Physical Sciences and Mathematics Commons^™

Data-Driven Multiscale Modeling Reveals The Role Of Metabolic Coupling For The Spatio-Temporal Growth Dynamics Of Yeast Colonies, Jukka Intosalmi, Adrian C. Scott, Michelle Hays, Nicholas Flann, Olli Yli-Harja, Harri Lähdesmäki, Aimée M. Dudley, Alexander Skupin

Computer Science Faculty and Staff Publications

Background: Multicellular entities like mammalian tissues or microbial biofilms typically exhibit complex spatial arrangements that are adapted to their specific functions or environments. These structures result from intercellular signaling as well as from the interaction with the environment that allow cells of the same genotype to differentiate into well-organized communities of diversified cells. Despite its importance, our understanding how this cell–cell and metabolic coupling lead to functionally optimized structures is still limited.

Results: Here, we present a data-driven spatial framework to computationally investigate the development of yeast colonies as such a multicellular structure in dependence on metabolic capacity. For this …

Hot Fusion Vs Cold Fusion For Malware Detection, Snehal Bichkar

Master's Projects

A fundamental problem in malware research consists of malware detection, that is, dis- tinguishing malware samples from benign samples. This problem becomes more challeng- ing when we consider multiple malware families. A typical approach to this multi-family detection problem is to train a machine learning model for each malware family and score each sample against all models. The resulting scores are then used for classification. We refer to this approach as “cold fusion,” since we combine previously-trained models—no retraining of these base models is required when additional malware families are considered. An alternative approach is to train a single model …

Image-Based Malware Classification With Convolutional Neural Networks And Extreme Learning Machines, Mugdha Jain

Master's Projects

Research in the field of malware classification often relies on machine learning models that are trained on high level features, such as opcodes, function calls, and control flow graphs. Extracting such features is costly, since disassembly or code execution is generally required. In this research, we conduct experiments to train and evaluate machine learning models for malware classification, based on features that can be obtained without disassembly or execution of code. Specifically, we visualize malware samples as images and employ image analysis techniques. In this context, we focus on two machine learning models, namely, Convolutional Neural Networks (CNN) and Extreme …

Environmental And Energy Assessment Of Biomass Residues To Biochar As Fuel: A Brief Review With Recommendations For Future Bioenergy Systems, Mengshan Lee, Yi-Li Lin, Pei-Te Chiueh, Walter Den

Water Resources Science and Technology Faculty Publications (Archived)

This study explores the environmental and energy benefits of biomass residues, including crop residues and agricultural waste, for the production of renewable energy in the form of biochar as fuel, in order to offer recommendations for policy makers, by reviewing information regarding the key environmental issues associated with the implementation of the systems. The highest environmental benefits for biochar-to-fuel systems were most observed in reduction of global warming potentials (i.e., carbon abatement), particularly for those integrated with combined heat and power technology, or for those incorporating electricity offsets from biochar combustion and co-firing. But all of these practices come …

Student Sustainability Leadership Development At Portland State University: Developing Holistic Sustainability Leaders, Megan Suzanne Schneider

Dissertations and Theses

In order to address the myriad of social, economic, and environmental challenges the world is facing, we need to be able to engage in leadership that fosters collective action towards sustainable solutions. Higher education is an institution that can equip people with the abilities to engage in sustainability leadership. This master's thesis research explores how students develop sustainability leadership through their college experience. Nine students, who had been identified as sustainability leaders through their participation in the Student Sustainability Center (SSC), a co-curricular sustainability program at Portland State University, were selected to be part of this grounded theory research project. …

Application Development For Goods Management System Towards Waste Minimization Options, Wan Ahmad Nadzim

Student Works (2020-2029)

Waste is a global concern. Increasing waste generation levels are causing the increase of waste management costs. In fact, the greatest costs of waste are measured by its impacts to the environment, society and economy. Prevention is better than cure—since all wastes come from goods, thus the best way to manage wastes is to manage goods. An application model of goods management system has been developed using GIS (Geographic Information System) and app prototyping. The primary purpose of goods management is to maximize goods and minimize waste by promoting reduction and reuse. GIS was used to perform spatial analyses on …

Impact Of Motor Therapy With Dynamic Body-Weight Support On Functional Independence Measures In Traumatic Brain Injury: An Exploratory Study, Emily F. Anggelis, Elizabeth Salmon Powell, Philip M. Westgate, Amanda C. Glueck, Lumy Sawaki

Physical Medicine and Rehabilitation Faculty Publications

BACKGROUND: Contemporary goals of rehabilitation after traumatic brain injury (TBI) aim to improve cognitive and motor function by applying concepts of neuroplasticity. This can be challenging to carry out in TBI patients with motor, balance, and cognitive impairments.

