Digital Commons Network^™

Investigation Of Biomolecular Interactions For Development Of Sensors And Diagnostics, Xiaojuan Zhang

Theses and Dissertations

The highly specific recognition processes between biomolecules mediate various crucial biological processes. Uncovering the molecular basis of these interactions is of great fundamental and applied importance. This research work focuses on understanding the interactions of several biomolecular recognition systems and processes that can provide fundamental information to aid in the rational design of sensing and molecular recognition tools. Initially, a reliable and versatile platform was developed to investigate biomolecular interactions at a molecular level. This involved several techniques, including biomolecule functionalization to enable attachment to self-assembled monolayers as well as atomic force microscopy (AFM) based force spectroscopy to uncover the …

Investigations On The Corrosion Resistance Of Metallic Bipolar Plates (Bpp) In Proton Exchange Membrane Fuel Cells (Pemfc) - Understanding Of The Effects Of Material, Coating And Manufacturing, Ender Dur

Theses and Dissertations

Polymer Electrolyte Membrane Fuel Cell (PEMFC) systems are promising technology for contributing to meet the deficiency of world`s clean and sustainable energy requirements in the near future. Metallic bipolar plate (BPP) as one of the most significant components of PEMFC device accounts for the largest part of the fuel cell`s stack. Corrosion for metallic bipolar plates is a critical issue, which influences the performance and durability of PEMFC. Corrosion causes adverse impacts on the PEMFC`s performance jeopardizing commercialization. This research is aimed at determining the corrosion resistance of metallic BPPs, particularly stainless steels, used in PEMFC from different aspects. Material …

Differential Gene Expression To Investigate The Effects Of Low-Level Electrochemical Currents On Bacillus Subtilis., Robert Szkotak, Tagbo H R Niepa, Nikhil Jawrani, Jeremy L. Gilbert, Marcus B. Jones, Dacheng Ren

Biomedical and Chemical Engineering - All Scholarship

With the emergence and spread of multidrug resistant bacteria, effective methods to eliminate both planktonic bacteria and those embedded in surface-attached biofilms are needed. Electric currents at uA-mA/cm2 range are known to reduce the viability of bacteria. However, the mechanism of such effects is still not well understood. In this study, Bacillus subtilis was used as the model Gram-positive species to systematically investigate the effects of electrochemical currents on bacteria including the morphology, viability, and gene expression of planktonic cells, and viability of biofilm cells. The data suggest that weak electrochemical currents can effectively eliminate B. subtilis both as planktonic …

Comparative Life Cycle Assessments Of Lignocellulosic And Algae Biomass Conversion To Various Energy Products Through Different Pathways, Maria Juliana Pinilla

USF Tampa Graduate Theses and Dissertations

Bioenergy has the potential to reduce the world's dependence on fossil fuels, and to decrease the CO2 emissions due to fossil combustion. Lignocellulosic and algae biomass have been presented as promising feedstocks for bioenergy production.

In this study, a comparative Life Cycle Assessment (LCA) has been developed to evaluate the environmental impacts associated with different energy products via different routes across the whole life of algal and lignocellulosic bioenergy. Results were compared per energy basis, the production of 1 million BTU of energy products.

For the development of the comparative algae biomass conversion LCA, algal biomass was converted to liquid …

Resource Letter No-1: Nonlinear Optics, Elsa Garmire

Dartmouth Scholarship

This Resource Letter provides a guide to the literature on nonlinear optics. Books, journals, and websites are introduced that cover the general subject. Journal articles and websites are cited covering the following topics: second-order nonlinearities in transparent media including second-harmonic generation and optical parametric oscillation, third-order and higher nonlinearities, nonlinear refractive index, absorptive nonlinearities such as saturable absorption and multiphoton absorption, and scattering nonlinearities such as stimulated Raman scattering and stimulated Brillouin scattering. Steady-state and transient phenomena, fiber optics, solitons, nonlinear wave mixing, optical phase conjugation, nonlinear spectroscopy, and multiphoton microscopy are all outlined.

