Digital Commons Network^™

The Benefits Of High Phosphate Concentration (10n : 1p) And Diagonal Orientation On The Ex Situ Grow-Out Of Caribbean Coral Juveniles, Ashley Shen

All HCAS Student Capstones, Theses, and Dissertations

As coral reefs keep declining, it is imperative to increase coral production ex situ for restoration, but this requires culture protocols to be optimized. This study examined the impacts of grow-out orientation and phosphate concentration (and nitrate (N): phosphate (P) ratio) on the survival and growth of Montastraea cavernosa and Pseudodiploria clivosa juveniles from 3 to 9 months old. Pristine reefs typically have low nitrate (0.12μmol/L) and low phosphate (0.03μmol/L) concentrations, leading to N:P ratios of 4-16 N: 1P. In recirculating tanks, it is difficult to lower nitrate concentrations below 25μmol/L. Here we hypothesized that increasing the phosphate concentration in …

“Asking For Help Feels Like A Weakness”: Factors Shaping First-Year Students’ Expectations Of Stem Course Office Hours, Jeremy L. Hsu, Grace Holick, Rebecca M. Green, Elaine Benaksas Schwartz, Melissa Rowland-Goldsmith

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background

Office hours are one of the most ubiquitous resources for students in STEM courses. However, there has been only limited work examining what students think of STEM course office hours, and we are not aware of any past work that has examined (1) how students perceive STEM course office hours upon entering college, and (2) how these perceptions change over time and the factors that shape these perceptions and expectations of what will occur in office hours. Here, we utilize a longitudinal series of surveys to capture first-year students’ perceptions and expectancies for office hours at the beginning of …

Gated Recurrent Unit With Decay Has Real-Time Capability For Postoperative Ileus Surveillance And Offers Cross-Hospital Transferability, Xiaoyang Ruan, Sunyang Fu, Heling Jia, Kellie L Mathis, Cornelius A Thiels, Schaeferle M Gavin, Patrick M Wilson, Curtis B Storlie, Hongfang Liu

Faculty, Staff and Student Publications

Background: Ileus, a postoperative complication after colorectal surgery, increases morbidity, costs, and hospital stays. Assessing risk of ileus is crucial, especially with the trend towards early discharge. Prior studies assessed risk of ileus with regression models, the role of deep learning remains unexplored.

Methods: We evaluated the Gated Recurrent Unit with Decay (GRU-D) for real-time ileus risk assessment in 7349 colorectal surgeries across three Mayo Clinic sites with two Electronic Health Record (EHR) systems. The results were compared with atemporal models on a panel of benchmark metrics.

Results: Here we show that despite extreme data sparsity (e.g., 72.2% of labs, …

Crop Yield Prediction At Multiple Spatial Scales With Statistical Machine Learning, Vaibhav Charan, Pratishtha Poudel

Discovery Undergraduate Interdisciplinary Research Internship

Understanding and accurately predicting crop yield is becoming increasingly important today in the face of global food security challenges, and thus, the availability of standardized data and scalable models is the need of the hour. To support this, researchers have developed CY-Bench (Crop Yield Benchmark), a comprehensive dataset that helps forecast maize and wheat yields on a global scale. This research project primarily involved working with the CY-Bench dataset aiming to improve crop yield prediction through machine learning. Initially, papers explaining the CY-Bench dataset and other papers for agriculture modeling were studied and analyzed in detail. The research then progressed …

Opposing Roles For Iron Transport Systems In Gallium Tolerance In Extraintestinal Pathogenic Escherichia Coli, Nagama Parveen

Theses and Dissertations

Iron is required for bacterial growth because it serves as a co-factor for enzymes involved in DNA synthesis, cellular respiration, and other processes. Disrupting bacterial iron homeostasis is an effective strategy to prevent the growth of antibiotic-resistant bacteria, and gallium (Ga³⁺) has emerged as a promising candidate due to its ability to displace iron (Fe³⁺) and prevent essential iron-dependent pathways. However, Escherichia coli are naturally less sensitive to gallium than many other bacteria, and the mechanisms that control gallium tolerance are not completely understood. To address this, we performed a genome-wide transposon sequencing (TnSeq) screen to identify genes important for …

