VictorJuiz/thesis huggingface dataset:
Biomaterials Design for Control of Cell Behavior by Femtosecond Laser Processing

The last decade has seen exciting and unprecedented work at the interface between biology and materials science, particularly in the form of exquisite control of cell attachment, shape, traction, motility, and differentiation. Recent progress in developing techniques for microfabrication of biomaterials helps recapitulate many extracellular matrix (ECM) cues, making them progressively more useful for applications in biology and tissue engineering. This dissertation presents a study of femtosecond laser assisted micro- and nano-fabrication applicable for the biomaterials design aiming at achieving deliberate control of the cell behavior. Cell mechanics connected to cell alignment and migration, from speculation of cell response to the biomaterials surface to control of the response by topographic and chemical patterns, was studied./nCell migration is an essential cellular process for a variety of physiological and pathological phenomena. Migration of leukocytes mediates phagocytic and immune responses. Migration of fibroblasts, vascular endothelial cells, and osteoblasts contributes to wound healing and tissue regeneration, and tumor cell migration is essential to metastasis. The cell migration process can be initiated by mechanical and chemical cues from the extracellular microenvironment. Factors affecting cell migration can be both soluble and insoluble macromolecules that comprise the ECM or mediate extracellular communication./nWe apply femtosecond laser induced two-photon polymerization and multiphoton laser ablation lithography to fabricate precisely defined two-dimensional patterned surface in nanometer to micrometer length scale and three-dimensional filamentous materials to be used in studies addressing fundamental issues concerning control of cell adhesion and migration. We studied microscale topographical patterned surface for cell alignment and migration. Anisotropic micronscale ridge/groove patterned surfaces are powerful cues to control cell shape and to enhance or obstruct cell migration. However, they have limited ability to independently control the size and the distribution of the cell adhesive domains and the ligand density. Thus, we applied chemically and topographically patterned surfaces in the nanoscale to control cell adhesion and guide directional cell migration to overcome constraints of microscale patterns. During cell migration, contractile force is needed to move the cell body forward. We also studied the contractile force exerted by an individual locomoting cell using fiber scaffolds.

Advisor: Grigoropoulos, Costas P
El quiebre de los dogmas: Debate feminista, transgresión y duelo en obras escogidas de Gioconda Belli, Diamela Eltit y Cristina Peri Rossi

Abstract/nShattering Dogma: Feminist Debate, Transgression and Mourning/nin Selected Works by Gioconda Belli, Diamela Eltit and Cristina Peri Rossi/nby/nTanya V. Varela/nDoctor of Philosophy in Hispanic Languages and Literatures/nUniversity of California, Berkeley/nProfessor Francine Masiello, Chair/nThis dissertation examines selected works of renowned authors Gioconda Belli, Diamela Eltit and Cristina Peri Rossi, with the objective of identifying the various levels of resistance that emerge from their texts against authoritative and dogmatic discourses -especially feminism-- prevalent in 1980's Latin America. Assessing how these women writers manage to break away from the decade's normative discursive tone, the introductory chapter discusses the cultural and historical factors that contribute to produce the distinctive qualities that define Latin American feminist thought./nAn elaborate comparative analysis in the core chapters leads me to examine to what extent Belli, Eltit and Peri Rossi both address and erode the ideological dogmatism and the essentialist tendencies that prevail in feminism. In these chapters, I also study their proposals for alternative representations of gender through innovative aesthetic quests. I argue that through ideological and aesthetic transgression, these writers attempt, with varying degrees of success, to drastically subvert and dismantle notions such as `patriarchy,' `femininity,' `motherhood' and `family'. In doing so, they liberate their respective texts from heavy categorical burdens and allow these politically disputed concepts to be aesthetically produced, reformulated, and modified. I propose that by positing a profoundly self-critical brand of feminism, these novelists rearticulate the theoretical and aesthetic debates in each of their selected works, and establish a healthy distance between the rigidity of militant ideological discourses and their literary production./nIn the last chapter, I analyze three recent novels by this trio of authors, seen in light of their contributions -in the 1980's-- to reformulating the dogmatically-oriented feminist discourse and now, at the start of the millennium, under the shadow of a less strident post-feminism that has settled in Latin America. I conclude that, just as the act of transgression was indeed necessary as a means to break away from the rigid symptoms detected in 1980's feminism, these recent texts are framed within an equally forceful imperative of mourning, which stems from the vacuum left by a shattered feminist dogma and the installation of a new global cultural context that has effectively co-opted and neutralized debates on gender. In the end, though this outcome is seemingly ironic, it has nevertheless propelled Belli, Eltit and Peri Rossi to continue their creative quests for contestatory new discursive proposals, while still searching for balance in the never-ending negotiation between aesthetics and ideology.

