Digital Commons Network^™

Estimating Spatial Probit Models In R, Stefan Wilhelm, Miguel Godinho De Matos

The R Journal

In this article we present the Bayesian estimation of spatial probit models in R and provide an implementation in the package spatialprobit. We show that large probit models can be estimated with sparse matrix representations and Gibbs sampling of a truncated multivariate normal distribution with the precision matrix. We present three examples and point to ways to achieve further performance gains through parallelization of the Markov Chain Monte Carlo approach.

The R User Conference 2013, User 2013 Organising Committee

The R Journal

The ninth R user conference will take place at the University of Castilla-La Mancha, Albacete, Spain from Wednesday 10 July 2013 to Friday 12 July 2013. Following previous useR! conferences, this meeting of the R user community will

• focus on R as the ‘lingua franca’ of data analysis and statistical computing;
• provide a platform for R users to discuss and exchange ideas on how R can be used for statistical computation, data analysis, visualization and exciting applications in various fields;
• give an overview of the new features of the ever evolving R project.

An Introduction To The Ecotroph R Package: Analyzing Aquatic Ecosystem Trophic Networks, Mathieu Colléter, Jérôme Guitton, Didier Gascuel

The R Journal

Recent advances in aquatic ecosystem modelling have particularly focused on trophic network analysis through trophodynamic models. We present here a R package devoted to a recently developed model, EcoTroph. This model enables the analysis of aquatic ecological networks and the related impacts of fisheries. It was available through a plug-in in the well-known Ecopath with Ecosim software or through implementations in Excel sheets. The R package we developed simplifies the access to the EcoTroph model and offers a new interfacing between two widely used software, Ecopath and R.

Cyclic Peptides Containing Tryptophan And Arginine As Src Kinase Inhibitors, Amir Nasrolahi Shirazi, Rakesh Tiwari, Alex Brown, Dindyal Mandal, Gongqin Sun, Keykavous Parang

Pharmacy Faculty Articles and Research

A number of cyclic and linear peptides containing various combinations of amino acids were evaluated for their Src kinase inhibitory potency. Among all the peptides, cyclic decapeptide C[RW]5 containing alternative arginine (R) and tryptophan (W) residues was found to be the most potent Src kinase inhibitor. C[RW]5 showed higher inhibitory activity (IC50=2.8 μM) than C[KW]5, L(KW)5, C[RW]4, and C[RW]3 with IC50 values of 46.9, 69.1, 21.5, and 25.0 μM, respectively, as determined in a fluorescence intensity-based assay. Thus, the cyclic nature, the presence of arginine, ring size, and the number of amino acids in the structure of the peptide were …

Surprisingly Little Population Genetic Structure In A Fungus-Associated Beetle Despite Its Exploitation Of Multiple Hosts, Corlett W. Wood , '08, H. M. Donald, Vincent A. Formica, E. D. Brodie Iii

Biology Faculty Works

In heterogeneous environments, landscape features directly affect the structure of genetic variation among populations by functioning as barriers to gene flow. Resource-associated population genetic structure, in which populations that use different resources (e.g., host plants) are genetically distinct, is a well-studied example of how environmental heterogeneity structures populations. However, the pattern that emerges in a given landscape should depend on its particular combination of resources. If resources constitute barriers to gene flow, population differentiation should be lowest in homogeneous landscapes, and highest where resources exist in equal proportions. In this study, we tested whether host community diversity affects population genetic …

A Review Of P300, Ssvep, And Hybrid P300/Ssvep Brain-Computer Interface Systems, Reza Fazel-Rezai, Setare Amiri, Ahmed Rabbi, Leila Azinfar

Electrical Engineering Faculty Publications

No abstract provided.

The Genome Sequence Of The Most Widely Cultivated Cacao Type And Its Use To Identify Candidate Genes Regulating Pod Color, Juan C. Motamayor, Keithanne Mockaitis, Jeremy Schmutz, Niina Haiminen, Donald Livingstone Iii, Omar Cornejo, Seth Findley, Ping Zheng, Filippo Utro, Stefan Royaert, Christopher Saski

Publications

Background

Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders.

