Physical Sciences and Mathematics Commons^™

Individual Based Modeling And Analysis Of Pathogen Levels In Poultry Chilling Process, Zachary Mccarthy, Ben Smith, Aamir Fazil, Jianhong Wu, Shawn D. Ryan, Daniel Munther

Mathematics and Statistics Faculty Publications

Pathogen control during poultry processing critically depends on more enhanced insight into contamination dynamics. In this study we build an individual based model (IBM) of the chilling process. Quantifying the relationships between typical Canadian processing specifications, water chemistry dynamics and pathogen levels both in the chiller water and on individual carcasses, the IBM is shown to provide a useful tool for risk management as it can inform risk assessment models. We apply the IBM to Campylobacter spp. contamination on broiler carcasses, illustrating how free chlorine (FC) sanitization, organic load in the water, and pre-chill carcass pathogen levels affect pathogen levels …

Barth Syndrome: Exploring Cardiac Metabolism With Induced Pluripotent Stem Cell-Derived Cardiomyocytes, Erica M. Fatica, Gina A. Deleonibus, Alisha House, Jillian V. Kodger, Ryan W. Pearce, Rohan R. Shah, Liraz Levi, Yana Sandlers

Chemistry Faculty Publications

© 2019 by the authors. Licensee MDPI, Basel, Switzerland. Barth syndrome (BTHS) is an X-linked recessive multisystem disorder caused by mutations in the TAZ gene (TAZ, G 4.5, OMIM 300394) that encodes for the acyltransferase tafazzin. This protein is highly expressed in the heart and plays a significant role in cardiolipin biosynthesis. Heart disease is the major clinical manifestation of BTHS with a high incidence in early life. Although the genetic basis of BTHS and tetralinoleoyl cardiolipin deficiency in BTHS-affected individuals are well-established, downstream metabolic changes in cardiac metabolism are still uncovered. Our study aimed to characterize TAZ-induced metabolic perturbations …

On Vibration Suppression And Trajectory Tracking In Largely Uncertain Torsional System: An Error-Based Adrc Approach, R. Madonski, M. Ramirez-Neria, M. Stankovic, Sally Shao, Zhiqiang Gao, J. Yang, S. Li

Mathematics and Statistics Faculty Publications

In this work, a practically relevant control problem of compensating harmonic uncertainties is tackled. The problem is formulated and solved here using an active disturbance rejection control (ADRC) methodology. A novel, custom ADRC structure is proposed that utilizes an innovative resonant extended state observer (RESO), dedicated to systems subjected to harmonic interferences. In order to make the introduced solution more industry-friendly, the entire observer-centered control topology is additionally restructured into one degree-of-freedom, compact, feedback error-based form (similar to ubiquitous in practice PID controller). Such reorganization enables a straightforward implementation and commission of the proposed technique in wide range of industrial …

An Individual-Carcass Model For Quantifying Bacterial Cross-Contamination In An Industrial Three-Stage Poultry Scalding Tank, Zachary Mccarthy, Ben Smith, Aamir Fazil, Shawn D. Ryan, Jianhong Wu, Daniel Munther

Mathematics and Statistics Faculty Publications

No abstract provided.

Advances In Remote Sensing To Understand Extreme Hydrological Events, Dongkyun Kim, Minha Choi, Jongho Kim, Ungtae Kim

Civil and Environmental Engineering Faculty Publications

No abstract provided.

