Now showing items 21-40 of 1629

    • On The Large-Scale Deployment of Laser-Powered Drones for UAV-Enabled Communications

      Lahmeri, Mohamed Amine (2021-04) [Thesis]
      Advisor: Alouini, Mohamed-Slim
      Committee members: Ooi, Boon S.; Sun, Ying; Park, Kihong
      To meet the latest requirements of the 6G standards, several techniques have been proposed in the open literature, such as millimeter waves, terahertz communication, and massive MIMO. In addition to these recent technologies, the use of unmanned aerial vehicles (UAVs) is strongly advocated for 6G networks, as the 6G standard will not be dedicated to broadband services, but will rather be oriented towards reduced geographical cellular coverage. In this context, the deployment of UAVs is considered a key solution for seamless connectivity and reliable coverage. Although UAVs are characterized by their high mobility and their ability to establish line-of-sight links, their use is still impeded by several factors such as weather conditions, their limited computing power, and, most importantly, their limited energy. In this work, we are aiming for the novel technology that enables indefinite wireless power transfer for UAVs using laser beams. We propose a novel UAV deployment strategy, based on which we analyze the overall performance of the system in terms of wireless coverage and provide some useful insights. To this end, we use tractable tools from stochastic geometry to model the complex communication system.
    • Transient Analysis of Electromagnetic and Acoustic Scattering using Second-kind Surface Integral Equations

      Chen, Rui (2021-04) [Dissertation]
      Advisor: Bagci, Hakan
      Committee members: Ooi, Boon S.; Wu, Ying; Shanker, Balasubramaniam
      Time-domain methods are preferred over their frequency-domain counterparts for solving acoustic and electromagnetic scattering problems since they can produce wide- band data from a single simulation. Among the time-domain methods, time-domain surface integral equation solvers have recently found widespread use because they offer several benefits over differential equation solvers. This dissertation develops several second-kind surface integral equation solvers for analyzing transient acoustic scattering from rigid and penetrable objects and transient electromagnetic scattering from perfect electrically conducting and dielectric objects. For acoustically rigid, perfect electrically conducting, and dielectric scatterers, fully explicit marching-on-in-time schemes are developed for solving time domain Kirchhoff, magnetic field, and scalar potential integral equations, respectively. The unknown quantity (e.g., velocity potential, electric current, or scalar potential) on the scatterer surface is discretized using a higher-order method in space and Lagrange interpolation in time. The resulting system is cast in the form of an ordinary differen- tial equation and integrated in time using a predictor-corrector scheme to obtain the unknown expansion coefficients. The explicit scheme can use the same time step size as its implicit counterpart without sacrificing from the stability of the solution and is much faster under low-frequency excitation (i.e., for large time step size). In addition, low-frequency behavior of vector potential integral equations for perfect electrically conducting scatterers is also investigated in this dissertation. For acoustically penetrable scatterers, presence of spurious interior resonance modes in the solutions of two forms of time domain surface integral equations is investigated. Numerical results demonstrate that the solution of the form that is widely used in the literature is corrupted by the interior resonance modes. But, the amplitude of these modes in the time domain can be suppressed by increasing the accuracy of discretization especially in time. On the other hand, the proposed one in the combined form shows a resonance-free performance verified via numerical experiments. In addition to providing detailed formulations of these solvers, the dissertation presents numerical examples, which demonstrate the solvers’ accuracy, efficiency, and applicability in real-life scenarios.
    • Ultra-Thin AMC for Gain-Enhancement of a 94 GHz Antenna-On-Chip

      Yu, Yiyang (2021-04) [Thesis]
      Advisor: Shamim, Atif
      Committee members: Bagci, Hakan; Wu, Ying
      The surge in transistor scaling and integration processes has driven the growth of wireless technology, especially low-cost millimeter-wave systems. Based on mainstream Silicon technology, System-on-Chip (SoC) has become an attractive approach to achieve the required high level of on-chip integration for modern wireless systems. However, the low resistivity (ρ=10 Ω-cm) and high relative permittivity (εr=11.9) of the silicon substrate are unsuitable for hosting antennas on it, because the Radio Frequency (RF) power is lost in the lossy silicon substrate, and some of it gets radiated in a certain undesired direction due to the surface waves. This has caused such antennas, typically known as Antenna-on-chip (AoC), to be poor radiators. Introducing an on-chip artificial magnetic conductor (AMC) between the substrate and the antenna can isolate the silicon substrate from the antenna and provide in-phase reflection, thereby improving the radiation performance. However, the drawback of conventional on- chip AMC is its relatively large thickness, which is extremely difficult to achieve on the thin silicon dioxide layer of typical CMOS processes (~10-15 μm). To resolve this problem, the embedded guiding structures have been designed between the periodic structure layer and the ground plane to realize an ultra-thin AMC which is suitable for thin oxide stack up of typical CMOS processes. Specifically, a patch-based AMC with embedded guiding structures has been designed for an on-chip monopole antenna operating at 94 GHz. The performance of the AMC has been studied for different resistivity substrates (from 10-3 to 103 Ω-cm). The AMC-backed on- chip antenna has been fabricated through an in-house CMOS-compatible process. The adhesion of the metallic layer to the substrate has been improved without using a seed layer, which is typically a low conductivity metal and has a negative impact on the radiation of the AoC. The measured input impedance and radiation performance of the AMC-backed AoC are fairly consistent with the simulations. It provides 5.85 dBi gain with the return loss of 16 dB at 94 GHz. According to the author’s best knowledge, this is the thinnest AMC-based AoC design in the literature.
    • Study of Miniaturization Techniques for a UHF RFID Tag on Package

