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System-Scale Patterns Of Karst Ventilation In A Mediterranean Karst Massif And Their Implications For The Subsurface Thermal Regime, José Luis Yanes, Francisco Moral

International Journal of Speleology

Karst systems are heterogeneous environments in which water flow is commonly assumed to control subsurface thermal dynamics. However, the role of air circulation at the system scale remains poorly constrained. This study presents a characterization of the thermal expression of ventilation processes in a western Betic Range (southern Spain) karst massif, based on the continuous monitoring of air temperature in multiple conduits distributed along an altitudinal gradient, combined with the analysis of external atmospheric conditions. Results show that ventilation is strongly seasonal and controlled by the interaction between thermal gradients, transient atmospheric variations and system geometry. The observations reveal recurrent …

Calcite Spar Of Kryštálová Cave (Slovakia): Insights Into Formation Conditions From Fluid Inclusions, Stable Isotopes, And Noble Gases, Petronela Ševčíková, Yuri Dublyansky, Stanislava Milovská, László Palcsu, Marjan Temovski, Kata Molnár, Gabriella I. Kiss, Mário Olšavský, Pavel Herich, Gabriella Koltai, Christoph Spötl

International Journal of Speleology

Phreatic calcite spar is an infrequently used yet promising archive for paleohydrology, a diagnostic tool for speleogenesis, and a robust geothermometer. In this study, we investigated phreatic calcite from Kryštálová cave (Malá Fatra Mts., Slovakia) to constrain its formation conditions, reconstruct the composition of its parent fluid, determine precipitation temperatures, and assess its potential for paleohydrology. Fluid-inclusion microthermometry and stable isotope analyses of inclusion water indicate that calcite precipitated at 45-80°C from a meteoric fluid (δ²H_meas = -87.4 to -84.4‰; δ¹⁸O_calc = -12.2 to -11.8‰) with a purely crustal noble gas signature. Stable …

The Conquest For Information V The Fermi Paradox, Matthew A. Kramer

PANDION: The Osprey Journal of Research and Ideas

The concepts of intelligent life beyond earth and extraterrestrial civilizations have intrigued scientists and scholars alike. Intellectuals have suggested that extraterrestrial intelligence should be detectable somewhere in the grand universe; however, despite continued effort, no one has reliably documented evidence supporting extraterrestrial life, culminating in the Fermi Paradox. One perspective to solve the Fermi Paradox involves using logic and analytical reasoning skills to deduce the limits of detection based on what is most probabilistically determinable via the Drake equation. However, with information comes costs and these emergent energetic complexities drive civilizations to maximize computing power, converging into a blackhole transcendent …

Gravitational Constraints And Graviphilic Systems, Bradley E. Cantrell

PANDION: The Osprey Journal of Research and Ideas

Astronomical observation is revealing thousands of new worlds while inferentially suggesting the existence of countless others, as advances in gravitational-wave astronomy and cosmology continue to expand our grasp of the observable universe. This study introduces the gravitational viability factor, 𝐺v, and the concept of graviphilic systems as a framework for organizing astrobiological inquiry. 𝐺v is proposed as a conceptual framework for connecting universal biological constraints with contingent biological outcomes. Gravity is not merely a constraint on life but a useful organizing parameter for evaluating biological plausibility across environments. An abundance of potential telescope targets is available through …

Salvia Rosmarinus L.-Mediated Synthesis Of Silver Nanoparticles: Physicochemical Characterization And In Vitro Evaluation Of Antimicrobial Activity And Cytotoxicity, Raghad Ahmed Alhawi, Hawazin Ahmed Abid

Karbala International Journal of Modern Science

This study describes the biosynthesis of silver nanoparticles (AgNPs) using an aqueous Salvia rosmarinus L. (SRL) extract (Family: Lamiaceae) as a natural source of reducing and capping agents through an easy and green method assisted by blue diode laser irradiation (450 nm, 5 W, 5 min). The formation of rosemary-mediated AgNPs was verified by observing a color change in the solution and the presence of a surface plasmon resonance (SPR) band at 454 nm in the UV–Vis spectrum. XRD and FESEM revealed crystalline silver-containing nanostructures with an average estimated crystallite size of 15.53 ± 3.54 nm and particles with an …

