Digital Commons Network^™

Greenhouse Evaluation Of Great Plains Native Grasses And Forbs Tolerance To Postemergence Herbicides Used For Roadside Weed Control, Rachel C. Woody-Pumford, Matthew B. Bertucci, Mike D. Richardson, Dirk Philipp, Hannah E. Wright-Smith

Horticulture Faculty Publications and Presentations

To combat the decline in North American grasslands and prairies, innovative strategies to establish new native grass and forb plantings must be considered. Integrated vegetation management entails the use of many practices to cultivate desirable vegetation along roadsides, including mowing, applying herbicides, burning, and replanting. Currently, only a limited selection of postemergence herbicides are available to improve native plant establishment along roadsides. A greenhouse herbicide screen that included four postemergence herbicides registered for use on Conservation Reserve Program (CRP) acres and rights-of-way was conducted to test their safety for use on four native grasses (big bluestem, buffalograss, sideoats grama, and …

Timing Of Nodal Metastasis In Patients With Eyelid Sebaceous Carcinoma And Implications For Surveillance And Survival, Tracy Lu, Casey Anthony, Xinyang Jiang, Jing Ning, Ryan Goepfert, Bita Esmaeli

Faculty, Staff and Student Publications

Background/aims: Sebaceous carcinoma (SC) is a rare cancer with periocular predilection. Studies focused on patterns and timing of nodal metastasis are scarce.Our aim is to report patterns of regional nodal metastasis in patients with eyelid SC, including results of sentinel lymph node biopsy (SLNB).

Methods: All consecutive patients with eyelid SC treated during 1999-2023 were retrospectively reviewed.All subjects had standard of care surgery for eyelid SC and regional lymph node evaluation using physical examination and ultrasonography (US) at baseline and during the surveillance period. 38 patients with negative findings on US had SLNB to rule out microscopic metastasis.The frequency and …

Longitudinal Analysis Of Gut Microbiome And Metabolome Correlates Of Response And Toxicity With Idecabtagene Vicleucel, Satabdi Saha, Lubna Rehman, Abdur Rehman, Faezeh Darbaniyan, Donna M Weber, Melody Becnel, Mahmoud Gaballa, Sheeba K Thomas, Hans C Lee, Chia-Chi Chang, Reetakshi Arora, Meghan Menges, Salvatore Corallo, Marco L Davila, Frederick L Locke, Mark R Tanner, Sattva S Neelapu, Elizabeth J Shpall, Christopher R Flowers, Robert Z Orlowski, Robert R Jenq, Michael D Jain, Christine Peterson, Doris K Hansen, Neeraj Y Saini, Krina K Patel

Faculty, Staff and Student Publications

Increasing evidence suggests that the gut microbiome may influence the responses and toxicities associated with chimeric antigen receptor T-cell (CAR-T) therapy. We conducted whole-genome shotgun sequencing on stool samples (N = 117) collected at various times from patients with multiple myeloma (n = 33) who underwent idecabtagene vicleucel (ide-cel) anti-B-cell maturation antigen CAR-T therapy. We observed a significant decrease in bacterial diversity after ide-cel infusion, along with significant differences in the bacterial composition linked to therapy response and toxicities. Specifically, we found significant enrichment of Flavonifractor plautii, Bacteroides thetaiotaomicron, Blautia fecis, and Dysosmobacter species in ide-cel responders. A notable finding …

Belumosudil Reduces Oral Chronic Graft-Versus-Host Disease Tissue Inflammation And Fibrosis: A Rockstar Companion Study, Rubina Sharma, Noa G Holtzman, Iskra Pusic, Corey Cutler, Nathaniel Treister, Rohtesh S Mehta, Amin S Alousi, Nadarajah Vigneswaran, Ayesha Javaid, Francis Boksa, Drashty P Mody, Ana C Costa-Da-Silva, Olivier Schueller, Sandrine Macé, Yu Yao, Ran Ji, Beifang Hu, Kathy Marshall, Bruce R Blazar, Stephanie J Lee, Steven Z Pavletic, Jacqueline W Mays

