VictorJuiz/thesis huggingface dataset:
Cultural competence in teaching immigrant-origin youth : the ethic of Cariño
Keywords: Education.

This dissertation documents the elements that characterize the perspectives and practices of four high school teachers identified as highly effective educators working with immigrant-origin Latina and Latino students in urban settings. They are distinguished in consistently taking into account their students' cultural backgrounds and personal narratives. Using portraiture methodology, this study examines the development of their cultural competencies and the myriad ways each one promotes, supports, and celebrates the learning of their immigrant-origin Latinx students. Data sources include semi-structured interviews with the teachers, administrators, and members of the community, classroom observations and audio files, extensive field notes, and demographic data about the local context of the school where the four teachers have been teaching. The teachers' commitment to serve immigrant-origin students was manifested in their persistent efforts to get to know their students well, to build strong relationships and to validate their voices. With rigor and thoughtfully planned lessons, they engaged their students in Socratic discourse about controversial current political issues and debates. These teachers demonstrated cariño, an ethical and moral foundation of teaching and education more generally. The ethic of cariño is explored and further conceptualized throughout this work. Eight emergent themes were found to demonstrate the ethic of cariño—four focused on perspectives and four on practices. The four perspectives that drove these teachers ranged from critical consciousness and equity-driven perspectives to embracing a reflective ethos viewing their students wholistically. The practices they manifested included curricular rigor and building relationships with students as well as engaging them and developing relevant curricula. The four perspectives and practices were not fixed categories, and all four teachers illustrated them in different degrees. The data sources revealed a fluid and dynamic relationship between the teacher practices and the teacher perspectives—a cyclical process that was generative in nature and informed the teacher's instructional choices. What was the same was how these eight themes combined in their teaching to illustrate the ethic of cariño that teachers used in approaching their immigrant-origin students. The portraits of the four teachers affirm existing research on the potential equity and culturally responsive contributions that teachers who work with immigrant-origin Latinx youth can provide in their classroom context. This work raises questions to the field about how teachers understand and make sense of the lived experiences of immigrant-origin youth and how they might develop their teaching craft to promote equity and social justice in their approaches to culturally and linguistically diverse students
Dark, dreary mines : bituminous coal in the United States, 1865-1900
Keywords: History.

In 1900, the bituminous coal industry was highly competitive—a fact that set it apart from many other industries. Both miners and the people who operated the mines believed that too many miners and too many mines produced too much coal. The competition made the industry dysfunctional; miners regularly had too little work to do. This dissertation focuses on the groups that caused this problem and those who tried to fix it. It answers questions about how labor unions came to be considered monopolies at the same time that bituminous coal had no monopoly. Railroads caused mines to open because they needed traffic. Highly speculative, very expensive, and politically connected new railroads in the southern Appalachian Mountains were particularly desperate to recoup their costs. Coal provided a solution. Railroads offered preferential freight deals to those to whom they owed money and pursued other means of influencing the coal market. As a result, railroads expanded the scope of the coal market and intensified competition within and among coal-mining regions. The steel industry also contributed to the dysfunction. Andrew Carnegie, the nation's largest steel producer, developed a close partnership with Henry Clay Frick, the nation's largest producer of metallurgical coal. The close partnership seemed to portend stability for Frick's coal company. The steel industry was remarkably stable—exactly the opposite of the bituminous coal industry. Carnegie, by investing deeply, helped Frick quickly grow his business beyond even Carnegie's demands for coal. While Frick wanted to use his excess capacity to bring stability to the coal industry, Carnegie wanted to use Frick's excess capacity to control his competitors. Carnegie, who always had the upper hand, always won out, and the coal industry suffered as a result. Coal mine operators made slim or sometimes no profits. Coal miners suffered even more. In what was known as the Central Competitive Field, miners and operators teamed up to try to bring stability to the industry in a series of Joint Conferences of Miners and Operators. They looked to maintain power against the railroads by forming democratic associations to fix wages and ensure profits to operators. They had measured success in the 1880s and 1890s. But by the end of the century, changing tactics and decreasing attention to democracy led them to more closely resemble a trust
"Death, Where Is Thy Sting?" : British spiritualists and the First World War
Keywords: History.

