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. This review explores the challenges and some of the solutions in transforming software from the terascale to the petascale and now to the upcoming exascale computers. While discussing the field in general, NWChem and its redesign, NWChemEx, will be highlighted as one of the early codesign projects to take advantage of massively parallel computers and emerging software standards to enable large scientific challenges to be tackled.

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. There are several barriers, including curricular space, equipment and physical space, adequate faculty, and performing assessment. METHODS: At West Virginia University, we began a longitudinal ultrasound curriculum in 2012 with incorporation of didactic and practical sessions into gross anatomy, our systems-based second-year curriculum, physical diagnosis course, and clinical rotations. We included both written and practical assessment from the onset. After the initial 4 years, the first graduates were surveyed on their perceptions of the curriculum. Responses were correlated with specialty choice and clinical campus site. RESULTS: Based on our survey (90% response rate), students felt sonography was useful for anatomical understanding and patient care. Overall, 93% of our respondents reviewed the curriculum favorably. Qualitative feedback was very positive, with students desiring more ultrasound education and more required components, specifically in clinical rotations. CONCLUSIONS: Based on these results, some changes have already been implemented, including decreased student-to-instructor ratios, more open scan time, and more required components. The breadth of formal assessment has increased. Multiple pilot programs for clinical rotations are being developed. There is an ongoing need for faculty development and continued assessment of ultrasound competency.

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. It presents clinically with cutaneous, renal, and pulmonary manifestations due to an autosomal dominant mutation in a tumor suppressor gene, FLCN, on chromosome 17p11.2. We present a case of a 22-year-old male with Birt-Hogg-Dubé syndrome, showing typical features consistent with the classical type of EDS, with genetic testing revealing a COL5A1 mutation of "uncertain clinical significance", not yet reported in clinical literature. We discuss the treatment of this patient and describe the presentations of the two pathologies. Lastly, we put forth guidelines for the management of a dilated ascending aorta, with which this patient presents, for future patients who may present with this novel EDS mutation.

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. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.

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. This "find-the-brain-structure" (FBS) event included teaching students to identify brain structures and other regions of interest in the central nervous system (and potentially in head and neck gross anatomy), which are traditionally taught using brain anatomy atlases and anatomical specimens. The interactive, small group exercise can be conducted in person or virtually on-line in as little as 30 min depending on the scope of objectives being covered. The learning exercise involves coordinated interaction between MS1s with one or several non-clinical faculty and may include one or several physicians (clinical faculty and/or qualified residents). It further allows for varying degrees of instructor interaction online and is easy to convey to instructors who do not have expertise in neuroimaging. Anonymous pre-event survey (n = 113, 100% response rate) versus post-event surveys (n = 92, 81% response rate) were attained from a cohort of MS1s in a neurobiology course. Results showed multiple statistically significant group-level shifts in response to several of the questions, showing an increase in MS1 confidence with reading MRI images (12% increase shift in mean, p < 0.001), confidence in their approaching physicians for medical training (9%, p < 0.01), and comfort levels in working online with virtual team-based peers and with team-based faculty (6%, p < 0.05). Qualitative student feedback revealed highly positive comments regarding the experience overall, encouraging this virtual medium as a desirable educational approach.

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. In a direct comparison to the current state-of-the-art organic terahertz generation crystals, these new materials excel. The discovery and characterization of these novel terahertz generators validate the approach of combining data mining with density functional theory calculations to predict properties of high-performance organic materials, potentially for a host of exciting applications.

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. The time correlation functions between properties in different grid cells are calculated and can be used as the basis for a fitting procedure for extracting spatially varying diffusion coefficients from the simulation. Results for the Lennard-Jones system show that transport behavior varies sharply near the liquid-solid boundary and that the changes depend on the details of the liquid-solid interaction. A quantitative difference between the reduced and detailed models is discussed. It is found that the difference could be associated with assumptions about the form of the transport equations at molecular scales in lieu of problems with the method itself. The study suggests that this approach to fitting molecular simulations to continuum equations may guide the development of appropriate coarse-grained equations to model transport phenomena at nanometer scales.

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. The formalism is demonstrated on a discrete particle simulation of diffusion with a spatially dependent diffusion coefficient. Correlation functions are calculated from the particle simulation and the spatially varying diffusion coefficient is recovered using a fitting procedure.

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.g., plume to aquifer scales and years to centuries). While the multiscale nature of hydrogeologic problems is widely recognized, technological limitations in computation and characterization restrict most practical modeling efforts to fairly coarse representations of heterogeneous properties and processes. For some modern problems, the necessary level of simplification is such that model parameters may lose physical meaning and model predictive ability is questionable for any conditions other than those to which the model was calibrated. Recently, there has been broad interest across a wide range of scientific and engineering disciplines in simulation approaches that more rigorously account for the multiscale nature of systems of interest. In this article, we review a number of such approaches and propose a classification scheme for defining different types of multiscale simulation methods and those classes of problems to which they are most applicable. Our classification scheme is presented in terms of a flowchart (Multiscale Analysis Platform), and defines several different motifs of multiscale simulation. Within each motif, the member methods are reviewed and example applications are discussed. We focus attention on hybrid multiscale methods, in which two or more models with different physics described at fundamentally different scales are directly coupled within a single simulation. Very recently these methods have begun to be applied to groundwater flow and transport simulations, and we discuss these applications in the context of our classification scheme. As computational and characterization capabilities continue to improve, we envision that hybrid multiscale modeling will become more common and also a viable alternative to conventional single-scale models in the near future.

