Digital Commons Network^™

A Framework To Validate Fluorescently Labeled Dna-Binding Proteins For Single-Molecule Experiments, Miranda Molina, Lindsey E. Way, Zhongqing Ren, Qin Liao, Bianca Guerra, Brandon Shields, Xindan Wang, Hyeongjun Kim

Physics & Astronomy Faculty Publications

Highlights

• KCK tag can alter protein properties both quantitatively and qualitatively

• Electrostatic interactions between the KCK tag and DNA contribute to the artifacts

• Adding a short peptide tag to ParB protein does not lead to its in vivo changes

• Single-molecule DNA flow-stretching assay can detect protein property changes

Motivation

Single-molecule fluorescence microscopy has been extensively used in modern biology to define the molecular action of proteins. Appending short peptide tags is a common strategy to enhance fluorescence labeling. Here, we evaluate the impact of a commonly used tag, the lysine-cysteine-lysine (KCK) tag, on protein behavior in single-molecule DNA flow-stretching assay, …

Nutritional Challenges Of Substituting Farmed Animals For Wild Fish In Human Diets, Sebastian A. Heilpern, Rafael M. Almeida, Kathryn J. Fiorella, Alexander S. Flecker, Demetra Williams, Peter B. Mcintyre

School of Earth, Environmental, & Marine Sciences Faculty Publications

Wild fisheries provide billions of people with a key source of multiple essential nutrients. As fisheries plateau or decline, nourishing more people will partially rely on shifting consumption to farmed animals. The environmental implications of transitions among animal-sourced foods have been scrutinized, but their nutritional substitutability remains unclear. We compared concentrations of six essential dietary nutrients across >5000 species of wild fishes, aquaculture, poultry and livestock species, representing >65% of animals consumed globally. Wild fishes are both more nutrient-dense and variable than farmed animals; achieving recommended intake of all nutrients with farmed species could require consuming almost four times more …

Fast-Askap Synergy: Quantifying Coexistent Tidal And Ram Pressure Strippings In The Ngc 4636 Group, Xuchen Lin, Jing Wang, Virginia Kilborn, Eric W. Peng, Luca Cortese, Alessandro Boselli, Ze-Zhong Liang, Bumhyun Lee, Dong Yang, Juan P. Madrid

Physics & Astronomy Faculty Publications

Combining new H I data from a synergetic survey of Australian Square Kilometre Array Pathfinder (ASKAP) Widefield ASKAP L-band Legacy All-sky Blind surveY and Five-hundred-meter Aperture Spherical radio Telescope with the Arecibo Legacy Fast ALFA data, we study the effect of ram pressure and tidal interactions in the NGC 4636 group. We develop two parameters to quantify and disentangle these two effects on gas stripping in H I-bearing galaxies: the strength of external forces at the optical-disk edge, and the outside-in extents of H I-disk stripping. We find that gas stripping is widespread in this group, affecting 80% of H …

On The Vanishing Of The Coefficients Of Cm Eta Quotients, Timothy Huber, Chang Liu, James Mclaughlin, Dongxi Ye, Miaodan Yuan, Sumeng Zhang

School of Mathematical & Statistical Sciences Faculty Publications

This work characterizes the vanishing of the Fourier coefficients of all CM (Complex Multiplication) eta quotients. As consequences, we recover Serre’s characterization about that of η(12z)2 and recent results of Chang on the pth coefficients of η(4z)6 and η(6z)4 . Moreover, we generalize the results on the cases of weight 1 to the setting of binary quadratic forms.

