Duquesne University (Virtual) Undergraduate Research Program Vi… · (Virtual) Undergraduate Research Program 23rd Annual (Virtual) Summer Research Symposium Sponsored by The Bayer

Duquesne University (Virtual) Undergraduate

Research Program

23rd Annual (Virtual) Summer Research Symposium

Sponsored by

The Bayer School of Natural and Environmental Sciences

Keynote Address:

Dr. Allison Roessler Assistant Professor of

Chemistry Oglethorpe University

“From Pre-Med to Ph.D.: My Journey through Higher Education”

Friday, July 31, 2020 1:00 p.m. – 4:15 p.m.

Welcome to the 2020 (Virtual) Summer Undergraduate Research

Symposium!

It is a pleasure and privilege to welcome you to today’s virtual version of the 23rd Annual Summer Undergraduate Research Symposium at Duquesne University. Each year the number of student participants and the quality and breadth of the research presented at this symposium continue to grow. The abstracts in this year’s program highlight the remarkable quality of the student research that we will see and discuss at today’s symposium. In an era in which we hear persistent concerns regarding our nation’s ability to sustain global competitiveness and global pre-eminence in the STEM disciplines, events such as today’s conference should reassure all of us of the superb caliber of the scientific research and training that occurs on a daily basis in our colleges, universities and research centers. Today’s presentations reinforce our conviction and confidence that we are preparing an emerging cadre of future scientific leaders who will possess the creativity, motivation, and intellect to meet and solve the challenges that our society faces. On behalf of the faculty, students, and staff of the Bayer School and Duquesne University, I am pleased to offer my sincerest congratulations to each of the student researchers participating in today’s symposium and to convey our best wishes for continued success in your academic and professional careers!

Sincerely,

Philip Reeder, Ph.D. Dean, Bayer School of Natural and Environmental Sciences Schedule:

1:00 PM Opening Remarks and Keynote Address

2:00 PM – 4:15 PM Poster Sessions

Contents:

Welcome Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

About Dr. Allison Roessler, Keynote Speaker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Index of Authors and Posters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-5

Poster Sessions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-9

Abstracts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-33

Colleges and Universities Represented . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .34

Instructions to Authors:

Authors can locate their assigned poster sessions and the time of their presentations, starting at page six. The abstracts of all the authors’ research begin at page ten. Please remember all presentations are up to seven minutes, with two minutes of questions and answers. All Q&A will be conducted on the chat feature in each room.

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ABOUT ALLISON ROESSLER, Ph.D.

Allison Roessler is an Assistant Professor of Chemistry at Oglethorpe University, a liberal arts college in Atlanta. She is an expert in the field of polymer mechanochemistry and applies theoretical tools to solve complex problems in materials chemistry and catalysis. Dr. Roessler recently earned her Ph.D. in Physical Chemistry and Scientific Computing from the University of Michigan where she served as a leader in the department. During her time at Michigan, she served as president of the Chemistry Graduate Student Council, planned a symposium to be held at an American Chemical Society National Meeting, and was recognized by awards for her research and leadership. Dr. Roessler is a native of Kentucky and a graduate of Franciscan University of Steubenville. Zoom Link to Dr. Roessler’s Keynote Address

https://duq.zoom.us/j/98083760114?pwd=NGdEWVpWazlvckVEU01kRkh1Umxldz09 Meeting ID: 980 8376 0114 Passcode: 919551

https://duq.zoom.us/j/98083760114?pwd=NGdEWVpWazlvckVEU01kRkh1Umxldz09

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INDEX OF POSTERS AND AUTHORS

NAME POSTER # PAGE #

NAME POSTER PAGE #

Armen, Jennifer

26,41 22,30 Koch, Andrew 42 30

Aruru, Meghana

5 12 Kolber, Benedict

24 21

Aumer, Thomas

38 28 Kotsikorou, Evangelia

39 29

Babyok, Olivia

24 21 Krishna, Neal

14 16

Bachtlin, Alanna

21 20 Lackey, Patrick

1,22,23 10,20

Barwatt, Holly

36 27 Lakani, Chirag M.

