VictorJuiz/thesis huggingface dataset:
Actomyosin Dynamics During Coordinated Cell Movements in Embryonic Wound Repair

Embryos repair epithelial wounds rapidly, in a process driven by collective cell behaviors. Upon wounding, filamentous actin and the motor protein non-muscle myosin II polarize in the cells adjacent to the wound, forming a supracellular cable around the lesion. Contraction at the wound margin coordinates cell movements and drives rapid wound closure. Using FRAP in Drosophila embryos, we found that myosin turnover at the wound margin was slower than in actomyosin networks with reduced contractility. Using laser ablation we showed that tension in the wound margin cable increased as wound closure progressed, which was associated with reduced myosin turnover. Reducing tension resulted in increased turnover and loss of myosin from the wound edge. Finally, myosin motor activity was necessary for its stabilization around the wound and for efficient wound closure. Our results indicate that mechanical forces regulate myosin dynamics during embryonic wound repair, however we could not discount regulation of myosin through its binding partner, actin. To investigate a role for tension in regulating actin during wound repair, we used FRAP to show that actin was stabilized around embryonic wounds. Loss of tension through laser ablation led to loss of actin fluorescence, however, photobleaching experiments after laser severing showed no change in actin turnover. We found no changes in actin dynamics between early and late wound closure, when tension is higher. Together these data suggest that tension may be partially necessary for actin localization, but it is neither necessary nor sufficient to regulate actin turnover. To begin to pick apart the relationship between actin and myosin at the wound margin, we inhibited myosin activity and measured actin turnover. Actin stabilization was independent of myosin activity, suggesting actin may be regulated independently. To understand whether myosin turnover is independent of actin, we stabilized actin networks pharmacologically and monitored for changes in myosin dynamics. Myosin turnover was unaffected by actin stabilization. These results suggest that actin and myosin are independently regulated, and that these networks are more complex than expected. This work provides insights into the mechanisms used by cells to coordinate their behaviour and could have implications for development and disease.

Keywords: actomyosin contractility
collective migration
FRAP
fruit fly
Laser ablation
wound repair
Advisor: Fernandez-Gonzalez, Rodrigo
Reconstructing Rural Chengdu: Urbanization as Development in the Post-Quake Context

On 12 May 2008 Western China was struck by an 8.0-magnitude earthquake (the Wenchuan Earthquake) that left over 87,000 people dead or missing, and destroyed nearly 8 million homes. The epicenter of the quake lay less than 100 km away from Chengdu, the capital city of Sichuan Province. Although the central city itself was not damaged by the quake, many settlements in Chengdu’s rural periphery had to be completely rebuilt. This dissertation examines how the Chengdu government used post-quake reconstruction as an opportunity to urbanize rural areas in the metropolitan region under the policy of “urban-rural integration”. But urban-rural integration was not merely urbanization in the sense of an expansion of the built-up urban core; it was a far more comprehensive project that was framed as a means of developing the rural economy, improving living environments, and bolstering peasants’ rights. I argue that Chengdu’s urbanization is best understood as a developmental project—a form of “development qua urbanization”—and as a form of governmental power in the Foucauldian sense. I further interpret the underlying logics of urban-rural integration—that rural areas are best developed through urbanization—in the context of China’s current historical conjuncture. In doing so, I turn to Polanyi’s description of the transition to a market society, and Lefebvre’s prediction of the transition to an urban society. Drawing on media and policy analysis, academic debates on Chengdu’s urban-rural integration project, and participant observation work and in-depth interviews conducted in peri-urban Chengdu over a period of nearly two years, I examine the multiple forms that post-quake urbanization in Chengdu took, including rationalizing land use throughout the metropolitan region, building concentrated villages, assigning individual titles to rural collective land, developing markets for rural property rights, encouraging large-scale agribusiness, extending social services to rural areas, reforming rural governance institutions, and transforming peasants into self-managing citizens.

Keywords: Chengdu
China
development
earthquake
planning
urbanization
Advisor: Boland, Alana
Graceful Symmetry: The Politics of Grace in Shakespeare, Spenser, and Milton

