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- ItemModeling the Pulmonary Effects of Respiratory Protective Masks During Physical Activity(2001) Coyne, Karen Marie; Johnson, Arthur T.; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md)Current respirator design involves developing and testing a prototype, making modifications, and then re-testing until a suitable mask is obtained. If the physiological effects of the respirator could be modeled, design could proceed more rapidly. Such a model would be an important design tool that would provide valuable information on the potential physiological and psychological compatibility of a respirator with the wearer. The model would not eliminate the need for human testing, but would decrease the number of prototypes required, saving time and money. A successful model would be very complex because of the many factors to consider. And, because of the variability of human response to exercise, work, and respirator wear, the initial development of the model will include many assumptions that may limit the expected accuracy of the predictions. The goal of this research was to develop a model of the pulmonary effects of respirator wear during physical activity that would form the framework of a larger model that would include other factors as well. Empirical equations were developed that related oxygen consumption to physiological work rate, anaerobic threshold, minute ventilation and tidal volume to oxygen consumption, and exhalation time to respiratory period. Respirator resistance and dead volume effects were quantified. The model was implemented in Visual BASIC. The model predicted oxygen consumption, minute ventilation, and tidal volume well for a limited number of subjects exercising below 70% of maximal oxygen consumption. For three subjects wearing respirators and exercising at 80-85%, the errors in the model parameters were greater than those of the original equations. As model equations were based on average responses, predictions for any one individual may have large errors. Model simulations of a subject exercising at five different work rates with and without a respirator showed that the model made rational predictions of the effects of a respirator on respiratory parameters. More data is needed to completely validate the model. These results showed that the model structure was valid and that overall the model was capable of making rational predictions of the average effects of respirator wear on pulmonary system parameters during physical activity.
- ItemDecrease of resistance to air flow with nasal strips as measured with the airflow perturbation device(Springer Nature, 2004-10-22) Wong, Lily S; Johnson, Arthur TNasal strips are used by athletes, people who snore, and asthmatics to ease the burden of breathing. Although there are some published studies that demonstrate higher flow with nasal strips, none had directly measured the effect of the strips on nasal resistance using the airflow perturbation device (APD). The APD is an inexpensive instrument that can measure respiratory resistance based on changes in mouth pressure and rate of airflow. This study tested forty-seven volunteers (14 men and 33 women), ranging in age from 17 to 51. Each volunteer was instructed to breathe normally into the APD using an oronasal mask with and without nasal strips. The APD measured respiratory resistance during inhalation, exhalation, and an average of the two. Results of a paired mean t-test comparing nasal strip against no nasal strip were statistically significant at the p = 0.05 level. The Breathe Right™ nasal dilator strips lowered nasal resistance by an average of 0.5 cm H20/Lps from an average nasal resistance of 5.5 cm H20/Lps. Nasal strips reduce nasal resistance when measured with the APD. The effect is equal during exhalation and during inhalation.
- ItemMaximum static inspiratory and expiratory pressures with different lung volumes(Springer Nature, 2006-05-05) Lausted, Christopher G; Johnson, Arthur T; Scott, William H; Johnson, Monique M; Coyne, Karen M; Coursey, Derya CMaximum pressures developed by the respiratory muscles can indicate the health of the respiratory system, help to determine maximum respiratory flow rates, and contribute to respiratory power development. Past measurements of maximum pressures have been found to be inadequate for inclusion in some exercise models involving respiration. Maximum inspiratory and expiratory airway pressures were measured over a range of lung volumes in 29 female and 19 male adults. A commercial bell spirometry system was programmed to occlude airflow at nine target lung volumes ranging from 10% to 90% of vital capacity. In women, maximum expiratory pressure increased with volume from 39 to 61 cmH2O and maximum inspiratory pressure decreased with volume from 66 to 28 cmH2O. In men, maximum expiratory pressure increased with volume from 63 to 97 cmH2O and maximum inspiratory pressure decreased with volume from 97 to 39 cmH2O. Equations describing pressures for both sexes are: Pe/Pmax = 0.1426 Ln( %VC) + 0.3402 R2 = 0.95 Pi/Pmax = 0.234 Ln(100 - %VC) - 0.0828 R2 = 0.96 These results were found to be consistent with values and trends obtained by other authors. Regression equations may be suitable for respiratory mechanics models.
