• Ultimate Cavity Dynamics of Hydrophobic Spheres Impacting on Free Water Surfaces

      Mansoor, Mohammad M. (2012-12)
      Cavity formation resulting from the water-entry of solid objects has been the subject of extensive research owing to its practical relevance in naval, military, industrial, sports and biological applications. The cavity formed by an impacting hydrophobic sphere normally seals at two places, one below (deep seal) and the other above the water surface (surface seal). For Froude numbers , the air flow into the resulting cavity is strong enough to suck the splash crown above the surface and disrupt the cavity dynamics before it deep seals. In this research work we eliminate surface seals by means of a novel practice of using cone splash-guards and examine the undisturbed transient cavity dynamics by impact of hydrophobic spheres for Froude numbers ranging . This enabled the measurement of extremely accurate pinch-off heights, pinch-off times, radial cavity collapse rates, and jet speeds in an extended range of Froude numbers compared to the previous work of Duclaux et al. (2007). Results in the extended regime were in remarkable agreement with the theoretical prediction of scaled pinch-off depth, and experimentally derived pinch-off time for . Furthermore, we investigated the influence of confinement on cavity formation by varying the cross-sectional area of the tank of liquid. In conjunction with surface seal elimination we observed the formation of multiple pinch-off points where a maximum of four deep seals were obtained in a sequential order for the Froude number range investigated. The presence of an elongated cavity beneath the first pinch-off point 5 resulted in evident "kinks" primarily related to the greatly diminished air pressure at the necking region caused by supersonic air flows (Gekle et al. 2010). Such flows passing through second pinch-offs were also found to choke the cavities beneath the first pinch- off depths causing radial expansion and hence disappearance of downward jets.
    • Ultra-High Speed Visualization of the Flashing Instability in Micron Size Nozzles under Vacuum Conditions

      Alghamdi, Tariq A. (2017-11)
      I visualized the flash-boiling atomization of liquid jets released into a low pressure environment at frame rates of up to five million frames per second. Such a high temporal resolution allowed us to observe for the first time the bubble expansion mechanism that atomizes the jet. To visualize the dynamics in detail, I focused closely to the outflow of the nozzle using a long distance microscope objective. I documented an abrupt transition from a laminar to a fully external flashing jet by systematically reducing the ambient pressure. I performed experiments with different volatile liquids and using nozzles with different inner diameters. The inner diameters of the nozzles varied from 30 to 480 µm. Perfluorohexane (PFnH) was our main working fluid, but also methanol, ethanol and 1-bromopropane were tested. Surprisingly, minimum intensity profiles revealed spray angles close to θs ~360°, meaning drops are ejected in all directions. Also, I measured speeds of bubble expansion up to 140 m/s. That is 45 times faster than the upper bound for inertial growth speed in complete vacuum from the Rayleigh-Plesset equation. I also calculated the trajectories of the ejected droplets as well as the drop speed distribution using particle tracking. I expect that our results bring new insight into the flash-boiling atomization mechanism.
    • Ultrafiltration Membrane Fouling and the Effect of Ion Exchange Resins

