Digital Commons Network^™

Isquest: Finding Insertion Sequences In Prokaryotic Sequence Fragment Data, Abhishek Biswas, David T. Gauthier, Desh Ranjan, Mohammad Zubair

Computer Science Faculty Publications

Motivation: Insertion sequences (ISs) are transposable elements present in most bacterial and archaeal genomes that play an important role in genomic evolution. The increasing availability of sequenced prokaryotic genomes offers the opportunity to study ISs comprehensively, but development of efficient and accurate tools is required for discovery and annotation. Additionally, prokaryotic genomes are frequently deposited as incomplete, or draft stage because of the substantial cost and effort required to finish genome assembly projects. Development of methods to identify IS directly from raw sequence reads or draft genomes are therefore desirable. Software tools such as Optimized Annotation System for Insertion Sequences …

Photosynthetic Performance And Anti-Oxidative Response Of Cornus Controversa Seedlings Under Cadmium And Lead Stress, Xinyu Huang, Yonglei Jiang, Xiaomao Cheng, Lilan Deng, Xuncheng Liu

Faculty Publications

The photosynthetic efficiency of Cornus controversa leaves was decreased significantly under Cd treatment while it was not affected by Pb exposure. Cd decreased while Pb treatment increased the chlorophyll contents of Cornus controversa leaves. Furthermore, the peroxidase (GPX) activities were decreased after Cd treatment while elevated by Pb exposure in Cornus controvera seedlings. In addition, both Cd and Pb exposures increased the malondialdehyde (MDA) and proline contents and elevated the superoxide dismutase (SOD) activities of Cornus controvera seedlings. Collectively, these results indicated that Cornus controversa may be more tolerant to Pb than Cd toxicity. This finding will contribute to the …

Protein Domain Linker Prediction: A Direction For Detecting Protein-Protein Interactions, Maad Mohammad Shatnawi

Dissertations

Protein chains are generally long and consist of multiple domains. Domains are the basic elements of protein structures that can exist, evolve, and function independently. The accurate and reliable identification of protein domains and their interactions has very important impacts in several protein research areas. The accurate prediction of protein domains is a fundamental stage in both experimental and computational proteomics. The knowledge of domains is an initial stage of protein tertiary structure prediction which can give insight into the way in which proteins work. The knowledge of domains is also useful in classifying proteins, understanding their structures, functions and …

Mongolians In The Genetic Landscape Of Central Asia: Exploring The Genetic Relations Among Mongolians And Other World Populations, Jane E. Brissenden, Judith R. Kidd, Baigalmaa Evsanaa, Ariunaa Togtokh, Andrew J. Pakstis, Françoise Friedlaender, Kenneth K. Kidd, Janet M. Roscoe

Human Biology Open Access Pre-Prints

Genetic data on North Central Asian populations are underrepresented in the literature, especially autosomal markers. In the present study we use 812 single nucleotide polymorphisms that are distributed across all the human autosomes and that have been extensively studied at Yale to examine the affinities of two recently collected, samples of populations: rural and cosmopolitan Mongolians from Ulaanbaatar and nomadic, Turkic-speaking Tsaatan from Mongolia near the Siberian border. We compare these two populations to one another and to a global set of populations and discuss their relationships to New World populations. Specifically, we analyze data on 521 autosomal loci (single …

Facilities Forum, Georgia Southern University

Auxiliary Services (2013-2021)

• Bicycle Parking Facility at Paulson Stadium
• Sweetheart Circle Pedestrian Island
• Military Science
• Fire Hydrant Makeover
• Decaying Pecan Tree Removal
• Safety Week Training
• Campus Garden
• Creating a Safety Culture
• Congratulations Mr. Gray!
• New Hires & Promotions

Lessons From Pollution Control: Response To Heller And Hobbs 2014, Robert L. Fischman, James Salzman

Articles by Maurer Faculty

Heller and Hobbs (2014) provide an incisive analysis of the challenges inherent in setting endpoint states as conservation goals. The social construct of nature, nonequilibrium ecosystems, global climate change, large-scale transformations of the landscape, and increasing population and economic activity confound efforts to establish conservation goals. Stakeholders often disagree on endpoint targets, whereas competing notions of historic fidelity and future flexibility frustrate our ability to articulate success, never mind actually achieve it. As Heller and Hobbs describe, this leaves managers in the bind of finding the “balance between future-looking management emphasizing change and past-looking management emphasizing persistence.” As a result, …

