Digital Commons Network^™

Fundamental Limits In Measuring The Anisotropic Rotational Diffusion Of Single Molecules, Weiyan Zhou, Tingting Wu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Many biophysical techniques, such as single-molecule fluorescence correlation spectroscopy, Förster resonance energy transfer, and fluorescence anisotropy, measure the translation and rotation of biomolecules to quantify molecular processes at the nanoscale. These methods often simplify data analysis by assuming isotropic rotational diffusion, e.g., that molecules wobble within a circular cone. This simplification ignores the anisotropy present in many biological contexts that may cause molecules to exhibit different degrees of diffusion in different directions. Here, we loosen this assumption and establish a theoretical framework for describing and measuring anisotropic rotational diffusion using fluorescence imaging. We show that anisotropic wobble is directly quantified …

Identification And Characterization Of Intrinsically Disordered Protein Regions, Guy Wayne Dayhoff Ii

USF Tampa Graduate Theses and Dissertations

This dissertation investigates protein intrinsic disorder and intrinsically disordered protein regions (IDPRs) through the development and application of advanced computational and experimental techniques. Chapter 1 provides an introduction to protein intrinsic disorder, outlining the historical context and fundamental concepts that highlight the importance of intrinsically disordered proteins (IDPs) and IDPRs in various biological processes. Chapter 2 focuses on the rapid prediction and analysis of protein intrinsic disorder. We introduce RIDAO (Rapid Intrinsic Disorder Analysis Online), a high-efficiency web-based tool that integrates multiple disorder predictors. RIDAO significantly outperforms existing predictors in computational efficiency, making it suitable for large-scale proteomic studies. We …

Securing Body Area Networks With Fingerprint Cryptography And Authentication In Manet, Alaa M. Elbanaa, Roayat Ismail Abdelfatah, Mohamed E. Nasr

Journal of Engineering Research

Standard MANETs face issues like incorrect transmission and vulnerability to unauthorized node access, posing significant security concerns, especially regarding authentication procedures. To address these challenges, researchers are exploring innovative approaches to enhance authentication mechanisms within MANETs. In this paper, we present a novel solution integrating a Body Area Network (BAN) scheme to capture biomedical data from sensors such as ECG and EEG, facilitating data transmission across MANETs. Furthermore, we employ a hybrid Elgamal algorithm for encrypting biomedical data, bolstered by fingerprint biometrics to fortify the cryptographic process, enhancing network security. Additionally, we conduct comparative analyses, exploring different key sizes and …

Prediction Of Noise From A Construction Site, Amira Mostafa Ibrahim Miss, Nashwa Mohamed Yossef Prof, Adel Ibrahim Eldosouky Emeritus Professor

Journal of Engineering Research

Construction activities significantly contribute to environmental noise pollution, affecting workers' health and the surrounding community, posing significant challenges to human well-being and productivity. This paper presents a prediction method and a modelling technique used to assess construction site noise. Various factors influencing noise generation and propagation, such as equipment types, operational conditions, site characteristics, and environmental factors, are discussed. This paper explores the application of Monte Carlo technique as an effective method for predicting construction site noise and planning noise mitigation strategies.

Survey And Analysis Of Safety Components And Costs In Construction Projects In Egypt, Emad E. Etman Prof., Haytham Sanad Prof., Asmaa Ibrahim Khater

Journal of Engineering Research

The difficulty of determining the factors that achieve safety on Egyptian construction sites as a result of multiple and different criteria and different relative weights of the criteria represents a challenge to achieve safety and a secure environment on construction sites. This issue has been of interest for many decades and continues to be a topic of discussion today because of construction project management is rapidly modernizing. The paper aims to identify the safety standards most commonly used on construction sites, and determine their relative weights as seen by the target audience and also estimate the cost of safety measures …