T-Cinnamaldehyde-Driven Fe2o3 Nps: Activity Against Resistant Salmonella, Gallbladder Cancer, And Molecular Docking Focused On Bacterial Targets, Arshad Mahdi Hamad, Sarab Dalaf Khalaf, Suha Maher Abed

Karbala International Journal of Modern Science

Iron oxide nanoparticles (t-CA-Fe₂O₃ NPs) were synthesized in this study using a green preparation method with trans-cinnamaldehyde (t-CA) as a reducing agent. After observing the first sign of successful preparation, namely the color change, the properties were studied using X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDX), ultraviolet-visible spectroscopy (UV-Vis), and Fourier transform infrared spectroscopy (FTIR) techniques. All characterization results were satisfactory, indicating the success of the preparation process and the purity of the prepared nanoparticles (NPs). The molecular docking process of several proteins important in antibiotic resistance and virulence …

Dynamical Behavior In A Three-Dimensional Rational Discrete-Time System, Zafar Saydimaxmudovich Boxonov

Turkish Journal of Mathematics

In this paper, we investigate the dynamic behavior of a three-dimensional rational discrete system with nine parameters. We analyze the system's local and global dynamics, determining conditions for parameter values to ensure positivity of trajectories. We prove the absence of periodic points and conduct global stability analysis using invariant sets. Furthermore, we give biological interpretations of our results.

Shrub Density And Associated Microclimatic Impacts On Rates Of Leaf Litter Decomposition, Evan N. Kraus, Natasha Cudjoe, Ava Loth, Darlene Panvini

Science University Research Symposium (SURS)

Shrub Density and Associated Microclimatic Impacts on Rates of Leaf Litter Decomposition  

Evan Kraus | Ava Loth | Natasha Cudjoe | Darlene Panvini

Leaf litter decomposition is an important ecological process that contributes to nutrient cycling and soil health. Environmental factors, including vegetation density and moisture availability, may influence decomposition rates. This study investigated whether differences in shrub density affect leaf litter decomposition in chives. Two environmental conditions were compared: wet areas with higher shrub density and dry areas with lower shrub density. Each condition included two replicates, with four leaf litter bags attached to each string. A total of …

Native Versus Nonnative Species: Decomposition Rates In Blue False Indigo And Sulfur Cosmos Leaf Litter, Christine Pattillo, Shahtaj Chaudhry, Andrew Golden, Darlene Panvini

Science University Research Symposium (SURS)

Measuring leaf litter decomposition rates provides insight into nutrient cycling within ecosystems and the contribution of plant matter to soil composition. Different plant species show different decomposition rates depending on their chemical makeup and structural characteristics. Using litterbags, it is possible to track and measure the breakdown of plant material by comparing its initial and final mass over a designated period of time. Tennessee has a range of native and non-native plant species. This study focused on two plants; native Blue False Indigo (Baptisia australis) and non-native Sulfur Cosmos (Cosmos sulphureus). It was hypothesized that native plants would decompose more …

Computation Of Minimum Numbers Of Tile And Bond-Edge Types For Dna Self-Assembly Of Select Archimedean Graphs, Tabitha Merrithew, Jessica Sorrells

Theory & Applications of Graphs

This project mathematically models the self-assembly of DNA nanostructures in the shape of select Archimedean graphs using the flexible tile model. Under the most strict set of conditions of this model, we employ principles of linear algebra and graph theory to determine the minimum number of different DNA branched molecules needed to construct the desired shapes, theoretically reducing laboratory costs and the waste of biomaterials. We determine exact values for $T_3(G)$, the minimum number of molecule (or ``tile") types needed for all six order 12 and 24 Archimedean graphs. We also determine exact values for $B_3(G)$, the minimum number of …

Codee Expects That Every Mathematician Will Do Their Odes: From The Battle Of Trafalgar To Calculus (Or Nelson To Newton), Steven Miller