Effects Of Carbon Nanotube-Tethered Nanosphere Density On Amperometric Biosensing: Simulation And Experiment, Jonathan Caussen, James Hengenius, Monique Wickner, Timothy Fisher, David Umulis, Marshall Porterfield

Birck and NCN Publications

Nascent nanofabrication approaches are being applied to reduce electrode feature dimensions from the microscale to the nanoscale, creating biosensors that are capable of working more efficiently at the biomolecular level. The development of nanoscale biosensors has been driven largely by experimental empiricism to date. Consequently, the precise positioning of nanoscale electrode elements is typically neglected, and its impact on biosensor performance is subsequently overlooked. Herein, we present a bottom-up nanoelectrode array fabrication approach that utilizes low-density and horizontally oriented single-walled carbon nanotubes (SWCNTs) as a template for the growth and precise positioning of Pt nanospheres. We further develop a computational …

Migration And Invasion Of Brain Tumors, Richard A. Able, Jr., Veronica Dudu, Maribel Vazquez

Publications and Research

Recent advances in molecular biology have led to new insights in the development, growth and infiltrative behaviors of primary brain tumors (Demuth and Berens, 2004; Huse and Holland, 2010; Johnson et al., 2009; Kanu et al., 2009). These tumors are derived from various brain cell lineages and have been historically classified on the basis of morphological and, more recently, immunohistochemical features with less emphasis on their underlying molecular pathogenesis (Huse and Holland, 2010). The detailed molecular characterization of brain tumors has laid the groundwork for augmentation of standard treatment with patient-specific designed targeted therapies (Johnson et al., 2009; Kanu et …

The Effectiveness Of Anaerobic Baffled Reactor And Rotating Biological Contactor In Batik Wastewater Treatment, Augustinus Ignatius Kristijanto, Widhi Handayani, Purwanti Asih Anna Levi

Makara Journal of Technology

Batik is one of popular arts of Indonesia. The batik industries in Sragen, Central Java, are prepared to compete in global market. In order to realize that objective, batik products should fulfill some qualifications, one of which is “environmental friendliness”. As batik production is usually generating wastewater which pollutes the environment, the technology of wastewater treatment should be developed to solve the problem. This preliminary study has been done to assess the effectiveness of anaerobic baffled reactor (ABR) and rotating biological contactor (RBC) in batik wastewater treatment. In 40 days of treatment period, the ABR performance in reducing pollutants showed …

Medium Density Fibreboard Made Of Acetylated Sludge From Paper Mill, Luthfi Hakim, Evalina Herawati, I Nyoman Jaya Wistara

Makara Journal of Technology

Medium Density Fibreboard Made of Acetylated Sludge from Paper Mill. Research of using sludge as raw material for making medium density fibreboard (MDF) was useful to create additional value of sludge. The objective of the research was to evaluate physical properties, mechanical properties, and durability of MDF from acetylated sludge in 4 levels of acetate anhydride (0%, 3%, 5%, and 7%) with 3 replicates. The MDF was made using dry process. After materials were mixed with adhesives, they were pressed using hotpress under 170 oC temperature and 45 Pa pressure for 25 minutes. The size of the MDF sample was …

Antibacterial Activity Of Papaya Leaf Extracts Against Pathogenic Bacteria, Elisa Friska Romasi, Jessica Karina, Adolf Jan Nexson Parhusip

Makara Journal of Technology

It was reported that the extracts of papaya leaves could inhibit the growth of Rhizopus stolonifer. Antibacterial activity of Carica papaya leaf extracts on pathogenic bacteria was observed in this study. Papaya leaves were extracted by using maceration method and three kinds of solvents: ethanol, ethyl acetate, and hexane. Papaya leaf extracts were tested against Bacillus stearothermophilus, Listeria monocytogenes, Pseudomonas sp., and Escherichia coli by agar diffusion method. The objectives of this study were to determine extract ability against pathogenic bacteria, to observe the influence of pH, NaCl, and heat on extracts ability, and to observe extract ability against B. …

Investigating The Role Of The Internet In Women And Minority Stem Participation: A Case Study Of Two Florida Engineering Programs, Arland Nguema Ndong

USF Tampa Graduate Theses and Dissertations

Despite our awareness of the fascination modern humans have with the Internet, little is known about how and why colleges and universities create and maintain Websites. At the most general level, in this case study, I hypothesize that university Websites serve as communication and marketing tools in attracting students. At the most specific level, I postulate that civil engineering programs with Web pages depicting images of women and minorities would be more successful in recruiting and retaining women and students of color than civil engineering programs with Web pages displaying fewer or no images of women and minorities. The primary …

Velocity Contour Weighting Method. I: Algorithm Development And Laboratory Testing, Daniel J. Howes, Brett F. Sanders

