2019-2020 Open Access Publishing Fund
Permanent URI for this collectionhttp://hdl.handle.net/10342/7572
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Item Open Access Circular Single-Stranded DNA Virus (Microviridae: Gokushovirinae: Jodiemicrovirus) Associated with the Pathobiome of the Flat-Back Mud Crab, Eurypanopeus depressus(2019-11-21) Bojko, Jamie; McCoy, Krista A.; Behringer, Donald C.; Blakeslee, AprilA single-stranded DNA (ssDNA) virus is presented from a metagenomic data set derived from Alphaproteobacteria-infected hepatopancreatic tissues of the crab Eurypanopeus depressus. The circular virus genome (4,768 bp) encodes 14 hypothetical proteins, some similar to other bacteriophages (Microviridae). Based on its relatedness to other Microviridae, this virus represents a member of a novel genus.Item Open Access Life in a contaminant milieu: PPCP mixtures generate unpredictable outcomes across trophic levels and life stagest(2019-12-05) Parrish, Samantha C.; Dormio, Samantha M.; Richards, Stephanie L.; McCoy, Krista A.; McCoy, Michael W.Nearly all aquatic ecosystems are affected by sublethal levels of anthropogenic chemical contamination, but other agents of large‐scale anthropogenic disruption of ecosystems have received more attention. Consequently, ecologists do not fully appreciate how sublethal contaminant exposure affects ecosystems. Sublethal contaminants can affect ecological systems directly via their impacts on an organism's fitness or indirectly by changing the strengths of species interactions. This study investigated how an emerging class of contaminants—pharmaceuticals and personal care products (PPCPs)—influences food webs by affecting the biology of organisms and by interfering with predator–prey interactions. Specifically, we investigated how three common PPCPs—caffeine, DEET (N, N‐diethyl‐meta‐toluamide), and triclosan—affect the strength of the interaction between a common mosquito predator (i.e., mosquito fish) and mosquito larvae as well as how these PPCPS affect mosquito survival, life history traits, and oviposition site choices. We found that all three PPCPs, individually and combined as a mixture, reduced predator consumption rates. Relative to a contaminant‐free control, the presence of predator cues reduced mosquito oviposition and larval abundance for all PPCP treatments except for DEET. Predator cues reduced mosquito adult emergence across PPCP treatments; however, mosquitoes that were exposed to caffeine did not emerge as adults even in the absence of predator cues. This study shows that the effects of PPCPs are diverse and can interact with mosquitoes and their predators in ways that cannot be predicted by their individual effects. In a contaminated world, ecologists need to better understand how sublethal concentrations of ubiquitous, biologically active pollutants might challenge what we think we know about how ecological systems function.Item Open Access Differential gene expression and gene variants drive color and pattern development in divergent color morphs of a mimetic poison frog(2019-07-21) Stuckert, Adam M. M.; Linderoth, Tyler; MacManes, Matthew D.; Summers, KyleEvolutionary biologists have long investigated the ecological contexts, evolutionary forces, and proximate mechanisms that produce the diversity of animal coloration we see in the natural world. In aposematic species, color and pattern is directly tied to survival and thus understanding the origin of the phenotype has been a focus of both theoretical and empirical inquiry. In order to better understand this diversity, we examined gene expression in skin tissue during development in four different color morphs of the aposematic mimic poison frog, Ranitomeya imitator. We identified a suite of candidate color-related genes a priori and identified the pattern of expression in these genes over time, differences in expression of these genes between the mimetic morphs, and genetic variants that differ between color morphs. We identified several candidate color genes that are differentially expressed over time or across populations, as well as a number of color genes with fixed genetic variants between color morphs. Many of the color genes we discovered in our dataset are involved in the canonical Wnt signaling pathway, including several fixed SNPs between color morphs. Further, many genes in this pathway were differentially expressed at different points in development (e.g., lef1, tyr, tyrp1). Importantly, Wnt signaling pathway genes are overrepresented relative to expression in Xenopus tropicalis. Taken together, this provides evidence that the Wnt signaling pathway is contributing to color pattern production in R. imitator, and is an excellent candidate for producing some of the differences in color pattern between morphs. In addition, we found evidence that sepiapterin reductase is likely important in the production of yellow-green coloration in this adaptive radiation. Finally, two iridophore genes (arfap1, gart) draw a strong parallel to previous work in another dendrobatid, indicating that these genes are also strong candidates for differential color production. We have used high throughput sequencing throughout development to examine the evolution of coloration in a rapid mimetic adaptive radiation and found that these divergent color patterns are likely to be affected by a combination of developmental patterns of gene expression, color morph-specific gene expression, and color morph-specific gene variants.Item Open Access Customer Reviews Analysis With Deep Neural Networks for E-Commerce Recommender