VictorJuiz/thesis huggingface dataset:
Interpreting contact interactions to overcome failure in robot assembly tasks

A key challenge towards the goal of multi-part assembly tasks is finding methods for robust sensorimotor control in the presence of uncertainty. In contrast to previous works that rely on a priori knowledge on whether two parts match, we propose a method to learn this through physical interaction. This method involves a hierarchical approach that enables a robot to autonomously assemble parts while being uncertain about part types and positions. In particular, the method's probabilistic approach learns a set of differentiable filters that leverage the tactile sensorimotor trace from failed assembly attempts to update a robot's belief about part position and type. This enables the robot to overcome assembly failure. Through experiments, we demonstrate the effectiveness of the proposed approach on a set of object fitting tasks. The experimental results indicate that the proposed approach achieves higher precision in object position and type estimation, and accomplishes object fitting tasks faster than baselines

Keywords: Mechanical Engineering.
Advisor: Bohg Jeannette
The intersections of education with housing and affordability : essays on impacts to schools, students, and teachers

This dissertation explores the question of how housing policy and the availability of affordable housing affect education. It consists of three papers that collectively provide evidence on the ways that shortages of affordable housing impact students and teachers, as well as examine the effects that policies addressing these shortages can have on educational equity and opportunities for disadvantaged students. In the first chapter, I examine the effect that low-income housing development has had on the racial, ethnic, and economic diversity of neighborhood public schools using evidence from the Low-Income Housing Tax Credit (LIHTC), the most important federal policy instrument incentivizing the supply of affordable housing. Using a regression discontinuity design, I find that LIHTC development did not result in a change in school composition on the nationwide level, but significantly increased minority student enrollment in predominantly white areas. In the second chapter, I estimate the short- and medium-term impacts that a rapid rehousing and homelessness prevention program has on homeless students, focusing on the outcomes of school and district mobility, attendance, and behavioral referrals. I use generalized difference-in-difference and event study models to find, among other results, that participation in the program had positive behavioral impacts but increased absences for students rehoused to faraway cities. In the final chapter, I and co-authors explore the prevalence and implications of economic anxiety among teachers in a high cost urban district using a combination of survey and administrative data. We find that economic anxiety is widespread among surveyed teachers and that it is highly predictive of teacher departure from the district, increased teacher absences, and more negative attitudes toward their jobs

Keywords: Education.
Advisor: Dee Thomas S. (Thomas Sean) 
Loeb Susanna
Reardon Sean F.
The inter-subject variability of ventral visual cortex

The human ventral visual stream is a processing stream in the human brain that is involved in visual perception and recognition. This stream contains a multitude of brain regions spanning the occipital lobe and the ventral aspect of the temporal lobe. An unanswered question is: How consistent are functional and microanatomical characteristics of the ventral visual stream across individuals? In study 1, I quantified if and how cytoarchitectonic areas, defined as areas that vary significantly in their cell density across the 6-layered cortical ribbon, of the ventral stream are linked to macroanatomical landmarks and if they are consistent across people. In study 2, I quantified the degree to which functional regions in ventral temporal cortex (VTC) and lateral occipito-temporal cortex (LOTC) are consistent across individuals. In study 3 I tested how responses in functional re- gions processing faces and bodies in VTC relate to behavioral judgements of ambiguous images and to what degree this relationship is consistent across individuals. Results of studies 1 -- 3 revealed strik- ingly high consistency of functional regions and cytoarchitectonic areas relative to macronanatomical landmarks and across people, and a consistent relationship of responses in face- and body-selective regions to behavioral judgements. These findings led me to ask in study 4: what principles drive this organization? Thus, in study 4, I investigated the role of experience in shaping the functional layout of the ventral stream by studying the functional organization of VTC in congenital blind partici- pants. I found that without visual input, the functional organization of VTC is substantially more heterogeneous in congenitally blind than sighted participants. This discovery suggests that common experience in sighted people contributes to their common functional organization of VTC. Together, results of these studies suggest that both the function and cytoarchitectonic organization of VTC is much more consistent across individuals that previously thought, and that visual experience plays an important role in shaping its functional organization. These data provide an important foundation for future studies that investigate both innate and experience-related organizational principles of the human ventral stream

