Life Sciences Commons^™

Your Sco/Eco Policy Under The Hood: What County Yield Is The Rma Using?, Cory Walters, Ken Harrison, Connor Whalen

Cornhusker Economics

Over the past decade, crop insurance has continued to expand contract offerings through new area-based policies. Supplemental Coverage Option (SCO) was introduced in the mid-2010s. Enhanced Coverage Option (ECO) was introduced in the early 2020s, and Margin Protection (MP) was introduced in the mid-to-late 2010s. The ECO premium subsidy was recently increased for the 2025 crop year to further encourage producer participation. Both the SCO and ECO programs have experienced increased participation for a variety of reasons.

Phenormgpt: A Framework For Extraction And Normalization Of Key Medical Findings

Faculty, Staff and Student Publications

This manuscript presents PheNormGPT, a framework for extraction and normalization of key findings in clinical text. PheNormGPT relies on an innovative approach, leveraging large language models to extract key findings and phenotypic data in unstructured clinical text and map them to Human Phenotype Ontology concepts. It utilizes OpenAI's GPT-3.5 Turbo and GPT-4 models with fine-tuning and few-shot learning strategies, including a novel few-shot learning strategy for custom-tailored few-shot example selection per request. PheNormGPT was evaluated in the BioCreative VIII Track 3: Genetic Phenotype Extraction from Dysmorphology Physical Examination Entries shared task. PheNormGPT achieved an F1 score of 0.82 for standard …

Neuregulin1 Nuclear Signaling Influences Adult Neurogenesis And Regulates A Schizophrenia Susceptibility Gene Network Within The Mouse Dentate Gyrus, Prithviraj Rajebhosale, Alice Jone, Kory R Johnson, Rohan Hofland, Camille Palarpalar, Lorna W Role

Faculty, Staff and Student Publications

Neuregulin1 (Nrg1) signaling is critical for neuronal development and function from fate specification to synaptic plasticity. Type III Nrg1 is a synaptic protein which engages in bidirectional signaling with its receptor ErbB4. Forward signaling engages ErbB4 phosphorylation, whereas back signaling engages two known mechanisms: (1) local axonal PI3K-AKT signaling and (2) cleavage by γ-secretase resulting in cytosolic release of the intracellular domain (ICD), which can traffic to the nucleus (Bao et al., 2003; Hancock et al., 2008). To dissect the contribution of these alternate signaling strategies to neuronal development, we generated a transgenic mouse with a missense mutation (V

Therapeutic Approaches To Modulate The Immune Microenvironment In Gliomas, Andreas Sarantopoulos, Chibawanye Ene, Elisa Aquilanti

Faculty, Staff and Student Publications

Immunomodulatory therapies, including immune checkpoint inhibitors, have drastically changed outcomes for certain cancer types over the last decade. Gliomas are among the cancers that have seem limited benefit from these agents, with most trials yielding negative results. The unique composition of the glioma immune microenvironment is among the culprits for this lack of efficacy. In recent years, several efforts have been made to improve understanding of the glioma immune microenvironment, aiming to pave the way for novel therapeutic interventions. In this review, we discuss some of the main components of the glioma immune microenvironment, including macrophages, myeloid-derived suppressor cells, neutrophils …

Impact Of Select Actionable Genomic Alterations On Efficacy Of Neoadjuvant Immunotherapy In Resectable Non-Small Cell Lung Cancer, Nicolas Zhou, Cheuk H Leung, William N William, Annikka Weissferdt, Apar Pataer, Brett W Carter, Anne S Tsao, George R Blumenschein, Xiuning Le, Jianjun Zhang, Ferdinandos Skoulidis, Jonathan M Kurie, Mehmet Altan, Charles Lu, Bonnie S Glisson, Lauren A Byers, Yasir Y Elamin, Reza J Mehran, David C Rice, Garrett L Walsh, Wayne L Hofstetter, Jack A Roth, Hai T Tran, Jia Wu, Luisa M Solis Soto, Humam Kadara, Stephen G Swisher, Ara A Vaporciyan, Don L Gibbons, Heather Y Lin, J Jack Lee, John V Heymach, Marcelo V Negrao, Boris Sepesi, Tina Cascone

Faculty, Staff and Student Publications

Background: Neoadjuvant immune checkpoint inhibitors (ICIs) have improved survival outcomes compared with chemotherapy in resectable non-small cell lung cancer (NSCLC). However, the impact of actionable genomic alterations (AGAs) on the efficacy of neoadjuvant ICIs remains unclear. We report the influence of AGAs on treatment failure (TF) in patients with resectable NSCLC treated with neoadjuvant ICIs.