Systems(2019-08-26) SHOJA, BABAK MALEKI; TABRIZI, NASSEHAn essential prerequisite of an effective recommender system is providing helpful information regarding users and items to generate high-quality recommendations. Written customer review is a rich source of information that can offer insights into the recommender system. However, dealing with the customer feedback in text format, as unstructured data, is challenging. In this research, we extract those features from customer reviews and use them for similarity evaluation of the users and ultimately in recommendation generation. To do so, we developed a glossary of features for each product category and evaluated them for removing irrelevant terms using Latent Dirichlet Allocation. Then, we employed a deep neural network to extract deep features from the reviews-characteristics matrix to deal with sparsity, ambiguity, and redundancy. We applied matrix factorization as the collaborative ltering method to provide recommendations. As the experimental results on the Amazon.com dataset demonstrate, our methodology improves the performance of the recommender system by incorporating information from reviews and produces recommendations with higher quality in terms of rating prediction accuracy compared to the baseline methods.Item Open Access MELPF Version 1: Modeling Error Learning Based Post-Processor Framework for Hydrologic Models Accuracy Improvement(2019-09-23) Wu, Rui; Yang, Lei; Chen, Chao; Ahmad, Sajjad; Dascalu, Sergiu M.This paper studies how to improve the accuracy of hydrologic models using machine-learning models as postprocessors and presents possibilities to reduce the workload to create an accurate hydrologic model by removing the calibration step. It is often challenging to develop an accurate hydrologic model due to the time-consuming model calibration procedure and the nonstationarity of hydrologic data. Our findings show that the errors of hydrologic models are correlated with model inputs. Thus motivated, we propose a modeling-error-learning-based post-processor framework by leveraging this correlation to improve the accuracy of a hydrologic model. The key idea is to predict the differences (errors) between the observed values and the hydrologic model predictions by using machine-learning techniques. To tackle the nonstationarity issue of hydrologic data, a movingwindow- based machine-learning approach is proposed to enhance the machine-learning error predictions by identifying the local stationarity of the data using a stationarity measure developed based on the Hilbert–Huang transform. Two hydrologic models, the Precipitation–Runoff Modeling System (PRMS) and the Hydrologic Modeling System (HEC-HMS), are used to evaluate the proposed framework. Two case studies are provided to exhibit the improved performance over the original model using multiple statistical metrics.Item Open Access Construction of realistic hybrid computational fetal phantoms from radiological images in three gestational ages for radiation dosimetry applications(2019-10-10) Makkia, Rasha; Nelson, Keith; Zaidi, Habib; Dingfelder, MichaelRadiation exposure and associated radiation risks are major concerns for fetal development for pregnant patients who undergo radiation therapy or diagnostic imaging procedures. In order to accurately estimate the radiation dose to the fetus and assess the uncertainty of fetal position and rotation, three hybrid computational fetus phantoms were constructed using magnetic resonance imaging (MRI) for each fetus model as a starting point to construct a complete anatomically accurate fetus, gravid uterus, and placenta. A total of 27 fetal organs were outlined from radiological images via the Velocity Treatment Planning System. The DICOM-Structure set was imported to Rhinoceros software for further reconstruction of 3D fetus phantom model sets. All fetal organ masses were compared with ICRP-89 reference data. Our fetal model series corresponds to 20, 31, and 35 weeks of pregnancy, thus covering the second and third trimester. Fetal positions and locations were carefully adapted to represent the real fetus locations inside the uterus for each trimester of pregnancy. The new series of hybrid computational fetus models together with pregnant female models can be used in evaluating fetal radiation doses in diagnostic imaging and radiotherapy procedures.xt-tItem Open Access Imaging of morphological and biochemical hallmarks of apoptosis with optimized optogenetic tools(2019-10-03) Godwin, Walton C.; Hoffmann, George F.; Gray, Taylor J.; Hughes, Robert M.Creation of optogenetic switches for specific activation of cell death pathways can provide insights into apoptosis and could also form a basis for noninvasive, next-generation therapeutic strategies. Previous work has demonstrated that cryptochrome 2 (Cry2)/cryptochrome-interacting β helix–loop–helix (CIB), a blue light–activated protein–protein dimerization module from the plant Arabidopsis thaliana, together with BCL2-associated X apoptosis regulator (BAX), an outer mitochondrial membrane–targeting pro-apoptotic protein, can be used for light-mediated initiation of mitochondrial outer membrane permeabilization (MOMP) and downstream apoptosis. In this work, we further developed the original light-activated Cry2-BAX system (hereafter referred to as OptoBAX) by improving the photophysical properties and light-independent interactions of this optogenetic switch. The resulting optogenetic constructs significantly reduced the frequency of light exposure required for membrane permeabilization activation and also