Engineering Commons^™

Visualization Of Deep Convolutional Neural Networks, Dingwen Li

McKelvey School of Engineering Graduate Student Theses & Dissertations

Deep learning has achieved great accuracy in large scale image classification and scene recognition tasks, especially after the Convolutional Neural Network (CNN) model was introduced. Although a CNN often demonstrates very good classification results, it is usually unclear how or why a classification result is achieved. The objective of this thesis is to explore several existing visualization approaches which offer intuitive visual results. The thesis focuses on three visualization approaches: (1) image masking which highlights the region of image with high influence on the classification, (2) Taylor decomposition back-propagation which generates a per pixel heat map that describes each pixel's …

Improving Radiation Therapy Through Motion Tracking, Hanlin Wan

McKelvey School of Engineering Graduate Student Theses & Dissertations

Radiation therapy is a widely-used cancer treatment method in which lethal doses of ionizing radiation are delivered to cancerous cells. Given the high dose requirements and the risk of associated complications, it is essential that radiation be targeted to cancerous cells while minimizing the dose to surrounding tissue. While current technology allows for accurate targeting of radiation dose, there is one major hurdle: Respiratory motion causes movement of up to a few centimeters of tumors in the abdomen and thorax, rendering even the most accurate radiation delivery machine highly inaccurate. Imaging devices integrated with the treatment machines allow us to …

Translational Photoacoustic Tomography, Yong Zhou

McKelvey School of Engineering Graduate Student Theses & Dissertations

Combining optical excitation and ultrasonic detection, photoacoustic tomography (PAT) offers deep imaging with high resolution. With optical excitation, PAT maintains the high contrast of optical imaging. Because of the low scattering of ultrasonic waves in tissue, PAT achieves high spatial resolution at depths. Several advantages make PAT suitable for clinical application, including its scalable penetration and resolution, high optical absorption contrast, fast imaging speed, and ability to perform spectral decomposition. Based on different image reconstruction mechanisms, PAT can be further divided into two embodiments: raster-scanning-based photoacoustic microscopy (PAM) and reconstruction-algorism-based photoacoustic computed tomography (PACT). This dissertation aims to advance the …

Development And Investigation Of Sparse Co-Adaptive Algorithms In Ecog Based Closed-Loop Brain Computer Interface, Piyush Karande

McKelvey School of Engineering Graduate Student Theses & Dissertations

Electrocorticography (ECoG) has gained a lot of momentum and has become a serious contender as a recording modality for the implementation of Brain-Computer Interface (BCI) systems in the last few years. ECoG signals provide the right balance between minimal invasiveness and robust spectral information to accomplish a BCI task. However, all the BCI studies until now have used signals recorded from a large number of implanted electrodes and a larger number of spectral features. The recording and processing of these signals uses a lot of electrical power and thus hinders its use outside the research setting. To translate this research …

Theory Of Carrier Transport From First Principles: Applications In Photovoltaic And Thermoelectric Materials, Alireza Faghaninia

McKelvey School of Engineering Graduate Student Theses & Dissertations

New sources of energy that are environmentally friendly, cost-effective, and renewable are essential if we are to combat the effects of global climate change. Two of these sources are solar photovoltaic (PV) cells to convert sunlight into electricity and thermoelectric (TE) devices to convert heat to electricity. To be practical on a large scale, the properties (e.g. electrical conductivity, band gap, Seebeck coefficient, etc) of the the underlying materials must be improved significantly through judicious control of structure and composition. Significant understanding of materials properties is required to design and engineer new high-performing materials. First principles calculations using density functional …

Multi-Static Mimo Along-Track Interferometry (Atl), Chad Knight, Ross Deming, Jake Gunther

Space Dynamics Laboratory Publications

Along-track interferometry (ATI) has the ability to generate high-quality synthetic aperture radar (SAR) images and concurrently detect and estimate the positions of ground moving target indicators (GMTI) with moderate processing requirements. This paper focuses on several different ATI system configurations, with an emphasis on low-cost configurations employing no active electronic scanned array (AESA). The objective system has two transmit phase centers and four receive phase centers and supports agile adaptive radar behavior. The advantages of multistatic, multiple input multiple output (MIMO) ATI system configurations are explored. The two transmit phase centers can employ a ping-pong configuration to provide the multistatic …

