A novel computational framework for fast, distributed computing and knowledge integration for microarray gene expression data analysis

The healthcare burden and suffering due to life-threatening diseases such as cancer would be significantly reduced by the design and refinement of computational interpretation of micro-molecular data collected by bioinformaticians. Rapid technological advancements in the field of microarray analysis, an important component in the design of in-silico molecular medicine methods, have generated enormous amounts of such data, a trend that has been increasing exponentially over the last few years. However, the analysis and handling of these data has become one of the major bottlenecks in the utilization of the technology. The rate of collection of these data has far surpassed our ability to analyze the data for novel, non-trivial, and important knowledge. The high-performance computing platform, and algorithms that utilize its embedded computing capacity, has emerged as a leading technology that can handle such data-intensive knowledge discovery applications. In this dissertation, we present a novel framework to achieve fast, robust, and accurate (biologically-significant) multi-class classification of gene expression data using distributed knowledge discovery and integration computational routines, specifically for cancer genomics applications. The research presents a unique computational paradigm for the rapid, accurate, and efficient selection of relevant marker genes, while providing parametric controls to ensure flexibility of its application. The proposed paradigm consists of the following key computational steps: (a) preprocess, normalize the gene expression data; (b) discretize the data for knowledge mining application; (c) partition the data using two proposed methods: partitioning with overlapped windows and adaptive selection; (d) perform knowledge discovery on the partitioned data-spaces for association rule discovery; (e) integrate association rules from partitioned data and knowledge spaces on distributed processor nodes using a novel knowledge integration algorithm; and (f) post-analysis and functional elucidation of the discovered gene rule sets. The framework is implemented on a shared-memory multiprocessor supercomputing environment, and several experimental results are demonstrated to evaluate the algorithms. We conclude with a functional interpretation of the computational discovery routines for enhanced biological physiological discovery from cancer genomics datasets, while suggesting some directions for future research

Ultrasound Assisted Facile Synthesis of 2-Benzylidenebenzofuran-3(2H)-ones

2-Benzylidenebenzofuran-3(2H)-ones commonly known as aurones, are an important class of oxygen heterocyclic compounds of flavonoid family. They exhibit some biological activities such as antioxidant, antifungal, anticancer, enzyme inhibitory, antiparasitic and antileishmanial activities. They are also responsible for imparting yellow color to the flowers and fruits. Owing to their varied importance, a simple and efficient method for the synthesis of 2-benzylidenebenzofuran-3(2H)-ones involving the reaction of 1-(2'-hydroxy-phenyl)-3-phenyl-propenones with copper acetate in ethanol under ultrasonic irradiation conditions has been described. The present method offers a faster reaction and a higher yield than conventional methods

Comparative evaluation of the chlorhexidine and cinnamon extract as ultrasonic coolant for reduction of bacterial load in dental aerosols

Background: Ultrasonic instruments generate aerosols with significantly greater number of bacteria. Preprocedural mouthrinses or chemotherapeutic coolants are used for the reduction of bacterial load in dental aerosols. The use of chlorhexidine as an ultrasonic coolant has been well established. However, this application has not yet been investigated for cinnamon extract which is known to have antibacterial and anti-inflammatory properties in vivo. Aim: The aim of this study is to compare and evaluate the efficacy of chlorhexidine and cinnamon extract as an ultrasonic coolant in reduction of aerosol contamination and biofilm formation during ultrasonic scaling in comparison with the distilled water (DW). Materials and Methods: Sixty patients diagnosed with moderate-to-severe gingivitis were randomly divided into three groups of twenty patients each undergoing ultrasonic scaling. For Group I, chlorhexidine was used as an ultrasonic coolant; for Group II, cinnamon extract was used; and Group III was served as control where DW was used. The aerosols from ultrasonic units were collected on two blood agar plates at three different positions. Both the plates from each position were incubated aerobically for 48 h. The total number of colony-forming units were counted as mean ± standard deviation and statistically analyzed. In addition, biofilm sampling of dental unit waterlines (DUWLs) was also done to evaluate the effect of these antimicrobials. Apart from microbial examination, clinical parameters such as plaque index and gingival index were also evaluated at baseline and 1-month follow-up. Results: Chlorhexidine and cinnamon both were equally effective (P > 0.05) in reducing the bacterial count in aerosols and biofilm in DUWL as compared to DW when used as ultrasonic cooling agent. Conclusion: Both cinnamon and chlorhexidine used as an ultrasonic device coolant through DUWLs effectively helped in the reduction of bacterial count in dental aerosols

Comparative evaluation of chlorhexidine and cinnamon extract used in dental unit waterlines to reduce bacterial load in aerosols during ultrasonic scaling

Background: Dental unit waterlines (DUWL) are believed to be a source of infection. Ultrasonic instruments generate aerosols with significantly greater numbers of bacteria. Chlorhexidine (CHX) exhibits significant antiseptic effect. Recently, cinnamon (CIN) has been displayed to have antibacterial and anti-inflammatory properties in vivo. Aim: The aim of this study is to compare and evaluate the efficacy of CHX versus CIN extract in the reduction of bacterial count in dental aerosols when used as an irrigant through DUWL during ultrasonic scaling. Materials and Methods: Sixty patients with moderate-to-severe gingivitis were randomly divided into 3 groups of 20 patients each undergoing ultrasonic scaling. For experimental group I, CHX was added in dental unit reservoir before ultrasonic scaling. Similarly, in group II, CIN extract was used and group III served as control where distilled water (DW) was used. The aerosols from ultrasonic units were collected on two blood agar plates at three different positions. One plate from each position was incubated aerobically for 48 h and other plate anaerobically for 72 h. The total number of colony forming units (CFUs) was then calculated and statistically interpreted. Results: CHX and CIN both were equally effective (P > 0.05) in reducing the bacterial count in aerosols as compared to DW (P < 0.05) when used through DUWL. Maximum contamination was seen on the agar plate placed at the chest of the patient. Conclusion: Both CIN and CHX used as an irrigant through DUWL effectively helped in the reduction of bacterial count in dental aerosols

Comparative evaluation of platelet count and antimicrobial efficacy of injectable platelet-rich fibrin with other platelet concentrates: An in vitro study

Background: Platelet concentrates are used in various medical procedures to promote soft- and hard-tissue regeneration. In recent times, their antimicrobial efficacy is also explored. However, various platelet concentrates have evolved which differ in the centrifugation protocols. One such recently introduced platelet concentrate is injectable platelet-rich fibrin (i-PRF) concentrate. Hence, the aim was to evaluate the antimicrobial property, and platelet count of i-PRF in comparison to other platelet concentrates, i.e., PRF, platelet-rich plasma (PRP), and control (whole blood). Materials and Methods: Blood samples were obtained from 10 chronic generalized marginal gingivitis patients. Platelet concentrates were prepared using standardized centrifugation protocol. Platelet count was evaluated by manual counting method using smear preparation of each sample. Subsequently, antimicrobial activity against oral bacteria was examined on blood agar using disc diffusion method to quantify the inhibitory effects. Results: Statistical significance was analyzed by one-way analysis of variance (ANOVA). P 0.05). i-PRF showed statistically significant difference (P < 0.001) in platelet count when compared to control. It was also significant when compared to PRP (P < 0.01), PRF (P < 0.001). Conclusion: i-PRF has maximum antimicrobial efficacy and higher platelet count in comparison to other platelet concentrates, thereby indicating to have a better regenerative potential then others