Disaggregating non-volatile memory for throughput-oriented genomics workloads

Massive exploitation of next-generation sequencing technologies requires dealing with both: huge amounts of data and complex bioinformatics pipelines. Computing architectures have evolved to deal with these problems, enabling approaches that were unfeasible years ago: accelerators and Non-Volatile Memories (NVM) are becoming widely used to enhance the most demanding workloads. However, bioinformatics workloads are usually part of bigger pipelines with different and dynamic needs in terms of resources. The introduction of Software Defined Infrastructures (SDI) for data centers provides roots to dramatically increase the efficiency in the management of infrastructures. SDI enables new ways to structure hardware resources through disaggregation, and provides new hardware composability and sharing mechanisms to deploy workloads in more flexible ways. In this paper we study a state-of-the-art genomics application, SMUFIN, aiming to address the challenges of future HPC facilities.This work is partially supported by the European Research Council (ERC) under the EU Horizon 2020 programme (GA 639595), the Spanish Ministry of Economy, Industry and Competitivity (TIN2015-65316-P) and the Generalitat de Catalunya (2014-SGR-1051).Peer ReviewedPostprint (author's final draft

Secondary Organic Aerosol Formation from Healthy and Aphid-Stressed Scots Pine Emissions.

One barrier to predicting biogenic secondary organic aerosol (SOA) formation in a changing climate can be attributed to the complex nature of plant volatile emissions. Plant volatile emissions are dynamic over space and time, and change in response to environmental stressors. This study investigated SOA production from emissions of healthy and aphid-stressed Scots pine saplings via dark ozonolysis and photooxidation chemistry. Laboratory experiments using a batch reaction chamber were used to investigate SOA production from different plant volatile mixtures. The volatile mixture from healthy plants included monoterpenes, aromatics, and a small amount of sesquiterpenes. The biggest change in the volatile mixture for aphid-stressed plants was a large increase (from 1.4 to 7.9 ppb) in sesquiterpenes-particularly acyclic sesquiterpenes, such as the farnesene isomers. Acyclic sesquiterpenes had different effects on SOA production depending on the chemical mechanism. Farnesenes suppressed SOA formation from ozonolysis with a 9.7-14.6% SOA mass yield from healthy plant emissions and a 6.9-10.4% SOA mass yield from aphid-stressed plant emissions. Ozonolysis of volatile mixtures containing more farnesenes promoted fragmentation reactions, which produced higher volatility oxidation products. In contrast, plant volatile mixtures containing more farnesenes did not appreciably change SOA production from photooxidation. SOA mass yields ranged from 10.8 to 23.2% from healthy plant emissions and 17.8-26.8% for aphid-stressed plant emissions. This study highlights the potential importance of acyclic terpene chemistry in a future climate regime with an increased presence of plant stress volatiles

Microfibers for juice analysis by solid-phase microextraction.

In view of the interest in analyzing volatile compounds by SPME, the following five microfibers were tested, polydimethylsiloxane; polyacrylate; polydimethylsiloxane/divinylbenzene; carboxen/polydimethylsiloxane, and carbowax/divinylbenzene, to select the one which presents the best performance for the adsorption of the volatile compounds present in the headspace of acid lime juice samples. Sample stabilization time variations (30 and 60 minutes) were assessed as well the addition of NaCl to the samples. It was verified that the chromatogram with the most adsorbed volatile compounds was obtained with PDMS/DVB microfiber at 30 minutes and the addition of 0.2 g NaCl

The role of Volatile Anesthetics in Cardioprotection: a systematic review.

This review evaluates the mechanism of volatile anesthetics as cardioprotective agents in both clinical and laboratory research and furthermore assesses possible cardiac side effects upon usage. Cardiac as well as non-cardiac surgery may evoke perioperative adverse events including: ischemia, diverse arrhythmias and reperfusion injury. As volatile anesthetics have cardiovascular effects that can lead to hypotension, clinicians may choose to administer alternative anesthetics to patients with coronary artery disease, particularly if the patient has severe preoperative ischemia or cardiovascular instability. Increasing preclinical evidence demonstrated that administration of inhaled anesthetics - before and during surgery - reduces the degree of ischemia and reperfusion injury to the heart. Recently, this preclinical data has been implemented clinically, and beneficial effects have been found in some studies of patients undergoing coronary artery bypass graft surgery. Administration of volatile anesthetic gases was protective for patients undergoing cardiac surgery through manipulation of the potassium ATP (KATP) channel, mitochondrial permeability transition pore (mPTP), reactive oxygen species (ROS) production, as well as through cytoprotective Akt and extracellular-signal kinases (ERK) pathways. However, as not all studies have demonstrated improved outcomes, the risks for undesirable hemodynamic effects must be weighed against the possible benefits of using volatile anesthetics as a means to provide cardiac protection in patients with coronary artery disease who are undergoing surgery

Lactic Acid Bacteria and Yeast Inocula Modulate the Volatile Profile of Spanish-Style Green Table Olive Fermentations

