Physical Sciences and Mathematics Commons^™

Editorial, Deepayan Sarkar

The R Journal

On behalf of the editorial board, I am pleased to publish Volume 6, Issue 2 of the R Journal.

Mvn: An R Package For Assessing Multivariate Normality, Selcuk Korkmaz, Dincer Goksuluk, Gokmen Zararsiz

The R Journal

Assessing the assumption of multivariate normality is required by many parametric multivariate statistical methods, such as MANOVA, linear discriminant analysis, principal component analysis, canonical correlation, etc. It is important to assess multivariate normality in order to proceed with such statistical methods. There are many analytical methods proposed for checking multivariate normality. However, deciding which method to use is a challenging process, since each method may give different results under certain conditions. Hence, we may say that there is no best method, which is valid under any condition, for normality checking. In addition to numerical results, it is very useful to …

Coordinate-Based Meta-Analysis Of Fmri Studies With R, Andrea Stocco

The R Journal

This paper outlines how to conduct a simple meta-analysis of neuroimaging foci of activation in R. In particular, the first part of this paper reviews the nature of fMRI data, and presents a brief overview of the existing packages that can be used to analyze fMRI data in R. The second part illustrates how to handle fMRI data by showing how to visualize the results of different neuroimaging studies in a so-called orthographic view, where the spatial distribution of the foci of activation from different fMRI studies can be inspected visually.

Functional MRI (fMRI) is one of the most important …

Bshazard: A Flexible Tool For Nonparametric Smoothing Of The Hazard Function, Paola Rebora, Agus Salim, Marie Reilly

The R Journal

The hazard function is a key component in the inferential process in survival analysis and relevant for describing the pattern of failures. However, it is rarely shown in research papers due to the difficulties in nonparametric estimation. We developed the bshazard package to facilitate the computation of a nonparametric estimate of the hazard function, with data-driven smoothing. The method accounts for left truncation, right censoring and possible covariates. B-splines are used to estimate the shape of the hazard within the generalized linear mixed models frame work. Smoothness is controlled by imposing an autoregressive structure on the baseline hazard coefficients. This …

Prinsimp, Jonathan Zhang, Nancy Heckman, Davor Cubranic, Joel G. Kingsolver, Travis Gaydos, J.S. Marron

The R Journal

Principal Components Analysis (PCA) is a common way to study the sources of variation in a high-dimensional data set. Typically, the leading principal components are used to understand the variation in the data or to reduce the dimension of the data for subsequent analysis. The remaining principal components are ignored since they explain little of the variation in the data. However, the space spanned by the low variation principal components may contain interesting structure, structure that PCA cannot find. Prinsimp is an R package that looks for interesting structure of low variability. “Interesting” is defined in terms of a simplicity …

Taming Pitchf/X Data With Xml2r And Pitchrx, Carson Sievert

The R Journal

XML2R is a framework that reduces the effort required to transform XML content into tables in a way that preserves parent to child relationships. pitchRx applies XML2R’s grammar for XML manipulation to Major League Baseball Advanced Media (MLBAM)’s Gameday data. With pitchRx, one can easily obtain and store Gameday data in a remote database. The Gameday website hosts a wealth of XML data, but perhaps most interesting is PITCHf/x. Among other things, PITCHf/x data can be used to recreate a baseball’s flight path from a pitcher’s hand to home plate. With pitchRx, one can easily create animations …

Applying Spartan To Understand Parameter Uncertainty In Simulations, Kieran Alden, Mark Read, Paul S. Andrews, Jon Timmis, Mark Coles

The R Journal

In attempts to further understand the dynamics of complex systems, the application of computer simulation is becoming increasingly prevalent. Whereas a great deal of focus has been placed in the development of software tools that aid researchers develop simulations, similar focus has not been applied in the creation of tools that perform a rigorous statistical analysis of results generated through simulation: vital in understanding how these results offer an insight into the captured system. This encouraged us to develop spartan, a package of statistical techniques designed to assist researchers in understanding the relationship between their simulation and the real system. …

Teachers' Curricular Reasoning And Mkt In The Context Of Algebra And Statistics, Kolby J. Gadd

Theses and Dissertations

This study investigates 7th grade teachers' curricular reasoning and MKT in algebra and statistics. Although the use of curriculum materials and MKT both influence the quality of mathematics instruction, no relationship between teachers' curricular reasoning and MKT was found. Further, teachers' curricular reasoning across algebra and statistics was very similar despite differences in these fields and differences in MKT. A model for thinking about the knowledge needed to provide high quality instruction is proposed by considering the role of curricular reasoning and MKT in instruction.

