Recently, through reporter gene studies, the novel BTB/POZ protein, Kaiso, has been identified as a transcriptional repressor. The purpose of this study was to determine if Kaiso recruited the Histone Deacetylase Complex to mediate repression and if the previously identified Kaiso Binding Site (KBS; TCCTGCNA) is a physiological target regulated by Kaiso. The two objectives are complementary because an HDAC interaction identifies the mechanism of transcriptional regulation used by Kaiso and regulation of the KBS element identifies a novel, non-methylation dependent, physiological target under transcriptional regulation by Kaiso. Through coimmunoprecipitation and Western blot analyses, Kaiso does not interact with HDAC1, HDAC2 or mSIN3A. These results were surprising since all three of these proteins are common to a variety of repression complexes. mSIN3A is a common component of SIN3 mediated repression and HDAC1/HDAC2 are part of various repression complexes including SIN3, NuRD and CtBP. Although the remaining HDAC proteins were not assayed for an interaction, Kaiso transcriptional activity was demonstrated to be insensitive to the HDAC inhibiting drug, Trichostatin A (TSA). These results indicate either a non-HDAC mechanism of action or alternatively, transcriptional activation. Complementary to the observations of no Kaiso-HDAC interaction and TSA insensitivity was the findings that Kaiso activates transcription of the KBS cis-element in HCT116, HCA-7 and 293 cells, but not MOCK cells in reporter gene assays. Taken together, these results indicate that Kaiso is a dual functioning protein capable of both transcriptional activation and repression and that the mechanism of repression is not through the direct recruitment of HDAC proteins. / Thesis / Master of Science (MSc)

In this thesis, low-cost free chlorine sensors for monitoring drinking water have been developed. The starting material, pencil lead, was modified using a ammonium carbamate solution. The main emphasis for this technology is the low cost, scalable and environmental friendly process. The resultant materials were highly sensitive to free chlorine. The second discovery was an advanced understanding of the unsteady state mass transfer during the sensing process, using the customly expanded Cottrell equation. This method could qualitatively indicated the absence of free chlorine, for applications where the removal of free chlorine is the goal. This method allowed better interpretation of transient data and simplified setup. The third discovery was the use of pulsed amperometric detection to detect free chlorine at a much higher sensitivity, while reducing the complexity of the setup, further reducing the cost. This method was based on the previous findings plus understanding of the reaction kinetics. The resultant sensors detected free chlorine with a detection of 0.0414 ppm, while the regulations require the free chlorine to be above 0.2 ppm. The response time was less than three seconds. The range of detection was up to around 20 ppm. The cost of materials for one sensor was less than ten dollars. The maintenance was minimal due to the lack of consumables. The operation could be as a meter or as a device in a large instrument. The target use of the sensors include small and distant communities, bottling industries, fruit and vegetable washing industries. The free chlorine sensing techniques can be readily expanded to biology, environment, and big data applications, based on the knowledge gained through the study. / Thesis / Doctor of Philosophy (PhD) / Low-cost sensors were developed to monitor free chlorine in drinking water for end users, especially in small and distant communities. Free chlorine keeps lethal microorganism pathogens from re-growing after disinfection. Re-growth is more likely to happen in these communities due to poor infrastructure and less usage-driven flow. The contributions include: • A low-cost sensing material for free chlorine based on pencil lead • Determination of operating range of the sensor • Study of sensing mechanisms • Efficiency improvement and cost reduction • Research articles, conference presentations, patent applications, and industrial collaboration based on above research The resultant sensor is easy to use, robust in practical conditions and requires low maintenance, suitable for small and distant communities. Future work is the integration with sensing systems and the application of knowledge gained in this thesis for sensing applications in other fields.

