Challenges and Opportunities for RISC-V Architectures towards Genomics-based Workloads

The use of large-scale supercomputing architectures is a hard requirement for scientific computing Big-Data applications. An example is genomics analytics, where millions of data transformations and tests per patient need to be done to find relevant clinical indicators. Therefore, to ensure open and broad access to high-performance technologies, governments, and academia are pushing toward the introduction of novel computing architectures in large-scale scientific environments. This is the case of RISC-V, an open-source and royalty-free instruction-set architecture. To evaluate such technologies, here we present the Variant-Interaction Analytics use case benchmarking suite and datasets. Through this use case, we search for possible genetic interactions using computational and statistical methods, providing a representative case for heavy ETL (Extract, Transform, Load) data processing. Current implementations are implemented in x86-based supercomputers (e.g. MareNostrum-IV at the Barcelona Supercomputing Center (BSC)), and future steps propose RISC-V as part of the next MareNostrum generations. Here we describe the Variant Interaction Use Case, highlighting the characteristics leveraging high-performance computing, indicating the caveats and challenges towards the next RISC-V developments and designs to come from a first comparison between x86 and RISC-V architectures on real Variant Interaction executions over real hardware implementations

On search for new Higgs physics in CDF at the Tevatron

We discuss the Higgs boson mass sum rules in the Minimal Supersymmetric Standard Model in order to estimate the upper limits on the masses of stop quarks as well as the lower bounds on the masses of the scalar Higgs boson state. The bounds on the scale of quark-lepton compositeness derived from the CDF Collaboration (Fermilab Tevatron) data and applied to new extra gauge boson search is taken into account. These extra gauge bosons are considered in the framework of the extended SU(2)_h \times SU(2)_l model. In addition, we discuss the physics of rare decays of the MSSM Higgs bosons in both CP-even and CP-odd sectors and also some extra gauge bosons.Comment: 24 pages, LaTeX, 8 figure

Effect of Ambrotose AO® on resting and exercise-induced antioxidant capacity and oxidative stress in healthy adults

<p>Abstract</p> <p>Background</p> <p>The purpose of this investigation was to determine the effects of a dietary supplement (Ambrotose AO^®) on resting and exercise-induced blood antioxidant capacity and oxidative stress in exercise-trained and untrained men and women.</p> <p>Methods</p> <p>25 individuals (7 trained and 5 untrained men; 7 trained and 6 untrained women) received Ambrotose AO^®(4 capsules per day = 2 grams per day) or a placebo for 3 weeks in a random order, double blind cross-over design (with a 3 week washout period). Blood samples were collected at rest, and at 0 and 30 minutes following a graded exercise treadmill test (GXT) performed to exhaustion, both before and after each 3 week supplementation period. Samples were analyzed for Trolox Equivalent Antioxidant Capacity (TEAC), Oxygen Radical Absorbance Capacity (ORAC), malondialdehyde (MDA), hydrogen peroxide (H₂O₂), and nitrate/nitrite (NOx). Quality of life was assessed using the SF-12 form and exercise time to exhaustion was recorded. Resting blood samples were analyzed for complete blood count (CBC), metabolic panel, and lipid panel before and after each 3 week supplementation period. Dietary intake during the week before each exercise test was recorded.</p> <p>Results</p> <p>No condition effects were noted for SF-12 data, for GXT time to exhaustion, or for any variable within the CBC, metabolic panel, or lipid panel (p > 0.05). Treatment with Ambrotose AO^®resulted in an increase in resting levels of TEAC (p = 0.02) and ORAC (p < 0.0001). No significant change was noted in resting levels of MDA, H₂O₂, or NOx (p > 0.05). Exercise resulted in an acute increase in TEAC, MDA, and H₂O₂(p < 0.05), all which were higher at 0 minutes post exercise compared to pre exercise (p < 0.05). No condition effects were noted for exercise related data (p > 0.05), with the exception of ORAC (p = 0.0005) which was greater at 30 minutes post exercise for Ambrotose AO^®compared to placebo.</p> <p>Conclusion</p> <p>Ambrotose AO^®at a daily dosage of 4 capsules per day increases resting blood antioxidant capacity and may enhance post exercise antioxidant capacity. However, no statistically detected difference is observed in resting or exercise-induced oxidative stress biomarkers, in quality of life, or in GXT time to exhaustion.</p

