Digital Commons Network^™

Integrated Rules Classifier For Predicting Pathogenic Non-Synonymous Single Nucleotide Variants In Human, Ahmed Barakat Hosseny, Marwa Said Hassan, A A. Shalan, Shymaa Khamis, M I. Dessouky

Basic Science Engineering

The most prevalent kind of genetic variants in humans are non-synonymous single nucleotide variants (nsSNVs). Several prediction tools have been launched to forecast the effect of amino acid substitutes on human protein function. These tools sort variants as pathogenic or neutral. We developed an Integrated Rules Classifier (Integration Score through JRip “ISTJRip”), which integrates the four individual tools that are publicly available; iFish, Mutation Assessor, FATHMM, and SIFT-based on the JRip machine learning technique. Additionally, we compared the ISTJRip approach with the other three created integration classifiers; Integration Score through J48 “ISTJ48”, Integration Score through RF “ISTRF”, and Integration …

Effects Of Electrode Materials And Potential Gradient On Electro-Osmotic Consolidation For Marine Clayey Soils, Haihui Jin, Lei Zhang, Binghui Wang, Chen Fang, Liyan Wang

Department of Civil and Environmental Engineering: Faculty Publications

This study conducted experimental investigations into the effects of electrode material and potential gradient on the effectiveness of electro-osmotic consolidation (EO) in strengthening soft soils. Seven laboratory tests were conducted on high-water-content marine clayey soils through EO. In these experimental tests, four different types of electrodes made of steel, copper, aluminum, and composite carbon fiber (CCF) were employed in four tests each to evaluate the consolidation effectiveness. Additionally, four tests, one was the comparitive study for different eletrode materials, were carried out to determine the optimal gradient for the EO using CCF electrode. Several critical properties of the tested soils …

Obstacle Avoidance Motion In Mobile Robotics, Yunchao Tang, Shaojun Qi, Lixue Zhu, Xianrong Zhuo, Yunqi Zhang, Fan Meng

Journal of System Simulation

Abstract: The advancement of artificial intelligence technology has significantly enhanced the utilization of mobile robots in various fields such as industry, aerospace, and agriculture. The autonomous obstacle avoidance capability of these robots is crucial to the safety and efficiency of their operations in diverse settings. Path planning, a key technology in obstacle avoidance, plays an essential role in the overall performance of these systems. This paper presents a comprehensive review of path planning technology for mobile robots, categorizing the algorithms into global planning and local obstacle avoidance according to their operational requirements. Specific focus is given to the global planning …

Research On Campus Epidemic Evolution Based On Multi-Scale Modeling And Simulation In Microscopic & Microscopic View, Mingwei Hu, Wenjie Yang

Journal of System Simulation

Abstract: High density of population leads to high possibility of cross-infection. It is necessary to focus on campus epidemic prevention and control. Basing on existing studies in macroscopic or microscopic view, this paper proposed a multi-scale means to analyze a short-term evolution of Corona virus disease 2019 (COVID-19) on campus and estimated the efficiency of prevention strategies. Macroscopic model was based on the susceptible-exposed-infections-recovered(SEIR) model, which exported the time curve of the number of asymptomatic patients and symptomatic patients. Microscopic model combined discrete event simulation modeling and agent-based modeling to simulate the behavior of campus students and the state evolution …

Impacts Of Farrowing Pen Design, Season, And Sow Parity On Litter Performance And Piglet Mortality, Verônica Madeira Pacheco, Tami M. Brown-Bandl, Gary A. Rohrer, Rafael Vieira De Sousa, Luciane Silva Martello

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Piglet mortality during lactation is a significant concern in swine production, influenced by complex interactions involving sow, piglet, environmental, and management factors. While crushing by the sow may be the ultimate cause of piglet mortality, there are many factors influencing the outcome, including parity, thermal stress, and animal housing systems. New farrowing systems are continuously being developed; however, it is difficult for producers to make decisions without any scientific basis. This study aimed to assess the impact of different farrowing pen layouts on piglet performance, considering parity and season. A total of 546 sows and 9123 piglets were monitored across …

