Digital Commons Network^™

Strprofiler: Efficient Comparisons Of Short Tandem Repeat Profiles For Biomedical Model Authentication., Jared M Andrews, Michael W Lloyd, Steven Neuhauser, Margaret Bundy, Emily L Jocoy, Susan Airhart, Carol J Bult, Yvonne A Evrard, Jeffrey Chuang, Suzanne Baker

Faculty Research 2024

SUMMARY: Short tandem repeat (STR) profiling is commonly performed for authentication of biomedical models of human origin, yet no tools exist to easily compare sets of STR profiles to each other or an existing database in a high-throughput manner. Here, we present STRprofiler, a Python package, command line tool, and Shiny application providing methods for STR profile comparison and cross-contamination detection. STRprofiler can be run with custom databases or used to query against the Cellosaurus cell line database.

AVAILABILITY AND IMPLEMENTATION: STRprofiler is freely available as a Python package with a rich CLI from PyPI https://pypi.org/project/strprofiler/ with source code available …

Hypertonic Saline Induces Host Protective Immune Responses Against, Tran Xuan Ngoc Huy, Trang Thi Nguyen, Said Abdi Salad, Ched Nicole Turbela Aguilar, Alisha Wehdnesday Bernardo Reyes, Lauren Togonon Arayan, Wongi Min, Hu Jang Lee, Huynh Tan Hop, Suk Kim

Faculty Research 2024

Hypertonic saline (HTS) resuscitation can enhance immune responses against various pathogens, however, the effect of HTS on brucellosis is yet to be defined. In this study, we found that HTS inhibited Brucella infection in mice by augmenting Th1 immunity. HTS treatment enhanced the serum cytokines production and the expression of nitric oxide synthase (NOS2) and nuclear factor kappa B (NF-ĸB) p50 and p65, crucial anti-Brucella effectors in splenocytes. In addition, HTS treatment also inhibited the phosphorylation of MAPK signaling, accompanied by the down-regulation of the autophagy marker LC3B-II. Due to directing an appropriate immune response, HTS treatment substantially decreased bacterial …

A Comprehensive Analysis Of In-Hospital Adverse Events After Scopolamine Administration: Insights From A Retrospective Cohort Study Using A Large Nationwide Inpatient Database, George Sun, Marc Torjman, Kevin Min

Department of Anesthesiology Faculty Papers

BACKGROUND: Scopolamine is a widely used antiemetic in anesthetic practice, particularly for postoperative and post-discharge nausea and vomiting. Despite its frequent usage and recognized efficacy, concerns have emerged regarding the potential for increased side effects, particularly in elderly patients. Further research is needed to assess safety and determine age thresholds for adverse events. This study hypothesizes associations between perioperative scopolamine use, worse clinical outcomes, increased pneumonia, delirium, urinary retention, and readmissions.

METHODS: A large, retrospective cohort study was performed using the TriNetX Analytics Network database on patients undergoing major surgical procedures between Jan 1, 2009, and March 21, 2018, to …

Role Of Myeloid Cell-Specific Adenylyl Cyclase Type 7 In Lipopolysaccharide- And Alcohol-Induced Immune Responses, Yawen Hu, Sonika Patial, Yogesh Saini, Masami Yoshimura

School of Graduate Studies Faculty Publications

Clinical and experimental evidence indicates that alcohol use causes various abnormalities in the immune system and compromises immune functions. However, the mechanistic understanding of ethanol’s effects on the immune system remains limited. Cyclic AMP (cAMP) regulates multiple processes, including immune responses. Earlier research indicated that type 7 adenylyl cyclase (AC7) regulates the immune system and is highly responsive to ethanol. Therefore, we hypothesized that AC7 is a central player in regulating the effects of alcohol on innate immune responses. To test this hypothesis, we utilized a myeloid lineage-specific AC7 KO mouse model and compared the effects of acute and chronic …

Effective Nutrient Management Of Surface Waters In The United States Requires Expanded Water Quality Monitoring In Agriculturally Intensive Areas, Christopher Oates, Hactor Fajardo, Khara Grieger, Daniel Obenaur, Rebecca Muenich, Natalie G. Nelson

