A controller display technique for a terminal air traffic control system.

"Contract no. FAA/BRD-15, Task order no. 14. Prepared for Federal Aviation Agency, Bureau of Research and Development, Systems Analysis Division."

Entanglement induced by spontaneous emission in spatially extended two-atom systems

The role of the collective antisymmetric state in entanglement creation by spontaneous emission in a system of two non-overlapping two-level atoms has been investigated. Populations of the collective atomic states and the Wootters entanglement measure (concurrence) for two sets of initial atomic conditions are calculated and illustrated graphically. Calculations include the dipole-dipole interaction and a spatial separation between the atoms that the antisymmetric state of the system is included throughout even for small interatomic separations. It is shown that spontaneous emission can lead to a transient entanglement between the atoms even if the atoms were prepared initially in an unentangled state. It is found that the ability of spontaneous emission to create transient entanglement relies on the absence of population in the collective symmetric state of the system. For the initial state of only one atom excited, entanglement builds up rapidly in time and reaches a maximum for parameter values corresponding roughly to zero population in the symmetric state. On the other hand, for the initial condition of both atoms excited, the atoms remain unentangled until the symmetric state is depopulated. A simple physical interpretation of these results is given in terms of the diagonal states of the density matrix of the system. We also study entanglement creation in a system of two non-identical atoms of different transition frequencies. It is found that the entanglement between the atoms can be enhanced compared to that for identical atoms, and can decay with two different time scales resulting from the coherent transfer of the population from the symmetric to the antisymmetric state. In addition, it was found that a decaying initial entanglement between the atoms can display a revival behaviour.

MMTV-trBrca 1 mice display strain-dependent abnormalities in vaginal development

The breast cancer susceptibility gene Brca1 encodes a large multi-functional protein which is implicated as a caretaker of the genome, through its role in regulation of DNA damage response pathways, including apoptosis. Here we show that in mice expressing a dominant-negative Brca1 transgene on a BALB/c background, vaginal entrance remodeling is inhibited, and that the incidence of this phenotype is increased on a p53 +/- genotype. Given that this developmental process is mediated primarily by apoptosis, we hypothesized that disruption of BRCA1 may confer a resistance to apoptosis in normal epithelial cells. Consistent with this, we show that expression of this transgene in vitro leads to resistance to ionizing radiation induced cell killing in mammary epithelial cells. This is the first time that BRCA1 has been implicated in an apoptosis-mediated normal developmental process.

A cationic vaccine adjuvant based on a saturated quaternary ammonium lipid have different in vivo distribution kinetics and display a distinct CD4 T cell-inducing capacity compared to its unsaturated analog

Adjuvants are often composed of different constituents that can be divided into two groups based on their primary activity: the delivery system which carries and presents the vaccine antigen to antigen-presenting cells, and the immunostimulator that activates and modulates the ensuing immune response. Herein, we have investigated the importance of the delivery system and in particular its physical characteristics by comparing the delivery properties of two lipids which differ only in the degree of saturation of the acyl chains, rendering the liposomes either rigid (DDA, dimethyldioctadecylammonium) or highly fluid (DODA, dimethyldioleoylammonium) at physiological temperature. We show that these delivery systems are remarkably different in their ability to prime a Th1-directed immune response with the rigid DDA-based liposomes inducing a response more than 100 times higher compared to that obtained with the fluid DODA-based liposomes. Upon injection with a vaccine antigen, DDA-based liposomes form a vaccine depot that results in a continuous attraction of antigen-presenting cells that engulf a high amount of adjuvant and are subsequently efficiently activated as measured by an elevated expression of the co-stimulatory molecules CD40 and CD86. In contrast, the fluid DODA-based liposomes are more rapidly removed from the site of injection resulting in a lower up-regulation of co-stimulatory CD40 and CD86 molecules on adjuvant-positive antigen-presenting cells. Additionally, the vaccine antigen is readily dissociated from the DODA-based liposomes leading to a population of antigen-presenting cells that are antigen-positive but adjuvant-negative and consequently are not activated. These studies demonstrate the importance of studying in vivo characteristics of the vaccine components and furthermore show that physicochemical properties of the delivery system have a major impact on the vaccine-induced immune response. © 2012 Elsevier B.V. All rights reserved.