Improving Communication Through Writing, Christopher N. Jacques

The Prairie Naturalist

Greetings GPNSS members! By the time you read this editorial, most of us will be enjoying the summer vacation and all that the Great Plains has to offer. Warmer temperatures, increasing day length, and time in the field are a welcomed change from the seemingly endless grip of “old man” winter (for those of us in the northern Great Plains). Of course, believing that anyone could truly enjoy the clouds of tormenting, biting insects and high humidity across the Great Plains is hard to imagine, in my opinion. There are plenty of summer activities for the outdoor enthusiasts among us, …

Inter- And Intra-Specific Interactions In Germination And Seedling Establishment Of Cheatgrass And Russian Wildrye, Erin K. Espeland

The Prairie Naturalist

Cheatgrass (Bromus tectorum) is an invasive species in the arid and semi-arid west of the USA, and is weedy in disturbed prairie landscapes. Perennial Russian wildrye (Psathyrostachys juncea) limits population growth of cheatgrass, but the mechanism is unclear. I conducted glasshouse and greenhouse experiments to test if intra- and interspecific competitive interactions of seeds and seedlings of cheatgrass and Russian wildrye were different across a geographic soil gradient with different cultivation legacies in eastern Montana, USA. Seed-seed interactions occurred in both species. Cheatgrass and Russian wildrye inhibited one another’s emergence in one edaphic condition in one experiment. Cheatgrass growth was …

West Nile Virus And Ferruginous Hawks (Buteo Regalis) In The Northern Great Plains, Shubham Datta, Jonathan A. Jenks, David E. Knudsen, Kent C. Jensen, Will M. Inselman, Christopher C. Swanson, Troy W. Grovenburg

The Prairie Naturalist

Emerging infectious diseases (EID) present significant threats to the conservation of global biodiversity (Daszak et al. 2000). Evaluating impacts (spatial, temporal and demographic) of EIDs on sensitive and declining wildlife populations is challenging because quantitative information is usually dependent on estimates rather than counts (Wobeser 2007) and mortality rates are seldom quantified with conventional monitoring (Naugle et al. 2005).

West Nile virus (WNv), a mosquito-borne Flavivirus (family Flaviviridae; Komar 2001), was discovered in northwest Uganda in 1937 (Smithburn et al. 1940). First encountered in the western hemisphere in New York in 1999 (Nash et al. 2001), WNv has become enzootic …

Using Otolith Microchemistry To Classify Yellow Perch As Stocked Or Naturally Produced, Andrew K. Carlson, Matthew J. Ward, Brian D.S Graeb

The Prairie Naturalist

Fisheries managers routinely use stocking to supplement fish populations (Schramm and Piper 1995, Fisher 1996). Stocking eyed-eggs offers substantial cost savings compared to stocking fry and fingerlings (PFBC 2011); however, traditional stocking evaluation using oxytetracycline (OTC) marking of otoliths is ineffective for eyed-eggs of some species (e.g., yellow perch, [Perca fla- vescens]). Thus, there is a need for additional approaches to be able to classify fish as stocked or naturally produced. Fish otoliths are paired calcified structures in the inner ear that permanently deposit trace elements in proportion to water column concentrations (Campana 1999, Campana et al. 2000). Coupled with …

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New packages in CRAN task views

New contributed packages

Other changes

R As An Environment For Reproducible Analysis Of Dna Amplification Experiments, Stefan Rödiger, Michał Burdukiewicz, Konstantin Blagodatskikh, Michael Jahn, Peter Schierack

The R Journal

There is an ever-increasing number of applications, which use quantitative PCR (qPCR) or digital PCR (dPCR) to elicit fundamentals of biological processes. Moreover, quantitative isothermal amplification (qIA) methods have become more prominent in life sciences and point-of-care diagnostics. Additionally, the analysis of melting data is essential during many experiments. Several software packages have been developed for the analysis of such datasets. In most cases, the software is either distributed as closed source software or as monolithic block with little freedom to perform highly customized analysis procedures. We argue, among others, that R is an excellent foundation for reproducible and transparent …