OBJECTIVE: To determine whether use of dynamic body-weight support (DBWS) would allow safe administration of intensive motor therapy during inpatient rehabilitation and whether its use would yield greater improvement in functional recovery than standard-of-care (SOC) therapy in adults with TBI.

METHODS: Data in this retrospective cohort study was collected from patients with TBI who receive inpatient rehabilitation incorporating DBWS (n = …

The Vden: An Ipt Designed For Usability, Alexander Jaeger

Theses and Dissertations

Currently, headsets are the emphasis of Virtual Reality and the primary reason is that they are easy to develop and demo, lightweight, simple, and aordable. Historically, IPTs have required dedicated rooms due to their large size and experts in order to run and maintain them. These devices are expensive and can be complicated due to mirrors, the number of displays, and the overwhelming size of the infrastructure and computing clusters.The research in minimial IPTs have led up to the use of front-projection and dual GPU gaming computers, however this only works in a few cases. This thesis presents new work …

Exploratory Measurements Of Large Winds And Shears In The Lower Thermosphere And Their Variability Using An Enhanced Sodium Lidar, Tao Yuan

Funded Research Records

No abstract provided.

Performance Of Nitrogen As A Carrier Gas In Capillary Gas Chromatography Using A Thin Film Column, Brittany A. Handzo

Seton Hall University Dissertations and Theses (ETDs)

Gas chromatography (GC) is one of the most widely used analytical techniques for the separation and analysis of volatile compounds. Solids, liquids, and gases, organic and inorganic materials, and large molecular weight compounds can all be analyzed via this technique. Gas chromatographic separations are fast, accurate, and reliable. One of the reasons why these separations are so efficient is because of the carrier gas. The purpose of the carrier gas is to carry the injected sample through the column. It is known as the mobile phase and does not interact chemically with the sample. Common carrier gases include helium, hydrogen, …

Is Contact Nucleation Caused By Pressure Perturbation?, Fan Yang, Will Cantrell, Alexander Kostinski, Raymond Shaw, Andrew M. Vogelmann

Michigan Tech Publications, Part 1

The reason why ice nucleation is more efficient by contact nucleation than by immersion nucleation has been elusive for over half a century. Six proposed mechanisms are summarized in this study. Among them, the pressure perturbation hypothesis, which arose from recent experiments, can qualitatively explain nearly all existing results relevant to contact nucleation. To explore the plausibility of this hypothesis in a more quantitative fashion and to guide future investigations, this study assessed the magnitude of pressure perturbation needed to cause contact nucleation and the associated spatial scales. The pressure perturbations needed were estimated using measured contact nucleation efficiencies for …

Heuristic One-Time Pad Encryption, James B. Joyce

Theses and Dissertations

Heuristic One-Time Pad (HOP) represents a methodology that is compliant with the requirements as established by Claude Shannon for a globally scalable and permanent encryption solution. The technique is not limited to encryption, rather, it also encompasses dynamic hashing and authentication. The two key Shannon-identified problems of continuous random number generation and secure distribution of encryption keys have been solved and are integral to the method. At each step of the algorithms, entropy is ‘1’ and unicity is ‘infinite’. All encryption key generation is independent of the value of the data being encrypted, and is dependent upon a combination of …

Development Of A Low-Cost, Open Source Miniature Rotary Cell Culture System To Simulate Microgravity Within An Irradiated Environment, Elizabeth Vargis, Jr Dennison

Browse all Datasets

A major challenge for astronauts in long-duration space travel is combatting the hazardous spaceflight environment caused by microgravity and increased levels of ionizing radiation. Microgravity damages cellular DNA by increasing the production of harmful reactive oxygen species, while ionizing radiation damages DNA by creating double-stranded DNA (dsDNA) breaks. Cellular damage due to microgravity and radiation has been investigated using ground-based models, but most models consider microgravity and ionizing radiation alone, or asynchronously. Synchronous modeling better mimics spaceflight conditions and can be used to understand the combined effects of microgravity and ionizing radiation. However, commercially available devices to model microgravity and …