Context-Dependent T-Box Transcription Factor Family: From Biology To Targeted Therapy, Siwen Li, Xiangyuan Luo, Mengyu Sun, Yijun Wang, Zerui Zhang, Junqing Jiang, Dian Hu, Jiaqian Zhang, Zhangfan Wu, Yufei Wang, Wenjie Huang, Limin Xia

Faculty, Staff and Student Publications

T-BOX factors belong to an evolutionarily conserved family of transcription factors. T-BOX factors not only play key roles in growth and development but are also involved in immunity, cancer initiation, and progression. Moreover, the same T-BOX molecule exhibits different or even opposite effects in various developmental processes and tumor microenvironments. Understanding the multiple roles of context-dependent T-BOX factors in malignancies is vital for uncovering the potential of T-BOX-targeted cancer therapy. We summarize the physiological roles of T-BOX factors in different developmental processes and their pathological roles observed when their expression is dysregulated. We also discuss their regulatory roles in tumor …

Phylogenomics Recovers Multiple Origins Of Portable Case Making In Caddisflies (Insecta: Trichoptera), Nature's Underwater Architects, Paul B. Frandsen, Ralph W. Holzenthal, Marianne Espeland, Jesse Breinholt, Jessica A. Thomas Thorpe, Sabrina Simon, Akito Y. Kawahara, David Plotkin, Scott Hotaling, Yiyuan Li, C. Riley Nelson, Oliver Niehuis, Christoph Mayer, Lars Podsiadlowski, Alexander Donath, Bernhard Misof, Emily Moriarty Lemmon, Alan Lemmon, John C. Morse, Shanlin Liu, Steffen U. Pauls, Xin Zhou

Watershed Sciences Faculty Publications

Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16 000 describes species. They play a fundamental role in freshwater ecology and environmental engineering in streams, rivers and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programmes. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case making, remain unanswered owing to the lack of a well-resolved phylogeny. Here, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 207 species, representing 48 of 52 …

The Protective Efficacy Of A Sars-Cov-2 Vaccine Candidate B1351v Against Several Variant Challenges In K18-Hace2 Mice, Jie Yang, Huifen Fan, Anna Yang, Wenhui Wang, Xin Wan, Fengjie Lin, Dongsheng Yang, Jie Wu, Kaiwen Wang, Wei Li, Qian Cai, Lei You, Deqin Pang, Jia Lu, Changfu Guo, Jinrong Shi, Yan Sun, Xinguo Li, Kai Duan, Shuo Shen, Shengli Meng, Jing Guo, Zejun Wang

Faculty, Staff and Student Publications

The emergence of SARS-CoV-2 variants of concern (VOCs) with increased transmissibility and partial resistance to neutralization by antibodies has been observed globally. There is an urgent need for an effective vaccine to combat these variants. Our study demonstrated that the B.1.351 variant inactivated vaccine candidate (B.1.351V) generated strong binding and neutralizing antibody responses in BALB/c mice against the B.1.351 virus and other SARS-CoV-2 variants after two doses within 28 days. Immunized K18-hACE2 mice also exhibited elevated levels of live virus-neutralizing antibodies against various SARS-CoV-2 viruses. Following infection with these viruses, K18-hACE2 mice displayed a stable body weight, a high survival …

Human Centered Approaches And Taxonomies For Explainable Artificial Intelligence, Helen Sheridan, Emma Murphy, Dympna O'Sullivan

Conference papers

Recent interest within the research community related to explainable artificial intelligence (XAI) has led to a profuse amount of literature on the subject. Those who wish to tackle the domain from an HCI focus may be presented with overwhelming material, most of which does not pertain to human aspects of XAI. Taxonomies can serve to categorize a subject into topic areas and distill content into an overview of the field. This late breaking work intends to help those within the HCI community with a focus on XAI to understand relevant aspects of human centered XAI. We also present a taxonomy …

Valorization Of Seafood Waste For Food Packaging Development, Zhijing Zhan, Yiming Feng, Jikai Zhao, Mingyu Qiao, Qing Jin

