AJUR Volume 15 Issue 1 (June 2018)

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AJUR Volume 15 Issue 1 (June 2018)

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p.5 An All-Atomistic Molecular Dynamics Study to Determine the Structural Importance of Disulfide Bonds in Immunoglobulin G and Bovine Serum Albumin
Akshay Mathavan, Akash Mathavan, Michael E. Fortunato, & Coray M. Colina
ABSTRACT: A fully-atomistic molecular dynamics study was performed to determine the importance of disulfide bonds on the stability of immunoglobulin G (IgG) and bovine serum albumin (BSA).The transferability of a previous prescreening methodology to assess contributions from individual disulfide bonds on conformational stability was tested on both proteins. In IgG, it was apparent that inter-chain and intra-chain disulfide bonds play different roles in maintaining structure, evidenced by clear separation of inter-chain cysteine residues upon cleavage of disulfide bonds. In BSA, a set of double disulfide bonds required both to be broken in order to observe significant structural changes, equivalently seen in a previous study of human serum albumin (HSA), a structurally similar protein. Structural analysis of IgG showed deviations in distances between domains, while analysis of BSA suggested more local structural changes. This work helps confirm the efficacy and reproducibility of the prescreening methodology on both a novel, larger protein such as IgG and a more homologous (to HSA), globular protein such as BSA. The results provide insight into the role of specific disulfide bonds in the stability of IgG and BSA.
KEYWORDS: Molecular Dynamics; Atomistic Simulations; Immunoglobulin G; Bovine Serum Albumin; Disulfide Bonds

p.23 Syndecan Affects Odor Response as well as Learning and Memory in Drosophila melanogaster
Dena Arizanovska, Jonathan King, &Karl G. Johnson
ABSTRACT: Syndecan (Sdc) is a transmembrane heparan sulfate proteoglycan that plays a crucial role in axon guidance and synapse formation during CNS development in Drosophila melanogaster. To further examine the effect of syndecan on CNS function, Sdc23 mutant D. melanogaster larvae were used to examine odor preference and the capacity for learning and memory. A series of olfaction assays in both wild type and mutant larvae were performed to characterize naive odor responses before adding a training period to identify the capacity for associative learning. These results showed that Sdc23 larvae prefer odors that wild type larvae do not respond to, suggesting a difference in odor receptor pathways and wiring. In addition, associative learning has been documented in wild type larvae, yet no evidence of associative learning in Sdc23 larvae was found, suggesting that the syndecan also plays a role in learning and memory in D. melanogaster larvae.
KEYWORDS: Syndecan; Proteoglycans; Neurodevelopment; Axon Guidance; Olfaction; Attraction Index; Associative Learning; Drosophila

p.33 Investigation of Flow Rate on Chemical Bath Deposition of Silver Films Inside Hollow Polymer Cylinders
M. Ehrsam, H. Taz, A. Malasi, C. Carr, & R. Kalyanaraman
In thin film solar cells made as planar structures, the absorption of solar light and hence, the solar conversion efficiency, is heavily determined by the position and orientation of the sun. One way to overcome this is to use solar cell geometries that could better absorb sunlight from different angles. One potential geometry is a hollow cylinder, which has the ability to better absorb the sun’s rays incident at various angles due to the light trapping nature of the cylindrical geometry. If such solar cells could be fabricated inside polymer tubes with micrometer diameters, many potential applications built around non-woven or woven textiles could be realized. Here we investigate the deposition of homogeneous thin metallic films inside hollow polymer cylinders using the process of chemical bath deposition (CBD). Although films deposited via CBD have been studied extensively, mechanisms to achieve high quality deposition inside hollow cylinders are still not well understood. The objective of this project was to deposit a smooth, homogeneous silver film inside a hollow cylindrical structure using varying flow rates. The early stage film growth for very short deposition times was observed by the localized surface plasmon resonance of the silver nanoclusters via absorption spectra along the length of the tube. For longer deposition times, silver films formed and were analyzed for their morphology, thickness, roughness, and resistance using a combination of optical microscopy, scanning electron microscopy, and two-probe conductivity. The findings from this study showed that deposition under flow with different Reynolds numbers had a strong influence on the morphology and electrical resistance of the deposited films.
KEYWORDS: Thin-films; Chemical Bath Deposition; Nanoparticles; Solar Cells; Silver

p.43 Feasibility of Man-Portable Power Generation Systems
Earl C. Allen & Nelson Fumo
ABSTRACT: Electric power is the most common source of power for many portable devices used in outdoor recreation, emergency scenarios, and military applications. Batteries that have limitations regarding power and energy are currently meeting the power demand for most of these devices. There is a search to use alternative power sources for portable energy needs. This search has mostly been researched particularly for the military to satisfy functions necessary for soldiers. However, any alternative that would provide electricity in an efficient and timely manner is useful in many applications beyond the military. The feasibility of man-portable power generation systems using thermal energy from any kind of fuels needs to be studied further, to understand if they are truly an option for situations where batteries are currently used. In this study, the feasibility of fueled power systems is investigated. Commercially available small power systems show that they are not small enough to satisfy the definition of man-portable power system. However, power systems working on an internal combustion engine show to be a better option when compared to batteries and fuel cells.
KEYWORDS: Fueled Power Generation; Man-portable Power; Power Density; Energy Density

p.55 The Role of Gender Stereotypes in Gubernatorial Campaign Coverage
Karen Bjerre
ABSTRACT: Through a content analysis of 1,152 articles covering 20 different gubernatorial races between 2004 and 2014, I examine how the presence of a woman candidate in a gubernatorial race affects media coverage of that campaign. This paper considers the prevalence of gender biases and stereotypes and examines whether print media outlets perpetuate these stereotypes or subvert them. Existing research suggests that voters favor traditionally masculine traits over traditionally feminine traits when evaluating candidates for public office. The difference in media coverage may therefore influence women’s chances of getting elected, and thereby influence women’s descriptive and substantive representation. I find that races with a woman candidate receive less issue coverage and more horse race coverage than races with two men running. Additionally, the types of adjectives used in campaign coverage differ depending on the gender of the candidate: women are more likely to be described as able to “change government,” while men are more likely to be described as “experienced.”
KEYWORDS: Media Coverage; Gender; Gubernatorial Campaigns; Women in Politics; Gender Stereotypes; Newspaper Coverage; American Politics

AJUR Volume 14 Issue 4 (March 2018)

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AJUR Volume 14 Issue 4 (March 2018)

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p.5. Thermodynamics of Concanavalin A Self-Association in the Presence of Osmolytes
Tyler Pfister*, Shamus Cooper, & Jeffrey K. Myers
Department of Chemistry, Davidson College, NC
Students: Typfister17@alumni.davidson.edu*, Shcooper16@alumni.davidson.edu
Mentor: Jemyers@davidson.edu
ABSTRACT: Protein-protein interactions are critical for biological function and depend significantly on environmental factors. A wide variety of small organic molecules that comprise the cellular environment are capable of interacting with proteins to affect folding, binding, and association. The plant lectin concanavalin A (ConA) undergoes a reversible, pH dependent dimer-to-tetramer equilibrium and has been used in our laboratory as a model system to study the effect of osmolytes on protein self-association. Previous research determined that trimethylamine N-oxide (TMAO) stabilizes the tetrameric conformation, while urea favors the dimer. Studying the equilibrium over a range of temperatures allowed quantification of the enthalpy change (∆H) and entropy change (∆S) of tetramer formation. Urea increased both the ∆H and ∆S of tetramer formation, while TMAO decreased both.  These effects are consistent with preferential hydration of the dimer-dimer interface in TMAO solution and preferential binding of urea to the interface.
KEYWORDS: Concanavalin A; Osmolytes; Trimethylamine N-oxide; Urea; Protein-Protein Interaction; Equilibrium; Enthalpy; Preferential Hydration

p.13. Perception of peer drinking and access to alcohol mediate the effect of residence status on alcohol consumption
KatrinaA.Williams*a, Nathaniel S. Thomas b,c, Amy E. Adkins b,c, & Danielle M. Dick b,c,d
a Department of Kinesiology and Health Sciences, Virginia Commonwealth University, Richmond, VA, United States
b College Behavioral and Emotional Health Institute, Virginia Commonwealth University, Richmond, VA,  United States
c Department of Psychology, Virginia Commonwealth University, Richmond, VA,  United States
d Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA,  United States
Student: williamska5@vcu.edu*
Mentor: thomasns@vcu.edu
ABSTRACT: Alcohol consumption is common in college attending populations and can have a negative impact on an individual’s academic, physical, and mental health. Previous research suggests that living at home could act as a protective measure. The current research looks at potential mediators of the association between living with parents while attending college and amount of alcohol consumed. In particular, this study examined access to alcohol, parental involvement, and perception of peer drinking as mediators of the association.  This study examined freshman data collected from a survey conducted at a large public university in the mid-Atlantic United States.  A pathway model was fit to test the relationships between residence status, access to alcohol, parental involvement, and perception of peer drinking on alcohol consumption.  We observed statistically significant indirect effects of residence status on alcohol consumption through the perception of peer drinking and access to alcohol. Parental involvement was significantly related to lower alcohol consumption and there was a direct effect of residence status on alcohol consumption.  There were significant indirect effects of residence status on alcohol consumption through both peer drinking and access to alcohol. Parental involvement was associated with decreased alcohol consumption, with no indirect effect in association with residence status. These effects were persistent in the presence of a range of covariates, including age, gender, ethnicity, and parental education.
KEYWORDS: Emerging Adult; Alcohol; Residence Status; Peer Drinking; Access to Alcohol; Parental involvement; Path Analysis

p.23. Speedup Potential for Reconstruction Techniques for Prompt Gamma Imaging During Proton Radiotherapy
James Della-Giustina*a, Johnlemuel Casilagb, Elizabeth Gregorioc, & Aniebiet Jacobsb
aDepartment of Information Technology & Computer Science, Community College of Baltimore County, Baltimore, MD
bDepartment of Computer Science & Electrical Engineering, University of Maryland, Baltimore County, Baltimore, MD
cDepartment of Physics, Hamline University, St. Paul, MN
dDepartment of Mathematics and Statistics, University of Maryland, Baltimore County, Baltimore, MD
eDepartment of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD
fDepartment of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
Students: jdella@umbc.edu*, cas6@umbc.edu, anie1@umbc.edu, egregorio01@gmail.com
Research Assistant: Carlos Barajasd, barajasc@umbc.edu
Faculty Mentor: Matthias K. Gobbertd, gobbert@umbc.edu
Clients: Dennis Mackinf, dsmackin@mdanderson.org, Jerimy Polfe, jpolf@umm.edu
ABSTRACT: Proton beam radiation treatment was first proposed by Robert Wilson in 1946. The advantage of proton beam radiation is that the lethal dose of radiation is delivered by a sharp increase toward the end of the beam range. This sharp increase, known as the Bragg peak, allows for the possibility of reducing the exposure of healthy tissue to radiation when comparing to x-ray radiation treatment. As the proton beam interacts with the molecules in the body, gamma rays are emitted. The origin of the gamma rays gives the location of the proton beam in the body, therefore, gamma ray imaging allows physicians to better take advantage of the benefits of proton beam radiation. These gamma rays are detected using a Compton Camera (CC) while the SOE algorithm is used to reconstruct images of these gamma rays as they are emitted from the patient. This imaging occurs while the radiation dose is delivered, which would allow the physician to make adjustments in real time in the treatment room, provided the image reconstruction is computed fast enough. This project focuses on speeding up the image reconstruction software with the use of of parallel computing techniques involving MPI. Additionally, we demonstrate the use of the VTune performance analyzer to identify bottlenecks in a parallel code.
KEYWORDS: Proton Beam Therapy; Image Reconstruction; SOE Algorithm; Parallel Computing; High Performance Computing; Medical Imaging; Prompt Gamma Imaging; Radiotherapy

