Digital Commons Network^™

Metabolic Network Analysis Of Filamentous Cyanobacteria, Daniel Alexis Norena-Caro

LSU Doctoral Dissertations

Cyanobacteria were the first organisms to use oxygenic photosynthesis, converting CO₂ into useful organic chemicals. However, the chemical industry has historically relied on fossil raw materials to produce organic precursors, which has contributed to global warming. Thus, cyanobacteria have emerged as sustainable stakeholders for biotechnological production. The filamentous cyanobacterium Anabaena sp. UTEX 2576 can metabolize multiple sources of Nitrogen and was studied as a platform for biotechnological production of high-value chemicals (i.e., pigments, antioxidants, vitamins and secondary metabolites). From a Chemical engineering perspective, the biomass generation in this organism was thoroughly studied by interpreting the cell as a microbial …

Data-Driven Modeling And Prediction For Reservoir Characterization And Simulation Using Seismic And Petrophysical Data Analyses, Xu Zhou

LSU Doctoral Dissertations

This study explores the application of data-driven modeling and prediction in reservoir characterization and simulation using seismic and petrophysical data analyses. Different aspects of the application of data-driven modeling methods are studied, which include rock facies classification, seismic attribute analyses, petrophysical properties prediction, seismic facies segmentation, and reservoir dimension reduction.

The application of using petrophysical well logs to predict rock facies is explored using different data analytics methods including decision tree, random forest, support vector machine and neural network. Different models are trained from a set of well logs and pre-interpreted rock facies data. Among the compared methods, the random …

Empathy, Fiction, And An Educational Ecosystem: A Narrative Case Study Of A High School Ela Classroom, Danielle Marie Klein

LSU Doctoral Dissertations

This study explores how empathy exists, as an experience, in an English Language Arts classroom. The research was conducted in an 11^th grade classroom during an instructional unit with Arthur Miller’s The Crucible as the anchor text. The study relies upon Transactional Reader Response Theory (Rosenblatt, 1988) to justify the exploration of the aesthetic, evocative nature of a text. Narrative inquiry methodology was used to collect and assemble the instances of empathy as inspired by the play. Guided by Doll’s (1993) premise of the classroom as an ecological, open system with multiple contributing forces, data was collected through classroom …

Identifying Human Trafficking Networks In Louisiana By Using Authorship Attribution And Network Modeling, Hassan Marzoughi Ardakani

LSU Doctoral Dissertations

Human trafficking or modern slavery is a problem that has plagued every U.S. state, in both urban and rural areas. During the past decades, online advertisements for sex trafficking have rapidly increased in numbers. The advancement of the Internet and smart phones have made it easier for sex traffickers to contact and recruit their victims and advertise and sell them online. Also, they have made it more difficult for law enforcement to trace the victims and identify the traffickers. Sadly, more than fifty percent of the victims of sex trafficking are children, many of which are exploited through the Internet. …

Investigating Geochemical Processes Of Fluid-Rock Interactions On Materials Related To Energy And Environment, Zelong Zhang

LSU Doctoral Dissertations

Understanding the potential processes of radionuclides released from nuclear waste forms is essential to the safe disposal and containment of nuclear waste. Iodoapatite, a potential waste form for radioiodine, was chosen as a model system to examine the impact by common aqueous anions on iodine release processes. Four semi-dynamic leaching tests were performed using 0.1 mol/L NaCl, Na₂CO₃, Na₃PO₄, and Na₂SO₄ solutions respectively under 90 °C, 1 bar, fixed S/V ratio 5/m (sample surface area to solution volume), and with 24-hour replacement of the leaching solutions. Solution analysis and …

Insights Into Desiccation Tolerance: Properties Of Late Embryogenesis Abundant Proteins From Embryos Of Artemia Franciscana, Blase Matthew Leblanc

