Life Sciences Commons^™

Effect Of Solvent Treatments On Intake And Digestibility Of Corn Stover, D M. Schaefer, M R. Ladisch, C H. Noller, V L. Lechtenberg

IGC Proceedings (1977-2023)

Treatment of crop residues with low levels of sodium hydroxide has been shown to improve organic-matter digestibility and animal performance. One objective of these experiments was to evaluate the effects of three treatments -water, sodium hydrox­ide, and chelating metal cellulose-swelling solution-on solubilization of cell-wall components in corn (Zea m£rys) stover. The two latter treatments were balanced for level of sodium hydroxide application, which was .3 .2 % of stover dry matter. The second objective was to determine the effects of these treatments on in-vitro and in-vivo digestibility as well as on consumption of corn stover. Twelve growing ram lambs were …

Factors Causing Greater In-Vitro Than In-Vivo Digestibility Of Sodium Hydroxide - Treated Roughages, L L. Berger, T J. Klopfenstein, R A. Britton

IGC Proceedings (1977-2023)

Research on sodium hydroxide (NaOH) treatment oflow-quality roughages generally indicates that in-vivo digestion is lower than in-vitro digestion. The purpose of this research was to identify factors that may cause less of the potentially digestible fiber to be digested in vivo than in vitro. Corn (Zea mays) cobs were raised to 60% moisture and treated to contain 0%, 2.5%, 5.0%, 7.5 % , and 10.0% NaOH. Lambs were fed diets containing 80% cobs and 20% supplement, giving a complete mixed diet con· taining 0%, 2.0%, 4.0%, 6.0%, and 8.0% NaOH. Five abomasally cannulated lambs were assigned to a 5 x …

Relationship Between Silage Quality And 15 N-Nitrate Reduction During Ensilage, K Ataku, M Horiguchi, T Matsumoto

IGC Proceedings (1977-2023)

Nitrate in forage has been proven to occasionally poison ruminants. Our recent studies, however, have shown that a high con­centration of nitrate inhibits butyric acid fermentation to the advantage of the silage quality. This work was undertaken to see the relationship between silage quality and the pattern of nitrate reduction during ensilage.

Oregon State Rank Assessment For Willamette Navarretia (Navarretia Willamettensis), Nora Dunkirk

Institute for Natural Resources Publications

Oregon state conservation status assessment for Willamette Navarretia (Navarretia willamettensis) using NatureServe methodology, 2026.

Examining The Relationship Between Civic Agriculture Participation And Civic Engagement In South Texas, Allison Kaika, Dongkyu Kim, William Donner, Alexis Racelis, Owen Temby

School of Earth, Environmental, & Marine Sciences Faculty Publications

Civic agriculture is often credited with strengthening democratic life by encouraging civic and political engagement, yet this claim has scarcely been tested in socioeconomically marginalized regions. Using original survey data collected through a combination of random and purposive sampling, this study assesses that relationship in the Lower Rio Grande Valley of Texas, a majority-Hispanic agricultural region marked by high poverty and low civic participation. Phone and online surveys were administered in English and Spanish to reach both the general population and individuals involved in civic agriculture initiatives, yielding over 400 responses. We examine whether civic agriculture participation predicts greater community …

Agrivoltaic Shading Reduces Soil Greenhouse Gas Fluxes In A Semi-Arid Vineyard, Marcelo Gomes Da Silva, Rafael M. Almeida, Carine Cocco, Engil Pereira

School of Earth, Environmental, & Marine Sciences Faculty Publications

Agrivoltaic systems are expanding in semi-arid regions, raising questions about how panel driven shading alters soil greenhouse gas exchange. We used automated chambers to measure high frequency soil CO2, N2O, and CH4 fluxes in a newly established vineyard agrivoltaic system in Texas across three shading intensities (0%, 35%, 88%) that represent the light environment beneath panels as shaped by panel tilt and solar trajectory. Shading primarily cooled the soil, reducing mean soil temperature from 35.9 °C (0%) to 32.5 °C (35%) and 30.5 °C (88%), while mean soil water content shifted modestly (0.125, 0.106, and 0.130 m3 m−3, respectively). Over …

