Digital Commons Network^™

The Effect Of The Species, Stage Of Maturity And Level Of Intake Of Grass On The Efficiency Of Microbial Protein Synthesis In The Rumen Of Cattle, F J. Hart, Jane Leibholz

IGC Proceedings (1977-2023)

This study was undertaken because there is a paucity of information in the literature on the efficiency of microbial protein synthesis in the rumen of cattle when grass is fed as the sole diet. There is also little experimental data available on the factors which affect the efficiency of microbial protein synthesis. The work involved feeding six rumen fistulated Friesian steers with three species of grass which were harvested at various tages of maturity. In addition each maturity of forage was fed at three 15levels of orp5 nic matter ( OM) intake.

as sampled at the omasum and microbial protein …

The Influence Of Aging On Forage Quality Of Individual Switchgrass Leaves And Stems, B Anderson

IGC Proceedings (1977-2023)

Cattle selectrively graze switchgrass (Panicum virgatum L.) tops prior to the boot stage and prefer vegetative culms and new tillers following heading. Therefore, a study was conducted to evaluate the changes in forage composition of individual leaves and stems during growth to determine if grazing selection may be influenced by aging. Plants were cut periodically at ground level from collaring of the first leaf until anthesis. Leaves (leaf blade plus sheath) of different ages, stems, and the whorl were hand separated at each harvest. Crude protein, in vitro dry matter disappearance (IVDMD), neutral and acid detergent fiber, lignin, and …

Harvesting Alyceclover For Maximum Dry Matter Yield And Nutrient Value, D D. Baltensperger, W G. Blue, W H. Anderson

IGC Proceedings (1977-2023)

Limited information is available on the quality of alyceclover (Alysicarpus vaginalis) in relation to plant stress. This study was undertaken to clarify the relationship between plant maturity and forage yield, quality and mineral composition in order to optimize each at harvest. Alyceclover was grown for two summers and new plots were harvested weekly through the pod-fill stage of development beginning eight weeks after planting. Samples were analyzed for dry matter, organic matter, In vitro dry matter digestibility, nitrogen, phosphorus, potassium, calcium, magnesium, manganese, copper, iron and zinc. Dry matter yields increased through the flowering stage of development except …

Adaptation Of The Inra System Of Determination And Expression Of The Nutritive Value Of Forages To The Tropical Conditions In The Caribbean Island, A Xande, R Garcia-Trujillo

IGC Proceedings (1977-2023)

This program have undertaken a series of trials of systematic measure of nu tritive value on the tropical forages. The choice of the calculation and of the way of expression of energetic and nitrogen values required comparation measures in different systems as well as attempts in alimentation before adopting the new french INRA system of energy (UFL-UFV) and of the protein value (POI). The general results of this study is a preamble to the diffusion of the table of nutritive value of the tropical forages. For this purpose 450 samples of forages have been analysed on sheep in cage of …

Gene Regulatory Network Prediction Using Machine Learning, Deep Learning, And Hybrid Approaches, Sai Teja Mummadi, Md Khairul Islam, Victor Busov, Hairong Wei

Michigan Tech Publications

Construction of gene regulatory networks (GRNs) is essential for elucidating the regulatory mechanisms underlying metabolic pathways, biological processes, and complex traits. In this study, we developed and evaluated machine learning, deep learning, and hybrid approaches for constructing GRNs by integrating prior knowledge and large-scale transcriptomic data from Arabidopsis thaliana, poplar, and maize. Among these, hybrid models that combined convolutional neural networks and machine learning consistently outperformed traditional machine learning and statistical methods, achieving over 95% accuracy on the holdout test datasets. These models not only identified a greater number of known transcription factors regulating the lignin biosynthesis pathway but also …

Non-Spectator Behavior Of A Neutral Phosphine Ligand Driven By A Redox-Active Boron Cluster, Jared R. Riffle, Cash L. Jowers, Sarah Luna, Mark D. Smith, Dmitry V. Peryshkov

