Digital Commons Network^™

The Transcriptome Of Human Oocytes, Arif Murat Kocabas, Javier Crosby, Pablo J. Ross, Hasan H. Otu, Zeki Beyhan, Handan Can, Wai-Leong Tam, Guilherme J. M. Rosa, Robert G. Halgren, Bing Lim, Emilio Fernandez, Jose Bernardo Cibelli

Department of Electrical and Computer Engineering: Faculty Publications

The identification of genes and deduced pathways from the mature human oocyte can help us better understand oogenesis, folliculogenesis, fertilization, and embryonic development. Human metaphase II oocytes were used within minutes after removal from the ovary, and its transcriptome was compared with a reference sample consisting of a mixture of total RNA from 10 different normal human tissues not including the ovary. RNA amplification was performed by using a unique protocol. Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays were used for hybridizations. Compared with reference samples, there were 5,331 transcripts significantly up-regulated and 7,074 transcripts significantly down-regulated in the …

Biological Opinion On The Operation Of The Missouri River Main Stem System, Missouri River Bank Stabilization And Navigation Project, And Operation Of The Kansas River Reservoir System

United States Army Corps of Engineers, Omaha District

The U.S. Army Corps of Engineers (Corps) prepares an annual report for interested parties in accordance with the reporting requirements of the “Biological Opinion (BiOp) on the Operation of the Missouri River Main Stem System, Operation and Maintenance of the Missouri River Bank Stabilization and Navigation Project (BSNP), and Operation of the Kansas River Reservoir System” prepared by the U.S. Fish and Wildlife Service (Service) dated November 30, 2000 and the Amendment, thereto, dated December 16, 2003.

This annual report documents the Corps threatened and endangered species conservation activities to comply with the provisions of the 2000 BiOp and the …

Missouri River Mainstem Reservoir System Master Water Control Manual Missouri River Basin

United States Army Corps of Engineers, Omaha District

In 2003, the United States Fish and Wildlife Service (USFWS) issued an Amended Biological Opinion (2003 Amended BiOp) on the United States Army Corps of Engineers’ (Corps’) Missouri River System operations. Among other actions, the 2003 Amended BiOp called for bimodal spring pulse releases from Gavins Point Dam for the benefit of the listed pallid sturgeon. Working with the USFWS, Tribes, states, and other basin stakeholders, the Corps has developed technical criteria for the bimodal spring pulse releases which, under the terms of the 2003 Amended BiOp, are to be implemented by March 2006. By my approval of the attached …

Modeling, Analysis, And Experimental Study Of In Vivo Wheeled Robotic Mobility, Mark E. Rentschler, Jason Dumpert, Stephen R. Platt, Karl Iagnemma, Dmitry Oleynikov, Shane M. Farritor

Department of Mechanical and Materials Engineering: Faculty Publications

Laparoscopy is abdominal surgery performed with long tools inserted through small incisions. The use of small incisions reduces patient trauma, but also eliminates the surgeon’s ability to view and touch the surgical environment directly. These limitations generally restrict the application of laparoscopy to procedures less complex than those performed during open surgery. This paper presents a theoretical and experimental analysis of miniature, wheeled, in vivo robots to support laparoscopy. The objective is to develop a wireless mobile imaging robot that can be placed inside the abdominal cavity during surgery. Such robots will allow the surgeon to view the surgical environment …

Circular Ultrasound Compounding By Designed Matrix Weighting, Gregory Bashford, Jonathan Morse

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Spatial compounding is an imaging technique that aims to improve image contrast by combining partially decorrelated images acquired at different angles or positions. In conventional spatial compounding, data sets are combined with equal weighting. Here, we describe an alternative method of reconstruction using algorithms which weight the data based on a “quality” matrix. The quality matrix is derived from beam-forming characteristics. For each data set, the reliability of the data is assumed to vary spatially. By compounding the data based on the quality matrix, a complete image is formed. Here, we describe the construction of a rotational translation stage and …