The R Journal (June 2015) 7(1): Complete Issue, The R Foundation

The R Journal

Editorial, Bettina Grün

Contributed Research Articles

Peptides: A Package for Data Mining of Antimicrobial Peptides, Daniel Osorio, Paola Rondón-Villarreal, and Rodrigo Torres

fanplot: An R Package for Visualising Sequential Distributions, Guy J. Abel

sparkTable: Generating Graphical Tables for Websites and Documents with R, Alexander Kowarik, Bernhard Meindl, and Matthias Templ

rdrobust: An R Package for Robust Nonparametric Inference in Regression-Discontinuity Designs, Sebastian Calonico, Matias D. Cattaneo, and Rocío Titiunik

Frames2: A Package for Estimation in Dual Frame Surveys, Antonio Arcos, David Molina, Maria Giovanna Ranalli, and María del Mar Rueda

The Complex Multivariate Gaussian Distribution, Robin K. S. Hankin

sae: …

Effects Of Minimum Winter Temperatures On Southern Pine Beetle (Dendroctonus Frontalis) Mortality On Long Island, N.Y., Jessica Cancelliere

Department of Entomology: Distance Master of Science Projects

Dendroctonus frontalis (the southern pine beetle) was discovered on Long Island, New York in 2014. Additional infestations have since been located in upstate New York, Rhode Island, Connecticut and Massachusetts. Previously found as far north as New Jersey and Pennsylvania, this range expansion now represents the current northern distribution limits of D. frontalis. Minimum winter temperatures are a meaningful driver of population dynamics and mortality in D. frontalis, and understanding this relationship at the northern range limits can help forest managers better predict and prepare for outbreaks. Studies addressing the relationship between temperature and beetle mortality, and the …

Dietary Microrna Database (Dmd): An Archive Database And Analytic Tool For Food-Borne Micrornas, Kevin Chiang, Jiang Shu, Janos Zempleni, Juan Cui

School of Computing: Faculty Publications

With the advent of high throughput technology, a huge amount of microRNA information has been added to the growing body of knowledge for non-coding RNAs. Here we present the Dietary MicroRNA Databases (DMD), the first repository for archiving and analyzing the published and novel microRNAs discovered in dietary resources. Currently there are fifteen types of dietary species, such as apple, grape, cow milk, and cow fat, included in the database originating from 9 plant and 5 animal species. Annotation for each entry, a mature microRNA indexed as DM0000*, covers information of the mature sequences, genome locations, hairpin structures of parental …

Water And Energy Use And Wastewater Production In A Beef Packing Plant, Rami Ziara

Department of Civil and Environmental Engineering: Dissertations, Theses, and Student Research

Accurate information about water and energy use and wastewater production in beef packing plants is scarce. The objective of this study was to collect baseline water and energy use data within a beef packing plant with a special focus on antimicrobial interventions and to collect preliminary wastewater production data in addition. Permanent and portable water flow meters were installed on the plant’s plumbing system to collect water flow data from March 2014 to March 2015. A local utility company was hired to meter electricity at antimicrobial interventions using portable data loggers. Metered water flows and temperatures were combined with fundamental …

A Prototype On-Line Aotf Hyperspectral Image Acquisition System For Tenderness Assessment Of Beef Carcasses, Govindarajan Konda Naganathan, Kim Cluff, Ashok Samal, Chris Calkins, David D. Jones, Carol Lorenzen, Jeyamkondan Subbiah

Department of Food Science and Technology: Faculty Publications

A prototype on-line acousto-optic tunable filter (AOTF)-based hyperspectral image acquisition system (λ = 450– 900 nm) was developed for tenderness assessment of beef carcasses. Hyperspectral images of ribeye muscle on stationary hanging beef carcasses (n = 338) at 2-day postmortem were acquired in commercial beef slaughter or packing plants. After image acquisition, a strip steak was cut from each carcass, vacuum packaged, aged for 14 days, cooked, and slice shear force tenderness scores were collected by an independent lab. Beef hyperspectral images were mosaicked together and principal component (PC) analysis was conducted to reduce the spectral dimension. Six different textural …

