VictorJuiz/thesis huggingface dataset:
Computational Methods for Scalable Interpretation and Exploration of Single-Cell Transcriptomes

Methods for genome-wide gene expression characterization have proven transformative in the study of biology, facilitating the identification of new types of cells, the unraveling of regulatory and signaling pathways, and the discovery of novel pharmaceutical targets for the treatment of human diseases. Beginning with microarrays and accelerated by the introduction of next-generation sequencing, the technology has progressively increased in its scale, sensitivity, and accuracy. Now, with the recent advent of single-cell RNA-seq (scRNA-seq), it is possible to survey the full heterogeneity of complex tissue. This work deals with the analysis of scRNA-seq data and the development of computational methods to extract new biological insights from single-cell experiments./nChapter 1 provides some background on the experimental developments enabling single-cell RNA-seq as well as existing methods for the analysis of single-cell data products. Chapter 2 develops an algorithm for the functional interpretation of scRNA-seq data through the use of previous high-throughput experimental results. As a departure from existing methods, this procedure can be utilized with both linear and non-linear dimensionality reduction methods and does not require a pre-partitioning of cells into discrete clusters. In Chapter 3 this approach is further extended for the systematic extraction of informative features (genes) that underlie the heterogeneity of scRNA-seq experiments and the organization of these features into co-regulated gene modules. We additionally demonstrate that this approach can be used with multi-modal datasets to identify genes that vary in accordance with a similarity map specified by a different modality - such as spatial or lineage measurements. Chapter 4 details the development of open source computational tools which make these methods accessible to the larger research community and provide additional capabilities in data exploration, visualization, and collaboration. Finally, in Chapter 5, a case study is described in which single-cell RNA-seq is used to investigate the relevance of the Interleukin 23 receptor in a model of T helper cell type 1 driven autoimmunity.

Advisor: Yosef, Nir
Stretchable Electronics and Soft Actuators via Elastic Instability Design and Facile Fabrication

Soft and deformable electronics and actuators have attracted high research interests toward practical applications. This work focuses on two goals: (1) applying the concept of elastic instability in the structural design for soft systems; and (2) exploring rapid and low-cost schemes for their facile fabrications. Specifically, Kirigami, curved serpentines, auxetics, bistable and multistable structures, have all been utilized in different electronics and actuator systems to obtain unique and desirable properties, such as ultrahigh deformability, omnidirectional stretchability, and impact-resistant mechanics in this work./nFirst, a construct inspired by Kirigami designs has been developed to make highly deformable micro-supercapacitor patches with high areal coverages of electrode and electrolyte materials. These patches are fabricated in simple and efficient steps by a laser assisted graphitic conversion and cutting process, utilizing different laser power and scanning speeds on a laser cutter. The Kirigami cuts significantly increase the structural compliance such that individual segments in the patches can buckle, rotate, bend and twist to accommodate large overall deformations with only a small strain in active electrode areas. Electrochemical testing results have proved that electrochemical performances are preserved under large deformations up to 282.5% of overall structural elongations./nA time- and cost-effective fabrication approach to construct stretchable electronics with the “island-bridge” constructs has been established without using photomasks. A low-cost commercially available vinyl cutter is used to define patterns by adjusting the cutting force and depth on the blade. Metal interconnects and pads can be patterned via the “tunnel cut” process and the flexible overall structure can be defined via the “through cut” process. The capabilities of the proposed method is shown by two demonstration devices, a skin-mounted module for monitoring breathing and a water-resistant supercapacitor array with omni-directionally stretchable capability. These devices can accommodate large deformations through the buckling and post-buckling instability without affecting their functions./nFinally, a class of magnetically powered, untethered soft actuators has been built based on a bioinspired “flesh-and-bone” construct. This construct has both key attributes of fast actuation and compliant impact-resistant mechanics and it also renders a simple fabrication process using generic 3D printers and off-the-shelf neodymium magnets as well as silicone elastomers. Actuators of diverse shapes of elastomeric “fleshes” and different placements of magnetic “bones” have displayed several distinct types of tasks, including auxetic expansion and shrinking, out-of-plane transformations, transition among multiple stable states, and manipulation of small objects.