08.04.2025 Ored Connect, Liz Williamson

ORED Newsletter

NIH limits AI use and annual proposals accepted per PI

Buffalo Stories & Science For 4th Graders, Ashley A. Duffy, Larry M. Browning, Matt Miller, Jiyul Chang, Srinivas Janaswamy, Lydia Yellow Hawk, Jessica Larson, Michael Prate, Madhav P. Nepal

iLEARN Teaching Resources

In this culturally responsive science lesson, students explore the ecological and historical importance of buffalo through story and hands-on learning. Using Paul Goble’s Return of the Buffaloes, learners’ journey into Lakota legend to discover how buffalo sustained communities and symbolized connection to land and spirit. Through guided reading, students uncover how buffalo supported Indigenous survival—providing food, shelter, clothing, and tools—while developing an appreciation for traditional knowledge systems and biodiversity. Students then deepen their understanding of food science by making buffalo jerky, connecting past and present preservation methods. As they mix ingredients, shape meat into strips, and observe dehydration techniques, students …

Indirect Dna Transfer To Duct Tape Rolls Stored In Cars, Yuching Chung

Student Theses

This project investigated the accumulation of DNA on duct tape rolls stored in cars. Specifically, we analyzed samples recovered from three areas (the inside, outside, and flat sides) of unused duct tape stored under the driver's seat and trunk of cars for seven days. Twelve volunteers were recruited, resulting in 64 DNA samples from 12 cars. We evaluated DNA quantities and STR genotyping outcomes after amplification with the GlobalFiler™ kit. On average, the DNA yields from under the driver's seat were higher than from the trunk, but the difference was not significant. The inside of the tape roll yielded significantly …

The Ring-Finger Ubiquitin E3 Ligase Rfel1 Targets Wheat Npr3 For Degradation To Confer Broad-Spectrum Resistance Against Biotrophic Fungal Pathogens, Liuhui Qiao, Kunpu Zhang, Jinyan Li, Ziming Zhang, Xiao Sun, Huiyun Liu, Ziyue Li, Nannan Ni, Ximei Ma, Jianhui Zhao, Guangwei Li, Xiaohuan Jin, Wenming Zheng, Daowen Wang, Zheng Qing Fu, Huan Wang

Faculty Publications

No abstract provided.

Staff Education For Improved Diabetes Management: Enhancing Knowledge And Patient Outcomes, Carissa Martine Bolden

Walden Dissertations and Doctoral Studies

An increase in patients’ hemoglobin A1c levels in a South Mississippi organization suggests that inadequate type 2 diabetes (T2DM) knowledge among the staff hindered them from delivering competent care. The gap in practice at the site revealed a deficiency in knowledge in nutrition education for healthcare providers and staff, which led to the practice question: Does educating providers and staff on nutrition for adults with type 2 diabetes improve knowledge, as evidenced by pre- and post-surveys? This educational initiative employed the analysis, design, development, implementation, and evaluation (ADDIE) model, the John Hopkins evidence-based practice (JHEBP) model, the Walden University Doctor …

Integrating Ctdna Analysis And Radiomics For Dynamic Risk Assessment In Localized Lung Cancer, Everett J Moding, Mohammad Shahrokh Esfahani, Cheng Jin, Angela B Hui, Barzin Y Nabet, Yufei Liu, Jacob J Chabon, Michael S Binkley, David M Kurtz, Emily G Hamilton, Aadel A Chaudhuri, Chih Long Liu, Zhe Li, Rene F Bonilla, Alice L Jiang, Brianna C Lau, Pablo Lopez, Jianzhong He, Yawei Qiao, Ting Xu, Luyang Yao, Saumil Gandhi, Zhongxing Liao, Millie Das, Kavitha J Ramchandran, Sukhmani K Padda, Joel W Neal, Heather A Wakelee, Michael F Gensheimer, Billy W Loo, Ruijiang Li, Steven H Lin, Ash A Alizadeh, Maximilian Diehn

