Engineering Commons^™

Mutations Of Adjacent Amino Acid Pairs Are Not Always Independent, Jyotsna Ramanan, Peter Revesz

School of Computing: Conference and Workshop Papers

Evolutionary studies usually assume that the genetic mutations are independent of each other. This paper tests the independence hypothesis for genetic mutations with regard to protein coding regions. According to the new experimental results the independence assumption generally holds, but there are certain exceptions. In particular, the coding regions that represent two adjacent amino acids seem to change in ways that sometimes deviate significantly from the expected theoretical probability under the independence assumption.

The Contribution Of Syntrophic Fatty-Acid Degrading Microbial Communities To Anaerobic Digester Function And Stability, Prince Peter Mathai

Dissertations (1934 -)

Anaerobic digestion (AD), the conversion of complex organic matter to methane, occurs through a series of reactions mediated by different guilds of microorganisms. AD process imbalances, such as organic overload or high organic loading rates (OLR), can result in the accumulation of volatile fatty acids (VFA) e.g., propionate, which must be degraded to maintain stable reactor function. VFAs are metabolized by syntrophic fatty-acid degrading bacteria (SFAB) in association with methanogenic archaea (collectively, syntrophic microbial communities, SMC). Despite their indispensable role in AD, little is known about the ecology of SFAB, especially under stressed conditions. To facilitate ecological studies, four quantitative …

Heterogeneous Oxidation Of Catechol, Elizabeth A. Pillar, Ruixin Zhou, Marcelo I. Guzman

Chemistry Faculty Publications

Natural and anthropogenic emissions of aromatic hydrocarbons from biomass burning, agro-industrial settings, and fossil fuel combustion contribute precursors to secondary aerosol formation (SOA). How these compounds are processed under humid tropospheric conditions is the focus of current attention to understand their environmental fate. This work shows how catechol thin films, a model for oxygenated aromatic hydrocarbons present in biomass burning and combustion aerosols, undergo heterogeneous oxidation at the air–solid interface under variable relative humidity (RH = 0–90%). The maximum reactive uptake coefficient of O₃(g) by catechol γ_O3 = (7.49 ± 0.35) × 10^–6 occurs for …

A Machine Learning Approach To Post-Market Surveillance Of Medical Devices, Jonathan Bates, Shu-Xia Li, Craig Parzynski, Ronald Coifman, Harlan Krumholz, Joseph Ross

Yale Day of Data

Post-market surveillance is a collection of processes and activities used by product manufacturers and regulators, such as the U.S. Food and Drug Administration (FDA) to monitor the safety and effectiveness of medical devices once they are available for use “on the market”. These activities are designed to generate information to identify poorly performing devices and other safety problems, accurately characterize real-world device performance and clinical outcomes, and facilitate the development of new devices, or new uses for existing devices. Typically, a device is monitored by comparing adverse events in the exposed population to a matched unexposed population. This research considers …

Lessons For Life, Story Musgrave

The Transdisciplinary STEAM+ Journal

This piece explores the creation of character and talent through a wide diversity of education and experience.

Ecoscience + Art Initiative: Designing A New Paradigm For College Education, Scholarship, And Service, Changwoo Ahn

The Transdisciplinary STEAM+ Journal

The paper presents a new initiative, EcoScience + Art, which blooms at George Mason University. The creator explains the background, history, and recent activities of the initiative, and also introduces an on-going special project called “The Rain Project”, a student participatory project to design, construct, and monitor a green infrastructure (i.e., floating wetland) for sustainable stormwater management on campus. The special project is geared to design and present a new paradigm to integrate college education, scholarship, and service. The relevance of the initiative and the special project to STEAM education is discussed.

Beer And Brewing In German Culture: Bridging The Gaps Within Steam, John D. Sundquist

The Transdisciplinary STEAM+ Journal

A university-level course on science, history, and culture of beer and brewing offers students from a wide range of disciplines a unique opportunity to learn from each other. They gain an appreciation for STEAM and the interaction of a number of disciplines while examining a subject of growing interest. This paper provides a brief description of such a course and includes specific examples of ways in which students explore science, engineering, humanities and the arts, as these areas of research come together in the study of beer and brewing.

