A pipeline structure for the block QR update in digital signal processing

[EN] There exist problems in the field of digital signal processing, such as filtering of acoustic signals that require processing a large amount of data in real time. The beamforming algorithm, for instance, is a process that can be modeled by a rectangular matrix built on the input signals of an acoustic system and, thus, changes in real time. To obtain the output signals, it is required to compute its QR factorization. In this paper, we propose to organize the concurrent computational resources of a given multicore computer in a pipeline structure to perform this factorization as fast as possible. The pipeline has been implemented using both the application programming interface OpenMP and GrPPI, a library interface to design parallel applications based on parallel patterns. We tackle not only the performance challenge but also the programmability of our idea using parallel programming frameworks.This work was supported by the Spanish Ministry of Economy and Competitiveness under MINECO and FEDER projects TIN2014-53495-R and TEC2015-67387-C4-1-R.Dolz, MF.; Alventosa, FJ.; Alonso-Jordá, P.; Vidal Maciá, AM. (2019). A pipeline structure for the block QR update in digital signal processing. The Journal of Supercomputing. 75(3):1470-1482. https://doi.org/10.1007/s11227-018-2666-1S14701482753Huang Y, Benesty J, Chen J (2006) Acoustic MIMO signal processing (signals and communication technology). Springer, BerlinRamiro C, Vidal AM, González A (2015) MIMOPack: a high performance computing library for MIMO communication systems. J Supercomput 71:751–760Alventosa FJ, Alonso P, Piñero G, Vidal AM (2016) Implementation of the Beamformer algorithm for the NVIDIA Jetson. In: Actas de la Conferencia, Granada, Spain, pp 201–211. ISBN 978-3-319-49955-0Alventosa FJ, Alonso P, Vidal AM, Piñero G, Quintana-Ortí ES (2018) Fast block QR update in digital signal processing. J Supercomput. https://doi.org/10.1007/s11227-018-2298-5del Rio D, Dolz MF, Fernández J, García JD (2017) A generic parallel pattern interface for stream and data processing. Concurr Comput Pract Exp 29(24):e4175Benesty J, Chen J, Huang Y, Dmochowski J (2007) On microphone-array Beamforming from a MIMO acoustic signal processing perspective. IEEE Trans Audio Speech Lang Process 15(3):1053–1065Lorente J, Piñero G, Vidal AM, Belloch JA, González A (2011) Parallel implementations of Beamforming design and filtering for microphone array applications. In: 19th European Signal Processing Conference (EUSIPCO), Barcelona, Spain, pp 501–505Belloch JA, Ferrer M, González A, Martínez-Zaldívar FJ, Vidal AM (2013) Headphone-based virtual spatialization of sound with a GPU accelerator. J Audio Eng Soc 61:546–561Belloch JA, González A, Martínez-Zaldívar FJ, Vidal AM (2011) Real-time massive convolution for audio applications on GPU. J Supercomput 58(3):449–457Golub GH, Van Loan CF (2013) Matrix computations. Johns Hopkins studies in the mathematical sciences. Johns Hopkins University Press, BaltimoreGunter BC, van de Geijn RA (2005) Parallel out-of-core computation and updating the QR factorization. ACM Trans Math Softw 31(1):60–78Buttari A, Langou J, Kurzak J, Dongarra J (2009) A class of parallel tiled linear algebra algorithms for multicore architectures. Parallel Comput 35(1):38–53Dolz MF, Alventosa FJ, Alonso-Jordá P, Vidal AM (2018) A pipeline for the QR update in digital signal processing. In: Proceedings of the 18th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2018), Rota, Cádiz, Spain, pp 1–5Quintana-Ortí G, Quintana-Ortí ES, Van De Geijn RA, Van Zee FG, Chan E (2009) Programming matrix algorithms-by-blocks for thread-level parallelism. ACM Trans Math Softw 36(3):14:1–14:2

Micro-spectroscopic investigation of selenium-bearing minerals from the Western US Phosphate Resource Area