      Lopez Reyes, Zulma (2021-04) [Thesis]
      Advisor: Shamim, Atif
      Committee members: Shamim, Atif; Bagci, Hakan; Salama, Khaled N.; Wu, Ying
      With the increasing demand of compact and lightweight wireless devices, there is a significant need to miniaturize the antennas, which are one of the largest radiofrequency components. The radiation performance of antennas degrades as their physical size becomes smaller in terms of operating wavelength [1]. The key challenge in antenna design, therefore, lies in the compromise between size and radiation performance. This challenge becomes critical for low frequency antennas such as for the RFID band. The Antenna-in-Package (AiP) concept, where the antenna is realized as part of the package along with the driving electronics, provides some console in terms of size as the antenna does not need any additional space. In this approach, the package becomes a functional module along with its primary job of protecting the components from the environment. This work aims to investigate various miniaturization techniques for a UHF RFID tag on package. Firstly, a dipole is given a 3D shape by carefully folding it over a package, in a manner that the currents on different segments add constructively. Secondly, the package material (which acts as the substrate for the antenna) is chosen to have a dielectric constant of 5.3 which further helps in size reduction. Finally, loading of slow-wave structures, comprising of inductors and capacitors, is used to achieve further miniaturization. The Artificial Transmission Line approach 5 is utilized to determine the required values of the lumped components, and its location is optimized by analyzing the current distribution of the antenna to maintain a good efficiency. The RFID chip with a large capacitive impedance is conjugately matched to the antenna without an external matching network. This is done by carefully selecting the values of the lumped components as well as by adjusting the trace width of the antenna. The package has been realized through a low-loss filament (𝑡𝑎𝑛(𝛿) = 0.004) with the Raise3D Pro2 printer, and the conductor has been realized by copper tape using laser patterning technology with the laser platform PLS6MW. At an operational frequency of 866 MHz, a 𝑘𝑎 of 0.26, a read-range of 2.7 𝑚, and a radiation efficiency of approximately 32% is achieved.
    • Layered double hydroxide (LDH)-mediated topical delivery of dsRNA for protection against Tomato yellow leaf curl virus (TYLCV) in Nicotiana benthamiana

      Hernandez, Edith Sanchez (2021-04) [Thesis]
      Advisor: Mahfouz, Magdy M.
      Committee members: Habuchi, Satoshi; Ghaffour, NorEddine
      Cell wall is the major barrier in the delivery of biomolecules such as nucleic acids into the plant cell. Biological (bacteria or viruses) and biolistic (particle-based) methods are used to deliver nucleic acids into the plant cell. However, these methods have significant limitations when it comes to species range, scalability, and field assays. In this work, we report the use of layered double hydroxide (LDH) topically applied to deliver RNA molecules into the plant cell. LDH were assembled by methanol-based co-precipitation of magnesium and aluminum nitrate solution with sodium hydroxide and finally dispersed in deionized water. The assembled LDH were physically characterized by AFM, zeta-sizer and their binding to RNA was confirmed by gel electrophoresis. LDH complexed with double stranded RNA (dsRNA) was topically applied to Nicotiana benthamiana leaves. As a model system, virus specific dsRNA-LDH complexes were used to activate cellular RNAi machinery against Tomato Yellow leaf Curl Virus (TYLCV) in N. benthamiana plants. Our results demonstrated that topical application of the TYLCV specific dsRNA-LDH complexes reduce viral genome accumulation and viral symptoms development. Similarly, dsRNA-LDH protected plants produce typical leaves, flowers, and seeds, confirming efficient virus resistance compared unprotected TYLCV infected plants. Topical application and noninvasive delivery of nucleic acid has several advantages, as these methods are specie independent, easy to scale up, applied with low-pressure spray, requires no tissue culture and no sophisticated equipment. The LDH based noninvasive delivery of nucleic acids has the capability to overcome the cell wall barrier limitations and will open new opportunities to exploit the full potential of cellular machinery to produce resilient plants and insure sustainable food production.
    • Propylene and Propane Separation Though Carbon Molecular Sieve Membranes Derived from a Tetraphenylethylene-Based Polymer of Intrinsic Microporosity (TPE-PIM)