CODEE Journal

Using the historical Battle of Trafalgar as a case study, we introduce students to mathematical modeling to describe and explore real-world systems. Starting with the question—how do force sizes and combat effectiveness determine which side wins?—we show how to use a blend of mathematics and computational tools to investigate the answer. Beginning by defining a simple differential equation model for combat dynamics, we analyze its behavior using differential equations and accessible algebraic techniques. We show how computational methods and simulations can support systematic, visual exploration and suggest conjectures that mathematical analysis can then establish. This material could serve as the …

Conserved Iq Motifs, Divergent Apo-Calmodulin Recognition In Ube3b And Ube3c, Emily G. Schaffter, Xiaohuan Lu, Anna E. Tinklenberg, Megan G. Hill, Rafael H. Levin, Javier F. Tabima, Shuanghong Huo, Donald E. Spratt

Chemistry

Calmodulin (CaM) regulates diverse signaling proteins through recognition of short linear motifs, including isoleucine-glutamine (IQ) motifs that commonly bind Ca2+-free CaM (apo-CaM). The homologous to E6AP carboxyl terminus (HECT) E3 ubiquitin ligases ubiquitin protein ligase E3B (UBE3B) and ubiquitin protein ligase E3C (UBE3C) are closely related enzymes that both contain N-terminal IQ motifs, yet whether these motifs encode conserved modes of apo-CaM recognition has remained unclear. Here, we combined isothermal titration calorimetry, nuclear magnetic resonance (NMR) spectroscopy, and computational modeling to compare apo-CaM binding by the UBE3B and UBE3C IQ motifs. The UBE3B IQ motif bound apo-CaM with high affinity …

Data Centre Litigation And Climate Change: Can Claims Against Data Centres Resolve Tensions Between Ai Growth And Climate Goals?, Nick Scott, Heng Wang

Research Collection Yong Pung How School Of Law

As artificial intelligence (AI) has become ubiquitous, climate-related impacts of data centres used to power these technologies have emerged as a growing concern for governments, civil society groups, and the public. As a result of this, a wave of data centre litigation has started to sweep multiple jurisdictions, in particular the United States, often leveraging environmental law. However, many claims do not directly target data centres’ impacts on climate change, and the challenges of aligning AI growth with climate goals may extend far beyond energy use in this infrastructure. This article analyses two research questions: (1) how are mismatched governance …

Managing Collaboration Under Conservation Crisis: Trust, Risk, And Control In The Gulf Of Maine Fishery Management Network, Evelyn Roozee, Owen Temby, Dongkyu Kim, Antonia Sohns, Anthony Rocha Lima, Jasper R. De Vries, Gordon M. Hickey

School of Earth, Environmental, & Marine Sciences Faculty Publications

Transboundary fishery management and the intertwined conservation of critically endangered species represent significant governance challenges that require ongoing inter-organizational communication, collaboration, and collective action to achieve shared objectives. Previous research suggests that inter-organizational collaborative performance depends heavily on different dimensions of trust and complementary control mechanisms to mitigate the perceived risks of collaborating and enable the reciprocal sharing of resources and the coordination of activities. However, it is unclear how proposed relationships between trust, risk, and control are shaped by disruptions to established transboundary management networks. This study presents the results of survey research conducted in the Gulf of Maine …

Understanding The Adaptability Of Wild Thyme And Lavender Using Temperature, Leslie De Leon, Elizabeth Reyes, Lillian Mitchell, Harris Memon, Darlene Panvini

Science University Research Symposium (SURS)

Green roofs are partially or completely covered with vegetation and provide several ecosystem services, including stormwater management, reducing the heat island effect, supporting biodiversity, and providing aesthetic value. Our research investigated how surface temperature affects the growth of two perennial plants, Wild Thyme and English Lavender, under green roof conditions. We hypothesized that both species would adapt well to temperature fluctuations because of their drought-tolerant and low-maintenance characteristics. For this study, we utilized Wild Thyme (Thymus serpyllum) and English Lavender (Lavandula angustifolia). Wild Thyme is a low-growing ground cover that tolerates drought and varying environmental …