End-Point Modification Of Recombinant Thrombomodulin With Enhanced Stability And Anticoagulant Activity, Xia Liu, Mallorie Boron, Yu Zhao, Xue-Long Sun

Chemistry Faculty Publications

Thrombomodulin (TM) is an endothelial cell membrane protein that plays essential roles in controlling vascular haemostatic balance. The 4, 5, 6 EGF-like domain of TM (TM₄₅₆) has cofactor activity for thrombin binding and subsequently protein C activation. Therefore, recombinant TM₄₅₆ is a promising anticoagulant candidate but has a very short half-life. Ligation of poly (ethylene glycol) to a bioactive protein (PEGylation) is a practical choice to improve stability, extend circulating life, and reduce immunogenicity of the protein. Site-specific PEGylation is preferred as it could avoid the loss of protein activity resulting from nonspecific modification. We report herein …

Validating The Water Vapor Variance Similarity Relationship In The Interfacial Layer Using Observations And Large-Eddy Simulations, M. K. Osman, D. D. Turner, Thijs Heus, V. Wulfmeyer

Physics Faculty Publications

In previous work, the similarity relationship for the water vapor variance in the interfacial layer (IL) at the top of the convective boundary layer (CBL) was proposed to be proportional to the convective velocity scale and the gradients of the water vapor mixing ratio and the Brunt‐Vaisala frequency in the entrainment zone. In the presence of wind shear in the IL, the similarity relationship was hypothesized to also include a dependence on the gradient Richardson number. Simultaneous measurements of the surface buoyancy flux, wind‐shear profiles from a radar wind profiler, water vapor mixing ratio and temperature measurements and their gradients …

Modeling Of Free Chlorine Consumption And Escherichia Coli O157:H7 Cross-Contamination During Fresh-Cut Produce Wash Cycles, Mohammadreza Dehghan Abnavi, Ali Alradaan, Daniel Munther, Chandrasekhar R. Kothapalli, Partha Srinivasan

Mathematics and Statistics Faculty Publications

Controlling the free chlorine (FC) availability in wash water during sanitization of fresh produce enhances our ability to reduce microbial levels and prevent cross-contamination. However, maintaining an ideal concentration of FC that could prevent the risk of contamination within the wash system is still a technical challenge in the industry, indicating the need to better understand wash water chemistry dynamics. Using bench-scale experiments and modeling approaches, we developed a comprehensive mathematical model to predict the FC concentration during fresh-cut produce wash processes for different lettuce types (romaine, iceberg, green leaf, and red leaf), carrots, and green cabbage as well as …

Cobalt(Ii) Diphenylazodioxide Complexes Induce Apoptosis In Sk-Hep-1 Cells, Norah J. Alghamdi, Lakshmi Balaraman, Kylin A. Emhoff, Ahmed M.H. Salem, Ruhan Wei, Aimin Zhou, W. Christropher Boyd

Chemistry Faculty Publications

The cobalt(II) complex salts [Co(bpy)(az)₂](PF₆)₂ and [Co(az)₄](PF₆), each bearing the unusual cis-N,N'-diphenylazodioxide ligand, were both screened as possible anticancer agents against SK-HEP-1 liver cancer cells. Both compounds were found to induce substantial apoptosis as an increasing function of concentration and time. Measurement of apoptosis-related proteins indicated that both the extrinsic and intrinsic pathways of apoptosis were activated. The apoptotic activity induced by these salts is not displayed either by simple cobalt(II) salts or complexes or by the free nitrosobenzene ligand. Additionally, these compounds did not induce apoptosis, as assessed by poly(adenosine …

Shifts In Plant Functional Composition Following Long-Term Drought In Grasslands, Robert J. Griffin‐Nolan, Dana M. Blumenthal, Scott L. Collins, Timothy E. Farkas, Ava M. Hoffman, Kevin E. Mueller, Troy W. Ocheltree, Melinda D. Smith, Kenneth D. Whitney, Alan K. Knapp

Biological, Geological, and Environmental Faculty Publications

1. Plant traits can provide unique insights into plant performance at the community scale. Functional composition, defined by both functional diversity and community-weighted trait means (CWMs), can affect the stability of above-ground net primary production (ANPP) in response to climate extremes. Further complexity arises, however, when functional composition itself responds to environmental change. The duration of climate extremes, such as drought, is expected to increase with rising global temperatures; thus, understanding the impacts of long-term drought on functional composition and the corresponding effect that has on ecosystem function could improve predictions of ecosystem sensitivity to climate change.

