Digital Commons Network^™

Bayesian Counterfactual Machine Learning Individualizes Radiation Modality Selection To Mitigate Immunosuppression, Duo Yu, Michael J Kane, Yiqing Chen, Steven H Lin, Radhe Mohan, Brian P Hobbs

Faculty, Staff and Student Publications

Purpose: Lymphocytes play critical roles in cancer immunity and tumor surveillance. Radiation-induced lymphopenia (RIL) is a common side effect observed in patients with cancer undergoing chemoradiation therapy (CRT), leading to impaired immunity and worse clinical outcomes. Although proton beam therapy (PBT) has been suggested to reduce RIL risk compared with intensity-modulated radiation therapy (IMRT), this study used Bayesian counterfactual machine learning to identify distinct patient profiles and inform personalized radiation modality choice.

Methods: A novel Bayesian causal inferential technique is introduced and applied to a matched retrospective cohort of 510 patients with esophageal cancer undergoing CRT to identify patient profiles …

Saliva & Circadian Rhythm In Medical Profiling For Early Disease Prevention, Joseph Lewis

Graduate Student Dissertations, Theses, Capstones, and Portfolios

Circadian rhythms affect almost every biological process from hormone secretion, gene expression, immune regulation, and metabolism. Studies show that disruption to these internal rhythms through irregular sleep, artificial sleep, and irregular sleep can significantly increase risk for chronic disease such as diabetes, cardiovascular disorders, neurodegeneration, and cancer. Saliva presents a viable alternative for capturing biomarkers found through blood or cerebrospinal fluid, offering substantial utility for diagnostic and chronobiological profiling. Saliva contains hormones such as cortisol and melatonin while containing inflammatory markers that fluctuate rhythmically throughout the day. Due to its ease of collection, saliva is well suited for longitudinal monitoring, …

Regulation Of Icer Degradation And Its Role In Melanoma, Justin Wheelan

Theses, Dissertations and Culminating Projects

Melanoma is the deadliest form of skin cancer, with 100,640 new cases and 8,290 deaths estimated in the United States in 2024. While targeted therapies and immunotherapy have improved patient outcomes, resistance remains a major challenge, necessitating new therapeutic approaches. Approximately 50% of melanomas harbor BRAFⱽ⁶⁰⁰ᴱ mutations, leading to constitutive MAPK pathway activation. Targeted small molecule therapies such as BRAF and MEK inhibitors are available and initially reduce tumor burden, however resistance frequently occurs, likely through many pathways including compensatory activation of cAMP signaling. ICER (Inducible cAMP Early Repressor), a transcriptional repressor of CREB-mediated gene expression, is absent in melanoma …

Examining The Use Of Two-Dimensional Video Capture And A Pressure Sensing Walkway For Collection Of Obstacle Crossing Measures, Ashlyn M. Jendro

Graduate Theses and Dissertations

Obstacle crossing research is crucial for providing insights into how and why people trip and fall. However, a growing body of literature has proposed that laboratory-based studies may not directly translate into real-world settings due to the complex nature beyond the sterile lab. Unfortunately, the absence of real-world obstacle crossing literature is likely due to a lack of available validated methods for collection of data outside the laboratory. This dissertation explored two potential methodologies (i.e., 2D motion capture and a pressure sensing walkway) that are more portable and cost-effective for collecting real-world obstacle crossing measures. It is hypothesized that 2D …

Advanced Analytical Biosensing For Cancer Detection And Neural Diagnostics Using Tapered Optical Fiber (Tof), Protonic, And High Throughput Microplate –Based Technologie, Bayan Hassan Alharbi

Chemistry & Biochemistry Theses & Dissertations

This dissertation investigates the development and application of advanced biosensing technologies to enhance early disease detection, neurological diagnostics, and bioactive compound evaluation. The research spans four key areas. First, it introduces tapered optical fiber (TOF)-based plasmonic biosensors for the non-invasive detection of prostate cancer, demonstrating high sensitivity and specificity compared to conventional diagnostic methods.

