Slicing of Aspect-Oriented Software and Its Application to Software Refactoring

This thesis first presents some program slicing techniques for Aspect-Oriented Programs (AOPs) and then presents a technique for refactoring of software using the proposed slicing technique. Main aim of all the proposed slicing algorithms in this thesis is to compute accurate and precise dynamic slices of AOPs. In order to compute the slices of aspect-oriented programs, first we extend the System Dependence Graph (SDG) for Object-Oriented Programs (OOPs) to handle AOPs. We have named the extended SDG Extended Aspect-Oriented System Dependence Graph (EAOSDG). The EAOSDG successfully represents different aspect- oriented features such as class representation, method invocation, inheritance, aspect declaration, point-cuts, advices etc. The EAOSDG of an aspect-oriented program consists of System Dependence Graph (SDG) for the non-aspect code, a group of Aspect-Oriented Dependence Graphs (ADGs) for aspect code and some additional dependence edges that are used to connect the SDG of the non-aspect code (base code) to ADG of the aspect code. Then, we propose an extended two-phase algorithm to compute the static slices of AOPs, using the proposed EAOSDG. Subsequently, we present a context-sensitive slicing algorithm to compute the dynamic slices of AOPs, using the proposed EAOSDG. The context-sensitivity makes the computed slice more precise and accurate. We have developed a slicer to implement our proposed algorithms. We have compared the performance of extended two-phase algorithm and context-sensitive algorithm, in terms of the average slice extraction time. We have considered five open source projects for comparison of slicing algorithms. We have observed that the context-sensitive algorithm computes the slices faster than the extended-two phase algorithm. Next, we extends our intermediate representation (EAOSDG) to be able to represent concurrent aspect-oriented programs. We have named this intermediate representation Multithreaded Aspect-Oriented Dependence Graph (MAODG). Our MAODG correcly represents the concurrency dependencies in concurrent AOPs. Then, we extend our context-sensitive dynamic slicing technique to handle concurrent AOPs having multiple threads. We have named our algorithm Context-Sensitive Concurrent Aspect (CSCA) slicing algorithm. Due to the presence of inter-thread synchronization and communication dependencies, some control and data flows in the threads become interdependent. This interdependency causes difficulty in finding accurate slices of concurrent AOPs. Our algorithm takes the MAODG of the concurrent AOP and a slicing criterion as input and vii computes the dynamic slice for the given concurrent AOP. We have developed a slicer Concurrent AspectJ slicer to implement our proposed CSCA algorithm. We have compared CSCA algorithm with two other existing algorithms using five case studies. The experiment shows that, our proposed CSCA algorithm computes precise slices in less time as compared to the other two existing algorithms. Further, we propose an approach for dynamic slicing of distributed AOPs. We first represent distributed aspect-oriented program using dependence based intermediate representation which we have named Distributed Aspect Dependence Graph (DADG). Based on the DADG, we present a slicing algorithm Parallel Context-sensitive Dynamic Slicing (PCDS) algorithm for distributed AOPs. We introduce parallelism in our algorithm to make slice computation faster. We have developed a tool called D-AspectJ slicer to implement the PCDS algorithm. The proposed slicing algorithm is compared with two other existing algorithms using seven case studies. The experimentation shows that our proposed PCDS algorithm generates smaller slices in less time as compared to the other two existing algorithms. Finally, we present a technique for software refactoring using program slicing. We use slice-based cohesion metrics to identify the target methods of a software that require refactoring. After identifying the target methods, we use program slicing to divide the target method into two parts. Then, we use the concept of aspects to alter the code structure in a manner that does not change the external behavior of the original module. We have implemented our proposed refactoring technique and evaluated its effectiveness through eleven case studies. We have also evaluated the effect of our proposed refactoring technique based on an open source code coverage tool EclEmm

Automatic semantic segmentation and classification of remote sensing data for agriculture

