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The R Journal (December 2014) 6(2): Complete Issue, The R Foundation

The R Journal

Editorial, Deepayan Sarkar

Contributed Research Articles

Coordinate-Based Meta-Analysis of fMRI Studies with R, Andrea Stocco

Automatic Conversion of Tables to LongForm Dataframes, Jimmy Oh

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

phaseR: An R Package for Phase Plane Analysis of Autonomous ODE Systems, Michael J. Grayling

Flexible R Functions for Processing Accelerometer Data, with Emphasis on NHANES 2003-2006, Dane R. Van Domelen and W. Stephen Pittard

Applying spartan to Understand Parameter Uncertainty in Simulations, Kieran Alden, Mark Read, Paul S. Andrews, Jon Timmis, and Mark Coles

ngspatial: A Package for Fitting …

Sgof: An R Package For Multiple Testing Problems, Irene Castro-Conde, Jacob De Uña-Álvarez

The R Journal

In this paper we present a new R package called sgof for multiple hypothesis testing. The principal aim of this package is to implement SGoF-type multiple testing methods, known to be more powerful than the classical false discovery rate (FDR) and family-wise error rate (FWER) based methods in certain situations, particularly when the number of tests is large. This package includes Bi nomial and Conservative SGoF and the Bayesian and Beta-Binomial SGoF multiple testing procedures, which are adaptations of the original SGoF method to the Bayesian setting and to possibly correlated tests, respectively. The sgof package also implements the Benjamini-Hochberg …

Phaser: An R Package For Phase Plane Analysis Of Autonomous Ode Systems, Michael J. Grayling

The R Journal

When modelling physical systems, analysts will frequently be confronted by differential equations which cannot be solved analytically. In this instance, numerical integration will usually be the only way forward. However, for autonomous systems of ordinary differential equations (ODEs) in one or two dimensions, it is possible to employ an instructive qualitative analysis foregoing this requirement, using so-called phase plane methods. Moreover, this qualitative analysis can even prove to be highly useful for systems that can be solved analytically, or will be solved numerically anyway. The package phaseR allows the user to perform such phase plane analyses: determining the stability of …

Judah Aristobulus And Alexander Jannaeus In The Dead Sea Scrolls, Kenneth Atkinson

Faculty Publications

The reigns of Judah Aristobulus and Alexander Jannaeus marked a major turning point in the history of the Hasmonean dynasty. Judah Aristobulus transformed his family’s state into a monarchy in which a single person held the offices of king and high priest. His brother, Alexander Jannaeus, succeeded him as king and high priest and expanded the boundaries of the Hasmonean state. He also preserved the territorial integrity of the Hasmonean state when he fought off invasions by Egyptian and Seleucid rulers. Although the reigns of Judah Aristobulus and Alexander Jannaeus are widely known from the writings of Josephus, the authors …

Protein Expression, Characterization And Activity Comparisons Of Wild Type And Mutant Dusp5 Proteins, Jaladhi Nayak, Adam J. Gastonguay, Marat R. Talipov, Padmanabhan Vakeel, Elise A. Span, Kelsey S. Kalous, Raman G. Kutty, David R. Jensen, Phani Raj Pokkuluri, Daniel S. Sem, Rajendra Rathore, Ramani Ramchandran

Chemistry Faculty Research and Publications

Background

The mitogen-activated protein kinases (MAPKs) pathway is critical for cellular signaling, and proteins such as phosphatases that regulate this pathway are important for normal tissue development. Based on our previous work on dual specificity phosphatase-5 (DUSP5), and its role in embryonic vascular development and disease, we hypothesized that mutations in DUSP5 will affect its function.