Recent Advances In Indoor Chemistry, Glenn Morrison

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

Just as the chemistry creates urban smog and aerosols that influence climate change, chemistry in building air can alter the indoor environment for better or worse. This review focuses on chemical pathways initiated by oxidants that infiltrate from outdoor air and other indoor-sourced reactants and surfaces that make these environments unique chemical reactors. Ozone reacts with fragrance molecules, tobacco smoke residues, and even human skin oils to generate a host of oxidized organic compounds, secondary organic aerosols, and irritants. Nitrous acid is formed on indoor surfaces and is subsequently cleaved by even the relatively dim light indoor. This raises the …

Comparing Yield Monitors With Weigh Wagons For On-Farm Corn Hybrid Evaluation, Bjorn P. Nelson, Roger Wesley Elmore, Andrew W. Lenssen

Department of Agronomy and Horticulture: Faculty Publications

For many years, on-farm yield evaluations of corn (Zea mays L.) hybrids were done with weigh wagons, handheld moisture testers, and measuring wheels. Today, most combines have continuous flow yield and moisture sensors. Published research results comparing the accuracy of combine-mounted sensor systems with that of weigh wagons are limited for on-farm corn hybrid evaluation. This study examined the accuracy of combine-mounted yield sensors with traditional weigh wagon methodology in on-farm corn hybrid strip trials. Data from combine-mounted sensors for plot weight, moisture percentage, and yield were compared with weigh wagon weight, handheld moisture testers, and calculated yield …

Design And Analysis Of A Reconfigurable Hierarchical Temporal Memory Architecture, Abdullah M. Zyarah

Theses

Self-learning hardware systems, with high-degree of plasticity, are critical in performing spatio-temporal tasks in next-generation computing systems. To this end, hierarchical temporal memory (HTM) offers time-based online-learning algorithms that store and recall temporal and spatial patterns. In this work, a reconfigurable and scalable HTM architecture is designed with unique pooling realizations. Virtual synapse design is proposed to address the dynamic interconnections occurring in the learning process. The architecture is interweaved with parallel cells and columns that enable high processing speed for the cortical learning algorithm.

HTM has two core operations, spatial and temporal pooling. These operations are verified for two …

Forma Naturalis, Patrick Kana

Theses

Mankind’s fascination with natural form is undeniably long-lived. From collecting and preserving specimens for evolutionary research, to documenting and expressing natural form through artistic practice, Mankind continues to embrace for scientific and aesthetic benefit that which surrounds us. I believe that botany, marine biology, and environmental phenomena—all areas of influence and study from my childhood—are sources that illustrate perfection in form and utility. The sheer beauty evident in these scientific forms continues to inspire me, and I will celebrate them and explore my relationship with them through an experimental making process in wood.

Carved objects, form studies, and functional furniture …

Biological Significance Of Dual Oriented P6 From Nontypeable Haemophilus Influenzae: Assessing Surface P6 Levels In Different Strains Of Nthi, Cultured Under Various Physiologically Relevant Environmental Conditions, Casey Reulbach

Theses

Nontypeable Haemophilus influenzae (NTHi) or nonencapsulated Haemophilus influenzae has been connected to such diseases as pneumonia, bacteremia, meningitis and sepsis in adults. NTHi is also linked to 25-35% of the roughly 25 million annual cases (within The United States) of acute otitis media (ear infections) in children. Vaccines against encapsulated strains of Haemophilus influenzae have been proven effective; yet, no vaccines have been produced to protect against NTHi infection. The 16-kDa outer membrane lipoprotein P6 has been shown to be nearly homologous between NTHi strains, making it one of the leading vaccine candidates for NTHi. However, it was recently demonstrated, …

The Apnaase/Mrna Decapping Nudix Hydrolases From M. Tuberculosis And M. Leprae, Peipei Zhu

Theses

Throughout history, Mycobacterium tuberculosis (MTB) has killed more people than any other infectious agent, while Mycobacterium leprae is an ancient human pathogen that still causes disease today. Each has developed drug resistance, thus the discovery of potential novel antibiotic targets is essential. The diadenosine polyphosphatases (ApnAases) / mRNA decapping enzymes of the Nudix hydrolase superfamily have been found to be essential for a number of pathogens (Bartonella bacilliformis, Legionella pneumophila) to invade human host cells, a process often essential for pathogenesis, and thus potential novel drug targets. There are two ApnAases in MTB: Rv2985 and Rv3908 and two corresponding orthologs …

