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

https://doi.org/10.33697/ajur.2016.010

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
APPENDIXES 

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

p. 5 Robust Nonlinear Control of BLDC Motor in Quadcopter Applications

https://doi.org/10.33697/ajur.2016.011

Steven T. Elliott & Thomas W. Carr
ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2016.012

Jenna Wilson, Tabitha Ricketts, Ian Bentley & Ewa Misiolek
ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2016.013

Sheikh Tijan Tabban & Nelson Fumo
ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2016.014

Forrest Picher
ABSTRACT
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.
KEYWORDS
Food; Film; Representations; Ghetto; Purim; Kosher

p. 57 hTERT Suppression via Small Interference RNA in Cervical Cancer Cells

https://doi.org/10.33697/ajur.2016.015

Shawn Gray & Douglas Christensen
ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2016.016

Zabrina Ebert, Preston Jacob, Katrina Jose, Lina Fouad, Katherine Vercellino, Steven Van Dorn, Mahaa Sidiqqi & Eve M. Mellgren
ABSTRACT
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.
KEY WORDS
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

https://doi.org/10.33697/ajur.2016.017

Ashleigh Moore, Kristy Lynn Daniel & Aimée K. Thomas
ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2016.018

Nilofer Sayed & Vandana Barve
ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2016.019

Audrene S. Edwards & Kumer Pial Das
ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2016.020

Kaitlyn Parsons, Tyler Reichanadter, Andi Vicksman & Harvey Segur
ABSTRACT
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.
KEYWORDS
Heat Equation; Bessel-Fourier Decomposition; Cylindrical; Time-dependent Boundary Conditions; Orthogonality; Partial Differential Equation; Separation of Variables; Green’s Functions
APPENDIXES 

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

https://doi.org/10.33697/ajur.2016.001

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 S_o and S_o’ 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 read “Einstein uses the symbols E and H to distinguish quantities in the S_o and S_o’ 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

https://doi.org/10.33697/ajur.2016.002

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

 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 read “Einstein 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)

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

https://doi.org/10.33697/ajur.2016.003

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 3B7, DNMT3B7, 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

https://doi.org/10.33697/ajur.2016.004

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

https://doi.org/10.33697/ajur.2016.005

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

https://doi.org/10.33697/ajur.2016.006

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

https://doi.org/10.33697/ajur.2016.007

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

https://doi.org/10.33697/ajur.2016.008

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

https://doi.org/10.33697/ajur.2016.009

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 interactive high-resolution pdf

https://doi.org/10.33697/ajur.2015.018

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

https://doi.org/10.33697/ajur.2015.019

p. 5 Category Theoretic Interpretation of Rings
by Edward Poon

https://doi.org/10.33697/ajur.2015.020

ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2015.021

ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2015.022

ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2015.023

ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2015.024

ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2015.025

ABSTRACT
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.
KEYWORDS
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

https://doi.org/10.33697/ajur.2015.026

ABSTRACT
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.
KEYWORDS
Essential Tremors, Archimedes Spiral, Accelerometry, Spiral Analysis, Acoustic Tremor Monitoring, Rhythmic Spirals.

Volume 12, Issue 3, May 2015 interactive high-resolution pdf

https://doi.org/10.33697/ajur.2015.009

Abstracts, key words, information about student authors, and press summaries for these articles are provided in the section below links to individual papers. The complete 12-3 issue prepared for the double sided printing is available at the bottom of the page.

p.2 Editorial “Citizen Science: Contribute to a Common Good, Collaborate, and Communicate!“

https://doi.org/10.33697/ajur.2015.010

Dr. John R. Jungck

p. 5 Investigating the Response of a Small Urbanized Watershed to Acute Toxicity Events via Analysis of High-frequency Environmental Data

Holly Adelle Clark , Walter M. McDonald, Vinod K. Lohani & Randel L. Dymond

p. 19 Occurrence of Multiple Antibiotic Resistant Bacteria in Aquatic Environments in Central Minnesota

Megan Bollin, Dr. Ellen Jensen & Dr. David Mitchell

p. 37 Effect of a Worksite Walking Competition on Health-Related Quality
of Life Among University Employees

Breanna Z. Orozco, Lisa J. Leininger & Kendra L. Contente

p. 45 Approximation of Euler Number Using Gamma Function

Shekh Mohammed Zahid & Dr. Prasanta Kumar Ray

p. 53 Direct and Indirect Effects of Pseudoephedrine on the Intrinsic Conduction System of the Embryonic Chicken Heart

Samely Gonzalez, Fatima Afzal & Dr. Jacqueline S. McLaughlin

p. 63 Nutritional Stress of Cultured Vero Cells Causes Altered Growth and Morphology as Seen in Neoplastic Transformation

Tyler Adams, Rabia Anwar, Michael Mfarej, Taylor Rundatz, Melissa Coyle &
Dr. Jacqueline S. McLaughlin

p. 77 Searching for Gravitational Waves from the Coalescence of High-mass Black Hole Binaries

Liting Xiao, Alan J. Weinstein, Dr. Tjonnie G. F. Li & Surabhi Sachdev

Abstracts, key words, information about student authors, and press summaries for these articles are provided below:

p. 5 Investigating the Response of a Small Urbanized Watershed to Acute Toxicity Events via Analysis of High-frequency Environmental Data

https://doi.org/10.33697/ajur.2015.011

Holly Adelle Clark , Walter M. McDonald, Vinod K. Lohani & Randel L. Dymond
ABSTRACT
This study, conducted over 10 weeks by an undergraduate student in an NSF REU (U.S. National Science Foundation Research Experiences for Undergraduates) program under mentorship of the co-authors, investigates responses of a small urban watershed, located in Blacksburg, Virginia, to acute toxicity events. High-frequency water and weather data were collected using monitoring equipment maintained by the Learning Enhanced Watershed Assessment System (LEWAS) lab, including a weather station, rain gauge, water quality sonde, and an Acoustic Doppler Current Profiler. The location and attributes of local stormwater catchments were surveyed and recorded using GIS software to determine the overall contributing area of the LEWAS lab watershed. This fieldwork resulted in the construction of an accurate stormwater network map, which in turn allowed the identification of sources of sedimentation and other pollution from runoff events. A case study presents the response of the watershed to a winter storm event that resulted in acute chloride toxicity from runoff containing road salts.
KEYWORDS
Water; Stormwater, Urban Watersheds; Watershed Responses; Acute Toxicity; High-frequency Data; Data Analysis; Data Collection; Environmental Monitoring; Flow Measurements; Hydrologic Data.
ABOUT THE STUDENT AUTHORS
Holly A. Clark is in her sixth year of undergraduate study at the University of Idaho. She is pursuing Bachelor of Science degrees in both Environmental Science (with a physical science emphasis) and Music History and Literature (with a clarinet emphasis). She will graduate in May 2015.
PRESS SUMMARY:
A 10 week U.S. National Science Foundation Research Experiences for Undergraduates study investigated responses of a small urban watershed, located in Blacksburg, Virginia, to acute toxicity events. High-frequency water and weather data were collected using monitoring equipment maintained by the Learning Enhanced Watershed Assessment System (LEWAS) lab, including a weather station, rain gauge, water quality sonde, and an Acoustic Doppler Current Profiler. Stormwater infrastructure fieldwork resulted in the construction of an accurate stormwater network map, which in turn allowed the identification of sources of sedimentation and other pollution from runoff events. A case study presents the response of the watershed to a winter storm event that resulted in acute chloride toxicity from runoff containing road salts.