- ItemMULTI-SCALE INVERSE MODELING IN BIOLOGICAL MASS TRANSPORT PROCESSES(2006-11-24) SADEGH ZADEH, KOUROUSH; MONTAS, HUBERT J; Fischell Department of Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)A state-of-the-art inverse modeling strategy was developed, analyzed, and applied in two different biological mass transport processes. The strategy was developed in the framework of the nonlinear optimization problem in which model parameters were estimated by minimizing an appropriate objective function which represents the discrepancy between the observed and predicted responses of the biological systems. The forward problems were solved numerically using the mass conservative Galerkin based linear finite element and finite difference methods. Before incorporating in the framework of the inverse code, the numerical simulators were validated with either analytical or reference solutions. In the inverse code, the Osborne- Moré extended version of the Levenberg- Marquardt algorithm was used to determine the search direction. The Jacobian matrix was constructed using partial derivatives of the state variables with respect to model parameters by one and two-sided finite difference approximations. A mixed termination criterion was used to end the optimization. The strategy was applied to parameter identification problem in Fluorescence Recovery after Photobleaching (FRAP) protocol to estimate the optimized values of the mass transport and binding rate parameters for GFP-tagged glucocorticoid receptor. Results indicate that the protocol provides enough information to uniquely estimate one parameter. It also provides enough information to uniquely estimate the individual values of the binding rate coefficients given the value of the molecular diffusion coefficient is known. However, the protocol provides insufficient information for unique simultaneous estimation of three parameters (diffusion coefficient and binding rate parameters) owing to the high intercorrelation between the molecular diffusion coefficient and pseudo-association rate parameter. Attempts to estimate macromolecule mass transport and binding rate parameters simultaneously from FRAP data result in misleading conclusions regarding concentrations of free macromolecule and bound complex inside the cell, average binding time per vacant site, average time for diffusion of macromolecules from one site to the next, and slow or rapid mobility of biomolecules in cells. To obtain unique values for molecular diffusion coefficient and binding rate parameters of biomolecule, two FRAP experiments should be conducted on the same class of macromolecule and cell. One experiment should be used to measure the molecular diffusion coefficient independently of binding in an effective diffusion regime and the other should be conducted in a reaction dominant or reaction-diffusion regime to quantify the binding rate parameters. The inverse modeling strategy was also successfully used to identify hydraulic parameters for both single and multi-objective optimization problems in homogeneous and heterogeneous variably saturated soils. Incorporating both soil water content information and soil water pressure head data in the framework of the multi-objective parameter optimization, produced excellent result for both soil water content and pressure head profiles.
- ItemINTEGRATED ECONOMIC DECISION SUPPORT SYSTEM MODEL FOR DETERMINING IRRIGATION APPLICATION AND PROJECTED AGRICULTURAL WATER DEMAND ON A WATERSHED SCALE(2006-11-27) Hanna, Kalim; Shirmohammadi, Adel; Biological Resources Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This study involves the development of an irrigation economic model used to determine the estimated net benefit of various irrigation systems when used in temperate zones. The model processes SWAT (Soil and Water Assessment Tool) output data together with user supplied economic data as a basis for identifying agricultural fields likely to result in the greatest economic return for irrigation installations, based on irrigation installation costs, water costs, and the expected revenue from increased yields due to applied water. The model is capable of not only identifying those agricultural fields within the area of interest likely to result in the greatest net benefit, but is able to prescribe the most profitable irrigation system from an array of possible systems, based on user supplied economic and performance data. The model can also be used to determine the optimal average monthly irrigation volume to be applied to a given field, by balancing the expected revenue due to the estimated yield increase as a result of irrigation application verses the cost of water. The model is applied in this study to a range of water cost levels and crop types from which general conclusions about the use of irrigation in temperate zones are made. The primary product of this study is an irrigation economic tool capable of determining the profitability of irrigation installations verses non-irrigated systems for a wide range of hydrological and environmental conditions. The project included the collection and compilation of required data on land-use, topography, and soil properties, into a GIS project, used as a data input basis for the SWAT model. For demonstration purposes the model is applied to the Pocomoke River basin located in the Coastal Plain of Maryland's Eastern Shore. Input data for the model is taken from multiple SWAT simulations for various crops, modeled with a statistically generated artificial weather pattern typical of the region. Further analysis is conducted on the environmental impact of irrigation, using SWAT model simulations over a range of irrigation application levels. General conclusions are drawn on the effects of irrigation on water quality parameters and the nutrient/sediment transport processes involved.
