Digital Commons Network^™

The Global Regulator Mftr Controls Virulence And Siderophore Production In Burkholderia Thailandensis, Sudarshan S. Thapa, Ahmed Al-Tohamy, Anne Grove

Faculty Publications

Burkholderia thailandensis is a member of the Burkholderia pseudomallei complex. It encodes the transcription factor MftR, which is conserved among the more pathogenic Burkholderia spp. and previously shown to be a global regulator of gene expression. We report here that a B. thailandensis strain in which the mftR gene is disrupted is more virulent in both Caenorhabditis elegans and onion. The DmftR strain exhibits a number of phenotypes associated with virulence. It is more proficient at forming biofilm, and the arcDABC gene cluster, which has been linked to anaerobic survival and fitness within a biofilm, is upregulated. Swimming and swarming …

Phase Contrast X-Ray Interferometry, Joyoni Dey, Narayan Bhusal, Leslie Butler, Jonathan P. Dowling, Kyungmin Ham, Varshni Singh

College of Science Patents

A phase contrast X-ray imaging system includes: an illumination source adapted to illuminate a region of interest; a diffraction grating adapted to receive illumination from the illuminated region of interest, the diffraction grating comprising a spatial structure having a first periodicity superimposed with a second periodicity that is different from the first periodicity; and a detector adapted to detect illumination passing through the diffraction grating, wherein the spatial structure is defined by varying height and/or pitch, and wherein the spatial structure imparts a first phase dependence based on the first periodicity and an additional phase dependence based on the second …

Understanding The Role Of Activated Sludge In Oxygen Transfer: Effects Of Sludge Settleability, Solids Retention Time, And Nitrification Reaction, Ken Campbell, Jianmin Wang

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

The current understanding on the oxygen transfer in activated sludge process is primarily developed based on two-phase systems, focusing only on oxygen transfer from air to water. However, this research demonstrates that activated sludge particles significantly impact oxygen transfer from air all the way to the microorganisms. Three bench-scale complete-mix activated sludge reactors, operated under the same influent loading and dissolved oxygen level but different solids retention times (SRTs), were used to develop oxygen transfer performance data as effects of different sludge property parameters. These reactors were also operated under batch modes to further validate the effect of nitrification reaction …

Louis Pasteur Signature Saying: Science Brings Men Closer To God Bicentenary Year: 200 Years After His Birth, Alan L. Gillen, Justin A. Ambrose

Faculty Publications and Presentations

This year (2022) marks the bicentenary birth (December 27, 1822) of Louis Pasteur. He has a global reputation. His contributions can be seen in our homes, in the "pasteurized" products derived from one of his discoveries and in disease prevention. It was in his discovery of gently heating beverages and food for what we today call pasteurization that he first said: “Man's first look at the universe discovers only variety, diversity, multiplicity of phenomena. Let this gaze be enlightened by science — by science which brings man closer to God — and simplicity and unity shine everywhere.” Louis Pasteur (Vallery-Radot, …

A Guided Chatbot Learning Experience In The Science Classroom, Jennifer Davis

Department of Teaching, Learning, and Teacher Education: Theses and Other Student Research

This dissertation describes a practitioner’s design-based development of a prototype chatbot to guide students in learning biological concepts of genetic mutations and protein synthesis. This chatbot’s architecture provides learning activities, feedback, and support throughout a series of short, connected lessons. The chatbot is designed to scaffold learners through a predict, observe, explain model of inquiry learning. It utilizes real-world phenomena to lead students through biology core ideas, science and engineering practices, and crosscutting concepts. Results of prototype testing include survey results in support of the proof of concept among both students and teachers, as well as accuracy measurements of chatbot …

Disparities In Covid-19 Case Counts And Incidence In Florida By Race And Ethnicity At The County And State Level, Elizabeth Weaver

Florida Public Health Review

Background: In 2020, as COVID-19 spread across the United States, reports of disparities in COVID-19 incidence and mortality by race and ethnicity soon followed. This study assessed COVID-19 case counts and incidence by race and ethnicity at county and state levels focusing on Florida.

Methods: Counts of COVID-19 were collected from June through December 2020. Chi square analyses assessed disparities in case distribution and linear regressions assessed disparities in incidence and potential interaction between predictors.