Assessing Biodiversity Of Native Lichen In Parks Along Major Interstates Of Davidson County, Leslie De Leon, Ross Andrew

Science University Research Symposium (SURS)

Lichens are unique biological entities formed through a symbiotic partnership between a fungus and a photosynthetic partner, such as algae or cyanobacteria. This mutualistic relationship allows lichens to survive in diverse environments and colonize a variety of substrates. Previous studies have examined air pollution at broad spatial scales and its impact on human health; however, less is understood about how air pollution and its potential ecological effects vary in areas surrounding major interstate highways. As biological indicators, lichens can provide insight into environmental conditions and air quality due to their sensitivity to atmospheric pollutants. This study examined lichen diversity and …

The Structure And Regulatory Mechanism Of The Emrb Rna Motif In Lactobacillus Acidophilus, Isabella J. Mezzenga, Brian M. Lee

Journal of the South Carolina Academy of Science

Major facilitator superfamily (MFS) transporters aid bacteria in expelling toxic compounds such as antibiotics, bile acids, and other substances. Previous bioinformatic studies identified the emrB motif as a potential regulatory RNA element. In Lactobacillus, this RNA motif is generally found in the intergenic region upstream of an MFS transporter gene with homology to the emrB gene from Escherichia coli. Secondary structure predictions of the intergenic region were used to define the structural features of this RNA motif. The emrB motif comprises two hairpins, though inclusion of neighboring regions is predicted to stabilize alternative secondary structures. A potential rho independent terminator …

A Philosophical Introduction To Elements And Relations: Aspects Of A Scientific Metaphysics, Martin Zwick

Complex Systems Faculty Publications and Presentations

My book, Elements and Relations*, amplifies Bunge’s characterization of the systems project as the construction an “exact and scientific metaphysics” (ESM) different from and broader than the reductionist and physicalist ontology of conventional science. This paper discusses the scientific theories constituting this project and the central notion of “system” as a structure-function dyad, where “structure” is the system’s internal order and “function” is its participation in the external order of its environment. The paper also discusses the book’s proposal of ontology and ethics as a structure-function dyad for the systems field, an ontology of problems that exemplifies the ESM idea.

Development And Validation Of An Ai-Assisted Eco-Batik Gringsing Student Worksheet, Intan Kurniawati, Arif Widiyatmoko, Bambang Subali 5, Novi Ratna Dewi

Jurnal Pendidikan dan Pembelajaran

Background: Science literacy among Indonesian students remains low, indicating a need for contextual learning resources that connect scientific concepts with students’ environments. Local cultural heritage such as Batik Gringsing, combined with artificial intelligence (AI) as a supporting tool, offers a promising context, yet their integration in a single student worksheet remains underexplored.

Objectives: This study aimed to develop and validate an AI-assisted Eco-Batik Gringsing student worksheet for science learning.

Methods: The study employed a research and development (R&D) approach adapted from the 4D model, covering the Define, Design, and Develop stages. The evaluation focused on the validity and practicality of …

Confluence: Linking Citizen Science And Extension Education To Inspire Environmental Stewardship, Dave Smaldone, Evan Harms, Jason Burnside, Chad Pierskalla, Jinyang Deng

Journal of Extension

Citizen science has rapidly moved beyond simply crowdsourcing data to become a novel platform for environmental and informal science education. However, few studies document the informal learning outcomes of citizen science, particularly in youth or Extension education. This quantitative study evaluated individual learning outcomes of an environmental education and citizen science experience about water quality at 4-H summer camps. Outcomes of interest, knowledge, and stewardship intentions were evaluated using pre- and post-participation surveys. The results showed an overall success of the program. By understanding these outcomes, we can better plan citizen-science-focused Extension learning experiences to meet strategically targeted outcomes.