Automatic semantic segmentation has expected increasing interest for researchers in recent years on multispectral remote sensing (RS) system. The agriculture supports 58 % of the population, in which 51 % of geographical area is under cultivation. Furthermore, the RS in agriculture can be used for identification, area estimation and monitoring, crop detection, soil mapping, crop yield modelling and production modelling etc. The RS images are high resolution images which can be used for agricultural and land cover classifications. Due to its high dimensional feature space, the conventional feature extraction techniques represent a progress of issues when handling huge size information e.g., computational cost, processing capacity and storage load. In order to overcome the existing drawback, we propose an automatic semantic segmentation without losing the significant data. In this paper, we use SOMs for segmentation purpose. Moreover, we proposed the particle swarm optimization technique (PSO) algorithm for finding cluster boundaries directly from the SOMs. On the other hand, we propose the deep residual network to achieve faster training process. Deep Residual Networks have been proved to be a very successful model on RS image classification. The main aim of this work is to achieve the overall accuracy greater than 85 % (OA > 85 %). So, we use a convolutional neural network (CNN), which outperforms better classification of certain crop types and yielding the target accuracies more than 85 % for all major crops. Furthermore, the proposed methods achieve good segmentation and classification accuracy than existing methods. The simulation results are further presented to show the performance of the proposed method applied to synthetic and real-world datasets

Serum gamma-glutamyl transferase level in acute stroke

Background: Stroke is the second leading cause of death worldwide, causing 6.2 million deaths in 2011. Serum Gamma-Glutamyl Transferase (GGT) has been conventionally considered as a marker of excessive alcohol intake and/or liver dysfunction. There are accumulating evidences suggesting association of raised serum GGT level in stroke. So, this study was conducted to determine the association between the serum GGT level and stroke in population without history of alcohol consumption.Methods: This cross-sectional comparative study was carried out at Department of General medicine, Veer Surendra Sai Institute of Medical Sciences and Research (VIMSAR), Burla from November 2016 to October 2018. 100 cases and 100 controls were included in this study. Cases were the patients admitted to Department of General Medicine, VIMSAR, Burla, presenting within 24 hours of first episode of stroke. Controls were the age (+/-5 years) and sex matched healthy attendants of the patients. Alcoholics or patients suffering from hepatitis, cirrhosis of liver, cholestasis or patients taking drugs like Phenytoin, Valproic acid, Carbamazepine etc or patients with past episode of stroke were excluded from this study. Serum GGT level of both cases and controls were measured and compared.Results: In stroke patients, the mean serum GGT level was 54.95 IU/L with standard deviation of 20.54. In controls, the mean serum GGT level was 32.14 IU/L with standard deviation of 5.07. The p-value was less than 0.0001 i.e. highly significant.Conclusions: Serum GGT level is significantly increased in stroke patients than healthy persons without stroke

Crystalline silicon surface passivation by thermal ALD deposited Al doped ZnO thin films

The evidence of good quality silicon surface passivation using thermal ALD deposited Al doped zinc oxide (AZO) thin films is demonstrated. AZO films are prepared by introducing aluminium precursor in between zinc and oxygen precursors during the deposition. The formation of AZO is confirmed by ellip-sometry, XRD and Hall measurements. Effective minority carrier lifetime (tau(eff)) greater than 1.5ms at intermediate bulk injection levels is realized for symmetrically passivated p-type silicon surfaces under optimised annealing conditions of temperature and time in hydrogen ambient. The best results are realised at 450 degrees C annealing for > 15min. Such a layer may lead to implied open circuit voltage gain of 80mV

Influence of deposition temperature of thermal ALD deposited Al2O3 films on silicon surface passivation

The effect of deposition temperature (T-dep) and subsequent annealing time (t(anl)) of atomic layer deposited aluminum oxide (Al2O3) films on silicon surface passivation (in terms of surface recombination velocity, SRV) is investigated. The pristine samples (as-deposited) show presence of positive fixed charges, Q(F). The interface defect density (D-it) decreases with increase in T-dep which further decreases with tanl up to 100s. An effective surface passivation (SRV= 200 degrees C. The present investigation suggests that low thermal budget processing provides the same quality of passivation as realized by high thermal budget process (tanl between 10 to 30 min)

Multi-OMICs analysis reveals metabolic and epigenetic changes associated with macrophage polarization

