VictorJuiz/thesis huggingface dataset:
Capacitive micromachined ultrasonic transducers (CMUTs) for therapeutic applications [electronic resource]

High-intensity focused ultrasound (HIFU) is a noninvasive method to treat a variety of diseases. Most of the HIFU machines in clinic typically consist of a piezoelectric transducer array and an imaging system for temperature monitoring and anatomical location guidance. One of the limitations of piezoelectric transducers is self-heating, which requires cooling systems to protect both transducers and patients. Capacitive micromachined ultrasonic transducers (CMUTs) are another type of transducers fabricated with silicon micromachining. CMUTs are promising candidates as therapeutic transducers, as they experience a lot less self-heating compared to piezoelectric transducers. This dissertation mainly focuses on describing the design, simulation, fabrication, characterization, and experimental results of CMUTs for HIFU applications. Single-element transducers are fabricated using local oxidation of silicon (LOCOS)-wafer-bonding process. The measurement part compares the self-heating of a PZT and a CMUT, and discusses the charging issue of CMUTs. Geometric focusing using multiple single-element CMUTs is also demonstrated. The fabrication of 1-D CMUT arrays to enhance the output pressure for HIFU applications is discussed. Higher output pressure of a CMUT cell can be achieved by adding one extra fabrication step to the existing fabrication process. Two-dimensional transducer arrays are required for electronic focusing and beam steering. An 8-channel continuous wave (CW) excitation system is developed to drive a 2-D CMUT array. This 8-channel system minimizes the system complexity without significant loss of focusing capability, compared to a full system with hundreds to thousands of channels. The first successful 2-D CMUT array fabricated using the thick-buried-oxide (BOX) process is presented. The breakdown issue of the insulation layer observed in the test stage is investigated as well. Another type of 2-D CMUT array fabricated using the sacrificial-release process is also tested for HIFU applications. Using the 8-channel CW excitation system, the 2-D CMUT array has proven to be able to produce enough output pressure for thermal ablation. This dissertation presents the result of ex-vivo experiments, which created thermal lesions on bovine tissue using a CMUT array for the first time.

Keywords: Electrical Engineering.
Advisor: Khuri-Yakub Butrus T.
Arbabian Amin advisor. Thesis advisor
Pauly Kim Butts (Kim Rosemary Butts)
Capacitive micromachined ultrasonic transducers with substrate-embedded springs [electronic resource]

After the first capacitive micromachined ultrasonic transducer (CMUT) was invented in 1994, it became one of the candidate technologies to advance the state-of-the-art of medical ultrasound imaging. Benefiting from its fabrication technique based on the semiconductor industry, CMUT technology has broadened the medical and therapeutic applications such as real-time volumetric ultrasound imaging, catheter-based forward-looking intravascular ultrasound (IVUS), photoacoustic imaging, high-intensity focused ultrasound (HIFU) and so on. In spite of many advantages, however, CMUT technology has been criticized with its relatively low transmit sensitivity (~10 kPa/V) or low average volume displacement efficiency (0.1 nm/V) as well as large drive and bias voltage requirements (in a range of a few hundreds of volts). In order to resolve these issues and open up new potential of clinical applications, this dissertation describes the design, fabrication, and system implementation of CMUTs with substrate-embedded springs, so-called post-CMUT (PCMUT). Since PCMUT structure resembles an ideal piston transducer, the improvements in performance mainly stem from the higher average displacement of the top plate for a given gap height. The overview of the first generation PCMUT is introduced and two main issues in simulation and fabrication aspects of the first generation PCMUT is discussed. To further improve the PCMUT device, a 3D finite element analysis (FEA) model of the PCMUT is demonstrated to predict the performance of the first generation PCMUT. In addition, the design guideline of the second generation PCMUT is proposed for achieving the maximum fractional bandwidth (100 %) as well as with the highest transmit sensitivity (~28 kPa/V). The second generation PCMUT is fabricated by using three combination MEMS processes: usage of two silicon-on-insulator (SOI) wafers, wafer bonding process, and wafer polishing process. The second generation PCMUT achieves high transmit sensitivity (~21 kPa/V) or large average volume displacement efficiency (1.1 nm/V) with a low bias voltage (55 V). Compared to a commercial piezoelectric transducer, the second generation PCMUT improves 2.75 times of the maximum output pressure and 5.25 times of the average volume displacement efficiency with respect to the same voltage. After fabrication and performance characterization of the second generation PCMUT, this dissertation demonstrates the feasibility of PCMUT to use it in medical imaging system by integrating PCMUT with a custom-built integrated circuit (IC). Photoacoustic imaging is also presented for one of its application examples.