Investigation Of The Effective Parameters On The Phenol Removal From The Groundwater By Response Surface Method, Khatereh Ahmadi, Farhad Qaderi, S. Mustapha Rahmaninezhad, Reza Shidpour

Civil Engineering Faculty Publications

The discharge of industrial waste containing organic pollutants like phenol has caused a surge in environmental complications in water, soil, and air. In recent years, the concentration of phenolic pollutants has risen due to their high toxicity and environmental persistence. This research used geotextile/activated carbon (GTX/AC) adsorbent to purify groundwater contaminated with phenol, owing to its easy availability. A low-cost geotextile carrier was utilized to avoid the dispersion of active carbon in the groundwater. Response surface method (RSM) was used in the present research to design and optimize experimental tests. The results indicate that the initial concentration, pH, and adsorbent …

Poster: No Fly-Zone: Drone Policies For Ensuring Safe Operations In Restricted Areas, Arturo Gonzalez, Amani Davidson, Carlos Rubio-Medrano

Computer Science Faculty Publications

As the use of drones continues to proliferate across various industries, ensuring their safe and secure operation becomes increasingly important. This abstract explores the techniques and strategies employed for drone identification and communication, aiming to enhance safety, security, and compliance. The paper highlights the significance of reliable drone recognition methods and effective communication protocols between drones and relevant parties. Specifically, it emphasizes the need for drones to adapt to restrictions, follow protocols, and communicate information in designated zones. Furthermore, the abstract emphasizes the importance of strict adherence to no-fly rules, precise identification of restricted airspace, and the establishment of robust …

Sublinear Time Motif Discovery From Multiple Sequences, Bin Fu, Yunhui Fu, Yuan Xue

Computer Science Faculty Publications

In this paper, a natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are k background sequences, and each character in a background sequence is a random character from an alphabet, Σ. A motif G = g1g2 . . . gm is a string of m characters. In each background sequence is implanted a probabilistically-generated approximate copy of G. For a probabilistically-generated approximate copy b1b2 . . . bm of G, every character, bi , is probabilistically generated, such that the probability for bi 6= gi is …

Use And Effectiveness Of Wildlife Exits Designed For Ocelots And Other Mesocarnivores On A South Texas Highway, Zarina N. Sheikh, Jamie E. Langbein, Kevin W. Ryer, Md Saydur Rahman, Christopher A. Gabler, John H. Young Jr., Richard Kline

School of Earth, Environmental, & Marine Sciences Faculty Publications

Movement is a key component of survival and reproduction, often causing wildlife to cross heavily trafficked highways, resulting in road mortalities by oncoming vehicles. Fencing and crossing structures are commonly regarded as effective mitigation structures to reduce these mortalities. In south Texas, ten wildlife exits (WE) were installed along State Highway 100 in conjunction with existing mitigation structures to provide the US endangered ocelot (Leopardus pardalis), a medium-sized spotted wild cat, a safe option to escape the right of way (ROW). The objectives of this study were to determine the effectiveness and species usage and to estimate the …

Widespread Dominance Of Methane Ebullition Over Diffusion In Freshwater Aquaculture Ponds, Renske J. E. Vroom, Sarian Kosten, Rafael M. Almeida, Raquel Mendonça, Ive S. Muzitano, Icaro Barbosa, Jonas Nasário, Ernandes S. Oliveira Junior, Alexander S. Flecker, Nathan Barros

School of Earth, Environmental, & Marine Sciences Faculty Publications

An ever-increasing demand for protein-rich food sources combined with dwindling wild fish stocks has caused the aquaculture sector to boom in the last two decades. Although fishponds are potentially strong emitters of the greenhouse gas methane (CH₄), little is known about the magnitude, pathways, and drivers of these emissions. We measured diffusive CH₄ emissions at the margin and in the center of 52 freshwater fishponds in Brazil. In a subset of ponds (n = 31) we additionally quantified ebullitive CH₄ fluxes and sampled water and sediment for biogeochemical analyses. Sediments (n = 20) were …

Explainable Machine Learning Reveals The Relationship Between Hearing Thresholds And Speech-In-Noise Recognition In Listeners With Normal Audiograms, Jithin Raj Balan, Hansapani Rodrigo, Udit Saxena, Srikanta K. Mishra

School of Mathematical & Statistical Sciences Faculty Publications

Some individuals complain of listening-in-noise difficulty despite having a normal audiogram. In this study, machine learning is applied to examine the extent to which hearing thresholds can predict speech-in-noise recognition among normal-hearing individuals. The specific goals were to (1) compare the performance of one standard (GAM, generalized additive model) and four machine learning models (ANN, artificial neural network; DNN, deep neural network; RF, random forest; XGBoost; eXtreme gradient boosting), and (2) examine the relative contribution of individual audiometric frequencies and demographic variables in predicting speech-in-noise recognition. Archival data included thresholds (0.25–16 kHz) and speech recognition thresholds (SRTs) from listeners with …