44 31

Bayto, Mikayla

3 11 Landsittel, Douglas

14 16

Bedillion, Derek

18 18 Lim, Min Soo

6 12

Bloomfield, Aaron

17 18 Lugo-Martinez, Jose

45 32

Boorgu, Devi Sai Sri Kavya

44 31 Mackenstein, Nicole

22 20

Boyer, Aiden

27 23 Majetic, Gabrielle

24 21

Bravo, Naila

39 29 Makowski, Joseph

28,30 23,24

Castile, Erin

28,30 23,24 Matthews, Emily

20 19

Catagena, Sofia

45 32 Mazza, William

8 13

Cava, Kacie

35 27 McClure, Taylor

37 28

Cawley, Hannah

4 11 Meng, Wilson S.

41 30

Chennubhotla, Chakra

47 33 Mihailescu, Mihaela-Rita

1,22,23 10,20

Cocolas, Alex

33 26 Montgomery, Thomas

7,10,33,42 13,14,26,30

Corcovilos, Theodore

16,38 17,28 Morsey, Yasser

12 15

Coufal, Sarah

34 26 Moskal, Lindsay

33 26

Deal, Brooke

11 15 Neal, Martin

10 14

Dembowski, Jill

31,32,36 25,27 Onyeador, Jeffrey

46 32

Demjanenko, Peter

26 22 Packard, Jessica

31,32,36 25,27

Enderby, Hannah

21 20 Palumbo, Rosalia

13 16

Esenwein, Raegen

31 25 Pamuku, Matt

29 24

Evans, Anton

9 14 Patel, Chirag J.

44 31

Evanseck, Jeffrey

1,6,7,10,13,19,22,23,28,30,

33,39,42

10,12,13,14,

16,19,20,23,

24,26,29,30

Patel, Yash

47 33

Ferrara, Lyndsie

4 11 Pellegrene, Kendy

1,6,22,23 10,12,20

Frederic, Wrebekah

17 18 Plyler, Alexandria

43 31

Furman, Samantha

47 33 Pollock, John

11 15

Gawalt, Ellen

26,41 22,30 Porter, Brady

40 29

Ghobrial, Jessica

40 29 Quinones-Fernandez, Rosalynn

18 18

Gil-Silva, Mauricio

24 21 Rebel, Lauren

2 10

Hejnosz, Sarah

10 14 Reynolds, Laura

11 15

Hoke, Tiffany

29 24 Robinson, Taylor

5 12

Iuliucci, Robbie

18 18 Rodo, Edgar

28,30 23,24

Janjic, Jelena

11 15 Rohde, Jeffrey

10 14

Jemison, Kezia

19 19 Roth, Talia

8 13

Jensen-Seaman, Michael

37 28 Saleem, Muzamil

11 15

Kelleher, Bryan

23 21 Santoro, Ava

8 13

Kessler, Collin

9 14 Santos, Raziel

9 14

Kim, Wook

8,9 13,14 Senathirajah, Yalini

46 32

Kington, H.M. “Skip”

29 24 Seybert, David

13,15 16,17

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INDEX OF POSTERS AND AUTHORS

NAME POSTER # PAGE #

Shide, Jasper 42 30

Shine, Morgan 1,22,23 10,20

Sipko, Emily

15 17

Slater, Tasia

25 22

Sobus, Michael

10 14

Spadavecchia, Katelyn

16 17

Srnec, Matthew

13 16

Stevens, Andrea

11 15

Stolz, John

2 10

Tamez, Angel

19,33,39 19,26,29

Taylor, Ethan

6 12

Teitelbaum, Taylor

29 24

Tressler, Serina

7,35 13,26

Van Stipdonk, Michael

43,48 31,33

Venkatesh, Shruthi

44 31

Weber, Hannah

41 30

Weier, Hao

29 24

Williams, Maya

32 25

Woerpel, Keith

28,30 23,24

Woodley, Sarah

25 22

Yuan, Mingyang

8 13

Xia, Zongqi

44 31

Farmen, Chris 48 33

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Poster Session 1 - 2 p.m. to 4:15 p.m. Moderator: Dr. Patrick Lackey, Westminster College Zoom Link: https://duq.zoom.us/j/97827416481?pwd=REkxTldEM1d0ZGdTYUJTOUJRY0FKdz09 Meeting ID: 978 2741 6481 Passcode: 357439

1. Morgan Shine: “Computational modeling of a uridylated histone mRNA degradation intermediate bound to SLBP and 3’hExo, individually and together.” (2 p.m.)