Variable Upper And Lower Crop Water Stress Index Baselines For Corn And Soybean, J. O. Payero, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Upper and lower crop water stress index (CWSI) baselines adaptable to different environments and times of day are needed to facilitate irrigation scheduling with infrared thermometers. The objective of this study was to develop dynamic upper and lower CWSI baselines for corn and soybean. Ten-minute averages of canopy temperatures from corn and soybean plots at four levels of soil water depletion were measured at North Platte, Nebraska, during the 2004 growing season. Other variables such as solar radiation (R_s), air temperature (T_a), relative humidity (RH), wind speed (u), and plant canopy height (h) were …

Use Of Time Domain Reflectometry For Continuous Monitoring Of Nitrate-Nitrogen In Soil And Water, J. O. Payero, David D. Tarkalson, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Nitrate-Nitrogen (NO₃-N) losses to ground and surface water are an environmental and agronomic concern in modern crop production systems in the Central Great Plains. Monitoring techniques for nitrogen use in agricultural production are needed to increase crop yield, optimize nitrogen use, and reduce NO₃-N leaching. Time domain reflectometry (TDR) could potentially be calibrated to continuously measure NO₃-N in soil and water. The objectives of this study were to: (1) evaluate the effect of different factors affecting the response of the bulk electrical conductivity (ECb) sensed by TDR, (2) compare the sensitivity and differences between …

Land Application Of Manure For Beneficial Reuse, L. M. Risse, M. L. Cabrera, A. J. Franzluebbers, J. W. Gaskin, John E. Gilley, R. Killorn, D. E. Radcliffe, W. E. Tollner, H. Zhang

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The concentration of animal production systems has increased efficiency and improved overall economic return for animal producers. This concentration, along with the advent of commercial fertilizers, has led to a change in the way animal producers view manure. Manure, once valued as a resource by farmers, is now treated as a waste. Air and water quality concerns that arise primarily from the under-utilization or inefficient use of manure contribute to these changing views. However, when properly used, manure is a resource and should be regulated as such. In the United States, the USDA/EPA Unified National Strategy for Animal Feeding Operations …

Properties Of Chitosan Films As A Function Of Ph And Solvent Type, Ki Myong Kim, Jeong Hwa Son, Sung-Koo Kim, Curtis L. Weller, Milford Hanna

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Two different deacetylated chitosans were dissolved in formic, acetic, lactic, or propionic acid to prepare chitosan films. The pH values of the film-forming solutions were adjusted to 3, 4, and 5. Water vapor permeability (WVP), tensile strength (TS), elongation (E), and total soluble matter (TSM) were significantly (P < 0.05) affected by acid type, pH, and degree of deacetylation (DA). Low DA (LDA) chitosan films had lower WVP and TSM, higher TS compared with high DA (HDA) chitosan films. The E values were not affected by DA. As pH increased, WVP and TSM of chitosan films tended to increase while TS decreased significantly (P < 0.05). Chitosan films with acetic and propionic acid solvents had low WVP and TSM and high TS, while films with lactic acid solvent had high E and TSM and the lowest TS. Fourier-transform infrared showed peak shifting in the spectra with different solvents and at different pH values. Chitosan films with lactic acid solvent showed a peak shift to a lower frequency range. The NH3+ band was absent in the pH 5.0 chitosan film spectra.

