Comparison on OpenStack and OpenNebula performance to improve multi-Cloud architecture on cosmological simulation use case

With the increasing numbers of Cloud Service Providers and the migration of the Grids to the Cloud paradigm, it is necessary to be able to leverage these new resources. Moreover, a large class of High Performance Computing (HPC) applications can run these resources without (or with minor) modifications. But using these resources come with the cost of being able to interact with these new resource providers. In this paper we introduce the design of a HPC middleware that is able to use resources coming from an environment that compose of multiple Clouds as well as classical \hpc resources. Using the \diet middleware, we are able to deploy a large-scale, distributed HPC platform that spans across a large pool of resources aggregated from different providers. Furthermore, we hide to the end users the difficulty and complexity of selecting and using these new resources even when new Cloud Service Providers are added to the pool. Finally, we validate the architecture concept through cosmological simulation RAMSES. Thus we give a comparison of 2 well-known Cloud Computing Software: OpenStack and OpenNebula.Avec l'augmentation du nombre de fournisseurs de service Cloud et la migration des applications depuis les grilles de calcul vers le Cloud, il est nécessaire de pouvoir tirer parti de ces nouvelles ressources. De plus, une large classe des applications de calcul haute performance peuvent s'exécuter sur ces ressources sans modifications (ou avec des modifications mineures). Mais utiliser ces ressources vient avec le coût d'être capable d'intéragir avec des nouveaux fournisseurs de ressources. Dans ce papier, nous introduisons la conception d'un nouveau intergiciel HPC qui permet d'utiliser les ressources qui proviennent d'un environement composé de plusieurs Clouds comme des ressources classiques. En utilisant l'intergiciel \diet, nous sommes capable de déployer une plateforme HPC distribuée et large échelle qui s'étend sur un large ensemble de ressources aggrégées entre plusieurs fournisseurs Cloud. De plus, nous cachons à l'utilisateur final la difficulté et la complexité de sélectionner et d'utiliser ces nouvelles ressources quand un nouveau fournisseur de service Cloud est ajouté dans l'ensemble. Finalement, nous validons notre concept d'architecture via une application de simulation cosmologique RAMSES. Et nous fournissons une comparaison entre 2 intergiciels de Cloud: OpenStack et OpenNebula

In Situ Diazotroph Population Dynamics Under Different Resource Ratios in the North Pacific Subtropical Gyre.

Major advances in understanding the diversity, distribution, and activity of marine N2-fixing microorganisms (diazotrophs) have been made in the past decades, however, large gaps in knowledge remain about the environmental controls on growth and mortality rates. In order to measure diazotroph net growth rates and microzooplankton grazing rates on diazotrophs, nutrient perturbation experiments and dilution grazing experiments were conducted using free-floating in situ incubation arrays in the vicinity of Station ALOHA in March 2016. Net growth rates for targeted diazotroph taxa as well as Prochlorococcus, Synechococcus and photosynthetic picoeukaryotes were determined under high (H) and low (L) nitrate:phosphate (NP) ratio conditions at four depths in the photic zone (25, 45, 75, and 100 m) using quantitative PCR and flow cytometry. Changes in the prokaryote community composition in response to HNP and LNP treatments were characterized using 16S rRNA variable region tag sequencing. Microzooplankton grazing rates on diazotrophs were measured using a modified dilution technique at two depths in the photic zone (15 and 125 m). Net growth rates for most of the targeted diazotrophs after 48 h were not stimulated as expected by LNP conditions, rather enhanced growth rates were often measured in HNP treatments. Interestingly, net growth rates of the uncultivated prymnesiophyte symbiont UCYN-A1 were stimulated in HNP treatments at 75 and 100 m, suggesting that N used for growth was acquired through continuing to fix N2 in the presence of nitrate. Net growth rates for UCYN-A1, UCYN-C, Crocosphaera sp. (UCYN-B) and the diatom symbiont Richelia (associated with Rhizosolenia) were uniformly high at 45 m (up to 1.6 ± 0.5 d-1), implying that all were growing optimally at the onset of the experiment at that depth. Differences in microzooplankton grazing rates on UCYN-A1 and UCYN-C in 15 m waters indicate that the grazer assemblage preyed preferentially on UCYN-A1. Deeper in the water column (125 m), both diazotrophs were grazed at substantial rates, suggesting grazing pressure may increase with depth in the photic zone. Constraining in situ diazotroph growth and mortality rates are important steps for improving parameterization for diazotrophs in global ecosystem models

