Volume 13, Issue 1, January 2016

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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 So and So’ frames, respectively.  For the energy of the particle before the emission of radiation he uses the symbol E and he uses H to denote the energy of the particle after the emission of light.” it should readEinstein uses the symbols E and H to distinguish quantities in the So and So’ frames, respectively.  For the energy of the particle before the emission of radiation he uses the subscript 0 and he uses the subscript 1 to denote the energy of the particle after the emission of light.” (posted on 06/25/2017)

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

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

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

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

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

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

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

 

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

Einstein’s 1905 Paper on E=mc2

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

 

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

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

 

Numerical Prediction of Microbubble Attachment in Biological Flows

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