Second, it explores the use of fluorescent biosensors to test the Transmembrane Electrostatically Localized Proton (TELP) theory, shedding light on the role of localized protons in neuronal signaling and energy transfer. Third, the work presents a high-throughput, microplate-based biosensing platform for analyzing mitochondrial function under nanosecond …

Towards Improving Computational Modeling Of The Lumbar Spine - Impact Of Material Properties And Laminotomy On Spinal Biomechanics, Isaac K. Kumi

Mechanical & Aerospace Engineering Theses & Dissertations

Spinal ligaments play a crucial role in maintaining the mechanical stability of the lumbar spine. These dense, collagenous tissues not only resist excessive motion but also distribute loads between spinal components to protect neural structures. Traditionally, the mechanical response of ligaments has been modeled using linear elastic assumptions, which treat the tissue as having a constant stiffness regardless of loading history. While this simplifies analysis, it fails to capture the time-dependent behaviors, such as creep, stress relaxation, and hysteresis, that are characteristic of biological tissues.

Viscoelastic modeling may provide a more physiologically accurate representation by incorporating both elastic and viscous …

Multi-Crop Systems And Crop-Switching Strategies To Enhance Water Use Efficiency And Climate Resilience In Arid Agricultural Regions, Shahryar Fazli, Wenzhao Li, Surendra Maharjan, Hesham El-Askary

Mathematics, Physics, and Computer Science Faculty Articles and Research

Agriculture in the Lower Colorado River (LCR) region faces mounting challenges from climate change, arid conditions, and water scarcity. This study evaluates water use efficiency (WUEc) and crop-switching strategies under SSP2-4.5 and SSP5-8.5 scenarios for 2025–2049, 2050–2074, and 2075–2099. Using historical data, climatic drivers such as temperature and precipitation were analyzed for their influence on key crops, including durum wheat, winter wheat, and corn. Results show SSP2-4.5 supports water use reductions up to 16%, stable profits (80–90%), and modest calorie increases (up to 15%), while SSP5-8.5 poses severe challenges, with water use reductions of 2–5%, profits dropping to around 20%, …

A Simple Guide For Describing Soils, 2nd Edition, Angela Stuart-Street, Nicolyn Short Dr, Paul Galloway, Noel R. Schoknecht

Natural resources published reports

Soils are enormously diverse and can be very confusing to understand and talk about. This simple guide for describing soils helps to identify the most important parts of a soil profile and provide an easy way to understand and explain what you see. It gives you a step-by-step guide of what soil properties to describe and how to describe them, along with the tools to make basic soil classifications. The soil descriptors help you to identify the soil type and aid in assigning a simple and standardised name to the soil. While this guide is designed to link with a …

Computed Tomography Radiomics-Based Cross-Sectional Detection Of Mandibular Osteoradionecrosis In Head And Neck Cancer Survivors, Serageldin Kamel, Laia Humbert-Vidan, Zaphanlene Kaffey, Sarah Mirbahaeddin, Abdulrahman Abusaif, David T A Fuentes, Kareem Wahid, Cem Dede, Mohamed A Naser, Renjie He, Ahmed W Moawad, Khaled M Elsayes, Melissa M Chen, Adegbenga O Otun, Jillian Rigert, Mark S Chambers, Andrew Hope, Erin Watson, Kristy K Brock, Katherine Hutcheson, Lisanne Van Dijk, Amy C Moreno, Stephen Y Lai, Clifton D Fuller, Abdallah S R Mohamed, Md Anderson Head And Neck Cancer Symptom Working Group

Faculty, Staff and Student Publications

Purpose: This study aims to identify radiomic features from contrast-enhanced CT (CECT) scans that differentiate osteoradionecrosis (ORN) from normal mandibular bone in head and neck cancer (HNC) patients treated with radiotherapy (RT).

