Digital Commons Network^™

Focus: A Graph Approach For Data-Mining And Domain-Specific Assembly Of Next Generation Sequencing Data, Julia Sommer

Theses & Dissertations

Next Generation Sequencing (NGS) has emerged as a key technology leading to revolutionary breakthroughs in numerous biomedical research areas. These technologies produce millions to billions of short DNA reads that represent a small fraction of the original target DNA sequence. These short reads contain little information individually but are produced at a high coverage of the original sequence such that many reads overlap. Overlap relationships allow for the reads to be linearly ordered and merged by computational programs called assemblers into long stretches of contiguous sequence called contigs that can be used for research applications. Although the assembly of the …

Hester, Lanny Ray, 1950-2015 (Fa 1120), Manuscripts & Folklife Archives

Folklife Archives Finding Aids

Finding aid only for Folklife Archives Project FA 1120. Student folk studies project titled: "Traditional Farming Methods & Tools," which includes survey sheets with brief descriptions of traditional farming using horses or mules in Warren County, Kentucky. Sheets may include a description of the traditional tack or implement, photo, informant's name, and text classification.

Cavin, Debbie And Sharman Mullins (Fa 1119), Manuscripts & Folklife Archives

Folklife Archives Finding Aids

Finding aid only for Folklife Archives Project 1119. Student paper titled “The Stewart Farm” in which Debbie Cavin and Sharman Mulls provide an expansive look at the homestead of Garrett Graham Stewart, a native of Warren County, Kentucky. The log house, which was built by Stewart in 1850, was originally part of a 400-acre farmstead. Cavin and Mullins collected their historical data from Bill and Bell Muth, a couple who were in the process of renovating and restoring the Stewart home. In addition to a history of the land, Cavin and Mullins also provide commentary on the home’s various architectural …

This Is Just A Phase : The Impact Of Population Structure On Haplotype Phasing And Linkage Disequilibrium Measures At Functional Genetic Sites., Roxanne Kaaren Leiter

Electronic Theses and Dissertations

The block-like structure of the human genome has been the subject of many scientific papers and is of practical significance in large-scale genome-wide association studies. How stringent haplotype block boundaries are within and between populations has been the subject of ongoing debate within human population genetics. This thesis will contribute to the description of universal and population-specific haplotype blocks at functional sites, namely across the IL-10 gene family (including IL-10, IL-19, IL-20 and IL-24), which is involved in a number of immune system processes, and MAPKAP-K2, an adjacent and functionally significant kinase gene. Beyond the description of blocks across these …

Human Dispersal From Siberia To Beringia: Assessing A Beringian Standstill In Light Of The Archaeological Evidence, Kelly E. Graf, Ian Buvit

All Faculty Scholarship for the College of the Sciences

With genetic studies showing unquestionable Asian origins of the first Americans, the Siberian and Beringian archaeological records are absolutely critical for understanding the initial dispersal of modern humans in the Western Hemisphere. The genetics-based Beringian Standstill Model posits a three-stage dispersal process and necessitates several expectations of the archaeological record of northeastern Asia. Here we present an overview of the Siberian and Beringian Upper Paleolithic records and discuss them in the context of a Beringian Standstill. We report that not every expectation of the model is met with archaeological data at hand.

Genetic Differentiation Of Two Species Of Buckwheat (Eriogonum), Jenessa Blotter Lemon

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Limestone mining in the San Franicso Mountain Range of west central Utah threatens the survival of a rare endemic species of buckwheat (Eriogonum soredium). This species is an edaphic endemic, only found growing on the outcrops of the Ordovician limestone mines in the area. Eriogonum soredium is a candidate for governmental protection under the Endangered Species Act (ESA). However, a common, widespread buckwheat (Eriogonum shockleyi) appears to be closely related to the narrow endemic. The genetic relatedness of the rare and and common species will greatly influence the decision of United States Fish and Wildlife Service …

Ancient Amazonian Populations Left Lasting Impacts On Forest Structure, Michael W. Palace, Crystal H. H. Mcmichael, Bobby H. Braswell, Stephen C. Hagen, Mark B. Bush, Eduardo Góes Neves, Eduardo K. Tamanaha, Christina Herrick, Steve E. Frolking

Ocean Engineering and Marine Sciences Faculty Publications

Amazonia contains a vast expanse of contiguous tropical forest and is influential in global carbon and hydrological cycles. Whether ancient Amazonia was highly disturbed or modestly impacted, and how ancient disturbances have shaped current forest ecosystem processes, is still under debate. Amazonian Dark Earths (ADEs), which are anthropic soil types with enriched nutrient levels, are one of the primary lines of evidence for ancient human presence and landscape modifications in settings that mostly lack stone structures and which are today covered by vegetation. We assessed the potential of using moderate spatial resolution optical satellite imagery to predict ADEs across the …

