Digital Commons Network^™

A Generative Model Of Cognitive State From Task And Eye Movements, W. Joseph Macinnes, Amelia R. Hunt, Alasdair D. F. Clarke, Michael D. Dodd

Department of Psychology: Faculty Publications

The early eye tracking studies of Yarbus provided descriptive evidence that an observer’s task influences patterns of eye movements, leading to the tantalizing prospect that an observer’s intentions could be inferred from their saccade behavior. We investigate the predictive value of task and eye movement properties by creating a computational cognitive model of saccade selection based on instructed task and internal cognitive state using a Dynamic Bayesian Network (DBN). Understanding how humans generate saccades under different conditions and cognitive sets links recent work on salience models of low-level vision with higher level cognitive goals. This model provides a Bayesian, cognitive …

Factor Structure And Gender Invariance Testing For The Sport Anxiety Scale-2 (Sas-2), Leilani Madrigal, Vincenzo Roma, Todd Caze, Arthur C. Maerlender, Debra Hope

Center for Brain, Biology, and Behavior: Faculty Publications

This study aimed to provide further psychometric validation of the Sport Anxiety Scale-2 (SAS-2) by assessing the factor structure, invariance across gender, and convergent and divergent validity of the SAS-2 by correlating both related (i.e., anxiety sensitivity, brief fear of negative evaluation, intolerance of uncertainty, and negative affect) and unrelated constructs (i.e., positive affect, self-confidence). A total of 542 current and former competitive athletes completed a questionnaire through Amazon’s Mechanical Turk system. All data were collected via online survey. Participants were randomly assigned to an exploratory factor analysis (n = 271) and confirmatory factor analysis group (n = 271). Results …

Accumulating Data To Optimally Predict Obesity Treatment (Adopt): Recommendations From The Biological Domain, Michael Rosenbaum, Tanya Agurs-Collins, Molly S. Bray, Kevin D. Hall, Mark Hopkins, Maren Laughlin, Paul S. Maclean, Padma Maruvada, Cary R. Savage, Dana M. Small, Luke Stoeckel

Center for Brain, Biology, and Behavior: Faculty Publications

Background: The responses to behavioral, pharmacological, or surgical obesity treatments are highly individualized. The Accumulating Data to Optimally Predict obesity Treatment (ADOPT) project provides a framework for how obesity researchers, working collectively, can generate the evidence base needed to guide the development of tailored, and potentially more effective, strategies for obesity treatment. Objectives: The objective of the ADOPT biological domain subgroup is to create a list of high-priority biological measures for weight-loss studies that will advance the understanding of individual variability in response to adult obesity treatments. This list includes measures of body composition, energy homeostasis (energy intake and output), …

Left Lateralized Cerebral Glucose Metabolism Declines In Amyloid-Β Positive Persons With Mild Cognitive Impairment, Christopher M. Weise, Kewei Chen, Yinghua Chen, Xiaoying Kuang, Cary R. Savage, Eric M. Reiman

Center for Brain, Biology, and Behavior: Faculty Publications

Background: Previous publications indicate that Alzheimer's Disease (AD) related cortical atrophy may develop in asymmetric patterns, with accentuation of the left hemisphere. Since fluorodeoxyglucose positron emission tomography (FDG PET) measurements of the regional cerebral metabolic rate of glucose (rCMRgl) provide a sensitive and specific marker of neurodegenerative disease progression, we sought to investigate the longitudinal pattern of rCMRgl in amyloid-positive persons with mild cognitive impairment (MCI) and dementia, hypothesizing asymmetric declines of cerebral glucose metabolism. Methods: Using florbetapir PET and cerebrospinal fluid (CSF) measures to define amyloid-β (Aβ) positivity, 40 Aβ negative (Aβ-) cognitively unimpaired controls (CU; 76 ± 5y), …