This dissertation examines the widespread yet underexamined phenomenon of spiritualism in Britain during and immediately following the First World War. While contemporary and historiographical interpretations of the war tend to emphasize its futility and senselessness, this dissertation highlights a population of Britons who, in their belief that death was not extinction, managed to find meaning and consolation in the midst of a seemingly irredeemable conflict. Primarily cultural in its approach, the dissertation draws on a range of sources, including séance transcripts, spirit photographs, letters, diaries, and spiritualist publications. The dissertation examines the complex ways in which spiritualism incorporated and refigured elements of British culture. It highlights the women at the forefront of wartime spiritualism who, by developing their own psychic faculties, sought direct communion with their dead. While the patriarchal British state was sending their loved ones to die and dictating their burials, spiritualist women re-domesticated death, re-feminized mourning, and found novel forms of agency. Meanwhile, séance rituals also provided a way to re-imagine elements of the traditional Victorian "good death." In the religious realm, spiritualism was, for some, an alternative to orthodox Christianity; for others, Christianity and spiritualism were complementary and compatible, with spiritualism providing objective assurance of life after death at a time when the Church's response to the war seemed insufficient. Wartime spiritualists also had complex and contradictory understandings of colonial subjects and racial others, particularly in their conceptions of the far and Middle East: many spiritualists revered the East as a paragon of spiritual evolution—yet with this evolution came a certain naïveté and childishness. Mediums channeled not only dead soldiers, but also Eastern spirits who delivered psychic wisdom in broken English. Though sometimes unruly, these subaltern spirits were always eventually subdued, reaffirming British supremacy at a time of unstable imperial politics and colonial agitation. Finally, wartime spiritualism not only reconnected the living and the dead, but also provided a philosophical and theological justification for the conflict. Spirits relayed redemptive prophecies, often socialist in tone, declaring that the war would result in the spiritual evolution of humanity, the end of sectarianism and national strife, and the dawn of universal brotherhood
Decentralized data analysis : genome-wide association studies and other biomedical applications
Keywords: Physics.

The recent growth of data with potential medical ramifications has led to a better understanding of complex disease pathways and risk factors. Currently, much of the medically and clinically-relevant data is generated and maintained in decentralized silos. As the size and sensitivity of this data increases, it is becoming exorbitantly expensive, unsafe, and impractical to host entire datasets in a centralized location. Meta-analysis techniques offer a feasible solution; however, they can introduce bias or may not be applicable in certain cases (e.g. small sample sizes). Federated learning can be used to combine some of the advantages of both data centralization and meta-analysis. I will describe how three optimization algorithms (Newton's method, alternating directions method of multiplier and Anderson accelerated Douglas-Rachford splitting) can be used with secure sum or partially-homomorphic encryption techniques to perform decentralized regression-based association analysis. I will show that these techniques are practical in many low-dimensional settings and that some can be scaled to computationally intensive tasks such as genome-wide association studies (GWAS) at consortium scale. Finally, I will introduce our federated GWAS platform, HyDRA
Deep learning for predicting antigen presentation
Keywords: Genetics.

The presentation of antigens by Human Leukocyte Antigen (HLA) class II molecules is an essential component of adaptive immune responses. Accurate prediction of which antigen fragments are likely to be presented by class II molecules will be of great value for vaccine development and cancer immunotherapies. However, current computational methods trained on in vitro binding data have limitations for accurately predicting class II antigen presentation. Here, we describe MARIA (MHC Analysis with Recurrent Integrated Architecture), a multimodal recurrent neural network for predicting the likelihood of presentation for a given candidate peptide. In addition to in vitro binding measurements, MARIA is trained on peptide HLA ligand sequences identified by mass spectrometry, antigen gene expression levels, and protease cleavage signatures. By integrating these diverse features and leveraging both improved training data and a novel machine learning framework, MARIA (AUC=0.89-0.92) outperformed existing methods in validation data sets and allowed identification of immunogenic epitopes in lymphomas and celiac disease. Across several independent early phase cancer vaccine studies, peptides with high MARIA scores were more likely to elicit strong CD4 T-cell responses. In summary, MARIA improves identification of human peptide immunogens for diverse applications and can be accessed at https://maria.stanford.edu
Deep learning in vision-based robotic manipulation : towards generalization and fast inference
Keywords: Electrical Engineering.

