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  • Control of the CDC48A segregase by the plant UBX-containing (PUX) protein family

    Zhang, Junrui (2021-05) [Thesis]
    Advisor: Arold, Stefan T.
    Committee members: Blilou, Ikram; Jaremko, Lukasz
    In plants, AAA-adenosine triphosphatase (ATPase) Cell Division Control Protein 48 (CDC48) uses the force generated through ATP hydrolysis to pull, extract, and unfold ubiquitylated or sumoylated proteins from the membrane, chromatin, or protein complexes. The resulting changes in protein or RNA content are an important means for plants to control protein homeostasis and thereby adapt to shifting environmental conditions. The activity and targeting of CDC48 are controlled by adaptor proteins, of which the plant ubiquitin regulatory X (UBX) domain-containing (PUX) proteins constitute the largest and most versatile family. However, few PUX proteins have been structurally or functionally characterized and how they participate in the substrate processing of CDC48A is not fully understood. Here, we first performed a comparative bioinformatic analysis, in which we found that the PUX proteins can be functionally divided into six types. We used this classification as a guide for our experimental efforts to elucidate how PUX proteins mediate client recognition and delivery for CDC48A-mediated unfolding. As a first step in this experimental analysis, we cloned and expressed a number of PUX protein constructs, we assessed their interaction features, and obtained crystals for several PUX domains. These bioinformatic and experimental results provide a basis for the in-depth structural and functional analysis of how PUX proteins control the CDC48A segregase.
  • Toward Improving the Internet of Things: Quality of Service and Fault Tolerance Perspectives

    Alaslani, Maha S. (2021-04-13) [Dissertation]
    Advisor: Shihada, Basem
    Committee members: Alouini, Mohamed-Slim; Zhang, Xiangliang; Bessani, Alysson
    The Internet of Things (IoT) is a technology aimed at developing a global network of machines and devices that can interact and communicate with each other. Supporting IoT, therefore, requires revisiting the Internet's best e ort service model and reviewing its complex communication patterns. In this dissertation, we explore the unique characteristics of IoT tra c and examine IoT systems. Our work is motivated by the new capabilities o ered by modern Software De ned Networks (SDN) and blockchain technology. We evaluate IoT Quality of Service (QoS) in traditional networking. We obtain mathematical expressions to calculate end-to-end delay, and dropping. Our results provide insight into the advantages of an intelligent edge serving as a detection mechanism. Subsequently, we propose SADIQ, SDN-based Application-aware Dynamic Internet of things QoS. SADIQ provides context-driven QoS for IoT applications by allowing applications to express their requirements using a high-level SQL-like policy language. Our results show that SADIQ improves the percentage of regions with an error in their reported temperature for the Weather Signal application up to 45 times; and it improves the percentage of incorrect parking statuses for regions with high occupancy for the Smart Parking application up to 30 times under the same network conditions and drop rates. Despite centralization and the control of data, IoT systems are not safe from cyber-crime, privacy issues, and security breaches. Therefore, we explore blockchain technology. In the context of IoT, Byzantine fault tolerance-based consensus protocols are used. However, the blockchain consensus layer contributes to the most remarkable performance overhead especially for IoT applications subject to maximum delay constraints. In order to capture the unique requirements of the IoT, consensus mechanisms and block formation need to be redesigned. To this end, we propose Synopsis, a novel hierarchical blockchain system. Synopsis introduces a wireless-optimized Byzantine chain replication protocol and a new probabilistic data structure. The results show that Synopsis successfully reduces the memory footprint from Megabytes to a few Kilobytes with an improvement of 1000 times. Synopsis also enables reductions in message complexity and commitment delay of 85% and 99.4%, respectively.
  • Frequency-modulation Stimulated Raman Scattering microscopy with an Acousto-Optic Tunable Filter

    Grassi, Elisa (2021-04) [Thesis]
    Advisor: Liberale, Carlo
    Committee members: Habuchi, Satoshi; Hauser, Charlotte
    Stimulated Raman Scattering (SRS) is a Coherent Raman microscopy method that has been increasingly employed in recent years for highly-speci c, label-free, and high-speed bioimaging. Compared to a similar Coherent Raman method, the so-called Coherent Anti-Stokes Scattering (CARS) microscopy, it exhibits advantages such as the absence of nonresonant background (NRB) and the linearity of the signal intensity on the concentration of molecules of interest. However, SRS can be a ected by unwanted background signals that hinder the acquisition of an accurate Raman information. These unwanted signals are generated by parasitic e ects that are dif- cult to suppress in standard SRS setups. Here, I present a frequency-modulation (FM) SRS technique via an Acousto-Optic Tunable Filter (AOTF), describing its implementation on Vibra Lab setup and assessing its e ciency with imaging results. The FM technique provides a cancellation of the unwanted background signals, maintaining intact the SRS information. It is based on the weak spectral dependence of the parasitic e ects as compared to the high spectral speci city of the SRS signal. The proposed scheme presents a few advantages when compared with other solutions presented in the literature. In particular, it doesn't require a complex setup con guration, and it can be used seamlessly in a very broad range of the vibrational spectrum.
  • Optimization of UV and bacteriophages as an alternative chemical-free approach for membrane cleaning