School of Earth, Environmental, & Marine Sciences Faculty Publications

Packaging plays a crucial role in protecting food by providing excellent mechanical properties as well as effectively blocking water vapor, oxygen, oil, and other contaminants. The low degradation of widely used petroleum-based plastics leads to environmental pollution and poses health risks. This has drawn interest in renewable biopolymers as sustainable alternatives. The seafood industry generates significant waste that is rich in bioactive substances like chitin, chitosan, gelatins, and alginate, which can replace synthetic polymers in food packaging. Although biopolymers offer biodegradability, biocompatibility, and non-toxicity, their films often lack mechanical and barrier properties compared with synthetic polymer films. This comprehensive review …

A/B Testing Of User Enrollment Forms To Enhance Diversity In The Biomedical Workforce Via The National Research Mentoring Network: User-Centered Design Case Study, Toufeeq Ahmed Syed, Erika L Thompson, Jason Johnson, Zainab Latif, Nan Kennedy, Damaris Javier, Katie Stinson, Jamboor K Vishwanatha

Faculty, Staff and Student Publications

BACKGROUND: The National Research Mentoring Network (NRMN) is a National Institutes of Health-funded program for diversifying the science, technology, engineering, math, and medicine research workforce through the provision of mentoring, networking, and professional development resources. The NRMN provides mentoring resources to members through its online platform-MyNRMN.

OBJECTIVE: MyNRMN helps members build a network of mentors. Our goal was to expand enrollment and mentoring connections, especially among those who have been historically underrepresented in biomedical training and the biomedical workforce.

METHODS: To improve the ease of enrollment, we implemented the split testing of iterations of our user interface for platform registration. …

A Systematic Approach For Evaluating And Selecting Healthcare Waste Treatment Devices Using Owcm-Codas And Triangular Neutrosophic Sets, Asmaa Elsayed, Bilal Arain

Neutrosophic Systems with Applications

Healthcare is a fundamental aspect of human life, impacting individuals, communities, and societies. Investing in healthcare infrastructure, services, and education is essential for fostering a healthy, thriving population. Healthcare waste management is a critical aspect of public health, and it requires a concerted effort from healthcare facilities, governments, and communities to ensure that waste is managed in a way that minimizes risks to human health and the environment. This paper proposes a hybrid methodology combining the Opinion Weight Criteria Method (OWCM) and the Combinative Distance-Based Assessment (CODAS) within the framework of Triangular Neutrosophic Sets (TNS) to evaluate and select the …

The Fishing Cat: New Insights On Distribution In The Northern Sector Of Chitwan National Park, Nepal, Rupesh Maharjan, Rama Mishra, Jhamak Bahadur Karki

School of Earth, Environmental, & Marine Sciences Faculty Publications

Fishing cat Prionailurus viverrinus (Bennett, 1833) is an elusive and medium-sized feline species with distinguished marking patterns on their head and body separating them from other feline species. Despite being distributed widely among diverse geographic locations, their abundance has declined due to significant habitat loss and human disturbances. There exists a substantial research gap regarding their abundance and distribution in Nepal. In this article, we presented the updated documentation of the fishing cat distribution in the northern sector of Chitwan National Park through our species-focused camera trapping survey. The study was carried out between April and May 2021 with a …

Review: Protection Of Wooden Structures With Nano-Titanium Dioxide Coating, Zienab Zienab A. Ahmed1*, And M. M. Mosallem2

Journal of Engineering Research

Wood is widely used for various purposes with good performance. Wood works as the main material for furniture, monuments, decorations and constructions. which has the close relationship with human. Durability of wood is important in ensuring an appropriate life for the structure being designed. Wooden construction deteriorates easily due to UV radiation and weather conditions. Many of wood types need a preservative treatment. Several compounds are available for chemical protection, but not all are completely safe for human health. New technologies with low environmental impact and economically feasible are developed, which improves the life cycle of wood. Titanium dioxide is …

Math 75: Introduction To Linear Algebra, Sarah K. Merz

Pacific Open Texts

This text is intended to use in a first course of Linear Algebra with a prerequisite of Calculus 1. Topics covered include systems of linear equations, matrix operations and inverses, linear transformations, Markov chains, determinants, eigenvalues and eigenvectors, diagonalization, vector geometry, projections and planes, homogeneous coordinates, subspaces, spanning sets, linear independence, orthogonality, fundamental subspaces, and least squares.