Modeling Of Transport Phenomena And Melting Kinetics Of Starch In A Co-Rotating Twin-Screw Extruder, Lijun Wang, David D. Jones, Curtis L. Weller, Milford Hanna

Department of Agricultural and Biological Systems Engineering: Faculty Publications

A mathematical model was developed to simulate fluid flow, heat transfer, and melting kinetics of starch in a co-rotating intermeshing twin-screw extruder (TSE). The partial differential equations governing the transport phenomena of the biomaterial in the extruder were solved by a finite element scheme. For validating the model, the predicted product pressure, bulk temperature at the entrance of the die, and minimum residence time of the biomaterial in the extruder were compared with experimental data. Standard errors of product pressure, bulk temperature at the die entrance, and minimum residence time were about 8.8, 2.8, and 17.3%. Simulations were carried out …

Impact Of Tillage And Placement Of Terbufos Insecticide Runoff, Mitiku Mamo, William L. Kranz, Elaine R. Douskey, Shripat T. Kamble, John F. Witkowski

Department of Agricultural and Biological Systems Engineering: Faculty Publications

On a national scale, the damage caused by corn rootworm (Diabrotica virgifera virgifera LeConte), can cause economic loss of up to $650 million annually. To limit these losses, corn producers apply terbufos insecticide to approximately 11% of all corn acres at a time when there is a high probability of intense precipitation. When combined with low vegetative cover and disturbed soil surfaces, there is a high potential for terbufos transport into surface water bodies. Increased public concern for environmental contamination from the use of agricultural chemicals has prompted many crop growers to look for crop production practices that minimize …

Nonintrusive Mapping Of Near-Surface Preferential Flow, R. S. Freeland, Lameck O. Odhiambo, J. S. Tyner, J. T. Ammons, W. C. Wright

Department of Agricultural and Biological Systems Engineering: Faculty Publications

A unique survey protocol has been developed that maps near-subsurface preferential flow using integrated ground-penetrating radar (GPR) and a differential geographical positioning system (DGPS). The survey protocol consists of a mobile GPR system that spirals outward along a prescribed course, continuously gathering subsurface data for an extended period. Metered water is applied to a centrally located water-ponding ring, after first capturing the initial dry-state pattern signatures. The water radiates outward beneath the surface as it follows preferential flow pathways, which the GPR instrumentation spiraling above highlights. After data are collected, pre- and post-water time-elapsed images profiles are segmented by pattern …

Purification And Scale-Up Of A Recombinant Heavy Chain Fragment C Of Botulinum Neurotoxin Serotype E In Pichia Pastoris Gs115, Michael P. Dux, Rick Barent, Jayanta Sinha, Mark Gouthro, Todd Swanson, Ardis Barthuli, Mehmet Inan, John T. Ross, Leonard A. Smith, Theresa J. Smith, Robert Webb, Bonnie Loveless, Ian Henderson, Michael M. Meagher

Michael Meagher Publications

A recombinant C-terminus heavy chain fragment from botulinum neurotoxin serotype E (BoNT/E) is proposed as a vaccine against the serotype E neurotoxin. This fragment, rBoNTE(H_c), was produced intracellular in Pichia pastoris GS115 by a three-step fermentation process, i.e., glycerol batch phase and a glycerol fed-batch phase to achieve high cell densities, followed by a methanol fed-batch induction phase. The rBoNTE(H_c) protein was purified from the soluble fraction of cell lysates using three ion-exchange chromatography steps (SP Sepharose Fast Flow, Q Sepharose Fast Flow, Sp Sepharose High Performance) and polished with a hydrophobic charge induction chromatography step …

Dissolution Kinetics Of High Explosives Particles In A Saturated Sandy Soil, Matthew C. Morley, Hiroshi Yamamoto, Gerald E. Speitel, Jr., Jay Clausen

Department of Civil and Environmental Engineering: Faculty Publications

Solid phase high explosive (HE) residues from munitions detonation may be a persistent source of soil and groundwater contamination at military training ranges. Saturated soil column tests were conducted to observe the dissolution behavior of individual components (RDX, HMX, and TNT) from two HE formulations (Comp B and C4). HE particles dissolved readily, with higher velocities yielding higher dissolution rates, higher mass transfer coefficients, and lower effluent concentrations. Effluent concentrations were below solubility limits for all components at superficial velocities of 10–50 cm day^-1. Under continuous flow at 50 cm day^-1, RDX dissolution rates from Comp …