p. 19 Occurrence of Multiple Antibiotic Resistant Bacteria in Aquatic Environments in Central Minnesota

https://doi.org/10.33697/ajur.2015.012

Megan Bollin, Dr. Ellen Jensen & Dr. David Mitchell
ABSTRACT
The purpose of this study was to investigate the possibility that antibiotic resistant bacteria could be isolated and identified in aquatic ecosystems in the lakes on the campus of Saint John’s University and the nearby Sauk and Watab Rivers. A total of 125 isolates were collected. Seventy-nine percent of the isolates were gram negative rods. Twenty-six isolates that were resistant to seven or more antibiotics were selected for further investigation. The 26 isolates were all gram negative and members of seven different genera with Flavobacterium and Acinetobacter being the most common. Resistance coefficients were calculated based on optical density values relative to cells grown without antibiotics. Multi-drug resistant, gram negative bacteria were shown to be common in aquatic environments in central Minnesota.
ABOUT THE STUDENT AUTHOR
Megan Bollin worked on this project in the summer of 2013 as part of her honors thesis in Biology at the College of Saint Benedict/Saint John’s University. She graduated with a Bachelor of Arts degree in Biology in May 2014 and while an undergraduate spent a semester studying in London. She currently works for a biotechnology firm in the Twin Cities.
PRESS SUMMARY
The (over)use of antibiotics in agriculture and medicine over the last few decades has raised serious questions about the evolution of bacteria that have become resistant to standard antibiotics. In this paper, we sampled several local waterways in and around St.John’s University in central Minnesota to determine if bacteria growing in these smaller, isolated areas had developed resistance to standard antibiotics and if so which classes of antibiotics were they now able to resist. The results indicate that bacteria growing in these areas are resistant to many common antibiotics.

p. 37 Effect of a Worksite Walking Competition on Health-Related Quality
of Life Among University Employees

https://doi.org/10.33697/ajur.2015.013

Breanna Z. Orozco, Lisa J. Leininger & Kendra L. Contente
ABSTRACT
Worksite health promotion programs (WHPPs) aim to improve the health and wellness of employees in an effort to improve health related quality of life (HRQOL). The effect of exercise on improving HRQOL is well documented among clinical populations. However, few studies have examined the effect of WHPPs on HRQOL. The purpose of this study was to investigate the effect of a six-week “Workplace Walk-Off Competition” (WWC) on HRQOL among university employees. One hundred and nine university employees were included in this study (WWC group: n=47, Control group: n=62). All study participants completed the Short Form 12 Question, Version 2 (SF-12v2), a HRQOL questionnaire, before and after the WWC. The SF-12v2 questionnaire determines HRQOL based on two components and reports scores for a physical component summary (PCS) score and a mental component summary (MCS) score. A two-way repeated measures ANOVA was performed on PCS and MCS scores, followed by dependent t-tests for each group. There was no significant difference in PCS or MCS scores between the groups. Further, there were no statistically significant changes in PCS or MCS scores (p>.05) among either group, following the six-week WWC. Although much research deems WHPPs effective for improving many health indicators, this short-term program was not effective in improving PCS and MCS components of HRQOL.
KEYWORDS
Quality of Life, Health Promotion, Walking Competition, University Employees
ABOUT THE STUDENT AUTHORS
Breanna Orozco will graduate from California State University, Monterey Bay in Spring 2015 with a Bachelor’s degree in Kinesiology – Exercise Science and a Minor in Statistics. Breanna is a McNair scholar, and has received many other prestigious awards, including the American College of Sports Medicine Golding Scholarship. Each summer, Breanna travels to the University of Southern California to work in the Women’s Health and Exercise Laboratory. She has presented at many national conferences including the American College of Sports Medicine Annual meetings, and the Hawaiian International Conference on Education. Her future endeavors include pursuing a Ph.D. in Biokinesiology and a career as a research professor.
Kendra Contente will graduate from California State University, Monterey Bay in Spring 2015 with a Bachelor’s degree in Kinesiology — Exercise Science. Kendra has been involved in many projects at CSU Monterey Bay, including the annual Workplace Walkoff Challenge. Kendra will be presenting at several national conferences in the next year. Kendra is interested in health and exercise, and her main focus of research for the upcoming year will be interventions to increase physical activity among employees at universities. Kendra plans to pursue medical school.
PRESS SUMMARY
Research indicates that exercise can help improve health-related quality of life, which adds to the importance of participating in regular physical activity. Worksite health promotion programs aim to improve the health of employees, in an effort to reduce individual disease risk and benefit the organization by reducing health care costs. This study examined if quality of life could be improved among employees with participation in a walking competition at a university. This study did not find that quality of life was improved, however there are many other benefits to worksite health promotion programs, and therefore, studies should continue in this field.

p. 45 Approximation of Euler Number Using Gamma Function

https://doi.org/10.33697/ajur.2015.014

Shekh Mohammed Zahid & Dr. Prasanta Kumar Ray
ABSTRACT
This research presents a formula to calculate Euler number using gamma function. The representation is somewhat similar to Taylor series expansion of e. The number e is presented as sum of an integral and decimal part. But it is well known that e is an irrational number, and therefore such an expression for e does not exist in principle, that is why we are approximately representing it for use in computation. The approximation of our formula increases as we increase the value of index in the summation formula. We also analyse the approximation of our formula by both numerical and graphical methods.
KEYWORDS
Euler Number, Gamma Function, Approximation, Computing, L’Hospital’s Rule
ABOUT THE STUDENT AUTHOR
Shekh Mohammed Zahid is a first year undergraduate student of BSc (Hons) in Mathematics and Computing in the Institute of Mathematics and Applications, Bhubaneswar, Odisha, India. His research interests include number theory and theoretical physics.
PRESS SUMMARY
In this paper, we developed a formula that gives an approximate value of the Euler number e using gamma function. Its expansion is the sum of integer part and the fractional part. Also, the expansion of series can be terminated as per our preference by choosing favourable index in the summation formula. We have approximated the Euler number e in the given formula for a specific value; however, there is a scope to extend the formula for approximating e in a new way using asymptotic notation.

p. 53 Direct and Indirect Effects of Pseudoephedrine on the Intrinsic Conduction System of the Embryonic Chicken Heart

https://doi.org/10.33697/ajur.2015.015

Samely Gonzalez, Fatima Afzal & Dr. Jacqueline S. McLaughlin
ABSTRACT
Pseudoephedrine (PSE) is an over the counter (OTC) medication used to temporarily relieve nasal congestion, hay fever or other upper respiratory allergies by shrinking blood vessels in the nasal passages. Aside from its vasoconstriction properties it is also known to elevate heart rate, and blood pressure, thus being a sympathomimetic drug. There are two hypotheses on how this drug increases heart rate (HR): (1) a direct mechanism wherein PSE works by binding to adrenergic receptors in the heart’s intrinsic conduction system; and, (2) an indirect mechanism wherein PSE causes the release of norepinephrine from sympathetic nerves to activate adrenergic receptors. This research utilized the chick embryonic heart as a model system to examine the chronotropic effects and mechanisms of PSE on the developing vertebrate heart. Research suggests that this drug has both direct and indirect effects, and induces dangerous heart arrhythmias such as atrial flutter, in high doses.
KEYWORDS
Pseudophedrine, Sympathomimetic Drugs, Pseudophedrine and Pregnancy, Pseudophedrine and Norepinephrine, Pseudophedrine Related Arrhythmias, Over–the-counter Drugs; Chick Heart Development
ABOUT THE STUDENT AUTHORS
Samely Gonzalez is a current undergraduate student at Penn State Abington, Philadelphia, PA set to graduate in May, 2016 with a B.S. degree in Genetics and Developmental Biology. She plans to utilize her skills and knowledge from undergraduate research and other science experiences in her pursuit to become a physician assistant. Her overall objective is to have a career in the medical field that allows her to help others achieve a healthy way of living.
Fatima Afzal is from Bethlehem, Pennsylvania and is currently enrolled as an undergraduate sophomore at Penn State Berks, Reading, PA. She has declared her major in biochemistry, pursing the cell and molecular biology option. She plans on applying the acquired research skills to future careers in pharmaceutical companies or as a medicinal chemist, working alongside eager scientists to develop and manufacture pharmaceuticals in order to grow and expand the drug industry.
PRESS SUMMARY
Pseudophedrine (PSE) is an over the counter (OTC) medication commonly used to temporarily relieve nasal congestion, upper respiratory allergies, and sinus pressure. Previous research has shown, however, that this drug elevates heart rate and blood pressure in humans and other mammals. This research utilized the chick embryonic heart as a model system to study the effects of (PSE) on the developing, vertebrate four-chambered heart and to determine whether this drug has either direct or indirect effects, i.e., it works by binding directly to receptors in the heart’s pacemaker or indirectly by causing the release of norepinephrine from sympathetic nerve terminals to activate the same receptors. To do this, isolated developing chick hearts without innervation and whole chick embryos were exposed to varying PSE concentrations and heart rates were recorded. Research suggests that this drug has both direct and indirect effects and induces atrial flutter when exposed to high dosages.