Biological and Agricultural Engineering Faculty Publications and Presentations

The U.S. Clean Water Act is believed to have driven widespread decreases in pollutants from point sources and developed areas, but has not substantially affected nutrient pollution from agriculture. Today, the highest nutrient concentrations in surface waters are often associated with agricultural production. In this Perspective, we explore whether challenges stemming from the Clean Water Act’s inability to mitigate agricultural nutrient pollution are also exacerbated by coarse nutrient monitoring. We evaluate the current state of nutrient monitoring in surface waters of the contiguous U.S. relative to agricultural nutrient inputs to assess how monitoring effort varies across agriculturally intensive areas. The …

Complement Immune System In Pulmonary Hypertension-Cooperating Roles Of Circadian Rhythmicity In Complement-Mediated Vascular Pathology, Hunter Devaughn, Haydn E Rich, Anthony Shadid, Priyanka K Vaidya, Marie-Francoise Doursout, Pooja Shivshankar

The Brown Foundation: Institute of Molecular Medicine

Originally discovered in the 1890s, the complement system has traditionally been viewed as a "compliment" to the body's innate and adaptive immune response. However, emerging data have shown that the complement system is a much more complex mechanism within the body involved in regulating inflammation, gene transcription, attraction of macrophages, and many more processes. Sustained complement activation contributes to autoimmunity and chronic inflammation. Pulmonary hypertension is a disease with a poor prognosis and an average life expectancy of 2-3 years that leads to vascular remodeling of the pulmonary arteries; the pulmonary arteries are essential to host homeostasis, as they divert …

Blood Matters: The Hematological Signatures Of Coronavirus Infection, Ayelen Toro, Ana P Arévalo, Marianoel Pereira-Gómez, Agustina Sabater, Eric A Zizzi, Paula Perbolianachis, Gaston Pascual, Sofia Lage-Vickers, Jorge L Pórfido, Ines Achinelli, Rocio Seniuk, Juan Bizzotto, Pablo Sanchis, Alvaro Olivera, Alejandro Leyva, Pilar Moreno, Alicia Costábile, Alvaro Fajardo, Federico Carrión, Martín Fló, Natalia Olivero-Deibe, Fernando Rodriguez, Nicolas Nin, Nicolas Anselmino, Estefania Labanca, Elba Vazquez, Javier Cotignola, Daniel F Alonso, Maria P Valacco, Marcelo Marti, Francesco Gentile, Artem Cherkasov, Martina Crispo, Gonzalo Moratorio, Geraldine Gueron

Faculty, Staff and Student Publications

Recent developments have broadened our perception of SARS-CoV-2, indicating its capability to affect the body systemically beyond its initial recognition as a mere respiratory pathogen. However, the pathways of its widespread are not well understood. Employing a dual-modality approach, we integrated findings from a Murine Hepatitis Virus (MHV) infection model with corroborative clinical data to investigate the pervasive reach of Coronaviruses. The novel presence of viral particles within red blood cells (RBCs) was demonstrated via high-resolution transmission electron microscopy, with computational modeling elucidating a potential heme-mediated viral entry mechanism via Spike protein affinity. Our data affirm viral localization in RBCs, …

The Laboratory Opossum (Monodelphis Domestica) Is A Unique Model For Research On Zika Virus: Robust Immune Response, Widespread Dissemination, And Long-Term Persistence, André Filipe Pastor, Susan M. Mahaney, Juan Garcia Jr., Marisol Morales, Oscar Quintanilla, Marco Arriaga, John M. Thomas, John L. Vandeberg

School of Medicine Publications

The Zika virus (ZIKV) epidemic elicited a rapid commitment to the development of animal models for ZIKV research. Non-human primates (NHPs) and mice have made significant contributions to this research, but NHPs are expensive, have a long gestation period, and are available only in small numbers; non-genetically modified mice are resistant to infection. To address these deficiencies, we have established the laboratory opossum, Monodelphis domestica, as a small animal model that complements the mouse and monkey models. We developed and validated an indirect ELISA for measuring antibodies to ZIKV in opossums, as well as an immunohistochemistry (IHC) method to detect …

