Evaluating the impact of OpenMP 4.0 extensions on relevant parallel workloads

OpenMP has been for many years the most widely used programming model for shared memory architectures. Periodically, new features are proposed and some of them are finally selected for inclusion in the OpenMP standard. The OmpSs programming model developed at the Barcelona Supercomputing Center (BSC) aims to be an OpenMP forerunner that handles the main OpenMP constructs plus some extra features not included in the OpenMP standard. In this paper we show the usefulness of three OmpSs features not currently handled by OpenMP 4.0 by deploying them over three applications of the PARSEC benchmark suite and showing the performance benefits. This paper also shows performance trade-offs between the OmpSs/OpenMP tasking and loop parallelism constructs and shows how a hybrid implementation that combines both approaches is sometimes the best option.This work has been partially supported by the European Research Council under the European Union's 7th FP, ERC Grant Agreement number 321253, by the Spanish Ministry of Science and Innovation under grant TIN2012-34557 and by the HiPEAC Network of Excellence. It has been also supported by the Severo Ochoa Program awarded by the Spanish Government (grant SEV-2011-00067) M. Moreto has been partially supported by the Ministry of Economy and Competitiveness under Juan de la Cierva postdoctoral fellowship number JCI- 2012-15047. M. Casas is supported by the Secretary for Universities and Research of the Ministry of Economy and Knowledge of the Government of Catalonia and the Co- fund programme of the Marie Curie Actions of the 7th R&D Framework Programme of the European Union (Contract 2013 BP_B 00243).Peer ReviewedPostprint (author's final draft

The G1/S Specific Cyclin D2 Is a Regulator of HIV-1 Restriction in Non-proliferating Cells

Macrophages are a heterogeneous cell population strongly influenced by differentiation stimuli that become susceptible to HIV-1 infection after inactivation of the restriction factor SAMHD1 by cyclin-dependent kinases (CDK). Here, we have used primary human monocyte-derived macrophages differentiated through different stimuli to evaluate macrophage heterogeneity on cell activation and proliferation and susceptibility to HIV-1 infection. Stimulation of monocytes with GM-CSF induces a non-proliferating macrophage population highly restrictive to HIV-1 infection, characterized by the upregulation of the G1/S-specific cyclin D2, known to control early steps of cell cycle progression. Knockdown of cyclin D2, enhances HIV-1 replication in GM-CSF macrophages through inactivation of SAMHD1 restriction factor by phosphorylation. Co-immunoprecipitation experiments show that cyclin D2 forms a complex with CDK4 and p21, a factor known to restrict HIV-1 replication by affecting the function of the downstream cascade that leads to SAMHD1 deactivation. Thus, we demonstrate that cyclin D2 acts as regulator of cell cycle proteins affecting SAMHD1-mediated HIV-1 restriction in non-proliferating macrophage

Prevalence of contagious and environmental mastitis-causing bacteria in bulk tank milk and its relationships with milking practices of dairy cattle herds in São Miguel Island (Azores)

This study aimed to assess the degree of contamination of bulk tank milk (BTM) by Staphylococcus spp. and coliform bacteria and to identify major milking practices that help perpetuate them in dairy cattle herds in São Miguel Island. In July 2014, BTM was sampled and a survey concerning local milking practices was conducted on 100 herds. Semi quantitative multiplex polymerase chain reaction detected coagulase-negative staphylococci, Escherichia coli, Staphylococcus aureus, and other coliform bacteria (Klebsiella oxytoca, Klebsiella pneumoniae, andSerratia marcescens) in 100, 75, 59, and 35 % of BTM, respectively. According to multivariable univariate models, on herds not using hot water for cleaning the milking machine and teat liners, there was at least 3.4 more odds (P<0.01) to have S. aureus or coliform bacteria contamination in BTM. The likelihoodoffinding S.aureus inBTMwas higher(P<0.001)on herds without high hygiene during milking, when milking mastitic cows at the end, on abrupt cessation of milking at dry-off, and official milk control implementation. The glove use also favored (odds ratio (OR) 5.8; P<0.01)thedetection ofcoliformbacteriainBTM.Poormilkingpracticesidentified in this study should be avoided in order to decrease S. aureus and coliform bacteria contamination of BTM. Other factors associated with milk quality in São Miguel Island also should be further investigated