Faculty Publications

A new concept of ligand ambiphilicity that relies on the redox behavior of the indirectly coordinated boron cluster scaffold instead of the direct involvement of a single center in a ligand is introduced. A copper(I) complex of a carboranyl-based triphosphine, [t^BuP-closo-{C₂B₁₀}-^PhP-closo-{C₂B₁₀}-t^BuP]CuPF₆, in acetonitrile solution coordinates an exogenous X− anion (X− = Cl− or N3−) at the phosphorus center of the ligand and not at the cationic metal site to form [t^BuP(X)-nido-{C₂B …

Computational And In Vitro Investigation Of P. Crocatum Bioactive Compounds As Pancreatic Lipase Inhibitors, Gusnia Meilin Gholam, Dimas Andrianto, Dewi Anggraini Septaningsih, Mega Safithri

Karbala International Journal of Modern Science

Obesity, a prevalent metabolic disorder characterized by excessive fat accumulation, can severely affect overall health if left untreated. This study investigated the potential of a 70% ethanol extract from Piper crocatum (red betel) leaves as an in vitro inhibitor of pancreatic lipase (PL), supported by computational analyses to identify alternative compounds to orlistat. The phytochemical profile was characterized using LC-MS/MS, revealing alkaloids and terpenoids with contents of 1.1 ± 0.01 mg CE/g and 3.14 ± 0.3 mg UAE/g, respectively. The extract exhibited 49 ± 9.1% inhibition of PL activity. Molecular docking identified three promising compounds: calanolide A (10.43 kcal/mol), myricanone …

In Silico Prediction Of Cytotoxic T-Cell Epitopes From Helicobacter Pylori Virulence Factors Using An Immunoinformatics Approach, Demy Valerie Chacon, Kiana Alika Co, Daphne Noreen Enriquez, Aubrey Love Labarda, Reanne Eden Manongsong, Edward Kevin B. Bragais

Biology Faculty Publications

Background: Helicobacter pylori infects approximately half of the global population, leading to gastric and duodenal ulcers. Despite the availability of antibiotics, challenges such as patient reluctance, high treatment costs, and antibiotic resistance limit their effectiveness, making vaccination a promising alternative. This study used immunoinformatics to identify candidate epitopes for a multiepitope vaccine construct against H. pylori.

Material and methods: The protein variability server was utilized for conservation analysis. The epitopes were screened for antigenicity, allergenicity, toxicity, cross-reactivity, and population coverage. Selected epitopes were docked with their corresponding human leukocyte antigen (HLA) alleles, and thermodynamic quantities were determined. Five virulence …

Derivation Of Adjoint Based Error Estimates For Nonlinear Ordinary Differential Equations With Application To Multistage Sir Models With Demographics, Daniel Alcala

Mathematics & Statistics ETDs

Ordinary Differential Equations (ODEs) are central to the mathematical modeling of various real-world phenomena, from mechanical systems governed by Newton’s laws to epidemic dynamics described by SIR-type ODEs. Since many ODEs do not admit closed-form analytic solutions, we approximate them numerically (e.g., with Euler’s, Runge–Kutta, or other such methods). This raises the key question: How accurate are these numerical solutions? In particular, reliably estimating the error in some quantity of interest (QoI) at time T without having an exact solution is of great scientific interest.

The first main contribution of this thesis is the development and analysis of adjoint-based error …

Using Triple Oxygen Isotopes To Investigate Water Usage In Desert Ecosystems, Cloe V. Knutson

Earth and Planetary Sciences ETDs

In arid environments, maintaining water balance can be more critical for survival than obtaining food. As droughts intensify, understanding how animals manage body water is essential. Triple oxygen isotope analysis provides a novel way to trace water sources in animals, distinguishing contributions from free water, food-derived oxygen, and atmospheric O₂. We developed an equilibration method using CO₂–H₂O oxygen exchange and measured δ^’18O and Δ^’17O values via tunable infrared laser direct spectroscopy (TILDAS). Validated against traditional fluorination methods, this technique enables streamlined analysis of whole blood and plant samples. Applied to …

A Mutational Analysis Of Thatisin: How Single Point Mutations Impact The Biosynthetic Process Of A Group 16 Graspetide, John F. Boynton Jr

