Digital Commons Network^™

Exploring The Connection Between Rna Splicing And Intellectual Disability, Anthony Caputo, Ashleigh E. Schaffer

Faculty Scholarship

Intellectual disability (ID) is a broad diagnostic category that encompasses individuals with impaired cognitive ability. While these disorders have heterogeneous causes, recent developments in next-generation sequencing (NGS) are revealing the prevalence of genetic etiologies. In particular, germline mutations in genes that affect RNA splicing are increasingly common causes of ID disorders. Research to elucidate the functional relationship between splicing and neurodevelopment is critical since molecular therapeutics require a nuanced understanding of the pathological mechanism. In this review, we first summarize the trends that have led to the discovery of the RNA splicing–ID relationship, then discuss recent progress and future directions …

Probing The Stability Of Designed Protein, Axel Irianni, Shuvo Chakraborty, Maral Afshinpour

SDSU Data Science Symposium

Naturally occurring proteins have evolved to perform specific biochemical functions, and their amino acid sequences are optimized for those functions rather than for stability. Enhancing protein stability without compromising its function is highly desirable for biotechnological applications, such as vaccine design. Computational protein design algorithms offer a solution by making targeted amino acid changes to the native protein sequence, potentially enhancing stability without the need for the lengthy, labor-intensive, and costly experimental processes typically involved in stabilizing proteins. There are various categories of computational protein design algorithms, and it remains unclear which approach is the most effective. In this study, …

Filters For Forecasting Crop Health: Analyzing And Projecting The Temporal Evolution Of Landsat Ndvi Data Using Dynamic Linear Models And The Kalman Filter, Kamal Albousafi, Hossein Moradi, Jung-Han Kimn

SDSU Data Science Symposium

Accurately forecasting food availability is a critical task. One approach involves utilizing remote sensing data, such as satellite images, to observe the health of crop fields using different Vegetation Indices (VI). The Normalized Difference Vegetation Index (NDVI) provides a sound metric to track the “greenness” of crops over time. In this research, we develop statistical models that capture the dynamics of NDVI time series data to make better predictions of its future values. The median NDVI of the pixels of a farm located in Edmunds County, South Dakota, is obtained using imagery from the Landsat 5 and Landsat 8 satellites, …

Corn Tolerance To Florpyrauxifen-Benzyl Rates And Its Mixture With Atrazine And Mesotrione, Amar Godar, Jason K. Norsworthy, L. Tom Barber

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Florpyrauxifen-benzyl is a new synthetic auxin herbicide labeled in rice with a broad spectrum of control, typically more potent on broadleaf weeds. It has garnered some interest as a potential broadleaf weed control option for use in corn at low rates. Field experiments were conducted in Fayetteville, Arkansas, from 2019 through 2021 to examine the response of corn to postemergence applications of florpyrauxifen-benzyl at three rates (7.5, 15, and 30 g ae ha-1), as well as mixtures of the herbicide with atrazine (at half or full rate), mesotrione, or a combination of atrazine (at half rate) and mesotrione. Injury and …

A Mechanistic Exploration Of How Neighborhood Crime Exposure Relates To Neonatal Brain Function, Early Externalizing Behaviors, And Callous-Unemotional Traits, Rebecca Brady

Arts & Sciences Graduate Student Theses and Dissertations

Pregnancy through early childhood is a period of tremendous neural and behavioral development. Neuronal birth and migration occur prenatally and result in the formation of neonatal functional and structural networks. These early brain networks are a building block for postnatal development wherein infants rapidly learn a variety of new skills, including socioemotional skills such as emotion regulation and moral understanding. During the acquisition of these skills, even typically developing toddlers can act aggressively or impulsively; however, toddlers with high levels of externalizing behaviors are more likely to develop clinical externalizing disorders later in childhood and adolescence. As such, it is …

Environmental Release Of A Safener Fenclorim From Rice (Oryza Sativa L.) Following Seed Treatment, Jeong-In R. Hwang, Jason K. Norsworthy, Nanda Kumar, Tae-Hwa Kim

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

The safener fenclorim, effective in protecting rice (Oryza sativa L.) from the phytotoxicity of some herbicides, is regarded as a contaminant of emerging concern that may cause toxicological issues to ecosystems and humans who may consume the final harvested rice. This study investigated time-dependent environmental releases of fenclorim from rice seeds treated with the safener and insecticide with five different treatments. The treatment with fenclorim alone caused the greatest fenclorim releases from the seed, and the release magnitude was similar to the treatment that had fenclorim and insecticide in mixture. The fenclorim release was the least when treated with safener …

