VictorJuiz/thesis huggingface dataset:
Transformations in Death: The Archaeology of Funerary Practices and Personhood in the Bronze Age Levant

Burials in the Middle and Late Bronze Age Levant (ca. 2000-1200 B.C.E.) exhibit a high degree of mortuary diversity and experimentation with body disposal methods in primary, secondary, and co-mingled inhumations. Previous research has explained the process of multiple-successive burial as a result of the functional need to make room inside of a re-used burial space such as a chamber tomb. This explanation misses the opportunity to investigate the social and ritual meaning of repeated, close contact with the corporeal remains of the deceased after death and burial. Indeed, written sources from the ancient Near East attest to the existence of posthumous persons such as ancestors, ghosts, and the deified dead. Therefore, this dissertation poses four research questions to investigate the roles of the dead body and person in funerary rituals of the second millennium B.C.E. Levant: (1) What is the status of the dead after burial? (2) What roles do the corpse play in the funerary sequence? (3) What do textual sources and mortuary practices reveal about relationships between the post-mortem body and person? (4) Under what circumstances does personhood continue or transform after death?/nThe treatment of the dead body determines the posthumous social roles of the deceased after burial and explains the high degree of burial diversity of the Middle and Late Bronze Age Levant. This work combines theoretical frameworks of personhood and embodiment with methods derived from mortuary archaeology, specifically funerary taphonomy, biological profiles of age and sex, and distributions of burial type, architecture, context, and grave goods. Drawing from a broad mortuary dataset from across the Levant, including three mortuary case studies from Tel Megiddo (Israel), patterns of deposition and corpse modification in residential burials are identified. These results are compared with contemporaneous textual evidence drawn from a variety of sources across the Levant and Mesopotamia which address the dead body and person. This study presents a new model of the extended funerary sequence in residential burials of the second millennium B.C.E., asserting that the bodies of the dead were treated differently according to their membership within the household. It is also argued that repeated fragmentation and intermixing of skeletal remains in residential burials was the primary pathway to achieving ancestor status after death and burial. The results provide new insight into the society of the Bronze Age Levant, a context in which the household encompassed the living and the dead and served as the primary social unit.

Advisor: Porter, Benjamin W
Predictive models of auditory perception in human electrophysiology

It has long been thought that sensory systems operate by representing information in a hierarchy of sensory features, and that these features build upon one another. From low-level information such as spectral content, to high-level information such as word content, the sensory system must rapidly extract all of these features from the world. However, the precise nature of these levels of representation, as well as how they interact with one another, is not well-understood. In audition, intermediate sensory representations are often studied in animals, using techniques that treat neurons as a linear filter for incoming sensory inputs. If those inputs are spectro-temporal features (e.g., a spectrogram), then the result is a Spectro Temporal Receptive Field (STRF). This describes how the neural unit in question (e.g., a neuron) will respond to patterns in spectro-temporal space. It has been a crucial tool in understanding sensory processing in low-level neural activity. Using this approach it is also possible to study how this neural representation changes under different experimental conditions. STRF plasticity has been shown in both reward- and context-modulated experiments in animals./nIn recent years, it has been suggested that similar techniques may work in modeling the activity of neural signals recorded from humans. As we cannot generally record from single unit activity in humans, this approach relies on proxies for neural activity – specifically in the high-frequency activity (HFA) of electrocorticography electrodes. This poses a unique opportunity for two reasons: First, human language is a natural stimulus set for studying hierarchical feature representations in the brain. There are many ways to decompose speech into both auditory and linguistic components, and each of these could serve as inputs to the modeling technique described above. Second, humans are especially skilled at using high-level context such as their experience and assumptions about the world in order to change their behavior. This poses a unique opportunity to study the plasticity of speech representations in the brain./nThis thesis reports several new approaches towards studying the sensory representation of speech in the human brain, as well as how these representations may change due to experience. It aims to bridge the literature in rodents and songbirds with ideas in human electrophysiology in order to pursue new approaches to studying perception in humans.