Keywords: Psychology.
Advisor: Grill-Spector Kalanit 
Norcia Anthony Matthew
Yamins Daniel
Intimate radicals and radical intimacies : East European Jewish women in the early twentieth-century Anglo-American Imaginary

This dissertation tells the story of romantic ties between a handful of East European Jewish women and patrician-born, Anglo-American intellectuals on the radical left in the early twentieth century. Through the use of personal archives, published and unpublished book manuscripts, memoirs, and poetry, the English and Yiddish press, and oral histories, it adds a much needed chapter to existing scholarship about Jews and modern American discourses of race, class, and gender. I argue that these interclass and interethnic relationships were an attempt on both sides to transcend the provincial trappings of their births - whether it be the East European shtetl or victorian America - and lay claim to new modern, cosmopolitan identities. My research demonstrates that young, Anglo-American intellectuals and writers articulated a sense of crisis about the United States by exploring emerging racial paradigms, shifting definitions of masculinity, and new modes in American culture through their desires for young East European Jewish women. At the same time, I challenge existing models of Jewish women's Americanization that rely on traditional feminine roles of marriage, domesticity, and motherhood. I argue instead that the romantic interests of these East European Jewish women in Anglo-American men were an attempt to meld class aspirations and a desire to integrate with deeply felt political views rooted in foreign revolutionary traditions and cosmopolitan identities. As committed socialists, American-born men and East European Jewish women hoped to put ideological principles into practice at the most intimate level

Keywords: History.
Advisor: Zipperstein Steven J.
Freedman Estelle B.
Michels Tony
Rodrigue Aron
Intimate strangers : cross-cultural exchanges between Indian and Western musicians, 1800-1950

In my dissertation, I examine the ways in which musical practices in two different geographical spaces, Europe and South Asia, changed as a result of cross-cultural encounters with each other's musical traditions from the nineteenth century onwards. I combine a relational approach—one that highlights the interconnectedness of such exchanges—with insights provided by adaptation theory, which enables such practices to be located "thickly" in their cultural, historical, and social contexts, and reveals parallels between Indian and European strategies for incorporating non-autochthonous elements. Starting with Abbé Vogler and Carl Maria von Weber, pioneers with regard to European engagements with non-European musical traditions, and ending with the South Asian musicians Qazi Nazrul Islam and Baba Allauddin Khan (the guru and mentor of Pandit Ravi Shankar, the internationally-acclaimed sitar maestro), I examine some key figures from Europe and India, notably Rabindranath Tagore, John Foulds, Maurice Delage, and Albert Roussel, and assess their contributions to the development of their own musical traditions through their engagement with and incorporation of foreign musical elements. By doing so, my dissertation also seeks to examine how music contributed to the development of local cosmopolitanisms in South Asia and Europe, and to determine the long-term impact of such exchanges. It focuses on the challenges faced by musicians, both European and South Asian, in incorporating elements from outside their own traditions. These include the examination of the difficulties involved in transmitting music across cultures when sound recordings could not be made; the interpretive obstacles posed by non-autochthonous music to composers, performers, and audiences of the receiving culture; and the limits to incorporating different techniques of performance, whether vocal or instrumental. Analyses of cross-cultural exchanges also call for the judicious use of an approach that Mantle Hood has termed "bi-musical." The methodology adopted in this dissertation pays especial attention to all these aspects in the project of reassessing the cross-cultural exchanges that took place between Indian and European musicians in the colonial era. The dissertation, thus, draws attention to the challenges and constraints within which numerous agential choices and adaptive decisions that go into the making of august musical traditions, often erroneously assumed to be pure and whole, but which are, actually, profoundly shaped by productive contacts with non-autochthonous traditions. Without at all ignoring the question of power relations, this dissertation also seeks to highlight the necessity of examining the material and semiotic dimensions of cross-cultural exchanges, through the study of the contributions of some of the most important European and Indian musicians from the nineteenth to the mid-twentieth centuries