Rape Pregnancies And Consequent Ptsd Resulting From The Overturn Of Roe V. Wade, Emma Lindenfelser, Yulia Garaeva, Nenette Nti-Agyemang, Ellen Davis, Anna Kabwa, Alexandra M Calaman

Binghamton University Undergraduate Journal

Prior to the 1973 Roe v. Wade ruling, access to safe legal abortions was limited and often restricted along racial, economic, and geographic lines. Nearly fifty years later, women’s health policy evolved again following the 2022 Dobbs v. Jackson Women’s Health Organization decision overturning Roe v. Wade. This court ruling decimated federal protections of abortion. This paper presents the research that the 2022 Dobbs judicial decision may contribute to and exacerbate rape-related PTSD on 1 out of 20 American who are unable to access a safe abortion after a rape-related pregnancy. Pregnant women living in conservative states that have outlawed …

Synthesis And Characterization Of Organometallic Polymers And Their Cytotoxicity Towards Human Cancer Cell Lines, Paul Peter Slawek

Electronic Theses and Dissertations 2020 - Present

This research aimed to synthesize organometallic polymers from dialkyl (methyl, ethyl, butyl, cyclohexyl, and octyl) and diaryl (phenyl) tin dichlorides and three organic monomers, dipicolinic acid (DPA), chloramphenicol (CH), and isomannide (IS), using interfacial polymerization. Structure-activity relationships were investigated through physicochemical characterization (light-scattering photometry, proton NMR, and IR spectroscopy) and cytotoxicity was evaluated against six human cancer cell lines (AsPC-1, PANC-1, MCF-7, MDA-MB-231, HT-29, PC-3), with cisplatin serving as the reference standard.

Five DPA/tin polymers were synthesized, with IC₅₀ values in the range of 0.60–0.71 μg/mL. Their cytotoxicity was significantly lower than that of cisplatin (0.0023-0.044 μg/mL), suggesting that …

Synthesis And Characterization Of Synergistic Bioactive– Organometallic Condensation Polymers, Francesca Isabel Mosca

Electronic Theses and Dissertations 2020 - Present

This research focuses on the synthesis and structural characterization of polymers with anticipated anticancer and antiviral properties by combining metal-containing Lewis acids, organotin dichlorides (R2SnCl2), Group 4 metallocene dichlorides (Cp2TiCl2, Cp2ZrCl2 and Cp2HfCl2), and triphenyl Group 15 metal dichlorides (Ph3AsCl2, Ph3SbCl2 and Ph3BiCl2), with biologically active Lewis bases, lamivudine, a synthetic nucleoside, and camphoric acid, a dicarboxylic acid, to achieve synergistic effect.

Five classes of polymers were synthesized using interfacial polymerization: lamivudine and organotin dichlorides, lamivudine and Group 4 metallocene dichlorides, camphoric acid and triphenyl Group 15 metal dichlorides, camphoric acid and organotin dichlorides, and camphoric acid and Group 4 …

Comparison Of Fish Biomass And Fish Carbon Content Associated With Reef Sites At The Rio Grande Valley Artificial Reef In The Gulf Of Mexico, Allison K. White, Md Saydur Rahman, Richard J. Kline

School of Earth, Environmental, & Marine Sciences Faculty Publications

As global fisheries stocks have decreased due to overfishing and climate change, artificial reefs have gained significant attention. In addition to providing or restoring habitat, artificial reefs may serve as carbon capture sinks and potential climate mitigation strategies. The Rio Grande Valley (RGV) Reef is an artificial reef located in the northwestern Gulf of Mexico off the coast of Texas. The RGV Reef area spans 1,650 acres and is comprised of hundreds of groupings of recycled and pre-formed materials ranging from low relief (1–2 ft) to high relief (8–30 ft) reef structures. This reef provides a variety of novel habitat …

Biologically Informed Negative Samplingfor Antibody Chain Pairing Classification, Ishita Singh

Computer Science Senior Theses

Antibody heavy and light chain (H/L) pairing is fundamental to antigen recognition and stability. While single-cell sequencing preserves native pairing information, widely used bulk repertoire and spatial transcriptomics platforms do not, motivating the need for efficient ML methods to infer H/L pairing. Training a binary classifier for this task faces the methodological challenge of a lack of true biological negatives, since natural selection eliminates B cells with incompatible H/L pairs.