Efficient Discovery And Industrialized Manufacture Of Terpenoids, Haoming Chi, Liying Er, Tiangang Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Terpenoids, a class of chemical entities with diverse biological activities in nature, demonstrate significant potential for applications in fields such as drug discovery, flavor industry, and agriculture. However, traditional methods face challenges, including inefficiency and high costs, in the discovery and industrialization of terpenoids. The rapid development of synthetic biology, genomics, artificial intelligence, and automation provides new opportunities for efficient terpenoid discovery and industrialization. This study comprehensively analyzes how these technologies synergistically contribute to the discovery, optimization, and large-scale production of terpenoids, and summarizes the current high-yield situations of terpenoids. The aim is to propose innovative strategies to accelerate technological …

Implantation Of A Capsular Tension Ring During Cataract Surgery Attenuates Predicted Remodeling Of The Post-Surgical Lens Capsule Along The Visual Axis, Kurt A. Ameku, Caleb C. Berggren, Ryan M. Pedrigi

Department of Mechanical and Materials Engineering: Faculty Publications

Introduction: Cataract surgery permanently alters the mechanical environment of the lens capsule by placing a hole in the anterior portion and implanting an intraocular lens (IOL) that has a very different geometry from the native lens. We hypothesized that implant configuration and mechanical interactions with the post-surgical lens capsule play a key role in determining long-term fibrotic remodeling.

Methods: We developed the first finite element-growth and remodeling (FE-G&R) model of the post-surgical lens capsule to evaluate how implantation of an IOL with and without a capsular tension ring (CTR) impacted evolving lens capsule mechanics and associated fibrosis over …

Electron Trajectories And Critical Current In A Two-Dimensional Planar Magnetically Insulated Crossed-Field Gap, Xiaojun Zhu, Jack K. Wright, N. R. Sree Harsha, Jim Browning, Allen L. Garner

Electrical and Computer Engineering Faculty Publications and Presentations

The critical current in a one-dimensional (1D) crossed-field gap is defined by the transition from a cycloidal flow to a near-Brillouin (nB) state characterized by electron flow orthogonal to both the electric and magnetic fields and uniform virtual cathode formation. Motivated by recent studies on space-charge-limited current in non-magnetic diodes, we assess the meaning of critical current in a magentically insulated two-dimensional (2D) planar crossed-field geometry. Particle-in-cell (PIC) simulations demonstrate that binary behavior between a laminar and turbulent state does not occur in 2D because the virtual cathode is nonuniform. Rather than a distinct nB state above the critical current …

Electron Effective Mass In Gan Revisited: New Insights From Terahertz And Mid-Infrared Optical Hall Effect, Nerijus Armakavicius, Sean Knight, Philipp Kühne, Vallery Stanishev, Dat Q. Tran, Steffen Richter, Alexis Papamichail, Megan Stokey, Preston Sorensen, Ufuk Kilic, Mathias Schubert, Plamen P. Paskov, Vanya Darakchieva

Department of Electrical and Computer Engineering: Faculty Publications

Electron effective mass is a fundamental material parameter defining the free charge carrier transport properties, but it is very challenging to be experimentally determined at high temperatures relevant to device operation. In this work, we obtain the electron effective mass parameters in a Si-doped GaN bulk substrate and epitaxial layers from terahertz (THz) and mid-infrared (MIR) optical Hall effect (OHE) measurements in the temperature range of 38–340 K. The OHE data are analyzed using the well-accepted Drude model to account for the free charge carrier contributions. A strong temperature dependence of the electron effective mass parameter in both bulk and …

Polymerizing Actin Regulates Myosin-Independent Mechanosensing By Modulating Actin Elasticity And Flow Fluctuation, Nikhil Mittal, Etienne Michels, Kathleen Pakenas, Shaina P. Royer-Weeden, Sangyoon J. Han