Keywords: Music.
Advisor: Grey Thomas C. 
Hinton Stephen
Schultz Anna C.
Investigating Allopregnanolone’s Effect on α3-NKA and GABAR-delta Subunit Through BDNF-TrkB Pathway in Undercut Model of Injury in Mice

Post-traumatic epilepsy is a recurrent seizure disorder marked by over-excitation in the brain after injury. Allopregnanolone (ALLO), a metabolite of progesterone, has previously been used as an anticonvulsant, though not as the first line of treatment. It has also been shown to have neuroprotective effects in other neurodegenerative diseases such as Parkinson’s and amyotrophic lateral sclerosis (ALS). It has not been extensively studied as a possible neuroprotectant in epilepsy. Currently, little is known about allopregnanolone’s mechanism of action. Using the undercut (UC) model of injury in mice, this study demonstrates allopregnanolone’s anatomical effects on post-traumatic brain tissue and further explores its mechanism of action. After partial neocortical isolation (UC injury) several allopregnanolone injections were given and immunohistochemistry was used to visualize and compare density of molecules relevant to inhibition in the brain amongst treatment groups, namely BDNF, Na+/K+ ATPase (NKA), and the GABA receptor (GABAR) delta subunit. It was originally proposed to assess the expression of BDNF, a neurotrophic factor known to be decreased after brain trauma; but, this was not possible due to time constraints. However, a literature review, past studies in this lab and preliminary images suggest that BDNF does decrease after undercut injury. As expected, the density of NKA in UC tissue significantly decreases compared to naïve tissue. Interestingly, in these experiments ALLO did not increase the expression of NKA and even slightly decreased it further in injured tissue. It was originally thought that the increased presence of NKA should make the membrane potentials of inhibitory interneurons less negative and promote inhibition in the brain, protecting against epileptogenesis. In the presence of ANA 12, a TrkB receptor blocker, there were small decreases in NKA that did not reach statistical significance. This indicates that ALLO’s mechanism of action may not primarily involve NKA. As another potential target of allopregnanolone, the GABA receptor (GABAR) delta subunit was studied as a modulator of inhibitory activity. There was an insignificant decrease in the subunit after injury and a slight recovery after treatment with ALLO. These results highlight the complicated nature of the possible targets and mechanism of action for allopregnanolone as a potential protectant against post-traumatic epilepsy.

Keywords:  Department of Biology
Biology
Traumatic brain injury
Allopregnanolone
BDNF
NKA
GABA receptor
Epilepsy
Thesis
Advisor: Prince David A.
Heller H. Craig
Investigating mechanisms of repeat-associated non-aug translation in neurodegenerative disease

A novel form of translation has been discovered in several neurodegenerative and muscular diseases which contain causative microsatellite expansions. This Repeat-Associated Non-ATG translation (RAN translation) occurs in the absence of a canonical AUG codon at disease-causing expansions. Expansion-harboring transcripts form com-plex secondary structures such as hairpins or G-quadruplexes. The protein products of RAN translation are toxic in cell culture and disease models ranging from yeast to mice and are found to accumulate in disease-relevant patient tissues. The basic mechanisms of RAN translation initiation have not been thoroughly investigated. The inhibition of RAN translation to prevent toxic protein production has been proposed as one therapeutic option for this class of diseases. Thus, a comprehensive characterization of machinery involved in and molecular mechanisms underlying RAN translation are of utmost importance in designing therapeutic strategies. Understanding how these mechanisms differ from AUG-initiated translation will broaden our understanding of non-canonically initiated translation. In Chapter 2, I perform a genetic screen in yeast in order to identify novel trans regulators of RAN translation. I found that RPS25 specifically regulates the efficient RAN translation of GGGGCC repeat expansions in the C9orf72 gene. Moreover, I found that RPS25 can also regulate the RAN translation of ATXN2 and HTT CAG expansions. Importantly, the reduction of RPS25 in patient-derived cell lines reduced the amount of DPRs detected and extended survival in a c9ALS Drosophila model. The result in Drosophila provides further evidence to support the model that DPRs are the predominant toxic species driving neurodegeneration. I provide data for one of the first protein factors identified to be involved in RAN translation and future work will delve into the precise mechanisms by which RPS25 coordinates an increase in efficiency of RAN translation. Ribosomal protein deficiencies are known to cause a whole host of consequences including ribosomal biogenesis defects and subsequent nucleolar stress. The effect of the deletion of RPS25 in cells is investigated in Chapter 3. I find that in our system, RPS25 is likely not functioning through a p53 axis to account for the effects seen in Chapter 2. Furthermore, I generate two mouse models: one strain harbors a deletion of exon 2 in the mouse RPS25 gene and the second strain is an RPS25 exon 2 floxed strain. I dis-cuss phenotypes observed in a small cohort of the RPS25 knockout strain mice and end with a discussion of future studies that will utilize these two strains

