VictorJuiz/thesis huggingface dataset:
In situ vascular graft generation and drug delivery system modeled by stromal cell- derived factor 1a and polylactide-co-caprolactone

Biodegradable polymers have potential as a scaffold material for making small diameter artery bypass grafts. To resist thrombosis, maintain biocompatibility and enhance the remodeling of the grafts, it is crucial to modify polymer scaffolds so that the grafts have anti-thrombogenic capacity and allow cell infiltration. In this study, two methods of aminolysis on electrospun poly-lactide-co-caprolactone (PLCL) nanofibers vascular graft are compared: plasma treatment method and Fmoc-PEG-diamine insertion method. Both methods successfully inserted amino groups on the polymer graft for heparin conjugation. However, plasma treatment resulted in significantly higher initial heparin density and higher heparin stability under simulated physiological conditions on PLCL nanofibers than Fmoc-PEG-diamine treatment. In addition, mechanical testing demonstrated that the plasma treatment method maintained PLCL nanofiber tensile strength after heparin conjugation while Fmoc-PEG-diamine insertion method compromised the mechanical property due to partial fiber melting and structure disruption. Subcutaneous implantation of the grafts in a rat model showed that heparin coating with both methods promoted cell infiltration. This study provides a rationale to optimize the biomolecule conjugation on electrospun PLCL scaffolds, and will have applications in tissue engineering vascular grafts and other tissues.

Advisor: Li, Song
Chronicles of Disappearance: The Novel of Investigation in the Arab World, 1975-1985

This dissertation identifies investigation as an ironic narrative practice through which Arab authors from a range of national contexts interrogate certain forms of political language, contest the premises of historiography, and reconsider the figure of the author during periods of historical upheaval. Most critical accounts of twentieth-century Arabic narrative identify the late 1960s as a crucial turning point for modernist experimentation, pointing particularly to how the defeat of the Arab Forces in the 1967 June War generated a self-questioning “new sensibility” in Arabic fiction. Yet few have articulated how these intellectual, spiritual, and political transformations manifested themselves on the more concrete level of literary form. I argue that the investigative plot allows the authors I consider to distance themselves from the political and literary languages they depict as rife with “pulverized,” “meaningless,” “worn out,” or “featureless” words. Faced with the task of distilling meaning from losses both physical and metaphysical, occasioned by the traumas of war, exile, colonialism, and state violence, these authors use investigation to piece together new narrative forms from the debris of poetry, the tradition’s privileged mode of historical reckoning./nIn the first two chapters, I bring together two novels with remarkable formal and structural similarities, Jabra Ibrahim Jabra’s al-Baḥth ʿan Walīd Masʿūd (In Search of Walid Masoud; 1978) and Elias Khoury’s al-Wujūh al-bayḍāʾ (White Masks; 1981). From these two works, I shape a general typology: the novel of investigation begins with the mysterious disappearance or death of its protagonist and proceeds as a search for causes and answers conducted by a metafictional frame narrator. In the second two chapters, I observe how the investigative model manifests both in Egypt, with Yūsuf al-Qaʿīd’s Yaḥduth fī Miṣr al-ān (It’s happening now in Egypt; 1977) and in Morocco, with Driss Chraïbi’s Francophone detective novel Une enquête au pays (1981), at approximately the same historical moment. In all of these novels, I argue, the absent protagonist represents a figure for political resistance that seemed to have disappeared in the disillusionment occasioned by the 1967 defeat—the peasant, the freedom fighter, the exilic intellectual, the Berber, etc.—while the self-questioning frame narrator stands in for the author himself, attempting to wrest meaning from the scattered, chaotic events of recent history.

Advisor: Larkin, Margaret
Interactions between computability theory and set theory

In this thesis, we explore connections between computability theory and set theory. We investigate an extension of reverse mathematics to a higher-order context, focusing in particular on determinacy principles, and an extension of computable structure theory to uncountable structures via set-theoretic forcing. We also look at computability-theoretic operations induced by ultrafilters, and the classical computable structure theory of ordinals as clarified by set-theoretic results.

