Digital Commons Network^™

Relationships Between The Nutrient Content Of Irrigated Pasture On Offer And That Selected By Grazing Dairy Cows, W J. Wales, C R. Stockdale, P T. Doyle

IGC Proceedings (1977-2023)

An experiment was conducted to determine the dry matter, energy, crude protein and fibre intake by dairy cows in late lactation when grazing perennial pasture offered at allocations of 15, 20, 30 and 40 kg DM/cow.day. The cows consistently selected a diet 10% higher in digestibility than that on offer. In contrast, cows selected diets with crude protein levels increasing from 22% to 40%, above that in pasture on offer, as pasture allocation increased. A similar pattern was observed for the intake of white clover (Trifolium repens L). The increase in the concentration of crude protein in the diet …

Species Preference Influences On Cattle Grazing Behaviour, G P. Cosgrove, C B. Anderson, R H. Fletcher

IGC Proceedings (1977-2023)

Lotus corniculatus offers specific nutritional benefits to animals, but exploiting these advantages in grazing systems depends on the proportion of lotus in the feed offered and the animals' preference, hence desire to select for it. To determine preference for lotus, heifers were offered free-choice in contrasting, spatially separated but adjacent monocultures of ryegrass-lotus or red clover-lotus. Following a one-week period to adjust to the species offered and their arrangement, 10 young heifers were observed at 10-minute intervals during daylight hours, and the species they were on and whether or not they were grazing was recorded. This procedure was conducted in …

Partial Preference Of Grazing Cattle For Contrasting Legume Swards, C.H. E.C. Poli, J Hodgson, G P. Cosgrove, G C. Arnold

IGC Proceedings (1977-2023)

Yearling heifers in groups of 3 grazed 405 m2 plots made up of alternating 2.4m wide strips of white clover/birdsfoot trefoil (WC+BT) or red clover (RC) in the proportions of 80:20, 67:33, 33:67 and 20:80 for periods of 3 days over four replicates in time, balanced for effects of previous treatment. Observation of the distribution of grazing activity and biting rate were made over 3 hour periods each evening. Biting rates were consistently higher on (WC+BT) than RC (52.3 vs 46.3 ± 0.59 bites.min-1 P(0.0001). Animals initially showed partial preference for the minor sward component in each treatment but regression …

The Use Of Vibration Analysis And Telemetry To Measure Bite Frequency And Intensity In Free-Ranging Horned Ruminants, P R. Lawrence, K Becker

IGC Proceedings (1977-2023)

An apparatus is described which detects and measures the vibrations in a ruminant’s horn especially those produced by the animal’s teeth. Vibrations are transmitted by radio to a portable computer where those produced as a result of eating and ruminating can be characterised by their intensity, length and frequency.

Influence Of Vegetation Patch Characteristics On Discriminatory Grazing By Dairy Cows, W M. Griffiths, J Hodgson, G C. Arnold, C W. Homes

IGC Proceedings (1977-2023)

Two studies involving the sequential grazing of sets of patches on a perennial ryegrass (Lolium perenne) sward were carried out to investigate the effects of patch characteristics on the selective behaviour of grazing cattle. Experiment 1 involved a range of combinations of sward height (8.9 - 19.6 cm) and bulk density (1.33 - 1.67 mg DM/cm3). Distribution of grazing activity (number of bites or residence time) was strongly and positively related to patch height, but additional effects of variation in bulk density were limited. In Experiment 2 patches were manipulated to offer contrasts in both height (13.4 and …

Shade For Cattle On Pasture: A Guide For Ontario Producers, E J. Finegan, T M. Widowski

IGC Proceedings (1977-2023)

In tropical climates, adequate shade may be essential to ensure the survival and productivity of grazing animals, but in the temperate Ontario climate, the necessity or benefits of providing shade for grazing cattle are less clear, and have proved controversial. Meteorological data indicate that beef cattle in Ontario may be at risk of suffering from heat stress on more than 25% of days during July and August, and may decrease feed intake and benefit from the provision of shade for more than 50% of days during the two hottest summer months. A booklet, entitled ‘Beat the Heat. A Guide …

