Physical Sciences and Mathematics Commons^™

Intergenic Transcription In In Vivo Developed Bovine Oocytes And Pre-Implantation Embryos, Saurav Ranjitkar, Mohammad Shiri, Jiangwen Sun, Xiuchun Tian

Computer Science Faculty Publications

Background

Intergenic transcription, either failure to terminate at the transcription end site (TES), or transcription initiation at other intergenic regions, is present in cultured cells and enhanced in the presence of stressors such as viral infection. Transcription termination failure has not been characterized in natural biological samples such as pre-implantation embryos which express more than 10,000 genes and undergo drastic changes in DNA methylation.

Results

Using Automatic Readthrough Transcription Detection (ARTDeco) and data of in vivo developed bovine oocytes and embryos, we found abundant intergenic transcripts that we termed as read-outs (transcribed from 5 to 15 kb after TES) and …

Numerical Study Of Sediment Suspension Affected By Rigid Cylinders Under Unidirectional And Combined Wave-Current Flows, Sha Lou, Xiaolan Chen, Shengyu Zhou, Gangfeng Ma, Shuguang Liu, Larisa Dorzhievna Radnaeva, Elena Nikitina, Irina Viktorovna Fedorova

Civil & Environmental Engineering Faculty Publications

Sediment transport modeling for flows with cylinders is very challenging owing to the complicated flow–cylinder–sediment interactions, especially under the combined wave-current flows. In this paper, an improved formulation for incipient sediment suspension considering the effect of cylinder density (i.e., solid volume fraction) is employed to simulate the bottom sediment flux in the flow with cylinders. The proposed model is calibrated and validated using laboratory measurements under unidirectional and combined wave-current flows in previous studies. It is proved that the effects of cylinders on sediment suspension can be accounted for through a modified critical Shields number, and the proposed model is …

Transfer Learning Using Infrared And Optical Full Motion Video Data For Gender Classification, Alexander M. Glandon, Joe Zalameda, Khan M. Iftekharuddin, Gabor F. Fulop (Ed.), David Z. Ting (Ed.), Lucy L. Zheng (Ed.)

Electrical & Computer Engineering Faculty Publications

This work is a review and extension of our ongoing research in human recognition analysis using multimodality motion sensor data. We review our work on hand crafted feature engineering for motion capture skeleton (MoCap) data, from the Air Force Research Lab for human gender followed by depth scan based skeleton extraction using LIDAR data from the Army Night Vision Lab for person identification. We then build on these works to demonstrate a transfer learning sensor fusion approach for using the larger MoCap and smaller LIDAR data for gender classification.

Prediction Of Rapid Early Progression And Survival Risk With Pre-Radiation Mri In Who Grade 4 Glioma Patients, Walia Farzana, Mustafa M. Basree, Norou Diawara, Zeina Shboul, Sagel Dubey, Marie M. Lockheart, Mohamed Hamza, Joshua D. Palmer, Khan Iftekharuddin

Electrical & Computer Engineering Faculty Publications

Rapid early progression (REP) has been defined as increased nodular enhancement at the border of the resection cavity, the appearance of new lesions outside the resection cavity, or increased enhancement of the residual disease after surgery and before radiation. Patients with REP have worse survival compared to patients without REP (non-REP). Therefore, a reliable method for differentiating REP from non-REP is hypothesized to assist in personlized treatment planning. A potential approach is to use the radiomics and fractal texture features extracted from brain tumors to characterize morphological and physiological properties. We propose a random sampling-based ensemble classification model. The proposed …

An Explainable Artificial Intelligence Framework For The Predictive Analysis Of Hypo And Hyper Thyroidism Using Machine Learning Algorithms, Md. Bipul Hossain, Anika Shama, Apurba Adhikary, Avi Deb Raha, K. M. Aslam Uddin, Mohammad Amzad Hossain, Imtia Islam, Saydul Akbar Murad, Md. Shirajum Munir, Anupam Kumur Bairagi