    Myshkevych, Yevhen (2021-03) [Thesis]
    Advisor: Hong, Pei-Ying
    Committee members: Nunes, Suzana Pereira; Daffonchio, Daniele
    Anaerobic membrane bioreactors (AnMBR) have been established as an efficient method of wastewater treatment to obtain high-quality effluent with low energy consumption. However, membrane fouling leading to flux reduction and an increase in operational costs can negate potential benefits associated with AnMBR. Today’s conventional membrane cleaning process includes physical and chemical approaches, both of which have their own drawback. For this reason, the biological approach was proposed as an alternative to dangerous, energy-consuming, and environmentally unsafe treatment techniques. The combination of UV-C and bacteriophage offers an alternative chemical-free approach for biofouling control. This dissertation aims to test the different order of using UV-C and bacteriophage to clean anaerobic membrane. This dissertation also demonstrates a proof-of-concept to achieve semi-online cleaning using UV-C and bacteriophage, thus increasing the feasibility of described technology. As a result of this work, it was shown that preliminary UV exposure enhances bacteriophage propagation into thick biofilms, and that the bacteriophages are able to affect total cell number and extracellular polymeric substances (EPS) compared to the control. Compared to the control, the semi-online cleaning strategy also resulted in a membrane that took a longer time for the transmembrane pressure to increase in the next operation cycle after cleaning.
  • High-Dimensional Analysis of Regularized Convex Optimization Problems with Application to Massive MIMO Wireless Communication Systems

    Alrashdi, Ayed (2021-03) [Dissertation]
    Advisor: Al-Naffouri, Tareq Y.
    Committee members: Alouini, Mohamed-Slim; Shihada, Basem; Kammoun, Abla; Al-Dhahir, Naofal; Davidson, Tim
    In the past couple of decades, the amount of data available has dramatically in- creased. Thus, in modern large-scale inference problems, the dimension of the signal to be estimated is comparable or even larger than the number of available observa- tions. Yet the desired properties of the signal typically lie in some low-dimensional structure, such as sparsity, low-rankness, finite alphabet, etc. Recently, non-smooth regularized convex optimization has risen as a powerful tool for the recovery of such structured signals from noisy linear measurements in an assortment of applications in signal processing, wireless communications, machine learning, computer vision, etc. With the advent of Compressed Sensing (CS), there has been a huge number of theoretical results that consider the estimation performance of non-smooth convex optimization in such a high-dimensional setting. In this thesis, we focus on precisely analyzing the high dimensional error perfor- mance of such regularized convex optimization problems under the presence of im- pairments (such as uncertainties) in the measurement matrix, which has independent Gaussian entries. The precise nature of our analysis allows performance compari- son between different types of these estimators and enables us to optimally tune the involved hyper-parameters. In particular, we study the performance of some of the most popular cases in linear inverse problems, such as the LASSO, Elastic Net, Least Squares (LS), Regularized Least Squares (RLS) and their box-constrained variants. In each context, we define appropriate performance measures, and we sharply an- alyze them in the High-Dimensional Statistical Regime. We use our results for a concrete application of designing efficient decoders for modern massive multi-input multi-output (MIMO) wireless communication systems and optimally allocate their power. The framework used for the analysis is based on Gaussian process methods, in particular, on a recently developed strong and tight version of the classical Gor- don Comparison Inequality which is called the Convex Gaussian Min-max Theorem (CGMT). We use some results from Random Matrix Theory (RMT) in our analysis as well.
  • Synthesis of novel bridged-pentanidiums and their performance in asymmetric phase-transfer catalysis

    Aresu, Emanuele (2021-03) [Dissertation]
    Advisor: Huang, Kuo-Wei
    Committee members: Rueping, Magnus; Bakr, Osman; Tan, Choon-Hong
    Abstract: Chiral phase-transfer catalysis (CPTC) is an efficient industrial process used to produce enantiomerically pure chemicals, such as agrochemicals, active pharmaceuticals ingredients (API), and monomers.1 CPTC has been applied successfully in various organic reactions with many advantages,2–6 such as mild reaction conditions, high product yields, elimination of hazardous or expensive reagents and solvents, and large- scale asymmetric productions.7 In the last decade, a chiral sp2-quaternary ammonium salt, pentanidium, reported by Tan et al. in 2011, has represented a breakthrough in this field.8 Since pentanidium catalysts have a high impact on asymmetric synthesis and are highly amenable to modification, a new class of bridged-pentanidium catalysts is discussed in this dissertation. The first part focuses on the retrosynthesis of chiral bridged-pentanidium catalysts and how they might be differently functionalized, starting the synthesis from commercial chiral diamines. As a proof-of-concept, a non-chiral bridged-pentanidium was synthesized and fully characterized. The reaction conditions were optimized for each step, particularly the critical seven-membered ring closure reaction, which proved that the retrosynthetic pathway was reliable. Next more sophisticated structures of chiral bridged-pentanidium catalysts were developed. These synthetic pathways involved the discovery of new compounds, such as chiral tertiary bisthioureas, chiral tetraamides, and chiral bisureas. Thus, various chiral bridged-pentanidium catalysts bearing various functional groups and counterions to tune their reactivity were produced. In the second part, the reactivity of chiral bridged-pentanidium catalysts was assessed in various asymmetric reactions. In particular, direct alkylation and Michael addition reactions were applied to synthesize natural and unnatural amino acids. Then, an asymmetric organocascade Michael-Michael reaction for the synthesis of chiral trisubstituted indanes was investigated. Lastly, additional control experiments involving various substrates and reagents were performed. The third part of this work investigated enantioselective induction through computational studies, including density functional theory (DFT), topographic steric maps, and topographic electrostatic maps.9 These studies characterized the properties of the previously synthesized chiral bridged-pentanidium catalysts and revealed how their enantioselectivity is affected by the structure of the catalyst. Finally, the structures and asymmetric induction of the novel chiral bridged-pentanidium catalysts were compared with those of open-pentanidium catalysts reported in the literature.
  • An Empirical Study of the Distributed Ellipsoidal Trust Region Method for Large Batch Training

