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Articles 1 - 16 of 16
Full-Text Articles in Life Sciences
Using Computational Fluid Dynamics And Optical Sensor Technology To Scale Cell Culture Platforms, Mandar Makwana
Using Computational Fluid Dynamics And Optical Sensor Technology To Scale Cell Culture Platforms, Mandar Makwana
KGI Theses and Dissertations
Different cell culture vessels ranging from micro scale to laboratory scale to commercial scale play critical role in upstream process development for biologics manufacturing. Based on the mode of operation, cell culture vessels have different hydrodynamic environments, making it challenging to scale. Integrated approaches using computational tools supported by experimental studies can overcome these challenges. Computational Fluid Dynamics (CFD) is one such tool that can simulate hydrodynamics within the cell culture vessels and can provide insights at macro and micro-scale. Accuracy of a CFD model significantly depends on the fluid model and assumptions. Traditionally, simple two-equation fluid models were developed …
Analysis Of Biologically Effective Dose For Retroactive Yttrium-90 Trans-Arterial Radioembolization Treatment Optimization, Mj Lindsey
CMC Senior Theses
Trans-arterial radioembolization (TARE) is a protracted modality of radiation therapy where radionuclides labeled with Yttrium-90 (90Y) are inserted inside a patient's hepatic artery to treat hepatocellular carcinoma (HCC). While TARE has been shown to be a clinically effective and safe treatment, there is little understanding of the radiobiological relationship between absorbed dose and tissue response, and thus there is no dosimetric standard for treatment planning. The Biologically Effective Dose (BED) formalism, derived from the Linear-Quadratic model of radiobiology, is used to weigh the absorbed dose by the time pattern of delivery. BED is a virtual dose that can …
Modeling Residence Time Distribution Of Chromatographic Perfusion Resin For Large Biopharmaceutical Molecules: A Computational Fluid Dynamic Study, Kevin Vehar
KGI Theses and Dissertations
The need for production processes of large biotherapeutic particles, such as virus-based particles and extracellular vesicles, has risen due to increased demand in the development of vaccinations, gene therapies, and cancer treatments. Liquid chromatography plays a significant role in the purification process and is routinely used with therapeutic protein production. However, performance with larger macromolecules is often inconsistent, and parameter estimation for process development can be extremely time- and resource-intensive. This thesis aimed to utilize advances in computational fluid dynamic (CFD) modeling to generate a first-principle model of the chromatographic process while minimizing model parameter estimation's physical resource demand. Specifically, …
Complex Ciliary Flows Around Stentor Polymorphus In Solutions Of 2% Buttermilk And Chlamydomonas Reinhardtii, Eliana B. Smithstein
Complex Ciliary Flows Around Stentor Polymorphus In Solutions Of 2% Buttermilk And Chlamydomonas Reinhardtii, Eliana B. Smithstein
Scripps Senior Theses
Stentor are large, unicellular ciliates of the Heterotricha order. They live in both freshwater and marine habitats and are mostly found in ponds. I studied Stentor polymorphus, which is a species of Stentor only recently discovered to be lab culturable. They range from 0.5-1.5mm in length and are unusual because they live with endosymbiotic algae and are much more likely than other, more widely studied, species of Stentor to form aggregates while they are eating. There are three main components to this thesis: First, I established protocols for keeping a viable S. polymorphus culture, since no protocols had been …
Gravity-Drawing Flexible Silicone Filaments As Fiber Optics And Model Foldamers, Katherine Snell
Gravity-Drawing Flexible Silicone Filaments As Fiber Optics And Model Foldamers, Katherine Snell
CMC Senior Theses