Keywords: Biology.
Advisor: Gitler Aaron D.
Brandman Onn
Frydman Judith
Puglisi Joseph D.
Stearns Tim
Investigating mitochondrial transport and quality control in drosophila melanogater models of neurodegenerative disease

Mitochondria are the major source of cellular ATP in eukaryotic cells and play several roles critical to cellular health and functionality including Ca2+ buffering and cell death signaling. Neurons have complex architectures with specialized subcompartments and local energetic and metabolic needs. To ensure constant mitochondrial integrity and supply, neurons rely on axonal transport of mitochondria, fission, fusion, and mitophagy. Evidence suggests that neurons with particularly long axons, high metabolic demands, or toxic loads may be more vulnerable to defects in mitochondrial transport or quality control processes. Parkinson's Disease and Amyotrophic Lateral Sclerosis are just two neurodegenerative diseases associated with defects in mitochondrial dynamics. In this dissertation, we address the role of mitochondrial transport and quality control in Drosophila models of neurodegenerative disease. In particular, we investigate Valosin Containing Protein (VCP/p97), a ubiquitously expressed ATPase with diverse cellular functions. By employing live-imaging methods in Drosophila larval axons and performing genetic interaction experiments, we discover that VCP regulates dynein-dependent axonal transport of mitochondria. Additionally, we investigate human pathogenic VCP mutations in our flies and discover pathogenic VCP mutations impact mitochondrial motility in a similar way as knocking down VCP. Finally, we demonstrate that enhancing Miro restores mitochondrial density loss in axons, rebalances directional mitochondrial motility, and improves ATP production. Additionally, we investigate the function of Leucine-Rich Repeat Kinase 2 (LRRK2) protein in mediating mitochondrial quality control. We identify a novel role for LRRK2 in promoting the removal of Miro from the OMM and facilitating mitophagy. We show this function of LRRK2 is disrupted by pathogenic mutations in Drosophila and patient derived cellular models of PD. Further, we demonstrate that impaired Miro degradation is a shared feature across several forms of PD. Finally, in our Drosophila model of LRRK2G2019S PD, we observed beneficial impacts in locomotive behavior and neuron survival by reducing Miro. This work highlights the link between mitochondrial motility and quality control, and the importance of these pathways in neuronal health and disease. We provide evidence to implicate impaired mitochondrial motility and quality control in the pathophysiology of VCP- relevant ALS and LRRK2- relevant Parkinson's Disease. Finally, our work suggests that Miro exists at the nexus of several important mitochondrial signaling pathways and may be a promising therapeutic target as we seek to develop treatments for diseases of the aging brain

Advisor: Wang Xinnan
Fuller Margaret T.
Lu Bingwei
Reimer Richard J.
Investigating the Cardiotoxicity of Proteasome Inhibitors on iPSC Cardiomyocytes