2. We experimentally …

Google Funds Cold Fusion Research; Results Still Negative, David W. Ball

Chemistry Faculty Publications

No abstract provided.

Experiences With Implementing Parallel Discrete-Event Simulation On Gpu, Janche Sang, Che-Rung Lee, Vernon Rego, Chung-Ta King

Electrical and Computer Engineering Faculty Publications

Modern graphics processing units (GPUs) offer much more computational power than recent CPUs by providing a vast number of simple, data-parallel, multithreaded cores. In this study, we focus on the use of a GPU to perform parallel discrete-event simulation. Our approach is to use a modified service time distribution function to allow more independent events to be processed in parallel. The implementation issues and alternative strategies will be discussed in detail. We describe and compare our experience and results in using Thrust and CUB, two open-source parallel algorithms libraries which resemble the C++ Standard Template Library, to build our tool. …

Long-Dose Intensive Therapy Is Necessary For Strong, Clinically Significant, Upper Limb Functional Gains And Retained Gains In Severe/Moderate Chronic Stroke, Janis J. Daly, Jessica P. Mccabe, John P. Holcomb, Michelle Monkiewicz, Jennifer Gansen, Svetlana Pundik

Mathematics and Statistics Faculty Publications

Background. Effective treatment methods are needed for moderate/severely impairment chronic stroke. Objective. The questions were the following: (1) Is there need for long-dose therapy or is there a mid-treatment plateau? (2) Are the observed gains from the prior-studied protocol retained after treatment? Methods. Single-blind, stratified/randomized design, with 3 applied technology treatment groups, combined with motor learning, for long-duration treatment (300 hours of treatment). Measures were Arm Motor Ability Test time and coordination-function (AMAT-T, AMAT-F, respectively), acquired pre-/posttreatment and 3-month follow-up (3moF/U); Fugl-Meyer (FM), acquired similarly with addition of mid-treatment. Findings. There was no group difference in …

Power-Law Scaling In The Internal Variability Of Cumulus Cloud Size Distributions Due To Subsampling And Spatial Organization, R. A. J. Neggers, P. J. Griewank, Thijs Heus

Physics Faculty Publications

In this study, the spatial structure of cumulus cloud populations is investigated using three-dimensional snapshots from large-domain LES experiments. The aim is to understand and quantify the internal variability in cloud size distributions due to subsampling effects and spatial organization. A set of idealized shallow cumulus cases is selected with varying degrees of spatial organization, including a slowly organizing marine precipitating case and five more quickly organizing diurnal cases over land. A subdomain analysis is applied, yielding cloud number distributions at sample sizes ranging from severely undersampled to nearly complete. A strong power-law scaling is found in the relation between …

Natural Kinds And Ceteris Paratis Generalizations: In Praise Of Hunches, W. Christropher Boyd, Richard N. Boyd

Chemistry Faculty Publications

According to stereotypical logical empiricist conceptions, scientific findings are approximately true (or perhaps true ceteris paribus) law-like generalizations used to predict natural phenomena. They are deployed using topic-neutral, generally reliable inferential principles like deductive or statistical inferences. Natural kinds are the kinds in such generalizations. Chemical examples show that such conceptions are seriously incomplete. Some important chemical generalizations are true often enough, even though not usually true, and they are applied using esoteric topic- and discipline-specific inference rules. Their important methodological role is to underwrite often-enough reliable, often socially implemented, scientifically informed guessing about chemical phenomena. Some chemical natural …

Ph Dependent C-Jejuni Thermal Inactivation Models And Application To Poultry Scalding, Zachary Mccarthy, Ben Smith, Aamir Fazil, Jianhong Wu, Shawn D. Ryan, Daniel Munther