Graceful Symmetry explores the relationship between grace and political agency in the work of William Shakespeare, Edmund Spenser, and John Milton. These writers were part of a Protestant culture that understood grace through the slogan sola gratia, or “grace alone,” which means that God has the prerogative to save or condemn human beings freely. Protestants inherited this vision of salvation from St. Paul, who imagines grace as a form of liberation within submission to God—so that liberty is, paradoxically, the experience of being bound. Shakespeare, Spenser, and Milton explore the political ramifications of these scriptural paradoxes. They suggest that, by magnifying the freedom of God, and by redefining the believer’s agency as a form of submission to the divine, grace challenges existing political obligations between subjects and their human sovereign. Shakespeare and Spenser deploy the rhetoric of religious grace to explore the degree to which monarchical power is compatible with active political participation from Protestant citizens. Taking this approach to a radical extreme, Milton argues that grace regenerates ordinary Christians to the extent that that they become capable of wielding sovereignty as citizens of a free republic, thus making monarchy unnecessary. Shakespeare, Spenser, and Milton ultimately coopt the religious language of grace to reimagine a wide range of political concepts—such as imperialism, absolutism, nationalism, and republicanism—during political crises such as Tyrone’s rebellion in Ireland and the English Civil Wars. I argue that grace is central not only for Protestant theology but also for the political ideals of Renaissance humanism, such as republicanism. The interdisciplinary resonance of grace was ultimately due to the tendency among a wide variety of early modern writers—including the literary writers I explore—to use Paul as an authority on legal and political questions as well as religious ones. By demonstrating how Paul’s writing on grace influenced early modern culture and religion, I argue that politics is inseparable from theology in post-Reformation English literature.

Keywords: Early Modern literature
Edmund Spenser
Intellectual History
John Milton
Protestant theology
William Shakespeare
Advisor: Stevens, Paul
Applications of Piers-Rubinsztajn Chemistry: Synthesis of Materials for Organic Electronics

Since the advent of the age of organic electronics, new materials are being developed regularly for use in these types of devices. Their processing methods have also evolved over the years, resulting in new, commercially-available applications. The application of these materials from solution, also known as solution processing, is lower-cost and less energy intensive with many other added benefits. To that end, this thesis explores the Piers-Rubinsztajn reaction as a tool to enable the solution processing of organic electronic materials. Piers-Rubinsztajn chemistry is a versatile, expedient reaction using an organic Lewis acidic catalyst tris(pentafluorophenyl)borane to couple a Si-H bond with an oxygen based nucleophile. This type of chemistry is underexplored in the field of materiasl development for organic electronics applications. This chemistry can be used to incorporate different types of siloxane oligomers into the structure of an organic electronic material, thus merging the properties of siloxane materials, such as flexibility, with those of the original compound. This methodology is used in this thesis to alter the physical properties of a variety of organic electronic materials to enable and ameliorate their solution processing. Chapters 2 to 5 explore the use of Piers-Rubinsztajn chemistry to cross-link triarylamine derivatives, to allow sequential solution processing for its application in an organic light emitting diode. Chapter 6 involves the synthesis of phenoxylated siloxane polymers, via Piers-Rubinsztajn chemistry, as a new material with improved organic-phase miscibility, for potential application in an organic electronic device. Chapters 7 and 8 follow the scale-up synthesis and application of a liquid triarylamine derivative in a dye-sensitized solar cell. Finally, Chapter 9 will cover the use of Piers-Rubinsztajn chemistry to functionalize insoluble silicon phthalocyanine derivatives to enable their use in bulk-heterojunction organic photovoltaics.

Keywords: Organic Electronics
Piers-Rubinsztajn
silicon phthalocyanine
siloxane
triarylamine
Advisor: Bender, Timothy P
Path Dependence, Abnormal Times Missed Opportunities: Exploring factors that facilitate or constrain implementation of institutional reforms post catastrophic natural disasters

Path dependence literature largely accepts that large-scale disasters trigger abnormal times that weaken path dependence and create windows of opportunity to bring about institutional reforms. Yet experience suggests that institutional reforms are rarely implemented post catastrophic disasters. This thesis examines factors that might explain why the windows of opportunity triggered by disasters are missed in some cases, while seized in others. This question is explored by juxtaposing two case studies: the Gorkha 2015 earthquakes (Nepal) and the Uttarakhand 2013 flood (India). My analysis reveals the critical role of (a) gradual reforms taken during normal times and its influence on actions taken during abnormal times, (b) negative feedback by external and internal actors, and (c) denial or acknowledgement of negative feedback by internal actors. Based on the findings, I elaborate policy suggestions that may aid in mitigating the possibility of abnormal times repeatedly becoming missed opportunities.