Results

We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina

1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of …

Schizophrenia: Causes, Crime, And Implications For Criminology And Criminal Justice, Anthony Walsh, Ilhong Yun

Criminal Justice Faculty Publications and Presentations

This paper is aimed at criminologists and criminal justicians seeking to understand their role in educating law enforcement and correctional personnel who must deal with the mentally ill. It is motivated by William Johnson's (2011) recent call for rethinking the interface between mental illness, criminal justice, and academia, and his call for advocacy. We concur with his concerns, and insist that this rethinking must necessarily include grounding in the etiology of mental illness (specifically, with schizophrenia) as it is currently understood by researchers in the area. Advocacy must go hand in hand with a thorough knowledge of the condition of …

Cave Talk, June 2013, Robert A. Holt

Cave Talk

Contents: Message from the President -- Red Bull Winch Sessions: Lost River Cave -- Steiner Scholarship Awarded to Ruby Falls Employees -- Post NCA Convention 2013 Canoe Trip on Current River, Salem, Mo -- NCA Buyers Group Talk -- WNS Committee Report -- the Address Given By David Summers, President of the International Show Caves Association to ACKMA’s Waitomo 2013 Conference in New Zealand 13th May 2013 -- NCA Convention Vendor Show Update -- from Deep Down in the Archives… Timeline 1977 -- Mark Your Calendar!

The R Journal (June 2013) 5(1): Complete Issue, The R Foundation

The R Journal

Editorial, Hadley Wickham

Contributed Research Articles

RTextTools: A Supervised Learning Package for Text Classification, Timothy P. Jurka, Loren Collingwood, Amber E. Boydstun, Emiliano Grossman, and Wouter van Atteveldt

Generalized Simulated Annealing for Global Optimization: The GenSA Package, Yang Xiang, Sylvain Gubian, Brian Suomela, and Julia Hoeng

Multiple Factor Analysis for Contingency Tables in the FactoMineR Package, Belchin Kostov, Mónica Bécue-Bertaut, and François Husson

Hypothesis Tests for Multivariate Linear Models Using the car Package, John Fox, Michael Friendly, and Sanford Weisberg

osmar: OpenStreetMap and R, Manuel J. A. Eugster and Thomas Schlesinger

ftsa: An R Package for Analyzing Functional Time Series, …

Design And Cost Analysis Of A Wetland Project, Matthew Rolen

BioResource and Agricultural Engineering

This senior project discusses the cost and design of a thirty acre wetland habitat project. This project demonstrates the importance that wetlands play for waterfowl as well as wildlife. The project will also discuss the changes made to the habitat and the importance of that. Also the unique design of the habitat will be explained. The main purpose of the project is the cost analysis of it. The budget of the project and the funding it takes to develop or preserve such a project.

Strategic Plan For Wine Tourism 2013, Templeton, California, Krista Galatolo, Nicole De La Rosa

City and Regional Planning

No abstract provided.

The Message 2.0: Perceptions Of Success From Members Of The Founding Class Of Mc Squared Stem High School, Jeffrey D. Mcclellan

Dissertations

This dissertation examines the methods of learning from the student’s perspective in order to understand what made the first graduating class of MC Squared successful. The conceptual model of student success composed of non-academic factors of motivation, social connectedness, and self-management was used for the lens from which to understand the six students in depth. Through the research, it was uncovered that diversified learning environments, a mastery based assessment system, and an unwavering acceptance of students within a challenging and supportive environment are essential to the success achieved at MC Squared STEM High School. Lastly, the seminal contribution of this …

Two Decades Of Rpl/Apel In Ireland: Practitioner Views, Phil O’Leary

Level 3

I was first involved with RPL in 1996. I began working in CIT in July of that year to run a project trialing APL. It was a two year project, funded under the EU Adapt programme to develop and deliver policy and procedures for APL and to trial its use. The project proposal was written by CIT staff members Ray Coughlan and Michael Delaney.