Keywords: Electrical Engineering.
Advisor: Khuri-Yakub Butrus T.
Howe Roger Thomas advisor. Thesis advisor
Solgaard Olav advisor. Thesis advisor
Capacitive micromachined ultrasonic transducers with vented cavities [electronic resource]

Capacitive micromachined ultrasonic transducers (CMUTs) are increasingly seen as a better alternative than piezoelectric transducers for many ultrasound applications. Ultrasonic flow metering presents one such case where CMUTs are much better suited. Due to their lower mechanical impedance, CMUTs are more efficient at coupling sound into a fluid medium than piezoelectric transducers. Unlike piezoelectric transducers which suffer from depoling at temperatures above their Curie point, CMUTs can easily be used in higher temperatures. This should make CMUTs ideal candidates for ultrasonic flow metering in extreme environments such as those that exist in flare stacks, high temperature steam lines in industrial plants, etc. Despite these benefits, conventional CMUTs are not suited for the highly variable pressure conditions that many flowmeters have to operate under. CMUTs with vented or pressurized cavities can overcome this limitation. This dissertation presents the design and modeling for such CMUTs. A reliable fabrication process for CMUTs vented through the plate or through the substrate is also presented. The fluid squeeze film formed in the cavity between the CMUT plate and the substrate provides a way to control the bandwidth and sensitivity of such CMUTs. The dissertation presents CMUTs with bandwidth ranging from 1% to over 20% in air. These CMUTs were tested under a pressure of up to 20 bar and maintained good bandwidth and SNR. The dissertation also discusses the importance of packaging for CMUTs vented through the substrate and presents a way to utilize acoustic resonances in the package for maintaining a steady operating frequency under varying pressure. The wide bandwidth of such CMUTs can be utilized in many other application of ultrasound in air. The dissertation briefly discussed the application of these CMUTs for thermoacoustic imaging as well as for gesture sensing.

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William primary advisor. Thesis advisor
Khuri-Yakub Butrus T.
Arbabian Amin advisor. Thesis advisor
Catalytic enantioselective dihalogenation of allylic alcohols and its application to the stereoselective total syntheses of chlorosulfolipids [electronic resource]

The dihalogenation reaction is one of the most fundamental reactions in organic chemistry, but few methods exist which render the transformation asymmetric. Here, a catalytic, enantioselective dihalogenation reaction is described which is capable of effecting selective dibromination, dichlorination, and bromochlorination to allylic alcohols of wide scope. This methodology was applied to a short, stereoselective synthesis of the chlorosulfolipid, danicalipin A. The reaction was further applied to the synthesis and crystallographic stereochemical confirmation of deschloromytilipin A and polybrominated analogs.

Keywords: Chemistry.
Advisor: Burns Noah
Du Bois Justin advisor. Thesis advisor
Trost Barry M. advisor. Thesis advisor
Cell free metabolic engineering for the production of hydrogen from cellulosic biomass [electronic resource]

