VictorJuiz/thesis huggingface dataset:
Towards Ubiquitous Augmented Reality in Structured Environments

Augmented reality has incredible potential to change the way we interact with information. Smart mobile devices have enabled us to be constantly connected to an ever expanding source of information known as the internet. Augmented Reality devices can present a method for organizing this information and ensure that relevant information is present in the location where it is most useful. Similarly, the spatial organization of information alongside physical objects can present new forms of creativity and artistry. These devices use computer vision algorithms to understand the structure of objects in the world as well as the devices' location relative to these objects. This understanding is used to display virtual objects in such a way as to appear present in the physical world. While these algorithms present a viable solution in many situations, they still have many failure cases that can prevent the ubiquitous adoption of these devices./nThis thesis discusses methods for improving the localization and mapping capabilities of these Augmented Reality devices by exploiting the structure that is present in many man-made environments. A discussion of some open problems in augmented reality is presented in the context of the open source package OpenARK. The remainder of thesis discusses methods for improving localization and mapping and 3D reconstruction. A method is presented for incorporating planar structures from a Time of Flight depth sensor into a state of the art Visual Inertial Odometry algorithm. This algorithm is demonstrated to improve localization accuracy in low light and low texture environments and maintain realtime performance on a mobile device with limited Time of Flight depth sensing range and limited compute resources. A method is presented for enabling the realtime matching of image wireframes. Image wireframes represent the junctions, lines and intersection relationships that form the structure of the scene. This algorithm exploits these relationships to improve the matching of image wireframes beyond standard feature matching. This method is further demonstrated to be capable of exploiting the additional constraints introduced by multiple cameras.

Advisor: Sastry, Sosale S
New Materials for Life Inter Vivos: Experimentation with Living Matter at the Biopolis-Dresden, Germany

New Materials for Life Inter Vivos: Experimentation with Living Matter at the Biopolis-Dresden, Germany, is premised on extensive participant-observation with life and material scientists in German laboratories. It chronicles a historical and scientific situation taking shape around the conceptualization and constitution of new materials for life: biomaterials. These are man-made materials designed to interface more ably with living systems, and their application in tissue engineering, stem-cell technologies, and drug development increasingly drives the trajectory of ambitious research programs at the intersection of basic biology and translational medicine. Through the figure of the biomaterial, I demonstrate how shifting notions of life and inchoate techniques for its commercial fabrication reconfigure the relationship between the biological and chemical sciences as they endeavor to create new objects of potential value for emerging medical markets and therapeutic milieus. The dissertation attends to the interplay of incipient knowledges and technical practices in the experimental life and materials sciences, the scientists who practice them, and their equivocations regarding the existential and ethical stakes of their pursuits. It seeks, ultimately, to situate novel conceptions of and interventions into living matter within a renewed vision of German engineering and technology manufacture, one that is particular to Dresden’s political and economic history as well as its post-socialist urban and industrial revitalization. Finally, by attending to the new relationships being forged between the biological and chemical sciences, their technologies for manipulating living matter, and their evolving conceptions of life, I argue for an anthropological approach to life and science inter vivos—one conceived in the relations between laboratories, disciplines, and experimental forms of both embodied and disembodied life.

Advisor: Cohen, Lawrence
Ong, Aihwa
Assembly of Extracellular Matrix Hydrogel Arrays and Phosphorylated Intrinsically Disordered Protein Brushes

Living cells sense and respond to the biophysical cues of extracellular matrix (ECM) in a complex and reciprocal manner. Towards a comprehensive understanding of the regulatory roles of matrix biophysical properties, there is an emerging need for high-throughput matrix platforms that enable parallel culture of cells in various matrix conditions, and for systems biology approaches that can investigate cell-ECM interactions in a parallelized fashion. We provide an overview of recent progress in developing synthetic biomaterial platforms to probe cell-ECM interactions in a high-throughput manner and to profile such interactions at the systems level. We then describe a multi-well hyaluronic acid (HA) array platform in which cells are cultured on combinatorial arrays of gels spanning a range of elasticities and adhesivities. We validated the platform by recapitulating expected relationships between matrix stiffness, adhesivity and cell mechanosensing in human mesenchymal stem cells (hMSCs). We also showed that on this platform, hMSCs maintain the capability of adipogenesis and osteogenesis, and inguinal white adipose tissue (WAT) cells were capable of developing into beige adipocytes. This hydrogel array platform provides a versatile tool for dissecting molecular mechanisms of cell-ECM interactions./nIntrinsically disordered proteins (IDPs) play central roles in numerous cellular processes. While the structure and function of many IDPs are regulated by multisite phosphorylation, biophysical insights into the relationship between the modifications and structure are limited. The challenge calls for paradigms in which IDP conformational responses can be measured in the context of controlled phosphorylation. By engineering the disordered neurofilament heavy subunit sidearm domain (NFH-SA), we established recombinant NFH-SA (rNFH-SA) brushes on glass that can be controllably phosphorylated in situ with pre-activated mitogen-activated protein kinase 1, and monitored brush conformations with atomic force microscopy. Phosphorylation induced significant brush swelling to an extent that strongly depends upon pH and ionic strength. The phosphorylated rNFH-SA brush was also dramatically condensed with micromolar concentrations of divalent cations. Our study demonstrates that multisite phosphorylation controls NFH-SA structure through modulation of chain electrostatics and points to a general strategy for engineering IDP-based interfaces that can be reversibly and dynamically modulated by enzymes.