Electrical & Computer Engineering Faculty Publications

The thyroid gland is the crucial organ in the human body, secreting two hormones that help to regulate the human body's metabolism. Thyroid disease is a severe medical complaint that could be developed by high Thyroid Stimulating Hormone (TSH) levels or an infection in the thyroid tissues. Hypothyroidism and hyperthyroidism are two critical conditions caused by insufficient thyroid hormone production and excessive thyroid hormone production, respectively. Machine learning models can be used to precisely process the data generated from different medical sectors and to build a model to predict several diseases. In this paper, we use different machine-learning algorithms to …

Commentary On Healthcare And Disruptive Innovation, Hilary Finch, Affia Abasi-Amefon, Woosub Jung, Lucas Potter, Xavier-Lewis Palmer

Electrical & Computer Engineering Faculty Publications

Exploits of technology have been an issue in healthcare for many years. Many hospital systems have a problem with “disruptive innovation” when introducing new technology. Disruptive innovation is “an innovation that creates a new market by applying a different set of values, which ultimately overtakes an existing market” (Sensmeier, 2012). Modern healthcare systems are historically slow to accept new technological advancements. This may be because patient-based, provider-based, or industry-wide decisions are tough to implement, giving way to dire consequences. One potential consequence is that healthcare providers may not be able to provide the best possible care to patients. For example, …

How Do Sustainability Stakeholders Seize Climate Risk Premia In The Private Cleantech Sector, Lingyu Li, Xianrong Zheng

Information Technology & Decision Sciences Faculty Publications

This paper explores the strategies and practices of capturing climate risk premia for venture capital (VC) fund managers and entrepreneurs in the private cleantech sector. It also examines the impact of the feed-in tariffs (FITs) policy on the management of cleantech investments. It is shown that a longer investment period, less investment capital in cleantech investment management strategies, and optimistic climate risk management practices will help investors to better capture climate risk premia. In fact, the FITs policy will give rise to VC fund managers and entrepreneurs having a positive view regarding the prospects of the cleantech sector, motivating them …

Inventions In The Area Of Nanotechnologies And Nanomaterials. Part I, Leonid A. Ivanov, Li Da Xu, Zhanna V. Pisarenko, Svetlana R. Muminova, Nadezda G. Miloradova

Information Technology & Decision Sciences Faculty Publications

Introduction. Advanced technologies inspire people by demonstrating the latest achievements (materials, methods, systems, technologies, devices etc.) that dramatically change the world. This, first of all, concerns nanotechnological inventions designed by scientists, engineers and specialists from different countries. Main part. The article provides an abstract overview of inventions of scientists, engineers and specialists from different countries: Germany, Russia, China, USA et al. The results of the creative activity of scientists, engineers and specialists, including inventions in the field of nanotechnology and nanomaterials allow, when introduced to industry, achieving a significant effect in construction, housing and communal services, and related sectors of …

Assessing Univariate And Multivariate Normality In Pls-Sem, Kathy Qing Ma, Weiyong Zhang

Information Technology & Decision Sciences Faculty Publications

Partial least squares structural equation modeling (PLS-SEM) has gained popularity among researchers in part due to its relaxed requirement for multivariate normality. One important step in performing structural equation modeling (SEM) is to test the normality assumption. In this paper, we illustrate how to assess univariate and multivariate normality in PLS-SEM using WarpPLS.

Outstanding Advantages, Current Drawbacks, And Significant Recent Developments In Mechanochemistry: A Perspective View, Silvina Pagola

Chemistry & Biochemistry Faculty Publications

Although known since antiquity, mechanochemistry has remained dormant for centuries. Nowadays, mechanochemistry is a flourishing research field at the simultaneous stages of gathering data and (often astonishing) observations, and scientific argumentation toward their analysis, for which the combination of interdisciplinary expertise is necessary. Mechanochemistry’s implementation as a synthetic method is constantly increasing, although it remains far from being fully exploited, or understood on the basis of fundamental principles. This review starts by describing many remarkable advantages of mechanochemical reactions, simplifying and “greening” chemistry in solutions. This description is followed by an overview of the current main weaknesses to be addressed …

More On The Demons Of Thermodynamics, Daniel P. Sheehan, Garret Moddel, James W. Lee

Chemistry & Biochemistry Faculty Publications

No abstract provided.