Learning From Oversampling: A Systematic Exploitation Of Oversampling To Address Data Scarcity Issues In Deep Learning- Based Magnetic Resonance Image Reconstruction, Ibsa Kumara Jalata, Reeshad Khan, Ukash Nakarmi

Computer Science and Computer Engineering Faculty Publications and Presentations

Data acquisitions in Magnetic Resonance Imaging (MRI) are inherently slow due to sequential acquisition protocol. Image reconstruction from under-sampled data is posed as an inverse problem in traditional model-based learning paradigms. Recent data-centric learning frameworks such as deep learning (DL) frameworks are data hungry, and demand a large, labeled training data sets. To address the lack of large training datasets, in MRI reconstructions, researchers approach the problem in two ways: (1) unsupervised method where the model is trained without the presence of fully sampled data. (2) using a method that efficiently use the limited dataset for training purpose. In this …

National Parks Field Journal, Isadora Davis

Art and Design Student Scholarship and Projects

A handwritten, richly illustrated field journal by Binghamton University art major Isadora Davis, recording a trip through national parks in the American West via SUNY Broome's BIO 217: Ecology of National Parks. Davis uses colored pencil drawings and pressed botanical specimens to record landscapes, birds, mammals, and plant life in Grand Teton, Yellowstone, Wind Cave, and Badlands National Parks, as well as Custer State Park. Davis's sketches and diagrams visually explore how to decode past landscapes from current formations, while her written entries explain species diversity, animal behavior, and the mechanisms causing geological formations and geothermal events. Part memoir of …

Ocular Gene Transfer In The Spotlight: Implications Of Newspaper Content For Clinical Communications, Shelly Benjaminy, Tania M. Bubela

Office of the Provost

Background: Ocular gene transfer clinical trials are raising hopes for blindness treatments and attracting media attention. News media provide an accessible health information source for patients and the public, but are often criticized for overemphasizing benefits and underplaying risks of novel biomedical interventions. Overly optimistic portrayals of unproven interventions may influence public and patient expectations; the latter may cause patients to downplay risks and over-emphasize benefits, with implications for informed consent for clinical trials. We analyze the news media communications landscape about ocular gene transfer and make recommendations for improving communications between clinicians and potential trial participants in light of …

Carbon-Based Nanocomposite Membranes For Membrane Distillation: Progress, Problems And Future Prospects, Chhabilal Regmi, Yuwaraj K. Kshetri, S. Ranil Wickramasinghe

Chemical Engineering Faculty Publications and Presentations

The development of an ideal membrane for membrane distillation (MD) is of the utmost importance. Enhancing the efficiency of MD by adding nanoparticles to or onto a membrane’s surface has drawn considerable attention from the scientific community. It is crucial to thoroughly examine state-of-the-art nanomaterials-enabled MD membranes with desirable properties, as they greatly enhance the efficiency and reliability of the MD process. This, in turn, opens up opportunities for achieving a sustainable water–energy–environment nexus. By introducing carbon-based nanomaterials into the membrane’s structure, the membrane gains excellent separation abilities, resistance to various feed waters, and a longer lifespan. Additionally, the use …

Mapping Recent Timber Harvest Activity In A Temperate Forest Using Single Date Airborne Lidar Surveys And Machine Learning: Lessons For Conservation Planning, G. Bursh Fisher, Andrew J. Elmore, Matthew C. Fitzpatrick, Darin J. Mcneil, Jeff W. Atkins, Jeffery L. Larkin