      Elahi, Fawwaz (2021-04) [Thesis]
      Advisor: Pinnau, Ingo
      Committee members: Han, Yu; Lai, Zhiping
      Efficient propylene and propane separation is a major challenge in the modern chemical industry. With current separation methods being highly energy-intensive, there is a pressing need to find alternative green technology. Membrane separation emerged as a promising candidate for propylene and propane separation. Their small footprint, low cost, reliability, and environmental friendliness give membrane separation systems a competitive edge in the race towards sustainable development. The continuous advancements in material science created avenues for new membrane materials such as carbon molecular sieve (CMS) membranes which exhibit exceptional gas separation performances for challenging applications due to their strong size-sieving capabilities. In this work, a carbon molecular sieve (CMS) membrane derived from a polymer of intrinsic microporosity (TPE-PIM) has been investigated for propylene/propane separation made by pyrolysis at 400, 450, 500, 550, 600, 650, and 700 ºC. TPE-PIM-derived CMS films showed excellent pure and mixed-gas permeability and selectivity, exceeding the upper bound limits for propylene and propane. Observed in this work was the presence of an optimal pyrolysis temperature at 600 ºC, where the film showed the best performance with a permeability of 41.6 Barrer and a selectivity of 197 based on pure-gas measurements but dropping to 34 Barrer and selectivity of 33 under equimolar mixed-gas conditions. Such performance could be attributed to the unique internal structural changes that occurred during the pyrolysis. In addition, propane permeability though the CMS films was slow and required long times to reach steady-state values. Such slow kinetics illustrates the molecular sieving capabilities of CMS membranes for bigger and more condensable gases. Several characterization techniques have been performed on the films to confirm CMS formation and showcase deeper molecular structure insights. X-ray diffraction of all TPE-PIM films showed a broad spectrum at each peak due to the material’s amorphous nature. Diffraction patterns also revealed a gradual peak shift for the (002) plane towards smaller values closer to that of pure graphite. Raman spectra showed the characteristic D and G peaks for carbon films prepared at 500 ºC and above. FTIR analysis was also performed to investigate the potential formation of triazine crosslinks in the thermally treated samples, but no conclusive results were obtained.
    • Spatio-temporal changes in Red Sea benthic coral reef communities

      Gonzalez-Martinez, Karla Paola (2021-04) [Thesis]
      Advisor: Berumen, Michael L.
      Committee members: Carvalho, Susana; Benzoni, Francesca
      Understanding how coral reefs respond to natural disturbances is fundamental to assess their resistance and resilience, particularly in a context of climate change. Therefore, and given the escalating frequency and intensity of bleaching events, it is essential to evaluate responses of communities in space and time to disentangle the mechanisms underlying ecological changes. Here, I analyzed a dataset comprising 59 reefs, resulting from 6 years (2014-2016) of a coral reef benthic monitoring program in the Saudi Arabian Red Sea. It encompasses the 2015/2016 mass bleaching event and spans three different geographic regions: north (Duba and Al Wajh), central (Jeddah and Thuwal), and south (Al Lith, Farasan Islands and Farasan Banks). The results indicate significant differences between regions and through time. Coral assemblages from the southern region were the most affected by the 2015 bleaching event, where in some reefs, hard and soft corals cover dropped to <2% in 2017. Important changes in community structure were observed through time in the three regions, with a shift to a macroalgae, turf algae and CCA dominance. Different environmental drivers (salinity, sea surface temperature, fishing index, distance to shore, and photosynthetically active radiation) were analyzed, and highlighted a regionally-based response of the communities to these potential drivers of change. Overall, the examined Red Sea benthic communities presented dynamic patterns in composition. Distance decay plots based on presence/absence showed a general increase in similarity throughout multiple spatial scales in 2019, when compared to previous years. This finding suggests a loss in biodiversity due to thermal anomalies and bleaching events, evidenced by a homogenization (i.e., increase similarity) in the composition of the benthic communities. I document here a patterns of dominance of a few benthic groups with time and a decrease in branching corals. This study provides baseline information about changes in coral reef benthic community structure and identifies environmental factors with a higher impact on a regional scale. This information can be used to guide conservation efforts in these highly biodiverse ecosystems.The resulting datasets can be valuable for anticipating responses of coral communities under future climate scenarios.
    • Discriminant Analysis and Support Vector Regression in High Dimensions: Sharp Performance Analysis and Optimal Designs