Methods: Tumor molecular profiles were obtained from patients with stage I-IIIA resectable NSCLC (American Joint Committee on Cancer seventh edition) treated with either neoadjuvant nivolumab (N, n=23) or nivolumab+ipilimumab (NI, n=21) followed by surgery in a previously reported phase-2 randomized study (NCT03158129). TF …

The Dleu2/Mir-15a/Mir-16-1 Cluster Shapes The Immune Microenvironment Of Chronic Lymphocytic Leukemia, Ronghua Zhang, Priyanka Khare, Priyanka Banerjee, Cristina Ivan, Sarah Schneider, Karen Clise-Dwyer, Erika Thompson, Marisela Mendoza, Nicholas Chiorazzi, Shih-Shih Chen, Xiao-Jie Joy Yan, Nitin Jain, Paolo Ghia, Federico Caligaris-Cappio, Rima Mendonsa, Sashi Kasimsetty, Ryan Swoboda, Recep Bayraktar, William Wierda, Varsha Gandhi, George A Calin, Michael J Keating, Maria Teresa Sabrina Bertilaccio

Faculty, Staff and Student Publications

The development and progression of chronic lymphocytic leukemia (CLL) depend on genetic abnormalities and on the immunosuppressive microenvironment. We have explored the possibility that genetic drivers might be responsible for the immune cell dysregulation that shapes the protumor microenvironment. We performed a transcriptome analysis of coding and non-coding RNAs (ncRNAs) during leukemia progression in the Rag2-/-γc-/- MEC1-based xenotransplantation model. The DLEU2/miR-16 locus was found downmodulated in monocytes/macrophages of leukemic mice. To validate the role of this cluster in the tumor immune microenvironment, we generated a mouse model that simultaneously mimics the overexpression of hTCL1 and the germline deletion of the …

San Diego Collaboration For Conservation: Sustaining The Region's Legacy Of Biodiversity Conservation, Tessa Tinkler, Darbi Berry, A-Bel Gong, Bryan Cardenas, Daniela Olguin, Connelly Meschen, Eo Hanabusa

Environment

We are living through significant environmental, social, political, and economic challenges. These challenges have strained our communities and humanbuilt systems, as well as our interconnected habitats, wildlife, and natural systems. Lack of adequate infrastructure to withstand natural disasters and climate change, as well as historical and presentday inequities in resources across neighborhoods, are examples of the multifaceted and interconnected threats contributing to the accelerated loss of our rich biodiversity. This natural abundance is integral to our region’s health, history, and continued prosperity.

Differential Hepatic Expression Of Mirna In Response To Aflatoxin B1 Challenge In Domestic And Wild Turkeys, Kade Jorud, Kristelle M. Mendoza, Thomas Kono, Roger A. Coulombe, Kent M. Reed

Animal, Dairy, and Veterinary Science Faculty Publications

Aflatoxin B1 (AFB₁) is a major foodborne mycotoxin that poses a significant economic risk to poultry due to a greater degree of susceptibility compared to other agricultural species. Domesticated turkeys (Meleagris gallopavo) are especially sensitive to AFB₁; however, wild turkeys (M. g. silvestris) are more resistant. A lack of functional isoforms of hepatic glutathione S-transferases (GSTs), an enzyme that plays a role in the detoxification of aflatoxin, is suspected as the reason for the increased sensitivity. Previous studies comparing the gene expression of domesticated and wild turkeys exposed to AFB₁ identified …

Preparation And Efficacy Evaluation Of Chicken Egg Yolk Sourced Igy Against The Venoms Of Cobra, Krait, Russell’S Viper, And Saw-Scaled Viper, Gayathri G

Theses and Dissertations

Envenomation resulting from snakebites is widely recognized as an alarming health risk in tropical and sub-tropical areas. The big four snakes including Naja naja, Bungarus caeruleus, Daboia russelli, Echis carinatus are responsible for most of the envenomation in India. The current therapy for snake envenomation is immunoglobulins, produced from serum or plasma of horses or sheep. To overcome the drawbacks of current antivenom, chicken egg yolk (IgY) antibodies have recently emerged as one of the most promising research avenues.

