VictorJuiz/thesis huggingface dataset:
Wittgenstein and Köhler on Seeing and Seeing Aspects: A Comparative Study

This thesis examines the relation between philosopher Ludwig Wittgenstein’s 1940s writings on seeing and seeing aspects and Gestalt psychologist Wolfgang Köhler’s theory of perception as set out in his Gestalt Psychology (1929). I argue that much of the existing literature on the Wittgenstein-Köhler relation distorts Köhler’s ideas and thus also Wittgenstein’s engagement with Köhler’s ideas. This double distortion underrates Köhler’s insights, misconstrues Wittgenstein’s complaints against Köhler, and masks points of contact between the two concerning the nature and description of human perceptual experience. In my view, Wittgenstein sympathizes with Köhler’s call to reflect on basic psychological categories such as “experience”, his respect for the “naïve” experience of the layperson, his method of “rediscovering” pervasive features of experience that escape our notice, and his efforts to identify intellectual prejudices that stymie inquiry. But a warning emerges from Wittgenstein’s discussions of seeing and seeing aspects: It is especially difficult to command a clear view of 'seeing' and its interrelations with other everyday, psychological concepts. I argue that Wittgenstein’s far-reaching criticism of Köhler is that the latter's account of visual “organization” overextends an analogy between seeing and seeing aspects and pushes aside other justifiable comparisons, for example between seeing and thinking and seeing and imagining. A consequence of Wittgenstein's criticism is that Kohler falls short of his aim to depict faithfully naïve visual experience. Moreover, despite Kohler's commitment to battling prejudices, the latter's emphasis on similarities between seeing and seeing aspects to the exclusion of their differences is a form of intellectual prejudice. For Wittgenstein various comparisons are justifiable by appeal to the interrelations between ‘seeing’ and other psychological concepts. A perspicuous view of the concept 'seeing' involves steady appreciation of the multitude of justifiable, criss-crossing comparisons. So although Wittgenstein does not deny Köhler’s claim that organization is a feature of visual experience rather than thinking, he does not unqualifiedly endorse it either. We have conceptual grounds for various ways of speaking about our experiences of aspects.

Keywords: Wittgenstein
Gestalt Psychology
seeing as
Kohler
perception
visual experience
aspect
Advisor: Canfield, John
A Modified Yeast One-hybrid Sytem to Investigate Protein-protein and Protein: DNA Interactions

A modified yeast one-hybrid (MY1H) system has been developed for in vivo investigation of simultaneous protein-protein and protein:DNA interactions. The traditional yeast one-hybrid assay (Y1H) permits examination of one expressed protein targeting one DNA site, whereas our MY1H allows coexpression of two different proteins and examination of their activity at the DNA target. This single-plasmid based MY1H was validated by use of the DNA-binding protein p53 and its inhibitory partners, large T antigen (LTAg) and 53BP2. The MY1H system could be used to examine proteins that contribute inhibitory, repressive, coactivational or bridging functions to the protein under investigation, as well as potential extension toward library screening for identification of novel accessory proteins. After development and validation of the MY1H with the p53/LTAg/53BP2 system, we applied the MY1H system to investigate the DNA binding activities of heterodimeric proteins, the bHLH/PAS domains of AhR and Arnt that target the xenobiotic response element (XRE). The AhR/Arnt:XRE interaction, which served as our positive control for heterodimeric protein binding of the XRE DNA site, showed negative signals in initial MY1H experiments. These false negative observations were turned into true positives by increasing the number of DNA target sites upstream of the reporter genes and increasing the number of activator domains fused to the two monomers. This methodology may help trouble-shooting false negatives stemming from unproductive transcription in yeast genetic assays, which can be a common problem. In the study of XRE-binding proteins, two bHLHZ-like hybrid proteins, AhRJunD and ArntFos were designed and coexpressed in the MY1H and yeast two-hybrid (Y2H) systems; these proteins comprise the bHLH domains of AhR and Arnt fused to the leucine zipper (LZ) elements from bZIP proteins JunD and Fos, respectively. The in vivo assays revealed that in the absence of the XRE DNA site, heterodimers and homodimers formed, but in the presence of the nonpalindromic XRE, only heterodimers bound to the XRE and activated reporter transcription. The present results provide valuable information on DNA-mediated protein heterodimerization and specific DNA binding, as well as the relationship between protein structure and DNA-binding function.

