Highly-parallelized simulation of a pixelated LArTPC on a GPU

The rapid development of general-purpose computing on graphics processing units (GPGPU) is allowing the implementation of highly-parallelized Monte Carlo simulation chains for particle physics experiments. This technique is particularly suitable for the simulation of a pixelated charge readout for time projection chambers, given the large number of channels that this technology employs. Here we present the first implementation of a full microphysical simulator of a liquid argon time projection chamber (LArTPC) equipped with light readout and pixelated charge readout, developed for the DUNE Near Detector. The software is implemented with an end-to-end set of GPU-optimized algorithms. The algorithms have been written in Python and translated into CUDA kernels using Numba, a just-in-time compiler for a subset of Python and NumPy instructions. The GPU implementation achieves a speed up of four orders of magnitude compared with the equivalent CPU version. The simulation of the current induced on 10^3 pixels takes around 1 ms on the GPU, compared with approximately 10 s on the CPU. The results of the simulation are compared against data from a pixel-readout LArTPC prototype

McMillan-Ginzburg-Landau theory of singularities and discommensurations in charge density wave states of transition metal dichalcogenides

Abstract: The McMillan-Ginzburg-Landau (MGL) model for charge density waves (CDW) is employed in a systematic phenomenological study of the different phases that have been probed in recent experiments involving transition metal dichalcogenides. We implemented an efficient imaginary time evolution method to solve the MGL equations, which enabled us to investigate the role of different coupling parameters on the CDW patterns and to perform calculations with different energy functionals that lead to several experimentally observed singularities in the CDW phase profiles. In particular, by choosing the appropriate energy functionals, we were able to obtain phases that go beyond the well-known periodic phase slips (discommensurations), exhibiting also topological defects (i.e., vortex-antivortex pairs), domain walls where the CDW order parameter is suppressed, and even CDW with broken rotational symmetry. Finally, we briefly discuss the effect of these different CDW phases on the profile and critical temperature of the competing superconducting state

Coronary artery calcification score is an independent predictor of the no-reflow phenomenon after reperfusion therapy in acute myocardial infarction

Abundant evidence shows that coronary artery calcification (CAC) is a strong marker of structural and functional changes within the artery wall. Thus far, the implications of CAC in patients with acute coronary syndromes remain unclear. We aimed to investigate whether the CAC score is associated with impaired reperfusion during the acute phase of ST-elevation myocardial infarction (STEMI). We enrolled 60 consecutive STEMI patients to undergo cardiac computed tomography for assessment of the CAC score within 1 week after STEMI. Coronary thrombus burden, coronary blood flow (TIMI flow), and myocardial blush grade (MBG) were evaluated systematically. Patients with maximal TIMI flow and MBG were grouped as optimal reperfusion (n=27) and their counterparts as no-reflow (NR, n=33). There were no differences in the clinical characteristics between groups. Patients in the NR group had higher heart rate, coronary angiographic severity, and CAC score. CAC score greater than 100 was associated independently with the presence of NR (odds ratio 4.4, 95% confidence interval 1.17-16.3). The CAC score of nonculprit coronary arteries was higher in NR individuals than in their counterparts (P=0.04). In addition, the CAC score of the isnfarct-related artery correlated negatively with the TIMI-flow rate (r=-0.54, P<0.001) and with the MBG (r=-0.32, P=0.04). The CAC score is associated with the presence of the NR phenomenon in STEMI patients.Abundant evidence shows that coronary artery calcification (CAC) is a strong marker of structural and functional changes within the artery wall. Thus far, the implications of CAC in patients with acute coronary syndromes remain unclear. We aimed to investigate whether the CAC score is associated with impaired reperfusion during the acute phase of ST-elevation myocardial infarction (STEMI). We enrolled 60 consecutive STEMI patients to undergo cardiac computed tomography for assessment of the CAC score within 1 week after STEMI. Coronary thrombus burden, coronary blood flow (TIMI flow), and myocardial blush grade (MBG) were evaluated systematically. Patients with maximal TIMI flow and MBG were grouped as optimal reperfusion (n=27) and their counterparts as no-reflow (NR, n=33). There were no differences in the clinical characteristics between groups. Patients in the NR group had higher heart rate, coronary angiographic severity, and CAC score. CAC score greater than 100 was associated independently with the presence of NR (odds ratio 4.4, 95% confidence interval 1.17-16.3). The CAC score of nonculprit coronary arteries was higher in NR individuals than in their counterparts (P=0.04). In addition, the CAC score of the isnfarct-related artery correlated negatively with the TIMI-flow rate (r=-0.54, P<0.001) and with the MBG (r=-0.32, P=0.04). The CAC score is associated with the presence of the NR phenomenon in STEMI patients2656256

Low Zinc Levels Is Associated With Increased Inflammatory Activity But Not With Atherosclerosis, Arteriosclerosis Or Endothelial Dysfunction Among The Very Elderly