In this work, Manzanilla Spanish-style green table olive fermentations were inoculated with Lactobacillus pentosus LPG1, Lactobacillus pentosus Lp13, Lactobacillus plantarum Lpl15, the yeast Wickerhanomyces anomalus Y12 and a mixed culture of all them. After fermentation (65 days), their volatile profiles in brines were determined by gas chromatography-mass spectrometry analysis. A total of 131 volatile compounds were found, but only 71 showed statistical differences between at least, two fermentation processes. The major chemical groups were alcohols (32), ketones (14), aldehydes (nine), and volatile phenols (nine). Results showed that inoculation with Lactobacillus strains, especially L. pentosus Lp13, reduced the formation of volatile compounds. On the contrary, inoculation with W. anomalus Y12 increased their concentrations with respect to the spontaneous process, mainly of 1-butanol, 2-phenylethyl acetate, ethanol, and 2-methyl-1-butanol. Furthermore, biplot and biclustering analyses segregated fermentations inoculated with Lp13 and Y12 from the rest of the processes. The use of sequential lactic acid bacteria and yeasts inocula, or their mixture, in Spanish-style green table olive fermentation could be advisable practice for producing differentiated and high-quality products with improved aromatic profile.Gobierno de España-OliFilm-AGL-2013-48300-

Impact of Ohmic Heating on Coconut Water Volatile Compounds

Immature coconut water (CW) is a low acid fruit juice mainly composed of sugars and minerals. Beside its healthy feature, it can also be a pleasant refreshing drink especially when coming from aromatic coconut varieties. Unlike conventional thermal processes, ohmic heating is an innovative technology using volumetric heating technique to pasteurize or sterilize food products. As such, it is known to overcome the overheating problem in fruit juices and to improve aroma preservation. This work aimed at obtaining a commercially safe CW beverage by ohmic heating while looking at the volatile compounds kinetic evolution. Coconut water from an aromatic Thailand Green Dwarf variety was submitted to different ohmic heating time-temperature treatments ranging from 100°C to 140°C and from 0 to 600 seconds. Volatile compounds from the fresh and heated samples were extracted by headspace-solid phase microextraction before being identified by gas chromatography coupled to mass spectrum analysis. Volatile compounds variations were described thanks to principal component analysis and chemical kinetics. Sixty volatile compounds were identified. Even after high temperature ohmic heating treatment, flavor compounds responsible for the typical CW aroma remained in samples headspace. None of the Strecker degradation molecules was detected in the GC analysis of CW after a 5s or 10s treatment at 140°C. The variations of the volatile compounds composition and levels during ohmic treatment confirmed that the higher the temperature is, the less the impact on the chemical reactions thus on flavor quality. At least two volatile molecules were apparently good indicators of the heating treatment level: 3-penten-2-one and ethyloctanoate. During the isothermal stage, the kinetic approach lead to Ea=67.7 kJ.mol-1 for the 3-penten-2-one increase. These results proved that ohmic HT-ST treatments could ensure a commercially safe high quality beverage thanks to a better retention of the original volatile compounds of immature coconut water. (Résumé d'auteur

Volatile Interest Rates, Volatile Crime Rates: A new argument for interest-rate smoothing

Good monetary policy requires estimates of all of its effects: monetary policy impacts traditional economic variables such as output, unemployment rates, and inflation. But does monetary policy influence crime rates? By extending the vector autoregression literature, we derive estimates of the dynamic effect of higher interest rates on crime rates. Higher interest rates have socially and statistically significant positive effects on rates of theft and knife robberies, while effects on rates of burglary and assault are smaller and statistically insignificant. Higher interest rates have no effect on homicide rates. We conclude that monetary policy influences the rate of economically-motivated crimes.http://deepblue.lib.umich.edu/bitstream/2027.42/40080/3/wp694.pd

Characterization of mesostasis regions in lunar basalts: Understanding late-stage melt evolution and its influence on apatite formation

Recent studies geared toward understanding the volatile abundances of the lunar interior have focused on the volatile-bearing accessory mineral apatite. Translating measurements of volatile abundances in lunar apatite into the volatile inventory of the silicate melts from which they crystallized, and ultimately of the mantle source regions of lunar magmas, however, has proved more difficult than initially thought. In this contribution, we report a detailed characterization of mesostasis regions in four Apollo mare basalts (10044, 12064, 15058, and 70035) in order to ascertain the compositions of the melts from which apatite crystallized. The texture, modal mineralogy, and reconstructed bulk composition of these mesostasis regions vary greatly within and between samples. There is no clear relationship between bulk-rock basaltic composition and that of bulk-mesostasis regions, indicating that bulk-rock composition may have little influence on mesostasis compositions. The development of individual melt pockets, combined with the occurrence of silicate liquid immiscibility, exerts greater control on the composition and texture of mesostasis regions. In general, the reconstructed late-stage lunar melts have roughly andesitic to dacitic compositions with low alkali contents, displaying much higher SiO2 abundances than the bulk compositions of their host magmatic rocks. Relevant partition coefficients for apatite-melt volatile partitioning under lunar conditions should, therefore, be derived from experiments conducted using intermediate compositions instead of compositions representing mare basalts