A Model For The Prediction Of Antimicrobial Resistance In Escherichia Coli Based On A Comparative Evaluation Of Fatty Acid Profiles, Randal S. Stahl, Bledar Bisha, Sebabrata Mahapatra, Jeffrey C. Chandler

United States Department of Agriculture Wildlife Services: Staff Publications

Antimicrobial resistance is a threat to agricultural production and public health. In this proof-of-concept study, we investigated predicting antimicrobial sensitive/resistant (S/R) phenotypes and host sources of Escherichia coli (n = 128) based on differential fatty acid abundance. Myristic (14:0), pentadecanoic acid (15:0), palmitic (16:0), elaidic (18:19) and steric acid (18:0) were significantly different (α = 0.05) using a two-way ANOVA for predicting nalidixic acid, ciprofloxacin, aztreonam, cefatoxime, and ceftazidime S/R phenotypes. Additionally, analyses of palmitoleic (16:1), palmitic acid (16:0), methyl palmitate (i-17:0), and cis-9,10-methyleneoctadecanoic acid (19:0Δ) showed these markers were significantly different (α = 0.05) between isolates obtained from cattle …

Identifying Customer Churn In After-Market Operations Using Machine Learning Algorithms, Vitaly Briker, Richard Farrow, William Trevino, Brent Allen

SMU Data Science Review

This paper presents a comparative study on machine learning methods as they are applied to product associations, future purchase predictions, and predictions of customer churn in aftermarket operations. Association rules are used help to identify patterns across products and find correlations in customer purchase behaviour. Studying customer behaviour as it pertains to Recency, Frequency, and Monetary Value (RFM) helps inform customer segmentation and identifies customers with propensity to churn. Lastly, Flowserve’s customer purchase history enables the establishment of churn thresholds for each customer group and assists in constructing a model to predict future churners. The aim of this model is …

Personalized Detection Of Anxiety Provoking News Events Using Semantic Network Analysis, Jacquelyn Cheun Phd, Luay Dajani, Quentin B. Thomas

SMU Data Science Review

In the age of hyper-connectivity, 24/7 news cycles, and instant news alerts via social media, mental health researchers don't have a way to automatically detect news content which is associated with triggering anxiety or depression in mental health patients. Using the Associated Press news wire, a semantic network was built with 1,056 news articles containing over 500,000 connections across multiple topics to provide a personalized algorithm which detects problematic news content for a given reader. We make use of Semantic Network Analysis to surface the relationship between news article text and anxiety in readers who struggle with mental health disorders. …

A Data Science Approach To Defining A Data Scientist, Andy Ho, An Nguyen, Jodi L. Pafford, Robert Slater

SMU Data Science Review

In this paper, we present a common definition and list of skills for a Data Scientist using online job postings. The overlap and ambiguity of various roles such as data scientist, data engineer, data analyst, software engineer, database administrator, and statistician motivate the problem. To arrive at a single Data Scientist definition, we collect over 8,000 job postings from Indeed.com for the six job titles. Each corpus contains text on job qualifications, skills, responsibilities, educational preferences, and requirements. Our data science methodology and analysis rendered the single definition of a data scientist: A data scientist codes, collaborates, and communicates – …

Resin And Magnetic Nanoparticle-Based Free Radical Probes For Glycan Capture, Isolation, And Structural Characterization, Kimberly Fabijanczuk, Kaylee Gaspar, Nikunj Desai, Jungeun Lee, Daniel A. Thomas, J. L. Beauchamp, Jinshan Gao

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

By combining the merits of solid supports and free radical activated glycan sequencing (FRAGS) reagents, we develop a multifunctional solid-supported free radical probe (SS-FRAGS) that enables glycan enrichment and characterization. SS-FRAGS comprises a solid support, free radical precursor, disulfide bond, pyridyl, and hydrazine moieties. Thio-activated resin and magnetic nanoparticles (MNPs) are chosen as the solid support to selectively capture free glycans via the hydrazine moiety, allowing for their enrichment and isolation. The disulfide bond acts as a temporary covalent linkage between the solid support and the captured glycan, allowing the release of glycans via the cleavage of the disulfide bond …

Answering Global Warming’S Hottest Debate: A Better Way To Tax Carbon, Saleh Husseini