In this study, the efficacy of chicken egg yolk sourced antisnake venom (ASV) IgY against the big four venoms was evaluated …

Subsoil Testing Required To Detect The Rundown Of Soil Potassium To Deficient Levels For Wheat Production On Loam-Textured Soils, Craig Scanlan, Richard Bell, Miaomiao Cheng, Tim Boyes

Grain and Other Field Crops Research Articles

Context

Long-term negative potassium (K) balances in crop production have depleted soil K levels in Western Australia (WA). Previous research has focussed on sand-textured soils, but recently, monitoring of crops grown on loam-textured soils has shown deficient or marginal shoot K concentrations where Colwell K 0–10 cm is above current critical levels.

Aims

The aims were to examine whether grain yield responses to fertiliser K can be detected on loam-textured soils and if soil test calibration curves can be identified for these soils.

Methods

Eight field trials were conducted with wheat on loam-textured soils. The same experimental design was used …

A Home Dyer's Garden, Part Ii: Extracting Pigment From Japanese Indigo, Wesley Crump, Toree Park, Elizabeth Cohen

All Current Publications

Several indigo dyeing methods use powdered pigment. This fact sheet outlines a simple, inexpensive method of extracting the pigment from plants. For information on growing Japanese indigo or dyeing with plant and pigment, see the other fact sheets in the Utah State University (USU) Extension series A Home Dyer’s Garden, including Part I: Growing Japanese Indigo and Part III: Dyeing With Japanese Indigo.

A Home Dyer's Garden, Part Iii: Dyeing With Japanese Indigo, Wesley Crump, Toree Park, Elizabeth Cohen

All Current Publications

Dyeing with Japanese indigo grown in the home garden can be an exciting and satisfying way to incorporate gardening into more aspects of your life and create unique products for yourself and others. This resource provides information to those who would like to experience the process from growing the plant until the final dyed project and those who would like to purchase the pigment and use it for dyeing. After preparing the fabric, there are many ways to dye with indigo. Two well-established methods, accessible and achievable for the beginning dyer, are included.

Unmasking Neuroendocrine Prostate Cancer With A Machine Learning-Driven Seven-Gene Stemness Signature That Predicts Progression, Agustina Sabater, Pablo Sanchis, Rocio Seniuk, Gaston Pascual, Nicolas Anselmino, Federico Cayol, Marcelo Marti, Javier Cotignola, Ayelen Toro, Estefania Labanca, Juan Bizzotto, Geraldine Gueron

Faculty, Staff and Student Publications

Prostate cancer (PCa) poses a significant global health challenge, particularly due to its progression into aggressive forms like neuroendocrine prostate cancer (NEPC). This study developed and validated a stemness-associated gene signature using advanced machine learning techniques, including Random Forest and Lasso regression, applied to large-scale transcriptomic datasets. The resulting seven-gene signature (KMT5C, DPP4, TYMS, CDC25B, IRF5, MEN1, and DNMT3B) was validated across independent cohorts and patient-derived xenograft (PDX) models. This signature demonstrated strong prognostic value for progression-free, disease-free, relapse-free, metastasis-free, and overall survival. Importantly, the signature not only identified specific NEPC subtypes, …

Optical Genome Mapping For Detection Of Bcr::Abl1-Another Tool In Our Toolbox, Zhenya Tang, Wei Wang, Gokce A Toruner, Shimin Hu, Hong Fang, M James You, Joseph D Khoury, Guilin Tang

Faculty, Staff and Student Publications

Background:BCR::ABL1 fusion is mostly derived from a reciprocal translocation t(9;22)(q34.1;q11.2) and is rarely caused by insertion. Various methods have been used for the detection of t(9;22)/BCR::ABL1, such as G-banded chromosomal analysis, fluorescence in situ hybridization (FISH), quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) and optical genome mapping (OGM). Understanding the strengths and limitations of each method is essential for the selection of appropriate method(s) of disease diagnosis and/or during the follow-up.

