Accelerating time series motif discovery in the Intel Xeon Phi KNL processor

Presented at HiPEAC Conference 2020, Bologna (Italy)Time series analysis is an important research topic of great interest in many fields. However, the memory-bound nature of the state-of-the-art algorithms limits the execution performance in some processor architectures. We analyze the Matrix Profile algorithm from the performance viewpoint in the context of the Intel Xeon Phi Knights Landing architecture (KNL). The experimental evaluation shows a performance improvement up to 190x with respect to the sequential execution and that the use of the HBM memory improves performance in a factor up to 5x with respect to the DDR4 memory.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Exploring the efficiency of gallic acid-based dendrimers and their block copolymers with PEG as gene carriers

The synthesis of a new family of amino-functionalized gallic acid-triethylene glycol (GATG) dendrimers and their block copolymers with polyethylene glycol (PEG) has recently being disclosed. In addition, these dendrimers have shown potential for gene delivery applications, as they efficiently complex nucleic acids and form small and homogeneous dendriplexes. On this basis, the present study aimed to explore the interaction of the engineered dendriplexes with blood components, as well as their stability, cytotoxicity and ability to enter and transfect mammalian cells. Results show that GATG dendrimers can form stable dendriplexes, protect the associated pDNA from degradation, and are biocompatible with HEK-293T cells and erythrocytes. More importantly, dendriplexes are effectively internalized by HEK-293T cells, which are successfully transfected. Besides, PEGylation has a marked influence on the properties of the resulting dendriplexes. While PEGylated GATG dendrimers have improved biocompatibility, the long PEG chains limit their uptake by HEK-293T cells, and thus, their ability to transfect them. As a consequence, the degree of PEGylation in dendriplexes containing dendrimer/block copolymer mixtures emerges as an important parameter to be modulated in order to obtain an optimized stealth formulation able to effectively induce the expression of the encoded proteinThe authors gratefully acknowledge support from the Spanish Ministry of Science and Innovation (SAF2004‐09230‐004‐01, CTQ2006‐12222/BQU, and CTQ2009‐10963) and the Xunta de Galicia (10CSA209021PR). M. Raviña and A. Sousa‐Herves also acknowledge fellowships from the Spanish Government (FPI and FPU, respectively)S

Speed of sound measurements of biogas from a landfill biomethanation process

Producción CientíficaBiogas is drawing attention as it can be a solution both to increase the renewable energy for heat or power supply and to help achieve a decarbonized economy. In this work, the measurements of the speed of sound of three mixtures of biogas from the biomethanation plant of the municipal waste of Valdemingómez, Madrid (Spain), are presented. The measurements were performed using an acoustic resonator, which is able to measure the speed of sound of gas mixtures with a relative expanded uncertainty of approximately 0.08%. A virial-type equation was also applied to fit the experimental values of the speed of sound, and the heat capacities as perfect gas were derived with uncertainties below 0.8%. In addition, the experimental results were compared with those calculated with the reference equations of state for natural gas mixtures such as GERG-2008 and AGA8-DC92. For both equations, the average relative deviations were less than 0.02% and 0.2% for the speed of sound and the heat capacities, respectively. These values are less than the uncertainties of these equations, demonstrating their reliability in predicting the thermodynamic behavior of biogas.Junta de Castilla y León y Unión Euopea (UE)-Fondo Europeo de Desarrollo Regional (FEDER) - (grants VA280P18 and CLU-2019-04

Aceleración del análisis de series temporales en el procesador Intel Xeon Phi KNL

El análisis de series temporales es un campo de investigación de gran interés con innumerables aplicaciones. Recientemente, el método Matrix Profile, y particularmente una de sus implementacio nes, el algoritmo SCRIMP, ha empezado a cobrar relevancia en este campo. En este trabajo analizamos la estructura y el ren dimiento del algoritmo SCRIMP en el contexto de una arquitectura Intel Xeon Phi Knights Landing (KNL), que integra módulos de memoria HBM (High-Bandwidth Memory). En este análisis combinamos diferentes técnicas para explotar el potencial de la arquitectura. Por un lado, explotamos la capacidad multihilo y vectorial de la arquitectura. Por otro lado, exploramos cómo ubicar los datos en la memoria para extraer el máximo rendimiento de la arquitectura de memoria hı́brida disponible, haciendo uso tanto de la memoria 3D de alto ancho de banda como de la memoria convencional DRAM DDR4.Sociedad de Arquitectura y Tecnología de Computadores (SARTECO) Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

USP7 and VCP define the SUMO/Ubiquitin landscape at the DNA replication fork

The AAA+ ATPase VCP regulates the extraction of SUMO and ubiquitin-modified DNA replication factors from chromatin. We have previously described that active DNA synthesis is associated with a SUMO-high/ubiquitin-low environment governed by the deubiquitylase USP7. Here, we unveil a functional cooperation between USP7 and VCP in DNA replication, which is conserved from Caenorhabditis elegans to mammals. The role of VCP in chromatin is defined by its cofactor FAF1, which facilitates the extraction of SUMOylated and ubiquitylated proteins that accumulate after the block of DNA replication in the absence of USP7. The inactivation of USP7 and FAF1 is synthetically lethal both in C. elegans and mammalian cells. In addition, USP7 and VCP inhibitors display synergistic toxicity supporting a functional link between deubiquitylation and extraction of chromatin-bound proteins. Our results suggest that USP7 and VCPFAF1 facilitate DNA replication by controlling the balance of SUMO/Ubiquitin-modified DNA replication factors on chromatinMINECO (BFU2014-55168-JIN; RTI2018-093485-B-I00) and a Ramo´ n y Cajal Fellowship from MINECO (RYC-2016-20705), co-funded by European Regional Development Funds (FEDER) to E.L.; by grants from the Spanish Ministry of Science, Innovation and Universities (RTI2018-102204-B-I00, co-financed with European FEDER funds) and the European Research Council (ERC-617840) to O.F.-C.; fellowships from Fundacion Ramón Areces-UAM and La Caixa Foundation to P.V. (LCF/BQ/ES18/11670008