Faculty, Staff and Student Publications

Belumosudil (KD025), an oral, selective, Rho-associated, coiled-coil-containing protein kinase 2 (ROCK2) inhibitor, is approved for third-line treatment of chronic graft-versus-host disease (cGVHD). Previous studies demonstrated that ROCK2 inhibition reduces blood interleukin-17 (IL-17) activity and promotes regulatory T-cell (Treg cell) recovery. However, these studies did not evaluate immune responses within cGVHD-affected tissues. This study assessed tissue-level immune dynamics in 20 patients with oral cGVHD from the phase 2 ROCKstar trial, before and after 6 months of belumosudil treatment, focusing on key effector sites (oral mucosa [OM], minor salivary glands [MSGs], and skin) and the peripheral blood. After belumosudil treatment, reduction in …

An Alternative Neural Basis Underlying Leptin Resistance, Hongli Li, Cunjin Su, Yuanzhong Xu, Mette Q Ludwig, Jon Davis, Qingchun Tong

Faculty, Staff and Student Publications

Overconsumption of a palatable Western diet, a condition linked to central leptin resistance, contributes extensively to the current obesity epidemic. In this context, intensive efforts have focused on detailing the molecular mechanisms underlying leptin resistance. Here, we demonstrate that chronic inhibition of hypothalamic arcuate GABAergic neurons (ArcGABA) effectively reduced diet-induced obesity (DIO). Interestingly, palatable food exposure increased the activity level of ArcGABA neurons, which do not express the leptin receptor (non-LepR neurons; nonresponsive to leptin). Chronic activation of ArcGABA non-LepR neurons led to massive obesity, which was associated with normal leptin-induced pSTAT3 signaling but phenotypic leptin resistance; i.e., high leptin …

Detection Of Oncogenic Fusions In Colorectal Cancer Using A Partner-Agnostic Next-Generation Sequencing Approach, Andrew J Pellatt, Reagan M Barnett, Sante Gnerre, Kristin Edwards, Jason A Willis, Michael J Overmann, Kanwal Raghav, Christine M Parseghian, Arvind Dasari, M Pia Morelli, Alisha Bent, Madhulika Eluri, Nicholas Hornstein, Leylah M Drusbosky, Scott Kopetz, Van K Morris

Faculty, Staff and Student Publications

Background: Gene fusions exist with low prevalence in colorectal cancer (CRC), and the clinical utility of fusion testing in advanced CRC remains unclear. We sought to identify oncogenic fusions in patients with advanced CRC using a fusion partner-agnostic circulating tumor DNA (ctDNA) assay to better understand their clinical relevance.

Methods: We performed a retrospective analysis using de-identified data from 18,558 patients with advanced CRC who underwent ctDNA next-generation sequencing with Guardant360® from 2017 to 2022. These samples were subsequently reanalyzed with a partner-agnostic bioinformatics method to identify both clonal and non-clonal fusions. We analyzed for associations between fusions and MSI-H …

A Caffeine And Theacrine Combination Improves Cognitive Performance In Tactical Personnel Under Physically Fatiguing Conditions, Blaine S. Lints, Adam T. Harrison, Sten O. Stray-Gundersen, Gianna F. Mastrofini, Riccardo F. Romersi, Noah K. Nakagawa, Mackenzie B. Yonder, Chimaobim E. Martin-Diala, Alexa J. Chandler, R. Davis Moore, Shawn M. Arent Ph.D., Cscs*D, Fissn, Facsm, Fnak

Faculty Publications

Background

Optimizing human performance under stressful physical and cognitive conditions is paramount during high-stakes military operations. As such, interventions to improve warfighter performance by mitigating task-induced cognitive performance deficits are necessary. While caffeine is the most widely consumed psychoactive substance in the world, common side effects (i.e. anxiousness, micro-saccades, irritability) may be detrimental to warfighter operations. Theacrine, a purine alkaloid similar in structure to caffeine but with a longer half-life, less habituation, and fewer side effects, is proposed as a caffeine-alternative to enhance cognitive resilience.