Advisor: Lin, Liwei
Practical and Scalable Serverless Computing

Serverless computing is a new paradigm for developing cloud applications popularized by Amazon's AWS Lambda service. In serverless computing, applications are decomposed into fine-grained serverless functions developed in high-level languages such as Python and Javascript. Developers can then submit these functions to serverless providers which then deploy and execute them. Unlike VM-based platforms, in serverless computing applications run inside containerized execution environments called "lambdas" or "lambda functions". Due to the lightweight and fine-grained nature of lambdas, serverless computing can provide higher elasticity and higher resource utilization. Furthermore, in serverless computing infrastructure and operational aspects of running applications in the cloud are delegated to the cloud provider, and this relieves developers from many complex and onerous tasks. This paradigm shift towards serverless computing is poised to radically change the way developers build cloud applications./nWe identify two main challenges with leveraging serverless computing for highly-distributed applications, such as Big Data Analytics and Machine Learning. The first challenge has to do with automatic management of resources through higher-level abstractions for serverless applications. The second has to do with the performance and scalability of distributed network communication on serverless platforms. In this thesis we present two systems that tackle both of these challenges. We solve the first one with a system, Cirrus, for automatic serverless ML end-to-end workflows. We solve the second one with Zip, a system that provides high-performance and scalable distributed primitives for inter-lambda serverless communication./nIn this thesis we show that it is possible to provide simple APIs to developers with significantly better performance than today's approaches. For instance, Cirrus provides 2 orders of magnitude more updates per second in model training than when using PyWren, a MapReduce serverless framework, because it provides a high-level API backed by a highly optimized backend for ML tasks. Similarly, Zip provides 1.3-12x speedup for different communication patterns compared to the next best alternative, using a memory-backed store for inter-lambda communication.

Advisor: Katz, Randy
Fonseca, Pedro
Echo Otherwise

In Echo Otherwise, I bring together two writers, Lucretius and Ferdinand de Saussure, whose kinship might seem to resist notice at first. However, the affinities between this unlikely pair are to be discovered along the wandering paths this dissertation forges, and in the conversation animated by my readings of their attention to sound. Indeed, the pairing of Lucretius’s De Rerum Natura and Saussure’s unpublished anagram notebooks discloses a set of remarkably interconnected and overlapping concerns. Both writers are interested in how sound works and in what sounds and resounds in the universe of poems and atoms, and both are attentive to what sound tells us about poems and atoms. I take them as models for the kinds of attention they perform as readers, writers, and theorists who in turn demand the same of their readers. These demands, as I understand them, instruct us to be guided by our sense perceptions, even if this warrants a disobedience to the conventions of disciplines and the decorum of genre. In the Coda, the modes of instruction I find in Lucretius and Saussure inform my approach to reading M. NourbeSe Philip’s Zong! and several works by Saidiya Hartman. I turn to Philip’s work because of the urgent questions it asks of us, among them: How are we formed in and by languages at once already determined by histories of subjugation and open to linguistic indeterminacy and surplus, the excess that eludes capture? Like Philip, Hartman writes within and against the archives of transatlantic slavery, and asks what forms and modes of writing this archive blocks and enables. In the Coda I thus disclose and perform a reading of (a listening to) the sounds that other writers have made resound from depths that ordinary, or ordinarily organized language, text, or speech could not otherwise body forth. The writing that my listening induces, then, carries forward what they may have heard in what wasn’t quite or couldn’t be said—an echo and a trace—as an offering towards an otherwise to the aftermath of ongoing catastrophes.

Advisor: Oliensis, Ellen
Inductive Wireless Power Transfer to Multiple Biomedical Implants

Recent progress in smart devices and the Internet of Things has led to a huge growth in smart systems. Phones, homes, cars, and appliances can all communicate with each other in order to expand their functionality and offer new ways of interaction. Unfortunately, human input/output modalities are still limited to our five senses - sight, hearing, touch, taste, and smell - leading to a gap between humans and the evolving world around us./nThe Human Intranet (HI) is the vision that human capabilities will be extended through human-device interaction. It is an open, scalable platform that seamlessly integrates an ever- increasing number of sensor, actuation, computation, storage, communication, and energy nodes located on, in, or around the human body acting in symbiosis with the functions provided by the body itself. A major challenge is providing reliable energy to these devices, as they are inherently distributed and modular, have widely varying energy requirements, and must operate chronically./nThis thesis focuses on powering distributed implants inside the body. Two dimensional tessellations of magnetic coils are used to generate a homogeneous magnetic field across a large area and energize implants within. A system for distributed recording of electromyography (EMG) signals in the forearm is presented. Single-channel recording implants located under- neath the skin and fat are wirelessly powered through a custom inductive link and transmit uplink data through FDM passive backscatter, enabling chronic EMG recording for use in gesture recognition platforms.