decreased dark-state cytotoxicity. We used OptoBAX in a series of experiments in Neuro-2a and HEK293T cells to measure the timing of the dramatic morphological and biochemical changes occurring in cells after light-induced MOMP. In these experiments, we used OptoBAX in tandem with fluorescent reporters to image key events in early apoptosis, including membrane inversion, caspase cleavage, and actin redistribution. We then used these data to construct a timeline of biochemical and morphological events in early apoptosis, demonstrating a direct link between MOMP-induced redistribution of actin and apoptosis progression. In summary, we created a next-generation Cry2/CIB–BAX system requiring less frequent light stimulation and established a timeline of critical apoptotic events, providing detailed insights into key steps in early apoptosis.Item Open Access Developing high performance concrete for precast/prestressed concrete industry(2019-12) Akhnoukh, Amin K.; Elia, HalaHigh performance concrete (HPC) is a new class of concrete that has superior characteristics compared to conventional concrete. Despite of its superior characteristics, HPC is not widely used in local and international markets due to its high constituent materials cost. This paper presents the research done to develop economic HPC mixes using local materials and conventional mixing and curing techniques. HPC characteristics were attained using supplementary cementitious materials as silica fume and class C fly in partial replacement of Portland cement. Superplasticizers were used to maintain a high flowing ability using a low water-to-powder ratio. Concrete mixes were produced using a high energy mixer to maintain sufficient mix consistency. As a result, concrete mixes with 24 -h compressive strength of 70 MPa and 28-day strength of 105 MPa were produced. Concrete samples tested for expansion using accelerated mortar bar test (AMBT) showed that developed concrete is not susceptible to alkali-silica reaction. Improved characteristics can be used in improving the performance of concrete construction projects, reduce required maintenance, and increase construction projects life-span.Item Open Access Measuring Workplace Discrimination among Sexual and Gender Minority Workers(2019-11-01) Lee, Joseph G. L.; Chaney, Beth H.; Cabacungan, Ashley N.As inequities in health for sexual and gender minority (SGM; eg, lesbian, gay, bisexual, and transgender [LGBT]) populations become increasingly well documented, it is important to investigate causes of inequities to inform intervention work. One area of importance is in employment discrimination, as there are limited or no protections against sexual orientation and gender identity discrimination in approximately half of US states. We sought to assess the internal consistency and validity of a brief, adapted scale to measure SGM workplace discrimination. Methods: We modified an existing workplace age discrimination scale to assess SGM workplace discrimination. We assessed internal consistency, criterion validity, construct validity, and conducted a confirmatory factor analysis. Data came from a convenience sample of employed, SGM-identified adults (N = 124) attending a pride festival in Durham, NC, in September 2016. Results: The 5-item scale was significantly associated with poorer health, greater internalized homonegativity, reporting workplace bullying, SGM isolation, gender expression discrimination, and having filed a formal complaint of workplace discrimination. The scale had a single factor solution. Conclusions: This 5-item scale may be useful in efficiently documenting and addressing SGM workplace discrimination; it assesses material forms of discrimination (eg, pay and job tasks assigned) against SGM employees.Item Open Access An endemic plant and the plant-insect visitor network of a dune ecosystem(2019-04) Jolls, Claudia L.; Inkster, Jaclyn N.; Scholtens, Brian G.; Vitt, Pati; Havens, KayriNetwork theory increasingly is used to quantify and evaluate mutualistic interactions, such as those among plants and their flower-visiting insects or pollinators. Some plant species have been shown to be important in community structure using network metrics; however, the roles of plant taxa, particularly rare species, are not well understood. Pitcher's thistle (Cirsium pitcheri), a threatened endemic of Great Lakes shorelines, flowers late-June to early-August, when other floral resources may be less abundant or unavailable. We performed 10 min insect visitor observations on all insect pollinated plants in 44–10 m by 10 m plots at Sturgeon Bay, northern lower MI, USA, during C. pitcheri flowering and recorded plant species, number of open flowers, species of insect visiting, and number of visits by insects. Pitcher's thistle received 18.2% of all 600 recorded visits, 61.1% more than the next most visited plant. Pitcher's thistle also received visits from 22 of the 59 different insect species in the network, twice as many as the next most visited plant species. Species-level network analysis metrics showed that Pitcher's thistle was most generalized, with greatest species strength, betweenness, and connectance scores of any other plant taxon, demonstrating network topological importance. Pitcher's thistle received significantly more insect visits relative to its abundance that did any other plant species. Therefore, conservation of C. pitcheri and of other rare taxa, particularly in xeric and low diversity systems, can be significant beyond species-level management and may extend to conservation of the plant-insect community.