In this thesis, I introduce a biologically informed negative sampling strategy for H/L pairing classification, drawing on known V-gene biases in heavy and light chain pairing. Pseudo-negatives are constructed by …

Exploring Regenerative Vegetable Systems On The Central Coast Of California, Una S. O'Connell

Master's Theses

As climate change and current agricultural practices place pressure on the long term sustainability and resilience of food production systems, there is growing interest in whether existing agricultural systems can adapt to maintain productivity while improving environmental outcomes.

This study evaluated the effects of regenerative versus standard organic vegetable production systems on yield, insect communities, and weed suppression across three field trials conducted on California's Central Coast. In addition, I collected baseline soil health data for all trials. Trials 1 and 2 were carried out at the Cal Poly San Luis Obispo Organic Farm using cabbage and broccoli as cash …

Updates To The Caniform Fauna (Carnivora, Caniformia) Of The John Day Formation, Oregon, Usa, John D. Orcutt, Kevin C. Talbott, Michael J. Monroe, Nicholas A. Famoso

Biology Faculty Scholarship

The John Day Formation of central Oregon preserves a diversity of Oligo-Miocene caniform carnivorans, many of which were first described from the formation. However, many historically important specimens lack detailed locality or stratigraphic information, complicating any analysis of faunal change through time. Here, we describe 16 new specimens of caniforms from the John Day Formation, most with precise stratigraphic information. We report multiple specimens of the amphicyonids Daphoenus Leidy, 1853, Paradaphoenus cuspigerus (Cope, 1878), and Temnocyon altigenis (Cope, 1878), all previously known from the formation. We also report the first definitive occurrence of the hesperocyonine canid Osbornodon Wang, 1994 from …

3dcotton, Md Ahmed Al Muzaddid, William J. Beksi

Agriculture - Archive

3DCotton is an image dataset consisting of 8 cotton plants recorded at the Texas A&M University Research Farm. The images were captured using an Apple iPhone at a resolution of 1040x1920 pixels. Approximately 150 images per plant were taken from a distance of 1 m by recording multiple viewpoints. These images can be utilized for developing 3D reconstruction methods.

Developing A High-Resolution Off-Axis Common-Mode Digital Holographic Microscope, Lucy Cook

University Honors Theses

Off-axis digital holographic microscopy (DHM) is a powerful tool for 3D, non-invasive live-cell tracking without moving parts. However, traditional setups face an inherent dilemma: split-path interferometers offer high spatial resolution but poor temporal stability, while more stable common-mode configurations are historically limited to lower numerical aperture (NA) regimes. This thesis bridges that gap by scaling a common-mode DHM architecture into a high-resolution benchtop instrument featuring NA = 0.65 objectives, paired with a high-power 520 nm laser source to combat transmission losses and sustain imaging frame rates across an expanded optical footprint. We map the multi-variable design space required to satisfy …

Shallow-Marine Crinoid Genera May Have Been More Resilient Across Permian Extinction Events In Terms Of Richness Than Deep-Marine Crinoid Genera, Amelia C. Kolstad

University Honors Theses

Throughout the Phanerozoic, one of the most successful phyla of marine invertebrates has been Echinodermata. Echinodermata was particularly successful throughout the Paleozoic, with class Crinoidea making up a majority of occurrences. The proportion of echinoderm occurrences that are crinoids declined massively at the end of the Permian and continued to decrease into modern day, never fully recovering. One of the factors thought to have been so important for crinoid success in the Paleozoic and their decreasing success throughout geologic time has been their propensity for success in shallow-marine environments, though crinoids also exist within deep-marine environments. This study seeks to …