A Multi-Omics Investigation Into The Mechanism Of Action Of An Anti-Tubercular Fatty Acid Analog, Isin T. Sakallioglu, Amith S. Maroli, Aline De Lima Leite, Darrell D. Marshall, Boone W. Evans, Denise K. Zinniel, Patrick H. Dussault, Raul G. Barletta, Robert Powers

Patrick Dussault Publications

The mechanism of action (MoA) of a clickable fatty acid analogue 8-(2-Cyclobuten-1-yl)octanoic acid (DA-CB) has been investigated for the first time. Proteomics, metabolomics, and lipidomics were combined with a network analysis to investigate the MoA of DA-CB against Mycobacterium smegmatis (Msm). The metabolomics results showed that DA-CB has a general MoA related to that of ethionamide, a mycolic acid inhibitor that targets enoyl-ACP reductase (InhA), but DA-CB likely inhibits a step downstream from InhA. Our combined multi-omics approach showed that DA-CB appears to disrupt the pathway leading to the biosynthesis of mycolic acids, an essential mycobacterial fatty acid …

Combining Multi-View Uav Photogrammetry, Thermal Imaging, And Computer Vision Can Derive Cost-Effective Ecological Indicators For Habitat Assessment, Qiao Hu, Ligang Zhang, Jeff Drahota, Wayne Woldt, Dana Varner, Andy Bishop, Ted Lagrange, Christopher M. U. Neale, Zhenghong Tang

School of Natural Resources: Faculty Publications

Recent developments in Unmanned Aircraft Vehicles (UAVs), thermal imaging, and Automachine learning (AutoML) have shown high potential for precise wildlife surveys but have rarely been studied for habitat assessment. Here, we propose a framework that leverages these advanced techniques to achieve cost-effective habitat quality assessment from the perspective of actual wildlife community usage. The framework exploits vision intelligence hidden in the UAV thermal images and AutoML methods to achieve cost-effective wildlife distribution mapping, and then derives wildlife use indicators to imply habitat quality variance. We conducted UAV-based thermal wildlife surveys at three wetlands in the Rainwater Basin, Nebraska. Experiments were …

Leveraging The Hmbc To Facilitate Metabolite Identification, Fatema Bhinderwala, Thao Vu, Thomas G. Smith, Julian Kosacki, Darrell D. Marshall, Yuhang Xu, Martha D. Morton, Robert Powers

Department of Chemistry: Faculty Publications

The accuracy and ease of metabolite assignments from a complex mixture are expected to be facilitated by employing a multi-spectral approach. The 2D ¹H-¹³C HSQC and 2D ¹H-¹H-TOCSY are the experiments commonly used for metabolite assignments. The 2D ¹H-¹³C HSQC-TOCSY and 2D ¹H-¹³C HMBC are routinely used by natural products chemists but have seen minimal usage in metabolomics despite the unique information, the nearly complete ¹H-¹H and ¹H-¹³C and spin systems provided by these experiments that may improve the accuracy and reliability …

Dissolved Nitrogen Removal In Biochar Amended, High Permeability Media For Urban Stormwater Treatment, Mark Vicciardo

USF Tampa Graduate Theses and Dissertations

Nutrient pollution in stormwater drives the eutrophication of inland and costal waterbodies which leads to sea grass retreat and the proliferation of harmful algal blooms (HAB). These anthropogenic effects destabilize ecosystems, and some HABs can pose direct human health risk. Bioretention, or the storage and controlled discharge of stormwater run-off in an ecologically engineered setting, is a potential solution to this problem. However, it relies heavily on the settling of particles as a nutrient removal mechanism, and thus struggles with pollutants, such as dissolved nitrogen, which is a particular problem in Florida where the geological prominence of phosphorus leaves nitrogen …

Challenges To Reindeer, Reciprocity, And Indigenous Sami Sovereignty Amidst The Impact Of Green Energy Developments, Lisa Heikka-Huber