Op-Eds from ENSC230 Energy and the Environment: Economics and Policies

Some of you are sick of hearing about it, some of you don’t really care, and the rest of you are probably the reason the first group is sick of hearing about it, but regardless of which category you fall into, one thing is certain: climate change is real and it’s already happening. With that said, I’m moving forward under the assumption that all of us here believe in science and understand this phenomenon to be largely a result of post-industrial anthropogenic activity. In which case, reducing our emissions is the only way to prevent climate change from becoming a …

Low Temperature Liquid Metal Batteries For Energy Storage Applications, Cameron A. Lippert, Kunlei Liu, James Landon, Susan A. Odom, Nicolas E. Holubowitch

Center for Applied Energy Research Faculty Patents

The present invention relates to a molten metal battery of liquid bismuth and liquid tin electrodes and a eutectic electrolyte. The electrodes may be coaxial and coplanar. The eutectic electrolyte may be in contact with a surface of each electrode. The eutectic electrolyte may comprise ZnC1₂:KCI.

Individual Based Modeling And Analysis Of Pathogen Levels In Poultry Chilling Process, Zachary Mccarthy, Ben Smith, Aamir Fazil, Jianhong Wu, Shawn D. Ryan, Daniel Munther

Mathematics and Statistics Faculty Publications

Pathogen control during poultry processing critically depends on more enhanced insight into contamination dynamics. In this study we build an individual based model (IBM) of the chilling process. Quantifying the relationships between typical Canadian processing specifications, water chemistry dynamics and pathogen levels both in the chiller water and on individual carcasses, the IBM is shown to provide a useful tool for risk management as it can inform risk assessment models. We apply the IBM to Campylobacter spp. contamination on broiler carcasses, illustrating how free chlorine (FC) sanitization, organic load in the water, and pre-chill carcass pathogen levels affect pathogen levels …

Detecting Myocardial Infarctions Using Machine Learning Methods, Aniruddh Mathur

Master's Projects

Myocardial Infarction (MI), commonly known as a heart attack, occurs when one of the three major blood vessels carrying blood to the heart get blocked, causing the death of myocardial (heart) cells. If not treated immediately, MI may cause cardiac arrest, which can ultimately cause death. Risk factors for MI include diabetes, family history, unhealthy diet and lifestyle. Medical treatments include various types of drugs and surgeries which can prove very expensive for patients due to high healthcare costs. Therefore, it is imperative that MI is diagnosed at the right time. Electrocardiography (ECG) is commonly used to detect MI. ECG …

Major Lower Paleozoic Horizons Of The Southern Illinois Basin, John B. Hickman

Report of Investigations--KGS

The geology exposed at the surface in the southern Illinois Basin has been mapped in great detail by countless workers over the past century. With the exception of limited and scattered exposures in incised river valleys, the oldest rocks exposed outside of the Jessamine, Nashville, and Ozark Domes surrounding the Illinois Basin are Mississippian in age. Extensive deposits of Cambrian–Devonian sediments occur in the subsurface above crystalline basement in this region, however. All available data for the region were analyzed to produce a single, comprehensive set of interpretations. The data used in this study include 1:24,000-scale geologic quadrangle maps, oil …

Subglacial Meltwater Supported Aerobic Marine Habitats During Snowball Earth, Maxwell A. Lechte, Malcolm W. Wallace, Ashleig Van Smeerdijk Hooda, Weiqiang Li, Ganqing Jiang, Galen P. Halverson, Dan Asael, Stephanie L. Mccoll, Noah J. Planavsky

Geoscience Faculty Research

The Earth’s most severe ice ages interrupted a crucial interval in eukaryotic evolution with widespread ice coverage during the Cryogenian Period (720 to 635 Ma). Aerobic eukaryotes must have survived the “Snowball Earth” glaciations, requiring the persistence of oxygenated marine habitats, yet evidence for these environments is lacking. We examine iron formations within globally distributed Cryogenian glacial successions to reconstruct the redox state of the synglacial oceans. Iron isotope ratios and cerium anomalies from a range of glaciomarine environments reveal pervasive anoxia in the ice-covered oceans but increasing oxidation with proximity to the ice shelf grounding line. We propose that …

In‐Situ Extraction And Impregnation Of Black Walnut Husk Into Polyethylene Film Using Supercritical Carbon Dioxide With An Ethanol Modifier, Jonathan Wenzel, Veronica R. Moorman, Lihua Wang, Isaiah Spencer-Williams, Mitchell Hall, Cheryl Samaniego, Michelle Ammerman