- ItemEffects of cytoskeletal protein disruption on the deformation of MSCs during chondrogenesis(2007-05-07) Vigfusdottir, Agusta Thuridur; Hsieh, Adam H; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Intervertebral disc degeneration has been identified as a main cause for low back pain, a large health problem in the Western world today with 60%-80% of people affected at some point during their lives. Current treatments alleviate the symptoms rather than repair the tissue, but tissue engineering the intervertebral discs to stem degeneration or to repair damaged tissues may be a realistic alternative. Adult bone marrow derived mesenchymal stem cells are undifferentiated, multipotent cells that have the ability to differentiate into the chondrocyte-like cells found within the nucleus pulposus of the adult intervertebral disc. This study examines one determinant of the cellular mechanotransduction pathway, an important aspect of cell-based therapies. Specifically, we investigate the role of cytoskeletal proteins on resisting mesenchymal stem cell deformation. An improved understanding of the relative contributions of microfilaments and microtubules to cell deformation characteristics will aid in the interpretation of cellular mechanotransduction mechanisms in future studies.
- ItemA finite element model for protein transport in vivo(Springer Nature, 2007-06-28) Sadegh Zadeh, Kouroush; Elman, Howard C; Montas, Hubert J; Shirmohammadi, AdelBiological mass transport processes determine the behavior and function of cells, regulate interactions between synthetic agents and recipient targets, and are key elements in the design and use of biosensors. Accurately predicting the outcomes of such processes is crucial to both enhancing our understanding of how these systems function, enabling the design of effective strategies to control their function, and verifying that engineered solutions perform according to plan. A Galerkin-based finite element model was developed and implemented to solve a system of two coupled partial differential equations governing biomolecule transport and reaction in live cells. The simulator was coupled, in the framework of an inverse modeling strategy, with an optimization algorithm and an experimental time series, obtained by the Fluorescence Recovery after Photobleaching (FRAP) technique, to estimate biomolecule mass transport and reaction rate parameters. In the inverse algorithm, an adaptive method was implemented to calculate sensitivity matrix. A multi-criteria termination rule was developed to stop the inverse code at the solution. The applicability of the model was illustrated by simulating the mobility and binding of GFP-tagged glucocorticoid receptor in the nucleoplasm of mouse adenocarcinoma. The numerical simulator shows excellent agreement with the analytic solutions and experimental FRAP data. Detailed residual analysis indicates that residuals have zero mean and constant variance and are normally distributed and uncorrelated. Therefore, the necessary and sufficient criteria for least square parameter optimization, which was used in this study, were met.The developed strategy is an efficient approach to extract as much physiochemical information from the FRAP protocol as possible. Well-posedness analysis of the inverse problem, however, indicates that the FRAP protocol provides insufficient information for unique simultaneous estimation of diffusion coefficient and binding rate parameters. Care should be exercised in drawing inferences, from FRAP data, regarding concentrations of free and bound proteins, average binding and diffusion times, and protein mobility unless they are confirmed by long-range Markov Chain-Monte Carlo (MCMC) methods and experimental observations.
- ItemSustained Delivery and Pharmacodynamics of an Integrin Antagonist for Ocular Angiogenesis(2007-11-19) Fu, Yingli; Wang, Nam Sun; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Ocular angiogenesis, or the formation of new blood vessels in the eye, is the leading cause of blindness in a variety of clinical conditions. Success in elucidation of several key steps in angiogenesis cascade has opened a door for anti-angiogenesis therapies. Development of novel therapeutic agents provides effective treatment for ocular disorders. However, treatment of many posterior segment diseases like age-related macular degeneration (AMD) and diabetic retinopathy (DRP) is far from satisfactory due to the limited availability of novel therapeutic drugs and the low efficiency of traditional drug delivery methods. In the present study, we investigated the anti-angiogenic properties of a novel small integrin antagonist, EMD478761, and developed sustained release systems to locally and continuously deliver this compound. In part I, sustained delivery implants were designed and investigation of their anti-angiogenic efficacy, including inhibition and regression, was performed using in vivo chick chorioallantoic membrane (CAM) assay. In part II, laser-induced choroidal neovascularization (CNV) rat model was employed to further examine the angiogenic inhibitory effect of EMD478761 from a sustained release microimplant. And in part III, the pharmacodynamics of EMD478761 was studied to reveal the mechanisms by which EMD478761 inhibited angiogenesis. Results from in vivo CAM assay and CNV rat model demonstrated that EMD478761 inhibited and regressed basic fibroblast growth factor (bFGF)-induced angiogenesis, and suppressed laser-induced CNV via sustained release implants. The pharmacodynamics of this drug was studied to better understand the mechanisms of the drug's action mode in preventing neovascularization. In vitro, EMD478761 inhibited human umbilical vein endothelial cell (HUVEC) proliferation, caused HUVEC detachment in vitronectin-coated surfaces in a time- and dose-dependent manner, and disrupted endothelial cell tube formation on Matrigel. In addition, EMD478761 induced HUVEC apoptosis on vitronectin via caspase-3 activation pathway. In vivo, EMD478761 induced endothelial cell apoptosis within CNV lesions as demonstrated by terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) assay. In addition, EMD478761 increased the integrin αvβ3 internalization in HUVECs, while it did not affect integrin αvβ3 expression levels after 12 hours treatment. Taken together, these findings demonstrate that sustained delivery of EMD478761 may provide an effective antiangiogenic approach for the treatment of ocular angiogenesis.