Results: Race and ethnicity were significant predictors of COVID-19 incidence. Mean incidence was 4.9, 6.6, and 14.3 per 1,000 people among White, Black, and Other …

Meta-Complementing The Semantics Of Short Texts In Neural Topic Models, Ce Zhang, Hady Wirawan Lauw

Research Collection School Of Computing and Information Systems

Topic models infer latent topic distributions based on observed word co-occurrences in a text corpus. While typically a corpus contains documents of variable lengths, most previous topic models treat documents of different lengths uniformly, assuming that each document is sufficiently informative. However, shorter documents may have only a few word co-occurrences, resulting in inferior topic quality. Some other previous works assume that all documents are short, and leverage external auxiliary data, e.g., pretrained word embeddings and document connectivity. Orthogonal to existing works, we remedy this problem within the corpus itself by proposing a Meta-Complement Topic Model, which improves topic quality …

Missed Pathological Femoral Neck Fracture Undergoes Spontaneous Healing, Stephanie Zarate, Ana Cecilia Belzarena Genovese

All Publications

No abstract provided.

Skin Lesion Segmentation By Using Object Detection Networks, Deeplab3+, And Active Contours, Fatemeh Bagheri, Mohammad Jafar Tarokh, Majid Ziaratban

Turkish Journal of Electrical Engineering and Computer Sciences

Developing an automatic system for detection, segmentation, and classification of skin lesions is very useful to aid well-timed diagnosis of skin diseases. Lesion segmentation is a crucial task for automated diagnosis of skin cancers, as it affects significantly the accuracy of the subsequent steps. Varieties in sizes and locations of lesions, and the lesions with low-contrast boundaries make this task very challenging. In this paper, a three-stage CNN-based method is presented for accurate segmentation of lesions from dermoscopic images. At the first step, normalization, approximate locations and sizes of lesions are estimated. Due to the importance of the normalization stage, …

Mocmin: Convex Inferring Of Modular Low-Rank Contact Networks Over Covid Diffusion Data, Emre Sefer

Turkish Journal of Electrical Engineering and Computer Sciences

SEIR (which consists of susceptible, exposed, infected, and recovered states) is a common diffusion model which could model different disease propagation dynamics across various domains such as influenza and COVID diffusion. As a motivation, across these domains, observing the node states is relatively easier than observing the network edges over which the diffusion is taking place, or it may not even be possible to observe the underlying network. This paper focuses on the problem of predicting modular low-rank human contact network edges only if a SEIR diffusion dynamics spreading among the human on their contact network can be observed. Such …

Monte-Carlo Method Based Simulations For Photothermal Mucosa Coagulation With Accurate Depth Limits, Merve Türker Burhan, Serhat Tozburun

Turkish Journal of Electrical Engineering and Computer Sciences

The mucosa layer, the innermost layer of the gastrointestinal (GI) system, is of great importance in carcinogenesis since most cancerous tissues occur as superficial lesions. Although various treatment strategies exist, the main difficulty in eradicating lesions is unintentional damage to healthy tissues with the uncontrolled depth of treatment. This study proposes a computer modeling approach for simulating depth-resolved photothermal (laser) mucosal coagulation therapy. Computer modeling mimics the thermal dynamics of mucosal tissue to characterize the total heat energy required for successful superficial coagulation, which can be controlled by the scan rate, scan time, output power, and beam diameter of the …

Detection And Classification Of White Blood Cells With An Improved Deep Learning-Based Approach, Fatma Akalin, Nejat Yumuşak

Turkish Journal of Electrical Engineering and Computer Sciences

The analysis of white blood cells, which defend the body against deadly infections and disease-causing substances, is an important issue in the medical world. The concentrations of these cells in the blood, examined in 5 classes, i.e. monocytes, eosinophils, basophils, lymphocytes, and neutrophils, vary according to the types of diseases in the body. The peripheral blood smear is widely used to analyze blood cells. Manual evaluation of this method is laborious and time-consuming. At the same time, many environmental and humanistic parameters affect the method's performance. Therefore, in the presented study, a real-time detection process is realized. Firstly, YOLOv5s, YOLOv5x, …