Advisor: Montalban, Antonio
Neural Representation Learning with Denoising Autoencoder Framework

Understanding of how the brain works and how it can solve difficult problems like image recognition is very important, especially for the progress in developing an autonomous intelligent system. Even though we have a lot of experimental data in neuroscience, we are lack of theories which can glue all the observations together. One approach to understand the brain is to investigate the representation of sensory information in the brain at each stage, and try explains it with some computational level principle, for example an efficient coding principle. This thesis follows this approach./nIn this thesis, I use the denoising autoencoder framework to approach two unsolved problems in Computational Neuroscience. The first problem is learning the group structure in the group sparse coding model. I propose that it is possible to learn the group structure using gradient descent with a data denoising objective function. To verify the method, I train a model on the van Hateren's natural image dataset. The model with the learned group structure shows an improvement in denoising performance 15% (SNR) over the regular sparse coding model. Moreover, the group structure learned groups together sparse coding basis functions with similar location, orientation and scale./nThe second problem is to understand why we have grid cells. I proposed that a population of place cells and grid cells should be modeled as an attractor network with noisy neurons. Furthermore, this attractor network can be trained with the denoising autoencoder framework to memorized a location in 1D space (simplification of the actual problem where the location is in 2D space). I show that the retrieved location accuracy of the network with both place cells and grid cells is higher than the network with place cells alone. The performance difference is due to the activity of the grid cells acts as an efficient error-correcting code.

Advisor: DeWeese, Michael R
Lagrangian and Eulerian Forms of Finite Plasticity

Over the past half century, much work has been published on the theory of elastic-plastic materials undergoing large deformations. However, there is still disagreement about certain basic issues. In this dissertation, the strain-based Lagrangian theory developed by Green, Naghdi and co-workers is re-assessed. Its basic structure is found to be satisfactory. For the purpose of applications, the theory is recast in Eulerian form. Additionally, a novel three-factor multiplicative decomposition of the deformation gradient is employed to define a unique intermediate configuration. The resulting theory of finite plasticity contains an elastic strain tensor measured from the intermediate stress-free configuration. The constitutive equations involve the objective stress rate of the rotated Cauchy stress, which can be expressed in terms of the rate of deformation tensor. In their general forms, the Lagrangian theory can be converted into the Eulerian theory and vice versa. Because the Green-Naghdi theory has a strain measure that represents the difference between total strain and plastic strain, rather than representing elastic strain, it does not lend itself to a physically realistic linearization for the case of small elastic deformations accompanied by large plastic deformations. The proposed theory is well suited to describe this case as it can be linearized about the intermediate configuration while allowing the plastic deformations to be large. Differences between the linearized Green-Naghdi theory and the new theory are illustrated for uniaxial tension and compression tests.

Advisor: Casey, James
Policing China: Struggles of Capacity, Order, and Organization

Why would police officers look the other way when criminals run? Why would an officer fix a busted lock in exchange for the victim calling to say she reported a break-in by mistake? This dissertation investigates issues of front-line policing and security capacity in the People’s Republic of China. It probes the challenges faced by ground-level officers and their superiors as they attempt to do their jobs in the face of funding limitations, reform challenges, and structural issues that complicate police response. Drawing from 22 months of fieldwork in eight cities, the project uses interviews, station data, news reports, internal documents, and social media postings to understand how local policing in today’s China works./nThe data show that, despite China’s reputation as a highly securitized state that spends more on internal security than national defense, ground-level policing is plagued by problems of capacity that even a well-organized central ministry is, for the most part, unable to resolve. As a result, the local state has difficulty responding to nearly every type of crime except public protest. Only in the domain of stability maintenance are police able to overcome the problem of low capacity by redirecting limited resources, implementing reforms that overcome institutionalized biases, and centralizing ministerial control by wresting power away from local actors. Security capacity remains low, however, for other areas of policing such as response to theft, violent crimes, and drug control, all of which continue to face problems of limited resources, poorly devised or executed reforms, and insufficient assistance from higher ups./nThe result is that the internal security state in China suffers from weak capacity but can work well when Central officials redirect resources, bring local forces in line, and overcome institutional and cultural barriers to effective policing. This pattern explains why scholars and journalists who focus exclusively on protest control mistakenly bill the Chinese internal security state as strong and robust. It also gives us cause to rethink how we assess security capacity in authoritarian states, since scholars tend to look at protest control capacity and ignore everything else. In the Chinese case, a comprehensive review of ground-level police operations raises questions about capacity that challenge claims of authoritarian resilience. Capacity failures also demonstrate the limits of decentralized control over the Chinese local state, which for the police bureaucracy only exacerbates strains on frontline response.