Incorporating Vehicle Mix In Stimulus-Response Car-Following Models, S Siuhi, Mohamed Kaseko

Civil and Environmental Engineering and Construction Faculty Research

The objective of this paper is to incorporate vehicle mix in stimulus-response car-following models. Separate models were estimated for acceleration and deceleration responses to account for vehicle mix via both movement state and vehicle type. For each model, three sub-models were developed for different pairs of following vehicles including “automobile following automobile,” “automobile following truck,” and “truck following automobile.” The estimated model parameters were then validated against other data from a similar region and roadway. The results indicated that drivers' behaviors were significantly different among the different pairs of following vehicles. Also the magnitude of the estimated parameters depends on …

Can Neuromorphic Computer Vision Inform Vision Science? Disparity Estimation As A Case Study, Guido Maiello, Manuela Chessa, Peter J. Bex, Fabio Solari

MODVIS Workshop

The primate visual system efficiently and effectively solves a multitude of tasks from orientation detection to motion detection. The Computer Vision community is therefore beginning to implement algorithms that mimic the processing hierarchies present in the primate visual system in the hope of achieving flexible and robust artificial vision systems. Here, we reappropriate the neuroscience “borrowed” by the Computer Vision community and ask whether neuromorphic computer vision solutions may give us insight into the functioning of the primate visual system. Specifically, we implement a neuromorphic algorithm for disparity estimation and compare its performance against that of human observers. The algorithm …

Fuzzy Control Of Flexible Multibody Spacecraft: A Linear Matrix Inequality Approach, Chokri Sendi

Engineering Ph.D. Theses

To reduce the cost of lifting to orbit, modern spacecraft and structures used in space applications are designed from light material as flexible multibody system. Moreover The unprecedented requirements for rapid retargeting, precision pointing and tracking capability have made these multibody highly flexible spacecraft vulnerable to dynamic excitation caused by the slewing/pointing maneuver, vibration and external disturbances. As a result, this will degrade the performance of the spacecraft including the pointing accuracy. Thus the aspect of modeling and control become extremely important for the safe and effective operation. Despite the numerous research, the development of high performance, nonlinear control laws …

Fed-Batch Process Development Using Metabolically Efficient Cho Cells, Cecile Toussaint

Cell Culture Engineering XV

The development and application of fed-batch strategies have greatly contributed to the improvement of the productivity of cell culture processes. However, in such processes, lactate and ammonia accumulation in the culture medium over time can have detrimental impacts on cell growth and product quality. Continuous cell lines typically exhibit an inefficient metabolism whereby most of the pyruvate derived from glucose is diverted to lactate and only a small percentage is incorporated into the TCA cycle. Thus, further process improvements can be expected by combining the application of rational fed-batch strategies with targeted metabolic engineering of cells to reduce waste metabolite …

Deepening Knowledge On Cho Cells Metabolism Using Multiple Tracer Substrates, Ana Teixeira, Manuel Carrondo

Cell Culture Engineering XV

Optimization of culture conditions through trial-and-error has led to much of the past progress on animal cell culture. Today, a renewed account of the underlying biologies through a “systems” view is providing a deeper knowledge of cellular physiology and laying the basis to reengineer desirable states of further increased culture performance. In this work, we took a comprehensive view of cellular metabolism by extensively profiling extracellular and intracellular metabolomes after ¹³C‑label supplementation in parallel labelling cultures of [1,2-¹³C]Glucose, [U-¹³C,¹⁵N]Asn, [U-¹³C,¹⁵N]Ser and [1-¹³C]Pyruvate. This integrative approach was used …

A Holistic Approach To Facility Protection From Adventitious Agents – A Case Study, Matthew Osborne, Ronan Kelly, Ann Maria Mccrohan, Marie Murphy

Cell Culture Engineering XV

The Eli Lilly biologics manufacturing facility in Kinsale, Ireland has been operational since 2010 with a 100% cell culture contamination control success rate. The presentation will review the holistic approach to facility protection from adventitious agents that underpins this success including:

• The risk assessment approach to points of entry and management via detectability and control measures
• The approach to personnel training that considers human factors, increased vigilance and event simulations following strategies that are used in chemical synthesis process safety

The presentation will then focus on control of adventitious virus. The talk will briefly comment on the early warning measures …

Building Qbd Frameworks Retrospectively For Commercial Products And The Use Of Scale-Down Model Qualification Strategies To Support Continuous Improvement, Jose Menezes, Francisca Gouveia, Pedro Felizardo

Cell Culture Engineering XV

A science-based justification for many continuous improvement and post-approval submissions on ‘legacy products’ (i.e., commercial products developed without a QbD rationale) requires that some of those missing QbD elements in the original filing, be defined retrospectively.