p.39. Knowledge and Behaviors Associated with a Campus Tobacco-Free Policy
Sarah Powell*a, Cassie Odahowskib,c, Elizabeth Crouchd, Erica Sercyb,c, Jackie Knighte, & Jan M. Eberthb,c
a Department of Epidemiology and Biostatistics, College of Public Health, University of South Florida, Tampa, FL
b Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC
c Statewide Cancer Prevention and Control Program, Arnold School of Public Health, University of South Carolina, Columbia, SC
d Department of Health Services Policy and Management, Arnold School of Public Health, University of South Carolina, Columbia, SC
e Healthy Carolina Coalition, University of South Carolina, Columbia, SC
Student: sepowell1@health.usf.edu *
Mentor: jmeberth@mailbox.sc.edu
ABSTRACT: Objective: Nearly half of U.S. colleges/universities have implemented tobacco-free campus policies. This study analyzed knowledge, attitudes, and practices associated with the tobacco-free policy at a large public university. It is important to study public university tobacco policies to determine the most efficient and cost-effective way to reduce tobacco related disease due to tobacco use and exposure. Methods: This study used a cross-sectional, campus-wide electronic survey distributed in November 2016. The primary outcomes of interest included 1) correct knowledge of the tobacco-free policy, 2) community member willingness to approach observed violation of the policy, and 3) a positive opinion of the policy’s effectiveness. Descriptive statistics and logistic regression were used to examine the impact of demographic factors on the outcomes. Results: After analysis, the team found that 23% of university faculty, staff, and students had incorrect knowledge about the campus tobacco-free policy. Almost 70% of the university community reported not having approached a smoking violator. Males were significantly less likely to understand the tobacco-free policy in full, approach a violator, or have a positive opinion about its effectiveness.  Staff had better knowledge of the policy, a higher likelihood of approaching a violator, and a better opinion about the policy’s effectiveness compared to graduate and undergraduate students. Conclusions: Interventions are needed to increase awareness and confidence regarding implementation and enforcement of the tobacco-free policy on campus, particularly among faculty and students. This paper expands on the currently increasing knowledge of tobacco-free policy enforcement and benefits.
KEYWORDS: Campus; Tobacco Regulation; Tobacco; Secondhand Smoke; Cross-Sectional Survey

p.49. Conduction Mechanism in Electrically Conducting Polymers
Daniel L.Gochnauer & T. H. Gilani*
Department of Physics, Millersville University, P. O. Box 1002, Millersville PA-17551
Student: dlg15@uw.edu
Mentor: tariq.gilani@millersville.edu
ABSTRACT: The conduction mechanism in conducting polymers is reviewed and experimental results of temperature dependence of electrical conductivity of PF6 doped polypyrrole in temperature range of 77 to 300 K are discussed. The room-temperature conductivitywas experimentally determined to be 73 ± 3.4 S/m and temperature dependence follows the Mott’s variable range hopping model. The average hopping distance at 298 K was (6.75 ± 0.97) ×10-8 cm. The coefficient of decay of the localized states, the density states at the Fermi level, and the hopping activation energy were calculated to be (3.5±0.51) ×107 cm-1, (1.92 ± 0.83) ×1022 cm-3 eV-1, and 0.040 ± 0.001 eV respectively.
KEYWORDS: Electrically Conducting Polymers; Doped Polypyrrole; Temperature Dependence of Conductivity; Hopping Activation Energy; Density of State at Fermi level

AJUR Volume 14 Issue 3 (November 2017)

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AJUR Volume 14 Issue 3 (November 2017)

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p.5 Strategies for Making Best Offers on eBay
William J. Britt, William E. Gryc, Jamie A. Oliva, Brittney N. Tuff, & Charli E. White
ABSTRACT: We model for “Buy-It-Now or Best Offer” auctions on eBay using two different models. In the first model, risk-neutral bidders submit bids in serial and try to surpass a stochastic seller threshold while taking into account how many previous failed bids were made by other bidders. We compute optimal strategies for this model and show that bidder expected surplus decreases in the number of previous failed bids. In the second model we assume bidders do not know how many previous failed bids have been made, and instead use a first-price sealed-bid mechanism with a buy-out price where bidders serially submit bids with the knowledge that no previous bidders have used the buy-out price. We derive a unique equilibrium bidding strategy for risk-neutral bidders in this serial model, show that any equilibrium in a similar parallel bidding model is the same as the equilibrium in the serial model, and compute seller revenue. In particular, under certain circumstances, bidders will bid more in this format than they would in a standard first-price sealed-bid auction, but that a seller maximizes expected revenue by setting a buy-out price higher than any bidder is willing to pay thereby making the auction essentially a first-price auction.
KEYWORDS: Auction Theory; eBay; Buy-It-Now or Best Offer; Symmetric Bayesian Nash Equilibrium; Buy-Out Price; First-Price Sealed-Bid

p. 37 The Relationship Between Parenting Styles and Substance Use Among University Students
Zackaria I. Niazi, Danielle Dick, Amy Adkins, & Megan Cooke
ABSTRACT: Parenting styles are important in the behavioral development of adolescents. The environment created by the parent, in regards to communication with their child and level of independence given to their child, may influence the child’s susceptibility to risk behaviors. This study examines the relationship between parenting style and substance use among university students. We hypothesized that university students exposed to lower levels of autonomy granting (AG) or parental involvement (PI) parenting styles would have an increased likelihood of alcohol and nicotine use. We also hypothesized that religiosity, parental education level, ethnicity, and gender would act as moderators of parenting styles and alcohol and nicotine use. Data from a diverse university-wide sample was collected in the fall semester of the student’s freshman year from 2011-2014 (N = 9889, 61.5% female). Results demonstrated that AG had a significant, negative association with alcohol use (B = -0.033, p = 0.006) and nicotine use (B = -0.066, p <0.001). All moderators were found to be significant predictors of alcohol use, however only father education level demonstrated a borderline significant moderation of the relationship between PI and alcohol use. Religiosity, Black race, Asian race, and gender were found to be significant predictors of nicotine use. Only gender moderated the association between PI and nicotine use. Even though alcohol and nicotine use and AG were associated, our results indicate that once students enter university, previous parenting style does not have a strong effect on alcohol and nicotine use behaviors in our sample.
KEYWORDS: Parenting Styles; University Students; Risky Behaviors; Autonomy Granting; Parental Involvement; Alcohol; Nicotine; Drug; Behavioral Biology; Substance Use

p.45 Matricial Representations of Certain Finitely Presented Groups Generated by Order-2 Generators and Their Applications
Ryan Golden & Ilwoo Cho
ABSTRACT: In this paper, we study matricial representations of certain finitely presented groups Γ2Nwith N-generators of order-2. As an application, we consider a group algebra Aof Γ22; under our representations. Specifically, we characterize the inverses g-1of all group elements g in Γ22; in terms of matrices in the group algebra A2. From the study of this characterization, we realize there are close relations between the trace of the radial operator of A2; and the Lucas numbers appearing in the Lucas triangle.
KEYWORDS: Matricial Representation; Group Presentation; Group Algebras; Lucas Numbers; Lucas Triangle; Finitely Presented Group;Group Relations; Free Probability

p.69 Evolution of Leucyl-tRNA Synthetase Through Eukaryotic Speciation
Katelyn E. Unvert, Frank A. Kovacs, Chi Zhang, Rachel A. Hellmann-Whitaker, & Katelin N. Arndt
ABSTRACT: Aminoacyl-tRNA synthetases (aaRSs) are part of the cellular translation machinery and as such, they are essential enzymes for every known cell. Due to their ubiquitous nature, their evolutionary history has been intensely researched to better understand the origins of life on a molecular level. Herein, we examine the evolutionary relatedness of leucyl-tRNA synthetases (LeuRS) from each major eukaryotic branch through the speciation process. This research effort was centered on amino acid sequence data as well as generating homology protein models for each LeuRS enzyme. Comparative analysis of this sequence and structural data for LeuRS amongst eukaryotes has indicated a high level of conservation within the active sites of these enzymes. Phylogenetic analysis confirmed this high degree of conservation as well as established evolutionary relatedness between these LeuRS enzymes. Based on this data, vertical gene transfer propagated LeuRS throughout the eukaryotic domain. Horizontal gene transfer and domain acquisition events were not observed within the eukaryotic organisms studied. Our data also highlighted LeuRS adaptation through the speciation process due to slight variability of scaffolding residues outside of the active site regions. We hypothesize that this variability may be due to mechanistic differences amongst LeuRS enzymes that have assumed non-translational functionality through the evolutionary process.
KEYWORDS: tRNA Synthetase; Leucyl-tRNA Synthetase; Eukaryotic Evolution; LeuRS Conservation; Vertical Gene Transfer; Horizontal Gene Transfer; Convergent Evolution; Primordial Enzymes

p.85 The Effect of CO2, Intracellular pH and Extracellular pH on Mechanosensory Proprioceptor Responses in Crayfish and Crab
Viresh Dayaram, Cole Malloy, Sarah Martha, Brenda Alvarez, Ikenna Chukwudolue, Nadera Dabbain, Dlovan Mahmood, Slavina Goleva, Tori Hickey, Angel Ho, Molly King, Paige Kington, Matthew Mattingly, Samuel Potter, Landon Simpson, Amanda Spence, Henry Uradu, Jacob Van Doorn, dlovan faiq, & Robin L. Cooper
ABSTRACT: Proprioceptive neurons monitor the movements of limbs and joints to transduce the movements into electrical signals. These neurons function similarly in species from arthropods to humans. These neurons can be compromised in disease states and in adverse environmental conditions such as with changes in external and internal pH. We used two model preparations (the crayfish muscle receptor organ and a chordotonal organ in the limb of a crab) to characterize the responses of these proprioceptors to external and internal pH changes as well as raised CO2. The results demonstrate the proprioceptive organs are not highly sensitive to changes in extracellular pH, when reduced to 5.0 from 7.4. However, if intracellular pH is decreased by exposure to propionic acid or saline containing CO2, there is a rapid decrease in firing rate in response to joint movements. The responses recover quickly upon reintroduction of normal pH (7.4) or saline not tainted with CO2. These basic understandings may help to address the mechanistic properties of mechanosensitive receptors in other organisms, such as muscle spindles in skeletal muscles of mammals and tactile as well as pressure (i.e., blood pressure) sensory receptors.
KEYWORDS: Proprioception; Sensory; Invertebrate; Carbon Dioxide; Protons; Mechanosensory; Intracellular pH; Extracellular pH

p.101 Derivation of Explicit Solutions Describing Early Stages of Platelet Activation
Rachel Austin, Scott Fones, Dominic Santoleri, Kaitlyn Thomesen, & Pak-Wing Fok
ABSTRACT: The formation of blood clots is vital for biological repair of injured blood vessels. When a blood vessel is injured, platelets come into contact with collagen, causing glycoprotein VI (GPVI) to undergo a conformational change and initialize the clotting process. This project aimed to simplify and solve a system of coupled ordinary differential equations (ODEs) proposed in Model A of Regulation of Early Steps of GPVI Signal Transduction by Phosphatase: A Systems Biology Approach by JL Dunster et al., modeling early platelet activation kinetics. In doing so, the ODEs were non-dimensionalized and the approximate analytical solutions were then found. The approximate solutions compare favorably to the numerical solutions and provide deeper insight into the signal regulation pathway. Most notably, the solutions expose a time at which the pathway dynamics change drastically. This illustrates the critical role of cytosolic spleen tyrosine kinase (Syk) as a molecular timer in the cascade.
KEYWORDS: Platelet Activation; Signal Cascade; Coupled Differential Equations; Asymptotic Analysis; Systems Biology; Mathematical Modeling; Model Simplification; Glycoprotein VI; Spleen Tyrosine Kinase; Syk Activation Dynamics


AJUR Volume 14 Issue 2 (June 2017)

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AJUR Volume 14 Issue 2 (June 2017)

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Blackseed (Nigella sativa) Oil and its Active Ingredient, Thymoquinone, Suppress the Aggressive Phenotype of Breast Cancer Cells

Sabrina Chaudhry, Safia Siddiqui, Tyrnnon K. Steffen, & Stacey L. Raimondi 

ABSTRACT Breast cancer is a leading cause of cancer deaths in women within the United States. However, current treatment methods for the disease present deleterious side effects themselves. Therefore, there is a move towards finding natural cures in order to mitigate negative side effects while still providing effective treatment for the cancer. Blackseed (Nigella sativa) oil is one particular natural remedy, alongside its active ingredient thymoquinone (TQ), which has been successfully tested for suppressing certain types of breast cancer cell proliferation. TQ itself has been seen to be capable of preventing proliferation of both non-aggressive MCF-7 and highly aggressive MDA-MB-231 cancer cells. However, studies which looked at the effects of TQ on MCF-7 cells alone were limiting in their use of high concentrations of the chemical without emphasis on finding a minimum effective dosage. Additionally, a second study which tested the effects of TQ on both MCF-7 and MDA-MB-231 cell lines conducted the experiments in the presence of a lipid-carrier molecule. This, in turn, may have served as a confounding variable in the results. Therefore, it was hypothesized that a minimal effective dosage for both blackseed oil and TQ could be determined, where a significantly greater suppression of MDA-MB-231, in comparison to MCF-7, cell proliferation would be observed. Cell proliferation, cell adhesion, and soft agar assays were used to test the hypothesis of this study. The minimum effective dosage for each substance, characterized by proliferation of the non-aggressive MCF-7 cells to some extent and suppression of the aggressive MDA-MB-231 cells, were determined to be 0.5 µL for blackseed oil and 1.0 µM for TQ. Additionally, TQ’s effectiveness was noted to be more time-dependent than blackseed oil. This study supports the use of minimal effective doses for blackseed oil or TQ to naturally treat breast cancer while preventing damage to non-aggressive cells.

