434 research outputs found
A fast sparse block circulant matrix vector product
In the context of computed tomography (CT), iterative image reconstruction techniques are gaining attention because high-quality images are becoming computationally feasible. They involve the solution of large systems of equations, whose cost is dominated by the sparse matrix vector product (SpMV). Our work considers the case of the sparse matrices being block circulant, which arises when taking advantage of the rotational symmetry in the tomographic system. Besides the straightforward storage saving, we exploit the circulant structure to rewrite the poor-performance SpMVs into a high-performance product between sparse and dense matrices. This paper describes the implementations developed for multi-core CPUs and GPUs, and presents experimental results with typical CT matrices. The presented approach is up to ten times faster than without exploiting the circulant structure.Romero Alcalde, E.; Tomás Domínguez, AE.; Soriano Asensi, A.; Blanquer Espert, I. (2014). A fast sparse block circulant matrix vector product. En Euro-Par 2014 Parallel Processing. Springer. 548-559. doi:10.1007/978-3-319-09873-9_46S548559Bian, J., Siewerdsen, J.H., Han, X., Sidky, E.Y., Prince, J.L., Pelizzari, C.A., Pal, X.: Evaluation of sparse-view reconstruction from flat-panel-detector cone-beam ct. Physics in Medicine and Biology 55, 6575–6599 (2010)Dalton, S., Bell, N.: CUSP: A C++ templated sparse matrix library version 0.4.0 (2014), http://cusplibrary.github.com/Feldkamp, L., Davis, L., Kress, J.: Practical cone-beam algorithm. Journal of the Optical Society of America 1, 612–619 (1984)Ganine, V., Legrand, M., Michalska, H., Pierre, C.: A sparse preconditioned iterative method for vibration analysis of geometrically mistuned bladed disks. Computers & Structures 87(5-6), 342–354 (2009)Hara, A.K., Paden, R.G., Silva, A.C., Kujak, J.L., Lawder, H.J., Pavlicek, W.: Iterative reconstruction technique for reducing body radiation dose at CT: Feasibility study. American Journal of Roentgenology 193, 764–771 (2009)Heroux, M.A., Bartlett, R.A., Howle, V.E., Hoekstra, R.J., Hu, J.J., Kolda, T.G., Lehoucq, R.B., Long, K.R., Pawlowski, R.P., Phipps, E.T., Salinger, A.G., Thornquist, H.K., Tuminaro, R.S., Willenbring, J.M., Williams, A., Stanley, K.S.: An overview of the Trilinos project. ACM Trans. Math. Softw. 31(3), 397–423 (2005)Im, E.J., Yelick, K., Vuduc, R.: Sparsity: Optimization framework for sparse matrix kernels. International Journal of High Performance Computing Applications 18(1), 135–158 (2004)Jones, E., Oliphant, T., Peterson, P., et al.: SciPy: Open source scientific tools for Python (2001), http://www.scipy.org/Kaveh, A., Rahami, H.: Block circulant matrices and applications in free vibration analysis of cyclically repetitive structures. Acta Mechanica 217(1-2), 51–62 (2011)Kourtis, K., Goumas, G., Koziris, N.: Optimizing sparse matrix-vector multiplication using index and value compression. In: Proceedings of the 5th Conference on Computing Frontiers, CF 2008, pp. 87–96. ACM, New York (2008)Krotkiewski, M., Dabrowski, M.: Parallel symmetric sparse matrix–vector product on scalar multi-core CPUs. Parallel Computing 36(4), 181–198 (2010)Lee, B., Vuduc, R., Demmel, J., Yelick, K.: Performance models for evaluation and automatic tuning of symmetric sparse matrix-vector multiply. In: International Conference on Parallel Processing, ICPP 2004, vol. 1, pp. 169–176 (2004)Leroux, J.D., Selivanov, V., Fontaine, R., Lecomte, R.: Accelerated iterative image reconstruction methods based on block-circulant system matrix derived from a cylindrical image representation. In: Nuclear Science Symposium Conference Record, NSS 2007, vol. 4, pp. 2764–2771. IEEE (2007)NVIDIA: CUSPARSE library (2014), https://developer.nvidia.com/cusparsePan, X., Sidky, E.Y., Vannier, M.: Why do commercial CT scanners still employ traditional, filtered back-projection for image reconstruction? Inverse Problems 25, 123009 (2008)Rodríguez-Alvarez, M.J., Soriano, A., Iborra, A., Sánchez, F., González, A.J., Conde, P., Hernández, L., Moliner, L., Orero, A., Vidal, L.F., Benlloch, J.M.: Expectation maximization (EM) algorithms using polar symmetries for computed tomography CT image reconstruction. Computers in Biology and Medicine 43(8), 1053–1061 (2013)Sheep, L., Vardi, Y.: Maximum likelihood reconstruction for emmision tomography. IEEE Transactions on