An Experimental Investigation Of Guided Wave Propagation In Corrugated Plates Showing Stop Bands And Pass Bands, Tribikram Kundu, Sourav Banerjee, Kumar V. Jata

Faculty Publications

Nonplanar surfaces are often encountered in engineering structures. In aerospace structures, periodically corrugated boundaries are formed by friction-stir-welding. In civil engineering structures, rebars used in reinforced concrete beams and slabs have periodic surface. Periodic structures are also being used to create desired acoustic band gaps. For health monitoring of these structures, a good understanding of the elastic wave propagation through such periodic structures is necessary. Although a number of research papers on the wave propagation in periodic structures are available in the literature, no one experimentally investigated the guided wave propagation through plates with periodic boundaries and compared the experimental …

Elastic Wave Propagation In Sinusoidally Corrugated Waveguides, Sourav Banerjee, Tribikram Kundu

Faculty Publications

The ultrasonicwave propagation in sinusoidally corrugated waveguides is studied in this paper. Periodically corrugated waveguides are gaining popularity in the field of vibration control and for designing structures with desired acoustic band gaps. Currently only numerical method (Boundary Element Method or Finite Element Method) based packages (e.g., PZFlex) are in principle capable of modeling ultrasonic fields in complex structures with rapid change of curvatures at the interfaces and boundaries but no analyses have been reported. However, the packages are very CPU intensive; it requires a huge amount of computation memory and time for its execution. In this paper a new …

A Mathematical Model For The Validation Of Safe Air-Blast Chilling Of Cooked Hams, L. J. Wang, A Amézquita, Curtis L. Weller

Department of Agricultural and Biological Systems Engineering: Faculty Publications

An integrated mathematical model of heat transfer and temperature-dependent bacterial growth was developed to validate the safety of cooked hams during air-blast chilling. Heat transfer through a cooked ham was mathematically modeled and analyzed with a finite element method. Response of bacteria to temperatures was quantitatively described using predictive microbiology. The cumulative effect of temperature history on the bacterial growth was taken into account in the model. For chilling cooked hams from 71°C to 10°C, the maximum error between the predicted and experimental core temperature was within 2.2°C, and the deviation between the predicted and measured total weight losses was …

Hydrodynamics And Morphology In The Ems/Dollard Estuary: Review Of Models, Measurements, Scientific Literature, And The Effects Of Changing Conditions, Stefan A. Talke, Huib E. De Swart

Civil and Environmental Engineering Faculty Publications and Presentations

The Ems estuary has constantly changed over the past centuries both from man-made and natural influences. On the time scale of thousands of years, sea level rise has created the estuary and dynamically changed its boundaries. More recently, storm surges created the Dollard sub-basin in the 14th -15th centuries. Beginning in the 16th century, diking and reclamation of land has greatly altered the surface area of the Ems estuary, particularly in the Dollard. These natural and anthropogenic changes to the surface area of the Ems altered the flow patterns of water, the tidal characteristics, and the patterns of sediment deposition …

Fabrication Of Array Microstructures By Localized Electro-Deposition, Nidal Khalaf Alshwawreh

Theses

Localized Electro-Deposition (LED) is now highly receiving scientists and researchers attention for its advantages over conventional fabrication techniques. These advantages include simplicity of the setup thus reducing the overall fabrication cost, capability of producing 2D and 3D high aspect ratio microstructures and its ability to fabricate microstructures from various raw materials. Efforts now are taking place in order to standardize the fabrication by LED to develop a commercial setup that is capable of producing complex microstructures which, in tum, can be integrated in different applications including microelectronics, microelectrochemical systems (MEMS) and sensors applications. The standardization process is performed by studying …

Composting Of Biodegradable Municipal Waste In Ireland, Niamh Power, Jerry D. Murphy

