Time Series Heterogeneous Co-execution on CPU+GPU

Time series motif (similarities) and discords discovery is one of the most important and challenging problems nowadays for time series analytics. We use an algorithm called “scrimp” that excels in collecting the relevant information of time series by reducing the computational complexity of the searching. Starting from the sequential algorithm we develop parallel alternatives based on a variety of scheduling policies that target different computing devices in a system that integrates a CPU multicore and an embedded GPU. These policies are named Dynamic -using Intel TBB- and Static -using C++11 threads- when targeting the CPU, and they are compared to a heterogeneous adaptive approach named LogFit -using Intel TBB and OpenCL- when targeting the co-execution on the CPU and GPU.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Solving Large-Scale Markov Decision Processes on Low-Power Heterogeneous Platforms

Markov Decision Processes (MDPs) provide a framework for a machine to act autonomously and intelligently in environments where the effects of its actions are not deterministic. MDPs have numerous applications. We focus on practical applications for decision making, such as autonomous driving and service robotics, that have to run on mobile platforms with scarce computing and power resources. In our study, we use Value Iteration to solve MDPs, a core method of the paradigm to find optimal sequences of actions, which is well known for its high computational cost. In order to solve these computationally complex problems efficiently in platforms with stringent power consumption constraints, high-performance accelerator hardware and parallelised software come to the rescue. We introduce a generalisable approach to implement practical applications for decision making, such as autonomous driving on mobile and embedded low-power heterogeneous SoC platforms that integrate an accelerator (GPU) with a multicore. We evaluate three scheduling strategies that enable concurrent execution and efficient use of resources on a variety of SoCs embedding a multicore CPU and integrated GPU, namely Oracle, Dynamic, and LogFit. We compare these strategies for solving an MDP modelling the use-case of autonomous robot navigation in indoor environments on four representative platforms for mobile decision-making applications with a power use ranging from 4 to 65 Watts. We provide a rigorous analysis of the results to better understand their behaviour depending on the MDP size and the computing platform. Our experimental results show that by using CPU-GPU heterogeneous strategies, the computation time and energy required are considerably reduced with respect to multicore implementation, regardless of the computational platform.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. This work was partially supported by the Spanish project TIN 2016-80920-R

Lightweight asynchronous scheduling in heterogeneous reconfigurable systems

The trend for heterogeneous embedded systems is the integration of accelerators and general-purpose CPU cores on the same die. In these integrated architectures, like the Zynq UltraScale+ board (CPU+FPGA) that we target in this work, hardware support for shared memory and low-overhead synchronization between the accelerator and the CPU cores make the case for exploring strategies that exploit a tight collaboration between the CPUs and the accelerator. In this paper we propose a novel lightweight scheduling strategy, FastFit, targeted to FPGA accelerators, and a new scheduler based on it, named MultiFastFit, which asynchronously tackles heterogeneous systems comprised of a variety of CPU cores and FPGA IPs. Our strategy significantly reduces the overhead to automatically compute the near-optimal chunksizes when compared to a previous state-of-the-art auto-tuned approach, which makes our approach more suitable for fine-grained applications. Additionally, our scheduler MultiFastFit has been designed to enable the efficient co-execution of work among compute devices in such a way that all the devices are busy while minimizing the load unbalance. Our approaches have been evaluated using four benchmarks carefully tuned for the low-power UltraScale+ platform. Our experiments demonstrate that the FastFit strategy always finds the near-optimal FPGA chunksize for any device configuration at a reasonable cost, even for fine-grained and irregular applications, and that heterogeneous CPU+FPGA co-executions that exploit all the compute devices are usually faster and more energy efficient than the CPU-only and FPGA-only executions. We have also compared MultiFastFit with other state-of-the-art scheduling strategies, finding that it outperforms other auto-tuned approach up to 2x and it achieves similar results to manually-tuned schedulers without requiring an offline search of the ideal CPU-FPGA partition or FPGA chunk granularity.This work was partially supported by the Spanish projects PID2019-105396RB-I00, UMA18-FEDERJA-108, and UK EPSRC projects ENEAC (EP/N002539/1), HOPWARE (EP/V040863/1) and RS MINET (INF\R2\192044). Funding for open access charge: Universidad de Málaga / CBUA