Results

In this study, we tested this hypothesis by generating full-length glutathione-S-transferase-tagged DUSP5 and serine 147 proline mutant (S147P) proteins from bacteria. Light scattering analysis, circular dichroism, enzymatic assays and molecular modeling approaches have been performed to extensively characterize the protein form and function. …

A Novel Method For Confirming The Presence Of Volatile Reduced Sulfide Compounds Via Inductively Coupled Plasma-Optical Emission Spectroscopy, Krystal Lynne Parker

Master's Theses

Millions of dollars in destruction in the past decade have resulted from the use of Chinese drywall in homes. There are also potential health hazards related to this corrosive material. As such, it is important to find a way to identify Chinese drywall. Drywall can be tested for certain markers, such as strontium, sulfur, and carbonates to identify it as corrosive Chinese drywall. The laboratory preparation and analysis should be efficient and cost effective. The methods previously used, such as an X-ray fluorescence gun have had issues with getting a proper reading due to the layers of other materials found …

The Effects Of The Tootling Intervention Using Daily Reinforcement, Melissa Bryanne Mchugh

Master's Theses

The current study was designed to replicate and extend the literature on the effectiveness of a classroom intervention known as Tootling (Skinner, Skinner, & Cashwell, 1998) in decreasing disruptive classroom behavior as well as increasing academically engaged classroom behavior. Tootling is a strategy that encourages and prompts students to report instances of their peers’ positive behaviors. Thus far, only three studies have utilized direct observation data for disruptive behavior during Tootling (Cihak, Kirk, & Boon, 2009; Lambert, 2012, 2014). To extend the research on Tootling, direct observation data of disruptive and academically engaged behaviors were collected on both entire classes …

A Vegetation Analysis On Horn Island, Mississippi, Ca. 1940 Using Characteristic Dimensions Derived From Historical Aerial Photography, Guy Wilburn Jeter Jr.

Master's Theses

Horn Island is part of the MS/AL barrier island chain in the northern Gulf of Mexico located approximately 18kn off the coast of Mississippi. This island’s habitats have undergone many transitions over the last several decades. The goal of this study was to quantify habitat change over a seventy year period using historical black and white photography from 1940. Using present NAIP imagery from the USDA, habitat structure was estimated by using geo-statistics, and second order statistics, from a co-occurrence matrix, to characterize texture for habitat classification. Percent land cover was then calculated to determine overall land cover change over …

Contents May Have Shifted: Disentangling The Best Evidence Rule From The Rule Against Hearsay, Colin Miller

Washington and Lee Law Review Online

The rule against hearsay covers a statement offered to prove the truth of the matter asserted but does not cover a statement offered for another purpose. Meanwhile, the Best Evidence Rule states that a party seeking to prove the content of a writing, recording, or photograph must produce the original or account for its nonproduction. Does this mean that the Rule is inapplicable when a party seeks to prove something other than the truth of the matter asserted in a writing, recording or photograph? Most courts have answered this question in the affirmative. This essay argues these courts are wrong.

Promoting Innovation While Preventing Discrimination: Policy Goals For The Scored Society, Frank Pasquale, Danielle K. Citron

Faculty Scholarship

There are several normative theories of jurisprudence supporting our critique of the scored society, which complement the social theory and political economy presented in our 2014 article on that topic in the Washington Law Review. This response to Professor Tal Zarsky clarifies our antidiscrimination argument while showing that is only one of many bases for the critique of scoring practices. The concerns raised by Big Data may exceed the capacity of extant legal doctrines. Addressing the potential injustice may require the hard work of legal reform.

Promoting Progress: A Qualitative Analysis Of Creative And Innovative Production, Jessica Silbey

Faculty Scholarship

This chapter is based on data collected as part of a larger qualitative empirical study based on face-to-face interviews with artists, scientists, engineers, their lawyers, agents and business partners. Broadly, the project involves the collecting and analysis of these interviews to understand how and why the interviewees create and innovate and to make sense of the intersection between intellectual property law and creative and innovative activity from the ground up. This chapter specifically investigates the concept of “progress” as discussed in the interviews. “Promoting progress” is the ostensible goal of the intellectual property protection in the United States, but what …

The Duty To Maintain, Nadav Shoked

Duke Law Journal

Property is closely associated with freedom. Following the demise of the feudal property system, property ownership in Anglo-American law came to imply an individual's freedom to act as she pleases on her land. For their part, modern property theories—whether right-based, utilitarian, or relational—employ the normative value of freedom to justify ownership. Courts and scholars have always acknowledged the fact that this freedom of the owner cannot be absolute: an owner's freedom to do as she pleases on her land is often limited to protect other owners. However, the consensual assumption remains that an owner is not subject to affirmative duties. …

50 Years Of Legal Education In Ethiopia: A Memoir, Stanley Z. Fisher

Faculty Scholarship

In this paper I describe my experience as one of the early members of the Haile Selassie I University (H.S.I.U.), Law Faculty, and share my reflections on developments in the ensuing years.