- ItemDynamics of Erythrocytes and Microcapsules(2008-04-25) Dodson, Walter; Dimitrakopoulos, Panagiotis; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The erythrocytes are the primary carriers of oxygen and carbon dioxide to and from the systemic tissue. The ability of these cells to deform and navigate through the capillary beds is of fundamental importance for proper functioning of the cardiovascular transport system. The erythrocyte is essentially a capsule, and flow-induced erythrocyte deformation involves the interfacial dynamics of a membrane-enclosed fluid volume stressed in a viscous flow. Elastic capsule dynamics is a complicated problem involving the coupling of fluid and membrane forces; it is also found in a variety of scientific and engineering applications. In this work, we investigate the dynamics of elastic capsules and erythrocytes using the Spectral Boundary Element (SBE) method, a high-order / high-accuracy method for capsule and cellular dynamics. For strain-hardening Skalak elastic capsules in an extensional flow, our investigations demonstrate a shape transition in accordance with experimental observations to a cusped conformation at high flow rates, which allows the capsule to withstand the increased hydrodynamic forces. Our computational methodology reveals a region of bifurcation, in which both spindled and cusped steady-state geometries coexist for a single flow rate. The method is also used to investigate the dynamics of strain-softening Neohookean capsules in the same flow pattern. The strain-softening capsules become highly extended at weaker flow rates than strain-hardening capsules, and do not form steady-state cusped shapes. The SBE method has been extended to model the erythrocyte by using a biconcave disc reference geometry and adaptive prestress to enforce area incompressibility. The method accurately reproduces experimental data from erythrocyte ektacytometry, but allows examination of the erythrocyte dynamics beyond the geometric constraints inherent in ektacytometry and other experimental techniques, including observation of the three-dimensional oscillatory behavior over a range of capillary numbers and viscosity ratios. Our results support a prediction by Fischer, Skalak, and coworkers that the erythrocyte shear modulus decreases at small shear deformations. Our work also suggests that cellular deformation is largely independent of the flow pattern, consistent with the findings of experimental investigators.
- ItemSynthetic biology: enormous possibility, exaggerated perils(Springer Nature, 2008-04-25) Russ, Zachary NThe following essay was written by a freshman undergraduate student majoring in Bioengineering at the University of Maryland, Mr. Zachary Russ. Mr. Russ was one of 94 students who submitted a 1000 to 1200 word essay to the 3rd Annual Bioethics Essay Contest sponsored by the Institute of Biological Engineering (IBE). A group of professionals in Biological Engineering assessed and ranked the essays in a blinded process. Five semi-finalists were invited to present their essays at a session at the annual meeting of IBE in Chapel Hill, NC on March 8, 2008. Five judges scored the presentations at the annual meeting and selected Mr. Russ's contribution as the overall winner (1st Place). Below is his essay.