A Virtual Scalable Model Of The Hepatic Lobule For Acetaminophen Hepatotoxicity Prediction, Stelian Camara Dit Pinto, Jalal Cherkaoui, Debarshi Ghosh, Valentine Cazaubon, Kenza E Benzeroual, Steven M Levine, Mohammed Cherkaoui, Gagan K Sood, Sharmila Anandasabapathy, Sadhna Dhingra, John M Vierling, Nicolas R Gallo

Faculty, Staff and Students Publications

Addressing drug-induced liver injury is crucial in drug development, often causing Phase III trial failures and market withdrawals. Traditional animal models fail to predict human liver toxicity accurately. Virtual twins of human organs present a promising solution. We introduce the Virtual Hepatic Lobule, a foundational element of the Living Liver, a multi-scale liver virtual twin. This model integrates blood flow dynamics and an acetaminophen-induced injury model to predict hepatocyte injury patterns specific to patients. By incorporating metabolic zonation, our predictions align with clinical zonal hepatotoxicity observations. This methodology advances the development of a human liver virtual twin, aiding in the …

Human Single Cell Rna-Sequencing Reveals A Targetable Cd8+ Exhausted T Cell Population That Maintains Mouse Low-Grade Glioma Growth, Rasha Barakat, Jit Chatterjee, Rui Mu, Xuanhe Qi, Xingxing Gu, Igor Smirnov, Olivia Cobb, Karen Gao, Angelica Barnes, Jonathan Kipnis, David H Gutmann

2020-Current year OA Pubs

In solid cancers, T cells typically function as cytotoxic effectors to limit tumor growth, prompting therapies that capitalize upon this antineoplastic property (immune checkpoint inhibition; ICI). Unfortunately, ICI treatments have been largely ineffective for high-grade brain tumors (gliomas; HGGs). Leveraging several single-cell RNA sequencing datasets, we report greater CD8

Dungeons & Dragons In Times Of Transmedia, Nazario Robles Bastida, Ricardo Victoria Uribe

Journal of Roleplaying Studies and STEAM

This paper explores the current state of transmedia storytelling, that is, the art of developing a cohesive narrative through a variety of media. Using Dungeons & Dragons as a case study, this study explores the complex nature of current forms of transmedia storytelling, as well as the complex relationships between media producers and consumers that have arisen due to this narrative technique. Focusing in three specific examples within the franchise: Drizzt Do'Urden, the Dungeons & Dragons Saturday morning cartoon series and the 2023 film Honor among Thieves, our analysis illustrate the fact that current media franchises are constituted by a …

Comparison Of Toxic Element Cadmium Levels In Female Patients With ‎Benign And ‎‎‎Malignant Uterine Tumors‎ By Flame Atomic Absorption ‎Spectrometry ., Hiba Ghmeedh Adhab, Liwaa Hussein Mahdi, Eman M. Al-Hilo

Maaen Journal for Medical Sciences

Cadmium is a toxic heavy metal known to be associated with various health issues, including cancer. Elevated blood cadmium levels can be a concern and may require medical evaluation and intervention. Some studies describing the etiology of cancer have focused on heavy metals, however, there is little information available for uterine cancer. This study assessed the levels of cadmium in the serum of 60 women with benign and malignant uterine tumors. Blood samples were obtained and analyzed using FAAS spectrometry in Najaf City, Iraq. Serum cadmium levels exhibited higher concentration in patients with malignant uterine tumors than those with benign …

Saan A Maymaysat' Aldaw: Education In Democracy, Social Justice, And Inclusion In Ilokano Life, Aurelio S. Agcaoili

Budhi: A Journal of Ideas and Culture

The essay argues that there has been a cognitive dissonance between the country’s formal education system (adal) and the Ilokano people’s vocation to knowledge (sursuro). Unless this dissonance is addressed, fundamental problems relative to education in democracy, social justice, and inclusion will never be solved. The Ilokano people’s sense of education—sursuro—shows us the way to correct that dissonance.