KEYWORDS Breast cancer; Blackseed oil; Nigella sativa; Thymoquinone; Effective dose; Natural remedies

Speech-Language Pathologists’ Perceptions of the Common Core State Standards: A Multi-State Study

Nicole Ariza & Patrick R. Walden

ABSTRACT This study investigated the Common Core State Standards (CCSS) from the perspective of Speech-Language Pathologists (SLPs) working with students with communication disorders in public schools. An invitation to participate in an anonymous, online questionnaire with both closed- and open-ended questions was posted to three online communities comprised of SLP’s working in schools across the United States of America (U.S.). Eighty-seven SLPs working in states using the CCSS completed the survey. The survey focused on four primary areas—the perceived impact of the CCSS on service delivery, student outcomes, professional workload and continuing professional education. Participants reported consistent incorporation of standards into services, but varied methods of implementation, primarily unchanged student outcomes, increased professional workload and a need for additional training. Overall, the CCSS’ intent to create consistent goals may not be accomplished due to variability in approaches in implementation of the standards. Additionally, more resources and trainings for SLPs are needed to fully implement CCSS into speech-language intervention in the schools.

KEYWORDS Common Core State Standards; School-Based Services; School-Based Issues; Speech-Language Pathology; Service Delivery; Student Outcomes; Professional Workload; Continuing Professional Education

A Comparative Study of All-atom Molecular Dynamics Simulation and Coarse-grained Normal Mode Analysis in Identifying Pre-existing Residue Interaction Networks that Promote Coupled-Domain Dynamics in Escherichia coli Methionyl-tRNA Synthetase

Samuel C. Fehling, Alexander M. Strom, Brent P. Lehman, Ryan J. Andrews, Sudeep Bhattacharyya, & Sanchita Hati

ABSTRACT Inter-domain communication plays a key role in the function of modular proteins. Earlier studies have demonstrated that the coupling of domain motions is important in mediating site-to-site communications in modular proteins. In the present study, bioinformatics and molecular simulations were usedto trace “pre-existing” residue-residue interaction networks that mediate coupled-domain dynamics in multi-domain Escherichia coli methionyl-tRNA synthetase (Ec MetRS). In particular, a comparative study was carried out to evaluate the effectiveness of coarse-grained normal mode analysis and all-atom molecular dynamic simulation in predicting pre-existing pathways of inter-domain communications in this enzyme. Integration of dynamic information of residues with their evolutionary features (conserved and coevolved) demonstrated that multiple residue-residue interaction networks exist in Ec MetRS that promote dynamic coupling between the anticodon binding domain and the connective polypeptide I domain, which are > 50Å apart, through correlated motions. Mutation of residues on these pathways have distinct impact on the dynamics and function of this enzyme. Moreover, the present study revealed that the dynamic information obtained from the coarse-grained normal mode analysis is comparable to the atomistic molecular dynamics simulations in predicting the interaction networks that are essential for promoting coupled-domain dynamics in Ec MetRS.

KEYWORDS Domain-domain Communication; Molecular Dynamics; Methionyl-tRNA Synthetase; Normal Mode Analysis; Coupled-domain Dynamics; Course-grained Normal Mode Analysis; Aminoacyl tRNA Synthetases; Statistical Coupling Analysis

Skewed and Flexible Skewed Distributions: A Modern Look at the Distribution of BMI

Thao Tran, Cara Wiskow, Mohammad Abdus Aziz

ABSTRACT The purpose of this study is to find distributions that best model body mass index (BMI) data. BMI has become a standard health indicator and numerous studies have been done to examine the distribution of BMI. Due to the skew and bimodal nature, we focus on modeling BMI with flexible skewed distributions. The distributions are fitted to University of Wisconsin–Eau Claire (UWEC) BMI data and to a data obtained from National Health and Nutrition Survey (NHANES). The model parameters are obtained using maximum likelihood estimation method. We compare flexible models to more conventional distributions, such as skew-normal, and skew-t distributions using AIC and BIC and Kolmogorov-Smirnov (K-S) goodness-of-fit test. Our results indicate that the skew-t and Alpha-Skew-Laplace distributions are reasonably competitive when describing unimodal BMI data whereas Alpha-Skew-Laplace and finite mixture of scale mixture of skew-normal and skew-t distributions are better alternatives to both unimodal and bimodal conventional distributions. The results we obtained are useful because we believe the models discussed in ours study will offer a framework for testing features such as bimodality, asymmetry, and robustness of the BMI data, thus providing a more detailed and accurate understanding of the distribution of BMI.

KEYWORDS Body Mass Index; Skew-normal distribution; Skew-t distribution; Flexible skewed distributions; Mixture distributions; Scale mixture of skew-normal distribution; K-S test

Exploration of the Influence of Smiling on Initial Reactions Across Levels of Facial Attractiveness

Stephanie M. Shields, Caitlin E. Morse, Paige Arrington, & David F. Nichols

ABSTRACT Both attractiveness and emotionality independently affect perception and interact to influence how a person perceives others. It has previously been shown that expressing positive emotions increases perceived attractiveness in general, but the relative influence of smiling across attractiveness levels and timing of this interaction is unknown. Such an interaction could entail dependent brain processing with interactions between brain areas or independent processing within each brain area. The present studies aimed to investigate this interaction and how it occurs through behavioral, specifically self-report, and physiological, specifically electrophysiological, methods. In each study, female undergraduate participants were shown images of male faces with smiling or neutral expressions. Study 1 used participant ratings to provide insight into the interaction and to establish an image subset of faces of high attractiveness (HA) and low attractiveness (LA). An interaction was found wherein HA faces were rated significantly higher on attractiveness when smiling whereas LA faces were rated similarly attractive regardless of emotional expression. Study 2 used electroencephalography (EEG) to examine the timing of brain responses to attractiveness, emotionality, and their interaction. Though a main effect of attractiveness consistently occurred prior to a main effect of emotional expression across two data sets, the presence of an interaction effect was inconsistent. There was some evidence for independent processing wherein the earliest brain responses are predominantly affected by attractiveness and are influenced by emotional expression, but dependent interactions between modular processing areas cannot be ruled out. Together, these results help to shed light on the interplay of attractiveness and emotionality though additional research could help to clarify the timing of the interaction on a neural level.

KEYWORDS Attractiveness, Emotionality, Emotional Expression, Smiling, Electroencephalography, Event Related Potentials

How to Become a “Real Chicagoan” in No Time: The Promise and Pedagogy of Walking Tourism

Jacob Henry

ABSTRACT This study takes seriously the tourist’s desire to feel like a local and examines how walking tour guides work toward fulfilling that desire. The paper examines some of the techniques used by urban walking tour guides to convey local cultural cues. The tourist, armed with these cues, may feel able to fit into a new culture as a quasi-insider. Through qualitative methods, primarily participant observation, the researcher identifies three tactics that guides implement to make the tourist to feel like a local. These tactics are labeled agent alignment, urban alchemy, and material action. These tactics take place within a borderzone, the liminal time-space between insider and outsider status. A successful guide facilitates the border crossing, allowing the tourist to transition from tourist to perceived ‘real Chicagoan.’ However, the unsuccessful guide forces tourists to exit the borderzone unchanged, still as tourists. These findings highlight the uniqueness of walking tourism as a niche tourism and wade into the conceptual milieu of ‘localism’ and ‘the local.’

KEYWORDS Walking Tourism; Urban Tourism; Tour Guides; Localization; Interculturalism; Urban Alchemy; Agent Alignment; Chicago

Characterization of Rectifying and Sphere Curves in 3

Julie Logan & Yun Myung Oh

ABSTRACT Studies of curves in 3D-space have been developed by many geometers and it is known that any regular curve in 3D space is completely determined by its curvature and torsion, up to position. Many results have been found to characterize various types of space curves in terms of conditions on the ratio of torsion to curvature. Under an extra condition on the constant curvature, Y. L. Seo and Y. M. Oh found the series solution when the ratio of torsion to curvature is a linear function. Furthermore, this solution is known to be a rectifying curve by B. Y. Chen’s work. This project, uses a different approach to characterize these rectifying curves.

This paper investigates two problems. The first problem relates to figuring out what we can say about a unit speed curve with nonzero curvature if every rectifying plane of the curve passes through a fixed point  in ℝ3. Secondly, some formulas of curvature and torsion for sphere curves are identified.

KEYWORDS Space Curve; Rectifying Curve; Curvature; Torsion; Rectifying Plane; Tangent Vector; Normal Vector; Binormal Vector

Previvors’ Perceptions of Hereditary Breast and Ovarian Cancer Health-related Information 

Rachel Koruo, Marleah Dean, Courtney L. Scherr, Meredith Clements, Amy A. Ross

ABSTRACT The purpose of this study is to identify female previvors’ perceptions of hereditary breast and ovarian cancer (HBOC) health-related information. Previvors are individuals who have tested positive for a harmful BRCA genetic mutation, which increases their lifetime risk for HBOC, but who have never been diagnosed with cancer. As a part of a larger research project where 25 qualitative interviews were conducted, this manuscript reports on the analysis of ten interviews which are most relevant to the research focus. Using the constant comparative method, themes were created and developed from the interview data. The results indicate previvors view information as a source of power. These women reported feeling personally responsible for seeking and sharing information, while also relying on medical professionals to provide credible sources of information. Furthermore, previvors emphasized a desire for medical professionals to be more informed about BRCA in order to assist them in making personal health decisions.  This study presents the perceptions regarding HBOC information as reported by this population of previvors. The findings indicate that information is not provided in an organized way relative to their specific needs. Therefore, the authors recommend an educational intervention tool for previvors and their medical professionals.

KEYWORDS BRCA; Communication; Qualitative; Hereditary Cancer; Health Experiences; Previvors; Medicine; Patient Perspectives; Health Information

Determination of Fitted Size Distribution for Atmospheric Aerosols

Kaitlin M. DuPaul, Adam T. Whitten

ABSTRACT A synthetic set of aerosol optical depths (AODs) generated from a standard set of aerosol size distributions was analyzed by a parameter based particle swarm optimization (PBPSO) routine in order to test the reproducibility of the results. Junge and lognormal size distributions were consistently reproduced. Gamma and bimodal distributions showed large variability in solutions.  values were used to determine the best subset of possible solutions allowing quantification of parameters with uncertainties when using PBPSO. AODs measured by a sun photometer on a clear day (20160413) and a foggy day (20160508) were then processed by the PBPSO program for both bimodal and lognormal distributions. Results showed that in general the foggy day has smaller  values indicating that the PBPSO algorithm is better able to match AODs when there is a larger aerosol load in the atmosphere. The bimodal distribution from the clear day best describes the aerosol size distribution since the  values are lower. The lognormal distribution best describes the aerosol size distribution on the foggy day (20160508).

KEYWORDS Atmospheric Aerosols; Size Distributions; Junge; Bimodal; Gamma; Lognormal; Particle Swarm Optimization; Inverse Problem; Aerosol Optical Depth

Strategy Abandonment Effects in Cued Recall

Stephanie A. Robinson, Amy A. Overman, & Joseph D.W. Stephens

ABSTRACT Decades of research have investigated the effects of encoding strategies in the formation of associations in memory. Despite this, it is not known whether or how changes in the use of strategies within a brief time span may affect memory. For example, what is the effect on memory of abandoning a recent strategy or switching to a different strategy? The present study systematically varied the strategies used by participants in two closely-spaced associative memory tasks. Results indicated that intentional abandonment of a verbal (sentence-generation) strategy had disproportionately negative consequences on memory for semantically unrelated word pairs. The findings suggest that memory encoding is affected by differences in strategy use across recent memory tasks, and have implications for effective use of memory strategies in practical settings.

