Strategies to parallelize a finite element mesh truncation technique on multi-core and many-core architectures

Achieving maximum parallel performance on multi-core CPUs and many-core GPUs is a challenging task depending on multiple factors. These include, for example, the number and granularity of the computations or the use of the memories of the devices. In this paper, we assess those factors by evaluating and comparing different parallelizations of the same problem on a multiprocessor containing a CPU with 40 cores and four P100 GPUs with Pascal architecture. We use, as study case, the convolutional operation behind a non-standard finite element mesh truncation technique in the context of open region electromagnetic wave propagation problems. A total of six parallel algorithms implemented using OpenMP and CUDA have been used to carry out the comparison by leveraging the same levels of parallelism on both types of platforms. Three of the algorithms are presented for the first time in this paper, including a multi-GPU method, and two others are improved versions of algorithms previously developed by some of the authors. This paper presents a thorough experimental evaluation of the parallel algorithms on a radar cross-sectional prediction problem. Results show that performance obtained on the GPU clearly overcomes those obtained in the CPU, much more so if we use multiple GPUs to distribute both data and computations. Accelerations close to 30 have been obtained on the CPU, while with the multi-GPU version accelerations larger than 250 have been achieved.Funding for open access charge: CRUE-Universitat Jaume

Combination of qualitative and quantitative methods for developing a new Health Related Quality of Life measure for patients with anogenital warts

BACKGROUND: Anogenital warts are the most easily recognized sign of genital Human Papilloma Virus infection. The objective was to develop a short, valid and reliable questionnaire to measure Health Related Quality of Life (HRQL) in patients with anogenital warts. METHODS: First a literature review was performed to identify relevant papers describing the impact of anogenital warts in HRQL; second the main domains were identified by some experts in a focus group, and third in-depth-semi-structured interviews were conducted in patients with anogenital warts to identify the initial set of items. A qualitative reduction of the initial set of items was performed based on the mean scoring of the experts for the three scales: clarity, frequency and importance. The initial questionnaire was pilot tested in 135 patients. Rasch analysis was performed with the results of the questionnaire in order to refine the instrument. Spearman's correlation was calculated between the initial questionnaire and the reduced version. Additionally the measurement properties (validity and reliability) of the resulting final questionnaire were tested and compared using standard procedures (Cronbach's Alpha and item-total correlation). RESULTS: the main domains identified as affected in patient's life were: sexual, colleagues and partner relationships. After a proper qualitative reduction the initial set of 134 items was reduced to 22. The questionnaire was pilot tested in 135 patients and two dimensions were identified after the multifactorial analysis: emotional dimension and sexual activity dimension. As a result of the Rasch analysis the questionnaire was reduced to 10 items. High correlation was found between the initial and the reduced version for the two dimensions. Cronbach's alpha values were acceptable (0.86). CONCLUSION: The initial 22 items questionnaire was reduced by Rasch analysis to a version of 10 items, with two dimensions: emotional and sexual. The results suggest the adequacy of the 10 items to evaluate HRQL of patients with anogenital warts in a valid and reliable way

Out-of-core macromolecular simulations on multithreaded architectures

We address the solution of large-scale eigenvalue problems that appear in the motion simulation of complex macromolecules on multithreaded platforms, consisting of multicore processors and possibly a graphics processor (GPU). In particular, we compare specialized implementations of several high- performance eigensolvers that, by relying on disk storage and out-of-core (OOC) techniques, can in principle tackle the large memory requirements of these biological problems, which in general do not fit into the main memory of current desktop machines. All these OOC eigensolvers, except for one, are composed of compute-bound (i.e., arithmetically-intensive) operations, which we accelerate by exploiting the performance of current multicore processors and, in some cases, by additionally off-loading certain parts of the computation to a GPU accelerator. One of the eigensolvers is a memory-bound algorithm, which strongly constrains its performance when the data is on disk. However, this method exhibits a much lower arithmetic cost compared with its compute- bound alternatives for this particular application. Experimental results on a desktop platform, representative of current server technology, illustrate the potential of these methods to address the simulation of biological activity