Here we present a new proposal to achieve that, that is general and very capable of supporting the transition of ‘legacy’ non-QbD into quasi-QbD filings. It is based on (1) a formal criticality analysis to the current process version to support the choice of quality attributes and process parameters in the filing, and identification of additional ones that may impact the quality target-product profile …

Separation Of Igg Glycoforms For Biosimilars Development Using Fc Gamma Receptors As Affinity-Based Chromatography Ligands, Austin Boesch

Cell Culture Engineering XV

Abstract: In biosimilars development, matching the glycosylation pattern of the innovator molecule can be a significant challenge in cell culture development. Here we present a novel downstream method using Fc gamma receptors as chromatography affinity ligands to separate monoclonal antibody glycoforms. Additional data is presented highlighting glycoform potentiation of effector functions such as antibody-dependent cellular cytotoxicity (ADCC) and phagocytosis which can be important mechanisms of action to consider in biosimilars development

Nanofiltration As An Effective Means To Prevent Virus Contamination Of Cell Culture Processes, Christina Carbrello

Cell Culture Engineering XV

While cell culture media is typically sterile filtered to remove bacteria and mycoplasma, many bioreactors remain unprotected from viral contamination. As awareness of the risk for viral contamination of cell culture processes grows, manufacturers are seeking virus barrier technologies to remove or inactivate viruses. Filtration is an ideal technology in terms of familiarity, ease of use and scalability. However, hurdles to its implementation remain, most notably, the high cost and large footprints required to implement filters designed for the downstream process and the concern that the small pore size of virus filters could impact cell culture performance. A filter specifically …

Improvement Of Cho Specific Productivity Using Amino Acid Derivatives, Aline Zimmer, Caroline Hecklau, Sascha Pering, Alisa Schnellbaecher, Thomas Eichhorn

Cell Culture Engineering XV

Industrial fed-batch cultivation of mammalian cells is used for the production of therapeutic proteins such as monoclonal antibodies. Besides medium ensuring initial growth, feeding is necessary to improve growth, viability and antibody production. Amino acids are key elements for the cellular metabolism but also for the quality of the recombinant protein produced. Several studies have already demonstrated the link between amino acid availability and sequence variants [1-3] or specific modifications like trisulfide bonds [4]. To avoid such modifications, the chemical modification of amino acids is an interesting alternative to modulate their overall solubility [5], …

Development Of An Enriched Cho Feed Media For Quality Therapeutic Antibody Production From High Performing Clones, David Ho

Cell Culture Engineering XV

The use of feed media during protein production is essential to sustain viable cell densities and facilitate high productivity for modern high performing clones. However, the introduction of feed media can also have a significant impact on product quality attributes, such as glycosylation for therapeutic antibodies, which can ultimately impact therapeutic efficacy. For certain antibodies, the absence of fucose on the N-glycan at Asparagine 297 of the Fc domain has been shown to significantly increase binding to the FcgammaRIII receptor on NK cells and results in increased ADCC activity. Here we have incorporated product quality analysis including N-glycan analysis into …

Using Definitive Screening Design To Effectively Assess The Combinatorial Impacts Of Media Supplements On Monoclonal Antibody Production In Mammalian Cells, Aaron Chen

Cell Culture Engineering XV

Process understanding is an essential component of QbD principles. Cell culture media composition can impact many process performance parameters such as viable cell density, product yield and product quality attributes. In order to enhance process understanding and exert better process control, numerous media supplements have previously been tested. However, their combinatorial effects on process and product quality have largely been unexplored. This is partially due to the resource and efforts required to execute relatively large size of experiment and data analysis.