Chemistry and Chemical Biology ETDs

Abstract:

Graspetides are a family of Ribosomally synthesized and Post-translationally modified Peptide (RiPP) natural products named for their ATP Grasp Macrocyclases. We identified several Graspetide Biosynthetic Gene Clusters containing common double glycine cleavage motifs and attempted characterization of the mature Graspetides. One of the resulting peptides, Thatisin, has a topology with two interlocking macrolactones installed by a single ATP Grasp Ligase named ThtC. Here we use single and double point mutations to observe the impact or variation on the installation of these macrocycles. Alanine scan mutagenesis is used to assess leader peptide residues in the precursor peptide ThtA to determine …

Advancing Diamond Quantum Sensors: Isotropic Flux Concentrators And Phase Noise Mitigation, Maziar Saleh Ziabari

Optical Science and Engineering ETDs

Two methods for improving the sensitivity of nitrogen vacancy quantum sensors in diamond are explored. First, by passively concentrating the magnetic flux, three orthogonally oriented ferrite truncated cone pairs amplify the field isotropically by 19 times, allowing measurement of Earth's field without a bias field and increasing sensitivity. Through thorough analysis, modeling and tuning a novel 3-dimensional flux concentrator system, we achieve a fractional standard deviation of less than 1% anisotropy and quantify minimal deadzones and ambient temperature-limited variations below 40 nT/hour. Second, we characterize, model and calculate phase noise in NV experiments, which in NV sensors is effectively indistinguishable …

Datasets Associated With Caballero Et Al. (2025): Sentinel-3 Coastal Analysis Ready Data (S3card): An Operational Framework For Coastal Water Applications, Cassia B. Caballero, Vitor S. Martins, Rejane S. Paulino, Thainara M. A. Lima, Elliott Butler, Eric Sparks

Research Data

This dataset provides access to twelve .zip archives containing pre-processed tiles from the S3CARD (Sentinel-3 Coastal Analysis Ready Data) framework. Each archive corresponds to a 2.5° × 2.5° coastal grid that includes an AERONET-OC (Aerosol Robotic Network – Ocean Color) station used for validation in Caballero et al. (2025). The data include atmospherically corrected, glint- and adjacency-corrected surface reflectance images derived from Sentinel-3 OLCI imagery.

Each tile includes:

- 21-band surface reflectance images in GeoTIFF format (valid water pixels only)

- Metadata files with acquisition geometry and processing details

These datasets support reproducibility and enable users to evaluate the S3CARD …

Optimizing Distributed Boundary Exchanges For Benchmarks, Solvers And Sparse Matrix Operations, Gerald Collom

Computer Science ETDs

Boundary exchanges dominate the cost of both stenciled codes and those that rely on sparse matrix operations. The performance of large boundary exchanges is limited by synchronization overheads and injection bandwidth limitations. Irregular boundary exchanges incur additional overheads due to the large number of required messages. This thesis investigates multiple methods for improving the performance and scalability of both Cartesian and irregular boundary exchanges. Since boundary exchanges are typically performed iteratively, persistent communication presents an opportunity for optimization by sharing and amortizing setup costs. Partitioned communication is also explored to increase asynchrony, reducing bottlenecks from synchronization overheads and data congestion. …

The Nature Of Anthropogenically Driven River Drying: Spatiotemporal Causes And Consequences, Eliza Inez Gilbert

Biology ETDs

Streambed drying naturally occurs in over 60% of rivers and streams worldwide. Climate change and human regulation of surface and groundwater have increased drying in naturally intermittent systems and caused perennial systems to transition to intermittency, impacting water security, water quality, and biodiversity. To understand human-induced drying dynamics, we used 12 years of daily drying data along a 154-km regulated reach of the Rio Grande. We conceptualized river drying as a regime analogous to the natural flow regime paradigm and quantified drying magnitude, rate of change, and duration. Although linear models predicting drying magnitude and rate of change were uninterpretable, …

Optimization And Model Averaging Of Histogram-Based Place Cell Firing Rate Maps Using The Point Process Framework, Murat Okatan