The human factors of automatic speech recognition in control room systems

This thesis addresses the viability of automatic speech recognition for control room systems; with careful system design, automatic speech recognition (ASR) devices can be useful means for human computer interaction in specific types of task. These tasks can be defined as complex verbal activities, such as command and control, and can be paired with spatial tasks, such as monitoring, without detriment. It is suggested that ASR use be confined to routine plant operation, as opposed the critical incidents, due to possible problems of stress on the operators' speech.  It is proposed that using ASR will require operators to adapt a commonly used skill to cater for a novel use of speech. Before using the ASR device, new operators will require some form of training. It is shown that a demonstration by an experienced user of the device can lead to superior performance than instructions. Thus, a relatively cheap and very efficient form of operator training can be supplied by demonstration by experienced ASR operators. From a series of studies into speech based interaction with computers, it is concluded that the interaction be designed to capitalise upon the tendency of operators to use short, succinct, task specific styles of speech. From studies comparing different types of feedback, it is concluded that operators be given screen based feedback, rather than auditory feedback, for control room operation. Feedback will take two forms: the use of the ASR device will require recognition feedback, which will be best supplied using text; the performance of a process control task will require task feedback integrated into the mimic display. This latter feedback can be either textual or symbolic, but it is suggested that symbolic feedback will be more beneficial. Related to both interaction style and feedback is the issue of handling recognition errors. These should be corrected by simple command repetition practices, rather than use error handling dialogues. This method of error correction is held to be non intrusive to primary command and control operations. This thesis also addresses some of the problems of user error in ASR use, and provides a number of recommendations for its reduction.

Benefits of electronic vision enhancement systems (EVES) for the visually impaired

PURPOSE: To examine whether objective performance of near tasks is improved with various electronic vision enhancement systems (EVES) compared with the subject's own optical magnifier. DESIGN: Experimental study, randomized, within-patient design. METHODS: This was a prospective study, conducted in a hospital ophthalmology low-vision clinic. The patient population comprised 70 sequential visually impaired subjects. The magnifying devices examined were: patient's optimum optical magnifier; magnification and field-of-view matched mouse EVES with monitor or head-mounted display (HMD) viewing; and stand EVES with monitor viewing. The tasks performed were: reading speed and acuity; time taken to track from one column of print to the next; follow a route map, and locate a specific feature; and identification of specific information from a medicine label. RESULTS: Mouse EVES with HMD viewing caused lower reading speeds than stand EVES with monitor viewing (F = 38.7, P < .001). Reading with the optical magnifier was slower than with the mouse or stand EVES with monitor viewing at smaller print sizes (P < .05). The column location task was faster with the optical magnifier than with any of the EVES (F = 10.3, P < .001). The map tracking and medicine label identification task was slower with the mouse EVES with HMD viewing than with the other magnifiers (P < .01). Previous EVES experience had no effect on task performance (P > .05), but subjects with previous optical magnifier experience were significantly slower at performing the medicine label identification task with all of the EVES (P < .05). CONCLUSIONS: Although EVES provide objective benefits to the visually impaired in reading speed and acuity, together with some specific near tasks, some can be performed just as fast using optical magnification. © 2003 by Elsevier Inc. All rights reserved.

Polymerisable octahedral rhenium cluster complexes as precursors for photo/electroluminescent polymers

New polymerisable photoluminescent octahedral rhenium cluster complexes trans-[{Re6Q8}(TBP)4(VB)2] (Q = S or Se; TBP-p-tert-butylpyridine; VB-vinyl benzoate) have been synthesised, characterised and used to construct rhenium cluster-organic polymer hybrid materials. These novel polymer systems are solution-processable and the rhenium clusters retain their photoluminescent properties within the polymer environment. Notably, when the rhenium cluster complexes are incorporated into the matrix of the electroluminescent polymer poly(N-vinylcarbazole), the resultant cluster polymer hybrid combined properties of both components and was used successfully in the construction of a polymer light emitting diode (PLED). These prototype devices are the first PLEDs to incorporate octahedral rhenium clusters and provide the first direct evidence of the electroluminescent properties of rhenium clusters and indeed, to the best of our knowledge, of any member of the family of 24-electron hexanuclear cluster complexes of molybdenum, tungsten or rhenium.