Gis Framework For Spatiotemporal Mapping Of Urban Flooding And Analyze Watershed Hydrological Response To Land Cover Change, Sayed Joinal Hossain Abedin

UNLV Theses, Dissertations, Professional Papers, and Capstones

Urban flooding is a manmade disaster, and a recurrent problem in cities around the globe. Increased surface imperviousness due to urbanization along with inadequate drainage infrastructure system are the chief culprits for urban flooding. Flooding in an urban area brings about severe economic, structural, and environmental damages, and can be associated with casualties too. In order to evade flooding, an efficient flood model is imperative to study current flooding, and analyze flooding behavior to urban surface characteristics.

This research aims to develop a framework using Geographic Information System (GIS) to perform modeling and mapping of flood spatiotemporal variation in urban …

Effect Of Caliche On The Behavior Of Drilled Shafts, Rouzbeh Afsharhasani

UNLV Theses, Dissertations, Professional Papers, and Capstones

The current design methodology for a drilled shaft foundation in cohesionless soil is primarily based on ultimate skin friction values of drilled shafts. In order to obtain these values for each soil type, load tests such as Osterberg test are designed and performed. The Osterberg test layout is designed to estimate the capacity of drilled shaft by applying an upward load during the test and then calculating the downward capacity assuming the upward and downward capacity are the same. This method is appropriate for soils not containing caliche layers because caliche layers bond to the shaft and prevent skin friction …

Design And Implementation Of An Instruction Set Architecture And An Instruction Execution Unit For The Rez9 Coprocessor System, Daniel Spencer Anderson

UNLV Theses, Dissertations, Professional Papers, and Capstones

While the use of RNS has provided groundbreaking theory and progress in this field, the applications still lack viable testing platforms to test and verify the theory. This Thesis outlines the processing of developing an instruction set architecture (ISA) and an instruction execution unit (IEU) to help make the first residue based general processor a viable testing platform to address the mentioned problems.

Consider a 32-bit ripple adder. The delay on this device will be 32N where N is the delay for each adder to complete its operation. The delay of this process is due to the need to propagate …

Morphometric Assessment Of The Internal Auditory Canal For Sex Determination In Subadults Using Cone Beam Computed Tomography (Cbct), Saoly Benson

UNLV Theses, Dissertations, Professional Papers, and Capstones

This study reports on the use of three methods for sex determination in subadults using the petrous portion of the temporal bone. The purpose of this study was to validate and refine two previously published methods of sex determination for the internal auditory canal as well as to develop a novel method. The sample was comprised of 276 cone beam computed tomography (CBCT) scans of a population of subadults age 6-24 (165 females, 111 males) divided into 5 age groups for analysis: Group 1 (age 6-10), Group 2 (age 11-13), Group 3 (age 14-16), Group 4 (age 17-19), and Group …

International City/County Management Association 1999 Revenue Estimation Survey Revisited, Benjamin Bond

UNLV Theses, Dissertations, Professional Papers, and Capstones

In 1899 the National Municipal League declared that it was the duty of the Mayor to submit to the Council the annual budget of current expenses of the city, for almost as long, the budgeting process has been researched (Hou, 2006). Researching budgets is important and needed but comparatively little attention has been paid to revenue forecasts or to those responsible for the generation of revenue forecasts. Professional public administrators responsible for generating revenue forecasts have largely been overlooked in research. Judging by the lack of scholarly material available in academic journals, it appears the political process in which budget …

Speciation Of Pentavalent Technetium Complexes With Aniline And Thiobenzene Derivatives, Kyle E. Childs

UNLV Theses, Dissertations, Professional Papers, and Capstones

The reaction of bidentate aniline oligomers with pentavalent technetium has been investigated previously through the reaction of (n-Bu4N)TcOCl4 with o-phenylenediamine (PDA). The initial studies found that PDA reacted in a 1 to 2 molar ratio with pentavalent technetium in in ethanol. This study was expanded by the examination of a second aniline derivatives, 2-aminophenol (AMP)) and two thiobenzene derivatives (2-mercaptophenol (MP) and thiosalicylic acid (TSA)) to evaluate the kinetic formation of these complexes with pentavalent technetium. The pentavalent technetium complexes all showed reactivity with technetium having a coordination numbers of 5 with all ligands reacting in a 1 to 2 …