Therapeutic Targeting Of The Janus Kinase/Signal Transducer And Activator Of Transcription Pathway In Cutaneous T-Cell Lymphoma, Alisha Kashyap, Julia Dai, Xiao Ni

Faculty, Staff and Student Publications

Background/Objectives: Cutaneous T-cell lymphoma (CTCL) is a rare group of non-Hodgkin lymphomas characterized by the clonal expansion of malignant T cells. While current treatments can alleviate symptoms and significant progress has been made in treating leukemic CTCL, a definitive cure remains elusive. Dysregulation of the Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway is a key driver of CTCL pathogenesis. As a result, therapeutic strategies targeting JAK/STAT signaling have gained momentum, with the increasing use of JAK inhibitors and other agents that effectively suppress this pathway. These immune-modulating therapies have broad effects on physiological processes, inflammation, and …

Additional Geographic Records Of Dekay’S Brownsnake (Storeria Dekayi) In Nebraska, Including A Late Seasonal Observation And Likely Range Expansion, Lauren Bahe, Dan D. Fogell, Keith Geluso

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Dekay’s Brownsnake (Storeria dekayi) occurs across much of eastern North America, inhabiting diverse environments such as marshes, woodlands, woodland edges, and urban areas. In Nebraska, recent studies documented its presence beyond the extreme southeastern region of the state, indicating a potential range expansion to the west and north. Our study continues to update its distribution with four additional county records. Two counties, Franklin and Harlan, represent the farthest west observations for Dekay’s Brownsnake in the state, further indicating a likely westward expansion. An observation from 6 December 2023 also represents the latest seasonal observation in the state. Despite …

Understanding The Relationship Between Food And Connection To God, Angela M. Hall

Doctoral Dissertations and Projects

A person’s relationship with God is a personal one, as is the choice of the food we eat. Today we see more and more people struggle with unhealthy relationships with food. And our relationship with food affects more than just our physical health. Food and diet can play a role in how we hear from God. The present qualitative study aimed to understand the relationship between food and connection to God. Specifically, this study aimed to explain lived experiences with food and if diet affected connection to God. A total of twelve Christian, adult men and women participated in 1:1 …

Comprehensive Sumo Proteomic Analyses Identify Hiv Latency-Associated Proteins In Microglia., Fergan Imbert, Dianne Langford

Rowan-Virtua School of Osteopathic Medicine Departmental Research

SUMOylation, the post-translational modification of proteins by small ubiquitin-like modifiers, plays a critical role in regulating various cellular processes, including innate immunity. This modification is essential for modulating immune responses and influencing signaling pathways that govern the activation and function of immune cells. Recent studies suggest that SUMOylation also contributes to the pathophysiology of central nervous system (CNS) viral infections, where it contributes to the host response and viral replication dynamics. Here, we explore the multifaceted role of SUMOylation in innate immune signaling and its implications for viral infections within the CNS. Notably, we present novel proteomic analyses aimed at …

Trichromacy Is Insufficient For Mate Detection In A Mimetic Butterfly, Andrew Dang, Gary D. Bernard, Furong Yuan, Aide Macias-Muñoz, Ryan I. Hill, J. P. Lawrence, Aline Giselle Rangel Olguin, Armando Luis-Martínez, Sean P. Mullen, Jorge Llorente-Bousquets, Adriana D. Briscoe

Pacific Faculty Work

Color vision is thought to play a key role in the evolution of animal coloration, while achromatic vision is rarely considered as a mechanism for species recognition. Here we test the hypothesis that brightness vision rather than color vision helps Adelpha fessonia butterflies identify potential mates while their co-mimetic wing coloration is indiscriminable to avian predators. We examine the trichromatic visual system of A. fessonia and characterize its photoreceptors using RNA-seq, eyeshine, epi-microspectrophotometry, and optophysiology. We model the discriminability of its wing color patches in relation to those of its co-mimic, A. basiloides, through A. fessonia and avian eyes. Visual …

Winter Hay-Feeding Effects On Soil Properties In A Rotationally Grazed Pasture System In The Ozark Highlands, Larry Berry, Kristofor R. Brye, Andrew Sharpley, Ron Morrow, Dirk Phillip, Tim A. Glover, James M. Burke, Mike B. Daniels