Medical Imaging 1, 113–122 (1982)Sidky, E.Y., Pan, X.: Image reconstruction in circular cone-beam computed tomography by constrained, total-variation minimization. Physics in Medicine and Biology 53, 4777–4807 (2008)Soriano, A., Rodríguez-Alvarez, M.J., Iborra, A., Sánchez, F., Carles, M., Conde, P., González, A.J., Hernández, L., Moliner, L., Orero, A., Vidal, L.F., Benlloch, J.M.: EM tomographic image reconstruction using polar voxels. Journal of Instrumentation 8, C01004 (2013)Thibaudeau, C., Leroux, J.D., Pratte, J.F., Fontaine, R., Lecomte, R.: Cylindrical and spherical ray-tracing for ct iterative reconstruction. In: 2011 IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), pp. 4378–4381 (2011)Vuduc, R., Demmel, J.W., Yelick, K.A.: OSKI: A library of automatically tuned sparse matrix kernels. Journal of Physics: Conference Series 16(1), 521 (2005)Vuduc, R.W., Moon, H.-J.: Fast sparse matrix-vector multiplication by exploiting variable block structure. In: Yang, L.T., Rana, O.F., Di Martino, B., Dongarra, J. (eds.) HPCC 2005. LNCS, vol. 3726, pp. 807–816. Springer, Heidelberg (2005)Williams, S., Oliker, L., Vuduc, R., Shalf, J., Yelick, K., Demmel, J.: Optimization of sparse matrix-vector multiplication on emerging multicore platforms. Parallel Computing 35(3), 178–194 (2009
Expectation maximization (EM) algorithms using polar symmetriesfor computed tomography(CT) image reconstruction
We suggest a symmetric-polar pixellation scheme which makes possible a reduction of the computational cost for expectation maximization (EM) iterative algorithms. The proposed symmetric-polar pixellation allows us to deal with 3D images as a whole problem without dividing the 3D problem into 2D slices approach. Performance evaluation of each approach in terms of stability and image quality is presented. Exhaustive comparisons between all approaches were conducted in a 2D based image reconstruction model. From these 2D approaches, that showing the best performances were finally implemented and evaluated in a 3D based image reconstruction model. Comparison to 3D images reconstructed with FBP is also presented. Although the algorithm is presented in the context of computed tomography (CT) image reconstruction, it can be applied to any other tomographic technique as well, due to the fact that the only requirement is a scanning geometry involving measurements of an object under different projection angles. Real data have been acquired with a small animal (CT) scanner to verify the proposed mathematical description of the CT system.This work was supported by the Spanish Plan Nacional de Investigacion Cientifica, Desarrollo e Innovacion Tecnologica (I+D+I) under Grant, FIS2010-21216-CO2-01, Valencian Local Government under Grant Nos. PROMETEO 2008/114 and APOSTD/2010/012. The authors would like to thank Brennan Holt for checking and correcting the text.Rodríguez Álvarez, MJ.; Soriano Asensi, A.; Iborra Carreres, A.; Sánchez Martínez, F.; González Martínez, AJ.; Conde, P.; Hernández Hernández, L.... (2013). Expectation maximization (EM) algorithms using polar symmetriesfor computed tomography(CT) image reconstruction. Computers in Biology and Medicine. 43(8):1053-1061. https://doi.org/10.1016/j.compbiomed.2013.04.015S1053106143
La subnutrición preparto y el hidroxitirosol en el equilibrio pro- y anti-oxidante de la sangre durante la etapa de lactación
La suplementación materna con HT mejoró la respuesta antioxidante de los terneros de vacas subnutridas. La capacidad antioxidante en vacas y el MDA en vacas y terneros incrementaron al avanzar la
gestación.: Proyecto financiado por MCIN/AEI/ 10.13039/501100011033 (FETALNUT). Contrato predoctoral de la Universitat de Lleida N. Escalera-Moreno. Los autores agradecen a M. Joy y a J.R. Bertolín (CITA-IA2(UNIZAR)) la ayuda proporcionada en el análisis de las muestras
Patients receiving a high burden of antibiotics in the community in Spain: a cross-sectional study
