VictorJuiz/thesis huggingface dataset:
ATP-dependent chromatin remodeling BRG/Brahma-associated factors (BAF) complexes in the regulation of mammalian stem cell self-renewal and development [electronic resource]

Mammalian SWI/SNF (also called BAF) ATP-dependent chromatin remodeling complexes are essential for formation of the pluripotent cells of the early embryo, and are also crucial for the self-renewal and pluripotency of mouse embryonic stem cells (ESCs). To understand the molecular mechanism of BAF complexes in regulating the chromatin of pluripotent stem cells, we performed both proteomic and genomic studies of endogenous complexes in ESCs. Proteomic studies reveal that ESCs express distinctive BAF complexes (esBAF), and this specialized subunit composition is required for ESC maintenance and pluripotency. High-resolution genome-wide mapping of the core ATPase subunit, Brg, using ChIP-Seq technology indicates that esBAF is a core component of the pluripotent transcriptional network. This is consistent with findings that esBAF interacts both physically and genetically with key regulators of pluripotency such as Stat3, Oct4 and Sox2. In addition, esBAF is critical for Stat3-mediated gene activation and repression in mESCs in response to Leukemia Inhibitory Factor (LIF), the cytokine that maintains mESCs in a self-renewing state. Brg maintains open accessibility of Stat3 target sites to allow continuous binding of Stat3 in response to LIF signaling, and prevents the expansion of Polycomb activity and the inappropriate deposition of the silencing mark H3K27me3 at both Stat3 targets and other sites. We propose that one integral mechanism of esBAF action in maintaining pluripotency is to maintain Stat3 responsiveness in ESCs by regulating the accessibility of its target sites. The role of BAF complexes in self-renewal and differentiation extend to adult multipotent stem cells. Using mouse adult hematopoietic development as a model, we show that Brg is required for the transition of quiescent long-term hematopoietic stem cells (LT-HSCs) to their downstream progenitors, and for the multilineage differentiation of transit amplifying hematopoietic progenitors. Hence, we propose that chromatin remodeling is generally required for the function and maintenance of stem cells by the regulation of their specialized chromatin landscape.

Advisor: Crabtree Gerald R. primary advisor. Thesis advisor
Cleary Michael L. advisor. Thesis advisor
Scott Matthew P. advisor. Thesis advisor
Weissman Irving L. advisor. Thesis advisor
Automatic biomedical information extraction from free text [electronic resource]

Advances in medical research, pharmaceuticals, treatment options, and biotechnology are occurring at an explosive rate. As of 2009, there are 19 million of biomedical research abstracts available on MEDLINE and 1.3 billion searches of MEDLINE are done in 2009. Most of the popular search engines, from Google to PubMed, use keyword-based information retrieval methods, often overloading users with irrelevant information. At the same time, keyword-based search engines cannot answer simple biomedical questions, such as "what are the breast cancer treatment drugs" or "what are the breast cancer associated genes". Answering such questions requires machine understandable knowledge to be extracted from free text. My thesis represents an automated system to extract machine understandable biomedical information from MEDLINE abstracts using machine learning and natural language processing ( NLP ) techniques. The system is different from current biomedical information extraction systems in the following: 1.the system is semi-supervised where the only human supervision is a single pattern for each information type; 2. it can be used to extract broad types of information, including named entities and relationships among entities.

Advisor: Das Amar K. (Amar Kumar) primary advisor. Thesis advisor
Garber Alan M. primary advisor. Thesis advisor
Altman Russ advisor. Thesis advisor
Manning Christopher D. advisor. Thesis advisor
Background calibration of timing skew in time-interleaved A/D converters [electronic resource]

The increasing data rate of wireline communication systems leads to more inter-symbol interference, due to the dispersive properties of the communication channel. This requires more complex equalization blocks to meet the required bit-error rate. One solution is to use an Analog-to-Digital Converter (ADC) in the front-end, thus enabling a digitally-equalized serial link. To achieve the high-data rates of these communication systems, a time-interleaved ADC is typically used. However, this type of ADC suffers from several time-varying errors, the most prominent of which is timing skew. This thesis introduces a statistics-based background calibration algorithm that compensates for the effect of timing skew. To demonstrate the background calibration algorithm, a proof-of-concept 5 bit 12 GS/s flash ADC has been fabricated in a 65 nm CMOS process. The design of this ADC takes into consideration the tight power bounds imposed on serial links by optimizing both the time-interleaved and the sub-ADC architecture. Power consumption is further reduced by using calibration circuits to correct the offset of the flash ADC's comparators. In the measured results, the timing skew correction improves the dynamic performance of the time-interleaved ADC by 12 dB, and the proof-of-concept ADC has the lowest published power consumption for ADCs with sample rates higher than 10 GS/s.