A novel partial agonist of the exchange protein activated by cAMP isoform 1 (EPAC1), I942, was recently discovered and shown to reduce the guanine exchange factor activity of cAMP-bound EPAC1 to approximately 10% relative to cAMP activation. However, the inhibition mechanism of I942 remains unknown. Here, we utilize NMR spectroscopy to probe the inhibitory I942 - EPAC1 interactions at atomic resolution. The EPAC1 - I942 interface was mapped through intermolecular NOEs measured by 15N and 13C filtered NOESY-HSQC experiment. Intermolecular NOE mapping combined with other protein NMR methods, such as saturation transfer difference, transfer Nuclear Overhauser Effect spectroscopy and chemical shift mapping, we revealed that I942 interacts with the phosphate binding cassette (PBC) and base binding region (BBR) of the EPAC1 cyclic nucleotide binding (CNB) domain, similar to cAMP. The PBC controls the conformation of the hinge region, and subsequently, allosterically shifts the hinge region between its active/inactive states. Molecular dynamics simulation based on the NMR spectroscopy data revealed that EPAC1-CNB adopts an intermediate conformation between its inactive and active states, which explains the partial agonist nature of I942. / Thesis / Master of Science (MSc) / The exchange protein activated by cAMP (EPAC) is a receptor for the classical secondary messenger cAMP. EPAC is present in multiple human systems and plays a pivotal role in the development of a wide range of diseases. In this study, we aim to establish the inhibition mechanism of a novel small molecule EPAC inhibitor/partial agonist I942 using NMR spectroscopy with the goal of achieving a better understanding of EPAC inhibition and paving the way for new small molecule EPAC inhibitors that can potentially treat EPAC-related diseases such as heart failure and diabetes.

Object-oriented programming has had a significant impact on software development because it provides programmers with a clear structure of a large system. It encapsulates data and operations into objects, groups objects into classes and dynamically binds operations to program code. With the emergence of multi-core processors, application developers have to explore concurrent programming to take full advantage of multi-core technology. However, when it comes to concurrent programming, object-oriented programming remains elusive as a useful programming tool. Most object-oriented programming languages do have some extensions for concurrency, but concurrency is implemented independently of objects: for example, concurrency in Java is managed separately with the Thread object. We employ a programming model called Lime that combines action systems tightly with object-oriented programming and implements concurrency by extending classes with actions and guarded methods. This provides programmers with a unified and straightforward design view for a concurrent object-oriented program. In this work, using coroutines with guarded methods and actions is proposed as a means of implementing the concurrency extension for objects. Mapping objects to coroutines can result in stack overflow as the number of objects increases. A dynamically segmented stack mechanism, which does not introduce runtime overhead, is implemented to support large-scale concurrency. Since Lime allows guarded methods and actions to "get stuck," a new user-level cooperative scheduler, and a fast coroutine context switch mechanism are implemented to improve the performance. Compared with the traditional segmented stack mechanisms, the new dynamically segmented stack mechanism gets equal performance for more common scenarios. Besides, it outperforms the contemporary stack mechanisms for deep recursion scenarios. Above all, Lime does not only provide the programmers with a unified and straightforward object-oriented programming model for concurrency, but also accomplishes a better performance than concurrent programming languages such as Erlang and Go, in fine-grained, highly concurrent benchmarks. / Thesis / Doctor of Philosophy (PhD)

No / Increasing number of sophisticated services provided by the current wireless communication systems have caused a significant transition from E-commerce to M-commerce. Enterprises have provided considerable new opportunities to promote their businesses accessible from small mobile devices such as personal digital assistant (PDA) or mobiles phones. These facilities are envisioned as the most convenient way of using M-commerce. Using such services from mobile phones or PDAs equipped with GSM/GPRS involve effective mobility management mechanisms in cellular networks¿a popular architecture for wireless networks. Success of such systems will largely depend on the reliable connection for the roaming users. Consequently, Quality of Service (QoS) provision is one of the most challenging issues in the heterogeneous wireless network-based m-commerce systems. Such m-commerce systems enable users to roam between different wireless networks operators and geographical areas while providing interactive broadband services and seamless connectivity. This paper presents an analytical framework to model scarce channels in any cell for maximizing channel utilization and efficient handling of handover requests. Typical numerical experiments are presented to validate the analytical solution against simulation to study the effect of bursty traffic upon the performance of the cell in any cellular networks.