Advisor: Rabaey, Jan M
Not Above Suspicion: Perceived Socioeconomic Status Impacts Judgments of Prosocial Behavior

Socioeconomic status (SES), one’s educational and financial status, has an enormous impact on one’s quality of life and how one is perceived in modern America, with those of lower (vs. higher) SES seen negatively along a number of important dimensions, including morality and competence. Research suggests that those who engage in behaviors that benefit others (i.e., prosocial behavior) are rated more positively and are rewarded with interpersonal rewards such as peer acceptance and status. However, this process depends upon observers perceiving the prosocial behavior of low (vs. high) SES individuals as prosocial, rather than perceiving the same behaviors through a different lens and, perhaps, undercutting such actions and perceiving them as less prosocial or even self-serving in some way. Three experiments examined the relation between a target’s perceived SES (low vs. high) and perceptions (positive vs. negative) of prosocial behavior. It was hypothesized that the prosocial behaviors of those perceived to be low (vs. high) SES would be perceived as less prosocial. Specifically, it was predicted that low-SES targets would be rated as having more self-serving intentions for their prosocial behaviors than high-SES targets. Experiment 1 conceptually replicates and extends prior work (Flynn, Reagans, Amanatullah, & Ames, 2006), finding that prosocial actors are not only perceived as higher status, but are also perceived to be of higher SES than their non-prosocial counterparts. Experiment 2 found that observers perceive targets of high SES to engage in prosocial behaviors more frequently than low-SES individuals, despite believing that these behaviors are no costlier to either group. Finally, Experiment 3 found evidence that perceivers are more suspicious of the intentions underlying the prosocial behaviors of low-SES individuals, as compared to high-SES individuals. These findings suggest that observers used perceived SES as a cue to interpret the intentions behind prosocial behavior. This provides further insight into one of the challenges encountered by low-SES individuals in modern America, as their good deeds are interrogated rather than rewarded. There are a number of promising directions for future work.

Advisor: Carney, Dana R.
Schroeder, Juliana
Intracranial Electrophysiological Correlates of Visual Perception in the Human Brain

Interaction with our environment involves a constant influx of visual inputs. There has been significant investigation into the complex neural transformations that reflect sensory input as a series of neural activity patterns. However, a paucity of human studies have captured the canonical early and late neural activity patterns that occur across stages of visual processing. Thus, we leverage the millimeter spatial and millisecond temporal resolution of invasive recordings in neurosurgical patients to explore how visual information is rapidly represented in the human brain over time. Chapter 1 investigates visual repetition suppression, the phenomenon where repeated presentations of a stimulus produce a decreased neural response. Repetition suppression occurs ubiquitously across sensory modalities and has been widely studied using non-human primate electrophysiology and human neuroimaging. Here, we investigate the temporal profile of repetition suppression in humans when images are repeated over long time lags. We find robust repetition suppression associated with smaller peak magnitudes, lower total responses, and earlier peak responses. We discuss these findings in the context of theoretical models of repetition suppression and the early and late temporal windows of perception. Chapter 2 explores visual perception using binocular rivalry, a unique experience in which different images are simultaneously presented to each eye, and perception dynamically alternates between the two images. This provides a rare opportunity to disentangle conscious perception and sensory inputs since perception alternates between the two possible percepts, while the stimulus remains static. Significant debate surrounds whether binocular rivalry is the result of competitive interactions between populations in visual areas, top-down influence from associative cortices, or a combination of the two. Chapter 2 attempts to resolve these disagreements using intracranial recordings across the human brain. The first portion explores the initial perception of an ambiguous binocular image. We compare neural responses to ambiguous and unambiguous images and explore their temporal profile across regions. We find that early neural activity predicts subsequent perception. The latter portion investigates changes in perception by studying the neural correlates of endogenous switching from seeing one percept to the other. We find that associative cortices initiate changes in perception and precede sensory reactivation in visual cortices. We find a bi-directional relationship distributed across visual and associative cortices that i) encode and represent ambiguous percepts and ii) are engaged at temporally distinct periods across perception. Overall, this dissertation reports several novel findings in studying sensory networks supporting perception. It aims to bridge the literature in nonhuman primates and human neuroimaging with novel data in human electrophysiology to further understand how the human brain supports visual perception.