Methods: We compared the results of OGM, chromosomal analysis, FISH, and/or RT-PCR in 12 cases with BCR::ABL1.

Results:BCR:ABL1 was detected by FISH and RT-PCR …

Impact Of Pik3ca Gain And Pten Loss On Mantle Cell Lymphoma Biology And Sensitivity To Targeted Therapies, Nardjas Bettazova, Jana Senavova, Kristyna Kupcova, Dana Sovilj, Anezka Rajmonova, Karla Svobodova, Zuzana Zemanova, Lenka Daumova, Vaclav Herman, Alexandra Dolníkova, R Eric Davis, Marek Trneny, Pavel Klener, Ondrej Havranek

Faculty, Staff and Student Publications

Besides many other mutations in known cancer driver genes, mantle cell lymphoma (MCL) is characterized by recurrent genetic alterations of important regulators of the phosphoinositol-3-kinase (PI3K) cascade including PIK3CA gains and PTEN losses. To evaluate the biological and functional consequences of these aberrations in MCL, we have introduced transgenic expression of PIK3CA (PIK3CA UP) and performed knockout/knockdown of PTEN gene (PTEN KO/KD) in 5 MCL cell lines. The modified cell lines were tested for associated phenotypes including dependence on upstream B-cell receptor (BCR) signaling (by an additional BCR knockout). PIK3CA overexpression decreased the dependence of the tested MCL on prosurvival …

Nutritional Intervention As Adjuvant Therapy For T-Cell Acute Lymphoblastic Leukemia, Miriam B Garcia, Palaniraja Thandapani

Faculty, Staff and Student Publications

No abstract provided.

The Interaction Of Treadmill Type And Incline Slope On Biomechanics And Muscle Activation During Human Locomotion, Rohit Kundu, Ricardo Sanchez, Taj Krieger, Eli Lankford

International Journal of Exercise Science

International Journal of Exercise Science 17(1): 1478-1492, 2024. To investigate the effects of differing treadmills on impact acceleration and muscle activation. Methods: 15 males and 7 females (27.8 ± 7.7yrs), engaged in two sessions of high-incline walking (HIW), and low-incline jogging (LIJ) on different deck systems (cushioned) treadmills (TM1 and TM2). Sessions lasted 5-minutes, and participants maintained a self-selected pace matched for each session. EMG markers were placed over the Tibialis Anterior (TA), Soleus (SOL), Lateral Gastrocnemius (LG), Biceps Femoris (BF), Gluteus Maximus (GM), Anterior Deltoid (AD), Vastus Lateralis (VL), and the Erector Spinae (ES). Trident Inertial Measurement Units (IMU) …

Effect Of Crop Age On Seed Yield Of Arachis Pintoi At Two Sites In Costa Rica, Pedro J. Argel, Alfredo Valerio

IGC Proceedings (1977-2023)

Arachis pintoi is a forage legume well adapted to the humid tropics of Costa Rica. Seed production studies were carried out at two contrasting localities within the country, Gulipiles (very humid tropics) and San Isidro (seasonal evergreen tropical forest). The accessions CIAT 18748, 18744 and 17434 cv. Amarillo of A. pinloi were vegetatively planted at both sites. Seed yields were measured at 8, 12, 16 and 20 months post- planting inGulipiles, and at·8, 16 and 20 months in San Isidro. Mean seed yields among accessions were similar in San Isidro but significantly different in Gulipiles; however, the contrary occurred in …

Efficient Nitrogen Fertilization In Grass Seed Crops With Regard To Soil Mineral Nitrogen Content And Analyzing Grass Tillers In Spring, W Schoberlein, H J. Wahl

IGC Proceedings (1977-2023)