Acute Salivary Steroid Hormone Responses During Coalitional And Dyadic Competitions In Hong Kong Juvenile Children, Timothy Mchale

UNLV Theses, Dissertations, Professional Papers, and Capstones

A large body of research links testosterone and cortisol responses to competition during adulthood. Little psychoneuroendocrine research has explored salivary steroid hormone responses to competition during middle childhood. This project investigated the relationship between acute salivary steroid hormone change, performance, competitor type, and outcome effects in three different field studies, while controlling for Body Mass Index (BMI) and pubertal development, in a population of ethnically Chinese, Hong Kong juvenile children, 8-11 years of age. The relative dynamics of salivary steroid change were assessed during a 1) coalitional physical competition (soccer) in boys, 2) a non-physical mixed-sex coalitional competition (math contest), …

Developing Algorithms For Quantifying The Super Resolution Microscopic Data: Applications To The Quantification Of Protein-Reorganization In Bacteria Responding To Treatment By Silver Ions, Sai Divya Challapalli

Graduate Theses and Dissertations

Histone-like nucleoid structuring proteins (HNS) play significant roles in shaping the chromosomal DNA, regulation of transcriptional networks in microbes, as well as bacterial responses to environmental changes such as temperature fluctuations. In this work, the intracellular organization of HNS proteins in E. coli bacteria was investigated utilizing super-resolution fluorescence microscopy, which surpasses conventional microscopy by 10–20 fold in spatial resolution. More importantly, the changes of the spatial distribution of HNS proteins in E. coli, by addition of silver ions into the growth medium were explored. To quantify the spatial distribution of HNS in bacteria and its changes, an automatic method …

A Culture Of Health: Herbal Remedies Of The Peruvian Highlands, Jarred Rimby

Whittier Scholars Program

I have divided this paper into three related sections, and each subsequent section of this paper builds on the conclusions of the previous sections. Section I seeks to define a “model of health” for people living in the Peruvian Highlands. Section I draws heavily on one month of fieldwork that I conducted. Section II catalogues and describes the use of culturally significant herbs in the Peruvian Highlands. Section III explores the physiological function of the therapeutic agents in coca, muna, ayahuasca, and sangre de grado, drawing on a review of scientific literature to summarize what is known about each. By …

Mansfield, Sherry R. And Bruce Greene (Fa 1112), Manuscripts & Folklife Archives

Folklife Archives Finding Aids

Finding aid only for Folklife Archives Project 1112. Student folk studies project titled: “Just a Man—Captain William Hicks” which includes an interview of C. Jeff Hicks, the son of Confederate Captain William Hicks. The interview includes a description of the life of the son and his father while living in Barren County, Kentucky and Sumner County, Tennessee.

Genetic Signatures For Helicobacter Pylori Strains Of West African Origin, Kennady K. Bullock, Carrie L. Shaffer, Andrew W. Brooks, Ousman Secka, Mark H. Forsyth, Mark S. Mcclain, Timothy L. Cover

Veterinary Science Faculty Publications

Helicobacter pylori is a genetically diverse bacterial species that colonizes the stomach in about half of the human population. Most persons colonized by H. pylori remain asymptomatic, but the presence of this organism is a risk factor for gastric cancer. Multiple populations and subpopulations of H. pylori with distinct geographic distributions are recognized. Genetic differences among these populations might be a factor underlying geographic variation in gastric cancer incidence. Relatively little is known about the genomic features of African H. pylori strains compared to other populations of strains. In this study, we first analyzed the genomes of …

In Place: November 27, 2017, Place

PLACE Historical Documents

In PLACE is a newsletter designed to keep the Linfield College community apprised of information related to PLACE activities, as well as ways to bring the program into classes. Included in this issue:

• Spotlight On: "What's the Big Idea"
• Upcoming Events
• PLACE in the News

Leveraging Multiple Populations Across Time Helps Define Accurate Models Of Human Evolution: A Reanalysis Of The Lactase Persistence Adaptation, Chenling Xu Antelope, Davide Marnetto, Fergal Casey, Emilia Huerta-Sanchez

Human Biology Open Access Pre-Prints

Access to a geographically diverse set of modern human samples from the present time and from ancient remains, combined with archaic hominin samples, provides an unprecedented level of resolution to study both human history and adaptation. The amount and quality of ancient human data continues to improve, and enables tracking the trajectory of genetic variation over time. These data have the potential to help us redefine or generate new hypotheses of how human evolution occurred, and revise previous conjectures. In this review, we argue that leveraging all these data will help us better detail adaptive histories in humans. As a …

Evolution, Function And Deconstructing Histories: A New Generation Of Anthropological Genetics, Omer Gokcumen

Human Biology Open Access Pre-Prints

Introduction to the Special Issue, mainly based on contributions by the speakers in the 2016 AAAG symposium, “Ancient alleles in modern populations: Ancient structure, introgression, and variation-maintaining adaptive forces.”