      Sifaou, Houssem (2021-04) [Dissertation]
      Advisor: Alouini, Mohamed-Slim
      Committee members: Shihada, Basem; Zhang, Xiangliang; Kammoun, Abla; McKay, Matthew
      Machine learning is emerging as a powerful tool to data science and is being applied in almost all subjects. In many applications, the number of features is com- parable to the number of samples, and both grow large. This setting is usually named the high-dimensional regime. In this regime, new challenges arise when it comes to the application of machine learning. In this work, we conduct a high-dimensional performance analysis of some popular classification and regression techniques. In a first part, discriminant analysis classifiers are considered. A major challenge towards the use of these classifiers in practice is that they depend on the inverse of covariance matrices that need to be estimated from training data. Several estimators for the inverse of the covariance matrices can be used. The most common ones are estimators based on the regularization approach. In this thesis, we propose new estimators that are shown to yield better performance. The main principle of our proposed approach is the design of an optimized inverse covariance matrix estimator based on the assumption that the covariance matrix is a low-rank perturbation of a scaled identity matrix. We show that not only the proposed classifiers are easier to implement but also, outperform the classical regularization-based discriminant analysis classifiers. In a second part, we carry out a high-dimensional statistical analysis of linear support vector regression. Under some plausible assumptions on the statistical dis- tribution of the data, we characterize the feasibility condition for the hard support vector regression and, when feasible, derive an asymptotic approximation for its risk. Similarly, we study the test risk for the soft support vector regression as a function of its parameters. The analysis is then extended to the case of kernel support vector regression under generalized linear models assumption. Based on our analysis, we illustrate that adding more samples may be harmful to the test performance of these regression algorithms, while it is always beneficial when the parameters are optimally selected. Our results pave the way to understand the effect of the underlying hyper- parameters and provide insights on how to optimally choose the kernel function.
    • Using Google Earth Engine for the Automated Mapping of Center Pivot Irrigation fields in Saudi Arabia

      Alwahas, Areej (2021-04) [Thesis]
      Advisor: McCabe, Matthew
      Committee members: Johansen, Kasper; Picioreanu, Cristian; Schuster, Gerard T.
      Groundwater is a vital non-renewable resource that is being over exploited at an alarming rate. In Saudi Arabia, the majority of groundwater is used for agricultural activities. As such, the mapping of irrigated lands is a crucial step for managing available water resources. Even though traditional in-field mapping is effective, it is expensive, physically demanding, and spatially restricted. The use of remote sensing combined with advanced computational approaches provide a potential solution to this scale problem. However, when attempted at large scales, traditional computing tends to have significant processing and storage limitations. To address the scalability challenge, this project explores open-source cloud-based resources to map and quantify center-pivot irrigation fields on a national scale. This is achieved by first applying a land cover classification using Random Forest which is a machine learning approach, and then implementing a circle detection algorithm. While the analysis represents a preliminary exploration of these emerging cloud-based techniques, there is clear potential for broad application to many problems in the Earth and environmental sciences.
    • Index Modulation Schemes for Terahertz Communications

      Loukil, Mohamed Habib (2021-04) [Thesis]
      Advisor: Al-Naffouri, Tareq Y.
      Committee members: Alouini, Mohamed-Slim; Shihada, Basem; Amin, Osama
      Terahertz (THz)-band communication is envisioned as a critical technology that could satisfy the need for much higher data rates in sixth generation wireless communi- cation (6G) systems and beyond. Although THz signal propagation suffers from huge spreading and molecular absorption losses that limit the achievable commu- nication ranges, ultra-massive multiple-input multiple-output (UM-MIMO) antenna arrays can introduce the required beamforming gains to compensate for these losses. The reconfigurable UM-MIMO systems of small footprints motivate the use of spatial modulation techniques. Furthermore, the ultra-wideband fragmented THz spectrum motivates the use of index modulation techniques over multicarrier channels. In this thesis, we consider the problem of efficient index mapping and data detection in THz- band index modulation paradigms. We first propose an accurate frequency-domain statistical UM-MIMO channel model for wideband multicarrier THz-band commu- nications by considering THz-specific features. We then propose several THz-band generalized index modulation schemes that provide various performance and complex- ity tradeoffs. We propose efficient algorithms for mapping information bits to antenna and frequency indices at the transmitter side to enhance the achievable data rates in THz channel uses. We further propose complementary low-complexity parameter estimation and data detection techniques at the receiver side that can scale efficiently with very high rates. We derive theoretical bounds on the achievable performance gains of the proposed solutions and generate extensive numerical results promoting the corresponding future 6G use cases.
    • Spatial dynamics of Red Sea coral reef fish assemblages: a taxonomic and ecological trait approach

