Digital Commons Network^™

Identification And Replication Of Rna-Seq Gene Network Modules Associated With Depression Severity, Trang T. Le, Jonathan Savitz, Hideo Suzuki, Masaya Misaki, T. Kent Teague, Bill C. White, Julie H. Marino, Graham Wiley, Patrick M. Gaffney, Wayne C. Drevets, Brett A. Mckinney, Jerzy Bodurka

Department of Educational Psychology: Faculty Publications

Genomic variation underlying major depressive disorder (MDD) likely involves the interaction and regulation of multiple genes in a network. Data-driven co-expression network module inference has the potential to account for variation within regulatory networks, reduce the dimensionality of RNA-Seq data, and detect significant geneexpression modules associated with depression severity. We performed an RNA-Seq gene co-expression network analysis of mRNA data obtained from the peripheral blood mononuclear cells of unmedicated MDD (n = 78) and healthy control (n = 79) subjects. Across the combined MDD and HC groups, we assigned genes into modules using hierarchical clustering with a dynamic …

Science Literacy: Using Research-Based Facts To Make Real-World Decisions, Shelby Cammack, Michael J. Boehm, Kathleen Lodl, Mark Balschweid, Mary Garbacz, Tiffany Heng-Moss, Katherine Mundorf, Charles Hibberd, Tala Awada, Emily Frenzen, Dirac L. Twidwell Jr., Riley Nichols, Nicholas Brozovic, Lindsay J. Hastings, Alexandria Lundvall, Brad Barker, Jamie Loizzo, Tiffany Messer, Scott Schrage, Abby Steffen, Ashu Guru, Jenny Keshwani, Jeyam Subbiah, Matt Kreifels, Jenny Dauer, Andrea Wach Tenney, Deepak Keshwani, Joesph Dauer, Sydney Everhart, Julie Obermeyer

Strategic Discussions for Nebraska

Science Literacy: Using Research-Based Facts to Make Real-World Decisions

As the next generation of leaders is entering the educational pipeline, it’s important to have an emphasis on science, technology, engineering and mathematics (STEM) to solve the grand challenge of feeding 9 billion people by 2050.

Rnai-Mediated Knockdown Of Vatpase Subunits Affects Survival And Reproduction Of Bed Bugs (Hemiptera: Cimicidae), Sanjay Basnet, Shripat T. Kamble

Department of Entomology: Faculty Publications

The common bed bug, Cimex lectularius L. (Hemiptera: Cimicidae) has resurged as one of the most troublesome household pests affecting people across the globe. Bed bug infestations have increased in recent years primarily due to the evolution of insecticide resistance and the insect’s ability to hitchhike with travelers. vATPases are one of the most evolutionarily conserved holoenzymes in eukaryotes, which are mainly involved in proton transport across the plasma membranes and intracellu­lar organelles. RNA interference (RNAi) has been developed as a promising tool for insect control. In this study, we used RNAi as an approach to knock down subunits A …

Research And Creative Activity, July 1, 2017–June 30, 2018: Major Sponsored Programs And Faculty Awards For Research And Creative Activity, University Of Nebraska–Lincoln, Office Of Research And Economic Development, University Of Nebraska–Lincoln

Office of Research and Economic Development: Publications

Foreword by Bob Wilhelm, Vice Chancellor for Research and Economic Development:

This booklet highlights successes in research, scholarship and creative activity by University of Nebraska–Lincoln faculty during the fiscal year July 1, 2017– June 30, 2018.

It lists investigators, project titles and funding sources on major grants and sponsored program awards received during the year; fellowships and other recognitions and honors bestowed on our faculty; books published by faculty; performances, exhibitions and other creative activity by our faculty; and patents and licensing agreements issued for products of Nebraska research.

Notably, the university reached a major milestone in FY2017: earning $302 …

An Engineer Cantonment Bestiary: The Art Of Titian Ramsay Peale, Hugh H. Genoways, Thomas E. Labedz

University of Nebraska State Museum: Mammalogy Papers

Includes an overview of the work of American nature artist Titian Ramsay Peale as part of the Stephen H. Long Expedition, 1819-1820, at Engineer Cantonment in eastern Nebraska, USA.