Methods

Tactically trained participants (n = 20; F = 5; M = 16; age …

Genetic Diversity And Historical Demography Of The Imperiled Rattlesnake-Master Borer Moth (Papaipema Eryngii), Donald B. Shepard, James R. Wilker, James A. Bess, Terry L. Esker, John A. Crawford, Michael J. Dreslik

Biological Sciences Faculty Publications and Presentations

Large-scale habitat loss and degradation have triggered a global biodiversity crisis with ecological-specialist species at increased risk of extinction. The Rattlesnake-Master Borer (Papaipema eryngii) is a small noctuid moth whose larvae feed exclusively on rattlesnake master (Eryngium yuccifolium), a native grassland plant ranging throughout the eastern United States. Widespread loss of grassland habitats has resulted in declines of P. eryngii and the species has been considered for listing under the U.S. Endangered Species Act. We analyzed the mitochondrial COI barcode sequences of 76 P. eryngii from across the species' distribution to examine genetic diversity and structure, and to test for …

Scorpions Of The Horn Of Africa (Arachnida: Scorpiones). Part Xli. Pandinops Sahil Sp. N. From Somaliland (Scorpionidae), František Kovařík

Euscorpius

Pandinops sahil sp. n. from Somaliland is described and compared with other species of the genus, fully complemented with color photos of specimens of both sexes of the new species, as well as of their habitat. Pandinops bambii Rossi, 2017 is synonymyzed with Pandinops turieli Kovařík, 2016, syn. n. A key for the species of Pandinops and a map of the distribution of the genus are provided.

Global Incidence Of Female Birdsong Is Predicted By Territoriality And Biparental Care In Songbirds, Karan J. Odom, Marcelo Araya-Salas, Lauryn Benedict, Kristi Lim, James Dale, Wesley H. Webb, Catherine Sheard, Joseph A. Tobias, Gregory F. Ball, Michelle L. Hall, Naomi E. Langmore, Michael S. Webster, Katharina Riebel

Pacific Faculty Work

Pronounced sexual dimorphism is generally assumed to evolve through sexual selection for elaborate male traits. However, there is increasing evidence that sexual dimorphism in traits such as birdsong may also evolve through loss of elaboration in females, but the evolutionary drivers underlying this process are obscure. Here we analyse ecological and natural history traits for over 1300 songbird species and show that increased female song incidence and elaboration are most directly associated with year-round territoriality, biparental care, and large body size. Phylogenetic path analysis indicates that mating system and breeding latitude primarily have indirect effects on female song evolution. Stable, …

Ethical Implications Of Being A Holobiont, Scott F. Gilbert

Biology Faculty Works

Developmental plasticity and holobiont theory have undermined the normative concepts of biological individuality. However, such traditional ideas of biological individuality have helped define and support Western ethical views into the 21st century. Guided by some of the ethical formulae of Simone Weil, Hans Jonas, and Alastair MacIntyre, this essay attempts to outline some possible trajectories for an ethics that is bounded by these new biological paradigms of environmental agency. Specifically, the ecological developmental biology concepts of plasticity and holobiont theory permit the “ethics of attention” to focus on the partnerships of living beings. Highlighting environmentally integrated life cycles and their …

A Deep-Learning-Based Dehazing Framework For Non-Homogenous Scenes, Shimaa Mohammed Abd Elghany, Doaa A. Altantawy, Hossam El-Din Moustafa Moustafa

Mansoura Engineering Journal

The advancement of single-image dehazing techniques has been rapid in recent years. Several existing algorithms that are based on deep learning have shown remarkable efficiency for dealing with homogeneous hazing-free issues, but convolutional neural networks (CNNS) frequently fail on non-homogeneous dehazing datasets. Meanwhile, dehaze results from dense haze regions are often blurry because the information of these regions is typically unknown and difficult to estimate. To address these issues, an efficient image enhancement dehazing algorithm that utilizes deep learning techniques, and a non-uniform atmospheric scattering model had been proposed. Unlike the majority of existing dehazing methods, the medium transmission function …