A series of niobium-containing nitride and carbides were prepared by a temperature-programmed synthesis method. The catalysts synthesized comprised a monometallic niobium oxynitride and a new bimetallic oxycarbide supported system, Nb-Mo-O-C/Al₂O₃ (Mo/Nb = 1.2; 1.6; 2.0). In the case of the niobium oxynitride, the progress of formation was analyzed by interrupting the synthesis at various stages. The effect of the heating rate on product properties was also investigated. The solid intermediates and the final niobium oxynitride were characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM), elemental analysis (CHNS), and gas adsorption techniques. The solid state transformation occurred directly from Nb₂O₅ to NbN_xO_y without any suboxide intermediates. The bimetallic supported oxycarbide materials were also characterized by X-ray diffraction (XRD), gas adsorption techniques, X-ray photoelectron spectroscopy (XPS), and near-edge X-ray absorption fine structure (NEXAFS). It was found that the electronic properties of the oxycarbide were modified by the interaction with the Al₂O₃ support, and that most of the oxygen atoms were associated with the niobium rather than the molybdenum atom. All of the niobium-containing catalysts were tested in a three-phase trickle-bed reactor for the simultaneous hydrodenitrogenation (HDN) of quinoline and hydrodesulfurization (HDS) of dibenzothiophene. The niobium oxynitride presented low HDS activity and moderate HDN activity, whereas the supported bimetallic oxycarbide was found to be highly active for both, HDN and HDS, demonstrating higher activities than the commercial sulfided Ni-Mo/Al₂O₃ when compared on the basis of active sites. In addition to these studies a comprehensive investigation of the HDN reaction mechanism was carried out over bulk unsupported Mo₂C, NbC, NbMo₂-O-C, and compared with the mechanism over a sulfide catalyst, MoS₂/SiO₂. For this purpose, a comparison of the HDN rate of a series of isomeric amines was performed, and the reaction occurred mainly through a β-elimination mechanism for all catalysts. Temperature programmed desorption of ethylamine was used to investigate the acid properties of the catalytic surfaces, and a good agreement between the specific rate of reaction and the number of Brønsted acid-sites was obtained. Infrared spectroscopy showed that the amines interacted with acidic centers to form adsorbed quartenary ammonium species. The deamination reaction over the carbide and sulfide catalysts probably occurs by a concerted push-pull mechanism involving basic sulfur species and Brønsted-acidic centers. In order to obtain more insight into the mechanism a study of the pyridine HDN network was carried out.All of the catalysts showed the same activity trend: the reactivity of n-pentylamine was high, while those of piperidine and pyridine were relatively low. The carbide catalysts showed higher selectivity towards HDN products than the sulfide catalyst at the same conversion levels. The higher selectivity was related to the higher ratio (r = k₂/k₁) between the rate constants of the two consecutive reactions, hydrogenation of pyridine (k₁) and ring opening of piperidine (k₂). The order of activity of the carbides and sulfide differed considerably depending on the substrate. However, for the pyridine reaction network the similarity in product distribution suggested that a similar surface composition, a carbosulfide, was attained during the reaction. / Ph. D.

We present and analyze two arm exoskeletons based on a pantograph linkage that allow for the support of 89~N (20~pounds) at the user's hand. Using a pantograph linkage allows for a constant force to be created at the hand in any orientation when a constant vertical force is supplied to the other side of the pantograph. We present several topologies and analyze them based on feasibility of manufacture and ability to provide a near vertical force to the pantograph linkage. Simulations are created using the best topologies and the resulting forces at the hand are reported. The mechanical design of an unpowered (passive) exoskeleton which uses a gas spring mechanism is presented. Additionally, simulations and block-CAD of a powered (active) exoskeleton which uses a motor for the supply of force are presented. The performance of the passive exoskeleton is qualitatively compared with simulations. / Master of Science / A wearable device or exoskeleton is presented which is designed to help a user support a weight of 20 pounds (89~N) at their hand. A pantograph linkage arm exoskeleton provides forces to the hand which are equal to the force provided to the linkage divided by the linkage's ratio. Providing a force to the linkage that is purely vertical will result in a purely vertical force at the hand. Layouts of the exoskeleton components which produce a near-vertical force for the linkage are explored. The more promising layouts are simulated and the forces are compared based on how vertical the forces are. The design of an unpowered exoskeleton is also presented, which uses a gas spring mechanism to provide force. Additionally, simulation results for the unpowered exoskeleton and the basic design and analysis of a powered exoskeleton are presented.