      Jamaly, Sanaa (2011-12)
      Membrane fouling is a challenging process for the ultrafiltration membrane during wastewater treatment. This research paper determines the organic character of foulants of different kinds of wastewater before and after adding some ion exchange resins. Two advanced organic characterization methods are compared in terms of concentration of dissolved organic carbons: The liquid chromatography with organic carbon (LC-OCD) and Shimadzu total organic carbon (TOC). In this study, two secondary wastewater effluents were treated using ultrafiltration membrane. To reduce fouling, pretreatment using some adsorbents were used in the study. Six ion exchange resins out of twenty were chosen to compare the effect of adsorbents on fouling membrane. Based on the percent of dissolved organic carbon’s removal, three adsorbents were determined to be the most efficient (DOWEX Marathon 11 anion exchange resin, DOWEX Optipore SD2 polymeric adsorbent, and DOWEX PSR2 anion exchange), and three other ones were determined to the least efficient (DOWEX Marathon A2 anion exchange resin, DOWEX SAR anion exchange resin, and DOWEX Optipore L493 polymeric adsorbent). Organic characterization for feed, permeate, and backwash samples were tested using LC-OCD and TOC to better understand the characteristics of foulants to prevent ultrafiltration membrane fouling. The results suggested that the polymeric ion exchange resin, DOWEX SD2, reduced fouling potential for both treated wastewaters. All the six ion exchange resins removed more humic fraction than other organic fractions in different percent, so this fraction is not the main for cause for UF membrane fouling. The fouling of colloids was tested before and after adding calcium. There is a severe fouling after adding Ca2+ to effluent colloids.
    • Ultrastructural Analysis of Human Breast Cancer Cells during Their Overtime Interaction with Cerium Oxide Nanoparticles

      AlAbbadi, Shatha H. (2016-12)
      Cerium oxide nanoparticles have been proposed as an anticancer agent, thanks to their ability of tuning the redox activity in accordance to different conditions, which lead to selective roles on healthy and cancer cells. Recent evidence suggested the ability of these nanoparticles to be toxic against cancer cells, while confer protection from oxidative stress, toward healthy cells. The main focus of this study was to determine the ultrastructural effects of cerium oxide nanoparticles over multiple incubation time of 1, 3, and 7 days on breast healthy and cancer cells. Cellular characterizations were carried out using electron microscopes, both transmission and scanning electron microscopes, while the viability assessments were performed by propidium iodide and trypan blue viability assays. The obtained results of the viability assays and electron microscopy suggested higher toxic effects on the cancer cell line viability by using a nanoceria dose of 300 μg/mL after 1 day of treatment. Such effects were shown to be preserved at 3 days, and in a longer time point of 7 days. On the contrary, the healthy cells underwent less effects on their viability at time point of 1 and 7 days. The 3 days treatment demonstrated a reduction on the number of cells that did not correlate with an increase of the dead cells, which suggested a possible initial decrease of the cell growth rate, which could be due to the high intracellular loading of nanoparticles. To conclude, the overall result of this experiment suggested that 300 μg/mL of CeO2 nanoparticles is the most suitable dose, within the range and the time point tested, which induces long-lasting cytotoxic effects in breast cancer cells, without harming the normal cells, as highlighted by the viability assays and ultrastructural characterization of electron microscopy analysis.
    • Underwater Animal Monitoring Magnetic Sensor System

      Kaidarova, Altynay (2017-10)
      Obtaining new insights into the behavior of free-living marine organisms is fundamental for conservation efforts and anticipating the impact of climate change on marine ecosystems. Despite the recent advances in biotelemetry, collecting physiological and behavioral parameters of underwater free-living animals remains technically challenging. In this thesis, we develop the first magnetic underwater animal monitoring system that utilizes Tunnel magnetoresistance (TMR) sensors, the most sensitive solid-state sensors today, coupled with flexible magnetic composites. The TMR sensors are composed of CoFeB free layers and MgO tunnel barriers, patterned using standard optical lithography and ion milling procedures. The short and long-term stability of the TMR sensors has been studied using statistical and Allan deviation analysis. Instrumentation noise has been reduced using optimized electrical interconnection schemes. We also develop flexible NdFeB-PDMS composite magnets optimized for applications in corrosive marine environments, and which can be attached to marine animals. The magnetic and mechanical properties are studied for different NdFeB powder concentrations and the performance of the magnetic composites for different exposure times to sea water is systematically investigated. Without protective layer, the composite magnets loose more than 50% of their magnetization after 51 days in seawater. The durability of the composite magnets can be considerably improved by using polymer coatings which are protecting the composite magnet, whereby Parylene C is found to be the most effective solution, providing simultaneously corrosion resistance, flexibility, and enhanced biocompatibility. A Parylene C film of 2μm thickness provides the sufficient protection of the magnetic composite in corrosive aqueous environments for more than 70 days. For the high level performance of the system, the theoretically optimal position of the composite magnets with respect to the sensing direction of the sensor has been estimated using finite element modeling software. The magnetic sensing system has been practically implemented for monitoring the belly size of a model fish and for monitoring the behavior of the largest living bivalve, giant clam (Tridacna maxima) in an aquarium. In both of these experiments, the sensing system showed a high performance, indicating its potential for novel marine monitoring applications.
    • An Underwater Superoleophobic Sepiolite Fibrous Membrane (SFM) for Oil­‐in­‐water Emulsion Separation