Growing Climate Literacy In Urban Green Spaces: An Extension Youth Climate Education Experience, Brad Bessler, Justin Hougham

Journal of Extension

Capturing Your Environment (CYE) is an environmental education framework that engages youth in place-based climate exploration. CYE was implemented with youth participating in a Milwaukee summer internship program funded by the Children, Youth, and Families at Risk (CYFAR) Sustainable Community Projects grant. The primary objective of CYE was to create an engaging climate-centered experience for youth. The experience aimed to improve science efficacy, climate content knowledge, science skills, and confidence using scientific tools. A paired t-test compared the learners' pre- and post-experience responses on a 16-item self-report survey. Following participation in CYE, youth reported increases across all measured outcomes.

A Comprehensive Review On The Role Of Deep Learning For Detecting And Identifying Obscured Objects, Baraa Hasan Hadi, Jamila Harbi Saud

Karbala International Journal of Modern Science

Human operators frequently encounter eye fatigue that typically comes from workload and sleep deprivation. This could affect the efficiency and performance of vigilance significantly. In safety-sensitive applications such as traffic systems, healthcare, and security, this issue is essential. To address this issue, there is a need for situational awareness and maintaining continuous monitoring of the workload of the person. To this end, advanced artificial intelligence (AI) methods, denoted by a deep learning (DL) based approach, can be used. Such methods are also supported by computer vision (CV) to detect and identify obscured objects. Combining CV with AI can overcome the …

Risk Prioritization Of ``Digital Drug'' And Consumer Neurostimulation Modalities: A Reproducible Interval-Valued Fermatean Fuzzy Entropy–Topsis Framework, Rawan Emad El-Saadany, Ahmed Samy, Mohamed M. Abdelhafeez, Mahmoud M. Ismail

Neutrosophic Systems with Applications

Consumer audio and multisensory stimulation technologies are increasingly accessible through streaming platforms, mobile applications, and immersive media. The expression digital drug is sometimes used for binaural-beat content intended to alter subjective states, but the term is a consumer/cultural label and does not imply pharmacological equivalence. Risk prioritization in this area is difficult because evidence is heterogeneous, several relevant criteria are qualitative, and judgments may be imprecise rather than point-valued. This paper develops a transparent interval-valued Fermatean fuzzy (IVFF) group decision framework that combines interval-preserving aggregation, Shannon entropy weighting, and TOPSIS for prioritizing digital drug risk scenarios under uncertainty. The method …

Autofield-Poa: A Hybrid Automl–Metaheuristic Framework For Automated Feature Selection In Recommender Systems, Mohammed Dheyaaldeen Taha, Waleed Kareem Ahmed, Rana Saad Mohammed, Zied O. Ahmed

Karbala International Journal of Modern Science

The problem of automated feature selection is one of the most important aspects of modern recommender systems, as overestimating the number of feature fields used, which can increase model complexity, inference latency, and performance degradation due to redundancy and noise. Although differentiable Automated Machine Learning (AutoML) based feature selection methods, including AutoField, are effective, they remain susceptible to initialization and local optima. Conversely, population-based metaheuristic algorithms are effective at global exploration, but are often inefficient in high-dimensional discrete spaces when randomly initialized. This paper presents AutoField-POA, a hybrid AutoML-metaheuristic framework that combines a differentiable controller with the Pelican Optimization Algorithm …

Resolving Satellite And In Situ Mismatches In Net Primary Production Using High-Frequency In Situ Bio-Optical Observations In The Subpolar Northwest Atlantic, Kitty Warsi Kam, Emmanuel Devred, Stephanie Alam Clay, Mohammad M. Amirian, Andrew J. Irwin, Dariia Atamanchuk, Uwe Send, Douglas W. R. Wallace

Publications and Research

Net primary productivity (NPP) plays a central role in biological carbon pump (BCP) and global carbon cycling, but NPP estimates in high-latitude regions remain highly uncertain despite their disproportional contribution to the global carbon sink. Previous studies identified discrepancies among satellite- and in situ-derived NPP estimates, but the drivers of disagreement remain poorly resolved due to limited high-frequency observations. Here, we present continuous depth-resolved estimates of in situ NPP from the Central Labrador Sea (56°N) in the subpolar Northwest Atlantic, reconstructed from daily bio-optical profiles collected between May and November 2016, and a 40-year dataset of photosynthesis parameters derived from …