Abiotic Stress Mitigation: A Case Study From 21 Trials Using A Natural Organic Matter Based Biostimulant Across Multiple Geographies, Rachel L. Sleighter, Terry Hanson, David Holden, Kristen M. Richards

Chemistry & Biochemistry Faculty Publications

Crop productivity and yields can be greatly diminished by abiotic stress events including drought, extreme temperatures, excess moisture, and saline irrigation water. Multiple stressors occurring simultaneously can further exacerbate the strain on plants. Various types of biostimulants have been shown to mitigate abiotic stress and here, the results of 21 trials on corn, wheat, soybean, and various high-value crops are discussed in the context of the abiotic stress that either occurred naturally or was experimentally induced. Treatments in these trials included stressed and non-stressed plants, as well as either an untreated control or grower standard fertilizer applications alone and in …

Enhancing The Conformational Stability Of The Cl-Par-4 Tumor Suppressor Via Site-Directed Mutagenesis, Samjhana Pandey, Krishna K. Raut, Andrea M. Clark, Antoine Baudin, Lamya Djemri, David S. Libich, Komala Ponniah, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Intrinsically disordered proteins play important roles in cell signaling, and dysregulation of these proteins is associated with several diseases. Prostate apoptosis response-4 (Par-4), an approximately 40 kilodalton proapoptotic tumor suppressor, is a predominantly intrinsically disordered protein whose downregulation has been observed in various cancers. The caspase-cleaved fragment of Par-4 (cl-Par-4) is active and plays a role in tumor suppression by inhibiting cell survival pathways. Here, we employed site-directed mutagenesis to create a cl-Par-4 point mutant (D313K). The expressed and purified D313K protein was characterized using biophysical techniques, and the results were compared to that of the wild-type (WT). We have …

Reduced Metal Nanocatalysts For Selective Electrochemical Hydrogenation Of Biomass-Derived 5-(Hydroxymethyl)Furfural To 2, 5-Bis(Hydroxymethyl)Furan In Ambient Conditions, Baleeswaraiah Muchharla, Moumita Dikshit, Ujjwal Pokharel, Ravindranath Garimella, Adetayo Adedeji, Kapil Kumar, Wei Cao, Hani Elsayed-Ali, Kishor Kumar Sadasivuni, Naif Abdullah Al-Dhabi, Sandeep Kumar, Bijandra Kumar

Chemistry & Biochemistry Faculty Publications

Selective electrochemical hydrogenation (ECH) of biomass-derived unsaturated organic molecules has enormous potential for sustainable chemical production. However, an efficient catalyst is essential to perform an ECH reaction consisting of superior product selectivity and a higher conversion rate. Here, we examined the ECH performance of reduced metal nanostructures i.e., reduced Ag (rAg) and reduced copper (rCu) prepared via electrochemical or thermal oxidation and electrochemical reduction process, respectively. Surface morphological analysis suggests formation of nanocoral and entangled nanowire structure formation for rAg and rCu catalysts. rCu exhibits slight enhancement in ECH reaction performance in comparison to the pristine Cu. However, the rAg …

Thermotrophy Exploratory Study, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

The question of whether environmental heat energy could be utilized as a source of energy for biological metabolism is the center of this exploratory research. In 1979, this author postulated a hypothesis for the existence of thermotrophs that could isothermally utilize environmental heat energy as a source of their energy on Earth. According to this hypothesis, the thermotrophs could be the first primitive forms of life in the early Earth environment. The chemotrophs and phototrophs that we currently are all well familiar with might have been evolved somehow from the primitive thermotrophs. Furthermore, all the organisms currently regarded as the …

Halogen Bonding Interactions Of Haloaromatic Endocrine Disruptors And The Potential For Inhibition Of Iodothyronine Deiodinases, Craig A. Bayse