Advisor: Kumar, Sanjay
Francis, Matthew B
Wearable Biosensors for Perspiration Monitoring

Sweat is an emerging biofluid that is non-invasively accessible and rich in biochemical information. It has traditionally been used for diagnosis of medical conditions, including cystic fibrosis, autonomic and small fiber neuropathy. Historically, sweat testing has been limited to clinical and research settings due to the need of specialized equipment with trained personnel. In this regard, wearable sensors open up opportunities for expanding sweat testing beyond the specialized environment and the established diagnosis of medical conditions. Major challenges in wearable sweat sensing research include (1) obtaining reliable sensors which can accurately provide the target’s signals and do not require repeated calibration for the wear duration, (2) designing an integrated device that mitigates the rapid evaporation, mixing, and contamination of freshly secreted sweat, and (3) interpreting potential sweat biomarkers to realize its role in health management. In this thesis, I demonstrated different wearable sweat sensors to address these challenges. Specifically, the first part of the thesis focuses on electrochemical sensors which allow multiplexed detection of target chemicals through modulation of sensing surfaces with suitable chemicals and materials on flexible plastic substrates. The second part includes integration of microfluidics with electrochemical and electrical sensors to deliver a device that can guide sweat flow and achieve ultra-low sweat measurement for sedentary individuals with and without active sweat stimulation. Lastly, a method for rapid and mass production of sweat sensors via roll-to-roll process is demonstrated, along with subject studies to explore the significance of sweat in relation to health.

Advisor: Javey, Ali
The Positive Selection of T cells with Different Degrees of Self Reactivity

During positive selection, thymocytes avoid death by sensing and adjusting to homeostatic signals from self-peptide:major histocompatibility complexes (MHCs) in a process known as functional tuning. As a result, thymocytes mature into a diverse repertoire of T cells with different degrees of self reactivity, and cells with high and low self reactivity exhibit differences in effector function in the periphery. CD5 is a known tuning molecule for thymocytes with high self reactivity. However, the molecules involved in the functional tuning of cells with low self reactivity during positive selection are yet to be identified, and overall little is known about the positive selection of T cells with low self reactivity. To investigate this, we identified TG6, a functionally relevant, MHCI-restricted TCR transgenic (tg), as a novel model for studying CD8 T cells with low self reactivity. Using this model, we show that cells with low self reactivity have relatively brief TCR signals, not associated with a migratory pause, during positive selection, and that these truncated signals are correlated with delayed progress through positive selection. Cells with low self reactivity can take a week or more to mature—compared to just 3 days for cells with high self reactivity. Though all polyclonal thymocytes have increased TCR sensitivity at the beginning of positive selection, we provide evidence that cells with low self reactivity retain a gene expression signature consistent with increased TCR sensitivity late into development. Furthermore, we identify two genes, Kcna2 and Tmie, that have high expression in cells with low self reactivity and may increase TCR sensitivity. The expression of Kcna2 and Tmie is set in cells with low self reactivity during positive selection and maintained in the periphery—a characteristic expression pattern of functional tuning genes. Our results fit with a model where self reactivity directs the rate of TCR signal accumulation, TCR sensitivity, and the time to reach maturation. These differences in positive selection may be important for appropriate functional tuning of T cells, based on their self reactivity.