When applying the Nmln method in grass seed crops analogously lo that in cereal crops we proceed from the experience that for a mean level of mineralisation, the sum total of soil-borne Nm1n available to plants at the beginning of the growth period and Nd Input in the form of fertiliser will provide sufficient N to the crop. The total quantity of mineral soil-borne N and fertiliser N is considered as the nominal value. The required N input can be derived from the difference between nominal value and mineral soil-borne N (Nd = nominal value• Nrnin>· For Dactylis glomerata …

Effects Of Aneuploidy On Seed Production In Autopolyploid Forage Crops, A Elgersma

IGC Proceedings (1977-2023)

Between the selection of a population and its commercial use, several generations of multiplication are necessary. The essential feature in variety maintenance is that no genetic changes occur during multiplication. In seed-propagated species, however, during each multiplication cycle natural selection takes place at ihe gamete, zygote, seed and plant level. In induced autopolyploids high frequencies of aneuploids can occur. Aneuploidy not only affects the seed yield level, but also the selection processes that occur during multiplication. It may cause genetic shift and affect variety stability. Species differ in their tolerance to aneuploids. It is not possible to eliminate aneuploidy by …

Effects Of Ratooning And Protection From Diseases And Birds On Seed Production In Guinea Grass, Okoro Oji, F N. Madubuike, F.O C. Ezedinma

IGC Proceedings (1977-2023)

Effects of ratooning and protection from diseases and birds on seed production in guinea grass (Pannicum maximum L.) were assessed in a study from October 1986 to April 1987. Treatments included ratooning and mancozeb application with or without protection from birds (netting). Highest yield occurred with combined netting and mancozeb application. Mancozeb sp,aying without netting gave lower seed yield than netting without fungicide spraying. Seed yield, which generally decreased with ratooning, was lowest among unnetted and unsprayed crops. Prom anthesis to seed maturation lasted, on average, 9 days, and seeds borne on the upper part of the panicle matured …

Potential For Improved Honey Bee Pollination Efficiency From Easy-To-Trip Lucerne, L R. Teuber, E E. Knapp

IGC Proceedings (1977-2023)

The principal pollinator of lucerne (Medicago sativa L.) in California, USA is the honey bee (Apis mellifera L.). However, honey bees are notoriously inefficient pollinators of lucerne because they learn to avoid tripping the floret. Easy-to-trip lucerne florets could reduce this problem. These studies were designed to determine the inheritance of ease of tripping and assess the effect of ease of tripping on the rate of outcrossing. Both additive and digenic variance for ease of tripping were significant, resulting in a heritability of 34.0:1:16.2%. Ease of tripping had no influence on outcrossing rate, which was estimated to average …

Effect Of Final Cutting For Fodder On Seed Yield And Seed Quality In Berseem, S L. Saini, R K. Chowdhury

IGC Proceedings (1977-2023)

The study was conducted to determine the appropriate time of final culling (closing) for fodder to optimise the seed yield and seed quality in berseem (Trifolium alexandrinum L.). Based on 2 years' experimentation, the maximum seed yield was obtained when the final cut for fodder was taken in mid•March and the crop was then closed for seed. Seed yield was reduced drastically when the final cut was delayed to late March•April. The seed quality parameters of standard germination, seed weight and vigour index were also reduced when the final cut for fodder was delayed to late March•early April. Based …

Effect Of Post-Harvest Management Practices On Seed Yields On Fine-Leaf Fescue, Gale A. Gingrich, William C. Young Iii, Thomas B. Silberstein

IGC Proceedings (1977-2023)

Public opposition and legislative actions have restricted the practice of open-field burning of grass seed fields in Western Oregon's Willamette Valley. Finding economically acceptable alternatives to straw residue removal has become a priority for valley grass seed growers. Trials using 4 residue management practices were established on 2 commercial fine fescue (Festuca rubra) seed fields. Seed yields varied significantly between residue management practices. Seed yields from thermal-treated plots were equal or significantly greater than yields from the non-thermal treatments. Fertile tiller number was also greater with thermal treatments. Most fine fescue fields produce 4-6 seed crops before replanting, …

Floret Site Utilization Of White Clover, A H. Marshall, D H. Hides

IGC Proceedings (1977-2023)