Faculty, Staff and Student Publications

The complementarity and clinical utility of combining liquid biopsies and radiomic image analysis has not been demonstrated. Circulating tumor DNA (ctDNA) minimal residual disease after chemoradiotherapy (CRT) for non-small cell lung cancer (NSCLC) is highly prognostic, but on-treatment biomarkers are needed to enable response-adapted therapies. Here, we analyzed 418 patients with NSCLC undergoing CRT to develop and validate a novel dynamic risk model that accurately predicts ultimate progression-free survival during treatment. We optimize tissue-free variant calling from plasma samples to facilitate ctDNA monitoring and demonstrate the importance of accounting for persistent clonal hematopoiesis variants. We show that mid-CRT ctDNA concentration …

Depletion Of Effector Regulatory T Cells Associates With Major Response To Induction Dual Immune Checkpoint Blockade, Xianli Jiang, Nils-Petter Rudqvist, Bo Jiang, Shengbin Ye, Shan He, Qingnan Liang, Jinzhuang Dou, Michelle D Williams, Joe Dan Dunn, Jason M Johnson, Keiko Akagi, Weihong Xiao, Shaoheng Liang, Satvik Elayavalli, Baohua Sun, Edwin R Parra, Renata Ferrarotto, Adam S Garden, Clifton David Fuller, Jay Reddy, Neil D Gross, Miriam N Lango, Cheuk Hong Leung, Suyu Liu, Diane D Liu, Meng Li, J Jack Lee, Michael A Curran, Jack Phan, Ken Chen, Maura L Gillison

Faculty, Staff and Student Publications

In a phase II trial, patients with local-regionally advanced human papillomavirus-positive oropharyngeal carcinoma (n = 35) received ipilimumab (anti-CTLA4) and nivolumab (anti-PD-1) as induction immunotherapy and concurrently with radiotherapy (NCT03799445). Coprimary endpoints included 6-month complete metabolic response rate (94%) and 2-year progression-free survival (84%). Induction yielded a 46% major histopathologic response rate. Single-cell profiling revealed responders had higher baseline intratumoral CD8+ T cells with a tumor-reactive, tissue-resident memory (TRM) phenotype and a treatment-related decrease in effector regulatory T (eTreg) cells. The eTreg decrease correlated with CD8+ T-cell clonotype transitioning from TRM to effector memory and IFNG+ effector cells. …

Car-Macrophage Cell Therapy: A New Era Of Hope For Pancreatic Cancer, Daoyan Wei, Liang Wang, Yi Liu, Xiangsheng Zuo, Xiling Shen, Robert S Bresalier

Faculty, Staff and Student Publications

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest malignancies, characterized by late diagnosis, early metastasis, and resistance to conventional therapies. A major barrier to effective treatment is its desmoplastic and immunosuppressive tumor microenvironment (TME), which restricts T cell infiltration and dampens responses to immune checkpoint inhibitors (ICIs). These features highlight the urgent need for innovative immunotherapeutic strategies capable of overcoming PDAC's immunologic and physical barriers. Chimeric antigen receptor (CAR)-macrophage (CAR-M) therapy has emerged as a promising approach to address these challenges. Unlike CAR-T or CAR-NK cells, CAR-Ms can efficiently infiltrate tumors, remodel the TME, phagocytose tumor cells, and stimulate …

Landscape Of Clinical Trials In Cancer Cachexia: Assessment Of Trends From 1995-2024, Ana Regina Cabrera, Kaitlyn Parker, Deena B. Snoke, Bart Hammig, Nicholas P. Greene

Health, Human Performance and Recreation Faculty Publications and Presentations

Background Cancer cachexia, a multifactorial syndrome characterized by unintentional weight loss, is a frequent complication of cancer that impacts patients' quality of life and survival.

Methods In this retrospective review, we evaluated the landscape of clinical trials registered on ClinicalTrials.gov for the consideration of potential factors contributing to biological human heterogeneity in their design and analyses.