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Soil nutrient management for pastures in Arkansas often ignores nutrients applied from feeding hay to cattle. Discounting nutrient contributions from hay may increase the likelihood of unnecessary fertilizer over-application. This study evaluated the effects of unrolling bales (unroll fed, UF) and using a ring feeder (ring fed, RF), compared to an unamended control, on changes in soil properties in the top 4 inches in a rotationally grazed, beef [red angus (Bos taurus)] pasture on silt-loam soils in northwest Arkansas. Forty-six cow-calf pairs were fed hay at 6.6 tons acre(-1) year(-1) (14.8 Mg ha(-1) year(-1); dry-weight basis) from December to February …

Starting Vegetable Seeds Indoors: I. Planning, Wesley Crump, Taun Beddes, Michael Caron, Milena Oliveira

All Current Publications

For many Utah gardeners, starting vegetable seeds indoors offers both an exciting opportunity to experiment with new varieties and a practical necessity for ensuring the successful growth and production of certain crops in their unique environmental conditions. Vegetable gardening involves inherent risks, particularly for the plants, with weather being a significant and largely uncontrollable factor. Because of this, many gardeners are unsure about when to start certain crops and whether the crops should be started indoors or sown directly in the garden. This fact sheet, the first in a series of four, discusses planning considerations when starting seeds indoors.

Same Data, Different Analysts: Variation In Effect Sizes Due To Analytical Decisions In Ecology And Evolutionary Biology, Elliot Gould, Hannah S. Fraser, Timothy H. Parker, Shinichi Nakagawa, Simon C. Griffith, Peter A. Vesk, Fiona Fidler, Daniel G. Hamilton, Robin N. Abbey-Lee, Jessica K. Abbott, Erica F. Stuber, Et Al.

Wildland Resources Faculty Publications

Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small “many analyst” study found similar variability in ecology. We expanded the scope …

Genomic And Phenotypic Correlates Of Mosaic Loss Of Chromosome Y In Blood, Yasminka A Jakubek, Xiaolong Ma, Adrienne M Stilp, Fulong Yu, Jason Bacon, Justin W Wong, Francois Aguet, Kristin Ardlie, Donna K Arnett, Kathleen Barnes, Joshua C Bis, Tom Blackwell, Lewis C Becker, Eric Boerwinkle, Russell P Bowler, Matthew J Budoff, April P Carson, Jiawen Chen, Michael H Cho, Josef Coresh, Nancy J Cox, Paul S De Vries, Dawn L Demeo, David W Fardo, Myriam Fornage, Xiuqing Guo, Michael E Hall, Nancy Heard-Costa, Bertha Hidalgo, Marguerite Ryan Irvin, Andrew D Johnson, Eric Jorgenson, Eimear E Kenny, Michael D Kessler, Daniel Levy, Yun Li, Joao A C Lima, Yongmei Liu, Adam E Locke, Ruth J F Loos, Mitchell J Machiela, Rasika A Mathias, Braxton D Mitchell, Joanne M Murabito, Josyf C Mychaleckyj, Kari E North, Peter Orchard, Stephen C J Parker, Yash Pershad, Patricia A Peyser, Katherine A Pratte, Bruce M Psaty, Laura M Raffield, Susan Redline, Stephen S Rich, Jerome I Rotter, Sanjiv J Shah, Jennifer A Smith, Aaron P Smith, Albert Smith, Margaret A Taub, Hemant K Tiwari, Russell Tracy, Bjoernar Tuftin, Alexander G Bick, Vijay G Sankaran, Alexander P Reiner, Paul Scheet, Paul L Auer

Faculty, Staff and Student Publications

Mosaic loss of Y (mLOY) is the most common somatic chromosomal alteration detected in human blood. The presence of mLOY is associated with altered blood cell counts and increased risk of Alzheimer disease, solid tumors, and other age-related diseases. We sought to gain a better understanding of genetic drivers and associated phenotypes of mLOY through analyses of whole-genome sequencing (WGS) of a large set of genetically diverse males from the Trans-Omics for Precision Medicine (TOPMed) program. We show that haplotype-based calling methods can be used with WGS data to successfully identify mLOY events. This approach enabled us to identify differences …

Differentiating Between Renal Medullary And Clear Cell Renal Carcinoma With A Machine Learning Radiomics Approach, Rahim Jiwani, Koustav Pal, Iwan Paolucci, Bruno Odisio, Kristy Brock, Nizar M Tannir, Daniel D Shapiro, Pavlos Msaouel, Rahul A Sheth

Faculty, Staff and Student Publications

Background: The objective of this study was to develop and validate a radiomics-based machine learning (ML) model to differentiate between renal medullary carcinoma (RMC) and clear cell renal carcinoma (ccRCC).

