Digital Commons Network^™

One-Step Production Of Fully Biotinylated And Glycosylated Human Fc Gamma Receptors

Faculty, Staff and Student Publications

Initiating and regulating humoral immunity, Fc gamma receptors (FcγRs) have been identified both as therapeutics and as drug targets, and thus production of biologically active FcγRs is highly demanded for biopharmaceutical development. Focusing on low-affinity FcγRs IIA (131H/R allotypes), IIB, and IIIA (176F/V), this study used human 293-F cells to achieve correct post-translational modifications (PTMs) including biotinylation, N-glycosylation, and disulfides. Approaches involving co-expression of FcγR-AviTag and Escherichia coli biotin ligase BirA, endoplasmic reticulum retention, stable and transient transfections, and optimization of transgene ratio were investigated. Protein electrophoresis under reducing and non-reducing conditions, enzymatic deglycosylation, streptavidin pull-down assays, and binding kinetic …

Metarnn: Differentiating Rare Pathogenic And Rare Benign Missense Snvs And Indels Using Deep Learning, Laila Rasmy, Xinyue Hu, Jianping He, Yifang Dang, Jingna Feng, Jianfu Li, Yichen Wang, Tianchen Lyu, Naomi Braun, Si Pham, Michael Gharacholou, Delisa Fairweather, Degui Zhi, Jiang Bian, Cui Tao

Faculty, Staff and Student Publications

BACKGROUND: Effective management of dual antiplatelet therapy (DAPT) following drug-eluting stent (DES) implantation is crucial for preventing adverse events. Traditional prognostic tools, such as rule-based methods or Cox regression, despite their widespread use and ease, tend to yield moderate predictive accuracy within predetermined timeframes. This study introduces a new contrastive learning-based approach to enhance prediction efficacy over multiple time intervals.

METHODS: We utilized retrospective, real-world data from the OneFlorida + Clinical Research Consortium. Our study focused on two primary endpoints: ischemic and bleeding events, with prediction windows of 1, 2, 3, 6, and 12 months post-DES implantation. Our approach first …

Contrastive Learning With Transformer For Adverse Endpoint Prediction In Patients On Dapt Post-Coronary Stent Implantation, Laila Rasmy, Xinyue Hu, Jianping He, Yifang Dang, Jingna Feng, Jianfu Li, Yichen Wang, Tianchen Lyu, Naomi Braun, Si Pham, Michael Gharacholou, Delisa Fairweather, Degui Zhi, Jiang Bian, Cui Tao

Faculty, Staff and Student Publications

Background: Effective management of dual antiplatelet therapy (DAPT) following drug-eluting stent (DES) implantation is crucial for preventing adverse events. Traditional prognostic tools, such as rule-based methods or Cox regression, despite their widespread use and ease, tend to yield moderate predictive accuracy within predetermined timeframes. This study introduces a new contrastive learning-based approach to enhance prediction efficacy over multiple time intervals.

Methods: We utilized retrospective, real-world data from the OneFlorida + Clinical Research Consortium. Our study focused on two primary endpoints: ischemic and bleeding events, with prediction windows of 1, 2, 3, 6, and 12 months post-DES implantation. Our approach first …

Tfeb-Vacuolar Atpase Signaling Regulates Lysosomal Function And Microglial Activation In Tauopathy, Baiping Wang, Heidi Martini-Stoica, Chuangye Qi, Tzu-Chiao Lu, Shuo Wang, Wen Xiong, Yanyan Qi, Yin Xu, Marco Sardiello, Hongjie Li, Hui Zheng

Center on Aging Staff Publications

Transcription factor EB (TFEB) mediates gene expression through binding to the coordinated lysosome expression and regulation (CLEAR) sequence. TFEB targets include subunits of the vacuolar ATPase (v-ATPase), which are essential for lysosome acidification. Single-nucleus RNA sequencing of wild-type and PS19 (Tau) transgenic mice expressing the P301S mutant tau identified three unique microglia subclusters in Tau mice that were associated with heightened lysosome and immune pathway genes. To explore the lysosome-immune relationship, we specifically disrupted the TFEB-v-ATPase signaling by creating a knock-in mouse line in which the CLEAR sequence of one of the v-ATPase subunits, Atp6v1h, was mutated. CLEAR mutant exhibited …