Bioactive glass-derived trabecular coating: a smart solution for enhancing osteointegration of prosthetic elements

In this work, the use of foam-like glass-ceramic scaffolds as trabecular coatings on ceramic prosthetic devices to enhance implant osteointegration is proposed. The feasibility of this innovative device was explored in a simplified, flat geometry: glass-ceramic scaffolds, prepared by polymeric sponge replication and mimicking the trabecular architecture of cancellous bone, were joined to alumina square substrates by a dense glass coating (interlayer). The role played by different formulations of starting glasses was examined, with particular care to the effect on the mechanical properties and bioactivity of the final coating. Microindentations at the coating/substrate interface and tensile tests were performed to evaluate the bonding strength between the sample's components. In vitro bioactive behaviour was assessed by soaking in simulated body fluid and evaluating the apatite formation on the surface and inside the pores of the trabecular coating. The concepts disclosed in the present study can have a significant impact in the field of implantable devices, suggesting a valuable alternative to traditional, often invasive bone-prosthesis fixatio

The phylogenetically-related pattern recognition receptors EFR and XA21 recruit similar immune signaling components in monocots and dicots

During plant immunity, surface-localized pattern recognition receptors (PRRs) recognize pathogen-associated molecular patterns (PAMPs). The transfer of PRRs between plant species is a promising strategy for engineering broad-spectrum disease resistance. Thus, there is a great interest in understanding the mechanisms of PRR-mediated resistance across different plant species. Two well-characterized plant PRRs are the leucine-rich repeat receptor kinases (LRR-RKs) EFR and XA21 from Arabidopsis thaliana (Arabidopsis) and rice, respectively. Interestingly, despite being evolutionary distant, EFR and XA21 are phylogenetically closely related and are both members of the sub-family XII of LRR-RKs that contains numerous potential PRRs. Here, we compared the ability of these related PRRs to engage immune signaling across the monocots-dicots taxonomic divide. Using chimera between Arabidopsis EFR and rice XA21, we show that the kinase domain of the rice XA21 is functional in triggering elf18-induced signaling and quantitative immunity to the bacteria Pseudomonas syringae pv. tomato (Pto) DC3000 and Agrobacterium tumefaciens in Arabidopsis. Furthermore, the EFR:XA21 chimera associates dynamically in a ligand-dependent manner with known components of the EFR complex. Conversely, EFR associates with Arabidopsis orthologues of rice XA21-interacting proteins, which appear to be involved in EFR-mediated signaling and immunity in Arabidopsis. Our work indicates the overall functional conservation of immune components acting downstream of distinct LRR-RK-type PRRs between monocots and dicots

The influence of semantic and phonological factors on syntactic decisions: An event-related brain potential study

During language production and comprehension, information about a word's syntactic properties is sometimes needed. While the decision about the grammatical gender of a word requires access to syntactic knowledge, it has also been hypothesized that semantic (i.e., biological gender) or phonological information (i.e., sound regularities) may influence this decision. Event-related potentials (ERPs) were measured while native speakers of German processed written words that were or were not semantically and/or phonologically marked for gender. Behavioral and ERP results showed that participants were faster in making a gender decision when words were semantically and/or phonologically gender marked than when this was not the case, although the phonological effects were less clear. In conclusion, our data provide evidence that even though participants performed a grammatical gender decision, this task can be influenced by semantic and phonological factors