Establishing alternative methods to produce petrochemicals from renewable resources is a critical step toward a sustainable society. Hydrogen is a key commodity chemical with over 50 million metric tons produced annually with a market value of over 0 billion. The majority of this hydrogen is used for synthesis of ammonia and petroleum refining but also has the potential for use as a clean burning fuel. However, current methods rely primarily on the steam reformation of natural gas. We sought to develop a new platform for synthesis of hydrogen from cellulosic biomass using E.coli cell free extracts. By coupling the native E.coli metabolic pathways with a heterologous synthetic pathway, we established a method to produce hydrogen from glucose. In order to accomplish this, a synthetic pathway to produce hydrogen from a native redox source, NADPH, was developed using a ferredoxin NADP+ reductase, ferredoxin, and a [FeFe] hydrogenase. The pathway was constructed by screening natural proteins for the capacity to support maximal hydrogen production rates. Careful characterization of the interactions of the three protein synthetic pathway through UV/Vis spectroscopy and gas chromatography enabled further improvements. The synthetic pathway was then coupled to a cell free extract to demonstrate the feasibility of producing hydrogen from glucose with a cell extract. In order to maximize the yields of hydrogen from the cell extract, we knocked out three metabolic proteins, phosphofructokinase, 6-phosphogluconate dehydratase, and glyceraldehyde-3-phosphate dehydrogenase that eliminate undesirable side reactions in glycolysis and Entner Doudoroff pathways. With these cell lines, we established protocols for cell extract production and in vitro hydrogen production that demonstrate significant improvements in hydrogen yield. Finally, in order to further improve the cell extracts, we then developed a strategy for selective metabolic silencing (SeMs) of key enzymatic activities. Using this technique, specific enzymatic activities could be provided in vivo for efficient cell growth and enzyme production, but then these activities could be inactivated in the cell extract to avoid the loss of the reducing equivalents required for hydrogen production. To demonstrate this principle, we engineered a library of glyeraldehyde-3-phosphate dehydrogenase mutants with insertion of a recognition sequence for human rhinovirus 3C protease. Many of these mutants were active in vivo, but through protease treatment could be inactivated to improve hydrogen production. Together, these advances explore the feasibility of using cell free extracts for biochemical synthesis, as well as contribute to ongoing research on in vitro enzymatic biocatalysis.

Keywords: Chemical Engineering.
Advisor: Swartz James R. primary advisor. Thesis advisor
Dunn Alexander Robert advisor. Thesis advisor
Smolke Christina D. advisor. Thesis advisor
Challenges, solutions, and biological applications of three-dimensional nanoscale spatial localization of single molecules [electronic resource]

Single fluorescent molecules and particles can be localized in space with precision on the order of tens of nanometers (i.e. "super localized") using state-of-the-art microscopy techniques. The ability to probe complex environments at the sub-diffraction size scale has proven invaluable in revealing fundamental heterogeneity and improving overall understanding across the applied physical sciences. Super-localization microscopy is at the heart of both single-molecule super-resolution microscopy and single-particle tracking. The work presented in this dissertation concerns the application of super-localization microscopy to problems of biophysical interest, as well as theoretical and experimental advances in the methodology of this class of techniques. While the most common methods of super-localized position estimation ensure high localization precision, they might not always ensure high accuracy. In particular, the anisotropy of single-molecule dipole emission can result in mislocalizations of hundreds of nanometers, depending on the orientation of the molecule and its distance from the focal plane. In this dissertation I discuss different ways to correct this potential source of error. On the one hand, a theory based on a wobbling-in-a-cone model is presented that shows how this error is mitigated by molecular rotational mobility. On the other hand, for the worst-case scenario of a rotationally fixed emitter, an experimental approach based on Fourier optics is also discussed that allows for estimation of molecular orientation and enables active correction of mislocalization effects. The last third of this dissertation discusses applications of super-localization microscopy to three-dimensional tracking of fluorescently labeled genetic loci in budding yeast. In order to localize loci in the axial dimension, I used a Fourier optics approach to engineer the point spread function of the microscope into a Double-Helix Point Spread Function (DH-PSF). With this method, many single copies of a specific locus were analyzed, each with 3D spatial precision on the order of 10 nm at a rate of 10 Hz. A two-color implementation of the microscope allowed measurement of the correlations of 3D motion between pairs of loci under variable transcriptional pressure. I also discuss the importance of properly accounting for the inescapable effects of static and dynamic tracking errors caused by finite photon statistics and motion blur, respectively. These errors affect the statistics of the estimated motion and distort common metrics for characterizing stochastic motion such as the mean-squared displacement (MSD) and velocity autocorrelation (VAC). Analytical expressions for the MSD and VAC in the presence of these errors are given, along with applications to chromosomal locus tracking.