Replication And Knowledge Production In Empirical Software Engineering Research, Jonathan L. Krein

Theses and Dissertations

Although replication is considered an indispensable part of the scientific method in software engineering, few replication studies are published each year. The rate of replication, however, is not surprising given that replication theory in software engineering is immature. Not only are replication taxonomies varied and difficult to reconcile, but opinions on the role of replication contradict. In general, we have no clear sense of how to build knowledge via replication, particularly given the practical realities of our research field. Consequently, most replications in software engineering yield little useful information. In particular, the vast majority of external replications (i.e., replications performed …

The Existence Of A Discontinuous Homomorphism Requires A Strong Axiom Of Choice, Michael Steven Andersen

Theses and Dissertations

Conner and Spencer used ultrafilters to construct homomorphisms between fundamental groups that could not be induced by continuous functions between the underlying spaces. We use methods from Shelah and Pawlikowski to prove that Conner and Spencer could not have constructed these homomorphisms with a weak version of the Axiom of Choice. This led us to define and examine a class of pathological objects that cannot be constructed without a strong version of the Axiom of Choice, which we call the class of inscrutable objects. Objects that do not need a strong version of the Axiom of Choice are scrutable. We …

Microchip Thermal Gradient Gas Chromatography, Anzi Wang

Theses and Dissertations

Although the airbath oven is a reliable heating method for gas chromatography (GC), resistive heating is needed for higher analytical throughput and on-site chemical analysis because of size, heating rate and power requirements. In the last thirty years, a variety of resistive heating methods were developed and implemented for both benchtop and portable GC systems. Although fast heating rates and low power consumption have been achieved, losses in column efficiency and resolution, complex construction processes and difficulties experienced in recovering damaged columns have also become problematic for routine use of resistively heated columns. To solve these problems, a new resistively …

Framework To Implement Authentication, Authorization And Secure Communications In A Multiuser Collaborative Cax Environment, Francis Mensah

Theses and Dissertations

Computer Aided Design (CAD) applications have historically been based on a single user per application architecture. Although this architecture is still popular to date, it does have several drawbacks. First of all the single user CAD architecture inhibits a concurrent engineering design process where several designers can work on the same model simultaneously. This limitation introduces time inefficiency especially when a project involves geographically dispersed designers. A solution to these drawbacks could be a transition from the traditional single user CAD architecture to a multiuser collaborative architecture. Advances in computer networking technologies, especially relating to the Internet, have provided the …

A Covering System With Minimum Modulus 42, Tyler Owens

Theses and Dissertations

We construct a covering system whose minimum modulus is 42. This improves the previous record of 40 by P. Nielsen.

The Bioluminescence Heterozygous Genome Assembler, Jared Calvin Price

Theses and Dissertations

High-throughput DNA sequencing technologies are currently revolutionizing the fields of biology and medicine by elucidating the structure and function of the components of life. Modern DNA sequencing machines typically produce relatively short reads of DNA which are then assembled by software in an attempt to produce a representation of the entire genome. Due to the complex structure of all but the smallest genomes, especially the abundant presence of exact or almost exact repeats, all genome assemblers introduce errors into the final sequence and output a relatively large set of contigs instead of full-length chromosomes (a contig is a DNA sequence …

Damage And Alteration Of Mangroves Inhabited By A Marine Wood-Borer, Timothy Mathias Davidson, Catherine E. De Rivera, Hwey-Lian Hsieh

Environmental Science and Management Faculty Publications and Presentations

Animals can exert a strong influence on the structure and function of foundation species such as mangroves. Because mangroves live at the interface of land and sea, both terrestrial and marine species affect them, including numerous herbivores and boring species. These organisms can affect the fecundity, performance, and morphology of mangroves. In a mangrove stand in southwestern Taiwan, we discovered that mangroves were extensively damaged by woodboring isopods Sphaeroma terebrans. We examined the relationships between burrowing damage from S. terebrans and metrics of mangrove fecundity, performance, and morphology. Individuals of Rhizophora stylosa that were more burrowed by isopods had significantly …