There is a recent surge in the development of spatio-temporal forecasting models in many applications, and traffic forecasting is one of the most important ones. Long-range traffic forecasting, however, remains a challenging task due to the intricate and extensive spatio-temporal correlations observed in traffic networks. Current works primarily rely on road networks with graph structures and learn representations using graph neural networks (GNNs), but this approach suffers from over-smoothing problem in deep architectures. To tackle this problem, recent methods introduced the combination of GNNs with residual connections or neural ordinary differential equations (NODEs). The existing graph ODE models are still limited in feature extraction due to (1) having bias towards global temporal patterns and ignoring local patterns which are crucial in case of unexpected events; (2) missing dynamic semantic edges in the model architecture; and (3) using simple aggregation layers that disregard the high-dimensional feature correlations. In this thesis, we propose a novel architecture called Graph-based Multi-ODE Neural Networks (GRAM-ODE) which is designed with multiple connective ODE-GNN modules to learn better representations by capturing different views of complex local and global dynamic spatio-temporal dependencies. We also add some techniques to further improve the communication between different ODE-GNN modules towards the forecasting task. Extensive experiments conducted on four real-world datasets demonstrate the outperformance of GRAM-ODE compared with state-of-the-art baselines as well as the contribution of different GRAM-ODE components to the performance. / Master of Science / There is a recent surge in the development of spatio-temporal forecasting models in many applications, and traffic forecasting is one of the most important ones. In traffic forecasting, current works limited in correctly capturing the key correlation of spatial and temporal patterns. In this thesis, we propose a novel architecture called Graph-based Multi-ODE Neural Networks (GRAM-ODE) to tackle the problem by using the separate ODE modules to deal with spatial and temporal patterns and further improve the communication between different modules. Extensive experiments conducted on four real-world datasets demonstrate the outperformance of GRAM-ODE compared with state-of-the-art baselines.

Grasp stability was studied and researched upon by various research groups, but mainly focused on robotic grippers by devising conditions for a stable grasp. Maintaining grasp stability is important so as to reduce the chances of the object slipping and dropping. But there was little focus on the grasp stability of robotic exoskeleton gloves and most of the research was focused on mechanical design. A robotic exoskeleton glove was developed as well as novel methods to improve the grasp stability. The exoskeleton glove developed is intended for patients who have suffered paralysis of the hand due to stroke or other factors. The robotic glove aids them in grasping objects as part of daily life activities. The glove is constructed with rigidly coupled 4-bar linkages attached to the finger tips. Each linkage mechanism has 1- Degree of Freedom (DOF) and is actuated by a linear Series Elastic Actuator (SEA). Two methods were developed to satisfy two of the conditions required for a stable grasp. These include deformation prevention of soft objects, and maintaining force and moment equilibrium of the objects being grasped. Simulations were performed to validate the performance of the algorithms. A battery of experiments was performed on the integrated prototype in order to validate the performance of the algorithms developed. / Master of Science / An exoskeleton glove is robotic device that can aid people who suffer from paralysis of their hands caused by a stroke or other factors with the primary goal of allowing them to regain the basic ability of grasping objects and thereby improving their quality of life. The exoskeleton glove developed in this research is focused on objects grasping assistance rather than for rehabilitation purposes. Since the exoskeleton glove lacks conscious senses like a human hand typically possesses, it may not be able to apply sufficient grasping force or may apply excessive force than required irrespective of the object being grasped. In order to ensure that the exoskeleton glove applies the proper amount of force, two novel methods were developed which help improve the overall grasping performance of the robotic glove. These methods use sensors that enable the glove to react to the force interaction changes that exists between the hand and the object being grasped through the exoskeleton glove. The first method detects any deformation that may occur while grasping a soft object and applies lesser force accordingly to prevent further damage to the object. The second method uses motion sensor to detect any movement by the user while grasping the object and applies corrective forces so that the object doesn’t slip from the hand. A prototype was designed and integrated and the two methods were tested on the prototype to validate them.