KEYWORDS Cued Recall; Encoding Strategies; Inhibition

AJUR Volume 14 Issue 1 (April 2017)

Click on the link below to download the full high-definition interactive pdf for

AJUR Volume 14 Issue 1 (April 2017)

Links to individual manuscripts, abstracts, and keywords are provided below.


pp. 5-10 Identifying Issues Surrounding First Generation Students
Lena Rubio, Candi Mireles, Quinlan Jones, & Melody Mayse
Social Work Department, Tarleton State University
First-generation students compose a subpopulation within the institution of higher education, which exhibits its own set of resources in areas such as academic preparation, support systems, family background, and finances to apply to education. This quantitative study examined gaps and barriers to resources currently available to assist the population. The researchers utilized four pre-developed demographic questions along with a 34-item survey instrument assessing the experiences of first generation students, to gather the data presented in the study. The analysis involved coding and elementary data analysis of demographics and reporting frequencies. The 200 participants in the study identified as first-generation students at four-year universities within the United States. The majority of the participants surveyed were white (69.5%; n= 139), between the ages of 17 and 26 (94.5%; n=189), and from families within the middle-class income bracket of (39.5%; n= 79). The results indicated that most common barrier to participants attending college was tuition-cost (63%; n=126), followed by a lack of information about a college, such as financial aid availability and required documents (34.5%; n=69). Over 64% (n=129) received support or guidance from support networks in the form of parents and/or guardians. The study provided information about the issues encountered by first-generation students, as well as the accessed support networks, and preferred resources.
First-Generation Student; College Retention; Academic Preparation; Financial Assistance; Support Systems

pp. 11-16 A Comparative Analysis of the Fitness of Collegiate Dancers as compared to Collegiate Volleyball and Softball Players
Leanna Miller* & Fred L. Miller III
Department of Kinesiology, Anderson University, Anderson, IN
Few studies directly compare the various fitness components of collegiate dancers and athletes in acknowledged sports. The limited studies that do exist fail to consider certain variables or to assess multiple fitness components. The purpose of this study was to provide a more comprehensive comparison of collegiate dancers and collegiate volleyball and softball players. We used multiple fitness components as an indicator of the comparative physical demands of these activities, to assess whether the physical demands of collegiate dance may warrant a comparable level of medical support as afforded to the volleyball and softball players. Thirty dancers and thirty volleyball and softball players were tested using six different measurements of physical fitness commonly used in athletic assessments at universities. A two-tailed independent t-test was performed to determine differences between dancers and athletes in each fitness component. Three tests revealed significant differences between the groups, with the dancers having a lower percent body fat and greater flexibility, and the athletes having greater relative upper body strength. No significant differences were found in relative leg strength, core strength, or estimated VO2max. The results of the current study suggest that dance provides training adaptations equivalent to traditional intermittent sports and thus support the use of similar levels of medical care for collegiate dancers to that afforded to collegiate volleyball and softball players.
Physical Fitness; Dance; Dance Medicine; Athletics; Dance Health Benefits

pp. 17-24 Adaptation of Esherichia coli to Antiobiotic Cycling via Single Nucleotide Polymorphisms
Samuel E. Hager, Ellen Jensen, Timothy J. Johnson, & David Mitchell*
Department of Biology, College of Saint Benedict/Saint John’s University, Collegeville, MN
Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN
Bacteria are quick to adapt and evolve, especially under the effects of selective pressures from chemical antibiotics. In addition, bacteria may develop resistance to antibiotics from multiple classes simultaneously, making their eradication from the human body particularly challenging. This study aims to demonstrate that bacterial multiple-drug resistance can be developed and retained in a laboratory setting. Escherichia coli B was grown in tryptic soy broth in the presence of a small, increasing concentration of streptomycin. This exposure resulted in a strain of E. coli, which had an increased minimum inhibitory concentration (MIC) towards streptomycin, or “resistance.” This resistant strain was then grown in like manner in nalidixic acid and then penicillin G. The result was a strain that became resistant to streptomycin and nalidixic acid, and increasingly resistant to nalidixic acid after penicillin G exposure. Additionally, the bacteria retained resistance to streptomycin and nalidixic acid even after exposure to those chemicals ceased. Genome sequencing and comparison to E. coli B reference strain REL606 revealed the emergence of point mutations with each exposure to an antibiotic. Of particular interest is a mutation associated with the appearance of nalidixic acid resistance. Base pair 4,553,488 was changed from adenine to guanine, resulting in a change from aspartate to glycine in the protein helicase. Previous studies have not indicated mutations to this locus as nalidixic acid resistance conferring. Thus, this mutation may be a novel mutation conferring E. coli B nalidixic acid resistance. Since the region of the mutated helicase is functionally undefined, a mechanism is not apparent. Further research needs to be done to confirm this hypothesis and illuminate a mechanism.
Bacteria; Escherichia coli; Evolution; Antibiotic Resistance; Nalidixic Acid; Streptomycin; Point Mutation; Single-nucleotide Polymorphism; Helicase; Minimum Inhibitory Concentration

pp. 25-34 Constructing the Imaginative Bridge: Third-Generation Holocaust Narratives
Megan Reynolds*
Department of English, Trinity University, San Antonio, TX
Reynolds’s research examines the ways in which third-generation Holocaust writers, the grandchildren of Holocaust survivors, approach the subject of their own traumatic history and the intergenerational transmission of trauma and memory. Despite the two generational divide that separates the third generation from the preceding two generations of Holocaust writers, the trans-generational transmission of trauma continues to preoccupy contemporary narratives. This research examines the ways the grandchildren of survivors, represented in this paper by Margot Singer and Jonathan Safran Foer, confront and include lost worlds in their narratives as well as their attempts to resurrect these fractured pasts through innovative uses of imaginative leaps. The third generation continues to suffer from the intergenerational transmission of trauma and memory yet discovers innovative ways to share that trauma, evidence of evolving modes of bearing witness.
Holocaust Narratives; Third-Generation; Intergenerational Transmission of Trauma; Literature; Trauma; Memory Studies; Jewish Identity; Grandchildren of Survivors

pp. 35-48 Mathematical Modeling Analysis to Simulate the Dynamics of Immune Cells, HIV, and Tuberculosis
Rumana Ahmed & Mahbubur Rahman
Department of Biology, the City College of the City University of New York, New York, NY
Department of Mathematics and Statistics, University of North Florida, Jacksonville, FL
The dynamics of immune cells, HIV, and tuberculosis can be described by a system of differential equations. We developed the formulations for this dynamical system. To evaluate the system as time goes to infinity, we investigated the equilibrium solutions. We established the criteria for stability based on the characteristics of the Jacobian matrix associated with the dynamical system. To investigate the bifurcation of the solution, we developed phase plane diagrams for the sets of assumed values of the parameters. we have investigated the curves for different values of the starting conditions of immune cells and the antigens. Along the curves, we observed the growth and decay processes. The stability of the system has been established by examining the phase plane diagrams as the solution approaches the equilibrium point. Based on phase diagrams, both stable and unstable systems have been simulated and examined in this study. Finally, we developed and evaluated the graphs for the unsteady variations of immune cells, HIV, and tuberculosis to see how the antigens grow because of the diminishing effects of immune cells in the system as time increases.
Mathematical Biology; Infectious Disease Modeling; Dynamical System; Simulation of Immune Cells and Antigens

pp. 49-60 Gender and Sexuality in Medieval Islamic Mysticism: A Comparative Study of Ibn ‘Arabi and al-Ghazali
Emily Dovel*
History Department, University of Portland, Portland, OR
Mysticism, defined as a direct experience with God that cannot occur through intellectual knowledge, has the potential to offer women opportunities disallowed by a patriarchal society. Because mysticism exists outside of religious institutions and hierarchies, female mystics could receive opportunities for public expression often prohibited by Medieval Islamic societies. Islamic Mysticism, or Sufism, has a long history of prominent female mystics. However, Sufi thought in the 12th and 13th centuries was certainly affected by the misogynistic influences of the greater society. In order to explore the ideological conflict within medieval Sufism, between the potential for gender egalitarianism within mysticism and the influences of patriarchy, this paper examines the theology of two prominent Sufi mystics, Ibn ‘Arabi and al-Ghazali, and proposes some explanations for the large disparity between the two Sufis’ opinions on gender and sexuality. Specifically, al-Ghazali fully supports the subjugation of women, and even equates the perpetuation of patriarchy to religious piety. This paper argues that, living under the politically turbulent and authoritarian reign of the Seljuks in Iraq, during the late 11th and early 12th centuries, al-Ghazali was particularly disinclined to question traditional orthodoxy, particularly with regard to gender. Ibn ‘Arabi, by contrast, accepts the spiritual, intellectual, and legal equality of women to a remarkable extent. Raised in Muslim Spain in the late 12th and early 13th centuries, Ibn ‘Arabi was exposed to female mystics as teachers and experienced little political pressure to conform to traditional doctrine. Further, Ibn ‘Arabi subscribes to Oneness of Being theology in which the created, material universe is an emanation of God, and is ultimately part of the same divine being. As such, unlike many religious thinkers within patriarchal societies, who tend to reject worldliness—along with women and female sexuality—in an attempt to reach God, Ibn ‘Arabi believes that all things material—including women and the human body—are ultimately connected to divinity.
Islam; Sufism; Gender; Sexuality; Theology; Medieval History

pp. 61-77 Breaking the Chain of Silence: Political Activism and Social Justice in Omar Offendum’s Syrian-American Hip-Hop
Harry Olafsen, Mohammed Ali, Mikayla McCord, and Dr. Roxana Cazan*
Department of Literature and Languages, Saint Francis University, PA
Pre-Medicine Track, Indiana University of Pennsylvania, PA
Department of Business, University of South Carolina in Columbia, SC
Dissatisfied with the decisions of the Western political class to remain uninvolved in helping settle the conflict in Syria, many hip-hop, rap, and pop artists from Syria and the surrounding region have been creating and performing politically charged music that promotes liberty, and justice in the Middle East. One artist in particular, Omar Offendum (in the United States), writes and brings to the stage his hip-hop music in a way that continues and enhances this political-artistic movement across the Atlantic. Employing rhymes and rhythms that foster commotion and make noise, Offendum breaks the global indifference accumulated around the topics of the Syrian war and the unsolvable debates about allowing a certain number of Syrian asylum seekers to apply for refugee status in Western nations. He underscores that apathy is not an option for those who oppose the oppressor. In this paper, we argue that Offendum’s music constitutes an effective tool of political propaganda that can raise social consciousness of the needs of Syrians today and inspire social justice. Because the political-ideological space that feeds his creative act is set in a civil-rights-conscious U.S., Offendum often appeals to a heritage, reminding the listener of the activism of the Black Panthers, the legacy of Malcom X, and the freedom battles of Rodney King and his followers. In many of his songs, Offendum uses Arabic, both as a means of highlighting the authenticity of his hybrid identity and as a method of marking a cultural space for a diverse audience to come together. In this paper, we offer a brief historical look at the role of hip-hop in the struggle for civil rights in the US in order to locate the legacy Offendum’s music builds on and to assess its power. We then perform a close analysis of three of his most famous songs and conclude with a brief discussion of the impact of Offendum’s on social media platforms globally.
Hip-Hop; Activism; Social Justice; Omar Offendum; Social Consciousness; Syrian War; Syrian Refugees; Civil Rights

AJUR Volume 13 Issue 4 (December 2016)

Click on the link below to download the full high-definition interactive pdf for
AJUR Volume 13 Issue 4 (December 2016)

Links to individual manuscripts, abstracts, and keywords are provided below.

