The distorted-wave impulse approximation for electron capture into excited states

Total cross sections for electron capture are calculated for collisions of fast protons and a-particles with atomic hydrogen. The distorted-wave impulse approximation is applied over the energy range 10-1500 keV/u. State-selective results are given for the 1s, 2s and 2p levels. Both the post and prior forms of the model are calculated and compared with results from other theories and experimental measurements. In general the model performs very well in comparison with experiment over this energy range though discrepancies arise at lower energies.

Design of an intravaginal ring for the controlled delivery of 17b-estradiol as its 3-acetate ester

Suitable ester prodrugs of 17b-estradiol are identified, thus permitting effective sustained and controlled estrogen replacement therapy (ERT) from an elastomeric, silicone intravaginal ring (IVR). IVR devices of reservoir design were prepared by blending silicone elastomer base with n-propylorthosilicate (cross-linker) and 10% w/w of 17b-estradiol or an ester prodrug, the mix being activated with 0.5% w/w stannous octoate and cured at 808C for 2 min. A rate-controlling membrane was similarly prepared, without the active agent. IVR devices were of cross-sectional diameter 9 mm, outer diameter 54 mm, with core cross-sectional diameter of 2 mm and core length varied as required. Sink conditions were evident for the 17b-estradiol esters in 1.0% aqueous benzalkonium chloride solution. The low release rates into 0.9% w/v saline of the lipophilic valerate and benzoate esters were due to their intrinsically low aqueous solubilities. In vivo, these esters failed to raise plasma estradiol above baseline levels in postmenopausal human volunteers, despite good in vitro release characteristics under sink conditions. The best release rates under sink conditions, in combination with substantial aqueous solubilities as indicated by the release rates into saline, were observed for the acetate and propionate esters. A
combination of drug release characteristics, short plasma half-life and a toxicologically acceptable hydrolysis product indicated that 17b-estradiol-3-acetate was the prodrug of choice for IVR delivery of ERT. In vivo, an IVR device releasing
100 mg/day of estradiol as its 3-acetate ester maintained over 84 days a circulating plasma concentration in the region of 300 pmol l , within the clinically desirable range for ERT.

Scalable black-box prediction models for multi-dimensional adaptation on NUMA multi-cores

This paper presents a scalable, statistical ‘black-box’ model for predicting the performance of parallel programs on multi-core non-uniform memory access (NUMA) systems. We derive a model with low overhead, by reducing data collection and model training time. The model can accurately predict the behaviour of parallel applications in response to changes in their concurrency, thread layout on NUMA nodes, and core voltage and frequency. We present a framework that applies the model to achieve significant energy and energy-delay-square (ED2) savings (9% and 25%, respectively) along with performance improvement (10% mean) on an actual 16-core NUMA system running realistic application workloads. Our prediction model proves substantially more accurate than previous efforts.

PLUMED 2: New feathers for an old bird

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here a,complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Program summary

Program title: PLUMED 2

Catalogue identifier: AEEE_v2_0

Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEE_v2_0.html

Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland

Licensing provisions: Yes

No. of lines in distributed program, including test data, etc.: 700646

No. of bytes in distributed program, including test data, etc.: 6618136

Distribution format: tar.gz

Programming language: ANSI-C++.

Computer: Any computer capable of running an executable produced by a C++ compiler.

Operating system: Linux operating system, Unix OSs.

Has the code been vectorized or parallelized?: Yes, parallelized using MPI.

RAM: Depends on the number of atoms, the method chosen and the collective variables used.

Classification: 3, 7.7, 23. Catalogue identifier of previous version: AEEE_v1_0.

Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1961.

External routines: GNU libmatheval, Lapack, Bias, MPI. (C) 2013 Elsevier B.V. All rights reserved.