A Yolov8x Framework For Breast Lesion Localization Using Real-World Mammographic Images, Hadeel Abdul Majeed Ghazi, Yarub Alazzawi, Hussein Hasan Nsaif

Karbala International Journal of Modern Science

Breast cancer is one of the leading causes of mortality among women worldwide, and early and accurate mammographic assessment is important for timely diagnosis and improved patient survival. However, accurate breast lesion detection requires overcoming the issues of low lesion contrast, dense breast tissue, image noise, and variation in mammographic acquisition. In this study, we present a YOLOv8x-based computer-aided detection framework for automated breast lesion localization in full-field digital mammography (FFDM) and digital breast tomosynthesis (DBT) images acquired under heterogeneous clinical conditions. The framework was developed and evaluated using 501 clinical mammographic images obtained from multiple mammography systems, namely GE …

An Object-Level Semantic Video Transmission Framework For Iomt Based On Lightweight Yolo And Motion Triggering, Iman Kadhum Abbood, Alaa Shawqi Jaber

Karbala International Journal of Modern Science

In Internet of Multimedia Things (IoMT) environments, video capture and frame transmission consume substantial sensor energy and impose considerable network overhead because of redundant data transmission. Traditional approaches often rely on repeated pixel-level operations and frequent execution of deep segmentation models, thereby increasing computational and transmission costs. This paper proposes an Object-Level Semantic Video Transmission Framework (OSVT) for resource-constrained IoMT environments in which high-definition visual data must be transmitted over low-bandwidth wireless multimedia sensor networks (WMSNs). The proposed OSVT incorporates a dual-stage wake-up mechanism that remains in sleep mode during static scenes, thereby reducing transmission load. The high-power YOLOv11-seg module …

Phenological Flexibility In Nesting Grassland Birds Over A Half Century Informs Timing Of Management, Kristin S. Ellis, Michael J. Anteau, Lawrence D. Igl, Garrett J. Macdonald, Neal D. Niemuth, Aaron T. Pearse, Jill A. Shaffer, Christine A. Ribic, Josh L. Vest, Masanori Abe, Daniel S. Ackerman, Marissa A. Ahlering, Johanna N. Alpert, Anahit Amiri, Kent Andersson, Jacqueline K. Augustine, Kristel K. Bakker, Jeffrey L. Beck, Adam C. Behney, Jacy S. Bernath-Plaisted, Todd R. Bogenschutz, Eric K. Bollinger, Lauren E. Bortolotti, Andy J. Boyce, Jeffrey D. Brawn, Fred C. Bryant, Andrew J. Campomizzi, Jay D. Carlisle, J Matthew Carroll, Rachel Carroll, John P. Carroll, Justin R. Clarke, Michael R. Conover, Reesa Y. Conrey, Jaime J. Coon, Kyle A. Cutting, Stephen K. Davis, Dawn M. Davis, Duane R. Diefenbach, Jonathan B. Dinkins, R Andrew Dreelin, Victoria J. Dreitz, Courtney J. Duchardt, Michael W. Eichholz, Susan N. Ellis-Felege, Kevin S. Ellison, Bradley C. Fedy, Samantha D. Fino, Robert J. Fletcher Jr, Dillon T. Fogarty, Samuel D. Fuhlendorf, Pamela R. Garrettson, Robert J. Gates, Erin L. Gelling, James J. Giacomo, Alex Glass, Cheri L. Gratto-Trevor, Ryan D. Haffele, Christian A. Hagen, Vanessa B. Harriman, Samuel W H Harryman, David A. Haukos, Robert T. Haynam, Heather A. Herakovich, James R. Herkert, Fidel Hernandez, Jason M. Hill, H Jeffrey Homan, Torre J. Hovick, Jonathan A. Jenks, William E. Jensen, Aaron N. Johnston, Sydney-Marie Jones, Carly S. Kelly, Kaylan M. Kemink, Silka L F Kempema, Dylan C. Kesler, Christopher P. Kirol, Robert W. Klaver, Page E. Klug, Jesse L. Kolar, Nicola Koper, Kyle J. Kuechle, Jonathan D. Lautenbach, Zoe M. Lebrun-Southcott, David W. Londe, Scott R. Loss, Cullen M. Mackenzie, Patrick A. Magee, Douglas L. Manzer, John P. Mccarty, Gywm Mckee, Ann E. Mckellar, Lance B. Mcnew, James R. Miller, Megan C. Milligan, Ashlee K. Minor, Rocco J. Murano, Les D. Murray, David E. Naugle, Clayton K. Nielsen, Christopher J. Norment, Sarah B. Ogden, Lindsay A. Parsons, Brian D. Peer, Noah G. Perlut, James C. Pittman, Christopher D. Pollentier, Larkin A. Powell, Aaron C. Pratt, John P. Pulliam, Nancy M. Raginski, Dan R. Reinking, Kaitlyn M. Reintsma, Terry Z. Riley, Kevin M. Ringelman, Joseph R. Robb, Scott K. Robinson, Andres N. Rosales, Charlotte L. Roy, Kayla A. Ruth, Brett K. Sandercock, Kevin K. Sedivec, Steve K. Sherrod, Justin J. Shew, Mason L. Sieges, Jenny L. Sika, Susan K. Skagen, Cassandra G. Skaggs, Joseph Smith, Jennifer A. Smith, Kurt D. Smith, Alex J. Solem, Joshua D. Stafford, Glenn E. Stauffer, Matthew D. Stephenson, Lee Sutcliffe, Amber E. Swicegood, Jason Tack, Evan P. Tanner, Catrina V. Terry, Wendy P. Tori, Ashley M. Unger, Kelly R. Vanbeek, William E. Vetter, Jay A. Vonbank, Brett L. Walker, Michael D. Whitson, Maiken Winter, Kimberly A. With, Donald H. Wolfe, Amy A. Yakel Adams, Benjamin Zuckerberg

