Digital Commons Network^™

Collections In R: Review And Proposal, Timothy Barry

The R Journal

R is a powerful tool for data processing, visualization, and modeling. However, R is slower than other languages used for similar purposes, such as Python. One reason for this is that R lacks base support for collections, abstract data types that store, manipulate, and return data (e.g., sets, maps, stacks). An exciting recent trend in the R extension ecosystem is the development of collection packages, packages that provide classes that implement common collections. At least 12 collection packages are available across the two major R extension repositories, the Comprehensive R Archive Network (CRAN) and Bioconductor. In this article, we compare …

Pstat: An R Package To Assess Population Differentiation In Phenotypic Traits, Stéphane Blondeau Da Silva, Anne Da Silva

The R Journal

The package Pstat calculates P_ST values to assess differentiation among populations from a set of quantitative traits and provides bootstrapped distributions and confidence intervals for P_ST. Variations of P_ST as a function of the parameter c/h² are studied as well. The package implements different transformations of the measured phenotypic traits to eliminate variation resulting from allometric growth, including calculation of residuals from linear regression, Reist standardization, and the Aitchison transformation.

Advanced Bayesian Multilevel Modeling With The R Package Brms, Paul-Christian Bürkner

The R Journal

The brms package allows R users to easily specify a wide range of Bayesian single-level and multilevel models which are fit with the probabilistic programming language Stan behind the scenes. Several response distributions are supported, of which all parameters (e.g., location, scale, and shape) can be predicted. Non-linear relationships may be specified using non-linear predictor terms or semi-parametric approaches such as splines or Gaussian processes. Multivariate models can be fit as well. To make all of these modeling options possible in a multilevel framework, brms provides an intuitive and powerful formula syntax, which extends the well known formula syntax of …

Support Vector Machines For Survival Analysis With R, Césaire J.K. Fouodo, Inke R. König, Claus Weihs, Andreas Ziegler, Marvin N. Wright

The R Journal

This article introduces the R package survivalsvm, implementing support vector machines for survival analysis. Three approaches are available in the package: The regression approach takes censoring into account when formulating the inequality constraints of the support vector problem. In the ranking approach, the inequality constraints set the objective to maximize the concordance index for comparable pairs of observations. The hybrid approach combines the regression and ranking constraints in a single model. We describe survival support vector machines and their implementation, provide examples and compare the prediction performance with the Cox proportional hazards model, random survival forests and gradient boosting using …

Mglm: An R Package For Multivariate Categorical Data Analysis, Juhyun Kim, Yiwen Zhang, Joshua Day, Hua Zhou

The R Journal

Data with multiple responses is ubiquitous in modern applications. However, few tools are available for regression analysis of multivariate counts. The most popular multinomial-logit model has a very restrictive mean-variance structure, limiting its applicability to many data sets. This article introduces an R package MGLM, short for multivariate response generalized linear models, that expands the current tools for regression analysis of polytomous data. Distribution fitting, random number generation, regression, and sparse regression are treated in a unifying framework. The algorithm, usage, and implementation details are discussed.

An Investigation Of Pair-Bonded Humboldt Penguins (Spheniscus Humboldti) In Captivity: The Differences Between Male-Female Pairs And Male-Male Pairs, Emily Allen

The Plymouth Student Scientist

Same-sex sexual and pair-bonding behaviours are seen in a wide range of species. This study compared opposite-sex and same-sex pair-bond behaviours, both affiliative within pairs, and agonistic between pairs and individuals, in Humboldt penguins (Spheniscus humboldti). This study also looked at where area preferences were within the enclosure to determine possible territory behaviour. A total of 200 minutes of footage of four pairs were analysed; two oppositesex pairs, and two male-male pairs. It was found that there was no difference between agonistic behaviours (P = 0.054), but affiliative behaviours were seen significantly more in opposite-sex pairs (P = 0.002). More …

The Development And Evaluation Of A First-Year Undergraduate Physical Chemistry Experiment, Carolina Uncles