Here, we present a method of gravity-drawing polydimethylsiloxane (PDMS) silicone fibers with application as fiber optics and as model foldamers. Beginning as a viscous liquid, PDMS is cured using heat until its measured viscosity reaches 4000 mPa•s. The semi-cured elastomer is then extruded through a tube furnace to produce thin (diameters on the order of hundred micrometers) filaments with scalable lengths. PDMS is biocompatible, gas-permeable, flexible, and hydrophobic. Additionally, the PDMS surface hydrophobicity can be modified via UV exposure, O2 plasma, and corona discharge. We demonstrate the patternibility (i.e patterns of hydrophobicity) of PDMS fibers, adding complexity to potential foldamer …
Giardia Lamblia Growth In Viscoelastic Fluids, Kelly Watanabe
Giardia Lamblia Growth In Viscoelastic Fluids, Kelly Watanabe
CMC Senior Theses
Giardia lamblia is a single-celled protozoan parasite that when ingested, causes diarrheal disease and infects 33% of people in developing countries. Previous studies observe Giardia in water-like fluids, but Giardia's infectious environment consists of viscoelastic mucus in the small intestine. Therefore, Giardia was cultured in viscoelastic fluids, and its population growth was observed in vitro. To create shear-thinning viscoelastic fluids, 0.2% and 0.4% long-chain polyacrylamide (LCPAM) was added to cell culture media. Giardia was cultured in control media, 0.2% LCPAM, and 0.4% LCPAM, and population growth was quantitatively determined over time. Increasing LCPAM concentration resulted in a solution with …
Can A Comprehensive Transition Plan To Barefoot Running Be The Solution To The Injury Epidemic In American Endurance Runners?, Michael A. Scarlett
Can A Comprehensive Transition Plan To Barefoot Running Be The Solution To The Injury Epidemic In American Endurance Runners?, Michael A. Scarlett
CMC Senior Theses
Fossils belonging to the genus Homo, dating as far back as two million years ago, exhibit uniquely efficient features suggesting that early humans had evolved to become exceptional endurance runners. Although they did not have the cushion or stability-control features provided in our modern day running shoes, our early human ancestors experienced far less of the running-related injuries we experience today. The injury rate has been estimated as high as 90% annually for Americans training for a marathon and as high as 79% annually for all American endurance runners. There is an injury epidemic in conventionally shod populations that …
Evolution Of Spur-Length Diversity In Aquilegia Petals Is Achieved Solely Through Cell-Shape Anisotropy, Joshua R. Puzey, Sharon J. Gerbode, Scott A. Hodges, Elena M. Kramer, L. Mahadevan
Evolution Of Spur-Length Diversity In Aquilegia Petals Is Achieved Solely Through Cell-Shape Anisotropy, Joshua R. Puzey, Sharon J. Gerbode, Scott A. Hodges, Elena M. Kramer, L. Mahadevan
All HMC Faculty Publications and Research
The role of petal spurs and specialized pollinator interactions has been studied since Darwin. Aquilegia petal spurs exhibit striking size and shape diversity, correlated with specialized pollinators ranging from bees to hawkmoths in a textbook example of adaptive radiation. Despite the evolutionary significance of spur length, remarkably little is known about Aquilegia spur morphogenesis and its evolution. Using experimental measurements, both at tissue and cellular levels, combined with numerical modelling, we have investigated the relative roles of cell divisions and cell shape in determining the morphology of the Aquilegia petal spur. Contrary to decades-old hypotheses implicating a discrete meristematic zone …
Effect Of Substrate Composition And Alignment On Corneal Cell Phenotype, Donna Phu '09, Lindsay S. Wray '08, Robert V. Warren '10, Richard C. Haskell, Elizabeth J. Orwin
Effect Of Substrate Composition And Alignment On Corneal Cell Phenotype, Donna Phu '09, Lindsay S. Wray '08, Robert V. Warren '10, Richard C. Haskell, Elizabeth J. Orwin
All HMC Faculty Publications and Research