Understanding Ten-Eleven Translocation-2 in Hematological and Nervous Systems

I proposed the study of two distinct aspects of Ten-Eleven Translocation 2 (TET2) protein for understanding specific functions in different body systems. In Part I, I characterized the molecular mechanisms of Tet2 in the hematological system. As the second member of Ten-Eleven Translocation protein family, TET2 is frequently mutated in leukemic patients. Previous studies have shown that the TET2 mutations frequently occur in 20% myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN), 10% T-cell lymphoma leukemia and 2% B-cell lymphoma leukemia. Genetic mouse models also display distinct phenotypes of various types of hematological malignancies. I performed 5-hydroxymethylcytosine (5hmC) chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) of hematopoietic stem/progenitor cells to determine whether the deletion of Tet2 can affect the abundance of 5hmC at myeloid, T-cell and B-cell specific gene transcription start sites, which ultimately result in various hematological malignancies. Subsequent Exome sequencing (Exome-Seq) showed that disease-specific genes are mutated in different types of tumors, which suggests that TET2 may protect the genome from being mutated. The direct interaction between TET2 and Mutator S Homolog 6 (MSH6) protein suggests TET2 is involved in DNA mismatch repair. Finally, in vivo mismatch repair studies show that the loss of Tet2 causes a mutator phenotype. Taken together, my data indicate that TET2 binds to MSH6 to protect genome integrity. In Part II, I intended to better understand the role of Tet2 in the nervous system. 5-hydroxymethylcytosine regulates epigenetic modification during neurodevelopment and aging. Thus, Tet2 may play a critical role in regulating adult neurogenesis. To examine the physiological significance of Tet2 in the nervous system, I first showed that the deletion of Tet2 reduces the 5hmC levels in neural stem cells. Mice lacking Tet2 show abnormal hippocampal neurogenesis along with 5hmC alternations at different gene promoters and corresponding gene expression downregulation. Through the luciferase reporter assay, two neural factors Neurogenic differentiation 1 (NeuroD1) and Glial fibrillary acidic protein (Gfap) were down-regulated in Tet2 knockout cells. My results suggest that Tet2 regulates neural stem/progenitor cell proliferation and differentiation in adult brain.

Dedication and Display of Portrait Statues in Hellenistic Greece: Spatial Practices and Identity Politics

This dissertation models a new approach to the study of ancient portrait statues—one that situates them in their historical, political, and spatial contexts. By bringing into conversation bodies of evidence that have traditionally been studied in discrete categories, I investigate how statue landscapes articulated and reinforced a complex set of political and social identities, how space was utilized and manipulated on a local and a regional level, and how patrons responded to the spatial pressures and visual politics of statue dedication within a constantly changing landscape.

Instead of treating sites independently, I have found it to be more productive—and, indeed, necessary—to examine broader patterns of statue dedication. I demonstrate that a regional perspective, that is, one that takes into account the role of choice and spatial preference in setting up a statue within a regional network of available display locations, can illuminate how space shaped the ancient practice of portrait dedication. This level of analysis is a new approach to the study of portrait statues and it has proved to be a productive way of thinking about how statues and context were used together to articulate identity. Understanding how individual monuments worked within these broader landscapes of portrait dedications, how statue monuments functioned within federal systems, and how monuments set up by individuals and social groups operated along side those set up by political bodies clarifies the important place of honorific statues as an expression of power and identity within the history of the site, the region, and Hellenistic Greece.

Out-of-equilibrium dynamical fluctuations in glassy systems

"In this paper we extend the earlier treatment of out-of-equilibrium mesoscopic fluctuations in glassy systems in several significant ways. First, via extensive simulations, we demonstrate that models of glassy behavior without quenched disorder display scalings of the probability of local two-time correlators that are qualitatively similar to that of models with short-ranged quenched interactions. The key ingredient for such scaling properties is shown to be the development of a criticallike dynamical correlation length, and not other microscopic details. This robust data collapse may be described in terms of a time-evolving "extreme value" distribution. We develop a theory to describe both the form and evolution of these distributions based on a effective sigma model approach."

