Janus: a framework to boost HPC applications in the cloud based on SDN path provisioning

Data centers, clusters, and grids have historically supported High-Performance Computing (HPC) applications. Due to the high capital and operational expenditures associated with such infrastructures, we have witnessed consistent efforts to run HPC applications in the cloud in the recent past. The potential advantages of this shift include higher scalability and lower costs. If, on the one hand, app instantiation—through customized Virtual Machines (VMs)—is a well-solved issue, on the other, the network still represents a significant bottleneck. When switching HPC applications to be executed on the cloud, we lose control of where VMs will be positioned and of the paths that will be traversed for processes to communicate with one another. To bridge this gap, we present Janus, a framework for dynamic, just-in-time path provisioning in cloud infrastructures. By leveraging emerging software-defined networking principles, the framework allows for an HPC application, once deployed, to have interprocess communication paths configured upon usage based on least-used network links (instead of resorting to shortest, pre-computed paths). Janus is fully configurable to cope with different operating parameters and communication strategies, providing a rich ecosystem for application execution speed up. Through an extensive experimental evaluation, we provide evidence that the proposed framework can lead to significant gains regarding runtime. Moreover, we show what one can expect in terms of system overheads, providing essential insights on how better benefiting from Janus.

     

Selective antibacterial activity of the cationic peptide PaDBS1R6 against Gram-negative bacteria

Infections caused by Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa foremost among them, constitute a major worldwide health problem. Bioinformatics methodologies are being used to rationally design new antimicrobial peptides, a potential alternative for treating these infections. One of the algorithms used to develop antimicrobial peptides is the Joker, which was used to design the peptide PaDBS1R6. This study evaluates the antibacterial activities of PaDBS1R6 in vitro and in vivo, characterizes the peptide interaction to target membranes, and investigates the PaDBS1R6 structure in contact with mimetic vesicles. Moreover, we demonstrate that PaDBS1R6 exhibits selective antimicrobial activity against Gram-negative bacteria. In the presence of negatively charged and zwitterionic lipids the structural arrangement of PaDBS1R6 transits from random coil to α-helix, as characterized by circular dichroism. The tertiary structure of PaDBS1R6 was determined by NMR in zwitterionic dodecylphosphocholine (DPC) micelles. In conclusion, PaDBS1R6 is a candidate for the treatment of nosocomial infections caused by Gram-negative bacteria, as template for producing other antimicrobial agents.     

Improving bioreactor production of a recombinant glycoprotein in Escherichia coli: Effect of specific growth rate on protein glycosylation and specific productivity

In the last decades bacterial glycoengineering emerged as a new field as the result of the ability to transfer the Campylobacter jejuni N- glycosylation machinery into Escherichia coli for the production of recombinant glycoproteins that can be used as antigens for diagnosis, vaccines, and therapeutics. However, the identification of critical parameters implicated in the production process and its optimization to jump to a productive scale is still required. In this study, we developed a dual expression glycosylation vector for the production of the recombinant glycoprotein AcrA-O157, a novel antigen that allows the serodiagnosis of the infection with enterohemorrhagic E. coli O157 in humans. Volumetric productivity was studied in different culture media and found that 2xYP had 6.9-fold higher productivity than the extensively used LB. Subsequently, bioreactor batch and exponential-fed-batch cultures were designed to determine the influence of the specific growth rate (μ) on AcrA-O157 glycosylation efficiency, production kinetics, and specific productivity. At μ_max, AcrA glycosylation with O157-polysaccharide and the specific synthesis rate were maximal, constituting the optimal physiological condition for AcrA-O157 production. Our findings should be considered for the design, optimization, and scaling up of AcrA-O157 production and other recombinant glycoproteins attractive for industrial applications.     

In silico and in vivo analysis of ABI3 and VAL2 genes during somatic embryogenesis of Coffea arabica: competence acquisition and developmental marker genes

Plant Cell, Tissue and Organ Culture (PCTOC) - The employment of biotechnology-based approaches such as somatic embryogenesis has been applied to several plants including Coffea sp. Despite the...     

Length–weight relationships of eight fish species from Guyana coastal drainages,Amapá, Brazil

The present study provides the length–weight relationships (LWR) for eight fish species in 19 streams from the Pedreira River basin, a small tributary of the Guyana coastal drainages from Amapá State, Brazil. Fishes were collected at two occasions, one in November 2016, the other in July 2018, using hand nets, with 0.5 mm of mesh size and 0.25 m² of mouth area, and trawl nets, with 0.5 mm of mesh size and 3 m long. Standard length and total weight were measured to determine the LWRs. The results show that the coefficient b varied between 2.798 and 3.380 and thus the values were within the expected range.     

Genetic Diversity of the Cryptococcus gattii Species Complex in Mato Grosso State,Brazil

Mycopathologia - Cryptococcosis is caused by fungi of the genus Cryptococcus. Owing to its importance, this study aimed to analyze the genetic diversity of C. gattii isolates from animals, humans,...     