p. 5 Green Chemistry: Comparison of Ionic Liquid vs Conventional Solvent for
Indole Alkylation
Jonathan G. Redrico & John L. Krstenansky
A comparison of the effectiveness of two synthetic methods was done for a green chemistry method using an ionic liquid-based solvent relative to a conventional method using organic solvents for the N-alkylation of indole. The green method used potassium hydroxide in the ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate, followed by addition of the alkyl halide. The conventional method used sodium hydride in dimethylformamide. Possible advantages of the green method would be the use of a non-volatile solvent, the possibility of recycling the solvent, and the use of a less reactive base. However, its reaction yield was lower than for the conventional method, the reagent expense was higher, and recycling and reuse of the ionic solvent require considerable amounts of conventional solvent to clean it up sufficiently for reuse. On a laboratory scale, the ionic liquid method yielded neither a “green” nor an efficiency advantage. It is possible that with optimization on an industrial scale involving solvent reclamation that the green method could realize its promise.
Green Chemistry; Sustainable Chemistry; Ionic Liquids; N-alkylation; Indole; Solvent Recycling; Organic Chemistry; 1-Butyl-3-methylimidazolium Tetrafluoroborate; Synthesis

p. 11 Use of the Bruker AXS SMART BREEZE™ System for Macromolecular
X-ray Data Collection
Christiana Standler, G. Blake Overson, Cody A. Black, Guizella A. Rocabado,
& Bruce R. Howard
The Bruker AXS SMART BREEZE™ system is a single-crystal X-ray diffractometer designed to collect data from crystals of small organic or inorganic compounds. It is typically equipped with a Molybdenum-anode sealed tube to facilitate data collection from small unit cells. We recently acquired this system, but chose to have it installed with a copper-anode sealed tube with the hope of using it to collect data from larger unit cells such as those found in crystals of proteins or other macromolecules. This is the first and only BREEZE™ system installed by Bruker AXS with a copper-anode to date. Here we show that this system is capable of efficiently collecting quality X-ray diffraction data from crystals of the enzymes lysozyme and xylanase. This capability to collect diffraction data from both macromolecular and small-molecule crystals greatly expands the scope of undergraduate research projects that can be addressed using this instrument.
X-ray; Diffraction; Crystallography; Diffractometer; Protein; Enzyme; Crystal; Structure

p. 21 Ebola Impact and Quarantine in a Network Model
Anca Radulescu & Joanna Herron
Much effort has been directed towards using mathematical models to understand and predict contagious disease, in particular Ebola outbreaks. Classical SIR (susceptible-infected-recovered) compartmental models capture well the dynamics of the outbreak in certain communities, and accurately describe the differences between them based on a variety of parameters. However, repeated resurgence of Ebola contagions suggests that there are components of the global disease dynamics that we don’t yet fully understand and can’t effectively control. In order to understand the dynamics of a more widespread contagion, we placed SIR models within the framework of dynamic networks, with the communities at risk of contracting the virus acting as nonlinear systems, coupled based on a connectivity graph. We study how the effects of the disease (measured as the outbreak impact and duration) change with respect to local parameters, but also with changes in both short-range and long-range connectivity patterns in the graph. We discuss the implications of optimizing both these measures in increasingly realistic models of coupled communities.
Epidemic Spread; Network Dynamics; Network Connectivity; Coupled Differential Equations; Compartmental Model; Information Transfer; Outbreak Impact; Outbreak Duration

p. 37 Analysis of Vortex Pool-and-Chute Fishway
Mathew Nyberg, Brian Draeger, Brian Weekly, Eileen Cashman, & Michael Love
Fishways are constructed in riverine habitats where structures such as culverts, dams, and flood channels have negatively impacted flow conditions suitable for the movement of native and migratory fish species. These auxiliary channels are engineered to resist gravitational force with frictional force, resulting in sustained depth and reduced velocity over a range of design flow rates. The Chézy hydraulic resistance coefficient accounts for such forces and provides a metric useful for determining the effectiveness of a fishway to alter flow conditions prohibitive to the passage of fish. The objective of this analysis was to use a scale model of an innovative vortex pool-and-chute fishway, that operates with both plunging and streaming flow simultaneously, designed by Michael Love and Associates, to determine the Chézy resistance coefficients over a range of flow rates under controlled hydraulic conditions. Using dimensional analysis to ensure proper scaling allowed laboratory measurements of the model to be translated into a real-world prototype design. The conceptual prototype fishway is a 144-foot-long by 30-foot-wide channel with an 8% slope. A 1:15 scale model was constructed to evaluate the design at prototype equivalent flow rates between 58 and 283 cubic feet per second (cfs). Chézy coefficients were estimated by two different calculation methods; the streaming flow method and the streaming and plunging flow method. Coefficients ranging between 22.3 and 39.2 ft1/2/s were determined by the streaming flow calculation method, whereas the streaming and plunging flow calculation method yielded estimates from 18.9 to 25.0 ft1/2/s at corresponding flow rates. For flows that were exclusively plunging, values of 32.2 to 41.9 ft1/2/s were found. In general, Chézy coefficient estimates were observed to decrease with increasing discharge and values were found to be comparable to those calculated for fishways implemented at similar slopes. The preliminary model fishway results indicated that implementation of a prototype fishway could effectively alter flows for adequate fish passage under the given conditions.
Hydraulics; Fish Passage; Fishway; Chézy Coefficient; Geometric Scaling; Froude Scaling; Streaming Flow; Plunging Flow; Dimensional Analysis; Similitude

p. 59 Dynamic Visualization of Time-Based Changes to Data Generated by
Reddit.com: The Real Time Conversation Project
Daniel Wang, Andy Luse, & Jim Burkman
With the increased amount of data generated by social networking sites there is also increased difficulty in the analysis of this data, including time-based changes, which can provide unique insights in social network analysis. Information visualization is a vital tool in assisting social scientists with analysis of large quantities of data; however, the gathering, formatting, and visualizing of time-related data from social networking sites still remains an obstacle. This research explores the process of gathering time-based data in real time and using dynamic visualization techniques to visualize and analyze time-based changes in data generated by discussions on the social networking site Reddit. The outcome culminates in our deliverable, the Real Time Conversation Project.
Visualization; Network Analysis; Social Network; Reddit; Gephi

p. 69 Effects similar to anxiolysis in an organic extract of Stypopodium zonale on an anxiety-related behavior in Drosophila melanogaster
Keysh Mejías, Grisel Robles, Zulmari Martínez, Anamaris Torres, Lee Algarín, Genesis López, & Ricardo Chiesa
Nature has a great diversity of organisms whose bioactive compounds may potentially be studied. When it comes to aquatic life we find that algae are organisms that are well suited for screening and identification of bioactive compounds due to their widespread distribution in both salt and freshwater. Our hypothesis is that a crude organic extract of the brown algae Stypopodium zonale can decrease anxiety-related behaviors in Drosophila melanogaster. Stypopodium zonale was collected in the south coast of Puerto Rico and the potential anxiolytic-like effects of the extract were studied in an anxiogenic-like behavioral paradigm in Drosophila melanogaster. This behavior is called centrophobia and is measured using an Open Field Arena (OFA). Validation of the paradigm gave the expected results as reported in the literature, in which Drosophila exhibits a phobia (avoidance) of remaining in the center of the OFA, which corresponds to a behavior with anxiety components. The organic extract was dissolved with dimethyl sulfoxide (DMSO). Toxicity tests were performed both for DMSO and the crude organic extract, and neither showed positive results. To perform the behavioral trials, 1 mL of the crude extract and 4 mL of water were mixed with 1.8 g of Drosophila food. The final concentration of the crude extract in the food was 5.4 mg/mL. The adult flies were grown in a tube with the extract until a considerable quantity of larvae was observed, and then the adults were removed. These new larvae, once turned into adult flies, were used for the behavioral trials. The behavior of control flies (food without extract) and experimental flies (extract containing food) was recorded with a video camera and the results of the centrophobic behavior were analyzed and compared using quantitative criteria. Both the control and experimental trials were performed in triplicate. The results show that flies grown in food containing the crude extract present a significant reduction in centrophobia compared with control flies. In conclusion, our results suggest that the organic crude extract from Stypopodium zonale has anxiolytic-like effects in a Drosophila melanogaster model with anxiety components. We are currently performing Nuclear Magnetic Resonance (NMR) studies on the crude extracts to identify the most abundant secondary metabolites. Future experiments should include the administration of the crude extracts (or fractions of the most abundant secondary metabolites) to a vertebrate model in to test the effect in a behavior with anxiety components. We are also in the process of developing a preliminary model of possible mechanisms of action of the crude organic extract in the reduction of centrophobia.
Anxiety; Algae; Drosophila melanogaster; Open Field Arena; Organic extracts; Centrophobia; Stypopodium zonale

AJUR Volume 13 Issue 3 (August 2016)

Click on the link below to download the full high-definition interactive pdf for
AJUR Volume 13 Issue 3 (August 2016)

Links to individual manuscripts, abstracts and keywords are provided in the section below:


p. 5 Effects of the Electronegativity of Second Row Elements on Their Bonding to Boron
Xavier Shiu & J. Conceicao
ABSTRACT The effects of electronegativity on the bonding between boron and second row elements are studied in this paper. Calculations using Density Functional Theory (DFT), Moller-Plesset Theory (MP2) and Natural Bonding Orbital (NBO) analysis were performed on BF3, B(OH)3 and B(NH2)3 and the localized bonding properties of these molecules were elucidated. All of these molecules showed the absence of pi-bonding and did not obey the octet rule. With decreasing electronegativity of the terminal atoms, F, O and N in BF3, B(OH)3, B(NH2)3 there is increasing the propensity of electron donation from these terminal atoms to the empty p-orbital of the central boron.  Within the BH2−F, BH2−OH and BH2−NH2 series, the amino-borane showed the largest change in relative bond length and angle across this set. Furthermore, the borate anion, O−B(OH) 2 was subjected to identical analysis and pi-bond formation was observed. Our results show that a good match orbital energies between the donor and acceptor orbitals are important for pi-bond formation.
KEYWORDS Electronegativity; Boron Trifluoride; Boric Acid; Triaminoborane; Borate Anion; Octet Rule; Density Functional Theory; Natural Bonding Orbital; Pi-Bond; Double Bond

p.13 What Angle Will You Take? Patterns of Perspective-Taking in a Body-Based Task
Tegan Garon
ABSTRACT When people conceptualize abstract ideas, different perspectives can help them to make connections and develop their reasoning. In this study, three third grade students who engaged in a body-based angle task, using the Kinect for Windows, were analyzed. Descriptions of their interviews are presented, including a detailed analysis of their patterns of perspective-taking and factors that might have been conducive to their learning. It was observed that students typically adopted a body-based perspective before transitioning to other perspectives. Further, the design of the task and interviewer comments were important factors that prompted students to take different perspectives. The implications for perspectives and their impacts on learning are discussed.
KEYWORDS Embodied Cognition; Angles; Mathematics Education; Perspectives; Movement

p.27 Affine Symmetry Tensors in Minkowski Space
Isaac Ahern & Sam Cook
ABSTRACT Killing vectors are generators of symmetries in a spacetime. This article defines certain generalizations of Killing vectors, called affine symmetry tensors, or simply affine tensors. While the affine vectors of the Minkowski spacetime are well known, and partial results for valence n = 2 have been discussed, affine tensors of valence n > 2 have never been exhibited. In this article, we discuss a computational algorithm to compute affine tensors in Minkowski spacetime, and discuss the results for affine tensors of valence 2 ≤ n ≤ 7. After comparison with analogous results concerning Killing tensors, we make several conjectures about the spaces of affine tensors in Minkowski spacetime.
KEYWORDS Affine Symmetry Tensors; Affine Vectors; Killing Tensors; Killing Vectors; Minkowski Spacetime; Dimension; Maple CAS; Lie Derivative; Generalized Killing Tensor

p.33 A Relationship Between Time Perception and State-Anxiety
James Brown
ABSTRACT Participants in this study were randomly assigned to one of three interval groups of either one, three, or five minutes. All participants were asked to estimate a group-assigned time interval and complete the state portion of the State Trait Anxiety Inventory (STAI). It was hypothesized that higher levels of state anxiety would cause participants to overestimate the passage of time. It was also hypothesized that shorter interval durations would be estimated more accurately than longer interval durations. Results of a t-test did not support the first hypothesis. Results of a linear trend analysis did support the second hypothesis (P < .05). These results indicate that state-anxiety does not cause the passage of time to be overestimated and that interval duration length affects how accurately time is estimated. Implications of this study are important to the understanding of human time-management ability and time estimation errors.
KEYWORDS Time estimation; Perception; State-anxiety; Attention; Working memory; Emotion

p.41 On Closure Properties of Irrational and Transcendental Numbers under Addition and Multiplication
Shekh Mohammed Zahid & Prasanta Kumar Ray
ABSTRACT In the article ‘There are Truth and Beauty in Undergraduate Mathematics Research’, the author posted a problem regarding the closure properties of irrational and transcendental numbers under addition and multiplication. In this study, we investigate the problem using elementary mathematical methods and provide a new approach to the closure properties of irrational numbers. Further, we also study the closure properties of transcendental numbers.
KEYWORDS Irrational numbers; Transcendental numbers; Dedekind cuts; Algebraic numbers