- ItemBioelectronic Sensor for Cellular Assays Using Polyelectrolyte Multilayer-Modified Electrodes(2008-04-25) Mijares, Geraldine; DeVoe, Donald L; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Cell-based impedance biosensors provide non-invasive, quantitative, and instantaneous detection of cellular responses to applied stimuli. Extracellular matrix proteins, which degrade over time, are commonly used as cell adhesion promoters on planar electrodes, but decrease the lifetime of biosensors. In this work, the feasibility of using non-biological polyelectrolyte multilayers (PEMs) to facilitate cell attachment on titanium-tungsten alloy/gold electrodes for cell assays is investigated. The PEMs-modified electrode system is modeled as an equivalent electrical circuit and the addition of cells to the system is defined by their electrical properties. Electrode performance is characterized by cyclic voltammetry and impedance spectroscopy. The electrodes are found to have the ability to specifically probe non-faradaic processes and show a 15% increase in impedance due to cell proliferation. This thesis work demonstrates the use of PEMs-modified electrodes for the continuous monitoring of cell proliferation and for the future application of probing cell confluency in microfluidic cytotoxicity assays.
- ItemMACHINE VISION TECHNOLOGY FOR FOOD QUALITY AND SAFETY INSPECTIONS(2008-10-02) Jin, Fenghua; Tao, Yang; Fischell Department of Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)With increased expectations for food products of high quality and safety standards, the need for accurate, fast and objective determination of these characteristics in food products continues to grow. Machine vision as a non-destructive technology, provides an automated and economic way to accomplish these requirements. This research thus explored two applications of using machine vision techniques for food quality and safety inspections. The first application is using a combined X-ray and laser range imaging system to detect bone and other physical contaminants inside poultry meat. For this project, our research focuses on how to calibrate the imaging system. A unique three-step calibration method was developed and results showed that high accuracy has been achieved for the whole system calibration - a root mean square error of 0.20 mm, a standard deviation of 0.20 mm, and a maximum error of 0.48 mm. The second application is separating walnuts' shells and meat. A backlight imaging system was developed based on our finding that the backlit images of walnut shells and meat showed quite different texture patterns due to their different light transmittance properties. The texture patterns were characterized by several rotation invariant texture analysis methods. The uncorrelated and redundant features were further removed by a support vector machine (SVM) based recursive feature elimination method, with the SVM classifier trained concurrently for separations of walnuts' shells and meat. The experimental results showed that the proposed approach was very effective and could achieve an overall 99.2% separation accuracy. This high separation accuracy and low instrument cost make the proposed imaging system a great benefit to the walnut processing industry.
- ItemProgrammable Biomolecule Assembly and Activity in Prepackaged BioMEMS(2008-10-21) Luo, Xiaolong; Rubloff, Gary W.; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Antibiotic resistance is an increasing public health concern and few new drugs for bacterial pathogenesis have been obtained without addressing this resistance. Quorum sensing (QS) is a newly-discovered system mediated by extracellular chemical signals known as "autoinducers", which can coordinate population-scale changes in gene regulation when the number of cells reaches a "quorum" level. The capability to intercept and rewire the biosynthesis pathway of autoinduer-2 (AI-2), a universal chemical signaling molecule, opens the door to discover novel antimicrobial drugs that are able to bypass the antibiotic resistance. In this research, chitosan-mediated in situ biomolecule assembly has been demonstrated as a facile approach to direct the assembly of biological components into a prefabricated, systematically controlled bio-microelectromechanical system (bioMEMS). Our bioMEMS device enables post-fabricated, signal-guided assembly of labile biomolecules such as proteins and DNA onto localized inorganic surfaces inside microfluidic channels with spatial and temporal programmability. Particularly, the programmable assembly and enzymatic activity of the metabolic pathway enzyme Pfs, one of the two AI-2 synthases, have been demonstrated as an important step to reconstruct and interrogate the AI-2 synthesis pathway in the bioMEMS environment. Additionally, the bioMEMS has been optimized for studies of metabolic pathway enzymes by implementing a novel packaging technique and an experimental strategy to improve the signal-to-background ratio of the site-specific enzymatic reactions in the bioMEMS device. I envision that the demonstrated technologies represent a key step in progress toward a bioMEMS technology suitable to support metabolic engineering research and development.
