A Deep Learning Framework for Unsupervised Affine and Deformable Image Registration

Image registration, the process of aligning two or more images, is the core technique of many (semi-)automatic medical image analysis tasks. Recent studies have shown that deep learning methods, notably convolutional neural networks (ConvNets), can be used for image registration. Thus far training of ConvNets for registration was supervised using predefined example registrations. However, obtaining example registrations is not trivial. To circumvent the need for predefined examples, and thereby to increase convenience of training ConvNets for image registration, we propose the Deep Learning Image Registration (DLIR) framework for \textit{unsupervised} affine and deformable image registration. In the DLIR framework ConvNets are trained for image registration by exploiting image similarity analogous to conventional intensity-based image registration. After a ConvNet has been trained with the DLIR framework, it can be used to register pairs of unseen images in one shot. We propose flexible ConvNets designs for affine image registration and for deformable image registration. By stacking multiple of these ConvNets into a larger architecture, we are able to perform coarse-to-fine image registration. We show for registration of cardiac cine MRI and registration of chest CT that performance of the DLIR framework is comparable to conventional image registration while being several orders of magnitude faster.Comment: Accepted: Medical Image Analysis - Elsevie

Intermittent permeation of cylindrical nanopores by water

Molecular Dynamics simulations of water molecules in nanometre sized cylindrical channels connecting two reservoirs show that the permeation of water is very sensitive to the channel radius and to electric polarization of the embedding material. At threshold, the permeation is {\emph{intermittent}} on a nanosecond timescale, and strongly enhanced by the presence of an ion inside the channel, providing a possible mechanism for gating. Confined water remains surprisingly fluid and bulk-like. Its behaviour differs strikingly from that of a reference Lennard-Jones fluid, which tends to contract into a highly layered structure inside the channel.Comment: 4 pages, 4 figure

Wetting and contact-line effects for spherical and cylindrical droplets on graphene layers: A comparative molecular-dynamics investigation

In Molecular Dynamics (MD) simulations, interactions between water molecules and graphitic surfaces are often modeled as a simple Lennard-Jones potential between oxygen and carbon atoms. A possible method for tuning this parameter consists of simulating a water nanodroplet on a flat graphitic surface, measuring the equilibrium contact angle, extrapolating it to the limit of a macroscopic droplet and finally matching this quantity to experimental results. Considering recent evidence demonstrating that the contact angle of water on a graphitic plane is much higher than what was previously reported, we estimate the oxygen-carbon interaction for the recent SPC/Fwwater model. Results indicate a value of about 0.2 kJ/mol, much lower than previous estimations. We then perform simulations of cylindrical water filaments on graphitic surfaces, in order to compare and correlate contact angles resulting from these two different systems. Results suggest that modified Young's equation does not describe the relation between contact angle and drop size in the case of extremely small systems and that contributions different from the one deriving from contact line tension should be taken into account.Comment: To be published on Physical Review E (http://pre.aps.org/

Assessment of the validity of intermolecular potential models used in molecular dynamics simulations by extended x-ray absorption fine structure spectroscopy:A case study of Sr2+ in methanol solution

Molecular dynamics simulations have been carried out for Sr2+ in methanol using different Sr2+ Lennard-Jones parameters and methanol models. X-ray absorption fine structure. (EXAFS) spectroscopy has been employed to assess the reliability of the ion-ion and ion-methanol potential functions used in the simulations. Radial distribution functions of Sr2+ in methanol have been. calculated for each simulation and compared with the EXAFS experimental data. This procedure has allowed the determinations of reliable Sr2+-methanol models which have been used in longer simulations providing an accurate description of the dynamic and structural properties of this system

Formation energy and interaction of point defects in two-dimensional colloidal crystals