Investigation Of Bovine Serum Albumin (Bsa) Attachment Onto Self-Assembled Monolayers (Sams) Using Combinatorial Quartz Crystal Microbalance With Dissipation (Qcm-D) And Spectroscopic Ellipsometry (Se), Hanh T.M. Phan, Shannon L. Bartelt-Hunt, Keith B. Rodenhausen, Mathias Schubert, Jason C. Bartz

Department of Civil and Environmental Engineering: Faculty Publications

Understanding protein adsorption kinetics to surfaces is of importance for various environmental and biomedical applications. Adsorption of bovine serum albumin to various selfassembled monolayer surfaces including neutral and charged hydrophilic and hydrophobic surfaces was investigated using in-situ combinatorial quartz crystal microbalance with dissipation and spectroscopic ellipsometry. Adsorption of bovine serum albumin varied as a function of surface properties, bovine serum albumin concentration and pH value. Charged surfaces exhibited a greater quantity of bovine serum albumin adsorption, a larger bovine serum albumin layer thickness, and increased density of bovine serum albumin protein compared to neutral surfaces at neutral pH value. The …

Thermodynamic Analysis Of Phenylpropanoid Pathway In Arabidopsis Thanliana, Patrick J. Ioerger, Rohit Jaini, John A. Morgan

The Summer Undergraduate Research Fellowship (SURF) Symposium

Biofuels represent a renewable alternative to traditional fossil fuels. As dependence on fossil fuels rise so does the importance of improving the production of alternative fuels. Lignin poses one obstacle in the development of such alternative fuels. Its presence strengthens cell walls and hinders degradation of polysaccharides into monosaccharides, increasing cost and time while decreasing efficiency of the process. Lignin is composed of three monolignols, each of which is produced through the Phenylpropanoid pathway; a series of chemical reactions. This work aims to determine which reactions in the pathway are least thermodynamically favorable and thus most limiting. From metabolic mapping …

Long-Term Tillage System Impacts On Soil Erodibility, Julianne R. Chechanover, Dennis C. Flanagan

The Summer Undergraduate Research Fellowship (SURF) Symposium

Conservation tillage practices, such as no-till agriculture, have the potential of reducing the erodibility of a soil compared to conventional agricultural practices. This research sought to determine whether long-term agricultural practices affect the baseline erodibility properties of a soil. Two soils from Throckmorton-Purdue Agricultural Center in Tippecanoe County, Indiana were used during this experiment. One soil was treated with a long-term conventional tillage (fall chisel, spring disk) system and the other soil was treated with a long-term no-till system. The soils’ interrill erodibility, and rill erodibility and critical hydraulic shear stress were measured under a rainfall simulator using soil boxes …

Visualization And Analysis Of Sensory Data, Luke Neumann, Sung Yeon Choi, Brian Olsen, Sungahn Ko, David Ebert Dr.

The Summer Undergraduate Research Fellowship (SURF) Symposium

Recently, California has suffered a severe drought, making water a scarce resource to its population. Many viticulturists are based in this area who rely on heavy irrigation to produce a better grape and a better wine. Not just in California, but throughout the nation, irrigation must be applied intelligently for efficient use of water and funding. By taking measurements of physical characteristics of a vineyard over time, one may be able to visualize trends in the data which lend itself to describing preferred growing methods. Wireless sensors can be used to take measurements including moisture, temperature, sunlight, and more. Sensors …

A Novel Synthetic Yeast For Enzymatic Biodigester Pretreatment, Tianyu Tan, Mark S. Aronson, Arren Liu, Jill H. Osterhus, Melissa Robins, Suraj Mohan, Erich Leazer, Bowman Clark, Alexa Petrucciani, Katherine Lowery, James Welch, Casey Martin, Helena Lysandrou, Michael E. Scharf, Jenna Rickus

The Summer Undergraduate Research Fellowship (SURF) Symposium

Lignin, a complex organic polymer, is a major roadblock to the efficiency of biofuel conversion as it both physically blocks carbohydrate substrates and poisons biomass degrading enzymes, even if broken down to monomer units. A pretreatment process is often applied to separate the lignin from biomass prior to biofuel conversion. However, contemporary methods of pretreatment require large amounts of energy, which may be economically uncompelling or unfeasible. Taking inspiration from several genes that have been isolated from termites and fungi which translate to enzymes that degrade lignin, we want to establish a novel “enzymatic pretreatment” system where microbes secrete these …

