Towards Automatic Memory Tuning for In-Memory Big Data Analytics in Clusters

Hadoop provides a scalable solution on traditional cluster-based Big Data platforms but imposes performance overheads due to only supporting on-disk data. Data Analytic algorithms usually require multiple iterations over a dataset and thus, multiple, slow, disk accesses. In contrast, modern clusters possess increasing amounts of main memory that can provide performance benefits by efficiently using main memory caching mechanisms. Apache Spark is an innovative distributed computing framework that supports in-memory computations. Even though this type of computations is very fast, memory is a scarce resource and this can cause bottlenecks to execution or, even worse, lead to failures. Spark offers various choices for memory tuning but this requires in-depth systems-level knowledge and the choices will be different across various workloads and cluster settings. Generally, the optimal choice is achieved by adopting a trial and error approach. This work describes a first step towards an automated selection mechanism for memory optimization that assesses workload and cluster characteristics and selects an appropriate caching scheme. The proposed caching mechanism decreases execution times by up to 25% compared to the default strategy and reduces the risk of main memory exceptions

Genetic diversity and risk factors for the transmission of antimicrobial resistance across human, animals and environmental compartments in East Africa: a review.

BACKGROUND The emergence and spread of antimicrobial resistance (AMR) present a challenge to disease control in East Africa. Resistance to beta-lactams, which are by far the most used antibiotics worldwide and include the penicillins, cephalosporins, monobactams and carbapenems, is reducing options for effective control of both Gram-positive and Gram-negative bacteria. The World Health Organization, Food and Agricultural Organization and the World Organization for Animal Health have all advocated surveillance of AMR using an integrated One Health approach. Regional consortia also have strengthened collaboration to address the AMR problem through surveillance, training and research in a holistic and multisectoral approach. This review paper contains collective information on risk factors for transmission, clinical relevance and diversity of resistance genes relating to extended-spectrum beta-lactamase-producing (ESBL) and carbapenemase-producing Enterobacteriaceae, and Methicillin-resistant Staphylococcus aureus (MRSA) across the human, animal and environmental compartments in East Africa. MAIN BODY The review of the AMR literature (years 2001 to 2019) was performed using search engines such as PubMed, Scopus, Science Direct, Google and Web of Science. The search terms included 'antimicrobial resistance and human-animal-environment', 'antimicrobial resistance, risk factors, genetic diversity, and human-animal-environment' combined with respective countries of East Africa. In general, the risk factors identified were associated with the transmission of AMR. The marked genetic diversity due to multiple sequence types among drug-resistant bacteria and their replicon plasmid types sourced from the animal, human and environment were reported. The main ESBL, MRSA and carbapenem related genes/plasmids were the CTX-Ms (45.7%), SCCmec type III (27.3%) and IMP types (23.8%), respectively. CONCLUSION The high diversity of the AMR genes suggests there may be multiple sources of resistance bacteria, or the possible exchange of strains or a flow of genes amongst different strains due to transfer by mobile genetic elements. Therefore, there should be harmonized One Health guidelines for the use of antibiotics, as well as regulations governing their importation and sale. Moreover, the trend of ESBLs, MRSA and carbapenem resistant (CAR) carriage rates is dynamic and are on rise over time period, posing a public health concern in East Africa. Collaborative surveillance of AMR in partnership with regional and external institutions using an integrated One Health approach is required for expert knowledge and technology transfer to facilitate information sharing for informed decision-making

Frequency and antimicrobial resistance patterns of bacteria implicated in community urinary tract infections: a ten-year surveillance study (2000-2009)