    Alnasser, Ali (2021-02-10) [Thesis]
    Advisor: Keyes, David E.
    Committee members: Wonka, Peter; Zhang, Xiangliang
    Neural networks optimizers are dominated by rst-order methods, due to their inexpensive computational cost per iteration. However, it has been shown that rstorder optimization is prone to reaching sharp minima when trained with large batch sizes. As the batch size increases, the statistical stability of the problem increases, a regime that is well suited for second-order optimization methods. In this thesis, we study a distributed ellipsoidal trust region model for neural networks. We use a block diagonal approximation of the Hessian, assigning consecutive layers of the network to each process. We solve in parallel for the update direction of each subset of the parameters. We show that our optimizer is t for large batch training as well as increasing number of processes.
  • Monitoring Agricultural Water Use Using High-Resolution Remote Sensing Technologies

    Aragon Solorio, Bruno Jose Luis (2021-02) [Dissertation]
    Advisor: McCabe, Matthew
    Committee members: Hong, Pei-Ying; Jones, Burton; Miralles, Diego G.
    Over the coming decades, both food consumption and agricultural water use are expected to increase in response to growing populations. In light of these concerns, there has been a growing awareness and appreciation of the objectives of agricultural sustainability, which has the broad aim of securing food and water resources, without adversely affecting the environment or disenfranchising future generations. To ensure that irrigated fields optimize their water use towards a more sustainable application while remaining compliant with any imposed restrictions on access to water supplies (i.e. through water licensing), it is necessary to understand and quantify the water consumption of crops at appropriate spatial and temporal scales. Evaporation (E), also commonly referred to as evapotranspiration (ET), is the physical process of water vapor transport from the surface into the atmosphere. Evaporation can be estimated via interpretive modeling approaches that combine meteorological, radiative, vegetation, and other related properties to estimate land surface fluxes at any given time. The research presented herein aims to investigate the evaporative response of agricultural croplands across a range of spatial and temporal scales, with a focus on high-resolution and field-scale estimation. In particular, we explore the utility of novel CubeSat imagery to produce the highest spatial resolution (3 m) crop water use estimates ever retrieved from space. These high-resolution results are expanded through time by retrieving a daily evaporation product, offering an enhanced capacity to provide new insights into precision agriculture. The effects and implications of higher spatiotemporal resolutions are explored and contrasted against governmental satellite missions that operate at lower resolutions. An exploratory study on the use of unmanned aerial vehicles (UAVs) is also performed, specifically in the context of their capacity to mount miniaturized thermal sensors: with the accuracy and limitations of these sensors for deriving evaporation-type products examined. The overarching goal of this research is to advance the utility of space-based estimates of evaporation for precision agricultural applications, and to provide new high-spatial and temporal agricultural insights that can be directed towards improving water management and address food security concerns in a more sustainable manner.
  • Exploring the Reactivity of Well-defined Oxide-supported Metal­Alkyl and Alkylidyne Complexes via Surface Organometallic Chemistry