BioResource and Agricultural Engineering

An algorithm is developed for real-time estimation of the cross-sectional average velocity of a channel flow by using an upward-looking pulsed wave acoustic Doppler velocity meters (ADVM). The Velocity Contour Weighting Method (VCWM) is applicable to gradually varied flows in prismatic channels and requires little to no calibration. VCWM estimates the average velocity as a weighted average of ADVM bin velocities. Weights are based on the velocity distribution sampled by the ADVM. Collectively, the VCWM is able to adapt to a wide range of channel geometry and roughness features. Expressions for the velocity weights are developed by first applying a …

The Genome Portal Of The Department Of Energy Joint Genome Institute, Igor V. Grigoriev, Henrik Nordberg, Igor Shabalov, Andrea Aerts, Mike Cantor, David Goodstein, Alan Kuo, Simon Minovitsky, Roman Nikitin, Robin A. Ohm, Robert Otillar, Alex Poliakov, Igor Ratnere, Robert Riley, Tatyana Smirnova, Daniel Rokhsar, Inna Dubchak

United States Department of Energy: Publications

The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal (http://genome.jgi.doe.gov) provides a unified access point to all JGI genomic databases and analytical tools. A user …

Unstable Spinocerebellar Ataxia Type 10 (Attct) (Agaat) Repeats Are Associated With Aberrant Replication At The Atx10 Locus And Replication Origin-Dependent Expansion At An Ectopic Site In Human Cells, Guoqi Liu, John J. Bissler, Richard R. Sinden, Michael Leffak

Biomedical Engineering and Sciences Faculty Publications

Spinocerebellar ataxia type 10 (SCA10) is associated with expansion of (ATTCT)n repeats (where n is the number of repeats) within the ataxin 10 (ATX10/E46L) gene. The demonstration that (ATTCT)n tracts can act as DNA unwinding elements (DUEs) in vitro has suggested that aberrant replication origin activity occurs at expanded (ATTCT)n tracts and may lead to their instability. Here, we confirm these predictions. The wild-type ATX10 locus displays inefficient origin activity, but origin activity is elevated at the expanded ATX10 loci in patient-derived cells. To test whether (ATTCT)n tracts can potentiate origin activity, cell lines were constructed that contain ectopic copies …

Liquid Crystal Devices For Optical Communications And Sensing Applications, Sunish Mathews

Doctoral

This thesis is focussed on the design and development of liquid crystal based tunable photonic devices for applications in optical communications and optical sensing, with an emphasis on all-fiber device configuration. The infiltration of liquid crystals into photonic crystal fiber provides a suitable common platform to design and fabricate simple and compact all-fiber tunable photonic devices which can be easily integrated with optical fiber networks and sensing systems. Based on the infiltration of liquid crystals – materials with high dielectric anisotropy, into photonic crystal fibers a common platform is developed to address the need for electronically tunable photonic devices with …

Differential Il-21 Signaling In Apcs Leads To Disparate Th17 Differentiation In Diabetes-Susceptible Nod And Diabetes-Resistant Nod.Idd3 Mice., Sue M. Liu, David H. Lee, Jenna M. Sullivan, Denise Chung, Anneli Jäger, Bennett O V. Shum, Nora E. Sarvetnick, Ana C. Anderson, Vijay K. Kuchroo

Journal Articles: Regenerative Medicine

Type 1 diabetes (T1D) is an autoimmune disease that shows familial aggregation in humans and likely has genetic determinants. Disease linkage studies have revealed many susceptibility loci for T1D in mice and humans. The mouse T1D susceptibility locus insulin-dependent diabetes susceptibility 3 (Idd3), which has a homologous genetic interval in humans, encodes cytokine genes Il2 and Il21 and regulates diabetes and other autoimmune diseases; however, the cellular and molecular mechanisms of this regulation are still being elucidated. Here we show that T cells from NOD mice produce more Il21 and less Il2 and exhibit enhanced Th17 cell generation compared with …

Gait Verification Using Knee Acceleration Signals, L. W. Hang, C. Y. Hong, C. W. Yen, D. J. Chang, Mark L. Nagurka

Mechanical Engineering Faculty Research and Publications

A novel gait recognition method for biometric applications is proposed. The approach has the following distinct features. First, gait patterns are determined via knee acceleration signals, circumventing difficulties associated with conventional vision-based gait recognition methods. Second, an automatic procedure to extract gait features from acceleration signals is developed that employs a multiple-template classification method. Consequently, the proposed approach can adjust the sensitivity and specificity of the gait recognition system with great flexibility. Experimental results from 35 subjects demonstrate the potential of the approach for successful recognition. By setting sensitivity to be 0.95 and 0.90, the resulting specificity ranges from 1 …

