VictorJuiz/thesis huggingface dataset:
Modulating phagocytosis [electronic resource] : therapeutic targeting of the anti-phagocytic signal CD47 in human malignancies
Keywords: Cancer Biology.

Growing evidence indicates that cancers are composed of functionally heterogeneous cells that are organized by a cellular hierarchy and are maintained by a stem cell-like population. Given their unique ability to initiate tumor growth, eradication of these cancer stem cells (CSC) is necessary for cure. Thus, the development of CSC targeted therapies is necessary to improve current clinical outcomes. This body of work identifies CD47 as a therapeutic target on CSC and bulk cells in several human malignancies. CD47 is a cell surface protein that functions to inhibit phagocytosis through binding its ligand SIRP[Alpha], expressed on phagocytes. Compared to normal cell counterparts, CD47 was highly expressed on several human tumors including acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), and non-Hodgkin lymphoma (NHL), suggesting that higher CD47 levels on tumors allow evasion of immune phagocytosis. Higher CD47 expression in these tumors correlated with a worse clinical prognosis and was an independent prognostic factor. Furthermore, a monoclonal blocking antibody against CD47 enabled phagocytosis of human AML, ALL, and NHL in vitro and eliminated disease in vivo. When combined with the Fc receptor-activating antibody, rituximab, anti-CD47 antibody therapy achieved high cure rates in pre-clinical models of NHL in contrast to partial responses with either agent alone. Lastly, anti-CD47 antibody treatment specifically targeted tumor but not normal cells, resulting in minimal toxicity in vitro and in vivo. The selective targeting of tumor cells by anti-CD47 antibody was due to the selective expression of the pro-phagocytic signal, calreticulin on tumor but not normal cells. In summary, this body of work identifies CD47 as a therapeutic target on several human cancers and that a monoclonal blocking antibody against CD47 has pre-clinical efficacy in eliminating these tumors through the promotion of phagocytosis.
Moduli spaces of pseudo-holomorphic disks and floer theory of cleanly intersecting immersed lagrangians [electronic resource]
Keywords: Mathematics

In this thesis we investigate moduli spaces of pseudo-holomorphic disks with Lagrangian boundary conditions, in which the Lagrangians are immersed with clean self-intersections. We then discuss the compactification of these moduli spaces, and show that under specific assumptions, the moduli spaces can be oriented. Finally, we use these moduli spaces to construct and compute Lagrangian Floer cohomology for sphere and orientation covers of the real projective space embedded as a Lagrangian submanifold of the complex projective space.
Moduli spaces of PT-stable objects [electronic resource]
Keywords: Mathematics

We develop techniques for performing semistable reduction on a flat family of objects in the heart of a t-structure on the bounded derived category of coherent sheaves of a smooth projective three-fold. Then we show that, with respect to Bayer's PT-stability function, the semistable objects in the heart of perverse sheaves form a proper Artin stack of finite type, provided the rank is nonzero, and the rank and degree are coprime.
Molecular characterization of cell division machinery in caulobacter crescentus [electronic resource]
Keywords: Chemistry

Cell division is a major developmental event in the life cycle of a bacterial cell. Caulobacter crescentus division is asymmetric, producing daughter cells that differ in morphology and polar features: a sessile stalked cell and a motile swarmer cell that subsequently differentiates into a stalked cell. In this work we investigate the assembly of the Caulobacter cell division machinery (the divisome) using genetics, biochemistry, and microscopy. In Caulobacter, the cell division process requires a set of approximately twenty-three proteins localizing from the cytoplasm to the outer membrane. To understand divisome assembly as a function of the cell cycle, we generated fluorescent fusions to analyze the temporal regulation of 19 representative divisome and division-site localized proteins. In Chapter 2, we identified a series of stages and transitions in divisome assembly and the associated events yielding a comprehensive temporal picture of the process. The assembly interdependency for divisome formation in Caulobacter appears to involve cooperative rather than sequential recruitment, suggesting that it is a multiprotein subcomplex model. In Chapter 3, we describe our investigation of the Tol-Pal complex where we demonstrated that it plays a vital role for membrane integrity maintenance and that it is essential for viability. Cryo-electron microscope images of the Caulobacter cell envelope exhibited outer membrane disruption, and cells failed to complete cell division in TolA, TolB, or Pal mutant strains. The Tol-Pal complex is required to maintain the position of the transmembrane TipN polar marker, and indirectly the PleC histidine kinase, at the cell pole, but it is not required for the polar maintenance of other transmembrane and membrane-associated polar proteins tested. Thus, the Caulobacter trans-envelope Tol-Pal complex is a key component of cell envelope structure and function, mediating outer membrane constriction at the final step of cell division, as well as the positioning of a protein localization factor. In Chapter 4, we describe our examination of the FtsZ binding protein, ZapA. FtsZ is the most highly conserved divisome protein that polymerizes into a contractile ring near midcell, defining the future site of cell division. We showed that ZapA is required to maintain a normal cell length, and promotes Z ring assembly. The biochemical and functional studies suggest that Caulobacter ZapA is a positive regulator of Z-ring assembly. In summary, we have addressed three major stages in developments of the divisome in Caulobacter: Z-ring assembly, divisome maturation and outer membrane invagination. These experiments have provided a new understanding of how the Caulobacter cell temporally executes the cell division program to propagate reliably and how Caulobacter cell division is performed.
Molecular counting [electronic resource] : from noninvasive prenatal diagnostics to whole-genome haplotyping
Keywords: Bioengineering.