The Catalan Surveillance Network of SARS-CoV-2 in Sewage: design, implementation, and performance

Wastewater-based epidemiology has shown to be an efficient tool to track the circulation of SARS-CoV-2 in communities assisted by wastewater treatment plants (WWTPs). The challenge comes when this approach is employed to help Health authorities in their decision-making. Here, we describe the roadmap for the design and deployment of SARSAIGUA, the Catalan Surveillance Network of SARS-CoV-2 in Sewage. The network monitors, weekly or biweekly, 56 WWTPs evenly distributed across the territory and serving 6 M inhabitants (80% of the Catalan population). Each week, samples from 45 WWTPs are collected, analyzed, results reported to Health authorities, and finally published within less than 72 h in an online dashboard ( https://sarsaigua.icra.cat ). After 20 months of monitoring (July 20-March 22), the standardized viral load (gene copies/day) in all the WWTPs monitored fairly matched the cumulative number of COVID-19 cases along the successive pandemic waves, showing a good fit with the diagnosed cases in the served municipalities (Spearman Rho = 0.69). Here we describe the roadmap of the design and deployment of SARSAIGUA while providing several open-access tools for the management and visualization of the surveillance data.The authors wish to thank the staff from all the WWTPs monitored for their help and technical support during the sampling campaigns. The authors acknowledge the funding received from the ACA and the ASPCAT from the Catalan Government (Generalitat de Catalunya). ICRA authors acknowledge the funding provided by the Generalitat de Catalunya through the Consolidated Research Group grants ICRA-ENV 2017 SGR 1124 and ICRA-TiA 2017 SGR 1318. ICRA researchers also thank the funding from the CERCA program of the Catalan Government.Peer reviewe

Emissió de Compostos Orgànics Volàtils en vegetació mediterrània: COVs oxigenats de cadena curta, interacció entre organismes i impacte atmosfèric