BACKGROUND Urinary tract infection (UTI) is one of the most common infectious diseases at the community level. In order to assess the adequacy of the empirical therapy, the prevalence and the resistance pattern of the main bacteria responsible for UTI in the community (in Aveiro, Portugal) was evaluated throughout a ten-year period. METHODS In this retrospective study, all urine samples from patients of the District of Aveiro, in ambulatory regime, collected at the Clinical Analysis Laboratory Avelab during the period 2000-2009 were analysed. Samples with more than 105 CFU/mL bacteria were considered positive and, for these samples, the bacteria were identified and the profile of antibiotic susceptibility was characterized. RESULTS From the 155597 samples analysed, 18797 (12.1%) were positive for bacterial infection. UTI was more frequent in women (78.5%) and its incidence varied with age, affecting more the elderly patients (38.6%). Although E. coli was, as usual, the most common pathogen implicated in UTI, it were observed differences related to the other bacteria more implicated in UTI relatively to previous studies. The bacteria implicated in the UTI varied with the sex of the patient, being P. aeruginosa a more important cause of infection in men than in women. The incidence of the main bacteria changed over the study period (P. aeruginosa, Klebsiella spp and Providencia spp increased and Enterobacter spp decreased). Although E. coli was responsible for more than an half of UTI, its resistance to antibiotics was low when compared with other pathogens implicated in UTI, showing also the lowest percentage of multidrug resistant (MDR) isolates (17%). Bacteria isolated from females were less resistant than those isolated from males and this difference increased with the patient age. CONCLUSIONS The differences in sex and age must be taken into account at the moment of empirical prescription of antimicrobials. From the recommended antimicrobials by the European Association of Urology guidelines, the first line drugs (pivmecillinam and nitrofurantoin) and the alternative antibiotic amoxicillin-clavulanic acid (AMX-CLA) are appropriate to treat community-acquired UTI, but the fluoroquinolones should not be suitable to treat male infections and the trimethoprim-sulfamethoxazole (SXT) shall not be used in the treatment of UTI at this level.Thanks are due to the University of Aveiro, Centre for Environmental and Marine Studies (CESAM) for funding the Microbiology Research Group (Project Pest-C/MAR/LA0017/2011) and to Clinical Analysis Laboratory Avelab (Portugal) for supplying the data.publishe

Comparison of Au(III) and Ga(III) ions' binding to calf thymus DNA: Spectroscopic characterization and thermal analysis

Metals have been studied as potential chemotherapeutic agents for cancer therapies due to their high reactivity toward a wide variety of substances. The characterization of metal ion-binding capacities is essential to understand the possible effects of metals on target biomolecules. In the present study, biochemical effects of Au(III) and Ga(III) ions on calf thymus DNA (ctDNA) were studied comparatively via bioanalytical, spectroscopic, and thermal methods. Briefly, UV-Vis absorbance spectroscopy, fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and Fourier transform infrared (FT-IR) spectroscopy were utilized for spectroscopic characterization, and isothermal titration calorimetry (ITC) measurements were performed for thermal analysis. Our results reveal that both Au(III) and Ga(III) ions are capable of interacting with ctDNA, and Au(III) ions display a more favorable interaction and a higher binding affinity. ITC analyses indicate that the Au(III)-DNA interaction displays a binding affinity (Ka) around 1.43×106 M -1, while a Ka around 1.17×105 M -1 was observed for the Ga(III)-DNA binding. It was suggested that both metal ions are unlikely to change the structural B-conformation while interacting with ctDNA. © 2014 Springer Science+Business Media

Parallel data mining-case study

Abstract. The continuing rapid growth of data and knowledge in scientific domain has spurred huge interest in distributed/parallel data and text mining. This paper reports the investigation of a large scale data mining application to supercomputing environment. The aim is to explore some of the issues that may arise in porting and working with the C++/MPI implementation of the ensemble knn application on supercomputers. In this paper we evaluate behaviour of MFS on several large data sets. The aim of this study is to identify how the performance of the ensemble application depends on the nature of the algorithm used, and on the characteristics of the datasets and the analysis to be performed. This can then be used to select the most appropriate algorithm for a given analysis/dataset, and to indicate the optimum number of processors to be used

A study on the antioxidant activities of some new benzazole derivatives

The in vitro antioxidant properties of some new benzazole derivatives ( 1–10 ) such as benzoxazoles, ben- zimidazoles, and benzothiazoles were determined by their effects on the rat liver microsomal NADPH- dependent lipid peroxidation (LP) level, the scavenging of superoxide anion and the stable radical 2,2- diphenyl-1-picrylhydrazyl (DPPH). Compounds 1 , 2 , 4 and 6 , showed potent scavenging effect on super- oxide radical at 10 –3 M. Compound 8, 5-nitro-2-(phenoxymethyl)benzimidazole, strongly inhibited lipid peroxidation at 10 –3 M concentration