Includes textual descriptions and/or reproductions of watercolors and lined drawings by Peale of banded killifish (Fundulus diaphanous), American White Pelican (Pelecanus erythrothynchos), Wood Duck (Aix sponsa), Rough-legged Hawk (Buteo lagopus/Falco lagopus), Sandhill Crane (Grus canadensis tabida), Pectoral Sandpiper (Calidris melanotos), Scarlet Tanager (Piranga olivacea), American Tree Sparrow (Spizella arborea), Yellow-headed Blackbird (Xanthocephalus …

Field Evaluation Of Commercially Available Small Unmanned Aircraft Crop Spray Systems, Wayne Woldt, D. Martin, M. Latheef, Greg Kruger, Robert J. Wright, Justin Mcmechan, Christopher A. Proctor, Tamra Jackson-Ziems

Department of Plant Pathology: Faculty Publications

Agricultural research and development on small unmanned aircraft systems (UAS) has been directed toward UAS enabled sensing to detect features of interest. While compelling, there is an immediate need to increase the breadth and depth of UAS-based research, to move beyond sensing, and explore active intervention in agricultural production systems. This paper is focused on the concept of crop protection through ultra-precise, unmanned aerial application systems, and seeks to initiate research discussion in this important area of opportunity. Toward this end, two different, commercially available, small Unmanned Aerial Application Systems (sUAAS - defined as less than 55 lbs. maximum take-off …

Examining The Roles Of Child Temperament And Teacher-Child Relationships As Predictors Of Turkish Children’S Social Competence And Antisocial Behavior, Ibrahim H. Acar, Traci Kutaka, Kathleen Moritz Rudasill, Julia C. Torquati, Robert J. Coplan, Süleyman Yıldız

Department of Child, Youth, and Family Studies: Faculty Publications

The present study examined the concurrent contribution of Turkish children’s temperament and teacher-child relationship quality to their social competence and antisocial behavior, with a specific focus on the moderating role of teacher-child relationships (closeness and conflict) on children’s temperament (inhibitory control and shyness) when predicting social competence and antisocial behavior. Participants were 94 children (56 boys) with mean age of 7.05 years (SD = .88) enrolled in 24 classrooms from five elementary schools in a suburban school district in Turkey. Mothers reported on children’s temperament and teachers reported on their relationships with children as well as children’s social competence …

Fictive Kinships And The Remaking Of Family Life In The Context Of Paid Domestic Work: The Case Of Philippine Yayas, Maria Rosario De Guzman, Aileen S. Garcia, Minerva D. Tuliao

Department of Child, Youth, and Family Studies: Faculty Publications

In this chapter, we draw from our study on Filipina rural-to-urban migrant workers in the domestic care sector to illustrate how migrants make and remake family in the context of separation. The setting of our study is in Quezon City, Philippines, and our participants are women employed as yayas-domestic care workers employed to care for children. They live in their employers' homes, and most of our respondents live apart from their own children and all are living away from their nuclear families. Details of this study are laid out in an earlier paper that focused on the experience of family …

Isolation Of Mitochondrial Dna From Single, Short Hairs Without Roots Using Pressure Cycling Technology, Kathryn A. Harper, Kelly A. Meiklejohn, Richard T. Merritt, Jessica Walker, Constance L. Fisher, James M. Robertson

United States Department of Justice: Publications

Hairs are commonly submitted as evidence to forensic laboratories, but standard nuclear DNA analysis is not always possible. Mitochondria (mt) provide another source of genetic material; however, manual isolation is laborious. In a proof-of-concept study, we assessed pressure cycling technology (PCT; an automated approach that subjects samples to varying cycles of high and low pressure) for extracting mtDNA from single, short hairs without roots. Using three microscopically similar donors, we determined the ideal PCT conditions and compared those yields to those obtained using the traditional manual micro-tissue grinder method. Higher yields were recovered from grinder extracts, but yields from PCT …

A Review And Conceptual Model Of Factors Correlated With Postmortem Root Band Formation, Joseph Donfack, Hilda S. Castillo

United States Department of Justice: Publications

It is generally accepted within the forensic trace evidence community that a postmortem root band (PMRB) can appear in the root of hairs attached to remains during decomposition. Presently, the specific sequences of events and/or exact molecular signals that lead to the formation of a PMRB are not well understood. The published literature addressing the abiotic and biotic factors that correlate with the formation of PMRBs is reviewed and a conceptual model for the formation of PMRBs is proposed.