Japanese Philosophy Of Moral Education: From Watsuji Tetsurô To Mori Akira, Anton Sevilla-Liu

Budhi: A Journal of Ideas and Culture

This article builds on the ethics of Watsuji Tetsurô (1889 1960) through a comparison with Mori Akira’s (1915–1976) the philosophy of education to show how Watsuji’s “ethics of emptiness” can be concretely manifested in human formation. While keeping Watsuji’s ethics in view, this article examines Mori Akira’s early philosophy of moral education in the 1950s, which can be found in his philosophy book, his teacher’s manual, and his moral education student textbooks. This article begins with Watsuji’s idea of “human existence” and its similarities with Mori Akira’s idea of “human becoming,” which adds a developmental angle to Watsuji’s tensional view …

Cutting Across The Waves Of The Web: The "Care Of The Self" As An Ethical Response To Post-Truth Politics In Social Media, Roberto Paolo T. Sangil

Budhi: A Journal of Ideas and Culture

Uttering “facts are passé” captures the spirit of post-truth. However, it often leads to addressing facts rather than why they pass off as passé. “Post-truth” was dubbed the 2016 Word of the Year due to its increased usage during the Brexit referendum and the US presidential election in the same year. The issue presses at least twenty-six countries, including the Philippines, as they face widespread disinformation and misinformation. This paper offers an overview of the social media manipulation from Samantha Bradshaw and Philip Howard, and networked disinformation in the Philippines from Jonathan Corpus Ong and Jason Vincent Cabañes. This paper …

Circum-Navigating The World Island, Among Enemies, John T. Giordano

Budhi: A Journal of Ideas and Culture

Everyday our vision travels across time and space. We see images in the media about atrocities, disruptions, crises, famine, and wars. And in each case, our sense of injustice is awakened. We feel outrage and indignation based upon our ideals and value systems, which were formed through our traditions and religions. But in this age where the power of media and information is so powerful, what we see is often manufactured to appeal to our values. While these values circulate among the images we see in cyberspace, these manipulations are rooted in certain realities: geography, natural resources, and power relationships. …

Sanut, Wayawaya, And The Naimbag A Biag In Ilokano Philosophy, Aurelio S. Agcaoili

Budhi: A Journal of Ideas and Culture

The essay articulates the fundamental connection of some of the basic concepts in Ilokano ethos as lived in the everyday in order to understand the basic contradictions of the Ilokano way of being in the world (Ilokano ontology), of being in a society marked by good intentions but evil practices. The notion of the good life as a political concept is explored, and its connection to knowledge (Ilokano epistemology) and freedom is established.

A Tale Of Two Walls: A Comparison Of The Green Wall Projects In Inner Mongolia And The Sahelo-Saharan Regions, Daniel Chen Ratilla

Budhi: A Journal of Ideas and Culture

Desertification as a bio-physical stressor threatens food and water security, and is exacerbated by climate change. Other issues such as peace, gender equity, and livelihood are some examples of socio-economic issues also connected to desertification. This is apparent in the cases of Inner Mongolia and the Sahelo-Saharan region, where desertification has spurred the creation of afforestation projects, colloquially known as “Green Walls”: these are the Three-North Shelterbelt Project, and the Great Green Wall of the Sahara and the Sahel Initiative, respectively. This paper explores the principles of environmental ethics (such as vulnerability, common goods, biological and cultural diversity, and environmental …

Bukusu And Amazonian Perspectives On Harmonious Relations With The Other, Gail M. Presbey

Budhi: A Journal of Ideas and Culture

The article follows the theme of dealing with adversaries and conflict resolution. As an exercise in intercultural philosophy, the paper explores the philosophies of two different regions, the Amazon of South America (Jivaro and Yanesha/Amuesha people of Peru) and Western Province of Kenya, East Africa (with a focus on the Bukusu people). Exploring the insights of other researchers as well as drawing upon interviews by the author, the article explains each group’s philosophy of conflict resolution referencing myths, folktales, proverbs, and interviews with sages. In the case of both communities, practitioners of peace must engage in bravery to reach out …