Composition and degradation of salp fecal pellets: Implications for vertical flux in oceanic environments

Changes in the sinking rates, ash-free dry weights, particulate carbon and nitrogen content, and carbon:nitrogen ratios from the fecal pellets of several species of oceanic salps were examined in ten-day decomposition studies. Although bacteria and protozoa became abundant in the incubation vessels, most of the fecal pellets remained physically intact throughout the study. Bacterial activity in the pellets (measured by the rate of uptake of 3H-thymidine) increased, but microbial degradation had little effect on the sinking speeds of most of the fecal pellets. The average losses of ash-free dry weight and carbon and nitrogen content, along with changes in carbon:nitrogen ratio, were small compared to their initial values. We conclude that microbial degradation of large salp fecal pellets would not prevent the vertical flux to the deep ocean of a significant fraction of the particulate organic material contained in the pellets. The fecal pellets of oceanic salps provide a rapid, and potentially important, mechanism for the consolidation and vertical transport of organic and lithogenic material associated with minute particles in the open ocean

Plenum a la Mode - Augmented Reality Fashions

Inspired by ideas portrayed in science fiction, the authors sought to develop a set of augmented reality fashions that showcased scenes from a science fiction novel recently published by the principal author. The development team included artists and designers, a programmer, and the writer. Significant technical challenges needed to be overcome for success, including fabric construction and manipulation, image enhancement, robust image recognition and tracking capabilities, and the management of lighting and suitable backgrounds. Viewing geometries were also a non-trivial problem. The final solution permitted acceptable but not perfect real-time tracking of the fashion models and the visualization of both static and dynamic 3D elements overlaid onto the physical garments

Ergodic encoding for single-element ultrasound imaging in vivo

Conventional ultrasound imaging relies on the computation of geometric time delay from multiple sensors to detect the position of a scatterer. In this paper, we present Ergodic Relay Ultrasound Imaging (ERUI), a method that utilizes an ergodic cavity down to a single ultrasonic sensor for ultrasound imaging. With the proposed method, the ergodic cavity creates a unique temporal signature that encodes the position of a scatterer. When compared to standard approaches, ERUI enables the generation of images of comparable quality while utilizing fewer detector elements. Our results suggest that ERUI has the potential to achieve image resolution similar to that of traditional imaging techniques, shifting the complexity from hardware to sofware. The demonstrated feasibility offers a promising path towards ultrasound probes with reduced costs and complexity for more portable scanning devices.Comment: 5 pages, 4 figures, Lette

Chromatin recruitment of activated AMPK drives fasting response genes co-controlled by GR and PPARα

Adaptation to fasting involves both Glucocorticoid Receptor (GRα) and Peroxisome Proliferator-Activated Receptor α (PPARα) activation. Given both receptors can physically interact we investigated the possibility of a genome-wide cross-talk between activated GR and PPARα, using ChIP- and RNA-seq in primary hepatocytes. Our data reveal extensive chromatin co-localization of both factors with cooperative induction of genes controlling lipid/glucose metabolism. Key GR/PPAR co-controlled genes switched from transcriptional antagonism to cooperativity when moving from short to prolonged hepatocyte fasting, a phenomenon coinciding with gene promoter recruitment of phosphorylated AMP-activated protein kinase (AMPK) and blocked by its pharmacological inhibition. In vitro interaction studies support trimeric complex formation between GR, PPARα and phospho-AMPK. Long-term fasting in mice showed enhanced phosphorylation of liver AMPK and GRα Ser211. Phospho-AMPK chromatin recruitment at liver target genes, observed upon prolonged fasting in mice, is dampened by refeeding. Taken together, our results identify phospho-AMPK as a molecular switch able to cooperate with nuclear receptors at the chromatin level and reveal a novel adaptation mechanism to prolonged fasting

Oxygen transfer rate model for cell-free and predictive D.O. control in intensified bioreactor processes

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MODELLING OF ALLOMETRIC EQUATIONS FOR BIOMASS ESTIMATE IN DECIDUOUS FOREST