      Yao, Pinjiang (2014-12)
      Separating oil/water emulsions is significant for the ecosystem and the petroleum and processing industry. To this end, we prepared an underwater superoleophobic membrane inspired by unique wettability of the fish scales. This membrane was fabricated by a facile vacuum filtration process of sepiolite nanofibers and chitosan, and after the cross-linking via glutaraldehyde, a self-standing membrane was obtained. The as-prepared membrane exhibited excellent capability of separating both the surfactant-free and surfactant-stabilized oil-in-water emulsions with high efficiency. This sepiolite fibrous membrane offers a convenient, reliable and efficient way for the large-scale de-emulsification process.
    • Underwater wireless optical communication system under reciprocal turbulence

      Guo, Yujian (2018-11)
      Underwater communication systems are in high demanded for subaquatic environment activities as the sea is an enormous and mostly unexplored place. The ten-meter long and few giga-bit per second range optical communication technique is feasible and has bright future compared to the mature but low data rate (few kilobits per second) acoustic technology and short distance (several meters) radio-frequency signaling schemes. The underwater wireless optical communication (UWOC) technique takes advantage of wide bandwidth, low attenuation effect in the visible range for multiple applications such as seafloor and offshore exploration, oil pipe control and maintenance, and pipeline leak detection. Nowadays, visible light-emitting diode (LED)-based and laser diode (LD)-based UWOC system are attractive and much related research is being conducted in the field. However, the major challenges of developing UWOC systems are the attenuation, scattering and turbulence effects of the underwater environment. The temperature gradient, salinity gradient, and bubbles make underwater optical channel predictable challenging and degrade the optical beam propagating distance and quality. Most studies focus on the statistical distribution of intensity fluctuations in underwater wireless optical channels with random temperature and salinity variations as well as the presence of air bubbles. In this thesis, we experimentally investigate the reciprocity nature of underwater turbulence caused by the turbidity, air bubbles, temperature variations, and salinity. Bit error rate measurement and statistical data analysis reveal the high reciprocal nature of turbulence that can be induced by the presence of bubbles, temperature, and salinity. The mitigation strategies for the different turbulence scenarios are discussed.
    • Unveiling the role of PAK2 in CD44 mediated inhibition of proliferation, differentiation and apoptosis in AML cells

      Aldehaiman, Mansour M. (2018-04)
      Acute myeloid leukemia (AML) is a heterogeneous disease characterized by the accumulation of immature nonfunctional highly proliferative hematopoietic cells in the blood, due to a blockage in myeloid differentiation at various stages. Since the success of the differentiation agent, All-trans retinoic acid (ATRA), in the treatment of acute promyelocytic leukemia (APL), much effort has gone into trying to find agents that are able to differentiate AML cells and specifically the leukemic stem cell (LSC). CD44 is a cell surface receptor that is over-expressed on AML cells. When bound to anti-CD44 monoclonal antibodies (mAbs), this differentiation block is relieved in AML cells and their proliferation is reduced. The molecular mechanisms that AML cells undergo to achieve this reversal of their apparent phenotype is not fully understood. To this end, we designed a study using quantitative phosphoproteomics approaches aimed at identifying differences in phosphorylation found on proteins involved in signaling pathways post-treatment with CD44-mAbs. The Rho family of GTPases emerged as one of the most transformed pathways following the treatment with CD44-mAbs. The P21 activated kinase 2(PAK2), a target of the Rho family of GTPases, was found to be differentially phosphorylated in AML cells post-treatment with CD44-mAbs. This protein has been found to possess a role similar to that of a switch that determines whether the cell survives or undergoes apoptosis. Beyond confirming these results by various biochemical approaches, our study aimed to determine the effect of knock down of PAK2 on AML cell proliferation and differentiation. In addition, over-expression of PAK2 mutants using plasmid cloning was also explored to fully understand how levels of PAK2 as well as the alteration of specific phospohorylation sites could alter AML cell responses to CD44-mAbs. Results from this study will be important in determining whether PAK2 could be used as a potential therapeutic target for AML once its levels are altered.
    • User Oriented Trajectory Search for Trip Recommendation