LSU Doctoral Dissertations

LEA proteins are a family of intrinsically disordered proteins that are expressed in various life stages of anhydrobiotic organisms and have been strongly associated with survival during water stress. The brine shrimp Artemia franciscana is the only known anhydrobiotic animal that expresses LEA proteins from Groups 1, 3, and 6. Here, I report that AfrLEA6, a novel Group 6 LEA protein, is most highly expressed in embryos during diapause and decreases throughout pre-emergence development. Notably, there is an acute drop in expression upon termination of the diapause state and the titer of AfrLEA6 during diapause is 10-fold lower than values …

Neural Stimulator, Jose A. Parodi Amaya, Edward F. Austin, Jin-Woo Choi

Pennington Biomedical Research Center Patents

Methods and apparatus are disclosed relating to the stimulating of tissue including nerve tissue based on combinations of capacitors and resistors. Application and removal of voltage to an electrical circuit is taught as part of a method of creating voltage waveforms for nerve and other tissue with such waveforms creating neural signals. The electrical circuits taught may, include a first electrical node grounded through a first resistor; a second electrical node grounded through a second resistor; a first capacitor connected to both the first electrical node and the second electrical node; a second capacitor separating the second electrical node from …

Evidence Of Pathogen-Induced Immunogenetic Selection Across The Large Geographic Range Of A Wild Seabird, Hila Levy, Stephen R. Fiddaman, Julianna A. Vianna, Daly Noll, Gemma Clucas, Jasmine K. H. Sidhu, Michael J. Polito, Charles A. Bost, Richard A. Phillips, Sarah Crofts, Gary D. Miller, Pierre Pistorius, Francesco Bonnadonna, Celine Le Bohec, Andres Barbosa, Phil Trathan, Andrea Raya Rey, Laurent A. F. Frantz, Tom Hart, Adrian L. Smith

Faculty Publications

Over evolutionary time, pathogen challenge shapes the immunepheno type of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between ''different clades. Inthis study, we examine the …

Effects Of A Tropical Cyclone On Salt Marsh Insect Communities And Post-Cyclone Reassembly Processes, Xuan Chen, Benjamin J. Adams, William J. Platt, Linda M. Hooper-Bùi

Faculty Publications

© 2020 The Authors. Ecography published by John Wiley & Sons Ltd on behalf of Nordic Society Oikos Concepts regarding effects of recurrent natural disturbances and subsequent responses of communities are central to ecology and conservation biology. Tropical cyclones constitute major disturbances producing direct effects (damage, mortality) in many coastal communities worldwide. Subsequent reassembly involves changes in composition and abundance for which the underlying mechanisms (deterministic and stochastic processes) are still not clear, especially for mobile organisms. We examined tropical cyclone-induced changes in composition and reassembly of entire insect communities in 16 Louisiana coastal salt marshes before and after Hurricane …

Altered Gut Microbiota In Infants Is Associated With Respiratory Syncytial Virus Disease Severity, Jeffrey N. Harding, David Siefker, Luan Vu, Dahui You, John Devincenzo, J. F. Pierre, Stephania A. Cormier

Faculty Publications

© 2020 The Author(s). Background: Respiratory syncytial virus (RSV) is the number one cause of lower respiratory tract infections in infants. There are still no vaccines or specific antiviral therapies against RSV, mainly due to the inadequate understanding of RSV pathogenesis. Recent data suggest a role for gut microbiota community structure in determining RSV disease severity. Our objective was to determine the gut microbial profile associated with severe RSV patients, which could be used to help identify at-risk patients and develop therapeutically protective microbial assemblages that may stimulate immuno-protection. Results: We enrolled 95 infants from Le Bonheur during the 2014 …

A Simple Index To Quantify And Compare The Magnitude Of Intraspecific Geographic Plumage Colour Variation In Typical Antbirds (Aves: Passeriformes: Thamnophilidae), R S. Marcondes, R T. Brumfield

Faculty Publications

Intraspecific geographic phenotypic variation is a crucial theme in evolutionary biology. Comparing its magnitude across species can provide insights into its ecological and genetic correlates. Here, we developed an index, which we dub the V index, to quantify intraspecific plumage colour variation in typical antbirds (Thamnophilidae), a family which has long interested ornithologists due to a high prevalence of intraspecific variation. The V index is based on a bivariate colour space defined by brightness and redness. Its value for each species equals the mean area occupied by each of its subspecies in that colour space, divided by the area of …