Michigan Tech Publications

The stiffness of the extracellular matrix induces differential tension within integrin-based adhesions. However, it has been unclear if the stiffness-dependent differential tension is induced solely by myosin activity. Here, we report that in the absence of myosin contractility, 3T3 fibroblasts still transmit stiffness-dependent differential levels of traction. This myosin-independent differential traction is regulated by polymerizing actin assisted by actin nucleators Arp2/3 and formin where formin has stronger contribution than Arp2/3. Interestingly, we report a four-fold reduction in traction of cells when both Arp2/3 and myosin were inhibited, compared to cells with only myosin inhibition, while there was only a slight …

Heterologous Expression Of Arabidopsis Laccase2, Laccase4 And Peroxidase52 Driven Under Developing Xylem Specific Promoter Dx15 Improves Saccharification In Populus, Yogesh Ahlawat, Ajaya K. Biswal, Sarahani Harun, Anne E. Harman-Ware, Crissa Doeppke, Nisha Sharma, Chandrashekhar P. Joshi, Bertrand B. Hankoua

Michigan Tech Publications

Background: Secondary cell wall holds considerable potential as it has gained immense momentum to replace the lignocellulosic feedstock into fuels. Lignin one of the components of secondary cell wall tightly holds the polysaccharides thereby enhancing the recalcitrance and complexity in the biomass. Laccases (LAC) and peroxidases (PRX) are the major phenyl-oxidases playing key functions during the polymerization of monolignols into lignin. Yet, the functions of laccase and peroxidases gene families remained largely unknown. Hence, the objective of this conducted study is to understand the role of specific LAC and PRX in Populus wood formation and to further investigate how the …

Market Analysis And Bidding Strategy Of Hybrid Renewable Energy Systems Considering Emissions, Fatma Elzahraa, Mohamed Elnemr, Samir Dawoud

Journal of Engineering Research

The competition in the electricity markets makes it difficult to choose a suitable strategy for maximizing profit while reducing harmful emissions. To have an adequate energy price for consumers while minimizing the harmful emissions to the atmosphere and maximizing profits of all participants in the electricity market needs an aggressive bidding strategy. Developing these bidding strategies with the integration of renewable energy (RE) in the electricity market became important. This research studies various bidding strategies for maximizing profits in the deregulated energy market since participants are keen on developing bidding strategies considering emissions. These bidding strategies will consider the integration …

Pestel And 3r Waste Management Model For Construction Companies Operating In Central Tanta: A Comprehensive Construction And Demolition Waste Management Model, Moaaz Ali Bastaweesy, Mahmoud Ahmed Zaki, Marwa Ahmed Kamer Eldawla

Journal of Engineering Research

Due to a recent economic boom, Tanta's construction sector has seen fast expansion, which has resulted in high construction and demolition waste (C&DW) creation and waste management operations that lag below international best practices. The current study uses PESTEL analysis, a thorough environmental screening method, to first identify and evaluate significant external and internal elements that may have an impact on C&DW management in a top Central Egyptian construction business. Then, this firm is the topic of a case study that applies the 3R (reduce-reuse- recycle) principles. The offered context-specific current international practices, the described current firm practices, and the …

Kinetic Applications Of Smart Materials In Architecture: A Descriptive Analysis, Youssef Elkhayat

Journal of Engineering Research

In recent years, many smart materials for architectural applications have been invented. Some smart materials can adapt and interact with the surrounding environment and its variants, whether temperature, humidity, daylight or electric current. Smart material changes its shape without any need for assistance, and it can return to its original state without any significant deformation in shape with the end of the external influence. The invention of smart materials stimulated several architects and facade designers to consider using them in various architectural applications such as sun shading, sun breakers, and windows, significantly impacting the concept and technology of movement in …

Optimum Design Of Metallic And Plastic Cylindrical Gears Using Naturally-Inspired Algorithms: A Review, Marah Elsiedy, Hesham Hegazi, Ahmed Elkassas, Abdelhameed Zayed

Journal of Engineering Research

Abstract- Nowadays, several machinery and vehicles utilize mechanical elements which transmit power ranges from low, middle, and high levels depending on the type of equipment needed. Gears are the most influential design elements on any process during the running of a specific application, moreover engineers tried to obtain the optimality of a gear design which is a more compact, reliable- long service with simply operating features by following a systematic calculation of the mathematical model from standards and handbooks, however this process doesn't give the optimal design of the gears. Optimization techniques have been added to the design process for …