Exploring protein-RNA interactions with site-directed mutagenesis and phage display

The importance of RNA as a mediator of genetic information is widely appreciated. RNA molecules also participate in the regulation of various post-transcriptional activities, such as mRNA splicing, editing, RNA stability and transport. Their regulatory roles for these activities are highly dependent on finely tuned associations with cognate proteins. The RNA recognition motif (RRM) is an ancient RNA binding module that participates in hundreds of essential activities where specific RNA recognition is required. We have applied phage display and site-directed mutagenesis to dissect principles of RRM-controlled RNA recognition. The model systems we are investigating are U1A and CUG-BP1. In this dissertation, the molecular basis of the binding affinity of U1A-RNA beyond individual contacts was investigated. We have identified and evaluated the contributions of the local cooperativity formed by three neighboring residues (Asn15, Asn16 and Glu19) to the stability of the U1A-RNA complex. The localized cooperative network was mapped by double-mutant cycles and explored using phage display. We also showed that a cluster of these residues forms a “hot spot” on the surface of U1A; a single substitution at position 19 with Gln or His can alter the binding properties of U1A to recognize a non-cognate G4U RNA. Finally, we applied a deletion analysis of CUG-BP1 to define the contributions of individual RRMs and RRM combinations to the stability of the complex formed between CUG-BP1 and the GRE sequence. The preliminary results showed RRM3 of CUG-BP1 is a key domain for RNA binding. It possibly binds to the GRE sequence cooperatively with RRM2 of CUG-BP1. RRM1 of CUG-BP1 is not required for GRE recognition, but may be important for maintaining the stability of the full-length CUG-BP1.

Interaction techniques with novel multimodal feedback for addressing gesture-sensing systems

Users need to be able to address in-air gesture systems, which means finding where to perform gestures and how to direct them towards the intended system. This is necessary for input to be sensed correctly and without unintentionally affecting other systems. This thesis investigates novel interaction techniques which allow users to address gesture systems properly, helping them find where and how to gesture. It also investigates audio, tactile and interactive light displays for multimodal gesture feedback; these can be used by gesture systems with limited output capabilities (like mobile phones and small household controls), allowing the interaction techniques to be used by a variety of device types. It investigates tactile and interactive light displays in greater detail, as these are not as well understood as audio displays. Experiments 1 and 2 explored tactile feedback for gesture systems, comparing an ultrasound haptic display to wearable tactile displays at different body locations and investigating feedback designs. These experiments found that tactile feedback improves the user experience of gesturing by reassuring users that their movements are being sensed. Experiment 3 investigated interactive light displays for gesture systems, finding this novel display type effective for giving feedback and presenting information. It also found that interactive light feedback is enhanced by audio and tactile feedback. These feedback modalities were then used alongside audio feedback in two interaction techniques for addressing gesture systems: sensor strength feedback and rhythmic gestures. Sensor strength feedback is multimodal feedback that tells users how well they can be sensed, encouraging them to find where to gesture through active exploration. Experiment 4 found that they can do this with 51mm accuracy, with combinations of audio and interactive light feedback leading to the best performance. Rhythmic gestures are continuously repeated gesture movements which can be used to direct input. Experiment 5 investigated the usability of this technique, finding that users can match rhythmic gestures well and with ease. Finally, these interaction techniques were combined, resulting in a new single interaction for addressing gesture systems. Using this interaction, users could direct their input with rhythmic gestures while using the sensor strength feedback to find a good location for addressing the system. Experiment 6 studied the effectiveness and usability of this technique, as well as the design space for combining the two types of feedback. It found that this interaction was successful, with users matching 99.9% of rhythmic gestures, with 80mm accuracy from target points. The findings show that gesture systems could successfully use this interaction technique to allow users to address them. Novel design recommendations for using rhythmic gestures and sensor strength feedback were created, informed by the experiment findings.

Dielectric studies of Liquid Crystal Nanocomposites and Nanomaterial systems.