      Gil Ramos, Gloria Lisbet (2021-04) [Thesis]
      Advisor: Berumen, Michael Lee
      Committee members: Carvalho, Susana; Peixoto, Raquel
      Despite the increases in the intensity and frequency of disturbances on coral reefs in the Red Sea over the past decade, patterns of variability in fish communities are still poorly understood. This study aims to contribute to a better understanding of how fish communities vary along multiple spatial scales (10-100’ of kilometers) and to provide a baseline for future comparisons, fundamental to assess responses to climate change and other disturbances. Coral reefs along the Saudi Arabian Red Sea coast were surveyed from 2017 to 2019. The reefs ranged from 28° N to 18 °N and were categorized according their geographical location and grouped within three regions, namely north (24-28.5°N; 12 reefs), central (20.4-22.3°N; 11 reefs), and south (18.5-21.2°N; 30 reefs). The quantification of spatial patterns was conducted based on both taxonomic- and trait-based approaches. Considering the dependence of fish communities on the benthic habitat the relationship between different attributes of the fish assemblages and coral cover was also investigated. A consistent pattern of separation between assemblages of the northern and central region from the ones in the south was observed in nearshore reefs but was not evident for offshore reefs. The southern region supported higher densities, biomass, and species richness than the other two regions. The analysis showed that transect and reef scales contributed to the greatest variation in fish communities, suggesting higher levels of variability within small spatial scales. Several parameters of the fish community (total species, total density, total biomass, total functional entities, functional richness, functional redundancy) were positively correlated to coral cover, particularly in the northern region. Responses were not consistent across the Red Sea basin, suggesting that management plans should be regionally based. This study can be helpful to design management strategies as it provides a current baseline from both taxonomic and trait perspectives for Red Sea reefs that can be used to evaluate future changes due to natural and human-based disturbances.
    • Antennas on Floating Transceivers for Internet of Sea Applications

      Liao, Hanguang (2021-04) [Thesis]
      Advisor: Shamim, Atif
      Committee members: Salama, Khaled N.; Bagci, Hakan; Abualnaja, Yasser
      The extensive industrialization and human expansion has caused environmental protection wildlife conservation to become paramount concerns of the 21st century. The ecosystems of oceans and seas have particularly been affected due to activities like oil spills and increased fishing. This has led to a growing interest in monitoring of the oceans and marine animals to detect signs of distress in aquatic species. However, acquisition of data from oceans to land has been a challenging and expensive task. The concept of Internet of Sea provides a solution to this data transfer between the ocean nodes, like animal tags or deployed floating transceivers, and our land Internet, and can potentially eliminate the need of expensive monitoring ships or underwater cables. The Internet of Sea is system that comprises of sensor nodes in the form of detachable marine animal tags as the data acquisition platforms and distributed floating transceivers as the intermedium nodes which then transfer the data to the base-stations located on lands. The data acquired by animal tags are first to be stored in the tag, and once the tag comes to the sea surface, the data is transferred to the nearby floating transceivers. The floating transceivers have multi- hopping capability so the data can be passed to the land base-stations through a small number of transceivers. Due to the specific geometric shapes and size constraints of the tag and floating transceivers, as well as the harsh ocean environment, novel integrated antennas are required for this type of system. In this thesis, we propose several antenna designs suitable for Internet of Sea applications. The first design is a quasi-isotropic Antenna in Package (AiP), operating in the Bluetooth band, which has been designed for semi-real-time monitoring. Secondly, a large frequency-ratio dual- band microstrip antenna array, working at Extended Global System for Mobile communications (E-GSM900), Long Range (LoRa), and Bluetooth bands, has been designed for large-area wireless communication. Lastly, a circularly polarized microstrip antenna array has also been designed for Global Positioning System (GPS). Throughout the work, the measured results are consistent with the design strategies and simulation results.
    • Low-Noise High-Precision Readout Circuits for Capacitive MEMS Accelerometer