An Assessment Of A 13-Week Teaching Gardens Intervention On Healthy Behavior Outcomes In 4th And 5th Grade Students At Crestwood Elementary School In Las Vegas, Nevada, Miranda Corgiat

UNLV Theses, Dissertations, Professional Papers, and Capstones

Nearly 13 million children and adolescents are considered to be obese in the United States, with children enrolled in Clark County School District showing elevated overweight and obese weight statuses compared to national averages. Carrying an excessive amount of weight can lead children to experience a multitude of complications with their physical and mental health as well as increase their risk of developing various chronic diseases. The American Heart Association's Las Vegas Teaching Gardens program implemented a school-based garden pilot study to target environmental causes of obesity in 4th and 5th grade students at Crestwood Elementary School. The objective of …

Investigation Of Chloride Induced Corrosion Of Bridge Pier And Life-Cycle Repair Cost Analysis Using Fiber Reinforced Polymer Composites, Dinesh Dhakal

UNLV Theses, Dissertations, Professional Papers, and Capstones

Bridges are the long term investment of the highway agencies. To maintain the required service level throughout the life of a bridge, a series of maintenance, repair, and rehabilitation (MR&R) works can be performed. To investigate the corrosion deterioration and maintenance and repair practices in the bridge pier columns constructed in chloride-laden environment, a questionnaire survey was conducted within the 50 state Departments of Transportation (DOTs). Based on the survey data, two corrosion deterioration phases were identified. They were corrosion crack initiation phase and corrosion propagation phase. The data showed that the mean corrosion crack initiation phase for bridge pier …

Keeping In Touch: Exchange As An Adaptive Strategy In Southern Nevada, Timothy Joshua Ferguson

UNLV Theses, Dissertations, Professional Papers, and Capstones

Archaeologists have always wondered about the extent of vessel movement in the American Southwest. Identifying vessel movement allows for the study of social interactions across a region and the role of ceramics in the adaptive processes of agriculturalists living in marginal, highly variable environments. In many instances, exchange may act as a way to reduce the risk of resource shortfalls by creating social ties in other areas. This research investigated the changing risk reduction strategies of households in the lowland Virgin region of southern Nevada by using geochemical methods to trace the exchange of locally produced pottery. It was hypothesized …

Simultaneous Determination Of Multiple Actinide Elements In A Variety Of Soils Utilizing A Standardized Sequential Extraction Protocol, Sherry Alina Faye

UNLV Theses, Dissertations, Professional Papers, and Capstones

To obtain a better understanding of the mobility of actinide element contaminants in the environment, the association of the contaminants with specific host phases of soils and sediments must be investigated. This investigation is most commonly conducted using sequential extraction techniques that employ the selective dissolution of soil phases with increasingly aggressive chemical treatment. Though several sequential extraction studies exist in literature, conclusions cannot be made by direct comparison of data due to the lack of uniformity in the protocols used. This work aims to continue development of a standard sequential extraction protocol and expanding its capabilities to include the …

Spectroscopic Investigation Of The Chemical And Electronic Properties Of Chalcogenide Materials For Thin-Film Optoelectronic Devices, Kimberly Horsley

UNLV Theses, Dissertations, Professional Papers, and Capstones

Chalcogen-based materials are at the forefront of technologies for sustainable energy production. This progress has come only from decades of research, and further investigation is needed to continue improvement of these materials.