Mining activities in the US Western Phosphate Resource Area (WPRA) have released Se into the environment. Selenium has several different oxidation states and species, each having varying degrees of solubility, reactivity, and bioavailability. In this study we are investigating the speciation of Se in mine-waste rocks. Selenium speciation was determined using bulk and micro-x-ray absorption spectroscopy (XAS), as well as micro-x-ray fluorescence mapping. Rocks used for bulk-XAS were ground into fine powders. Shale used for micro-XAS was broken along depositional planes to expose unweathered surfaces. The near edge region of the XAS spectra (XANES) for the bulk rock samples revealed multiple oxidation states, with peaks indicative of Se(-II), Se(IV), and Se(+VI) species. Micro-XANES analysis of the shale indicated that three unique Se-bearing species were present. Using the XANES data together with ab initio fitting of the extended x-ray absorption fine structure region of the micro-XAS data (micro-EXAFS) the three Se-bearing species were identified as dzharkenite, a di-selenide carbon compound, and Se-substituted pyrite. Results from this research will allow for a better understanding of the biogeochemical cycling of Se in the WPRA

Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass

Abstract Background Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield. Despite its importance as a prominent bioenergy crop, a genome-wide comprehensive analysis of NB-LRR disease resistance genes has yet to be performed in switchgrass. Results In this study, we used a homology-based computational approach to identify 1011 potential NB-LRR resistance gene homologs (RGHs) in the switchgrass genome (v 1.1). In addition, we identified 40 RGHs that potentially contain unique domains including major sperm protein domain, jacalin-like binding domain, calmodulin-like binding, and thioredoxin. RNA-sequencing analysis of leaf tissue from ‘Alamo’, a rust-resistant switchgrass cultivar, and ‘Dacotah’, a rust-susceptible switchgrass cultivar, identified 2634 high quality variants in the RGHs between the two cultivars. RNA-sequencing data from field-grown cultivar ‘Summer’ plants indicated that the expression of some of these RGHs was developmentally regulated. Conclusions Our results provide useful insight into the molecular structure, distribution, and expression patterns of members of the NB-LRR gene family in switchgrass. These results also provide a foundation for future work aimed at elucidating the molecular mechanisms underlying disease resistance in this important bioenergy crop

Association of APOE polymorphism with chronic kidney disease in a nationally representative sample: a Third National Health and Nutrition Examination Survey (NHANES III) Genetic Study

<p>Abstract</p> <p>Background</p> <p>Apolipoprotein E polymorphisms (<it>APOE</it>) have been associated with lowered glomerular filtration rate (GFR) and chronic kidney disease (CKD) with e2 allele conferring risk and e4 providing protection. However, few data are available in non-European ethnic groups or in a population-based cohort.</p> <p>Methods</p> <p>The authors analyzed 5,583 individuals from the Third National Health and Nutrition Examination Survey (NHANES III) to determine association with estimated GFR by the Modification of Diet in Renal Disease (MDRD) equation and low-GFR cases. Low-GFR cases were defined as GFR <75 ml/min/1.73 m²; additionally, GFR was analyzed continuously.</p> <p>Results</p> <p>In univariate analysis, the e4 allele was negatively associated with low-GFR cases in non-Hispanic whites, odds ratio (OR): 0.76, 95% confidence interval (CI): 0.60, 0.97. In whites, there was a significant association between increasing <it>APOE </it>score (indicating greater number of e2 alleles) and higher prevalence of low-GFR cases (OR: 1.21, 95%CI: 1.01, 1.45). Analysis of continuous GFR in whites found the e4 allele was associated with higher levels of continuous GFR (β-coefficient: 2.57 ml/min/1.73 m², 95%CI: 0.005, 5.14); in non-Hispanic blacks the e2 allele was associated with lower levels of continuous GFR (β-coefficient: -3.73 ml/min/1.73 m², 95%CI: -6.61, -0.84). <it>APOE </it>e2 and e4 alleles were rare and not associated with low-GFR cases or continuous GFR in Mexican Americans.</p> <p>Conclusion</p> <p>In conclusion, the authors observed a weak association between the <it>APOE </it>e4 allele and low-GFR cases and continuous GFR in non-Hispanic whites, and the <it>APOE </it>e2 allele and continuous GFR in non-Hispanic blacks, but found no association with either measure of kidney function in Mexican Americans. Larger studies including multiethnic groups are needed to determine the significance of this association.</p