Advisor: O'Brien, Kevin J.
Impact of residential versus outpatient substance abuse treatment on child welfare outcomes: A secondary analysis of NSCAW II data

Between 40–80% of substantiated child maltreatment cases in the United States contain some/ndegree of parental substance abuse. After child welfare becomes involved, outcomes for/nchildren of parents with substance abuse issues are substantially worse than for children of nonsubstance-/nabusing parents. While some studies have demonstrated that substance abuse/ntreatment can improve child welfare outcomes, results are largely inconclusive as to whether/nresidential substance abuse treatment is more effective than outpatient options. Using data from/nthe National Survey of Child and Adolescent Well-Being II, this study evaluates the effects of/nresidential versus outpatient substance abuse treatment on family progress for families involved/nin the child welfare system./nUsing propensity score weighting to control for substance abuse severity and other variables that/nmay select parents into treatment, results indicate that child welfare workers were more likely/n(RRR = 4.40, p = 0.026) to indicate that families had deteriorated or made no progress in cases/nwhere parents attended residential treatment. Placement of children in out-of-home care also/nincreased the likelihood that workers would indicate that a family had deteriorated or made no/nprogress./nAt the same time, results from this study indicate that child welfare workers were also more/nlikely (RRR = 3.77, p = 0.022) to believe that a family had made substantial progress when a/nparent attended residential treatment. This finding was especially true for parents when the/ncaseworker assessed domestic violence as a pre-existing condition (RRR = 7.89, p = 0.044),/nsuggesting a moderating relationship between treatment setting and caseworker assessment./nConsidering the importance of worker assessments to child welfare outcomes such as/nreunification and case closure, this study’s findings have implications for treatment assignment/nfor child welfare involved parents. Findings from this study also provide support for the/nprovision of ancillary services, such as domestic violence counseling in residential programs.

Advisor: Berrick, Jill
Empowering Teachers to Change: A Mixed Methods Examination of Equity-Oriented STEM Instruction

In this dissertation study, I employed mixed methods to examine the varied perspectives teachers have about equity-oriented STEM instruction and how their equitable teaching practices make certain academic and STEM identities available to their students. Both qualitative and quantitative data sources were collected from eight case study teachers and 24 focal high school students who participated in a summer residential college preparatory program for students from nondominant communities. Based on the eight case study teachers’ pre- and post-survey data, teaching philosophy statements, and other teacher materials (lesson plans, reflection responses, etc.), I highlight the two main perspectives on equity-oriented STEM instructions that teachers exhibited across the summer session: equity is equality and empowering students for success. The findings revealed how five teachers’ perspectives shifted over the summer from equity is equality to empowering students for success. Teacher learning was supported by the use of cultural artifacts and by the development of both collegial and teacher-student relationships./nThis study also analyzed the equitable teaching practices of two focal teachers. Specifically, the equity-minded focal teachers: 1) utilized culturally relevant teaching practices; 2) developed relationships with students; and 3) emphasized diverse perspectives and participation in the STEM fields. Drawing upon the practice-linked identity framework (Nasir, 2012; Nasir & Cooks, 2009; Nasir & Hand, 2008) I examined qualitative and quantitative data sources to show how material, ideational, and relational resources available in the focal teachers’ classrooms supported students’ identity development. These teachers’ teaching and classroom environments made three identities available to focal students, including capable learners, potential change agents, and future STEM professionals. Statistical analyses (p < 0.05) of students’ pre- and post-surveys indicated that students made significant gains in their identity development./nFindings from this research can inform the design of professional development experiences to develop equity-minded teachers. These include supports for teacher learning, developing equitable teaching practices, and fostering equitable learning environments.

Advisor: Nasir, Na'ilah
Bioconjugate materials for the study of pigment mobility in light-harvesting systems, protein-based formulations for hydrophobic actives, and conformational changes in conjugate vaccines

Techniques for the preparation, purification, and characterization of protein-based materials have allowed for advances in fields ranging from medicine to materials science. While great attention has been paid to the chemistries used in the attachment of molecules of interest to proteins, the importance of the linking group is often overlooked. Each chapter of this dissertation describes the use of linkers as functional design elements in three distinct projects. In Chapter One, the development and characterization of a minimal model for investigating the role of pigment mobility in photosynthetic light-harvesting antenna systems will be discussed. In this model system, pigment-protein and pigment-pigment interactions were altered through the use of pigment-protein linkers of various lengths and rigidities. Chapter Two explores new biocompatible bond cleavage reactions for the preparation of a new class of general protein-based formulations for hydrophobic actives, wherein the linker group imparts the critical properties to the system. Chapter Three will examine conformational changes in peptide-protein conjugate vaccines. The roles of specific methods of covalent modification and linker composition in these conformational changes are emphasized.