This paper aimed at testing and adjusting the allometric models for the biomass estimate in deciduous forest. The data result from seven 12 x 12 m plots, where 91 trees were cut down. Their diameter at breast height (DBH) was greater than 5 cm, and the measurement was made based on the DBH, total height (H) and total dry biomass (DAB) for each individual. The adjusted equations, without stratification, present an adjusted determination coefficient (R2aj) between 0.726 and 0.972, and estimate standard error in percentage (Syx%) ranging from 33.5 to 119.6. The best-adjusted model for the non-stratified data set was obtained through the Stepwise procedure, which resulted in the following equation: dab = β0 + β1.(DBH3) + β2.H + β3.(DBH3.H), with R2aj of 0.954 and Syx% of 44.0. For the stratified form, only the diameter class above 15 cm presented acceptable parameters, with R2aj of 0.968 and Syx% of 26.5.  That way, the current database has shown good results in the adjustment of stochastic models to estimate the DAB of each tree

TRUNK BIOMASS ESTIMATION BY DIFFERENT METHODS IN A SUBTROPICAL FOREST

The aim of the work was to estimate trunk biomass in a Deciduous Seasonal Forest by using direct and indirect methods. The data were obtained from seven 12 x 12 m plots, bringing to a total of 64 trees. Trunk biomass was determined by direct method and indirect methods which consisted of: 1) Real Volume (RV) of the trunk multiplied by the Weighted Average (WA) and Arithmetic Average (AA) of the specific basic mass of the wood species found, resulting in Real Volume for Weighted Average (RVWA)  and Real Volume for Arithmetic Average (RVAA), and 2) by the Estimated Volume (EV) multiplied by WAand by AA, resulting in Estimated Volume for Weighted Average (EVWA)  and Estimated Volume for Arithmetic Average (EVAA). The trunk biomass of the three plots determined by the direct method was 11,451 Kg. The indirect method that had the most similar to the real trunk biomass (TB) value result was the EVAA (13,142 Kg), and the one that showed the largest difference was the RVWA,which was estimated at 20,061 Kg. The t-test showed significant difference of trunk biomass for indirect methods that used the RV; and the methods that used the EV did not differ statistically.Key-words: Forest biomass; arboreal biomass; Decidual Stational Forest.ResumoEstimativa da biomassa do fuste por diferentes métodos em floresta subtropical. O trabalho teve como objetivo estimar a biomassa do fuste em um fragmento de Floresta Estacional Decidual Montana utilizando métodos diretos e indiretos. Os dados de biomassa foram obtidos de sete parcelas de 12 x 12 m, totalizando 64 árvores. A biomassa do fuste foi determinada pelo método direto e por métodos indiretos que consistiram em: 1º) Volume Rigoroso (VR) do fuste multiplicado pela Média Ponderada (MP) e Média Aritmética (MA) da massa específica básica da madeira das espécies encontradas, resultando em Volume Rigoroso para Média Ponderada (VRMP)e Volume Rigoroso para Média Aritmética (VRMA), e 2º) pelo Volume Estimado (VE) multiplicado pela MPe pela MA, resultando em Volume Estimado para Média Ponderada (VEMP) e Volume Estimado para a Média Aritmética (VEMA). O TB das três parcelas determinado diretamente foi de 11451 Kg. O método indireto que mais se aproximou da biomassa do fuste foi o VEMA (13142 Kg), e o que apresentou a maior diferença foi o VRMP que totalizou 20061 Kg. O teste t indicou diferença significativa da biomassa do fuste para os métodos indiretos que utilizam o VR; e os métodos que utilizaram o VE não diferiram estatisticamente.Palavras-chaves: Biomassa florestal; biomassa arbórea; Floresta Estacional Decidual

Non-redundant Functions of ATM and DNA-PKcs in Response to DNA Double-Strand Breaks

DNA double-strand breaks (DSBs) elicit the so-called DNA damage response (DDR), largely relying on ataxia telangiectasia mutated (ATM) and DNA-dependent protein kinase (DNA-PKcs), two members of the PI3K-like kinase family, whose respective functions during the sequential steps of the DDR remains controversial. Using the DIvA system (DSB inducible via AsiSI) combined with high-resolution mapping and advanced microscopy, we uncovered that both ATM and DNA-PKcs spread in cis on a confined region surrounding DSBs, independently of the pathway used for repair. However, once recruited, these kinases exhibit non-overlapping functions on end joining and γH2AX domain establishment. More specifically, we found that ATM is required to ensure the association of multiple DSBs within “repair foci.” Our results suggest that ATM acts not only on chromatin marks but also on higher-order chromatin organization to ensure repair accuracy and survival.Spanish Government SAF2010-21017Spanish Government BES-2011-0473