Macrophages (MФ) are an essential immune cell for defense and repair that travel to different tissues and adapt based on local stimuli. A critical factor that may govern their polarization is the cross-talk between metabolism and epigenetics. However, simultaneous measurements of metabolites, epigenetics, and proteins (phenotype) has been a major technical challenge. To address this, we have developed a novel triomics approach using mass spectrometry to comprehensively analyze metabolites, proteins, and histone modifications, in a single sample. To demonstrate this technique, we investigated the metabolic-epigenetic-phenotype axis following polarization of human blood-derived monocytes into either \u27pro-inflammatory M1\u27- or \u27anti-inflammatory M2-\u27 MФs. We report here a complex relationship between arginine, tryptophan, glucose, and the citric acid cycle (TCA) metabolism, protein and histone post-translational modifications, and human macrophage polarization that was previously not described. Surprisingly, M1-MФs had globally reduced histone acetylation levels but high levels of acetylated amino acids. This suggests acetyl-CoA was diverted, in part, towards acetylated amino acids. Consistent with this, stable isotope tracing of glucose revealed reduced usage of acetyl-CoA for histone acetylation in M1-MФs. Furthermore, isotope tracing also revealed MФs uncoupled glycolysis from the TCA cycle, as evidenced by poor isotope enrichment of succinate. M2-MФs had high levels of kynurenine and serotonin which are reported to have immune-suppressive effects. Kynurenine is upstream of de novo NAD+ metabolism which is a necessary cofactor for Sirtuin-type histone deacetylases. Taken together, we demonstrate a complex interplay between metabolism and epigenetics that may ultimately influence cell phenotype

Human Macrophages Exhibit GM-CSF Dependent Restriction of Mycobacterium tuberculosis Infection via Regulating Their Self-Survival, Differentiation and Metabolism

GM-CSF is an important cytokine that regulates the proliferation of monocytes/macrophages and its various functions during health and disease. Although growing evidences support the notion that GM-CSF could play a major role in immunity against tuberculosis (TB) infection, the mechanism of GM-CSF mediated protective effect against TB remains largely unknown. Here in this study we examined the secreted levels of GM-CSF by human macrophages from different donors along with the GM-CSF dependent cellular processes that are critical for control of M. tuberculosis infection. While macrophage of different donors varied in their ability to produce GM-CSF, a significant correlation was observed between secreted levels of GM-CSF, survial of macrophages and intra-macrophage control of Mycobacterium tuberculosis bacilli. GM-CSF levels secreted by macrophages negatively correlated with the intra-macrophage M. tuberculosis burden, survival of infected host macrophages positively correlated with their GM-CSF levels. GM-CSF-dependent prolonged survival of human macrophages also correlated with significantly decreased bacterial burden and increased expression of self-renewal/cell-survival associated genes such as BCL-2 and HSP27. Antibody-mediated depletion of GM-CSF in macrophages resulted in induction of significantly elevated levels of apoptotic/necrotic cell death and a simultaneous decrease in autophagic flux. Additionally, protective macrophages against M. tuberculosis that produced more GM-CSF, induced a stronger granulomatous response and produced significantly increased levels of IL-1β, IL-12 and IL-10 and decreased levels of TNF-α and IL-6. In parallel, macrophages isolated from the peripheral blood of active TB patients exhibited reduced capacity to control the intracellular growth of M. tuberculosis and produced significantly lower levels of GM-CSF. Remarkably, as compared to healthy controls, macrophages of active TB patients exhibited significantly altered metabolic state correlating with their GM-CSF secretion levels. Altogether, these results suggest that relative levels of GM-CSF produced by human macrophages plays a critical role in preventing cell death and maintaining a protective differentiation and metabolic state of the host cell against M. tuberculosis infection

Human monocyte-derived macrophage responses to M. tuberculosis differ by the host’s tuberculosis, diabetes or obesity status, and are enhanced by rapamycin

Human macrophages play a major role in controlling tuberculosis (TB), but their anti-mycobacterial mechanisms remain unclear among individuals with metabolic alterations like obesity (TB protective) or diabetes (TB risk). To help discern this, we aimed to: i) Evaluate the impact of the host’s TB status or their comorbidities on the anti-mycobacterial responses of their monocyte-derived macrophages (MDMs), and ii) determine if the autophagy inducer rapamycin, can enhance these responses. We used MDMs from newly diagnosed TB patients, their close contacts and unexposed controls. The MDMs from TB patients had a reduced capacity to activate T cells (surrogate for antigen presentation) or kill M. tuberculosis (Mtb) when compared to non-TB controls. The MDMs from obese participants had a higher antigen presenting capacity, whereas those from chronic diabetes patients displayed lower Mtb killing. The activation of MDMs with rapamycin led to an enhanced anti-mycobacterial activity irrespective of TB status but was not as effective in patients with diabetes. Further studies are warranted using MDMs from TB patients with or without metabolic comorbidities to: i) elucidate the mechanisms through which host factors affect Mtb responses, and ii) evaluate host directed therapy using autophagy-inducing drugs like rapamycin to enhance macrophage function