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

The Indigenous people of Europe known as the Sami, (also spelled Saami) many of whom live throughout the world, have continued to maintain active nomadic communities today as their ancestors did. A wide spanning region of Northern Europe’s Arctic Zone or Sampi often referred to as Fennoscandia, encompasses four countries, Norway, Sweden, Finland, and Russia’s Kola Peninsula (Roland & Löffler, 2012). The nomadic Sami people follow the migration pathways of their reindeer herds through the wilderness bi-annually. This paper will discuss many perspectives, including the battle Sami people and other Indigenous communities have endured while combating green energy development from …

Automatic Image-Based Nutritional Calculator App, Kejvi Cupa

USF Tampa Graduate Theses and Dissertations

Nutrition plays a pivotal role in shaping an individuals’ health and quality of life, making the evaluation of dietary intake crucial for promoting healthier lifestyle choices. Various solutions, particularly mobile apps, have been developed to facilitate the process of dietary estimation. Accurate nutritional intake assessment relies on two key components: ingredient recognition and food portion estimation. For a mobile app to offer a comprehensive solution for automatic nutritional assessment, it must address both components.

In this work, we focus on a mobile app pipeline: the semi-automatic pipeline which focuses on automatic food ingredient recognition. This pipeline integrates state-of-the-art models for …

Bird Strike Hazard Assessment For The Tampa International Airport, Florida, Usa, Yakubu Ogwu Isah

USF Tampa Graduate Theses and Dissertations

Managing wildlife at airports poses a challenge for ensuring safety for aviation traffic. Airports, with their surrounding habitats and infrastructure, serve as attractants for avian species. Threats created by these species have led managers to develop management techniques in and around airports (DeVault et al 2013). One approach is the use of geographic information systems (GIS) for analyzing avian strike data and airport bird surveys. Spatial analysis of strike data identifies species of threat by categorizing strike occurrence, species sizes, phase of flight, and risk of damage. In addition, GIS can be used to map hotspots of bird strikes. These …

Semi-Automated Cell Annotation Framework Using Deep Learning, Abhiram Kandiyana

USF Tampa Graduate Theses and Dissertations

Unbiased stereology refers to a field of applied mathematics \cite{intro-to-stereology} focused on accurate (model and assumption-free) quantification of three-dimensional (3D) objects, typically based on their appearance in 2D sections (planes) through the objects. In the biological sciences, these techniques are widely used for making unbiased estimates of arbitrary-shaped (stochastic) objects such as stained cells, blood vessels, region volumes, etc., in tissue sections through a region of interest (ROI).

This fundamental methodology is widely used for evaluating structural changes that occur in diseases, aging, and pharmaceutical interventions, thereby ensuring reliable outcomes. In terms of limitations, stereology is tedious, time- and labor-intensive, …

The Polyglutamine Domain Is The Primary Driver Of Seeding In Huntingtin Aggregation, Adam Skeens, Chathuranga Siriwardhana, Sophia E. Massinople, Michelle M. Wunder, Zachary L. Ellis, Kaitlyn M. Keith, Tyler Girman, Shelli L. Frey, Justin Legleiter

Chemistry Faculty Publications

Huntington’s Disease (HD) is a fatal, neurodegenerative disease caused by aggregation of the huntingtin protein (htt) with an expanded polyglutamine (polyQ) domain into amyloid fibrils. Htt aggregation is modified by flanking sequences surrounding the polyQ domain as well as the binding of htt to lipid membranes. Upon fibrillization, htt fibrils are able to template the aggregation of monomers into fibrils in a phenomenon known as seeding, and this process appears to play a critical role in cell-to-cell spread of HD. Here, exposure of C. elegans expressing a nonpathogenic N-terminal htt fragment (15-repeat glutamine residues) to preformed htt-exon1 fibrils induced …

Advanced Hyperthermia Treatment: Optimizing Microwave Energy Focus For Breast Cancer Therapy, Burak Acar, Tuba Yilmaz Abdolsaheb, Ali Yapar