Can Generative Ai Make Farming Decisions? Current Status And Future Pathways: A Case Study In Row Crop Production With Chatgpt, Nipuna Chamara, Yufeng Ge, Joe Luck, Yu Pan, Saleh Taghvaeian, Cory Walters, Christopher Proctor, Daran Rudnick, Daren Redfearn

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The agricultural decision-making process is experience-based, knowledge-dependent, time-sensitive, complex, and driven by historical data. Planting, fertilization, irrigation, and chemigation are key categories in farm decision-making, and currently there is no one-shot decision-support tool that covers all these activities. Generative Artificial Intelligence (AI) models are more advanced than traditional machine learning and deep learning models. These models have been trained on vast amounts of data from the internet, allowing them to accept unstructured data in various forms and generate human-like text, solutions to problems, and scenario predictions. Given this capability, we became interested in exploring the potential of generative AI in …

Invasion Patterns And Niche Dynamics Of The Pollinivorous Florida Calligrapher, Toxomerus Floralis (Diptera: Syrphidae) In The Afrotropical Region, Burgert Muller, John Midgley, Georg Goergen, Ali Al Jahdhami, Michelson Azo'o Ela, Terence Bellingan, Simon Cavaillès, Robert Copeland, Marc De Meyer, Martin Hauser, Allen Holmes, Ximo Mengual, Gabriel Nève, Menno Reemer, Jeff Skevington, Gunilla Ståhls, Eugène Sinzinkayo, John Smit, Axel Ssymank, Genevieve Theron, Kurt Jordaens

All Peer-Reviewed Publications

The rapid spread of Toxomerus floralis (Fabricius, 1798) (Diptera: Syrphidae) within the Afrotropical region is described. We characterise and compare the climatic niches of T. floralis in its native (Southern North America, Central America and South America) and invaded (Afrotropical Region) range to assess the potential for further expansion across Africa and beyond, and included future global climate models and socioeconomic pathways as projections. Occurrence data for native and invaded ranges were obtained from field sampling by authors, major collections of Afrotropical Syrphidae, collections records and occurrence data from the Global Biodiversity Information Facility (GBIF), including iNaturalist data. Single and …

Supramolecular Assembly In Short Peptide Systems For Selective Metabolite Recognition And Drug Nanoencapsulation, Maithreyi Ramakrishnan

Dissertations, Theses, and Capstone Projects

Short peptides can form adaptive supramolecular assemblies, and understanding how minimal sequences organize around neurometabolites or hydrophobic cancer drugs enables the rational design of functional materials. This thesis combines molecular dynamics with experimental validation to establish design rules linking peptide sequence to emergent structure and function. Chapter 1 outlines the molecular determinants governing peptide assembly. Chapter 2 reviews computational workflows that reveal sequence-dependent conformations and supramolecular organization. Chapter 3 applies these principles to Dynamic Peptide Libraries which identify tetrapeptides that selectively interact with neurometabolites. Chapter 4 extends the same interaction-driven framework to design tryptophan-rich pentapeptides that co-assemble with kinase inhibitors …

Climate Change Reduces Pollination Services And Sunflower Yields Across Europe And Northern Africa, Stella Gachoki, Clémence Riva, Danilo Bevk, Yamina Haider, Noureddine Adjlane, Ioannis Manthos, Bojan Stipešević, Zlatko Puškadija, Marin Kovačić, Leonidas Charistos, Fani Hatjina, Fabrice Requier

All Peer-Reviewed Publications

Sunflower (Helianthus annuus) productivity is highly dependent on pollinators, yet the effects of climate on pollination services and crop yield remain poorly understood. In this study, we investigate how temperature gradients influence flower-visiting communities, pollination services, and sunflower productivity across Europe and Northern Africa. We conducted standardized two-year (2022 and 2023) pollination exclusion experiments across 36 sunflower fields spanning a broad climatic gradient, from temperate regions in Slovenia to arid conditions in Algeria. We found that sunflower production (seed set, seed number, and oil content) relied heavily on insect pollination. However, this benefit declined with rising temperatures, likely due to …