Publications

The implementation of the Landfill Directive (96/31/EC) will lead to a massive reduction in quantities of Biodegradable Municipal Waste (BMW), which may be landfilled. In 2016, an estimated 2.6 million tonnes of BMW will require diversion from landfill in Ireland. Recycling of dry paper, reuse of textiles and home composting will divert significant quantities of BMW. However, to divert the quantities required to comply with the Directive a significant proportion of the Organic Fraction of Municipal Solid Waste (OFMSW) will require treatment in centralised biological facilities. A survey was undertaken of composting facilities in Ireland to ascertain present capacity, present …

Corrosion Mechanisms And Kinetics Of Steels In Lead-Bismuth Eutectic: Quaterly Report, Allen L. Johnson, John Farley

Transmutation Sciences Materials (TRP)

A large number of studies of corroded samples were conducted using SEM, XPS, probe, and the TEM. Samples from the DELTA loop at LANL and from other sources were examined. Also, the investigation of 316 class stainless steel in LBE is continuing.

Corroded samples of D-9 steel have been in the process of being studies, which is a variant of 316 stainless steel that is optimized for resistance to swelling. The D-9 samples are notable for the process in which a localized failure of the protective oxide layer becomes widespread corrosion. The research group is examining the D-9 samples using …

Cross Chip Probe Matching Tool: A Tool For Linking Probes From Microarrays Within And Across Species, Ruchi Ghanekar

All ETDs from UAB

raditionally, but not exclusively, a microarray experiment is conducted on a single type of microarray. However, different labs often use different chip types, and new versions of chips may be developed. Comparing experiments can be problematic in such cases, as it is not always clear which probe sets correspond to the same gene across experiments. The goal of this research was to develop a tool that allows investigators to identify probe sets that correspond to the gene within and across species. The Cross Chip Probe Matching Tool (CCPMT) makes use of the probe sequences for all features on arrays from …

Interactions Between Trains Of Premature Stimuli And Anatomically Anchored Reentrant Wavefronts: Implications For Antitachycardia Pacing, Israel A. Byrd

All ETDs from UAB

Implantable cardioverter defibrillators can terminate accelerated heart rhythms with either high energy shocks or antitachycardia pacing. Shocks are highly effective, but they reduce the quality of life in patients that receive them. Antitachycardia pacing is a train of pulses administered at a rate slightly faster than the arrhythmia rate. These pulses are low energy, and terminate ventricular tachycardia in patients without causing pain. The paced wavefronts penetrate the reentrant circuit, and interact with the underlying reentrant wavefront to block all arrhythmic activity. Currently, these interactions between paced wavefronts and reentrant wavefronts are not well understood. A better understanding of these …

Double-Matching In Anti-Correlated Random Dot Stereograms Of Panum's Limiting Case Reveals The Interactions Among The Elementary Disparity Signals Across Scale, Hwan Sean Lee

All ETDs from UAB

A fundamental problem in binocular vision is to understand the rules that govern matching of features in the two eyes. We adopted Panum’s limiting case (PLC) into random-dot stereograms (RDS) to determine whether our visual system permits non-unique binocular matching for stereopsis. Using PLC RDS, we found that i.) the PLC-defined depth was compatible with the disparity-defined depth, which suggests that our visual system detects the relative disparity in PLC; ii.) the upper depth limits discriminating the PLC-defined surfaces and disparity-defined surfaces were almost identical, which suggests that there is a common mechanism – correlation-based stereopsis – responsible for the …

Development And Modeling Of Thermally Conductive Resins For Fuel Cell Bipolar Plate Applications, Michael G. Miller

Dissertations, Master's Theses and Master's Reports - Open

Thermally conductive resins are a class of material that show promise in many different applications. One growing field for their use is in the area of bipolar plate technology for fuel cell applications. In this work, a LCP was mixed with different types of carbon fillers to determine the effects of the individual carbon fillers on the thermal conductivity of the composite resin. In addition, mathematical modeling was performed on the thermal conductivity data with the goal of developing predictive models for the thermal conductivity of highly filled composite resins.