Keywords: Electrical Engineering
Advisor: Murmann Boris primary advisor. Thesis advisor
Meng Teresa H. advisor. Thesis advisor
Wooley Bruce A.
Barriers and Facilitators to Adoption of Personal Health Records: A Study of Families with Children with Special Health Care Needs

This project explores the barriers and facilitators to adoption of electronic Personal Health Records (PHRs) in low income families/caregivers of children with special healthcare needs (CSHCN). Focus groups at two community support organizations were conducted in English, Spanish, and Cantonese. Usability studies of Google Health, a personal health record that is partnering with Lucile Packard Children’s Hospital, were also conducted in English with parents. These studies will help explain: 1) the current methods by which parents manage healthcare information, 2) the knowledge, needs, and concerns of caregivers about PHRs, and 3) design goals for improving PHR accessibility.
Focus groups and interviews following the usability studies consistently showed that parents rely on paper-based methods even though healthcare providers may not always give full copies of records. This incomplete record frustrates parents and impedes information flow between the multiple healthcare providers of special needs children. The PHR was met with excitement by families, but few families were aware of the PHR’s availability before participating in the study. However, the majority of parents expressed a desire to learn and begin using a PHR to complement their information management needs. Although privacy concerns, technology literacy, and health literacy remain as foreseeable barriers to PHR adoption, families
with CSHCN can derive immediate benefit if they are informed and educated about the availability of the PHR to manage healthcare information. Developers of PHRs can support this goal by ensuring that sound usability is a priority, thereby presenting a compelling option for parents.

Keywords: Medical records
Personal information management
Medical informatics
Electronic health records
Thesis
Advisor: Winograd Terry
Bergman David
Slayton Rebecca
Visconti Virginia
A Bayesian method for construction of Markov models to describe dynamics on various time scales [electronic resource]

The dynamics of many biological processes of interest, such as the folding of a protein, are slow and complicated enough that a single molecular dynamics simulation trajectory of the entire process is difficult to obtain in any reasonable amount of time. Moreover, one such simulation may not be sufficient to develop an understanding of the mechanism of the process, and multiple simulations may be necessary. One approach to circumvent this computational barrier is the use of Markov state models. These models are useful because they can be constructed using data from a large number of shorter simulations instead of a single long simulation. This thesis presents a new Bayesian method for the construction of Markov models from simulation data. A Markov model is specified by (t, P, T), where t is the mesoscopic time step, P is a partition of configuration space into mesostates, and T is an N x N transition rate matrix for transitions between the mesostates in one mesoscopic time step, where N is the number of mesostates in P. The method presented here is different from previous Bayesian methods in several ways. 1. The method uses Bayesian analysis to determine the partition as well as the transition probabilities. 2. The method allows the construction of a Markov model for any chosen mesoscopic time scale t. 3. It constructs Markov models for which the diagonal elements of T are all equal to or greater than 0.5. Such a model will be called a 'consistent mesoscopic Markov model' (or CMMM). Such models have important advantages for providing an understanding of the dynamics on a mesoscopic time scale. The Bayesian method uses simulation data to find a posterior probability distribution for (P, T) for any chosen t. This distribution can be regarded as the Bayesian probability that the kinetics observed in the atomistic simulation data on the mesoscopic time scale t was generated by the CMMM specified by (P, T). An optimization algorithm is used to find the most probable CMMM for the chosen mesoscopic time step. We applied this method of Markov model construction to several toy systems (random walks in one and two dimensions) as well as the dynamics of alanine dipeptide in water and of trpzip2 in water. The resulting Markov state models were indeed successful in capturing the dynamics of our test systems on a variety of mesoscopic time scales.

Keywords: Chemistry
Advisor: Andersen Hans
Fayer Michael D. advisor. Thesis advisor
Pande Vijay advisor. Thesis advisor
Bayesian statistics and single-molecule trajectories [electronic resource]

Bayesian statistics is a powerful method for inference--possibly the uniquely correct method for inference. As described herein, when applied to a few degrees of freedom from single molecule trajectories, Bayesian statistics yield useful insights into rates, states, and motions.