      Ding, Ruogu (2012-07-08)
      Trajectory sharing and searching have received significant attention in recent years. In this thesis, we propose and investigate the methods to find and recommend the best trajectory to the traveler, and mainly focus on a novel technique named User Oriented Trajectory Search (UOTS) query processing. In contrast to conventional trajectory search by locations (spatial domain only), we consider both spatial and textual domains in the new UOTS query. Given a trajectory data set, the query input contains a set of intended places given by the traveler and a set of textual attributes describing the traveler’s preference. If a trajectory is connecting/close to the specified query locations, and the textual attributes of the trajectory are similar to the traveler’s preference, it will be recommended to the traveler. This type of queries can enable many popular applications such as trip planning and recommendation. There are two challenges in UOTS query processing, (i) how to constrain the searching range in two domains and (ii) how to schedule multiple query sources effectively. To overcome the challenges and answer the UOTS query efficiently, a novel collaborative searching approach is developed. Conceptually, the UOTS query processing is conducted in the spatial and textual domains alternately. A pair of upper and lower bounds are devised to constrain the searching range in two domains. In the meantime, a heuristic searching strategy based on priority ranking is adopted for scheduling the multiple query sources, which can further reduce the searching range and enhance the query efficiency notably. Furthermore, the devised collaborative searching approach can be extended to situations where the query locations are ordered. Extensive experiments are conducted on both real and synthetic trajectory data in road networks. Our approach is verified to be effective in reducing both CPU time and disk I/O time.
    • Using Proteomics to 1) Identify the Bone Marrow Homing Receptors Expressed on Human Hematopoietic Stem Cells and 2) Elucidate Critical Signaling Pathways Responsible for the Blockage of Hematopoietic Differentiation in Leukemia

      Chin, Chee J. (2011-05-22)
      Successful hematopoiesis requires the trafficking of hematopoietic stem/progenitor cells (HSPCs) to their bone marrow (BM) niche, where they can differentiate to produce all blood lineages. Leukemia arises when there is a blockage of differentiation and uncontrolled proliferation in the hematopoietic cells during their development. To refine therapies for leukemia, this study sought to improve the homing of healthy donor HSPCs for better transplantation and to find new candidates for differentiating and blocking proliferation in leukemic cells. Characterizing the molecular effectors mediating cell migration forms the basis for improving clinical transplantation of HSPCs. E-selectin/ligand interactions play a critical role in the homing of HSPCs to the BM, however, the identity of E-selectin ligands remains elusive. We aimed to use mass spectrometry (MS) to fully analyze the E-selectin ligands expressed on HSPCs. Immunoprecipitation studies coupled with MS confirmed the expression of three known E-selectin ligands, the hematopoietic cell E-/L-selectin ligand (HCELL), P-selectin glycoprotein ligand-1 (PSGL-1) and CD43, and revealed the presence of many interesting candidates on HSPCs-like cell line and on primary human BM CD34+ cells. The MS dataset represents a rich resource for further characterization of E-selectin ligands, which will lead to improvement of HSPCs transplantation. 4 Understanding the critical pathways underlying the initiation and maintenance of leukemia plays a key role in treating acute myeloid leukemia (AML). Ligation of the glycoprotein, CD44, using monoclonal antibodies or its natural ligand, hyaluronic acid, drives the differentiation of immature leukemic cells towards mature terminally differentiated cells, inhibits their proliferation and in some case induces their apoptosis. The aim of this study is to characterize the phosphoproteome of AML cells in response to CD44-induced differentiation. This will afford novel insights into the signaling events critical for proliferation and differentiation in AML cells. Stable isotope labeling with amino acids in cell culture is used to quantify the changes in the global phosphorylation profile upon CD44 activation. Preliminary results showed that the heavy isotope was fully incorporated and that anti-CD44 induction of myeloid differentiation was not perturbed in our culture conditions. We anticipate that this study will bring forth new candidates for a targeted therapy of AML.
    • Using Proteomics To Elucidate Critical Signaling Pathways