Sensing With The Motor Cortex, Nicholas G. Hatsopoulos, Aaron J. Suminski

Biomedical Engineering Faculty Research and Publications

The primary motor cortex is a critical node in the network of brain regions responsible for voluntary motor behavior. It has been less appreciated, however, that the motor cortex exhibits sensory responses in a variety of modalities including vision and somatosensation. We review current work that emphasizes the heterogeneity in sensorimotor responses in the motor cortex and focus on its implications for cortical control of movement as well as for brain-machine interface development.

Bs News November/December

Building Services Engineering

No abstract provided.

Neutron Imaging And Applications: A Reference For The Imaging Community, Edmund Perfect, Chu-Lin Cheng, Peter Lehmann

Civil Engineering Faculty Publications

No abstract provided.

A Test Method For Optimal Micro-Screen Drum Filter Selection, Eoin Dolan, Ronan Oliver, Niall Murphy, Michael O'Hehir

Other resources

In order to meet increasing demand for seafood worldwide Recirculation Aquaculture Systems (RAS) are frequently used. These systems are susceptible to contamination by waste matter including faecal material in the water. It is imperative that this material is removed from the system. The maintenance of good water quality is a pre-requisite to the success of the operation. Negligence in this area will adversely affect animal growth rates and also the economic performance of the system.

Micro-screen drum filters are a popular solution for the removal of this material (Cripps, Simon J. and Bergheim, Asbjørn., 2000). These screens are nominally rated …

Combined Fluorescence And Reflectance Spectroscopy For In Vivo Quantification Of Cancer Biomarkers In Low- And High-Grade Glioma Surgery, Pablo A. ValdéS, Anthony Kim, Keith D. Paulsen, Frederic Leblond, Olga M. Conde, Brent T. Harris, David W. Roberts

Dartmouth Scholarship

Biomarkers are indicators of biological processes and hold promise for the diagnosis and treatment of disease. Gliomas represent a heterogeneous group of brain tumors with marked intra- and inter-tumor variability. The extent of surgical resection is a significant factor influencing post-surgical recurrence and prognosis. Here, we used fluorescence and reflectance spectral signatures for in vivo quantification of multiple biomarkers during glioma surgery, with fluorescence contrast provided by exogenously-induced protoporphyrin IX (PpIX) following administration of 5-aminolevulinic acid. We performed light-transport modeling to quantify multiple biomarkers indicative of tumor biological processes, including the local concentration of PpIX and associated photoproducts, total hemoglobin …

History Of The Biological Systems Engineering Program In Nebraska, University Of Nebraska-Lincoln, William E. Splinter

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The Farm Machinery/Agricultural Engineering/Biological Systems Engineering program current and former faculty members at the University of Nebraska, as demonstrated here, has made a statewide, national, and worldwide impact on the efficient production of food. The quality of this recognition is evidenced best by peer professionals through recognized ASABE awards received by Nebraska alumni or professors. Since its inception in 1909 and until 2010, there have been 10 national presidents, 19 gold medal recipients and 33 named national award recipients. Currently there are 31 ASABE Fellows and two members of the National Academy of Engineering. This national recognition comes as a …

Transient Response Of Long Bubbles In Volatile Organic Compounds, Cheng-Hsing Hsu, Ching-Chuan Chang, Chia-Chuan Kuo, Kuang-Yuan Kung

Journal of Marine Science and Technology–Taiwan

A mass flow controller (MFC) was used to control the injection gas amount into volatile organic compounds (VOCs), each having a different evaporation rate, within straight tubes. As the moving velocities of the air bubbles within the straight tube had changed, a specific transient response occurred. The transient shape was a mushroom bubbles. From the experiment results, as the evaporation rate of VOCs ≧ 1, mushroom bubbles occur as the Reynolds number (Re) of the moving air bubbles reach a certain region. Moreover, the shapes mushroom bubbles were more apparent when volatility of the solvent was higher. As VOCs evaporation …

A Reversibility Analysis Of Encoding Methods For Spiking Neural Networks, Catherine Johnson, S. Roychowdhury, Ganesh K. Venayagamoorthy

