Cost-aware job scheduling for cloud instances using deep reinforcement learning

As the services provided by cloud vendors are providing better performance, achieving auto-scaling, load-balancing, and optimized performance along with low infrastructure maintenance, more and more companies migrate their services to the cloud. Since the cloud workload is dynamic and complex, scheduling the jobs submitted by users in an effective way is proving to be a challenging task. Although a lot of advanced job scheduling approaches have been proposed in the past years, almost all of them are designed to handle batch jobs rather than real-time workloads, such as that user requests are submitted at any time with any amount of numbers. In this work, we have proposed a Deep Reinforcement Learning (DRL) based job scheduler that dispatches the jobs in real time to tackle this problem. Specifically, we focus on scheduling user requests in such a way as to provide the quality of service (QoS) to the end-user along with a significant reduction of the cost spent on the execution of jobs on the virtual instances. We have implemented our method by Deep Q-learning Network (DQN) model, and our experimental results demonstrate that our approach can significantly outperform the commonly used real-time scheduling algorithms.

     

BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology

Background

Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.

Results

We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology.

Conclusions

BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0486-3) contains supplementary material, which is available to authorized users.     

Alteration/deficiency in activation-3 (Ada3) plays a critical role in maintaining genomic stability

Cell cycle regulation and DNA repair following damage are essential for maintaining genome integrity. DNA damage activates checkpoints in order to repair damaged DNA prior to exit to the next phase of cell cycle. Recently, we have shown the role of Ada3, a component of various histone acetyltransferase complexes, in cell cycle regulation, and loss of Ada3 results in mouse embryonic lethality. Here, we used adenovirus-Cre-mediated Ada3 deletion in Ada3^fl/fl mouse embryonic fibroblasts (MEFs) to assess the role of Ada3 in DNA damage response following exposure to ionizing radiation (IR). We report that Ada3 depletion was associated with increased levels of phospho-ATM (pATM), γH2AX, phospho-53BP1 (p53BP1) and phospho-RAD51 (pRAD51) in untreated cells; however, radiation response was intact in Ada3^−/− cells. Notably, Ada3^−/− cells exhibited a significant delay in disappearance of DNA damage foci for several critical proteins involved in the DNA repair process. Significantly, loss of Ada3 led to enhanced chromosomal aberrations, such as chromosome breaks, fragments, deletions and translocations, which further increased upon DNA damage. Notably, the total numbers of aberrations were more clearly observed in S-phase, as compared with G₁ or G₂ phases of cell cycle with IR. Lastly, comparison of DNA damage in Ada3^fl/fl and Ada3^−/− cells confirmed higher residual DNA damage in Ada3^−/− cells, underscoring a critical role of Ada3 in the DNA repair process. Taken together, these findings provide evidence for a novel role for Ada3 in maintenance of the DNA repair process and genomic stability.     

On the topographical differences in the localization of alkaline and acid phosphatases in nerves of teleosts Saccobranchus fossilis and Mystus seenghala

Summary The present study describes the distribution of alkaline and acid phosphatases in the lateral line nerve of Saccobranchus fossilis and optic nerve of Mystus seenghala. The distribution of the phosphatases is quite different in these nerves, i.e., in the lateral line nerve the axons are intensely positive for alkaline and acid phosphatases whereas the myelin sheaths are negative for the enzymes. In the optic nerve, however, the axons are negative and the activity of the alkaline and acid phosphatases appear in the form of bands in the myelin sheaths. The significance of these differences is discussed with special reference to the controversy about the neurokeratin network and the physiological activities of nerves.The glial processes intervening between the myelinated axons of the optic nerve are also stained by the reactions for alkaline and acid phosphatases. The metabolic significance of phosphatases at these sites is discussed.     

