Digital Commons Network^™

Identifying Early-Life Behavior To Predict Mothering Ability In Swine Utilizing NuTrack System, Savannah Millburn, Ty B. Schmidt, Gary A. Rohrer, Benny Mote

Department of Animal Science: Faculty Publications

Early indicator traits for swine reproduction and longevity support economical selection decision-making. Activity is a key variable impacting a sow’s herd life and productivity. Early-life activities could contribute to farrowing traits including gestation length (GL), number born alive (NBA), and number weaned (NW). Beginning at 20 weeks of age, 480 gilts were video recorded for 7 consecutive days and processed using the NUtrack system. Activity traits included angle rotated (radians), average speed (m/s), distance traveled (m), time spent eating (s), lying lateral (s), lying sternal (s), standing (s), and sitting (s). Final daily activity values were averaged across the …

Integrating Glycolysis, Citric Acid Cycle, Pentose Phosphate Pathway, And Fatty Acid Beta‑Oxidation Into A Single Computational Model, Sylwester M. Kloska, Krzysztof Pałczyński, Tomasz Marciniak, Tomasz Talaśka, Beata J. Wysocki, Paul H. Davis, Tadeusz A. Wysocki

Department of Electrical and Computer Engineering: Faculty Publications

The metabolic network of a living cell is highly intricate and involves complex interactions between various pathways. In this study, we propose a computational model that integrates glycolysis, the pentose phosphate pathway (PPP), the fatty acids beta-oxidation, and the tricarboxylic acid cycle (TCA cycle) using queueing theory. The model utilizes literature data on metabolite concentrations and enzyme kinetic constants to calculate the probabilities of individual reactions occurring on a microscopic scale, which can be viewed as the reaction rates on a macroscopic scale. However, it should be noted that the model has some limitations, including not accounting for all the …

Taz2 Truncation Confers Overactivation Of P300 And Cellular Vulnerability To Hdac Inhibition, Longxia Xu, Hongwen Xuan, Wei He, Liang Zhang, Mengying Huang, Kuai Li, Hong Wen, Han Xu, Xiaobing Shi

Faculty, Staff and Student Publications

The histone acetyltransferase p300/CBP is composed of several conserved domains, among which, the TAZ2 domain is known as a protein-protein interaction domain that binds to E1A and various transcription factors. Here we show that TAZ2 has a HAT autoinhibitory function. Truncating p300/CBP at TAZ2 leads to hyperactive HAT and elevated histone H3K27 and H3K18 acetylation in cells. Mechanistically, TAZ2 cooperates with other HAT neighboring domains to maintain the HAT active site in a 'closed' state. Truncating TAZ2 or binding of transcription factors to TAZ2 induces a conformational change that 'opens' the active site for substrate acetylation. Importantly, genetic mutations that …

Aenmd: Annotating Escape From Nonsense-Mediated Decay For Transcripts With Protein-Truncating Variants, Jonathan Klonowski, Qianqian Liang, Zeynep Coban-Akdemir, Cecilia Lo, Dennis Kostka

Faculty, Staff and Student Publications

DNA changes that cause premature termination codons (PTCs) represent a large fraction of clinically relevant pathogenic genomic variation. Typically, PTCs induce transcript degradation by nonsense-mediated mRNA decay (NMD) and render such changes loss-of-function alleles. However, certain PTC-containing transcripts escape NMD and can exert dominant-negative or gain-of-function (DN/GOF) effects. Therefore, systematic identification of human PTC-causing variants and their susceptibility to NMD contributes to the investigation of the role of DN/GOF alleles in human disease. Here we present aenmd, a software for annotating PTC-containing transcript-variant pairs for predicted escape from NMD. aenmd is user-friendly and self-contained. It offers functionality not currently available …

Enhanced Presynaptic Mitochondrial Energy Production Is Required For Memory Formation, Erica L Underwood, John B Redell, Kimberly N Hood, Mark E Maynard, Michael Hylin, M Neal Waxham, Jing Zhao, Anthony N Moore, Pramod K Dash