Keywords: protein engineering
yeast one-hybrid assay
protein:DNA interaction
protein-protein interaction
Advisor: Shin, Jumi A.
Timed State Tree Structures: Supervisory Control and Fault Diagnosis

It is well known that the optimal nonblocking supervisory control problem of timed discrete event systems is NP-hard, subject in particular to state space explosion that is exponential in the number of system components. In this thesis, we propose to manage complexity by organizing the system as a Timed State Tree Structure (TSTS). TSTS are an adaptation of STS to timed Supervisory Control Theory (SCT). Based on TSTS we present an e±cient recursive symbolic algorithm that can perform nonblocking supervisory control design for systems of state size 10^12 and higher. Failure diagnosis is the process of detecting and identifying deviations of a system from its normal behavior using the information available through sensors. A method for fault diagnosis of the TSTS model is proposed. A state based diagnoser is constructed for each timed holon of TSTS. Fault diagnosis is accomplished using the state estimates provided by the timed holon diagnosers. The diagnosers may communicate among each other in order to update their state estimates. At any given time, only a subset of the diagnosers are operational, and as a result, instead of the entire model of the system, only the models of the timed holons associated with the operational diagnosers are used. It is shown that the computational complexity of constructing and storing the transition systems required for diagnosis in the proposed approach is polynomial in the number of system components, whereas in the original monolithic approach the computational complexity is exponential.

Keywords: Discrete Event Systems
Hierarchical Systems
Supervisory Control
Fault Diagnosis
State Tree Structures
Advisor: Wonham, Murray
Leaf Conjugacies on the Torus

If a partially hyperbolic diffeomorphism on a torus of dimension d greater than 3 has stable and unstable foliations which are quasi-isometric on the universal cover, and its center direction is one-dimensional, then the diffeomorphism is leaf conjugate to a linear toral automorphism. In other words, the hyperbolic structure of the diffeomorphism is exactly that of a linear, and thus simple to understand, example. In particular, every partially hyperbolic diffeomorphism on the 3-torus is leaf conjugate to a linear toral automorphism.

Keywords: Partially Hypberbolic Systems
Leaf Conjugacies
Advisor: Pugh, Charles Chapman
The Double-edged Sword: A Critical Race Africology of Collaborations between Blacks and Whites in Racial Equity Work

In recent years, there has been a significant amount of new attention to white dominance and privilege (or whiteness) as the often unmarked inverse of racial oppression. This interest has spawned the academic domain called Critical Whiteness Studies (CWS). While the critical investigation of whiteness is not new, and has been pioneered by Black scholars beginning at least since the early 1900s in the work of W. E. B. Du Bois, what is notable about this new interest in whiteness is its advancement almost exclusively by white scholars. The paucity of literature centering the Black voice in the study of whiteness both suggests the lack of appreciation for the importance of this perspective when researching the phenomenon of racial dominance, and raises questions about the manner in which racial equity work is approached by some Whites who do work that is intended to advance racial equity. This study investigates the context of racial equity collaborations between Blacks and Whites, responding to this knowledge deficit in two ways: a) it centers the Black voice, specifically and intentionally seeking the perspectives of Blacks about racial equity collaborations b) it investigates the nature and effects of the relationships between Blacks and Whites in these collaborative endeavours. This qualitative research study uses in-depth interview data collected from ten Black racial equity workers who collaborate with Whites in doing racial equity work. The data makes evident that the Black participants find these collaborations to be necessary and strategic while at the same time having the potential to undermine their own agency. The study examines this contradiction, discussing several manifestations of it in the lives of these Black racial equity workers. It outlines the importance of Black embodied knowledge to racial equity work and to these collaborations, and outlines an epistemology of unknowing and a politics of humility that these Blacks seek in their white colleagues. The study also outlines the collective and individual strategies used by these Black racial equity workers to navigate and resist the contradictory terrain of their collaborations with Whites in racial equity work.

Keywords: Anti-racism
Critical Study of Whiteness
Embodied Knowledge
Collaboration
Afrocentricity
Critical Whiteness Studies
Epistemology of Ignorance
Resistance
African Agency
Racism
Race
Salience of Race
Interest Convergence
Advisor: Dei, George Jerry Sefa
Mechanical Forces Regulate Cartilage Tissue Formation by Chondrocytes via Integrin-mediated cell Spreading