Riparian Revegetation: Re-Indigenizing The Powers Creek Tributary Of The Baduwa’T Watershed At Blue Lake Rancheria, California, Genesis Beltran, Ruben Lopez, Ben Stock

Undergraduate Scholarship

This project focuses on the ecological and cultural restoration of Powers Creek, a tributary of the Baduwa’t watershed at Blue Lake Rancheria, California. Riparian ecosystems play a critical role in biodiversity, water quality, and climate resilience, particularly for species like salmonids reliant on cold-water refugia. The restoration efforts, guided by Indigenous knowledge, addressed the removal of non-native competitive species such as Scotch broom (Cytisus scoparius) and French broom (Genista monspessulana) – which are shown to increase wildfire severity and challenge native plant communities – in addition to freeing established plantings of vegetative competition. Through collaborative planning …

Community-Based Respiratory Health Measures In Children And Young People With Cerebral Palsy: A Scoping Review, Rachel Knight Lozano, Harriet Shannon, Jonathan Gilby, Sian Goddard, Leanne Turner, Jonathan Marsden

School of Health Professions

Aim: To identify, map, and describe outcome measurement domains and instruments used within a community setting to assess respiratory health in children and young people aged 1 to 18 years, diagnosed with cerebral palsy (CP). Method: A scoping review methodology informed structured searches in nine databases, grey literature, and registries, conducted in August 2021 (updated in February 2023). Articles were screened for eligibility by two independent researchers. Any outcome measurement instruments used to assess respiratory health or associated impact were extracted, categorized, and mapped to health and health-related domains of the International Classification of Functioning, Disability, and Health. Results: Seventy-six …

Transmission+Interference: A New Materialist And Machine-Oriented Approach To Collectively Make-With Noise, David Strang

School of Art, Design and Architecture Theses

This thesis explores the materiality at play within installation and performance artworks from across the interdisciplinary fields of media arts, digital arts and contemporary technological arts and is positioned at the noisier end of the artistic spectrum of these disciplines. The practice-led research presented here deals with the shift away from clean digital media environments of production in order to embrace a more material focused approach that has emerged within recent years (see the emergence of physical computing and electronics practices), especially across sonic arts practices (see also the re-emergence of modular synthesis). The aim is to unfold an understanding …

Mapping A Lived Experience In Landscape: An Artist’S Analysis Of Gps And Gis Data, Becalelis Brodskis

School of Art, Design and Architecture Theses

This thesis involves a critical analysis of data types and digital interfaces used in a socially engaged arts practice aligned with the concerns of participatory mapping. The research identifies a problem which occurs when the development and use of technologies begins to conflate data with its visual representation or, conversely, reduces the experience of reality to what can be documented. The thesis aligns with a concern that this impacts the perception of, and sensitivity to, available qualities or indeed possibilities of experience. Responding to this concern questions are raised relating to how and why qualities of objectivity or subjectivity are …

Climate Change And Sustainability Literacy: A Mixed-Methods Study Of Attitudes To Climate Education In Secondary Schools, Alison Anderson

School of Law, Humanities and Social Sciences

Climate change and sustainability are inherently socio-political issues and education plays a key role in mobilising action on climate change and environment. This study builds on interdisciplinary work on youth and climate change education including science communication, environmental education, environmental psychology, and sociology. It reports on novel mixed-methods research on attitudes to climate change and sustainability education in secondary schools in the UK. The study was undertaken in conjunction with the British Science Association (BSA) Future Forums. Drawing on the findings of a national cross-sectional survey of young people aged 14-18 (n= 1000) and two follow up in-depth workshops (n= …

Practical Actions To Strengthen Capacity For Deep-Water Research In Africa, Kirsty A Mcquaid, Kerry Howell, Agnes W.N. Muthumbi, Olusola Adeoye, Isa Elegbede, Luther Adams, Blessing Charuka, Ana Hilário, Hendrina Kadila, Sophia Laarissa, Randa Mejri, Sidi Mohamed, Damaris Mutia, Angela Nyangwe, Angus Paterson, Sinothando Shibe, Kerry Sink, Sheena Talma, Urias Taylor, Arthur Tuda