How Prepared are UK Medical Graduates for Practice? Final report from a programme of research commissioned by the General Medical Council

This programme of research aimed to understand the extent to which current UK medical graduates are prepared for practice. Commissioned by the General Medical Council, we conducted: (1) A Rapid Review of the literature between 2009 and 2013; (2) narrative interviews with a range of stakeholders; and (3) longitudinal audio-diaries with Foundation Year 1 doctors. The Rapid Review (RR) resulted in data from 81 manuscripts being extracted and mapped against a coding framework (including outcomes from Tomorrow's Doctors (2009) (TD09)). A narrative synthesis of the data was undertaken. Narrative interviews were conducted with 185 participants from 8 stakeholder groups: F1 trainees, newly registered trainee doctors, clinical educators, undergraduate and postgraduate deans and foundation programme directors, other healthcare professionals, employers, policy and government and patient and public representatives. Longitudinal audio-diaries were recorded by 26 F1 trainees over 4 months. The data were analysed thematically and mapped against TD09. Together these data shed light onto how preparedness for practice is conceptualised, measured, how prepared UK medical graduates are for practice, the effectiveness of transition interventions and the currently debated issue of bringing full registration forward to align with medical students’ graduation. Preparedness for practice was conceptualised as both a long- and short-term venture that included personal readiness as well as knowledge, skills and attitudes. It has mainly been researched using self-report measures of generalised incidents that have been shown to be problematic. In terms of transition interventions: assistantships were found to be valuable and efficacious for proactive students as team members, shadowing is effective when undertaken close to employment/setting of F1 post and induction is generally effective but of inconsistent quality. The August transition was highlighted in our interview and audio-diary data where F1s felt unprepared, particularly for the step-change in responsibility, workload, degree of multitasking and understanding where to go for help. Evidence of preparedness for specific tasks, skills and knowledge was contradictory: trainees are well prepared for some practical procedures but not others, reasonably well prepared for history taking and full physical examinations, but mostly unprepared for adopting an holistic understanding of the patient, involving patients in their care, safe and legal prescribing, diagnosing and managing complex clinical conditions and providing immediate care in medical emergencies. Evidence for preparedness for interactional and interpersonal aspects of practice was inconsistent with some studies in the RR suggesting graduates were prepared for team working and communicating with colleagues and patients, but other studies contradicting this. Interview and audio-diary data highlights concerns around F1s preparedness for communicating with angry or upset patients and relatives, breaking bad news, communicating with the wider team (including interprofessionally) and handover communication. There was some evidence in the RR to suggest that graduates were unprepared for dealing with error and safety incidents and lack an understanding of how the clinical environment works. Interview and audio-diary data backs this up, adding that F1s are also unprepared for understanding financial aspects of healthcare. In terms of being personally prepared, RR, interview and audio diary evidence is mixed around graduates’ preparedness for identifying their own limitations, but all data points to graduates’ difficulties in the domain of time management. In terms of personal and situational demographic factors, the RR found that gender did not typically predict perceptions of preparedness, but graduates from more recent cohorts, graduate entry students, graduates from problem based learning courses, UK educated graduates and graduates with an integrated degree reported feeling better prepared. The longitudinal audio-diaries provided insights into the preparedness journey for F1s. There seems to be a general development in the direction of trainees feeling more confident and competent as they gain more experience. However, these developments were not necessarily linear as challenging circumstances (e.g. new specialty, new colleagues, lack of staffing) sometimes made them feel unprepared for situations where they had previously indicated preparedness.

Finding Relevant Tweets

When a user of a microblogging site authors a microblog
post or browses through a microblog post, it provides cues as to what
topic she is interested in at that point in time. Example-based search
that retrieves similar tweets given one exemplary tweet, such as the one
just authored, can help provide the user with relevant content. We investigate
various components of microblog posts, such as the associated
timestamp, author’s social network, and the content of the post, and
develop approaches that harness such factors in finding relevant tweets
given a query tweet. An empirical analysis of such techniques on real
world twitter-data is then presented to quantify the utility of the various
factors in assessing tweet relevance. We observe that content-wise similar
tweets that also contain extra information not already present in the
query, are perceived as useful. We then develop a composite technique
that combines the various approaches by scoring tweets using a dynamic
query-specific linear combination of separate techniques. An empirical
evaluation establishes the effectiveness of the composite technique, and
that it outperforms each of its constituents.

