pClay: A Precise Parallel Algorithm for Comparing Molecular Surfaces

Comparing binding sites as geometric solids can reveal conserved features of protein structure that bind similar molecular fragments and varying features that select different partners. Due to the subtlety of these features, algorithmic efficiency and geometric precision are essential for comparison accuracy. For these reasons, this paper presents pClay, the first structure comparison algorithm to employ fine-grained parallelism to enhance both throughput and efficiency. We evaluated the parallel performance of pClay on both multicore workstation CPUs and a 61-core Xeon Phi, observing scaleable speedup in many thread configurations. Parallelism unlocked levels of precision that were not practical with existing methods. This precision has important applications, which we demonstrate: A statistical model of steric variations in binding cavities, trained with data at the level of precision typical of existing work, can overlook 46% of authentic steric influences on specificity (p <= .02). The same model, trained with more precise data from pClay, overlooked 0% using the same standard of statistical significance. These results demonstrate how enhanced efficiency and precision can advance the detection of binding mechanisms that influence specificity

Brass Ensembles Showcase

Kennesaw State University School of Music presents Brass Ensembles Showcase featuring performances by various brass ensembles showcasing the KSU brass faculty and students.https://digitalcommons.kennesaw.edu/musicprograms/1777/thumbnail.jp

Management of patients at the hepatopancreatobiliary unit of a London teaching hospital during the COVID-19 pandemic

To mitigate COVID-19-related shortage of treatment capacity, the hepatopancreatobiliary (HPB) unit of the Royal Free Hospital London (RFHL) transferred its practice to independent hospitals in Central London through the North Central London Cancer Alliance. The aim of this study was to critically assess this strategy and evaluate perioperative outcomes. Prospectively collected data were reviewed on all patients who were treated under the RFHL HPB unit in six hospitals between November 2020 and October 2021. A total of 1541 patients were included, as follows: 1246 (81%) at the RFHL, 41 (3%) at the Chase Farm Hospital, 23 (2%) at the Whittington Hospital, 207 (13%) at the Princess Grace Hospital, 12 (1%) at the Wellington Hospital and 12 (1%) at the Lister Hospital, Chelsea. Across all institutions, overall complication rate were 40%, major complication (Clavien-Dindo grade ≥ 3a) rate were 11% and mortality rates were 1.4%, respectively. In COVID-19-positive patients (n = 28), compared with negative patients, complication rate and mortality rates were increased tenfold. Outsourcing HPB patients, including their specialist care, to surrounding institutions was safe and ensured ongoing treatment with comparable outcomes among the institutions during the COVID-19 pandemic. Due to the lack of direct comparison with a non-pandemic cohort, these results can strictly only be applied within a pandemic setting

Treatment as prevention: preparing the way

Potent antiretroviral therapy (ART) reduces mortality and morbidity in people living with HIV by reducing viral load and allowing their immune systems to recover. The reduction in viral load soon after starting ART has led to the hypothesis that early and widespread ART could prevent onward transmission and therefore eliminate the HIV epidemic in the long term. While several authors have argued that it is feasible to use HIV treatment as prevention (TasP), provided treatment is started sufficiently early, others have reasonably drawn attention to the many operational difficulties that will need to be overcome if the strategy is to succeed in reducing HIV transmission. Furthermore, international public health policy must be based on more than theoretical studies, no matter how appealing. Community randomized controlled trials provide the gold standard for testing the extent to which early treatment reduces incidence, but much still needs to be understood and the immediate need is for operational studies to explore the practical feasibility of this approach. Here, we examine some of the issues to be addressed, the obstacles to be overcome, and strategies that may be necessary if TasP is to be effective. Studies of this kind will provide valuable information for the design of large-scale trials, as well as essential information that will be needed if early treatment is to be incorporated into public health policy

Selector’s Guide for Resources in the Humanities: An Open Access Student Publication