The concept of a personal genome stems from the fact that every human genome is unique. Measuring the unique features of a personal genome would help uncover the genetic basis of diseases and traits, and would be increasingly important in clinical diagnosis especially with the growing emphasis on personalized medicine. This thesis focuses on exploring the power of molecular counting to develop novel strategies that address the inadequacy of existing technologies in measuring the unique features of a human genome. The first focus of the thesis is aneuploidy detection, which has major application in prenatal diagnosis. While karyotyping of fetal cells is well-established for detecting aneuploidy, invasive sampling of fetal materials impose a small but significant risk to the health of both the mother and the fetus. A major research focus in the field of prenatal diagnosis has been to develop a noninvasive test for detecting fetal aneuploidy. Here, the concept of single molecule counting was applied to the problem of aneuploidy detection. The concept was first tested with digital PCR on invasively collected fetal materials, and subsequently extended to the noninvasive setting by shotgun sequencing maternal plasma DNA, which contains a small amount of fetal DNA. The former work led to the development of a polymorphism-independent method for rapid invasive diagnosis of aneuploidy, while the later work marked the development of the first polymorphism-independent method for the noninvasive diagnosis of fetal aneuploidy documented in the literature. The second focus of the thesis is molecular haplotyping. Present sequencing and other molecular techniques concentrate at identifying variants at isolated locations throughout a genome but largely ignore the haplotypes formed by these variants. Direct experimental determination of the haplotypes of an individual is challenging because of the lack of techniques to separate the two highly similar homologous copies of a chromosome. Here, a whole-genome haplotyping method was devised by analyzing amplified materials from single intact chromosomes within single cells, made possible by microfluidics. Such strategy enabled, for the first time, completely deterministic measurement of personal whole-genome haplotypes. It sets the stage for the direct sequencing of the two unique haploid genomes of any individual human, which has not been achieved by any personal genomes sequenced to date, and can potentially facilitate noninvasive fetal genome sequencing.
Molecular logic of adult stem cell self-renewal and the commitment to differentiation in the Drosophila testis stem cell niche [electronic resource]
Keywords: Developmental Biology.

Adult stem cells both self-renew and give rise to differentiating progeny that maintain and repair tissues throughout an individual's lifetime. Adult stem cells reside in specialized microenvironments, or niches, that regulate stem cell behavior in vivo. The Drosophila testis contains a complex niche that maintains two adult stem cell populations, germline stem cells (GSCs) and somatic cyst stem cells (CySCs), which are directly anchored to a plug of post-mitotic support cells called the hub. A short-range, cytokine-like signal from the hub, the ligand Unpaired (Upd), activates the JAK-STAT pathway in adjacent GSCs and CySCs to promote stem cell maintenance. To map the regulatory circuitry downstream of Upd signaling from the hub, I identified genomic sites of STAT binding in GSCs and CySCs by performing chromatin immunoprecipitation with antibodies against activated STAT, followed by high throughput Solexa sequencing (ChIP-Seq). My analysis suggests that forked regulatory circuits lay downstream of activated STAT in GSCs and CySCs, with different tines containing target gene(s) that regulate unique aspects of stem cell identity and behavior, including sustained receptivity to niche signals, expression of transcriptional regulators required for stem cell fate, and cell-cell communication between germline and soma. Adult stem cell behavior is also influenced by cell-intrinsic factors, including transcription and chromatin remodeling factors, which enable stem cells to interpret and execute appropriate responses to niche signals. I discovered that the transcriptional regulator longitudinals lacking (lola) is required cell autonomously for GSC and CySC maintenance: stem cells homozygous mutant for lola detach from the hub and differentiate. In addition, I found that activity of lola is also required for proper execution of key developmental transitions during germ cell differentiation, including the timely switch from the transit amplification divisions to the spermatocyte growth and gene expression program, and subsequently for the meiosis and spermatid differentiation.
Molecular mechanisms of the innate immune response to Francisella tularensis [electronic resource]
Keywords: Microbiology and Immunology