Proteasome inhibitors (PIs) are a class of chemotherapeutic drug in treating multiple myeloma (MM), a cancer of plasma cells. PIs are an integral part of MM therapy, but their usage is limited by its cardiovascular side effects. Clinical cases show that patients have suffered from complications such as heart failure and sudden cardiac death after taking these drugs. The mechanism through which PIs cause these effects remains unknown. This study aims to use an iPSC-CM model to recapitulate and investigate the mechanism of cardiotoxicity caused by PIs. First, human iPSC-CMs were treated with three types of PIs (carfilzomib, ixazomib, and bortezomib) at doses and schedules relevant to their clinical usages. Doxorubicin, a well characterized chemotherapeutic known to have cardiac adverse side effects, was used as a positive control. We then conducted a series of in vitro investigations including contractility and viability assays to 1) determine whether iPSC-CMs adequately model clinical features of PI-induced cardiotoxicities and 2) to better understand their effects on the contraction of cardiomyocytes. Results show that the mechanism through which cardiotoxicity occurs is linked to the cells’ inability to contract when treated with moderate to high concentration of the drugs. Cells treated with carfilzomib, bortezomib, and ixazomib respectively showed high, moderate, and low levels of cardiotoxicity. The iPSC-CM model used in this study serves as a high-throughput, efficient approach to screen drugs associated with deaths due to cardiac adverse events in MM patients and will enable future studies to further investigate the effects of PIs on cardiomyocytes.

Keywords:  Department of Biology
Biology
induced pluripotent stem cell
cardiomyocytes
proteasome inhibitors
cardiotoxicity
Thesis
Advisor: Wu Joseph C
Cyert Martha S
Investigating the function of a mitochondrial phosphatase, PTPMT1, in Drosophila melanogaster

Mitochondria are complex organelles that play a variety of critical roles in the cell beyond the generation of ATP. Reversible phosphorylation, mediated by mitochondrially-localized kinases and phosphatases, is a central mechanism by which mitochondrial activities are regulated and by which tissue-specific mitochondrial functions can be achieved. PTPMT1 is a mitochondrial phosphatase and a vital regulator of mitochondrial activities. Current work points to roles for PTPMT1 in the regulation of mitochondrial respiration, dynamics, and ultrastructure through the modulation of pyruvate importation, the tuning of TCA cycle activity, and the synthesis of cardiolipin. PTPMT1 is ubiquitously expressed; however, little is known about its tissue-specific functions. Additionally, PTPMT1 has predominately been studied in vertebrate models, even though invertebrate models, namely Drosophila melanogaster, provide powerful genetic tools for the dissection of gene function. In Chapter 1 of this dissertation, I review the current knowledge surrounding PTPMT1 in vertebrate models. In Chapter 2, I introduce the Drosophila tracheal system and briefly review what is known concerning the mechanisms of tracheal liquid clearance and gas filling in the fly. In Chapter 3, I use RNA interference and CRISPR-Cas9 technologies to generate and validate Drosophila models of dPTPMT1 depletion. Using these models, I discover a new physiological role for dPTPMT1 in the process of tracheal liquid clearance and gas filling. I further show that gas-filling defects occur following molting in first instars with tracheal-specific knockdown of dPTPMT1 and are accompanied by subsequent activation of innate immune responses. First instars with dPTPMT1-depleted tracheae show mitochondrial clustering prior to failure of liquid clearance and gas filling, suggesting that an initial mitochondrial defect may be responsible for this phenotype. I further ask whether other mutants in the cardiolipin synthesis pathway phenocopy the tracheal phenotypes observed in dPTPMT1-depletion and find that they do not, indicating that dPTPMT1 likely acts through one of its other known substrates or perhaps through a novel substrate to mediate tracheal liquid clearance and gas filling in Drosophila. My work demonstrates a new cell-type specific role for dPTPMT1 in fly tracheal epithelial cells and establishes a new model for the exploration of dPTPMT1's physiological and cellular functions

Keywords: Developmental Biology.
Advisor: Wang Xinnan
Fuller Margaret T.
Reimer Richard J. 
Talbot William S.