Affective States Classification Performance Of Audio-Visual Stimuli From Eeg Signals With Multiple-Instance Learning, Yaşar Daşdemi̇r, Rüstem Özakar

Turkish Journal of Electrical Engineering and Computer Sciences

Throughout various disciplines, emotion recognition continues to be an essential subject of study. With the advancement of machine learning methods, accurate emotion recognition from different data modalities (facial images, brain EEG signals) has become possible. Success of EEG-based emotion recognition systems depends on efficient feature extraction and pre/postprocessing of signals. Main objective of this study is to analyze the efficacy of multiple-instance learning (MIL) on postprocessing features of EEG signals using three different domains (time, frequency, time-frequency) for human emotion classification. Methods and results are presented for single-trial classification of valence (V), arousal (A), and dominance (D) ratings from EEG …

A Comparison Of Methods To Harmonize Cortical Thickness Measurements Across Scanners And Sites, Delin Sun, Gopalkumar Rakesh, Courtney C. Haswell, Mark Logue, C. Lexi Baird, Erin N. O'Learly, Andrew S. Cotton, Hong Xie, Marijo Tamburrino, Tian Chen, Emily L. Dennis, Neda Jahanshad, Lauren Salminen, Sophia I. Thomopoulos, Faisal Rashid, Christopher R.K. Ching, Saskia B.J. Koch, Jessie L. Frijling, Laura Nawijn, Mirjam Van Zuiden, Xi Zhu, Benjamin Suarez-Jimenez, Anika Sierk, Henrik Walter, Antje Manthey, Jennifer S. Stevens, Negar Fani, Sanne J.H. Van Rooij, Murray Stein, Jessica A. Bomyea, Inga K. Koerte, Kyle Choi, Steven J.A. Van Der Werff, Robert R.J.M. Vermeiren, Julia Herzog, Lauren A. M. Lebois, Justin T. Baker, Elizabeth A. Olson, Thomas Straube, Mayuresh S. Korgaonkar, Elpiniki Andrew, Ye Zhu, Gen Li, Jonathan Ipser, Anna R. Hudson, Matthew Peverill, Kelly Sambrook, Evan Gordon, Lee A. Baugh, Gina L. Forster, Raluca M. Simons, Jeffrey S. Simons, Vincent A. Magnotta, Adi Maron-Katz, Stefan Du Plessis, Seth Disner, Nicholas Davenport, Daniel W. Grupe, Jack B. Nitschke, Terri A. Deroon-Cassini, Jacklynn M. Fitzgerald, John H. Krystal, Ifat Levy, Miranda Olff, Dick J. Veltman, Li Wang, Yuval Neria, Michael D. De Bellis, Tanja Jovanovic, Judith K. Daniels, Martha E. Shenton, Nic J.A. Van De Wee, Christian Schmahl, Milissa L. Kaufman, Isabelle M. Rosso, Scott R. Sponheim, David Hofmann, Richard A. Bryant, Kelene A. Fercho, Dan J. Stein, Sven C. Mueller, Bobak Hosseini, K. Luan Phan, Katie A. Mclaughlin, Richard J. Davidson, Christine L. Larson, Geoffrey May, Steven M. Nelson, Chadi G. Abdallah, Hassaan Gomaa, Amit Etkin, Soraya Seedat, Ilan Harpaz-Rotem, Israel Liberzon, Theo G.M. Van Erp, Yann Quidé, Xin Wang, Paul M. Thompson, Rajendra A. Morey

Psychology Faculty Research and Publications

Results of neuroimaging datasets aggregated from multiple sites may be biased by site-specific profiles in participants’ demographic and clinical characteristics, as well as MRI acquisition protocols and scanning platforms. We compared the impact of four different harmonization methods on results obtained from analyses of cortical thickness data: (1) linear mixed-effects model (LME) that models site-specific random intercepts (LMEINT), (2) LME that models both site-specific random intercepts and age-related random slopes (LMEINT+SLP), (3) ComBat, and (4) ComBat with a generalized additive model (ComBat-GAM). Our test case for comparing harmonization methods was cortical thickness data aggregated from 29 sites, which included 1,340 …