Els compostos orgànics volàtils (COVs) presents a l'atmosfera poden tenir fonts naturals o antròpiques. Els COVs estan implicats en reaccions químiques que afecten la química atmosfèrica i poden tenir impactes indirectes sobre el clima a través de la generació d'aerosols i compostos oxidants. Globalment, la vegetació és la font principal de COVs naturals, mentre que els COVs antropogènics són la majoria de vegades producte d'emissions industrials i de motors de vehicles. D'entre els COVs biogènics, els isoprenoids són els més coneguts i estudiats. La nostra recerca es va centrar en el grup de COVs de cadena curta oxigenats (oxCOVs), un grup poc conegut format per metanol, etanol, formaldehid, acetaldehid, acids fòrmic i acètic, i acetona. Els oxCOVs poden ser emesos directament tant per les plantes com per les activitats humanes, i també es poden formar per la degradació atmosfèrica d'altres COVs de major massa molecular. Entre d'altres raons, han estat menys estudiats degut a problemes analítics, que s'han resolt en part recentment amb l'aparició de noves tecnologies, especialment l'espectrometria de masses per transferència de protons. Els oxCOVs tenen diverses propietats que els diferencien d'altres COVs com els isoprenoids. Els oxCOVs són més solubles en aigua i això fa la seva emissió en plantes depenent dels estomes. També tenen una vida atmosfèrica relativament llarga i presenten concentracions considerables a l'atmosfera en el nivell de ppbv (1 part en 109 en volum). Les emissions d'oxCOVs en plantes mediterrànies són molt poc conegudes, per això vam estudiar-ne l'intercanvi en els arbres típicament mediterranis Quercus ilex i Pinus halepensis. Es va confirmar el control estomàtic i de la concentració atmosfèrica del seu intercanvi. Per exemple, es va observar un punt de compensació de 20 ppbv pel formaldehid en les dues espècies d'arbre, mentre que per l'acetaldehid va ser de 6 ppbv en P. halepensis. Un tractament de sequera i posterior reg va mostrar que la sequera afecta l'intercanvi d'oxCOVs perquè afecta la conductància estomàtica. A més, es va confirmar que Q. ilex emet isoprè, encara que amb taxes petites, i que l'emissió d'isoprenoids en Q. ilex va disminuir per la sequera. Els COVs poden tenir també un paper ecològic molt important: participar en les comunicacions entre organismes. En interaccions planta-planta la nostra hipòtesi era que el metanol podia jugar un paper senyalitzador, ja que el metanol s'emet en grans quantitats des de les fulles quan són atacades per un herbívor. Un experiment de fumigació amb metanol va mostrar que les respostes de Q. ilex al metanol arribat per l'aire eren similars a les respostes a l'herbivoria i també que l'emissió de monoterpens es va incrementar lleugerament. En la comunicació entre animals, vam identificar alguns components volàtils emesos pels capolls i els excrements d'una espècie d'abella solitària (Osmia cornuta), essent-ne l'àcid acètic un dels més abundants. Llavors vam provar l'atracció exercida per l'àcid acètic sobre femelles de Monodontomerus aeneus, una vespa parasitoide d'O. cornuta, que busquen capolls per ovipositar-hi. Encara que l'àcid acètic sol atreia M. aeneus, probablement un senyal volàtil complex intervé en el procés d'atracció, ja que la ràtio àcid acètic-acetaldehid característica dels excrements va resultar més atractiva que altres ràtios. L'objectiu final de la tesi va ser observar quin impacte tenen les emissions de COVs en l'atmosfera mediterrània, ja sigui pel nivell de concentració que atanyen els COVs a l'aire com també per la seva participació en la formació de compostos com l'ozó. Per això vam mesurar (hivern i estiu) les concentracions d'oxCOVs, isoprenoids i COVs aromàtics en una zona boscosa situada dins del parc natural del Montseny, a uns 60 km al NE de la ciutat de Barcelona. Mentre que els COVs aromàtics no varen presentar gairebé cap variació estacional, les concentracions dels oxCOVs van assolir nivells més alts a l'estiu degut a les majors emissions de la vegetació i a l'increment de les reaccions fotoquímiques resultants de les altes temperatures i radiació solar de l'estiu. Els COVs isoprenoids van mostrar el canvi entre estacions més gran: les concentracions van augmentar un ordre de magnitud a l'estiu, degut a l'increment de l'activitat fisiològica de la vegetació i de les seves taxes d'emissió. També les concentracions diürnes màximes d'ozó van augmentar a l'estiu, per la major activitat fotoquímica i la presència de més COVs a l'aire. La variació diària de concentracions de COVs seguia bàsicament el règim de vent de la muntanya. La brisa marina que es desenvolupa quan surt el sol transporta cap a la muntanya masses d'aire que prèviament han passat sobre la regió metropolitana de Barcelona, on han estat enriquides en NO2 i en COVs d'origen biòtic i abiòtic. A més, aquestes masses d'aire contaminades poden reaccionar amb els COVs biogènics emesos de forma local per la vegetació, tot afavorint la formació d'O3 en aquesta zona boscosa. L'únic tipus de COV que presentava un cicle diari diferent dels demés van ser els monoterpens, perquè tenien un origen biogènic local. L'isoprè també compartia parcialment el cicle diari dels monoterpens, però només a l'estiu quan les seves fonts biòtiques eren més fortes.Volatile organic compounds (VOCs) present in the atmosphere can have natural or anthropic sources. VOCs are involved in atmospheric chemistry reactions that can have indirect climatic impacts through the generation of aerosols and oxidant compounds. Globally, vegetation is the main source of natural VOC emission, while anthropogenic VOCs are in most cases product of vehicle exhaust and industry emissions. Within biogenic VOCs, isoprenoids are the most studied and known group. Our research was focused in a group of short-chain oxygenated VOCs (oxVOCs), a poorly known group composed by methanol, ethanol, formaldehyde, acetaldehyde, formic and acetic acids, and acetone. They can be emitted directly either by plants or by human activities, and they can also be formed through degradation in the air of other higher molecular mass VOCs. Among other reasons, they have been less studied due to analytical problems than have been partly solved in recent years with the advent of new technologies, specially proton transfer reaction mass spectrometry. OxVOCs have several properties that set them apart of other VOCs like isoprenoids. OxVOCs are more soluble in water and this fact makes their release from plants stomatal-dependent. In addition, these compounds have relatively long atmospheric halflives and reach considerable concentrations in the atmosphere in the range of parts per billion in volume (ppbv). Emissions of oxVOCs in Mediterranean plants are scarcely known, for this reason we studied oxVOCs exchange in the typically Mediterranean tree species Quercus ilex and Pinus halepensis. The stomatal and atmospheric mixing ratios control of their exchange was confirmed. For instance, a compensation point of 20 ppbv for formaldehyde was observed for both tree species, while for acetaldehyde it was of 6 ppbv in P. halepensis. A treatment of drought and posterior re-watering showed that drought affects oxVOC exchange because it affects stomatal conductance. In addition, it was confirmed that Q. ilex emits isoprene, although at small rates, and that isoprenoid emission in Q. ilex decreased due to drought. VOCs can also have an important ecological role: taking part in the communication between organisms. In plant-plant interaction our hypothesis was that methanol could have a signalling role, given that methanol is emitted in big amounts from leaves upon herbivore attack. An experiment of fumigation with methanol showed that Q. ilex responses to airborne methanol were similar to responses to herbivory and also that monoterpene emission was slightly increased. In communication between animals, we identified some volatile components emitted by the cocoons and frass of a solitary bee species (Osmia cornuta), being acetic acid an abundant one among them. We then tested acetic acid attractiveness for Monodontomerus aeneus female wasps, parasitoids of O. cornuta, that look for cocoons to oviposit. Although acetic acid alone attracted M. aeneus, a complex volatile signal is probably involved in the attraction process since the ratio acetic acid-acetaldehyde characteristic of the frass was more attractive than other ratios. The last objective of this thesis was to observe the impact that VOC emissions have on the Mediterranean atmosphere, either by the mixing ratios that VOC reach in the air or also by their participation in the formation of compounds like ozone. To achieve this, the mixing ratios of oxVOCs, isoprenoids, and aromatic VOCs were measured (winter and summer) in a forest site located within a densely forested natural park (Montseny) about 60 km NE of the city of Barcelona. While aromatic VOCs showed almost no seasonal variability, short-chain oxygenated VOCs presented higher mixing ratios in summer due to the increased emission by vegetation and the increased photochemistry, both enhanced by the high temperatures and solar radiation in summer. Isoprenoid VOCs showed the biggest seasonal change in mixing ratios:they increased by one order of magnitude in summer, as a result of the increased vegetation physiological activity and emission rates. Ozone highest diurnal concentrations increased in summer too, due to more photochemical activity and the presence of more VOCs in the air. The daily variation of the VOC mixing ratios was mainly governed by the wind regime of the mountain. Sea breeze that develops after sunrise advects to the mountain polluted air masses that previously had passed over the Barcelona metropolitan region, where they were enriched in NO2 and in VOCs of biotic and abiotic origin. Furthermore, these polluted air masses can react with biogenic VOCs emitted at the local valley by the vegetation, thus enhancing O3 formation in this forest site. The only VOC species that showed a different daily pattern were monoterpenes because of their local biogenic emission. Isoprene also shared partially the daily pattern of monoterpenes, but only in summer when its biotic sources were stronger

Proportion of 894 bulk milk samples that were positive for bovine mastitis pathogens in China from April 2012 to October 2013.

<p>Proportion of 894 bulk milk samples that were positive for bovine mastitis pathogens in China from April 2012 to October 2013.</p

Effect of regions on the presence of mastitis pathogens.

<p>Effect of regions on the presence of mastitis pathogens.</p