      Yang, Kuilian (2021-04) [Thesis]
      Advisor: Fariborzi, Hossein
      Committee members: Alouini, Mohamed-Slim; Eltawil, Ahmed; Sarathy, Mani
      Over the past two decades, Micro-Electro-Mechanical System (MEMS) based accelerometers, benefiting from relatively simple structure, low-power consumption, high sensitivity, and easy integration, have been widely used in many industrial and consumer electronics applications. For the high precision accelerometers, a significant technical challenge is to design a low-noise readout circuit to guarantee the required high resolution of the entire integrated system. There are three main approaches for improvement of the noise and offset of the readout circuit, namely auto-zero (AZ) and correlated double sampling (CDS) for the switched- capacitor (SC) circuit and chopper stabilization (CHS) for the continuous-time circuit. This thesis investigates the merits and drawbacks of all three techniques for reading the capacitance of a low noise MEMS accelerometer developed in our group. After that, we compare the different effects of the three technologies on noise, offset, output range, linearity, dynamic range, and gain. Next, we present the design of the most suitable structure for our sensor to achieve low noise, low offset, and high precision within the working frequency. In this thesis, the design and post-layout simulation of the circuit is proposed, and the fabrication is currently in progress. The readout circuit has reached the noise floor of the sub-μg, which meets the strict requirements of low noise MEMS capacitance-to-voltage converter. A high-performance accelerometer system is regarded as the core of a low-noise, high-resolution geophone. We show that together with the MEMS accelerometer sensor, the readout circuit provides competitive overall system noise and guarantees the required resolution.
    • Reconstruction of Cell and Tissue-specific Immune-protein Interactomes Using Single-cell RNA Sequencing Data

      Althobaiti, Atheer (2021-04) [Thesis]
      Advisor: Tegner, Jesper
      Committee members: Gao, Xin; Arold, Stefan T.
      Protein molecules and their interactions via protein-protein interactions (PPIs) are at the core of cellular functions. While such global PPI networks have been useful for analyzing gene function and effects of genetic variants, they do not resolve tissue and cell-typespecific interactions. Here we leverage recent advances in single-cell RNA sequencing (scRNA-seq) to reconstruct cell-type-specific PPI networks across different tissues to enable a context-sensitive analysis of immune cells’ gene-protein pathways. Targeting B cells, T cells, and macrophage cells as a proof-of-principle, we used scRNA-seq data across different tissues from the Tabula Muris mouse consortium. We mapped the protein-coding DEGs to a protein-protein interaction network database (STRING v.11). Topological and global similarity analysis of the networks revealed distinct properties between tissues highlighting tissue-specific behaviors for each cell type. For example, we found that degree and clustering coefficients distributions were tissue-specific. Different cell types and tissues displayed specific characteristics, and in particular, the splenic PPI networks were different compared to other analyzed tissues for all the immune cell types examined. For example, the pairwise comparison of the Jaccard index for node similarity and the mantel test correlation analysis showed that the spleen’ node and PPI networks are more different than any other tissues for each cell type examined. The physiological and anatomical properties that distinguish the spleen from other examined tissues might explain why the splenic PPI networks tend to be less similar compared to other tissues. The cell-type-specific network analyses using the different distance measures between the adjacency matrices on the hub nodes such as Euclidean, Manhattan, Jaccard, and Hamming distances showed a macrophage-specific behavior not observed in B cells and T cells, confirming their lineage differences. Finally, we explored the rewiring of selected hub nodes and transcription factors in the PPI networks along with their biological enrichments to validate our observations. The suggested biological validity of our results confirms the relevance of data-driven reconstruction of these context-sensitive networks using more advanced network inference algorithms. In conclusion, scRNA-seq enables the reconstruction of global unspecific PPI networks into cell and tissue-specific networks, thereby providing an increased resolution of the biological context.
    • Harnessing a novel compact CRISPR-Cas13b for SARS-CoV-2 diagnostics

      Wang, Qiaochu (2021-04) [Thesis]
      Advisor: Mahfouz, Magdy M.
      Committee members: Li, Mo; Jensen, Christian Froekjaer
      The outbreak of infectious diseases across the world results in huge disasters for public health. Rapid and effective diagnostic methods are crucial for disease identification and transmission control. Since first identified in late 2019, the pandemic of COVID-19 caused by the SARS-CoV-2 virus resulted in unprecedented catastrophe globally. To control the further spread of COVID-19, there is an urgent need for rapid, accurate, cost-effective, and efficient diagnostics. Recently, many CRISPR-based diagnostics have been developed by coupling isothermal amplification methods with Cas proteinmediated nucleic acid detection. Compared with conventional methods like RT-qPCR, CRISPR-based assays are more cost-effective and efficient without sacrificing sensitivity and specificity. Here, I developed a Cas13-based assay for SARS-CoV-2 detection with a novel compact Cas13b protein. In this assay, the Cas13 detection is combined with RT-LAMP, achieving the detection of viral RNA as low as 4 copies/μl. By utilizing a simple LED-based visualizer (P51™) instead of a plate reader, the detection result can be visualized directly without using sophisticated instruments. The compact Cas13b-mediated viral detection together with P51™-based visualization enable rapid, sensitive, and portable diagnostics for SARS-CoV-2, showing great potential in application to point-of-care testing.
    • Non-Newtonian Drop Impact on Textured Solid Surfaces: Bouncing and Filaments Formation