Identification Of Light Sources Using Machine Learning, Chenglong You, Mario A. Quiroz-Juárez, Aidan Lambert, Narayan Bhusal, Chao Dong, Armando Perez-Leija, Amir Javaid, Roberto De J. León-Montiel, Omar S. Magaña-Loaiza

Faculty Publications

The identification of light sources represents a task of utmost importance for the development of multiple photonic technologies. Over the last decades, the identification of light sources as diverse as sunlight, laser radiation, and molecule fluorescence has relied on the collection of photon statistics or the implementation of quantum state tomography. In general, this task requires an extensive number of measurements to unveil the characteristic statistical fluctuations and correlation properties of light, particularly in the low-photon flux regime. In this article, we exploit the self-learning features of artificial neural networks and the naive Bayes classifier to dramatically reduce the number …

A Noble-Transition Alloy Excels At Hot-Carrier Generation In The Near Infrared, Sara K.F. Stofela, Orhan Kizilkaya, Benjamin T. Diroll, Tiago R. Leite, Mohammad M. Taheri, Daniel E. Willis, Jason B. Baxter, William A. Shelton, Phillip T. Sprunger, Kevin M. Mcpeak

Faculty Publications

Above-equilibrium “hot”-carrier generation in metals is a promising route to convert photons into electrical charge for efficient near-infrared optoelectronics. However, metals that offer both hot-carrier generation in the near-infrared and sufficient carrier lifetimes remain elusive. Alloys can offer emergent properties and new design strategies compared to pure metals. Here, it is shown that a noble-transition alloy, AuxPd1−x, outperforms its constituent metals concerning generation and lifetime of hot carriers when excited in the near-infrared. At optical fiber wavelengths (e.g., 1550 nm), Au50Pd50 provides a 20-fold increase in the number of ≈0.8 eV hot holes, compared to Au, and a threefold increase …

Fine Structure Of Angular Distribution Of X-Ray Transition Radiation From Multilayered Radiator In Geant4, A. A. Savchenko, A. A. Tishchenko, D. Yu Sergeeva, N. Belyaev, M. Cherry, F. Dachs, S. Doronin, K. Filippov, P. Fusco, F. Gargano, S. Konovalov, F. Loparco, V. Mascagna, M. N. Mazziotta, S. Nechaeva, D. Ponomarenko, A. Romaniouk, E. J. Schioppa, S. Smirnov, Y. Smirnov, M. Soldani, P. Spinelli, M. N. Strikhanov, P. Teterin, V. O. Tikhomirov, K. Vorobev, K. Zhukov

Faculty Publications

The present version of the Transition Radiation (TR) simulation module implemented in the Geant4 toolkit describes very well experimental data for the TR energy distribution; however, it does not allow reproducing the details of angular distribution at small angles. In order to solve this problem, corrections to the existing x-ray TR module in Geant4 are proposed. With these corrections, the results of the simulations are in a good agreement with the angular TR distributions predicted by theory and obtained in the test beam measurements using a 480 um Si pixel detector and Mylar radiator.

Biomolecular Complex Viewed By Dynamic Nuclear Polarization Solid-State Nmr Spectroscopy, Arnab Chakraborty, Fabien Deligey, Jenny Quach, Frederic Mentink-Vigier, Ping Wang, Tuo Wang

Faculty Publications

© 2020 Portland Press Ltd. All rights reserved. Solid-state nuclear magnetic resonance (ssNMR) is an indispensable tool for elucidating the structure and dynamics of insoluble and non-crystalline biomolecules. The recent advances in the sensitivity-enhancing technique magic-angle spinning dynamic nuclear polarization (MAS-DNP) have substantially expanded the territory of ssNMR investigations and enabled the detection of polymer interfaces in a cellular environment. This article highlights the emerging MAS-DNP approaches and their applications to the analysis of biomolecular composites and intact cells to determine the folding pathway and ligand binding of proteins, the structural polymorphism of low-populated biopolymers, as well as the physical …

