The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases

One of the most intriguing groups of enzymes, the feruloyl esterases (FAEs), is ubiquitous in both simple and complex organisms. FAEs have gained importance in biofuel, medicine and food industries due to their capability of acting on a large range of substrates for cleaving ester bonds and synthesizing high-added value molecules through esterification and transesterification reactions. During the past two decades extensive studies have been carried out on the production and partial characterization of FAEs from fungi, while much less is known about FAEs of bacterial or plant origin. Initial classification studies on FAEs were restricted on sequence similarity and substrate specificity on just four model substrates and considered only a handful of FAEs belonging to the fungal kingdom. This study centers on the descriptor-based classification and structural analysis of experimentally verified and putative FAEs; nevertheless, the framework presented here is applicable to every poorly characterized enzyme family. 365 FAE-related sequences of fungal, bacterial and plantae origin were collected and they were clustered using Self Organizing Maps followed by k-means clustering into distinct groups based on amino acid composition and physico-chemical composition descriptors derived from the respective amino acid sequence. A Support Vector Machine model was subsequently constructed for the classification of new FAEs into the pre-assigned clusters. The model successfully recognized 98.2% of the training sequences and all the sequences of the blind test. The underlying functionality of the 12 proposed FAE families was validated against a combination of prediction tools and published experimental data. Another important aspect of the present work involves the development of pharmacophore models for the new FAE families, for which sufficient information on known substrates existed. Knowing the pharmacophoric features of a small molecule that are essential for binding to the members of a certain family opens a window of opportunities for tailored applications of FAEs

Candidate Effectors From Uromyces appendiculatus, the Causal Agent of Rust on Common Bean, Can Be Discriminated Based on Suppression of Immune Responses

Rust fungi are devastating pathogens for several important crop plants. The biotrophic lifestyle of rust fungi requires that they influence their host plants to create a favorable environment for growth and reproduction. Rust fungi secrete a variety of effector proteins that manipulate host target proteins to alter plant metabolism and suppress defense responses. Because of the obligate biotrophic lifestyle of rust fungi, direct evidence for effector function is difficult to obtain, and so suites of experiments utilizing expression in heterologous systems are necessary. Here, we present results from a yeast cell death suppression assay and assays for suppression of PAMP-triggered immunity (PTI) and effector triggered immunity (ETI) based on delivery of effectors through the bacterial type III secretion system. In addition, subcellular localization was tested using transient expression of GFP fusion proteins in Nicotiana benthamiana through Agrobacterium infiltration. We tested 31 representative effector candidates from the devastating common bean rust pathogen Uromyces appendiculatus. These effector candidates were selected based on features of their gene families, most important lineage specificity. We show that several of our effector candidates suppress plant defense. Some of them also belong to families of effector candidates that are present in multiple rust species where their homologs probably also have effector functions. In our analysis of candidate effector mRNA expression, some of those effector candidates that gave positive results in the other assays were not up-regulated during plant infection, indicating that either these proteins have functions at multiple life stages or that strong up-regulation of RNA level in planta may not be as important a criterion for identifying effectors as previously thought. Overall, our pipeline for selecting effector candidates based on sequence features followed by screening assays using heterologous expression systems was successful in discriminating effector candidates. This work lays the foundation for functional characterization of U. appendiculatus effectors, the identification of effector targets, and identification of novel sources for resistance in common bean

DATA DRIVEN INTELLIGENT AGENT NETWORKS FOR ADAPTIVE MONITORING AND CONTROL

To analyze the characteristics and predict the dynamic behaviors of complex systems over time, comprehensive research to enable the development of systems that can intelligently adapt to the evolving conditions and infer new knowledge with algorithms that are not predesigned is crucially needed. This dissertation research studies the integration of the techniques and methodologies resulted from the fields of pattern recognition, intelligent agents, artificial immune systems, and distributed computing platforms, to create technologies that can more accurately describe and control the dynamics of real-world complex systems. The need for such technologies is emerging in manufacturing, transportation, hazard mitigation, weather and climate prediction, homeland security, and emergency response. Motivated by the ability of mobile agents to dynamically incorporate additional computational and control algorithms into executing applications, mobile agent technology is employed in this research for the adaptive sensing and monitoring in a wireless sensor network. Mobile agents are software components that can travel from one computing platform to another in a network and carry programs and data states that are needed for performing the assigned tasks. To support the generation, migration, communication, and management of mobile monitoring agents, an embeddable mobile agent system (Mobile-C) is integrated with sensor nodes. Mobile monitoring agents visit distributed sensor nodes, read real-time sensor data, and perform anomaly detection using the equipped pattern recognition algorithms. The optimal control of agents is achieved by mimicking the adaptive immune response and the application of multi-objective optimization algorithms. The mobile agent approach provides potential to reduce the communication load and energy consumption in monitoring networks. The major research work of this dissertation project includes: (1) studying effective feature extraction methods for time series measurement data; (2) investigating the impact of the feature extraction methods and dissimilarity measures on the performance of pattern recognition; (3) researching the effects of environmental factors on the performance of pattern recognition; (4) integrating an embeddable mobile agent system with wireless sensor nodes; (5) optimizing agent generation and distribution using artificial immune system concept and multi-objective algorithms; (6) applying mobile agent technology and pattern recognition algorithms for adaptive structural health monitoring and driving cycle pattern recognition; (7) developing a web-based monitoring network to enable the visualization and analysis of real-time sensor data remotely. Techniques and algorithms developed in this dissertation project will contribute to research advances in networked distributed systems operating under changing environments

Aspect of Code Cloning Towards Software Bug and Imminent Maintenance: A Perspective on Open-source and Industrial Mobile Applications

As a part of the digital era of microtechnology, mobile application (app) development is evolving with lightning speed to enrich our lives and bring new challenges and risks. In particular, software bugs and failures cost trillions of dollars every year, including fatalities such as a software bug in a self-driving car that resulted in a pedestrian fatality in March 2018 and the recent Boeing-737 Max tragedies that resulted in hundreds of deaths. Software clones (duplicated fragments of code) are also found to be one of the crucial factors for having bugs or failures in software systems. There have been many significant studies on software clones and their relationships to software bugs for desktop-based applications. Unfortunately, while mobile apps have become an integral part of today’s era, there is a marked lack of such studies for mobile apps. In order to explore this important aspect, in this thesis, first, we studied the characteristics of software bugs in the context of mobile apps, which might not be prevalent for desktop-based apps such as energy-related (battery drain while using apps) and compatibility-related (different behaviors of same app in different devices) bugs/issues. Using Support Vector Machine (SVM), we classified about 3K mobile app bug reports of different open-source development sites into four categories: crash, energy, functionality and security bug. We then manually examined a subset of those bugs and found that over 50% of the bug-fixing code-changes occurred in clone code. There have been a number of studies with desktop-based software systems that clearly show the harmful impacts of code clones and their relationships to software bugs. Given that there is a marked lack of such studies for mobile apps, in our second study, we examined 11 open-source and industrial mobile apps written in two different languages (Java and Swift) and noticed that clone code is more bug-prone than non-clone code and that industrial mobile apps have a higher code clone ratio than open-source mobile apps. Furthermore, we correlated our study outcomes with those of existing desktop based studies and surveyed 23 mobile app developers to validate our findings. Along with validating our findings from the survey, we noticed that around 95% of the developers usually copy/paste (code cloning) code fragments from the popular Crowd-sourcing platform, Stack Overflow (SO) to their projects and that over 75% of such developers experience bugs after such activities (the code cloning from SO). Existing studies with desktop-based systems also showed that while SO is one of the most popular online platforms for code reuse (and code cloning), SO code fragments are usually toxic in terms of software maintenance perspective. Thus, in the third study of this thesis, we studied the consequences of code cloning from SO in different open source and industrial mobile apps. We observed that closed-source industrial apps even reused more SO code fragments than open-source mobile apps and that SO code fragments were more change-prone (such as bug) than non-SO code fragments. We also experienced that SO code fragments were related to more bugs in industrial projects than open-source ones. Our studies show how we could efficiently and effectively manage clone related software bugs for mobile apps by utilizing the positive sides of code cloning while overcoming (or at least minimizing) the negative consequences of clone fragments

Design and validation of structural health monitoring system based on bio-inspired algorithms