Rudimentary G-Quadruplex-Based Telomere Capping In Saccharomyces Cerevisiae

Telomere capping conceals chromosome ends from exonucleases and checkpoints, but the full range of capping mechanisms is not well defined. Telomeres have the potential to form G-quadruplex (G4) DNA, although evidence for telomere G4 DNA function in vivo is limited. In budding yeast, capping requires the Cdc13 protein and is lost at nonpermissive temperatures in cdc13-1 mutants. Here, we use several independent G4 DNA-stabilizing treatments to suppress cdc13-1 capping defects. These include overexpression of three different G4 DNA binding proteins, loss of the G4 DNA unwinding helicase Sgs1, or treatment with small molecule G4 DNA ligands. In vitro, we show that protein-bound G4 DNA at a 3\u27 overhang inhibits 5\u27-\u3e 3\u27 resection of a paired strand by exonuclease I. These findings demonstrate that, at least in the absence of full natural capping, G4 DNA can play a positive role at telomeres in vivo

Probing superfast quarks in nuclei through dijet production at the LHC

We investigate dijet production from proton-nucleus collisions at the Large Hadron Collider (LHC) as a means for observing superfast quarks in nuclei with Bjorken $x>1$. Kinematically, superfast quarks can be identified through directly measurable jet kinematics. Dynamically, their description requires understanding several elusive properties of nuclear QCD, such as nuclear forces at very short distances, as well as medium modification of parton distributions in nuclei. In the present work, we develop a model for nuclear parton distributions at large $x$ in which the nuclear dynamics at short distance scales are described by two- and three-nucleon short range correlations (SRCs). Nuclear modifications are accounted for using the color screening model, and an improved description of the EMC effect is reached by using a structure function parametrization that includes higher-twist contributions. We apply QCD evolution at the leading order to obtain nuclear parton distributions in the kinematic regime of the LHC, and based on the obtained distributions calculate the cross section for dijet production. We find not only that superfast quarks can be observed at the LHC, but also that they provide sensitivity to the practically unexplored three-nucleon SRCs in nuclei. Additionally, the LHC can extend our knowledge of the EMC effect to large $Q^2$ where higher-twist effects are negligible.Comment: 44 pages, 17 figures, final version to be published in EJP

Analysis of norfloxacin ecotoxicity and the relation with its degradation by means of electrochemical oxidation using different anodes

[EN] In this work, ecotoxicological bioassays based on Lactuca sativa seeds and bioluminescent bacterium (Vibrio fischeri) have been carried out in order to quantify the toxicity of Norfloxacin (NOR) and sodium sulfate solutions, before and after treating them using electrochemical advanced oxidation. The effect of some process variables (anode material, reactor configuration and applied current) on the toxicity evolution of the treated solution has been studied. A NOR solution shows an EC50 (5 days) of 336 mg L-1 towards Lactuca sativa. This threshold NOR concentration decreases with sodium sulfate concentration, in solutions that contain simultaneously Norfloxacin and sodium sulfate. In every case considered in this work, the electrochemical advanced oxidation process increased the toxicity (towards both Lactuca sativa and Vibrio fischeri) of the solution. This toxicity increase is mainly due to the persulfate formation during the electrochemical treatment. From a final solution toxicity point of view, the best results were obtained using a BDD anode in a divided reactor applying the lowest current intensity.The authors are very grateful to the Ministerio de Economia y Competitividad (Projects CTQ2015-65202-C2-1-R and RTI2018-101341-B-C21) for their economic support.Montañés, M.; García Gabaldón, M.; Roca-Pérez, L.; Giner-Sanz, JJ.; Mora-Gómez, J.; Pérez-Herranz, V. (2020). Analysis of norfloxacin ecotoxicity and the relation with its degradation by means of electrochemical oxidation using different anodes. Ecotoxicology and Environmental Safety. 188:1-10. https://doi.org/10.1016/j.ecoenv.2019.109923S110188Banks, M. K., & Schultz, K. E. (2005). Comparison of Plants for Germination Toxicity Tests in Petroleum-Contaminated Soils. Water, Air, and Soil Pollution, 167(1-4), 211-219. doi:10.1007/s11270-005-8553-4Barreto, J. P. d. P., Araujo, K. C. d. F., de Araujo, D. M., & Martinez-Huitle, C. A. (2015). 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Internet-based medical education: a realist review of what works, for whom and in what circumstances

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