Bhaskara’S Approximation For The Sine, Karel Stroethoff

The Mathematics Enthusiast

The 7th century Indian mathematician Bhaskara (c.600 – c.680) obtained a remarkable approximation for the sine function. Many subsequent ancient authors have given versions of this rule, but none provided a proof or described how the result was obtained. Grover [1] provides a possible explanation, but I think the rule can be explained more clearly. Rather than give the rule first, we will derive it, and then discuss its accuracy, and explore some alternative approximations. Our derivation is simply an exercise in modeling.

Numerically Integrating Irregularly-Spaced (X, Y) Data, B. Cameron Reed

The Mathematics Enthusiast

This article describes a computer program for numerically integrating under a y(x) curve of experimental data where the abscissa values are not equally-spaced. This technique is based on fitting parabolas to successive groups of three data points, and may be regarded as a generalization of Simpson’s rule.

Math As A Tool Of Anti-Semitism, Jay Egenhoff

The Mathematics Enthusiast

At Moscow State University’s Department of Mathematics during the 1970’s and 1980’s, there was rampant discrimination against Jewish and other unwanted students. The professors at the math department made a strong effort to keep Jewish students out of the department. They designed "killer" or "coffin" problems and Jewish students had to answer them during an oral exam. These problems have simple solutions, but require a clever strategy to solve them. This paper explores some of the context of this episode and provides several problems with detailed solutions.

An Examination Of Pre-Service Secondary Mathematics Teachers’ Conceptions Of Angles, Melike Yigit

The Mathematics Enthusiast

The concept of angles is one of the foundational concepts to develop of geometric knowledge, but it remains a difficult concept for students and teachers to grasp. Exiting studies claimed that students’ difficulties in learning of the concept of angles are based on learning of the multiple definitions of an angle, describing angles measuring the size of angles, and conceiving different types of angles such as 0-line angles, 1- line angles, and 2-line angles. This study was designed to gain better insight into pre-service secondary mathematics teachers’ (PSMTs) mental constructions of the concept of angles from the perspective of Action-Process-Object-Schema …

Common Sense About The Common Core, Alan H. Schoenfeld

The Mathematics Enthusiast

Is the Common Core the best thing since sliced bread, or the work of the devil? Is it brand new, or a rehash of old ideas? Is it anything more than a brand name, or is there substance? Can it work, given the implementation challenges in our political and school systems? Opinions about the Common Core are everywhere, but the op-eds I’ve seen are often short on facts, and equally short on common sense. A mathematician by training, I’ve worked for nearly 40 years as an education researcher, curriculum materials developer, test developer, standards writer, and teacher. What follows is …

Book Review Of The Tower Of Hanoi: Myths And Maths (Birkhäuser), Cory Palmer

The Mathematics Enthusiast

As the title of the book suggests, the central topic of “The Tower of Hanoi – Myths and Maths” by Hinz, Klavˇzar, Milutinovi´c, and Petr is the famous puzzle of the same name. The classic Tower of Hanoi puzzle along with a number of its variations and related puzzles are examined in a rigorous mathematical framework.

Proper Handling And Transportation Of Eggs For Sale At Kentucky Farmers’ Markets, Anthony J. Pescatore, Jacquie Jacob

Agriculture and Natural Resources Publications

Regardless of the number of eggs produced, and whether the eggs are for home use or sale, careful egg handling is very important. The United States Food and Drug Administration (FDA) lists eggs as a potentially hazardous food, therefore careful handling is important. In Kentucky, if you sell more than 60 dozen eggs a week you need to purchase a retail license. The same holds true if you want to sell your eggs to a retail store to be re-sold or to a distributor that will sell them for you. If you produce fewer than 60 dozen eggs a week …

Sheep Breeding: Heritability, Ebvs, Epds And The Nsip, Debra K. Aaron

Agriculture and Natural Resources Publications

Genetic improvement in a flock depends on the producer’s ability to select breeding sheep that are genetically superior for traits of economic importance. This is complicated by the fact that an animal’s own performance is not always a true indicator of its genetic potential as a parent.