p. 63 Nutritional Stress of Cultured Vero Cells Causes Altered Growth and Morphology as Seen in Neoplastic Transformation

https://doi.org/10.33697/ajur.2015.016

Tyler Adams, Rabia Anwar, Michael Mfarej, Taylor Rundatz, Melissa Coyle &
Dr. Jacqueline S. McLaughlin
ABSTRACT
In this report, the authors describe the effects of stressed culture conditions on Vero cells, which are a form of epithelial cells derived from the African green monkey kidney. This project was designed in large part to replicate a previously published report on the effects of nutritional stress on the growth patterns of these cells. Culture conditions that include nutritional limitation and cell crowding have been shown to transform these cells into cells that differ morphologically, develop into spheroid- shaped clusters, as well as exhibit altered protein expression. It was suggested that these changes might mirror those occurring in metastatic cancer cells, and could therefore provide a useful experimental model system. In the current study, the investigators successfully cultured Vero cells in control cultures, and then compared their growth patterns and morphology to cells grown in nutritionally stressed and overcrowded cell culture conditions defined by extensive days in culture in unchanged media which did or did not contain glucose. The results confirmed that nutritionally stressed and over-crowded cultures result in cells that change morphologically, detach from the substrate, and exhibit spheroid-shaped clusters of cells. Sub-culturing these detached cells demonstrated that the results were permanent, meaning that the new growth patterns and clustering persisted. The results suggest that deprivation of nutrition and other factors essential to life may facilitate aberrant growth.
KEYWORDS
Vero Cells, Nutritional Stress, Cell Morphology, Neoplastic Transformation, Malignant Cells, Spheroid Formation.
ABOUT THE STUDENT AUTHORS
Tyler Adams is currently a third year student at Penn State Berks. He is pursuing a B.S. in Biology. After graduation, he intends on earning his M.D. and specializing in cardiology.
Rabia Anwar is a third year student at Penn State Berks. She is pursuing a B.S. in Genetics and Developmental Biology and a minor in Entrepreneurship and Innovation. After graduation, she intends on earning her M.D. and specializing in cardiology.
Michael Mfarej is currently a fourth year Penn State Berks student. He is pursuing a B.S. in Genetics and Developmental Biology. He will be graduating in the Spring of 2015. After graduation, he plans to pursue a Ph.D. in Cellular and Molecular Biology with interests of continuing his research training in cancer biology.
Taylor Rundatz is currently a fourth year Penn State Berks student. She intends on graduating in the Spring of 2015 with a B.S. in Biology. After graduation, she plans to pursue an M.D. and Ph.D. dual degree program. With her medical education she is interested in a career as a pathologist.
PRESS SUMMARY
Vero cells were monitored for nine and fifteen day periods under nutritional deprivation and over-crowding conditions. The stressed cells remained viable and underwent a transformation in growth patterns and morphology analogous to behavior seen other models of mammalian cell transformation. These alterations were maintained in the stressed cells after re-plating, suggesting that the transformation was permanent. The results suggest that deprivation of nutrition and other factors essential to life may facilitate aberrant growth.

p. 77 Searching for Gravitational Waves from the Coalescence of High-mass Black Hole Binaries

https://doi.org/10.33697/ajur.2015.017

Liting Xiao, Alan J. Weinstein, Dr. Tjonnie G. F. Li & Surabhi Sachdev
ABSTRACT
We search for gravitational waves from the coalescence (inspiral, merger and ringdown) of binary black holes with data from the Laser Interferometer Gravitational-Wave Observatory (LIGO). Provided with well-described waveform models from General Relativity, matched filtering is employed in the GSTLAL analysis pipeline as the optimal detection technique for weak signals in Gaussian noise. The GSTLAL analysis pipeline filters data with waveform template banks, identifies triggers with SNR greater than 4, forms coincident triggers between multiple detectors in the LSC-Virgo Collaboration, and attempts to optimally separate signal from detector background noise fluctuations using a Chisquared test. We analyze high-statistics simulations of binary merger waveforms injected into LIGO recolored S6 data to evaluate the pipeline search sensitivity and to test the readiness of the pipeline for Advanced LIGO. With Advanced LIGO fully in operation by 2015 and the upgraded analysis pipelines, the expected detection rate is increased to as much as 100 events/year or more as compared to 0.01–1 events/year in Initial LIGO. Our work will make it possible to detect gravitational waves from binary black hole coalescence in Advanced LIGO data with high confidence.
KEYWORDS
LIGO, Gravitational Waves, General Relativity, Coalescence, Black Hole Binaries, Noise Fluctuations, Matched Filtering, Chi-squared Test, Simulations, GSTLAL Analysis Pipeline
ABOUT THE STUDENT AUTHOR
Liting Xiao is a fourth year Astronomy-Physics and Mathematics student at the University of Virginia. After graduation, she plans to pursue a Ph.D. degree in physics, specialized in experimental particle physics, astrophysics and cosmology. In the past, she has worked on Indirect Dark Matter Searches in the NOνA Experiment at Fermi National Accelerator Laboratory, student-led JefferSat Cosmic Ray Mission funded by NASA, and LIGO Gravitational Waves Searches at the California Institute of Technology. She is currently investigating time evolution of the population of compact galaxy groups in different epochs of the Universe for her honors senior thesis.
PRESS SUMMARY
Gravitational waves are the ripples of space-time curvature according to Einstein’s General Relativity. We search for gravitational waves as binary black holes spiral in towards each other and dissipate energy. We develop the GSTLAL analysis pipeline to match data from the Laser Interferometer Gravitational- wave Observatory (LIGO) with astrophysically modeled templates. Our pipeline evaluation and optimization work will improve the pipeline sensitivity and make it possible to detect gravitational waves from binary black hole coalescence in Advanced LIGO data with high confidence.

Volume 12, Issue 3, May 2015 print pdf

Volume 12, Issue 2, January 2015 interactive pdf

 

https://doi.org/10.33697/ajur.2015.001

Editor’s Note “American Journal of Undergraduate Research Impact Factor“

 

https://doi.org/10.33697/ajur.2015.002

Design and Development of the Telescope-deployment High-vacuum teleOperated Rover (THOR) in an Airless Body Environment
Chris Womack, Miles Crist, Laura Kruger, Kelsey DeGeorge, Karynna Tuan, & Jack Burns

 

A Study of Subracks
Samantha Driskill

Cardiac Myocardial Hypertrophy and Altered Swimming Behavior in Xenopus laevis Embryos in Incrementally Increasing Hypergravity
Stacey Howes & Darrell Wiens

 

Can An Algebraic Diagnostic Test be Used to Predict Final Grades in an Introductory Statistics Class?
Justine Kirksey & Anthony Cooper

 

A Curve Satisfying K/T = s with constant K>0
Yun Myung Oh and Ye Lim Seo

 

Does Altering Local Water Availability for an Invasive Plant (Raphanus raphanistrum) Affect Floral Morphology and Reproductive Potential?
Natalia Pirimova, Alison J. Parker, and Lesley G. Campbell

 

Full details are provided below:

 

Design and Development of the Telescope-deployment High-vacuum teleOperated Rover (THOR) in an Airless Body Environment

https://doi.org/10.33697/ajur.2015.003

Chris Womack, Miles Crist, Laura Kruger, Kelsey DeGeorge, Karynna Tuan, & Jack Burns