Faculty, Staff and Student Publications

Some of the prominent features of long-term memory formation include protein synthesis, gene expression, enhanced neurotransmitter release, increased excitability, and formation of new synapses. As these processes are critically dependent on mitochondrial function, we hypothesized that increased mitochondrial respiration and dynamics would play a prominent role in memory formation. To address this possibility, we measured mitochondrial oxygen consumption (OCR) in hippocampal tissue punches from trained and untrained animals. Our results show that context fear training significantly increased basal, ATP synthesis-linked, and maximal OCR in the Shaffer collateral-CA1 synaptic region, but not in the CA1 cell body layer. These changes were …

Integrate-Circ And Integrate-Vis: Unbiased Detection And Visualization Of Fusion-Derived Circular Rna, Jace Webster, Hung Mai, Amy Ly, Christopher Maher

2020-Current year OA Pubs

MOTIVATION: Backsplicing of RNA results in circularized rather than linear transcripts, known as circular RNA (circRNA). A recently discovered and poorly understood subset of circRNAs that are composed of multiple genes, termed fusion-derived circular RNAs (fcircRNAs), represent a class of potential biomarkers shown to have oncogenic potential. Detection of fcircRNAs eludes existing analytical tools, making it difficult to more comprehensively assess their prevalence and function. Improved detection methods may lead to additional biological and clinical insights related to fcircRNAs.

RESULTS: We developed the first unbiased tool for detecting fcircRNAs (INTEGRATE-Circ) and visualizing fcircRNAs (INTEGRATE-Vis) from RNA-Seq data. We found that …

Acorn: An R Package For De Novo Variant Analysis, Tychele N Turner

2020-Current year OA Pubs

BACKGROUND: The study of de novo variation is important for assessing biological characteristics of new variation and for studies related to human phenotypes. Software programs exist to call de novo variants and programs also exist to test the burden of these variants in genomic regions; however, I am unaware of a program that fits in between these two aspects of de novo variant assessment. This intermediate space is important for assessing the quality of de novo variants and to understand the characteristics of the callsets. For this reason, I developed an R package called acorn.

RESULTS: Acorn is an R …

The Effects Of Different Training Types On Phase Angle In Men - An Exploratory Study, Trevor Short, Paulette Yamada

Topics in Exercise Science and Kinesiology

Topics in Exercise Science and Kinesiology Volume 4: Issue 1, Article 12, 2023. Phase Angle (PhA) has emerged as a valuable measure in clinical and sports settings due to its predictive relationship with health and sports performance. Fitness is related to PhA, but the type of exercise training that is most influential over PhA has yet to be determined. The purpose was to explore the effects of endurance training (ET), strength-based resistance training (RT), and sprint-interval training (SIT) on PhA, resistance (R), and reactance (Xc) in men. Thirty-five recreationally-trained healthy young adult males (24±4 years) were randomly assigned to one …

Comparative Investigations On Microextraction And Conventional Air Sampling Techniques: Challenges And Future Directions, Firoz Ahmed, Mehedi Hasan Roni, Ashiqur Rahman, Sayed M A Salam

Al-Bahir

Microextraction technique (e.g., solid phase microextraction, thin film microextraction, in-tube extraction) brings a revolutionary change in air sampling techniques over the recent few years. This advanced technique exhibits a high pollutant extraction rate, a low retention time, and a lower error margin compared to conventional air sampling techniques. The accuracy range of microextraction technique (MET) was recorded ~90-95% to isolate the volatile organic components, oxygenated and halogenated carbon particles from the air. However, the efficiency of MET increases additional >3-5% when employed by coupled with gas chromatography or gas chromatography-mass spectrometry. The conventional sampling techniques (e.g., bag sampling, grab sampling) …

Concentration Of Spraying Solution Effect On The Structural, Morphological And Optical Properties Of Nio Thin Films, Radhiyah M. Aljarrah, Ali Madlool Naamah, Adel H. Omran Alkhayatt

Al-Bahir

In the present study nickel oxide NiO thin films of thickness ranging about 250-350 nm which were prepared on glass substrates by using chemical spray pyrolysis as a simple and low cost method. The impact of thickness and aqueous solution molarity concentration on the crystal structure and optical characteristics were investigated. The results showed that the deposited films is homogenous and have a good adherent to the glass substrates. The crystal structure results showed that all films have polycrystalline in nature, of rock salt phase, and the preferential orientation is an along (111) plane. The diffraction intensity was increased with …

Proportional Hazard Bivariate Kumaraswamy Model Applied On Fish Mercury Concentration, W. A. Hassanein, A. M. Sobhy, M. M. E. Abd El-Monsef

