Portable simulation framework for diffusion MRI

The numerical simulation of the diffusion MRI signal arising from complex tissue micro-structures is helpful for understanding and interpreting imaging data as well as for designing and optimizing MRI sequences. The discretization of the Bloch-Torrey equation by finite elements is a more recently developed approach for this purpose, in contrast to random walk simulations, which has a longer history. While finite element discretization is more difficult to implement than random walk simulations, the approach benefits from a long history of theoretical and numerical developments by the mathematical and engineering communities. In particular, software packages for the automated solutions of partial differential equations using finite element discretization, such as FEniCS, are undergoing active support and development. However, because diffusion MRI simulation is a relatively new application area, there is still a gap between the simulation needs of the MRI community and the available tools provided by finite element software packages. In this paper, we address two potential difficulties in using FEniCS for diffusion MRI simulation. First, we simplified software installation by the use of FEniCS containers that are completely portable across multiple platforms. Second, we provide a portable simulation framework based on Python and whose code is open source. This simulation framework can be seamlessly integrated with cloud computing resources such as Google Colaboratory notebooks working on a web browser or with Google Cloud Platform with MPI parallelization. We show examples illustrating the accuracy, the computational times, and parallel computing capabilities. The framework contributes to reproducible science and open-source software in computational diffusion MRI with the hope that it will help to speed up method developments and stimulate research collaborations.La Caixa 201

Effect of Segmental Bronchoalveolar Lavage on Quantitative Computed Tomography of the Lung

Rationale and Objectives: With employment of both multidetector computed tomography (MDCT) and endobronchial procedures in multicenter studies, effects of timing of endobronchial procedures on quantitative imaging (Q-MDCT) metrics is a question of increasing importance.Materials and Methods: Six subjects were studied via MDCT at baseline, immediately following and at 4 hours and 24 hours post-bronchoalveolar lavage (SAL) (right middle lobe and lingula). Through quantitative image analysis, non-air, or "tissue" volume (TV) in each lung and lobe was recorded. Change in TV from baseline was used to infer retention and redistribution of lavage fluid.Results: Bronchoscopist reported unrecovered BAL volume correlated well with Q-MDCT for whole lung measures, but less well with individual lobes indicating redistribution. TV in all lobes except the right lower lobe differed significantly (P &lt;.05) from baseline immediately post lavage. At 24 hours, all lobes except the left lower lobe (small 1% mean difference at 24 hours) returned to baseline.Conclusions: These findings suggest fluid movement affecting Q-MDCT metrics between lobes and between lungs before eventual resolution, and preclude protocols involving the lavage of one lung and imaging of the other to avoid interactions. We demonstrate that Q-MDCT is sensitive to lavage fluid retention and redistribution, and endobronchial procedures should not precede Q-MDCT imaging by less than 24 hours.</p

Ising model with periodic pinning of mobile defects

A two-dimensional Ising model with short-range interactions and mobile defects describing the formation and thermal destruction of defect stripes is studied. In particular, the effect of a local pinning of the defects at the sites of straight equidistant lines is analysed using Monte Carlo simulations and the transfer matrix method. The pinning leads to a long-range ordered magnetic phase at low temperatures. The dependence of the phase transition temperature, at which the defect stripes are destabilized, on the pinning strength is determined. The transition seems to be of first order, with and without pinning.Comment: 7 pages, 7 figure

The High Voltage Feedthroughs for the ATLAS Liquid Argon Calorimeters

The purpose, design specifications, construction techniques, and testing methods are described for the high voltage feedthrough ports and filters of the ATLAS Liquid Argon calorimeters. These feedthroughs carry about 5000 high voltage wires from a room-temperature environment (300 K) through the cryostat walls to the calorimeters cells (89 K) while maintaining the electrical and cryogenic integrity of the system. The feedthrough wiring and filters operate at a maximum high voltage of 2.5 kV without danger of degradation by corona discharges or radiation at the Large Hadron Collider