Viewing The Extracellular Matrix: An Imaging Method For Tissue Engineering, Michael Drakopoulos, Sarah Calve

The Summer Undergraduate Research Fellowship (SURF) Symposium

The field of regenerative medicine seeks to create replacement tissues and organs, both to repair deficiencies in biological function and to treat structural damage caused by injury. Scaffoldings mimicking extracellular matrix (ECM), the structure to which cells attach to form tissues, have been developed from synthetic polymers and also been prepared by decellularizing adult tissue. However, the structure of ECM undergoes significant remodeling during natural tissue repair, suggesting that ECM-replacement constructs that mirror developing tissues may promote better regeneration than those modeled on adult tissues. This work investigated the effectiveness of a method of viewing the extracellular matrix of developing …

Processing Methods And Storage Conditions On Chocolate And Coffee Powder Flow Properties, Sunland L. Gong, Andrea Della Bella, Teresa M. Carvajal

The Summer Undergraduate Research Fellowship (SURF) Symposium

Powders are widely used in a countless number of industries, and are crucial to the quality control of products in areas such as pharmaceuticals and food. Particle physicochemical properties (morphology, solid state – crystalline, amorphous or both) are important factors for powder flow, which in turn can have significant impact on the stability, performance, and presentation of powders. Different processing methods as well as storage conditions such as relative humidity (RH) can drastically affect powder flow. Due to the widespread use of chocolate and coffee powder around the world, and their importance to the food industry, this work investigates two …

Visualization Of The Growth And Production Of Grapes Through Analysis Of Sensory Data, Sung Yeon Choi, Luke Neumann, Brian Olsen, Sungahn Ko, David Ebert Ph.D

The Summer Undergraduate Research Fellowship (SURF) Symposium

Grapes used in the wine industry have been one of the highest value crops in the United States. However, with unpredictable weather changes and recent drought in the Western United States, vineyard owners and grape growers have faced difficulties on producing good quality grapes suited for wine making. Therefore, a technology that would keep record of environmental data and incorporate the data to support agricultural decisions will help the growers to produce quality grapes even in extreme conditions. As such, this research focuses on developing an interactive system that uses sensory data and visual analytics to facilitate vineyard management and …

Optical Emission Spectroscopy Diagnostics Of Cold Plasmas For Food Sterilization, Abhijit Jassem, Michael Lauria, Russell Brayfield Ii, Kevin M. Keener, Allen L. Garner

The Summer Undergraduate Research Fellowship (SURF) Symposium

There is a growing need for economical, effective, and safe methods of sterilizing fresh produce. The most common method is a chlorine wash, which is expensive and may introduce carcinogens. High voltage cold atmospheric pressure plasmas are a promising solution that has demonstrated a germicidal effect; however, the responsible chemical mechanisms and reaction pathways are not fully understood. To elucidate this chemistry, we used optical emission spectroscopy to measure the species produced in the plasma generated by a 60 Hz pulsed dielectric barrier discharge in a plastic box containing various fill gases (He, N₂, CO₂, dry …

Development Of A Novel Enzymatic Pre-Treatment For Lignocellulosic Biomass, Melissa Robins, Jenna Rickus

The Summer Undergraduate Research Fellowship (SURF) Symposium

Biofuels, fuels derived directly from living matter, present a renewable and environmentally friendly alternative to petroleum based fuels. Bioethanol produced from low input energy crops or agricultural waste is a promising fuel source because it does not interfere with the human food supply chain and the ethanol produced can be blended with gasoline. These potential sources of bioethanol are not yet commercially viable due to a polymer called lignin present in the plant’s cell wall which impedes the conversion of cellulose to glucose and the eventual fermentation of glucose to ethanol. Developing new methods for the pretreatment of lignocellulosic biomass …

Spontaneous Synchrony On Graphs And The Emergence Of Order From Disorder, Dylan Linville, Daniel Trugillo Martins Fontes

Rose-Hulman Undergraduate Research Publications

From pulsars to pedestrians and bacteria to brain cells, objects that exhibit cyclical behavior, called oscillators, are found in a variety of different settings. When oscillators adjust their behavior in response to nearby oscillators, they often achieve a state of synchrony, in which they all have the same phase and frequency. Here, we explore the Kuramoto model, a simple and general model which describes oscillators as dynamical systems on a graph and has been used to study synchronization in systems ranging from firefly swarms to the power grid. We discuss analytical and numerical methods used to investigate the governing system …

