The HPCG benchmark: analysis, shared memory preliminary improvements and evaluation on an Arm-based platform

The High-Performance Conjugate Gradient (HPCG) benchmark complements the LINPACK benchmark in the performance evaluation coverage of large High-Performance Computing (HPC) systems. Due to its lower arithmetic intensity and higher memory pressure, HPCG is recognized as a more representative benchmark for data-center and irregular memory access pattern workloads, therefore its popularity and acceptance is raising within the HPC community. As only a small fraction of the reference version of the HPCG benchmark is parallelized with shared memory techniques (OpenMP), we introduce in this report two OpenMP parallelization methods. Due to the increasing importance of Arm architecture in the HPC scenario, we evaluate our HPCG code at scale on a state-of-the-art HPC system based on Cavium ThunderX2 SoC. We consider our work as a contribution to the Arm ecosystem: along with this technical report, we plan in fact to release our code for boosting the tuning of the HPCG benchmark within the Arm community.Postprint (author's final draft

Looking up or down on the social ladder: how socioeconomic comparisons shape judgments about monetary and time donations

The increasing inequality rate within countries worldwide makes social comparisons more evident. In seven experiments, we demonstrate that people comparing themselves to others in a superior socioeconomic position (upward comparison) judge that wealthier others should donate more time and money to charity. However, social comparison to others in an inferior position (downward comparison) does not always increase monetary donations. This discrepancy in prescriptions for monetary donations between those who make upward and downward social comparisons is driven by judgments about relative spare money; while people making upward comparisons believe that others have more spare money, people making downward comparisons only think they have more spare money, and should donate more, when reminded of their hierarchical position at the time of judgment. Low meritocracy beliefs exacerbate the difference between the prescriptions of how much oneself and others should donate given their socioeconomic position. This differential pattern among individuals making upward and downward social comparisons helps to propagate economic inequality. People making upward comparisons prescribe to wealthier others the responsibility to donate to charity, who in turn may not think they should donate more money. These findings have implications for charitable and non-profit organizations and contribute to research on social comparison, inequality, and judgments about monetary and time donations.info:eu-repo/semantics/publishedVersio

Estudo da recuperação e hidrólise de isoflavonas e carboidratos obtidos a partir do melaço de soja