Solid-State Nmr Of Plant And Fungal Cell Walls: A Critical Review, Wancheng Zhao, Liyanage D. Fernando, Alex Kirui, Fabien Deligey, Tuo Wang

Faculty Publications

© 2020 Elsevier Inc. The cell walls of plants and microbes are a central source for bio-renewable energy and the major targets of antibiotics and antifungal agents. It is highly challenging to determine the molecular structure of complex carbohydrates, protein and lignin, and their supramolecular assembly in intact cell walls. This article selectively highlights the recent breakthroughs that employ 13C/15N solid-state NMR techniques to elucidate the architecture of fungal cell walls in Aspergillus fumigatus and the primary and secondary cell walls in a large variety of plant species such as Arabidopsis, Brachypodium, maize, and spruce. Built upon these pioneering studies, …

Reduction Of Phakopsora Pachyrhizi Infection On Soybean Through Host- And Spray-Induced Gene Silencing, Dongfang Hu, Zhi Yuan Chen, Chunquan Zhang, Mala Ganiger

Faculty Publications

Asian soybean rust (ASR), caused by the obligate fungal pathogen Phakopsora pachyrhizi, often leads to significant yield losses and can only be managed through fungicide applications currently. In the present study, eight urediniospore germination or appressorium formation induced P. pachyrhizi genes were investigated for their feasibility to suppress ASR through a bean pod mottle virus (BPMV)-based host-induced gene silencing (HIGS) strategy. Soybean plants expressing three of these modified BPMV vectors suppressed the expression of their corresponding target gene by 45%–80%, fungal biomass accumulation by 58%–80%, and significantly reduced ASR symptom development in soybean leaves after the plants were inoculated with …

A Note On Species Richness And The Variance Of Epidemic Severity, Peter Shaffery, Bret D. Elderd, Vanja Dukic

Faculty Publications

© 2020, Springer-Verlag GmbH Germany, part of Springer Nature. The commonly observed negative correlation between the number of species in an ecological community and disease risk, typically referred to as “the dilution effect”, has received a substantial amount of attention over the past decade. Attempts to test this relationship experimentally have revealed that, in addition to the mean disease risk decreasing with species number, so too does the variance of disease risk. This is referred to as the “variance reduction effect”, and has received relatively little attention in the disease-diversity literature. Here, we set out to clarify and quantify some …

Multiscale-Spectral Gfem And Optimal Oversampling, Ivo Babuška, Robert Lipton, Paul Sinz, Michael Stuebner

Faculty Publications

In this work we address the Multiscale Spectral Generalized Finite Element Method (MS-GFEM) developed in Babuška and Lipton (2011). We outline the numerical implementation of this method and present simulations that demonstrate contrast independent exponential convergence of MS-GFEM solutions. We introduce strategies to reduce the computational cost of generating the optimal oversampled local approximating spaces used here. These strategies retain accuracy while reducing the computational work necessary to generate local bases. Motivated by oversampling we develop a nearly optimal local basis based on a partition of unity on the boundary and the associated A-harmonic extensions.

Vitamin D Actions In Neurons Require The Pi3k Pathway For Both Enhancing Insulin Signaling And Rapid Depolarizing Effects, Silvania Da Silva Teixeira, Keisha Harrison, Munachismo Uzodike, Kimal Rajapakshe, Cristian Coarfa, Yanlin He, Yong Xu, Stephanie Sisley

Division of Basic Science Faculty Publications

Despite correlations between low vitamin D levels and diabetes incidence/severity, supplementation with vitamin D has not been widely effective in improving glucose parameters. This may be due to a lack of knowledge regarding how low vitamin D levels physiologically affect glucose homeostasis. We have previously shown that the brain may be a critical area for vitamin D-mediated action on peripheral glucose levels. However, the mechanisms for how vitamin D acts in the brain are unknown. We utilized a multimodal approach to determine the mechanisms by which vitamin D may act in the brain. We first performed an unbiased search (RNA-sequencing) …