Prognostic factors of a lower CD4/CD8 ratio in long term viral suppression HIV infected children

CoRISpe (Cohorte Nacional de VIH pediátrica de la RED RIS).[Background] Combination antiretroviral therapy (cART) is associated with marked immune reconstitution. Although a long term viral suppression is achievable, not all children however, attain complete immunological recovery due to persistent immune activation. We use CD4/CD8 ratio like a marker of immune reconstitution.[Methods] Perinatal HIV-infected children who underwent a first-line cART, achieved viral suppression in the first year and maintained it for more than 5 years, with no viral rebound were included. Logistic models were applied to estimate the prognostic factors, clinical characteristics at cART start, of a lower CD4/CD8 ratio at the last visit.[Results] 146 HIV-infected children were included: 77% Caucasian, 45% male and 28% CDC C. Median age at cART initiation was 2.3 years (IQR: 0.5–6.2). 42 (30%) children received mono-dual therapy previously to cART. Time of undetectable viral load was 9.5 years (IQR: 7.8, 12.5). 33% of the children not achieved CD4/CD8 ratio >1. Univariate analysis showed an association between CD4/CD8 1 was not achieved in 33% of the children. Lower CD4 nadir and previous exposure to suboptimal therapy, before initiating cART, are factors showing independently association with a worse immune recovery (CD4/CD8 < 1).Peer reviewe

Clinical and pathological characteristics of peripheral T‐cell lymphomas in a Spanish population: a retrospective study

We investigated the clinicopathological features and prognostic factors of patients with peripheral T-cell lymphoma (PTCL) in 13 sites across Spain. Relevant clinical antecedents, CD30 expression and staining pattern, prognostic indices using the International Prognostic Index and the Intergruppo Italiano Linfomi system, treatments, and clinical outcomes were examined. A sizeable proportion of 175 patients had a history of immune-related disorders (autoimmune 16%, viral infections 17%, chemo/radiotherapy-treated carcinomas 19%). The median progression-free survival (PFS) and overall survival (OS) were 7·9 and 15·8 months, respectively. Prognostic indices influenced PFS and OS, with a higher number of adverse factors resulting in shorter survival (P 15% of cells were positive in anaplastic lymphoma kinase-positive and -negative anaplastic large-cell lymphoma and extranodal natural killer PTCL groups. We observed PTCL distribution across subtypes based on haematopathological re-evaluation. Poor prognosis, effect of specific prognostic indices, relevance of histopathological sub-classification, and response level to first-line treatment on outcomes were confirmed. Immune disorders amongst patients require further examination involving genetic studies and identification of associated immunosuppressive factors

Late gadolinium enhancement distribution patterns in non-ischemic dilated cardiomyopathy: Genotype-phenotype correlation.

AIMS Late gadolinium enhancement (LGE) is frequently found in patients with dilated cardiomyopathy (DCM), there is little information about its frequency and distribution pattern according to underlying genetic substrate. We sought to describe LGE patterns according to genotype and to analyze the risk of major ventricular arrhythmias (MVA) according to patterns. METHODS AND RESULTS Cardiac magnetic resonance findings and LGE distribution according to genetics was performed in a cohort of 600 DCM patients followed at 20 Spanish centers. After exclusion of individuals with multiple causative gene variants or with variants in infrequent DCM-causing genes, 577 patients (34% females, mean age 53.5 years, LVEF 36.9 ± 13.9%) conformed the final cohort. A causative genetic variant was identified in 219 (38%) patients and 147 (25.5%) had LGE. Significant differences were found comparing LGE patterns between genes (P < 0.001). LGE was absent or rare in patients with variants in TNNT2, RBM20 and MYH7 (0%, 5% and 20%, respectively). Patients with variants in DMD, DSP and FLNC showed predominance of LGE subepicardial pattern (50%, 41% and 18%, respectively) whereas patients with variants in TTN, BAG3, LMNA and MYBPC3 showed unspecific LGE patterns. Genetic yield differed according to LGE pattern. Patients with subepicardial, lineal midwall, transmural, right ventricular insertion points or with combination of LGE patterns showed increased risk of MVA compared with patients without LGE. CONCLUSION LGE patterns in DCM has a specific distribution according to the affected gene. Certain LGE patterns are associated with increased risk of MVA and with increased yield of genetic testing.This study has been funded by Instituto Salud Carlos III (ISCIII) through the projects ‘PI18/0004, PI19/01283, and PI20/0320’ (co-funded by the European Regional Development Fund/European Social Fund ‘A way to make Europe’/‘Investing in your future’). The Hospital Universitario Puerta de Hierro, the Hospital Universitario Vall Hebrón, the Hospital General Universitario Gregorio Marañón, and the Hospital Universitario Virgen de la Arrixaca are members of the European Reference Network for Rare, Low Prevalence, and Complex Diseases of the Heart (ERN GUARD-Heart). F.d.F. receives grant support from ISCIII (CM20/00101). R.B. receives funding from the Obra Social la Caixa Foundation. M.B. receives funding from ISCIII (PI19/01283). The CNIC is supported by the ISCIII, Ministerio de Ciencia e Innovación of the Spanish Government (MCIN), and Pro CNIC Foundation.S