Determining the molecular mechanisms at the origin of protein function remains a challenge due to the complex non-covalent interactions that shape their structure. Since the non-covalent interactions arise from charge fluctuations, electric fields can be used as a tool to quantify the interactions between a target and its environment. The contribution of each component of the system is reflected in the direction and strength of the electric field exerted on the target, which can be calculated from molecular dynamics simulations. The interactions experienced by ligands in enzymatic active sites determine the catalytic activity of the enzyme. Ligands in synthetic enzymes lack interactions with the protein scaffold, which limit their efficiency. To substitute for the role of non-effective protein scaffold, we introduced a polar DNA fragment to the enzyme vicinity, inducing electrostatic interactions that will facilitate the reaction. We found that the introduction of a DNA fragment enhanced the original interactions between the residues in the active site and the ligand, without creating new interaction hot spots. Using electric fields, we calculated a reduction in activation energy of 2.0 kcal/mol when introducing the DNA fragment, indicating a promising avenue for catalytic improvement. Inspired by the success in using electric fields to understand enzyme catalysis in the context of electrostatic preorganization theory, we generalized these fundamental concepts to another type of proteins: voltage-gated ion channels. Our results indicate that electric fields also report on channel activity. We find an asymmetry in the number of active residues for channel function between the four domains and between the two gating motifs of the permeation pathway, with domain I being the major contributor in both cases. The importance of residues for channel activity is not a simple linear correlation of their distance with the functional motif, but a relationship dominated by non-covalent interactions. Finally, we investigate the effects of loop dynamics on enzyme product inhibition. We modify the chemical nature of the unstructured loops that obstruct the active site of DszB by glycosylating serine and threonine residues. We monitor the corresponding variations in loop dynamics and their effect on the interaction between the enzyme and the product. Overall, promising results were found using electric fields in the investigation of protein mechanisms that are mainly dominated by non-covalent interactions and provide insight into the role of the individual components in the system. / Doctor of Philosophy / Although weaker than covalent interactions, non-covalent interactions play a crucial role in molecular biological processes, especially in protein mechanisms. In order to modify the properties of proteins to our advantage, we need a metric with which we can map these interactions onto the protein structure. Different types of non-covalent interactions share one similarity: they originate from the change of electron distribution of interacting atoms, therefore can be captured by analyzing the protein- generated electric fields. Synthetic enzymes are designed to better adapt to varying environments and catalyze a broader reaction range. However, they are less effective than natural enzymes because the protein scaffold does not contribute to catalysis. Indeed, protein scaffolds in natural enzymes generate an electric field that lowers the reaction activation energy in the active site. Protein scaffolds in synthetic enzyme do not generate such electric fields. To address this issue, we modified the environment of synthetic enzyme KE15, introducing a polar DNA fragment to induce interactions in the active site. This modification strengthen the interactions between protein and ligand, leading to a decrease in the energy required for the reaction. While enzymes are famous for their generation of electric fields facilitating function, we demonstrated that this phenomenon also exist in voltage-gated ion channels Nav1.7. Residues were found to exert an electric field that can facilitate ion permeation. This is not simply because of their distance to the key regions, but a result of the non-covalent interactions regulating the mechanism, with different regions showing asymmetric importance in the process. Since the governing non-covalent interactions are relatively weak, proteins are flexible, especially protein loops. In enzyme DszB, this loop flexibility enables a conformational change when the ligand binds the active site. The change in loop conformation traps the product inside the active site, limiting enzymatic turnover. To prevent active site obstruction by these flexible loops, we attached glucose to a few loop residues to modify the hydrophobicity profile near the active site. The introduction of hydrophilic glucoses helps to pull the loops towards the solvent, rather than towards the active site, limiting product inhibition while preserving catalytic activity. Overall, our results show that electric field can be applied as a general method for protein studies, relating structure to function.