GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

AbstractGROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported

Endovascular thrombectomy in patients with large core ischemic stroke: a cost-effectiveness analysis from the SELECT study

Background It is unknown whether endovascular thrombectomy (EVT) is cost effective in large ischemic core infarcts. Methods In the prospective, multicenter, cohort study of imaging selection study (SELECT), large core was defined as computed tomography (CT) ASPECTS(CTP) ischemic core volume (rCBF Results From 361 patients enrolled in SELECT, 105 had large core on CT or CTP (EVT 62, MM 43). 19 (31%) EVT vs 6 (14%) MM patients achieved modified Rankin Scale (mRS) score 0–2 (OR 3.27, 95% CI 1.11 to 9.62, P=0.03) with a shift towards better mRS (cOR 2.12, 95% CI 1.05 to 4.31, P=0.04). Over the projected lifetime of patients presenting with large core, EVT led to incremental costs of $33 094 and a gain of 1.34 QALYs per patient, resulting in ICER of$24 665 per QALY. EVT has a higher NMB compared with MM at lower (EVT -$42 747, MM -$76 740) and upper (EVT $155 041, MM$57 134) WTP thresholds. PSA confirmed the results and CEAC showed 77% and 92% acceptability of EVT at the WTP of $50 000 and$100 000, respectively. EVT was associated with an increment of $29 225 in societal costs. The pivotal EVT trials (HERMES, DAWN, DEFUSE 3) were dominant in a sensitivity analysis at the same inputs, with societal cost-savings of$37 901, $86 164 and$22 501 and a gain of 1.62, 2.36 and 2.21 QALYs, respectively. Conclusions In a non-randomized prospective cohort study, EVT resulted in better outcomes in large core patients with higher QALYs, NMB and high cost-effectiveness acceptability rates at current WTP thresholds. Randomized trials are needed to confirm these results. Clinical trial registration NCT0244658

Arte convenzionale – ovvero – perché non possono esistere artisti realmente anticonformisti

The representation of the artist is generally that of a nonconformist, a lonely Bohemian eager to revolutionise the world from his studio. From this perspective, the traditional interpretation of art history is one of linear progress, spurred on by moments of innovation aiming at new states of conventionalism. This article shows how such a perspective has much to do with the philosophy of modern times, even though it doesn’t provide a satisfactory explanation of the meaning and development of art throughout the centuries, bound as they are instead to the necessity of convention with the values of society (or of its élite) rather than on wild individualism

Site fidelity and movement patterns of reef manta rays (Mobula alfredi: Mobulidae) using passive acoustic telemetry in northern Raja Ampat, Indonesia

Though extremely valuable to the local marine tourism industry, there is a dearth of published information on the ecology and population dynamics of reef manta rays (Mobula alfredi) in Raja Ampat, West Papua, Indonesia. Knowledge of the movement ecology in particular of this large and scattered population is urgently needed to better manage the rapidly expanding manta-focused tourism. Here we report the results of an initial passive acoustic telemetry study designed to provide local managers with the first detailed knowledge of the site use and movement patterns of reef mantas in northern Raja Ampat. A total of 39 reef mantas were tagged with Vemco V16 acoustic transmitters over a 15-month period between 27 November 2013 and 22 February 2015. To monitor their movements, VR2W acoustic receivers were deployed at eight sites corresponding to known manta cleaning and feeding aggregation sites, with receivers downloaded every six months over a two-year initial monitoring period. The duration between tag deployments and last date of detections at sites ranged from 1 to 682 days (mean ± SE = 237 ± 27). The cumulative number of days of manta detections at receiver sites by individual mantas ranged from 1 to 188 days (mean ± SE = 42 ± 7). Manta Ridge was the most visited site with 565 days of detections. The tagged mantas demonstrated strong site fidelity to the observed aggregation sites. At the same time, they also exhibited seasonal movements within an approximately 150 km long corridor between sites in the Dampier Strait and the northwest of Waigeo Island. Data analysed from a nearby array of six VR2W receivers in southern Raja Ampat (approximately 180 km to the south of the study area) confirmed that none of the tagged mantas were detected in this array, providing further evidence of strong site fidelity and limited movements within northern Raja Ampat. More than 96% of detections occurred during the daytime. The number of detections reached a peak around noon at Yefnabi Kecil and Eagle Rock and slightly earlier at Manta Ridge. These findings have been shared with the Raja Ampat Marine Protected Area Management Authority and are now being used in the formulation of a management plan for this vulnerable and economically important species to ensure the long-term health of Raja Ampat's reef mantas and the sustainability of manta tourism in the region

Musical events and perceptual ecologies

This paper, followed by two responses, discusses the application of ecological theory to an understanding of a number of issues in the aesthetics of music. It argues for an understanding of music as based in event perception, with an expanded conception of the sources that are specified by those events. Building on the theory of affordances, it considers the limitations of an information theoretic conception of musical complexity, discusses the importance of perceptual learning (understood as shaping by a structured environment) in understanding the affordances of music for different listeners, and raises the challenging problem of the terms in which musical materials might be appropriately described. The apparent tension between ecological and aesthetic positions—in which adaptation and accommodation seem to be at odds with a modernist aesthetic perspective which prioritizes the unsettling and defamiliarizing function of art—is confronted, before the paper concludes with some observations about different disciplinary perspectives on aesthetics, and matters of specificity and generality

Improvement in Survival Associated With Adult-to-Adult Living Donor Liver Transplantation

More than 2000 adult-to-adult living donor liver transplants (LDLT) have been performed in the U.S., yet the potential benefit to liver transplant candidates of undergoing LDLT compared to waiting for deceased donor liver transplant (DDLT) is unknown. The aim of this study was to determine if there is a survival benefit of adult LDL