Novel Biomarkers Of Physical Activity Maintenance In Midlife Women: Preliminary Investigation, Kelly A. Bosak, Vlad B. Papa, Morgan G. Brucks, Cary R. Savage, Joseph E. Donnelly, Laura E. Martin

Center for Brain, Biology, and Behavior: Faculty Publications

The precision health initiative is leading the discovery of novel biomarkers as important indicators of biological processes or responses to behavior, such as physical activity. Neural biomarkers identified by magnetic resonance imaging (MRI) hold promise to inform future research, and ultimately, for transfer to the clinical setting to optimize health outcomes. This study investigated resting-state and functional brain biomarkers between midlife women who were maintaining physical activity in accordance with the current national guidelines and previously acquired age-matched sedentary controls. Approval was obtained from the Human Subjects Committee. Participants included nondiabetic, healthy weight to overweight (body mass index 19–29.9 kg/m …

Development Of Ifox-Hunting As A Functional Genomic Tool And Demonstration Of Its Use To Identify Early Senescence-Related Genes In The Polyploid Brassica Napus, Juan Ling, Renjie Li, Chinedu Charles Nwafor, Junluo Cheng, Maoteng Li, Qing Xi, Jian Wu, Lu Gan, Qingyong Yang, Chao Liu, Ming Chen, Yongming Zhou, Edgar B. Cahoon, Chunyu Zhang

Center for Plant Science Innovation: Faculty Publications

Functional genomic studies of many polyploid crops, including rapeseed (Brassica napus), are constrained by limited tool sets. Here we report development of a gain-of-function platform, termed ‘iFOX (inducible Full-length cDNA OvereXpressor gene)-Hunting’, for inducible expression of B. napus seed cDNAs in Arabidopsis. A Gateway-compatible plant gene expression vector containing a methoxyfenozide-inducible constitutive promoter for transgene expression was developed. This vector was used for cloning of random cDNAs from developing B. napus seeds and subsequent Agrobacterium-mediated transformation of Arabidopsis. The inducible promoter of this vector enabled identification of genes upon induction that are otherwise lethal when constitutively overexpressed and …

Conventional And Hyperspectral Time-Series Imaging Of Maize Lines Widely Used In Field Trials, Zhikai Liang, Piyush Pandey, Vincent Stoerger, Yuhang Xu, Yumou Qiu, Yufeng Ge, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Background: Maize (Zea mays ssp. mays) is 1 of 3 crops, along with rice and wheat, responsible for more than one-half of all calories consumed around the world. Increasing the yield and stress tolerance of these crops is essential to meet the growing need for food. The cost and speed of plant phenotyping are currently the largest constraints on plant breeding efforts. Datasets linking new types of high-throughput phenotyping data collected from plants to the performance of the same genotypes under agronomic conditions across a wide range of environments are essential for developing new statistical approaches and computer …

Single-Molecule Sequencing And Optical Mapping Yields An Improved Genome Of Woodland Strawberry (Fragaria Vesca) With Chromosome-Scale Contiguity, Patrick P. Edger, Robert Vanburen, Marivi Colle, Thomas J. Poorten, Ching Man Wai, Chad E. Niederhuth, Elizabeth I. Alger, Shujun Ou, Charlotte B. Acharya, Jie Wang, Pete Callow, Michael R. Mckain, Jinghua Shi, Chad Collier, Zhiyong Xiong, Jeffrey P. Mower, Janet P. Slovin, Timo Hytonen, Ning Jiang, Kevin L. Childs, Steven J. Knapp

Center for Plant Science Innovation: Faculty Publications

Background: Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Findings: Here we utilized a robust, cost-effective approach to produce high-quality reference genomes.We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ~7.9 million base pairs (Mb), representing a ~300-fold improvement of the previous version. The vast majority (>99.8%) …

Identification Of Bottlenecks In The Accumulation Of Cyclic Fatty Acids In Camelina Seed Oil, Xiao-Hong Yu, Rebecca E. Cahoon, Patrick J. Horn, Hai Shi, Richa R. Prakash, Yuanheng Cai, Maegan Hearney, Kent D. Chapman, Edgar B. Cahoon, Jorg Schwender, John Shanklin