Automating fault tolerance in high-performance computational biological jobs using multi-agent approaches

Background: Large-scale biological jobs on high-performance computing systems require manual intervention if one or more computing cores on which they execute fail. This places not only a cost on the maintenance of the job, but also a cost on the time taken for reinstating the job and the risk of losing data and execution accomplished by the job before it failed. Approaches which can proactively detect computing core failures and take action to relocate the computing core's job onto reliable cores can make a significant step towards automating fault tolerance. Method: This paper describes an experimental investigation into the use of multi-agent approaches for fault tolerance. Two approaches are studied, the first at the job level and the second at the core level. The approaches are investigated for single core failure scenarios that can occur in the execution of parallel reduction algorithms on computer clusters. A third approach is proposed that incorporates multi-agent technology both at the job and core level. Experiments are pursued in the context of genome searching, a popular computational biology application. Result: The key conclusion is that the approaches proposed are feasible for automating fault tolerance in high-performance computing systems with minimal human intervention. In a typical experiment in which the fault tolerance is studied, centralised and decentralised checkpointing approaches on an average add 90% to the actual time for executing the job. On the other hand, in the same experiment the multi-agent approaches add only 10% to the overall execution time

Runtime Support for Adaptive Power Capping on Heterogeneous SoCs

Power capping is a fundamental method for reducing the energy consumption of a wide range of modern computing environments, ranging from mobile embedded systems to datacentres. Unfortunately, maximising performance and system efficiency under static power caps remains challenging, while maximising performance under dynamic power caps has been largely unexplored. We present an adaptive power capping method that reduces the power consumption and maximizes the performance of heterogeneous SoCs for mobile and server platforms. Our technique combines power capping with coordinated DVFS, data partitioning and core allocations on a heterogeneous SoC with ARM processors and FPGA resources. We design our framework as a run-time system based on OpenMP and OpenCL to utilise the heterogeneous resources. We evaluate it through five data-parallel benchmarks on the Xilinx SoC which allows fully voltage and frequency control. Our experiments show a significant performance boost of 30% under dynamic power caps with concurrent execution on ARM and FPGA, compared to a naive separate approach.

Non-radial instabilities and progenitor asphericities in core-collapse supernovae

Since core-collapse supernova simulations still struggle to produce robust neutrino-driven explosions in 3D, it has been proposed that asphericities caused by convection in the progenitor might facilitate shock revival by boosting the activity of non-radial hydrodynamic instabilities in the post-shock region. We investigate this scenario in depth using 42 relativistic 2D simulations with multigroup neutrino transport to examine the effects of velocity and density perturbations in the progenitor for different perturbation geometries that obey fundamental physical constraints (like the anelastic condition). As a framework for analysing our results, we introduce semi-empirical scaling laws relating neutrino heating, average turbulent velocities in the gain region, and the shock deformation in the saturation limit of non-radial instabilities. The squared turbulent Mach number, 〈Ma2〉, reflects the violence of aspherical motions in the gain layer, and explosive runaway occurs for 〈Ma2〉 ≳ 0.3, corresponding to a reduction of the critical neutrino luminosity by ∼25∼25 per cent compared to 1D. In the light of this theory, progenitor asphericities aid shock revival mainly by creating anisotropic mass flux on to the shock: differential infall efficiently converts velocity perturbations in the progenitor into density perturbations δρ/ρ at the shock of the order of the initial convective Mach number Maprog. The anisotropic mass flux and ram pressure deform the shock and thereby amplify post-shock turbulence. Large-scale (ℓ = 2, ℓ = 1) modes prove most conducive to shock revival, whereas small-scale perturbations require unrealistically high convective Mach numbers. Initial density perturbations in the progenitor are only of the order of Ma2progMaprog2 and therefore play a subdominant role.