Chemistry & Biochemistry Faculty Publications

Halogen bonding (XB) is a potential mechanism for the inhibition of the thyroid-activating/deactivating iodothyronine deiodinase family of selenoproteins through interactions with halogenated endocrine disrupting compounds (EDCs). Trends in XB interactions were examined using density functional theory for a series of polyhalogenated dibenzo-1,4-dioxins, biphenyls, and other EDCs with methylselenolate, a simple model of the Dio active site selenocysteine. The strengths of the interactions depend upon the halogen (Br>Cl), the degree of substitution, and the position of the acceptor. In terms of donor-acceptor energies, interactions at the meta position are often the strongest, suggesting a link to the topology of THs, …

Synthesis And Self-Assembling Properties Of Carbohydrate- And Diarylethene-Based Photoswitchable Molecular Gelators, Pramod Aryal, Joedian Morris, Surya B. Adhikari, Jonathan Bietsch, Guijun Wang

Chemistry & Biochemistry Faculty Publications

Carbohydrate-based low-molecular-weight gelators are interesting new materials with many potential applications. These compounds can be designed to include multiple stimuli-responsive functional groups. In this study, we designed and synthesized several chemically responsive bola-glycolipids and dimeric carbohydrate- and diarylethene-based photoswitchable derivatives. The dimeric glycolipids formed stable gels in a variety of solvent systems. The best performing gelators in this series contained decanedioic and dithienylethene (DTE) spacers, which formed gels in eight and nine of the tested solvents, respectively. The two new DTE-containing esters possessed interesting photoswitching properties and DTE derivative 7 was found to have versatile gelation properties in many solvents, …

Extracting High-Molecular Weight Dna From Cyanobacteria Using Promega's Wizard® Hmw Dna Extraction Kit With A Modified Protocol, Metis, Megan A. Hept, Lesley H. Greene

Chemistry & Biochemistry Faculty Publications

Extraction of high molecular weight (HMW) DNA for long read sequencing with little to no fragmentation and high purity is difficult to acquire from cyanobacterial species. Here we describe a modified method of extraction using Promega's Wizard® HMW DNA Extraction Kit to acquire high molecular weight DNA from cyanobacterial species. The protocol used in the kit is the “3.D. Isolating HMW DNA from Gram-Positive and Gram-Negative Bacteria” protocol. During a key step in the protocol, the lingering remnants of the mucilage layer of the cyanobacterial species is removed, preventing it from sticking to the DNA pellet produced. This customized modification …

S-Type Stars: Line List For The A²Π-X²Σ⁺ Band System Of Lao, P. F. Bernath, R. Dodangodage, J. Liévin

Chemistry & Biochemistry Faculty Publications

LaO bands are found in the spectra of cool S-type stars. The bands of the A²Π–X²Σ⁺ transition with v' ⩽ 3 and v'' ≤ 4 are rotationally analyzed, providing spectroscopic constants for the A²Π state. Line strengths are calculated using an ab initio transition dipole moment function, and radiative lifetimes for the A²Π state have also been computed. A line list for the A²Π–X²Σ⁺ transition of LaO is provided and can be used to determine LaO stellar abundances.

Telp Theory: Elucidating The Major Observations Of Rieger Et Al. 2021 In Mitochondria, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

The transmembrane-electrostatically localized protons (TELP) theory may represent a complementary development to Mitchell's chemiosmotic theory. The combination of the two together can now excellently explain the energetics in mitochondria. Our calculated transmembrane-attractive force between an excess proton and an excess hydroxide explains how TELP may stay within a 1-nm thin layer at the liquid-membrane interface. Consequently, any pH sensor (sEcGFP) located at least 2–3 nm away from the membrane surface will not be able to see TELP. This feature as predicted from the TELP model was observed exactly in the experiment of Rieger et al., 2021. In contrast to their …

Expanding Our Grasp Of Two-Component Signaling In Clostridioides Difficile, Orlando Berumen Alvarez, Erin B. Purcell

Chemistry & Biochemistry Faculty Publications

The intestinal pathogen Clostridioides difficile encodes roughly 50 TCS, but very few have been characterized in terms of their activating signals or their regulatory roles. A. G. Pannullo, B. R. Zbylicki, and C. D. Ellermeier (J Bacteriol 205:e00164-23, 2023, https://doi.org/10.1128/jb.00164-23) have identified both for the novel C. difficile TCD DraRS. DraRS responds to antibiotics that target lipid-II molecules in the bacterial cell envelope, and regulates the production of a novel glycolipid necessary for bacitracin and daptomycin resistance in C. difficile.