Materials and methods: CECT images from 150 patients with confirmed ORN diagnosis (2008-2018) at MD Anderson Cancer Center (MDACC) were analyzed (80 % train, 20 % test). Radiomic features were extracted using PyRadiomics from manually segmented ORN regions and automated contralateral healthy mandible regions. Correlation analysis (r > 0.95) reduced features for model training. A random Forest (RF) classifier with Recursive Feature Elimination identified discriminative features. Explainability was assessed …

Nature-Inspired Metaheuristics For Optimizing Dose-Finding And Computationally Challenging Clinical Trial Designs, Weng Kee Wong, Yevgen Ryeznik, Oleksandr Sverdlov, Ping-Yang Chen, Xinying Fang, Ray-Bing Chen, Shouhao Zhou, J Jack Lee

Faculty, Staff and Student Publications

Metaheuristics are commonly used in computer science and engineering to solve optimization problems, but their potential applications in clinical trial design have remained largely unexplored. This article provides a brief overview of metaheuristics and reviews their limited use in clinical trial settings. We focus on nature-inspired metaheuristics and apply one of its exemplary algorithms, the particle swarm optimization (PSO) algorithm, to find phase I/II designs that jointly consider toxicity and efficacy. As a specific application, we demonstrate the utility of PSO in designing optimal dose-finding studies to estimate the optimal biological dose (OBD) for a continuation-ratio model with four parameters …

Crystal Structures Of Escherichia Coli Glucokinase And Insights Into Phosphate Binding, Joseph Andrews, Joshua Sakon, Chenguang Fan

Chemistry & Biochemistry Faculty Publications and Presentations

Here, we report the crystal structure of Escherichia coli glucokinase (GLK), which has phosphate bound in the cleft between the alpha and beta domains adjacent to the active site. A ternary complex consisting of GLK, glucose and phosphate is also reported in this work. Diffraction data were collected at 2.63 angstrom resolution for the phospate-bound form (R-work/R-free = 0.191/0.230) and at 2.54 angstrom resolution for the ternary complex (R-work/R-free = 0.202/0.258), both at 297 K. A B-factor analysis of the phosphate-bound GLK structure revealed consistently lower values for phosphate-interacting basic residues in the alpha 4, alpha 5 and alpha 9 …

Assessing Effectiveness Of Runnel Restoration In New England Salt Marsh Habitats, David M. Burdick, Grant Mckown, Gregg Moore, Jenny Gibson, Wenley Ferguson, John Herbert, Nancy Pau, Susan Adamowicz, Geoff Wilson

Faculty Publications

Rising sea levels that increase flooding in salt marshes recovering from hydrologic impairments is reducing nesting habitat for salt marsh sparrows. Abandonment of colonial farming practices (1600s through 1900s) has resulted in large, waterlogged basins characterized by shallow depressions (pannes) dominated by short-form Spartina alterniflora and unvegetated megapools that are subsiding. A relatively new technique designed to provide regular tidal flooding and drainage to the waterlogged basins that have formed on the marsh is runnelling – creation of shallow hydrologic features on the marsh surface. Will runnels result in revegetation of pannes and pools with productive perennial grasses that are …

The Crab Silvofishery System As A Conservation Strategy In Mangrove Restoration Area: A Case Study On The Coast Of Banyuasin, South Sumatra, Apriyanto Apriyanto, Rujito Agus Suwignyo, Tengku Zia Ulqodry, Sarno Sarno, Riris Aryawati, Muhtadi Muhtadi, Herry Purnomo, Beni Okarda

Journal of Environmental Science and Sustainable Development

Anthropogenic activities such as logging and converting mangrove forests into plantations have degraded coastal ecosystems and reduced their ecological stability. Silvofishery is a restoration system that balances the ecological and economic functions of mangroves. In Marga Sungsang Village, South Sumatra, mangrove restoration was integrated with mud crab (Scylla spp.) cultivation through a crab silvofishery system. This study aimed to analyze the contribution of mangrove restoration with a mud crab silvofishery system to mud crab growth. The study was conducted from August 2024 to January 2025. Growth parameters included carapace length, width, and body weight. Analyses covered absolute growth …