Fluidic Oscillator Design For Water Removal Enhancement In A Pem Fuel Cell, Sheng Han Tseng

Dissertations, Master's Theses and Master's Reports - Open

This research initiative was triggered by the problems of water management of Polymer Electrolyte Membrane Fuel Cell (PEMFC). In low temperature fuel cells such as PEMFC, some of the water produced after the chemical reaction remains in its liquid state. Excess water produced by the fuel cell must be removed from the system to avoid flooding of the gas diffusion layers (GDL). The GDL is responsible for the transport of reactant gas to the active sites and remove the water produced from the sites. If the GDL is flooded, the supply gas will not be able to reach the reactive …

Secure Digital Communication Using Chaotic Symbolic Dynamics, Ajeesh P. Kurian, Sadasivan Puthusserypady

Turkish Journal of Electrical Engineering and Computer Sciences

One of the major hurdles in implementing chaotic communication schemes is the synchronization of chaotic systems. For the last two decades, numerous contributions of varying successes have been made by researchers from different disciplines for the synchronization of chaotic systems. Symbolic dynamics based synchronization method is shown to be capable of providing high quality synchronization (HQS), which is essential for reliable communication. In this work, using this method, a secure digital communication system is proposed. The well known piece-wise linear 1-D map such as tent map and Bernoulli shift map are used for this study. Since the information is dynamically …

Stem Cells, Tgf-Ss, And The Adenoviral Mediated Overexpression Of Fibromodulin To Promo Te Incisional Wound Healing, Steven T. Moore

All ETDs from UAB

Incision wounds are a clinical problem due to insufficient strength with cosmeti-cally and functionally unacceptable scarring. The primary goals of therapy are increasing the rate of tissue repair and reducing scar stiffness. Assessment of the wounds is neces-sary to determine the state of the tissue in terms of strength, stiffness, and function as well as to compare the efficacy of various treatments and therapies. Mechanical testing can reveal both the speed in which a wound is healing in addition to the amount of scar-ring that is present in a wound. Presently, mesenchymal stem cells have shown potential to heal injured …

Impacts Of The 2004 Tsunami On Groundwater In Sri Lanka, T. Illangasekare, S. W. Tyler, T. P. Clement, K. G. Villholth, A. P.G.R.L. Perera, J. Obeysekera, A. Gunatilaka, C. R. Panabokke, D. W. Hyndman, K. J. Cunningham, W-G. Yeh, Jagath J. Kaluarachchi, M-Rien Van Genuchten, K. Jensen

Civil and Environmental Engineering Faculty Publications

The 26 December 2004 tsunami caused widespread destruction and contamination of coastal aquifers across southern Asia. Seawater filled domestic open dug wells and also entered the aquifers via direct infiltration during the first flooding waves and later as ponded seawater infiltrated through the permeable sands that are typical of coastal aquifers. In Sri Lanka alone, it is estimated that over 40,000 drinking water wells were either destroyed or contaminated. From February through September 2005, a team of United States, Sri Lankan, and Danish water resource scientists and engineers surveyed the coastal groundwater resources of Sri Lanka to develop an understanding …

Selective Growth Of Carbon Nanotubes And Oxide Nanowires: Applications In Shadow Lithography And Fabrication Of Aligned Carbon Nanotube Membranes, Nitin Chopra

University of Kentucky Doctoral Dissertations

A promising approach investigated here is to utilize thin film multilayer structures where the thickness of a catalyst layer at an exposed edge of photolithographically defined pattern determines the diameter of the nanotubes/nanowires grown from it. This can in turn be incorporated into photolithographically defined post structures resulting in an array of suspended nanowires for line-of-site shadow lithography. Success of the diameter control approach has been shown by selectively growing carbon nanotubes (CNTs) from narrow lines (12-60 nm) of SiO₂, Fe, Ni, Co on micron-scale patterned substrates in a ferrocene or nonferrocene catalyzed CVD process. In addition, the …