Liquid crystals (LCs) have revolutionized the display and communication technologies. Doping of LCs with inorganic nanoparticles such as carbon nanotubes, gold nanoparticles and ferroelectric nanoparticles have garnered the interest of research community as they aid in improving the electro-optic performance. In this thesis, we examine a hybrid nanocomposite comprising of 5CB liquid crystal and block copolymer functionalized barium titanate ferroelectric nanoparticles. This hybrid system exhibits a giant soft-memory effect. Here, spontaneous polarization of ferroelectric nanoparticles couples synergistically with the radially aligned BCP chains to create nanoscopic domains that can be rotated electromechanically and locked in space even after the removal of the applied electric field. The resulting non-volatile memory is several times larger than the non-functionalized sample and provides an insight into the role of non-covalent polymer functionalization. We also present the latest results from the dielectric and spectroscopic study of field assisted alignment of gold nanorods.

Understanding ten-eleven translocation-2 in hematological and nervous systems

I proposed the study of two distinct aspects of Ten-Eleven Translocation 2 (TET2) protein for understanding specific functions in different body systems. ^ In Part I, I characterized the molecular mechanisms of Tet2 in the hematological system. As the second member of Ten-Eleven Translocation protein family, TET2 is frequently mutated in leukemic patients. Previous studies have shown that the TET2 mutations frequently occur in 20% myelodysplastic syndrome/myeloproliferative neoplasm (MDS/MPN), 10% T-cell lymphoma leukemia and 2% B-cell lymphoma leukemia. Genetic mouse models also display distinct phenotypes of various types of hematological malignancies. I performed 5-hydroxymethylcytosine (5hmC) chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq) of hematopoietic stem/progenitor cells to determine whether the deletion of Tet2 can affect the abundance of 5hmC at myeloid, T-cell and B-cell specific gene transcription start sites, which ultimately result in various hematological malignancies. Subsequent Exome sequencing (Exome-Seq) showed that disease-specific genes are mutated in different types of tumors, which suggests that TET2 may protect the genome from being mutated. The direct interaction between TET2 and Mutator S Homolog 6 (MSH6) protein suggests TET2 is involved in DNA mismatch repair. Finally, in vivo mismatch repair studies show that the loss of Tet2 causes a mutator phenotype. Taken together, my data indicate that TET2 binds to MSH6 to protect genome integrity. ^ In Part II, I intended to better understand the role of Tet2 in the nervous system. 5-hydroxymethylcytosine regulates epigenetic modification during neurodevelopment and aging. Thus, Tet2 may play a critical role in regulating adult neurogenesis. To examine the physiological significance of Tet2 in the nervous system, I first showed that the deletion of Tet2 reduces the 5hmC levels in neural stem cells. Mice lacking Tet2 show abnormal hippocampal neurogenesis along with 5hmC alternations at different gene promoters and corresponding gene expression downregulation. Through the luciferase reporter assay, two neural factors Neurogenic differentiation 1 (NeuroD1) and Glial fibrillary acidic protein (Gfap) were down-regulated in Tet2 knockout cells. My results suggest that Tet2 regulates neural stem/progenitor cell proliferation and differentiation in adult brain.^

Motivating the use of public transit through a mobile glanceable display

With increasing concerns about the impact of global warming on human life, policy makers around the world and researchers have sought for technological solutions that have the potential to attenuate this process. This thesis describes the design and evaluation of an information appliance that aims to increase the use of public transportation. We developed a mobile glanceable display that, being aware of the user’s transportation routines, provides awareness cues about bus arrival time, grounded upon the vision of Ambient Intelligence. We present the design process we followed, from ideation to building a prototype and conducting a field study, and conclude with a set of guidelines for the design of relevant personal information systems. More specifically we seek to test the following hypotheses: 1) That the tangible prototype that provides ambient cues will be used more frequently than a similar purpose mobile app, 2) That the tangible prototype will reduce the waiting time at the bus stop, 3) That the tangible prototype will result to reduced anxiety on passengers, 4) That the tangible prototype will result to an increase in the perceived reliability of the transit service, 5) That the tangible prototype will enhance users’ efficiency in reading the bus schedules and 6) That the tangible prototype will make individuals more likely to use public transit. In a field study, we compare the tangible prototype against the mobile app and a control condition where participants were given no external support in obtaining bus arrival information, other than their existing routines. Using qualitative and quantitative data, we test the aforementioned hypotheses and explore users’ reactions to the prototype we developed.