Resilient Greenport Conceptual Model: Integrating Masterplan With Flood And Land Subsidence Disaster Management, Teuku Khamil Syamsura, Kosuke Mizuno, Supriatna Supriatna

Journal of Environmental Science and Sustainable Development

Hydrometeorological disasters, such as flooding by seawater intrusion and land subsidence from excessive water resource usage, significantly disrupt maritime traffic and port infrastructure, leading to severe economic and social consequences. This study aims to develop a conceptual model for a disaster-resilient and environmentally friendly port. The primary objective is to analyze the components of the Port Masterplan (RIP), the Greenport concept, current operational conditions, and surrounding disaster threats for develop conceptual model. A mixed-methods approach, integrating quantitative and qualitative analyses, was employed. The study examined various components of the Tanjung Priok Port Masterplan, operational data, and environmental and disaster risk …

The Effect Of Cellulolytic Enzyme Preparations As In Vitro Improvement For Forage Digestibility, G Bertin, Ph Hellings

IGC Proceedings (1977-2023)

The systematic study of commercial preparations of fungal cellulases has been undertaken with the aim of determining the principal components and the contribution of each to the digestion of the plant cell wall. These enzymes, normally have three fold role-silage preservative by hydrolysing the cellulosic wall of plant material, cellulases make available fermentable sugars to the lactic bacteria. -Improvement of digestibility we can increase gain by 1 % of the dry matter in forage. - Improvement of intake if the animal digests more quickly his gut will empty more rapidly thus making it available sooner for a new intake of …

Effect Of Cellulase Preparation On Fermentation Of Silage, E No, Y Harasawa, A Ataku, N Narasaki, T Sueyoshi

IGC Proceedings (1977-2023)

The effects of cellulase preparation (Meicelase) on silage fermentation were studied using the first cutting alfalfa and timothy. In one-liter laboratory silos with Meicelase of 0, 0.2, 0.4 and 0:8% of the fresh grasses, the fermentative quality was examined throughout a 30 day ensilage period. The amount of the lactic acid in the silage with the Meicelase was considerably greater than the control silage with no additive. In addition, the pH of that silage was low and the content of water soluble carbohydrate (WSC) was high. However, the differences in the amount of Meicelase applied had no effects in the …

Effects Of Sample Drying Method On Estimates Of Nutritive Value Value, S Uchida, H Hayashi, T Horigome

IGC Proceedings (1977-2023)

The influence of different drying methods for the sample used for analysis on the estimates of the nutritive value of silage was investigated. The silages and hay were made from the same grass and fed to three wethers to determine digestibilities. The samples for analytical use of silages and hay fed, and feces excreted, were prepared by three drying techniques of freeze drying (F), oven drying at 60 C (L) and oven drying at 100 C (H) and then each dried sample was ground in a Wiley mill to pass a 0.5 mm screen. The residual moisture in prepared samples …

Effect Of Lactic Acid Bacteria On Silage Fermentation, Ph Hellings, G Bertin, M Vanbelle

IGC Proceedings (1977-2023)

Inoculants were tested to determine their suitability for use as silage aids. Studies carried out in laboratory indicated (1) that the minimum inoculum should be at least 105 viable organisms per gram of fresh fodder and (2) of all bacterial strains tested, only the Lactobacillus and, specifically, L. casei improved storage characteristics. But the efficiency of an inoculant was subordinated to the fermentable sugars content of the crops. In this respect, alfalfa and second cut grass had the lowest potential for ensilage. Energy was supplied as a mixture of milled barley and amylolytic complex. The influence of a 1: 1: …

Ensilage Of Alfalfa Press-Cake. A Kinetic Model For Ph, Acidity And Nitrogen Evolution, G Amdrich, L Lencioni, R Florentini, G Anelli

IGC Proceedings (1977-2023)

A kinetic model to describe the time evolution of pH, acidity, metabolizable nitrogen and k1 • B, ( a function related to the bacteria concentration) during ensilage of alfalfa press-cake is suggested. The basic hypotheses of the model are given together with the related differential and integral equations. The kinetic model has been tested using experimental data obtained from two samples of alfalfa press-cake respectively ensiled with and without acid addition. The correlation coefficients obtained indicate the reliability of the suggested model.