Recent advancement in modern design of experiment methodology has alleviated this issue. The definitive screening design (DSD) allows for …

Adapting An In-Licensed/Acquired Cell Culture Process To Platform Conditions, Raghunath Shivappa

Cell Culture Engineering XV

The use of platform materials and processes for new products help streamline process development, enhance predictability and efficiency during manufacturing, and simplify the raw materials supply chain. Although common, adaptation of cell expression systems can require a significant amount of process development work to achieve desired product yield, quality, and comparability. Here, we present a progressive development approach for evaluating platform media and feeds for an acquired cell culture process.

A CHO-DG 44 cell line expressing a novel antibody product was procured through acquisition. The original non-platform media and fed-batch process yielded titers of approximately 3 g/L. A study was …

Antibody Production With Site-Specific Non-Natural Amino Acid Incorporation For Generation Of Antibody Drug Conjugates, Alyssa Powell

Cell Culture Engineering XV

Ambrx’s mammalian expression platform (EuCODE) enables site-specific incorporation of non-natural amino acids into antibodies. This EuCODE technology provides a means for stable payload linkages at defined sites and with a defined DAR of 2 for antibody drug conjugate (ADC) generation. While the ability to control the DAR and payload site can provide an advantage to an ADC, the incorporation of the non-natural amino acid into the antibody heavy chain introduces a unique challenge for antibody production.

To achieve high production of monoclonal antibodies (mAbs) containing non-natural amino acids, we engineered a CHO-K1 cell line which stably contains Ambrx’s patented tRNA …

Development Of A Chemically Defined Media And A Chemically Defined Feeding Strategy For Extended Growth And Enhanced Productivity In Cho-K1 And Cho Dg44 Cultures, Sagar Kokal, Kyle Liu, John Menton

Cell Culture Engineering XV

The biopharmaceutical industry utilizes Chinese Hamster Ovary (CHO) cells for the production of recombinant proteins. Due to regulatory restrictions, there has been much focus on using serum-free culture processes including chemically defined (CD) media and feed system. A great deal of time and cost has been invested by biopharmaceutical companies for the development of an optimal CD media. Currently, the fed-batch process is the most dominant method for the large cultivation of CHO cells. In response to these industry requirements, Kerry has developed a complete system including a CD media called Sheff-CHO CD complete and a CD feed system named …

Evaluating Sugar-Based Detergents As A Potential Alternative To Poloxamer Bubble Protectant, Jessica Wuu, Jayanthi Lakkyreddy, Steven Meier

Cell Culture Engineering XV

Poloxamer 188 (commonly referred to as Pluronic® F-68) is a commonly-used medium component which protects against bubble-induced shear in mammalian cell cultures. Recently, concerns have arisen due to limited sourcing and variable performance of this critical component. In 2008, Hu, et al.¹ proposed the use of sugar-based detergents – specifically, maltopyranosides and glucopyranosides – as potential bubble protectants based on their rheological properties and relatively low toxicity to cells. This work explores the feasibility of these detergents using commercially relevant CHO cell lines and media. Detergent candidates were evaluated based on their tolerance by cells, stability in cell culture …

Adaptation Of Cho Metabolism To Long Term Phosphate Limitation, Mugdha Gadgil

Cell Culture Engineering XV

Phosphate is an important component of abundant intracellular molecules like RNA, is a critical component of energy metabolism and is involved in substrate phosphorylation in cellular metabolism and signaling. Inorganic phosphate (P_i) is transported through specialized transporter proteins and limitation in the availability of phosphate in the growth medium limits cell growth. P_i concentrations have been reported to regulate the rates of aerobic glycolysis and oxygen uptake. Thus it is expected that cellular metabolism will adapt to long term phosphate restriction. Since complete phosphate deprivation will result in lack of growth, such an adaptation needs to be …

Impact Of Poloxamer 188 Variability On Biologics Manufacturing: Mitigations And Causal Investigation, Salim Charaniya

Cell Culture Engineering XV

Poloxamer 188 (P188), a water-soluble, synthetic copolymer with hydrophilic as well as lipophilic properties, is widely used as a cell protectant for bubble-induced shear during cultivation of suspension-adapted mammalian cells for large-scale production of protein-based therapeutics. Poor cell growth and lower product yield has been recently observed at commercial scales in more than one Chinese hamster ovary-based manufacturing process within Roche network when specific lots of P188 were used. An investigation is being conducted to unearth the root cause of “poor-performing” P188 lots and to identify means to mitigate the product supply risks. P188 raw material is currently sourced from …