Musculoskeletal Adaptation Of Young And Older Adults In Response To Challenging Surface Conditions, Amy E. Holcomb, Nicholas L. Hunt, Amanda K. Ivy, Aidan G. Cormier, Tyler N. Brown, Clare K. Fitzpatrick

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Over 36 million adults over 65 years of age experience accidental falls each year. The underlying neuromechanics (whole-body function) and driving forces behind accidental falls, as well as the effects of aging on the ability of the musculoskeletal system to adapt, are poorly understood. We evaluated differences in kinematics (lower extremity joint angles and range of motion), kinetics (ground reaction force), and electromyography (muscle co-contraction), due to changes in surface conditions during gait in 14 older adults with a history of falling and 14 young adults. We investigated the impact of challenging surfaces on musculoskeletal adaptation and compared the mechanisms …

High-Resolution Ribosome Profiling Reveals Translational Selectivity For Transcripts In Bovine Preimplantation Embryo Development, Linkai Zhu, Tong Zhou, Rajan Iyyappan, Hao Ming, Michal Dvoran, Yinjuan Wang, Qi Chen, R. Michael Roberts, Andrej Susor, Zongliang Jiang

Faculty Publications

High-resolution ribosome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscapes of early embryo development at an unprecedented level. We analyzed the transcriptome and the polysome- and non-polysome-bound RNA profiles of bovine oocytes (germinal vesicle and metaphase II stages) and early embryos at the two-cell, eight-cell, morula and blastocyst stages, and revealed four modes of translational selectivity: (1) selective translation of non-abundant mRNAs; (2) active, but modest translation of a selection of highly expressed mRNAs; (3) translationally suppressed abundant to moderately abundant mRNAs; and (4) mRNAs associated specifically with monosomes. …

Multiscale Analysis Of Cancer Service Areas In The United States, Changzhen Wang, Tracy Onega, Fahui Wang

Faculty Publications

The purpose of delineating Cancer Service Areas (CSAs) is to define a reliable unit of analysis, more meaningful than geopolitical units such as states and counties, for examining geographic variations of the cancer care markets using geographic information systems (GIS). This study aims to provide a multiscale analysis of the U.S. cancer care markets based on the 2014–2015 Medicare claims of cancer-directed surgery, chemotherapy, and radiation. The CSAs are delineated by a scale-flexible network community detection algorithm automated in GIS so that the patient flows are maximized within CSAs and minimized between them. The multiscale CSAs include those comparable in …

Modification Of The Tumor Microenvironment Enhances Anti-Pd-1 Immunotherapy In Metastatic Melanoma, Guilan Shi, Megan Scott, Cathryn G. Mangiamele, Richard Heller

Bioelectrics Publications

Resistance to checkpoint-blockade treatments is a challenge in the clinic. Both primary and acquired resistance have become major obstacles, greatly limiting the long-lasting effects and wide application of blockade therapy. Many patients with metastatic melanoma eventually require further therapy. The absence of T-cell infiltration to the tumor site is a well-accepted contributor limiting immune checkpoint inhibitor efficacy. In this study, we combined intratumoral injection of plasmid IL-12 with electrotransfer and anti-PD-1 in metastatic B16F10 melanoma tumor model to increase tumor-infiltrating lymphocytes and improve therapeutic efficacy. We showed that effective anti-tumor responses required a subset of tumor-infiltrating CD8⁺ and CD4 …

All The Brain's A Stage For Serotonin: The Forgotten Story Of Serotonin Diffusion Across Cell Membranes, Paul W. Andrews, Catherine Bosyj, Luke Brenton, Laura Green, Paul J. Gasser, Christopher A. Lowry, Virginia M. Pickel

Biomedical Sciences Faculty Research and Publications

In the conventional model of serotonin neurotransmission, serotonin released by neurons in the midbrain raphe nuclei exerts its actions on forebrain neurons by interacting with a large family of post-synaptic receptors. The actions of serotonin are terminated by active transport of serotonin back into the releasing neuron, which is mediated by the serotonin reuptake transporter (SERT). Because SERT is expressed pre-synaptically and is widely thought to be the only serotonin transporter in the forebrain, the conventional model does not include serotonin transport into post-synaptic neurons. However, a large body of evidence accumulating since the 1970s has shown that serotonin, despite …