Modeling Colony Collapse Disorder In Honeybees As A Contagion, Christopher Kribs, Christopher Mitchell

Mathematics Faculty Publications - Archive

Honeybee pollination accounts annually for over $14 billion in United States agriculture alone. Within the past decade there has been a mysterious mass die-off of honeybees, an estimated 10 million beehives and sometimes as much as 90% of an apiary. There is still no consensus on what causes this phenomenon, called Colony Collapse Disorder, or CCD. Several mathematical models have studied CCD by only focusing on infection dynamics. We created a model to account for both healthy hive dynamics and hive extinction due to CCD, modeling CCD via a transmissible infection brought to the hive by foragers. The system of …

Inbreeding In Sheep, Debra K. Aaron

Agriculture and Natural Resources Publications

Inbreeding is broadly defined as the mating of individuals that are related. Strictly speaking, however, all animals within a breed are related. So, in a sense, every purebred sheep producer practices some degree of inbreeding. In most cases this relationship is very slight. Therefore, inbreeding is more practically defined as the mating of individuals more closely related than the average of the breed. This practice includes mating brother to sister, sire to daughter and son to dam.

Umphlett Qci Dec 2014, Natalie A. Umphlett

High Plains Regional Climate Center: Staff Publications

Highlights for the Basin

Temperature and Precipitation Anomalies

Drought Conditions

Agriculture

Horticulture

Recreation and Tourism

3-Month Precipitation and Temperature Outlooks

Soil Moisture Conditions

Association Of G-Quadruplex Forming Sequences With Human Mtdna Deletion Breakpoints, D. W. Dong, F. Pereira, Steven Paul Barrett , '13, J. E. Kolesar, K. Cao, J. Damas, Liliya A. Yatsunyk, F. B. Johnson, B. A. Kaufman

Chemistry & Biochemistry Faculty Works

Background: Mitochondrial DNA (mtDNA) deletions cause disease and accumulate during aging, yet our understanding of the molecular mechanisms underlying their formation remains rudimentary. Guanine-quadruplex (GQ) DNA structures are associated with nuclear DNA instability in cancer; recent evidence indicates they can also form in mitochondrial nucleic acids, suggesting that these non-B DNA structures could be associated with mtDNA deletions. Currently, the multiple types of GQ sequences and their association with human mtDNA stability are unknown. Results: Here, we show an association between human mtDNA deletion breakpoint locations (sites where DNA ends rejoin after deletion of a section) and sequences with G-quadruplex …

First Proof Of Concept Of Sustainable Metabolite Production From High Solids Fermentation Of Lignocellulosic Biomass Using A Bacterial Co-Culture And Cycling Flush System, Wanying Yao, Sue E. Nokes

Biosystems and Agricultural Engineering Faculty Publications

To improve the lignocellulose conversion for ABE in high solids fermentation, this study explored the feasibility of cycling the process through the cellulolytic or/and solventogenic phases via intermittent flushing of the fermentation media. Five different flushing strategies (varying medium ingredients, inoculum supplement and cycling through phases) were investigated. Flushing regularly throughout the cellulolytic phase is necessary because re-incubation at 65 °C significantly improved glucose availability by at least 6-fold. The solvents accumulation was increased by 4-fold using corn stover (3-fold using miscanthus) over that produced by flushing only through the solventogenic phase. In addition, cycling process was simplified by re-incubating …

Quantifying The Basal Conditions Of A Mountain Glacier Using A Targeted Full-Waveform Inversion: Bench Glacier, Alaska, Usa, E. Babcock, J. Bradford

Geosciences Faculty Publications and Presentations

Glacier dynamics are inextricably linked to the basal conditions of glaciers. Seismic reflection methods can image the glacier bed under certain conditions. However, where a seismically thin layer of material is present at the bed, traditional analyses may fail to fully characterize bed properties. We use a targeted full-waveform inversion algorithm to quantify the basal-layer parameters of a mountain glacier: thickness (d), P-wave velocity (α) and density (ρ). We simultaneously invert for the seismic quality factor (Q) of the bulk glacier ice. The inversion seeks to minimize the difference between the data …

An Introduction To Sheep, Debra K. Aaron, Donald G. Ely

Agriculture and Natural Resources Publications

The information in this fact sheet was developed to provide a quick reference to the most frequently asked questions about sheep and sheep production.