Keywords: Abnormal Times
Incremental reforms
Institutional change
Natural Disaster
Negative feedback
Path Dependence
Advisor: Prado, Mariana Mota
Socratic Method and Moral Motivation

I argue for a new account of the role of philosophical argument in changing a person’s core values. As philosophers, we tend to think it is possible to cause someone to change his values by directing some piece of reasoning at him. But that is often naïve, as can be seen by the trajectory of many political disputes: one side takes an argument to be persuasive, and the other refuses to accept it. As it happens, this is the exact progression of many Platonic dialogues. Socrates argues that his interlocutor’s core values are mistaken, and his interlocutor, despite being unable to identify where, if anywhere, the argument goes astray, rejects its conclusion. Is, then, argument out of work when it comes to changing a person’s core values? Many scholars, including Martha Nussbaum, Gregory Vlastos, and Alexander Nehamas, hold that Plato believes as much. On the standard view, Plato thinks that philosophical argument is an ineffective way of reforming a person’s life, and he rejects Socrates’ project, as outlined in the Apology, of using philosophical argument to persuade his interlocutors to value wisdom more than money, honor, and everything else. Against this standard view, I argue that Plato offers a compelling account of how philosophical argument can be effective at transforming a person’s values. As has not been appreciated by other scholars, Socrates uses his methods of refutation and exhortation in most cases not to advocate wisdom’s overriding importance, but rather to motivate pursuing wisdom merely for its instrumental value, and this because it is the instrumental pursuit of wisdom that is meant to be transformative. Socrates’ overall strategy, then, is not unlike that of the professor who recruits a student to philosophy with the promise that it will improve her LSAT scores, all the while anticipating that, once the student experiences the thrill of abstract, intellectual inquiry, she will lose her legal ambitions and devote herself to philosophical studies. What justifies this strategy, in our eyes and Plato’s, is that, in some important contexts, including the choice of a way of life, the right reasons can come into view only after taking up some practice, and so the practice cannot be motivated by the right reasons until it is taken up on some other basis.

Keywords: Conversion
Eros
Exhortation
Plato
Refutation
Socrates
Advisor: Barney, Rachel
Philosophy, practice and implications of phylogenetic inference as exemplified by Neotropical microteiid lizards (Reptilia: Gymnophthalmidae, Alopoglossidae)

Understanding evolutionary processes involved in the diversity of life first requires knowledge of phylogeny. This knowledge is necessary to explain the evolutionary origins of features and provides a predictive framework to guide research. Biodiversity demands explanation, and heritable variation provides the evidential basis for formulating and testing phylogenetic hypotheses. My goal herein is to advance understanding of phylogenetic inference by addressing theoretical, analytical and empirical problems, and the rationale behind my approaches to solving them. To this end, I use a combination of approaches both to make phylogenetic inferences and to advance the field. Consequently, I present a collection of broadly overlapping contributions. I begin with a review of median-joining (MJ), a method for phylogeographic analysis. I show that MJ networks are theoretically untenable for phylogenetic inference. I also discuss the concept of phylogenetic network. Given the confusion that afflicts the implementation of concepts in some methods, I explore the concept of cladogram and argue that cladograms do not necessarily require synapomorphies, but synapomorphies are required to test and ultimately falsify cladograms. I conclude that both cladograms and synapomorphies are required to achieve phylogenetic explanation. I continue with an evaluation of the impact of phenotypic evidence on molecular datasets. I show that inclusion of phenotypic evidence can alter both topologies and support values in phylogenetic analyses. I use an optimal phylogenetic hypothesis to formulate and test biogeographic hypotheses involving Neotropical montane regions, and to analyze character evolution. I finish with the development of a theory of outgroup sampling, a fundamental step in phylogenetic analysis, grounded in the logic of scientific discovery. Its objective is to test hypotheses of ingroup topology and homology as severely as possible. This framework provides a logical basis for sampling and successively increases severity of hypothesis-testing, but it does not provide any grounds for limiting the sample. I then propose a heuristic procedure that provides an empirical basis to limit sampling. For most projects, I use Neotropical microteiid lizards. Finally, biodiversity also demands documentation, and my research often results in taxonomic novelties. Herein, I describe three new species and erect two new genera of microteiid lizards.

Advisor: Murphy, Robert W.
Entanglements: Volkswagen de MĂŠxico and Global Capitalism

This dissertation is an ethnographic study of global capitalism. It examines the multilayered presence of Volkswagen de México to grapple with the double-edged sword of transnational economic dependencies. Car manufacturing in Mexico has created jobs for a number of college graduates, middle class status, modes of relationality and care, and even the possibility to migrate to Germany. At the same time global car production relies on a large number of low-wage and uncertain jobs, on mechanisms that make labor cheap and discipline the labor force, as well as on land and water dispossession. While Volkswagen de México is a medium of inclusivity into 21st century global capitalism, it has also created contentious relations on the ground: among those who celebrate the presence of the factory, those who oppose it, those who have been violently excluded, and among unionized and non-unionized workers. To elucidate this complex and convoluted landscape of social relations, this study examines how transnational car production intersects with processes of nation-state formation, local ideas about status, and personal aspirations, as well as the conjunctures between global transformations, manufacturing, and the North American Free Trade Agreement. This dissertation shows how Volkswagen’s car economy has endured through forms of domination, subjugation and accommodation, and traces its not-always-predictable effects on the ground. Thereby it offers a nuanced and textured account of how global capitalism is constituted trans-locally.