Methods: This retrospective Institutional Review Board -approved study analyzed CT images and clinical data from patients with RMC (n = 87) and ccRCC (n = 93). Patients without contrast-enhanced CT scans obtained before nephrectomy were excluded. A standard volumetric software package (MIM 7.1.4, MIM Software Inc.) was used for contouring, after which 949 radiomics features were extracted with PyRadiomics 3.1.0. Radiomics analysis was then performed with RadAR for differential radiomics …

Proceedings Of The 1st Biannual Bridging The Gaps In Lung Cancer Conference, Narjust Florez, Sandip P Patel, Heather Wakelee, Lyudmila Bazhenova, Erminia Massarelli, Ravi Salgia, Brendon Stiles, Solange Peters, Jyoti Malhotra, Shirish M Gadgeel, Jorge J Nieva, Michelle Afkhami, Fred R Hirsch, Matthew Gubens, Tina Cascone, Benjamin Levy, Joshua Sabari, Hatim Husain, Patrick C Ma, Leah M Backhus, Puneeth Iyengar, Percy Lee, Russell Miller, Jacob Sands, Edward Kim

Faculty, Staff and Student Publications

Lung cancer is the leading cause of cancer death in the US and globally. The mortality from lung cancer has been declining, due to a reduction in incidence and advances in treatment. Although recent success in developing targeted and immunotherapies for lung cancer has benefitted patients, it has also expanded the complexity of potential treatment options for health care providers. To aid in reducing such complexity, experts in oncology convened a conference (Bridging the Gaps in Lung Cancer) to identify current knowledge gaps and controversies in the diagnosis, treatment, and outcomes of various lung cancer scenarios, as described here. Such …

Examination Of Protective Mucosal Immune Responses To Viral Sexually Transmitted Infections, Aisha Lee

Arts & Sciences Graduate Student Theses and Dissertations

Sexually transmitted infections (STI) are a prominent global health issue that affect the sexual and reproductive health of billions worldwide. Viral STIs present a particular challenge due to limited availability of treatment options and their frequent establishment of lifelong infection. One of the most common viral STIs is genital herpes, a recurrent ulcerative disease caused by chronic infection with the human alphaherpesviruses, HSV-1 or HSV-2. Women are particularly susceptible to morbidities of infection ranging from increased risk of HIV-1 acquisition to vertical transfer to neonates, for whom infection can be fatal. Previous efforts to develop a prophylactic vaccine for genital …

Same Data, Different Analysts: Variation In Effect Sizes Due To Analytical Decisions In Ecology And Evolutionary Biology, Elliot Gould, Hannah S. Fraser, Timothy H. Parker, Shinichi Nakagawa, Simon C. Griffith, Peter A. Vesk, Fiona Fidler, Daniel G. Hamilton, Robin N. Abbey-Lee, Andrea Contina

School of Integrative Biological & Chemical Sciences Faculty Publications

Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small “many analyst” study found similar variability in ecology. We expanded the scope …

Oncogenic Kras Mutations Confer A Unique Mechanotransduction Response To Peristalsis In Colorectal Cancer Cells, Abigail J Clevenger, Claudia A Collier, John Paul M Gorley, Sarah Colijn, Maygan K Mcfarlin, Spencer C Solberg, Scott Kopetz, Amber N Stratman, Shreya A Raghavan

Faculty, Staff and Student Publications

Colorectal cancer tumors start as polyps on the inner lining of the colorectum, in which they are exposed to the mechanics of peristalsis. Our previous work leveraged a custom-built peristalsis bioreactor to demonstrate that colonic peristalsis led to cancer stem cell enrichment in colorectal cancer cells. However, this malignant mechanotransductive response was confined to select colorectal cancer lines that harbored an oncogenic mutation in the Kirsten rat sarcoma virus (KRAS) gene. In this study, we explored the involvement of activating KRAS mutations on peristalsis-associated mechanotransduction in colorectal cancer. Peristalsis enriched cancer stem cell marker Leucine-rich repeat-containing G protein-coupled receptor 5 …

Antidiabetic Properties Of Prickly Pear (Opuntia Ficus-Indica) Fruit Extract, Kenzy Aidan Joseph Mckay