Shaky Ground: Educators At The Intersection Of Gender Diversity And Early Childhood Environments, Elizabeth Gragg Elizardi

LSU Doctoral Dissertations

This dissertation examines the hidden curriculum of gender socialization in early childhood classrooms. Purposes of this study included exploring how teachers’ beliefs about gender are enacted in activities, roles, and relationships with children to inform and recommend future directions for gender conscious education and pedagogies. This dissertation includes an assessment of participants’ gender schema, an analysis of participant interviews and focus groups, field notes from classroom observations and artifact collection. This study draws on Brofenbrenner’s (2005) bioecological theory of human development, positioning teachers as a primary engine of development in a child’s life. Cognitive-developmental theories are forwarded to explain gender …

Performance Of Full-Scale Anaerobic Co-Digestion Of Fog And Municipal Solids With An Emphasis On Syntrophomonas Populations, Thomas Solon

All Theses

Due to increased methane yields, anaerobic co-digestion of fats, oils, and grease (FOG) and municipal solids is an attractive process to employ at water resource recovery facilities (WRRFs). For many practitioners in the industry, the risks associated with anaerobic co-digestion of FOG have overshadowed the many benefits. In recent years, much effort has been given to understanding the chemical and microbial aspects of achieving stable co-digestion of FOG. To date, no full-scale studies have been conducted to understand how the current research applies to FOG co-digestion at scale. To fill this gap within the literature, two 1.36-million-gallon digesters receiving primary …

Neurodevelopment And Recovery From Wasting, Harriet M. Babikako, Celine Bourdon, Emmie Mbale, Peace Aber, Annet Birabwa, Josephine Chimoyo, Wieger Voskuijl, Zaubina Kazi, John Mukisa, Ali Faisal Saleem

Department of Paediatrics and Child Health

Background and objectives: Acute illness with malnutrition is a common indication for hospitalization among children in low- and middle-income countries. We investigated the association between wasting recovery trajectories and neurodevelopmental outcomes in young children 6 months after hospitalization for an acute illness.
Methods: Children aged 2 to 23 months were enrolled in a prospective observational cohort of the Childhood Acute Illness & Nutrition Network, in Uganda, Malawi, and Pakistan between January 2017 and January 2019. We grouped children on the basis of their wasting recovery trajectories using change in mid-upper arm circumference for age z-score. Neurodevelopment was assessed with the …

Risk Factors For Community-Acquired Bacterial Infection Among Young Infants In South Asia: A Longitudinal Cohort Study With Nested Case–Control Analysis, Nicholas E. Connor, Mohammad Shahidul Islam, Luke C. Mullany, Nong Shang, Zulfiqar Ahmed Bhutta, Anita K. M. Zaidi, Sajid Bashir Soofi, Muhammad Imran Nisar, Pinaki Panigrahi, Kalpana Panigrahi

Department of Paediatrics and Child Health

Objective: Risk factors predisposing infants to community-acquired bacterial infections during the first 2 months of life are poorly understood in South Asia. Identifying risk factors for infection could lead to improved preventive measures and antibiotic stewardship.
Methods: Five sites in Bangladesh, India and Pakistan enrolled mother-child pairs via population-based pregnancy surveillance by community health workers. Medical, sociodemographic and epidemiological risk factor data were collected. Young infants aged 0-59 days with signs of possible serious bacterial infection (pSBI) and age-matched controls provided blood and respiratory specimens that were analysed by blood culture and real-time PCR. These tests were used to build …

Levinas, Adorno, And The Ethics Of The Material Other By Eric Nelson, Suny Press, 2020 Pp. 480, Emilia Angelova, Curtis Hutt, Leah Klmanson, Eric Nelson

International Dialogue

This is a number of reviews and responses to Eric S. Nelson's Levinas, Adorno, and the Ethics of Materials Other (2020) SUNY Press. This includes:

The Relation of the Ethics of the Material Other to the Rights of the Stranger by Emilia Angelova

Nelson's Defense of Asymmetrical Ethics: On Religion and Human Rights by Curtis Hutt

On Nelson and East Asian Philosophies by Leah Kalmanson

Author Response: The Ethics of the Material Other and the Right of the Other by Eric S. Nelson