Results Among clinical trials registered from 1995-2024, we observed increased inclusion of female participants, but lack of reporting of sex as a biological variable. The majority (similar to 93%) of participants were of Caucasian descent. There was a substantial divergence in the diagnostic criteria …

Volumetric Imaging Of Cellular Dynamics Using Light-Sheet Microscopy: From Subcellular Structures To Whole Organisms, Md Nasful Huda Prince

Optical Science and Engineering ETDs

Advancing biomedical imaging requires platforms that combine high-resolution, speed, and stability across biological scales. This dissertation presents three innovations designed to address limitations of conventional light-sheet and oblique plane imaging. First, we introduce Reflected Inline Detection in Epi-Oblique Plane Microscopy (RIDE-OPM), a compact and drift-resistant system that eliminates a tertiary detection path while maintaining alignment flexibility, enabling robust long-term live imaging. Second, we present a high-speed Axially Swept Light-Sheet Microscopy (ASLM) platform for cleared tissues, using dual foci and synchronized sweeping to achieve isotropic sub-micron resolution at up to 40 frames-per-second, a fourfold improvement over standard ASLM. Integrated with a …

Silicon Is The Next Frontier In Plant Synthetic Biology, Aniruddha Acharya, Kaitlin Hopkins, Tatum Simms

Faculty Publications - Biological Sciences

Silicon has a striking similarity to carbon and is found in plant cells. However, there is no specific role that has been assigned to silicon in the life cycle of plants. The amount of silicon in plant cells is species specific and can reach levels comparable to macronutrients. Silicon is used extensively in artificial intelligence, nanotechnology, and the digital revolution, and thus can serve as an informational molecule such as nucleic acids. The diverse potential of silicon to bond with different chemical species is analogous to carbon; thus, it can serve as a structural candidate similar to proteins. The discovery …

Unci Maka’S Gift: An Outdoor Science Adventure For The First Graders, Arlene A. Abao, Larry M. Browning, Matt Miller, Jiyul Chang, Srinivas Janaswamy, Jessica Larson, Lydia Yellow Hawk, Michael Prate, Madhav P. Nepal

iLEARN Teaching Resources

In this super-fun lesson, kids are going outside to explore the schoolyard! They will look for all sorts of amazing plants, also called flora. They will use a special tablet to help us learn their names and then draw pictures of them. They will also dig a little to see the soil and learn why it's so important for plants to grow big and strong. And guess what? They’ll even look for little animals like ants or butterflies, also called fauna, that live near the plants, because everything in nature works together! They'll also hear cool stories about how people …

Culturally Responsive Teaching: Identifying Conifers Through Science And Tradition, Madhav P. Nepal

iLEARN Teaching Resources

This lesson on plant taxonomy introduces students to the scientific system used to name, classify, and identify plant species, with a focus on conifer trees found in local environments. Students explore how observable traits—such as needle shape, cone structure, and bark texture—are used to group plants into categories that reflect their evolutionary relationships. Through a hands-on tree-walk activity, students use a simplified dichotomous key to identify at least five conifer species on or near school grounds. They then use digital plant ID tools to confirm their findings and compare traditional and modern identification methods. The lesson also emphasizes the hierarchical …

Partial Cystectomy For Muscle-Invasive Bladder Cancer, Peter S Palencia, Nethusan Sivanesan, Syed Rahman, Fady Ghali, David Hesse, John Colberg, Ashwin Sridhar, John D Kelly, Byron H Lee, Ashish M Kamat, Wei-Shen Tan

Faculty, Staff and Student Publications

Partial cystectomy is a surgical bladder-sparing option for selected patients with muscle-invasive bladder cancer (MIBC), urachal adenocarcinoma and diverticular bladder tumors. Partial cystectomy hold several advantages. It allows for definite pathology and accurate staging while avoiding side effects from radiation therapy and preserves the option for salvage radical therapy (radical cystectomy or radical radiotherapy). Patients should have a CT urogram, prostatic urethral biopsy and mapping biopsies or blue light cystoscopy to rule out multifocal disease or CIS. Small solitary MIBC patients without carcinoma in situ in an area of the bladder where resection can be performed with negative margin would …

Bcl-2/Bcl-Xl Dual Inhibition Triggers Gasdermin D-Mediated Pyroptosis In Mantle Cell Lymphoma, Yijing Li, Joseph Mcintosh, Vivian Jiang, Fangfang Yan, Jovanny Vargas, Yuxuan Che, Wei Wang, Ching-Fei Li, Yue Fei, Celeste Lee, Lei Nie, Yixin Yao, Michael Wang, Heng-Huan Lee, Yang Liu

Faculty, Staff and Student Publications

No abstract provided.