Keywords: Chemistry.
Advisor: Moerner W. E. (William Esco)
Fayer Michael D. advisor. Thesis advisor
Pande Vijay advisor. Thesis advisor
Characterization of CD90 as a Therapeutic Antibody Target on Cancer Stem Cells

Cancer stem cells (CSCs) are essential for the growth and proliferation of some tumors, and therapies aimed at clearance of CSCs have potential as treatments, and possibly cures, of these cancers. Here we demonstrate that the cell surface antigen CD90 (Thy-1), which has been previously established as a marker of neoplastic stem cells, can be targeted by monoclonal anti-CD90 antibodies to modulate tumor growth. Anti-mouse and anti-human monoclonal CD90 antibodies were used to evaluate the potential of CD90 as a therapeutic antibody target in mouse breast, human bladder, and human breast cancers engrafted in mice. In treating transplanted mice with anti-CD90 antibodies, we found that anti-CD90 antibodies accelerated mouse breast tumor growth. Simultaneously, there was a decrease in T cell frequency when transplanted mice were treated with anti-mouse CD90 antibodies. However, bone marrow transplant and adoptive T cell transfer experiments revealed that hematopoietic cells or T cells did not mediate the increase in tumor growth. In the xenotransplantation models, we discovered that anti-CD90 antibodies inhibit growth of human bladder tumors engrafted in immunodeficient mice in a preliminary experiment, but in a second experiment, the antibodies had no significant effect on tumor growth. Anti-CD90 antibodies also had no significant effect on the growth of human breast cancer cells. These results indicate that in some tumors, antibody targeting of CD90 modulates proliferation or death of tumor cells via activating/blocking downstream CD90 signaling or affecting anti-cancer immune response. It may be possible to manipulate the CD90 signaling pathway or anti-CD90-mediated immune mechanism so as to promote or inhibit tumor growth. These findings can lead to the development of therapeutic agents that control CD90 signaling to inhibit tumor development, progression, and/or relapse.

Keywords: Stanford University
Stanford University Department of Biology
Stanford University School of Medicine
Institute for Stem Cell Biology and Regenerative Medicine
CD90
Thy-1
cancer stem cells
monoclonal antibody therapy
cancer immunotherapy
tumorigenesis
breast cancer
bladder cancer
xenotransplantation
Thesis
Advisor: Weissman Irving
Jones Patricia
Characterization of the INO80 Subfamily of Chromatin Remodelers in Microtubule Dynamics in S. cerevisiae

The INO80 subfamily of chromatin remodelers, which includes the complexes INO80 and SWR1, have been known to play an important role in rearranging chromatin, hydrolyzing ATP to change the structure of nucleosomes. However, recent research has suggested that these complexes may also play a role during mitosis, specifically in microtubule dynamics. Preliminary studies from our lab have shown that ino80Δ shows ploidy defects and abnormal microtubule dynamics. Furthermore, high-throughput genetic analyses have shown negative interactions for both INO80 and SWR1 with various mitotic genes of interest, further suggesting that these complexes are involved in mitosis. However, the exact mechanisms underlying INO80 and SWR1’s mitotic functions remain unknown, particularly for the latter. This study sought to elucidate the roles of both complexes during mitosis, using an integrative approach of genetics, molecular biology, and microscopy techniques to answer this question. We hypothesized that INO80 and SWR1 affect chromosome segregation by affecting microtubule dynamics. Our genetic analyses show that INO80 and SWR1 function in parallel pathways to BIM1 and BIK1, two genes critical for microtubule dynamics in S. cerevisiae. Our in vivo live-cell imaging reveals that ino80Δ mutants have short spindles and elongated cell morphology. These results suggest that INO80 is involved in stabilizing microtubules and potentially affects other components of the cytoskeleton, including actin. On the other hand, although swr1Δ mutants also show shortened spindles, they also tend to have exaggerated astral microtubules (aMTs) as opposed to ino80Δ mutants, which show fewer aMTs. This finding opens the possibility that SWR1 and INO80 have complementary but opposite roles during mitosis. Further studies conducted on domain and module mutants of INO80 revealed that the HSA and spacer domains are specifically involved in the complex’s microtubule-stabilizing activity, which also apparently requires the ATPase function of the catalytic subunit. Genetic and fitness assays of SWR1 in conjunction with various kinetochore genes (CBF1, BUB1, MCM21, and CHL4) show negative interactions between the two groups. These results suggest that SWR1 may be acting at the microtubule-kinetochore interface, helping to define a mechanism for its effect on microtubule dynamics as observed through live-cell imaging. The findings of this study provide a novel view of a subfamily of chromatin remodelers, defining a mechanistic level of understanding for their function in mitosis. Chromosome missegregation is associated with many diseases such as cancer and congenital disorders. Because proper chromosome segregation is largely dependent on microtubule dynamics, determining the INO80 subfamily’s role in this process has meaningful implications for disease treatment in the future.