Gc-Ms-Based Comparative Analysis Of Compounds In Host Plants And Insect Gut Extracts, Rita Dill, Kimberly Smith, Shelia Okoth, Xavier Cheseto, Anne Osano

All Peer-Reviewed Publications

Background/Objectives: Herbivorous insects feed on plant tissues to obtain nutrients necessary for growth and development while simultaneously ingesting diverse plant secondary metabolites. Understanding the fate of these compounds during digestion is important for advancing knowledge of insect nutritional physiology and diet-associated biochemical processes. This study aimed to comparatively profile metabolites in host plants and corresponding insect gut extracts to generate insights into compound transfer and compositional changes within these systems. Methods: Gas Chromatography-Mass Spectrometry (GC-MS) metabolomics was combined with Ultraviolet-Visible (UV–Vis) quantification of total phenols and flavonoids to compare host plant tissues and insect gut extracts in three systems: fall …

Climate-Driven Stochastic Modelling Of Crimean-Congo Haemorrhagic Fever Transmission In Uganda, P. G. Kpatchana, J. Aduda, K. M. Agboka

All Peer-Reviewed Publications

Crimean-Congo haemorrhagic fever (CCHF) is a climate-sensitive tick-borne zoonosis that remains a significant public health concern in Uganda, where temperature and vapour pressure deficit influence tick ecology and consequently disease transmission. This study aimed to develop and analyse a climate-driven stochastic model for CCHF transmission among ticks, livestock, and humans under environmental variability in Uganda. A compartmental transmission model was formulated and extended into a stochastic differential equation framework by incorporating multiplicative environmental noise. Climate-dependent tick recruitment, development, and mortality were parameterized using district-level temperature and vapour pressure deficit data to capture spatial heterogeneity in transmission risk. Theoretical analyses based …

Computational Insights Into Nucleosome Dynamics In Epigenetics Using Molecular Dynamics Simulations, Rutika Patel

Dissertations, Theses, and Capstone Projects

Nucleosome core particles (NCP) are the building blocks that form a highly organized and compact chromatin structure. Nucleosomes package DNA in the nucleus of eukaryotic cells. The NCP consists of about 147 base pairs of DNA wrapped around the histone octamer, with 1.65 superhelical turns in a left-handed manner. The histone octamer is composed of two copies of H3, H4, H2A, and H2B. Together with histone H1 and linker DNA, they further assemble into a higher-order chromatin structure. The nucleosome complex is stabilized by electrostatic interactions between positively charged histone residues and the negatively charged DNA backbone. To effectively access …

A Predictive Coding Account Of Spatial Working Memory Following Prophylactic Levetiracetam Administration Prior To Traumatic Brain Injury, Omeima Mutwali

Dissertations, Theses, and Capstone Projects

Traumatic brain injury (TBI) symptom prevention and remediation is an important area of research that would benefit vulnerable groups, including active-duty and veteran soldiers. These patients can sustain penetrative forces in fields of combat or in training, which result in focal lesions that trigger inflammatory and degenerative processes in the brain. Both primary and secondary injuries are associated with changes to cognition, behavior and affective state. This disease poses increased risk of epileptogenesis, as well. Given these outcomes, prior research has evaluated levetiracetam (LEV) as a prophylactic treatment for seizures, cognitive deficits and negative emotionality. LEV acts as a presynaptic …

Identifying Textual Predictors Of Early Termination In Clinical Trials In Medicine: An Explainable Machine-Learning Study, Rohan Ramnarain

Dissertations, Theses, and Capstone Projects

About one in five clinical trials in medicine ends early, wasting valuable resources and reducing the evidence available for developing life-saving medical treatments. This project uses a method called Trial2Vec, which is a self-supervised machine-learning method that converts clinical trial documents into dense numerical representations that capture their key design and clinical characteristics, to turn each proposed clinical trial’s written protocol into a compact numerical profile (a process referred to as embedding). These profiles are then paired with a predictive machine learning models to identify the words and phrases in the trial documents that can signal a higher risk of …