The Accumulation And Growth Of Pseudomonas Aeruginosa On Surfaces Is Modulated By Surface Mechanics Via Cyclic-Di-Gmp Signaling, Liyun Wang, Yu-Chern Wong, Joshua M. Correira, Megan Wancura, Chris J. Geiger, Shanice S. Webster, Ahmed Touhami, Benjamin J. Butler, George A. O’Toole, Richard M. Langford

Physics & Astronomy Faculty Publications

Attachment of bacteria onto a surface, consequent signaling, and accumulation and growth of the surface-bound bacterial population are key initial steps in the formation of pathogenic biofilms. While recent reports have hinted that surface mechanics may affect the accumulation of bacteria on that surface, the processes that underlie bacterial perception of surface mechanics and modulation of accumulation in response to surface mechanics remain largely unknown. We use thin and thick hydrogels coated on glass to create composite materials with different mechanics (higher elasticity for thin composites; lower elasticity for thick composites) but with the same surface adhesivity and chemistry. The …

Adjusting For Berkson Error In Exposure In Ordinary And Conditional Logistic Regression And In Poisson Regression, Tamer Oraby, Santanu Chakraborty, Siva Sivaganesan, Laurel Kincl, Lesley Richardson, Mary Mcbride, Jack Siemiatycki, Elisabeth Cardis, Daniel Krewski

School of Mathematical & Statistical Sciences Faculty Publications

Background

INTEROCC is a seven-country cohort study of occupational exposures and brain cancer risk, including occupational exposure to electromagnetic fields (EMF). In the absence of data on individual exposures, a Job Exposure Matrix (JEM) may be used to construct likely exposure scenarios in occupational settings. This tool was constructed using statistical summaries of exposure to EMF for various occupational categories for a comparable group of workers.

Methods

In this study, we use the Canadian data from INTEROCC to determine the best EMF exposure surrogate/estimate from three appropriately chosen surrogates from the JEM, along with a fourth surrogate based on Berkson …

The Rider (2023-10-09), Natalie Lapsley

The Rider Archives

Vol.9 No.7

Trauma Center Designation Effects On Clinical Outcomes In Pediatric Dog Bites: A Retrospective Study, Jessy Feng, Sabrina Orta, Alejandro Aquino, Lori Berry, Demba Fofana, Paul Berry

Research Colloquium

Introduction: Clinical outcomes associated with the American College of Surgeons (ACS) trauma center designation have been examined for many conditions. However, we sought to analyze the association between ACS pediatric trauma center designation and outcomes following pediatric dog bite trauma cases, which has rarely been studied.

Methods: The National Trauma Data Bank was queried to identify pediatric (0-19y) dog bite trauma patients admitted to ACS pediatric level I or II trauma centers from 2007-2016. Chi-Squared and Odds Ratio statistical analyses were used to compare the outcomes.

Results:We identified 6,196 pediatric dog bite trauma patients treated at ACS level …

Exploring High School Students’ Careless Or Insufficient Effort Survey Responses When Investigating Attitudes Toward Mathematics, Xiaohui Wang, Mayra Ortiz Galarza, Sergey Grigorian, Aaron T. Wilson, John Knight

School of Mathematical & Statistical Sciences Faculty Publications

A modified, bilingual Attitudes Toward Mathematics Inventory (ATMI) instrument was administered to 1,258 high school students in South Texas in an NSF-funded project on informal learning of mathematics and near peer mentoring. We explore students’ survey response behaviors and examine the existence of careless and insufficient effort (CIE) responses. This is empirical research for handling the challenge of CIE responses that leads to improved survey data quality, thus eventually validating the intervention effect of the mathematical informal learning project.