Orientador : Prof. Dr. Marcos Lúcio CorazzaCoorientador : Prof. Dr. Lúcio Cardozo FilhoTese (doutorado) - Universidade Federal do Paraná, Setor de Tecnologia, Programa de Pós-Graduação em Engenharia de Alimentos. Defesa: Curitiba, 18/10/2013Inclui referênciasResumo: O melaço de soja é um resíduo obtido no processo de geração do concentrado proteico. É um resíduo pouco aproveitado em aplicações biotecnológicas, mesmo dispondo de substâncias bioativas, como as isoflavonas, e presença de altas quantidades de carboidratos, em especial os oligossacarídeos de rafinose (RO). Este material apresenta grande potencial para atender demandas das indústrias alimentícias e farmacêuticas. Assim, este trabalho tem como objetivo estudar a conversão dos compostos de isoflavonas (formas glicosídicas) em formas agliconas por bioconversão com o uso de enzimas presentes no extrato enzimático. Foram utilizados três diferentes solventes extratores de isoflavonas (metanol, etanol e água), e bioconversões dos extratos utilizando o planejamento experimental 23 com variáveis independentes (agitação, razão de extrato enzimático e tempo). Foram utilizadas membranas de ultrafiltração com diferentes porosidades para obtenção dos carboidratos livres de sujidades e posterior bioconversão das formas RO em formas monossacarídicas e dissacarídicas, bem como estabelecer um protocolo eficiente para obtenção e aplicação industrial. O extrato enzimático obtido do Aspergillus niger contém enzimas _-glicosidase e _-galactosidase obtidas por fermentação em estado semissólido após incubação por 96 h. A caracterização bioquímica da enzima _-glicosidase presente no extrato (Gli) foi avaliada pelo pH e temperatura ótimas, valores 4,9 e 56,5 oC, respectivamente, e estabilidade enzimática na faixa de pH entre 3,5 a 5,5 e temperatura de 50 e 55 oC. O uso da técnica Api-Zym possibilitou um avanço em relação à presença de outras enzimas, antes desconhecidas, presentes no extrato enzimático. Testes de atividade antimicrobiana sobre o fungo Myrothecium verrucaria foram realizados com concentração de 0,2 mg/ L de isoflavonas bioconvertidas, com a obtenção de resultados satisfatórios em relação ao crescimento do micro-organismo nas proximidades do halo. Os valores da composição centesimal do melaço de soja apresentaram baixos teores proteicos e alto teor de carboidratos digeríveis (24,5%) e formas não digeríveis RO (19,5%). A ultrafiltração de compostos de isoflavonas totais possibilitou a obtenção de teores distintos (101,8 e 82,8 g/g). No entanto, para os teores de carboidratos totais o maior valor foi de 104,0 mg/g e o menor 39,4 mg/g. Os resultados de bioconversão, utilizando a enzima _-Gal sobre os compostos de carboidratos foram satisfatórios, com observação da redução dos valores de RO de 75,2% e 70%. O método adotado para bioconversão sobre os compostos de isoflavonas extraídos a partir dos solventes metanol, etanol e água, empregando a enzima _-Gli, foi satisfatório, especialmente em relação ao etanol. Ainda neste trabalho, a validação da metodologia de quantificação dos compostos de isoflavonas com obtenção das curvas de calibração e ajustes dentro de valores significativos a nível de (p<0,05), com utilização da análise de variância. Entretanto, para os teores de fenólicos totais, os resultados obtidos foram considerados coerentes por se tratar de um resíduo à base de soja, com valores variando entre 26,8 GAE/100g de extrato metanólico (80%) e 59,8mg GAE/100g de extrato etanólico (90% v/v).Abstract: Soybean molasses is a residue obtained during the process of generating protein concentrate. It has hardly been tapped in biotechnological applications even providing bioactive substances such as isoflavones and the presence of high levels of carbohydrates, especially raffinose oligosaccharides (RO). This material has great potential to meet the demands of food and pharmaceutical industries. Thus, this paper aims to study the conversion of isoflavone compounds (glycoside forms) into aglycone forms through bioconversion using enzymes from the enzyme extract. Three different isoflavone extractor solvents (methanol, ethanol, and water) were used as well as extract bioconversions using the experimental design 23 with independent variables (agitation, enzyme extract rate, and time). Ultrafiltration membranes were used with different porosity to obtain carbohydrates free of impurities and subsequent bioconversion of RO forms into monosaccharide and disaccharide forms, as well as establish an efficient protocol for industrial application. The enzyme extract obtained from Aspergillus niger has _-glucosidase and _- galactosidase enzymes obtained through semisolid state fermentation after incubation for 96 h. Biochemical characterization of the enzyme _-glucosidase present in the extract (Gli) was evaluated by pH and temperature conditions, values 4.9 and 56.5 °C respectively. Enzymatic stability showed pH ranging from 3.5 to 5.5 and temperature of 50 and 55 oC. The use of the technique Api-Zym enabled the improvement concerning the presence of previously unknown enzymes in the enzyme extract. Tests of antimicrobial activity against the fungus Myrothecium verrucaria were performed with 0.2 mg/ L of converted isoflavones. Results were satisfactory in relation to the growing of microorganisms near the halo. Proximate composition values of soybean molasses showed low levels of protein and high levels of digestible carbohydrates (24.5%) and non digestible RO forms (19.5%). The infiltration of total isoflavone compounds made it possible to get distinct concentrations (101.8 and 82.8 g/g). However, for total carbohydrate levels the highest value was 104.0 mg/g and the lowest 39.4 mg/g. Bioconversion results using the enzyme _-Gal on carbohydrate compounds were satisfactory and the reduction of RO values of 75.2% and 70% were observed. The method adopted for bioconversion on isoflavone compounds extracted from the solvents methanol, ethanol, and water using the enzyme _-Gli was satisfactory, especially with regards to ethanol. Also, the methodology for quantifying isoflavone compounds was validated and calibration curves and adjustments were obtained within significant levels at (p<0.05) using the variance analysis. However, the results for total phenolic levels were considered consistent since it is a soybean-based residue with values ranging from 26.8 GAE/100g of methanol extract (80%) and 59.8 mg GAE/100g of ethanol extract (90% v/v)

Implementation of the K-Means Algorithm on Heterogeneous Devices: A Use Case Based on an Industrial Dataset