Advisor: Robey, Ellen A
Shaping the Contours of Orthodoxy in the Fifth-Century West: Gennadius of Marseilles and the De viris illustribus Tradition

This dissertation is a historical study of Gennadius of Marseilles’ De viris illustribus, a catalog of 101 short, bio-bibliographical notices devoted to Christian authors and their works written by a member of the ascetic movement in Marseilles during the second half of the fifth century A.D. The study advances existing knowledge of the fifth century in three distinct ways. First, it establishes the Sitz im Leben of De viris illustribus. To do so, it has had to contend with not only a dearth of evidence relating to the life and literary practices of its author but also the longstanding but nevertheless erroneous assumption that in writing De viris illustribus Gennadius produced nothing more than a second part of what Jerome had written nearly eight decades earlier. Second, on the basis of the established context, it uses two case studies to explain how Gennadius presented three western theological controversies—Origenism, Pelagianism, and “Semipelagianism”—that took place during the eight decades that separated him from his literary predecessor. And third, it uses De viris illustribus, both its historical and theological contexts and its content, to reevaluate the character of southern Gallic asceticism during the second half of the fifth century, especially its close engagement with several eastern or eastern-oriented texts, most notably those of Origen of Alexandria, Evagrius Ponticus, and Rufinus of Aquileia. The effect of this reevaluation not only sheds light on the theological substrate that animated Massilianism but also explains its opposition to Augustine of Hippo’s late theology in what has been known since the sixteenth century as the Semipelagian Controversy.

Advisor: Elm, Susanna
Biomechanical Models and Robotic Systems for Human Motion Assessment

Over the past several decades, there have been advances in the development of complex robotic devices for daily assistance or rehabilitation. The use of such devices, however, has largely remained limited to a research setting due to the prohibitive cost and required operational engineering expertise. Likewise, dedicated biomechanics facilities perform quantitative motion analysis, contrasting the qualitative and static imaging methods which are standard in clinical care. The aim of this dissertation is to develop and validate affordable methods and devices for assessing and assisting human motion./nWe first present a framework for improved estimation of whole-body human kinematics with data from a single depth-camera. The algorithm incorporates biomechanical and dynamic constraints for near-real time analysis of human motion. The approach is validated against data from a ground-truth motion capture system on sit-to-stand (STS), an activity of daily living which requires significant torque generation and coordinated movement of multiple joints. We additionally present two methods for modeling the torso: a generalized relationship for the lower-lumbar angle and an optimization-based method for estimating a subject-specific model. Building on these modeling methods, we introduce a passive elastic knee orthotic device which provides bilateral knee assistance during STS. The device design and analysis integrate models of the human and device dynamics. Preliminary human subjects tests demonstrate a decrease in the human knee torque as well as positive changes in whole-body biomechanics. Finally, we introduce an affordable planar robotic manipulandum for upper limb assessment and assistance. The mechanical, electrical, and control architectures are presented, along with preliminary human subjects tests of reaching and elliptical trajectories with force field assistance under an admittance controller. A protocol for the assessment of strength and coordination is introduced and integrated with a biomechanical model of the arm. With a total material cost of less than $800, this device provides an accessible platform for clinical robotic assessment and rehabilitation.

Advisor: Bajcsy, Ruzena
Essays on the neuroeconomics of motivation

The ability to initiate goal-directed behaviors related to every day outcomes is a crucial component of motivation. Across clinical and subclinical domains, variability in motivated decision-making accounts for failures to both begin and complete actions towards improved health. When faced with decisions that involve expending our own energetic resources in order to attain rewards, whether for ourselves or others, individuals vary broadly in the behaviors they take, or fail to take, to reach said goals. In order to classify, and potentially provide a mechanistic account of, differences in these cost-benefit processes, an objective investigation into the computations underlying motivated behavior is tantamount. This is particularly relevant to the clinical domain, wherein the broad goal of computational psychiatry is a methodologically quantitative approach to taxonomic classification. The following essays offer an overview of three studies with the aim of providing formal accounts of integrating information from individual differences (chapters 1 and 2) and stereotype content (chapter 3) into mathematical models of motivated behavior. I will begin by discussing a computational approach towards predictive modeling of effort-based decision-making utilizing dimensions of clinical and subclinical approach and avoidant traits. In the first chapter, I will focus on modeling behavior in a community-recruited sample of adults by integrating a number of demographic and individual difference measures into behavioral economic models of effort discounting. In the second, I will focus my analyses on a separate but demographically similar cohort of adults who completed the same experimental paradigm during functional neuroimaging. Here, I will investigate changes in neural activity (inferred by blood-oxygen level dependent (BOLD) signal) responding to different levels of effort-reward tradeoffs. I will utilize the same behavioral modeling processes as the first chapter in order to extract individual difference measures by estimating free parameters specific to individual subjects, and relating them to changes in the neural responses to cost-benefit evaluations. Finally, I will discuss the manner in which evaluations of effort expenditure for other-rewarding outcomes are distinct from those with self-rewarding outcomes, and how social information – or stereotypes – about the recipient of said rewards robustly contributes to effort-related choice processes