Rogue Waves And Their Patterns In The Vector Nonlinear Schrödinger Equation, Guangxiong Zhang, Peng Huang, Bao-Feng Feng, Chengfa Wu

School of Mathematical & Statistical Sciences Faculty Publications

In this paper, we study the general rogue wave solutions and their patterns in the vector (or M-component) nonlinear Schrödinger (NLS) equation. By applying the Kadomtsev–Petviashvili reduction method, we derive an explicit solution for the rogue wave expressed by τ functions that are determinants of K × K block matrices ( 1 ≤ K ≤ M ) with an index jump of M + 1 . Patterns of the rogue waves for M = 3 , 4 and K = 1 are thoroughly investigated. It is found that when one of the internal parameters is large enough, the wave pattern …

A Review On Antibacterial Activity Of Nanoparticles, Badr-Edine Sadoq, Mohammed Reda Britel, Adel Bouajaj, Ramzi Maâlej, Ahmed Touhami, Marwa Abid, Hanen Douiri, Fakhita Touhami, Amal Maurady

Physics & Astronomy Faculty Publications

The increasing resistance of bacteria to antibiotic agents is a main global public health problem. The use of nanoparticles is one of the promising ways to overcome microbial resistance to antimicrobial agents. Metal nanoparticles are increasingly used to target bacterial strains. Advances in nanotechnology, in particular the ability to synthesize nanoparticles of specific size and shape, are likely to lead to the development of new antibacterial agents. The antibacterial activities of nanoparticles are largely influenced by their sizes and large surface area/mass ratio. The antibacterial mechanisms of nanoparticles are poorly understood, but the currently accepted mechanisms include oxidative stress induction, …

Rubin Observatory Lsst Transients And Variable Stars Roadmap, Kelly M. Hambleton, Federica B. Bianco, Rachel Street, Keaton Bell, David Buckley, Melissa Graham, Nina Hernitschek, Michael B. Lund, Elena Mason, Liliana Rivera Sandoval

Physics & Astronomy Faculty Publications

The Vera C. Rubin Legacy Survey of Space and Time (LSST) holds the potential to revolutionize time domain astrophysics, reaching completely unexplored areas of the Universe and mapping variability time scales from minutes to a decade. To prepare to maximize the potential of the Rubin LSST data for the exploration of the transient and variable Universe, one of the four pillars of Rubin LSST science, the Transient and Variable Stars Science Collaboration, one of the eight Rubin LSST Science Collaborations, has identified research areas of interest and requirements, and paths to enable them. While our roadmap is ever-evolving, this document …

Conformational Landscapes Of Symmetrically Fluorine-Substituted Benzoic Acids Ii: Calculations And Measurements For The Rotational Spectrum And Structure Of 3,4,5-Trifluorobenzoic Acid, Jingling Hong, Alitza Gracia, Savannah Romero, Mingfei Zhou, Wei Lin, Weixing Li

Physics & Astronomy Faculty Publications

Calculations on the structure of 3,4,5-trifluorobenzoic acid were made using the Gaussian 16 program. The potential energy surfaces were scanned along CCCO and OCOH dihedral angles at the B3LYP/6-311G level to analyze its conformational landscape. Two conformations were identified and reoptimized at the B3LYP/aug-cc-pVTZ level. The result indicates that 3,4,5-trifluorobenzoic acid prefers a planar structure in its global minimum conformation. The pure rotational spectra of 3,4,5-trifluorobenzoic acid were measured in the frequency range of 6 – 12.5 GHz using a chirped pulse Fourier transform microwave (CP-FTMW) spectrometer. The spectra of the parent, seven 13C, and one deuterium singly substituted isotopologues …

Figured Worlds Of Women Mathematics Education Scholars, Lili Zhou, Ricki L. Geller-Mckee, Brooke Max, Hyunyi Jung, Bima Sapkota, Jill Newton, Lindsay M. Keazer

School of Mathematical & Statistical Sciences Faculty Publications

Drawing on the concept of figured worlds (Holland et al., 1998), this project focuses on addressing, responding to, and understanding the self within the figured world of the mathematics education community. Specifically, we examine a group of women with diverse backgrounds in terms of race, class, and cultural contexts, who are engaged in various roles as mathematics education scholars, including teachers, teacher educators, and researchers. Using a dialogical self approach, we facilitate both internal and external discourses, exploring personal histories, narratives, and the development of evolving identities. Our findings reveal that culture and social positions, such as gender, class, and …