Turkish Journal of Electrical Engineering and Computer Sciences

This paper presents a fast antenna phase optimization scheme to enable microwave power focusing for breast cancer hyperthermia. The power focusing is achieved through the maximization of the deposited electric field on the target malignant tumor tissue. To do so, a malignant breast tumor, the surrounding breast medium, and the skin of the breast are modeled as a cylindrical structure composed of eccentric cylinders, and electric field distribution is computed analytically in terms of cylindrical harmonics. This approach minimized the computational cost and simplified the breast medium model. To ensure applicability across various breast types, the dielectric properties (DPs) of …

Atomic Comagnetometer Gyroscopes For Inertial Navigation Systems: A Review, Murat Salim Karabinaoglu, Bekir Çakir, Mustafa Engin Başoğlu

Turkish Journal of Electrical Engineering and Computer Sciences

In recent years, developments in quantum sensing, laser, and atomic sensor technologies have also enabled advancement in the field of quantum navigation. Atomic-based gyroscopes have emerged as one of the most critical atomic sensors in this respect. In this review, a brief technology statement of spin exchange relaxation free (SERF) and nuclear magnetic resonance (NMR) type atomic comagnetometer gyroscope (CG) is presented. Related studies in the literature have been gathered, and the fundamental compositions of CGs with technical basics are presented. A comparison of SERF and NMR CGs is provided. A basic simulation of SERF CG was carried out because …

Consensus-Based Virtual Leader Tracking Algorithm For Flight Formation Control Of Swarm Uavs, Berat Yıldız, Akif Durdu, Ahmet Kayabaşi

Turkish Journal of Electrical Engineering and Computer Sciences

Technological developments in industrial areas also impact unmanned aerial vehicles (UAVs). Recent improvements in both software and hardware have significantly increased the use of many UAVs in social and military fields. In particular, the widespread use of these vehicles in social areas such as entertainment, shipping, transportation, and delivery and military areas such as surveillance, tracking, and offensive measures has accelerated the research on swarm systems. This study examined the previous investigations on swarm UAVs and aimed to create a more efficient algorithm. The effectiveness of the proposed algorithm was compared with other leader-based applications. A swarm consisting of 5 …

Label-Aware Distance Mitigates Temporal And Spatial Variability For Clustering And Visualization Of Single-Cell Gene Expression Data, Shaoheng Liang, Jinzhuang Dou, Ramiz Iqbal, Ken Chen

Faculty, Staff and Student Publications

Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. The batch effect, i.e., the variability among samples gathered from different times, tissues, and patients, introduces large between-group distance and obscures the true identities of cells. To solve this problem, we introduce Label-Aware Distance (LAD), a metric using temporal/spatial locality of the batch effect to control for such factors. We validate LAD on simulated data as well as apply it to a mouse retina development dataset and a lung dataset. We also found the utility of our …

Deep Learning Approaches For Cancer Prognosis Prediction Using Histopathological, Omics, And Clinical Data, Shuai Jiang

Dartmouth College Ph.D Dissertations

Accurate prediction of patient outcomes is crucial for shared clinical decision-making, treatment planning, and patients' psychological adjustment. Histopathological features of cancer, including tumor size, lymph node involvement, and metastasis, are commonly incorporated into survival prediction models, underscoring the prognostic value of whole slide images (WSIs). Concurrently, studies have highlighted the significance of omics data, such as transcriptomics, in providing valuable insights into cancer prognosis.

The emerging deep learning methods have brought new opportunities in biomedical informatics. Despite a growing body of studies on the application of deep learning methods for predicting prognosis using WSIs, the results are varied, primarily due …

An Exposome Atlas Of Serum Reveals The Risk Of Chronic Diseases In The Chinese Population, Lei You, Jing Kou, Mengdie Wang, Guoqin Ji, Xiang Li, Chang Su, Fujian Zheng, Mingye Zhang, Yuting Wang, Tiantian Chen, Ting Li, Lina Zhou, Xianzhe Shi, Chunxia Zhao, Xinyu Liu, Surong Mei, Guowang Xu