Self-perception of leadership styles and behaviour in primary health care

Background: The concept of leadership has been studied in various disciplines and from different theoretical approaches. It is a dynamic concept that evolves over time. There are few studies in our field on managers' self-perception of their leadership style. There are no pure styles, but one or another style is generally favoured to a greater or lesser degree. In the primary health care (PHC) setting, managers' leadership style is defined as a set of attitudes, behaviours, beliefs and values. The objectives of this study were to describe and learn about the self-perception of behaviours and leadership styles among PHC managers; to determine the influence of the leadership style on job satisfaction, efficiency, and willingness to work in a team; and to determine the relationship between transformational and transactional styles according age, gender, profession, type of manager years of management experience, and the type of organization. Methods: To describe leadership styles as perceived by PHC managers, a cross sectional study was performed using an 82 items-self-administered Multifactor Leadership Questionnaire (MLQ). This questionnaire measures leadership styles, attitudes and behaviour of managers. The items are grouped into three first order variables (transformational, transactional and laissez-faire) and ten second order variables (which discriminate leader behaviours). Additionally, the questionnaire evaluates organizational consequences such as extra-effort, efficiency and satisfaction. Results: One hundred forty responses from 258 managers of 133 PHC teams in the Barcelona Health Area (response rate: 54.26%). Most participants were nurses (61.4%), average age was 49 years and the gender predominantly female (75%). Globally, managers assessed themselves as equally transactional and transformational leaders (average: 3.30 points). Grouped by profession, nurses (28.57% of participants) showed a higher transactional leadership style, over transformational leadership style, compared to physicians (3.38 points, p < 0.003). Considering gender, men obtained the lowest results in transactional style (p < 0.015). Both transactional and transformational styles correlate with efficiency and job satisfaction (r = 0.724 and r = 0.710, respectively). Conclusions: PHC managers' self-perception of their leadership style was transactional, focused on the maintenance of the status quo, although there was a trend in some scores towards the transformational style, mainly among nurse managers. Both styles correlate with satisfaction and willingness to strive to work better. Keywords: Leadership, Primary health care, Self-concept, Job satisfaction, MLQ, Manager

Desarrollo de la técnica de FICTION como nueva herramienta para el diagnóstico precoz de cáncer de pulmón

El cáncer de pulmón es una de las causas de muerte más frecuentes en el mundo occidental. La supervivencia global de los pacientes no supera el 15% a los 5 años, debido principalmente a que la mayor parte de los casos se diagnostican en estadios avanzados. Además de la prevención primaria, mediante la reducción del consumo de tabaco, son necesarias nuevas tecnologías para el diagnóstico precoz de la enfermedad. Estudios recientes han demostrado que el TAC helicoidal del tórax es efectivo en la detección de nódulos pulmonares malignos en estadios precoces. En la actualidad se está valorando su eficacia en series amplias de pacientes de alto riesgo. Recientemente se ha desarrollado una nueva técnica de citogenética molecular, el FICTION (Fluorescence Immunophenotyping and Interphase Cytogenetics as a Tool for the Investigation of Neoplasms). Esta técnica permite el análisis simultáneo de marcadores inmunofenotípicos y alteraciones genéticas presentes en las células tumorales. El objetivo de nuestro proyecto es su puesta a punto para el estudio de muestras de esputo y lavado broncoalveolar de pacientes con cáncer de pulmón. El fin último es estudiar la posibilidad de que esta técnica pueda ser utilizada, junto con el TAC helicoidal, en programas de detección precoz de cáncer de pulmón, para pacientes de alto riesgo. En este trabajo presentamos una revisión de la contribución de las distintas técnicas de citogenética al estudio del cáncer de pulmón y la metodología de trabajo que vamos a llevar a cabo en nuestro proyecto

Development of a questionnaire to measure health-related quality of life (HRQoL) in patients with atrial fibrillation (AF-QoL)

<p>Abstract</p> <p>Background</p> <p>The Health-Related Quality of Life (HRQoL) assessment in atrial fibrillation (AF) patients has traditionally been carried out in a poorly standardised fashion, or via the use of non disease-specific HRQoL questionnaires. The development of a HRQoL questionnaire with a good measuring performance will allow for a standardised assessment of the impact of this disease on the patient's daily living.</p> <p>Methods</p> <p>A bibliography review was conducted to identify the most relevant domains of daily living in AF patients. Subsequently, a focus group was created with the aid of cardiologists, and 17 patients were interviewed to identify the most-affected HRQoL domains. A qualitative analysis of the interview answers was performed, which was used to develop a pilot questionnaire administered to a 112-patient sample. Based on patient responses, an analysis was carried out following the statistical procedures defined by the Classical Test Theory (CTT) and the Item Response Theory (IRT). Reliablility was assessed via Cronbach's coefficient alpha and item-total score correlations. A factorial analysis was performed to determine the number of domains. For each domain, a Rasch analysis was carried out, in order to reduce and stand hierarchically the questionnaire items.</p> <p>Results</p> <p>By way of the bibliography review and the expert focus group, 10 domains were identified. The patient interviews allowed for the identification of 286 items that later were downsized to 40 items. The resultant preliminary questionnaire was administered to a 112-patient sample (pilot study). The Rasch analysis led to the definition of two domains, comprising 7 and 11 items respectively, which corresponded to the psychological and physical domains (18 items total), thereby giving rise to the initial AF-QoL-18 questionnaire. Cronbach's coefficient alpha was acceptable (0.91).</p> <p>Conclusion</p> <p>An initial HRQoL questionnaire, AFQoL-18, has been developed to assess HRQoL in AF patients.</p

A model based on the quantification of complement C4c, CYFRA 21-1 and CRP exhibits high specificity for the early diagnosis of lung cancer