The Plymouth Student Scientist

The laboratory in chemistry has been a place for student learning for many years. The study here developed a practical experiment to form part of the curriculum of Plymouth University’s BSc (Hons) Chemistry course for first year students. The experiment focused on physical chemistry and explored rates of reaction using a modified crystal violet and sodium hydroxide reaction. The modifications from an original method included the concentrations of sodium hydroxide and the instrument used. The practical was finalised and lab script produced in eight weeks. Further studies were also conducted surrounding the effect of temperature on the reaction. The resultant …

Grove Gulch Stream Restoration Hydraulic Design, Alison Lunde

Graduate Theses & Non-Theses

Blacktail Creek (BTC) is a second order stream that joins Silver Bow Creek (SBC) within Butte’s watershed. This stream contained heavy metals since Butte’s mining boom in the 1900’s, the source of the contamination is seen today at a place known as the “BTC berm” (Tuccci, 2014). Grove Gulch is a tributary stream of Blacktail Creek and is located southwest of Butte, MT. The stream is approximately 6 miles long from its headwaters to its point of discharge into BTC. Historically, this stream discharged half a mile downstream from its current location and in the late 1800’s the stream was …

Hydrothermal Water-Rock Reaction Modeling With Microbial Considerations: Rabbit Creek Area, Yellowstone National Park, Wy, Shanna Law

Graduate Theses & Non-Theses

Water-rock reactions at depth are the main control on aqueous hydrothermal chemistries of hot springs and other thermal features. Thermophilic microbes living in the hydrothermal system are a secondary control on aqueous hydrothermal chemistries and are expected to have increasing influence as spring temperatures decrease. The Rabbit Creek area of Yellowstone National Park (YNP) is an ideal case study for investigating the geologic and biologic controls on aqueous hydrothermal chemistries due to the proximity of the drill core Y-5 to geochemically diverse hydrothermal features (17.3⁰C to 92.2⁰C ± 0.1⁰C; field pH values 6.50 to 9.60 ± 0.05).

The modeling program …

Continuous Flow Process For Recovery Of Metal Contaminants From Industrial Wastewaters With Magnetic Nanocomposites, David Hutchins

Graduate Theses & Non-Theses

Remediation of metal-containing industrial effluents presents both a technical challenge and an economic opportunity. Many industrial waste streams contain low levels of metal ions requiring treatment prior to discharge. Existing treatment technologies are frustrated by disparate compositions and low metal concentrations. Chemical precipitation is effective; however, it requires excessive reagents and discourages selective recovery. Ion-exchange enables recovery, but requires a batch process with extensive operational and maintenance demands, and is rarely implemented in large-scale applications. A continuous flow process capable of selective recovery would present many advantages over existing technologies.

This research examines and develops a continuous flow process for …

Differential Evolution Of Antiretroviral Restriction Factors In Pteropid Bats As Revealed By Apobec3 Gene Complexity, Joshua A. Hayward, Mary Tachedjian, Jie Cui, Adam Z. Cheng, Adam Johnson, Michelle L. Baker, Reuben S. Harris, Lin-Fa Wang, Gilda Tachedjian

KIP Articles

No abstract provided.

Teaching Calculus With Infinitesimals: New Perspectives, Luz Marina Hernandez, Jorge M. Lopez Fernandez

The Mathematics Enthusiast

The present research corroborates K. Sullivan's initial results as stated in her epoch making study about the effectiveness of teaching elementary calculus using Robinson's non standard approach. Our research added to her results related to the teaching of the elementary integral, with similar positive results. In this essay we propose a definition of the notion of cognitive advantage mentioned by Sullivan in expressing the dramatic differences in understanding of students of non standard calculus as opposed to those of its standard counterpart. Our proposal is based on ideas of Kitcher and Kuhn and allows us to better understand the didactics …

Abrf Proteome Informatics Research Group (Iprg) 2016 Study: Inferring Proteoforms From Bottom-Up Proteomics Data., Joon-Yong Lee, Hyungwon Choi, Christopher M Colangelo, Darryl Davis, Michael R Hoopmann, Lukas Käll, Henry Lam, Samuel H Payne, Yasset Perez-Riverol, Matthew The, Ryan Wilson, Susan T Weintraub, Magnus Palmblad

Articles, Abstracts, and Reports

This report presents the results from the 2016 Association of Biomolecular Resource Facilities Proteome Informatics Research Group (iPRG) study on proteoform inference and false discovery rate (FDR) estimation from bottom-up proteomics data. For this study, 3 replicate Q Exactive Orbitrap liquid chromatography-tandom mass spectrometry datasets were generated from each of 4