Keywords: Chemistry
Advisor: Pande Vijay primary advisor. Thesis advisor
Andersen Hans
Boxer Steven G. (Steven George)
Beyond "Spanglish" [electronic resource] : ideologies of language and identity in bilingual Chicana/o cultural production

Prompted by the following research question: How is the relationship between language and identity conceptualized, articulated, and represented in cultural productions by, for, and about Chicana/os?, this dissertation interrogates linguistic assumptions and expectations of Chicana/o identities. By foregrounding the study of bilingualism in analyses of coming-of-age novels, autobiographical narratives, and feminist writing, it argues for the identification of language ideologies in Chicana/o cultural production. Doing so allows for the necessary examination of social constructions of language and the systems of power they reproduce within Chicana/o cultural studies, as well as the recalibration of limiting linguistic expectations of Chicana/o identity. The first chapter presents a conceptual framework based on the study of bilingualism, identity work, language ideologies, and Chicana/o cultural studies as a critical entry into the analysis of representations of bilingualism and/or bilingual representations. The second chapter compares the proto-Chicano development of bilingualism and Mexican American identity in the protagonists and texts of José Antonio Villareal's Pocho and Américo Paredes's George Washington Gómez. The third chapter elucidates the intricate identity work required to choose and maintain a bilingual Chicana/o identity in Ernesto Galarza's Barrio Boy, Arturo Islas's The Rain God, and Sandra Cisneros's Caramelo. The fourth chapter examines the conflictive relationship to Spanish as a heritage language in writings by Michele Serros, Gloria Anzaldúa, Cherríe Moraga, and Vida Mía García that scrutinize the negation of bilingual Chicana/o identities.

Keywords: Iberian and Latin American Cultures.
Advisor: Valdés Guadalupe primary advisor. Thesis advisor
Yarbro-Bejarano Yvonne
Brotherston Gordon advisor. Thesis advisor
Saldívar Ramón
Biodegradable poly (hydroxyalkanoates) [electronic resource] : melt, solid, and foam

Plastic materials have a huge impact to the environment. EPA statistics shows that less than 7% of the plastic products are being recycled, and many of the rest are sent to landfills or, in worse scenarios, end up in our natural environment. Poly(hydroxyalkanoates) (PHAs), a family of biodegradable polyesters that can be produced by microbes fed on renewable carbon substrates, can be used as a "green" substitute to conventional plastics and help solve this environmental problem. However, difficulties remain for using PHAs at a sizable scale. Besides the high production cost, weaknesses in material properties, including narrow thermal processing window and insufficient melt elasticity, are also limiting the application of PHAs. Recent progress in PHA syntheses has resulted in new copolymers in the PHA family which are expected to possess improved properties. In this thesis, the melt properties of a series of one such copolymer, poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (P3HB-co-3HHx), with varying 3HHx content, were investigated. Results suggested that the presence of the propyl side groups on 3HHx increases the steric hindrance of the P3HB-co-3HHx chains, thus resulting in increased entanglement density, and subsequently, the melt elasticity. Solid-state properties of P3HB-co-3HHx were also studied, and the effects on biodegradability of thin films of P3HB-co-3HHx were investigated. Results show that varying copolymer composition in combination with modifying the crystalline morphology through heat treatment may enable control over biodegradation rates for PHAs materials. In addition, biodegradable cellular foams made of PHAs were synthesized through extrusion foaming, a standard melt processing for thermoplastics. A commercial PHA copolymer, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (P3HB-co-3HV), was used and evaluated for its foamability. Another naturally-derived polymer, cellulose acetate butyrate (CAB), was chosen to blend with P3HB-co-3HV to enhance its melt properties and processability. It was found that blending significantly improved the thermal processing window and enhanced melt elasticity. Results showed that selectively combining two types of bio-based renewable polymer could be an effective way to tune the melt properties and crystallinity and thus the processability.

Keywords: Chemical Engineering
Advisor: Frank C. W. primary advisor. Thesis advisor
Billington Sarah L. (Sarah Longstreth)
Criddle Craig advisor. Thesis advisor
Biomechanical guidelines for the treatment of crouch gait in children with cerebral palsy [electronic resource]

Many children with cerebral palsy walk with excessive knee flexion, an inefficient locomotion pattern known as crouch gait that progressively worsens over time without intervention. Patients often receive surgeries to lengthen tight or spastic muscles or to correct bone malalignments, but outcomes are variable and unpredictable. The goals of this dissertation were, first, to objectively identify biomechanical factors that cause a patient to walk with excess knee flexion and, second, to use these factors to predict whether a patient's crouch gait will improve after receiving treatment. We first determined the influence of abnormal bone geometry and crouched gait postures on the function of muscles during walking using a three-dimensional model of the musculoskeletal system. Our analysis revealed that a tibial torsion deformity, a common bone malalignment, reduces the capacity of lower limb muscles to generate extension of the knee and hip joints. Excess tibial torsion may thus be a significant contributor to crouch gait and warrant surgical correction. In addition, our analysis showed that a crouched gait posture markedly reduces the capacity of most lower limb muscles to extend the knee and hip joints. These findings help explain the altered muscle activations, increased energy requirements, and increased joint loading associated with walking in a crouch gait. We also developed a multi-variable linear regression model to estimate how much subjects' crouch gait would change between hospital visits by retrospectively analyzing patients' gait kinematics over time and surgical histories. The regression model was able to explain 49% of the variance in the change in knee flexion between gait visits for the 353 subject-limbs that we analyzed. Further, the regression model classified subject-limbs as 'Improved' or 'Unimproved' with approximately 70% accuracy, which contrasts with the observed improvement rate of 48% among subject-limbs in the study. We further demonstrated that more improvement in crouch gait was expected when subjects had i) adequate hamstrings lengths and velocities, ii) normal tibial torsion, and iii) greater extensor muscle strength, three variables drawn from our knowledge about the biomechanics of crouch gait. This work establishes a new framework--combining biomechanical modeling and statistical analysis--for understanding gait pathology and objectively planning treatment.