For this dissertation, a number of chalcogenide systems were studied, which have applications in optoelectronic devices, such as LEDs and Photovoltaics. The systems studied include Cu(In,Ga)Se2 (CIGSe) and CuInSe2 (CISe) thin-film absorbers, CdTe-based photovoltaic structures, and CdTe-ZnO nanocomposite materials. For each project, a sample set was prepared through collaboration with outside institutions, and a suite of spectroscopy techniques was employed to answer specific questions about the system. These …

Li+ Ion Transport In Select Lithium-Rich Antiperovskites, John William Howard

UNLV Theses, Dissertations, Professional Papers, and Capstones

Lithium-Rich Antiperovskites (LiRAPs) have been shown to possess relatively high ionic conductivity at room temperature, and become superionic conductors at elevated temperatures. These materials generally have a stoichiometry Li3BX, where B is a doubly deficient anion, and X is a monovalent anion. Ideally they belong to the high symmetry space group Pm-3m where lithium atoms occupy octahedral corners, B anions occupy octahedral centers, and X anions occupy the interstitial centers between the octahedra. LiRAPs were synthesized using several different methods and characterized by XRD, EIS, DSC, TGA, FTIR, and INS techniques. Chemical analyses were performed to determine the stoichiometries of …

Modeling And Analysis Of Pedestrian Flows, Romesh Khaddar

UNLV Theses, Dissertations, Professional Papers, and Capstones

According to the Traveler Opinion and Perception Survey of 2005, about 107.4 million Americans regularly use walking as a mode of transport during their commute, which amounts for 51% of the total American population. In 2009, 4092 pedestrian fatalities were reported nationwide, out of 59,000 pedestrian crashes. This amounts for 12% of the fatalities in the total traffic accidents recorded, and shows an over-representation of pedestrians incidents. Thus, it is imperative to understand the causes behind such statistics, and conduct a comprehensive research on pedestrian walking behavior and their interaction with surroundings.

A lot of researches on pedestrian flows have …

Songs By Hsiao Tyzen: The Interaction Between His Music And Taiwan, Pei-Ning Ku

UNLV Theses, Dissertations, Professional Papers, and Capstones

The purpose of this document is to understand Taiwanese composer Hsiao Tyzen's artistic persona through analysis of the textual and musical characteristics of his songs. This document is comprised of: 1) an historical overview of Taiwan, 2) a history of Taiwanese vocal music, 3) a description of Hsiao Tyzen's life and career, 4) an introduction to Taiwanese diction, 5) an examination and analysis of musical components (melody, rhythm, accompaniment and form) of four of Tyzen's songs, and 6) a conclusion based upon sociological factors, historical influences and musical devices to define what constitutes the stylistic characteristics of the songs of …

Who Or What Should I Be Like? The Self-Assessment Of Sexual Desire, Caroline Maykut

UNLV Theses, Dissertations, Professional Papers, and Capstones

The construct of sexual desire has been notoriously difficult to capture and measure, in part as a function of questionable methods of sexual desire assessment. Due to problems finding an accurate, objective marker of sexual desire, research has relied on self-report. One notable difficulty with self-reported desire assessment is the lack of information on the context in which these assessments are made. The only available data focuses on relative assessment of sexual desire within couples, and ignores broader social and cultural contexts. The present study investigated men and women's perception of sexual desire discrepancies between themselves and other people and …

Factors Associated With Rapid Readmission Among Nevada State Pyschiatric Hospital Patients, Christopher Owen Moore

UNLV Theses, Dissertations, Professional Papers, and Capstones

Rapid readmission (RR) of psychiatric patients within 30 days of discharge places a costly burden on state psychiatric facilities and may be an indicator of suboptimal service provision. Several studies have previously considered RR to inpatient facilities, but there is a lack of information available about the variables associated with RR of psychiatric patients to state-operated inpatient facilities in Nevada. This study attempts to identify factors associated with RR at a southern Nevada state psychiatric hospital. Participants included 7,177 patients admitted between May 1, 2012 and April 30, 2014. All 12,068 admissions, including 2,220 RR, were reviewed, and rapid readmits …

The Presentation Of Childhood Parental Divorce In Adulthood: A Retrospective Phenomenological Study, Sheala Catherine Morrison

UNLV Theses, Dissertations, Professional Papers, and Capstones

There has been a wealth of research aimed at developing an understanding of the way in which the experience of divorce impacts children. However, adult children of divorce have been widely underrepresented in this literature, much of which is outdated being at least ten years old. With shifting societal attitudes and the transformation of the family system since the 1990's it is crucial that the research is updated in order to stay up on the way children and families are impacted in today's society. The purpose of this study was to hear directly from adults who experienced their parents' divorce …