OBTENCIÓN DEL MÁXIMO ANCHO DE BANDA PARA LA ADQUISICIÓN Y RECONSTRUCCIÓN DE SEÑALES ANALÓGICAS CON LA TARJETA SPARTAN 3E

ResumenEn este trabajo se presenta un sistema en el cual se obtiene el máximo ancho de banda posible para la adquisición y reconstrucción de señales analógicas en la tarjeta de desarrollo Spartan-3E del fabricante Xilinx, utilizando los convertidores que contiene dicha tarjeta, tanto el ADC como el DAC. El sistema está desarrollado en VHDL empleando el concepto de máquina de estados finitos (FSM) y el administrador digital de reloj (DCM) incluido en el FPGA de la tarjeta. En aplicaciones tales como procesamiento digital de señales en tiempo real, comunicaciones digitales y control digital, por mencionar algunas, es muy importante tener un ancho de banda considerable en el sistema. El valor máximo obtenido para el ancho de banda del sistema fue de 161 kHz.Palabras Claves: ADC, ancho de banda, DAC, FPGA, Spartan-3E.OBTAINING THE MAXIMUM BANDWIDTH FOR THE ACQUISITION AND RECONSTRUCTION OF ANALOGUE SIGNALS WITH THE SPARTAN 3E CARDAbstractThis paper presents a system in which the maximum bandwidth possible for the acquisition and reconstruction of analog signals is obtained in the Spartan-3E development board of the Xilinx manufacturer, using the converters contained in this board, both the ADC and The DAC. The system is developed in VHDL using the concept of finite state machine (FSM) and the digital clock manager (DCM) included in the FPGA. In applications such as digital processing of real-time signals, digital communications and digital control, to mention a few, it is very important to have a considerable bandwidth in the system. The maximum value obtained for the system bandwidth was 161 kHz.Keywords: ADC, bandwith, DAC, FPGA, Spartan-3E

Anti-inflammatory and regenerative effects of MKARE® Eggshell Membrane: An in vitro osteoarthritis model and placebo-controlled clinical study

[EN]MKARE®, a 100% natural ingredient derived from fresh eggshell membrane (ESM), has a rich composition in bioactive compounds like collagen, hyaluronic acid, and elastin. These components are beneficial for managing osteoarthritis (OA) due to their anti-inflammatory and regenerative properties. Highlighting the significance of freshness, our research has shown that the effectiveness of MKARE® is higher than that of other commercial products based on ESM that have been stored for several days at room temperature, losing their bioactive compounds. This study explores the MKARE® anti-inflammatory capacity through an in vitro and clinical analyses, demonstrating its ability to alleviate OA symptoms and improve joint health. This underscores the crucial role of freshness in optimizing the therapeutic benefits.S

L-arginine ameliorates defective autophagy in GM2 gangliosidoses by mTOR modulation

Aims: Tay–Sachs and Sandhoff diseases (GM2 gangliosidosis) are autosomal recessive disorders of lysosomal function that cause progressive neurodegeneration in infants and young children. Impaired hydrolysis catalysed by β-hexosaminidase A (HexA) leads to the accumulation of GM2 ganglioside in neuronal lysosomes. Despite the storage phenotype, the role of autophagy and its regulation by mTOR has yet to be explored in the neuropathogenesis. Accordingly, we investigated the effects on autophagy and lysosomal integrity using skin fibroblasts obtained from patients with Tay–Sachs and Sandhoff diseases. Results: Pathological autophagosomes with impaired autophagic flux, an abnormality confirmed by electron microscopy and biochemical studies revealing the accelerated release of mature cathepsins and HexA into the cytosol, indicating increased lysosomal permeability. GM2 fibroblasts showed diminished mTOR signalling with reduced basal mTOR activity. Accordingly, provision of a positive nutrient signal by L-arginine supplementation partially restored mTOR activity and ameliorated the cytopathological abnormalities. Innovation: Our data provide a novel molecular mechanism underlying GM2 gangliosidosis. Impaired autophagy caused by insufficient lysosomal function might represent a new therapeutic target for these diseases. Conclusions: We contend that the expression of autophagy/lysosome/mTOR-associated molecules may prove useful peripheral biomarkers for facile monitoring of treatment of GM2 gangliosidosis and neurodegenerative disorders that affect the lysosomal function and disrupt autophagy

Intermediate Band Solar Cell with Extreme Broadband Spectrum Quantum Efficiency

We report, for the first time, about an intermediate band solar cell implemented with InAs/AlGaAs quantum dots whose photoresponse expands from 250 to ~ 6000  nm. To our knowledge, this is the broadest quantum efficiency reported to date for a solar cell and demonstrates that the intermediate band solar cell is capable of producing photocurrent when illuminated with photons whose energy equals the energy of the lowest band gap. We show experimental evidence indicating that this result is in agreement with the theory of the intermediate band solar cell, according to which the generation recombination between the intermediate band and the valence band makes this photocurrent detectable