Antibody-Mediated LILRB2-Receptor Antagonism Induces Human Myeloid-Derived Suppressor Cells to Kill Mycobacterium tuberculosis

Tuberculosis is a leading cause of death in mankind due to infectious agents, and Mycobacterium tuberculosis (Mtb) infects and survives in macrophages (MФs). Although MФs are a major niche, myeloid-derived suppressor cells (MDSCs) are an alternative site for pathogen persistence. Both MФs and MDSCs express varying levels of leukocyte immunoglobulin-like receptor B (LILRB), which regulate the myeloid cell suppressive function. Herein, we demonstrate that antagonism of LILRB2 by a monoclonal antibody (mab) induced a switch of human MDSCs towards an M1-macrophage phenotype, increasing the killing of intracellular Mtb. Mab-mediated antagonism of LILRB2 alone and its combination with a pharmacological blockade of SHP1/2 phosphatase increased proinflammatory cytokine responses and phosphorylation of ERK1/2, p38 MAPK, and NF-kB in Mtb-infected MDSCs. LILRB2 antagonism also upregulated anti-mycobacterial iNOS gene expression and an increase in both nitric oxide and reactive oxygen species synthesis. Because genes associated with the anti-mycobacterial function of M1-MФs were enhanced in MDSCs following mab treatment, we propose that LILRB2 antagonism reprograms MDSCs from an immunosuppressive state towards a pro-inflammatory phenotype that kills Mtb. LILRB2 is therefore a novel therapeutic target for eradicating Mtb in MDSCs

Comparative antioxidant and hepatoprotective potential quercetin and corycavidine from Hedyotis corymbosa (L.) Lam. and Solanum xanthocarpum Schrad & Wendl.

776-784Liver disease is the major health issues in current era. Antioxidants play the essential role in hepatoprotection by protecting the hepatic cells against free radicals. Flavonoids and alkaloids are the essential plants bioactive that play the major role in the antioxidant system. In our project we used diamond flower Hedyotis corymbosa (L.) Lam. and Yellow berried Nightshade Solanum xanthocarpum Schrad & Wendl., and both plants have major phytoconstituent which acts as antioxidants. Thus, the aim of the current study validates the isolation, characterization, and determination of in vivo antioxidant and hepatoprotective consequences of corycavidine and quercetin that were isolated from Diamond flower Hedyotis corymbosa (L.) Lam. and Yellow berried Nightshade Solanum xanthocarpum Schrad & Wendl.. The study intent to isolate and identify the antioxidant and hepatoprotective agent from two different plants and compare their hepatoprotective potential to obtain the most effective liver protective phytoconstituent. Quercetin was isolated from S. xanthocarpum by column chromatography employing n-butanol: acetic acid: H2O (2:2:6) as a solvent system, however, corycavidine was isolated from H. corymbosa by column chromatography employing chloroform: methanol: diethylamine (4:1:2.2) as mobile phase. Structural illustrations were confirmed by UV, FT-IR, 1H-NMR, and 13C-NMR, and mass spectroscopy. Both the phytoconstituents, corycavidine and quercetin, were explored for their antioxidant potential by investigating CAT, SOD GSH, and LPO in liver homogenates of experimental rats. Additionally, the in vivo hepatoprotective effect was examined against simvastatin (20 mg/kg, p.o.), which induced hepatotoxicity in experimental rodents. The liver protective activity was computed by determining distinct biochemical parameters like SGOT, SGPT, ALP, bilirubin, total protein, cholesterol and urea along with hematological parameters and histopathological studies. The results of spectroscopic methods confirmed that the isolated phytochemical constituent from the H. corymbosa is corycavidine, a benzylisoquinoline alkaloid, however from S. xanthocarpum is quercetin a flavonoid. Both phytoconstituents significantly (P <0.05 P <0.001) and dose-dependently reversed simvastatin induced elevated levels of SGOT, SGPT, cholesterol, urea, total bilirubin and restored the total protein and albumin level in experimental rats. Furthermore, it also signifies the blood parameters at a dose of 50 and 100 mg/kg and restored the body protection system. The histological examination exhibited that corycavidine and quercetin at a dose of 100 mg/kg showed regeneration of hepatocytes around the central vein with nearly normal liver architecture. The results expressed the hepatoprotective outcome of quercetin is preeminent than corycavidine and therefore, scientifically validates its traditional application