Some patients in the community receive a high burden of antibiotics. We aimed at describing the characteristics of these patients, antibiotics used, and conditions for which they received antibiotics. We carried out a cross-sectional study. Setting: Thirty Health Primary Care Areas from 12 regions in Spain, covering 5, 960, 191 inhabitants. Patients having at least 30 packages of antibacterials for systemic use dispensed in 2017 were considered. Main outcome measures: Prevalence of antibiotic use, conditions for which antibiotics were prescribed, clinical characteristics of patients, comorbidities, concomitant treatments, and microbiological isolates. Patient''s average age was 70 years; 52% were men; 60% smokers/ex-smokers; 54% obese. Overall, 93% of patients had, at least, one chronic condition, and four comorbidities on average. Most common comorbidities were cardiovascular and/or hypertension (67%), respiratory diseases (62%), neurological/mental conditions (32%), diabetes (23%), and urological diseases (21%); 29% were immunosuppressed, 10% were dead at the time of data collection. Patients received three antibiotic treatments per year, mainly fluoroquinolones (28%), macrolides (21%), penicillins (19%), or cephalosporins (12%). Most frequently treated conditions were lower respiratory tract (infections or prophylaxis) (48%), urinary (27%), and skin/soft tissue infections (11%). Thirty-five percent have been guided by a microbiological diagnosis, being Pseudomonas aeruginosa (30%) and Escherichia coli (16%) the most frequent isolates. In conclusion, high antibiotic consumers in the community were basically elder, with multimorbidity and polymedication. They frequently received broad-spectrum antibiotics for long periods of time. The approach to infections in high consumers should be differentiated from healthy patients receiving antibiotics occasionally
Evidence for a mixed mass composition at the `ankle' in the cosmic-ray spectrum
We report a first measurement for ultra-high energy cosmic rays of the
correlation between the depth of shower maximum and the signal in the water
Cherenkov stations of air-showers registered simultaneously by the fluorescence
and the surface detectors of the Pierre Auger Observatory. Such a correlation
measurement is a unique feature of a hybrid air-shower observatory with
sensitivity to both the electromagnetic and muonic components. It allows an
accurate determination of the spread of primary masses in the cosmic-ray flux.
Up till now, constraints on the spread of primary masses have been dominated by
systematic uncertainties. The present correlation measurement is not affected
by systematics in the measurement of the depth of shower maximum or the signal
in the water Cherenkov stations. The analysis relies on general characteristics
of air showers and is thus robust also with respect to uncertainties in
hadronic event generators. The observed correlation in the energy range around
the `ankle' at differs significantly from
expectations for pure primary cosmic-ray compositions. A light composition made
up of proton and helium only is equally inconsistent with observations. The
data are explained well by a mixed composition including nuclei with mass . Scenarios such as the proton dip model, with almost pure compositions, are
thus disfavoured as the sole explanation of the ultrahigh-energy cosmic-ray
flux at Earth.Comment: Published version. Added journal reference and DOI. Added Report
Numbe
The exposure of the hybrid detector of the Pierre Auger Observatory
The Pierre Auger Observatory is a detector for ultra-high energy cosmic rays.
It consists of a surface array to measure secondary particles at ground level
and a fluorescence detector to measure the development of air showers in the
atmosphere above the array. The "hybrid" detection mode combines the
information from the two subsystems. We describe the determination of the
hybrid exposure for events observed by the fluorescence telescopes in
coincidence with at least one water-Cherenkov detector of the surface array. A
detailed knowledge of the time dependence of the detection operations is
crucial for an accurate evaluation of the exposure. We discuss the relevance of
monitoring data collected during operations, such as the status of the
fluorescence detector, background light and atmospheric conditions, that are
used in both simulation and reconstruction.Comment: Paper accepted by Astroparticle Physic
Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set
We report a measurement of the bottom-strange meson mixing phase \beta_s
using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays
in which the quark-flavor content of the bottom-strange meson is identified at
production. This measurement uses the full data set of proton-antiproton
collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment
at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity.