- ItemTesting limits to airflow perturbation device (APD) measurements(Springer Nature, 2008-10-31) Lopresti, Erika R; Johnson, Arthur T; Koh, Frank C; Scott, William H; Jamshidi, Shaya; Silverman, Nischom KThe Airflow Perturbation Device (APD) is a lightweight, portable device that can be used to measure total respiratory resistance as well as inhalation and exhalation resistances. There is a need to determine limits to the accuracy of APD measurements for different conditions likely to occur: leaks around the mouthpiece, use of an oronasal mask, and the addition of resistance in the respiratory system. Also, there is a need for resistance measurements in patients who are ventilated. Ten subjects between the ages of 18 and 35 were tested for each station in the experiment. The first station involved testing the effects of leaks of known sizes on APD measurements. The second station tested the use of an oronasal mask used in conjunction with the APD during nose and mouth breathing. The third station tested the effects of two different resistances added in series with the APD mouthpiece. The fourth station tested the usage of a flexible ventilator tube in conjunction with the APD. All leaks reduced APD resistance measurement values. Leaks represented by two 3.2 mm diameter tubes reduced measured resistance by about 10% (4.2 cmH2O·sec/L for control and 3.9 cm H2O·sec/L for the leak). This was not statistically significant. Larger leaks given by 4.8 and 6.4 mm tubes reduced measurements significantly (3.4 and 3.0 cm cmH2O·sec/L, respectively). Mouth resistance measured with a cardboard mouthpiece gave an APD measurement of 4.2 cm H2O·sec/L and mouth resistance measured with an oronasal mask was 4.5 cm H2O·sec/L; the two were not significantly different. Nose resistance measured with the oronasal mask was 7.6 cm H2O·sec/L. Adding airflow resistances of 1.12 and 2.10 cm H2O·sec/L to the breathing circuit between the mouth and APD yielded respiratory resistance values higher than the control by 0.7 and 2.0 cm H2O·sec/L. Although breathing through a 52 cm length of flexible ventilator tubing reduced the APD measurement from 4.0 cm H2O·sec/L for the control to 3.6 cm H2O·sec/L for the tube, the difference was not statistically significant. The APD can be adapted for use in ventilated, unconscious, and uncooperative patients with use of a ventilator tube and an oronasal mask without significantly affecting measurements. Adding a resistance in series with the APD mouthpiece has an additive effect on resistance measurements, and can be used for qualitative calibration. A leak size of at least the equivalent of two 3.2 mm diameter tubes can be tolerated without significantly affecting APD measurements.
- ItemRNA Interference Mediated Suppression of Tn-Caspase-1 as a means of investigating apoptosis and improving recombinant protein production in Trichoplusia ni cells(2008-11-17) Hebert, Colin G; Bentley, William E; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The baculovirus expression system has proven to be a robust and versatile system for recombinant protein production in insect cells. A wide range of promoters is available for the facile expression of transgenes, and yields of up to 50% of total protein have been reported. However, in many cases production is decreased as a result of proteases and host cell apoptosis. To combat this problem, RNA interference (RNAi) has been used as a metabolic engineering tool to knockdown host genes responsible for decreasing the yield of recombinant protein. A novel caspase (Tn caspase-1) derived from Trichoplusia ni cells has been identified and characterized. Through modulation of caspase levels via either RNAi or through interaction with baculovirus protein p35, the overall level of apoptosis present in cell culture has been decreased. In addition, the use of in vitro RNAi targeted against Tn caspase-1 has increased the production of recombinant green fluorescent protein. To further study the effect of suppressing Tn caspase-1, a stable cell line producing in vivo RNAi was developed, resulting in a nearly 90% decrease in caspase enzymatic activity. This suppression was able to improve culture viability under adverse conditions and increase recombinant protein production levels up to two-fold that of standard cells.
- ItemPredicting Water Table Fluctuations Using Artificial Neural Network(2008-11-17) Wu, Chung-Yu; Shirmohammadi, Adel; Fischell Department of Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Correctly forecasting groundwater level fluctuations can assist water resource managers and engineers in efficient allocation of the regional water needs. Modeling such systems based on satellite remotely sensed data may be a viable option to predict water table fluctuations. Two types of water table prediction models based on Artificial Neural Network (ANN) technology were developed to simulate the water table fluctuations at two well sites in Maryland. One was based on the relationship between the variations of brightness temperature and water table depth. The other one was based on the relationship between the changes of soil moisture and water table depth. Water table depths recorded at these two wells, brightness temperature retrieved from the Advanced Microwave Scanning Radiometer, and soil moisture data produced by the Land Data Assimilation System were used to train and validate the models. Three models were constructed and they all performed well in predicting water table fluctuations. The root mean square errors of the water table depth forecasts for 12 months were between 0.043m and 0.047m for these three models. The results of sensitivity test showed that the models were more sensitive to the uncertainty in water table depth than to that in brightness temperature or in soil moisture content. This suggests that for situations where high resolution remotely sensed data is not available, an ANN water table prediction model still can be built if the trend of the time series of the data, such as brightness temperature or soil moisture, over the study site correlates well with the trend of the time series of the ground measurement at the study site. An extension of the study to a regional scale was also performed at 12 available well sites in Piedmont Plateau, Maryland. Hydrologic soil types, LDAS soil moistures, and water table depths at these locations were used in the ANN modeling. The root mean square error of one month long water table depth forecast was 0.142m. However, the accuracy of the monthly forecast decreases with the increase of time. A further study to improve the accuracy of long-term water table fluctuation forecast is recommended.
