VictorJuiz/thesis huggingface dataset:
Characteristics and implications of brief duration hydrodynamic forces in the intertidal zone [electronic resource]

The hydrodynamic forces produced by breaking waves make the rocky intertidal zone one of the most physical stressful environments on Earth. Although the classical in-line hydrodynamic forces are well studied and characterized, an undescribed force -- known as the impingement force -- may be the largest hydrodynamic force in the intertidal zone. Impingement is characterized by a sharp, transient spike in force at the instant of wave arrival, and very few measurements of it exist. I measured impingement in the laboratory, using a gravity-driven water cannon to simulate waves and tested which variables affect impingement magnitude. I show that impingement is likely drag, rather than an undescribed hydrodynamic force; it likely occurs due to brief increases in flow velocity at the front of a wave. To assess the frequency and magnitudes of impingement events in the field, I built a force transducer to record high-frequency forces in the intertidal zone. Impingement events occur in 2-7% of waves in the field, but surprisingly, the average magnitude of impingement events is lower than the average maximum force produced by all recorded waves in this study. This suggests that impingement is not the largest hydrodynamic risk to organisms, and future work measuring flows in the intertidal zone should focus on identifying large transient forces regardless of where they occur in a wave. Using these measurements, I explore the likely effects of brief forces on intertidal organisms in two ways: first, I model a limpet as a mechanical spring-mass-damper system and show that its foot has the capacity to reduce the effective force on the animal. I also predict dislodgment rates of three species of gastropod using the maximum forces recorded in my field study. At my site, snails are very susceptible to wave-induced dislodgment. This dissertation illustrates the necessity of recording high-frequency flows when studying intertidal hydrodynamics.

Keywords: Biology.
Advisor: Denny Mark W.
Fong Derek advisor. Thesis advisor
Monismith Stephen Gene advisor. Thesis advisor
Somero George N. advisor. Thesis advisor
Watanabe James Minoru
Characterization and application of vertical nanopillar-based sensors for probing cellular functions [electronic resource]

Vertically aligned nanopillars can serve as excellent electrical, optical and mechanical platforms for biological studies. To date, the interface between cells and nanopillars, particularly the conformation of the cell membrane and nucleus, has not been well characterized despite its importance to the choice of feasible applications for nanopillar substrates to cellular studies. We characterized the cell-nanopillar interface by fluorescence, scanning electron and transmission electron microscopy on nanopillars with a range of diameters, pitch and heights. We found that the cell membrane wraps around the entirety of the nanopillar without loss of membrane integrity, contrary to prior suggestions. We also observed that the membrane-surface gap of both cell bodies and neurites is smaller for nanopillars than for a flat substrate. These results support a tight interaction between the cell membrane and the nanopillars and previous findings of excellent sealing in electrophysiology recordings using nanopillar electrodes. Subsequently, we took advantage of the cell-nanopillar interface to develop applications of nanopillar arrays to mechanical and optical measurements in living cells. We observed that vertical nanopillar arrays significantly deform the nuclear envelope, and the extent of deformation is sensitive to both the stiffness of the nucleus and the stiffness of the cytoskeleton. Thus, nanopillar arrays constitute a novel approach for non-invasive, subcellular perturbation of nuclear mechanics and open up exciting new possibilities for the study of nuclear mechanotransduction in live cells. In addition to serving as mechanical probes, we developed a nanopillar-based platform for single molecule measurements in live cells. With a diameter much smaller than the wavelength of visible light, a transparent silicon dioxide nanopillar embedded in a nontransparent substrate restricts the propagation of light and affords evanescence wave excitation along its vertical surface. We showed that nanopillar illumination can be used for in vitro single molecule detection with high background. In addition, the tight interface between vertical nanopillars and live cells allows them to function as highly localized light sources inside the cell. Overall, nanopillar arrays are a powerful platform for studying cell function through electrical, optical and mechanical measurements.