ABSTRACT
The harsh environment on the lunar surface presents unique technological challenges for space exploration. This paper presents research on the design and development of the Telescope-deployment High-vacuum teleOperated Rover (THOR), currently being built and tested in the Lunar and Airless Bodies Simulator (LABS) facility at the University of Colorado Boulder. This rover is fabricated entirely out of cost-effective commercial off-the-shelf (COTS) components and materials. THOR can potentially survive for more than one simulated year in conditions similar to that of the lunar environment, demonstrating the successful initial results of a first phase research study on material and electronic survivability in an extreme environment such as the Moon.
KEYWORDS
Telerobotics, Space Exploration, LUNAR, High-vacuum, Electronic Survivability, Robotics, Engineering
ABOUT THE STUDENT AUTHORS
Chris Womack is currently pursuing a B.S. in both Mechanical Engineering, and Electrical and Computer Engineering. He has been with the LUNAR team for 2 years developing a teleoperated rover. Currently he is collaborating with Lockheed Martin to extend this application to remote control via web apps for telerobotic operations and testing. Miles Crist is a mechanical engineer who recently graduated from the University of Colorado at Boulder. He has worked for NASA’s Lunar Science Institute conducting material and electronic research in support of a lunar far side radio telescope array. Miles operated and maintained a thermal vacuum chamber and was part of a team that developed the Telescope Deployment High VacuumteleOperated Rover (THOR). Miles now works for Crane Aerospace and Electronics designing fuel pumps for a large variety of aircraft. Laura Kruger is a graduate student at the University of Colorado Boulder. She graduated with a BA in Astrophysics and is currently pursuing a MS in Aerospace Engineering and ME in Engineering Management. After working with the LUNAR team for five years as laboratory manager for CU’s lunar simulation thermal-vacuum facility, Laura joined Ball Aerospace as a Systems Engineer in August of 2014. Kelsey DeGeorge is a recent graduate receiving her Bachelor of Science in Mechanical Engineering from the University of Colorado at Boulder. She previously worked as an intern for Shear Engineering Corporation and Real D, Inc. She is currently a Manufacturing Engineer for Schlumberger in Houston, TX providing solutions for both design and manufacture of isolation valves for oilfield services. Karynna Tuan is currently working towards her graduate degree in the 5-year MS/BS program, majoring in Aerospace Engineering with a focus area in Bioastronautics, the study and support of human spaceflight at CU Boulder. She has worked at Space Grant with the PolarCube team for a year, developing a CubeSat to study the Earth’s tropospheric weather patterns and monitor and record temperature profiles. She is continuing her work experience in the industry field at Sierra Nevada Corporation, Space Systems as a Manufacturing Intern.
PRESS SUMMARY
Joint human-robotic space exploration involving the teleoperation of rovers on planetary surfaces is a key strategy defined by the ISECG’s Global Exploration Roadmap. In support of this goal, the LABS (Lunar and Airless Body Simulator) team at the University of Colorado Boulder has developed a lunar simulation thermal-vacuum facility to create an analog environment in which to conduct survivability testing. LABS built a rover, the Telescope-deployment High Vacuum teleOperated Rover, that can operate for extended periods of time in the harsh lunar environment. The rover is fabricated entirely out of cost-effective commercial off-the-shelf (COTS) components and materials, showing the potential of practical, low cost options for future space exploration.

A Study of Subracks

https://doi.org/10.33697/ajur.2015.004

Samantha Driskill

ABSTRACT
Racks were introduced in 1959 by G. Wraith and J. Conway as a wreckage of groups, and have been used in various topics of mathematics. In this project, we aim to establish certain classical results known for subgroups on subracks.
KEYWORDS
Racks, Subracks, Quandle, Group, Centralizer, Dimension
ABOUT THE STUDENT AUTHOR
Samantha Driskill worked on this project during her senior year (2012 – 2013) at Southwestern
Oklahoma State University. She graduated in the spring of 2014 with two Bachelor of Science degrees (Mathematics and Mathematics Education). She was the president of the Mathematics club and a recipient of multiple awards in the math department. Samantha is currently a full-time teacher at Del city high school in Oklahoma.
PRESS SUMMARY
The theory of racks is strongly connected to the theory of conjugation in groups. Roughly, racks are
described as groups in which the group operation is discarded and only the concept of conjugation is left. In this paper, we investigate and introduce on racks some notions well-developed in groups, and apply those notions in a few examples.

Cardiac Myocardial Hypertrophy and Altered Swimming Behavior in Xenopus laevis Embryos in Incrementally Increasing Hypergravity

https://doi.org/10.33697/ajur.2015.005

Stacey Howes & Darrell Wiens

ABSTRACT
Every living organism on earth has developed and evolved in unit gravity (1G) conditions.  It is likely that any deviation from Earth’s standard gravity will influence development, particularly at early stages.  Previous reports from this lab showed that total length is reduced and that ventricle size is increased during development at 7G.  The objective of the present study was to investigate the effect of increasing levels of hypergravity on the development of the ventricular myocardial wall and the neuromuscular responsiveness of Xenopus laevis.  At early gastrulation, embryos were placed in a centrifuge simulating 7G, 10G, 15G or 17G until they reached stage 45 (feeding tadpole stage, approximately 72 hours from initiation of gastrulation).  Mortality was low and only the 17G exposure induced significant mortality.  Immediately following centrifugation, the embryos were stimulated by touching with a probe to test neuromuscular responsiveness.  With increasing G forces, responsiveness to this test was incrementally reduced. A quarter of the embryos were fixed and their body dimensions were measured.  One group of remaining live embryos, those exposed to 7G, was maintained and swimming behavior was observed during daily 5-minute periods for 52 days.  Overall, abnormal swimming behavior was found in 33% of 7G embryos and in 2% of controls during this time.  These embryos were later subjected to an orientation-swimming test.  Hypergravity-exposed embryos required, on average, one second longer (9% of time required) to become oriented.  From the embryos exposed to increasing G levels and then fixed, we found that total length was reduced successively at increasing hypergravity levels, but the snout-vent proportion of total length increased.  Stained sections of the fixed embryos revealed that the thickness of the ventricle wall was increased, especially the interior ridge component (trabeculae / papillary muscles).  The data demonstrates that hypergravity has persistent effects on the development of the ventricular myocardial wall, neuromuscular responsiveness, and equilibrium organs.
KEYWORDS
Hypergravity, Xenopus, Embryo, Behavior, Myocardium, Hypertrophy
ABOUT THE STUDENT AUTHOR
Stacey Howes is from Fairfax, Iowa and graduated from the University of Northern Iowa (UNI) in May, 2014.  At UNI she majored in biology and carried out this research for her University and Biology Honors thesis.  She submitted an abstract describing aspect of this work for presentation at the 2013 annual meeting of the American Society for Space and Gravitational Research in New Orleans, La.  Her abstract was accepted and at the meeting she presented a poster and was also invited to give a talk.  She received recognition for one of the best talks given by an undergraduate student at the meeting.  Stacey is now pursuing studies at the University of Iowa College of Dentistry.
PRESS SUMMARY
Life on earth has developed and evolved in unit gravity (1G) conditions and it is likely that any deviation in this force would affect early development. The objective of this study was to investigate the effect of increasing levels of gravitational force on the development of body dimensions, the cardiac muscular wall and the neuromuscular responsiveness of the African Clawed frog Xenopus laevis.  Early embryos were placed in a centrifuge simulating 7G, 10G, 15G or 17G until they reached the feeding tadpole stage, and then they were examined and tested.  We found that with increasing G forces, responsiveness was incrementally reduced, aberrant swimming behavior was more frequent, and orientation ability was slower. Their total length was reduced successively at increasing hypergravity levels, but the snout-vent proportion of total length increased. The thickness of the ventricle wall was increased, especially the interior ridges, suggesting hypertrophy.  Our data demonstrate that hypergravity has persistent effects on the development of the ventricular myocardial wall, neuromuscular responsiveness, and equilibrium organs.

Can An Algebraic Diagnostic Test be Used to Predict Final Grades in an Introductory Statistics Class?

https://doi.org/10.33697/ajur.2015.006

Justine Kirksey & Anthony Cooper

ABSTRACT
The Department of Mathematics and Statistics at California State University Sacramento has been using the Intermediate Algebra Diagnostic (IAD) test as a proxy tool to screen students intending to enroll in an introductory statistics course (Stat 1). However, the use of an algebraic test as a diagnostic tool for a statistics course has been questioned by some faculty members and students at this university. The regression models used in this study (simple linear regression, hierarchical linear regression, and logistic regression) show that higher IAD scores are related to higher final grades in Stat 1, even after adjusting for different instructors. Inferences were also made in this study to predict a passing grade and passing rates in Stat 1 based on the bounds of the confidence and prediction intervals obtained for the IAD scores with these models.
KEYWORDS
Linear Regression, Logistic Regression, Statistics Diagnostic Test, Algebra Diagnostic Test, MDTP, Introductory Statistics
ABOUT THE STUDENT AUTHORS
Anthony Cooper is a mathematics major at California State University-Sacramento (CSUS). He is a
non-traditional student that returned to college after working in a bank for 10 years and then serving children and families in an afterschool program for over 15 years. He is currently finishing his major and teaching credential studies at CSUS preparing for a career in education.
Justine Kirksey graduated from CSU, Sacramento Spring 2014 with her BA degree in Biology, minor in Mathematics. She is beginning her teaching credential program at National University in September to pursue her career as a mathematics and science high school teacher.
PRESS SUMMARY
The use of the intermediate algebra diagnostic (IAD) test as a screening tool for a statistics course (Stat 1) in the Department of Mathematics and Statistics at California State University Sacramento has been questioned by some faculty members and students at this university. The statistical analysis in this study shows that higher IAD scores are indeed related to higher final grades in Stat 1, even after adjusting for different instructors when using a sample of over 550 students who have taken this course. Inferences were also made in this study to predict passing grades and passing rates in Stat 1 when using IAD scores as predictors.