Journal of Statistics Applications & Probability

International advisory bodies have developed guidelines for testing mercury and aquatic items to protect human health and international trade. The mercury absorption in fish has a great effect on human health. For modeling this problem, a new bivariate distribution using the proportional hazard rate (PHR) model with Kumaraswamy marginal called BKPH is derived and studied via statistical properties and reliability measures. Moreover, several methods of parameter estimation are discussed, including maximum likelihood estimation (MLE), method of moments estimation (MME), and inference function for margins estimation (IFM). In the simulation study, the performance of estimators depending on their estimation methodologies is …

Disease Progression Modelling Of Alzheimer's Disease Using Probabilistic Principal Components Analysis, Martin Saint-Jalmes, Victor Fedyashov, Daniel Beck, Timothy Baldwin, Noel G. Faux, Pierrick Bourgeat, Jurgen Fripp, Colin L. Masters, Benjamin Goudey

Natural Language Processing Faculty Publications

The recent biological redefinition of Alzheimer's Disease (AD) has spurred the development of statistical models that relate changes in biomarkers with neurodegeneration and worsening condition linked to AD. The ability to measure such changes may facilitate earlier diagnoses for affected individuals and help in monitoring the evolution of their condition. Amongst such statistical tools, disease progression models (DPMs) are quantitative, data-driven methods that specifically attempt to describe the temporal dynamics of biomarkers relevant to AD. Due to the heterogeneous nature of this disease, with patients of similar age experiencing different AD-related changes, a challenge facing longitudinal mixed-effects-based DPMs is the …

Alternative Microplastic Identification Methods Using Optical Components To Modify Standard Compound Microscopes For Fluorescence Microscopy, Malia R. Trujillo

Student Research and Creative Projects 2022-2023

This study aimed to use optical components to modify and convert a compound microscope into a functional fluorescence microscope as an alternative identification procedure for microplastics in water samples. The results of this study showed that Nile Red dye was most effective in emitting fluorescence in colorless or clear plastics. Plastics that were colored showed weaker fluorescence. Rit Fabric Dye was also analyzed for fluorescence while bound to microplastics, but no fluorescence was found with this method.

Establishing Optimal Seeding Density And Ideal Starvation Conditions Of Sf9 And Nih/3t3 Cell Lines, Ellyssa N. Wager, Kassandra Heranandez, Justin Johnson

Student Research and Creative Projects 2022-2023

Fibroblast Growth Factors (FGFs) are a family of structurally related polypeptide cytokines. 22 FGF genes (FGF1-14, FGF16-23) are found in the human genome. FGFs have various known intracrine, paracrine, and endocrine functions and are essential for the development and wound repair in organisms through these mechanisms. The role of FGFs in viruses has become an area of piqued interest in the field of pathology as several virus families have genomes that encode one or more growth factor homologues. It has been suggested that a virally encoded ortholog of FGF (vFGF) identified in the viral families of Baculoviridae and Iridoviridae is …

Preparation And Characterization Of New Titanocene(Iv) Curcuminoid Complexes, Krista L. Osteraas, Valeria A. Stepanova

Student Research and Creative Projects 2022-2023

Titanocene complexes and curcuminoid species have both independently been shown to exhibit a number of biologically relevant properties. While complexes of the type [(η5-cyclopentadienyl)Ti(β-diketonate)]+ have been reported, no curcumin-based analogue has ever been synthesized. Using a straight forward method, several [(η5-cyclopentadienyl)Ti("curc")]+ ("curc" = curcuminoidate) have been prepared using an array of synthetic curcumin analogues. 1H and 13C NMR spectroscopy, mass spectrometry and single crystal X-ray diffractometry have all been utilized to characterize these compounds.

Mutagenesis Of The Of Sars-Coronavirus-2 Spike Gene, Coltan M. Kline, Anna Anderson, Salina Acharya

Student Research and Creative Projects 2022-2023

Coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 virus, has become a global pandemic resulting in over 6 million deaths worldwide. The virus binds to host cells through its spike (S) attachment protein, composed of two subunits: S1 and S2. The S protein is a target for vaccine development, with neutralizing antibodies blocking ACE2 binding to prevent infection. However, SARS-CoV-2 continues to evolve and accumulate mutations in the S protein, including L452R, T478K, D614G, P681R, and D950N, which can increase infectivity and evade host immune functions. To study the functions of these mutations, we randomly combined them in the alpha …

Rights Of Nature: What Are They?, Stepan Wood

Centre for Law and the Environment

This guide is one in an evolving series of guides intended to provide a general introduction to RON laws in plain language. They are intended for anyone curious about the subject, from ordinary citizens to community organizers, business people, scientists, politicians, government officials and Indigenous leaders.