      Jalal Ahmed, Heba M. (2012-11)
      Despite important advances in the therapy of acute myeloid leukemia (AML) the majority of patients will die from their disease (Appelbaum, Rowe, Radich, & Dick, 2001). Characterization of the aberrant molecular pathways responsible for this malignancy provides a platform to discover alternative treatments to help alter the fate of patients. AML is characterized by a blockage in the differentiation of myeloid cells resulting in the accumulation of highly proliferating immature hematopoietic cells. Since treatments such as chemotherapy rarely destroy the leukemic cells entirely, differentiation induction therapy has become a very attractive treatment option. Interestingly, previous experiments have shown that ligation of CD44, a cell surface glycoprotein strongly expressed on all AML cells, with anti-CD44 monoclonal antibodies (mAbs) could reverse this block in differentiation of leukemic blasts regardless of the AML subtype. To expand the understanding of the cellular regulation and circuitry involved, we aim to apply quantitative phosphoproteomics to monitor dynamic changes in phosphorylation state in response to anti-CD44 treatment. Protein phosphorylation and dephosphorylation is a highly controlled biochemical process that responds to various intracellular and extracellular stimuli. As phosphorylation is a dynamic process, quantification of these phosphorylation events would be vastly insightful. The main objective of this project is to determine the differentiation-dependent phosphoproteome of AML cells upon treatment of cells with the anti-CD44 mAb.In these experiments, optimization of protein extraction, phosphopeptide enrichment and data processing and analysis has been achieved. The primary results show successful phosphoproteome extraction complemented with efficient phosphopeptide enrichment and informative data processing. Further quantification with stable isotope labeling techniques is anticipated to provide candidates for targeted therapy.
    • Using the Direct Sampling Multiple-Point Geostatistical Method for Filling Gaps in Landsat 7 ETM+ SLC-off Imagery

      Yin, Gaohong (2016-05)
      Since the failure of the Scan Line Corrector (SLC) instrument on Landsat 7, observable gaps occur in the acquired Landsat 7 imagery, impacting the spatial continuity of observed imagery. Due to the highly geometric and radiometric accuracy provided by Landsat 7, a number of approaches have been proposed to fill the gaps. However, all proposed approaches have evident constraints for universal application. The main issues in gap-filling are an inability to describe the continuity features such as meandering streams or roads, or maintaining the shape of small objects when filling gaps in heterogeneous areas. The aim of the study is to validate the feasibility of using the Direct Sampling multiple-point geostatistical method, which has been shown to reconstruct complicated geological structures satisfactorily, to fill Landsat 7 gaps. The Direct Sampling method uses a conditional stochastic resampling of known locations within a target image to fill gaps and can generate multiple reconstructions for one simulation case. The Direct Sampling method was examined across a range of land cover types including deserts, sparse rural areas, dense farmlands, urban areas, braided rivers and coastal areas to demonstrate its capacity to recover gaps accurately for various land cover types. The prediction accuracy of the Direct Sampling method was also compared with other gap-filling approaches, which have been previously demonstrated to offer satisfactory results, under both homogeneous area and heterogeneous area situations. Studies have shown that the Direct Sampling method provides sufficiently accurate prediction results for a variety of land cover types from homogeneous areas to heterogeneous land cover types. Likewise, it exhibits superior performances when used to fill gaps in heterogeneous land cover types without input image or with an input image that is temporally far from the target image in comparison with other gap-filling approaches.
    • VarB Plus: An Integrated Tool for Visualization of Genome Variation Datasets

