Accelerating COBAYA3 on multi-core CPU and GPU systems using PARALUTION

COBAYA3 is a multi-physics system of codes which includes two 3D multi-group neutron diffusion codes, ANDES and COBAYA3-PBP, coupled with COBRA-TF, COBRA-IIIc and SUBCHANFLOW sub-channel thermal-hydraulic codes, for the simulation of LWR core transients. The 3D multi-group neutron diffusion equations are expressed in terms of a sparse linear system which can be solved using different iterative Krylov subspace solvers. The mathematical SPARSKIT library has been used for these purposes as it implements among others, external GMRES, PGMRES and BiCGStab solvers. Multi-core CPUs and graphical processing units (GPUs) provide high performance capabilities which are able to accelerate many scientific computations. To take advantage of these new hardware features in daily use computer codes, the integration of the PARALUTION library to solve sparse systems of linear equations is a good choice. It features several types of iterative solvers and preconditioners which can run on both multi-core CPUs and GPU devices without any modification from the interface point of view. This feature is due to the great portability obtained by the modular and flexible design of the library. By exploring this technology, namely the implementation of the PARALUTION library in COBAYA3, we are able to decrease the solution time of the sparse linear systems by a factor 5.15x on GPU and 2.56x on multi-core CPU using standard hardware. These obtained speedup factors in addition to the implementation details are discussed in this paper

X-ray crystallographic structure of 3-(Propan-2-ylidene) benzofuran-2(3H)-one

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Patient satisfaction while enrolled in clinical trials: A literature review

Patient satisfaction surveys may not adequately reflect organizations that conduct research in patients who enroll in clinical trials. The purpose of this systematic literature review was to summarize the current state of knowledge of patient satisfaction while enrolled in clinical trials utilizing a widely used, validated patient satisfaction instrument. A comprehensive literature search was conducted using CINAHL, EMBASE, PsycInfo, PubMed and Web of Science. Studies were evaluated in terms of clinical trial participation; assessment conducted during or after participation; utilization of a validated instrument; a pharmacological intervention; and the paper was published in English. Only nine studies met this review’s inclusion criteria. Eight studies utilized investigator-developed patient satisfaction instruments and only one study used a widely-used, validated patient satisfaction instrument. Two studies evaluated patient satisfaction during the development of the instrument. Of the nine studies identified, only five patient satisfaction domains were common across the studies and only study evaluated the associations of patient satisfaction responses with clinical outcomes. Given the importance of patient satisfaction surveys, future studies need to focus on this subset of patients enrolled in clinical trials to evaluate a patient’s experience and its impact on protocol compliance and protocol outcomes. Future studies need to focus on domains associated with clinical trial participation and look beyond the current patients’ general expectations about healthcare accessibility, facilities, healthcare team clinical skills, and their ability to focus and listen to the patients’ concerns. Experience Framework This article is associated with the Policy & Measurement lens of The Beryl Institute Experience Framework. (https://www.theberylinstitute.org/ExperienceFramework). Access other PXJ articles related to this lens. Access other resources related to this lens

The Thioredoxin-Regulated α-Amylase 3 of Arabidopsis thaliana Is a Target of S-Glutathionylation

Reactive oxygen species (ROS) are produced in cells as normal cellular metabolic by-products. ROS concentration is normally low, but it increases under stress conditions. To stand ROS exposure, organisms evolved series of responsive mechanisms. One such mechanism is protein S-glutathionylation. S-glutathionylation is a post-translational modification typically occurring in response to oxidative stress, in which a glutathione reacts with cysteinyl residues, protecting them from overoxidation. α-Amylases are glucan hydrolases that cleave α-1,4-glucosidic bonds in starch. The Arabidopsis genome contains three genes encoding α-amylases. The sole chloroplastic member, AtAMY3, is involved in osmotic stress response and stomatal opening and is redox-regulated by thioredoxins. Here we show that AtAMY3 activity was sensitive to ROS, such as H2O2. Treatments with H2O2 inhibited enzyme activity and part of the inhibition was irreversible. However, in the presence of glutathione this irreversible inhibition was prevented through S-glutathionylation. The activity of oxidized AtAMY3 was completely restored by simultaneous reduction by both glutaredoxin (specific for the removal of glutathione-mixed disulfide) and thioredoxin (specific for the reduction of protein disulfide), supporting a possible liaison between both redox modifications. By comparing free cysteine residues between reduced and GSSG-treated AtAMY3 and performing oxidation experiments of Cys-to-Ser variants of AtAMY3 using biotin-conjugated GSSG, we could demonstrate that at least three distinct cysteinyl residues can be oxidized/glutathionylated, among those the two previously identified catalytic cysteines, Cys499 and Cys587. Measuring the pKa values of the catalytic cysteines by alkylation at different pHs and enzyme activity measurement (pKa1 = 5.70 ± 0.28; pKa2 = 7.83 ± 0.12) showed the tendency of one of the two catalytic cysteines to deprotonation, even at physiological pHs, supporting its propensity to undergo redox post-translational modifications. Taking into account previous and present findings, a functional model for redox regulation of AtAMY3 is proposed