In vitro grown cartilage is functionally inferior to native tissue, and improvements in its quality should be attempted so it can be used therapeutically. In these studies we investigated the effects of cell shape on tissue quality through alteration of substrate geometry and application of mechanical stimuli. Articular chondrocytes were isolated and cultured on the surface Ti-6Al-4V substrates with various geometries. When cultured on fully porous titanium alloy substrates, chondrocyte spreading was enhanced over those grown on substrates with solid bases. Chondrocytes which remained round did not synthesize significant amounts of matrix and were thus unable to form cartilaginous tissue. In contrast, chondrocytes which were directed to spread to a limited amount, resulting in a polygonal morphology, accumulated significantly more matrix molecules and in time formed cartilage-like tissue. Computational fluid dynamics analyses demonstrated that cells on fully porous substrates experience time-dependent shear stresses that differ from those experienced by cells on substrates with solid bases where media flow-through is restricted. Integrin-blocking experiments revealed that integrins are important regulators of cell shape, and appeared to influence the accumulation of collagen and proteoglycans by chondrocytes. Furthermore, compressive mechanical stimulation induced a rapid, transient increase in chondrocyte spreading by 10 minutes, followed by a retraction to pre-stimulated size within 6 hours. This has been shown to be associated with increased accumulation of newly synthesized proteoglycans. Blocking the α5β1 integrin, or its β1 subunit, inhibited cell spreading and resulted in a partial inhibition of compression-induced increases in matrix accumulation, thereby substantiating the role of β1 integrins in this process. These results suggest that both fluid induced shear forces and compressive forces regulate chondrocyte matrix accumulation by altering cell morphology, which is mediated by integrins. Identifying the molecular mechanisms that influence chondrocyte shape and thus tissue formation may ultimately lead to the development of a tissue that more closely resembles native articular cartilage.

Keywords: articular chondrocytes
tissue engineering
Advisor: Kandel, Rita A.
Polarity Control in Migrating Vascular Smooth Muscle Cells: N-cadherin Localization and Function

Vascular endothelial cell loss initiates directional migration of medial smooth muscle cells into the arterial intima contributing to in-stent restenosis, atherosclerosis and coronary arterial by-pass graft failure. N-cadherin is a cell-cell adhesion molecule that mediates the interaction between vascular endothelial cells and the innermost smooth muscle cells to stabilize the arterial wall. Upon injury, I reasoned that relocalization of N-cadherin on the inner most smooth muscle cells to the posterior-lateral borders stimulates cell polarization to enable directional migration. Using an in vitro scratch-wound model to stimulate cell polarity and locally remove cell-cell contacts at one pole of smooth muscle cells, I found that N-cadherin localization provides signaling cues via a Cdc42/GSK pathway that promote polarized reorganization of the cytoskeleton and directional cell migration. I also found that N-cadherin was important to functions of lamellipodia at the anterior of migrating cells. In lamellipodia, actin polymerization drives protrusion of the leading edge and coincident, but more posterior, actin depolymerization results in retrograde flow of actin and associated plasma membrane structures. Using live cell imaging, I found that clusters of N-cadherin-GFP repeatedly accumulated at the leading edge specifically at the neck of large pinocytotic vesicles called macropinosomes that were internalized and transported away from the leading edge. This localization is consistent with a role for N-cadherin in closure and scission of vesicles during macropinocytosis. These are the first studies to examine polarity in migrating vascular smooth muscle cells, and advance our understanding concerning cell-cell adhesions in controlling directional cell migration. My results suggest that N-cadherin may serve as a viable target for the treatment of arterial stenosis that would limit smooth muscle cell migration and stabilize the arterial wall. Furthermore, I report on a novel localization and function of N-cadherin in the biogenesis of macropinosomes in the lamellipodia that contribute to cell protrusion.

Keywords: Vascular Biology
Polarity
N-cadherin
Restenosis
Migration
Advisor: Bendeck, Michelle
Space-time Coded Modulation Design in Slow Fading

This dissertation examines multi-antenna transceiver design over flat-fading wireless channels. Bit Interleaved Coded Modulation (BICM) and MultiLevel Coded Modulation (MLCM) transmitter structures are considered, as well as the used of an optional spatial precoder under slow and quasi-static fading conditions. At the receiver, MultiStage Decoder (MSD) and Iterative Detection and Decoding (IDD) strategies are applied. Precoder, mapper and subcode designs are optimized for different receiver structures over the different antenna and fading scenarios. Under slow and quasi-static channel conditions, fade resistant multi-antenna transmission is achieved through a combination of linear spatial precoding and non-linear multi-dimensional mapping. A time-varying random unitary precoder is proposed, with significant performance gains over spatial interleaving. The fade resistant properties of multidimensional random mapping are also analyzed. For MLCM architectures, a group random labelling strategy is proposed for large antenna systems. The use of complexity constrained receivers in BICM and MLCM transmissions is explored. Two multi-antenna detectors are proposed based on a group detection strategy, whose complexity can be adjusted through the group size parameter. These detectors show performance gains over the the Minimum Mean Squared Error (MMSE)detector in spatially multiplexed systems having an excess number of transmitter antennas. A class of irregular convolutional codes is proposed for use in BICM transmissions. An irregular convolutional code is formed by encoding fractions of bits with different puncture patterns and mother codes of different memory. The code profile is designed with the aid of extrinsic information transfer charts, based on the channel and mapping function characteristics. In multi-antenna applications, these codes outperform convolutional turbo codes under independent and quasi-static fading conditions. For finite length transmissions, MLCM-MSD performance is affected by the mapping function. Labelling schemes such as set partitioning and multidimensional random labelling generate a large spread of subcode rates. A class of generalized Low Density Parity Check (LDPC) codes is proposed, to improve low-rate subcode performance. For MLCM-MSD transmissions, the proposed generalized LDPC codes outperform conventional LDPC code construction over a wide range of channels and design rates.