Francisella tularensis is a facultative intracellular pathogen that causes the disease tularemia. The ability of F. tularensis to escape phagosomal degradation and replicate in the macrophage cytosol is central to its pathogenesis. The macrophage responds to the presence of cytosolic F. tularensis with the production of type-I interferons (IFN) and subsequent activation of the inflammasome. We conducted a forward genetic screen of a F. novicida transposon library to identify mutants that resulted in an increased or decreased cytosolic response in macrophages. We identified 164 F. novicida mutants that lead to increased type-I IFN production and inflammasome activation in macrophages. We also identified 74 mutants that resulted in decreased type-I IFN and inflammasome responses in macrophages. Finally, we identified AIM2 as the host receptor responsible for inflammasome activation in response to cytosolic F. novicida. We showed that lysing cytosolic F. novicida leads to release of bacterial DNA that triggers type-IFN through a pathway involving the adaptor STING. STING-dependent type-I IFN production increases the expression of AIM2, which complexes with the bacterial DNA and initiates inflammasome activation. We further demonstrate that AIM2 is critical for innate immunity to F. novicida infection in vivo. Thus we identified a novel bacterial ligand and novel cytosolic sensing components that play a role in the host defense to bacterial infections.
Molecular origins of mechanical properties in hybrid glasses [electronic resource]
Keywords: Materials Science and Engineering

Hybrid organic-inorganic glasses are materials wherein organic and inorganic chemical components are intermixed and covalently bound at the molecular scale. This class of materials has great potential to enable and enhance a range of new technologies given their unique properties. To date, hybrid glasses have been used in a diverse range of applications including protective coatings, adhesion promoting films, ultra-low-k dielectrics, and optical waveguides. The successful integration of hybrid glasses requires that they possess sufficient mechanical properties to withstand often harsh processing and operating conditions. This dissertation presents results from several investigations of how molecular structure controls elastic and fracture properties of hybrid glasses. Two major sol-gel derived hybrid glass systems are discussed. The first is oxycarbosilane (OCS) glasses processed from small organosilane precursors. The second system is ZrOx/epoxysilane hybrids. For the OCS glasses, the primary focus of this work was to develop the capability to generate accurate molecular models of these materials and to simulate their mechanical properties using molecular dynamics as well as a novel fracture model that uses the mathematics of graph theory to predict the 3-D cohesive fracture path at the atomic scale. Using these computational tools, the impact of network connectivity on elastic stiffness and cohesive fracture energy has been elucidated. Also, the exceptionally high stiffness of OCS materials processed from 1,3,5-benzene precursors predicted by computational modeling is discussed. For the ZrOx/epoxysilane materials, linear elastic fracture mechanics experiments were done to characterize the fracture resistance of these glasses under monotonic, static, and cyclic loading conditions. The effects of glass composition, substrate composition, and silane crosslinking on the critical fracture energy were investigated. Additionally, plasticity-driven cyclic mechanical fatigue was observed, providing the first evidence of the importance of fatigue phenomena to hybrid glasses.
Molecular signatures of virome-host interactions [electronic resource]
Keywords: Microbiology and Immunology

Small RNAs that are 19-30 nucleotides in length use the genetic information encoded in their sequence to effect gene regulation in a sequence-directed manner. Infections with RNA viruses in plants, worms and flies generate short viral-derived RNAs ("vsRNAs") that map to the genome of the infecting virus. The regulated production of these vsRNAs and their engagement by the immune apparatus is essential for inhibiting viral growth, making vsRNAs important components of antiviral immunity in these organisms. RNA virus-derived vsRNA-mediated gene silencing is yet to be demonstrated in mammalian systems. We investigated diverse RNA virus-mammalian systems, and characterized changes in small RNA populations that occur during viral infection in animal cells using high-throughput sequencing. Due to the large number of samples to be analyzed, we designed DNA barcodes to 'tag' RNA samples from individual experiments, which facilitated sequencing in parallel from multiple samples. Our work demonstrated the generality of RNA virus-derived vsRNA production, and the ability of the cellular short RNA apparatus to engage these vsRNAs in worms during Flock House Virus replication, and in mammalian cells during infections with Hepatitis C, Polio, Dengue, Vesicular Stomatitis or West Nile virus. In addition to the appearance of vsRNAs during infection, we saw a number of specific changes in host-encoded small RNA (miRNA) profiles. For several infection models investigated in more detail, the RNAi and Interferon pathways modulated the abundance of vsRNAs. We found evidence for populations of vsRNAs that exist as duplexed small interfering RNAs ("siRNAs; " effectors of gene silencing) with zero to three nucleotide 3' overhangs. We also observed strand-selective loading of siRNAs onto Argonaute complexes, which are mediators of gene silencing. We quantitated the capacity of these HCVrep-derived vsRNAs to down-regulate target mRNAs in a sequence-specific manner in mammalian systems. We found that abundant HCVrep vsRNAs are not capable of mediating robust silencing (i.e. 2-fold or higher) of Luciferase reporters that have been engineered with vsRNA targets. Additionally, over-expression of siRNAs corresponding to five abundant vsRNAs failed to enhance silencing of Hepatitis C Virus mRNA. These results complement each other and suggest that in mammalian hosts, the virus may coexist with an abundant population of vsRNAs. Questions still remain as to whether robust gene silencing may be achieved by the cooperative action of abundant vsRNAs, or if abundant vsRNAs specifically inhibited from functioning in gene silencing, or alternatively, if they have novel roles in pathways distinct from gene silencing.
Monolingual and bilingual children's integration of multiple cues to understand a speaker's referential intent [electronic resource] : the role of experience in cognitive development
Keywords: Psychology