The need of ensure the proper performance of the structures in service has made of structural health monitoring (SHM) a priority research area. Researchers all around the world have focused efforts on the development of new ways to continuous monitoring the structures and analyze the data collected from the inspection process in order to provide information about the current state and avoid possible catastrophes. To perform an effective analysis of the data, the development of methodologies is crucial in order to assess the structures with a low computational cost and with a high reliability. These desirable features can be found in biological systems, and these can be emulated by means of computational systems. The use of bio-inspired algorithms is a recent approach that has demonstrated its effectiveness in data analysis in different areas. Since these algorithms are based in the emulation of biological systems that have demonstrated its effectiveness for several generations, it is possible to mimic the evolution process and its adaptability characteristics by using computational algorithms. Specially in pattern recognition, several algorithms have shown good performance. Some widely used examples are the neural networks, the fuzzy systems and the genetic algorithms. This thesis is concerned about the development of bio-inspired methodologies for structural damage detection and classification. This document is organized in five chapters. First, an overview of the problem statement, the objectives, general results, a brief theoretical background and the description of the different experimental setups are included in Chapter 1 (Introduction). Chapters 2 to 4 include the journal papers published by the author of this thesis. The discussion of the results, some conclusions and the future work can be found on Chapter 5. Finally, Appendix A includes other contributions such as a book chapter and some conference papers.La necesidad de asegurar el correcto funcionamiento de las estructuras en servicio ha hecho de la monitorización de la integridad estructural un área de gran interés. Investigadores en todas las partes del mundo centran sus esfuerzos en el desarrollo de nuevas formas de monitorización contínua de estructuras que permitan analizar e interpretar los datos recogidos durante el proceso de inspección con el objetivo de proveer información sobre el estado actual de la estructura y evitar posibles catástrofes. Para desarrollar un análisis efectivo de los datos, es necesario el desarrollo de metodologías para inspeccionar la estructura con un bajo coste computacional y alta fiabilidad. Estas características deseadas pueden ser encontradas en los sistemas biológicos y pueden ser emuladas mediante herramientas computacionales. El uso de algoritmos bio-inspirados es una reciente técnica que ha demostrado su efectividad en el análisis de datos en diferentes áreas. Dado que estos algoritmos se basan en la emulación de sistemas biológicos que han demostrado su efectividad a lo largo de muchas generaciones, es posible imitar el proceso de evolución y sus características de adaptabilidad al medio usando algoritmos computacionales. Esto es así, especialmente, en reconocimiento de patrones, donde muchos de estos algoritmos brindan excelentes resultados. Algunos ejemplos ampliamente usados son las redes neuronales, los sistemas fuzzy y los algoritmos genéticos. Esta tesis involucra el desarrollo de unas metodologías bio-inspiradas para la detección y clasificación de daños estructurales. El documento está organizado en cinco capítulos. En primer lugar, se incluye una descripción general del problema, los objetivos del trabajo, los resultados obtenidos, un breve marco conceptual y la descripción de los diferentes escenarios experimentales en el Capítulo 1 (Introducción). Los Capítulos 2 a 4 incluyen los artículos publicados en diferentes revistas indexadas. La revisión de los resultados, conclusiones y el trabajo futuro se encuentra en el Capítulo 5. Finalmente, el Anexo A incluye otras contribuciones tales como un capítulo de libro y algunos trabajos publicados en conferencias

Comparative Analysis of Techniques Used to Detect Copy-Move Tampering for Real-World Electronic Images

Evolution of high computational powerful computers, easy availability of several innovative editing software package and high-definition quality-based image capturing tools follows to effortless result in producing image forgery. Though, threats for security and misinterpretation of digital images and scenes have been observed to be happened since a long period and also a lot of research has been established in developing diverse techniques to authenticate the digital images. On the contrary, the research in this region is not limited to checking the validity of digital photos but also to exploring the specific signs of distortion or forgery. This analysis would not require additional prior information of intrinsic content of corresponding digital image or prior embedding of watermarks. In this paper, recent growth in the area of digital image tampering identification have been discussed along with benchmarking study has been shown with qualitative and quantitative results. With variety of methodologies and concepts, different applications of forgery detection have been discussed with corresponding outcomes especially using machine and deep learning methods in order to develop efficient automated forgery detection system. The future applications and development of advanced soft-computing based techniques in digital image forgery tampering has been discussed