Corneal blindness is a significant problem treated primarily by corneal transplants. Donor tissue supply is low, creating a growing need for an alternative. A tissue-engineered cornea made from patient-derived cells and biopolymer scaffold materials would be widely accessible to all patients and would alleviate the need for donor sources. Previous work in this lab led to a method for electrospinning type I collagen scaffolds for culturing corneal fibroblasts ex vivo that mimics the microenvironment in the native cornea. This electrospun scaffold is composed of small-diameter, aligned collagen fibers. In this study, we investigate the effect of scaffold nanostructure and composition …
Kinematic Evidence For Superfast Locomotory Muscle In Two Species Of Teneriffiid Mites, Grace C. Wu, Jonathan C. Wright, Dwight L. Whitaker, Anna N. Ahn
Kinematic Evidence For Superfast Locomotory Muscle In Two Species Of Teneriffiid Mites, Grace C. Wu, Jonathan C. Wright, Dwight L. Whitaker, Anna N. Ahn
All HMC Faculty Publications and Research
Locomotory muscles typically operate over a narrow range of contraction frequencies, characterized by the predominant fiber types and functional roles. The highest documented frequencies in the synchronous sound-producing muscles of insects (550 Hz) and toadfish (200 Hz) far exceed the contraction frequencies observed in weight-bearing locomotory muscles, which have maximum documented frequencies below 15-30 Hz. Laws of scaling, however, predict that smaller arthropods may employ stride frequencies exceeding this range. In this study we measured running speed and stride frequency in two undescribed species of teneriffiid mites from the coastal sage scrub of southern California. Relative speeds of both species …
Thermal Links For The Implementation Of An Optical Refrigerator, John Parker, David Mar, Steven Von Der Porten, John Hankinson, Kevin Byram, Chris Lee, Michael K. Mayeda, Richard C. Haskell, Qimin Yang, Scott R. Greenfield, Richard I. Epstein
Thermal Links For The Implementation Of An Optical Refrigerator, John Parker, David Mar, Steven Von Der Porten, John Hankinson, Kevin Byram, Chris Lee, Michael K. Mayeda, Richard C. Haskell, Qimin Yang, Scott R. Greenfield, Richard I. Epstein
All HMC Faculty Publications and Research
Optical refrigeration has been demonstrated by several groups of researchers, but the cooling elements have not been thermally linked to realistic heat loads in ways that achieve the desired temperatures. The ideal thermal link will have minimal surface area, provide complete optical isolation for the load, and possess high thermal conductivity. We have designed thermal links that minimize the absorption of fluoresced photons by the heat load using multiple mirrors and geometric shapes including a hemisphere, a kinked waveguide, and a tapered waveguide. While total link performance is dependent on additional factors, we have observed net transmission of photons with …
Motion-Sensitive 3-D Optical Coherence Microscope Operating At 1300 Nm For The Visualization Of Early Frog Development, Barbara M. Hoeling, Stephanie S. Feldman, Daniel T. Strenge, Aaron Bernard, Emily R. Hogan, Daniel C. Petersen, Scott E. Fraser, Yun Kee, J. Michael Tyszka, Richard C. Haskell
Motion-Sensitive 3-D Optical Coherence Microscope Operating At 1300 Nm For The Visualization Of Early Frog Development, Barbara M. Hoeling, Stephanie S. Feldman, Daniel T. Strenge, Aaron Bernard, Emily R. Hogan, Daniel C. Petersen, Scott E. Fraser, Yun Kee, J. Michael Tyszka, Richard C. Haskell
All HMC Faculty Publications and Research
We present 3-dimensional volume-rendered in vivo images of developing embryos of the African clawed frog Xenopus laevis taken with our new en-face-scanning, focus-tracking OCM system at 1300 nm wavelength. Compared to our older instrument which operates at 850 nm, we measure a decrease in the attenuation coefficient by 33%, leading to a substantial improvement in depth penetration. Both instruments have motion-sensitivity capability. By evaluating the fast Fourier transform of the fringe signal, we can produce simultaneously images displaying the fringe amplitude of the backscattered light and images showing the random Brownian motion of the scatterers. We present time-lapse movies of …
Immunogold Labeling To Enhance Contrast In Optical Coherence Microscopy Of Tissue Engineered Corneal Constructs, Chris B. Raub, Elizabeth J. Orwin, Richard C. Haskell