Children growing up in a dual-language environment have to constantly monitor the dynamic communicative context to determine what the speaker is trying to say and how to respond appropriately. Such self-generated efforts to monitor speakers' communicative needs may heighten children's sensitivity to and allow them to make better use of communicative cues to figure out a speaker's referential intent. Chapter 1 of this paper reviews the current models of bilingualism and literature on the impact of growing up bilingual, including benefits to the cognitive and communicative development of children. Chapter 2 presents a series of studies to examine how the experience of growing up bilingual may foster children's ability to integrate multiple cues to understand a speaker's referential intent, and how the experience of a communication breakdown of a bilingual nature may increase children's sensitivity to communicative cues. Overall, results provide evidence that growing up in a bilingual environment facilitates a more sophisticated understanding of the demands in a communicative context and support the hypothesis that children's self-generated efforts to cope with communicative challenges heighten their sensitivity to a speaker's communicative intent and foster their cognitive and linguistic development.
Monte Carlo simulation of particle production and decay at high-energy colliders [electronic resource]
Keywords: Physics

Detecting and understanding new physics at the LHC and other future colliders depends on having an understanding of what kinds of signals to look for above the Standard Model background. Event generators are used to simulate the physics events we can expect to see at these colliders and facilitate the search for and analysis of interesting signals. In this thesis we discuss the pandora event generator and its use for generating collider events with Beyond the Standard Model particles and their decays. First we will describe the physics fundamental to event generators, the particular philosophy behind the pandora generator, and how it compares to other available tools. Second, we will discuss how that particular philosophy was implemented and how the implementation facilitates incorporating new BSM physics. Finally we will discuss several physics results generated using pandora, displaying its various features.
Moving through the brain [electronic resource] : a study of movement preparation in the oculomotor and reach systems
Keywords: Neurosciences.

Movement preparation allows the rapid and accurate execution of voluntary move- ments, and can be influenced by factors that may change from moment to moment, such as attention and differences in stimulus properties. Consequently, movement preparation unfolds differently across many repetitions of the same movement. Averaging neural responses across many repetitions is necessary to interpret single-cell recordings, but diminishes our ability to characterize the dynamics of the underlying process. A central question in neuroscience, and also of fundamental clinical importance, is to understand how these plans develop in the brain. Several research groups are starting to build prosthetic devices that are controlled directly by neural activity in motor areas of the brain (Nicolelis, 2001; Donoghue, 2002; Musallam et al., 2004; Schwartz, 2004; Santhanam et al., 2006; Hochberg et al., 2006; Mulliken et al., 2008; Andersen et al., 2010), but the extent to which these can be developed may hinge critically upon our understanding of the neural basis of motor preparation. Simultaneous recording from populations of neurons allows dynamics of movement preparation to be estimated on single trials. Our goal is to characterize these dynamics, to gain insight into the process underlying movement preparation. Here, we recorded peri-saccadic activity from ensembles of neurons in an oculomotor area, prearcuate cortex, in two monkeys. While monkeys performed visually-guided eye movements, we measured firing rates of a population of neurons using a 96-electrode array. We studied (1) the responses from a heterogeneous population of prearcuate cortex neurons involved in decision-making and movement preparation, (2) the relationship between saccade initiation times and responses from the neural population, and (3) how these responses compared to those recorded in PMd, a cortical area involved in arm movements. The array data from prearcuate allowed us to compare responses from individual neurons with previous findings, but also allowed us to analyze the population dynamics of movement planning, by using techniques applied to the reach system. We found that ensemble responses from diverse populations of prearcuate neurons (1) can be visualized as trajectories moving through a low-dimensional neural state space, (2) reflect visual, decision-, and movement-related aspects of the task, and (3) correlate with a monkey's reaction time on a trial-by-trial basis. Further, the single-trial relationship between ensemble activity in prearcuate cortex and saccadic reaction times was qualitatively and quantitatively very similar to the relationship between ensemble activity in PMd and corresponding reach reaction times. This framework for analyzing neural population activity and dynamics should permit new extensions of single-neuron-level models, and may offer further insight into general mechanisms of movement preparation across motor systems.