Visible Light Generation Of High-Valent Corrole-Manganese(V)-Oxo Intermediates And Biomimetic Studies Of The Oxidation Of Organic Sulfides Catalyzed By Manganese Corroles With Iodobenzene Diacetate, Davis Ray Ranburger

Masters Theses & Specialist Projects

High-valent transition metal-oxo intermediates play essential roles as active oxidizing species in enzymatic and biomimetic catalytic systems. Extensive research has been conducted on a variety of transition metal catalysts being studied as models for the ubiquitous cytochrome P450 enzymes. In doing so, the production of enzyme-like oxidation catalysts and probing studies on the sophisticated oxygen atom transfer mechanism are taking place.

In this work, visible-light irradiation of highly-photo-labile corrole-manganese(IV) bromates and chlorates was studied in two corrole systems with differing electronic environments, i.e. 5,10,15-trisphenylcorrole (H3TPC) and 5,10,15- tris(pentafluorophenyl)corrole (H3TPFC). In both systems, homolytic cleavage of the O- …

Where's Dad? The Importance Of Integrating Fatherhood And Parenting Programming Into Substance Use Treatment For Men, Carla Smith Stover, Melissa Carlson, Sarika Patel, Raquel Manalich

Mental Health Law & Policy Faculty Publications

Large numbers of men enter substance use disorder treatment each year, yet very little attention is paid to the fatherhood and parenting status of these men. Substance use treatment programmes for men rarely incorporate a parenting component into their treatment planning, despite the increased success of women's treatment programmes that focus on gender and motherhood. This paper provides: (1) a review of the literature on the fathering of substance‐using men, what has been learned from substance use disorder treatment for mothers, and the implications for children and families; (2) pilot quantitative and qualitative outcomes resulting from the implementation of a …

Dizajnimi I Filtrave Digjital Rekurziv (Iir), Edona Selimi

Theses and Dissertations

Filtrat aktiv, sot paraqesin elementin krucial në pajisjet elektronike, sidomos të atyre për bartjen e sinjaleve dhe selektimit të tyre sipas frekuencave të caktuara për qëllime të ndryshme. Filtrat aktiv, gjatë lëshimit të sinjalve nëpër atë, e bëjnë forcimin e komponentës së dobishme të sinjalit, ndërsa komponentët e padëshiruara të atij sinjali i dobësojnë. Filtrat aktiv janë elemente katërpolare. Sipas frekuencave të sinjaleve që i lëshojnë, filtrat aktiv ndahen në më shumë grupe prej të cilave dallohen katër prej tyre: • Filtrat lëshues të frekuencave të ulëta (FLFU); • Filtrat lëshues të frekuencave të larta (FLFL); • Filtrat lëshues të …

Anemarrhena Asphodeloides Bunge And Its Constituent Timosaponin‐Aiii Induce Cell Cycle Arrest And Apoptosis In Pancreatic Cancer Cells, Catherine B. Marelia, Arielle Sharp, Tiffany A. Shemwell, Y. C. Zhang, Brant R. Burkhardt

Molecular Biosciences Faculty Publications

Pancreatic cancer is one of the most recalcitrant and lethal of all cancers. We examined the effects of Anemarrhena asphodeloides (AA) and timosaponin‐AIII (TAIII), a steroidal saponin present in AA, on pancreatic cancer cell proliferation and aimed to elucidate their potential apoptotic mechanisms of action. Viability assays and cell cycle analysis revealed that both AA and TAIII significantly inhibited pancreatic cancer cell proliferation and cell cycle progression compared to treatment with gemcitabine, the standard chemotherapeutic agent for advanced pancreatic cancer. We identified a dose‐dependent increase in caspase‐dependent apoptosis and activation of pro‐apoptotic PI3K/Akt pathway proteins, with a subsequent downregulation of …

The Influence Of Landscape And Environmental Factors On Ranavirus Epidemiology In A California Amphibian Assemblage, Brian J. Tornabene, Andrew R. Blausten, Cheryl J. Briggs, Dana M. Calhoun, Pieter T. J. Johnson, Travis Mcdevitt-Galles, Jason R. Rohr, Jason T. Hoverman