A Comprehensive Study Of Transportation Projects Impact In Congested Cities Through Travel Demand Modeling And Decision-Making Tools: A Case Study Of Zagazig City, Egypt, Amr M. Sakr, Metwally Gouda Mohamed Altaher, Mahmoud El-Saied Ali Solyman, Mohamed Ibrahim El-Sharkawi Attia

Mansoura Engineering Journal

Transportation projects are major resource-intensive projects that largely influence the transportation system’s resilience, human health, and quality of life. This study aims to assess and prioritize four transportation projects in Zagazig City, Egypt, in an attempt to build a more sustainable transport system. The travel demand model is used to determine various traffic characteristics and environmental impacts, and decision-making tools are used to evaluate the proposed projects. Benefit-cost analysis (BCA) is employed to investigate the economic feasibility of the proposed projects, and two hybrid multiple-criteria decision-making (MCDM) methods are used to prioritize the proposed projects. Through the work conducted in …

Collaborative Class Zine: Weekly Reflection Assignment With Powerpoint Template, Brett Whysel

Open Educational Resources

Abstract

This collaborative class zine assignment uses a shared PowerPoint format to deepen student learning while building community. Students contribute visual reflections (graphics, diagrams, quotes, or doodles) weekly or periodically throughout the semester. Faculty provide reflection prompts about key takeaways and unclear concepts (sample prompts included). The resource includes both sample LMS instructions and a ready-to-use PowerPoint zine template that works across all disciplines. By combining metacognitive reflection with creative expression, students consolidate learning by finding new connections and applications. The collaborative format creates community connections and joy while students learn from peers' diverse perspectives.

Biochar Type And Rate Effects On Greenhouse Gas Emissions Fromfurrow-Irrigated Rice, Lauren Gwaltney, Kristofor R. Brye, Diego Della Lunga, Trenton L. Roberts, Samuel B. Fernandes, Mike B. Daniels

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Biochar is a relatively new, potential climate-mitigation strategy, but biochar still requires investigation regarding biochar's ability to reduce greenhouse gas (GHG) emissions. Little research has been conducted to quantify the impacts of biochar on GHG production from upland (i.e., furrow-irrigated) rice (Oryza sativa) production systems. The objective of this study was to evaluate the effects of wood biochar type (powder and coarse particle size) and application rate (0, 2.5, and 5 Mg ha-1) on GHG emissions in greenhouse-grown, simulated furrow-irrigated rice grown in a silt-loam soil. Carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) fluxes were measured weekly throughout …

The Effect Of Transformer Based Pre-Trained Language Models On Biomedical Relation Extractions, Eman Saad, Sherif Kishk, Amr Ali-Eldin, Ahmed I. Saleh

Mansoura Engineering Journal

Biomedical relation extraction represents a critical advancement in healthcare research. As the volume of biomedical publications continues to grow exponentially, efficient extraction of entity relationships has become essential for accelerating knowledge discovery, drug development, and precision medicine initiatives. The field has evolved from focusing on simple binary relations, such as Protein-Protein Interactions (PPI), which are fundamental to understanding cellular processes and therapeutic development, to addressing more complex multi-class classification challenges like Drug-Drug Interactions (DDI) and Chemical-Protein Interactions (CPI).Pre-trained language models have become the cornerstone of modern approaches of extracting biomedical relations. Models like BioBERT, PubMedBERT, and SciBERT, along with general-purpose …

Scorpions Of The Horn Of Africa (Arachnida: Scorpiones). Part Xl. Barbaracurus Lowei Sp. N. From Ethiopia (Buthidae), František Kovařík, Hassan Sh A. Elmi

Euscorpius

Barbaracurus lowei sp. n. from Ethiopia is described and compared with other species of the genus, fully complemented with color photos of specimens of both sexes of the new species, as well as of their habitat. Included is a key for Barbaracurus and a map of the distribution of the genus in the Arabian Peninsula and the Horn of Africa.