Advisor: Knight, Robert T
Data Driven Algorithms For Perception With Applications To Autonomous Driving, Energy And Mixed Reality

The rise of autonomous and artificially intelligent systems promises to deliver efficient and optimal performance as well as unprecedented functionality in a variety of fields and human endeavors. As varied as these fields are, a common property of most autonomous systems is that they convert raw data about their relationship with the environment into optimal actions to achieve a desired goal. One may further divide this conversion into the sub-tasks of sensing and perception, planning, and actuation. Perception is an important part of this pipeline since it describes the set of algorithms for turning raw data into useful bits of information that can be used for planning./nAt its core, we may view perception using an estimation framework. Perception algorithms essentially seek to estimate information from noisy, incomplete and raw data obtained from sensors. However, the accuracy of the information obtained (and consequently effectiveness of the actions taken by the system) are dependent on the assumptions and models used in designing perception algorithms. Therefore, it is important to take care in designing accurate but tractable models for perception. Unfortunately, many perception tasks involve complex functions and sensor models relating observed data to information. These functions are difficult to model from physical properties. In these cases data-driven methods can provide complementary techniques that result in excellent models for very complex systems./nIn this dissertation, we present three perception algorithms designed for applications in Autonomous Driving, Energy Systems and Mixed Reality. We make use of data driven methods to provide approximations to complex sensor models and present tractable estimation algorithms for turning raw data into information. We verify our approach on both synthetic and real data and report excellent results.

Advisor: Sastry, Shankar S
Energy Transfer and the 17O Anomaly in Ozone

Whether formed in the atmosphere or laboratory, ozone has a highly unusual isotopic composition that deviates from predictions of traditional chemical kinetics models and from usual patterns of ‘mass-dependent’ fractionation. Previous research indicates that the anomalous mass-independent isotopic composition of ozone originates in the energy-transfer mechanism for ozone formation (O + O2 + M → O3* + M → O3 + M#), due to a unique, and not fully understood, difference in the behavior of isotopically symmetric versus asymmetric metastable ozone (O3*)./nIn this dissertation, I present photochemistry experiments that provide insight into the origin of the mass-independent isotopic composition of ozone (called the 17O anomaly). In these experiments, ozone was formed in different pressures of various bath gases, M, each with unique energy transfer properties. The product ozone was isolated, and its isotopic composition measured by isotope ratio mass spectrometry. The results of these experiments show that there is an exponential dependence on the 17O anomaly on , the average energy transferred per collision of O3* with M, and indicate that the unusual symmetric/asymmetric differences in ozone are most prominent at energies of O3* near the dissociation threshold./nThese experimental findings led me to design a modified master equation model that produces results in line with experimental bath gas dependent, pressure dependent, and temperature dependent measurements of the isotopic composition of ozone. This model demonstrates that all three of the aforementioned dependencies may be explained by mass-independent isotope effects in ozone that exist at energies up to merely ~100 cm-1 above the dissociation threshold. The model thus gives a plausible explanation for an array of previously unexplained experimental trends in the 17O anomaly in ozone. Moreover, the creation of this model allows relative isotope-specific rate coefficients in ozone to be calculated under the wide range of relevant atmospheric conditions. These kinetic values produced by the model can aid in the interpretation of the 17O anomaly in the many substances in the atmosphere and in and other parts of the Earth system that have acquired a 17O anomaly through reaction or isotope exchange with ozone./nOverall, the results of the experiments and modeling presented in this dissertation provide key insights into the origin of the 17O anomaly in ozone, as well as findings relevant for applications of the unique ozone isotope anomaly to atmospheric and Earth science studies.

Advisor: Boering, Kristie A
Ceramic Packaging for Wireless Implantable Medical Devices

Implantable medical devices have tremendous therapeutic potential for both treatment of/ndisease states as well as monitoring for preventative care. To be effective, implants must/nperturb host tissue as minimally as possible, while simultaneously being able to withstand/nthe tissue environment for a significant portion of a patient’s life. Advances in wireless/npower transfer technology have made it possible to implant millimeter to sub-millimeter/nscale devices fully within the body, but these devices have not been demonstrated to work/nfor decadal time spans./nTypical packaging material for medical implants are polymers such as silicone or parylene,/nor titanium. However, polymers are not chronically hermetic due to their high water va-/npor permeability and titanium is not easily amenable to electromagnetics-based wireless/ncommunication. Ceramic materials, however, have a low water vapor permeability and are/ntransparent to radio-frequency radiation. Furthermore, they have had a long history in medi-/ncal implants and semiconductor processing methods have greatly increased the compatibility/nof ceramics processing with other materials./nThis thesis explores the use of ceramics as packaging materials for wireless, miniaturized,/nimplantable medical devices. An alumina-titanium hybrid package is first demonstrated for/na millimeter-scale ultrasonically-coupled wireless implant. Sound propagation through solids/nin two different modes is investigated, test packages are assembled, and performance is eval-/nuated. Next, silicon carbide is explored as a potential packaging material for wireless radio-/nfrequency identification tags. A system for rapidly testing and aging silicon carbide thin-films/nis designed and demonstrated, and progress towards building chronic silicon-carbide encap-/nsulated radio-frequency identification tags is shown.

Advisor: Maharbiz, Michel M