Indigenous Liberation Theology And Spirituality: Looking To The Past For Answers In The Present, Kathleen Nadeau, Jojo M. Fung

Budhi: A Journal of Ideas and Culture

Pope Francis’s Laudato si’: On the Care of Our Common Home offers a framework for dealing with poverty, ecological degradation, and climate change in the Philippines. His interconnected and holistic ecological spirituality shares some commonalities with indigenous spirituality where the earth is a gift from God to be taken care of—not taken advantage of or taken for granted. In this paper, we explore how this integrated approach of indigenous spirituality and liberation theology offers some long-term solutions to the problems of poverty and climate-change. Taking the position of being politically engaged in the world accords well with indigenous spirituality, this …

Sustaining Temporal Peace: A Worldview For Sustainable Living Inspired By Saint Augustine's Philosophy, Joseph Emmanuel D. Sta. Maria

Budhi: A Journal of Ideas and Culture

My paper aims to use the philosophical resources of Saint Augustine’s thought, particularly as found in the City of God, in order to sketch a basic worldview which can educate and lead people towards living lives that promote sustainable development. Specifically, I wish to show how Saint Augustine’s concepts of order, rightly ordered love, and temporal peace can serve as material to create a rough metaphysical framework in which human beings are understood to be an integrated part of a greater whole which is the earth. The ethical corollary of this framework is that human beings should act in such …

Nakaparsuaan, Kadagaan, And Panaglunit Ti Daga: Climate Justice And Environmental Ethics In Ilokano Life, Aurelio S. Agcaoili

Budhi: A Journal of Ideas and Culture

The work offers an interpretation of the world as understood and being lived until today by Ilokanos. Such a reading involves the plumbing into linguistic and cultural data as proofs of an inchoate philosophy that has been preserved in the minds of the Ilokano people and which continues to guide their conduct. The world, understood as the physical environment, peoples, and communities, is linked back to the problem of social justice and stewardship of living and nonliving things, to the issue of who calls the shots in the unethical exploitation of these resources, and to the lessons that can be …

Benchmarking Pretrained Models For Speech Emotion Recognition: A Focus On Xception, Ahmed Hassan, Tehroom Masood, Hassan A. Ahmed, H. M. Shahzad, Hafiz Muhammad T. Khushi

Business Faculty Publications

Speech emotion recognition (SER) is an emerging technology that utilizes speech sounds to identify a speaker’s emotional state. Computational intelligence is receiving increasing attention from academics, health, and social media applications. This research was conducted to identify emotional states in verbal communication. We applied a publicly available dataset called RAVDEES. The data augmentation process involved adding noise, applying time stretching, shifting, and pitch, and extracting the features zero cross rate (ZCR), chroma shift, Mel-Frequency Cepstral Coefficients (MFCC), and a spectrogram. In addition, we used many pretrained deep learning models, such as VGG16, ResNet50, Xception, InceptionV3, and DenseNet121. Out of all …

Red Snapper (Lutjanus Campechanus) Neurocranium, Michelle Bassali, Anthony D'Auria, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Enhancing Muscle Health And Modulating Immune Response With Galectin-1 In Lgmd2b/R2 Models, Stefannia Esparza Pulido

Theses and Dissertations

Limb-Girdle Muscular Dystrophy Type 2B/R2 (LGMD2B/R2) is a type of dysferlinopathy, a progressive muscle-wasting disorder caused by mutations in the dysferlin gene. Hallmarks of the disease include chronic inflammation, impaired muscle regeneration, and eventual muscle degeneration. Currently, no FDA-approved therapies are available for dysferlinopathies. Recombinant human Galectin-1 (rHsGal-1) has shown multiple roles in maintaining skeletal muscle homeostasis, promoting muscle repair, enhancing myogenesis, and modulating inflammation by downregulating the NF-κB pathway. The ability of rHsGal-1 to modulate the immune response is particularly promising for therapeutic applications in patients with LGMD2B/R2. In this study, we evaluated the effects of rHsGal-1 in a …