Integration Of Paper Spray Ionization High‐Field Asymmetric Waveform Ion Mobility Spectrometry For Forensic Applications, Chia-Wei Tsai, Christopher A. Tipple, Richard A. Yost

United States Department of Justice: Publications

Rationale: Paper spray ionization (PSI) is an attractive ambient ionization source for mass spectrometry (MS) since it allows the combination of surface sampling and ionization. The minimal sample preparation inherent in this approach greatly reduces the time needed for analysis. However, the ions generated from interfering compounds in the sample and the paper substrate may interfere with the analyte ions. Therefore, the integration of PSI with high‐field asymmetric ion mobility spectrometry (FAIMS) is of significant interest since it should reduce the background ions entering the mass analyzer without complicating the analysis or increasing analysis time. Here we demonstrate the integration …

Potential Effects Of Ionizing Radiation On The Evidentiary Value Of Dna, Latent Fingerprints, Hair, And Fibers: A Comprehensive Review And New Results, Keith L. Monson, Sherine Ali, Michael D. Brandhagen, Martine C. Duff, Constance L. Fisher, Karen K. Lowe, Carna E. Meyer, Maria A. Roberts, Kyle R. Tom, Aaron L. Washington Ii

United States Department of Justice: Publications

An extensive literature review and new post-irradiation experimental results are presented of genotyping blood stains and hair, and physical examinations of latent fingerprints, hairs, and fibers. Results indicate that successful development of nuclear short tandem repeat (STR) and mitochondrial DNA sequence profiles from human blood and hair evidence is possible—up to a point—following exposure to gamma, neutron, beta, and alpha radiation at several levels that would most likely be present at this type of crime scene (i.e., a “dirty bomb,” etc.). Commencing at gamma radiation levels between 90 and 900 kGy, DNA analysis using conventional DNA techniques was unsuccessful. In …

A Protocol For Obtaining Dna Barcodes From Plant And Insect Fragments Isolated From Forensic-Type Soils, Kelly A. Meiklejohn, Megan L. Jackson, Libby A. Stern, James M. Robertson

United States Department of Justice: Publications

Soil is often collected from a suspect’s tire, vehicle, or shoes during a criminal investigation and subsequently submitted to a forensic laboratory for analysis. Plant and insect material recovered in such samples is rarely analyzed, as morphological identification is difficult. In this study, DNA barcoding was used for taxonomic identifications by targeting the gene regions known to permit discrimination in plants [maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL)] and insects [cytochrome oxidase subunit I (COI)]. A DNA barcode protocol suitable for processing forensic-type biological fragments was developed and its utility broadly tested with …

Use Of The Lus In Sequence Allele Designations To Facilitate Probabilistic Genotyping Of Ngs-Based Str Typing Results, Rebecca S. Just, Jodi A. Irwin

United States Department of Justice: Publications

Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input. Yet to leverage the benefits of NGS for …

Amphibians And Reptiles Of United States Department Of Defense Installations, Christopher E. Petersen, Robert E. Lovich, Sarah Stallings

United States Navy: Publications

The U.S. Department of Defense (DoD) occupies approximately 10.1 million ha of land within the U.S. spanning most ecosystems contained therein. To date, no comprehensive agency-wide inventory of amphibian and reptile species has been compiled. We developed an amphibian and reptile species inventory for 415 DoD installations/sites and evaluated species diversity. The amphibian and reptile species confirmed present on DoD sites represent 66% of the total native species documented in the continental U.S. Snakes are the most widespread group found on DoD lands. Of the military services, Army sites have the greatest number of confirmed species, federally listed, state-listed, and …

Seroprevalence Survey For Microsporidia In Common Bottlenose Dolphin (Tursiops Truncatus): Example Of A Quantitative Approach Based On Immunoblotting, Guillaume Desoubeaux, Roman Peschke, Carolina Le-Bert, Venessa Fravel, Jeny Soto, Eric D. Jensen, Jennifer E. Flower, Randall Wells, Anja Joachim, Carolyn Cray

United States Navy: Publications

Little is known about microsporidiosis pathogenicity in cetaceans. Here we report seroprevalence of 76% for microsporidia in blood samples from common bottlenose dolphins (Tursiops truncatus), from animals managed under human care (n=108) or captured for health assessments (n=13) and released.