Advisor: Masiello, Francine
Sticky Incentives and Dynamic Agency

I explicitly derive the optimal dynamic incentive contract in a general continuous time agency problem where inducing static first-best action is not always optimal. My framework generates two dynamic contracts new to the literature: (1) a ``quiet-life" arrangement and (2) a suspension-based endogenously renegotiating contract. Both contractual forms induce a mixture of first-best and non-first-best action. These contracts capture common features in many real life arrangements such as ``up-or-out", partnership, tenure, hidden compensation and suspension clauses. In applications, I explore the effects of taxes, bargaining and renegotiation on optimal contracting. My technical work produces a new type of incentive scheme I call sticky incentives which underlies the optimal, infrequent-monitoring approach to inducing a mixture of first-best and non-first-best action. Furthermore, I show how differences in patience between the principal and agent factor into optimal contracting.

Advisor: Anderson, Robert M.
Nanoscale SRAM Variability and Optimization

Robust SRAM design is one of the key challenges of process technology scaling. The steady pace of process technology scaling allows doubling memory array sizes, which requires thorough characterization of the impact of sources of process variability on SRAM operation. SRAM arrays are traditionally designed using static noise margins which are known to be optimistic in writeability and pessimistic in read stability. This work presents techniques for characterizing SRAM using dynamic stability metrics, which better represent actual SRAM operating conditions. Quantitative relationships between static and dynamic stability metrics are explored through statistical circuit simulations. Nano-scale SRAM design is traditionally complicated by sources of variability related to physical variability in the structure of the transistors, such as random dopant distribution. This work identifies temporal sources of variability in transistor intrinsic parameters, caused by random telegraph signaling (RTS) noise, which is directly correlated with fluctuation in SRAM performance. A large-scale dynamic stability characterization architecture is introduced and implemented in an early commercial low-power 45 nm CMOS process. This is used to experimentally verify the expected correlations between static and dynamic stability metrics. Outliers of up to 100X which are not correlated between static and dynamic stability metrics were observed and identified to be due to enhanced sensitivity of dynamic stability metrics to variability. Measurement techniques for characterizing temporal sources of variability caused by RTS noise, with particular emphasis on the large-signal bias change response typically encountered in SRAM operation, are used to collect large-scale statistics and to estimate the statistical impact of RTS noise on large SRAM arrays./nAn importance sampling algorithm adapted for dynamic stability metrics is developed in this work. This algorithm is used to estimate improvements in SRAM robustness expected from new process technology options such as FDSOI, different bitcell designs such as the 8T-SRAM, as well as several read-assist and write-assist techniques. An optimization framework enabled by this importance sampling algorithm is used to design SRAM arrays with maximum array efficiency through joint-optimization between process technology, bitcell design, and array organization. In conclusion, this dissertation identifies important sources of variability in nano-scale SRAM and also introduces the relevant optimization tools for performing variability-aware SRAM design.

Advisor: Nikolic, Borivoje
The effects of oxidative modifications on cardiac and skeletal muscle

Biological systems are frequently exposed to reactive oxygen species (ROS), which can be damaging to cellular function. Recent research suggests that ROS can also be used as signaling agents, modifying protein functions post-translationally, by reversibly modifying cysteines. The contractile functions of both skeletal and cardiac muscle are responsive to reactive oxygen species, but the mechanisms are unknown. We therefore developed methods to quantify, which cysteines are modified by exposure to oxidative reagents, and used these methods as a gateway for testing different mechanisms for how ROS affect function. From these techniques, we found that nearly every myofilament protein in both cardiac and skeletal muscle has one or more cysteines that can be modified by ROS in the environment of the myofilament lattice. Interestingly, we found that both the cysteines modified and the effects from ROS exposure depended on the contractile state of the muscle. Exposure in a relaxing buffer (ATP present) modified a large number of myosin thiols, and decreased the maximum ATPase and calcium sensitivity when compared to untreated myofibrils. In contrast, ROS exposure in a rigor buffer (no ATP) decreased the number of modified myosin thiols and increased the modification of actin when compared to treatment in relaxing buffer. Exposure in rigor buffer did not change the maximum myofibril ATPase, but did increase the basal ATPase and calcium sensitivity. Complementary studies in fast skeletal muscle tested the ability of different cysteine reagents to change calcium sensitivity. We found that different reagents affected calcium sensitivity in opposite directions, and found evidence that the difference in direction was due to differences in the type of modification, rather than a difference between cysteine sites. We narrowed down the proteins responsible for these effects to actin, essential light chain, tropomyosin and the myosin heavy chain. Further eliminating proteins with cysteines not unique to fast muscle, we found two cysteines in the myosin heavy chain, both in the neck region, that are the most likely to be responsible for the changes in calcium sensitivity. In summary these experiments shed significant light on a variety of mechanisms by which ROS can modify the contractile function of cardiac and skeletal muscle. These results may be important for understanding and eventually treatment of diseases that have been found to produce oxidative modifications and decreased function of muscle, including heart failure, muscular dystrophy, arthritis and cancer.