Integrative Biology Faculty and Staff Publications

1. A fundamental goal of disease ecology is to determine the landscape and environmental processes that drive disease dynamics at different biological levels to guide management and conservation. Although ranaviruses (family Iridoviridae) are emerging amphibian pathogens, few studies have conducted comprehensive field surveys to assess potential drivers of ranavirus disease dynamics.
2. We examined the factors underlying patterns in site‐level ranavirus presence and individual‐level ranavirus infection in 76 ponds and 1,088 individuals representing five amphibian species within the East Bay region of California.
3. Based on a competing‐model approach followed by variance partitioning, landscape and biotic variables explained the most variation in …

Holmium Laser For Endoscopic Treatment Of Benign Tracheal Stenosis, D J. Verret, Arneya Jategaonkar, Samuel Helman, Sameep Kadakia, Arash Bahrami, Eli Gordin, Yadranko Ducic

Otolaryngology (ENT) Resident Research

Introduction Laryngotracheal stenosis is a difficult problem with varied etiology and various treatment options. The holmium laser represents another tool for the treatment of benign tracheal stenosis.

Objectives To determine the utility of holmium laser treatment for benign tracheal stenosis with regards to safety and efficacy.

Methods This was a retrospective case study examining patients with benign tracheal stenosis from 1998–2016 who underwent holmium laser treatment. Determining the safety of this procedure was the primary goal, and complications were monitored as a surrogate of safety.

Results A total of 123 patients who underwent holmium laser treatment for benign tracheal stenosis …

Measuring The Interaction And Cooperativity Between Ionic, Aromatic, And Nonpolar Amino Acids In Protein Structure, Mason Scott Smith

Theses and Dissertations

Protein folding studies have provided important insights about the key role of non-covalent interactions in protein structure and conformational stability. Some of these interactions include salt bridges, cation-π, and anion-Ï€ interactions. Understanding these interactions is crucial to developing methods for predicting protein secondary, tertiary, quaternary structure from primary sequence and understanding protein-protein interactions and protein-ligand interactions. Several studies have described how the interaction between two amino acid side chains have a substantial effect on protein structure and conformational stability. This is under the assumption that the interaction between the two amino acids is independent of surrounding interactions. We are interested …

Methamphetamine Effects On Adolescent Brain Development In Both Sexes, Jessica Alvarez, Sarah Westbrook, Joshua Gulley

PRECS 2018

Vulnerability to drug addiction in adolescents (ADOLs) may lead to faster rates of addiction and higher rates of relapse. The brain is developing in adolescence, including the prefrontal cortex (PFC) and the nucleus accumbens (NAc), which are regions involved in self-control and reward systems, respectively. Further, females, both human and rat models, often exhibit faster rates of addiction than males. Research from this lab has found previously that adult rats of both sexes exposed to amphetamine during ADOL had reduced expression of dopamine D₁ receptors (D₁R) in the medial PFC but no change in the NAc. The …

Finding Dex-1 Phenotype Suppressing Components, Matthew Barnum, Kristen Flatt, Nathan E. Schroeder

PRECS 2018

Caenorhabditis elegans is a species of microscopic round worm that has been used as a genetic model for over forty years. When in an adverse environment, C. elegans larvae cease reproductive development and enter the stress-resistant dauer stage.

dex-1 mutants of C. elegans are deficient in this protein, resulting in shortened dendrites and a sensitivity to sodium dodecyl sulfate (SDS). SDS will kill any non-dauer C. elegans, but wild type dauers will survive well past the standard concentration of 1% SDS. Thus, treatment with SDS is commonly how labs isolate dauers. By contrast, dex-1 dauers (Fig.3) will …

Phosphorus Vs. Mycorrhiza: Mitigation Of Lead Uptake In Tomatoes, Helen Senerchia, Liz Miernicki, Andrew Margenot

PRECS 2018

This study seeks to understand how the mutualist relationship between arbuscular mycorrhizal fungi (AM) and Solanum lycopersicum (tomato) affects the uptake and distribution of iron (Pb) found in soil by tomatoes and how the effects of phosphorous (P) application may pose a trade-off between AM and P mitigation of bioavailability of Pb.