The manipulation of individual colloidal particles using optical tweezers has allowed vacancies to be created in two-dimensional (2d) colloidal crystals, with unprecedented possibility of real-time monitoring the dynamics of such defects (Nature {\bf 413}, 147 (2001)). In this Letter, we employ molecular dynamics (MD) simulations to calculate the formation energy of single defects and the binding energy between pairs of defects in a 2d colloidal crystal. In the light of our results, experimental observations of vacancies could be explained and then compared to simulation results for the interstitial defects. We see a remarkable similarity between our results for a 2d colloidal crystal and the 2d Wigner crystal (Phys. Rev. Lett. {\bf 86}, 492 (2001)). The results show that the formation energy to create a single interstitial is $12$ lower than that of the vacancy. Because the pair binding energies of the defects are strongly attractive for short distances, the ground state should correspond to bound pairs with the interstitial bound pairs being the most probable.Comment: 5 pages, 2 figure

Magnetic friction due to vortex fluctuation

We use Monte Carlo and molecular dynamics simulation to study a magnetic tip-sample interaction. Our interest is to understand the mechanism of heat dissipation when the forces involved in the system are magnetic in essence. We consider a magnetic crystalline substrate composed of several layers interacting magnetically with a tip. The set is put thermally in equilibrium at temperature T by using a numerical Monte Carlo technique. By using that configuration we study its dynamical evolution by integrating numerically the equations of motion. Our results suggests that the heat dissipation in this system is closed related to the appearing of vortices in the sample.Comment: 6 pages, 41 figure

Polarization forces in water deduced from single molecule data

Intermolecular polarization interactions in water are determined using a minimal atomic multipole model constructed with distributed polarizabilities. Hydrogen bonding and other properties of water-water interactions are reproduced to fine detail by only three multipoles $\mu_H$, $\mu_O$, and $\theta_O$ and two polarizabilities $\alpha_O$ and $\alpha_H$, which characterize a single water molecule and are deduced from single molecule data.Comment: 4 revtex pages, 3 embedded color PS figure

A Potential Energy Landscape Study of the Amorphous-Amorphous Transformation in H2_2O

We study the potential energy landscape explored during a compression-decompression cycle for the SPC/E (extended simple point charge) model of water. During the cycle, the system changes from low density amorphous ice (LDA) to high density amorphous ice (HDA). After the cycle, the system does not return to the same region of the landscape, supporting the interesting possibility that more than one significantly different configuration corresponds to LDA. We find that the regions of the landscape explored during this transition have properties remarkably different from those explored in thermal equilibrium in the liquid phase

Webifying the computerized execution of Clinical Practice Guidelines

The means through which Clinical Practice Guidelines are dissemi-nated and become accessible are a crucial factor in their later adoption by health care professionals. Making these guidelines available in Clinical Decision Sup-port Systems renders their application more personal and thus acceptable at the moment of care. Web technologies may play an important role in increasing the reach and dissemination of guidelines, but this promise remains largely unful-filled. There is a need for a guideline computer model that can accommodate a wide variety of medical knowledge along with a platform for its execution that can be easily used in mobile devices. This work presents the CompGuide frame-work, a web-based and service-oriented platform for the execution of Computer-Interpretable Guidelines. Its architecture comprises different modules whose in-teraction enables the interpretation of clinical tasks and the verification of clinical constraints and temporal restrictions of guidelines represented in OWL. It allows remote guideline execution with data centralization, more suitable for a work en-vironment where physicians are mobile and not bound to a machine. The solution presented in this paper encompasses a computer-interpretable guideline model, a web-based framework for guideline execution and an Application Programming Interface for the development of other guideline execution systems.This work is part-funded by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT – Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project FCOMP-01-0124-FEDER-028980 (PTDC/EEI-SII/1386/2012). The work of Tiago Oliveira is supported by doctoral grant by FCT (SFRH/BD/85291/2012)

Risk scoring for the primary prevention of cardiovascular disease.