The Paradox of Muscle Hypertrophy in Muscular Dystrophy

Mutations in the dystrophin gene cause Duchenne and Becker muscular dystrophy in humans and syndromes in mice, dogs, and cats. Affected humans and dogs have progressive disease that leads primarily to muscle atrophy. Mdx mice progress through an initial phase of muscle hypertrophy followed by atrophy. Cats have persistent muscle hypertrophy. Hypertrophy in humans has been attributed to deposition of fat and connective tissue (pseudohypertrophy). Increased muscle mass (true hypertrophy) has been documented in animal models. Muscle hypertrophy can exaggerate postural instability and joint contractures. Deleterious consequences of muscle hypertrophy should be considered when developing treatments for muscular dystrophy

Expansion of Vortex Cores by Strong Electronic Correlation in La2−x_{2-x}Srx_xCuO4_4 at Low Magnetic Induction

The vortex core radius \rv, defined as the peak position of the supercurrent around the vortex, has been determined by muon spin rotation measurements in the mixed state of \lscox for $x=0.13$, 0.15, and 0.19. At lower doping (x=0.13 and 0.15), \rv(T) increases with decreasing temperature T, which is opposite to the behavior predicted by the conventional theory. Moreover, \rv(T\to0) is significantly larger than the Ginsburg-Landau coherence length determined by the upper critical field, and shows a clear tendency to decrease with increasing the doping x. These features can be qualitatively reproduced in a microscopic model involving antiferromagnetic electronic correlations.Comment: 6 pages, 4 figures, to be published in Phys. Rev.

The Intentional Use of Service Recovery Strategies to Influence Consumer Emotion, Cognition and Behaviour

Service recovery strategies have been identified as a critical factor in the success of. service organizations. This study develops a conceptual frame work to investigate how specific service recovery strategies influence the emotional, cognitive and negative behavioural responses of . consumers., as well as how emotion and cognition influence negative behavior. Understanding the impact of specific service recovery strategies will allow service providers' to more deliberately and intentionally engage in strategies that result in positive organizational outcomes. This study was conducted using a 2 x 2 between-subjects quasi-experimental design. The results suggest that service recovery has a significant impact on emotion, cognition and negative behavior. Similarly, satisfaction, negative emotion and positive emotion all influence negative behavior but distributive justice has no effect

Indirect search for dark matter: prospects for GLAST

Possible indirect detection of neutralino, through its gamma-ray annihilation product, by the forthcoming GLAST satellite from our galactic halo, M31, M87 and the dwarf galaxies Draco and Sagittarius is studied. Gamma-ray fluxes are evaluated for the two representative energy thresholds, 0.1 GeV and 1.0 GeV, at which the spatial resolution of GLAST varies considerably. Apart from dwarfs which are described either by a modified Plummer profile or by a tidally-truncated King profiles, fluxes are compared for halos with central cusps and cores. It is demonstrated that substructures, irrespective of their profiles, enhance the gamma-ray emission only marginally. The expected gamma-ray intensity above 1 GeV at high galactic latitudes is consistent with the residual emission derived from EGRET data if the density profile has a central core and the neutralino mass is less than 50 GeV, whereas for a central cusp only a substantial enhancement would explain the observations. From M31, the flux can be detected above 0.1 GeV and 1.0 GeV by GLAST only if the neutralino mass is below 300 GeV and if the density profile has a central cusp, case in which a significant boost in the gamma-ray emission is produced by the central black hole. For Sagittarius, the flux above 0.1 GeV is detectable by GLAST provided the neutralino mass is below 50 GeV. From M87 and Draco the fluxes are always below the sensitivity limit of GLAST.Comment: 14 Pages, 7 Figures, 3 Tables, version to appear on Physical Review

Current constraints on Cosmological Parameters from Microwave Background Anisotropies