Concentrated Fish Oil (Lovaza®) Extends Lifespan And Attenuates Kidney Disease In Lupus-Prone Short-Lived (Nzbxnzw)F1 Mice, Ganesh V. Halade, Paul J. Williams, Jyothi M. Veigas, Jeffrey L. Barnes, Gabriel Fernandes

Internal Medicine Faculty Publications

A growing number of reports indicate that anti-inflammatory actions of fish oil (FO) are beneficial against systemic lupus erythematosus (SLE). However, the majority of pre-clinical studies were performed using 5-20% FO, which is higher than the clinically relevant dose for lupus patients. The present study was performed in order to determine the effective low dose of FDA-approved concentrated FO (Lovaza®) compared to the commonly used FO-18/12 (18-Eicosapentaenoic acid [EPA]/12-Docosahexaenoic acid [DHA]). We examined the dose-dependent response of Lovaza® (1% and 4%) on an SLE mouse strain (NZBxNZW)F1 and compared the same with 1% and 4% placebo, as well as 4% …

Inventory, Conservation, And Management Of Lava Tube Caves At El Malpais National Monument, New Mexico, J. Judson Wynne

KIP Articles

Lava tube caves at El Malpais National Monument have received little scientific attention with regard to their bat and arthropod populations. From an all taxa biological inventory of 11 caves,I identified seven new species of cave-dwelling arthropods (including two potential troglobites) and range expansions of two parasitoidal wasps. The presence of unique microhabitats, tree root "curtains" hanging from the ceilings, and moss gardens in cave entrances resulted in higher species richness of arthropods at four caves. For bats, I confirmed continued use of one large bat hibernaculum cave and one significant bat maternity roost. While several recommendations have been made …

Co-Rumination Partially Mediates The Relationship Between Social Support And Emotional Exhaustion Among Graduate Students, Justin P. Boren

Communication

Graduate students regularly report high levels of stress and burnout. Many of those same students utilize social support networks, which can act as stress buffers. This study evaluated excessive negative talk about issues (co-rumination) and its effects on that social-support to burnout (emotional exhaustion) relationship and predicted that co-rumination would act as a suppressor variable. Graduate student volunteers (N = 213) reported their levels of social support, co-rumination, and emotional exhaustion. Data indicated that co-rumination did mediate the social support-to-emotional exhaustion relationship on two dimensions. This project purports that, while social support is important, the content of socially-supportive interactions may …

Annual Report Of The Wally Cordes Teaching And Faculty Support Center For The Year Ended…, 2013, University Of Arkansas, Fayetteville. Wally Cordes Teaching And Faculty Support Center

Wally Cordes Teaching and Faculty Support Center Annual Report

No abstract provided.

Tourism And Karst Areas, Volume 6, No. 1, 2013, Heros Augusto Santos Lobo

KIP Articles

Contents: Caves: The most important geotouristic feature in the world -- Speleological heritage in Brazil's proposed geoparks, as presented in the book "Geoparques do Brasil: Propostas" -- Geotourism potential of underground sites in Costa Rica -- Consumer-based cave travel and tourism market characteristics in West Java, Indonesia

Novel Sars-Like Betacoronaviruses In Bats, China, 2011, Li Yang, Zhiqiang Wu, Xianwen Ren

KIP Articles

To clarify the evolutionary relationships among betavoronaviruses that infect bats, we analyzed samples collected during 2010–2011 from 14 insectivorous bat species in China. We identified complete genomes of 2 novel betacoronaviruses in Rhinolophus pusillus and Chaerephon plicata bats, which showed close genetic relationships with severe acute respiratory syndrome coronaviruses.

Espeleorevista Puerto Rico, No. 8, January-June 2013, Marianela Mercado Burgos

KIP Articles

Contenido: Mata la cucaracha... ¡AZAH! 6 por Daniel LugoPopeye: el curioso caso del camarón que llegó a Cueva del Agua por Cielo FiguerolaBosque Rocoso del Karso del Sur por Jorge Ariel TorresSirenios fósiles en las calizas de Puerto Rico por Jorge VélezCueva El Mamey por José Luis GómezGalería Subterránea: Cueva del Agua por Jan Paul ZegarraNCRC del Caribe Informa 52 Taller de Orientación Básica de Rescate en Cuevas - NRCR por Karel HilversumCuatro preguntas para una buena comunicación por Roberto Miranda

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New CRAN task views

New packages in CRAN task views

New contributed packages

Other changes

The New Hampshire, Vol. 102 [103], No. 50 (Summer 2013), The New Hampshire

The New Hampshire Print Edition

An independent student produced newspaper from the University of New Hampshire. This volume was printed as 102, but it is the 103rd volume in the series. This was corrected in pencil.