Anti-Dirt Hand Sanitizer: A Zeolite-Enhanced Approach To Hygiene And Microbial Protection, Theo Uskoković, Evangelina Uskoković, Victoria Wu, Vuk Uskoković

Administration and Staff Articles and Research

Children love to play with dirt and their outdoor activities oftentimes make their hands heavily soiled. Meanwhile, improper sanitation of the hands prior to making contact with food or bodily fluids can result in potentially dangerous infection. In situations where handwashing is not available, hand sanitizers present a common cleaning agent of choice. However, as it is shown here, standard sanitizers, albeit acting effectively against skin microbes, do not have the ability to remove the dirt deposits off children's hands, where microbial colonies may remain protected against the antiseptic effect of the sanitizer. To circumvent this limitation, we designed and …

Targeted Delivery Of Rapamycin Via Epidermal Growth Factor Receptors In Pancreatic Cancer Cells Inhibits Cell Proliferation And Induces Apoptosis, Nawab Ali, Adeolu S. Oluremi, Christopher Baldwin, Nickolas Gustavison, Mujeebat Bashiru, Adeniyi Oyebade, Noureen Siraj, Raj Raghavendra Rao

Faculty Scholarship

Pancreatic cancer (PC) is aggressive and deadly; most PC cells overexpress an epidermal growth factor receptor (EGFR). EGFR-targeting peptide (GE11) was conjugated to gold nanoparticles (AuNPs) for delivering rapamycin (Rap), an mTOR inhibitor that reduces proliferation and induces apoptosis. Biophysical techniques confirmed the conjugation. Rap loading efficiency was 41.5%, with sustained release at a lower pH. Conjugates showed higher uptake in PANC-1 cells than unmodified AuNPs. It also inhibited proliferation and induced apoptosis via pathways involving reactive oxygen species, mitochondrial damage, and caspase activation. This approach represents a promising nanoparticle-based therapeutic strategy targeting PC cells, utilizing GE11-EGFR interactions to minimize …

Accuracy Of Anthropometric Equations In Estimating Body Fat Percentage In Transgender Men Undergoing Gender-Affirming Hormone Therapy, Barbara Buosi, Yana Barros Hara, Rodolfo André Dellagrana, Rafael Martins Da Costa, Mateus Rossato

International Journal of Exercise Science

International Journal of Exercise Science 18(1): 686-694, 2025. Transgender people may opt for the use of sex steroids and, in some cases, hormone blockers, which can lead to changes in body fat distribution. The aim of this study was to verify the accuracy of anthropometric equations to estimate the body density (BD) of transgender men who are undergoing Gender-Affirming Hormone Therapy (GAHT). Four transgender men (25-32 years old), who had performed GAHT for at least six months and used the hormone testosterone cypionate participated in the study. The reference criteria for BD was air displacement plethysmography (ADP). In addition, BD …

Inter-Effort Recovery Intermittent Hypoxia And Force Parameters In Sprint Interval Exercise, Tarine Botta De Arruda, Felipe Alves Ribeiro Ms, Germano Marcolino Putti, Marcelo Papoti

International Journal of Exercise Science

International Journal of Exercise Science 18(3): 672-685, 2025. Performing training sessions in hypoxia leads to a decrease in effort quality. The inter-effort recovery intermittent hypoxia model seems to ensure training session performance. The aim of this study is to investigate the effects of sprint interval exercise under normoxic (NOR), continuous hypoxic (HYP), and inter-effort hypoxic (IEH) conditions on force parameters. Seven swimmers (age: 26.04 ± 4.64 years) volunteered and performed one session of the 10 × 30-s all-out tethered swimming efforts with 4-min passive recovery intervals for each condition. Considering the simulated altitude at F_iO₂ = 0.13 …

Executive Dysfunction In College Aged Students With And Without Mild Traumatic Brain Injury, Emily A. Veasey, Tyler Herring