      Al Julaih, Ali (2021-04) [Thesis]
      Advisor: Thoroddsen, Sigurdur T
      Committee members: Lacoste, Deanna; Mishra, Himanshu
      This work uses high-speed video imaging to study the formation of filaments, during impact and rebounding of drops with polymer additives. We use PEO of different concentrations from 10 to 1000 ppm and study how drops rebound from various different surfaces: superhydrophilic, hydrophilic, hydrophobic, and superhydrophobic. Bouncing occurs for all surfaces at low impact velocities. We specifically focus on the phenomenon of the generation of polymer filaments, which are pulled out of the free surface of the drop during its rebounding from micro-pillared or rough substrates. We map the parameter regime, in terms of polymer concentration and impact Weber number, where the filaments are generated in the most repeatable manner. This occurs for regularly pillared surfaces and drops of 100 ppm PEO concentrations, where numerous separated filaments are observed. In contrast, for superhydrophobic coatings with random roughness the filaments tend to merge forming a branching structure. Impacts on inclined surfaces are used to deposit the filaments on top of the pillars for detailed study.
    • Functional Diversity of Red Sea Coral Reef Fish Assemblages in Northern Saudi Arabia

      Ford, Kiana (2021-04) [Thesis]
      Advisor: Berumen, Michael Lee
      Committee members: Brainard, Rusty; Coker, Darren
      As a part of Saudi Arabia’s Vision 2030, the Al Wajh Bank will soon undergo major coastal development to be transformed into a sustainable luxury tourist destination, with goals to safeguard the marine and coastal habitats in order to achieve a net conservation benefit of 30%. To realize these objectives, it is essential to establish baseline data on the marine communities to gauge the success of conservation goals. In this study, we evaluated and compared the taxonomic and functional diversity of reef fish assemblages between two areas in the Al Wajh Bank, sites inside the lagoon and those outside of it, in order to establish differences in fish communities across environmental gradients. Conditions within the lagoon, such as temperature and salinity, have been shown to differ from most other Red Sea areas and are thought to result in unique fish assemblages. Underwater assessments of fish communities and benthic composition were conducted throughout the Al Wajh Bank during cruises in 2016 and 2017. We found that of the 168 fish species recorded, 75 species were exclusive outside the lagoon, 22 were exclusive inside the lagoon, and 71 species were shared between inside and outside. Sites within the lagoon had significantly less species richness as well as lower abundances. While taxonomic composition differed between the two areas, functionally they were very similar. Two functional metrics (functional richness and functional dispersion) indicated different levels of functional diversity, while two other metrics (functional evenness and functional specialization) showed no differences in functional diversity. The outside had five groups comprising eleven species with functional redundancy; in contrast, the inside had two species which were functionally redundant. This study was able to establish that the inside and outside habitats are different and have dissimilar species compositions, yet the functional characterization of fish assemblages in conserved. These results advocate for the use of functional diversity metrics as a way to evaluate changes to community composition, and is an initial assessment towards tracking changes in the fish communities as coastal development progresses
    • Characterization of full-scale KAUST RO desalination plant and RO produced drinking water

      Albassam, Hassah (2021-04) [Thesis]
      Advisor: Vrouwenvelder, Johannes
      Committee members: Santamarina, Carlos; Ghaffour, Noreddine; Farhat, Nadia
      Water samples were taken at the KAUST RO plant, the WDRC pilot plant and three other full-scale desalination installations in Saudi Arabia. The water was characterized using selected microbiological parameters, being conventional (heterotopic place count (HPC), total coliforms, Escherichia coli) and more novel and sensitive methods (adenosine tri-phosphate (ATP, a measure for bacterial activity), as well as total and intact bacterial cell concentrations (TDC using flow cytometry) and supporting parameters (pH, conductivity, residual chlorine and temperature). Selective samples were used to quantify the bacterial growth potential (“food for the bacteria”), applying a flow cytometer based easily Assimilable Organic Carbon (AOC) assay. Hypothesized was that no or very low bacterial numbers would occur after RO filtration in the plants due to the high rejection properties of the RO membranes and the produced water exceptionally low mineral and nutrient content. Key findings are that the (i) RO permeate contains bacterial cell concentrations exceeding 1.0 × 103 cells/mL. The highest percentage of cells are intact and active, based on the ATP and total cell counts (ii) advanced microbial parameters ATP and TDC enabled to detect and quantify bacteria numbers and activity while the less sensitive conventional plate counts based techniques did not, (iii) flow cytometer-based growth potential measurements indicate the presence of 8 µg AOC/L in the RO permeate. A typical last step in drinking water production is chlorination, effectively inactivating all the bacterial cells. The origin of the bacterial cells and the biodegradable nutrients enabling the bacterial growth in the RO permeate is not clear. There is a clear need to assess the origin of the nutrients and bacteria found in the RO produced water. It is not expected to be passing the RO membrane.
    • Exploring Cholinergic Mechanisms in Hydra through Pharmacological Intervention and Behavioral Observation