      Hidayah, Lailatul (2012-07)
      Research on genomic sequences has been improving significantly as more advanced technology for sequencing has been developed. This opens enormous opportunities for sequence analysis. Various analytical tools have been built for purposes such as sequence assembly, read alignments, genome browsing, comparative genomics, and visualization. From the visualization perspective, there is an increasing trend towards use of large-scale computation. However, more than power is required to produce an informative image. This is a challenge that we address by providing several ways of representing biological data in order to advance the inference endeavors of biologists. This thesis focuses on visualization of variations found in genomic sequences. We develop several visualization functions and embed them in an existing variation visualization tool as extensions. The tool we improved is named VarB, hence the nomenclature for our enhancement is VarB Plus. To the best of our knowledge, besides VarB, there is no tool that provides the capability of dynamic visualization of genome variation datasets as well as statistical analysis. Dynamic visualization allows users to toggle different parameters on and off and see the results on the fly. The statistical analysis includes Fixation Index, Relative Variant Density, and Tajima’s D. Hence we focused our efforts on this tool. The scope of our work includes plots of per-base genome coverage, Principal Coordinate Analysis (PCoA), integration with a read alignment viewer named LookSeq, and visualization of geo-biological data. In addition to description of embedded functionalities, significance, and limitations, future improvements are discussed. The result is four extensions embedded successfully in the original tool, which is built on the Qt framework in C++. Hence it is portable to numerous platforms. Our extensions have shown acceptable execution time in a beta testing with various high-volume published datasets, as well as positive feedback from several researchers in the field in terms of their usability and significance.
    • Variants Prioritization in Cancer: Understanding and Predicting Cancer Driver Genes and Mutations

      Althubaiti, Sara (2018-11-08)
      Millions of somatic mutations in human cancers have been identified by sequenc- ing. Identifying and distinguishing cancer driver genes amongst the millions of candi- date mutations remains a major challenge. Accurate identification of driver genes and mutations is essential for the progress of cancer research and personalizing treatment based on accurate stratification of patients. Because of inter-tumor genetic hetero- geneity, numerous driver mutations within a gene can be found at low frequencies. This makes them difficult to differentiate from other non-driver mutations. Inspired by these challenges, we devised a novel way of identifying cancer driver genes. Our approach utilizes multiple complementary types of information, specifically cellular phenotypes, cellular locations, function, and whole body physiological phenotypes as features. We demonstrate that our method can accurately identify known cancer driver genes and distinguish between their role in different types of cancer. In ad- dition to identifying known driver genes, we identify several novel candidate driver genes. We provide an external evaluation of the predicted genes using a dataset of 26 nasopharyngeal cancer samples that underwent whole exome sequencing. We find that the predicted driver genes have a significantly higher rate of mutation than non-driver genes, both in publicly available data and in the nasopharyngeal cancer samples we use for validation. Additionally, we characterize sub-networks of genes that are jointly involved in specific tumors.
    • Variation of the Symbiodinium Community Composition in Scleractinian Corals along a Cross-shelf and Depth Gradient