Mathematics and Statistics Faculty Publications

Campylobacter jejuni related outbreaks and prevalence on retail poultry products pose threats to public health and cause financial burden worldwide. To resolve these problems, it is imperative to take a closer look at poultry processing practices and standards. Using available data (D-values) on the thermal inactivation of C. jejuni we develop a comprehensive inactivation model, taking into account the variation of strain-specific heat resistance, experimental method, and suspension pH. Utilizing our C. jejuni thermal inactivation model, we study the poultry scalding process. We present a mechanistic model of bacteria transfer and inactivation during a typical immersion scald in a high-speed …

A Non-Natural Nucleotide Uses A Specific Pocket To Selectively Inhibit Telomerase Activity, Wilnelly Hernandez-Sanchez, Wei Huang, Brian Plucinsky, Nelson Garcia-Vazquez, Nathaniel J. Robinson, William P. Schiemann, Anthony J. Berdis, Emmanuel Skordalakes, Derek J. Taylor

Chemistry Faculty Publications

Telomerase, a unique reverse transcriptase that specifically extends the ends of linear chromosomes, is up-regulated in the vast majority of cancer cells. Here, we show that an indole nucleotide analog, 5-methylcarboxyl-indolyl-2′-deoxyriboside 5′-triphosphate (5-MeCITP), functions as an inhibitor of telomerase activity. The crystal structure of 5-MeCITP bound to the Tribolium castaneum telomerase reverse transcriptase reveals an atypical interaction, in which the nucleobase is flipped in the active site. In this orientation, the methoxy group of 5-MeCITP extends out of the canonical active site to interact with a telomerase-specific hydrophobic pocket formed by motifs 1 and 2 in the fingers domain and …

A Quantitative Lc-Ms/Ms Method For Determination Of A Small Molecule Agonist Of Epha2 In Mouse Plasma And Brain Tissue, Bo Zhong, Yaxin Li, Nethrie Idippily, Aaron Petty, Bin Su Ph.D., Bingcheng Wang

Chemistry Faculty Publications

Compound 27 {1, 12‐bis[4‐(4‐amino‐6,7‐dimethoxyquinazolin‐2‐yl)piperazin‐1‐yl]dodecane‐1,12‐dione} is a novel small molecule agonist of EphA2 receptor tyrosine kinase. It showed much improved activity for the activation of EphA2 receptor compared with the parental compound doxazosin. To support further pharmacological and toxicological studies of the compound, a method using liquid chromatography and electrospray ionization tandem mass spectrometry (LC–MS/MS) has been developed for the quantification of this compound. Liquid–liquid extraction was used to extract the compound from mouse plasma and brain tissue homogenate. Reverse‐phase chromatography with gradient elution was performed to separate compound 27 from the endogenous molecules in the matrix, followed by …

Tracking Decitabine Incorporation Into Malignant Myeloid Cell Dna In Vitro And In Vivo By Lc-Ms/Ms With Enzymatic Digestion, Sujatha Chilakala, Ye Feng, Lan Li, Reda Mahfouz, Ebrahem Quteba, Yogen Saunthararajah, Yan Xu

Chemistry Faculty Publications

The DNA hypomethylating agents decitabine and 5-azacytidine are the only two drugs approved for treatment of all subtypes of the myeloid malignancy myelodysplastic syndromes (MDS). The key to drug activity is incorporation into target cell DNA, however, a practical method to measure this incorporation is un-available. Here, we report a sensitive and specific LC-MS/MS method to simultaneously measure decitabine incorporation and DNA hypomethylation. A stable heavy isotope of 2'-deoxycytidine was used as an internal standard and one-step multi-enzyme digestion was used to release the DNA bound drug. Enzyme-released decitabine along with other mononucleosides were separated by a reverse-phase C-18 column …

Gluing Semigroups And Strongly Indispensable Free Resolutions, Mesut Sahin, Leah Gold Stella

Mathematics and Statistics Faculty Publications

We study strong indispensability of minimal free resolutions of semigroup rings focusing on the operation of gluing used in literature to take examples with a special property and producenew ones. We give a naive condition to determine whether gluing of two semigroup rings has astrongly indispensable minimal free resolution. As applications, we determine simple gluings of 3-generated non-symmetric, 4-generated symmetric and pseudo symmetric numerical semigroups as well as obtain infinitely many new complete intersection semigroups of any embedding dimensions, having strongly indispensable minimal free resolutions.