Sustainability Partnerships And Viticulture Management In California, Vicken Hillis, Mark Lubell, Matthew Hoffman

Human-Environment Systems Research Center Faculty Publications and Presentations

Agricultural regions in the United States are experimenting with sustainability partnerships that, among other goals, seek to improve growers' ability to manage their vineyards sustainably. In this paper, we analyze the association between winegrape grower participation in sustainability partnership activities and practice adoption in three winegrowing regions of California. Using data gathered from a survey of 822 winegrape growers, we find a positive association between participation and adoption of sustainable practices, which holds most strongly for practices in which the perceived private benefits outweigh the costs, and for growers with relatively dense social networks. We highlight the mechanisms by which …

Hyporheic Source And Sink Of Nitrous Oxide, W. Jeffery Reeder, Annika M. Quick, Tiffany B. Farrell, Shawn G. Benner, Kevin P. Feris, Alessandra Marzadri, Daniele Tonina

Geosciences Faculty Publications and Presentations

Nitrous oxide (N₂O) is a potent greenhouse gas with an estimated 10% of anthropogenic N₂O coming from the hyporheic zone of streams and rivers. However, difficulty in making accurate fine-scale field measurements has prevented detailed understanding of the processes of N₂O production and emission at the bedform and flowline scales. Using large-scale, replicated flume experiments that employed high-density chemical concentration measurements, we have been able to refine the current conceptualization of N₂O production, consumption, and emission from the hyporheic zone. We present a predictive model based on a Damköhler-type transformation (τ̃) in …

Natural Resource Condition Assessment, Scotts Bluff National Monument, Reilly R. Dibner, Nicole Korfanta, Gary Beauvais, Jonathan Bowler, Kit Freedman, Kelli C. Trujillo, Victoria H. Zero

United States National Park Service: Publications

Executive Summary

In collaboration with the National Park Service, the University of Wyoming Ruckelshaus Institute of Environment and Natural Resources and the Wyoming Natural Diversity Database completed the Natural Resource Condition Assessment (NRCA) for Scotts Bluff National Monument (NM). The purpose of the NRCA is to provide park leaders and resource managers with information on resource conditions to support near-term planning and management, long-term strategic planning, and effective science communication to decision-makers and the public.

Scotts Bluff NM was established in 1919. The purposes of the park include protecting and preserving the Mitchell Pass portion of the Oregon Trail and …

2018 - 2019 University Catalog, Loma Linda University

University Catalog (2005 - present)

This is a one-year CATALOG, effective beginning Summer Quarter 2018.

Volume 107, Number 1, July 2018.

Contrasting Governance Learning Processes Of Climate-Leading And -Lagging Cities: Portland, Oregon, And Phoenix, Arizona, Usa, Jonathan H. Fink

Geology Faculty Publications and Presentations

The contrasting histories and political ecologies of two U.S. cities—Portland Oregon and Phoenix Arizona—shed light on their ability to learn from and influence the climate governance of their peers. Portland's populace, political leadership, and business sectors are motivated by environmental and social values, resulting in a collective sense of responsibility for fixing global problems like climate change. The city's pioneering land-use policies, green infrastructure, and multimodal transportation systems solidify its place at the climate action forefront. In contrast, libertarian Phoenix prioritizes real estate, efficient government, tourism, and protection of individual rights—the antithesis of Portland's altruism. However, because Phoenix's economic success …

Moving Beyond Consent For Citizen Science In Big Data Health And Medical Research, Anne S.Y. Cheung

Northwestern Journal of Technology and Intellectual Property

Consent has been the cornerstone of the personal data privacy regime. This notion is premised on the liberal tenets of individual autonomy, freedom of choice, and rationality. The above concern is particularly pertinent to citizen science in health and medical research, in which the nature of research is often data intensive with serious implications for individual privacy and other interests. Although there is no standard definition for citizen science, it includes generally the gathering and volunteering of data by non-professionals, the participation of non-experts in analysis and scientific experimentation, and public input into research and projects. Consent from citizen scientists …

Enrollment Report, Summer 2018, Planning, Research, And Policy Analysis

Enrollment Reports (2004-2019)

Enrollment Report for Summer 2018 for Illinois State University