Advisor: Knight, Robert T
Using Instructional Rounds at the School Level to Improve Classroom Instruction

Despite the growing descriptions of effective teacher community —and lessons about the conditions needed for them to survive — more research has been done on exemplars of strong professional community than on efforts to produce professional community where it doesn’t already exist. Building professional community is important to school improvement as it promotes cooperative, job-embedded learning where teachers engage in serious discussions about teaching that could lead to shift in instructional practice. Research on individual and group change suggests that these shifts are unlikely to occur without a supportive environment that includes positive pressure for change. The introduction of organizational routines designed to make teaching more public and collaborative is one solution. Instructional Rounds is a collegial network based approach to improving teaching and learning. At the school site level, Instructional Rounds can create a system and structure where teachers engage in professional dialogue and take collective action in their schools./nUsing a modified design development format (with an action research component), this study focuses on the implementation of Instructional Rounds at a school site. The study documents teacher experience with Rounds and documents a second iteration of Rounds that more resembled the protocol of Lesson Study. The participants were 24 teachers from an urban elementary school in the Bay Area of California where I serve as Principal. The findings of this study indicate that Instructional Rounds is a promising practice at a school site that can further the goal of making teaching more public and collaborative. The findings also indicate that, due to embedded norms of privacy and a culture of isolation, teachers will receive Rounds with some resistance as it opens up a focus on classroom practice. A key component of the initial success of Rounds was the role played by a site instructional leadership team, which led the planning and endorsed the approach. A second implementation of the intervention, grade-level rounds that resembled Lesson Study, did not have sufficient buy-in and contained many competing foci, and was not as effective. Nonetheless, for the teachers who did complete the full parameters of the Lesson Study, there was evidence documenting the promise of this practice to promote in-depth conversations of instructional practice./nOverall, the findings in this study demonstrate the complexity in the introduction of organizational routines designed to make teaching more public and collective at a school site. From a perspective of distributed leadership, all leadership entities (teachers, administration, outside partners) need to be aligned and all potential resources in the school need to be sufficient for the introduction of the new routine to be successful.

Advisor: Warren Little, Judith
Conformational Coordination of Strand Passage by Type IIA and Type IIB Topoisomerases

Topoisomerases are essential molecular machines that manage physical challenges presented by DNA topology. Life has evolved two classes of enzyme, type IIA and type IIB topoisomerases, which unlink entangled chromosomes by coordinating a complex, ATP-dependent passage of one DNA segment through a transient double strand break generated in a second DNA segment. Both classes share functional modules and an overall mechanism, yet they possess distinct architectures. Type IIA topoisomerases must coordinate transient strand scission with the association and dissociation of three distinct dimer interfaces, whereas type IIB topoisomerases must accomplish the same using only two interfaces. The biophysical basis of communication between these interfaces underlies the action of frontline small-molecule therapeutics which corrupt these concerted movements. To address how type IIA topoisomerases coordinate strand scission with the dimerization status of their unique third interface, I used X-ray crystallography to determine the first structure of the DNA cleavage core of human topoisomerase II. Comparative analyses to previously determined structures revealed that the principal site of DNA engagement in type IIA topoisomerases undergoes highly-quantized conformational transitions between distinct binding, cleavage, and drug-inhibited states that correlate with the control of subunit-subunit interactions. Additional consideration of this model in light of an etoposide-inhibited complex of human topoisomerase IIβ suggests possible strategies for developing inhibitors specific to topoisomerase II, the primary target of these therapies. To address how type IIB topoisomerases faithfully coordinate strand scission using only two interfaces, I performed biochemical analyses which show that these enzymes actively recognize and utilizes DNA bends and crossings formed in supercoiled DNA to stimulate ATP binding and hydrolysis as a prerequisite for efficient DNA cleavage and strand passage. This finding indicates that binding of two DNA segments preferentially drives the ATP-triggered dimerization, a coordinated action with important ramifications for how both type II topoisomerase machineries control of double-strand break formation.

Advisor: Berger, James M
Martin, Andreas
Algebraic Defects and Boundaries in Integrable & Topological Systems

Topological and conformal field theories and integrable systems can be described by the algebraic structures of quantum groups and quantum affine algebras. Boundary conditions and defects for these theories are described via algebraic constructions from these quantum groups or quantum affine algebras./nIn the first third of this thesis we describe constructions associated with three dimensional topological field theories. First we compute some Brauer-Picard groups which characterize nontrivial invertible structures that can be assigned using the cobordism hypothesis with singularities. Then we give a construction of bimodule categories using the procedure of covariantization(transmutation) of coquasitriangular Hopf algebras. The first third closes with a reduction by taking $K_0$ which results in algebraic K-theory of fusion rings./nThe next third describes spin chains which are governed by quantum affine algebras. The first chapter gives a proof of the asymptotic completeness of the algebraic Bethe Ansatz for the XXZ chain. Then we describe a similar reduction of taking $K_0$ which results in algebraic K-theory of cluster algebras./nThe last third of this thesis describes the appearance of these defects in topological field theories constructed by the AKSZ procedure. In the three dimensional case, this gives perturbative perspectives on the theories covered in the first third of the thesis. The last chapter gives the connection with topological insulators as they fit into the general AKSZ paradigm.