We report confidence regions in the two-dimensional space of \beta_s and the
B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2,
-1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in
agreement with the standard model expectation. Assuming the standard model
value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +-
0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +-
0.009 (syst) ps, which are consistent and competitive with determinations by
other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012
Role of age and comorbidities in mortality of patients with infective endocarditis
Purpose: The aim of this study was to analyse the characteristics of patients with IE in three groups of age and to assess the ability of age and the Charlson Comorbidity Index (CCI) to predict mortality.
Methods: Prospective cohort study of all patients with IE included in the GAMES Spanish database between 2008 and 2015. Patients were stratified into three age groups:<65 years, 65 to 80 years, and = 80 years.The area under the receiver-operating characteristic (AUROC) curve was calculated to quantify the diagnostic accuracy of the CCI to predict mortality risk.
Results: A total of 3120 patients with IE (1327 < 65 years;1291 65-80 years;502 = 80 years) were enrolled.Fever and heart failure were the most common presentations of IE, with no differences among age groups.Patients =80 years who underwent surgery were significantly lower compared with other age groups (14.3%, 65 years; 20.5%, 65-79 years; 31.3%, =80 years). In-hospital mortality was lower in the <65-year group (20.3%, <65 years;30.1%, 65-79 years;34.7%, =80 years;p < 0.001) as well as 1-year mortality (3.2%, <65 years; 5.5%, 65-80 years;7.6%, =80 years; p = 0.003).Independent predictors of mortality were age = 80 years (hazard ratio [HR]:2.78;95% confidence interval [CI]:2.32–3.34), CCI = 3 (HR:1.62; 95% CI:1.39–1.88), and non-performed surgery (HR:1.64;95% CI:11.16–1.58).When the three age groups were compared, the AUROC curve for CCI was significantly larger for patients aged <65 years(p < 0.001) for both in-hospital and 1-year mortality.
Conclusion: There were no differences in the clinical presentation of IE between the groups. Age = 80 years, high comorbidity (measured by CCI), and non-performance of surgery were independent predictors of mortality in patients with IE.CCI could help to identify those patients with IE and surgical indication who present a lower risk of in-hospital and 1-year mortality after surgery, especially in the <65-year group
Cut-offs and response criteria for the Hospital Universitario la Princesa Index (HUPI) and their comparison to widely-used indices of disease activity in rheumatoid arthritis
Objective To estimate cut-off points and to establish response criteria for the Hospital Universitario La Princesa Index (HUPI) in patients with chronic polyarthritis. Methods Two cohorts, one of early arthritis (Princesa Early Arthritis Register Longitudinal PEARL] study) and other of long-term rheumatoid arthritis (Estudio de la Morbilidad y Expresión Clínica de la Artritis Reumatoide EMECAR]) including altogether 1200 patients were used to determine cut-off values for remission, and for low, moderate and high activity through receiver operating curve (ROC) analysis. The areas under ROC (AUC) were compared to those of validated indexes (SDAI, CDAI, DAS28). ROC analysis was also applied to establish minimal and relevant clinical improvement for HUPI. Results The best cut-off points for HUPI are 2, 5 and 9, classifying RA activity as remission if =2, low disease activity if >2 and =5), moderate if >5 and <9 and high if =9. HUPI''s AUC to discriminate between low-moderate activity was 0.909 and between moderate-high activity 0.887. DAS28''s AUCs were 0.887 and 0.846, respectively; both indices had higher accuracy than SDAI (AUCs: 0.832 and 0.756) and CDAI (AUCs: 0.789 and 0.728). HUPI discriminates remission better than DAS28-ESR in early arthritis, but similarly to SDAI. The HUPI cut-off for minimal clinical improvement was established at 2 and for relevant clinical improvement at 4. Response criteria were established based on these cut-off values. Conclusions The cut-offs proposed for HUPI perform adequately in patients with either early or long term arthritis
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