BMX: Biological modelling and interface exchange.

High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings.

Online interactive medical neuroimaging exercise to identify human brain structures.

A persisting need remains for developing methods for inspiring and teaching undergraduate medical students to quickly learn to identify the hundreds of human brain structures, tracts and spaces that are clinically relevant (viewed as three-dimensional volumes or two-dimensional neuroimages), and to accomplish this with the option of virtual on-line methods. This notably includes teaching the essentials of recommended diagnostic radiology to allow students to be familiar with patient neuroimages routinely acquired using magnetic resonance imaging (MRI) and computed tomography (CT). The present article includes a brief example video plus details a clinically oriented interactive neuroimaging exercise for first year medical students (MS1s) in small groups, conducted with instructors either in-person or as an entirely online virtual event.

Presentation and Management of a Novel Ehlers-Danlos COL5A1 Variant With Birt-Hogg-Dube Syndrome: A Case Study.

Ehlers-Danlos syndrome (EDS) is a hereditary disorder caused by a mutation in the COL gene, which leads to the faulty synthesis of the collagen protein. EDS can present with a wide array of manifestations depending upon which COL gene is mutated. Birt-Hogg-Dubé (BHD) syndrome is a rare hereditary disorder currently identified in 200 families worldwide.

Data Mining for Terahertz Generation Crystals.

A data mining approach to discover and develop new organic nonlinear optical crystals that produce intense pulses of terahertz radiation is demonstrated. The Cambridge Structural Database is mined for non-centrosymmetric materials and these structural data are used in tandem with density functional theory calculations to predict new materials that efficiently generate terahertz radiation. This enables us to (in a relatively short time) discover, synthesize, and grow large, high-quality crystals of four promising materials and characterize them for intense terahertz generation.

From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape.

Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the hardware and software have evolved, so have the theoretical and computational chemistry methods and algorithms. Parallel computers clearly changed the common computing paradigm in the late 1970s and 80s, and the field has again seen a paradigm shift with the advent of graphical processing units.

Correlation function approach for diffusion in confined geometries.

This paper describes a formalism for extracting spatially varying transport coefficients from simulations of a molecular fluid in a nanochannel. This approach is applied to self-diffusion of a Lennard-Jones fluid confined between two parallel surfaces. A numerical grid is laid over the domain confining the fluid, and fluid properties are projected onto the grid cells.

Longitudinal Ultrasound Curriculum Incorporation at West Virginia University School of Medicine: A Description and Graduating Students' Perceptions.

Objectives: Sonography is a clinical tool being incorporated in multiple medical specialties with evidence of improved patient care and cost. Some schools have begun implementing ultrasound curricula. We hope to build upon that foundation and provide another potential framework of incorporation.

Coarse-grained hydrodynamics from correlation functions.

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configurations from a molecular dynamics simulation or other atomistic simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilibrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system.

An analysis platform for multiscale hydrogeologic modeling with emphasis on hybrid multiscale methods.

One of the most significant challenges faced by hydrogeologic modelers is the disparity between the spatial and temporal scales at which fundamental flow, transport, and reaction processes can best be understood and quantified (e.g., microscopic to pore scales and seconds to days) and at which practical model predictions are needed (e.

A multicenter, randomized, double-blind, parallel group pilot evaluation of the efficacy and safety of intravesical sodium chondroitin sulfate versus vehicle control in patients with interstitial cystitis/painful bladder syndrome.

Objective: The goal of this pilot study was to gather information on differences between intravesical chondroitin sulfate and inactive vehicle control for treatment of interstitial cystitis/painful bladder syndrome (IC/PBS).

Methods: This was a prospective, randomized, double-blind, inactive vehicle-controlled, 12-week study (6-week treatment period, followed by a 6-week follow-up period) in patients with IC/PBS. Patients were randomized to weekly intravesical treatment with 2.

Activation energies and potentials of mean force for water cluster evaporation.