Resistant Starch Has No Effect On Appetite And Food Intake In Individuals With Prediabetes, Ursula White, Courtney M. Peterson, Robbie A. Beyl, Corby K. Martin, Eric Ravussin

Clinical Research Faculty Publications

Background: Type 2 resistant starch (RS2) has been shown to improve metabolic health outcomes and may increase satiety and suppress appetite and food intake in humans. Objective: This study assessed whether 12 weeks of daily RS2 supplementation could influence appetite perception, food intake, and appetite-related gut hormones in adults with prediabetes, relative to the control (CTL) group. Design: The study was a randomized controlled trial and analysis of secondary study end points. Participants/setting: Sixty-eight adults (body mass index ≥27) aged 35 to 75 years with prediabetes were enrolled in the study at Pennington Biomedical Research Center (2012 to 2016). Fifty-nine …

Projecting Stand Survival And Basal Area Based On A Self-Thinning Model For Chinese Fir Plantations, Xiongqing Zhang, Quang V. Cao, Hanchen Wang, Aiguo Duan, Jianguo Zhang

Faculty Publications

The self-thinning rule has played a critical role in controlling stand stocking and modeling stand development in forest stands. Chinese fir (Cunninghamia lanceolata) is a native and fast-growing tree species used for timber production and is widely grown in southern China. Effective management of this important tree species requires accurate and reasonable predictions of stand growth and survival. Remeasured data from 48 plots distributed in Fujian, Jiangxi, Guangxi, and Sichuan provinces were used to develop models to predict stand survival and basal area based on the self-thinning trajectories. These trajectories were constructed using a self-thinning slope of -1.605, as suggested …

Automated White Matter Hyperintensity Segmentation Using Bayesian Model Selection: Assessment And Correlations With Cognitive Change, Cassidy M. Fiford, Carole H. Sudre, Hugh Pemberton, Phoebe Walsh, Emily Manning, Ian B. Malone, Jennifer Nicholas, Willem H. Bouvy, Owen T. Carmichael, Geert Jan Biessels, M. Jorge Cardoso, Josephine Barnes

Clinical Research Faculty Publications

Accurate, automated white matter hyperintensity (WMH) segmentations are needed for large-scale studies to understand contributions of WMH to neurological diseases. We evaluated Bayesian Model Selection (BaMoS), a hierarchical fully-unsupervised model selection framework for WMH segmentation. We compared BaMoS segmentations to semi-automated segmentations, and assessed whether they predicted longitudinal cognitive change in control, early Mild Cognitive Impairment (EMCI), late Mild Cognitive Impairment (LMCI), subjective/significant memory concern (SMC) and Alzheimer’s (AD) participants. Data were downloaded from the Alzheimer’s disease Neuroimaging Initiative (ADNI). Magnetic resonance images from 30 control and 30 AD participants were selected to incorporate multiple scanners, and were semi-automatically segmented …

Towards Optimizing Quality Assurance Outcomes Of Knowledge-Based Radiation Therapy Treatment Plans Using Machine Learning, Phillip Douglas Hardenbergh Wall

LSU Doctoral Dissertations

Knowledge-based planning (KBP) techniques have been shown to provide improvements in plan quality, consistency, and efficiency for advanced radiation therapies such as volumetric modulated arc therapy (VMAT). While the potential clinical benefits of KBP methods are generally well known, comparatively less is understood regarding the impact of using these systems on resulting plan complexity and pre-treatment quality assurance (QA) measurements, especially for in-house KBP systems. Therefore, the overarching purpose of this work was to assess QA implications with using an in-house KBP system and explore data-driven methods for mitigating increased plan complexity and QA error rates without compromising dosimetric plan …

Temporal And Spatial Trends Of Dead Copepods In The Northern Gulf Of Mexico In Relation To The Deepwater Horizon Oil Spill, Jessica L. Tolan