Mefloquine induces ROS mediated programmed cell death in malaria parasite: Plasmodium

Recent studies pioneer the existence of a novel programmed cell death pathway in malaria parasite plasmodium and suggest that it could be helpful in developing new targeted anti-malarial therapies. Considering this fact, we evaluated the underlying action mechanism of this pathway in mefloquine (MQ) treated parasite. Since cysteine proteases play a key role in apoptosis hence we performed preliminary computational simulations to determine binding affinity of MQ with metacaspase protein model. Binding pocket identified using computational studies, was docked with MQ to identify it’s potential to bind with the predicted protein model. We further determined apoptotic markers such as mitochondrial dysregulation, activation of cysteine proteases and in situ DNA fragmentation in MQ treated/untreated parasites by cell based assay. Our results showed low mitochondrial membrane potential, enhanced activity of cysteine protease and increased number of fragmented DNA in treated parasites compared to untreated ones. We next tested the involvement of oxidative stress in MQ mediated cell death and found significant increase in reactive oxygen species generation after 24 h of treatment. Therefore we conclude that apart from hemozoin inhibition, MQ is competent to induce apoptosis in plasmodium by activating metacaspase and ROS production.     

Fine needle aspiration cytologic diagnosis of erythema nodosum leprosum: a case report

BACKGROUND: Erythema nodosum leprosum (ENL), the type 2 lepra reaction occurring in lepromatous or borderline lepromatous leprosy, presents clinically with acute manifestations that compel the patient to seek medical attention. Recognition and timely management of these patients is critical in order to avoid permanent disability. Fine needle aspiration cytology (FNAC) is a simple, effective tool that aids in correct diagnosis and management of ENL. CASE: A 30-year-old woman presented with history of fever, reddening of the face, and multiple raised, reddish, painful swellings of the bilateral forearms and legs for 7 days. One year previously, she was diagnosed and treated for lepromatous leprosy with type 2 reaction. After a thorough clinical examination a diagnosis of ENL was made. FNA smears from the forearm swellings showed pus-like material with intact and degenerated polymorphonuclear leukocytes and many foamy macrophages with strong granular acid-fast bacillus (AFB) positivity. A cytologic diagnosis of ENL was given, which was confirmed on histopathologic examination of skin biopsy. CONCLUSION: Cytologic features such as a large number of intact and degenerated neutrophils with foamy macrophages and strong granular AFB positivity, in an appropriate clinical background, allows a confident diagnosis of ENL.     

Mechanistic approach for fabrication of gold nanoparticles by Nitzschia diatom and their antibacterial activity

The problem of chemically synthesized nanoproducts motivated scientific community to explore ecofriendly methods of nanosynthesis. Diatoms belong to a group of aquatic, unicellular, photosynthetic microalgae have been scarcely investigated as a source of reducing and capping agents for nanosynthesis of pesticides and antibiotics. The present study reports a novel ecofriendly method for the fabrication of bioactive gold nanoparticles using locally isolated Nitzschia diatoms. The diatom-fabricated gold nanoparticles show characteristic ruby red colored with sharp absorbance peak at 529 nm. Electron microscopy confirmed irregular shape of gold nanoparticles, with average size of 43 nm and zeta potential of −16.8 mV. The effects of gold nanoparticles on diatom viability were investigated using light and electron microscopy. The mechanistic approach to shed light on how diatoms reacted after exposure to gold metal salt revealed that exposure to gold chloride triggers elevated levels of catalase and peroxidase (12.76 and 14.43 unit/mg protein, respectively) to relieve reactive oxygen species (ROS) stress induced by gold salt exposure. Investigation studies on mechanisms behind Nitzschia-mediated gold nanoparticles fabrication outlined the role of diatom proteins, polysaccharides in reduction, and stabilization of nanoparticles as confirmed by FT-IR analysis. Bioactivity of gold nanoparticles was accessed by coupling them with antibiotics (penicillin and streptomycin), which increased their antibacterial activity compared to individual nanoparticles and antibiotics (Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus). Overall, the present novel phyco-nanotechnological approach is a promising tool to be used as sustainable strategy in green nanotechnology as well as to reduce use of antibiotics in microbial control.