A Host Cell Protein That May Impact Polysorbate Degradataion, Kelvin Lee

Cell Culture Engineering XV

There is growing interest and concern related to host cell proteins. Current issues with host cell proteins include questions related to the various available analytical approaches and the sensitivity of those approaches as well as issues with purification strategies and the impact of host cell proteins downstream. The availability of a sequenced genome enables new opportunities to address problematic host cell proteins via cell line engineering. We studied difficult to remove host cell proteins in CHO cells with the goal of identifying host cell proteins that may be product associated with a number of monoclonal antibodies, that may copurify with …

The Differential Polarizability Of Cho Cells Can Be Used To Monitor Changes In Metabolism, Katrin Braasch

Cell Culture Engineering XV

The continuous monitoring of cell growth and viability is an integral part of biopharmaceutical production. Measurements of changes in the polarizability of individual cells can identify early emerging sub-populations of apoptotic cells in a dielectrophoretic (DEP) cytometer designed at the University of Manitoba. In this instrument the trajectory of individual cells was tracked as they passed through a bank of electrodes (sensitivity: 0.1 µm; rate: 5 cells per second) designed to differentially perturb the cells according to their polarizability. This perturbation was recorded as a force index (FI), which was related to the electrical displacement of the cells. Using this …

Development Of Antibody Detection Methods For Active Product At The Cell Culture Stage, Gregory Walsh, Matthew Schraut, Jon Barricelli, Lada Laenen

Cell Culture Engineering XV

Development of new analytical methods to characterize the manufacturing process became necessary when the site wanted to implement process improvements to increase output from the bioreactor. The bioreactor process is monitored and controlled for dissolved oxygen content, glucose concentration, temperature, etc. and samples of the harvest are analyzed daily using an endpoint assay and a total protein method. Neither of the two methods can detect the total amount of product at the harvest stage; the endpoint assay will only detect active product and the total protein method will not discriminate between the cellular proteins and the active product. We have …

Development And Application Of Glycosyltransferases For In Vitro Glycoengineering, Alfred Engel

Cell Culture Engineering XV

Glycosylation is an important posttranslational modification of proteins influencing protein folding, stability and regulation of the biological activity, e.g. IgG featuring terminal sialic acids were shown to suppress inflammatory response (ADCC) and increase serum half-life. Fully galactosylated structures seem to improve binding to the complement system (CDC).

Despite all efforts in cell-line engineering and process optimization to increase glycosylation homogeneity, today therapeutic proteins still show a heterogeneous glycosylation pattern, with large variations between bioprocesses and even from batch to batch. The use of glycosyltransferases for enzymatic synthesis of well-defined glycan structures will become an essential tool – at least in …

Comparison Of Commercial Cho Cell Media Formulations Using Material-Oriented Recurrent Spectral Libraries, Kelly Telu

Cell Culture Engineering XV

Chinese hamster ovary (CHO) cells are commonly used for the production of biological therapeutics. Metabolic profiles of media components can be used to monitor process variability and look for markers that discriminate between batches of product. Currently, there exists no database of CHO media components or a method for the comparison of commercial media formulations. We are creating material-oriented libraries of CHO media components that include LC-MS/MS and GC-MS data. The libraries represent all metabolites that can be detected by LC-MS/MS and GC-MS and consist of recurrent spectra that cover all known fragmentation conditions and precursors. Recurrent spectra occur repeatedly …

Integrating Emerging Trends In Upstream Process Development: Autosampling, Nutrient Feedback Control, And Single Use Tanks, T. Craig Seamans

Cell Culture Engineering XV

Key to effective upstream development is the presence of resource-efficient systems for examining complex process options. In this presentation, we report the design and characterization of a 3-L rigid single-use bioreactor (SUB), combined with a completely automated sampling and control system capable of evaluating different metabolic-based feed strategies.

Considerations in our development of a custom 3-L SUB, targeted to replace current workhorse glass reactors, encompassed proper technical functionality to flexibility and ease of use. Highlights include: vessel configuration details (impeller, sparger, baffles), perfusion readiness, agitation system design (magnetic bottom drive), and extra sensor ports and feed lines. The SUB was …