School of Biological and Marine Sciences

While Africa's deep marine biodiversity offers economic prospects it also supports crucial ecosystem services and sustainable development is dependent on knowledge of these systems. Building understanding of deep-water ecosystems is key, but there are substantial discrepancies in countries' abilities to achieve this. Coinciding with the 2024 Ocean Decade Conference, the Challenger 150 African Network of Deep-water Researchers is pleased to release a report on “Practical Actions to Strengthen Capacity for Deep-water Research in Africa”. Through a series of online workshops, the ANDR brought together 98 individuals from 19 African nations to discuss challenges for deep-water research in Africa, identify solutions …

Atmospheric Deposition Of Microplastics In Shiraz, Iran, Sajjad Abbasi, Farnaz Ahmadi, Nafiseh Khodabakhshloo, Haniye Pourmahmood, Atefeh Esfandiari, Zeinab Mokhtarzadeh, Shaqayeq Rahnama, Reza Dehbandi, Arya Vazirzadeh, Andrew Turner

School of Geography, Earth and Environmental Sciences

The atmosphere plays a critical role in the regional and global transportation and redistribution of microplastics (MPs). However, the significance of rainfall and its means of scavenging MPs are not well understood. In this study, MP deposition was determined during successive dry and rainy events over eight consecutive days in the Shiraz region of Iran. Flux magnitudes and temporal distributions at six sites within and outside the city (including a remote, non-urbanised location) were similar and revealed a progressive increase in MP abundance and deposition during dry periods (up to about 50 MP m−2 h−1) and subsequent relatively rapid wet …

Insights From Early Career Researcher Representatives At The Sustainability Research & Innovation Congress 2022 Asia Spotlight Event, Cho Kwong Charlie Lam

School of Geography, Earth and Environmental Sciences

The Sustainability Research & Innovation Congress 2022 Asia Spotlight Event (SRI-ASE 2022) was held virtually from June 21-24, 2022 and co-organized by Future Earth Global Secretariat Hubs in Asia based in Japan, Taipei, China, and South Asia, during the main sessions of the SRI 2022. SRI-ASE 2022 included over 70 speakers and more than 300 participants from within and outside the Asia region. The aim of the event was to provide space to reflect on inspiring research and discussions related to the themes: New Horizons, Different Ways of Knowing, Nexus Issues, and Cross-cutting Science and Innovation in Asia. This report …

Balancing Energy Transition: Assessing Decent Living Standards And Future Energy Demand In The Global South, Souran Chatterjee

School of Geography, Earth and Environmental Sciences

Achieving low energy demand in buildings is crucial in climate change mitigation. In the Global South, however, reducing the energy demand blanketly is not advisable due to critical gaps in access to the basic services supporting Decent Living Standards (DLS). Current energy demand scenarios mostly overlook achievement of DLS. Furthermore, model limitations in representing distributional aspects hinder modelling future energy demands to meet DLS. Supported by new evidence from a set of detailed sectoral and integrated assessment models, this research contributes to bridging this gap by exploring future trends in DLS achievement and linkages with energy demand in the Global …

Suitability Of 210pbex, 137cs And 239+240pu As Soil Erosion Tracers In Western Kenya, Sophia M. Dowell, Olivier S. Humphrey, Charles J.B. Gowing, Thomas S. Barlow, Simon R. Chenery, Job Isaboke, William H. Blake, Odipo Osano, Michael J. Watts

School of Geography, Earth and Environmental Sciences

Land degradation resulting from soil erosion is a global concern, with the greatest risk in developing countries where food and land resources can be limited. The use of fallout radionuclides (FRNs) is a proven method for determining short and medium-term rates of soil erosion, to help improve our understanding of soil erosion processes. There has been limited use of these methods in tropical Africa due to the analytical challenges associated with 137Cs, where inventories are an order of magnitude lower than in the Europe. This research aimed to demonstrate the usability of 239+240Pu as a soil erosion tracer in western …

International Ocean Discovery Program Expedition 399 Preliminary Report: Building Blocks Of Life, Atlantis Massif, Andrew M. Mccaig, S.Q. Lang, Peter Blum, Expedition 399 Scientists, Andrew Parsons

School of Geography, Earth and Environmental Sciences

No abstract provided.