LSU Master's Theses

Zooplankton are a critical link between primary producers and higher trophic levels in the marine environment. They play a critical role in carbon cycling, are an important food source for commercially important species, and are excellent indicator genera for environmental changes that take place in marine ecosystems. This research quantified temporal and spatial patterns of dead copepods in response to the Deepwater Horizon Oil Spill (DWH) site using ZooSCAN imaging technologies. Research showed that the proportion of dead copepods (showed evidence of decay but no physical damage due to predation) increased with depth, and at time periods closest to the …

Identification Of Top-Down, Bottom-Up, And Cement-Treated Reflective Cracks Using Convolutional Neural Network And Artificial Neural Network, Nirmal Dhakal

LSU Doctoral Dissertations

The objective of this study was to formulate a Convolutional Neural Networks (CNN) model and to develop a decision-making tool using Artificial Neural Networks (ANN) to identify top-down, bottom-up, and cement treated (CT) reflective cracking in in-service flexible pavements. The CNN’s architecture consisted of five convolutional layers with three max-pooling layers and three fully connected layers. Input variables for the ANN model were pavement age, asphalt concrete (AC) thickness, annual average daily traffic (AADT), type of base, crack orientation, and crack location. The ANN network architecture consisted of an input layer of six neurons, a hidden layer of ten neurons, …

Spatial Synchrony Is Related To Environmental Change In Finnish Moth Communities: Synchrony And Environmental Change, Tad A. Dallas, Laura H. Antão, Juha Pöyry, Reima Leinonen, Otso Ovaskainen

Faculty Publications

© 2020 The Author(s). Spatially distinct pairs of sites may have similarly fluctuating population dynamics across large geographical distances, a phenomenon called spatial synchrony. However, species rarely exist in isolation, but rather as members of interactive communities, linked with other communities through dispersal (i.e. a metacommunity). Using data on Finnish moth communities sampled across 65 sites for 20 years, we examine the complex synchronous/anti-synchronous relationships among sites using the geography of synchrony framework. We relate site-level synchrony to mean and temporal variation in climatic data, finding that colder and drier sites-and those with the most drastic temperature increases-are important for …

Evolution Of Computational Thinking Contextualized In A Teacher-Student Collaborative Learning Environment., John Arthur Underwood

LSU Doctoral Dissertations

The discussion of Computational Thinking as a pedagogical concept is now essential as it has found itself integrated into the core science disciplines with its inclusion in all of the Next Generation Science Standards (NGSS, 2018). The need for a practical and functional definition for teacher practitioners is a driving point for many recent research endeavors. Across the United States school systems are currently seeking new methods for expanding their students’ ability to analytically think and to employee real-world problem-solving strategies (Hopson, Simms, and Knezek, 2001). The need for STEM trained individuals crosses both the vocational certified and college degreed …

The Language Of Rats: Unwelcome Animals And Interspecies Connection In Contemporary Anglophone Fiction, Kieran Leigh Lyons

LSU Doctoral Dissertations

The Language of Rats: Unwelcome Animals and Interspecies Connection in Global Contemporary Fiction consists of three essays examining the representation of what I call unwelcome animals in contemporary Anglophone novels from the United States, Nigeria, and India. These animals often live alongside humans yet are perceived as threats or annoyances. Literary depictions of this fraught relationship reveal, and sometimes critique, the intellectual structures that shape how we understand and represent interspecies connections. This dissertation contributes to our understanding of the interspecies dimensions of contemporary fiction by bringing together the fields of environmental criticism, animal studies, postcolonialism, and U.S. Southern studies. …

The Evolution Of Bivalve Shell Matrix Proteins, Mark Ira Duhon Ii

LSU Doctoral Dissertations

This dissertation focuses on the molecular underpinnings surrounding the evolution of the biomineralized shells of marine bivalves. Bivalve molluscs synthesize remarkably complex shells from calcium carbonate and an organic matrix of proteins secreted from the dorsal edge of the mantle. Molecular analyses of shell matrix proteins (SMPs) have suggested high rates of gene turnover despite the conserved nature of the shell itself. Here, I used proteomic and transcriptomic data to identify the SMPs and other biomineralization proteins from seven bivalve species that diverged 3-513 Mya. Contrary to previous studies that identified only a few shared biomineralization transcripts across the Bivalvia, …