Students in the Master of Library and Information Science degree program at Valdosta State University who completed the elective course in Humanities Information Services in 2014 produced bibliographies on sub-disciplines of the humanities. These example bibliographies are compiled into the document titled Selector’s Guide for Resources in the Humanities: An Open Access Student Publication. The student authored sections of the Selector’s Guide focus on narrowly defined humanities areas and contain resources representative of professional organizations, major serials, online indexes and databases, primary sources, classic and contemporary monographs, standard reference works, vetted websites, media, and open access resources. The compilers of this guide offer it as a companion to the document entitled Teaching Guide for Resources in the Humanities: An Open Access Publication. The Teaching Guide references two tutorials, one on WorldCat and one on the Gale Literary Index. Copies of both tutorials are found in here. The authors of these materials invite professors seeking a guide to the providers and formats of information in the humanities to use the bibliographies therein as a starting point for creating assignments and to use materials from the teaching guide as class exercises, if appropriate

NuSTAR observatory science operations: on-orbit acclimation

The Nuclear Spectroscopic Telescope Array (NuSTAR) is the first focusing high energy (3-79 keV) X-ray observatory. The NuSTAR project is led by Caltech, which hosts the Science Operations Center (SOC), with mission operations managed by UCB Space Sciences Laboratory. We present an overview of NuSTAR science operations and describe the on-orbit performance of the observatory. The SOC is enhancing science operations to serve the community with a guest observing program beginning in 2015. We present some of the challenges and approaches taken by the SOC to operating a full service space observatory that maximizes the scientific return from the mission

Pulmonary fibrosis: tissue characterization using late-enhanced MRI compared with unenhanced anatomic high-resolution CT

PURPOSE:We aimed to prospectively evaluate anatomic chest computed tomography (CT) with tissue characterization late gadolinium-enhanced magnetic resonance imaging (MRI) in the evaluation of pulmonary fibrosis (PF).METHODS:Twenty patients with idiopathic pulmonary fibrosis (IPF) and twelve control patients underwent late-enhanced MRI and high-resolution CT. Tissue characterization of PF was depicted using a segmented inversion-recovery turbo low-angle shot MRI sequence. Pulmonary arterial blood pool nulling was achieved by nulling main pulmonary artery signal. Images were read in random order by a blinded reader for presence and extent of overall PF (reticulation and honeycombing) at five anatomic levels. Overall extent of IPF was estimated to the nearest 5% as well as an evaluation of the ratios of IPF made up of reticulation and honeycombing. Overall grade of severity was dependent on the extent of reticulation and honeycombing.RESULTS:No control patient exhibited contrast enhancement on lung late-enhanced MRI. All IPF patients were identified with late-enhanced MRI. Mean signal intensity of the late-enhanced fibrotic lung was 31.8±10.6 vs. 10.5±1.6 for normal lung regions, P < 0.001, resulting in a percent elevation in signal intensity from PF of 204.8%±90.6 compared with the signal intensity of normal lung. The mean contrast-to-noise ratio was 22.8±10.7. Late-enhanced MRI correlated significantly with chest CT for the extent of PF (R=0.78, P = 0.001) but not for reticulation, honeycombing, or coarseness of reticulation or honeycombing.CONCLUSION:Tissue characterization of IPF is possible using inversion recovery sequence thoracic MRI

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Spontaneous vortices in the formation of Bose-Einstein condensates

Phase transitions are ubiquitous in nature, ranging from protein folding and denaturisation, to the superconductor-insulator quantum phase transition, to the decoupling of forces in the early universe. Remarkably, phase transitions can be arranged into universality classes, where systems having unrelated microscopic physics exhibit identical scaling behaviour near the critical point. Here we present an experimental and theoretical study of the Bose-Einstein condensation phase transition of an atomic gas, focusing on one prominent universal element of phase transition dynamics: the spontaneous formation of topological defects during a quench through the transition. While the microscopic dynamics of defect formation in phase transitions are generally difficult to investigate, particularly for superfluid phase transitions, Bose-Einstein condensates (BECs) offer unique experimental and theoretical opportunities for probing such details. Although spontaneously formed vortices in the condensation transition have been previously predicted to occur, our results encompass the first experimental observations and statistical characterisation of spontaneous vortex formation in the condensation transition. Using microscopic theories that incorporate atomic interactions and quantum and thermal fluctuations of a finite-temperature Bose gas, we simulate condensation and observe vortex formation in close quantitative agreement with our experimental results. Our studies provide further understanding of the development of coherence in superfluids, and may allow for direct investigation of universal phase-transition dynamics.Comment: 14 pages, 6 figures. Accepted for publication in Nature. Supplementary movie files are available at http://www.physics.uq.edu.au/people/mdavis/spontaneous_vortice