Nutrition Recommendations For Patients On Weight Loss Drugs, Crystal M. Duque Rdn-Ldn, Toye Jackman

Department of Nutrition Student Projects

This paper provides a comprehensive, evidence-based framework for dietitians counseling patients who are using GLP-1 receptor agonists, such as Ozempic and Wegovy, for weight management. These medications are rapidly gaining popularity for their effectiveness in supporting weight loss; however, they come with unique nutritional considerations that require tailored guidance. This review outlines key aspects of GLP-1 mechanisms of action, emphasizing how these medications alter digestive processes, specifically impacting the absorption and metabolism of essential macronutrients, including proteins and dietary fibers. The paper also highlights hydration needs to support optimal health and weight loss outcomes in patients on GLP-1 therapies. Additionally, …

Functions Of Tam Receptors And Ligands Protein S And Gas6 In Atherosclerosis And Cardiovascular Disease, Teagan Prouse, Samarpan Majumder, Rinku Majumder

School of Medicine Faculty Publications

Atherosclerosis and cardiovascular disease are associated with high morbidity and mortality in industrialized nations. The Tyro3, Axl, and Mer (TAM) family of receptor tyrosine kinases is involved in the amplification or resolution of atherosclerosis pathology and other cardiovascular pathology. The ligands of these receptors, Protein S (PS) and growth arrest specific protein 6 (Gas6), are essential for TAM receptor functions in the amplification and resolution of atherosclerosis. The Axl-Gas6 interaction has various effects on cardiovascular disease. Mer and PS dampen inflammation, thereby protecting against atherosclerosis progression. Tyro3, the least studied TAM receptor in cardiovascular disease, appears to protect against fibrosis …

Association Mapping For Water Use Efficiency In Soybean Identifies Previously Reported And Novel Loci And Permits Genomic Prediction, Siva K. Chamarthi, Larry C. Purcell, Felix B. Fritschi, Jeffrey D. Ray, James R. Smith, Avjinder S. Kaler, C. Andy King, Jason D. Gillman

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Soybean is a major legume crop cultivated globally due to the high quality and quantity of its seed protein and oil. However, drought stress is the most significant factor that decreases soybean yield, and more than 90% of US soybean acreage is dependent on rainfall. Water use efficiency (WUE) is positively correlated with the carbon isotopic ratio ¹³C/¹²C (C13 ratio) and selecting soybean varieties for high C13 ratio may enhance WUE and help improve tolerance to drought. Our study objective was to identify genetic loci associated with C13 ratio using a diverse set of 205 soybean maturity …

Variation In Diet And Leafy Browse Offerings Amongcolobus Monkeys (Colobus Spp.) And Langurs(Trachypithecus Spp.) In Aza Facilities, Maura R. Plocek, Noah T. Dunham

Student Scholarship

Providing nutritionally balanced diets is a key aspect of successful husbandry and can help support sustainable ex situ populations. This study focuses on the diets of zoo‐housed colobus monkeys (Colobus angolensis and C. guereza) and langurs (Trachypithecus cristatus and T. francoisi) across AZA institutions. We utilized survey responses from 34 institutions to (1)document the extent of dietary variation with regard to food categories and macronutrients offered, (2) assess interspecific variation in diets offered, and (3) identify important aspects of browse provisioning among institutions. A total of 95 different food items and 229 common‐name browse types were …

Beyond Surrealism: The Developing Keyboard Style Of André Souris, Melanie T. Mallard

LSU Doctoral Dissertations

André Souris (1899-1970) is perhaps best known as a musical contributor to the Belgian surrealist group founded by Paul Nougé, but he assumed many roles throughout his life, including composer, writer, director, and promoter of modern music. His various interests influenced the style of his compositions, which remain largely unpublished and have received little scholarly attention beyond researchers of surrealism. Through this survey of many of Souris’ works for keyboard, I attempt to lay the groundwork for further discussion about Souris’ musical contributions not only through the lens of surrealism but also throughout his compositional career. This descriptive analysis of …