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.

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. Analyses were performed using enzymatic, immunoturbidimetric and ultracentrifugation assays. RESULTS: Data obtained for total cholesterol, triglyceride, HDL-cholesterol, LDL-cholesterol, HDL and LDL particle density, high sensitivity C-reactive protein, serum amyloid-A and apoprotein B-100 concentrations in arterial and venous blood did not demonstrate any significant difference in the means. CONCLUSION: Arterial and venous blood can be used interchangeably to study the effect of blood concentrations of common soluble surrogate markers of atherosclerosis.

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 2.0% sodium chondroitin sulfate in phosphate-buffered saline or intravesical vehicle control. Primary efficacy analysis compared responders (moderately or markedly improved) according to the 7-point Global Response Assessment. Secondary endpoints include questionnaires focused on symptoms and quality of life. RESULTS: Sixty-five evaluable patients were randomized. At the primary endpoint analysis (week 7), 22.6% of the vehicle control group were responders compared with 39.4% of the active therapy group (P = .15). There was no statistically significant difference for any of the secondary endpoints. Overall, 76.9% of the patients in the study reported at least 1 adverse event; most were mild or moderate, the majority associated with the vehicle control treatment. Nine nonserious intervention-related adverse events were reported in 3 patients in the vehicle control group compared with 2 in 1 patient in the active treatment group. CONCLUSION: The difference in treatment effect in this small underpowered study was not statistically significant, although twice as many patients reported a clinically significant benefit with intravesical chondroitin sulfate treatment compared with vehicle control treatment. This trial provides data required to design a well-powered randomized vehicle-controlled trial to determine the true efficacy of this potentially promising therapy.

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. These calculations employ a parallel sampling technique utilizing a Global Arrays toolkit. The resulting evaporation rate constants for each cluster are then fitted to Arrhenius equations to obtain activation energies. We discuss DNT evaporation rate constants and their relation to potentials of mean force, activation energies, and how to account for nonseparability of the reaction coordinate in the reactant state partition function.

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. The results show that very high levels of scalability can be achieved using processor groups with corresponding reductions in the time to completion. The main limitation to scaling appears to be a load imbalance due to variations in the execution times of the individual tasks.

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. The perylene cyclic dimer and its concatenated tetramer were characterized using both structural methods (NMR, mass spectroscopy) and photophysical measurements (UV-vis spectroscopy). Kinetic analyses offer informative insights about reaction pathways and possible mechanisms, which lead to the formation of complex concatenated rings. Molecular dynamic behaviors of both the monocyclic dimer and the concatenated dimer-dimer ring were modeled with the NWChem molecular dynamics software module, which shows distinct stacking activities for the monocyclic dimer and the concatenated tetramer.

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. Additionally, Ecce was architected with mechanisms to integrate alternative electronic structure codes. The successful integration of Amica within Ecce validates the architecture of the latter and brings the high-accuracy capabilities of Amica to a wider audience.

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. RESULTS: The rate of relapse, time to relapse and site of relapse were associated with pathological stage. Five-year progression-free probability was 93% for pT1, 81% for pT2, 67% for pT3A and 57% for pT3B (p <0.001). Compared to patients with pT1-2 those with pT3A-B lesions had earlier relapse after nephrectomy (median 12 vs 26 months, p = 0.001) and were at higher risk for relapse at abdominal sites (14% vs 1.8%, p < 0.001). Abdominal relapse was detected in the absence of symptoms, abnormal biochemical profile or thoracic metastases detectable by chest x-ray in 7 patients (1.4%) overall, including 3 (0.9%) with pT1, 3 (4%) with pT3A and 1 (3%) with pT3B. CONCLUSIONS: The risk and the pattern of relapse of RCC after nephrectomy are associated with pathological stage. For the surveillance of recurrent disease after nephrectomy we recommend annual clinical assessment and chest x-ray in pT1-2 cases. Patients with pT3A-B should be followed every 6 months for the first 3 years with clinical assessment and chest x-ray, and annual followup thereafter. The higher risk of abdominal relapse in patients with pT3A-B indicates that they should receive surveillance abdominal imaging. We recommend abdominal computerized tomography 6, 12, 24 and 36 months postoperatively.

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. Patients were assessed at baseline and at 3, 6, and 12 weeks with the NIH Chronic Prostatitis Symptom Index (NIH-CPSI) and global patient assessments (subjective global assessment and patient assessment questionnaire). RESULTS: Eighty men (average age 56.0 years, range 36 to 78; duration of symptoms 6.5 years, range 0.6 to 32) were randomized to receive levofloxacin (n = 45) or placebo (n = 35). All were evaluated in an intent-to-treat analysis. Both groups experienced progressive improvement in symptoms as measured by the NIH-CPSI. However, the difference in response was not statistically or clinically significant at end of treatment (6 weeks) or at the end of the follow-up visits (12 weeks). No patients withdrew because of adverse events. One patient withdrew before the 6-week assessment. Adverse events (all mild) were reported in 20% of the levofloxacin group and 17% of the placebo group. CONCLUSIONS: This pilot placebo-controlled study showed that 6 weeks of levofloxacin therapy in men diagnosed with CP/CPPS resulted in symptom improvement that was not significantly different from that with placebo at end of treatment or follow-up. The clinical ramifications of these findings need to be addressed.