Turkish Journal of Electrical Engineering and Computer Sciences

The firing rate of hippocampal place cells depends on the spatial position of the organism in an environment. This position dependence is often quantified by constructing spike-in-location and time-in-location histograms, the ratio of which yields a firing rate map. The purpose of this study is to present a new method for optimizing the spatial resolution of histogram-based firing rate maps. It is pointed out that histogram-based firing rate maps are conditional intensity functions of inhomogeneous Poisson process models of neural spike trains, and, as such, they can be optimized through model selection within the point process framework. The point process …

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

Ionic Liquid Enhanced Proton Transfer For Neutral Oxygen Evolution Reaction, Ming-Xing Chen, Nian Liu, Zi-He Dua, Jing Qi, Rui Cao

Journal of Electrochemistry

The development of highly active catalyst in pH-neutral media for oxygen evolution reaction (OER) is critical in the field of renewable energy storage and conversion. Nevertheless, the slow kinetics of proton-coupled electron transfer (PCET) hinders the overall OER efficiency. Herein, we report an ionic liquid (IL) modified CoSn(OH)₆ nanocubes (denoted as CoSn(OH)₆-IL), which could be prepared through a facile strategy. The modified IL would not change the structural characteristics of CoSn(OH)₆, but could effectively regulate the local proton activity near the active sites. The CoSn(OH)₆-IL exhibited higher intrinsic OER performances than the pristine …

High Spatial Resolution Crop Type And Land Use Land Cover Classification Without Labels: A Framework Using Multi-Temporal Planetscope Images And Variational Bayesian Gaussian Mixture Model, Minh Tri Le

Mathematics, Physics, and Computer Science Faculty Articles and Research

Previous studies often combined high spatial resolution data (e.g., PlanetScope) with wider spectral range data (e.g., Sentinel-2) and relied on supervised classification methods to produce land use and land cover (LULC) maps. This study proposed a new unsupervised framework to generate crop type and LULC maps at high spatial resolution (< 5 m) using available PlanetScope data solely without requiring ground truths. We used PlanetScope surface reflectance images and their derived spectral indices during growing seasons to create multi-temporal input features, which were fed into an unsupervised Variational Bayesian Gaussian Mixture Model (VBGMM). The VBGMM, unlike the traditional unsupervised classification methods, (1) first estimated optimal parameters that are most suitable based on the input features and then (2) assigned pixels to the cluster with maximum posteriori probability of a mixture of several Gaussian distributions. The crop type and LULC maps were then generated by labeling the derived clusters using the best possible assignment method, referring to the existing crop type or LULC products. We evaluated the produced PlanetScope-based crop type and LULC maps using true labels, corresponding reference maps, and other unsupervised classification methods. The results demonstrated the robustness and effectiveness of the proposed framework in mapping crop types and LULC at 3–5 m pixels across various ecosystems, climate zones, and human-managed landscapes. The spatial patterns of PlanetScope-based maps were (1) highly comparable with all the reference datasets at 10–30 m spatial resolution and (2) better than the traditional GMM and K-means clustering methods. The VBGMM produced classification maps with high confidence, yielding class probabilities above 0.9 for over 90 % of all study areas. The area percentage for all crop type and LULC classes agreed well with their reference maps, with R2 of 0.95 and RMSE of 1.04 %. The confusion matrices using true labels indicated that PlanetScope-based maps achieved a higher overall accuracy of 84 % than the supervised referenced maps of 81 %. Besides, the entropy comparison showed that our framework-based maps were better at capturing fine-scale features such as developed areas within cities that commonly mix with open space and vegetation, deforestation and cropland conversion in South America, smallholder croplands in Africa and Asia, and generating homogeneous crop fields in North America. This study further highlighted the potential for future research to implement our proposed framework to generate timely and extensive annotated datasets, which can be used for operationally training machine learning models to map crop types and LULC, track deforestation, detect wildfires, and delineate flooded areas at larger scales using medium/coarse Earth observations.