- ItemBiological Nanofactories: Altering Cellular Response via Localized Synthesis and Delivery(2008-11-19) Fernandes, Rohan; Bentley, William E; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Conventional research in targeted delivery of molecules-of-interest involves either packaging of the molecules-of-interest within a delivery mechanism or pre-synthesis of an inactive prodrug that is converted to the molecule-of-interest in the vicinity of the targeted area. Biological nanofactories provide an alternative approach to targeted delivery by locally synthesizing and delivering the molecules-of-interest at surface of the targeted cells. The machinery for synthesis and delivery is derived from the targeted cells themselves. Biological nanofactories are nano-dimensioned and are comprised of multiple functional modules. At the most basic level, a biological nanofactory consists of a cell targeting module and a synthesis module. When deployed, a biological nanofactory binds to the targeted cell surface and locally synthesizes and delivers molecules-of-interest thus altering the response of the targeted cells. In this dissertation, biological nanofactories for the localized synthesis and delivery of the 'universal' quorum sensing signaling molecule autoinducer-2 are demonstrated. Quorum sensing is process by which bacterial co-ordinate their activities at a population level through the production, release, sensing and uptake of signaling autoinducers and plays a role in diverse bacterial phenomena such as bacterial pathogenicity, biofilm formation and bioluminescence. Two types of biological nanofactories; magnetic nanofactories and antibody nanofactories are presented in this dissertation as demonstrations of the biological nanofactory approach to targeted delivery. Magnetic nanofactories consist of the AI-2 biosynthesis enzymes attached to functionalized chitosan-mag nanoparticles. Assembly of these nanofactories involves synthesis of the chitosan-mag nanoparticles and subsequent assembly of the AI-2 pathway enzymes onto the particles. Antibody nanofactories consist of the AI-2 biosynthesis enzymes self assembled onto the targeting antibody. Assembly of these nanofactories involves creation of a fusion protein that attaches to the targeting antibody. When added to cultures of quorum sensing bacteria, the nanofactories bind to the surface of the targeted cells via the targeting module and locally synthesize and deliver AI-2 there via the synthesis module. The cells sense and uptake the AI-2 and alter their natural response. Prospects of using biological nanofactories to alter the native response of targeted cells to a 'desired' state, especially with respect to down-regulating undesirable co-ordinated bacterial response, are envisioned.
- ItemNovel Statistical Pattern Recognition and 3D Machine Vision Technologies for Automated Food Quality Inspection(2008-12-02) Zhu, Bin; Tao, Yang; Fischell Department of Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Machine vision technologies have received a lot of attention for automated food quality inspection. This dissertation describes three techniques developed to improve the quality inspection of apple and poultry products. First, a Gabor feature-based kernel principal component analysis (PCA) method was introduced by combining Gabor wavelet representation of apple images and the kernel PCA method for apple quality inspection using near-infrared (NIR) imaging. Gabor wavelet decomposition was employed to extract appropriate Gabor features of whole apple NIR images. Then, the kernel PCA method with polynomial kernels was applied in the Gabor feature space to handle nonlinear separable features. The experimental results showed the effectiveness of the Gabor-based kernel PCA method. Using the proposed Gabor kernel PCA eliminated the need for local feature segmentation and also resolved the nonlinear separable problem in the Gabor feature space. An overall 90.5% detection rate was achieved. Second, a novel 3D-based apple near-infrared (NIR) data analysis strategy was utilized so that the apple stem-end/calyx could be identified, and hence differentiated from defects and normal tissue according to their different 3D shapes. Two automated 3D data processing approaches were developed in this research: 1) A 3D quadratic facet model fitting, which employed a small concave 3D patch to fit the 3D apple surface and the best fit could be found around stem-end/calyx area; and 2) A 3D shape enhanced transform (SET), which enhanced the apple stem-end/calyx area and made it easily detectable because of the 3D surface gradient difference between the stem-end/calyx and the apple surface. An overall 92.6% accuracy was achieved. Third, high resolution on-line laser 3D imaging was investigated for improving the 3D profile recovery for thickness compensation purposes. Parallel processing and memory management were also considered to improve the processing speed of the detection system. Multiple-lane coverage was fulfilled such that a wider conveyor could be used and overall throughput would be increased. To further improve the detection performance of the dual X-ray and laser imaging system, a dynamic thresholding approach was introduced to suppress the errors and noise involved by the imaging system. Unlike the traditional single threshold method, dynamic thresholding monitored the responses of the region of interest under a set of thresholds to determine the true physical contaminants, making it more tolerant to the noise than the single threshold method. An overall 98.6% detection rate was achieved.