Lung cancer screening detects early-stage cancers, but also a large number of benign nodules. Molecular markers can help in the lung cancer screening process by refining inclusion criteria or guiding the management of indeterminate pulmonary nodules. In this study, we developed a diagnostic model based on the quantification in plasma of complement-derived fragment C4c, cytokeratin fragment 21-1 (CYFRA 21-1) and C-reactive protein (CRP). The model was first validated in two independent cohorts, and showed a good diagnostic performance across a range of lung tumor types, emphasizing its high specificity and positive predictive value. We next tested its utility in two clinically relevant contexts: assessment of lung cancer risk and nodule malignancy. The scores derived from the model were associated with a significantly higher risk of having lung cancer in asymptomatic individuals enrolled in a computed tomography (CT)-screening program (OR = 1.89; 95% CI = 1.20–2.97). Our model also served to discriminate between benign and malignant pulmonary nodules (AUC: 0.86; 95% CI = 0.80–0.92) with very good specificity (92%). Moreover, the model performed better in combination with clinical factors, and may be used to reclassify patients with intermediate-risk indeterminate pulmonary nodules into patients who require a more aggressive work-up. In conclusion, we propose a new diagnostic biomarker panel that may dictate which incidental or screening-detected pulmonary nodules require a more active work-up

Efficacy and safety of acupuncture for the treatment of non-specific acute low back pain: a randomised controlled multicentre trial protocol [ISRCTN65814467]

BACKGROUND: Low back pain and its associated incapacitating effects constitute an important healthcare and socioeconomic problem, as well as being one of the main causes of disability among adults of working age. The prevalence of non-specific low back pain is very high among the general population, and 60–70% of adults are believed to have suffered this problem at some time. Nevertheless, few randomised clinical trials have been made of the efficacy and efficiency of acupuncture with respect to acute low back pain. The present study is intended to assess the efficacy of acupuncture for acute low back pain in terms of the improvement reported on the Roland Morris Questionnaire (RMQ) on low back pain incapacity, to estimate the specific and non-specific effects produced by the technique, and to carry out a cost-effectiveness analysis. METHODS/DESIGN: Randomised four-branch controlled multicentre prospective study made to compare semi-standardised real acupuncture, sham acupuncture (acupuncture at non-specific points), placebo acupuncture and conventional treatment. The patients are blinded to the real, sham and placebo acupuncture treatments. Patients in the sample present symptoms of non specific acute low back pain, with a case history of 2 weeks or less, and will be selected from working-age patients, whether in paid employment or not, referred by General Practitioners from Primary Healthcare Clinics to the four clinics participating in this study. In order to assess the primary and secondary result measures, the patients will be requested to fill in a questionnaire before the randomisation and again at 3, 12 and 48 weeks after starting the treatment. The primary result measure will be the clinical relevant improvement (CRI) at 3 weeks after randomisation. We define CRI as a reduction of 35% or more in the RMQ results. DISCUSSION: This study is intended to obtain further evidence on the effectiveness of acupuncture on acute low back pain and to isolate the specific and non-specific effects of the treatment

Insights into the deterministic skill of air quality ensembles from the analysis of AQMEII data

© 2016. This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited. Ioannis Kioutsioukis, et al, ‘Insights into the deterministic skill of air quality ensembles from the analysis of AQMEII data’, Atmospheric Chemistry and Physics, Vol 16(24): 15629-15652, published 20 December 2016, the version of record is available at doi:10.5194/acp-16-15629-2016 Published by Copernicus Publications on behalf of the European Geosciences Union.Simulations from chemical weather models are subject to uncertainties in the input data (e.g. emission inventory, initial and boundary conditions) as well as those intrinsic to the model (e.g. physical parameterization, chemical mechanism). Multi-model ensembles can improve the forecast skill, provided that certain mathematical conditions are fulfilled. In this work, four ensemble methods were applied to two different datasets, and their performance was compared for ozone (O3), nitrogen dioxide (NO2) and particulate matter (PM10). Apart from the unconditional ensemble average, the approach behind the other three methods relies on adding optimum weights to members or constraining the ensemble to those members that meet certain conditions in time or frequency domain. The two different datasets were created for the first and second phase of the Air Quality Model Evaluation International Initiative (AQMEII). The methods are evaluated against ground level observations collected from the EMEP (European Monitoring and Evaluation Programme) and AirBase databases. The goal of the study is to quantify to what extent we can extract predictable signals from an ensemble with superior skill over the single models and the ensemble mean. Verification statistics show that the deterministic models simulate better O3 than NO2 and PM10, linked to different levels of complexity in the represented processes. The unconditional ensemble mean achieves higher skill compared to each station's best deterministic model at no more than 60 % of the sites, indicating a combination of members with unbalanced skill difference and error dependence for the rest. The promotion of the right amount of accuracy and diversity within the ensemble results in an average additional skill of up to 31 % compared to using the full ensemble in an unconditional way. The skill improvements were higher for O3 and lower for PM10, associated with the extent of potential changes in the joint distribution of accuracy and diversity in the ensembles. The skill enhancement was superior using the weighting scheme, but the training period required to acquire representative weights was longer compared to the sub-selecting schemes. Further development of the method is discussed in the conclusion.Peer reviewedFinal Published versio