Advisor: Francis, Matthew B
When Public Participation Isn’t Enough: Community Resilience and the  Failure of Colorblind Environmental Justice Policies

Issues of health inequities and environmental hazards affect low-income communities of color throughout the US (Pastor et al, 2001; Morello-Frosch and Lopez, 2006). These communities are both rural and urban, and located in every corner of the US, but one area of California hosts a disproportionate share of environmental hazards in the form of toxic facilities, pollution, and health disparities. One San Joaquin Valley community, Kettleman City in Kings County, California is an unincorporated, rural community lacking political representation in environmental and land-use decision-making processes. This lack of influence in decision-making has led to the Kings County Planning Commission permitting a large, Class I landfill near Kettleman City that residents believe has a negative impact on their health./nUsing a single case study of Kettleman City and an environmental justice framework, this dissertation examined how rural communities with few resources can utilize community-based strategies to be meaningfully involved in the permitting process of a hazardous, Class I facility. Relying on planning and legal documents, participant observations at public meetings in 2013 and 2014, archival research, and in-depth interviews with 22 residents, organizers, and advocates, as well as government officials involved with the public meetings in 1990 and 2009, this study reveals the challenges and opportunities for meaningful involvement with local and state permitting processes that occurred in 1991 and 2009. By examining the community resident’s experiences with these two permitting processes, their challenges, strategies, and resilience for inclusion in the processes is demonstrated. Ultimately what is revealed are the limitations for using public participation to achieve environmental justice, the barriers to challenging state permitting decisions, and what is needed from government officials to work toward achieving environmental justice.

Advisor: Hutson, Malo
Corburn, Jason
The Making of Ignorance: Epistemic Design in Self-Tracking Health

This dissertation contributes to emergent scholarly work on the dynamics of ignorance in the production of power. Drawing on my study of the health self-trackers who identify under the banner of the “Quantified Self,” I examine the “choreography” of ignorance in two intersecting forces that arbitrate the experience of illness and well being. The first force reflects an emergent phenomenon of individuals co-opting the computational gaze of contemporary mass surveillance and turning it onto the embodied self, a redirection that sees its most vibrant and experimental manifestation in this self-tracking community. The second embraces newly formed and structured efforts that redistribute the attention of American medical science from treating illness to preventing illness. This new medical imperative is anchored to the individual, now called on to adopt tracking technologies not only as an act of self-care, but also as a remedial intervention into the very institutions and scientific processes that many self-trackers believe have failed them. Institutional actors, however, present such pursuits as a “democratization” of American medicine. The Quantified Self provides the anchoring social context from which I access the interplay of these two forces, allowing me to illustrate how three engagements with ignorance — selectivity, uncertainty and obscurity — are implicated in failures of epistemic justice./nEthnographic attention to ignorance remains minimal. Thus, the task of studying ignorance requires epistemic innovations. I explore Charis Thompson’s framework of ontological choreography as a tool to capture and analyze how ignorance is orchestrated to produce desired goals. I argue that the rhetoric of democratization of American medicine and the Quantified Self ethos is largely in service to the perceived needs of dominant groups and the establishment science the individual is called to help reform. I conclude that an analysis of ignorance offers an avenue to examine how novel technologies, new movements and fantastical speculations, all invested in rendering our bodies as “data,” reinforce existing dynamics of power.

Advisor: Saxenian, Annalee
Duguid, Paul
Speeding up distributed storage and computing systems using codes

Modern data centers have been providing exponentially increasing computing and storage resources, which have been fueling core applications ranging from search engines in the early 2000's to the real-time, large-scale data analysis of today. All these breakthroughs were made possible only due to the scalability in computing and storage resources offered by modern large-scale clusters, comprising individually small and unreliable low-end devices. Given the individually unpredictable nature of the underlying devices in these systems, we face the constant challenge of securing predictable and high-quality performance of such systems in the face of uncertainty./nIn this thesis, distributed storage and computing systems are viewed through a coding-theoretic lens. The role of codes in providing resiliency against noise has been studied for decades in many other engineering contexts, especially in communication systems, and codes are parts of our everyday infrastructure such as smartphones, WiFi, cellular systems, etc. Since the performance of distributed systems is significantly affected by anomalous system behavior and bottlenecks, which we call "system noise", there is an exciting opportunity for codes to endow distributed systems with robustness against such system noise./nOur key observation – channel noise in communication systems is equivalent to system noise in distributed systems – forms the key motivation of this thesis, and raises the fundamental question: "can we use codes to guarantee robust speedups in distributed storage and computing systems?". In this thesis, three main layers of distributed computing and storage systems – storage layer, computation layer, and communication layer – are robustified through coding-theoretic tools. For the storage layer, we show that coded distributed storage systems allow faster data retrieval in addition to the other known advantages such as higher data durability and lower storage overhead; for the computation layer, we inject computing redundancy into distributed algorithms that are robust to stragglers or nodes that are substantially slower than the other nodes; for the communication layer, we propose a novel data caching and communication protocol, based on coding-theoretic principles that can significantly reduce the network overhead of the data shuffling operation, which is necessary to achieve higher statistical efficiency when running parallel/distributed machine learning algorithms.

Advisor: Ramchandran, Kannan