Advisor: Reshetikhin, Nicolai
Moore, Joel
Posets, Polytopes and Positroids

This dissertation explores questions about posets and polytopes through the lenses of positroids and geometry. The introduction and study of positroids, a special class of matroids, was pioneered by Postnikov in his study of the totally nonnegative Grassmannian and has subsequently been applied to various fields such as cluster algebras, physics, and free probability. Postnikov showed that positroids, the matroids realized by full rank $k\times n$ real matrices whose maximal minors are nonnegative, are in bijection with several combinatorial objects: Grassmann necklaces, decorated permutations, Le-diagrams and plabic graphs./nIn the first chapter, following work of Skandera and Reed, we define the unit interval positroid arising from a unit interval order poset via its associated antiadjacency matrix. We give a simple description of the decorated permutation representation of a unit interval positroid, and show it can be recovered from the Dyck path drawn on the associated antiadjacency matrix. We also describe the unit interval positroid cells in the totally nonnegative Grassmannian and their adjacencies. Finally, we provide a new description of the $f$-vector of posets./nThe second chapter concerns the $f$-vector of a $d$-dimensional polytope $P$, which stores the number of faces of each dimension. When $P$ is a simplicial polytope the Dehn--Sommerville relations condense the $f$-vector into the $g$-vector, which has length $\lceil{\frac{d+1}{2}}\rceil$. Thus, to determine the $f$-vector of $P$, we only need to know approximately half of its entries. This raises the question: Which $\left(\lceil{\frac{d+1}{2}}\rceil\right)$-subsets of the $f$-vector of a general simplicial polytope are sufficient to determine the whole $f$-vector? We prove that the answer is given by the bases of the Catalan matroid./nIn the final chapter, we explore the combinatorial structure of Knuth equivalence graphs $G_{\lambda}$. The vertices of $G_{\lambda}$ are the permutations whose insertion tableau is a fixed tableau of shape $\lambda$, and the edges are given by local Knuth moves on the permutations. The graph $G_{\lambda}$ is the $1$-skeleton of a cubical complex $C_{\lambda}$, and one can ask whether it is CAT(0); this is a desirable metric property that allows us to describe the combinatorial structure of $G_{\lambda}$ very explicitly. We prove that $C_{\lambda}$ is CAT(0) if and only if $\lambda$ is a hook.

Advisor: Williams, Lauren K
Radical Empiricist Poetics in the New York School and Beyond

This dissertation contends that the first-generation New York School poets—especially John Ashbery, Frank O’Hara, and James Schuyler—develop the aesthetic possibilities of the philosophical stance that William James called “radical empiricism.” James followed the British empiricists in granting priority to parts, individuals, and unanalyzed sensations, but he radicalized the empiricist perspective by holding experiences of cohesion and relation to be as real as those of disjunction and discrete sensation. Schuyler, Ashbery, and O’Hara each practice an empiricist poetics: a poetics of the everyday, the felt, and the miscellaneous. At the same time, their poetries pose challenges to the conceptions of experience on which empiricism historically has been based, from the presumption of a unified experiencing subject to the relegation of sensation and abstraction to separate orders of reality. I argue that these challenges should not be seen as a denial of experience, as some postmodernist readings of New York School poetry allege, but as part of a careful and critical commitment to experience. As radical empiricists, these poets understand experience not as an inward phenomenon but as a field in which inner and outer are merely potential and constantly shifting divisions./nIn the first chapter, I locate a precedent for Ashbery’s radical-empiricist poetics in Gertrude Stein’s Stanzas in Meditation, arguing that both Stein and Ashbery confound the conceptions of experience that predominate in critical assessments of modern and postmodern poetry and art. In the second chapter, O’Hara’s poetry presses the necessity of distinguishing between radical-empiricist poetics and the influential poetics of pragmatism. O’Hara shares pragmatism’s conception of experience as fluid and precarious, but his poems highlight affective dimensions of experience that are lost when poetry is understood pragmatically, as an instrument designed to provide the reader, or the poet, with momentary clarity and provisional ideals conducive to her progress in an unsteady world. Chapter Three analyzes the technique of bathetic deflation that Schuyler employs to forestall the idealization of notions like experience, self, and nature in an effort to keep the phenomena that those terms describe thoroughly suspended in the matrix of the empirical. Finally, in a chapter linking the poetry of the New York School to the art of Jasper Johns and Robert Rauschenberg, I argue that these poets and artists respond in parallel ways to the models of experience associated with Abstract Expressionist painting. Johns and Rauschenberg recover the category of experience by unhooking it from the language of self, soul, and expression with which it had long been associated and resituating it in the world of material objects, including the human body.