Reversibility Of Stranded Cellular Automata, Allyn Loyd

Mathematical Sciences Technical Reports (MSTR)

Cellular automata, such as the Stranded Cellular Automaton (SCA) model created by Joshua and Lana Holden, can be used to model weaving patterns. Similar models can be constructed to model macrame patterns, where strands are knotted together. If a rule is injective, then it is reversible. If a rule is surjective, then every configuration has at least one predecessor. In this paper, we will discuss the injectivity and surjectivity of several new SCA models in order to find reversible rules. We will also analyze the number of configurations with no predecessors and the number of configurations that map to the …

Herbicide And Additive Impacts On Bradyrhizobium Japonicum Growth In Solution, Joy Amajioyi, Thandiwe Nleya, Senthil Subramanian, Sharon A. Clay

Agronomy, Horticulture and Plant Science Faculty Publications

Plant biostimulants include beneficial fungi and bacteria, and are often applied to foliage to improve crop growth, yield, and/or crop quality. Crop improvements due to biostimulant addition may be modest; therefore, solo applications may not be economical or climate smart. However, biostimulants combined with other postemergence treatments, such as herbicides, may provide an alternative application method, if mixtures do not harm the living organism(s). The growth of Bradyrhizobium japonicum, as a biostimulant surrogate, was assessed in solutions of glyphosate [N-(phosphonomethyl)glycine] and dicamba (3,6-dichloro-2-methoxybenzoic acid), with and without common spray additives (ammonium sulfate [AMS] and nonionic surfactant) in laboratory studies over …

Wofford Today Fall 2023, Wofford College. Office Of Marketing And Communications

Wofford Today

No abstract provided.

Convergence: Eos News And Updates, September 2023, Unh Institute For The Study Of Earth, Oceans And Space

Convergence: EOS News and Updates

No abstract provided.

The Price Of Competition: Analyzing Anticompetitive Tactics In Pharmaceutical Markets During The Hatch-Waxman Era, William Ulrich

Notre Dame Journal on Emerging Technologies

Pharmaceutical manufacturers can delay the generic entry for a blockbuster drug. In order to keep the generic system on track, it is critical to expose the various avenues of generic delay. Part I of this Note briefly describes the generic entry process as prescribed by the Hatch-Waxman Act. Part II details four well-known tactics used by brand-name manufacturers to block or delay the entry of generic competition, highlighting how the tactics are successful. Part III concludes by examining the nature of the various problems and arguing that the first step towards ending the different forms of anticompetitive behavior is through …

A Sleeping Giant: Mhelath Applications, The Gdpr, And The Need For Federal Privacy Regulation In The United States, Kali Peeples

Notre Dame Journal on Emerging Technologies

An analysis of privacy regulation concerning mHealth apps is a multifaceted process that requires the examination of changes within not only the healthcare space but also the technological world, as well as the legislative history and intent of various nations.The main issue being addressed in this paper is whether the United States should create nationwide legislation that directly relates to mHealth data protection or continue with a self-regulatory method. Part I focuses on the development and rapid creation of mHealth apps within the past decade. Part II seeks to illustrate the distinct privacy concerns of mHealth apps by concentrating on …

The Code Of Life And Death, Braden R. Leach

Notre Dame Journal on Emerging Technologies

Biotechnology is advancing at an astonishing clip, but our safeguards are decades behind. Given new technologies and economies of scale, it is possible for nefarious actors to assemble deadly viruses from scratch using synthetic DNA ordered off the internet. The Select Agents statute helps to prevent malicious actors from acquiring dangerous pathogens, but the Department of Health and Human Services has interpreted it to not cover synthetic DNA. Recognizing the gap, HHS issued guidance recommending that gene synthesis companies verify their customers to ensure their legitimacy and screen genetic sequences for matches to pathogen sequences. Unsurprisingly, voluntary guidance has not …