Keywords: Capitalism
Car Production
Cars
Mexico
NAFTA
Transnational Corporation
Advisor: Napolitano, Valentina
Ivan Goes Abroad: The Red Army in the Balkans and Central Europe, 1944-1945

Ivan Goes Abroad: The Red Army in the Balkans and Central Europe, 1944-1945 explores the Red Army’s occupation of Romania, Bulgaria, Yugoslavia, Hungary, and Austria in World War II, focusing on the issue of sexual violence against women. In order to explain the Soviet troops’ behavior, Ivan Goes Abroad examines the Kremlin’s policies in each country that they occupied, the Red Army’s propaganda line, the leadership’s disciplinary policies toward criminals in the ranks, and the frontline soldiers’ and officers’ attitudes to the local population. A potent mix of factors from above and below resulted in mass rapes. Many Soviet male troops viewed women primarily as sex objects, believing that their membership in a victorious Red Army entitled them to women’s bodies, even by force. Furthermore, as the Red Army’s soldiers and officers moved across the Balkans and Central Europe, they developed a series of stereotypes about countries that they encountered. These views were mostly independent of the official line, although they were extremely common among the rank and file and higher ranking officers. When soldiers attributed to a nation positive characteristics, as was the case in Bulgaria and Yugoslavia, they behaved with relative restraint. In contrast, when they assigned negative characteristics to a nation, as was the case in Romania, Hungary, and Austria, they wreaked havoc against the civilians. The high command sent mixed signals to the rank and file about the acceptability of violence against civilians. Although robberies, rapes, and murders of civilians were always illegal in the Red Army, the commanding officers’ permissive attitude towards the violence, the dehumanizing hate propaganda against Romanians, Hungarians, and Austrians, as well as the inability of the high command to impose discipline on the frontline troops, signalled to the rank and file that their crimes would go largely unpunished.

Keywords: Red Army
Sexual violence
World War II
Advisor: Viola, Lynne
â In the Language of the Patriarchâ : Patriarch Tikhon, the Russian Orthodox Church, and the Soviet State (1865-1925)

In 1917, the Russian Orthodox Church became independent from the state for the first time in two centuries. The first All-Russian Church Council voted to restore the institution of the patriarchate, and in the midst of the Bolshevik Revolution, Archbishop Tikhon (Bellavin) was chosen to become the Patriarch of Moscow and All-Rus. Tikhon’s eight-year tenure as patriarch spanned the crucial period during which two powerful currents—long-awaited ecclesiastical reform and unexpected political upheaval—converged and clashed. This dissertation reconstructs the language and worldview of Patriarch Tikhon, tracing the historical roots of the ideas and beliefs he espoused. The patriarch’s mode of speaking about Russia, the human person, and the meaning of life and history represented an alternative to Bolshevik definitions of those same terms. Patriarch Tikhon has been largely ignored by Western scholars of Russia. In recent years, historians of Soviet Russia have argued that we ought to take more seriously the discourse of Bolshevik actors and consider that Bolshevik language revealed a great deal about the worldview and practices of the Bolsheviks themselves. This dissertation proceeds on the assumption that the same can be said of the patriarch’s language. It analyzes how this language developed in the pre-revolutionary period, how it fit within larger trends in Orthodox thought and practice, and what it meant for Tikhon, his contemporaries, and the Bolsheviks. This centerpiece of this study is the published version of the sledstvennoe delo or “investigatory file” of Patriarch Tikhon. The file contains information gathered by the secret police about the patriarch from 1918 to 1925. Each chapter relies on different types of sources in order to parse the language of the investigatory file. These include archival documents from the Archive of the Russian Federation (GARF), the Russian State Archive of Socio-Political History (RGASPI), and the Russian State Historical Archive (RGIA), and from the Library of Congress in Washington D.C. Published sources include records of correspondence between Tikhon and government representatives, friends, and other clergymen; theological journals from the nineteenth century; diocesan newspapers from all of the dioceses in which Tikhon served; post-revolutionary Russian newspapers; foreign newspapers; and memoirs.

Keywords: canon law
Orthodox Church
Russian Revolution
Tikhon
Advisor: Viola, Lynne