Neuroscience Summer Fellows

Functional near-infrared spectroscopy (fNIRS) is a non-invasive tool used to measure cortical hemodynamics and has growing applications in studying executive functioning after mild traumatic brain injury (mTBI). In this study, fNIRS was used to examine prefrontal cortex activation in individuals with a history of concussion during the Iowa Gambling Task, which is used to measure decision making under uncertainty and risk. This task assesses key executive functions such as decision-making, inhibition, and planning. This study aimed to find a correlation between college-aged students with mTBIs and frontal lobe dysfunction. We are going to see that students with more concussions, a …

A Cancer Education Needs Assessment: Informing Middle-Aged Female Patients About The Relationships Between Obesity And Women’S Health Concerns In The Reproductive System, Breast, And Endometrial Health, Batul Mirza

MUSC Theses and Dissertations

Obesity significantly impacts women’s health, particularly among middle-aged women, by increasing the risk of hormone-sensitive cancers such as breast, endometrial, and reproductive system cancers. This study examines the educational needs of this demographic group regarding obesity-related cancer risks and explores effective intervention strategies. Obesity-induced mechanisms – hormonal imbalances, chronic inflammation, and insulin resistance – drive cancer susceptibility, emphasizing the need for targeted health education. The study employs a qualitative design, which includes interviews with subject matter experts (SMEs) and surveys of middle-aged women. The goal is to assess awareness, perceived barriers, and preferred learning methods. Findings suggest that with many …

Detection Of Neuron Derived Cfdna In Blood Plasma: A New Diagnostic Approach For Neurodegenerative Conditions, Chad Alan Pollard

Theses and Dissertations

Neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS) are characterized by the progressive loss of distinct neuronal subtypes, yet current diagnostic tools are either invasive, limited in resolution, or poorly suited for early detection and longitudinal monitoring. This dissertation began with a proof-of- concept study using bisulfite-PCR at a neuron-enriched locus to detect cortical neuron-derived cell-free DNA (cfDNA) in AD plasma samples, establishing the potential of cfDNA as a marker of neuronal injury. Building on these preliminary findings, a novel framework was developed utilizing Oxford Nanopore Technologies (ONT) to profile genome-wide native DNA …

Novel Tools And Datamining Techniques To Visualize And Interpret Historical Sugarcane Datasets, Zachary A. Taylor

LSU Master's Theses

Heritable genetic variation is an essential raw ingredient of variety development programs. This variation is acted upon via selection by identifying elite progeny that can be utilized agronomically or exploited as parents. Sugarcane breeders are tasked with creating optimal genetic variation through crossing. Prior knowledge of pedigree and parental performance allows breeders to discern which crosses to prioritize, since the time to make crossing decisions and the space to evaluate tens and thousands of progenies are both limited resources in sugarcane variety development programs. In this project, we have updated and validated the U.S. sugarcane pedigree …

Parthenocarpic Cucumber Cultivar Susceptibility Varies Among Common High Tunnel Insect And Mite Pests, Leslie Aviles, Elizabeth Maynard, Wenjing Guan, Laura Ingwell

Department of Horticulture & Landscape Architecture Faculty Publications

High tunnels (HTs) are a protected agriculture tool used by specialty crop farmers. Cucumbers (Cucumis sativa L.) are well suited for HT production because of their vertical growth habit, allowing for space optimization, and repeated flowering, providing multiple harvest opportunities. However, twospotted spider mites (Tetranychus urticae Koch; TSSM), striped cucumber beetles (Acalymma vittatum Fabricius), and melon aphids (Aphis gossypii Glover) are common pests of cucumbers in HT systems, limiting production. The unique environment of HTs lacks regulation of temperatures, which can reach high levels during summer, facilitating the rapid development of pests. Here, we present results …

Granulocyte-Colony Stimulating Factor Effects On The Mesolimbic Dopamine Circuitry And Adaptations With Chronic Ethanol Exposure, Rachel Ji-Hyae Campbell