      Mejia Restrepo, Alejandro (2017-12)
      Corals form a symbiotic relationship with photosynthetic zooxanthellae from the genus Symbiodinium; the breakdown of this symbiosis results in the phenomenon known as coral bleaching. This relationship is especially vulnerable to high temperature stress, although corals may survive if they have resistant types of symbionts, or switch their community composition towards them. To assess the variation of the symbiont community in different environmental conditions, I recorded the temperature and collected samples from six scleractinian coral species and one calcifying hydrozoan, in two inshore, two mid-shelf, and two offshore reefs at 1, 15, and 30m depth, analyzing Symbiodinium diversity using Next Generation Sequencing with the SymPortal profile typing approach. The temperature was very similar for all points in winter, when coral samples were collected, but variation between points increased until a maximum at summer, with the shallower parts of the inshore reefs showing higher temperatures and the points at 30m depth showing the lowest. The Symbiodinium composition was more similar between samples of the same host species than among samples of the same reefs or depths. Coral species from the Pocilloporidae family and Millepora dichotoma showed specific association with different profile types, specifically, intragenomic variants of Symbiodinium type A1, which appears to be dominant in the Red Sea although it has not been reported for these species in other regions. The other species showed specific associations with types previously reported in other regions, mostly from clade C and D, although also having different types and intragenomic variants. For most cases, certain profile types, which can reflect different species or populations, appeared to be dominant in particular environmental conditions, following a distribution related with depth, reef type, or both. In conclusion, this study showed that the Symbiodinium composition depends more on the host species than on the environmental conditions, and within each species the adaptation to environmental gradients can rely on tolerant symbiont species or populations characteristic of the Red Sea, or association with different types and clades that are common also in other regions.
    • Variations in the Produce-Associated Microbiota and the Occurrence Frequency of Extended-Spectrum Beta-Lactamase Gram-Negative Bacteria Result in Different Level of Ingestion Risks

      Bokhari, Osama (2016-04)
      A monitoring effort that spanned across one and a half years was conducted to examine three types of produce-associated microbiota. Produce type was determined to be the predominant factor affecting the microbial communities. Other significant factors that resulted in differences in the microbial populations were the origin and sampling date. Specifically, produce-associated microbiota among lettuce and tomatoes clustered based on the sampling period. Through molecular and cultivation-based approaches, sporadic presence of extended spectrum beta-lactamase (ESBL)-positive Klebsiella pneumoniae and Acinetobacter baumannii was detected on lettuce and cucumbers during certain periods of sampling. Quantitative microbial risk assessment denoted varying levels of ingestion risks associated with different types of produce. In particular, the risks arising from ESBL-positive K. pneumoniae in the lettuce were higher than the acceptable annual risk of 10-4. Commonly used approaches to clean and wash the produce were insufficient in removing majority of the produce-associated microbiota. More invasive cleaning approaches or thorough cooking of the produce would be required to mitigate the associated risks. Most of the current reports of ESBL-positive bacterial isolates were identified in nosocomial environment. However, the carriage of such drug-resistant bacteria in food that is consumed daily
    • A Vehicular Guidance Wireless Sensor/Actuator Network

      Boudellioua, Imene (2012-07)
      Sensor networks have been heralded as one of 21 most important technologies for the 21st century by Business Week [1]. Wireless sensor/actuator networks (WSANs)are emerging as a new generation of sensor networks with the potential for enhancing the versatility and effectiveness of sensor networks. However, the unreliability of wireless communications and the real-time requirements of control applications raise great challenges for WSAN design. In this thesis, we design a WSAN for a vehicular guidance system targeting environmental disaster management applications. In this system, actuators provide mobility to all sensor nodes in the observed area whenever needed. Moreover, nodes form clusters and their movement is controlled by a master node that is selected dynamically. We also discuss the factors affecting our network performance in real-life and propose a framework which accounts for real-time requirement and reliable actuation. We finally perform some experimental studies on our system to measure its performance in an indoor environment.
    • Virtual Reality Interaction Using Mobile Devices

