of, for example, host-defence peptides and ​p53. The metallohelices display high, structure-dependent toxicity to the human colon carcinoma cell-line HCT116 ​p53++, causing dramatic changes in the cell cycle without DNA damage. They have lower toxicity to human breast adenocarcinoma cells (MDA-MB-468) and, most remarkably, they show no significant toxicity to the bacteria methicillin-resistant Staphylococcus aureus and Escherichia coli. At a glanc

Simpson's Paradox, Lord's Paradox, and Suppression Effects are the same phenomenon – the reversal paradox

This article discusses three statistical paradoxes that pervade epidemiological research: Simpson's paradox, Lord's paradox, and suppression. These paradoxes have important implications for the interpretation of evidence from observational studies. This article uses hypothetical scenarios to illustrate how the three paradoxes are different manifestations of one phenomenon – the reversal paradox – depending on whether the outcome and explanatory variables are categorical, continuous or a combination of both; this renders the issues and remedies for any one to be similar for all three. Although the three statistical paradoxes occur in different types of variables, they share the same characteristic: the association between two variables can be reversed, diminished, or enhanced when another variable is statistically controlled for. Understanding the concepts and theory behind these paradoxes provides insights into some controversial or contradictory research findings. These paradoxes show that prior knowledge and underlying causal theory play an important role in the statistical modelling of epidemiological data, where incorrect use of statistical models might produce consistent, replicable, yet erroneous results