A Curve Satisfying K/T = s with constant K>0

https://doi.org/10.33697/ajur.2015.007

Yun Myung Oh and Ye Lim Seo

ABSTRACT
In the present paper, we investigate a space curve in which the curvature is constant and the torsion is a linear function. The aim of this paper is to find an explicit formula for this space curve when the ratioof the torsion to the curvature is a linear function when the curvature is constant.
KEYWORDS
Space Curve, Curvature, Torsion, General Helix, Frenet Frame, Series Solution, Rectifying Curve
ABOUT THE STUDENT AUTHOR
Ye Lim Seo is an undergraduate student at Andrews University. She has shown strong interest in mathematics
and has received several math awards.
PRESS SUMMARY
The first chapter of undergraduate differential geometry is about the curves in 3-dimensional space. Because one of famous results about the general helix is that it has the constant ratio of torsion to curvature, a natural question is to think about the next simple case: the ratio of torsion to curvature as a linear function. Using the idea of series solution to the differential equation, one can find the curve explicitly with the extra condition that the curvature is a constant.

Does Altering Local Water Availability for an Invasive Plant (Raphanus raphanistrum) Affect Floral Morphology and Reproductive Potential?

https://doi.org/10.33697/ajur.2015.008

Natalia Pirimova, Alison J. Parker, and Lesley G. Campbell

ABSTRACT
Abiotic environmental variation can have dramatic effects on plant floral morphology and nectar or
pollen rewards. In response, pollinators may change their foraging behavior and distribution and if
pollinators change their foraging behavior or distribution, this could have dramatic effects on the
reproductive success of plant populations. To start tackling this problem, we measured the response of floral morphology (corolla diameter, stamen length, and ovule number) of Raphanus raphanistrum to experimental manipulations of field soil moisture. As soil moisture increased, corolla diameter and anther length grew. We expect these changes to provide more visitation rewards for insects in moist conditions. Therefore, water availability influences growth and development of flowers, and may have dramatic effects on insect community dynamics.
KEYWORDS
Floral Rewards, Climate, Rain-out Shelters, Flower Morphology, Raphanus raphanistrum, Brassicaceae
ABOUT THE STUDENT AUTHOR
Natalia Pirimova graduated from Ryerson University in May, 2012 with a BS degree in Biology and then graduated from Centennial College in January, 2014 with a post-baccalaureate in a Medical Laboratory Technician field. She is currently a practicing phlebotomist and a medical laboratory technician at St. Michael’s Hospital in Toronto, Ontario.
PRESS SUMMARY
As has been widely discussed recently, climatic conditions and specifically rainfall patterns, of our
planet are changing dramatically. Changes in rainfall may alter the attractiveness of flowers to insect pollinators. We manipulated water availability (both increasing and decreasing soil moisture) and measured the consequences of water availability on flower size in an agricultural weed, wild radish. We concluded that increasing water availability may make flowers more attractive to insect visitors.

Volume 12 Issue 1 August 2014 interactive pdf

https://doi.org/10.33697/ajur.2014.001

Design Techniques for the DNA Cubic-Lattice

Tyler Hotte and Miranda LaRocque

A Student Approach to a Mathematical Simulation of a Racing Electric Vehicle

Fernando Daniel León-Cázares and Daniel Xoconostle-Luna

Proteomic Study of Ribosomal Proteins from Escherichia coli, Saccharomyces cerevisiae, Bos taurus, Gallus gallus, and Oncorhynchus tshawytscha: Application in a Teaching Laboratory Setting

Yoshihiro Miura, Eric Yeager, James A. MacKenzie, and Kestutis Bendinskas

A Cellular Automaton Model for Traffic Flow -Investigating the Effect of Turning

Tracy Finner and Matthew A. Beauregard

On Deflection of Potentially Dangerous Asteroids

Josh Fixelle and Mikhail Kagan

 

August 2014 articles (full details and links):

1) 

Design Techniques for the DNA Cubic-Lattice

https://doi.org/10.33697/ajur.2014.002

Tyler Hotte and Miranda LaRocque

Saint Michael’s College, One Winooski Park, Colchester, VT 05439 USA

Link to PDF  Link to Supplemental Information

Abstract: We use the Watson-Crick properties of DNA and the principles of graph theory to construct origami folding designs for self-assembling cubic lattices.  Our objective is a mathematical design strategy that can be expanded systematically to any size cubic lattice.  This design consists of threading a scaffolding strand of DNA through the lattice that is secured in place by short staple strands of DNA.  We first add augmenting edges to the cubic lattice to enable a single scaffolding strand threading.   We then thread the scaffolding strand through the augmented cube in a way that minimizes the number of different vertex configurations in the structure.

Key Words: Watson-Crick, DNA Self-Assembly, Origami folding, Cubic Lattice, Scaffolding Strand, Threading, Staple Strands

Student Authors’ Bios: Miranda LaRocque graduated from Saint Michael’s College with a BS degree in Mathematics in May 2014. She is currently working as an Actuarial Systems Analyst at National Life Group, a life insurance company in Montpelier, Vermont.
Tyler Hotte graduated from the Saint Michael’s College and the University of Vermont in May 2014 with a BS degree in Mechanical Engineering (minor in math). He is currently living in Burlington, VT and works as a Timber Framer for Vermont Frames in Starksboro, VT.

Press Summary: DNA nanostructures are nanoscale structures made of self-assembling DNA, which can be used for biomolecular computing, targeted drug delivery, and biosensors. We use the Watson-Crick properties of DNA and the principles of graph theory to construct origami folding designs for a cubic lattice. Our methods involve a single scaffolding strand of DNA and short staple strands of DNA that secure the scaffolding strand into the shape of a cubic lattice. Our objective was a mathematical design strategy that could be expanded systematically for self-assembly of any size cubic lattice.

2) 

A Student Approach to a Mathematical Simulation of a Racing Electric Vehicle

https://doi.org/10.33697/ajur.2014.003

Fernando Daniel León-Cázares and Daniel Xoconostle-Luna

Instituto Tecnológico y de Estudios Superiores de Monterrey Campus Estado de México

Link to PDF

Abstract: A program was developed using the software Mathematica to simulate the dynamical behavior of an electric racing car, an electrathon. In conjunction with experimental data it is focused to allow the Borregos-CEM Racing Team decide which settings have to be adjusted in order to increase the velocity of the racing car while decreasing its energy consumption, i.e. the current demanded to the batteries.

Keywords: Model, electric, racing, vehicle, dynamic, simulation, Electrathon

Student Authors’ Bios: Fernando León-Cázares is a senior student in the area of mechanical engineering in Instituto Tecnológico y de Estudios Superiores de Monterrey Campus Estado de México. He was the Electrathon Borregos CEM Racing’s captain for two years and he has participated in a research group in the same institute dealing with the mathematical modeling of a plasma nitriding process. Daniel Xoconostle-Luna is a mechatronics engineering student who began to work full time in 2013.

Press Summary: An Electrathon is a custom built electric vehicle, similar in appearance to a Go-Kart but powered by an electric motor. We developed a mathematical model to simulate the performance of such vehicle under different conditions so that it is possible to predict its velocity, acceleration and energy consumption at any point of any specific track. This allows for the optimization of different parameters of the vehicle to build the best Electrathon possible.