Center for Plant Science Innovation: Faculty Publications

Modified fatty acids (mFA) have diverse uses; for example, cyclopropane fatty acids (CPA) are feedstocks for producing coatings, lubricants, plastics and cosmetics. The expression of mFA-producing enzymes in crop and model plants generally results in lower levels of mFA accumulation than in their natural-occurring source plants. Thus, to further our understanding of metabolic bottlenecks that limit mFA accumulation, we generated transgenic Camelina sativa lines co-expressing Escherichia coli cyclopropane synthase (EcCPS) and Sterculia foetida lysophosphatidic acid acyltransferase (SfLPAT). In contrast to transgenic CPA-accumulating Arabidopsis, CPA accumulation in camelina caused only minor changes in seed weight, germination rate, oil accumulation and seedling …

Integrating Phylogenetic And Network Approaches To Study Gene Family Evolution: The Case Of The Agamous Family Of Floral Genes, Daniel Santana De Carvalho, James C. Schnable, Ana Maria R. Almeida

Center for Plant Science Innovation: Faculty Publications

The study of gene family evolution has benefited from the use of phylogenetic tools, which can greatly inform studies of both relationships within gene families and functional divergence. Here, we propose the use of a network-based approach that in combination with phylogenetic methods can provide additional support for models of gene family evolution. We dissect the contributions of each method to the improved understanding of relationships and functions within the well-characterized family of AGAMOUS floral development genes. The results obtained with the two methods largely agreed with one another. In particular, we show how network approaches can provide improved interpretations …

Functional Modeling Of Plant Growth Dynamics, Y. Xu, Y. Qiu, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

Recent advances in automated plant phenotyping have enabled the collection of time series measurements from the same plants of a wide range of traits at different developmental time scales. The availability of time series phenotypic datasets has increased interest in statistical approaches for comparing patterns of change among different plant genotypes and different treatment conditions. Two widely used methods of modeling growth with time are pointwise analysis of variance (ANOVA) and parametric sigmoidal curve fitting. Pointwise ANOVA yields discontinuous growth curves, which do not reflect the true dynamics of growth patterns in plants. In contrast, fitting a parametric model to …

Gipc Glcnac Glycosyltransferase, Toshiki Ishikawa, Lin Fang, Emilie A. Rennie, Julien Sechet, Jingwei Yan, Beibei Jing, William Moore, Edgar B. Cahoon, Henrik V. Scheller, Maki Kawai-Yamada, Jenny C. Mortimer

Center for Plant Science Innovation: Faculty Publications

Glycosylinositol phosphorylceramides (GIPCs), which have a ceramide core linked to a glycan headgroup of varying structure, are the major sphingolipids in the plant plasma membrane. Recently, we identified the major biosynthetic genes for GIPC glycosylation in Arabidopsis thaliana, and demonstrated that the glycan headgroup is essential for plant viability. However, the function of GIPCs and the significance of their structural variation are poorly understood. Here, we characterized the Arabidopsis glycosyltransferase GLUCOSAMINE INOSITOLPHOSPHORYLCERAMIDE TRANSFERASE1 (GINT1) and showed that it is responsible for the glycosylation of a subgroup of GIPCs found in seeds and pollen that contain N-acetylglucosamine (GlcNAc) and glucosamine …

Sma1, A Homolog Of The Splicing Factor Prp28, Has A Multifaceted Role In Mirna Biogenesis In Arabidopsis, Shengjun Li, Ran Xu, Aixia Li, Kan Liu, Liqing Gu, Mu Li, Hairui Zhang, Yueying Zhang, Shangshang Zhuang, Quanhui Wang, Gang Gao, Na Li, Chi Zhang, Yunhai Li, Bin Yu