The Undergraduate Research Journal

Diabetes mellitus is a metabolic disorder that claims 1.5 million lives annually. Opuntia ficus-indica, commonly known as the prickly pear, has been commonly used in traditional folk medicine for its hypoglycemic properties. It has been claimed that it has antimicrobial and antioxidant properties as well. The plant is native to Mexico and is commonly found in the middle east and India and folk medicine from all of these areas have been using prickly pear medicinally for years. To test these claims an extract of locally sourced Opuntia ficus-indica was prepared using the flesh and seeds of the fruit. The …

Single Amino Acid Changes Impact The Ability Of Drosophila Melanogaster Cecropins To Inhibit Growth Of Providencia Pathogens, Sarah Smith, Marla Forfar, Christopher Feudale, Lauren Shaffer, Grace Ginder, Marion Duval, Quinn Smith, Moria C. Chambers

Faculty Journal Articles

As antibiotic-resistant bacteria spread worldwide, the need to develop novel antimicrobial agents is urgent. One rich source of potential antimicrobials is the insect immune system, as insects produce a wide range of antimicrobial peptides (AMPs) with diverse sequences and structures. Insects also encounter many bacterial pathogens, some of which are closely related to pathogens of clinical relevance. However, despite interest in AMPs as therapeutics, the relationships between the amino acid sequence, biophysical properties, antimicrobial activity, and specificity are still not generalizable. To improve our understanding of these relationships, we assessed how single amino acid changes in cecropin AMPs produced by …

Brd7 Loss Reawakens Dormant Metastasis Initiating Cells In Lung By Forging An Immunosuppressive Niche, Jayanta Mondal, Junfeng Zhang, Feng Qing, Shunping Li, Dhiraj Kumar, Jason T Huse, Filippo G Giancotti

Faculty, Staff and Student Publications

Metastasis in cancer is influenced by epigenetic factors. Using an in vivo screen, we demonstrate that several subunits of the polybromo-associated BAF (PBAF) chromatin remodeling complex, particularly Brd7, are required for maintaining breast cancer metastatic dormancy in the lungs of female mice. Brd7 loss induces metastatic reawakening, along with modifications in epigenomic landscapes and upregulated oncogenic signaling. Breast cancer cells harboring Brd7 inactivation also reprogram the surrounding immune microenvironment by downregulating MHC-1 expression and promoting a pro-metastatic cytokine profile. Flow cytometric and single-cell analyses reveal increased levels of pro-tumorigenic inflammatory and transitional neutrophils, CD8+ exhausted T cells, and CD4+ stress …

Advanced External Beam Stereotactic Radiotherapy For Skull Base Reirradiation, He Wang, Fahed M Alsanea, Dong Joo Rhee, Xiaodong Zhang, Wei Liu, Jinzhong Yang, Zhifei Wen, Yao Zhao, Tyler D Williamson, Rachel A Hunter, Peter A Balter, Tina M Briere, Ronald X Zhu, Anna Lee, Amy C Moreno, Jay P Reddy, Adam S Garden, David I Rosenthal, Gary B Gunn, Jack Phan

Faculty, Staff and Student Publications

Background/objectives: Stereotactic body radiation therapy (SBRT) for skull base reirradiation is particularly challenging, as patients have already received substantial radiation doses to the region, and nearby normal organs may have approached their tolerance limit from prior treatments. In this study, we reviewed the characteristics and capabilities of four advanced external beam radiation delivery systems and four modern treatment planning systems and evaluated the treatment plan quality of each technique using skull base reirradiation patient cases.

Methods: SBRT plans were generated for sixteen skull base reirradiation patients using four modalities: the GK plan for the Elekta Leksell Gamma Knife Perfexion/ICON, the …

A Qualitative Analysis Of 14- To 17-Year-Olds’ Perceptions Of And Interest In Dietetics, Andrea Barney, Kelsey Mueller, Emily Patten

Journal of Dietetic Education

Objective: To understand 14-17-year-old youth’s perceptions of the field of dietetics and what would influence them to pursue or not pursue dietetics as a career. Design: Researchers developed an electronic survey asking about youth’s perceptions of the dietetics profession. Setting/Participants: The survey was distributed to a diverse population of youth aged 14-17 in the USA. Main Outcome Measures: Researchers aimed to understand what qualities 14-17-year-olds associate with dietetics professionals and if youth are interested in and/or view themselves as capable of becoming a dietitian. Analysis: SPSS software calculated descriptive statistics. Open-ended responses were analyzed using conventional content analysis. Results: Half …

Agricultural Drought Prediction From Multispectral Image Processing Using Deep Learning Models, Gowri L