- ItemControlled liposome formation and solute encapsulation with continuous-flow microfluidic hydrodynamic focusing(2008-12-11) Jahn, Andreas; DeVoe, Don L; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Liposomes enable the compartmentalization of compounds making them interesting as drug delivery systems. A drug delivery system (DDS) is a transport vehicle for a drug for in vivo drug administration. Drugs can be encapsulated, bound, or otherwise tethered to the carrier which can vary in size from tens of nanometers to a few micrometers. Liposomal DDSs have shown their capability to deliver drugs in a new fashion, allowing exclusive sales of encapsulated drugs to be extended beyond the initial compound's patent expiration date. However, existing methods to form liposomes and encapsulate drugs are based on bulk mixing techniques with limited process control and the produced liposomes frequently require post-processing steps. In this dissertation, a new method is demonstrated to control liposome formation and compound encapsulation that pushes beyond existing benchmarks in liposome size homogeneity and adjustable encapsulation. The technology utilizes microfluidics for future pharmacy-on-a-chip applications. The microfluidic system allows for precise control of mixing via molecular diffusion with reproducible and controlled physicochemical conditions compared to traditional bulk-phase preparation techniques (i.e. test tubes and beakers). The laminar flow and facile fluidic control in microchannels enables reproducible self-assembly of lipids into liposomes in a sheathed flow-field. Confining a water-soluble compound to be encapsulated to the immediate vicinity where liposome formation is expected to occur reduces sample consumption without affecting liposome loading. The ability to alter the concentration and control the amount of encapsulated compounds within liposomes in a continuous-flow mode is another interesting feature towards tailored liposomal drug delivery. The liposome formation strategy demonstrated in this dissertation offers potential for point-of-care drug encapsulation, eliminating shelf-life limitations inherent to current liposome preparation techniques.
- ItemComplete genomic sequence analysis of infectious bronchitis virus Ark DPI strain and its evolution by recombination(2008-12-22) Ammayappan, Arun; Upadhyay, Chitra; Gelb, Jack Jr.; Vakharia, Vikram NAn infectious bronchitis virus Arkansas DPI (Ark DPI) virulent strain was sequenced, analyzed and compared with many different IBV strains and coronaviruses. The genome of Ark DPI consists of 27,620 nucleotides, excluding poly (A) tail, and comprises ten open reading frames. Comparative sequence analysis of Ark DPI with other IBV strains shows striking similarity to the Conn, Gray, JMK, and Ark 99, which were circulating during that time period. Furthermore, comparison of the Ark genome with other coronaviruses demonstrates a close relationship to turkey coronavirus. Among non-structural genes, the 5'untranslated region (UTR), 3C-like proteinase (3CL pro) and the polymerase (RdRp) sequences are 100% identical to the Gray strain. Among structural genes, S1 has 97% identity with Ark 99; S2 has 100% identity with JMK and 96% to Conn; 3b 99%, and 3C to N is 100% identical to Conn strain. Possible recombination sites were found at the intergenic region of spike gene, 3'end of S1 and 3a gene. Independent recombination events may have occurred in the entire genome of Ark DPI, involving four different IBV strains, suggesting that genomic RNA recombination may occur in any part of the genome at number of sites. Hence, we speculate that the Ark DPI strain originated from the Conn strain, but diverged and evolved independently by point mutations and recombination between field strains.