Center for Plant Science Innovation: Faculty Publications

MicroRNAs (miRNAs) are a class of small non-coding RNAs that repress gene expression. In plants, the RNase III enzyme Dicer-like (DCL1) processes primary miRNAs (pri-miRNAs) into miRNAs. Here, we show that SMALL1 (SMA1), a homolog of the DEADbox pre-mRNA splicing factor Prp28, plays essential roles in miRNA biogenesis in Arabidopsis. A hypomorphic sma1-1 mutation causes growth defects and reduces miRNA accumulation correlated with increased target transcript levels. SMA1 interacts with the DCL1 complex and positively influences primiRNA processing. Moreover, SMA1 binds the promoter region of genes encoding pri-miRNAs (MIRs) and is required for MIR transcription. Furthermore, SMA1 also …

Generation And Evaluation Of Modified Opaque-2 Popcorn Suggests A Route To Quality Protein Popcorn, Ying Ren, Abou Yobi, Leandra Marshall, Ruthie Angelovici, Oscar Rodriguez, David R. Holding

Center for Plant Science Innovation: Faculty Publications

Introducing traits from dent corn to popcorn is challenging because it is difficult to recover adequate popping characteristics. QPM (Quality Protein Maize) is a dent corn variety carrying the opaque-2 (o2) mutation, specifying increased amounts of normally limiting essential amino acids, and modifier genes which restore the wild type vitreous kernel phenotype. In this study, we introgressed o2 and selected for endosperm modification using vitreousness and high 27-kD gamma zein content. In this way, we recovered high-lysine, fully poppable Quality Protein Popcorn (QPP). BC₂F₄ individuals with vitreous kernels were confirmed to be o2 mutants by …

Molecular Tools Enabling Pennycress (Thlaspi Arvense) As A Model Plant And Oilseed Cash Cover Crop, Michaela Mcginn, Winthrop B. Phippen, Ratan Chopra, Sunil Bansal, Brice A. Jarvis, Mary E. Phippen, Kevin M. Dorn, Maliheh Esfahanian, Tara J. Nazarenus, Edgar B. Cahoon, Timothy P. Durrett, M. David Marks, John C. Sedbrook

Center for Plant Science Innovation: Faculty Publications

Thlapsi arvense L. (pennycress) is being developed as a profitable oilseed cover crop for the winter fallow period throughout the temperate regions of the world, controlling soil erosion and nutrients run-off on otherwise barren farmland. We demonstrate that pennycress can serve as a user-friendly model system akin to Arabidopsis that is well-suited for both laboratory and field experimentation. We sequenced the diploid genome of the spring-type Spring 32-10 inbred line (1C DNA content of 539 Mb; 2n = 14), identifying variation that may explain phenotypic differences with winter-type pennycress, as well as predominantly a one-to-one correspondence with Arabidopsis genes, …

Lycophyte Plastid Genomics: Extreme Variation In Gc, Gene And Intron Content And Multiple Inversions Between A Direct And Inverted Orientation Of The Rrna Repeat, Jeffrey P. Mower, Peng-Fei Ma, Felix Grewe, Alex Taylor, Todd P. Michael, Robert Vanburen, Yin-Long Qiu

Center for Plant Science Innovation: Faculty Publications

Lycophytes are a key group for understanding vascular plant evolution. Lycophyte plastomes are highly distinct, indicating a dynamic evolutionary history, but detailed evaluation is hindered by the limited availability of sequences. Eight diverse plastomes were sequenced to assess variation in structure and functional content across lycophytes. Lycopodiaceae plastomes have remained largely unchanged compared with the common ancestor of land plants, whereas plastome evolution in Isoetes and especially Selaginella is highly dynamic. Selaginella plastomes have the highest GC content and fewest genes and introns of any photosynthetic land plant. Uniquely, the canonical inverted repeat was converted into a direct repeat (DR) …