Faculty, Staff and Student Publications

Although adverse environmental exposures are considered a major cause of chronic diseases, current studies provide limited information on real-world chemical exposures and related risks. For this study, we collected serum samples from 5696 healthy people and patients, including those with 12 chronic diseases, in China and completed serum biomonitoring including 267 chemicals via gas and liquid chromatography-tandem mass spectrometry. Seventy-four highly frequently detected exposures were used for exposure characterization and risk analysis. The results show that region is the most critical factor influencing human exposure levels, followed by age. Organochlorine pesticides and perfluoroalkyl substances are associated with multiple chronic diseases, …

Predicting Gender Of Author Using Large Language Models (Llms), Satya Uday Sanku

USF Tampa Graduate Theses and Dissertations

The advent of text data from social media, blogs, movie reviews, and other textual sources has opened new avenues for research, particularly in the domain of Author Profiling. Author Profiling helps in Capturing the Stylistic features and also useful for analyzing the required elements in the written text. This Study addresses one of the tasks in Author Profiling which is termed as gender detection or Classification of Gender from Text. The main goal of this research is to obtain valuable and relevant gender characteristics that will accurately classify the Author’s gender of a review extracted from an Anime Review website. …

Interrelationships Among Local Values Of Wet Bulb Globe Temperature, Heat Index, And Adjusted Temperature, Andrea Giraldo

USF Tampa Graduate Theses and Dissertations

Occupational heat stress significantly affects outdoor workers who face challenges due to increased heat exposure. Because of the prevalence of heat illness, it is important to measure heat stress for outdoor workers. Monitoring occupational heat stress most often relies on the Wet Bulb Globe Temperature (WBGT) measure. Heat Index (HI) is a widely used measure to account for air temperature and humidity. Adjusted Temperature (Tadj) considers air temperature, humidity and estimates radiant heat. There is interest in predicting WBGT from HI and HI from WBGT. This study builds on previous USF research by Bernard and Iheanacho and Irvin to evaluate …

Resolving The Nanoscale Structure Of Β-Sheet Peptide Self-Assemblies Using Single-Molecule Orientation–Localization Microscopy, Weiyan Zhou, Conor L. O'Neill, Tianben Ding, Oumeng Zhang, Jai S. Rudra, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Synthetic peptides that self-assemble into cross-β fibrils are versatile building blocks for engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarities to amyloid species have been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize Nile red (NR), an amyloidophilic fluorogenic probe, and single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers KFE8^L and KFE8^D and the pathological amyloid-beta peptide Aβ42. Importantly, NR SMOLM reveals the helical (bilayer) …

Β-Sheets Mediate The Conformational Change And Allosteric Signal Transmission Between The Aslov2 Termini, Sian Xiao, Mayar Terek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

Avena sativa phototropin 1 light-oxygen-voltage 2 domain (AsLOV2) is a model protein of Per-Arnt-Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change begins with the unfolding of the N-terminal A'α helix in the dark state followed by the unfolding of the C-terminal Jα helix. The light state is characterized by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, β-sheets are identified as crucial components for mediating allosteric signal transmission between the two termini. Through combined experimental and computational investigations, the Hβ …

Synthesis And Functional Properties Of Metal Chalcogenide Semiconductors, Jiang Luo

Arts & Sciences Graduate Student Theses and Dissertations

Metal chalcogenides exhibit perovskite, chiral, and layered structures, and accommodate many atoms from periodic table, providing abundant properties such as ferroelectricity, circular dichroism, and anisotropic carrier transport. Those various physical properties make metal chalcogenides promising for the applications from electronics to optoelectronics, such as thermoelectrics, photovoltaics, and photodetectors. The upper limit of carrier mobility, termed as intrinsic carrier mobility, is the key factor that determine the performance of the semiconductor-based applications. However, either experiments or first-principle calculations are challenging to obtain the intrinsic carrier mobility over a wide class of materials. I found a descriptor that have a good correlation …