Mass balance of the Greenland and Antarctic ice sheets from 1992 to 2020

Ice losses from the Greenland and Antarctic ice sheets have accelerated since the 1990s, accounting for a significant increase in the global mean sea level. Here, we present a new 29-year record of ice sheet mass balance from 1992 to 2020 from the Ice Sheet Mass Balance Inter-comparison Exercise (IMBIE). We compare and combine 50 independent estimates of ice sheet mass balance derived from satellite observations of temporal changes in ice sheet flow, in ice sheet volume, and in Earth's gravity field. Between 1992 and 2020, the ice sheets contributed 21.0±1.9g€¯mm to global mean sea level, with the rate of mass loss rising from 105g€¯Gtg€¯yr-1 between 1992 and 1996 to 372g€¯Gtg€¯yr-1 between 2016 and 2020. In Greenland, the rate of mass loss is 169±9g€¯Gtg€¯yr-1 between 1992 and 2020, but there are large inter-annual variations in mass balance, with mass loss ranging from 86g€¯Gtg€¯yr-1 in 2017 to 444g€¯Gtg€¯yr-1 in 2019 due to large variability in surface mass balance. In Antarctica, ice losses continue to be dominated by mass loss from West Antarctica (82±9g€¯Gtg€¯yr-1) and, to a lesser extent, from the Antarctic Peninsula (13±5g€¯Gtg€¯yr-1). East Antarctica remains close to a state of balance, with a small gain of 3±15g€¯Gtg€¯yr-1, but is the most uncertain component of Antarctica's mass balance. The dataset is publicly available at 10.5285/77B64C55-7166-4A06-9DEF-2E400398E452 (IMBIE Team, 2021)

Methylome Analysis and Epigenetic Changes Associated with Menarcheal Age

CAD received funding from EU-Europe aid grant CRIS 2009/223–507.The EPIC cohort is supported by the Europe Against Cancer Program of the European Commission (SANCO). The individual centres also received funding from: Denmark (Danish Cancer Society); France (Ligue centre le Cancer, Institut Gustave Roussy, Mutuelle Ge´ne´rale de l’Education Nationale, and Institut National de la Sante´ et de la Recherche Me´dicale (INSERM)); Greece (Hellenic Ministry of Health, the Stavros Niarchos Foundation and the Hellenic Health Foundation); Germany (German Cancer Aid, German Cancer Research Center, and Federal Ministry of Education and Research (Grant 01-EA-9401)); Italy (Italian Association for Research on Cancer and the National Research Council); The Netherlands (Dutch Ministry of Public Health, Welfare and Sports (VWS), Netherlands Cancer Registry (NKR), LK Research Funds, Dutch Prevention Funds, and Dutch ZON (Zorg Onderzoek Nederland), World Cancer Research Fund (WCRF)); Spain (Health Research Fund (FIS) of the Spanish Ministry of Health (Exp 96/0032) and the participating regional governments and institutions); Sweden (Swedish Cancer Society, Swedish Scientific Council, and Regional Government of Skane); and the United Kingdom (Cancer Research UK and Medical Research Council UK and Breast Cancer Campaign). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Inflammation gene variants and susceptibility to albuminuria in the U.S. population: analysis in the Third National Health and Nutrition Examination Survey (NHANES III), 1991-1994