Earth and Environmental Sciences Faculty Publications

Effective planning for natural resource management and wildlife conservation requires detailed information on vegetation structure at landscape scales and how structure is influenced by land- use practices. In many forested landscapes, the largest impacts of land use on forest structure are driven by forest management activities, which can include invasive species control, prescribed fire, partial harvests (e.g. shelterwood harvests) or overstory removals and clearcuts. Active timber management is often used to achieve forest conservation objectives, but to be used effectively, managers require knowledge of harvest frequency and extent in adjacent forests and at landscape scales. In this paper, we develop …

Effects Of Simulated Climate Change On Native Southeastern Grassland Vegetation Using Open Top Chambers, Makaila Carpenter

Theses

The southeastern United States is a critical biodiversity hotspot once covered in prairie grassland ecosystems and now facing significant threats due to urbanization, habitat destruction, over-exploitation, biological invasions, pollution, and climate change. This study analyzes the response of Alabama’s native prairie ecosystem to climate change. We used open top chambers (OTCs) to simulate climate change-induced warming. We assessed the response of ecosystem function and structure to higher temperatures (1-3^oC). The indicators of ecosystem function included phenology, leaf surface area (LSA), specific leaf area (SLA), and aboveground and below net primary productivity (ANPP and BNPP respectively). Ecosystem structure was …

Removing Methane Via Atmospheric Oxidation Enhancement: The Legal Framework, Romany M. Webb, Martin Lockman, Korey Silverman-Roati

Sabin Center for Climate Change Law

To achieve the Paris Agreement’s goal of limiting the increase in global average temperatures to “well below 2 degrees Celsius,” and ideally 1.5 degrees Celsius, above pre-industrial levels, global greenhouse gas (“GHG”) emissions must reach net zero in the second half of the century. The global community is not currently on track to achieve net zero emissions. In fact, with the exception of a slight dip during the Covid-19 pandemic, emissions have risen steadily in recent years. This, together with the increasingly visible impacts of climate change, has prompted growing interest in the possibility of removing GHGs directly from the …

Pressure And Temperature Conditions Across The Mct And Other High Strain Zones Along The Marsyangdi River; Comparison To Modi Khola River Results, Katherine Dudenhoefer

Nepal: Geoscience in the Himalaya

As a result of the Indo-Asia collision, the Main Central Thrust (MCT) is a ductile shear zone that extends across the Himalayas and marks the fault boundary between the Greater Himalayan Crystallines (GHC) and the Lesser Himalayan Sequence (LHS). Due to the nature of this thrust fault, the GHCs are being stacked on top of the LHS despite their older age and higher grade of metamorphism. However, previously published works show that the MCT is more active in certain regions of Nepal than others. The GHC in the Modi Khola region to the west is thicker than the Marsyangdi region …

Reproducibility Debt: Challenges And Future Pathways, Zara Hassan, Christoph Treude, Michael Norrish, Graham Williams, Alex Potanin

Research Collection School Of Computing and Information Systems

Reproducibility of scientic computation is a critical factor in validating its underlying process, but it is often elusive. Complexity and continuous evolution in software systems have introduced new challenges for reproducibility across a myriad of computational sciences, resulting in growing debt. This requires a comprehensive domain-agnostic study to dene and asses Reproducibility Debt (RpD) in scientic software, thus uncovering and classifying all underlying factors attributed towards its emergence and identication i.e., causes and eects. Moreover, an organised map of prevention strategies is imperative to guide researchers for its proactive management. This vision paper highlights the challenges that hinder eective management …

Population Demography, Occupancy, And Connectivity Of Invasive Bigheaded Carp In The Platte River, Nebraska And Its Tributaries, Blake W. Logan