The High Cost Of Pharmaceutical Acquisitions: Increasing Social Welfare Or Furthering Inequality?, Timothy J. Haltermann

Notre Dame Journal on Emerging Technologies

This note will argue that government and regulatory authorities should focus on easing access to downstream innovation by broadening research exemptions to patent infringement. Part I of this note will focus on the current state of patent protection and exclusivity afforded to pharmaceutical companies. Part II will discuss incentives created that lead rational actors to engage in M&A instead of through internal R&D. Part III will address the development of innovation as a standalone theory of harm in merger review, and the fallacies associated with labeling certain transactions as “killer acquisitions.” Finally, Part IV of the note will look at …

A Numerical Confirmation Of A Fractional Seitr For Influenza Model Efficiency, Dalal Khalid Almutairi, Mohamed A.Abdoon, Mohammed Berir, Rania Saadeh, Ahmad Qazza

Applied Mathematics & Information Sciences

The main idea of this study is to reduce the number of susceptible to infections so that ill patients can receive prompt hospitalization. Fractional SEITR was introduced for this purpose. Both endemic and disease-free equilibrium’s’ durability was examined. The fundamental reproduction number of the fractional SEITR model was determined using the next-generation matrix method. Our analytical results were supported by numerical models. Here, a graphical representation of the fractional order model is presented to validate the conclusion through numerical simulation. We have come to the conclusion that the fractional order model is more precise and provides more information about the …

On Weighted Discretized Fre ́Chet-Weibull Distribution With Application To Real Life Data, Diksha Das, Bhanita Das

Applied Mathematics & Information Sciences

Weighted distributions have great practical importance in mathematics, probability and statistics. In this study a new discrete distribution which is a weighted version of Discretized Fréchet-Weibull distribution (DFWD), known as Weighted Discretized Fréchet-Weibull distribution (WDFWD), is proposed. It has been shown that the distribution is unimodal, positively skewed and suitable for modelling with overdispersed count data sets. This distribution has bathtub shape and decreasing hazard rate function. Various statistical properties and simulation of the proposed distribution are obtained. The estimation of parameters have been handled by the method of maximum likelihood estimation. Finally, the proposed model has been fitted to …

Chaos In New Polynomial Discrete Logistic Maps With Fractional Derivative And Applications For Text Encryption, Kalsouabe Zoukalne, Ahamat Mahamat Hassane, Mahamoud Youssouf Khayal, Paul Woafo

Applied Mathematics & Information Sciences

In this paper, we propose new polynomial discrete logistic equations based on the classical logistic map, which exhibit chaotic behavior as control parameters vary. We also explore versions with fractional derivatives. Using the chaotic sequence generated by these equations, we develop an encryption scheme for text. The scheme relies on initial conditions, control parameters, and a transformation of text characters into values between 0 and 1, followed by a transformation to discrete chaotic values for transmission

Neutrosophic Adaptive Lsb And Deep Learning Hybrid Framework For Ecg Signal Classification, Abdallah Rezk, Ahmed S. Sakr, H. M. Abdulkader

Applied Mathematics & Information Sciences

This paper proposes a novel hybrid framework for ECG signal classification and privacy preservation. The framework includes two phases: the first phase uses LSTM+CNN with attention gate for ECG classification, while the second phase utilizes adaptive least signal bit with neutrosophic for hiding important data during transmission. The proposed framework converts data into three sets of degrees (true, false, and intermediate) using neutrosophic and passes them to an embedding layer. In the sender part, the framework hides important data in ECG signal as true and false degrees, using the intermediate set as a shared dynamic key between sender and receiver. …

Compatibility Of Clique Clustering Algorithm With Dimensionality Reduction, Ug ̆Ur Madran, Duygu Soyog ̆Lu

Applied Mathematics & Information Sciences

In our previous work, we introduced a clustering algorithm based on clique formation. Cliques, the obtained clusters, are constructed by choosing the most dense complete subgraphs by using similarity values between instances. The clique algorithm successfully reduces the number of instances in a data set without substantially changing the accuracy rate. In this current work, we focused on reducing the number of features. For this purpose, the effect of the clique clustering algorithm on dimensionality reduction has been analyzed. We propose a novel algorithm for support vector machine classification by combining these two techniques and applying different strategies by differentiating …