Advisor: Lehman, Steven L
Extensions to Metadata Languages for Environmental Primary Data

During the last decade environmental scientists and managers have found in the Internet a new communication venue that has improved their productivity by allowing them to share data and knowledge more fluently. Since the invention of the eXtensible Markup Language (XML), XML has brought the attention of many researchers to improve the communications among people working with data-centric documents since XML was supposed to be the correct approach to standardize data. During this decade, many papers have been published under the pretenses of XML being the new and paradigmatic standard to share data even though no study has proved that the XML languages have been used by researchers or managers working with data-centric documents during this period of time. This thesis by researching all possible spaces proves that, on the contrary, that after more than a decade from its invention, XML is still not used by the vast scientific community that works with data-centric documents who are still using data archives with legacy formats. Therefore, if data standardization is difficult to attain, and facilitating sharing data a goal to reach, the other clear venue to follow to achieve the goal is to use metadata information. However, metadata languages such as the Ecological Modeling Language (EML) and others have no intrinsic features to complete and directly describe the information conveyed in many important types of data-centric documents used by environmentalists. By carefully studying the nature of data-centric archives and the process of metadata creation, this thesis shows that any data archive can be easily described using an "a posteriori" approach where the lexical descriptors of the physical data from a data-centric file are developed by inspection of the file instead of by following the specifications of the format of the file. In addition, following the principles of the Linked Open Data project, the lexical tree is mapped into a simple logic model with semantic annotations from controlled vocabularies which can be easily serialized for data exchange or data syndicalization. With the metadata extensions researched in this thesis, metadata languages such as EML can be improved by increasing its expression power. Environmental scientists and researchers can us this to exchange data-centric documents, and multidisciplinary projects can easily syndicate data from different authors in different formats in a data-centric cloud.

Advisor: Biging, Greg
Patterning of the Ciona intestinalis Motor Ganglion

Patterning of the Ciona intestinalis Motor Ganglion/nby/nAlberto Sunao Stolfi/nDoctor of Philosophy in Molecular and Cell Biology/nUniversity of California, Berkeley/nProfessor Michael S. Levine, Chair/nSea squirts are the closest living relatives to the vertebrates. The Motor Ganglion (MG) of the sea squirt Ciona intestinalis provides the basic excitatory drive of the central pattern generator (CPG) underlying swimming behavior of the tadpole. Despite its cellular simplicity, the MG shows molecular and physiological parallels to the spinal cord of vertebrates. Here I uncover the morphological diversity of MG neuronal subtypes, and show that this diversity is generated by sequential Ephrin/FGF/MAPK and Delta/Notch signaling events. Despite the divergent signaling requirements for patterning of this motor pool, I believe that the conserved downstream transcription factors might be operating to specify neuronal subtypes that are similar to those in the vertebrate spinal cord. Taking advantage of the experimental tractability of the Ciona embryo, I can generate a series of tadpoles with differing composition of moto- and interneuron subtypes, which could serve as the basis for elucidating the development and connectivity of a chordate locomotor CPG.

Advisor: Levine, Michael S
Dynamics of Viral Packaging: Single-Molecule Observations in Multiple Dimensions