Keywords: MIM0
wireless communications
group detection
BICM
coded modulation
LDPC
irregular convolutional codes
unitary precoding
Advisor: Plataniotis, Konstantinos N.
Pasupathy, Subbarayan
Theodore Stanton: An American Editor, Syndicator, and Literary Agent in Paris, 1880-1920

Theodore Stanton’s career as a literary middleman exemplifies several of the intermediary professions in book and periodical publishing that were being created and tested in the late nineteenth century in response to expanded publishing opportunities in France, Great Britain, the United States, and Canada. The need for professional middlemen between writers and publishers developed differently in each country, thus their roles and activities, the literary agent’s in particular, varied according to regional demands. Different interpretations of intellectual property in copyright laws determined the balance of power between creators and producers of texts. In turn, writers’ relative ability to control copyrights shaped the middleman’s field of endeavour. The range of professional middleman specializations is described. A case study of some American publications of Émile Zola’s novels shows the legal and logistical difficulties of transatlantic publishing in practice. In chapter 3, Stanton’s beginnings as an American newspaper correspondent in Paris precede his middleman role as editor of the European Correspondent, a weekly galley-proof service printed in English in Paris and syndicated to American newspaper editors. Stanton’s work as a European sub-editor of the North American Review and other magazines is detailed in chapter 4. As the Paris representative of Harper & Brothers from 1899, Stanton presented previously unpublished writings of Honoré de Balzac, Victor Hugo, Émile Zola, and others to American readers, also co-operating with French publishers. Case studies portray the challenges and successes of a middleman position within a large, complex enterprise. In chapter 5, a more independent Stanton arranges the simultaneous, posthumous publication of the memoirs of Eugénie, ex-Empress of France, by D. Appleton and Company in New York and London, and in four European translations. Count Maurice Fleury compiled and authored the two-volume work, which was not published in France. The manuscript took a circuitous path to publication through Stanton’s efforts to ensure authenticity, maintain exclusivity, and protect copyright. Methodological approaches of correspondence editing, bibliography, and textual criticism reveal both the processes and the results of Stanton’s mediation and illuminate how the participation of literary middlemen shaped the way French culture was received and understood in North America.

Keywords: book history
Emile Zola
bibliography
literary agency
print culture
Advisor: Oliver, William Andrew
A Regulatory Theory of Cortical Organization and its Applications to Robotics

Fundamental aspects of biologically-inspired regulatory mechanisms are considered in a robotics context, using artificial neural-network control systems . Regulatory mechanisms are used to control expression of genes, adaptation of form and behavior in organisms. Traditional neural network control architectures assume networks of neurons are fixed and are interconnected by wires. However, these architectures tend to be specified by a designer and are faced with several limitations that reduce scalability and tractability for tasks with larger search spaces. Traditional methods used to overcome these limitations with fixed network topologies are to provide more supervision by a designer. More supervision as shown does not guarantee improvement during training particularly when making incorrect assumptions for little known task domains. Biological organisms often do not require such external intervention (more supervision) and have self-organized through adaptation. Artificial neural tissues (ANT) addresses limitations with current neural-network architectures by modeling both wired interactions between neurons and wireless interactions through use of chemical diffusion fields. An evolutionary (Darwinian) selection process is used to ‘breed’ ANT controllers for a task at hand and the framework facilitates emergence of creative solutions since only a system goal function and a generic set of basis behaviours need be defined. Regulatory mechanisms are formed dynamically within ANT through superpositioning of chemical diffusion fields from multiple sources and are used to select neuronal groups. Regulation drives competition and cooperation among neuronal groups and results in areas of specialization forming within the tissue. These regulatory mechanisms are also shown to increase tractability without requiring more supervision using a new statistical theory developed to predict performance characteristics of fixed network topologies. Simulations also confirm the significance of regulatory mechanisms in solving certain tasks found intractable for fixed network topologies. The framework also shows general improvement in training performance against existing fixed-topology neural network controllers for several robotic and control tasks. ANT controllers evolved in a low-fidelity simulation environment have been demonstrated for a number of tasks on hardware using groups of mobile robots and have given insight into self-organizing system. Evidence of sparse activity and use of decentralized, distributed functionality within ANT controller solutions are found consistent with observations from neurobiology.

Keywords: Evolutionary Robotics
Neural Networks
Developmental systems
Gene regulation
Space Robotics
Multiagent systems
Advisor: Gabriele, D'Eleuterio