      Tawfiq, Rund (2021-04) [Thesis]
      Advisor: Gojobori, Takashi
      Committee members: Hamdan, Samir; Jensen, Christian Froekjaer; Mineta, Katsuhiko
      Efforts to uncover a cholinergic neurotransmission system in Hydra have yielded conflicting results, where early studies suggested cholinergic agents affect the animal’s movement and later studies failed to reproduce these results. The identification of cholinergic mechanisms in the Cnidarian Nematostella vectensis and the presence of nicotinic Acetylcholine receptor (nAChR)-like sequences in the published Hydra genome have led us to revisit this issue. This study explores cholinergic mechanisms in Hydra through a comprehensive approach, including bioinformatics analysis, dose-response experiments, live-neuron imaging, and molecular approaches. Bioinformatics analysis identified 6 homologous nAChR sequences, one of which was confirmed by RT-qPCR. Dose-response experiments clearly showed that cholinergic agonists induced wholebody contractions and a nAChR antagonist sequestered this response. Live neuron imaging confirms that agonist treatment plays a role in neuron excitation that directly precedes behavior. Overall, my results confirm the existence of cholinergic mechanisms in Hydra. Further investigations can prove a direct or indirect mechanism of action on neurons.
    • Fish Movement in the Red Sea and Implications for Marine Protected Area Design

      Salinas-Akhmadeeva, Irene Antonina (2021-04) [Thesis]
      Advisor: Berumen, Michael L.
      Committee members: Green, Alison; Coker, Darren; Brainard, Rusty
      The Red Sea is valued for its biodiversity and the livelihoods it provides for many. It now faces overfishing, habitat degradation, and anthropogenic induced climate-change. Marine Protected Areas (MPAs) became a powerful management tool to protect vulnerable species and ecosystems, re-establish their balance, and enhance marine populations. For this, they need to be well designed and managed. There are 15 designated MPAs in the Red Sea but their level of enforcement is unclear. To design an MPA it is necessary to know if it will protect species of interest by considering their movement needs. In this thesis I aim at understanding fish movement in the Red Sea, specifically home range (HR) to inform MPA size designation. With not much empirical data available on HR for Red Sea fish, I used a Machine Learning (ML) classification model, trained with empirical literature HR measurements with Maximum Total Length (L Max), Aspect Ratio (AR) of the caudal fin, and Trophic Level as predictor variables. HR was classified into 5 categories: <.1 km, 0.1- 1.0 km, 2.0- 5.0 km, 5.0- 20 km, and >20 km. The model presents a 74.5% degree of accuracy. With it, I obtained the HR category for 337 Red Sea fish species. Having MPAs with a maximum linear dimension of at least 10km will meet the requirements of 90% of fish species evaluated in the model, which were small to medium size families (damselfishes, butterflyfishes, small wrasses, cardinalfishes, gobies and blennies). This percentage does not include larger species likely to move over much greater distances (10s, 100s or 1000s of km) (e.g., medium to large jacks, snappers,, groupers, sharks and rays). 60% of the Red Seas designated MPAs have the potential, if enforced as a No Take Area (NTA), to benefit more than 95% of reef fishes. However, larger MPAs will be required to protect more wide-ranging species. TRSP project in Al Wadj is proposing to close the entire SEZ to fishing. If they are successful in implementing and enforcing this fishing ban, TRSP will be the largest no take area in the Red Sea (~160 km long) that is likely to not only protect all of the species evaluated in the model, but also most wide-ranging species. Therefore, TRSP is not only likely to achieve and surpass its stated goal of increasing current fish biomass by 30%, but also to provide benefits to surrounding areas through the spillover of adults, juvenile and larvae to fished areas.