Keywords: Chemistry.
Advisor: Cui Bianxiao primary advisor. Thesis advisor
Cui Yi
Dai Hongjie
Characterization of Lin28-RNA interactions in human embryonic stem cells [electronic resource]

RNA binding proteins (RBPs) play essential roles in the post-transcriptional regulation of gene expression. The RBP Lin28 is highly expressed in human embryonic stem (hES) cells and is known to play important roles in hES cell self-renewal and pluripotency. However, it is not completely understood how Lin28 contributes to the regulation of stem cell properties. This dissertation aims to advance our understanding on the molecular mechanisms Lin28 utilizes to influence stem cell biology. The first goal of the study was to systematically identify the full complement of Lin28-associated RNAs in hES cells. Using crosslinking and immunoprecipitation (CLIP) in combination with other genome-wide in vivo and in vitro techniques, we discovered that Lin28 interacts with the large majority of cellular RNAs, including all major functional classes of cytosolic RNAs in hES cells. Among the large number of targets preferential association occurs with tRNAs and mRNAs. The high abundance of Lin28 in hES cells is sufficient to allow binding of multiple Lin28 molecules to most of its mRNA targets. The second goal of the study was to uncover Lin28 recognition sequences on the identified RNA targets. Bioinformatic analysis and in vitro testing of Lin28 binding regions showed that Lin28 recognition of RNA targets occurs through interactions with low complexity nucleotide motifs that vary among RNA classes. The motif preference was clearest in mRNAs where Lin28 bound preferentially but not exclusively to the 3'UTR and favored interactions with AU rich sequences. The third and final goal of the study was to better understand Lin28's role in regulation of its mRNA targets. The data showed that in hES cells Lin28 appears to play no more than a minor role in regulating mRNA stability. However, Lin28 binding is strongly associated with a Lin28-dependent decrease in the density of ribosomes associated with its mRNA targets. The multiplicity of Lin28's interactions with diverse functional classes of RNA in hES cells, and the evidence that these interactions systematically alter translation of its mRNA targets, suggest that Lin28 may have a general transcriptome-wide regulatory role in hES cells.

Keywords: Genetics.
Advisor: Brown Patrick primary advisor. Thesis advisor
Fire Andrew Zachary advisor. Thesis advisor
Greenleaf William James advisor. Thesis advisor
Stearns Tim advisor. Thesis advisor
Characterizing, identifying, and using tree-like structure in social and information networks [electronic resource]

In this work, a detailed empirical analysis of two kinds of tree-like structure, in a variety of real and synthetic networks, is presented. The two types of tree-like structure computed are Gromov hyperbolicity, originated from geometric group theory, and the tree decomposition, an object common in theoretical computer science. The relationship between these structures and core-periphery structure, measured using the k-core decomposition, is also presented. The computational methods for each of these measurements are discussed, including timing results using OpenMP in several different implementations of the algorithm for computing Gromov hyperbolicity. The results show that tree-like structure is present in many real networks, but, because of the inherent fragility of the measurements, that modified definitions (which are scale-sensitive) are required to identify meaningful structure. Additionally, it is shown that there is a strong connection between the core-periphery structure and both Gromov hyperbolicity and the structure of the resulting tree decompositions. The final chapter of this work is separate and self-contained. It describes a novel method for using persistent homology (a technique of computational topology) to classify computed tomography (CT) scans of hepatic lesions.