    Saidi, Aya (2021-02) [Dissertation]
    Advisor: Basset, Jean-Marie
    Committee members: Huang, Kuo-Wei; Saikaly, Pascal; Astruc, Didier
    Surface Organometallic Chemistry (SOMC) is an excellent approach to erase the gap between homogeneous and heterogeneous catalysis by grafting the molecular organometallic complex on various oxide surfaces, forming well-defined and single-site catalysts. This strategy allows for better characterization as well as the improvement and development of existing and new catalysts. These surface species could promote a wide range of catalytic applications (i.e., metathesis of hydrocarbons, hydrogenolysis of alkanes, and olefin polymerization reactions) depending on the metal center and its coordination sphere. In particular, the grafting of alkylated organometallic complexes of groups 4, 5, and 6 metals on the surface oxide is a thermodynamically favored reaction generally leading to strongly bonded well-defined surface species, which are highly reactive catalysts. This thesis has focused on the preparation, characterization, and catalytic investigation of different supported complexes that contain methyl, alkyl, and alkylidyne ligands. The first part compares the catalytic activity of [(≡Si−O−)W(-CH3)5] and [(≡Si-O-)Mo(≡CtBu)(-CH2tBu)2] surface species experimentally and by DFT calculations in the metathesis reactions of linear classical and functionalized olefins. Both pre-catalysts perform almost equally in the α-olefin metathesis reaction. However, in the functionalized olefin metathesis reaction, W pre-catalyst provides selective metathesis products and performs much better than Mo that gives a range of isomerization products. The second part deals with the synthesis and characterization of [(THF)2Zr(-CH3)4] and its grafting on silica support for the first time. The generated surface species [(≡Si−O−)Zr(CH3)3(THF)2] and [(≡Si−O−)2Zr(CH3)2(THF)2] are used for the conversion of CO2 and propylene oxide to cyclic propylene carbonates achieving a TON of 4227. The third part describes the first synthesis and characterization of the highly unstable homoleptic [Ti(-CH3)4] without any coordinating solvent. This complex was stabilized by grafting on SiO2-700, yielding two fully characterized surface species [(≡Si-O-)TiMe3] and [(≡Si-O-Si≡)(≡Si-O-)TiMe3], which were used in the hydrogenolysis reaction of propane and n-butane, with TONs of 419 and 578, respectively. Finally, the fourth part reports the immobilization and characterization of [TiMe2Cl2], an intermediate in the synthesis of [Ti(-CH3)4], on SiO2-700 resulting in [(≡Si-O-)TiMeCl2] and [(≡Si-O-)TiMe2Cl] surface species. These complexes reacted with a demethylating Lewis acid agent (BARF), forming the corresponding cationic Ti species [(≡Si-O-)TiMeCl]+ and [(≡Si-O-)TiCl2]+. Both neutral and cationic complexes were tested in the ethylene polymerization reaction affording linear HDPE with high molecular weights of 500,367 and 486,612 g/mol.
  • Autoignition and reactivity studies of renewable fuels and their blends with conventional fuels

    Issayev, Gani (2021-02) [Dissertation]
    Advisor: Farooq, Aamir
    Committee members: Sarathy, Mani; Fariborzi, Hossein; Curran, Henry J.
    Population growth and increasing standards of living have resulted in a rapid demand for energy. Our primary energy production is still dominated by fossil fuels. This extensive usage of fossil fuels has led to global warming, environmental pollution, as well as the depletion of hydrocarbon resources. The prevailing difficult situation offers not only a challenge but also an opportunity to search for alternatives to fossil fuels. Hence, there is an urgent need to explore environmentally friendly and cost-effective renewable energy sources. Oxygenates (alcohols, ethers) and ammonia are among the potential renewable alternative fuels of the future. This thesis investigates the combustion characteristics of promising alternative fuels and their blends using a combination of experimental and modelling methodologies. The studied fuels include ethanol, diethyl ether, dimethyl ether, dimethoxy methane, γ-valerolactone, cyclopentanone, and ammonia. For the results presented in this thesis, the studies may be classified into three main categories: 1. Ignition delay time measurements of ethanol and its blends by using a rapid compression machine and a shock tube. The blends studied include binary mixtures of ethanol/diethyl ether and ternary mixtures of ethanol/diethyl ether/ethyl levulinate. A chemical kinetic model has been constructed and validated over a wide range of experimental conditions. The results showed that a high-reactivity fuel, diethyl ether, may be blended with a low-reactivity fuel, ethanol, in varying concentrations to achieve the desired combustion characteristics. A ternary blend of ethanol/diethyl ether/ethyl levulinate may be formulated from a single production stream, and this blend is shown to behave similarly to a conventional gasoline. 2. Ignition delay time and flame speed measurements of ammonia blended with combustion promoters by utilizing a rapid compression machine and a constant volume spherical reactor. The extremely low reactivity of ammonia makes it unsuitable for direct use in many combustion systems. One of the potential strategies to utilize ammonia is to blend it with a combustion promoter. In this work, dimethyl ether, diethyl ether, and dimethoxy methane are explored as potential promoters of ammonia combustion. Chemical kinetic models were developed and validated in the high temperature regime by using flame speed data and in the low-to-intermediate temperature regime by using ignition delay time data. The results showed that even a small addition (~ 5 – 10%) of combustion promoters can significantly alter ammonia combustion, and diethyl ether was found to have the highest propensity to enhance ammonia ignition and flame propagation. Blends of combustion promoters with ammonia can thus be utilized in modern downsized turbo-charged engines. 3. Octane boosting and emissions minimization effects of next generation oxygenated biofuels. These studies were carried out using a cooperative fuel research engine operating in a homogenous charge compression ignition (HCCI) mode. The oxygenated fuels considered here include γ-valerolactone and cyclopentanone. The results showed that γ-valerolactone and cyclopentanone can be effective additives for octane boosting and emission reduction of conventional fuels. Overall, the results and outcomes of this thesis will be highly useful in choosing and optimizing alternative fuels for future transportation systems.
  • A versatile approach for combined algae removal and biofouling control in seawater reverse osmosis (SWRO) desalination systems