Augmented Reality Farm Mapper Development: Lessons Learned From An App Designed To Improve Rural Emergency Response, Bryan Weichelt, Aaron Yoder, Casper Bendixsen, Matthew Pilz, Gerald Minor, Matthew Keifer

United States Department of Veterans Affairs: Publications

Fire departments have right-of-entry to most commercial industrial sites and preemptively map them to identify the onsite resources and hazards they need to promptly and safely respond to an emergency event. This is not the case for private farms. Emergency responders are blind to resources and hazards prior to arrival and must spend critical minutes locating them during an emergency response at a farm location. The original 2013 Farm Mapping to Assist, Protect and Prepare Emergency Responders (Farm MAPPER) project was undertaken to develop a method to give emergency responders an up-to-date view of on-farm hazard information to safely and …

Prevalence Of Adhd In Publicly Insured Adults, Yanmin Zhu, Wie Liu, Yan Li, Xi Wang, Almut G. Winterstein

United States Food and Drug Administration: Publications

Objective: To estimate the prevalence of adult ADHD diagnosis and treatment in U.S. Medicaid beneficiaries. Method: Using outpatient, inpatient, and pharmacy billing records for patients eligible for Medicaid fee-for-service benefits within 29 states from 1999 to 2010, we estimated the annual prevalence of ADHD diagnosis and treatment. Results: The prevalence of ADHD diagnosis increased from 2.20 per 1,000 patients in 1999 to 10.57 in 2010. Likewise, prevalence of ADHD treatment increased from 1.95 per 1,000 patients in 1999 to 13.16 in 2010. Between 40% and 65%, patients had ADHD drug prescription fills 6 months after ADHD diagnosis, whereas 45% to …

Existing And Potential Statistical And Computational Approaches For The Analysis Of 3d Ct Images Of Plant Roots, Zheng Xu, Camilo Valdes, Jennifer Clarke

Department of Statistics: Faculty Publications

Scanning technologies based on X-ray Computed Tomography (CT) have been widely used in many scientific fields including medicine, nanosciences and materials research. Considerable progress in recent years has been made in agronomic and plant science research thanks to X-ray CT technology. X-ray CT image-based phenotyping methods enable high-throughput and non-destructive measuring and inference of root systems, which makes downstream studies of complex mechanisms of plants during growth feasible. An impressive amount of plant CT scanning data has been collected, but how to analyze these data efficiently and accurately remains a challenge. We review statistical and computational approaches that have been …

Development Of 11-Plex Mol-Pcr Assay For The Rapid Screening Of Samples For Shiga Toxin-Producing Escherichia Coli, Travis A. Woods, Heather M. Mendez, Sandy Ortega, Xiaorong Shi, David Marx, Jianfa Bai, Rodney A. Moxley, T. G. Nagaraja, Steven W. Graves, Alina Deshpande

Department of Statistics: Faculty Publications

Strains of Shiga toxin-producing Escherichia coli (STEC) are a serious threat to the health, with approximately half of the STEC related food-borne illnesses attributable to contaminated beef. We developed an assay that was able to screen samples for several important STEC associated serogroups (O26, O45, O103, O104, O111, O121, O145, O157) and three major virulence factors (eae, stx1, stx2) in a rapid and multiplexed format using the Multiplex oligonucleotide ligation-PCR (MOL-PCR) assay chemistry. This assay detected unique STEC DNA signatures and is meant to be used on samples from various sources related to beef production, providing a multiplex and high-throughput …

Application Of Transfer Learning For Cancer Drug Sensitivity Prediction, Saugato Rahman Dhruba, Raziur Rahman, Kevin Matlock, Souparno Ghosh, Ranadip Pal

Department of Statistics: Faculty Publications

Background: In precision medicine, scarcity of suitable biological data often hinders the design of an appropriate predictive model. In this regard, large scale pharmacogenomics studies, like CCLE and GDSC hold the promise to mitigate the issue. However, one cannot directly employ data from multiple sources together due to the existing distribution shift in data. One way to solve this problem is to utilize the transfer learning methodologies tailored to fit in this specific context.

Results: In this paper, we present two novel approaches for incorporating information from a secondary database for improving the prediction in a target database. The first …

Investigation Of Model Stacking For Drug Sensitivity Prediction, Kevin Matlock, Carlos De Niz, Raziur Rahman, Souparno Ghosh, Ranadip Pal

Department of Statistics: Faculty Publications

Background: A significant problem in precision medicine is the prediction of drug sensitivity for individual cancer cell lines. Predictive models such as Random Forests have shown promising performance while predicting from individual genomic features such as gene expressions. However, accessibility of various other forms of data types including information on multiple tested drugs necessitates the examination of designing predictive models incorporating the various data types.