3) 

Proteomic Study of Ribosomal Proteins from Escherichia coli, Saccharomyces cerevisiae, Bos taurus, Gallus gallus, and Oncorhynchus tshawytscha: Application in a Teaching Laboratory Setting

https://doi.org/10.33697/ajur.2014.004

Yoshihiro Miura1,2, Eric Yeager2, James A. MacKenzie2, Kestutis Bendinskas1*

1Department of Chemistry and 2Department of Biological Sciences, SUNY-Oswego

Link to PDF  Link to Supplemental Information

Abstract: Ribosomes are central to protein synthesis and our understanding of ribosomes has advanced antibiotics research. The proteomic study of ribosomes presented here utilizes a combination of differential centrifugation and matrix assisted laser desorption/ionization – time of flight mass spectrometry (MALDI-TOF MS) to analyze ribosomes from various species in a teaching laboratory setting. Five biologically varied species were used: Escherichia coli (bacteria), Saccharomyces cerevisiae (yeast), Bos taurus (cow), Gallus gallus (chicken), and Oncorhynchus tshawytscha (Chinook salmon). Samples were lysed, ribosomes were isolated via ultracentrifugation using a discontinuous sucrose gradient and the individual protein subunits were separated via sodium dodecyl sulfate polyacrylamide gel electrophoresis. Tryptic digest and MALDI-TOF MS were then conducted on fifteen bands excised from the gel, and the mass spectra of both the whole protein sample and peptides were analyzed. Five out of these fifteen bands were positively identified as various ribosomal proteins, with two uncertain identifications. Additionally, three of the five positively identified proteins that travelled the same distance on the gel were determined to be orthologous. Finally, a class of 14 Biochemistry II students utilized these protocols, identified 3 ribosomal proteins and provided their evaluations of the ultracentrifugation-proteomics teaching laboratory.

Key Words: Proteomics, MALDI-TOF MS, ultracentrifugation, ribosomes, teaching laboratory

Student Authors’ Bios: Yoshihiro Miura graduated from SUNY Oswego in December 2012 with a BS in Biochemistry and Biology. He chose to get his D.P.T. degree at Columbia University, NYC, New York.

Eric Yeager graduated from the State University of New York (SUNY) at Oswego in May, 2010 with a BS degree in Zoology (minor in Chemistry). He is currently living in Ithaca, NY, while attending the New York State College of Veterinary Medicine at Cornell University pursuing his Doctorate in Veterinary Medicine (DVM).

Press Summary: Ribosomes are central to protein synthesis and our understanding of ribosomes has advanced antibiotics research. We purified ribosomes and then ribosomal proteins and identified some of those proteins in five species: bacteria, yeast, salmon, chicken, and cow. We taught these advanced techniques to a class of biochemistry students. We suggest that other biochemists could use our protocols for teaching ultracentrifugation and proteomics in their teaching laboratories.

4) 

A Cellular Automaton Model for Traffic Flow -Investigating the Effect of Turning

https://doi.org/10.33697/ajur.2014.005

Tracy Finner1 & Matthew A. Beauregard2

1 Department of Mathematics, University of Arizona, AZ

2 Department of Mathematics, Baylor University, Waco, TX

Link to PDF 

Abstract: A cellular automaton model is proposed, modeling vehicular traffic flow on a two dimensional lattice in which the vehicles turn at an intersection with a given probability. It is shown that the introduction of turning reduces the long-term average velocity, and can be predicted by a power law depending on the probability of a vehicle turning and the density of cars. The reduction in speed decreases rapidly once the light cycle length surpasses a certain threshold, the value of which can be predicted from the observed power law.

Keywords: cellular automaton, traffic flow, traffic light strategy, turning, dynamical systems, power law

Student Authors’ Bios:

Tracy Finner worked on this project during her senior year (2010-2011) at the University of Arizona. She finished her M.Sc. in industrial engineering in the spring of 2014. She is now an Industrial Engineer at Raytheon.

Press Summary: “Traffic flow models are central to urban planners and developers.  In this paper, a traffic flow model is proposed that models the interaction between individual vehicles and subsequent driver behavior to the traffic light system.  The model is then used to develop empirical evidence for a statistical correlation between the density of vehicles, frequency of turning vehicles, and the timing of the traffic signal.”

5) 

On Deflection of Potentially Dangerous Asteroids

https://doi.org/10.33697/ajur.2014.006

Josh Fixelle and Mikhail Kagan

Department of Science and Engineering, The Pennsylvania State University, Abington, 1600 Woodland Road, Abington, PA 19116, USA

Link to PDF 

Abstract: As has been widely discussed recently, our planet may become a target for asteroids. We consider several scenarios proposed to prevent asteroid collisions with Earth. The asteroid 99942 Apophis is considered as a typical representative. Among others, the recent “gravitational tractor” scenario is discussed. For a simplistic toy-model we obtain estimates for both the mass of the tractor and the amount of fuel required to tow a potentially dangerous asteroid off-course so as to avoid a collision with the Earth. In addition, we analyze two more scenarios titled “sling-shot” and “bumping”, and comment on their relative efficiency compared to the ‘towing” scenario. Based on the analysis, the bumping scenario looks most promising.

KeyWords: Near-Earh Objects, 99942 Apophis, Asteroid Deflection, Gravitational Tractor, “Bumping” Scenario, “Sling-shot” Scenario

Student Authors’ Bios: Joshua Fixelle graduated from the Pennsylvania State University in December, 2013 with BS degrees in Astronomy & Astrophysics and Engineering Science & Mechanics (minors in Mathematics and Physics). He is currently living in Evanston, IL, while attending Northwestern University pursuing his Doctorate in Astrophysics (PhD).

Press Summary: As has been widely discussed recently, our planet may become a target for asteroids (the asteroid 99942 Apophis is considered as a typical representative). We considered several scenarios proposed to prevent asteroid collisions with Earth, including the “gravitational tractor”, “sling-shot”, and “bumping” scenarios. We analyzed and compared the scenarios in regards to their relative efficiency compared to the “gravitational tractor”, and concluded that the bumping scenario looks most promising.

Archives

https://doi.org/10.33697/ajur.2013.001

After 10 Years: Returning to the International Connection

https://doi.org/10.33697/ajur.2013.002

Author(s):

C. C. Chancey

Affiliation:

University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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Measuring Potassium in Muscle Tissue Utilizing an Atomic Absorption Spectrometer Validation of an Adaptation for a Whole-body Potassium Counting Method

https://doi.org/10.33697/ajur.2013.003

Author(s):

Anthony R. Horner, Rose A. Clark, Stephen M. LoRusso, and Edward P. Zovinka

Affiliation:

Department of Chemistry, Department of Physical Therapy, Saint Francis University, 117 Evergreen Drive, Loretto, Pennsylvania 15940 USA

ABSTRACT:

Potassium is a cation important for a properly functioning body. It is especially significant for nerves, kidneys, and muscles. The concentration of potassium ions in muscle tissue was determined using an atomic absorption spectrometer operating in emission mode. The meat samples were flash frozen using liquid nitrogen, further ground using a mortar and pestle and then digested by immersing the processed meat in a hydrochloric acid solution. The potassium concentrations in muscle tissue were found to range from 2.76 – 4.66 g K+/kg of beef sample.

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A Case Study on Developing a Classroom Web Application Using Behavior-Driven Development

https://doi.org/10.33697/ajur.2013.004

Author(s):

Austin Vance and Trevor Cickovski

Affiliation:

Eckerd College, 4200 54th Avenue South, Saint Petersburg, Florida 33712 USA

ABSTRACT:

Behavior-Driven Development (BDD) is a software design methodology which bridges the developer-client gap by evolving software through communication between the two sides and shaping it to the goals of shareholders. As a recently published iterative development strategy, BDD is slowly being adopted as a software practice in a wide range of domains. We study the applicability of BDD to designing Narwhal, a classroom drawing application that mimics a combination of PowerPoint slides and whiteboard. Through this case study, we employ junior and senior seminar students as clients and view the effects of BDD on Narwhal’s evolution over a three-month period. We conclude with a discussion on the general applicability of BDD to the design of classroom tools following lessons learned from this case study.