Becoming Human: A Theory Of Ontogeny Michael Tomasello. Cambridge: Harvard University Press, 2019 Pp. 392., Benjamin Gregg

International Dialogue

No philosophical question is older than What are we, we humans? Michael Tomasello contributes a splendid, empirically based answer to this hoary debate in Becoming Human, with a programmatic subtitle, A Theory of Ontogeny. We humans are an evolved organism with a capacity to create culture only by means of which we can realize aspects of our biological selves—and just as our biology can realize aspects of our cultural selves. That is, our biology evolved in ways that released in us capacities for “culture” that, in turn, released in us biologically relevant capacities, with “enormous and cascading phenotypic effects”—but effects …

Impacts Of Algal Morphology And Water Flow On Macroalgal Microplastic Capture, Cheyenne M. Adams

Honors College Theses

Microplastic pollution is a major area of concern in marine environments, especially as microplastics enter the food web. This study used pipe cleaners and two lichen species as algal mimics, and Chaetomorpha sp. and Chondrus crispus as model algal species to test the effects of morphology and biomass on microbead and foam capture. This study also utilized two different water flow methods: vortices and waves. Results suggest that water flow, as well as biomass and morphology, play a role in microplastic capture in macroalgae. For all mimics and algal species, except Cladonia lichens, turfs with increased biomass and length showed …

Regulation Of Tissue Mechanics And Adherens Junctions By Small Gtpase Rhoa During Drosophila Embryogenesis, Hanqing Guo

Dartmouth College Ph.D Dissertations

Actomyosin contractility plays an important role at both the cell and tissue level during developments. In this study, we developed an optogenetic tool that can acutely inhibit actomyosin contractility by targeting its main activator Rho1. This optogenetic tool can achieve myosin inhibition within one minute and thus enable further dissection of actomyosin function in development. In my first two projects, I used Drosophila mesoderm invagination (also known as ventral furrow formation) as a model to study epithelial folding, a fundamental mechanism for constructing complex 3D tissues. Apical constriction mediated by actomyosin contractility is a common mechanism for epithelial folding. However, …

Through The Library: A Study Of The Importance Of Women In Philosophy, Isabell A. Bowling

Theology Undergraduate Work

While researching women, this author found that a large portion of philosophical writings didn’t meet the academic and theological standards set forth. The desire was to find writings about the philosophy of women as a separate gender with Christ at the center of the musings. With this in mind, Through the Library was imagined. It begins with a short story, wherein the main character, Darius, has a crisis of confidence and falls asleep in a library. He dreams a conversation with Lady Wisdom, who gives him philosophical ideas on women in regard to motherhood, success, and God. Then, the paper …

Post-Fire Seed Dispersal Of A Wind-Dispersed Shrub Declined With Distance To Seed Source, Yet Had High Levels Of Unexplained Variation, Cara Applestein, T. Trevor Caughlin, Matthew J. Germino

Biology Faculty Publications and Presentations

Plant-population recovery across large disturbance areas is often seed-limited. An understanding of seed dispersal patterns is fundamental for determining natural-regeneration potential. However, forecasting seed dispersal rates across heterogeneous landscapes remains a challenge. Our objectives were to determine (i) the landscape patterning of post-disturbance seed dispersal, and underlying sources of variation and the scale at which they operate, and (ii) how the natural seed dispersal patterns relate to a seed augmentation strategy. Vertical seed trapping experiments were replicated across 2 years and five burned and/or managed landscapes in sagebrush steppe. Multi-scale sampling and hierarchical Bayesian models were used to determine the …

Influence Of Plant Density On Rainfall Interception By Spartina Alterniflora, Hannah K. Longaberger

Honors College Theses

Abstract

Spartina alterniflora is an abundant plant in eastern US and Gulf coast salt marshes; it is important in maintaining a diverse ecosystem. Salt marshes are impacted by rainstorms, which may affect erosion events. This project examined the partitioning of rainfall on single plants of various sizes and on central plants within different canopy densities of S. alterniflora. By calculating the rain stemflow (SF), throughfall (TF), and water adhered to the stem in S. alterniflora, we gained insight to rainfall partitioning with different plant features. My research found no statistically significant relationship between different plant features and SF, TF, …