Results: We explore the predictive performance of model stacking and the effect of stacking on the predictive bias and squarred error. In addition we discuss the analytical underpinnings supporting the advantages of stacking in reducing …

What Is My Role In Changing The System? A New Model Of Responsibility For Structural Injustice, Robin Zheng

Women's and Gender Studies Program: Faculty Publications

What responsibility do individuals bear for structural injustice? Iris Marion Young has offered the most fully developed account to date, the Social Connections Model. She argues that we all bear responsibility because we each causally contribute to structural processes that produce injustice. My aim in this article is to motivate and defend an alternative account that improves on Young’s model by addressing five fundamental challenges faced by any such theory. The core idea of what I call the Role-Ideal Model is that we are each responsible for structural injustice through and in virtue of our social roles, i.e. our roles …

The Promise Of Piezoelectric Polymers, Timothy D. Usher, Kimberley R. Cousins, Renwu Zhang, Stephen Ducharme

Stephen Ducharme Publications

Recent advances provide new opportunities in the field of polymer piezoelectric materials. Piezoelectric materials provide unique insights to the fundamental understanding of the solid state. In addition, piezoelectric materials have a wide range of applications, representing billions of dollars of commercial applications. However, inorganic piezoelectric materials have limitations that polymer ferroelectric materials can overcome, if certain challenges can be addressed. This mini-review is a practical summary of the current research and future directions in the investigation and application of piezoelectric materials with an emphasis on polymeric piezoelectric materials. We will assume that the reader is well versed in the subject …

Ncuwm Talk Abstracts 2018

Nebraska Conference for Undergraduate Women in Mathematics

No abstract provided.

Veterans And Agent Orange: Update 11 (2018) (2018), Irva Hertz-Picciotto, Nancy Berliner, Wendy B. Bernstein, Michael J. Carvan Iii, Aravinda Chakravarti, Dana C. Dolinoy, Mary A. Fox, Karl T. Kelsey, Molly L. Kile, Molly L. Kile, Andrew F. Olshan, Beate R. Ritz, Lori A. White

United States Department of Veterans Affairs: Publications

Contents

ACRONYMS AND ABBREVIATIONS xvii

SUMMARY 1

1 INTRODUCTION 17

Previous Veterans and Agent Orange Reports, 18

Charge to the Committee, 19

Information Gathering, 20

Organization of the Report, 21

2 BACKGROUND 25

The Current Population of Vietnam Veterans,25

Military Use of Herbicides in Vietnam, 27

Exposure of Different Groups of Vietnam Veterans, 30

Characterizing Exposure, 38

Determining Increased Risk in Vietnam Veterans, 43

Research At Nebraska, 2017-2018 Report, University Of Nebraska-Lincoln

Office of Research and Economic Development: Publications

This publication is a snapshot of the fiscal year’s activities. To read more stories about research and creativity at Nebraska, visit the online edition at https://research.unl.edu/annualreport/2018. Additional multimedia are available for many stories.

Seabirds As Regional Biomonitors Of Legacy Toxicants On An Urbanized Coastline, Corey A. Clatterbuck, Rebecca L. Lewison, Nathan G. Dodder, Catherine Zeeman, Kenneth Schiff

United States Fish and Wildlife Service: Publications

Seabirds are often cited as sentinels of the marine environment, but are rarely used in traditional ocean and coastal contaminant monitoring. Four classes of persistent organic pollutants (POPs, n=68) and three trace elements (mercury, selenium, and arsenic) were measured in the eggs of California least terns (Sterna antillarum browni), caspian terns (Hydroprogne caspia), double-crested cormorants (Phalacrocorax auritus), and western gulls (Larus occidentalis) that nest in the Southern California Bight. Building on a periodic five year regional monitoring program, we measured contaminant exposure and assessed the utility of seabirds as regional contaminant biomonitors. …

Altering Plant Defenses: Herbivore-Associated Molecular Patterns And Effector Arsenal Of Chewing Herbivores, Saumik Basu, Suresh Varsani, Joe Louis

Department of Entomology: Faculty Publications

Chewing herbivores, such as caterpillars and beetles, while feeding on the host plant, cause extensive tissue damage and release a wide array of cues to alter plant defenses. Consequently, the cues can have both beneficial and detrimental impacts on the chewing herbivores. Herbivore-associated molecular patterns (HAMPs) are molecules produced by herbivorous insects that aid them to elicit plant defenses leading to impairment of insect growth, while effectors suppress plant defenses and contribute to increased susceptibility to subsequent feeding by chewing herbivores. Besides secretions that originate from glands (e.g., saliva) and fore- and midgut regions (e.g., oral secretions) of chewing herbivores, …

2018 Annual Report Nebraska Game And Parks

Nebraska Game and Parks Commission: Publications

No abstract provided.