Biophilic Urbanism As A Tool To Conserve Urban Waterfront Of Submerged Heritage Cities, Fatma Ahmed Alashwah, Ayman Abdel Tawab Professor, Ingy Eldarwish Professor, Wesam Mehanna

Journal of Engineering Research

The Urban waterfronts of submerged heritage cities hold significant cultural and natural value that necessitates preservation. However, these sites suffer from a disconnection between nature and culture in heritage conservation practices, negatively impacting heritage sites, ecosystems, and human well-being. Biophilic urbanism offers a valuable tool to address this gap, creating healthier cities. This paper explores how to implement biophilic urbanism elements in conserving urban waterfronts of submerged heritage cities. Through a comprehensive literature review, the study discusses the gap between heritage and nature in conservation practices and explores the perception of biophilic urbanism elements in conserving the urban waterfront of …

The Ecological Responses To Hydroperiod Of Wetland Plant Species Determined By Manipulated Soil Surface Elevation (Marsh Organs), Brandon Wolff

LSU Master's Theses

As sea level rise, subsidence, and abandonment of natural deltaic processes due to a highly engineered Mississippi River continue to threaten Louisiana’s coastal wetlands, the need for a system-wide understanding of natural wetland land-building and preservation processes has never been greater. A key component of any wetland is the ever-changing water environment that periodically floods and dries the marsh platforms. The flooding depth, duration, and frequency, known as the hydroperiod, along with salinity and soil fertility are key determining factors of vegetation and marsh types at a particular location. Different types of vegetation will have different growth characteristics such as …

Digital Phobia: An Inquiry For Mapping The Unseen Dimension Of New Digital Anxiety, The ‘Digiphobia’, Amarjit Kumar Singh ,Library Assistant, Md. Arshad Ali , Professional Assistant, Dr. Pankaj Mathur, Deputy Librarian,

Library Philosophy and Practice (e-journal)

Background: As technology continues to advance, individuals' interactions with digital platforms have become integral to daily life. Amidst this technological evolution, a novel concern emerges—Digital Phobia, hereafter referred to as “Digiphobia.” This phenomenon, although not previously explored in scholarly literature, necessitates an in-depth investigation due to its potential impact on individuals' well-being. Our research employs a two-step methodology to investigate its existence, implications, and manifestations.

Introduction: This research paper introduces and proposes the term "Digiphobia" as a comprehensive conceptualization of anxiety arising from interactions with digital spaces, applications, and environments. The proliferation of digital technologies has led to the emergence …

Scaffold-Based 3d Cell Culture Models In Cancer Research, Waad H. Abuwatfa, William G. Pitt, Ghaleb A. Husseini

Faculty Publications

Three-dimensional (3D) cell cultures have emerged as valuable tools in cancer research, offering significant advantages over traditional two-dimensional (2D) cell culture systems. In 3D cell cultures, cancer cells are grown in an environment that more closely mimics the 3D architecture and complexity of in vivo tumors. This approach has revolutionized cancer research by providing a more accurate representation of the tumor microenvironment (TME) and enabling the study of tumor behavior and response to therapies in a more physiologically relevant context. One of the key benefits of 3D cell culture in cancer research is the ability to recapitulate the complex interactions …

Engineering Neurotoxin-Functionalized Exosomes For Targeted Delivery To The Peripheral Nervous System, Mena Asha Krishnan, Olawale A. Alimi, Tianshu Pan, Mitchell Kuss, Zeljka Korade, Guoku Hu, Bo Liu, Bin Duan

Department of Mechanical and Materials Engineering: Faculty Publications

The administration of therapeutics to peripheral nerve tissue is challenging due to the complexities of peripheral neuroanatomy and the limitations imposed by the blood–nerve barrier (BNB). Therefore, there is a pressing need to enhance delivery effectiveness and implement targeted delivery methods. Recently, erythrocyte-derived exosomes (Exos) have gained widespread attention as biocompatible vehicles for therapeutics in clinical applications. However, engineering targeted Exos for the peripheral nervous system (PNS) is still challenging. This study aims to develop a targeted Exo delivery system specifically designed for presynaptic terminals of peripheral nerve tissue. The clostridium neurotoxin, tetanus toxin-C fragment (TTC), was tethered to the …