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A Comparison of Skin Microbiota under Adhesive Bandages versus Uncovered Adjacent Skin

https://doi.org/10.33697/ajur.2013.005

Author(s):

Kendra Lemire, Felicia Maes, Marialis Ginart, Chris VanFleet and Tim Braun

Affiliation:

Biological Sciences Department, State University of New York at Oswego, 7060 Route 104, Oswego, New York 13126-3599 USA

ABSTRACT:

The skin is the largest organ in the human body and interacts directly with the exterior environment. It is also a habitat for bacteria. We are interested in the perturbing effects of adhesive bandages on the skin’s bacterial populations. We compared covered versus uncovered finger skin using three kinds of over the counter adhesive bandages. We found that skin covered with an adhesive bandage is home to approximately 80 fold more culturable bacteria than is uncovered skin and that type of bandage makes little difference to expansion of the bacterial population. Diversity of bacteria was measured by two different techniques: one culture dependent and one culture independent, both found no significant diversity difference between covered vs. uncovered skin in number of taxa present. The culture dependent analysis found that most samples were dominated by a single bacterium, whereas the culture independent 16S rDNA analysis found more diversity. Evidence of seasonal cycling of dominant culturable skin bacteria was observed.

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More on the Mathematics of the DLF Theory: Embedding of the Oscillator World L into Segal’s Compact Cosmos D

https://doi.org/10.33697/ajur.2013.006

Author(s):

J. Y. Feng* and A. V. Levichev

Affiliation:

Department of Mathematics, Boston University, Boston, Massachusetts 02215 USA

ABSTRACT:

The DLF theory can be understood as an attempt to modify the Standard Model by flexing the Poincare symmetry to certain 7-dimensional symmetries. The D part of the theory is known as Segal’s Chronometry which is based on compact cosmos D=U(2) with the SU(2,2) fractional linear action on it. The oscillator group is viewed as a subgroup LG of the conformal group G=SU(2,2) and certain LG-orbits L in D are studied. We prove existence of such L and of such an embedding of F=U(1,1) into D, that D differs from F by a certain torus whereas D differs from L by a circle on that torus. In the general U(p,q) vs U(p+q) case, the Sviderskiy formula is described – as a tribute to the late Oleg S. Sviderskiy (July 31 1969 – March 30 2011).

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SAR and Pharmacophore Based Designing of Some Antimalarial and Antiretroviral Agents: An INTERNET Based Drug Design Approach

https://doi.org/10.33697/ajur.2013.007

Author(s):

Soumendranath Bhakat

Affiliation:

Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Ranchi-835215 INDIA

ABSTRACT:

With the development of computational chemistry and molecular docking studies, Structure Activity Relationship or SAR- and pharmacophore-based drug design have been modified to target based drug discovery using sophisticated computational tools which is not very much user friendly and has got many incompatibility issues with many operating systems (OS) and other system configurations. In this paper SAR and pharmacophore based drug design approaches have been described by the used of free internet based tools which are very much user friendly and can almost compatible with any platform. Some antimalarial. And anti retroviral agents have been designed using pharmacophore study and their drug like properties, toxicity, metabolic sites and other parameters are predicted by the free internet based tools.

https://doi.org/10.33697/ajur.2012.006

After 10 Years: Back to Undergraduate Research Advisors

https://doi.org/10.33697/ajur.2012.007

Author(s):

C. C. Chancey

Affiliation:

University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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The Effects of Hypergravity on Xenopus Embryo Growth and Cardiac Hypertrophy

https://doi.org/10.33697/ajur.2012.008

Author(s):

Bryce Joseph Duchman and Darrell Wiens

Affiliation:

Department of Biology, University of Northern Iowa, Cedar Falls, Iowa 50614-0421 USA

ABSTRACT:

All life on earth has developed and evolved in a unity gravity (1G) environment. Any deviation below or above 1G could affect animal development, a period when much change occurs and sensitivity is high. We imposed simulated hypergravity through centrifugation and analyzed the effects on the overall body length and cardiac growth of Xenopus laevis embryos. We predicted that increased contractile force would be required from the heart to adequately circulate blood, dispersing nutrients, and that this would inhibit organism growth and possibly induce a state of hypertrophy. Embryos reaching gastrulation stage were exposed to a 7G or 1G (control) field via centrifugation for 96 hours. We then recorded behavior, mortality and took body length measurements. We found no significant differences in behavior or mortality, however, body length was significantly reduced by an average of 6.8% in the 7G group. We then fixed, embedded, sectioned and stained embryos in order to investigate the dimensions of cardiac tissue and of the cardiac region of the body using image analysis software. We found the 7G group had a significantly reduced average body cross-sectional area (-18%) and yet a significantly larger ventricular cross-sectional area (+36%) when compared to the 1G group. The average ratio of ventricle cross-sectional area to average body cross-sectional area was significantly higher in the 7G group when compared to the 1G. From these data, we conclude that hypergravity has a significant inhibitory impact on the Xenopus laevis embryo growth and causes a significant increase in ventricle size.

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Observing Program Calculator for Eclipsing Binary Star Systems

Appendix: ephemeris calculator

https://doi.org/10.33697/ajur.2012.009

Author(s):

Colby Neal and Michael Braunstein

Affiliation:

Central Washington University, Department of Physics, Ellensburg, Washington 98926 USA

ABSTRACT:

A Microsoft Excel application has been developed to utilize eclipsing binary elements to calculate binary ephemerides that are useful in a program of observing binary systems. Binary star systems consist of two stars orbiting a common center of mass. Consistent monitoring of eclipsing binary stars is important for establishing fundamental astronomical parameters, such as mass and composition of the stellar system. The application that was developed supports effective use of resources in such monitoring applications. The main quantities computed by the application at the time of the eclipse include: local time, Julian date, starting Epoch, altitude of the system, phase of the moon, Local Mean Sidereal Time, and Local Hour Angle. Other quantities computed by the application include current Universal Time (UT), UT/Local Time correction, Julian Date, and current moon phase/percent illuminated. The observing application has been demonstrated to be effective in practical application to obtain differential photometry data for SV Camelopardalis, a system of interest because of variability in its period caused by a third body. The application can be easily modified for use with other highly periodic astronomical systems, for instance transits of extrasolar planets.

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Isospectral Domains in Euclidean 3-Space

https://doi.org/10.33697/ajur.2012.010

Author(s):

Christopher Cox

Affiliation:

Department of Mathematics, Iowa State University, Ames, Iowa 50011 USA

ABSTRACT:

The question as to whether the shape of a drum can be heard has existed for around fifty years. The simple answer is ‘no’ as shown through the construction of isospectral domains. Isospectral domains are non-isometric domains that display the same spectra of frequencies of sound. These frequencies, deduced from the eigenvalues of the Laplacian, are determined by solving the wave equation in a domain omega , where alpha-omega is subject to Dirichlet boundary conditions. This paper presents methods to expand the already existing two dimensional transplantation proof into Euclidean 3-space and, through these means, provides a number of three dimensional isospectral domains.

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Memory Accuracy for Emotional and Neutral Narratives: Investigating the Influence of Suggestive Misinformation on the Frequency of False Memories

https://doi.org/10.33697/ajur.2012.011

Author(s):

Laura E. Paige and Elizabeth A. Kensinger

Affiliation:

Psychology Department, Boston College, Chestnut Hill, Massachusetts 02467 USA

ABSTRACT:

Memory is a reconstructive process, impressionable and not always vigilant in detecting devices working against its accuracy. False memory occurs when memory for an event is infiltrated by new information or alterations are made to the information that was previously stored. The present study investigated the effect of emotional valence on false memory occurrence through the misinformation effect – memory errors that arise as a consequence of exposure to misleading information – by presenting participants with narratives in one of three valence conditions (negative, positive, neutral) and subjecting them to suggestive questions providing credulous misinformation following a one-hour delay. Results revealed that when collapsing across negative and positive conditions, overall false memory occurrences were significantly reduced for these narratives compared to the neutral condition. Some of the effects of emotion on memory accuracy were more pronounced for negative information than for positive or neutral information; response rates in the negative condition, as compared to the two other valence conditions, revealed an increase in hits and a decrease in false alarms suggesting negative valence enhances discriminability.

