Parafrase restructuring of FORTRAN code for parallel processing

Parafrase transforms a FORTRAN code, subroutine by subroutine, into a parallel code for a vector and/or shared-memory multiprocessor system. Parafrase is not a compiler; it transforms a code and provides information for a vector or concurrent process. Parafrase uses a data dependency to reveal parallelism among instructions. The data dependency test distinguishes between recurrences and statements that can be directly vectorized or parallelized. A number of transformations are required to build a data dependency graph

<span style="font-size:11.0pt;font-family: "Times New Roman";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: Mangal;mso-ansi-language:EN-GB;mso-fareast-language:EN-US;mso-bidi-language: HI" lang="EN-GB">Analyzing time course microarray data of <i style="mso-bidi-font-style: normal">Toxoplasma gondii</i> and study the impact on host transcript levels using Bioconductor</span>

46-51Toxoplasma gondii is an obligate, intracellular, apicomplexan parasite that can infect a wide range of warm-blooded animals including humans. In humans and other intermediate hosts, Toxoplasma develops into chronic infection that cannot be eliminated by host’s immune response or by currently used drugs. The ability of the parasite to convert to the bradyzoite stage and to live inside slow-growing cysts that can go unnoticed by the host immune system allows for the persistence of parasite throughout the life of the infected host. Little is known, however, about how bradyzoites manipulate their host cell. Large scale microarray experiments are becoming increasingly routine, particularly those which track a number of different cell lines through time. This time course information provides valuable insight into dynamics of various biological processes. The proper statistical analysis, however, requires the use of more sophisticated tools and complex statistical models. In the current study, the open-source R programming environment in conjunction with the open-source Bioconductor software was used to analyze microarray data of T. gondii. Several statistical analysis procedures like (log) fold changes in conjunction with ordinary and moderated t-statistics were used to determine differentially expressed genes. The differentially expressed genes were subjected to cluster analysis, followed by the annotation of the up and down regulated genes based on the gene ontology. The findings in the present study suggest the overall effect of the gene expression changes is to modulate the key metabolic pathways leading to compromised host immune response, enhancement in programmed cell death, depression in cell proliferation process and induction of various diseases

Statistical analysis of differential gene expression profile for colon cancer

396-403To analyze differentially expressed genes in colon cancer, we compared expression profiles of colorectal cancer cells from normal colonic cells using data of DNA microarray consisting of 6584 human genes. Each probe set on the array consisted of EST (expressed sequence tag) sequence of 20 feature pairs of 25 bp sequence. The data set comprised of 61 samples, divided into two groups of 40 samples for tumor cells (Group 1) and 21 samples for normal cells (Group 2). In order to do background adjustments for the negative expression values, the data was transformed into log base 2 and estimation of missing values was performed by K-nearest neighbor method, followed by normalization using ‘minimum mean ratio’ among arrays. The basic statistics used for the significance analysis was J5 test, which was computed for each probe and for each contrast with a threshold value of 4.0 and mean as the measure of central tendency. The differentially expressed genes were expressed at high frequency in tumour samples. The Naive Bayes Classifier Algorithm was used to test defined classification of samples of genes. Correlation distance was measured with the help of Pearson’s correlation distance. On the basis of J5 test scores, top 5 upregulated genes, viz., vasopressin-neurophysin 2-copeptin preproprotein, cytochrome, P450 2A7 isoform, major centromere autoantigen B, myelin associated glycoprotein and bone morphogenetic protein 1 isoform 3 precursor, were selected for further analysis. The above said genes have not yet been reported to be differentially overexpressed in colon cancer cells, while their overexpression was reported in other cancers, such as, lung and breast cancer, etc. These genes can be used for prediction and analyses of the gene products, which will help in designing new diagnostic and treatment strategies for the colon cancer

An In-Vitro Evaluation of Microbial Adhesion on Different Types of Orthodontic Brackets