Chaco Canyon Dig Unearths Ethical Concerns, Katrina G. Claw, Dorothy Lippert, Jessica Bardill, Anna Cordova, Keolu Fox, Joseph M. Yracheta, Alyssa C. Bader, Deborah A. Bolnick, Ripan S. Malhi, Kimberly Tallbear, Nanibaa' A. Garrison

Human Biology Open Access Pre-Prints

The field of paleogenomics (the study of ancient genomes) is rapidly advancing with more robust methods of isolating ancient DNA and increasing access to next-generation DNA sequencing technology. As these studies progress, many important ethical issues have emerged that should be considered when ancient Native American remains, whom we refer to as ancestors, are used in research. We highlight a recent article by Kennett et al. (2017), “Archaeogenomic evidence reveals prehistoric matrilineal dynasty,” that brings several ethical issues to light that should be addressed in paleogenomics research (Kennett et al. 2017). The study helps elucidate the matrilineal relationships in ancient …

Genetic Differentiation In A Sample From Northern Mexico City Detected By Hla System Analysis: Impact In The Study Of Population Immunogenetics, Eva D. JuáRez CortéS, Miguel A. Contreras Sieck, AgustíN J. Arriaga Perea, Rosa M. MacíAs Medrano, Anaí Balbuena Jaime, Paola Everardo MartíNez, JoaquíN ZúÑIga, VíCtor AcuñA Alonzo, Julio Granados, Rodrigo Barquera

Human Biology Open Access Pre-Prints

The major histocompatibility complex is directly involved in the immune response and thus the genes coding for its proteins are useful markers for the study of genetic diversity, susceptibility to disease (autoimmunity and infections), transplant medicine, and pharmacogenetics, among others. The polymorphism of the system also allows researchers to use it as a proxy for population genetics analysis, such as genetic admixture and genetic structure. In order to determine the immunogenetic characteristics of a sample from the northern part of Mexico City and to use them to analyze the genetic differentiation from other admixed populations, including those from previous studies …

Chance, Nancy Fowler (Fa 1110), Manuscripts & Folklife Archives

Folklife Archives Finding Aids

Finding aid only for Folklife Archives Project 1110. Student folk studies project titled: “Butter making” which includes survey sheets with descriptions of the traditional butter making process in Allen County and Warren County, Kentucky. Sheets may include a brief description of pictured equipment, traditional practice, belief and motif index number.

Building Academic/Practitioner Teams For Human Rights Projects: Examples, Lessons Learned, And Pitfalls To Avoid, Theresa Harris

Biennial Conference: The Social Practice of Human Rights

Academics are increasingly interested in getting out of their classrooms and labs to contribute their knowledge, expertise, and resources to help communities develop evidence-based policies. In addition to post-election initiatives such as the March for Science and 314 Action, many academics are joining “without borders”-type programs and organizations that connect academics with opportunities to volunteer their time and talents for “social good.”

One of the longest-running of these is On-call Scientists, an initiative of the American Association for the Advancement of Science (AAAS) that connects human rights organizations with pro bono scientists across all fields — life, physical, behavioral, and …

Jaggers, Katie Thompson (Fa 1107), Manuscripts & Folklife Archives

Folklife Archives Finding Aids

Finding aid only for Folklife Archives Project 1107. Paper titled “Methods of Corn Production in an Edmonson Co[unty] Community” in which Katie Jaggers Charts the history of corn harvesting by traditional means, such as using mules, shovels, wagons, and A-harrows, up through the current practice of employing highly-tech machinery. Paper is based on information collected by Jaggers from two brothers, Edgar and Harry Thompson, who resided in Lindseyville, Kentucky. Collection also includes color photos and descriptions of traditional farming machinery.

Collins, Gary & Tammy Pickering (Fa 346), Manuscripts & Folklife Archives

Folklife Archives Finding Aids

Finding aid only for Folklife Archives Project 346. Paper titled "Hog Killing in Western Kentucky" in which Gary Collins and Tammie Pickering discuss the cultural significance of farm-raising hogs and the foodways traditions that result from the slaughtering process. Using slides and interviews, Collins and Pickering document a hog killing that took place in January 1986 on a farm in Trigg County, Kentucky.

Pickering, Tammie & Gary Collins (Fa 348), Manuscripts & Folklife Archives

Folklife Archives Finding Aids

Finding aid and full-text scan of paper (Click on “Additional Files” below) for Folklife Archives Project 348. Student paper titled “Trees in Folk Crafts” in which Tammie Pickering and Gary Collins explore the connection between trees and traditional folkways. Paper details the medicinal properties of sassafras tea, which is made from tree roots, the production of maple syrup, and the expressive crafts of wood-carving and carpentry. Data collected from three working-class residents of Caldwell County. Paper also includes field journals, recorded interviews, and transcripts.