Ensilage Of Alfalfa Press-Cake, G Anelli, G Andrich, M Contini, L Lencioni

IGC Proceedings (1977-2023)

The Istituto Industrie Agrarie of the University of Pisa has developed a wet green crop fractionation process which involves the ensilage of the press-cake. This note reports some experimental results on the alfalfa press-cake ensiled with or without addition of acid. The evolution of silages was evaluated through organoleptic and chemical parameters. The good behaviour· during the ensilage shows that alfalfa press-cake is suitable to be ensiled even without previous acidification.

Coagulation Of Sheep Milk Added With Alfalfa Juice And Protein Concentrate, L Lencioni, R Florentini, A M. Pisanelli, C Galoppini

IGC Proceedings (1977-2023)

This note reports some experimental results on the preparation of food-grade products obtained by enzyme coagulation of sheep milk added with alfalfa juice, decolourized whole protein concentrate and cytoplasmic protein concentrate. Working conditions are reported together with the yields, chemical composition and organoleptic properties of the coagula. Products obtained from milk supplemented with low alfalfa juice (��5% dry basis) or protein concentrates (;;;;:10% dry basis) show a good acceptability. The ripening greatly reduces grass flavour and taste.

Effect Of Remaining Brown Juice In Wet Protein Curd On The Quality Of Leaf Protein After Drying, Y S. Cho, J K. Kim, T Horigome, S Uchifa

IGC Proceedings (1977-2023)

The influence of remaining brown juice ( deproteinised juice) in wet protein curd on the quality of resulting leaf protein was examined. Freshly cut Italian ryegrass and red clover were fractionated into protein curd, brown juice and pressed cake. Various leaf proteins were prepared by drying the protein curds retaining different amounts of brown juice at 65°C followed by acetone-washing, and by immediate acetone-washing of the protein curd. Casein-brown juice mixtures at the ratio of 1 :3 and 1: 6 were also prepared. The crude protein content of the dry matter in brown juice was very low, 9. 9% for …

The Nutritive Value Of Mixtures Of White Leaf Protein And Other Food Proteins, R Carlsson, P Hanczakowski

IGC Proceedings (1977-2023)

The nutritive value of white leaf proteins were studied, as food supplements. The protein was obtained by heat­fractionation ( Chenopodium quinoa Willd.) or by de-pigmentation (Medicago sativa L. ). The leaf protein was substituting 50% of the protein in a diet, where the remaining 50% came from wheat gluten, soya bean meal, bone-meat meal, fish meal, skim milk or whey. The nutritive value was estimated by the Thomas-Mitchell nitrogen balance method. The proximate chemical composition of the food protein products, and their amino acid composition were analysed. In every mixture but the one with gluten the biological value was higher …

Effect Of Contamination By Aspergillus Flavus On The Nutritive Value Of Leaf Protein Concentrate Of Leucaena Leucocphala During Storage, H T. Ostrowski-Meissner, I Komang, W Supratman, I Barchia, S Cacang

IGC Proceedings (1977-2023)

Leaf protein concentrate extracted from tree legume Leucaena leucocephala cultivar Cunningham (LLP) was stored under humid tropical conditions (24-28°C and 84-92% rh) in the form of wet cake during a 10 day period. Samples of LLP were taken every second day for chemical analyses and protein quality assays. The effect of storage on dried LLP was also assessed against two control proteins: peanut meal (PNM) and fish meal (FM), either free of aflatoxins or infected by the aflatoxigenic fungus Aspergi_llus flavus to the level 280 mcg aflatoxin B1 equivalent/kg. Storage of wet LLP under such conditions resulted in infestation by …

Physiological Activity Of Alfalfa Lpc And Brown Juice, A Sagasaki, T Kawakami, M Naito, H Yamada, Y Kuroyanagi, K Suzumura, R Kayama

IGC Proceedings (1977-2023)

With the purpose of searching physiological active component(s) contained in alfalfa leaf, green leaf protein concentrate (LPC) and brown juice were tested against the effects on the inutagenicity of mutagen and hyperlipemia. LPC and brown juice were found to inactivate the mutagenicity of 2•aminoanthracene by the Ames test, and the capacity was more powerful in LPC than in brown juice. Further feeding of alfalfa LPC or its brown juice added diet to hamster reduced the total cholesterol and triglyceride levels in serum.