Novel Inhibitors To Mmpl3 Transporter Of Mycobacterium Tuberculosis By Structure-Based High-Throughput Virtual Screening And Molecular Dynamics Simulations, Hetanshi Choksi, Justin Carbone, Nicholas J. Paradis, Lucas Bennett, Candice Bui-Linh, Chun Wu

College of Science & Mathematics Departmental Research

Tuberculosis (TB)-causing bacterium Mycobacterium tuberculosis (Mtb) utilizes mycolic acids for building the mycobacterial cell wall, which is critical in providing defense against external factors and resisting antibiotic action. MmpL3 is a secondary resistance nodulation division transporter that facilitates the coupled transport of mycolic acid precursor into the periplasm using the proton motive force, thus making it an attractive drug target for TB infection. In 2019, X-ray crystal structures of MmpL3 from M. smegmatis were solved with a promising inhibitor SQ109, which showed promise against drug-resistant TB in Phase II clinical trials. Still, there is a pressing need to discover more …

Field-Based Measurement Tools To Distinguish Clonal Typha Taxa And Estimate Biomass: A Resource For Conservation And Restoration, Brian M. Ohsowski, Cassidy Redding, Pamela Geddes, Shane Lishawa

School of Environmental Sustainability: Faculty Publications and Other Works

Two species of clonal Typha [T. latifolia (native) and T. angustifolia (exotic)] hybridize to form the highly invasive, heterotic (high vigor) T. × glauca in North American wetlands leading to increased primary production, litter accumulation, and biodiversity loss. Conservation of T. latifolia has become critical as invasive Typha has overwhelmed wetlands. In the field, Typha taxa identification is difficult due to subtle differences in morphology, and molecular identification is often unfeasible for managers. Furthermore, improved methods to non-destructively estimate Typha biomass is imperative to enhance ecological impact assessments. To address field-based Typha ID limitations, our study developed a predictive …

Novel Lipid Mediator 7s,14r-Docosahexaenoic Acid: Biogenesis And Harnessing Mesenchymal Stem Cells To Ameliorate Diabetic Mellitus And Retinal Pericyte Loss, Yan Lu, Haibin Tian, Hongying Peng, Quansheng Wang, Bruce A. Bunnell, Nicolas G. Bazan, Song Hong

School of Medicine Faculty Publications

Introduction: Stem cells can be used to treat diabetic mellitus and complications. ω3-docosahexaenoic acid (DHA) derived lipid mediators are inflammation-resolving and protective. This study found novel DHA-derived 7S,14R-dihydroxy-4Z,8E,10Z,12E,16Z,19Z-docosahexaenoic acid (7S,14R-diHDHA), a maresin-1 stereoisomer biosynthesized by leukocytes and related enzymes. Moreover, 7S,14R-diHDHA can enhance mesenchymal stem cell (MSC) functions in the amelioration of diabetic mellitus and retinal pericyte loss in diabetic db/db mice. Methods: MSCs treated with 7S,14R-diHDHA were delivered into db/db mice i.v. every 5 days for 35 days. Results: Blood glucose levels in diabetic mice were lowered by 7S,14R-diHDHA-treated MSCs compared to control and untreated MSC groups, accompanied by …

6d Single-Fluorogen Orientation-Localization Microscopy For Elucidating The Architecture Of Beta-Sheet Assemblies And Biomolecular Condensates, Tingting Wu, Weiyan Zhou, Jai S. Rudra, Rohit V. Pappu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

We develop six-dimensional single-molecule orientation-localization microscopy (SMOLM) to measure the 3D positions and 3D orientations simultaneously of single fluorophores. We show how careful optimization of phase and polarization modulation components can encode phase, polarization, and angular spectrum information from each fluorescence photon into a microscope’s dipole-spread function. We used the transient binding and blinking of Nile red (NR) to characterize the helical structure of fibrils formed by designed amphipathic peptides, KFE8^L and KFE8^D, and the pathological amyloid-beta peptide Aβ42. We also deployed merocyanine 540 to uncover the interfacial architectures of biomolecular condensates.