Theses and Dissertations

Accurate and timely prediction of agricultural droughts is fundamental to the management of ecosystems, preservation of biodiversity, and environmental sustainability. It helps to reduce environmental exploitation, promotes eco-friendly irrigation techniques, and tackles climate change efficiently. Its social implications include food safety and financial stability through continuous rural employment. Drought prediction guarantees social progress and sustainability by ensuring zero hunger/poverty and effective water management. A multi-sensor image pre-processing framework that incorporates data from various satellite platforms like Landsat (30 metres), Sentinel-2 (10 metres, 20 metres, 30 metres), and MODIS (500 metres) is used to monitor and assess agricultural drought effectively.

Analysis …

Determining Spatial Responses Of Fishers (Pakania Pennanti) To Mechanical Treatments Of Forest Stands For Fuel Reduction, Tessa R. Smith, Eric M. Gese, R. David Clayton, Patricia A. Terletzky, Kathryn L. Purcell, Craig M. Thompson

Wildland Resources Faculty Publications

Historical forestry practices (e.g., fire suppression, heavy timber logging) have contributed to a discernable change in stand composition of western forests in the U.S., which now comprise a tinderbox mixture of increased surface and ladder fuels, dense stands, and fire-intolerant species. Forest managers are mitigating this concern by implementing silviculture practices (e.g., selective logging, thinning, prescribed burning) to reduce fuel loads and improve stand resiliency. Concern for habitat specialists, such as the fisher (Pekania pennanti), have arisen as they may be negatively influenced in the short-term by modifications to their environment that are needed to ensure long-term habitat …

Anatomy And Variations Of The Carina And Its Cartilaginous Makeup: A Cadaveric Study, Chung Yoh Kim, Kristen Rizzuto, Daniel Tahan, Devendra Shekhawat, Rarinthorn Samrid, Yoko Tabira, Stephen J. Bordes, Joe Iwanaga, R. Shane Tubbs

School of Medicine Faculty Publications

Purpose: The carina, located at the bifurcation of the trachea, has been regarded as a part of the trachea. Although clinically useful as an anatomical landmark, studies of its detailed morphology are lacking in the literature. Methods: The distal trachea and left and right main bronchi were harvested from 32 cadavers and the carina studied using microsurgical dissection, endoscopy, micro-CT, and histology. Results: The right bronchial cartilages were most commonly involved in forming the carina (72.41%), and the left bronchial cartilages were the second most commonly involved (37.93%). The carinal cartilages were slightly deviated to the left of midline in …

Ion Suppression Correction And Normalization For Non-Targeted Metabolomics, Iqbal Mahmud, Bo Wei, Lucas Veillon, Lin Tan, Sara Martinez, Bao Tran, Alexander Raskind, Felice De Jong, Yiwei Liu, Jibin Ding, Yun Xiong, Wai-Kin Chan, Rehan Akbani, John N Weinstein, Chris Beecher, Philip L Lorenzi

Faculty, Staff and Student Publications

Ion suppression is a major problem in mass spectrometry (MS)-based metabolomics; it can dramatically decrease measurement accuracy, precision, and sensitivity. Here we report a method, the IROA TruQuant Workflow, that uses a stable isotope-labeled internal standard (IROA-IS) library plus companion algorithms to: 1) measure and correct for ion suppression, and 2) perform Dual MSTUS normalization of MS metabolomic data. We evaluate the method across ion chromatography (IC), hydrophilic interaction liquid chromatography (HILIC), and reversed-phase liquid chromatography (RPLC)-MS systems in both positive and negative ionization modes, with clean and unclean ion sources, and across different biological matrices. Across the broad range …

Theranostic Nanoemulsions Suppress Macrophage-Mediated Acute Inflammation In Rats, Riddhi Vichare, Yalcin Kulahci, Rebecca Mccallin, Fatih Zor, Fatma Nurefsan Selek, Lu Liu, Caitlin Crelli, Anneliese Troidle, Michele Herneisey, James M Nichols, Andrew J Shepherd, Vijay S Gorantla, Jelena M Janjic

Faculty, Staff and Student Publications

In inflammatory diseases or following an injury, dysregulated inflammation is a common driver of pain and tissue damage. Macrophages are immune cells that contribute to the initiation, maintenance, and resolution of inflammation due to their phenotypic plasticity in response to signals from inflammatory microenvironments. Macrophages infiltrate and polarize toward a pro-inflammatory phenotype (M