Plants of white clover (Trifolium repensL.) cv. Olwen were grown in an open glasshouse at 20°C and ovule growth and development measured. Differences in the rate of growth of ovules within ovaries were observed as early as 2 days after pollination. Ovules reached a maximum size after 8 days, with the smallest only half the size of the largest. After 8 days the smallest ovules became flaccid and shrivelled. Ovule position within the ovary had no effect on the frequency of seed set. Inflorescence position and floret position on the inflorescence had a significant effect on the number …

Influence Of Harvest Date On The Yield And Quality Of Seed Of Phalaris, K Reddy, W R. Scott, R J. Lucas

IGC Proceedings (1977-2023)

Grasslands Maru phalaris (Phalaris aquatica L,) was harvested every third day commencing 12 days after mid-anthesis (DAA) to define the optimum time of harvest for seed yield and quality. Harvesting earlier than 21-24 DAA reduced 1000-seed weight and viability. Delaying harvest until 24 days reduced seed yield due to shattering but had no detrimental effect on seed weight and viability. Heavy seed losses occurred 24 DAA when seed moisture fell below 40%. The results of this experiment suggest that Maru phalaris should be harvested 21-24 DAA when the seed moisture is in the range of 40-42% to reduce the …

Annual Bluegrass And Rat's Tail Fescue Control In Perennial Ryegrass, M E. Mellbye, William C. Young Iii, George W. Mueller-Warrant

IGC Proceedings (1977-2023)

Annual bh1egrass (Poa annua L.) and rat's-tail fescue (Vulpia myruros (L.) C.C. Omel.) are common weed contaminants in seed from perennial ryegrass fields Lolium perenne L. grown in Oregon. A trial was conducted to evaluate post-harvest residue removal methods and herbicides to reduce the level of these impurities. The best weed control was obtained from herbicides following crew-cut management, a comparatively thorough non-thermal nppronch to residue removal. Control was good with sequential herbicide treatments, especially when an effective pre-emergence herbicide such as pendimethalin was used, although no treatment completely eliminated annual bluegrass and rat's-tail fescue from threshed seed samples …

Flowering And Seed Production Of Centrosema Spp. In Relation To Day Length And Temperature, R.J M. Gonzalez, R J. Clements, L R. Humphreys

IGC Proceedings (1977-2023)

The effcc1s of variation in daylength and temperature on the flowering processes leading to seed production were studied in genotypes of 5 Centrosema spp. Short days (11 h) enhanced flowering in accessions of C. virginatum from low latitude but flowering of lines from high latitude was more prolific in 16-h days. A quantitative long-short day response was evident in 2 intermediate latitude accessions. The critical photoperiod for flowering·varied: C. virginianum cross 31 flowered in 13.5 h or less, C. pubescens, C. pascuorum and C. macrocarpum in 12 h or less, and C. schiediam Oowcred only in a 10.5 …

Herbicide Treatments For Non-Thermal Grass-Seed Production, George W. Mueller-Warrant, William C. Young Iii

IGC Proceedings (1977-2023)

Legislation phasing down open-field burning in the Willamette Valley of Oregon is forcing grass seed growers to alter crop production piactices. Adoption of new mechanical means for straw removal has increased reliance on herbicides. Volunteer seedling control and crop tolerance for 15 herbicide treatment sequences were evaluated in established tall fcscue (Festuca arundinacea) and perennial ryegrass (Lolimn perenne) stands during 2 growing seasons using 5 methods of residue removal. Pre-emergence pendimethalin was extremely safe yet fairly effective on volunteer seedlings in both crops. For perennial ryegrass subsequently treated with post-emergence herbicides, pre-emergence metolachlor was slightly more …

A Development Scale For Perennial Ryegrass, Miriam L. Martin, Roger J. Field

IGC Proceedings (1977-2023)

Vernalised plants of perennial ryeg ra ss (Lolium prenne L. cv. Orasslonds Nui) were grown under controlled conditions and apical development followed by regular excision of apices, which were examined by light and scanning electron microscopy. A 12-point scale describing apical development from the vegetative stage to ear emergence has been produced that is presented in 2 forms: a developmental sequence describing organogenesis events at specific stages, and a commentary on easily recognised features of each stage. The developmental scale provides a detailed analysis that is of value as a botanical description and as a practical aid to those involved …