Designing A Remote Aerial System To Image And Analyze The Health Of Grape Crops At Cal Poly San Luis Obispo, Alexander D. Vice, Dylan Benton, Adipratnia Asmady, Andrew Mercier, Andrew Meyer, Eric Belfield, Aaron Drake

STAR Program Research Presentations

In the last decade the prevalence of unmanned aerial vehicles (UAVs) has exploded; however, the presence of UAVs in research situations is still a relatively new and untested field. The autonomous flight lab (AFL) at Cal Poly San Luis Obispo is a new lab site that is dedicated to using UAVs to benefit research for all backgrounds. Before AFL was able to fly missions we first needed to actually receive our vehicles, create a lab space that would provide all of the necessary resources and equipment necessary to fly, and to be granted permission by the Federal Aviation Administration (FAA) …

A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

With the advent of high-throughput next-generation sequencing (NGS) techniques, the amount of data being generated represents challenges including storage, analysis and transport of huge datasets. One solution to storage and transmission of data is compression using specialized compression algorithms. However, these specialized algorithms suffer from poor scalability with increasing size of the datasets and best available solutions can take hours to compress gigabytes of data. In this paper we introduce paraDSRC, a parallel implementation of DSRC algorithm using a message passing model that presents reduction of the compression time complexity by a factor of O(1/p ). Our experimental results show …

Dietary Strategies For Mitigation Of Methane Production By Growing And Finishing Cattle, Anna C. Pesta

Department of Animal Science: Dissertations, Theses, and Student Research

Interest in reducing methane (CH₄) emissions by cattle has increased recently. Loss of feed energy as CH₄ represents both an environmental concern and an energetic loss to the animal. Manipulation of dietary composition has proven to be an effective mitigation strategy. Experiments were conducted to evaluate the effect of several dietary characteristics on CH₄ production in growing and finishing cattle, and to develop a novel, non-invasive method for quantifying emissions from animals in a production setting. Short-term gaseous emissions of CH₄ and carbon dioxide (CO₂) were measured and the CH₄:CO_{2 …}

Land Use And Water And Soil Management Practices Impacts On Potential Groundwater Recharge In Loess Regions Of South Central Nebraska, Gustavo Bosch-Rubia

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Sustainability of agro-ecosystems must consider land use and water and soil management effects on groundwater recharge. Water flow beneath the plant root zone through the intermediate vadose zone determines potential groundwater recharge. Different land uses, water and soil management practices control deep percolation as a result of changes on evapotranspiration and infiltration. This study of the impact of surface activities on deep percolation was conducted at six locations across Nebraska: Two center-pivot irrigated no-till planting systems fields were compared with one tilled center-pivot irrigated field, a furrow irrigated field with multiple tillage treatments, an eco-fallow dryland farming system, and a …

Simulation And Validation Of Radio Frequency Heating Of Shell Eggs, Soon Kiat Lau

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Finite element models were developed with the purpose of finding an optimal radio frequency (RF) heating setup for pasteurizing shell eggs. Material properties of the yolk, albumen, and shell were measured and fitted into equations that were used as inputs for the model. When the egg was heated by itself, heating tend to be focused at the air cell to result in a “coagulation ring.” The focused heating near the air cell of the egg prevented satisfactory pasteurization of the egg, but deeper analysis of the simulation results offered a new perspective on how non-uniform RF heating could occur in …

Interdisciplinary Modeling For Water-Related Issues Graduate Course, Laurel Saito, Alexander Fernald, Timothy Link

All ECSTATIC Materials

The science and management of aquatic ecosystems is inherently interdisciplinary, with issues associated with hydrology, atmospheric science, water quality, geochemistry, sociology, economics, environmental science, and ecology. Addressing water resources issues in any one discipline invariably involves effects that concern other disciplines, and attempts to address one issue often have consequences that exacerbate existing issues or concerns, or create new ones (Jørgensen et al. 1992; Lackey et al. 1975; Straskraba 1994) due to the strongly interactive nature of key processes (Christensen et al. 1996). Thus, research and management of aquatic ecosystems must be interdisciplinary to be most effective, but such truly …

Monitoring The Progression Of Spontaneous Articular Cartilage Healing With Infrared Spectroscopy, Megan P. O'Brien, Madhuri Penmatsa, Uday Palukuru, Paul West, Xu Yang, Mathias P. G. Bostrom, Theresa Freeman, Nancy Pleshko