School of Natural Resources: Dissertations, Theses, and Student Research

Silver Carp Hypophthalmichthys molitrix and Bighead Carp H. nobilis, collectively referred to as bigheaded carp, are invasive species in the United States of America that have expanded their range throughout the Missouri River basin in the last three decades. It may be desirable to develop management plans directed at the monitoring, control, or removal of bigheaded carp within the Missouri River basin. However, a knowledge gap exists regarding bigheaded carp ecology in Missouri River tributaries, which may be important for the development of management plans. As such, this study characterized bigheaded carp population demographics, occupancy, and connectivity in …

Virtual Fencing In Livestock Management: Effects On Beef Cattle Stress And Enhancing Wildlife Conservation, Kaitlyn E. Dozler

School of Natural Resources: Dissertations, Theses, and Student Research

I examined the effects of virtual fencing on beef cattle stress and how implementing the technology can aid wildlife habitat conservation at the University of Nebraska Gudmundsen Sandhills laboratory (GSL) near Whitman, NE. First, I examined how virtual fencing influences acute heart rate changes in beef cattle fitted with the virtual fencing collars. No significant difference in the average heart rate of a cow (P > 0.05) was observed between the 30 min control and virtual fenced periods for both trial dates. Second, I examined the influence of topography on wildlife species richness and presence at GSL using wildlife camera …

Spatial Ecology Of Mountain Lions Throughout Their Distribution In California, Kyle D. Dougherty

School of Natural Resources: Dissertations, Theses, and Student Research

Mountain lions (Puma concolor) have been studied extensively throughout their wide geographic distribution in the Western Hemisphere, but most research has been conducted at relatively small spatial scales. We used GPS telemetry data contributed by researchers in 16 study areas throughout California to advance understanding of mountain lion spatial ecology. First, we investigated multi-scale resource selection of mountain lions relative to spatially varying risk of intentional human-caused mortality associated with livestock depredation management. We show that individuals that proactively avoided mortality risk when selecting home ranges were able to relax their avoidance of risk when making resource selection …

Hybridization Between The Rare Gray-Headed Chickadee And The Abundant Boreal Chickadee In The Midst Of Shifting Climate, Matthew R. Armstrong

School of Natural Resources: Dissertations, Theses, and Student Research

As species respond to changing climate, distributions and abundances may shift and alter species interactions. Hybridization, a relatively widespread phenomenon becoming more common with climate change, can have beneficial and detrimental effects on population growth rates and genetic integrity. Beneficial effects due to the introduction of advantageous alleles and increased genetic diversity may result from hybridization. Species may also accrue fitness costs associated with changing climates if mismatches occur between environmental variables and phenotypes. The gray-headed chickadee, Poecile cinctus lathami, is an extremely rare songbird that has experienced marked declines in recent decades within its restricted distribution in Alaska …

Phylogeny And Disparity Of Ammonoid Family Acanthoceratidae Over Ocean Anoxic Event 2, Lindsey Howard

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

The widespread use of genera as proxies for species in paleobiological studies might affect the results of these studies. Although most attention has been given to taxonomic diversity studies, this could also be true of disparity and phylogenetic studies. In particular, the assumption that particular character states truly diagnose all members of a genus might distort results. This study examines the disparity of Acanthoceratid ammonoids at both the generic and species level. 149 species from 42 genera were examined with 52 characters measured. Following the measurements, an inverse modeling simulation was run 100 times to generate a simulated phylogeny with …

Geospatial Distribution Of Rhizocarpon Lichens In The Peri Himal, Matt Lehmann, Daniel Havlat

Nepal: Geoscience in the Himalaya

Lichenometry, a technique used primarily in high latitudes and mountainous regions to date rock surface exposure, relies on estimations of lichen growth rates. Utilizing Rhizocarpon lichen, lichenometry has been extensively applied to date Late Holocene glacial landforms. In this study, we explore Rhizocarpon distribution in the Peri Himal of the Nepal Himalaya to understand the microclimatic and environmental mechanisms that dictate their growth location. We collected 25 data points throughout the western moraine of Ponkar Glacier near Kehcakyu Khola and around Ponkar Lake. Through this data we raised the question, under what conditions do Rhizocarpon lichen grow in high altitude …