Electrochemical Based Quantification Of Bacterial Growth In Media Using Square Wave Voltammetry And Low Cost Screen Printed Electrodes, Simon Peter Whelan, Shirin Naserikarimvand, Zari Tehrani, Martin Peacock, Owen Guy, David Gethin

School of Geography, Earth and Environmental Sciences

A novel method for determining the yield of bacterial growth using square wave voltammetry and screen printed electrodes is described here. This procedure was shown to be a reliable and accurate way to quickly determine the level of bacterial growth within culturing media and these results suggest that the combination of such sensors and the application of square wave voltammetry is suitable for applications such as within a bioreactor where the rapid determination of bacterial growth may be necessary.

Drone Imagery And Deep Learning For Mapping The Density Of Wild Pacific Oysters To Manage Their Expansion Into Protected Areas, Aser Mata, David Moffat, Sílvia Almeida, Marko Radeta, William Jay, Nigel Mortimer, Katie Awty-Carroll, Oliver Thomas, Vanda Brotas, Steve Groom

School of Geography, Earth and Environmental Sciences

The recent expansion of wild Pacific oysters already had negative repercussions on sites in Europe and has raised further concerns over their potential harmful impact on the balance of biomes within protected areas. Monitoring their colonisation, especially at early stages, has become an urgent ecological issue. Current efforts to monitor wild Pacific oysters rely on “walk-over” surveys that are highly laborious and often limited to specific areas of easy access. Remotely Piloted Aircraft Systems (RPAS), commonly known as drones, can provide an effective tool for surveying complex terrains and detect Pacific oysters. This study provides a novel workflow for automated …

The Importance Of Acoustic Output Measurement And Monitoring For The Replicability Of Transcranial Ultrasonic Stimulation Studies, Miriam C. Klein-Flügge, Elsa F. Fouragnan, Eleanor Martin

School of Psychology

No abstract provided.

Structural And Functional Studies Of The Human Members Of The Macrophage Migration Inhibitory Factor Family, Andrew Parkins

University of the Pacific Theses and Dissertations

Macrophage migration inhibitory factor (MIF) and D-dopachrome tautomerase (D-DT) are the two human members of the MIF superfamily, which are implicated in an array of autoimmune disorders, inflammatory diseases, and cancer via their pleiotropic functionality. Despite only sharing 34% sequence identity, MIF and D-DT have high structural homology and overlapping functional traits, including activation of the type II cell surface receptor CD74 and keto-enol tautomerase activity. The MIF and/or D-DT-induced activation of CD74 leads to signaling cascades pivotal for cell growth, proliferation, and inhibition of apoptosis. Such characteristics make MIF and D-DT attractive molecular targets for drug discovery.

Currently, all …

Transgenerational Effects Of Stress On The Plasma Proteome Of A Marine Mammal, Emily Voelkner

University of the Pacific Theses and Dissertations

The physiological stress response enables animals to respond to changes in their environment, and is mediated by the hypothalamic-pituitary-adrenal (HPA) axis in mammals. Increased activation of the HPA axis by repeated stress during critical life stages like reproduction could affect fitness. Information about a stressor can be communicated to offspring via hormone signals prenatally, or postnatally via milk, and affect offspring development and stress reactivity. Experimentally activating the HPA axis by adrenocorticotropic hormone (ACTH) administration results in the synthesis of the major glucocorticoid hormone cortisol, which has well-studied far-reaching effects on growth, metabolism, and immunity. Beyond cortisol levels alone, biomarkers …

Luminescent Solar Concentrators For Greenhouse Applications Based On Highly Luminescent Carbon Quantum Dots, Kambiz Hosseinpanahi, Mohammad Hossein Abbaspour-Fard, Mahmoud Reza Golzarian, Elaheh K. Goharshadi, Alberto Vomiero