p.45 Peaked T-Waves and Potassium: The Reliability of Peaked T-Waves as Indicators of Hyperkalemia in End-Stage Renal Patients Undergoing Hemodialysis
Ryan D. Pappal, Ilse M. Espina & Zubaid Rafique
ABSTRACT While peaked T-waves have traditionally been associated with hyperkalemia cases, previous studies have called their reliability for hyperkalemia diagnosis into question. This study examined 89 ESRD patients totaling to 736 patient visits. Linear regressions and receiver operating characteristic (ROC) analyses were utilized to assess the reliability of peaked T-waves as a diagnostic criterion for hyperkalemia. Poor correlations between T/R ratio (leads V2-V4) and serum potassium were found, r = 0.23, 0.17, and 0.17, p < 0.001. R2 values ranged from 0.03 to 0.05. ROC analysis found poor sensitivity and specificity of T/R as a predictor of hyperkalemia (area under the curve: 0.61 – 0.66), and the T/R ≥ 0.75 threshold yielded a sensitivity of 0.83 with a specificity of 0.40 when predicting hyperkalemia (serum potassium > 5.5 mEq/L). We conclude that the peaked T-wave is a poor indicator for the early identification of hyperkalemia in ESRD patients presenting to the emergency department.
KEYWORDS Hyperkalemia; Electrocardiography; End-stage Renal Disease; Hemodialysis; Arrhythmias, Potassium; Sensitivity and Specificity; ROC Curve

p.53 Modeling Internet Traffic Generations Based on Individual Users and Activities for Telecommunication Applications
Sara Stoudt, Pamela Badian-Pessot, Blanche Ngo Mahop, Erika Earley, Jordan Menter, Yadira Flores, Danielle Williams, Weijia Zhang, Liza Maharjan, Yixin Bao, Laura Rosenbauer, Van Nguyen, Veena Mendiratta & Nessy Tania
ABSTRACT A traffic generation model is a stochastic model of the data flow in a communication network. These models are useful during the development of telecommunication technologies and for analyzing the performance and capacity of various protocols,algorithms, and network topologies. We present here two modeling approaches for simulating internet traffic. In our models, we simulate the length and interarrival times of individual packets, the discrete unit of data transfer over the internet. Our first modeling approach is based on fitting data to known theoretical distributions. The second method utilizes empirical copulae and is completely data driven. Our models were based on internet traffic data generated by different individuals performing specific tasks (e.g., web browsing, video streaming, and online gaming). When combined, these models can be used to simulate internet traffic from multiple individuals performing typical tasks.
KEYWORDS Internet Traffic Simulation; Stochastic Models; Empirical Copula; Cumulative distribution function; Wireshark

Volume 13, Issue 2, June 2016

Click on the link below to download full interactive pdf for
AJUR Volume 13 Issue 2 (June 2016)

Quick links to individual manuscripts (abstracts and keywords are provided in the section below):

p. 5 Robust Nonlinear Control of BLDC Motor in Quadcopter Applications
Steven T. Elliott & Thomas W. Carr

p. 15 Development of Four-Square Fiducial Markers for Analysis of Paper Analytical Devices
Jenna Wilson, Tabitha Ricketts, Ian Bentley & Ewa Misiolek

p. 29 Sensitivity Analysis of Common Input Parameters in Tools for Modeling Energy in Homes
Sheikh Tijan Tabban & Nelson Fumo

p. 43 Feeding Anti-Semitism: Representations of Jewish Food Practices in Der ewige Jude
Forrest Picher

p. 57 hTERT Suppression via Small Interference RNA in Cervical Cancer Cells
Shawn Gray & Douglas Christensen

p. 65 Malate : Quinone Oxidoreductase and Malic Enzyme are required for the Plant Pathogen Pseudomonas syringae pv. tomato DC3000 to Utilize Malate
Zabrina Ebert, Preston Jacob, Katrina Jose, Lina Fouad, Katherine Vercellino, Steven Van Dorn, Mahaa Sidiqqi & Eve M. Mellgren

p. 73 Engaging Students in Science through a Nature Hike: A Case of Two Students with ADHD
Ashleigh Moore, Kristy Lynn Daniel & Aimée K. Thomas

p. 81 Evaluation of Antiulcer Activity of Laghusoothshekhar (an Ayurvedic Formula) in Pyloric Ligature Induced Gastric Ulcers in Albino Rats
Nilofer Sayed & Vandana Barve

p. 87 Using Statistical Approaches to Model Natural Disasters
Audrene S. Edwards & Kumer Pial Das

p. 105 Explicit Solution for Cylindrical Heat Conduction
Kaitlyn Parsons, Tyler Reichanadter, Andi Vicksman & Harvey Segur

Abstracts and keywords for articles published in AJUR Volume 13 Issue 2:

p. 5 Robust Nonlinear Control of BLDC Motor in Quadcopter Applications
Steven T. Elliott & Thomas W. Carr
This paper describes the development of a nonlinear closed loop motor control system for a quadcopter micro-unmanned aerial vehicle (micro-UAV) platform. Research groups have analyzed the performance of brushless direct current (BLDC) motors with nonlinear effects in various applications, focusing on areas such as friction’s effect on position. This paper analyzes the nonlinear effects of BLDC motors on speed when these motors are used in quadcopter flying robots. Notably, to account for nonlinear torque from the aerodynamic forces on a quadcopter rotor, a Control Lyapunov Function (CLF) approach is used in designing a stable feedback control system. The paper also explains the custom model and simulation of the system built in MATLAB/Simulink used to demonstrate and quantify the successful performance of the design.
Control Lyapunov Function; Micro-Unmanned Aerial Vehicle; Aerial Robotics; Quadcopters; Nonlinear Motor Control

p. 15 Development of Four-Square Fiducial Markers for Analysis of Paper Analytical Devices
Jenna Wilson, Tabitha Ricketts, Ian Bentley & Ewa Misiolek
Fiducial markers are used in image processing to determine locations of interest based on fixed points of reference. There are a number of applications for these markers across various fields ranging from advertising to radiation therapy. The four-square fiducial markers discussed in this manuscript allow for the determination of locations of interest on digital images. These new markers are easily detected, provide information about image orientation, and allow for local color sampling. The markers are intended for use in a pharmaceutical assessment process in which images of colorimetric chemical tests are taken by a smart-phone in the field, uploaded to a database, and analyzed to collect quantitative information about the colors resulting from the tests.
Image Processing; Digital Imaging; Fiducial Markers; Image Thresholding; Color Calibration; MATLAB; Paper Analytical Devices

p. 29 Sensitivity Analysis of Common Input Parameters in Tools for Modeling Energy in Homes
Sheikh Tijan Tabban & Nelson Fumo
Energy models of buildings can be developed and used for analysis of energy consumption. A model offers the opportunity to simulate a building under specific conditions for analysis of energy efficiency measures or optimum design. Due to the great amount of information needed to develop an energy model of a building, the number of inputs can be reduced by making variable the most relevant input parameters and making the others to take common or standard values. In this study, an analysis of input parameters required by computational tools to estimate energy consumption in homes was done in two stages. In the first stage, common input parameters were identified for three software and three webtools based on the criteria that the input parameter should be common for at least two software and at least one webtool. In the second stage, a sensitivity analysis was performed on the inputs identified in the first stage. The software BEopt, developed by the National Renewable Energy Laboratory, was used as the source of typical input parameters to be compared, and to perform the simulations for the sensitivity analysis. The base or reference model to perform simulations for the sensitivity analysis corresponds to a model developed with information from a research house located on the campus of the University of Texas at Tyler and default inputs for the BEopt B-10 reference benchmark. Results show that besides the location, and consequently the weather, common parameters are building orientation, air leakage, space conditioning settings, space conditioning schedule, water heating equipment, and terrain. Among these parameters, the sensitivity analysis identified the largest variations in energy consumption for variations on space conditioning schedule (heating and cooling setpoints), followed by the type of water heating equipment.
Residential Buildings; Energy Consumption; Energy Analysis; Input Parameters; Building Simulation; Source Energy

p. 43 Feeding Anti-Semitism: Representations of Jewish Food Practices in Der ewige Jude
Forrest Picher
The film Der ewige Jude has received a considerable amount of scholarship, but never solely in the context of its representations of Jewish food practices. This paper addresses this void arguing that the representations are used to de-civilize and dehumanize the Jewish people in the minds of the viewers. The representation of Jewish home life around the dinner table is done in such a way as to emphasize filth and bugs. Similarly the conditions of street food are naturalized and used as “evidence” that the Jewish people are a lower race. Later, as the film describes Jewish cultural practices it completely subverts the meaning of Purim in such a way as to access the longstanding prejudices of Jews as “bloodsuckers”. Finally, kosher slaughter is used to separate Jewish people from both a sense of Germanness and a European identity altogether. In fact, I argue this representation served as an argument to deny European Jews their humanity altogether. In all of these ways the film creates a cinematic argument that attempts to justify what would become the mass-murder and genocide of the European Jews.
Food; Film; Representations; Ghetto; Purim; Kosher

p. 57 hTERT Suppression via Small Interference RNA in Cervical Cancer Cells
Shawn Gray & Douglas Christensen
Telomerase (TERT) functions to extend the telomeric repeat terminus of each chromosome allowing embryonic cells to proliferate into an adult organism. The TERT gene is subsequently inactivated following maturation, consequently conveying a finite lifespan to every adult cell line, as shortened chromosome arms trigger cell apoptosis. This process ensures that older cells lines, which are invariably accumulating mutations, are eliminated from the body and replaced by stem cells containing founding DNA. One of the defining attributes of a cancer cell is the ability to divide perpetually. This capability to divide continually is often due to the reactivation of TERT. Therefore, the abolishment of TERT activity presents a promising avenue for cancer treatment. Here, we demonstrate through qRT-PCR and ELISA techniques that although small interference RNA (siRNA) results in a transcription knockdown of ninety-seven percent the actual protein activity reduction is far less dramatic.
Telomerase; Small Interference RNA; Cancer; Tumor; hTERT; qRT-PCR; RNA Interference; ELISA

p. 65 Malate : Quinone Oxidoreductase and Malic Enzyme are required for the Plant Pathogen Pseudomonas syringae pv. tomato DC3000 to Utilize Malate
Zabrina Ebert, Preston Jacob, Katrina Jose, Lina Fouad, Katherine Vercellino, Steven Van Dorn, Mahaa Sidiqqi & Eve M. Mellgren
Pseudomonas syringae pv. tomato strain DC3000 (DC3000) is a gram-negative bacterial plant pathogen that causes disease on tomato and the model plant Arabidopsis thaliana. Interestingly, previous studies showed that malate:quinone oxidoreductase (Mqo), an enzyme in the citric acid cycle, is required for DC3000 to cause disease on these plants. In addition, growth of DC3000 lacking the mqo gene in minimal medium with malate was significantly delayed, but eventually reached wild-type levels of growth, which is similar to growth in planta. This suggests that malate may be an important carbon source for DC3000. One reason the mqo::KO bacteria may be able to reach wild-type levels of growth in culture and plants is that the DC3000 malic enzyme may be used to complete the citric acid cycle. Our research shows that a mutant strain lacking a functional mqo gene and malic enzyme gene (mqo::KO;ME::pJP) fails to grow in minimal media cultures with malate and has reduced growth in media with citrate, indicating that both Mqo and ME are required for normal growth when utilizing these carbon sources. Future studies looking at growth of this double mutant in plants will identify how important the activities of both of these genes are for DC3000 to cause disease in plants.
Malate:quinone Oxidoreductase; Malic Enzyme; MQO; Pseudomonas syringae; Arabidopsis thaliana; Malate; Citrate; DC3000

p. 73 Engaging Students in Science through a Nature Hike: A Case of Two Students with ADHD
Ashleigh Moore, Kristy Lynn Daniel & Aimée K. Thomas
Attention-Deficit/Hyperactivity Disorder (ADHD) is becoming prevalent amongst elementary school aged students and can lead to learning disorders. Additionally, informal science education is a field of study that is becoming increasingly popular and important in the world of science, especially with elementary students. Thus, it is important to understand how students with ADHD react to informal learning experiences. We measured learning gains and changes in environmental awareness among 84 fifth grade students that participated in an informal nature hike associated with the Over, Under, and Through: Students’ Informal Discover the Environment program. We also used a case study approach to reveal the hike experiences of two students with ADHD. Both students demonstrated increased attention and interest in science during and after their participation in the nature hike. While this is a small scale, case study, findings from this work and related literature suggest that more informal experiential learning opportunities should be integrated into science classes as they help improve student attention, content recall, and attitude toward science.
ADHD; Engagement; Environmental Science Education; Informal Science Education; Mobile Technology; Nature Hike 