Influence Of The Age Of Chicken On The Metabolizable Energy Value Of Alfalfa Leaf Protein Concentrate, S Terapuntuwat, I Tasaki

IGC Proceedings (1977-2023)

Influence of the age of chicken on the nitrogen corrected metabolizable energy (MEn) value of alfalfa leaf protein concentrate (LPC) was investigated. Chickens of various ages were fed diets containing certain amounts of the LPC, and droppings were collected quantitatively. The MEn of the diets was determined as the difference between consumed energy and excreted energy which was corrected with retained energy as body protein. Then the MEn value of the LPC was calculated using the values of the LPC containing diets and that of cornstarch which was obtained from data for a LPC-free diet. As a result, the MEn …

High Value Productions From Lucerne: A New Zealand Perspective, R M. Mcdonald, P E. Donnelly, R A. Mills, S R. Vaughan

IGC Proceedings (1977-2023)

Research at Ruakura has aimed at improving the economics of lucerne protein extraction, by extracting more of the protein (up to 85%) and by searching for ways to get maximum value for each of the components in the lucerne. Presently most lucerne protein concentrate is sold on the basis of its protein and xanthophyll contents, which are valued by poultry growers. Other components, including carotene, chlorophyll and vitamin E, are not valued in poultry feed and consequently could be extracted and sold separately. Carotene and vitamin E have recently been associated with cancer prevention. The paper also discusses the value …

Effect Of Drying Methods On The Nutritive Value Of Leaf Protein Concentrates Coagulated By Acidification, Heat Or Anaerobic Fermentation, M Ohshima

IGC Proceedings (1977-2023)

SUMMARY To determine the effect of heat-treatments on the nutritive value of leaf protein concentrate(LPC), several LPCs prepared by different procedures were fed to rats. The nutritive value of ladino clover LPC separated centrifugally from acidified juice and freeze-dried was compared with that of LPC prepared from the same acidified juice by heating to 70°C with an electric heater before the centrifugation and oven-dried at 70°C. The heat-treatments reduced not only the apparent digestibility of crude protein by 5%, but also the nutritionally available lysine content of LPC. Response of rats to lysine supplementation in addition to methionine was observed …

Effect Of Anaerobic Fermentation Of Plant Juice On The Yield And The Nutritive Value Of Leaf Protein Concentration, M Ohshima, H Ueda

IGC Proceedings (1977-2023)

Effect of treatments of plant juice on the yield and nutritive value of leaf protein concentrate (LPC) was studied with special reference to anaerobic fermentation using lucerne and Italian rye grass as the materials. Lucerne juice was .subdivided into three portions. The two portions were heated to 70°C immediately or after being adjusted to pH 8 with NaOH. The other portion was anaerobically fermented for 7 days. One half of ryegrass juice was heated to 70°C after being adjusted to pH 4 with HCI and the other half was submitted to the fermentation. After the treatments, each juice was centrifuged …

Alkali Treatment Of Rice Whole Crop Silage, T Tobino, N Mikami, A Yamazaki, R Kobayashi, K Furugouri

IGC Proceedings (1977-2023)

Application of Na OH for rice whole crop at the time of ensiling increased digestibility, intake and body weight gain of Holstein steers. As rice whole crop silage is inclined to cause secondary fermentation, when the moisture content is not sufficient, water addition to the filling material is necessary. The suitable application level of NaOH is 3 to 4% of silage dry matter and it can be applied successfully using 20 to 30% solution. The rate of notreacted Na in the NaOH applied silages was 20 to 40% and it changed wholly to the form of Na2CO3 -Na. The greater …