Advisor: Altieri, Charles
Development and Assessment of Electronic Structure Approaches for Non-Covalent Interactions

This thesis is primarily concerned with the development and assessment of electronic structure approaches for intermolecular interactions. Various aspects of existing approaches -- most notably the choices of method, grid, and basis set -- are examined with respect to performance in novel ways, and new semi-empirical corrections intended to rectify deficiencies in standard methods are introduced.

Advisor: Head-Gordon, Martin P
Neaton, Jeffrey B
Automated Registration of Image Pairs with Dramatically Inconsistent Appearance

The objective of this research is to advance the state of the art in image matching algorithms, especially with regard to input image pairs that include dramatically inconsistent appearance (e.g., different sensor modalities, significant intensity/color changes, different times such as day/night and years apart, etc.). We denote this range of input as disparate input. To handle disparate input, one should be able to capture the underlying aspects not affected by superficial changes to appearance./nTo this end, we present a novel image descriptor based on the distribution of line segments in an image; we call it DUDE (DUality Descriptor). By exploiting line-point duality, DUDE descriptors are computationally efficient and robust to unstable line segment detection. Our experiments show that DUDE can provide more true-positive correspondences for challenging disparate datasets./nBeyond traditional image matching, we have designed an effective autograding system for multiview engineering drawings that also uses DUDE to improve its performance. The autograding system needs to be able to compare drawings that may include appearance changes due to students' mistakes, but also needs to differentiate between allowable and erroneous translation and/or scale changes./nIn the addition to hand-crafted descriptors, this research also investigates data-driven descriptors generated by new deep learning based approaches. Due to the lack of labeled disparate imagery datasets, it is still challenging to effectively target disparate input using deep learning approaches. Therefore we introduce an aggressive data augmentation strategy called Artificial Intensity Remapping (AIR). By applying AIR to standard datasets, one can obtain models that are more effective for registration of disparate data. Finally, we compare the DUDE descriptor to a deep learning based descriptor powered by AIR.

Advisor: McMains, Sara
Statistical Learning for Sparse Sensing and Agile Operation

Recent advancements in the study of cyber-physical systems (CPS) have addressed the combination of computation, networking, physical processes, and human involvement as an overall system to improve adaptability, autonomy, eciency, functionality, reliability, safety, and usability. Among other lines of CPS research, machine learning (ML) has emerged as an indispensable component for state estimation, prediction, diagnosis, structure identication, operation specication, event detection, etc. This work particularly discusses three learning tasks that are commonly encountered in CPS sensing and operation applications. The primary motivations underlying this dissertation are (1) to incorporate the unique characteristics of the data generated from system measurement, and (2) to facilitate the integration of ML into other components of CPS, such as sensing and control subsystems./nMore specically, we rst consider learning interaction structures for sparse sensing. With the generic directed information maximization as the learning objective, we discuss two subset selection problems and provide performance guarantees for greedy algorithms by extending the notion of submodularity. Practically, the proposed learning framework can be applied broadly to streaming feature selection, causality mining, sensor placement, as well as the construction of causal graphs. The second learning task discussed in this work is focused on the detection of outliers or novelties from multiple correlated time series data generated from CPS measurement. The key issue being addressed is the utilization of the correlation information in the smoothing process of multiple sequences. Two methods, one based on a multi-task extension of non-parametric time series modeling and the other based on merging hidden Markov model with matrix factorization, are established and analyzed. Lastly, we discuss the task of learning system requirement for agile operation and optimal control. The classical ML paradigm is modied with \shape constraints" to facilitate its usage for optimal control or to capture class imbalance for event detection. While developing new learning formulations, we also propose a novel global optimization procedure, namely parametric dual maximization, that is able to solve a class of modied machine learning problems having non-convex objectives.

Advisor: Spanos, Costas J