    Alshahri, Abdullah (2021-02) [Dissertation]
    Advisor: Ghaffour, NorEddine
    Committee members: Saikaly, Pascal; Pinnau, Ingo; Missimer, Thomas
    The goal of this study was to evaluate the feasibility of using advanced coagulation with Fe(VI) in coagulation-flocculation-sedimentation/ flotation systems for the pretreatment of SWRO desalination plants during algal bloom events. Algal organic matter (AOM) material extracted from marine diatom species (Chaetoceros affinis) was added to Red Sea water to mimic algal bloom conditions. Low dosage of Fe(VI) (<1 mg Fe/L) was very effective at improving feed water quality containing AOM (algal bloom conditions). Based on results from both a bench-scale DAF unit and Jar testing unit, 0.75 mg Fe/L of Fe (VI) proved to be effective at improving the raw water quality which is comparable to the performance of 1 and 3 mg Fe/L of Fe (III). The removal efficiency for both testing units with the use of Fe(VI) was up to 100% for algae , 99.99% for ATP, 99% for biopolymers and 70 % for DOC. The improvement in Fe(VI) performance is related to the simultaneous action of Fe(VI) as oxidant, disinfectant and coagulant. The performance of Fe(VI) coagulant was also evaluated with the use of coagulant aids (clays). The overall turbidity, DOC, biopolymers and algal cells removal was improved via using Fe(VI) and clays at very low dose. Generally, it was found that for the same pretreatment performance achieved, a much lower Fe(VI) dose was required compared to Fe (III), which make it important to study of cost effectiveness for using Fe(VI) instead of Fe(III) and estimate cost savings during algal bloom conditions. A detailed cost comparative study was conducted for Fe(III) vs. Fe(VI) coagulation process based on the removal efficiency. The use of Fe(VI) reduced the total pretreatment cost by 77% and sludge disposal cost by > 88% compared to the use of Fe(III) in the pretreatment process. The use of Fe(VI) reduces the operational and maintenance cost in SWRO desalination plant by 7% and the production cost by 4%. This study proved that the use of Fe(VI) during high turgidity and algal bloom conditions helped providing high raw water quality to the RO process with lower chemicals and operations cost as well as low chlorine and iron residuals.
  • Orientation and Dimensionality Control of Two-dimensional Transition Metal Dichalcogenides

    Aljarb, Areej (2021-01-17) [Dissertation]
    Advisor: Tung, Vincent
    Committee members: Anthopoulos, Thomas D.; Han, Yu; Li, Lain-Jong; Kim, Jeehwan
    Two-dimensional (2D) transition metal dichalcogenides (TMDs) have attracted significant attention owing to their unique electrical, optical, mechanical, and thermal properties not found in their 3D counterparts. They can be obtained by mechanical, chemical, or electrochemical exfoliation. However, these strategies lack uniformity and produce defect-rich samples, making it impossible for large-scale device fabrication. Chemical vapor deposition (CVD) method emerges as the viable candidate to create atomically thin specimens at the technologically relevant scale. However, the large-scale growth of monolayer TMD films with spatial homogeneity and high electrical performance remains an unsolved challenge. The spatial inhomogeneity and the associated grain boundaries between randomly oriented domains culminate to the deleterious quality of TMDs, breaking of the long-range crystalline periodicity and introduction of insidious strain. Recent research efforts have therefore dedicated to obtaining the single crystallinity of 2D materials by controlling the orientation and dimensionality to obtain a large-scale and grain boundary-free monolayer films for Si-comparable electron mobility and overcoming the scaling limitation of traditional Si-based microelectronics,. In the first part of this thesis, orientation and dimensionality controlling of TMDs are discussed. To this end, we systematically study the growth of stereotypical molybdenum disulfide (MoS2) monolayer on a c-plane sapphire with CVD to elucidate the factors controlling their orientation. We have arrived at the conclusion that the concentration of precursors- that is, the ratio between sulfur and molybdenum oxide, plays a key role in the size and orientation of seeds, subsequently controlling the orientation of MoS2 monolayers. Later, we demonstrate a ledge-directed epitaxy (LDE) of dense arrays of continuous, self-aligned, monolayer, and single-crystalline MoS2 nanoribbons on β-gallium (iii) oxide (β-Ga2O3) (100) substrates. LDE MoS2 nanoribbons have spatial uniformity over a long-range and transport characteristics on par with those seen in exfoliated benchmarks. In the second part, we theoretically reveal and experimentally determine the origin of resonant modulation of contrast as a result of the residual 3-fold astigmatism in modern scanning transmission electron microscopy (STEM) and its unintended impact on violating the power-law dependence of contrast on coordination modes between the transition metal and chalcogenide atoms.
  • Implications of irradiance for the Red Sea Tridacna giant clam holobiont