Chemistry & Biochemistry Publications

Walnuts are commonly cultivated for their kernel, which is a rich source of antioxidant phenolic compounds. The husk likewise contains antioxidant and antimicrobial compounds, but is typically discarded without further processing. Antioxidant compounds are useful in creating active packaging films, but typically decompose at melt extrusion temperatures in polymer processing. Due to carbon dioxide's low critical point and ability to swell polymer films, supercritical carbon dioxide may be used to impregnate phenolic compounds into polymers. For this study, a novel technique is used to simultaneously produce walnut husk extracts and impregnate the extract into polymer films in the same batch …

Analytic Non-Adiabatic Derivative Coupling Terms For Spin-Orbit Mrci Wavefunctions. I. Formalism, Lachlan T. Belcher, Gary S. Kedziora, David E. Weeks

Faculty Publications

Analytic gradients of electronic eigenvalues require one calculation per nuclear geometry, compared to at least 3n + 1 calculations for finite difference methods, where n is the number of nuclei. Analytic nonadiabatic derivative coupling terms (DCTs), which are calculated in a similar fashion, are used to remove nondiagonal contributions to the kinetic energy operator, leading to more accurate nuclear dynamics calculations than those that employ the Born-Oppenheimer approximation, i.e., that assume off-diagonal contributions are zero. The current methods and underpinnings for calculating both of these quantities, gradients and DCTs, for the State-Averaged MultiReference Configuration Interaction with Singles and Doubles (MRCI-SD) …

“Treat Me Covalently” – New Tools To Improve Covalent Drug Design For Advancement Of Cancer Treatments, Yuliya Mazo

Student Theses and Dissertations

The goal of this project was to investigate the complex mechanism of covalent bonding among different molecules and their targets in a modeling software ICM-Pro. Specifically, it included the identification of fundamental aspects of a covalent bonding mechanism of the Michael addition reaction. Michael addition reaction of electrophilic α, β-unsaturated carbonyl compounds with a nucleophilic cysteine residue in thymidylate synthase, papain, and EGFR tyrosine kinase were examined. Thymidylate synthase and EGFR were chosen because they are important targets in the treatment of various types of cancer. In order to find the most optimal parameters, identification and assessment of the effect …

Structural And Geochronologic Constraints On The Duration Of The Picuris Orogeny And Demise Of An Orogenic Plateau, Northern Nm, Daniel J. Young

Earth and Planetary Sciences ETDs

Metasedimentary and igneous basement rocks in northern New Mexico record episodic pulses of tectonism during cratonic growth from 1.8 to 1.38 Ga. Continued challenges involve parsing the deformational features attributable to the Yavapai Orogeny (1.71-1.68 Ga), Mazatzal orogeny (1.66-1.60 Ga), and Picuris orogeny (1.5-1.38 Ga) in this region and understanding how older structures may have been overprinted and reactivated to explain the observed strain. This paper presents regional cross-sections of the 1.7 Ga Vadito, 1.68 to 1.50 Ga Hondo, and 1.5-1.45 Ga Trampas groups of the Picuris Mountains and Rio Mora areas of northern New Mexico combined with new geochronologic …

Statistical Analysis Of Social Network Change, Teresa Danielle Schmidt

Dissertations and Theses

This project explores two statistical methods that infer social network structures and statistically test those structures for change over time: regression-based differential network analysis (R-DNA) and information theory-based differential analysis (I-DNA). R-DNA is adapted from bioinformatics and I-DNA employs reconstructability analysis.

This project applies both R-DNA and I-DNA to analyze Medicaid claims data from one-year periods before (May 2011- Apr 2012) and after (Jan 2013-Dec 2013) the formation of the Health Share of Oregon Coordinated Care Organization (CCO). The formation of CCOs was legislated by the state of Oregon in 2012 with the triple aim of improving health outcomes, reducing …

Achieving Optimal Horizontal Drill Operations, Daniel J. Serna, James Vasquez, Donald Markley

SMU Data Science Review

In this paper, we present a novel method of predicting the onset of a slide event in horizontal drilling operations. Horizontal drilling operations attempt to create a well through a subsurface as quickly as possible by rotating a drill through the subsurface. A slide event occurs when the drill begins to inefficiently rotate through the subsurface, resulting in a significantly reduced rate of penetration. Slide events can be prevented, or significantly reduced in their impact, when their onset is accurately predicted. We present a method of accurately predicting the onset of slide events with a time-series based predictive model that …