BACKGROUND: The current paradigm for cardiovascular disease (CVD) emphasises absolute risk assessment to guide treatment decisions in primary prevention. Although the derivation and validation of multivariable risk assessment tools, or CVD risk scores, have attracted considerable attention, their effect on clinical outcomes is uncertain. OBJECTIVES: To assess the effects of evaluating and providing CVD risk scores in adults without prevalent CVD on cardiovascular outcomes, risk factor levels, preventive medication prescribing, and health behaviours. SEARCH METHODS: We searched the Cochrane Central Register of Controlled Trials (CENTRAL) in the Cochrane Library (2016, Issue 2), MEDLINE Ovid (1946 to March week 1 2016), Embase (embase.com) (1974 to 15 March 2016), and Conference Proceedings Citation Index-Science (CPCI-S) (1990 to 15 March 2016). We imposed no language restrictions. We searched clinical trial registers in March 2016 and handsearched reference lists of primary studies to identify additional reports. SELECTION CRITERIA: We included randomised and quasi-randomised trials comparing the systematic provision of CVD risk scores by a clinician, healthcare professional, or healthcare system compared with usual care (i.e. no systematic provision of CVD risk scores) in adults without CVD. DATA COLLECTION AND ANALYSIS: Three review authors independently selected studies, extracted data, and evaluated study quality. We used the Cochrane 'Risk of bias' tool to assess study limitations. The primary outcomes were: CVD events, change in CVD risk factor levels (total cholesterol, systolic blood pressure, and multivariable CVD risk), and adverse events. Secondary outcomes included: lipid-lowering and antihypertensive medication prescribing in higher-risk people. We calculated risk ratios (RR) for dichotomous data and mean differences (MD) or standardised mean differences (SMD) for continuous data using 95% confidence intervals. We used a fixed-effects model when heterogeneity (I²) was at least 50% and a random-effects model for substantial heterogeneity (I² > 50%). We evaluated the quality of evidence using the GRADE framework. MAIN RESULTS: We identified 41 randomised controlled trials (RCTs) involving 194,035 participants from 6422 reports. We assessed studies as having high or unclear risk of bias across multiple domains. Low-quality evidence evidence suggests that providing CVD risk scores may have little or no effect on CVD events compared with usual care (5.4% versus 5.3%; RR 1.01, 95% confidence interval (CI) 0.95 to 1.08; I² = 25%; 3 trials, N = 99,070). Providing CVD risk scores may reduce CVD risk factor levels by a small amount compared with usual care. Providing CVD risk scores reduced total cholesterol (MD -0.10 mmol/L, 95% CI -0.20 to 0.00; I² = 94%; 12 trials, N = 20,437, low-quality evidence), systolic blood pressure (MD -2.77 mmHg, 95% CI -4.16 to -1.38; I² = 93%; 16 trials, N = 32,954, low-quality evidence), and multivariable CVD risk (SMD -0.21, 95% CI -0.39 to -0.02; I² = 94%; 9 trials, N = 9549, low-quality evidence). Providing CVD risk scores may reduce adverse events compared with usual care, but results were imprecise (1.9% versus 2.7%; RR 0.72, 95% CI 0.49 to 1.04; I² = 0%; 4 trials, N = 4630, low-quality evidence). Compared with usual care, providing CVD risk scores may increase new or intensified lipid-lowering medications (15.7% versus 10.7%; RR 1.47, 95% CI 1.15 to 1.87; I² = 40%; 11 trials, N = 14,175, low-quality evidence) and increase new or increased antihypertensive medications (17.2% versus 11.4%; RR 1.51, 95% CI 1.08 to 2.11; I² = 53%; 8 trials, N = 13,255, low-quality evidence). AUTHORS' CONCLUSIONS: There is uncertainty whether current strategies for providing CVD risk scores affect CVD events. Providing CVD risk scores may slightly reduce CVD risk factor levels and may increase preventive medication prescribing in higher-risk people without evidence of harm. There were multiple study limitations in the identified studies and substantial heterogeneity in the interventions, outcomes, and analyses, so readers should interpret results with caution. New models for implementing and evaluating CVD risk scores in adequately powered studies are needed to define the role of applying CVD risk scores in primary CVD prevention