Some Nonparametric Tests For High-Dimensional And Functional Data, Bilol Banerjee

Doctoral Theses

The advancement of information technology and sciences over the last few decades has facilitated the collection, storage and analysis of huge data sets. Many of these data sets contain observations having large number of features, and in some cases, this number is comparable to or even much larger than the sample size. Many traditional statistical methods cannot be meaningfully used in such situations. We develop some inferential tools for such high dimensional data. In particular, we consider the two-sample problem and the problem of testing spherical symmetry of a multivariate distributions. We construct some nonparametric tests in these contexts and …

Combination Of Irreversible Electroporation And Clostridium Novyi-Nt Bacterial Therapy For Colorectal Liver Metastasis, Zigeng Zhang, Guangbo Yu, Qiaoming Hou, Farideh Amirrad, Sha Webster, Surya M. Nauli, Jianhua Yu, Vahid Yaghmai, Aydin Eresen, Zhuoli Zhang

Pharmacy Faculty Articles and Research

Colorectal liver metastasis (CRLM) poses a significant challenge in oncology due to its high incidence and poor prognosis in unresectable cases. Current treatments, including surgical resection, systemic chemotherapy, and liver-directed therapies, often fail to effectively target hypoxic tumor regions, which are inherently more resistant to these interventions. This review examines the potential of a novel therapeutic strategy combining irreversible electroporation (IRE) ablation and Clostridium novyi-nontoxic (C. novyi-NT) bacterial therapy. IRE is a non-thermal tumor ablation technique that uses high-voltage electric pulses to create permanent nanopores in cell membranes, leading to cell death while preserving surrounding structures, and …

Transformation With Genes To Improve Lipid Production And Barcoding To Identify Unknown Algal Species, Michelle T. Rada

Theses and Dissertations

With the rising demand for alternative fuels, algal-based biofuels are a promising, sustainable source that meets commercial interest while producing lower greenhouse gas emissions compared to fossil fuels. This thesis explored two studies, evaluating microalgae for their future potential in lipid yield for biofuel production.

The first study involved developing a cost-efficient electroporation protocol that allowed for the genetic transformation of Chlamydomonas reinhardtii using the pChlamy_4 vector, which supports future cloning of genes to enhance lipid production. Parameters affecting DNA uptake and integration into algal genomes were studied: the effect of cell density, the settings of the electroporation device, and …

Detection Of Oil Pollution On The Tigris River In Iraq Using Fluorescence And Reflecting Techniques, Ahmad K. Ahmad, Thamer M. Mohammed

Karbala International Journal of Modern Science

In this study, a broadband light source (visible and ultraviolet) was used to name minerals via fluorescence spectra and estimate slick oil thickness, ranging from sub-millimetres, using the reflecting spectrum technique. Using a fluorescent technique, we obtained fluorescence spectra of the samples, converting and processing the signals to produce high-resolution data, which enabled the identification of the types of dissolved elements and oil slicks in the Tigris River, highlighting pollution sources and potential control measures. This system aims to show the faint signal in fluorescence samples collected from the cooling system outlet water throughout the refining process from AL-Dora (Baghdad) …

Advances In Key Technologies For The Management, Restoration, Development, And Utilization Of Coal Mining Subsidence Areas, Meng Zhuanghan, Wang Yutao, Tian Yanzhe

Coal Geology & Exploration

Background Coal mining subsidence areas, formed by the exploitation of coal resources, have emerged as severe challenges to the construction of ecological civilization and the sustainable development of the social economy in China. Their management, restoration, development, and utilization play a significant role in ecological security, food security, and energy transformation. Methods This study aims to address the unresolved and emerging issues in the management of coal mining subsidence areas. Based on the core concepts of management, restoration, development, and utilization, this study developed a dual-level zoning basis system combining theories and reality. Accordingly, coal mining subsidence areas in China …

Design And Efficiency Assessment Of A Passive Treatment System For Acid Mine Drainage, Yan Ruiwen, Zhu Jun, Zhu Junhao, Lin Gang, Zhang Wanqiu, Jia Zenghua, Wang Wenming, Xi Furui