The Role Of Type Iii Effectors From Xanthomonas Axonopodis Pv. Manihotis In Virulence And Suppression Of Plant Immunity, Cesar Augusto Medina, Paola Andrea Reyes, Cesar Augusto Trujillo, Juan Luis Gonzalez, David Alejandro Bejarano, Nathaly Andrea Montenegro, Jonathan M. Jacobs, Anna Joe, Silvia Restrepo, James R. Alfano, Adriana Bernal

Center for Plant Science Innovation: Faculty Publications

Xanthomonas axonopodis pv. manihotis (Xam) causes cassava bacterial blight, the most important bacterial disease of cassava. Xam, like other Xanthomonas species, requires type III effectors (T3Es) for maximal virulence. Xam strain CIO151 possesses 17 predicted T3Es belonging to the Xanthomonas outer protein (Xop) class. This work aimed to characterize nine Xop effectors present in Xam CIO151 for their role in virulence and modulation of plant immunity. Our findings demonstrate the importance of XopZ, XopX, XopAO1 and AvrBs2 for full virulence, as well as a redundant function in virulence between XopN and XopQ in susceptible cassava plants. We tested their role …

Xanthomonas Oryzae Pv. Oryzae Tale Proteins Recruit Ostfiiaγ1 To Compensate For The Absence Of Ostfiiaγ5 In Bacterial Blight In Rice, Wenxiu Ma, Lifang Zou, Zhiyuan Ji, Xiameng Xu, Zhengyin Xu, Yangyang Yang, James R. Alfano

Center for Plant Science Innovation: Faculty Publications

Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight (BB) of rice, uses transcription activator-like effectors (TALEs) to interact with the basal transcription factor gamma subunit OsTFIIAγ5 (Xa5) and activates the transcription of host genes. However, how OsTFIIAγ1, the other OsTFIIAγ protein, functions in the presence of TALEs remains unclear. In this study, we show that OsTFIIAγ1 plays a compensatory role in the absence of Xa5. The expression of OsTFIIAγ1, which is activated by TALE PthXo7, increases the expression of host genes targeted by avirulent and virulent TALEs. Defective OsTFIIAγ1 rice lines show reduced expression of the TALE-targeted …

Comparison Of Hematologic Effects Of Coronary Artery Bypass Grafting Surgery Performed With And Without Use Of Cardiopulmonary Bypass, Simon Kigwana

Yale Medicine Thesis Digital Library

Abstract: Coronary artery graft surgery (CABG) using a cardiopulmonary bypass (CPB)

pump to allow for stopping the heart, commonly designated as “on pump CABG” or

ONCAB, requires complete anticoagulation and is associated with significant

postoperative anemia. In addition, a reduction in postoperative platelet counts is relatively

common in large part due to heightened activation of hemostatic pathways and platelet

consumption secondary to blood passing through the CPB circuit. It has been

demonstrated that both anemia and nadir platelet counts after ONCAB are associated

with the incidence and severity of postoperative acute kidney injury (AKI). Over the past

several years, techniques …

Recurrent Neural Networks And Their Applications To Rna Secondary Structure Inference, Devin Willmott

Theses and Dissertations--Mathematics

Recurrent neural networks (RNNs) are state of the art sequential machine learning tools, but have difficulty learning sequences with long-range dependencies due to the exponential growth or decay of gradients backpropagated through the RNN. Some methods overcome this problem by modifying the standard RNN architecure to force the recurrent weight matrix W to remain orthogonal throughout training. The first half of this thesis presents a novel orthogonal RNN architecture that enforces orthogonality of W by parametrizing with a skew-symmetric matrix via the Cayley transform. We present rules for backpropagation through the Cayley transform, show how to deal with the Cayley …

New Frontiers 2018-19 Brochure

Annual Brochures

This year the series continues to grow and represent the interdisciplinary nature of biomedical research with seminars on diet and physiology, neuroscience, biomechanics, computational modeling, and medical visualization and communication.