Keywords: Electrical Engineering.
Advisor: Carlsson G. (Gunnar)
Boyd Stephen P. advisor. Thesis advisor
Montanari Andrea advisor. Thesis advisor
Characterizing sensory cell regeneration by facultative Lgr5+ cells in Mus musculus utricle

Recruitment of endogenous progenitors is critical during tissue repair. In the mammalian cochlea, damaged hair cells are not regenerated. As a result, hearing loss is permanent and negatively impacts the quality of life for over 48 million Americans. Adjacent to the cochlea in the inner ear are the vestibular organs responsible for our balance functions. Of the vestibular organs, the utricle requires mechanosensory hair cells to detect linear acceleration. After damage, non-mammalian utricles regenerate hair cells mitotically and non-mitotically. By contrast, mammalian utricles exhibit limited non-mitotic regeneration, with the source of regenerated hair cells currently unknown. Here, we used Lgr5-EGFP reporter mice to show that hair cell damage in neonatal mouse utricles activates the Wnt target gene, Lgr5, in supporting cells, which normally do not express Lgr5. Lineage tracing and time-lapse microscopy in utricles from Lgr5-EGFP-CreERT2; Rosa26R-tdTomato mice reveal that Lgr5+ cells non-mitotically become hair cell-like cells in vitro, a process termed “direct transdifferentiation.” Thus, Lgr5 marks damage-activated HC progenitors and may help reveal factors necessary for mammalian hair cell regeneration.

Keywords:  Department of Biology
Biology
Otolaryngology
regeneration
Wnt
Thesis
Advisor: Cheng Alan
Fernald Russell
ChIRP [electronic resource] : RNA interactome analysis

Abstract Long noncoding RNAs (lncRNAs) are key regulators of diverse cellular activities, yet their mechanisms of actions are largely unknown. Our understanding of lncRNA biology can be greatly improved by the development and deployment of novel technology, such as biochemical tools optimized for RNAs. Here we introduce Chromatin Isolation by RNA Purification (ChIRP), where tiling oligonucleotides retrieve specific lncRNAs and their interacting DNA sequences, which are enumerated by deep sequencing. ChIRP-seq reveals that RNA occupancy sites in the genome are focal, sequence-specific, and numerous. Drosophila roX2 RNA occupies male X-linked gene bodies with increasing tendency toward the 3' end, peaking at CES sites. ChIRP can also be modified for the purification of lncRNA-interacting transcripts and proteins, making it a universal tool for illuminating lncRNA-interactome with newfound precision.

Advisor: Chang Howard
Khavari Paul A. advisor. Thesis advisor
Sarnow P. (Peter) advisor. Thesis advisor
Wysocka Joanna
Chronotopes of a Continent: Ben Okri and the Spatial Dynamics of The Famished Road

This thesis examines the role of Ben Okri's The Famished Road (1991) in the canon of African literature. The unique narrative structure of the novel opens up possibilities of interpretation beyond the potentially limiting scales of analysis often associated with the African novel, including tribe, nation, race, and continent.

Keywords:  Department of English
Department of English
African novel
Nigeria
postcolonial literature
chronotope
twentieth century literature
Nigerian history
Negritude
Pan-Africanism
narrative theory
Thesis
Advisor: Woloch Alex
Hanretta Sean
Circuits underlying visual attention in primate neocortex [electronic resource]

Humans and many other species attend to only a small portion of available visual information at any given moment. They enhance perception of the attended stimulus either overtly, making an eye or head movement to orient toward it, or covertly, without any such movements. The neural circuits that underlie these two types of attention behaviors, and the relationship between them, remain unclear. To investigate the interdependence of them we trained monkeys on a task that behaviorally dissociated the location of covert attention from the location of a saccade target. Recordings in extrastriate visual cortical area V4 surprisingly revealed that enhanced firing rates and other modulations of neural activity accompanied both covert attention and saccade preparation. These results suggested a hypothesis about the circuits that could mediate the control of both behaviors. We recorded neurons in the frontal eye field, an area involved in controlling both behaviors, and found evidence contradicting our hypothesis. Separately, we examined the circuit underlying the integration of attention-related feedback signals with visual information in visual cortex by recording from distinct neuron populations, defined by laminar depth, within V4 during the covert attention task. We found that all neuron populations were modulated indistinguishably during attention. Finally, we constructed a large-scale model of FEF and V4 on neuromorphic hardware and used it to investigate a novel hypothesis about the way feedback from FEF influences V4, namely, via NMDA synapses. This model makes predictions for future experiments that could help uncover the mechanism of attention-related modulation of visual cortex. Taken together, these results have helped to elucidate our understanding of the circuits within and between frontal and visual cortical areas underlying attention.