This paper presents and analyzes a heterogeneous implementation of an industrial use case based on K-means that targets symmetric multiprocessing (SMP), GPUs and FPGAs. We present how the application can be optimized from an algorithmic point of view and how this optimization performs on two heterogeneous platforms. The presented implementation relies on the OmpSs programming model, which introduces a simplified pragma-based syntax for the communication between the main processor and the accelerators. Performance improvement can be achieved by the programmer explicitly specifying the data memory accesses or copies. As expected, the newer SMP+GPU system studied is more powerful than the older SMP+FPGA system. However the latter is enough to fulfill the requirements of our use case and we show that uses less energy when considering only the active power of the execution.This work is partially supported by the European Union H2020 project AXIOM (grant agreement n. 645496), HiPEAC (grant agreement n. 687698), and Mont-Blanc (grant agreements n. 288777, 610402 and 671697), the Spanish Government Programa Severo Ochoa (SEV-2015-0493), the Spanish Ministry of Science and Technology (TIN2015- 65316-P) and the Departament d’Innovació, Universitats i Empresa de la Generalitat de Catalunya, under project MPEXPAR: Models de Programaci´o i Entorns d’Execució Paral·lels (2014-SGR-1051).Peer ReviewedPostprint (author's final draft

Is Arm software ecosystem ready for HPC?

In recent years, the HPC community has increasingly grown its interest towards the Arm architecture with research projects targeting primarily the installation of Arm-based clusters. State of the art research project examples are the European Mont-Blanc, the Japanese Post-K, and the UKs GW4/EPSRC. Primarily attention is usually given to hardware platforms, and the Arm HPC community is growing as the hardware is evolving towards HPC workloads via solutions borrowed from mobile market e.g., big.LITTLE and additions such as Armv8-A Scalable Vector Extension (SVE) technology. However the availability of a mature software ecosystem and the possibility of running large and complex HPC applications plays a key role in the consolidation process of a new technology, especially in a conservative market like HPC. For this reason in this poster we present a preliminary evaluation of the Arm system software ecosystem, limited here to the Arm HPC Compiler and the Arm Performance Libraries, together with a porting and testing of three fairly complex HPC code suites: QuantumESPRESSO, WRF and FEniCS. The selection of these codes has not been totally random: they have been in fact proposed as HPC challenges during the last two editions of the Student Cluster Competition at ISC where all the authors have been involved operating an Arm-based cluster and awarded with the Fan Favorite award.The research leading to these results has received funding from the European Community's Seventh Framework Programme [FP7/2007-2013] and Horizon 2020 under the Mont-Blanc projects [3], grant agreements n. 288777, 610402 and 671697. The authors would also like to thank E4 Computer Engineering for providing part of the hardware resources needed for the evaluation carried out in this poster as well as for greatly supporting the Student Cluster Competition team.Postprint (author's final draft

IS PRINCIPAL COMPONENT ANALYSIS MORE EFFICIENT TO DETECT DIFFERENCES ON BIOMECHANICAL VARIABLES BETWEEN GROUPS?

The biomechanical analysis investigates variables such as angles, inter-segmental forces and moments at the joints. When the relevant parameters (e.g., range of motion, peak values) are selected a priori from these variables, they could not perfectly represent the information content of the original dataset. Therefore, in this study we want to validate the efficacy of the Principal Component Analysis (PCA) in overcoming the limitations of the a priori selection of the parameters. An application study is reported; the lower-limb joint mechanics between patients operated with two different surgical techniques for a total hip arthroplasty are analyzed with both the traditional analysis and the PCA. The findings from the two methods converged, but the PCA identified new sources of variability not previously detected

Influence of cold rolling on in vitro cytotoxicity and electrochemical behaviour of an Fe-Mn-C biodegradable alloy in physiological solutions

The properties of cold-worked Fe-13Mn-1.2C steel, as candidate material for scaffolding and stenting applications, have been investigated. The study of the electrochemical corrosion susceptibility of Fe-13Mn-1.2C alloy in protein bearing and non-protein bearing physiological solutions, revealed that there were no differences between the as-received, 10% and 20% cold worked Fe-13Mn-1.2C samples. Although protein addition reduces the overall corrosion rate in static immersion degradation tests for both the cold worked and non-cold worked alloys, there were no discernible differences in the corrosion rates of samples with different percentages of cold work deformations. Similarly, potentiodynamic testing showed no differences between the corrosion rates in solutions with and without protein addition. Atomic absorption spectroscopy (AAS) results—post static immersion—showed similar values of Fe and Mn concentrations in the electrolyte for all the investigated conditions. Cold working was found to increase Grain Average Misorientation (GAM) and deformation twins within the steel, and, consequently, this led to an increase in the elastic modulus. Hence, cold-rolling may be used to achieve smaller sections (volumes) in order to support the equivalent load of the non-cold worked counterpart, giving a larger surface area to the volume ratio, thereby increasing the corrosion rate, and, in turn, rendering the degradation process shorter. When considering cytocompatibility in vitro, the collected supernatant particulate free Fe-13Mn-1.2C steel electrolytes were seen to be equally cytocompatible with no differences being observed between the different percentage cold work conditions. The presence of solid 80 μm size particles in the seeded elutions were seen to change the results and render the Fe-13Mn-1.2C steel non-cytocompatible.peer-reviewe