Please join us in welcoming and learning from nationally recognized researchers and scientific communicators in our annual seminar series. You will learn about cutting-edge research that is changing the way we address problems in biological research and human health, the tools we use to study them, and the methods used to educate and inform patients.

Benzodiazepines I: Upping The Care On Downers: The Evidence Of Risks, Benefits And Alternatives, Jeffrey Guina, Brian Merrill

Psychiatry Faculty Publications

Benzodiazepines are some of the most commonly prescribed medications in the world. These sedative-hypnotics can provide rapid relief for symptoms like anxiety and insomnia, but are also linked to a variety of adverse effects (whether used long-term, short-term, or as needed). Many patients take benzodiazepines long-term without ever receiving evidence-based first-line treatments (e.g., psychotherapy, relaxation techniques, sleep hygiene education, serotonergic agents). This review discusses the risks and benefits of, and alternatives to benzodiazepines. We discuss evidence-based indications and contraindications, and the theoretical biopsychosocial bases for effectiveness, ineffectiveness and harm. Potential adverse effects and drug-drug interactions are summarized. Finally, both fast-acting/acute …

Repeatability Of The Heart Rate Variability Threshold During Treadmill Exercise, Shane Chambers

Senior Honors Projects, 2010-2019

Purpose: Heart rate variability threshold (HRVT) is a clinical parameter used to gain insight into autonomic balance. Various studies have validated the use of cycle ergometers in determining HRVT, although the literature lacks evidence that treadmill use is a viable means of determining this threshold. We examined the repeatability of HRVT occurrence using standard deviation of normal R-R intervals (SDNN), root mean square of successive differences of continuous R-R intervals (RMSSD), and standard deviation of instantaneous beat intervals (SD1) in college aged males using treadmill exercise to see if this is a reliable method of threshold determination.

Methods: Ten healthy, …

A Cure For Salmonella: Engaging Students In Pathogen Microbiology And Bioinformatics, Sophie Jurgensen

Senior Honors Projects, 2010-2019

Advances in Next Generation Sequencing (NGS) technology have generated a vast amount of publicly available genomic data, creating a need for students with training in computational analysis. This laboratory lesson is a course-based undergraduate research experience (CURE) focusing on environmental Salmonella, a common foodborne pathogen that is of great interest to public health laboratories but is relatively less virulent than most other such pathogens. As discovery is a central tenet of CUREs, students isolate novel Salmonella enterica and related strains from stream sediment, poultry litter, or other sources in the first half of the lesson (Module 1). They also …

Stem Stories, January 2018, #1, Ginger L'Heureux

STEM Stories

First Generation Series #1

The Mall: Writing From Butler University's First Year Seminar 2017-18, The Mall Staff

The Mall

No abstract provided.

Mechanical And Aerospace Engineering, 2017-2018, College Of Engineering And Applied Sciences

Mechanical and Aerospace Engineering News

• Letter from the Chair
• Introducing Dr. Jinseok Kim
• Use of 3D Printing at WMU Helps Borgess Cardiologist Plug Holes in the Heart
• Department of Mechanical and Aerospace Engineering Develops Semi-Virtual Reality Powered Wheelchair Simulator
• The Western Aerospace Launch Initiative (WALI)
• 2017 NSF I-Corps Experience of MAE team
• Matthew Baird's Internship Experiences at JPL and GRC
• More Department News
• Faculty Sabbaticals

2018-2019 Catalog, Wku Graduate School

Graduate School

Graduate School catalog regarding admissions, curriculum and policies.

Ua66/5 Department Of Agriculture 2018 Newsletter, Department Of Agriculture And Food Science

Agriculture Department Publications

No abstract provided.

Dr. Jonathan An Receives Ada Foundation Dentsply Sirona Research Award, American Dental Association

News Releases

This collection includes standard news releases, information kits and other documents distributed for publicity, information, announcements of events, etc. as issued from the ADA. Items included in this collection are archival and any costs, links, contact information, or other figures may be out of date. Please contact the ADA to verify information.