Convergence Of The Two-Point Modulus-Based Matrix Splitting Iteration Method, Ximing Fang, Ze Gu, Zhijun Qiao

School of Mathematical & Statistical Sciences Faculty Publications

In this paper, we discuss the convergence of the two-point modulus-based matrix splitting iteration method for solving the linear complementarity problem. Some convergence conditions are presented from the spectral radius and the matrix norm when the system matrix is a -matrix. Besides, the quasi-optimal cases of the method are studied. Numerical experiments are provided to show the presented results.

Elementary Mathematics Curriculum: State Policy, Covid-19, And Teachers’ Control, Mona Baniahmadi, Bima Sapkota, Amy M. Olson

School of Mathematical & Statistical Sciences Faculty Publications

In the U.S., state guidance to schools in response to the COVID-19 pandemic was politicized. We used state-level political affiliation to explore whether access to curricular resources differed pre-pandemic or during pandemic remote teaching and teachers' reported control over curricular resources during pandemic teaching. We found that pre-pandemic the percentage of teachers in Republican states reported higher levels of resources overall, and use of core and teacher-created curricular resources in particular. They also reported having greater control over their curricular decision-making during the pandemic. There were no state-level differences in teachers’ level of preparation for pandemic teaching, but teachers in …

Conformational Landscapes Of Symmetrically Fluorine-Substituted Benzoic Acids I: Microwave Spectroscopic And Theoretical Studies On 3,5-Difluorobenzoic Acid, Alitza Gracia, Jingling Hong, Rebakah Arismendi, Mingfei Zhou, Weixing Li, Wei Lin

Physics & Astronomy Faculty Publications

We report our combined theoretical and spectroscopic studies on 3,5-difluorobenzoic acid. Using a chirped pulse Fourier transform microwave (CP-FTMW) spectrometer, we recorded and analyzed the rotational spectrum spanning the frequency range of 6 – 12.5 GHz. Quantum chemical calculations were employed to analyze the conformational changes and landscapes of 3,5-difluorobenzoic acid. These calculations focused on studying the potential energy surfaces along the CCCO and OCOH dihedral angles at the B3LYP/6-311G level. Based on the computational results, we identified the global minimum conformer 1 as well as the local minimum conformer 2. We discussed and interpreted the geometric structures of the …

Rogue Waves In The Massive Thirring Model, Junchao Chen, Bo Yang, Bao-Feng Feng

School of Mathematical & Statistical Sciences Faculty Publications

In this paper, general rogue wave solutions in the massive Thirring (MT) model are derived by using the Kadomtsev–Petviashvili (KP) hierarchy reduction method and these rational solutions are presented explicitly in terms of determinants whose matrix elements are elementary Schur polynomials. In the reduction process, three reduction conditions including one index- and two dimension-ones are proved to be consistent by only one constraint relation on parameters of tau-functions of the KP-Toda hierarchy. It is found that the rogue wave solutions in the MT model depend on two background parameters, which influence their orientation and duration. Differing from many other coupled …

Complexity Of Reconfiguration In Surface Chemical Reaction Networks, Robert M. Alaniz, Josh Brunner, Michael Coulombe, Erik D. Demaine, Yevhenii Diomidov, Ryan Knobel, Timothy Gomez, Elise Grizzell, Jayson Lynch, Andrew Rodriguez, Robert Schweller, Tim Wylie

Computer Science Faculty Publications

We analyze the computational complexity of basic reconfiguration problems for the recently introduced surface Chemical Reaction Networks (sCRNs), where ordered pairs of adjacent species nondeterministically transform into a different ordered pair of species according to a predefined set of allowed transition rules (chemical reactions). In particular, two questions that are fundamental to the simulation of sCRNs are whether a given configuration of molecules can ever transform into another given configuration, and whether a given cell can ever contain a given species, given a set of transition rules. We show that these problems can be solved in polynomial time, are NP-complete, …

Semidefinite Programming Bounds For Distance Distribution Of Spherical Codes, Oleg R. Musin

School of Mathematical & Statistical Sciences Faculty Publications

We present an extension of known semidefinite and linear programming upper bounds for spherical codes. We apply the main result for the distance distribution of a spherical code and show that this method can work effectively In particular, we get a shorter solution to the kissing number problem in dimension 4.