Intervention Levers For Stunting Reduction In Indonesia: Evidence From The 2023 Indonesian Health Survey Data, Iwan Ariawan, Hafizah Jusril, Zahra Izza Afifa, Azka Fitri, Elmarizha Sekar Utami, Mikail Hasan, Dwi Puspasari

Kesmas

Stunting remains the largest public health challenge among macro-nutrition problems in Indonesia, affecting almost a quarter of children under five in 2023. The prevalence is considered high according to the World Health Organization standard. This study analyzed 15 aggregated provincial variables from the 2023 Indonesian Health Survey using Structural Equation Modeling (SEM), focusing on determinants of stunting among children under two to identify primary intervention levers. Findings indicated that intervention urgency should focus on the first 1,000 days, particularly the steep increase in stunting prevalence observed in the 12–24-month age range. While the highest prevalence is in Eastern provinces (e.g., …

Fate Of Nitrogen Applied To Grassland In Animal Wastes, M Sherwood

IGC Proceedings (1977-2023)

The experiment was designed to determine the effects of land spreading of animal manures on the nutrient content of surface runoff water and infiltrating soil water. This report deals only with nitrogen (N) and attempts to quantify the losses through runoff, leaching, and volatilization of ammonia (NH3) as well as N uptake in the grass over a 3-year period. Experimental plots sited on grassland, on two soil types (a moderately drained loam and an impermeable gley), were equipped to collect surface runoff water. Ceramic probes were installed in each plot at 15-, 30-, 60-, and 100-cm depths to extract in­filtrating …

Annual Losses Of Ammonia From A Grazed Pasture Fertilized With Urea, V R. Catchpoole, L A. Harper, R J.K Keyers

IGC Proceedings (1977-2023)

Nitrogen-balance studies have shown losses of applied nitrogen (N) from grazed pastures in southeastern Queensland. Losses as high as 80% have been observed from urea N broadcast at 376 kg N/ha/yr over 8 years on a Setaria sp1uu:elata cv. Nandi pasture. Management techniques aimed at reducing this loss and thereby increasing the efficiency of use of N by pastures cannot be devised until the pathways of loss are known. The objective of this research was to estimate the annual ammonia (NH3) loss by convective transport from a urea-fertilized pasture at Samford Pasture Research Station in southeastern Queensland. Urea was broadcast …

Nitrogen Losses From Urine-Affected Areas Of A New Zealand Pasture, Under Contrasting Seasonal Conditions, P R. Ball, D R. Keeney

IGC Proceedings (1977-2023)

Grazing ruminants aggregate large quantities of forage nitrogen (N) into urine patches. Pasture plots treated with urine N were studied to assess its fate under contrasting seasonal conditions: cool-moist (representing winter-spring); warm-moist (late spring-early summer), and warm-dry (late summer-autumn). A permanent ryegrass (Lolium perenne L.)-white clover (Trifolium repens L.) sward on free-draining alluvial soil was studied. 'freatments were replicated in randomized blocks. Urine N was applied at 30 or 60 g N/m2• Relevant measurements were then continued until treatment differences disappeared. Apparent N balances for urine treatments were compiled. Fixation by white clover was always greatly reduced in …

Effects Of Grazing Management On Seasonal Variation In Nitrogen Fixation, J L. Brock, J H. Hoglund, R H. Fletcher

IGC Proceedings (1977-2023)

Using the acetylene reduction assay, field studies in recent years have investigated the variation in N fixation in grazed systems, and some of the principles involved in the interaction with available soil N have been described. This experiment ex­tends this work to include the effect of grazing management on the factors influencing N fixation. Two self-contained sheep-grazed units, one a 10-paddock rotationally grazed system and the other set stocked, were estab­lished on a high-fertility ryegrass-white clover pasture, with a basic stocking rate of 22 sheep/ha. Over the 1975-1978 period, both units were monitored for pasture growth, N fixation, and associated …