Pcl And Dmso2 Composites As Biomaterials For Additive Manufacturing, Jae-Won Jang

Dissertations and Theses

Tissue engineering provides a viable solution to address the shortage of organ donors for allograft transplants. Its primary objective is the replacement or regeneration of damaged tissues which is developed by combining living cells, a scaffold, and a bioreactor. Among these components, the scaffold serves as an artificial extracellular matrix (ECM), which plays a pivotal role in supporting cell adhesion, proliferation, differentiation, and overall tissue development. Additive manufacturing (AM), commonly referred to as three-dimensional (3D) printing, emerges as a promising method for scaffold fabrication due to its capability to create complex and repeatable geometries.

Polycaprolactone (PCL) has been one of …

Soil Improvement Using Fungal Mycelium Of Trichoderma Virens And Construction Techniques Of Mud Dauber, Park Joon Soo

LSU Doctoral Dissertations

Traditional ground improvement techniques involve high energy consumption and expensive and invasive earthworks. To develop sustainable ground improvement techniques, extensive research has explored biological processes and strategies. This dissertation identifies two organisms, fungal mycelium and mud dauber wasp, as sources of utilization and inspiration for the development of sustainable soil improvement techniques.

Filamentous fungi can form a root-like interconnected complex network known as fungal mycelium. Fungal mycelium can extend through soil pores and secrete hydrophobic compounds, binding soil particles and increasing soil water repellency. This dissertation conducted experimental studies to investigate the effects of fungal mycelium on hydraulic and mechanical …

Diagnosis Of Disease Affecting Gait With A Body Acceleration‑Based Model Using Reflected Marker Data For Training And A Wearable Accelerometer For Implementation, Mohammad Ali Takallou, Farahnaz Fallahtafti, Mahdi Hassan, Ali Al‑Ramini, Basheer Qolomany, Iraklis I. Pipinos, Sara A. Myers, F. M. Alsaleem

Durham School of Architectural Engineering and Construction: Faculty Publications

This paper demonstrates the value of a framework for processing data on body acceleration as a uniquely valuable tool for diagnosing diseases that affect gait early. As a case study, we used this model to identify individuals with peripheral artery disease (PAD) and distinguish them from those without PAD. The framework uses acceleration data extracted from anatomical reflective markers placed in different body locations to train the diagnostic models and a wearable accelerometer carried at the waist for validation. Reflective marker data have been used for decades in studies evaluating and monitoring human gait. They are widely available for many …

Yap Mechanotransduction Under Cyclic Mechanical Stretch Loading For Mesenchymal Stem Cell Osteogenesis Is Regulated By Rock, Eunju Kim, Brandon D. Riehl, Tasneem Bouzid, Ruiguo Yang, Bin Duan, Henry J. Donahue, Jung Yul Lim

Department of Mechanical and Materials Engineering: Faculty Publications

While yes-associated protein (YAP) is now recognized as a potent mechanosensitive transcriptional regulator to affect cell growth and differentiation including the osteogenic transcription of mesenchymal stem cells (MSCs), most studies have reported the YAP mechanosensing of static mechanophysical cues such as substrate stiffness. We tested MSC response to dynamic loading, i.e., cyclic mechanical stretching, and assessed YAP mechanosensing and resultant MSC osteogenesis. We showed that cyclic stretching at 10% strain and 1 Hz frequency triggered YAP nuclear import in MSCs. YAP phosphorylation at S127 and S397, which is required for YAP cytoplasmic retention, was suppressed by cyclic stretch. We also …

Improvement Of Convective Drying Equipment, A Ponasenko, Jasur Safarov, Shaxnoza Sultanova

Technical science and innovation

Drying of agricultural raw materials is an energy-consuming but integral process. Therefore, increasing the efficiency of drying and improving the quality indicators of dried material at minimum material and energy costs is relevant for producers of agricultural products. By present time numerous researches on improvement of constructions and processes of work of dryers providing satisfactory parameters of energy saving have been carried out. In some scientific materials it is shown that the use of generative gas and straw as fuel allows to reduce energy costs for the drying process in the fluidised bed dryer by 10-30%, the quality of seeds …