Coal Geology & Exploration

Background Acid mine drainage (AMD) refers to highly acidic, heavy metal-rich effluent generated from mining activities, potentially causing severe environmental contamination. Methods Focusing on the Lujiang alum mine in Anhui Province, this study established a systematic framework for the design and assessment of an integrated passive AMD treatment system using the Phreeqc and AMDTreat software. Based on a comprehensive analysis of the on-site hydrogeochemical characteristics (pH: 2.93‒3.06, Fe: 5.98‒42.52 mg/L, and Al: 18.87‒32.14 mg/L) and physical conditions (flow rate: 50‒96 m³/h, available area: about 50 000 m²), this study proposed a hybrid passive treatment system comprising …

Fabrication, Calibration, And Deployment Of A Home-Made Radiometer, Callum Flowerday, Ryan Thalman, Jaron Hansen

ScholarsArchive Data

Subfolders and Contents:

Chamber Characterization: Contains emission spectrum measured from inside the chamber with converted spectra to power and photon flux.

LED Calibration: (Each calibration file contains folders of data from each LED used in calibration)

• Cone
• Cone 2
• Dome 2
• Flat Top
• Quartz Rod
• Uniform Dome

Outside:

• Cone 2 front porch
• Cone 2 roof
• Flat top

(Arise) Achievements In Research, Inquiry And Scholarship Exhibition 2025, Office Of Undergraduate Research

(ARISE) Achievements in Research, Inquiry and Scholarship Exhibition

Conference held at John A. Delaney Student Union on July 25, 2025

Patterns And Processes Behind Secretive Marshbird Movement, Abundance, And Distribution Across Southeastern Louisiana, Leah Moran

LSU Doctoral Dissertations

Restoration and conservation of coastal Louisiana hinges on understanding the patterns and processes underlying habitat heterogeneity on the landscape and therefore the species that inhabits this region, including secretive marshbirds. Elusive in nature, this guild of birds has evolved under dynamic hydroperiods, and myriad plant communities present within wetlands. Only recently, however, has research focused on the role of hydrologic dynamics and vegetative structure and distribution on abundance, movement and detection of marshbirds, specifically within southeastern Louisiana. This study aimed to quantify the ecological patterns and processes, particularly hydrologic processes and landscape structure, driving breeding secretive marshbird movement, abundance and …

How Effective Are Engineered And Non-Engineered Riparian Forest Restoration Projects In Providing Salmonid-Quality Habitat In The San Francisco Bay Area?, Alexander Ivanov

Master's Theses

Streams and their riparian zones in the San Francisco Bay Area have been degraded, severely harming salmonid populations in the region. Ecological restoration is a common approach to return stream function. Such restoration projects vary widely in intensity, from low-impact vegetation removal/planting to highly engineered projects involving structures and grading. This research investigated the effectiveness of streams restored using engineered versus non-engineered solutions in supporting salmonid habitat viability in San Francisco Bay Area streams. Fourteen streams, seven from each of the two types of restoration, were sampled in the wet and dry season in 2024, three times each season. Data …

Antibacterial Potential Of Tapanuli Orangutan (Pongo Tapanuliensis) Food In Batang Toru Forest Against Escherichia Coli And Salmonella Typhi, Herna Febrianty Sianipar, Wahyu Widoretno, Luchman Hakim, Rezi Rahmi Amolia, Fatchiyah Fatchiyah

Karbala International Journal of Modern Science

Diarrhea is a common disease affecting orangutans, primarily caused by Escherichia coli and Salmonella typhi bacteria. To treat this disease, antibacterial food sources are essential as therapeutic agents for orangutans. The fruits consumed by Tapanuli orangutans include Campnosperma auriculatum, Agathis borneensis, Artocarpus heterophyllus, Castanopsis argantea, and Aglaia tomentosa. This study aims to examine the amino acid and phytochemical components with potential antibacterial properties in these five fruit species and their inhibitory effects on E. coli and S. typhi growth through cell lysis, observed using a Scanning Electron Microscope (SEM). The samples were tested for amino acids, phytochemicals, vitamin C content, …