During the self-assembly of bacteriophage phi29, the viral genome is packaged into a pre-formed capsid by a molecular motor. The packaging motor is a complex of several oligomers including a dodecameric connector ring and a pentameric ATPase ring. These rings coordinate with each other, generating high forces in order to compact the dsDNA genome into the capsid at high pressures./nThe connector was proposed to engage and directly perform work on the DNA during packaging. Consideration of the symmetry of the connector and the capsid predicts that the connector must rotate relative to the capsid as part of the mechanism for translocating the DNA. An experiment designed to directly measure rotation of the connector is discussed in Chapter 2 of this dissertation. A combination magnetic tweezers and total internal reflection microscope is used to track the polarization of single fluorescent dyes attached to the connector. No evidence of polarization changes were found, indicating that the connector does not rotate at the expected rates. This further suggests that the connector does not directly perform mechanical work on the DNA during packaging./nViral packaging can be observed in optical tweezers by monitoring the length of the DNA as it is drawn into the capsid. Past studies have revealed many details of the packaging mechanism by following the dependence of the packaging velocity on factors like ATP concentration and applied load. In Chapter 3, I propose an experimental design intended to measure the effect of the packaging motor on the angle of the DNA in addition to its length and thus recover the full three-dimensional trajectory of the DNA as it passes into the capsid. In addition, this scheme can be used to apply torque and thus provides an additional tool with which to probe the packaging mechanism./nIn Chapter 4, we find that during packaging the downstream DNA is twisted in an underwinding direction, with a magnitude that depends on the extent to which the capsid is filled. The change in twisting can be attributed to cumulative looping of the DNA within the capsid, and the data predicts that the loops formed in the last kilobasepair of packaging are as small as 4 nm in radius. In addition, a non-lethal method of rupturing the viral capsids prior to packaging was discovered. Observations of DNA twisting by those packaging complexes revealed that, in the absence of internal pressure, the DNA is twisted by -1.2 °/bp. This number suggests that one of the packaging motor's five subunits makes contact with the DNA every ten basepairs, and that the cycle repeats with that subunit performing the same function every time. Such a strict functional segregation, in addition to the catalytic segregation revealed in previous high-resolution optical tweezers experiments, is an important part of the mechanism by which the motor packages DNA against high forces.

Advisor: Bustamante, Carlos J
Quantifying Uranium Isotope Ratios Using Resonance Ionization Mass Spectrometry: The Influence of Laser Parameters on Relative Ionization Probability

Resonance Ionization Mass Spectrometry (RIMS) has been developed as a method to measure relative uranium isotope abundances. In this approach, RIMS is used as an element-selective ionization process to provide a distinction between uranium atoms and potential isobars without the aid of chemical purification and separation. We explore the laser parameters critical to the ionization process and their effects on the measured isotope ratio. Specifically, the use of broad bandwidth lasers with automated feedback control of wavelength was applied to the measurement of 235U/238U ratios to decrease laser-induced isotopic fractionation. By broadening the bandwidth of the first laser in a 3-color, 3-photon ionization process from a bandwidth of 1.8 GHz to about 10 GHz, the variation in sequential relative isotope abundance measurements decreased from >10% to less than 0.5%. This procedure was demonstrated for the direct interrogation of uranium oxide targets with essentially no sample preparation. A rate equation model for predicting the relative ionization probability has been developed to study the effect of variation in laser parameters on the measured isotope ratio. This work demonstrates that RIMS can be used for the robust measurement of uranium isotope ratios.

Advisor: Prussin, Stanley G
Promote Chemistry Learning with Dynamic Visualizations: Generation, Selection, and Critique

Dynamic visualizations can strengthen chemistry instruction by illustrating atomic level phenomena. Visualizations can help students add ideas about unseen phenomena involving atomic particles. They allow students to interact with phenomena that cannot be investigated in hands-on laboratories. Connecting dynamic, atomic representations with associated observable phenomena and symbolic representations has the potential to increase the coherence and comprehensiveness of student understanding./nConsistent with the knowledge integration framework, students enter chemistry courses with multiple non-normative ideas about chemical reactions. Following the knowledge integration framework, an inquiry project entitled Hydrogen Fuel Cell Cars engaged students in making predictions, exploring new ideas, distinguishing among ideas, and reflecting while connecting atomic interactions to everyday issues such as cars and fuel. To add normative ideas, a dynamic visualization that shows bond breaking and formation during hydrogen combustion was embedded in the unit. Using an iterative design process, a series of studies compared four approaches to distinguishing ideas: unguided exploration of the visualization, generating drawings of the sequence of events in the visualization, critiquing sequences of drawings attributed to a peer, and selecting among alternatives sequences. Progress was assessed using assessments that required students to articulate coherent accounts of chemical reactions./nThe dissertation describes the design and development of the instruction, reports on a series of comparison studies conducted in typical middle schools that compare student performance in each of the four conditions: exploration, drawing, critique, and selection. The results reveal that visualizations can be deceptively clear so students may ignore important details when exploring a visualization. When learners generate, select, or critique drawings of atomic interactions, they recognize gaps in their knowledge, develop criteria for distinguishing among ideas, and increase in ability to select normative ideas. The dissertation demonstrates the importance of encouraging students to distinguish ideas when learning with visualizations. It suggests design principles for creating instructions featuring visualizations that can succeed in typical classrooms.

Advisor: Linn, Marcia C.