Complementing the Cancer-Immunity Cycle

Reactivation of cytotoxic CD8+ T-cell responses has set a new direction for cancer immunotherapy. Neutralizing antibodies targeting immune checkpoint programmed cell death protein 1 (PD-1) or its ligand (PD-L1) have been particularly successful for tumor types with limited therapeutic options such as melanoma and lung cancer. However, reactivation of T cells is only one step toward tumor elimination, and a substantial fraction of patients fails to respond to these therapies. In this context, combination therapies targeting more than one of the steps of the cancer-immune cycle may provide significant benefits. To find the best combinations, it is of upmost importance to understand the interplay between cancer cells and all the components of the immune response. This review focuses on the elements of the complement system that come into play in the cancer-immunity cycle. The complement system, an essential part of innate immunity, has emerged as a major regulator of cancer immunity. Complement effectors such as C1q, anaphylatoxins C3a and C5a, and their receptors C3aR and C5aR1, have been associated with tolerogenic cell death and inhibition of antitumor T-cell responses through the recruitment and/or activation of immunosuppressive cell subpopulations such as myeloid-derived suppressor cells (MDSCs), regulatory T cells (Tregs), or M2 tumor-associated macrophages (TAMs). Evidence is provided to support the idea that complement blocks many of the effector routes associated with the cancer-immunity cycle, providing the rationale for new therapeutic combinations aimed to enhance the antitumor efficacy of anti-PD-1/PD-L1 checkpoint inhibitors

Terminal-repeat retrotransposons in miniature (TRIMs) in bivalves

Terminal repeat retrotransposons in miniature (TRIMs) are small non-autonomous LTR retrotransposons consisting of two terminal direct repeats surrounding a short internal domain. The detection and characterization of these elements has been mainly limited to plants. Here we present the first finding of a TRIM element in bivalves, and among the first known in the kingdom Animalia. Class Bivalvia has high ecological and commercial importance in marine ecosystems and aquaculture, and, in recent years, an increasing number of genomic studies has addressed to these organisms. We have identified biv-TRIM in several bivalve species: Donax trunculus, Ruditapes decussatus, R. philippinarum, Venerupis corrugata, Polititapes rhomboides, Venus verrucosa, Dosinia exoleta, Glycymeris glycymeris, Cerastoderma edule, Magallana gigas, Mytilus galloprovincialis. biv-TRIM has several characteristics typical for this group of elements, exhibiting different variations. In addition to canonically structured elements, solo-TDRs and tandem repeats were detected. The presence of this element in the genome of each species is <1%. The phylogenetic analysis showed a complex clustering pattern of biv-TRIM elements, and indicates the involvement of horizontal transfer in the spreading of this elementXunta de Galicia | Ref. ED431C 2016-037Xunta de Galicia | Ref. ED481B/2018/091Ministarstvo Znanosti, Obrazovanja i Sporta | Ref. 098-0982913-275

Complementing the cancer-immunity cycle

Reactivation of cytotoxic CD8+ T-cell responses has set a new direction for cancer immunotherapy. Neutralizing antibodies targeting immune checkpoint programmed cell death protein 1 (PD-1) or its ligand (PD-L1) have been particularly successful for tumor types with limited therapeutic options such as melanoma and lung cancer. However, reactivation of T cells is only one step toward tumor elimination, and a substantial fraction of patients fails to respond to these therapies. In this context, combination therapies targeting more than one of the steps of the cancer-immune cycle may provide significant benefits. To find the best combinations, it is of upmost importance to understand the interplay between cancer cells and all the components of the immune response. This review focuses on the elements of the complement system that come into play in the cancer-immunity cycle. The complement system, an essential part of innate immunity, has emerged as a major regulator of cancer immunity. Complement effectors such as C1q, anaphylatoxins C3a and C5a, and their receptors C3aR and C5aR1, have been associated with tolerogenic cell death and inhibition of antitumor T-cell responses through the recruitment and/or activation of immunosuppressive cell subpopulations such as myeloid-derived suppressor cells (MDSCs), regulatory T cells (Tregs), or M2 tumor-associated macrophages (TAMs). Evidence is provided to support the idea that complement blocks many of the effector routes associated with the cancer-immunity cycle, providing the rationale for new therapeutic combinations aimed to enhance the antitumor efficacy of anti-PD-1/PD-L1 checkpoint inhibitors