Search For Subsolar-Mass Black Hole Binaries In The Second Part Of Advanced Ligo’S And Advanced Virgo’S Third Observing Run, R. Abbott, H. Abe, F. Acernese, Teviet Creighton, Mario C. Diaz, Francisco Llamas, Soma Mukherjee, Gaukhar Nurbek, Volker Quetschke, Wenhui Wang

Physics & Astronomy Faculty Publications

We describe a search for gravitational waves from compact binaries with at least one component with mass 0.2 –1.0M⊙ and mass ratio q ≥ 0.1 in Advanced Laser Interferometer Gravitational-Wave Observatory (LIGO) and Advanced Virgo data collected between 2019 November 1, 15:00 UTC and 2020 March 27, 17:00 UTC. No signals were detected. The most significant candidate has a false alarm rate of 0.2yr−1 ⁠. We estimate the sensitivity of our search over the entirety of Advanced LIGO’s and Advanced Virgo’s third observing run, and present the most stringent limits to date on the merger rate of binary black holes …

Effect Of Room Size, Shape, Ac Placement, And Air Leakage On Indoor Airborne Viral Transmission, K. Choudhary, K. A. Krishnaprasad, ‪Nadim Zgheib, M. Y. Ha, S. Balachandar

Mechanical Engineering Faculty Publications

Highlights

• Statistical overloading is used to obtain spatio-temporal pathogen concentration.

• Symmetrically placed AC limits pathogen propagation over long distances.

• Well-mixed model captures room-averaged concentration for any shape and AC location.

• The pathogens level of mixing is reduced when AC is symmetrically positioned.

• Air leakage has insignificant impact on indoor pathogen distribution.

Abstract

We conducted Euler–Lagrange Reynolds-Averaged Navier–Stokes simulations with statistical overloading to investigate the effect of room shape, air-condition (AC) location, and the presence of an open window on indoor airborne viral transmission, particularly as it relates to the spatio-temporal distribution of viral-laden droplet nuclei. Two room geometries were …

Thermal Dose Inactivation Of Escherichia Coli By Magnetic Induced Hyperthermia, Silverio A. Lopez, Carlos Trevino De Leo, Ivan Davila, Karen S. Martirosyan

Research Symposium

Background: Apoptosis of mutated cells via magnetic hyperthermia has gained advocacy as technology capable of being used in lieu of chemotherapy for targeting cancer tumors. Progress of nanotechnology offers effective remote heating of magnetic fluid via hyperthermia. The heating and specific power absorption of these nanoparticles use in the magnetic fluid are dependent on particle properties and treatment locations.

Methods: Nanoparticles were fabricated using microfluidic system by interaction of two solutions containing 2Fe(NO3)3+FeSO4 and NaOH+2%Dextran to create nanostructured media with a biocompatible dextran coating and a Fe3O4 core. The nanoparticles, of a concentration of 5mg/ml, were placed in a vile …

Precise Method To Identify Kinase Drug Targets In Complex Diseases: The First Step Towards Sustainable And Effective Treatment, Hasbanny Irisson, Marzieh Ayati

Research Symposium

Background: Kinases are enzymes that have proven to be important drug targets due to their role in critical biological mechanisms such as phosphorylation. Phosphorylation happens when a kinase catalyzes the transfer of a phosphate group to a protein in a phosphorylated site, which then becomes known as the substrate of the kinase. Any dysregulation of protein phosphorylation causes a wide range of complex diseases including cancer. Thus, discovering the links between kinases and their substrates (i.e. predicting kinase-substrate associations (KSAs)) is crucial in developing effective and sustainable treatments. Presently, less than 5% of phosphorylated sites have an associated kinase, and …