We compare the latest observations of Cosmic Microwave Background (CMB) Anisotropies with the theoretical predictions of the standard scenario of structure formation. Assuming a primordial power spectrum of adiabatic perturbations we found that the total energy density is constrained to be $\Omega_{tot}=1.03\pm0.06$ while the energy density in baryon and Cold Dark Matter (CDM) are $\Omega_bh^2=0.021\pm0.003$ and $\Omega_{cdm}h^2=0.12\pm0.02$, (all at 68% C.L.) respectively. The primordial spectrum is consistent with scale invariance, ($n_s=0.97\pm0.04$) and the age of the universe is $t_0=14.6\pm0.9$ Gyrs. Adding informations from Large Scale Structure and Supernovae, we found a strong evidence for a cosmological constant $\Omega_{\Lambda}=0.70_{-0.05}^{+0.07}$ and a value of the Hubble parameter $h=0.69\pm0.07$. Restricting this combined analysis to flat universes, we put constraints on possible 'extensions' of the standard scenario. A gravity waves contribution to the quadrupole anisotropy is limited to be $r \le 0.42$ (95% c.l.). A constant equation of state for the dark energy component is bound to be $w_Q \le -0.74$ (95% c.l.). We constrain the effective relativistic degrees of freedom $N_\nu \leq 6.2$ and the neutrino chemical potential $-0.01 \leq \xi_e \leq 0.18$ and $|\xi_{\mu,\tau}|\leq 2.3$ (massless neutrinos).Comment: The status of cosmological parameters before WMAP. In press on Phys. Rev. D., Rapid Communication, 6 pages, 5 figure

Optimizing research in symptomatic uterine fibroids with development of a computable phenotype for use with electronic health records

Background: Women with symptomatic uterine fibroids can report a myriad of symptoms, including pain, bleeding, infertility, and psychosocial sequelae. Optimizing fibroid research requires the ability to enroll populations of women with image-confirmed symptomatic uterine fibroids. Objective: Our objective was to develop an electronic health record–based algorithm to identify women with symptomatic uterine fibroids for a comparative effectiveness study of medical or surgical treatments on quality-of-life measures. Using an iterative process and text-mining techniques, an effective computable phenotype algorithm, composed of demographics, and clinical and laboratory characteristics, was developed with reasonable performance. Such algorithms provide a feasible, efficient way to identify populations of women with symptomatic uterine fibroids for the conduct of large traditional or pragmatic trials and observational comparative effectiveness studies. Symptomatic uterine fibroids, due to menorrhagia, pelvic pain, bulk symptoms, or infertility, are a source of substantial morbidity for reproductive-age women. Comparing Treatment Options for Uterine Fibroids is a multisite registry study to compare the effectiveness of hormonal or surgical fibroid treatments on women's perceptions of their quality of life. Electronic health record–based algorithms are able to identify large numbers of women with fibroids, but additional work is needed to develop electronic health record algorithms that can identify women with symptomatic fibroids to optimize fibroid research. We sought to develop an efficient electronic health record–based algorithm that can identify women with symptomatic uterine fibroids in a large health care system for recruitment into large-scale observational and interventional research in fibroid management. Study Design: We developed and assessed the accuracy of 3 algorithms to identify patients with symptomatic fibroids using an iterative approach. The data source was the Carolina Data Warehouse for Health, a repository for the health system's electronic health record data. In addition to International Classification of Diseases, Ninth Revision diagnosis and procedure codes and clinical characteristics, text data–mining software was used to derive information from imaging reports to confirm the presence of uterine fibroids. Results of each algorithm were compared with expert manual review to calculate the positive predictive values for each algorithm. Results: Algorithm 1 was composed of the following criteria: (1) age 18-54 years; (2) either ≥1 International Classification of Diseases, Ninth Revision diagnosis codes for uterine fibroids or mention of fibroids using text-mined key words in imaging records or documents; and (3) no International Classification of Diseases, Ninth Revision or Current Procedural Terminology codes for hysterectomy and no reported history of hysterectomy. The positive predictive value was 47% (95% confidence interval 39–56%). Algorithm 2 required ≥2 International Classification of Diseases, Ninth Revision diagnosis codes for fibroids and positive text-mined key words and had a positive predictive value of 65% (95% confidence interval 50–79%). In algorithm 3, further refinements included ≥2 International Classification of Diseases, Ninth Revision diagnosis codes for fibroids on separate outpatient visit dates, the exclusion of women who had a positive pregnancy test within 3 months of their fibroid-related visit, and exclusion of incidentally detected fibroids during prenatal or emergency department visits. Algorithm 3 achieved a positive predictive value of 76% (95% confidence interval 71–81%). Conclusion: An electronic health record–based algorithm is capable of identifying cases of symptomatic uterine fibroids with moderate positive predictive value and may be an efficient approach for large-scale study recruitment