    Rossbach, Susann (2021-01) [Dissertation]
    Advisor: Duarte, Carlos M.
    Committee members: Voolstra, Christian R.; Daffonchio, Daniele; Benzoni, Francesca; Todd, Peter A.
    Giant clams (Tridacninae subfamily) are prominent members of Indo-Pacific corals reefs, including the Red Sea, where they play multiple roles and are of distinct ecological significance for these communities. Tridacninae stand out among other bivalves as one of the few molluscan groups that live in a symbiosis with dinoflagellate Symbiodiniaceae. This relationship is comparable to the symbiosis of corals and their associated algae, where the symbionts provide a substantial amount of the respiratory carbon demand of the host through their photosynthetic activity. Their photosymbiosis restricts the distribution of the Tridacninae holobiont (i.e. giant clam host, symbiotic algae and associated bacteria) to the sunlit, shallow waters of the euphotic zone, where organisms receive sufficient incident light to maintain their high rates of primary production and calcification. However, giant clams in these shallow reefs are simultaneously exposed to potentially high and damaging levels of solar (UV) radiation. This thesis includes research on the Red Sea Tridacna spp. holobiont from an ecosystem to microscale level. It assess the abundance and distribution of Red Sea giant clams, including their associated symbiotic microalgae and bacterial microbiome. Further, it describes the strong light-dependency of calcification and primary production of Red Sea Tridacna maxima clams and reports on the effective photo-protective mechanisms that have been evolved by these clams to thrive in shallow reefs, despite levels of high solar irradiance. Tridacninae developed effective behavioral mechanisms for photo-protection, by which the clam is able to flexibly adjust its shell gaping behavior to incident light levels within a narrow time frame. On a microscale, Tridacninae use advanced photonic structures (iridocytes) within their tissues to mitigate the potential negative effects of high solar UV radiation, and to promote the photosynthesis of their symbiotic algae. Understanding the role of the Tridacna spp. holobiont for Red Sea coral reefs, its contributions to overall productivity, and its abundances in the region may serve as a baseline for further studies on this charismatic invertebrate. It may also contribute to the conservation efforts from local to regional scales, and eventually aid the protection of Tridacninae in the Red Sea and elsewhere.
  • Assembly of Two CCDD Rice Genomes, Oryza grandiglumis and Oryza latifolia, and the Study of Their Evolutionary Changes

    Alsantely, Aseel O. (2021-01) [Thesis]
    Advisor: Wing, Rod Anthony
    Committee members: Gojobori, Takashi; Zuccolo, Andrea
    Every day more than half of the world consumes rice as a primary dietary resource. Thus, rice is one of the most important food crops in the world. Rice and its wild relatives are part of the genus Oryza. Studying the genome structure, function, and evolution of Oryza species in a comparative genomics framework is a useful approach to provide a wealth of knowledge that can significantly improve valuable agronomic traits. The Oryza genus includes 27 species, with 11 different genome types as identified by genetic and cytogenetic analyses. Six genome types, including that of domesticated rice - O. sativa and O. glaberrima, are diploid, and the remaining 5 are tetraploids. Three of the tetraploid species contain the CCDD genome types (O. grandiglumis, O. latifolia, and O. alta), which arose less than 2 million years ago. Polyploidization is one of the major contributors to evolutionary divergence and can thereby lead to adaptation to new environmental niches. An important first step in the characterization of the polyploid Oryza species is the generation of a high-quality reference genome sequence. Unfortunately, up until recently, the generation of such an important and fundamental resource from polyploid species has been challenging, primarily due to their genome complexity and repetitive sequence content. In this project, I assembled two high-quality genomes assemblies for O. grandiglumis and O. latifolia using PacBio long-read sequencing technology and an assembly pipeline that employed 3 genome assemblers (i.e., Canu/2.0, Mecat2, and Flye/2.5) and multiple rounds of sequence polishing with 5 both Arrow and Pilon/1.23. After the primary assembly, sequence contigs were arranged into pseudomolecules, and homeologous chromosomes were assigned to their respective genome types (i.e., CC or DD). Finally, the assemblies were extensively edited manually to close as many gaps as possible. Both assemblies were then analyzed for transposable element and structural variant content between species and homoeologous chromosomes. This enabled us to study the evolutionary divergence of those two genomes, and to explore the possibility of neo-domesticating either species in future research for my PhD dissertation.
  • Zaxinone, a Natural Apocarotenoid, Regulates Growth and Strigolactone Biosynthesis in Rice

    Wang, Jian You (2021-01) [Dissertation]
    Advisor: Al-Babili, Salim
    Committee members: Gojobori, Takashi; Blilou, Ikram; Bouwmeester, Harro J.
    Carotenoids are the precursor of several metabolites with regulatory functions, which include the plant hormones abscisic acid (ABA) and strigolactones (SLs), and signaling molecules, such as β-cyclocitral. These carotenoid-derivatives originate from oxidative breakdown of the double bond resulting in carbonyl cleavage-products designated as apocarotenoids. The cleavage reaction causing apocarotenoid formation is catalyzed frequently by Carotenoid Cleavage Dioxygenases (CCDs). Several lines of evidence indicate the presence of yet unidentified apocarotenoids with regulatory or signaling function. Here, we first characterized the biological functions of the apocarotenoid zaxinone formed by ZAXINONE SYNTHASE (ZAS), a member of an overlooked, widely distributed plant CCD clade. The loss-of-function rice zas mutant contains less zaxinone, exhibiting retarded growth with elevated levels of SLs that determines plant architecture, mediates mycorrhization, and facilitates the germination of root parasitic seeds, such as Striga spp. The zaxinone treatment rescued zas phenotypes, down-regulated SL biosynthesis and release, and enhanced root growth in the wild-type rice seedlings. Next, we performed multi-omics analysis demonstrating zaxinone increased sugar metabolism and induced photosynthesis in a manner that led to phenotypical changes in rice roots. Besides, transcriptome analysis showed that zaxinone upregulated CYTOKININ GLUCOSYLTRANSFERASES expression in roots, which might explain the increase in the apex and meristem length, and in the number of cellular layers. Finally, the investigation of zaxinone biology and the utilization of its application is constrained by its laborious organic synthesis and low abundance in natural sources. Therefore, we developed easy-to-synthesize and highly efficient Mimic of Zaxinone (MiZax), based on the structure-activity-relationship study using a series of apocarotenoids. Activity-based experiments unraveled MiZax3 and MiZax5 were at least as active as zaxinone in rescuing root phenotypes of the zas mutant, promoting root growth in wild-type seedlings, and reducing SL biosynthesis and release. Taken together, zaxinone is a key regulator of rice growth and development, which regulates sugar metabolism, suppresses SL biosynthesis, fine-tunes cytokinins level, and modulates biotic interactions with arbuscular mycorrhizal (AM) fungi. Our work also provides easy-to-synthesize mimics for illuminating zaxinone biology and as a tool to improve crop growth and reduce the infestation by Striga hermonthica, a severe threat to food security worldwide.
  • Oxygen Modulation of thermal tolerance in the branching coral Stylophora pistillata