Introduction: Information regarding the adhesion of bacterial species and plaque accumulation to bracket material is limited. Adequate information is needed in order to offer patients orthodontic treatment without significantly increasing their risk of developing white spots, caries, or gingival inflammation. Aim: To determine the levels of the caries-inducing S. mutans species on metallic, self-ligating and ceramic brackets and to compare the total bacterial counts and counts of species present on these bracket materials. Materials and Methods: By means of an in-vitro study, six commercially available bracket systems {3M Gemini (A), American Ortho (B), Ormco (C), Begg (D), Ceramic (E) and Self-ligating (F)} were compared. The brackets were bonded in the cell well culture plate and the agar plates were prepared. Brain heart infusion medium including bacteria and artificial saliva was introduced to each bracket system containing 10 premolar brackets and were incubated. After 72 hours, the adherent bacteria were then detached by sonication and the Colony-Forming Units (CFU) of Streptococcus mutans were calculated on each bracket and were analysed using Statistical Package for the Social Sciences (SPSS) software version 17.0 for Windows. Results: Between the different bracket types, significant differences were found in terms of biofilm formation. The Begg brackets showed the least bacterial adhesion and the selfligating brackets showed the highest bacterial adhesion and was statistically significant among all the groups (p<0.05). Ceramic brackets also showed a higher bacterial adhesion after the self-ligating brackets. Among the three groups of metallic brackets, 3M brackets showed the least bacterial adhesion but was statistically insignificant (p>0.05). Conclusion: Different orthodontic brackets serve as different loci for biofilm formation showing that the Begg brackets are the most hygienic among all the brackets taken in this study

Laparoscopic Repair of Diaphragmatic Hernias: Experience of Six Cases

Laparoscopic diaphragmatic hernia repair is increasingly performed in adults for congenital diaphragmatic hernias and chronic traumatic diaphragmatic hernias. This study reviewed our experience with laparoscopic diaphragmatic hernia repair to evaluate its safety, efficacy and outcomes. Methods: Between January 1999 and December 2002, four male and two female patients presented to us with diaphragmatic hernias, three with traumatic and three with congenital hernias. The mean age of patients was 58.6 years (range, 42-83 years). Five patients presented with main complaints of postprandial retrosternal/chest discomfort and one patient had an acute gastric outlet obstruction. Dissection was performed laparoscopically to reduce the contents of the sac and the hernial defect was repaired using prolene sutures and a polypropylene mesh. Results: Laparoscopic repair of diaphragmatic hernias was completed successfully in all patients. The mean size of the defect was 6.8 cm (range, 3-12 cm) and the mean operative time was 100 minutes (range, 60-150 minutes). There were no major intraoperative complications. One patient required placement of a chest tube due to inadvertent opening of the pleura with the hernial sac and one patient had prolonged postoperative gastric ileus. The mean hospital stay was 2.3 days (range, 1-4 days) and the mean pain score was 4 (range, 2-6). All patients remained asymptomatic over a mean follow-up of 2.9 years. Conclusion: Adult congenital and chronic traumatic diaphragmatic hernias are amenable to laparoscopic repair. Laparoscopic repair is safe and feasible and confers all the advantages of minimal access surgery

Hypothesis Volume 8(3) Metabolic pathway analysis and molecular docking analysis for identification of putative drug targets in Toxoplasma gondii: novel approach

Abstract: Toxoplasma gondii is an obligate intracellular apicomplexan parasite that can infect a wide range of warm-blooded animals including humans. In humans and other intermediate hosts, toxoplasma develops into chronic infection that cannot be eliminated by host&apos;s immune response or by currently used drugs. In most cases, chronic infections are largely asymptomatic unless the host becomes immune compromised. Thus, toxoplasma is a global health problem and the situation has become more precarious due to the advent of HIV infections and poor toleration of drugs used to treat toxoplasma infection, having severe side effects and also resistance have been developed to the current generation of drugs. The emergence of these drug resistant varieties of T. gondii has led to a search for novel drug targets. We have performed a comparative analysis of metabolic pathways of the host Homo sapiens and the pathogen T. gondii. The enzymes in the unique pathways of T. gondii, which do not show similarity to any protein from the host, represent attractive potential drug targets. We have listed out 11 such potential drug targets which are playing some important work in more than one pathway. Out of these, one important target is Glutamate dehydrogenase enzyme; it plays crucial part in oxidation reduction, metabolic process and amino acid metabolic process. As this is also present in the targets of tropical diseases of TDR (Tropical disease related Drug) target database and no PDB and MODBASE 3D structural model is available, homology models for Glutamate dehydrogenase enzyme were generated using MODELLER9v6. The model was further explored for the molecular dynamics simulation study with GROMACS, virtual screening and docking studies with suitable inhibitors against the NCI diversity subset molecules from ZINC database, by using AutoDock-Vina. The best ten docking solutions were selected (ZINC01690699, ZINC17465979, ZINC17465983, ZINC18141294_03, ZINC05462670, ZINC01572309, ZINC18055497_01, ZINC18141294, ZINC05462674 and ZINC13152284_01). Further the Complexes were analyzed through LIGPLOT. On the basis of Complex scoring and binding ability it is deciphered that these NCI diversity set II compounds, specifically ZINC01690699 (as it has minimum energy score and one of the highest number of interactions with the active site residue), could be promising inhibitors for T. gondii using Glutamate dehydrogenase as Drug target