Escherichia Coli Strain Diversity In Humans: Effects Of Sampling Effort And Methodology, Emily R. Neal

Master's Theses

Studies investigating Escherichia coli strain diversity and demographics in human hosts are frequently inconsistent regarding sampling effort and methodology while current strain typing methods are often expensive or laborious. To rectify these inconsistencies, sampling effort was investigated by comparing the diversity of 15-isolate collections to 100-isolate collections from 3 human subjects. Temporal variation in E. coli strain diversity was also studied by collecting 15 isolates once every 6 months. Additionally, strain identification and diversity collected by different sampling methods (fecal swabs vs. anal swabs collected at different times around defecation) were compared to identify any inherent biases in sampling method. …

Evaluating Usability Evaluations, Allen Leo Dunlea

Master's Theses

We live in an age when consumers can now shop and browse the web using hand-held devices. This means that competitive companies need to have a website to represent their brand and to conduct business. E-commerce sites need to pay special attention to the usability of their sites, since it has such an impact on how potential costumers view their brand.

Jakob Nielsen defines usability as a "quality attribute that assesses how easy user interfaces are to use"; he separates usability into five quality components: learnability, efficiency, memorability, errors and satisfaction. The current standard for testing usability involves having …

Dna Purification Process Optimization At Life Technologies Corporation, Trevor J. Shepherd

Master's Theses

This project focused on optimizing the plasmid DNA purification process at Life Technologies. These plasmids are designed to code for specialized proteins used by research universities, national laboratories, or research companies. Once cultivated and harvested, the plasmids must be analyzed for quality and quantity. The project is divided into improving three aspects of the process: 1) plasmid identification, 2) plasmid purity evaluation, and 3) process yield. Plasmid identification is now simpler, more robust and has zero ambiguity. Plasmid purity evaluation is now measured with computer software, which reduces user error and eliminates subjectivity. Using the nascent metrics provided by the …

Cplop: The Cal Poly Library Of Pyroprints, Jan Lorenz Villaceran Soliman

Master's Theses

To date, microbial source tracking (MST), i.e. determining the source of microbial contamination based on the specific strains observed in the environment, often uses methods that are time-consuming, expensive and not always reliable. The biology department at Cal Poly, San Luis Obispo has developed a new method for MST called pyroprinting. Pyroprints can be used as DNA fingerprints for identifying sources of fecal contamination and studying bacterial populations in host animals. The MST method consists of two parts: the pyroprinting process and a database of pyroprints. The Cal Poly Library of Pyroprints (CPLOP) was developed to provide a database application …

Computational Modeling To Evaluate Helical Electrode Designs For Use In Vagus Nerve Stimulation, Anthony W. Cowley

Master's Theses

An estimated 0.5% of world’s population has been diagnosed with epilepsy. Of these patients 20-30% will be unable to achieve seizure control with anti-epileptic drugs. Vagus nerve stimulation (VNS) may be an appropriate treatment option for some patients with pharmaceutically refractory, partial-onset seizures.

VNS therapy uses a helical electrode to interface between the implantable pulse generator and the vagus nerve. While there have been several studies related to the mechanical and electrical safety of such electrodes, little work has been done toward understanding the effectiveness of the helical electrode in nerve stimulation. A better understanding of the voltage field and …

Latent Cysteine Residues From Polymers Prepared Via Free And Controlled Radical Polymerizations, Douglas Vincent Amato

Master's Theses

One less commonly used “click” reaction is thiazolidine chemistry. Thiazolidine chemistry is a commonly used reaction used in biological systems because the reaction requires the presence of both cysteine (a common amino acid) and an aldehyde or ketone. If cysteine residues could be incorporated into a polymer then a variety of applications could be developed. Polymers containing free thiols (aka thiomers) have developed in the last decade to become great mucoadhesives. If there was a facile route to control the amount of free thiols along the polymer then more fine-tuned and potentially stronger adhesives could be made. For these reasons …

Institutional Integrity And Respect For Precedent: Do They Favor Continued Adherence To An Abortion Right, Michael F. Moses

Notre Dame Journal of Law, Ethics & Public Policy

No abstract provided.