Keywords: Mechanical Engineering
Advisor: Delp Scott primary advisor. Thesis advisor
Andriacchi Th. P. (Thomas P.) advisor. Thesis advisor
Imrie Meghan advisor. Thesis advisor
Boundary ray analysis of radiometric optical systems [electronic resource]

Radiometric optical systems are designed to control the flow of radiant energy. The objective may be to collect energy from a source, transmit energy from the source to a point of use, or concentrate energy onto a receiver. These systems differ substantially from imaging systems both in application and design. Some radiometric applications must consider the fine, information-bearing structures of the light, but the objective is to destroy this structure, not carefully preserve it! The objective of this thesis is to provide insight and design methodology that result when the fine scale structure of the illumination is ignored. When fine scale brightness differences in the illumination are avoided or ignored, the remaining feature of the illumination is the boundary between rays that carry radiant energy and neighboring rays that don't. The rays that fall on this boundary between light and dark are the boundary rays. These rays have particular significance. By knowing the location of the boundary, the location of all the illumination is known. Furthermore, it is shown that the boundary is conserved during propagation through a continuous optical system. The illumination at the output may be determined by tracing just these rays from the input. This result is rigorously proven and called "the boundary mapping theorem for continuous optical systems". Conservation of boundary rays is a mixed blessing. It specifies both a simplification, only the boundary rays are important, but also a constraint, the boundary rays cannot be changed. Discontinuous optical systems have isolated discontinuities where the boundary rays of the illumination do change. Furthermore, discontinuous optical systems have great radiometric performance! A careful examination of discontinuities permits extension of the boundary mapping theorem to optical systems with discontinuities. The discontinuity at the edge of a reflector and the discontinuity at the critical angle are analyzed in detail. The changes that occur in the boundary, either addition of new boundary rays or deletion of old boundary rays, are specified for these discontinuities. If only a few rays determine radiometric behavior, then control of these rays controls the radiometric behavior. In two-dimensional light pipes, sufficient degrees of freedom exist to fully control the important rays. The resulting designs are optimal: all the rays that the system is designed to accept are transmitted to the output, and only those rays are transmitted to the output. Several light pipes are designed and analyzed in this thesis to exemplify this behavior.

Keywords: Electrical Engineering
Advisor: Gibbons James F. primary advisor. Thesis advisor
Hesselink Lambertus primary advisor. Thesis advisor
Macovski Albert
Building common instructional practice in a choice-driven district [electronic resource] : what reform brought to Milwaukee 1999-2009 [electronic resource]

Two competing strategies for school improvement have gained traction over the past twenty years. One approach centers on attempts to better manage instruction from the top as a way to improve school quality and student outcomes. The other strategy aims to loosen controls by giving schools more autonomy with the thought that educators will utilize increased autonomy as a mechanism for creating and redesigning schools that better meet the needs of students. At the district level, these two approaches have been loosely categorized as managed instruction or a portfolio reform strategy respectively. Although many districts have attempted variations of both of these models, few districts have attempted to actively manage instruction within a portfolio of schools. To better understand how these strategies can support and diminish one another this study examined Milwaukee Public Schools' attempt to build common instructional practice in its portfolio of schools. The study sought to answer two primary questions: How can a district attempt to build common instructional practice in a portfolio of schools and to what effect? To address these questions the study presents a case study on the implementation of the MPS instructional improvement plan and an examination of both student outcomes and instructional practice across the district. It was concluded that the outcomes are mixed: the district has made progress in creating the context necessary for building common practice, but wide variation in instructional still exists. MPS has created a common language for discussing instruction and implemented processes that support common practice, with a particularly strong effort in making instructional practice transparent. Despite success in these areas the district has not yet realized the system-wide changes in instructional practice it had sought because many of the policies and attitudes that support the portfolio approach frustrate the attempts at building common practice. It has been especially difficult for the district to build an instructional accountability system and create coherence and support for its principals and teachers.

Keywords: Education.
Advisor: Darling-Hammond Linda
Alvarado Anthony
Labaree David F.