On The Chronological Understanding Of The Homogeneous Dielectric Barrier Discharge, Xinpei Lu, Zhi Fang, Dong Dai, Tao Shao, Feng Liu, Cheng Zhang, Dawei Liu, Lanlan Nie, Chunqi Jiang

Bioelectrics Publications

Dielectric barrier discharges (DBD) are widely utilised non-equilibrium atmospheric pressure plasmas with a diverse range of applications, such as material processing, surface treatment, light sources, pollution control, and medicine. Over the course of several decades, extensive research has been dedicated to the generation of homogeneous DBD (H-DBD), focussing on understanding the transition from H-DBD to filamentary DBD and exploring strategies to create and sustain H-DBD. This paper first discusses the influence of various parameters on DBD, including gas flow, dielectric material, surface conductivity, and mesh electrode. Secondly, a chronological literature review is presented, highlighting the development of H-DBD and the …

The Post-Shock Nonequilibrium Relaxation In A Hypersonic Plasma Flow Involving Reflection Off A Thermal Discontinuity, Anna Markhotok

Physics Faculty Publications

The evolution in the post shock nonequilibrium relaxation in a hypersonic plasma flow was investigated during a shock’s reflection off a thermal discontinuity. Within a transitional period, the relaxation zone parameters past both, the reflected and transmitted waves, evolve differently compared to that in the incident wave. In a numerical example for the non-dissociating N₂ gas heated to 5000 K/10,000 K across the interface and M = 3.5, the relaxation time for the transmitted wave is up to 50% shorter and the relaxation depth for both waves is significantly reduced, thus resulting in a weakened wave structure. The …

Basics Of Factorization In A Scalar Yukawa Field Theory, F. Aslan, L. Gamberg, J.O. Gonzalez-Hernandez, T. Rainaldi, T. C. Rogers

Physics Faculty Publications

The factorization theorems of QCD apply equally well to most simple quantum field theories that require renormalization but where direct calculations are much more straightforward. Working with these simpler theories is convenient for stress testing the limits of the factorization program and for examining general properties of the parton density functions or other correlation functions that might be necessary for a factorized description of a process. With this view in mind, we review the steps of factorization in a real scalar Yukawa field theory for both deep inelastic scattering and semi-inclusive deep inelastic scattering cross sections. In the case of …

Observation Of Large Missing-Momentum (E, E' P) Cross-Section Scaling And The Onset Of Correlated-Pair Dominance In Nuclei, I. Korover, A. W. Denniston, A. Kiral, A. Schmidt, A. Lovato, N. Rocco, A. Nikolakopoulos, L. B. Weinstein, E. Piasetzky, O. Hen, M. J. Amaryan, Giovanni Angelini, H. Atac, N. A. Baltzell, L. Barion, M. Battaglieri, I. Bedlinskiy, Fatiha Benmokhtar, A. Bianconi, Z. W. Zhao, Et Al., Clas Collaboration

Physics Faculty Publications

We report the measurement of 𝒙_B scaling in (e,e′p) cross-section ratios off nuclei relative to deuterium at large missing momentum of 350 ≤ _Pmiss ≤ 600 MeV/c. The observed scaling extends over a kinematic range of 0.7 ≤ 𝒙_B ≤ 1.8, which is significantly wider than 1.4 ≤ 𝒙_B ≤ 1.8 previously observed for inclusive (e,e′) cross-section ratios. The 𝒙_B-integrated cross-section ratios become constant (i.e., scale) beginning at p_miss ≈ kF, the nuclear Fermi momentum. Comparing with theoretical calculations we find good agreement with generalized contact formalism calculations for high missing …