Keywords:  Department of Biology
Biology
mitosis
chromosome segregation
chromatin remodelers
INO80
SWR1
spindle assembly
microtubules
kinetochore
S. cerevisiae
Thesis
Advisor: Morrison Ashby
Hanawalt Philip
Characterization of zeta-tubulin and discovery of the ZED tubulin module [electronic resource]

Microtubules and microtubule-based structures play key roles in a variety of cellular processes, including cellular trafficking, motility, division, and signaling. In most animal cells, microtubules are organized by centrosomes, which contain a pair of specialized microtubule-based structures called centrioles surrounded by a meshwork of proteins known as pericentriolar material. In these cells, one centriole can elongate a single primary cilium that performs a number of sensory and signaling functions. In many specialized cell types of the adult vertebrate body plan, however, cells contain tens to hundreds of centrioles that nucleate motile cilia. Defects in centrioles, primary cilia, and motile cilia cause human diseases, both congenital and acquired. In this thesis, we have undertaken a study of zeta-tubulin, a member of the tubulin superfamily of proteins that are essential to the structure and function of microtubules and microtubule-based structures. Zeta-tubulin is a multiciliated-cell specific protein that orients the centrioles via localization to an important appendage known as the basal foot. As a confirmation of the co-conservation of zeta-, epsilon-, and delta- tubulin, we show that zeta- and epsilon-tubulin also co-localize at basal feet in multiciliated cells, suggesting concerted function of these ZED tubulins. We provide the basis for future studies of ZED tubulin biochemical function by purification of these tubulins from insect cells using the baculovirus expression system. Finally, we investigated the transcriptome of mouse multiciliated cells using bioinformatic approaches and utilized Xenopus datasets to discover potential new multiciliated cell specific proteins.

Advisor: Stearns Tim primary advisor. Thesis advisor
Cyert Martha S.
Goodman Miriam Beth advisor. Thesis advisor
Straight Aaron
Characterizing molecular interactions in polymer [electronic resource] : fullerene solar cells

The global demand for energy is on the rise, but reliance on power production via fossil fuels has resulted in the emission and accumulation of greenhouse gases which cause global warming. Solar energy provides a clean power generation alternative, and polymer solar cells (PSCs) composed of semiconducting polymers and functionalized fullerenes provide a path to solar power production on a large scale. In this dissertation, I will discuss the mixed polymer:fullerene phase and its implications for polymer solar cell (PSC) performance. Using X-ray diffraction, NMR, and computational modeling, the crystal structure of a polymer:fullerene bimolecular crystal is determined. Using electrochemistry and photoelectron spectroscopy, I show that a strong intermolecular coupling between the polymer and fullerene exists. This intermolecular interaction has a large impact on the PSC energetic landscape which not only drives the formation of the mixed phase, but also impacts device performance. I will also discuss the physical mechanisms responsible for this intermolecular interaction, and use vibrational spectroscopy to determine which mechanism is most likely occurring. Finally, I will discuss how the polymer:fullerene intermolecular interaction impacts open circuit voltage and energetic disorder. Using this understanding of the polymer:fullerene intermolecular interaction, design guidelines are provided for future semiconducting polymers to raise PSC PCE.

Keywords: Materials Science and Engineering.
Advisor: McGehee Michael
Salleo Alberto
Toney Michael Folsom