Advisor: Hsu, Ming
RNA decay during gammaherpesvirus infection reduces RNA polymerase II occupancy of host promoters but spares viral promoters

Gene expression is generally thought of as a linear pathway, beginning with transcription and processing of messenger RNA (mRNA), followed by export to the cytoplasm for translation and decay. Viruses have long been a key to discovering novel pathways and regulation in cells in their modulation of these pathways and gene expression is no different. Here we describe how infection with gammaherpesviruses is characterized by widespread mRNA degradation that leads to reduced RNA Polymerase II (Pol II) occupancy of host promoters by chromatin immuno- precipitation and sequencing (ChIP-seq) of infected cells. Pol II occupancy depends on RNA decay as infection with a decay-deficient virus does not broadly alter Pol II occupancy. In contrast to host promoters, viral promoters continue to recruit Pol II and transcribe their genes even at late stages in infection. This transcriptional escape of viral genes is all the more notable in light of a massive reduction in components of Pol II and general transcription factors (GTF) protein levels that we describe during infection. We further isolate the transcriptional capacity of viral genes to their presence on the replicating viral genome./nIn Chapter 1 of this thesis we provide an overview of RNA decay, transcription and the literature that investigates mechanistic links between these two processes. This situates our work as distinct from the majority of literature that finds RNA decay and transcription are modulated to maintain constant RNA levels in a cell; instead, during pathogenic stress RNA decay feeds forward to further inhibit transcription. Chapter 2 characterizes the transcriptional repression phenotype during murine herpesvirus 68 infection and highlights how viral genes are able to robustly transcribe their genome irrespective of widespread decay. In Chapter 3 we further investigate the protein depletions of Pol II subunits and GTFs that exacerbate transcriptional repression of the host that we uncover in Chapter 2. Chapter 4 delves into the dual roles of SOX, the viral nuclease that instigates RNA decay, as both an RNase and a DNase./nIn summary, this dissertation links disparate stages of the gene expression pathway and provides mechanistic details for how this occurs during MHV68 infection.

Advisor: Glaunsinger, Britt A
Measuring the Nuclear Level Density and gamma-Decay Strength for the 92Sr(n,g) Reaction

Neutron-induced reaction cross sections on short-lived neutron-rich nuclei, such as fission fragments play a crucial role for a wide range of nuclear physics applications, from nuclear energy and astrophysics to U.S. stockpile stewardship and other national security missions. However, our ability to model these cross sections are limited by theoretical uncertainties that range over orders of magnitude. Indirect methods are utilized to determine cross sections when direct measurements are not possible. These indirect methods can provide an experimental constraint on nuclear properties used in determining the (n,g) cross section using Hauser-Feshbach reaction modeling including the nuclear level density (NLD), gamma-ray strength function (gSF), and parameterizations of the optical model potential. One example of this is the fission fragment 92Sr. The direct measurement of 92Sr neutron-capture cross section is not possible, as the half-life of 2.66 hours is too short to allow the manufacturing of a target and subsequent irradiation of the target using neutrons. While it may not be possible to measure neutron capture on 92Sr, beta decay of 93Rb (Q=7.466(9) MeV) can be used to probe average nuclear properties of the 93Sr compound nucleus. In this dissertation we present the results of such a study where the emitted beta-delayed gamma rays were measured using a total absorption spectrometer (TAS) known as the Summing NaI(Tl) detector (SuN) to simultaneously determine the gamma-ray energies and excitation energies. The experiment utilized a combination of the SuN detector together with a plastic scintillator to measure coincidence events with the emitted beta particle, and a Tape Station for Active Nuclei (SuNTAN) to remove gamma-ray background from the decay daughter activity. The measured 93Sr gamma-ray energies as a function of excitation energy were analyzed using the beta-Oslo Method to extract statistical nuclear properties that were implemented in the reaction code TALYS. The resulting calculated 92Sr neutron capture cross section is constrained by the experimental uncertainty and systematic uncertainties of the beta-Oslo Method.

Advisor: Vujic, Jasmina