Theses and Dissertations

The mesolimbic dopamine (DA) system contributes to reward and reinforcement learning for ethanol (EtOH). The nucleus accumbens (NAc) receives DA input from the ventral tegmental area (VTA) encoding rewarding information. Acute EtOH increases NAc DA levels, and this DA response is attenuated with chronic EtOH exposure. Furthermore, chronic EtOH results in reduced DA release, increased DA clearance and presynaptic D2-type auto-receptor sensitization. Further research into EtOH-induced neural adaptations that modulate NAc DA release is explored herein, including changes in cholinergic interneurons (CIN), which are known regulators of DA transmission. One potential class of regulators are immune related cytokines, that can …

A Glyoxal-Specific Aldehyde Signaling Axis In Pseudomonas Aeruginosa That Influences Quorum Sensing And Infection, Christopher J. Corcoran, Bonnie J. Cuthbert, David G. Glanville, Mailyn Terrado, Diana Valverde Mendez, Benjamin P. Bratton, Daniel E. Schemenauer, Valerie L. Tokars, Thomas G. Martin, Lawrence W. Rasmussen, Matthew C. Madison, Andrew F. Maule, Joshua W. Shaevitz, Boo Shan Tseng, Julian P. Whitelegge, Catherine Putonti, Amit Gaggar, Jordan R. Beach, Jonathan A. Kirk, Alfonso Mondragón, Abby R. Kroken, Jonathan P. Allen, Celia W. Goulding, Andrew T. Ulijasz

Biology: Faculty Publications and Other Works

The universally conserved α-oxoaldehydes glyoxal (GO) and methylglyoxal (MGO) are toxic metabolic byproducts whose accumulation can lead to cell death. In the absence of a known, natural inducer of the GO-specific response in prokaryotes, we exploited RNA-seq to define a GO response in the bacterial pathogen Pseudomonas aeruginosa. The highest upregulated operon consisted of the known glyoxalase (gloA2) and an antibiotic monooxygenase (ABM) domain of unknown function - renamed here Aldehyde responsive quorum-sensing Inhibitor (ArqI). The arqI-gloA2 operon is highly specific to GO induction and ArqI protein responds by migrating to the flagellar pole. An ArqI atomic structure revealed several …

Image-Based Inference Of Tumor Cell Trajectories Enables Large-Scale Cancer Progression Analysis, Yang Liu, Ling Cai, Ruichen Rong, Shidan Wang, Liwei Jia, Peiran Quan, Qin Zhou, Guanghua Xiao, Yang Xie

Faculty, Staff and Student Publications

Current approaches to estimating cell trajectories, tumor progression dynamics, and cell population diversity of tumor microenvironment often depend on single-cell RNA sequencing, which is costly and resource intensive. To address this limitation, we developed an artificial intelligence (AI) model that leverages cell morphology features and histological spatial organization to classify tumor cell differentiation status, infer cell dynamic trajectories, and quantify tumor progression from hematoxylin and eosin (H&E)-stained whole-slide images. In three independent lung adenocarcinoma cohorts, our AI-based model accurately predicted cell differential status and provided quantifiable measures of tumor progression that were prognostic of patient survival. Spatial transcriptomic integrative analyses …

A Two-Stage Dual-Task Learning Strategy For Early Prediction Of Pathological Complete Response To Neoadjuvant Chemotherapy For Breast Cancer Using Dynamic Contrast-Enhanced Magnetic Resonance Images, Bowen Jing, Jing Wang

Faculty, Staff and Student Publications

Early prediction of treatment response can facilitate personalized treatment for breast cancer patients. Studies on the I-SPY 2 clinical trial demonstrate that multi-time point dynamic contrast-enhanced magnetic resonance (DCEMR) imaging improves the accuracy of predicting pathological complete response (pCR) to chemotherapy. However, previous image-based prediction models usually rely on mid- or post-treatment images to ensure the accuracy of prediction, which may outweigh the benefit of response-based adaptive treatment strategy. Accurately predicting the pCR at the early time point is desired yet remains challenging. To improve prediction accuracy at the early time point of treatment, we proposed a two-stage dual-task learning …