Immunogold Labeling To Enhance Contrast In Optical Coherence Microscopy Of Tissue Engineered Corneal Constructs, Chris B. Raub, Elizabeth J. Orwin, Richard C. Haskell
All HMC Faculty Publications and Research
Our lab has used an optical coherence microscope (OCM) to assess both the structure of tissue-engineered corneal constructs and their transparency. Currently, we are not able to resolve cells versus collagen matrix material in the images produced. We would like to distinguish cells in order to determine if they are viable while growing in culture and also if they are significantly contributing to the light scattering in the tissue. In order to do this, we are currently investigating the use of immunogold labeling. Gold nanoparticles are high scatterers and can create contrast in images. We have conjugated gold nanoparticles to …
Visualizing Early Frog Development With Motion-Sensitive 3-D Optical Coherence Microscopy, Richard C. Haskell, Mary E. Williams, Daniel C. Petersen, Barbara M. Hoeling, Andrew J. Schile, J. D. Pennington, M. G. Seetin, J. M. Castelaz, Scott E. Fraser, Cyrus Papan, Hongwu Ren, Johannes F. De Boer, Zhongping Chen
Visualizing Early Frog Development With Motion-Sensitive 3-D Optical Coherence Microscopy, Richard C. Haskell, Mary E. Williams, Daniel C. Petersen, Barbara M. Hoeling, Andrew J. Schile, J. D. Pennington, M. G. Seetin, J. M. Castelaz, Scott E. Fraser, Cyrus Papan, Hongwu Ren, Johannes F. De Boer, Zhongping Chen
All HMC Faculty Publications and Research
A motion-sensitive en-face-scanning 3-D optical coherence microscope (OCM) has been designed and constructed to study critical events in the early development of plants and animals. We describe the OCM instrument and present time-lapse movies of frog gastrulation, an early developmental event in which three distinct tissue layers are established that later give rise to all major organ systems. OCM images constructed with fringe-amplitude data show the mesendoderm migrating up along the blastocoel roof, thus forming the inner two tissue layers. Motion-sigma data, measuring the random motion of scatterers, is used to construct complementary images that indicate the presence of Brownian …
Phase Modulation At 125 Khz In A Michelson Interferometer Using An Inexpensive Piezoelectric Stack Driven At Resonance, Barbara M. Hoeling, Andrew D. Fernandez, Richard C. Haskell, Daniel C. Petersen
Phase Modulation At 125 Khz In A Michelson Interferometer Using An Inexpensive Piezoelectric Stack Driven At Resonance, Barbara M. Hoeling, Andrew D. Fernandez, Richard C. Haskell, Daniel C. Petersen
All HMC Faculty Publications and Research
Fast phase modulation has been achieved in a Michelson interferometer by attaching a lightweight reference mirror to a piezoelectric stack and driving the stack at a resonance frequency of about 125 kHz. The electrical behavior of the piezo stack and the mechanical properties of the piezo-mirror arrangement are described. A displacement amplitude at resonance of about 350 nm was achieved using a standard function generator. Phase drift in the interferometer and piezo wobble were readily circumvented. This approach to phase modulation is less expensive by a factor of roughly 50 than one based on an electro-optic effect.
A High-Bandwidth Frequency-Domain Photon Migration Instrument For Clinical Use, Steen J. Madsen, Eric R. Anderson, Richard C. Haskell, Bruce J. Tromberg
A High-Bandwidth Frequency-Domain Photon Migration Instrument For Clinical Use, Steen J. Madsen, Eric R. Anderson, Richard C. Haskell, Bruce J. Tromberg
All HMC Faculty Publications and Research
We have developed a high-bandwidth frequency-domain photon migration (FDPM) instrument which is capable of noninvasively determining the optical properties of biological tissues in near-real-time. This portable, inexpensive, diode-based instrument is unique in the sense that we employ direct diode laser modulation and avalanche photodiode detection. Diffusion models were used to extract the optical properties (absorption and transport scattering coefficients)of tissue-simulating solutions.from the 300 kHz to I GHz photon density wave data.