Research outputs 2022 to 2026

Carbon quantum dots (CQDs) are promising luminophores for luminescent solar concentrators (LSCs) in transparent photovoltaic greenhouse covers due to their high ultraviolet (UV)-light absorption coefficient, which is vital for plant growth. Herein, high quantum yield (75%) and large Stokes shift (0.706 eV) CQDs are synthesized by a simple, fast, cheap, and mass scalable method. A comprehensive study on the LSC engineering is carried out. Thin layers of CQDs with different concentrations of 1, 3, and 5 wt% and different number of layers (1–5) are coated on glass and poly(methyl methacrylate) (PMMA) waveguides, sized 5 × 5 × 0.6 and 15 …

The Impact Of Domain Name Server (Dns) Over Hypertext Transfer Protocol Secure (Https) On Cyber Security: Limitations, Challenges, And Detection Techniques, Muhammad Dawood, Shanshan Tu, Chuangbai Xiao, Muhammad Haris, Hisham Alasmary, Muhammad Waqas, Sadaqat Ur Rehman

Research outputs 2022 to 2026

The DNS over HTTPS (Hypertext Transfer Protocol Secure) (DoH) is a new technology that encrypts DNS traffic, enhancing the privacy and security of end-users. However, the adoption of DoH is still facing several research challenges, such as ensuring security, compatibility, standardization, performance, privacy, and increasing user awareness. DoH significantly impacts network security, including better end-user privacy and security, challenges for network security professionals, increasing usage of encrypted malware communication, and difficulty adapting DNS-based security measures. Therefore, it is important to understand the impact of DoH on network security and develop new privacy-preserving techniques to allow the analysis of DoH traffic …

The Integrated Behavioral Model Of Mental Health Help Seeking (Ibm-Hs): A Health Services Utilization Theory Of Planned Behavior For Accessing Care, Joseph H. Hammer, David L. Vogel, Patrick R. Grzanka, Nayeon Kim, Brian T. Keum, Claire Adams, Sarah A. Wilson

Research outputs 2022 to 2026

This article introduces the integrated behavioral model of mental health help seeking (IBM-HS), a theoretical model for understanding the constructs (e.g., systemic, predisposing, and enabling factors; mental health literacy; illness perceptions; perceived need; stigma; shame; perceived benefits, motivation) that influence people’s decision making around seeking professional mental health care and their ultimate access to formal treatment. The IBM-HS is a help-seeking-specific adaptation of the empirically supported integrated behavioral model and integrative model, which are themselves evolutions of the theory of planned behavior and theory of reasoned action. The IBM-HS posits that help-seeking determinants (e.g., structural forces; cultural influences; past help-seeking …

The Phase Behaviour And Stability Of An Environmentally Friendly Oil-In-Water Emulsion Produced Using Balanites Aegyptiaca Oil And Green Emulsifiers, Sami A.M. Yagoub, Swee P. Yeap, Nurudeen P. Yekeen, Mohammed A. Ayoub

Research outputs 2022 to 2026

Due to environmental concerns about extensively using chemical emulsifiers and hydrocarbon oil in emulsion systems formation, recent research has shifted to using natural emulsifiers and oil. This study produced green emulsion using Balanites aegyptiaca oil and various bio-emulsifiers (such as sodium alginate, carboxymethylcellulose, guar gum, and Saponin). Phase behavior and stability of the emulsion were tested at different NaCl concentrations over one month of ageing. The emulsion was also produced using Balanites aegyptiaca oil and synthetic emulsifiers (Tween 80 and Triton X-100). The critical micelle concentrations of emulsifiers were determined and used as the fixed concentration for the green emulsion …

Changes In Deadlift Six Repetition Maximum, Countermovement Jump Performance, Barbell Velocity, And Perceived Exertion Over The Duration Of A Microcycle, Stuart N. Guppy, Tsuyoshi Nagatani, Wayne C. K. Poon, Kristina L. Kendall, Jason P. Lake, G. Gregory Haff

Research outputs 2022 to 2026

The primary aim of this study was to investigate the stability of the six-repetition maximum (6RM) deadlift over the length of a five-day microcycle and whether the fatigue induced by maximal effort testing detrimentally impacted preparedness. Twelve participants performed four testing sessions, comprising a one-repetition maximum test and three 6RM tests separated by 48 hours. Countermovement jumps were performed before each testing session, and barbell velocity was measured during each warm-up set to assess changes in preparedness. The 6RM deadlift was not statistically different between any of the testing sessions (p  =  .056; η_p²  =  0.251). Similarly, …