Nuclear Magnetic Quadrupole Moment Of ¹⁷⁵Lu And Parity-Violating Polarization Degree Of Levels In ¹⁷⁵Luoh⁺, Igor Kurchavov, Daniel Maison, Leonid Skripnikov, Matt Grau, Alexander Petrov

Physics Faculty Publications

A calculation is performed of the parity-violating polarizations in the external electric field, which are associated with the electron electric dipole moment (eEDM) and magnetic quadrupole moment (MQM) of the ¹⁷⁵Lu nucleus, as well as the determination of the rovibrational structure for the ¹⁷⁵LuOH⁺ cation. Beyond the bending of the molecule, the slight effect of the stretching of the distance between Lu and OH is taken into account. This study is required for the preparation of the experiment and for the extraction of the eEDM and MQM values of ¹⁷⁵Lu from future measurements.

Liouvillian Dynamics Of The Open Schwinger Model: String Breaking And Kinetic Dissipation In A Thermal Medium, Kyle Lee, James Mulligan, Felix Ringer, Xiaojun Yao

Physics Faculty Publications

Understanding the dynamics of bound state formation is one of the fundamental questions in confining quantum field theories such as Quantum Chromodynamics (QCD). One hadronization mechanism that has garnered significant attention is the breaking of a string initially connecting a fermion and an antifermion. Deepening our understanding of real-time string-breaking dynamics with simpler, lower dimensional models like the Schwinger model can improve our understanding of the hadronization process in QCD and other confining systems found in condensed matter and statistical systems. In this paper, we consider the string-breaking dynamics within the Schwinger model and investigate its modification inside a thermal …

Machine-Assisted Discovery Of Integrable Symplectic Mappings, T. Zolkin, Y. Kharkov, S. Nagaitsev

Physics Faculty Publications

We present a new automated method for finding integrable symplectic maps of the plane. These dynamical systems possess a hidden symmetry associated with an existence of conserved quantities, i.e., integrals of motion. The core idea of the algorithm is based on the knowledge that the evolution of an integrable system in the phase space is restricted to a lower-dimensional submanifold. Limiting ourselves to polygon invariants of motion, we analyze the shape of individual trajectories thus successfully distinguishing integrable motion from chaotic cases. For example, our method rediscovers some of the famous McMillan-Suris integrable mappings and ultradiscrete Painlevé equations. In total, …

A User-Centered Mapping Design For Geomorphological Hazard Thematic Map, Su-Min Shen, Yin-Hsuen Chen, Chia-Ming Lo, Mu-Ti Yu, Si-Chin Lin, Sendo Wang, Chih-Hsin Chang, Sheng-Chi Lin

University Administration Publications

Numerous studies have concentrated on developing user-centered designs for hazard zone maps but rarely for hazard-oriented geomorphological maps, named as Geomorphological Hazard Thematic Maps (GHTMs) in this study, which provide more detailed information about natural hazards. This study developed a user-centered mapping design for GHTMs for nonexperts in geomorphology. We invited civil engineers and high school educators to evaluate a sample GHTM's design in group and focus group panel interviews. The civil engineers preferred maps with more geomorphological features, whereas the educators preferred simple designs. Both groups indicated that the inclusion of essential facilities and road networks is essential. The …

An Optimized And Scalable Blockchain-Based Distributed Learning Platform For Consumer Iot, Zhaocheng Wang, Xueying Liu, Xinming Shao, Abdullah Alghamdi, Md. Shirajum Munir, Sujit Biswas

School of Cybersecurity Faculty Publications

Consumer Internet of Things (CIoT) manufacturers seek customer feedback to enhance their products and services, creating a smart ecosystem, like a smart home. Due to security and privacy concerns, blockchain-based federated learning (BCFL) ecosystems can let CIoT manufacturers update their machine learning (ML) models using end-user data. Federated learning (FL) uses privacy-preserving ML techniques to forecast customers' needs and consumption habits, and blockchain replaces the centralized aggregator to safeguard the ecosystem. However, blockchain technology (BCT) struggles with scalability and quick ledger expansion. In BCFL, local model generation and secure aggregation are other issues. This research introduces a novel architecture, emphasizing …