Restoration At The Intersection Of Science And Outreach-The Working Woods Learning Forest, Katharine L. Stuble, David J. Burke, Samuel C. Harbol, Chad Knisely, Jessica Miller Mecaskey, Alexa S. Wagner, Michael Watson, Kevin E. Mueller

Biological, Geological, and Environmental Faculty Publications

Botanical gardens and arboreta have enormous (if often under-realized) potential to increase understanding of restoration as a predictive science while simultaneously serving as platforms promoting large-scale restoration by public and private stakeholders. Public gardens often have deep histories of both research and outreach and, increasingly, engagement in restoration efforts. As a team of researchers and practitioners, we share our experiences using a forest management manipulation at the Holden Arboretum for both research and outreach. Forest management is a key tool for enhancing biodiversity and ecosystem services in young forests. Known as the Working Woods Learning Forest, this restoration simultaneously serves …

Quantile Index Predictors Using R Package Hyper.Gam, Tingting Zhan, Misung Yi, Inna Chervoneva

Department of Pharmacology, Physiology, and Cancer Biology Faculty Papers

MOTIVATION: Evaluation of single-cell protein expression from immunohistochemistry images is used increasingly in biomedical research. Many proteins are used solely for phenotyping cells in the tumor microenvironment. Other proteins with meaningfully quantitative expression levels provide so-called functional protein biomarkers. There is still a limited number of methods and software tools available for utilizing the entire distributions of single-cell expression levels.

RESULTS: We present the R package hyper.gam, providing a supervised learning framework for deriving biomarkers based on single-cell distribution quantiles. The single-cell data are first converted into sample quantile functions, which are then used as predictors in scalar-on-function regression models …

Rna Sequencing And Immunohistochemistry Jointly Improve Tumor Biomarker Interpretation, Vladimir Kushnarev, Danil Stupichev, Suren Davitavyan, Kirill Kriukov, Basavaraja U Shanthappa, Anna Butusova, Sofia Menshikova, Anna Belozerova, Anastasia Shvyrkova, Arina Tkachuk, Olga Khatenkova, Linda Balabanian, Ekaterina Postovalova, Jochen K Lennerz, Funda Meric-Bernstam, Alexander Bagaev

Faculty, Staff and Student Publications

This study aimed to assess the correlation between RNA sequencing (RNA-seq) and immunohistochemistry (IHC) in detecting key cancer biomarkers across solid tumors, and then, to establish RNA-seq thresholds that accurately reflect clinical IHC classifications. Expression levels of nine biomarkers-ESR1, PGR, AR, MKI67, ERBB2, CD274, CDX2, KRT7, and KRT20-were analyzed in 365 formalin-fixed, paraffin-embedded samples from breast, lung, gastrointestinal, and other solid carcinomas. Correlations between RNA-seq data and IHC scores were determined using Spearman's correlation coefficients, with RNA-seq cut-offs established to distinguish positive from negative IHC scores. The results revealed strong correlations for most biomarkers, with coefficients ranging from 0.53 to …

Sex, Stress And Hormones : The Role Of Modifiable Risk Factors In The Kinetics Of Alzheimer’S Disease, Hannah Marie Edwards

Arts & Sciences Graduate Student Theses and Dissertations

Alzheimer’s Disease (AD) is a neurodegenerative disease hallmarked by the presence of amyloid- plaques and tau tangles in the brain. The process of the disease begins decades prior to the onset of symptoms and is thought to be driven first by a buildup of amyloid- peptide in the extracellular space, triggering a cascade of pathology and symptomology culminating in loss of cerebral volume and cognitive impairment. Women are diagnosed with AD at a rate 2/3 higher than their male counterparts, even when controlling for age. While most driving factors of the disease are thought to be genetic, roughly 40% of …