The Santa Clara, 2017-11-02, Santa Clara University

The Santa Clara

No abstract provided.

Creation Of Forest Edges Has A Global Impact On Forest Vertebrates, M. Pfeifer, V. Lefebvre, C. A. Peres, C. Banks-Leite, O. R. Wearn, C. J. Marsh, S. Butchart, V. Arroyo-Rodriguez, J. Barlow, A. Cerezo, L. Cisneros, N. D'Cruze, D. Faria, A. Hadley, S. M. Harris, B. T. Klingbeil, U. Kormann, L. Lens, G. F. Medina-Rangel, J. C. Morante-Filho, P. Olivier, S. L. Peters, A. Pidgeon, D. B. Ribeiro, C. Scherber, L. Schneider-Maunoury, M. Struebig, N. Urbina-Cardona, J. I. Watling, M. R. Willig, E. M. Wood, R. M. Ewers

2017 Faculty Bibliography

Forest edges influence more than half of the world's forests and contribute to worldwide declines in biodiversity and ecosystem functions. However, predicting these declines is challenging in heterogeneous fragmented landscapes. Here we assembled a global dataset on species responses to fragmentation and developed a statistical approach for quantifying edge impacts in heterogeneous landscapes to quantify edge-determined changes in abundance of 1,673 vertebrate species. We show that the abundances of 85% of species are affected, either positively or negatively, by forest edges. Species that live in the centre of the forest (forest core), that were more likely to be listed as …

2017 Program, Office Of Academic Affairs

Programs

Scholarship, creativity, innovation, and the many forms of collaborative engagement that shape faculty life and student learning are central to the mission of Eastern Illinois University. For that reason, our faculty, department chairs, college deans, the Provost, and the entire campus community celebrate the achievements and outstanding contributions of our colleagues and students to their disciplines and professions every year. And, as the following pages illustrate, faculty engaged in continuing scholarly and creative activities that have provided outstanding mentoring experiences for our undergraduate and graduate students.

In addition to recognizing faculty performances, shows, publications, grants and other professional efforts, the …

Dailey, Jan (Fa 1103), Manuscripts & Folklife Archives

Folklife Archives Finding Aids

Finding aid only for Folklife Archives Project 1103. Paper titled “Food Storage for Winter Consumption” in which Jan Dailey offers an in-depth exploration into the realm of traditional food preservation and storage practices, such as drying, peeling, dipping, husking, and “hilling up,” that have persisted in spite of modern mechanized methods. Paper is based on information gathered by Dailey from farmers and homemakers across McCracken and Metcalfe County.

Water Supply In Developing Countries: Student Experiences In The Dominican Republic, Albert Alwang, Margaret Busse, Audrey Caprio, Marieke Fenton, Jason Hawes, Andrew Kanach, Autumn Mcelfresh-Sutton

Purdue Journal of Service-Learning and International Engagement

In 2010, the United Nations established access to safe drinking water as a basic human right; however, many areas around the globe still lack access. The interdisciplinary service-learning course “Water Supply in Developing Countries” was established at Purdue in 2012 to address the complex issue of water insecurity around the world. Over the past five years, the course has produced teams involving students from nursing, engineering, agricultural economics, biology, and food science working together to develop sustainable, community-scale drinking water treatment systems. In partnership with Aqua Clara International, the student team in 2017 established a drinking water treatment system at …

Introgression Makes Waves In Inferred Histories Of Effective Population Size, John Hawks

Human Biology Open Access Pre-Prints

Human populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent “wave” of larger effective population size, found in both African and non-African populations, that appears to reflect events prior to the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations …

Evangelii Gaudium: A European Perspective, Salvatore Moccia

Journal of Vincentian Social Action

In order to understand the Apostolic Exhortation Evangelii Gaudium, we have to analyze the strategic roots of this Pope, a shepherd who lived his life with the smell of the sheep. Only if we recognize the “great enemy” we can fully understand all the Papal “No’s” of the Encyclical: no to an economy of exclusion, no to the new idolatry of money, no to a financial system which rules rather than serves, and no to the inequality which spawns violence. We believe that Pope Francis, with his Apostolic Exhortation Evangelii Gaudium, has updated most of the Franciscan reflections on the …

The Future Of Food In Blade Runner 2049, Diarmuid Cawley

Other resources

The science fiction genre has always been a hotbed for questions about the existence of life and what it means to be human. Food, like water and oxygen, is necessary to sustain life, but also is a key indicator of culture. One of the things that fascinates us about science fiction is how an imagined future culture might look. Blade Runner 2049, although not centred around food, interweaves food and agriculture into a dystopian narrative on evolution and a bio-engineered labour force, while asking us what it means to have memories and to be human.