United States Department of Agriculture Wildlife Services: Staff Publications

The timing of biological events for wildlife species reflects and influences ecological and evolutionary processes and helps guide management actions to meet conservation objectives. Climate change may cause phenological shifts across trophic levels and ecosystems, which can have broad ecological impacts. Shifts may also result in mistiming between management practices based on historical conditions and current biological events, reducing the effectiveness of natural resource management and conservation efforts. We analyzed nesting phenology patterns over recent decades across North America for 44 species of grassland-nesting birds, including waterfowl, upland gamebirds, shorebirds, and passerines, many of which have experienced precipitous population declines. …

Systematic Profiling Of Encoder Architectures And Multimodal Embeddings In Protein Foundation Models Reveals Data Set-Driven Separability Regimes In Prediction Of Allosteric And Orthosteric Binding Sites, Alina Bazarova, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Allosteric regulation represents a fundamental mechanism of protein function, yet distinguishing allosteric from orthosteric protein-binding sites remains a persistent computational challenge. While multimodal protein foundation models offer the potential to integrate complementary biological signals, including sequence, structure, functional annotations, and conformational dynamics, their performance determinants in allosteric binding site detection remain poorly understood. We introduce a unified computational framework for profiling multimodal protein foundation models across distinct binding site separability regimes. Rather than evaluating models solely by predictive accuracy, the framework combines systematic modality embedding ablations, encoder architecture comparisons, and variance decomposition to characterize how evolutionary, structural, functional, and dynamical …

Establishing Kinetic Lipidomic Methods For Quantifying In Vivo Shifts In Metabolic Homeostasis, Coleman Nielsen

Theses and Dissertations

Lipidomics conventionally measures molecular abundance, but abundance alone cannot distinguish a lipid pool that is actively turning over from one that is static. This dissertation develops kinetic lipidomics, a mass spectrometry approach that uses deuterated-water labeling to quantify in vivo turnover across an entire lipidome. We apply this framework to investigate how apolipoprotein E (ApoE) genotype alters brain metabolism in the context of Alzheimer's disease risk. The method simultaneously recovers three parameters for hundreds of lipid species: the fractional turnover rate (k), the fraction of the pool accessible to endogenous synthesis (Asyn), and the effective number of deuterium-incorporating sites (nL). …