    Parry, Anieka (2021-01) [Thesis]
    Advisor: Duarte, Carlos M.
    Committee members: Aranda, Manuel; Daffonchio, Daniele
    Coral reef ecosystems are under increasing threat from ocean warming and deoxygenation. Mass coral bleaching events in recent years have been linked to marine heatwaves but reporting of hypoxia-induced bleaching has also been increasing. Oxygen availability in coral reefs is driven by community metabolism and they experience a dynamic range of oxygen concentrations throughout diel cycles, hyperoxia during the day and hypoxia during the night. It has been suggested that the highest oxygen concentrations coincide with the hottest part of the day and this may protect marine taxa from high temperatures. We evaluated experimentally whether excess oxygen availability would increase the thermal threshold of the branching coral Stylophora pistillata, from the Southern Red Sea. We did this by exposing coral fragments of this species to varying dissolved oxygen concentrations (hypoxia, normoxia and hyperoxia) and a short-term temperature ramping regime (1˚C h-1). Hyperoxia did extend the thermal tolerance of S. pistillata fragments, with an LT50 of 39.1˚C as opposed to 39.0˚C for the normoxic treatment and 38.7˚C for the hypoxic treatment. Hyperoxia also increased respiration and gross photosynthesis and had a negative effect on photochemical efficiency at high temperatures. Net photosynthesis, P:R ratio and symbiont density were not significantly affected by oxygen concentration. Corals in this experiment displayed exceedingly high thermal thresholds, which were at least 2˚C higher than previously reported for the same species in the Central Red Sea. The corals used in the experiment had previously survived mass bleaching events in 2015 and hence we may have selected for individuals adapted to thermal stress. This is the first study to investigate the role of oxygen in the thermal tolerance of hermatypic corals and the first assessment of thermal thresholds from corals in the Southern Red Sea, where previously thermal thresholds have been based on a 1-2˚C increase in maximum mean monthly temperatures and visual bleaching observations. This highlights the need for increased experimental assessments of thermal thresholds in the Southern regions of the Red Sea and the important role of oxygen in moderating thermal stress.
  • Sustainability Evaluation of Hybrid Desalination Systems: Multi Effect Distillation – Adsorption (MED-AD) and Forward Osmosis – Membrane Distillation (FO-MD)

    Son, Hyuk Soo (2020-12) [Dissertation]
    Advisor: Ghaffour, NorEddine
    Committee members: Vrouwenvelder, Johannes S.; Pinnau, Ingo; Orfi, Jamel
    Water is life for all living organisms on earth, and all human beings need water for every socio-economic activity in their daily lives. However, constant challenges are faced in securing quality water resources due to environmental pollution, a growing demand, and climate changes. To overcome imminent worldwide challenges on water resources, desalination of seawater and saline wastewater became inevitable, and significant efforts have been deployed by the desalination research community to advance the technology. However, there is still a gap to take it to a higher sustainability and compatibility compared to conventional water treatment technologies. Among all efforts, the hybridization of two or more processes stands among the promising solutions for sustainable desalination, which synergizes benefits of multiple technologies. To evaluate the sustainability of hybrid desalination technologies, two different systems, namely; (i) multi-effect distillation – adsorption (MED-AD) and (ii) forward osmosis – membrane distillation (FO-MD), are investigated in this study. The method developed for the analysis of primary energy consumption in complex desalination systems is used to evaluate the performance of the MED-AD pilot facility at King Abdullah University of Science and Technology (KAUST). Results of the MED-AD pilot operation showed an improvement in water production with a higher energy efficiency under the same operating conditions (near the ambient temperature with the solar thermal system). For the FO-MD hybrid system, an investigation is carried out on a novel in-house integrated module and a comparative analysis with the conventional module is provided. An isolation barrier carefully placed in the novel design enhanced the hybrid performance by reducing both concentration and temperature polarization. In addition, the FO-MD hybrid process is evaluated for brine reclamation application in a SWRO-MD-FO system. The sustainability of the proposed system and the potential of a flexible sustainable operation are presented with the experimental study with real seawater and brine from the full-scale desalination plant.
  • Shales: Comprehensive Laboratory Characterization

