Evaluation of the MapReduce paradigm for parallel suffix array construction

The suffix array of a string, which is the lexicographic ordering of all its suffixes, is one of the most powerful string indexing data structures with a broad range of applications in bioinformatics and other scientific computing domains that rely on string processing and text mining. The problem of constructing the suffix array of a string is akin to integer sorting, and there are three well-known serial linear time solutions for construction. However, the problem becomes difficult to parallelize because of inherent irregularities and data locality/movement requirements that originate during computation. Yet parallelism is needed to be able to scale to large data sizes. In this research project, we evaluate the MapReduce paradigm in the context of constructing suffix arrays in parallel. The MapReduce paradigm is emerging to be the de facto standard for data-intensive scientific applications. Due to the relative nascency of the model, multiple open source implementations are being developed and made available for use by the community. We aim to cross-evaluate a couple of these implementations, viz. the Hadoop and Phoenix MapReduce libraries, for the construction of suffix arrays in parallel. We base our algorithms on the linear-time serial DC3 algorithm given by Karkainnen and Sanders, 2003. More specifically, we present recursive, multi-stage MapReduce parallel algorithms for constructing suffix arrays under the Hadoop and Phoenix frameworks. The Hadoop implementation represents parallelization under a distributed memory, IO-bound setting, whereas the Phoenix implementation represents parallelization under a shared memory, multicore setting. We tested our implementations on different platforms using as input chromosomal sequences extracted from the human genome. While our experimental results suggest that the Phoenix shared memory model is better suited for parallelizing this problem, the studies presented offer insights into the different design level challenges and the different tradeoffs imposed by these two platforms (distributed and shared memory) for parallelizing this problem. We believe that this research project can also serve as a case-study for those trying to parallelize an irregular combinatorial problem using MapReduce or those trying to implement recursive, multi-stage MapReduce methods under shared and/or distributed memory environments

Myelodysplastic syndrome among elderly patients with anemia: A Single institutional experience

BACKGROUND AND OBJECTIVES: Many geriatric patients with different cytopenias are symptomatically treated and miss the diagnosis of myelodysplastic syndrome (MDS). The study was done to estimate the prevalence of elderly presenting with cytopenias in hospital population and to assess karyotyping profile and gene expression in mTOR pathway and correlate with clinical course. PATIENTS AND METHODS: Blood samples of patients (> 60 years) who visited outpatient department and who were in - patients being evaluated for anemias, were included. 15 patients were diagnosed with myelodysplastic syndrome. Karyotype profile and gene expression studies for S6K1 and 4E-BP1 and IPSS –R scoring were done. RESULTS: Among 521 patients, normocytic normochromic anemias was most common (48.3%).15 MDS patients were classified (WHO classification) as - Single lineage dysplasia -6, multilineage dysplasia-5 multilineage dysplasia with excess blasts 1- and three with hypo plastic marrow. There was no significant correlation between the karyotype and subgroups of MDS and age. IPSS scoring showed patients, with very low score – n-1 (ARR-1.3) low score n-6 (ARR- 1.6-2.8) intermediate score n-4 (ARR 3.1-3.7). During follow up for two years one death was reported in the intermediate category. Quantification of mRNA expression of S6K1 and 4EBP1 showed absence or reduction in all cases. CONCLUSIONS: An incidence of 2.8% MDS was observed. The median age reported is consistent with Asian literature. IPSS-R scoring with inclusion of cytogenetic analysis helped in effective risk stratification of patients for management. Though no definite conclusions can be drawn on expression of S6K1 and 4EBP1 of mTOR pathway due to limited sample size, their role in the cytopenia cannot be ruled out

Prevalence and antibacterial resistance patterns of extended-spectrum beta-lactamase producing Gram-negative bacteria isolated from ocular infections

Purpose: Extended-spectrum beta-lactamases (ESBLs) mediated resistance is more prevalent worldwide, especially among Gram-negative bacterial isolates, conferring resistance to the expanded spectrum cephalosporins. As limited data were available on the prevalence of ESBLs in this area, the current study was undertaken to determine the prevalence, antibacterial resistance patterns, and molecular detection and characterization of ESBL encoding resistance genes among ocular Gram-negative bacterial isolates from ocular infections. Materials and Methods: A prospective study was done on 252 ocular Gram-negative bacterial isolates recovered from ocular infections during a study period from February 2011 to January 2014. All isolates were subjected to detection of ESBLs by cephalosporin/clavulanate combination disc test and their antibacterial resistance pattern was studied. Molecular detection and characterization of ESBL encoding blaTEM -, blaSHV , blaOXA -, and blaCTX-M (phylogenetic groups 1, 2, 9, and 8/25) resistance genes by multiplex polymerase chain reaction and DNA sequence analysis. Results: Of all Gram-negative bacteria, Pseudomonas aeruginosa (44%) was the most common strain, followed by Enterobacter agglomerans and Klebsiella pneumoniae each (10%). Among the 252, 42 (17%) were ESBL producers. The major source of ESBL producers were corneal scraping specimens, highest ESBL production was observed in P. aeruginosa 16 (38%) and Escherichia coli 7 (16.6%). Among ESBL-producing genes, the prevalence of blaTEM -gene was the highest (83%) followed by blaOXA -gene (35%), blaSHV -gene (18.5%), and blaCTX-M-1 -gene (18.5%) alone or together. Conclusion: The higher rate of prevalence of ESBLs-encoding genes among ocular Gram-negative bacteria is of great concern, as it causes limitation to therapeutic options. This regional knowledge will help in guiding appropriate antibiotic use which is highly warranted

Attenuation of virulence in an apicomplexan hemoparasite results in reduced genome diversity at the population level

BACKGROUND: Virulence acquisition and loss is a dynamic adaptation of pathogens to thrive in changing milieus. We investigated the mechanisms of virulence loss at the whole genome level using Babesia bovis as a model apicomplexan in which genetically related attenuated parasites can be reliably derived from virulent parental strains in the natural host. We expected virulence loss to be accompanied by consistent changes at the gene level, and that such changes would be shared among attenuated parasites of diverse geographic and genetic background. RESULTS: Surprisingly, while single nucleotide polymorphisms in 14 genes distinguished all attenuated parasites from their virulent parental strains, all non-synonymous changes resulted in no deleterious amino acid modification that could consistently be associated with attenuation (or virulence) in this hemoparasite. Interestingly, however, attenuation significantly reduced the overall population's genome diversity with 81% of base pairs shared among attenuated strains, compared to only 60% of base pairs common among virulent parental parasites. There were significantly fewer genes that were unique to their geographical origins among the attenuated parasites, resulting in a simplified population structure among the attenuated strains. CONCLUSIONS: This simplified structure includes reduced diversity of the variant erythrocyte surface 1 (ves) multigene family repertoire among attenuated parasites when compared to virulent parental strains, possibly suggesting that overall variance in large protein families such as Variant Erythrocyte Surface Antigens has a critical role in expression of the virulence phenotype. In addition, the results suggest that virulence (or attenuation) mechanisms may not be shared among all populations of parasites at the gene level, but instead may reflect expansion or contraction of the population structure in response to shifting milieus