p. 81 Evaluation of Antiulcer Activity of Laghusoothshekhar (an Ayurvedic Formula) in Pyloric Ligature Induced Gastric Ulcers in Albino Rats
Nilofer Sayed & Vandana Barve
Laghusoothshekhar is an ayurvedic formula widely used for gastritis and peptic ulcers that has been described in various ayurvedic texts such as Bharat Bhaishajya Ratnakar, Ayurved saar sangraha and Nav samhita with slight variations in their ingredients. Marketed formulas from the first two references are available but the study of this formula from nav samhita is not yet carried out nor is it available commercially. It is a simple formula of few ingredients and is widely prepared and used by ayurvedic practitioners for treating gastritis (both acute and chronic) and peptic ulcers. Hence, efforts were taken to evaluate its antiulcer activity. Four groups comprising of six animals each were studied. Control Group: vehicle (2% w/v gum acacia), Group A: (50 mg/kg), Group B: (100 mg/kg), Group C: ranitidine (25 mg/kg). One hour after the last dose, pyloric ligation was done and animals were deprived of food and water for 4 hours, thereafter sacrificed and the number of ulcers and their severity was calculated. Both the doses of Laghusoothshekhar showed significant anti-ulcer activity and the histopathological findings of the gastric tissues confirmed the same. The results proved that the drug is as efficient as the standard drug ranitidine used in the treatment of gastritis and peptic ulcers. Ranitidine inhibits acid production by reversibly blocking H2 receptors on the basolateral membrane of parietal cells in the stomach.
Laghusoothshekhar; Pyloric Ligation; Ranitidine; Nav Samhita; Ayurveda; Amlapitta; Peptic Ulcers; Gastritis; Naagvel Patra; Ginger; Suvarna Gairik 

p. 87 Using Statistical Approaches to Model Natural Disasters
Audrene S. Edwards & Kumer Pial Das
The study of extremes has attracted the attention of scientists, engineers, actuaries, policy makers, and statisticians for many years. Extreme value theory (EVT) deals with the extreme deviations from the median of probability distributions and is used to study rare but extreme events. EVT’s main results characterize the distribution of the sample maximum or the distribution of values above a given threshold. In this study, EVT has been used to construct a model on the extreme and rare earthquakes that have happened in the United States from 1700 to 2011.The primary goal of fitting such a model is to estimate the amount of losses due to those extreme events and the probabilities of such events. Several diagnostic methods (for example, QQ plot and Mean Excess Plot) have been used to justify that the data set follows generalized Pareto distribution (GPD). Three estimation techniques have been employed to estimate parameters. The consistency and reliability of estimated parameters have been observed for different threshold values. The purpose of this study is manifold: first, we investigate whether the data set follows GPD, by using graphical interpretation and hypothesis testing. Second, we estimate GPD parameters using three different estimation techniques.Third, we compare consistency and reliability of estimated parameters for different threshold values. Last, we investigate the bias of estimated parameters using a simulation study. The result is particularly useful because it can be used in many applications (for example, disaster management, engineering design, insurance industry, hydrology, ocean engineering, and traffic management) with a minimal set of assumptions about the true underlying distribution of a data set.
Extreme Value Theory; QQ Plot; Mean Excess Plot; Mean Residual Plot; Peak Over Threshold; Generalized Pareto Distribution; Maximum Likelihood Method; Method of Moments; Probability-Weighted Moments; Shapiro-Wilk test; Anderson- Darling Test

p. 105 Explicit Solution for Cylindrical Heat Conduction
Kaitlyn Parsons, Tyler Reichanadter, Andi Vicksman & Harvey Segur
The heat equation is a partial differential equation that elegantly describes heat conduction or other diffusive processes. Primary methods for solving this equation require time-independent boundary conditions. In reality this assumption rarely has any validity. Therefore it is necessary to construct an analytical method by which to handle the heat equation with time-variant boundary conditions. This paper analyzes a physical system in which a solid brass cylinder experiences heat flow from the central axis to a heat sink along its outer rim. In particular, the partial differential equation is transformed such that its boundary conditions are zero which creates a forcing function in the transform PDE. This transformation constructs a Green’s function, which admits the use of variation of parameters to find the explicit solution. Experimental results verify the success of this analytical method.
Heat Equation; Bessel-Fourier Decomposition; Cylindrical; Time-dependent Boundary Conditions; Orthogonality; Partial Differential Equation; Separation of Variables; Green’s Functions

Volume 13, Issue 1, January 2016

Click on this link to download full interactive pdf for AJUR Volume 13 Issue 1

Abstracts and keywords are provided in the section below.

p.5 Einstein’s 1905 Paper on E=mc∧2
Patrick Moylan, James Lombardi & Stephen Moylan

Erratum for AJUR, Volume 13, Issue 1, p.6., “Einstein’s 1905 Paper on E=mc^2″ by Patrick Moylan, James Lombardi & Stephen Moylan: instead of “Einstein uses the subscripts 0 and 1 to distinguish quantities in the So and So’ frames, respectively.  For the energy of the particle before the emission of radiation he uses the symbol E and he uses H to denote the energy of the particle after the emission of light.” it should readEinstein uses the symbols E and H to distinguish quantities in the So and So’ frames, respectively.  For the energy of the particle before the emission of radiation he uses the subscript 0 and he uses the subscript 1 to denote the energy of the particle after the emission of light.” (posted on 06/25/2017)

p. 11 Aberrant DNMT3B7 Expression Correlates to Age, Race, and Hormone Receptor Status in Breast Cancer Patients
Christian C.S. Mullin, Jennifer J. Busser, Anna M. Ciampanelli & Stacey L. Raimondi

p. 21 Numerical Prediction of Microbubble Attachment in Biological Flows
Joshua Gosney & Jeffrey J. Heys

p.31 Utilizing Machine Learning to Accelerate Automated Assignment of Backbone NMR Data
Joel Venzke, David Mascharka, Paxten Johnson, Rachel Davis, Katie Roth, Leah Robison, Adina Kilpatrick & Timothy Urness

p. 41 Approximate Formulae for Willmore Surfaces via Support Functions and Matlab
Phillip M. Galboa & Michael C. Barg

p. 51 Preparation of t-Butyldimethylphosphine Borane and t-Butyldiethylphosphine Borane by Selective Grignard Reagent Substitution of Phosphorus Trichloride
Auston G. Butterfield, Matthew B. Prater & Nathan S. Werner

p. 59 The Effect of Umbellularia californica Essential Oil on Blood Vessel Diameter in Frogs
Holden M. Wagstaff, Stephan R. Maman, Mary Jo Tufte & Matthew S. Weeg

p. 65 The Wellbeing of Young Adults as a Function of Parental Status in Rural Tanzania
H. Callie Silver


Abstracts and keywords for articles published in AJUR Volume 13 Issue 1:

Einstein’s 1905 Paper on E=mc2

Patrick Moylan, James Lombardi & Stephen Moylan

ABSTRACT It is well-known that Einstein’s first paper on E=mc2 as published in the Annalen der Physik in 1905 is problematic in that it suffers from the error of circular reasoning. This means that it uses as one of its premises a statement which is equivalent to the conclusion of the paper, namely, that E=mc2. This difficulty with the paper has been pointed out by many writers including Max Planck, Herbert Ives, Max Jammer and also biographers of Einstein including Gerald Holton and Arthur I. Miller. Unfortunately, the derivation is repeated today as being correct without any mention of the above criticisms of it. In view of this it seems to us worthwhile to have a clear and as simple as possible explanation of the logical difficulties associated with Einstein’s 1905 derivation, and it is to this end that this paper is written. Herewith we present a very simple treatment of the problem which makes absolutely clear the logical difficulties in Einstein’s first published work on E=mc2.

KEYWORDS History of Science; Origins of Special Relativity


Aberrant DNMT3B7 Expression Correlates to Age, Race, and Hormone Receptor Status in Breast Cancer Patients

Christian C.S. Mullin, Jennifer J. Busser, Anna M. Ciampanelli & Stacey L. Raimondi

ABSTRACT Invasive breast cancer caused almost 40,000 deaths last year alone. Deciphering a way to better understand aggressive phenotypes of breast cancer could potentially provide a novel approach to increase the efficacy of breast cancer treatments. The aberrant gene DNA methyltransferase 3B7DNMT3B7, has been observed in virtually all cancer types and has been shown to affect multiple facets of breast cancer progression including changes in cell adhesion, cellular proliferation, and anchorage-independent growth. A bioinformatics approach was taken to attempt to determine which clinical parameters are potentially altered by DNMT3B7 expression in breast cancer patients. Clinical parameters including age at initial diagnosis, menopausal status, race, and the status of three hormone receptors — estrogen, progesterone, and human epidermal growth factor 2 (ER, PR, HER2, respectively) — were collected from The Cancer Genome Atlas (TCGA) and analyzed using T-tests and ANOVA. Our results show increased expression of the aberrant gene, DNMT3B7, is correlated with age at initial diagnosis, race, and hormone receptor status (ER negative, PR negative, and HER2 positive) in breast cancer patients, but not with menopausal status. Taken together, these data indicate that DNMT3B7 expression may be an important marker in tumor progression.

KEYWORDS DNMT3B7, DNA Methylation; Bioinformatics; Breast Cancer; Tumor Progression; Estrogen Receptor; Progesterone Receptor: Human Epidermal Growth Factor Receptor 2


Numerical Prediction of Microbubble Attachment in Biological Flows

Joshua Gosney & Jeffrey J. Heys

ABSTRACT Biofilm infections pose a major threat to human health and are difficult to detect. Microbubbles provide an effective and inexpensive method of detection for biofilm-based infections and other diseases such as cancer. The approach studied here examines the potential of targeted microbubbles, with specific antibodies covalently linked to their surfaces for use as ultrasound contrast agents and drug delivery vehicle. This work presents a novel numerical model for estimating the forces on microbubble conjugates in the vascular system. A full computational fluid dynamics simulation of biological fluid flow and the resulting forces on attached microbubbles is presented as well as comparisons with simplified analytical models. Both the computational and analytical predictions are compared with experimental measurements from Takalkar et al. and Schmidt et al., and these comparisons indicate stable microbubble attachment can be anticipated when the total hydrodynamic force on the microbubble is less than 100 pN. Through the examination of typical biological flows, microbubble attachment can be expected up to an average fluid velocity of 0.025 cm/s near the microbubble (i.e., a particle Reynolds number on the order of .001). The Stokes drag law was shown to predict the drag force (the dominant force) on the microbubble within an order of magnitude of the force predicted by the numerical model. Finally, it was found that the lift force on a microbubble was small relative to the drag force, and that the Saffman equation prediction differed from the numerical model by more than an order of magnitude for the biological flows examined.

KEYWORDS Microbubble Attachment; Ultrasound Contrast Agent; Hydrodynamic Force; Computational Fluid Dynamics


Utilizing Machine Learning to Accelerate Automated Assignment of Backbone NMR Data

Joel Venzke, David Mascharka, Paxten Johnson, Rachel Davis, Katie Roth, Leah Robison, Adina Kilpatrick & Timothy Urness

ABSTRACT Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for determining three-dimensional structures of biomolecules, including proteins. The protein structure determination process requires measured NMR values to be assigned to specific amino acids in the primary protein sequence. Unfortunately, current manual techniques for the assignment of NMR data are time-consuming and susceptible to error. Many algorithms have been developed to automate the process, with various strengths and weaknesses. The algorithm described in this paper addresses the challenges of previous programs by utilizing machine learning to predict amino acid type, thereby increasing assignment speed. The program also generates place-holders to accommodate missing data and amino acids with unique chemical characteristics, namely proline. Through machine learning and residue-type tagging, the assignment process is greatly sped up, while maintaining high accuracy.