Publications and Research

Objective. Evaluation of early compositional changes in healing articular cartilage is critical for understanding tissue repair and for therapeutic decision-making. Fourier transform infrared imaging spectroscopy (FT-IRIS) can be used to assess the molecular composition of harvested repair tissue. Furthermore, use of an infrared fiber-optic probe (IFOP) has the potential for translation to a clinical setting to provide molecular information in situ. In the current study, we determined the feasibility of IFOP assessment of cartilage repair tissue in a rabbit model, and assessed correlations with gold-standard histology.

Design. Bilateral osteochondral defects were generated in mature white New Zealand rabbits, and …

The Effect Of Posterior Foot Positions On Electromyography, Joint Kinetics And Energetics During A Sit-To-Stand In Young And Older Adults, Eric A. Pitman

Human Movement Studies & Special Education Theses & Dissertations

The sit-to-stand (STS) movement, defined as standing up from a chair to an upright posture, is a common task performed daily. The inability to accomplish this task may lead to dependence, institutionalization and even death in older adults. A common strategy change for the STS is positioning the feet posteriorly by increasing flexion at the knee joint. This reduces the displacement of the center of mass to the base of support while increasing the joint moment of force at the knee while decreasing it at the hip. The aims of this study were to: 1) examine the joint kinetics, joint …

Synergy-Based Two-Level Optimization For Predicting Knee Contact Forces During Walking, Gil Serrancolí, Allison Kinney, Josep M. Font-Llagunes, Benjamin J. Fregly

Mechanical and Aerospace Engineering Faculty Publications

Musculoskeletal models and optimization methods are combined to calculate muscle forces. Some model parameters cannot be experimentally measured due to the invasiveness, such as the muscle moment arms or the muscle and tendon lengths. Moreover, other parameters used in the optimization, such as the muscle synergy components, can be also unknown. The estimation of all these parameters needs to be validated to obtain physiologically consistent results. In this study, a two-step optimization problem was formulated to predict both muscle and knee contact forces of a subject wearing an instrumented knee prosthesis. In the outer level, muscle parameters were calibrated, whereas …

Development Of A Muscle Model Parameter Calibration Method Via Passive Muscle Force Minimization, Allison Kinney, Benjamin J. Fregly

Mechanical and Aerospace Engineering Faculty Publications

Computational predictions of subject-specific muscle and knee joint contact forces during walking may improve individual rehabilitation treatment design. Such predictions depend directly on specified model parameter values. However, model parameters are difficult to measure non-invasively. Methods for muscle model parameter calibration have been developed previously. However, it is currently unknown how the musculoskeletal system chooses muscle model parameter values. Previous studies have hypothesized that muscles avoid injury during walking by generating little passive force and operating in the ascending region of the force-length curve. This hypothesis suggests that muscle model parameter values may be selected by the body to minimize …

Computer Vision System For Grading Mangos In Bangladesh, Md Abdul Momin, Md Towfiqur Rahman, Mst Sabrina Sultana, Igathinathane Cannayen

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Mango (Mangifera indica) is one of the most common, important, and popular fruits among fruits produced in Bangladesh. In Bangladesh, mango was cultivated in about 0.078 million acres with an annual production of 0.8 million tonne. However, the technologies used in post-harvest processing (e.g., grading, sorting, etc.) of mango are mostly traditional involving human labors; and the methods are far from satisfactory, in terms of accuracy and throughput. In order to grade mango according to size, we developed a machine vision system with image processing capabilities that can measure sizes of mango fruits from the images. In this system images …

A Cradle To Farm Gate Life Cycle Analysis Of Land Use In U.S. Pork Production, William Benjamin Putman

Graduate Theses and Dissertations

The goal of this study was to conduct a detailed Life Cycle Assessment (LCA) of the U.S. live swine production supply chain to quantify land use requirements and to assess the impact associated with various ration compositions. The functional unit was defined as one kilogram (2.2 pounds) of live swine at the farm gate, ready for transport to the abattoir. This assessment focused on the three highest producing USDA regions, which encompassed the Midwest (Regions 5 and 7) and the Southeast (Region 4), representing 86% of U.S. market hog production.

First, a literature review was conducted to summarize the most …