Valorization Of Spent Vetiver Roots For Biochar Generation, Sameer Neve, Dibyendu Sarkar, Manas Warke, Teresa Bandosz, Rupali Datta

Michigan Tech Publications

Vetiver root is widely used to produce essential oils in the aromatherapy industry. After the extraction of oil, the roots are disposed of as waste. The central objective of this research was to explore the conversion of this waste into a resource using a circular economy framework. To generate biochar, vetiver roots were pyrolyzed at different temperatures (300, 500, and 700 °C) and residence times (30, 60, and 120 min). Analysis showed the root biochar generated at 500 °C and held for 60 min had the highest surface area of 308.15 m2/g and a yield of 53.76%, in addition to …

Heating Capacity And Biocompatibility Of Hybrid Nanoparticles For Magnetic Hyperthermia Treatment, Aline Alexandrina Gomes, Thalita Marcolan Valverde, Vagner De Oliveira Machado, Emanueli Do Nascimento Da Silva, Daniele Alves Fagundes, Fernanda De Paula Oliveira, Erico Freitas, José Domingos Ardisson, José Maria Da Fonte Ferreira, Junnia Alvarenga De Carvalho Oliveira, Eliza Rocha Gomes, Caio Fabrini Rodrigues, Alfredo Miranda De Goes, Rosana Zacarias Domingues, Ângela Leão Andrade

Michigan Tech Publications

Cancer is one of the deadliest diseases worldwide and has been responsible for millions of deaths. However, developing a satisfactory smart multifunctional material combining different strategies to kill cancer cells poses a challenge. This work aims at filling this gap by developing a composite material for cancer treatment through hyperthermia and drug release. With this purpose, magnetic nanoparticles were coated with a polymer matrix consisting of poly (L-co-D,L lactic acid-co-trimethylene carbonate) and a poly(ethylene oxide)–poly(propylene oxide)–poly(ethylene oxide) triblock copolymer. High-resolution transmission electron microscopy and selected area electron diffraction confirmed magnetite to be the only iron oxide in the sample. Cytotoxicity …

Radiation Force Modeling For A Wave Energy Converter Array, Salman Husain, Gordon Parker, David Forehand, Enrico Anderlini

Michigan Tech Publications

The motivation and focus of this work is to generate passive transfer function matrices that model the radiation forces for an array of WECs. Multivariable control design is often based on linear time-invariant (LTI) systems such as state-space or transfer function matrix models. The intended use is for designing real-time control strategies where knowledge of the model’s poles and zeros is helpful. This work presents a passivity-based approach to estimate radiation force transfer functions that accurately replace the convolution operation in the Cummins equation while preserving the physical properties of the radiation function. A two-stage numerical optimization approach is used, …

Matthew Gaber: Peekaboo, Matthew Gaber, Mohiuddin Ahmed, Helge Janicke

Research Datasets

Cyber-attacks continue to evolve, increasing in frequency and sophistication where Artificial Intelligence (AI) is becoming essential in detecting modern malware. However, the accuracy of AI in malware detection is dependent on the quality of the features it is trained with. Static and dynamic analysis of malware is limited by the widespread use of obfuscation and anti-analysis techniques employed by malware authors, where if an analysis environment is detected the malware will hide its malicious behavior. However, Dynamic Binary Instrumentation (DBI) allows deep and precise control of the malware sample, thereby facilitating the extraction of authentic features from sophisticated and evasive …

The Hydrodynamics Of Double-Layered Vegetation Partially Occupying Both Banks In An Open Channel Flow, Maheshwara Ihala Gallangage Gedara

Research Datasets

This data delves into the hydrodynamic intricacies within an open channel featuring continuous double-layered vegetation along both banks. Measurements are undertaken using nonintrusive laser diagnostics (LDV) to assess velocity, shear stress, and turbulence intensity. Two double-layered vegetation configurations, uniform growth (A1) and mixed growth (A2), were examined in conjunction with four aspect ratios (AR-6.67, 5.00, 4.00, and 2.63). The raw data were acquired using "BSA Flow Software v5.00", provided by DANTEC DYNAMICS, Denmark, and the extracted data used for the analysis was included in the Excel sheets for the purpose of sharing.