Advisor: Boahen Kwabena (Kwabena Adu) primary advisor. Thesis advisor
Moore Tirin
Hestrin Shaul
Knudsen Eric I. advisor. Thesis advisor
Newsome William T. advisor. Thesis advisor
Cognitive and neural mechanisms of self-control [electronic resource]

Self-control, the ability to regulate impulses, is an important determinant of adaptive behavior and numerous significant life outcomes. This dissertation focuses on a class of decision-making known as intertemporal choices that require exertion of self-control. Intertemporal choices are decisions made between options that are available at different points in time. Delay discounting describes how individuals discount the value of future outcomes as a function of the delay until their receipt. The five experiments presented in this dissertation explore the cognitive and neural mechanisms of intertemporal decision making using a range of variables that predict differences in decision makers' discount rates. These variables include cultural differences (Experiment 1), cognitive framing of choice options (Experiments 2 and 4), and the magnitude of the reward under consideration (Experiment 3). Finally, we use repetitive transcranial magnetic stimulation (rTMS) to disrupt the processes identified in Experiments 2 and 3 to demonstrate their specificity and causality (Experiment 5).

Keywords: Psychology.
Advisor: McClure Samuel M. primary advisor. Thesis advisor
Dweck Carol S.
Gross James
Cohesion and decohesion kinetics of polymer solar cells [electronic resource]

Polymer organic solar cells (OSCs) possess many desirable properties include low temperature solution processibility of photoactive materials and the utilization of flexible substrates for conformal OSC design. However, challenges remain that may inhibit their adoption and implementation. Among these are thermochemical stability, optimized power conversion efficiency, and mechanical reliability. Indeed, for organic solar cells to be used on flexible substrates, mechanical reliability of the individual layers and interfaces is pertinent. In this dissertation, quantitative micromechanical testing techniques were employed to help characterize the mechanical reliability of the layers and interfaces for polymer OSCs. From testing, it was determined that the polymer:fullerene photoactive layer consistently failed cohesively. The cohesive strength of most photoactive layers generally ranged from 0.5 to 2.0 Joules per square meter. However, by using thermal annealing, manipulating the photoactive layer structure, and selecting polymer molecular weight, cohesion values as high as 17 Joules per square meter could be achieved. Indeed, polymer molecular weight affected cohesion the most due to significant plasticity within the photoactive layer. Conversely, improved cohesion did not always result in improved device electronic performance. By optimizing cohesion and efficiency, we are able to come closer to design guidelines for mechanically robust and efficient solar cells. Finally, because OSCs must operate in the environment at temperatures as high as 65 C, we analyzed OSCs under dry, inert environmental conditions and showed how temperature affects the decohesion kinetics within the device. It was demonstrated that the decohesion rate generally accelerated with increasing test temperature. We were able to develop a viscoelastic kinetic model that was able to describe and predict decohesion for these devices. This collective work and modeling will provide greater insight into the practical limitations of OSC design and will aid in future development of OSCs with greater mechanical reliability and in-service lifetimes.

Keywords: Chemistry.
Advisor: Dauskardt R. H. (Reinhold H.) primary advisor. Thesis advisor
Dai Hongjie
Waymouth Robert M. advisor. Thesis advisor
Collective governance in student housing cooperatives

Student housing cooperatives, or co-ops, are hybrid organizations that combine bureaucratic and communitarian organizational logics. Despite the inherent tension between these dual ways of organizing communal life, student co-ops are remarkably long-lived intentional communities, lasting over decades of constantly shifting membership and leadership. Collective governance, through which student co-ops manage to survive as communitarian projects in bureaucratic organizations, is the central phenomenon of interest in this study. How does the practice of collective governance in student co-ops enable students to negotiate between competing organizational forms and sustain a cooperative way of life? Through participant-observation of sixteen group decision-making meetings in two student co-ops, I depict the practice of collective governance in student co-ops as constituted in two parallel processes: managerial decision-making and collective decision-making. These systems reflect the hybridization of bureaucracy and communitarianism into a dynamic organizational form centered on negotiation and compromise. These findings suggest that while bureaucracy and communitarianism may be incompatible organizational logics, structured efforts toward compromise between them can itself be the basis for robust communal projects.