La sociología de la salud y los paradigmas de investigación

El presente libro se deriva del trabajo colegiado de la investigación científica, que realizan maestro y alumnos de las diferentes sedes académicas, para así contribuir mas a la investigación y que de igual manera sea un complemento de estudio para la Licenciatura en Educación para la Salud y para la Maestría en Sociología de la SaludEl libro contiene diversas temáticas que muestran conocimientos, metodologías, técnicas, herramientas y lenguajes necesarios utilizados comúnmente en el área de las Ciencias Sociales y de la Salud, desde un enfoque multi y transdisciplinario para poder indagar los elementos que componen la diversidad, la multiculturalidad y el medio ambiente que gira en torno a los temas de salud y de los estilos de vida saludabl

Integrative epigenomics in Sjögren´s syndrome reveals novel pathways and a strong interaction between the HLA, autoantibodies and the interferon signature

Primary Sjögren's syndrome (SS) is a systemic autoimmune disease characterized by lymphocytic infiltration and damage of exocrine salivary and lacrimal glands. The etiology of SS is complex with environmental triggers and genetic factors involved. By conducting an integrated multi-omics study, we confirmed a vast coordinated hypomethylation and overexpression effects in IFN-related genes, what is known as the IFN signature. Stratified and conditional analyses suggest a strong interaction between SS-associated HLA genetic variation and the presence of Anti-Ro/SSA autoantibodies in driving the IFN epigenetic signature and determining SS. We report a novel epigenetic signature characterized by increased DNA methylation levels in a large number of genes enriched in pathways such as collagen metabolism and extracellular matrix organization. We identified potential new genetic variants associated with SS that might mediate their risk by altering DNA methylation or gene expression patterns, as well as disease-interacting genetic variants that exhibit regulatory function only in the SS population. Our study sheds new light on the interaction between genetics, autoantibody profiles, DNA methylation and gene expression in SS, and contributes to elucidate the genetic architecture of gene regulation in an autoimmune population

Complement component C4 structural variation and quantitative traits contribute to sex-biased vulnerability in systemic sclerosis

Altres ajuts: Fondo Europeo de Desarrollo Regional (FEDER), "A way of making Europe".Copy number (CN) polymorphisms of complement C4 play distinct roles in many conditions, including immune-mediated diseases. We investigated the association of C4 CN with systemic sclerosis (SSc) risk. Imputed total C4, C4A, C4B, and HERV-K CN were analyzed in 26,633 individuals and validated in an independent cohort. Our results showed that higher C4 CN confers protection to SSc, and deviations from CN parity of C4A and C4B augmented risk. The protection contributed per copy of C4A and C4B differed by sex. Stronger protection was afforded by C4A in men and by C4B in women. C4 CN correlated well with its gene expression and serum protein levels, and less C4 was detected for both in SSc patients. Conditioned analysis suggests that C4 genetics strongly contributes to the SSc association within the major histocompatibility complex locus and highlights classical alleles and amino acid variants of HLA-DRB1 and HLA-DPB1 as C4-independent signals

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality