2,073 Works

Dissecting JACKDAW transcriptional regulatory module and protein– protein interaction domains

Louai Alidrissi
Many biological processes are regulated via the action of interacting transcription factors. Together, these proteins form a complex regulatory network that will lead to different outcomes according to the DNA context of their target. The transcriptional regulator JACKDAW (JKD) together with the transcription factors SHR (SHORT-ROOT) and (SCARECROW) form a regulatory module that control a variety cell type specific targets to maintain the stem cell niche and regulate asymmetric cell division in the Arabidopsis root...

Understanding the molecular functions of the spliceosomal protein SF3B14a/p14 via CRISPR/Cas9 system

Radwa Kamel
At the post-transcriptional level, the splicing of the pre-mRNA plays a vital role in cell fate determination and respond to biotic and abiotic stresses. Through alternative splicing, mRNAs variants can be produced from a single gene. SF3B is a heptameric protein complex that is essential for pre-mRNA splicing. It contains seven subunits: SF3b155, SF3b130, SF3b145, SF3b49, SF3b14b, P14/SF3b14a and SF3b10 and they play an important role in BS (branch point sequence) recognition. P14/SF3b14a interacts with...

AC ELECTROHYDRODYNAMICS PHENOMENON IN 2D AND 3D MICROELECTRODES

Raphaela Silva
Alternating current electrohydrodynamics (ac-EHD) has been reported as a promising technique for enhancing sensor performance by the intimate mixing of the analyte solution at the electrode surface. The lateral fluid motion created by the ac-EHD phenomenon can be tuned by changing the frequency, voltage, and electrode geometry. To date, various studies have been conducted on the use of 2D electrodes based ac- EHD devices for sensor applications. However, the use of 3D electrodes may provide...

New Algorithms to Solve the Positioning Problem of Outdoor Localization Using Constrained and Unconstrained Optimization Techniques

Muhanned Alsaif
The demand for outdoor precise location is increasing with the development of new applications such as autonomous vehicles, exploration robots and wireless sensor networks. Global Navigation Satellite System (GNSS) is the go-to system for outdoor localization. This thesis focuses on developing new methods for GNSS single-point positioning (SPP) model, where no access to a reference station or precise GNSS parameters is needed. We investigated the limitations of the standard method, least- squares adjustment (LSA), and...

A Multi-platform Comparison of Phenology for Semi-automated Classification of Crops

Sarah Kanee
Remote sensing has enabled unprecedented earth observation from space and has proven to be an invaluable tool for agricultural applications and crop management practices. Here we detect seasonal metrics indicating the start of the season (SOS), the end of the season (EOS) and maximum greenness (MAX) based on vegetation spectral signatures and the normalized difference vegetation index (NDVI) for a time series of Landsat-8, Sentinel-2 and PlanetScope imagery of potato, wheat, watermelon, olive and peach/apricot...

Polycyclic Aromatic Hydrocarbons and Soot Particle Formation in the Combustion Process

Can Shao
The threat to the environment and human health posed by the emission of soot particles and their precursors during the combustion process has attracted widespread attention for some time. Generation of soot particles includes the precursor’s formation, particle nucleation, and the growth and oxidation of soot particles; these processes are experimentally and numerically studied in this dissertation. Fuel composition is one of the most important parameters in the study of the combustion emissions. In the...

Multiscale factors that control hydrocarbon storage capacity, and successful hydrofracturing and refracturing in mudrocks

Syed Haider
Hydrocarbon production from mudrocks (“shales”) is vital to global economic growth and smooth transition to a clean energy infrastructure. The commercial development prospect of a shale play depends on its evolution history over millions of years. Economic hydrocarbon production from shale starts after hydraulic fracturing, that creates a multiscale fracture network leading to an increased overall permeability. The properties of the stimulated rock can be assessed via parameters at different scales (nano-, micro- and macro-scale)....

A Bayesian Approach to D2D Proximity Estimation using Radio CSI Measurements

Lucas Bezerra
Channel State Information (CSI) refers to a set of measurements used to characterize a radio communication link. Radio infrastructure collects CSI and derives useful metrics that indicate changes to modulation and coding to be made to improve the link performance (e.g. throughput, reliability). The CSI, however, has a wider potential use. It contains an environment-specific signature that can be used to extract information about users’ position and activity. In our work, we explore the problem...

Imaging and Characterization of the Multi-scale Pore System of Microporous Carbonates

Ahmed Hassan
Microporous carbonates host a significant portion of the remaining oil-in-place in the giant carbonate reservoirs of the Middle East. Improved understanding of petrophysical and multi-phase flow properties at the pore-scale is essential for the development of better oil recovery processes. These properties strongly depend on the 3D geometry and connectivity of the pore space. In this study, we harnessed the unique capabilities of fluorescence confocal laser scanning microscopy (CLSM) to capture both macroporosity and microporosity,...

Characterizing Power Consumption of a Fully Flexible System-on-Chip for Internet of Everything Applications

Abdullah Alquwayzani
Achieving an internet of everything requires flexible electronics capable of con- forming to non-flat dynamic surfaces. Flexible electronics made for the internet of everything must be capable of storing, processing, and communicating large volumes of data. While, early efforts in flexible electronics focused primarily on organic ma- terials due to their inherent flexibility, recent innovations have made it possible to transform mature bulky complementary metal-oxide semiconductor based integrated circuits into flexible electronics. Powered by state...

Cellular and Polymeric Membranes for Separation and Delivery Applications

Mram Z. Alyami
The primary focus of this research is to utilize cellular and polymeric membranes for biomedical applications: To date, several organic and inorganic materials have been used to synthesize nanoparticles (NPs). The question arises as to which criteria and design principles should be considered while selecting the best material. Based on the results of testing, three key roles of NPs have been identified. First, NPs need enough circulation time to reach their target. Then these NPs...

Unified Tractable Model for Large-Scale Networks Using Stochastic Geometry: Analysis and Design

Laila H. Afify
The ever-growing demands for wireless technologies necessitate the evolution of next generation wireless networks that fulfill the diverse wireless users requirements. However, upscaling existing wireless networks implies upscaling an intrinsic component in the wireless domain; the aggregate network interference. Being the main performance limiting factor, it becomes crucial to develop a rigorous analytical framework to accurately characterize the out-of-cell interference, to reap the benefits of emerging networks. Due to the different network setups and key...

Optimization of Algorithms Using Extensions of Dynamic Programming

Hassan M. AbouEisha
We study and answer questions related to the complexity of various important problems such as: multi-frontal solvers of hp-adaptive finite element method, sorting and majority. We advocate the use of dynamic programming as a viable tool to study optimal algorithms for these problems. The main approach used to attack these problems is modeling classes of algorithms that may solve this problem using a discrete model of computation then defining cost functions on this discrete structure...

On the role of thermal fluctuations in fluid mixing

Kiran Narayanan
Fluid mixing that is induced by hydrodynamic instability is ubiquitous in nature; the material interface between two fluids when perturbed even slightly, changes shape under the influence of hydrodynamic forces, and an additional zone called the mixing layer where the two fluids mix, develops and grows in size. This dissertation reports a study on the role of thermal fluctuations in fluid mixing at the interface separating two perfectly miscible fluids of different densities. Mixing under...

Potential of Bacterial Volatile Organic Compounds for Biocontrol of Fungal Phytopathogens and Plant Growth Promotion Under Abiotic Stress

Asma Soussi
Bacterial volatile organic compounds (VOCs) are signal molecules that may have beneficial roles in the soil-plant-microbiome ecosystem. In this Ph.D. thesis, I aimed to assess and characterize the role of bacterial VOCs in plant tolerance to drought and in the biocontrol of fungal pathogens. I started by studying two root endophytic bacteria isolated from pepper plants cultivated under desert farming conditions. They showed an enhancement of pepper tolerance to drought stress and an amelioration of...

Transcription Activator-Like Effectors (TALEs) Hybrid Nucleases for Genome Engineering Application

Anjar Wibowo
Gene targeting is a powerful genome engineering tool that can be used for a variety of biotechnological applications. Genomic double-strand DNA breaks generated by engineered site-specific nucleases can stimulate gene targeting. Hybrid nucleases are composed of DNA binding module and DNA cleavage module. Zinc Finger Nucleases were used to generate double-strand DNA breaks but it suffers from failures and lack of reproducibility. The transcription activator–like effectors (TALEs) from plant pathogenic Xanthomonas contain a unique type...

Spatial Exploration and Characterization of Endozoicomonas spp. Bacteria in Stylophora pistillata Using Fluorescence In Situ Hybridization

Areej Alsheikh-­Hussain
Studies of coral-­associated bacterial communities have repeatedly demonstrated that the microbial assemblages of the coral host are highly specific and complex. In particular, bacterial community surveys of scleractinian and soft corals from geographically diverse reefs continually uncover a high abundance of sequences affiliated with the Gammaproteobacteria genus Endozoicomonas. The role of these bacteria within the complex coral holobiont is currently unknown. In order to localize these cells and gain an understanding of their potential interactions...