      Aseeri, Sahar A. (2013-07)
      With the use of an immersive display system such as CAVE system, the user is able to realize a 3D immersive virtual environment realistically. However, interacting with virtual worlds in CAVE systems using traditional input devices to perform easy operations such as manipulation, object selection, and navigation is often difficult. This difficulty could diminish the immersion and sense of presence when it comes to 3D virtual environment tasks. Our research aims to implement and evaluate alternative approaches of interaction with immersive virtual environments on mobile devices for manipulation and object selection tasks. As many researchers have noted, using a mobile device as an interaction device has a number of advantages, including built-in display, built-in control, and touch screen facility. These advantages facilitate simple tasks within immersive virtual environments. This research proposes new methods using mobile devices like Smart-phones to perform di↵erent kinds of interactions both as an input device, (e.g. performing selection and manipulation of objects) and as an output device (e.g. utilizing the screen as an extra view for a virtual camera or information display). Moreover, we developed a prototype system to demonstrate and informally evaluate these methods. The research conclusion suggests using mobile devices as a 3D-controller. This will be a more intuitive approach to interact within the virtual environment.
    • Visualization and Simulation of Variants in Personal Genomes With an Application to Premarital Testing (VSIM)

      Althagafi, Azza Th. (2018-11-28)
      Interpretation and simulation of the large-scale genomics data are very challenging, and currently, many web tools have been developed to analyze genomic variation which supports automated visualization of a variety of high throughput genomics data. We have developed VSIM an automated and easy to use web application for interpretation and visualization of a variety of genomics data, it identifies the candidate diseases variants by referencing to four databases Clinvar, GWAS, DIDA, and PharmGKB, and predicted the pathogenic variants. Moreover, it investigates the attitude towards premarital genetic screening by simulating a population of children and analyze the diseases they might be carrying, based on the genetic factors of their parents taking into consideration the recombination hotspots. VSIM supports output formats based on Ideograms that are easy to interpret and understand, which makes it a biologist-friendly powerful tool for data visualization, and interpretation of personal genomic data. Our results show that VSIM can efficiently identify the causative variants by referencing well-known databases for variants in whole genomes associated with different kind of diseases. Moreover, it can be used for premarital genetic screening by simulating a population of offspring and analyze the disorders they might be carrying. The output format provides a better understanding of such large genomics data. VSIM thus helps biologists and marriage counsellor to visualize a variety of genomic variants associated with diseases seamlessly.
    • Volume Visualization and Compositing on Large-Scale Displays Using Handheld Touchscreen Interaction

      Gastelum, Cristhopper Jacobo Armenta (2011-07-27)
      Advances in the physical sciences have progressively delivered ever increasing, already extremely large data sets to be analyzed. High performance volume rendering has become critical to the scientists for a better understanding of the massive amounts of data to be visualized. Cluster based rendering systems have become the base line to achieve the power and flexibility required to perform such task. Furthermore, display arrays have become the most suitable solution to display these data sets at their natural size and resolution which can be critical for human perception and evaluation. The work in this thesis aims at improving the scalability and usability of volume rendering systems that target visualization on display arrays. The first part deals with improving the performance by introducing the implementations of two parallel compositing algorithms for volume rendering: direct send and binary swap. The High quality Volume Rendering (HVR) framework has been extended to accommodate parallel compositing where previously only serial compositing was possible. The preliminary results show improvements in the compositing times for direct send even for a small number of processors. Unfortunately, the results of binary swap exhibit a negative behavior. This is due to the naive use of the graphics hardware blending mechanism. The expensive transfers account for the lengthy compositing times. The second part targets the development of scalable and intuitive interaction mechanisms. It introduces the development of a new client application for multitouch tablet devices, like the Apple iPad. The main goal is to provide the HVR framework, that has been extended to use tiled displays, a more intuitive and portable interaction mechanism that can get advantage of the new environment. The previous client is a PC application for the typical desktop settings that use a mouse and keyboard as sources of interaction. The current implementation of the client lets the user steer and change the opacity transfer function of the visualization via simple multitouch gestures. Nonetheless, the user can freely move around, engage into discussion with other users and easily pass the tablet around for others to use. Before, this was not possible with the same ease of use. Ultimately, the collaborative possibilities are many and extremely interesting to explore.