Mining Engineering Faculty Research & Creative Works

There is much excitement surrounding the idea of using spiking neural networks (SNNs) as the next generation of function-approximating neural networks. However, with the unique mechanism of communication (neural spikes) between neurons comes the challenge of transferring real-world data into the network to process. Many different encoding methods have been developed for SNNs, most temporal and some spatial. This paper analyzes three of them (Poisson rate encoding, Gaussian receptor fields, and a dual-neuron n-bit representation) and tests to see if the information is fully transformed into the spiking patterns. an oft-neglected consideration in encoding for SNNs is whether or not …

Fabrication Of Size-Tunable Metallic Nanoparticles Using Plasmid Dna As A Biomolecular Reactor, Jacopo Samson, Irene Piscopo, Alex Yampolski, Patrick Nahirney, Andrea Parpas, Amit Aggarwal, Raihan Saleh, Charles Michael Drain

Publications and Research

Plasmid DNA can be used as a template to yield gold, palladium, silver, and chromium nanoparticles of different sizes based on variations in incubation time at 70 °C with gold phosphine complexes, with the acetates of silver or palladium, or chromium acetylacetonate. The employment of mild synthetic conditions, minimal procedural steps, and aqueous solvents makes this method environmentally greener and ensures general feasibility. The use of plasmids exploits the capabilities of the biotechnology industry as a source of nanoreactor materials.

Selecting Ports And Terminal Operators - An Application Of Pso, Tzay-An Shiau, Li-Mei Lin, Ding-Hsun Hsiao

Journal of Marine Science and Technology–Taiwan

Past literature has mostly discussed port selection. However, within a given region, any port which meets a carrier’s threshold conditions is eligible for consideration, and a terminal operator at any of these ports is a candidate for entering into a contract with the carrier. The choice is not restricted to terminal operators at a single given port. Thus the choice of terminal operator between ports within a given region is an important issue in the decision-making process and has rarely been addressed in the literature. The main purpose of this paper is to examine a situation in which all ports …

Quantifying Mass Sediment Movement In Deer Creek Reservoir During Spring Runoff And Potential Water Quality Impacts, Colin Rodger Ricks

Theses and Dissertations

The accurate prediction of water quality is essential for management of reservoirs used for drinking water supply. Since algae are a major source of taste and odor problems in drinking water, understanding and controlling algal growth and production is an important task. Deer Creek Reservoir supplies drinking water for over one million people in northern Utah and has been highly eutrophic in the past. Despite major reductions in external nutrient loading, including phosphorus, seasonal algal blooms in Deer Creek have not decreased to desired levels. Resuspension of sediment has been suggested as a potential source of internal nutrient loading for …

Enhanced Valence Force Field Model For The Lattice Properties Of Gallium Arsenide, Sebastian Steiger, Mehdi Salmani-Jelodar, Denis Areshkin, Abhijeet Paul, Tillmann Kubis, Michael Povolotskyi, Hong-Hyun Park, Gerhard Klimeck

Birck and NCN Publications

An enhanced valence force field model for zinc-blende crystals is developed to provide a unified description of the isothermal static and dynamical lattice properties of gallium arsenide. The expression for the lattice energy includes a second-nearest-neighbor coplanar interaction term, the Coulomb interaction between partially charged ions, and anharmonicity corrections. General relations are derived between the microscopic force constants and the macroscopic elastic constants in zinc-blende crystals. Applying the model to gallium arsenide, parameter sets are presented that yield quantitative agreement with experimental results for the phonon dispersion, elastic constants, sound velocities, and Gru ̈neisen mode parameters.

Design, Fabrication, And Implementation Of A Wireless, Passive Implantable Pressure Sensor Based On Magnetic Higher-Order Harmonic Fields, Ee Lim Tan, Andrew Derouin, Brandon D. Pereles, Keat Ghee Ong

Michigan Tech Publications, Part 1

A passive and wireless sensor was developed for monitoring pressure in vivo. Structurally, the pressure sensor, referred to as the magneto-harmonic pressure sensor, is an airtight chamber sealed with an elastic pressure membrane. A strip of magnetically-soft material is attached to the bottom of the chamber and a permanent magnet strip is embedded inside the membrane. Under the excitation of an externally applied AC magnetic field, the magnetically-soft strip produces a higher-order magnetic signature that can be remotely detected with an external receiving coil. As ambient pressure varies, the pressure membrane deflects, altering the separation distance between the magnetically-soft strip …