Acoustic Estimates of Distribution and Biomass of Different Acoustic Scattering Types Between the New England Shelf Break and Slope Waters

Alexander McLaren
Due to their great ecological significance, mesopelagic fishes are attracting a wider audience on account of the large biomass they represent. Data from the National Marine Fisheries Service (NMFS) provided the opportunity to explore an unknown region of the North-West Atlantic, adjacent to one of the most productive fisheries in the world. Acoustic data collected during the cruise required the identification of acoustically distinct scattering types to make inferences on the migrations, distributions and biomass...

Post-translational Analysis of Arabidopsis thaliana Proteins in Response to Cyclic Guanosine Monophosphate Treatment

Brian Parrott
The introduction of mass spectrometry techniques to the field of biology has made possible the exploration of the proteome as a whole system as opposed to prior techniques, such as anti-body based assays or yeast two-hybrid studies, which were strictly limited to the study of a few proteins at a time. This practice has allowed for a systems biology approach of exploring the proteome, with the possibility of viewing entire pathways over increments of time....

Cytotoxic Effects of Nickel Nanowires in Human Fibroblasts

Laura P. Felix Servin
There is an increasing interest for the use of nanostructures as potential tools in areas that include biology and medicine, for applications spanning from cell separation to treatments of diseases. Magnetic nanoparticles (MNPs) have been the most widely studied and utilized nanostructures in biomedical applications. Despite their popularity, the regular shape of MNPs limits their potential for certain applications. Studies have shown that magnetic nanowires (MNWs), due to their high-­-aspect ratio and specific magnetic properties,...

Efficient C-O and C-N bond forming cross-coupling reactions catalyzed by core-shell structured Cu/Cu2O nanowires

Ahmed M. Elshewy
Oxygen and Nitrogen containing compounds are of utmost importance due to their interesting and diverse biological activities. The construction of the C-O and C–N bonds is of significance as it opens avenues for the introduction of ether and amine linkages in organic molecules. Despite significant advancements in this field, the construction of C-O and C–N bonds is still a major challenge for organic chemists, due to the involvement of harsh reaction conditions or the use...

Fabrication and Characterization of Micro-membrane GaN Light Emitting Diodes

Hsien-Yu Liao
Developing etching of GaN material system is the key to device fabrications. In this thesis, we report on the fabrication of high throughput lift-off of InGaN/GaN based micro-membrane light emitting diode (LED) from sapphire substrate using UV-assisted photoelectroless chemical (PEsC) etching. Unlike existing bandgap selective etching based on unconventional sacrificial layer, the current hydrofluoric acid based wet etching process enables the selective etching of undoped GaN layer already incorporated in standard commercial LED structures, thus...

Reversibly Bistable Flexible Electronics

Nasir Alfaraj
Introducing the notion of transformational silicon electronics has paved the way for integrating various applications with silicon-based, modern, high-performance electronic circuits that are mechanically flexible and optically semitransparent. While maintaining large-scale production and prototyping rapidity, this flexible and translucent scheme demonstrates the potential to transform conventionally stiff electronic devices into thin and foldable ones without compromising long-term performance and reliability. In this work, we report on the fabrication and characterization of reversibly bistable flexible electronic...

ACCTuner: OpenACC Auto-Tuner For Accelerated Scientific Applications

Fatemah Alzayer
We optimize parameters in OpenACC clauses for a stencil evaluation kernel executed on Graphical Processing Units (GPUs) using a variety of machine learning and optimization search algorithms, individually and in hybrid combinations, and compare execution time performance to the best possible obtained from brute force search. Several auto-tuning techniques – historic learning, random walk, simulated annealing, Nelder-Mead, and genetic algorithms – are evaluated over a large two-dimensional parameter space not satisfactorily addressed to date by...

Combating Impairments in Multi-carrier Systems: A Compressed Sensing Approach

Shamael Al-Shuhail
Multi-carrier systems suffer from several impairments, and communication system engineers use powerful signal processing tools to combat these impairments and keep up with the capacity/rate demands. Compressed sensing (CS) is one such tool that allows recovering any sparse signal, requiring only a few measurements in a domain that is incoherent with the domain of sparsity. Almost all signals of interest have some degree of sparsity, and in this work we utilize the sparsity of impairments...

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