Activation energies for water cluster evaporation are of interest in many areas of chemical physics. We present the first computation of activation energies for monomer evaporation of small water clusters using the formalism of dynamical nucleation theory (DNT). To this end, individual evaporation rate constants are computed for water clusters (H(2)O)(i), where i=2-10 for temperatures ranging from 243 to 333 K.

The Use of Processor Groups in Molecular Dynamics Simulations to Sample Free-Energy States.

Molecular dynamics calculations composed of many independent simulations are frequently encountered in free-energy calculations, as well as many other simulation approaches. In principle, the availability of a large number of independent tasks should make possible the development of highly scalable parallel code that executes these tasks concurrently. This paper discusses the use of processor groups to write simulation codes of this type and describes results for a code that evaluates the volume dependence of the Helmholtz free energy for clusters of an immiscible fluid in a solvent.

Cyclization and catenation directed by molecular self-assembly.

We report here that molecular self-assembly can effectively direct and enhance specific reaction pathways. Using perylene pi-pi stacking weak attractive forces, we succeeded in synthesizing perylene bisimide macrocyclic dimer and a concatenated dimer-dimer ring from dynamic self-assembly of monomeric bis-N,N'-(2-(2-(2-(2-thioacetylethoxy)ethoxy)ethoxy)ethyl)perylenetetracarboxylic diimide. The monocyclic ring closure and the dimer-dimer ring concatenation were accomplished through formation of disulfide bonds, which was readily triggered by air oxidization under basic deacetylation conditions.

Registering the Amica electronic structure code in the extensible computational chemistry environment.

We describe the integration and use of the Amica software package ("Atoms & Molecules In Chemical Accuracy") within the Extensible Computational Chemistry Environment (Ecce). Amica is capable of accurately solving the electronic Schrodinger equation of small atoms and molecules using terms that are linear in the interelectronic distances, r(12), on multireference level of theory, but it requires expert knowledge to configure and execute its algorithms. Ecce is a comprehensive suite of tools that support the computational chemistry research processes of computation setup, execution, and analysis through a convenient graphical user interface.

Guidelines for the surveillance of localized renal cell carcinoma based on the patterns of relapse after nephrectomy.

Purpose: We characterized relapse patterns in patients with sporadic renal cell carcinoma (RCC) following radical and partial nephrectomy, and developed surveillance guidelines.

Materials And Methods: Between 1989 and 2000, 495 patients underwent nephrectomy for RCC at 1 of 5 Canadian referral centers. Median followup was 42 months.

Effectiveness and safety of manual hemostasis facilitated by the SyvekPatch with one hour of bedrest after coronary angiography using six-French catheters.

Manual hemostasis facilitated by a SyvekPatch with 1 hour of bedrest after coronary angiography using 6Fr catheters was evaluated in a study of 200 patients. There were no major adverse events and 2% minor adverse events, all of which were managed successfully with additional bedrest of 1 to 2 hours. The findings suggest that the 1-hour bedrest protocol using the SyvekPatch is safe and effective in low-risk patients.

Levofloxacin for chronic prostatitis/chronic pelvic pain syndrome in men: a randomized placebo-controlled multicenter trial.

Objectives: To perform a Canadian multicenter randomized placebo-controlled trial to evaluate the safety and efficacy of 6 weeks of levofloxacin therapy compared with placebo in chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). Uncontrolled studies have supported the use of antibiotics in CP/CPPS.

Methods: Men with a National Institutes of Health (NIH) diagnosis of CP/CPPS (specifically, no infection localized to the prostate) were randomized to levofloxacin (500 mg/day) or placebo for 6 weeks in 11 Canadian centers.

Comparison of lipid and non-lipid markers of atherosclerosis in arterial versus venous blood.

Background: Early studies have suggested that there may be differences in the concentration of lipoprotein particles and their associated apolipoproteins in arterial and venous blood and that this gradient might explain a proclivity to develop atherosclerotic lesions. The aim of this study was to use current methods of analysis to determine levels of these components, including particle densities and several common inflammatory markers in arterial and venous blood.

Methods: Samples of arterial and venous blood were obtained nearly simultaneously in 26 patients undergoing right and left heart catheterization.