<p>Abstract</p> <p>Background</p> <p>Albuminuria, a common marker of kidney damage, serves as an important predictive factor for the progression of kidney disease and for the development of cardiovascular disease. While the underlying etiology is unclear, chronic, low-grade inflammation is a suspected key factor. Genetic variants within genes involved in inflammatory processes may, therefore, contribute to the development of albuminuria.</p> <p>Methods</p> <p>We evaluated 60 polymorphisms within 27 inflammatory response genes in participants from the second phase (1991-1994) of the Third National Health and Nutrition Examination Survey (NHANES III), a population-based and nationally representative survey of the United States. Albuminuria was evaluated as logarithm-transformed albumin-to-creatinine ratio (ACR), as ACR ≥ 30 mg/g, and as ACR above sex-specific thresholds. Multivariable linear regression and haplotype trend analyses were conducted to test for genetic associations in 5321 participants aged 20 years or older. Differences in allele and genotype distributions among non-Hispanic whites, non-Hispanic blacks, and Mexican Americans were tested in additive and codominant genetic models.</p> <p>Results</p> <p>Variants in several genes were found to be marginally associated (uncorrected P value < 0.05) with log(ACR) in at least one race/ethnic group, but none remained significant in crude or fully-adjusted models when correcting for the false-discovery rate (FDR). In analyses of sex-specific albuminuria, <it>IL1B </it>(rs1143623) among Mexican Americans remained significantly associated with increased odds, while <it>IL1B </it>(rs1143623), <it>CRP </it>(rs1800947) and <it>NOS3 </it>(rs2070744) were significantly associated with ACR ≥ 30 mg/g in this population (additive models, FDR-P < 0.05). In contrast, no variants were found to be associated with albuminuria among non-Hispanic blacks after adjustment for multiple testing. The only variant among non-Hispanic whites significantly associated with any outcome was <it>TNF </it>rs1800750, which failed the test for Hardy-Weinberg proportions in this population. Haplotypes within <it>MBL2</it>, <it>CRP</it>, <it>ADRB2, IL4R</it>, <it>NOS3</it>, and <it>VDR </it>were significantly associated (FDR-P < 0.05) with log(ACR) or albuminuria in at least one race/ethnic group.</p> <p>Conclusions</p> <p>Our findings suggest a small role for genetic variation within inflammation-related genes to the susceptibility to albuminuria. Additional studies are needed to further assess whether genetic variation in these, and untested, inflammation genes alter the susceptibility to kidney damage.</p

Adverse effects of extra-articular corticosteroid injections: a systematic review

<p>Abstract</p> <p>Background</p> <p>To estimate the occurrence and type of adverse effects after application of an extra-articular (soft tissue) corticosteroid injection.</p> <p>Methods</p> <p>A systematic review of the literature was made based on a PubMed and Embase search covering the period 1956 to January 2010. Case reports were included, as were prospective and retrospective studies that reported adverse events of corticosteroid injection. All clinical trials which used extra-articular corticosteroid injections were examined. We divided the reported adverse events into major (defined as those needing intervention or not disappearing) and minor ones (transient, not requiring intervention).</p> <p>Results</p> <p>The search yielded 87 relevant studies:44 case reports, 37 prospective studies and 6 retrospective studies. The major adverse events included osteomyelitis and protothecosis; one fatal necrotizing fasciitis; cellulitis and ecchymosis; tendon ruptures; atrophy of the plantar fat was described after injecting a neuroma; and local skin effects appeared as atrophy, hypopigmentation or as skin defect. The minor adverse events effects ranged from skin rash to flushing and disturbed menstrual pattern. Increased pain or steroid flare after injection was reported in 19 studies. After extra-articular injection, the incidence of major adverse events ranged from 0-5.8% and that of minor adverse events from 0-81%. It was not feasible to pool the risk for adverse effects due to heterogeneity of study populations and difference in interventions and variance in reporting.</p> <p>Conclusion</p> <p>In this literature review it was difficult to accurately quantify the incidence of adverse effects after extra-articular corticosteroid injection. The reported adverse events were relatively mild, although one fatal reaction was reported.</p

Mixed Climatology, Non-synoptic Phenomena and Downburst Wind Loading of Structures

Modern wind engineering was born in 1961, when Davenport published a paper in which meteorology, micrometeorology, climatology, bluff-body aerodynamics and structural dynamics were embedded within a homogeneous framework of the wind loading of structures called today \u201cDavenport chain\u201d. Idealizing the wind with a synoptic extra-tropical cyclone, this model was so simple and elegant as to become a sort of axiom. Between 1976 and 1977 Gomes and Vickery separated thunderstorm from non-thunderstorm winds, determined their disjoint extreme distributions and derived a mixed model later extended to other Aeolian phenomena; this study, which represents a milestone in mixed climatology, proved the impossibility of labelling a heterogeneous range of events by the generic term \u201cwind\u201d. This paper provides an overview of this matter, with particular regard to the studies conducted at the University of Genova on thunderstorm downbursts