    Gramajo, Eduardo (2020-12) [Dissertation]
    Advisor: Santamarina, Carlos
    Committee members: Vahrenkamp, Volker C.; Mai, Paul Martin; Frost, David; Finkbeiner, Thomas
    Unconventional formations have become an increasingly important source of energy resources. Proper rock mechanic characterization is needed not only to identify the most promising areas for stimulation, but to increase our understanding of the sealing capabilities of cap-rock formations for carbon geological storage. However, shale assessment is challenging with current standard techniques. This research explores the index and rock mechanic properties of different shale specimens considered as source rocks for oil and gas (Eagle Ford, Wolfcamp, Jordanian, Mancos, Bakken, and Kimmeridge), and presents an in-depth analysis of tools and protocols to identify inherent biases. New test protocols proposed in this thesis provide robust and cost-effective measurement techniques to characterize shale formations in general; these include: 1) new energy methods computed from the area under the stress-strain curve or proposed boundary asymptotes (strength and stiffness) to assess brittle/ductile conditions in the field, 2) tensile strength analyses to determine anisotropy in shale formations, 3) Coda wave analysis to monitor pre-failure damage evolution during compression, and 4) a combination of index tests to anticipate the complicated geology or layered characteristics, which include high-resolution imaging, hardness, and scratch tests. Experimental results combined with extensive databases provide unprecedented information related to the mechanical behavior of shale formations needed for the enhanced design and analysis of geo-engineering applications. Calcareous shales display strong interlayer bonding and lower compressive strength anisotropy than siliceous shales. Tensile strength anisotropy is more pronounced than in compressive strength and reflects bedding orientation and loading conditions that affect fracture propagation and ensuing failure surface topography.
  • Modeling Human Learning in Games

    Alghamdi, Norah K. (2020-12) [Thesis]
    Advisor: Shamma, Jeff S.
    Committee members: Feron, Eric; Laleg-Kirati, Taous-Meriem
    Human-robot interaction is an important and broad area of study. To achieve success- ful interaction, we have to study human decision making rules. This work investigates human learning rules in games with the presence of intelligent decision makers. Par- ticularly, we analyze human behavior in a congestion game. The game models traffic in a simple scenario where multiple vehicles share two roads. Ten vehicles are con- trolled by the human player, where they decide on how to distribute their vehicles on the two roads. There are hundred simulated players each controlling one vehicle. The game is repeated for many rounds, allowing the players to adapt and formulate a strategy, and after each round, the cost of the roads and visual assistance is shown to the human player. The goal of all players is to minimize the total congestion experienced by the vehicles they control. In order to demonstrate our results, we first built a human player simulator using Fictitious play and Regret Matching algorithms. Then, we showed the passivity property of these algorithms after adjusting the passivity condition to suit discrete time formulation. Next, we conducted the experiment online to allow players to participate. A similar analysis was done on the data collected, to study the passivity of the human decision making rule. We observe different performances with different types of virtual players. However, in all cases, the human decision rule satisfied the passivity condition. This result implies that human behavior can be modeled as passive, and systems can be designed to use these results to influence human behavior and reach desirable outcomes.
  • Exploring Entity Relationship in Pairwise Ranking: Adaptive Sampler and Beyond

    Yu, Lu (2020-12) [Dissertation]
    Advisor: Zhang, Xiangliang
    Committee members: Moshkov, Mikhail; Hoehndorf, Robert; Karypis, George
    Living in the booming age of information, we have to rely on powerful information retrieval tools to seek the unique piece of desired knowledge from such a big data world, like using personalized search engine and recommendation systems. As one of the core components, ranking model can appear in almost everywhere as long as we need a relative order of desired/relevant entities. Based on the most general and intuitive assumption that entities without user actions (e.g., clicks, purchase, comments) are of less interest than those with user actions, the objective function of pairwise ranking models is formulated by measuring the contrast between positive (with actions) and negative (without actions) entities. This contrastive relationship is the core of pairwise ranking models. The construction of these positive-negative pairs has great influence on the model inference accuracy. Especially, it is challenging to explore the entity relationships in heterogeneous information network. In this thesis, we aim at advancing the development of the methodologies and principles of mining heterogeneous information network through learning entity relations from a pairwise learning to rank optimization perspective. More specifically we first show the connections of different relation learning objectives modified from different ranking metrics including both pairwise and list-wise objectives. We prove that most of popular ranking metrics can be optimized in the same lower bound. Secondly, we propose the class-imbalance problem imposed by entity relation comparison in ranking objectives, and prove that class-imbalance problem can lead to frequency 5 clustering and gradient vanishment problems. As a response, we indicate out that developing a fast adaptive sampling method is very essential to boost the pairwise ranking model. To model the entity dynamic dependency, we propose to unify the individual-level interaction and union-level interactions, and result in a multi-order attentive ranking model to improve the preference inference from multiple views.

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