Keywords: cooperatives
co-ops
student housing
collective governance
student groups
Thesis
Advisor: Stevens Mitchell
Stipek Deborah
Combined optical trapping and sm-FRET for nucleic acid folding studies [electronic resource]

By studying ancient RNA motifs found in all kingdoms of life, we are also looking back in time to a common evolutionary ancestor. Riboswitches and ribozymes are structured RNAs capable of gene regulation and catalysis. Their surprising catalytic/functional diversity and prevalence across species hints at an "RNA World" that predates our current paradigm which depends on DNA for information and protein for catalysis. The TPP riboswitch is an ancient ligand-binding RNA that regulates vitamin B1 (TPP) synthesis in bacteria, archaea, and even higher organisms like plants. Using single molecule optical trapping (OT) and the judicious application of piconewton forces, we have studied the folding pathways of the riboswitch and its response to TPP and other analogues. Ligand binding appears to form in two steps: TPP must first bind weakly before proceeding to a strongly bound state, as measured by the non-equilibrium work required to unfold it. To probe the physical origin of these states, we use a novel dual-beam optical trap combined with simultaneous FRET that can measure two orthogonal signals of the molecule's conformation. We demonstrate the direct observation of both the unfolding of secondary (base-paired) structures (via OT) and long-range tertiary contacts (via FRET) that form during ligand binding. In time, we anticipate this technique will become a sought-after tool that can expose the intricate folding pathways of complex biomolecules.

Keywords: Physics.
Advisor: Block Steven M.
Das Rhiju
Doniach S. advisor. Thesis advisor
Commitments not to communicate before and after digital media [electronic resource] : a study of the will and ways to disconnect under changing conditions

"Information wants to be free, " goes the catchphrase of the information age. Falsely attributing agency to inanimate information by anthropomorphizing it wears away at belief in the role of individual agency in people's own communicative lives. So-called "internet addiction" is one prominent example of this in its displacement of responsibility from the will to the body. Neither engineers nor policymakers nor individuals adrift in the disorienting superabundance of digital communication claim responsibility for it, and few are proposing serious solutions. Communication scholars of various stripes offer theories of why we do and do not choose certain media, do and do not use certain devices, but there has been no systematic treatment of the myriad ways people deliberately structure quiet into their lives. This dissertation is such an analysis. The economic concept of "commitment devices" is applied to communication, generating a new definition of communication avoidance: the willful choice to limit one's own future communication choices. Our present motivations and methods for preempting communication of different kinds are illuminated through three historical chapters devoted to accounts of communication avoidance in the religious, public, and personal spheres. "Information overload" is a new term for an old phenomenon, and although masses of messages are today a quantitatively and qualitatively different problem, examples reaching back thousands of years to the seventh day—that of rest—help to frame contemporary problems within older concerns both technical and normative. A number of taxonomies are developed in order to better understand the diversity of and relationships between different forms of disconnection. In the digital case, this includes an analysis in terms of four different categories of means of disconnection: practices, software, hardware, and location. The book concludes with a discussion of the social and political project of destigmatizing avoidance and envisioning infrastructures that would empower people to better control the silences in their own lives.

Keywords: Communication.
Advisor: Glasser Theodore Lewis
Gumbrecht Hans Ulrich primary advisor. Thesis advisor
Bailenson Jeremy advisor. Thesis advisor
Hamilton James advisor. Thesis advisor