General Error-Based Active Disturbance Rejection Control For Swift Industrial Implementations, R. Madonski, S. Shao, H. Zhang, Z. Gao, J. Yang, S. Li

Mathematics and Statistics Faculty Publications

In this article, a typical 2DOF active disturbance rejection control (ADRC) design is restructured into a 1DOF form, thus making it compatible with standard industrial control function blocks and enhancing its market competitiveness. This methodology integrates the previously separated components, such as the profile generator, state observer, feedback controller, feedforward terms, and disturbance rejection, into one unified structure. In doing so, certain ADRC components can be made simpler (or even obsolete) without sacrificing the nominal control performance, which further simplifies the control synthesis and tuning. A generalized version of the error-driven design is adopted and rigorously proved here using the …

Analysis Of Oxygen-18 Labeled Phosphate To Study Positional Isotope Experiments Using Lc-Qtof-Ms, Sujatha Chilakala, Iteen Cheng, Ireen Lee, Yan Xu

Chemistry Faculty Publications

A method is proposed in this paper for the determination of oxygen-18 labeled phosphate so that positional isotope experiments using sensitive and rapid liquid chromatography–QTOF–mass spectrometry (LC-QTOF-MS) experiments can be carried out. The positional isotope exchange technique is a useful tool in understanding the mechanisms and kinetics of many enzyme-catalyzed reactions. Detection of the positions and concentration of these exchanged isotopes is the key. Gas chromatography–mass spectrometry (GC-MS) and nuclear magnetic resonance imaging are commonly used analytical techniques for measurement of ¹⁸O/¹⁶O, ³¹P and ¹⁵N isotope enrichment. Since these techniques either require a time-consuming derivatization …

Fpc: A New Approach To Firewall Policies Compression, Yuzhu Cheng, Weiping Wang, Jianxin Wang, Haodong Wang

Electrical and Computer Engineering Faculty Publications

Firewalls are crucial elements that enhance network security by examining the field values of every packet and deciding whether to accept or discard a packet according to the firewall policies. With the development of networks, the number of rules in firewalls has rapidly increased, consequently degrading network performance. In addition, because most real-life firewalls have been plagued with policy conflicts, malicious traffics can be allowed or legitimate traffics can be blocked. Moreover, because of the complexity of the firewall policies, it is very important to reduce the number of rules in a firewall while keeping the rule semantics unchanged and …

Cold Fusion Thirty Years Later, David W. Ball

Chemistry Faculty Publications

In March 1989, the claim of a revolutionary discovery in nuclear energy production galvanized the scientific community. It turned into a classic case of pathological science—and a textbook example of the self-correcting nature of science.

Coordination Chemistry Of N,N’- Azodoxides, Lakshmi Balaraman

ETD Archive

The coordination chemistry of nitric oxide (NO) with transition metals has been extensively investigated, but that of organic NO derivatives as ligands less so. Some nitrosoalkanes RNO and nitrosoarenes ArNO are in equilibrium with dimeric species known as N,N'–azodioxides, R(O)NN(O)R or Ar(O)NN(O)Ar. The cis diastereomers of azodioxides have been proposed to act as bidentate chelating ligands for both main-group and transition metals, but only three azodioxide complexes, a dicationic iron (II) complex, a neutral scandium (III) complex, and a dicationic calcium (II) complex, have thus far been structurally characterized before our work in this area. The delocalized π system of …