Background: Reduced zinc intake has been related to atherogenesis and arteriosclerosis. We verified this assumption in very old individuals, which are particularly prone to both zinc deficiency and structural and functional changes in the arterial wall. Methods: Subjects (n. = 201, 80-102. years) with uneventful cardiovascular history and who were not in use of anti-inflammatory treatments in the last 30-days were enrolled. Daily intake of zinc, lipid profile, plasma C-reactive protein (CRP), plasma zinc, flow-mediated dilation (FMD), carotid ultrasonography and cardiac computed tomography were obtained. Young's Elastic Modulus, Stiffness Index and Artery Compliance were calculated. Results: There was no significant difference in clinical or laboratorial data between subjects grouped according to plasma zinc tertile, except for CRP (p. = 0.01) and blood leukocytes (p. = 0.002), of which levels were higher in the upper tertiles. The average daily intake of zinc was not significantly correlated with zinc or CRP plasma levels.The plasma zinc/zinc intake ratio was inversely correlated with plasma CRP levels (- 0.18; p. = 0.01). There was no significant difference between the plasma zinc tertiles and FMD, carotid intima-media thickness, coronary calcium score, carotid plaque presence, remodeled noncalcified coronary plaques, or low-attenuation noncalcified coronary plaques. Conclusion: Although plasma zinc level is inversely related to systemic inflammatory activity, its plasma levels of daily intake are not associated to alterations in structure or function of the arterial wall. General significance: In the very elderly plasma concentrations or daily intake of zinc is not related to endothelial dysfunction, arteriosclerosis or atherosclerotic burden at coronary or carotid arteries. © 2014.216Freitas, W.M., Carvalho, L.S., Moura, F.A., Sposito, A.C., Atherosclerotic disease in octogenarians: a challenge for science and clinical practice (2012) Atherosclerosis, 225, pp. 281-289Fraker, P.J., King, L.E., Reprogramming of the immune system during zinc deficiency (2004) Annu. Rev. Nutr., 24, pp. 277-298Wellinghausen, N., Rink, L., The significance of zinc for leukocyte biology (1998) J. Leukoc. Biol., 64, pp. 571-577Shankar, A.H., Zinc and immune function: the biological basis of altered resistance to infection (1998) Am. J. Clin. Nutr., 68, pp. 447S-463SHennig, B., Meerarani, P., Ramadass, P., Toborek, M., Malecki, A., Slim, R., McClain, C.J., Zinc nutrition and apoptosis of vascular endothelial cells: implications in atherosclerosis (1999) Nutrition, 15, pp. 744-748Khadilkar, A.V., Chiplonkar, S.A., Pandit, D.S., Kinare, A.S., Khadilkar, V.V., Metabolic risk factors and arterial stiffness in Indian children of parents with metabolic syndrome (2012) J. Am. Coll. Nutr., 31, pp. 54-62Vlachopoulos, C., Aznaouridis, K., Dima, I., Ioakeimidis, N., Vasiliadou, C., Zervoudaki, A., Gialernios, T., Stefanadis, C., Negative association between serum levels of matrix metalloproteinases-2 and -9 and aortic stiffness in healthy adults (2007) Int. J. Cardiol., 122, pp. 232-238Freitas, W.M., Quaglia, L.A., Santos, S.N., Soares, A.A., Japiassu, A.V., Boaventura, V., dos Santos Barros, E., Sposito, A.C., Association of systemic inflammatory activity with coronary and carotid atherosclerosis in the very elderly (2011) Atherosclerosis, 216, pp. 212-216Smith, R.A., Cokkinides, V., Eyre, H.J., Cancer screening in the United States, 2007: a review of current guidelines, practices, and prospects (2007) CA Cancer J. Clin., 57, pp. 90-104Alberti, K.G., Eckel, R.H., Grundy, S.M., Zimmet, P.Z., Cleeman, J.I., Donato, K.A., Fruchart, J.C., Smith, S.C., E. International Diabetes Federation Task Force on, Prevention, L. National Heart, I. Blood, A. American Heart, F. World Heart, S. International Atherosclerosis, O. International Association for the Study of, Harmonizing the metabolic syndrome: a joint interim statement of the International Diabetes Federation Task Force on Epidemiology and PreventionNational Heart, Lung, and Blood InstituteAm (2009) Circulation, 120, pp. 1640-1645Costa, A.P., de Paula, R.C., Carvalho, G.F., Araujo, J.P., Andrade, J.M., de Almeida, O.L., de Faria, E.C., Sposito, A.C., High sodium intake adversely affects oxidative-inflammatory response, cardiac remodelling and mortality after myocardial infarction (2012) Atherosclerosis, 222, pp. 284-291(2006) Version 2, , NEPA-UNICAMP, Campinas, Brazilian Table of Food Composition (TACO)Gottdiener, J.S., Bednarz, J., Devereux, R., Gardin, J., Klein, A., Manning, W.J., Morehead, A., Weissman, N.J., E. American Society of, American Society of Echocardiography recommendations for use of echocardiography in clinical trials (2004) J. Am. Soc. Echocardiogr.: Off. Publ. Am. Soc. Echocardiogr., 17, pp. 1086-1119Juonala, M., Jarvisalo, M.J., Maki-Torkko, N., Kahonen, M., Viikari, J.S., Raitakari, O.T., Risk factors identified in childhood and decreased carotid artery elasticity in adulthood: the Cardiovascular Risk in Young Finns Study (2005) Circulation, 112, pp. 1486-1493Motoyama, S., Sarai, M., Harigaya, H., Anno, H., Inoue, K., Hara, T., Naruse, H., Narula, J., Computed tomographic angiography characteristics of atherosclerotic plaques subsequently resulting in acute coronary syndrome (2009) J. Am. Coll. Cardiol., 54, pp. 49-57Prasad, A.S., Zinc: role in immunity, oxidative stress and chronic inflammation (2009) Curr. Opin. Clin. Nutr. Metab. Care, 12, pp. 646-652Giannoglou, G.D., Konstantinou, D.M., Kovatsi, L., Chatzizisis, Y.S., Mikhailidis, D.P., Association of reduced zinc status with angiographically severe coronary atherosclerosis: a pilot study (2010) Angiology, 61, pp. 449-455Murr, C., Pilz, S., Grammer, T.B., Kleber, M.E., Bohm, B.O., Marz, W., Fuchs, D., Low serum zinc levels in patients undergoing coronary angiography correlate with immune activation and inflammation (2012) J.Trace Elem. Med. Biol.: Organ. Soc. Miner. Trace Elem., 26, pp. 26-30Sesso, H.D., Christen, W.G., Bubes, V., Smith, J.P., MacFadyen, J., Schvartz, M., Manson, J.E., Gaziano, J.M., Multivitamins in the prevention of cardiovascular disease in men: the Physicians' Health Study II randomized controlled trial (2012) JAMA, 308, pp. 1751-1760Journal, N.B., (2012) NBJ's Supplement Business Report 2012Bailey, R.L., Gahche, J.J., Lentino, C.V., Dwyer, J.T., Engel, J.S., Thomas, P.R., Betz, J.M., Picciano, M.F., Dietary supplement use in the United States, 2003-2006 (2011) J. Nutr., 141, pp. 261-266(2001) F.A.N.B. Institute of Medicine, Dietary Reference Intakes for Vitamin A, Vitamin K, Arsenic, Boron, Chromium, Copper, Iodine, Iron, Manganese, Molybdenum, Nickel, Silicon, Vanadium, and Zinc, , National Academy Press, Washington, DCHonkanen, V.E., Lamberg-Allardt, C.H., Vesterinen, M.K., Lehto, J.H., Westermarck, T.W., Metsa-Ketela, T.K., Mussalo-Rauhamaa, M.H., Konttinen, Y.T., Plasma zinc and copper concentrations in rheumatoid arthritis: influence of dietary factors and disease activity (1991) Am. J. Clin. Nutr., 54, pp. 1082-1086Foster, M., Petocz, P., Samman, S., Inflammation markers predict zinc transporter gene expression in women with type 2 diabetes mellitus (2013) J. Nutr. Biochem., 24, pp. 1655-1661Noh, H., Paik, H.Y., Kim, J., Chung, J., The alteration of zinc transporter gene expression is associated with inflammatory markers in obese women (2014) Biol. Trace Elem. Res., 160, pp. 153-154Liuzzi, J.P., Lichten, L.A., Rivera, S., Blanchard, R.K., Aydemir, T.B., Knutson, M.D., Ganz, T., Cousins, R.J., Interleukin-6 regulates the zinc transporter Zip14 in liver and contributes to the hypozincemia of the acute-phase response (2005) Proc. Natl. Acad. Sci. U. S. A., 102, pp. 6843-6848Ghayour-Mobarhan, M., Taylor, A., New, S.A., Lamb, D.J., Ferns, G.A., Determinants of serum copper, zinc and selenium in healthy subjects (2005) Ann. Clin. Biochem., 42, pp. 364-37

Characterization of gene polymorphisms related to immune system physiology in Mangalarga horses

The objectives of this study were to standardize a PCR-RFLP genotyping method for the AY_731081:g.1900T>C SNP of the equine CD14 gene, and to characterize this SNP and two other polymorphisms (AY_005808: c.1530A>G of the TLR4 gene and AX_463789: g.133T>C of the Cε gene) in Mangalarga horses, in order to contribute to future studies investigating the association between DNA markers and traits related to immune system physiology in this breed. A total of 151 Mangalarga horses of both sexes and variable ages, representative of the population of São Paulo State, were used. PCR-RFLP was found to be adequate for genotyping of the AY_731081: g.1900T>C SNP of the equine CD14 gene. However, this polymorphism is probably not present in Mangalarga horses, thus impairing association studies using this marker in the breed. The population genetic parameters obtained for the TLR4 AY_005808:c.1530A>G and Cε AX_463789:g.133T>C polymorphisms suggest the use of these markers in association studies with immune system-related traits in Mangalarga horses