Breeding Season Bird Use Of And Non-Native Plants Found In Food Plots In The Southern Appalachian Mountains, Nathan A. Klaus, Kirk Stodola

Georgia Journal of Science

Traditional agricultural style food plots, or wildlife openings, are widely used for wildlife management and hunting opportunities on public and private lands in the Southeastern United States. These habitats are often cited as beneficial for game and nongame wildlife, but there are few published studies examining nongame bird use of food plots in recent decades. Modern concerns about the ecological costs of food plots, particularly fragmentation and invasive non-native species, warrant a new examination of this practice. We conducted avian surveys during the breeding season of 2008 at 39 sites composed of three different treatments: traditional food plots, novel food …

Tides, Tourists, And Tails: Exploring Human-Wildlife Overlap On The Homer Spit, Alaska, Serena Seiler

Masters Theses & Specialist Projects

Coastal areas present unique challenges for human-wildlife coexistence due to their shared use by people and marine species. The Homer Spit in Homer, AK (59.6481° N, 151.5299° W) is a projection of land into Kachemak Bay on which lodging, restaurants, campgrounds, RV parks, fishing, and a variety of coastal activities exist or occur, especially during the summer months. Two of the most popular nearshore marine mammals that attract visitors are sea otters (Enhydra lutris) and harbor seals (Phoca vitulina). These two species spend time swimming, foraging, and resting around the Spit, potentially resulting in co occurrences with humans. Using a …

Product Evaluation Plan For Under-Desk Treadmills, Alison Larocca

Waldo Library Student Exhibits

No abstract provided.

Fisheries Research Report No. 350: Recreational Vessel Retrievals In Western Australia - 2009 To 2024, Stephen C. Bradshaw, Claire B. Smallwood, Stuart J. Blight, Troy Matthews, Karina L. Ryan

Fisheries Research Reports

This report provides a time series (2009 – 2024) of the total number of recreational vessel (powerboat) retrievals at a spatial (boat ramp) and temporal (annual, month, hour) resolution for 32 boat ramps distributed from Wyndham to Esperance. This time series has been developed using a workflow that outlines each step, from acquiring raw video data to producing a completed time series of vessel retrievals. As part of this workflow, modelling was undertaken to impute counts of vessel retrieval for sites and hours for which data had not been read, or for which there were significant outages. Features within the …

Demographic Characteristics And Selected Personality Traits Of Women In Competitive Bodybuilding, Chloe A. Zeeuw

Master's Theses

This study investigated demographic characteristics and measures of personality (dimensions of performance perfectionism and five-factor model characteristics) in women in competitive bodybuilding between 18-25 years old. A total of 24 women completed an online survey which included a demographic questionnaire, the Five Factor Model Rating Form (FFMRF), and the Performance Perfectionism Scale for Sport (PPSS) inventories. Descriptive results for the FFMRF were Openness (18.17±3.12), Conscientiousness (25.58±3.33), Extraversion (19.96±3.46), Agreeableness (19.88±4.58), and Neuroticism (15.67±4.94), and for the PPS-S were Self-oriented performance perfectionism (20.96±3.53), Socially prescribed performance perfectionism (13.96±4.26), and Other-oriented performance perfectionism (10.54±4.23). Pearson’s correlation coefficients and Shapiro-Wilk tests revealed that …

Perspectives On Water Policies And Alternative Land Uses Among Alfalfa Farmers In The Great Salt Lake Basin, Bryn Watkins, Stacia Ryder

Publications

Climate change threatens many resources necessary for life. In arid and semiarid regions like Utah, water represents one of the key climate-related conflicts (1,2). In Utah, a changing climate paired with human overconsumption has contributed to the drying of the Great Salt Lake. Rising temperatures will lead to greater evapotranspiration and decreasing headwater streamflow and groundwater storage, resulting in increasing dryness in the Great Salt Lake Basin regardless of human water consumption (3). This in turn threatens the ecosystems, economies, and cultures of the Great Salt Lake Basin, accelerating the local impacts of climate change (4).