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Diffusion of Water and Diatomic Oxygen in Poly(3-hexylthiophene) Melt: A Molecular Dynamics Simulation Study

https://doi.org/10.33697/ajur.2012.012

Author(s):

Julia Deitz, Yeneneh Yimer, and Mesfin Tsige

Affiliation:

Department of Polymer Science, University of Akron, 302 Buchtel Common, Akron, Ohio 44325 USA

ABSTRACT:

Diffusion behavior of water, diatomic oxygen, and a mixture of both into a poly(3-hexylthiophene)[P3HT] melt were investigated using Molecular Dynamics Simulation. Once simulations were complete, the data was analyzed to determine the diffusion coefficient of those molecules in P3HT using Fick’s law. The diffusion coefficient values were then plotted as a function of concentration and temperature to determine if trends existed. For both water and oxygen, no dependence was observed of the diffusion coefficient on concentration and temperature for the ranges studied. However, a variation in the diffusion coefficient on concentration was observed due to the expected inhomogeneity of the P3HT melt. In the presence of O2, the diffusion of H2O decreased significantly by a factor between four and five, while in the presence of H2O, the diffusion of O2 slightly decreased.

https://doi.org/10.33697/ajur.2012.001

After 10 Years: Back to Where We Began

https://doi.org/10.33697/ajur.2012.002

Author(s):

C. C. Chancey

Affiliation:

University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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A New Vectorization Technique for Expression Templates in C++

https://doi.org/10.33697/ajur.2012.003

Authors and Affiliations:

J. Progsch and Y. Ineichen
Department of Computational Science, ETH-Zürich, CAB H 83.2, Universitätstrasse 6, 8092 Zürich SWITZERLAND

A. Adelmann
Paul Scherrer Institute, 5232 Villigen PSI, SWITZERLAND

ABSTRACT:

Vector operations play an important role in high performance computing and are typically provided by highly optimized libraries that implement the Basic Linear Algebra Subprograms (BLAS) interface. In C++ templates and operator overloading allow the implementation of these vector operations as expression templates which construct custom loops at compile time and providing a more abstract interface. Unfortunately existing expression template libraries lack the performance of fast BLAS implementations. This paper presents a new approach – Statically Accelerated Loop Templates (SALT) – to close this performance gap by combining expression templates with an aggressive loop unrolling technique. Benchmarks were conducted using the Intel C++ compiler and GNU Compiler Collection to assess the performance of our library relative to Intel’s Math Kernel Library as well as the Eigen template library. The results show that the approach is able to provide optimization comparable to the fastest available BLAS implementations, while retaining the convenience and flexibility of a template library.

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Determining the Efficacy of IonatorEXP™ Activated Tap Water on Growth of Staphyloccocus aures and Escherichia coli.

https://doi.org/10.33697/ajur.2012.004

Author(s):

Sara Schiedler, Rachelle Peterson, and Sasha Showsh (Department of Biology)

Thao Yang (Department of Chemistry)

Affiliation:

University of Wisconsin, PO Box 4004, Eau Claire, Wisconsin 54702 USA

ABSTRACT:

The efficacy in growth inhibition of Staphylococcus aureus and Escherichia coli of the IonatorEXP™ activated tap water was compared to plain tap water, Quatsyl™, and Butchers Neutral Disinfectant™. Treatment with Quatsyl™ or Butchers Morning Mist™ Neutral Disinfectant resulted in complete inhibition of growth for both S. aureus and E.coli. Treatments with IonatorEXP™ activated tap water, performed as directed by the manufacturer, or plain tap water, resulted in no observable inhibition of growth for either of the bacterial strains tested. This observation is not unexpected given that analysis of pH, conductivity and H2O2 on IonatorEXP™ activated tap water were statistically the same values as those determined for plain tap water that was not activated by the IonatorEXP™.

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A Multi-Objective, Linked-Simulation-Optimization of Henry’s Saltwater Intrusion Problem using HST3D and Box’s Method

https://doi.org/10.33697/ajur.2012.005

Author(s):

Emily Curtis and Robert Willis

Affiliation:

Department of Environmental Resources Engineering, Humboldt State University, Arcata, California 95521 USA

ABSTRACT:

A multi-objective linked simulation and optimization (LSO) model for a three dimensional saltwater intrusion problem has been developed. The LSO employs HST3D and Box’s algorithm. The weighting method of multi-objective optimization solves the multi-objective planning problem. The model is capable of determining the optimal pumping rates that minimize the saline concentration at the well sites, as well as, the cost associated with pumping, while satisfying an exogenous water demand. The model is valid for a wide range of applications as explicitly defined by the simulation model. The application of the model was limited to a modified version of Henry’s saltwater intrusion problem. Henry’s problem was modified to include a third spatial dimension and well sites. The multi-objective optimization yielded explicit tradeoff information between the two objectives.

https://doi.org/10.33697/ajur.2011.016

Editorial: The Lessons of Pittsburgh

https://doi.org/10.33697/ajur.2011.017

Author(s):

C. C. Chancey

Affiliation:

University of Northern Iowa, Cedar Falls, Iowa 50614-0150 USA

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The ERC Mechanism and the Formation of Abnormal Product in the Stevens Rearrangement

https://doi.org/10.33697/ajur.2011.018

Author(s):

Soumendranath Bhakat

Affiliation:

Nutanpalli, P.O. Suri, Dist. Birbhum, West Bengal, Pin: 731101 INDIA

ABSTRACT:

To explain the new abnormal product of the Stevens Rearrangement which is not explainable by different existing mechanisms like “radical pair mechanism”; “ionic pair mechanism”, I proposed a new mechanism scheme entitled the ERC (Elimination Recombination Coupling) mechanism and a new abnormal product of the Stevens Rearrangement. This mechanism also maintains parity between the “radical pair mechanism” and the “ionic pair mechanism.

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Physiological Versus Perceived Foot Temperature, and Perceived Comfort, during Treadmill Running in Shoes and Socks of Various Constructions

https://doi.org/10.33697/ajur.2011.019

Author(s):

Rachel M. Barkley, Mike R. Bumgarner, and Erin M. Poss (Biochemistry, Cell and Molecular Biology Program)

David S. Senchina (Biology Department)

Affiliation:

Drake University, Des Moines, Iowa 50311 USA

ABSTRACT:

The purpose of this investigation was to determine whether people could accurately perceive physiological foot temperature during brief bouts of treadmill running in different combinations of shoe and sock models, and also how perception of comfort was influenced. Sixteen young adult males (21.3  0.8 years, 181.8  1 cm, 74.6  1.5 kg) participated in two separate studies where they alternated running and resting for 10 min each with temperature probes attached at two sites on the lateral dorsal aspect of the right foot. Subjects reported perceptions of foot comfort and temperature after each run using 10 cm visual analogue scales. In the first experiment, different sock models were tested with the same shoe model; in the second experiment, different shoe models were tested with the same sock model. Foot temperature did not differ statistically as a function of shoe or sock model in either experiment. Subjects did not perceive any difference in foot temperature in the shoe experiment, but perceived their foot as being cooler when wearing either a polyester sock or a calf compression sleeve and more comfortable when wearing shoes with less mass. Taken together, the results suggest that subjects’ perceptions of foot temperature may not coincide with physiological foot temperature and are more strongly influenced by sock characteristics than shoe characteristics. Further, shoe mass (but not sock fiber weave or composition) may impact comfort perception by subjects.

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Determination of Cadmium and Lead in Northern Pike from the Missouri River

https://doi.org/10.33697/ajur.2011.020

Author(s):

Jennifer Even and Shahrokh Ghaffari

Affiliation:

Ohio University-Zanesville, Zanesville, Ohio 43701 USA

ABSTRACT:

Lead and cadmium are trace metals which accumulate in the body and are extremely toxic in living organisms. The purpose of this study was to find organ(s) with the greatest concentrations of these elements. In this study liver, gill, intestines, and kidney of five samples of Northern Pikes were analyzed. After the organs were dried and digested using nitric acid the anodic stripping voltammetry method was employed to analyze this samples. This method was used for its low detection limit of 10-9 to 10-10 M. However, no trace of either lead or cadmium was found in all 60 samples analyzed. Lack of detectable amount of both lead and cadmium is attribute to; first, Northern Pikes are not bottom dweller and thus would not be highly exposed to sediments that most commonly contain trace metals, second, the absence of a major industry which typically produces these contaminates in this area.

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Conic Sections in the Double-Slit Experiment

https://doi.org/10.33697/ajur.2011.021

Author(s):

Joe Hughes and Frederic Liebrand

Affiliation:

Walla Walla University, 204 S. College Avenue, College Place, Washington 99324 USA

ABSTRACT:

The use of conic sections in obtaining the locations of double-slit maxima is absent in many undergraduate treatments [1-3]. However, their inclusion is not conceptually difficult and increases the understanding not only of interference phenomena, but also of the underlying geometry. This paper illustrates how elliptic and hyperbolic conic sections arise naturally in a conceptual analysis of the double slit.