Reactivity Of Molybdenum And Tungsten Sulfido Complexes With First-Series Transition Metals, Khalil Mudarmah

ETD Archive

Ammonium tetrathiomolybdate (ATTM) is an important compound in bioinorganic chemistry, with medicinal applications. Metal complexes of sulfur-containing ligands have been widely used as building block in biology and inorganic chemistry. This project aims to increase the number of Mo-S and W-S complexes that may contribute to fields such as bioinorganic and medicinal chemistry, by the preparation of heterometallic complexes containing both Mo or S and a metal of the first transition series. The homobimetallic complex anion salts (Et4N)2[Mo2(S)2(μ-S)2(edt)2] (1) and (Et4N)2[W2(S)2(μ-S)2(edt)2] (2) have been prepared from ATTM and ammonium tetrathiotungstate (ATTW) in order to start our work. The overnight treatment …

Usability Engineering Of A Privacy-Aware Compliance Tracking System, Parameswara Reddy Annapureddy

ETD Archive

Software is useful when it is able to provide useful information to the end user with minimum effort. This thesis is about usability improvements to a privacy-aware human motion tracking system for healthcare professionals. The original system has a number of usability issues: (1) Users need to wear a smartwatch, which will be used to connect to the system; (2) Data are stored in XML, comma-separated-value format which is very difficult to analyze; (3) Data are available only at the local computer and there is no easy way to access them remotely via a Web or mobile interface; (4) Analysis …

Liquid Chromatography - Mass Spectrometric Analysis Of Clinicallyand Pharmacologically Relevant Molecules, Raghavi Kakarla

ETD Archive

Liquid Chromatography-Mass Spectrometry is an advanced analytical technique that offers high sensitivity and specificity and has been increasingly used for analysis of a wide variety of compounds including clinically and pharmacologically relevant molecules. In this dissertation we describe qualitative and quantitative liquid chromatographic mass spectrometric methods to analyze both small molecules and larger macromolecules that provide useful insights into diagnosis and management of several diseases. An LCMS(/MS) analytical method includes extraction of analytes of interest from the matrix followed by liquid chromatographic separation and mass spectrometric detection. Chapter I describes pre-analytical workflows and sample pretreatment techniques and theories underlying LC-MS …

Development Of An Spr Method To Monitor The Chemical Interaction Of Dna With A Small Reactive Molecule: Peroxynitrite As An Example, Divya Sharma

ETD Archive

Peroxynitrite is an anion with the formula ONOO-. It is an unstable structural isomer of nitrate, NO3-. Although its conjugate acid (ONOOH) is highly reactive, it is quite relatively stable in basic solutions. Generation of peroxynitrite in-vivo occurs through the diffusion-controlled reaction between superoxide anion and nitric oxide free radical. It is a strong oxidizing and nitrating agent, and its formation has been correlated with many pathological conditions. Because of its oxidizing properties, peroxynitrite can damage a wide array of molecules in cells, including DNA and proteins. Reactions of peroxynitrite with DNA, proteins, and lipids, trigger a wide array of …

In-Quest Of Biomarkers For Alzheimer’S Disease And Pharmacokinetic Profile Of Anticancer Agents Using Lc-Ms In Human Plasma, Chandana Mannem

ETD Archive

In this dissertation work, a semi-quantitative assay using a lipidomics approach and an absolute quantitative assay using liquid chromatography-mass spectrometry techniques were developed (LC-MS). In the lipidomics approach, ultra-high pressure liquid chromatography in tandem with quadrupole time of flight (UHPLC-QTOF) mass spectrometry was used to profile, compare and quantitate the human plasma lipids in Alzheimer’s disease subjects (AD) and normal cognitive controls (NCCs). The purpose of this study is to identify potential plasma lipid markers of AD and to explore the relationships between AD and lipid pathways in humans by using bioinformatic tools. The plasma samples of study subjects were …