Effects of chronic physical activity and of ultrasound treatment on bone consolidation

The objective of this study was to investigate the effects of ultrasound treatment and physical exercise on the velocity of bone consolidation and resistance to deformation. We performed osteotomy in the upper third of the right tibia of rats. Physical training consisted of swimming 1 h per day with a load of 5% b.w. for 30 days. Therapy with medium-intensity ultrasound was applied daily on the damaged area. Wistar rats were divided into the following groups: osteotomized sedentary animals with no ultrasound treatment (1.OSnUS), osteotomized trained animals with no ultrasound treatment (2.OTnUS), osteotomized sedentary animals with ultrasound treatment (3.OSwUS), and osteotomized trained animals with ultrasound treatment (4.OTwUS). The animals were sacrificed for the following analyses: muscle glycogen, serum alkaline phosphatase at the 5th, 10th, 20th, and 30th days, test of maximum resistance to flexion, rupture flexion and mean tibial rigidity at the 30th day. Muscle glycogen was increased at the 20th day; alkaline phosphatase was elevated at the 5th and 20th days in groups 3.OSwUS and 4.OTwUS, and decreased at the 10th day. Groups 1.OSnUS and 2.OTnUS did not show significant variations. In the mechanical resistance tests, we noted that ultrasound therapy and the association of physical activity used in the present study showed significant differences in bone resistance and bone rigidity after 30 days of treatment. These facts suggest that ultrasound or physical activity, or their combination may accelerate the process of bone tissue repair.     

Effect of different growth hormone dosages on the growth velocity in children born small for gestational age

To assess whether short-term growth hormone (GH) treatment can improve the linear growth in children who were born small for gestational age (SGA), we started a randomized multicenter trial in 26 age- and sex-matched prepubertal children born SGA. During the 1st year of GH therapy, all children received GH 0.23 mg/kg/week, then during the 2nd year, 13 children received the same dose (group A), and in the other 13 children, the dose of GH was doubled, i.e., 0.46 mg/kg/week (group B). During the 1st year of therapy, the growth velocity significantly (p<0.0001) increased in all patients. During the 2nd year, group A showed a significant decrease of the growth velocity (p<0.015), whereas group B maintained the growth rate. The height in group A children significantly increased during the 1st and the 2nd year of GH therapy (p<0.000002 and p<0.000001, respectively), reaching the normal range in 8 out of 13 children at the end of 2 years of GH therapy. The height in group B children significantly increased during the 1st and the 2nd year of GH therapy (p<0.000001 and p<0.000001, respectively), reaching the normal range in all 11 children who completed the GH therapy. The height gain was similar in groups A and B treated with the same GH dosage during the 1st year of therapy. A greater increase in height gain was found in children of group B treated with the higher GH dosage during the 2nd year of therapy as compared with group A (p<0.02). Significant increases in insulin-like growth factor I (p<0.0001), acid-labile subunit (p<0.0002), and bone/chronological age ratio (p<0.0001) were found after the 1st year of GH therapy, but no significant changes were observed during the 2nd year, independently of the GH dose. In conclusion, the height velocity of children born SGA significantly increases during the 1st year of GH therapy, diminishes, but can decrease during the 2nd year, if the GH dosage is not raised.     

Beneficial effects of GH/IGF-1 on skeletal muscle atrophy and function in experimental heart failure

Muscle atrophy is a determinant of exercise capacity in heart failure (CHF). Myocyte apoptosis, triggered by tumor necrosis factor- (TNF-) or its second messenger sphingosine (SPH), is one of the causes of atrophy. Growth hormone (GH) improves hemodynamic and cardiac trophism in several experimental models of CHF, but its effect on skeletal muscle in CHF is not yet clear. We tested the hypothesis that GH can prevent skeletal muscle apoptosis in rats with CHF. CHF was induced by injecting monocrotaline. After 2 wk, 2 groups of rats were treated with GH (0.2 mg·kg^–1·day^–1 and 1.0 mg·kg^–1·day^–1) subcutaneously. A third group of controls had saline. After 2 additional weeks, rats were killed. Tibialis anterior cross-sectional area, myosin heavy chain (MHC) composition, and a study on myocyte apoptosis and serum levels of TNF- and SPH were carried out. The number of apoptotic nuclei, muscle atrophy, and serum levels of TNF- and SPH were decreased with GH at high but not at low doses compared with CHF rats. Bcl-2 was increased, whereas activated caspases and bax were decreased. The MHC pattern in GH-treated animals was similar to that of controls. Monocrotaline slowed down both contraction and relaxation but did not affect specific tetanic force, whereas absolute force was decreased. GH treatment restored contraction and relaxation to control values and brought muscle mass and absolute twitch and tetanic tension to normal levels. These findings may provide an insight into the therapeutic strategy of GH given to patients with CHF to improve exercise capacity. apoptosis; cytokines; myosin heavy chains     

Relationships in subtribe Diocleinae (Leguminosae; Papilionoideae) inferred from internal transcribed spacer sequences from nuclear ribosomal DNA

The complete sequences of nuclear ribosomal DNA (nrDNA) internal transcribed spacer regions (ITS/5.8S) were determined for species belonging to six genera from the subtribe Diocleinae as well as for the anomalous genera Calopogonium and Pachyrhizus. Phylogenetic trees constructed by distance matrix, maximum parsimony and maximum likelihood methods showed that Calopogonium and Pachyrhizus were outside the clade Diocleinae (Canavalia, Camptosema, Cratylia, Dioclea, Cymbosema, and Galactia). This finding supports previous morphological, phytochemical, and molecular evidence that Calopogonium and Pachyrhizus do not belong to the subtribe Diocleinae. Within the true Diocleinae clade, the clustering of genera and species were congruent with morphology-based classifications, suggesting that ITS/5.8S sequences can provide enough informative sites to allow resolution below the genus level. This is the first evidence of the phylogeny of subtribe Diocleinae based on nuclear DNA sequences.