Phylogeographic Study Of Ctenosaura Similis, Hasret Ozturk

Theses

The genus Ctenosaura (spiny-tailed iguanas) represents the most diverse group of iguanas with 18 currently recognized species. Ctenosaura similis has the most widespread ranges of all the Ctenosaura species, and extends from southern Mexico to Panama including many coastal islands. The purpose of this study is to explore the genetic diversity within C. similis and look for correlations between genetic relationships and biogeographic patterns related to the spread of the species. This study sequenced and aligned 1140 bp from the cytochrome b (cytb) locus for 159 individuals and 847-878 bp from the rhodopsin locus for 127 individuals. A total of …

Content-Based Image Retrieval Using Deep Learning, Anshuman Vikram Singh

Theses

A content-based image retrieval (CBIR) system works on the low-level visual features of a user input query image, which makes it difficult for the users to formulate the query and also does not give satisfactory retrieval results. In the past image annotation was proposed as the best possible system for CBIR which works on the principle of automatically assigning keywords to images that help image retrieval users to query images based on these keywords. Image annotation is often regarded as the problem of image classification where the images are represented by some low-level features and the mapping between low-level features …

Fibroblast-Derived Extracellular Matrix: An Alternative Cell Culture Substrate That Alters Lung Cancer Cell Line Phenotype., Michael Thomas Scherzer

Electronic Theses and Dissertations

Poor lung cancer survival can largely be contributed to the metastatic cells that invade and spread throughout the body. The tumor microenvironment (TME) is composed of multiple cell types, as well as non-cellular components. The TME plays a critical role in the development of metastatic cancers by providing migratory cues that change the growing tumor’s properties. The Extracellular Matrix (ECM), a main component of the TME, has been shown to change composition during tumor progression, allowing cancer cells to invade tissue and survive away from the primary cancer site. Although the ECM is well-known to influence the fate of tumor …

Establishing An Effective National Environmental Information System, Rizah Hajdari

Theses

This Capstone project addresses the important problem of functional improvement of the National Environmental System in Kosovo. The main issues addressed are the legal requirements for data collection, data processing, validation, and reporting, as stipulated by the law on environment; and the practical needs for improvement in order to make the system more effective, more reliable, and more usable in order to provide timely and accurate environmental data to the policymakers and to overall public. In order to better address the problem, consideration is given to both international and national context of EIS requirements. This is very relevant given the …

Jurisdictional Roadside Ditches, Sarah M. Mccormack, Christopher W. Van Dyke, Doug Kreis

Kentucky Transportation Center Research Report

Section 404 of the Clean Water Act (CWA) mandates that state agencies and other entities perform compensatory mitigation when their activities impair jurisdictional waters. In the Commonwealth of Kentucky, the Kentucky Transportation Cabinet (KYTC) is required to pay in-lieu fees or purchase stream mitigation credits when a roadside ditch is impaired or relocated as part of a road construction project. In-lieu fees and stream mitigation credits are costly, and ditches that have suffered degraded habitat and loss of hydrogeomorphic functionality are treated as total losses when they are impacted by construction and maintenance activities. This raises the question of whether …

Commencement Program 2015, Loma Linda University

Commencement Programs

CONTENTS

1 | Message from the President

3 | 2015 Events of Commencement

5 | The Academic Procession

7 | Significance of Academic Regalia

9 | The Good Samaritan

10 | University History Highlights

12 | Loma Linda University Song - "Healing Love"

13 | The Speakers

23 | The University Honorees

45 | The School Honorees

72 | The Programs

• School of Medicine, 73
• School of Pharmacy, 95
• School of Dentistry, 103
• School of Allied Health Professions, 122
• School of Allied Health Professions - Physical Therapy, 143
• School of Public Health, 154
• School of Behavioral Health and School of …

Erika Dyck. Facing Eugenics: Reproduction, Sterilization, And The Politics Of Choice, Garland E. Allen

Biology Faculty Research

[Book review of Erika Dyck. Facing Eugenics: Reproduction, Sterilization, and the Politics of Choice. Toronto: University of Toronto Press, 2013.]