In the past decade, researchers are looking at bringing robots into our daily lives, and automating services such as taxis, delivery, house-works, and even medical procedures. One of the major roadblocks in making this leap is the diversity and uncertainty in the environments that the robots need to work in. Machine perception, i.e. understanding of the environment through visual, audio, and contact signals, is indispensable in such diverse and uncertain environments, and is a hard problem in itself. Further, the environment is changing, due to human activities and other factors, and robots need to react to the changes quickly. Recent developments in deep learning, especially computer vision, has brought us closer to achieving the goal of bringing robots into our daily environments. However, deep learning methods require a large amount of data with annotated labels, and new datasets and annotations need to be collected for each new task. Deep reinforcement learning algorithms have also achieved good performance on a range of locomotion or manipulation tasks, but the amount of interactions required to train most algorithms is so large that it could take days even with parallel simulation engines. Highly data-efficient models and learning algorithms are needed to help robots learn faster and with less human effort. Additionally, when designing a learning-based solution to a robotics task, inference speed needs to be taken into consideration so that the robot can respond to changes quickly. This thesis introduces methods to improve training data efficiency and inference speed for vision-based robotic manipulation. To improve data efficiency of models, we analyze properties and structures of the specific problems, and build structural biases into the models based on the insights obtained. In addition, we demonstrate self-supervised learning of the perception model on real images, enabling robots to collect their own training data without requiring human annotations. To improve robots' response speed, when learning motion policies we design learning algorithms to always explicitly learn the distribution of promising actions, instead of learning an action evaluation function which requires online optimization during runtime. The proposed methods are integrated into end-to-end systems and tested on real robots on two tasks: vision-based robotic grasping, and rope manipulation and knotting
De-essentializing 'Hispanic': A Critical Approach to Ancestry Estimation with FORDISC 3.1
Keywords:  Center for Latin American Studies
forensic anthropology
FORDISC
biological anthropology
physical anthropology
admixture
Stanford University
Center for Latin American Studies
Thesis

Latin American populations exhibit a high degree of admixture due to the region’s complicated history of colonialism, migration, and settlement. Commonly used methods currently employed in forensic anthropology, such as FORDISC 3.1, often fail to account for the diversity in morphological signatures of the peoples who comprise this region and, in turn, effectively estimate ancestry or affinity. This thesis explores this program’s limits and challenges, using both ideal and realistic preservation case measurements for Latin American populations. Mosaic plots, multiple correspondence analyses, principal components analyses, and mean posterior probability bar graphs were employed to examine the program’s outputs. It was found that FORDISC 3.1 needs improved reference samples and socially-relevant classification labels in order to more accurately classify Latinx individuals by ancestry. These results are especially useful and important now, given the context of the humanitarian crisis along the U.S.-México border. This thesis concludes by promoting the use of admixture approaches and a fuller disentanglement of the biological science of forensic anthropology from the socially-driven frameworks of law enforcement investigation.
Defining natural killer cell responses to HIV
Keywords: Immunology.

Human immunodeficiency virus (HIV) remains a major global public health issue, and in the continued absence of a cure or vaccine, novel treatment and prevention strategies are needed to combat the ongoing epidemic. Many lines of evidence have suggested that natural killer (NK) cells, effector cells of the innate immune system that rapidly respond to virus-infected and malignantly transformed cells, can contribute to protection against HIV acquisition and disease progression. Here provide a characterization of methods of NK cell targeting of HIV, encompassing both natural receptor-ligand interactions in the setting of in vitro infection as well as in HIV-infected individuals, as well as via the use of bispecific antibodies to specifically target NK cells to HIV-infected cells. We first optimize an in vitro co-culture system to detect HIV-specific NK cell responses to autologous infected cells. We then use a combination of single cell transcriptomics and mass cytometry to characterize the features of NK cells in these co-cultures. Using single cell RNA-seq, we find a dominant interferon-driven gene signature in NK cells responding to HIV-infected cells. In addition, by mass cytometry profiling of NK cell phenotype and function, paired with profiling of ligand expression on infected CD4 T cells, we identify candidate receptor-ligand interactions (NKG2D/MIC-A/B and ULBP-1/2/5/6, and NKp30-B7-H6) involved in recognition mechanisms, which we then validate using CRISPR knockout of the corresponding ligands on target cells. We thus identify mechanisms of NK cell activation and response against HIV. We then study whether HIV-infected individuals treated with antiretroviral therapy (ART) possess alterations in NK cells that may make them more responsive to a second, in vitro exposure to HIV. We once again use mass cytometry to profile NK cell phenotype and function in both treated, HIV-infected individuals and healthy controls and find that, while there is a shift in the pattern of expression of NK cell receptors including NKp30 and CD2, the overall phenotype and frequency of the subset of cells that respond to in vitro HIV stimulation is not changed. We thus find that while the NK cell repertoire is altered in treated, HIV-infected individuals, it does not become more HIV-specific. Lastly, we develop and test a bispecific antibody that targets HIV gp41 and the NK cell activating receptor CD16. We show that this bispecific antibody has increased affinity and avidity to CD16, and is thus able to robustly enhance NK cell targeting of infected cells. This provides a means for controlled targeting of NK cells to infected cells. Overall, we identify multiple mechanisms that may hold promise to improve NK cell activity against HIV-infected cells. We discuss the extension of these findings in improving NK cell-mediated immunotherapy in HIV infection
Defining the human innate immune response to dengue virus infection
Keywords: Immunology.