Mathematical Modeling Of Fruit Drying And System Analysis Of The Process (On The Example Of Persimmon), Gani Dadayev, Jasur Safarov, Shakhnoza Sultanova, Qobiljon Muxiddinov

Technical science and innovation

Vegetable raw materials, as an object of drying, are characterized by a large amount of water and a low content of dry substances. Vegetable raw materials have a capillary-porous structure. Food products contain both bound and free moisture at the same time. The removal of moisture from the material during drying depends on the total moisture content and the form of connection of moisture with the material. Adsorption and osmotic - bound moisture is retained at the interface of colloidal particles with the environment. Food products contain both bound and free moisture at the same time. The quantitative ratio between …

Cancer Treatment By Targeting Hdac4 Translocation Induced By Microsecond Pulsed Electric Field Exposure: Mechanistic Insights Through Kinases And Phosphatases, Zahra Safaei

Theses and Dissertations

Epigenetic modifications, arising from sub-cellular shifts in histone deacetylase (HDAC) activity and localization, present promising strategies for diverse cancer treatments. HDACs, enzymes responsible for post-translational histone modifications, induce these epigenetic changes by removing acetyl groups from ε-N-acetyl-lysine residues on histones, thereby suppressing gene transcription. Within the HDAC group, class IIa HDACs are notable for their responsiveness to extracellular signals, bridging the gap between external stimuli, plasma membrane, and genome through nuclear-cytoplasmic translocation. This localization offers two significant mechanisms for cancer treatment: nuclear accumulation of HDACs represses oncogenic transcription factors, such as myocyte-specific enhancer factor 2C (MEF2C), triggering various cell death …

Development Of A Xenograft For Annular Repair Using Pulsed Electric Field Exposures For Enhanced Decellularization, Prince Mensah Kwaku Atsu

Theses and Dissertations

Severe back injuries and chronic pain necessitate surgical replacement of damaged intervertebral disc (IVD) cartilage in advanced disease stages. Bovine IVD tissue has been exposed to an upper threshold pulsed electric field (PEF) dose, causing cell death without thermal damage to the tissue. Subsequent PEF exposures at lower magnitudes have accelerated the removal of immunogenic biomolecules though electrokinetic extraction using optimized aqueous solutions. This approach yields a natural scaffold, ready for biocompatibility and mechanical strength assessment. The effects of microsecond pulsed electric fields (µsPEF) on primary bovine AF fibroblast-like cells have been characterized in vitro. PEFs of 10 and 100 …

Statistical Analysis For Water Quality Data Using Anova (Case Study – Lake Burullus Influent Drains), Dr.Aya Hassan

Civil Engineering

Lake Burullus is considered one of the most valuable northern lakes in Egypt due to its unique ecological system and special location. Over the past four decades, the lake has suffered from high contamination levels due to expansion in fish farming and increasing of agricultural drainage water entering the southern side of the lake through eight influent drains. This research aims to assess the current situation of the lake’s influent drains. For this purpose, two types of statistical analysis, Mean average method, and Analysis of Variance (ANOVA) were used. The water quality conditions for six major drains (Therah (Tira), Nashart, …

Development Of A Suspended Aerobic Membrane Bioreactor (Sambr) For Sustainable Wastewater Treatment On Early Planetary Bases, Talon James Bullard

USF Tampa Graduate Theses and Dissertations

Environmental Control and Life Support Systems (ECLSS) ideally should treat all “waste” streams for recovery in a sustainable and near closed-loop manner. This will be critical for Partial Gravity Habitats (PGH) and Early Planetary Bases (EPB) that will be established on the Moon and Mars due to the lack of readily available resources. Currently, the Water Recovery System (WRS), onboard the International Space Station (ISS), recovers and purifies water from urine and graywater. While efficient, this system is not optimized for future missions and utilizes physical-chemical technologies that operate with single-use and hazardous consumables. In response to the lack of …