KEYWORDS Chemical Shift; Machine Learning; NMR; Artificial Intelligence; Proteins; Bioinformatics

Approximate Formulae for Willmore Surfaces via Support Functions and Matlab

Phillip M. Galboa & Michael C. Barg

ABSTRACT Bio-membrane shapes are calculated numerically by minimizing a bending energy with area and volume constraints. We use a modified Helfrich’s bending energy that includes buoyancy. Spheres, prolate and oblate discocytes, tori, Y -shapes, and dumbbells are some of the variety of bio-membranes that have been observed without buoyancy. Since the system of differential equations that minimizers must satisfy is extremely complex, many shapes are only known to exist through their numerical solutions. Indeed, exact analytical solutions for many shapes remain elusive. Here, we consider Y -shapes and dumbbells and give closed-form approximate formulae for these shapes using a support function method.

KEYWORDS Bio-membranes; Support Functions; Willmore Surfaces; Generating Curves; Polynomial Approximation; Numerical Solutions; Matlab; Helfrich’s Bending Energy


Preparation of t-Butyldimethylphosphine Borane and t-Butyldiethylphosphine Borane by Selective Grignard Reagent Substitution of Phosphorus Trichloride

Auston G. Butterfield, Matthew B. Prater & Nathan S. Werner

ABSTRACT The synthesis of differentially substituted trialkylphosphine boranes from the selective substitution reaction of Grignard reagents with phosphorus trichloride in a single reaction flask was studied. The reaction temperature, stoichiometric loading of the first equivalent of Grignard reagent and reaction time were found to be important for maximizing the yield and selectivity of the reaction. Reaction conditions were optimized to achieve maximum yield of t-butyldiethylphosphine borane. The optimized conditions were applied to the syntheses of t-butyldiethylphosphine borane and t-butyldimethylphosphine borane, which provided 60% and 62% isolated yields respectively. Products were characterized with mass spectrometry, infrared spectroscopy, 1H, 13C, and 31P nuclear magnetic resonance spectroscopy.

KEYWORDS Synthesis; Trialkylphosphine; Grignard Reagent; Selective; Substitution Reaction; t-Butyldiethylphosphine Borane; t-Butyldimethylphosphine Borane; Phosphorus Trichloride


The Effect of Umbellularia californica Essential Oil on Blood Vessel Diameter in Frogs

Holden M. Wagstaff, Stephan R. Maman, Mary Jo Tufte & Matthew S. Weeg

ABSTRACT Plant essential oils contain many chemicals that are physiologically active in vertebrates. Terpenoids, which represent the largest category of these compounds, have been shown to lower blood pressure by reducing cardiac output and causing vasodilation. Most studies on the vasoactivity of terpenoids have been done on aortic rings and mesenteric artery preparations, and little is known about their effects on microvasculature. We applied Umbellularia californica essential oil, which contains several different terpenoids, to the cutaneous microvasculature of frogs and measured changes in blood vessel diameter. The U. californica oil caused a sustained, reversible vasoconstriction of these blood vessels, whereas no significant change in diameter was caused by medical grade sesame oil, which served as our control. The vasoconstriction we observed was therefore induced by compounds in the U. californica oil, many of which have previously been shown to cause vasodilation in arteries. Our results suggest that the vasoactive effects of terpenoids may differ across blood vessel types, and are more variable than previously thought.

KEYWORDS Cardiovascular; Terpenoid; Vasoactive; Arteriole; Secondary Metabolite; Vasoconstriction; Essential Oil; Microvasculature


The Wellbeing of Young Adults as a Function of Parental Status in Rural Tanzania

H. Callie Silver

ABSTRACT The East-African nation of Tanzania has one of the highest HIV/AIDS rates in the entire world, and thus, an alarmingly high number of orphaned children. The present study sought to determine if being an orphan during childhood, either single or double, is related to one’s psychological wellbeing in young adulthood. Orphan status and psychological wellbeing information was gathered via surveys containing background information and standardized wellbeing scales. The oral survey was administered in person in Kiswahili, the national language of Tanzania. Sixty-three young adults, ages 18–25, in a small rural village community participated in the study. The results of the study found no significant association between orphan status in childhood and psychological wellbeing in young adulthood, leading to a discussion on how parental loss may be experienced in small, African, rural villages, under the framework of resilience. Conclusions were all speculative and further research is thus recommended.

KEY WORDS Psychological; Wellbeing; Orphan; Parental Loss; HIV/AIDS; Tanzania; Sub-Saharan Africa

Volume 12, Issue 4, November 2015

Volume 12, Issue 4, November 2015 interactive high-resolution pdf


p. 2 A Historical Context for Undergraduate Research: The Contribution of Wilhelm von Humboldt by David Vampola

p. 5 Category Theoretic Interpretation of Rings
by Edward Poon
We enhance the category of rings and the category of idempotented rings to 2-categories. After doing this, we prove an equivalence of 1-categories and 2-categories between the category of rings and the category of small preadditive categories with one object and between the category of idempotented rings and the category of small preadditive categories with finitely many objects. Under these equivalences, we demonstrate some analogues between notions in category theory and ring theory.
Ring, Idempotent, Preadditive Category

p. 31 Effect of Manual Ivy Removal on Seedling Recruitment in Forest Park, Portland, OR by Katelin D. Stanley & Dr. David W. Taylor
English and Irish ivy (Hedera helix and H. hibernica) are invasive lianas which have become especially intrusive in the Pacific Northwest, as evidenced by their invasion of many areas in Forest Park, Portland, OR. The most common strategy for ivy control is currently manual removal, though the potential consequences of this method have not been well studied. The purpose of this study was to evaluate the effectiveness of manual ivy removal with respect to its influence on native plant diversity, abundance, species richness, and evenness by comparing these parameters in 1-m2 plots manually cleared of ivy to paired control plots. Prior to plot establishment, evidence of deer herbivory of ivy was observed at this site. Four weeks after manual removal, treated plots were less diverse and hosted a lower abundance of native plants than control plots. Ten weeks after ivy removal, treated and control plots were equally diverse, and treated plots showed greater abundance of plant cover than controls. This trend persisted at twenty-six weeks after treatment. Treated and control plots were not significantly different in species richness or evenness at any time. These results suggest that manual ivy removal temporarily disturbs native plant life, but the negative effects are overcome as quickly as ten weeks after treatment, at which time native plants are more successful. Manual removal as a method to control ivy in this region appears effective within one growing season.
English Ivy, Irish Ivy, Invasive Species, Pacific Northwest, Forest Park, Hedera helix, Hedera hibernica

p. 43 Imaging Noisy Seismic Data using a One Dimensional Inverse Scattering Algorithm by Bogdan G. Nita & Christopher Smith
We test the capability of an inverse scattering algorithm for imaging noisy seismic data. The algorithm does not require a velocity model or any other a priori information about the medium under investigation. We use three different geometries which capture different types of one-dimensional media with variable velocity. We show that the algorithm can precisely locate the interfaces and discover the correct velocity changes at those interfaces under moderate noise condition. When the signal to noise ratio is too small, the data is de-noised using a threshold filter and then imaged with excellent results.
Seismic Imaging, Inversion, Amplitude Correction, Scattering Theory, Noise, Threshold Filter. 2000 MATHEMATICS SUBJECT CLASSIFICATION 86A22, 35J05, 35R30.

p. 57 Effect of Native American Bean-corn Biculture Planting on Free-living Bacterial Abundance and Plant Growth by Heather A. Miller, Justin Fiene & Tamara L. Marsh
Native American tribes with bountiful harvests. Today it is widely recognized that this associated intercropping system derives much of its success from symbiotic bacteria (e.g. Rhizobium). These bacteria colonize the roots of leguminous plants, allowing them to fix atmospheric nitrogen into ammonia. However, the effect of this intercropping practice on the microbial community, independent of the effect of the symbiotic nitrogen-fixing bacteria, is not well understood. Therefore, a study was designed to model the effects of simultaneously intercropping bean and corn on the abundance of aerobic heterotrophic, free-living nitrogen-fixing, and symbiotic nitrogen-fixing bacteria, as well as plant growth and fecundity markers. In parallel, the benefits mediated by rhizobia were evaluated by inoculating a duplicate set of treatments with N-Dure, a rhizobia-containing inoculum. Native American varieties of pole-bean (Phaseolus vulgaris L.) and corn (Zea mays mays L.) were planted in monoculture and biculture treatments. All cultivations were maintained under greenhouse conditions for 52 days with daily watering and no additional fertilizer or microbial amendments. Although a significant increase in weight per plant was noted for the inoculated biculture when compared to either the inoculated bean or corn monocultures (p ≤ 0.05), the abundance of heterotrophic and free-living nitrogen-fixing bacteria did not show a significant change from the related controls, with or without inoculation. However, symbiotic nitrogen-fixing bacteria, as measured by root nodulation, increased significantly (p ≤ 0.05) for the inoculated biculture and single planting. Thus, these data confirm that corn benefited from this associated intercropping system as shown by an increase in plant biomass that can be attributed to Rhizobium. However, neither the legume-bacteria symbiotic relationship nor the increase in plant biodiversity resulting from this intercropping practice appears to have had significant effects on the abundance of the two common soil-associated bacterial groups evaluated, though further research would be necessary to fully assess the changes to heterotrophic bacterial diversity at the species level.
Three Sisters; Nitrogen-fixing Bacteria; Inoculation with Rhizobia; Plant Growth Promoting Bacteria; Soil Microbial Biota; Corn and Bean Simultaneous Planting.

p. 73 Point-Spread Function (PSF) Photometric Analysis of Open Clusters: Melotte 72 & NGC 2158 by Muhammad Awais Mirza & Zain Rahim
Point Spread Function (PSF) photometry of open star clusters Melotte 72 and NGC 2158 was performed using g and r band data from the Sloan digital Sky Survey (SDSS) Data Release 7. Instrumental magnitudes of stars in both bands were transformed into calibrated magnitudes using standard equation. Color-Magnitude (CM) diagrams were produced and compared with the SDSS isochrones for AB stellar system for different ages and/or metallicities. The objective of this study was to determine the physical parameters (age, distance, metallicity, reddening) of open clusters from CM diagrams. The best fit isochrones were used to estimate cluster parameters. The observed parameters were then compared with the WEBDA data base.
PSF Photometry, Melotte 72, SDSS, NGC 2158, Isochrone Fitting, IRAF

p. 79 Synthesis of a MUC1 Mucin Cyclic Dimer Peptide and Its Antibody Binding Properties as Revealed by STD-NMR by Cheng Her & Thao Yang
In a previous study we showed that the shortened MUC1 mucin peptide GVTSAPD could bind monoclonal antibody (mAb). We proceeded on to make a cyclic peptide of the same sequence to see if it would be more effective in binding antibody. We were able to synthesize and isolate two different cyclic mucin peptides: 1) a monomer cyclic peptide with sequence GVTSAPD which we did not study due to difficulties in achieving homogeneity, and 2) a dimer cyclic peptide with sequence GVTSAPDGVTSAPD that was successfully isolated and studied. We describe here the results of the dimer cyclic peptide-antibody interactions obtained by Saturation Transfer Difference NMR (STDNMR). The results indicated that the protons of all residues experienced STD effects, notably being more pronounced at Pro, Val, Ala and Asp compared to the linear peptide GVTSAPD. The Pro residue exhibited STD peaks for all its side chain protons with stronger intensity at ProHγ while Ala, Val and Thr are localized to methyl groups.
Muc1 Antibody Recognition Epitope, STD NMR, Mucin Peptide-antibody Interactions, Cyclodimer Peptide.

p. 93 Methods for Essential Tremor Assessment: Acoustic Tremor Monitoring (ATM) and Rhythmic Spirals (RS) Methods by Emily Hart, Caroline Chow, Patricia Stan & Daniel King
There are several techniques of monitoring essential tremors, but there is not yet a standard method developed for the field. A quantitative way to track effects of medication and/or lifestyle treatment would be beneficial for future research in prevention or regression of essential tremors. The two methods evaluated are acoustic tremor monitoring (ATM) and rhythmic spirals (RS). The novel ATM measurement quantifies frequency and amplitude quickly and cost effectively. The tremor patient holds a microphone close to a speaker playing a single frequency tone. The Doppler Effect caused by the shaking microphone distorts the sound recording, and the encoded tremor information can be retrieved by using the Fast-Fourier Transform algorithm. The second method, RS, can be used by patients at home to measure frequency. The RS method is similar to the classic Archimedes spirals, but uses a different form and is timed which allows for the calculation of tremor frequency. The RS and ATM methods produce statistically similar frequency measurements, although ATM has greater precision.
Essential Tremors, Archimedes Spiral, Accelerometry, Spiral Analysis, Acoustic Tremor Monitoring, Rhythmic Spirals.