Dengue virus (DENV), a serious cause of morbidity in the Americas and Southeast Asia, is the most prevalent arthropod-borne virus in the world. During DENV infection, innate immune cells not only serve as a first line of defense, but also as sites of viral replication. Consequently, their response to infection affects the extent of viral spread and activation of the adaptive immune response. Here we present three stories exploring the innate immune response to DENV infection with a focus on natural killer (NK) cells and monocytes. We first examine how upregulation of HLA class I molecules by DENV-infected cells serves to suppress the NK cell response. Next, we investigate how the immune response to DENV infection differs between children and adults, with a particular focus on changes in the NK cell receptor-ligand repertoire. Finally, we explore the susceptibility of different monocyte subsets to the two different routes of dengue infection: direct infection and antibody-dependent enhancement (ADE). To conclude, we discuss some new questions that have arisen from this work and propose future studies
Deranging the Senses through Space and Time: European Classical Music Festivals in the Twenty-First Century
Keywords: Stanford Anthropology
classical music
festivals
arts management
Thesis

In the postwar period, classical music festivals have increased in number and risen in stature as more marketable alternatives to traditional forums like local symphony orchestras and opera houses. In the summer of 2019, I visited three festivals to experience firsthand their interventions in redefining classical music today. Cloistered gardens, concert halls, and open-air plazas filled with audiences and music became my field sites, and I interviewed festival organizers, music critics, and audience members to interrogate what compelled their decision-making. How do festivals toggle between a universal ideal latent in classical music and the inherent particularities of the audiences, venues, performers, and histories that form their identities? How do they participate in the cultivation of refined aesthetic palettes in their audiences, while proselytizing classical music as an inclusive pedagogy that might bridge differences in class, language, and culture? In the first chapter, I consider how festivals are impelled to beget the new, that evergreen mandate for sponsors of the arts. In the second chapter, I question how festivals forward their own interpretations of place, one that is always necessarily a “meeting place” between local, national, and global identities.
Design and clinical applications of protease-activated optical chemical probes
Keywords: Chemical and Systems Biology.

Tumor resection remains one of the best ways to ensure a positive outcome for cancer patients. Intraoperative differentiation between tumor and healthy tissue is critical and tools that can aid surgeons make these important surgical decisions are being pursued in various biomedical/engineering disciplines. Here, I describe chemical tools that are designed to sense the tumor microenvironment, activate in the tumors, and produce an observable signal, thus allowing for surgical margin detection. Proteases are enzymes that hydrolyze peptide bonds and play key roles in normal physiology as well as in disease. In cancer, tumor-associated macrophages, which are immune cells, release various proteases which cleave molecules used for signaling, tissue repair, angiogenesis, and degrade the extra-cellular matrix. While there are methods to analyze protease mRNA and protein levels, they do not reflect the proteolytic activity of the cancer micro-environment. Using fluorescently-quenched optical chemical probes, we are able to dynamically monitor this protease activity. This work is broadly divided into two parts: 1) Clinical applications of optical chemical probes for imaging disease and 2) Design strategies of protease-activated optical chemical probes. Chapters 2-4 describe how clinical considerations guided us to optimize chemical probes to be compatible with imaging equipment used in the clinic. We find that these optical chemical probes augment surgical workflows in the operating room and enhance pathology analyses, allowing clinicians to make more accurate diagnoses. In Chapter 6, we discuss the development of protease-activated chemical probes by directly screening tumor samples. This unbiased approach allows us to design chemical tools that responds more accurately to the complex milieu of proteolytic activity found in actual tumor microenvironments