6. Ethan Taylor: Frictional Properties of n-Alkyl Carboxylic Acid Self-Assembled Monolayers from an Adapted Steered

Molecular Dynamics Approach.” (2:10 p.m.)

7. Serina Tressler: “Squaramide Structure and Noncovalent Interactions with Benzene.” (2:20 p.m.)

10. Michael Sobus: “Epibatidine SAR Analogue Synthesis: Theoretical Mechanistic Study of 1,3-dipolar Cylcoadditions.” (2:30 p.m.)

13. Rosalia Palumbo: “Conformations that define the native fold of bovine serum albumin by molecular dynamics and multivariate analysis.” (2:40 p.m.)

15. Emily Sipko: “New approaches to in vitro macromolecular crowding studies with bovine serum albumin.” (2:50 p.m.) 10-minute break

19. Kezia Jemison: “Hybrid Quantum Mechanical-Molecular Mechanical Computational Approach to Modeling the Water Solvated Uncatalyzed Decarboxylation of Monoanionic Malonate.” (3:10 p.m.)

28. Edgar Rodo: “CCSD(T) and DFT torsional energy scan comparisons on 3-aryl substituted oxocarbenium ions.” (3:20 p.m.)

30. Joseph Makowski: “Distinguishing Between Steric and Electrostatic Effects on Stereochemistry of Nucleophilic Addition to Five- and Six-Membered Oxocarbenium Ions.” (3:30 p.m.)

33. Lindsay Moskal: “The Structure, Flexibilities, and Energies of the Urea/Thiourea Dual Hydrogen Bond Donor Core.” (3:40 p.m.)

39. Naila Bravo: “Molecular Dynamic Simulations Reveal Allosteric Communication Between the Androgen Receptor BF-3 Surface Binding Site and the Steroid Binding Pocket.” (3:50 p.m.)

42. Jasper Shide: “The Effect of Noncovalent Interactions on Reductive Elimination of Diaryliodoniums with Neutral Nucleophiles.” (4 p.m.)

https://duq.zoom.us/j/97827416481?pwd=REkxTldEM1d0ZGdTYUJTOUJRY0FKdz09

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Poster Session 2 - 2 p.m. to 4:15 p.m. Moderator: Dr. Michael Jensen-Seaman, Duquesne University Zoom Link: https://duq.zoom.us/j/94818401418?pwd=cGk0K2lNb1V6T05YQTFucnE3T25KQT09 Meeting ID: 948 1840 1418 Passcode: 972669

8. Talia Roth: “Unraveling the mysteries of dandruff and Malassezia restricta, the dominant fungus of human scalp.” (2 p.m.)

9. Raziel Santos: “Identification of unique genetic signatures underlying the functional divergence of bacterial Rsm homologs.” (2:10 p.m.)

11. Laura Reynolds: “A Review: Theranostic Nanoemulsion Treatment of Neuropathic Pain Alleviates Pain and May Influence Neuronal Damage Through Shifts in Transcriptome Expression and Cell Infiltration.” (2:20 p.m.)

22. Nicole Mackenstein: “Molecular dynamic simulations of folding and dimerization in mutations found in the s2m motif of SARS-CoV-2.” (2:30 p.m.)

24. Olivia Babyok: “Optimization of MatLab Code for Analysis of Urinary Bladder Distention for Visceromotor Response.” (2:40 p.m.)

25. Tasia Slater: “The Role of Female Behavior During Salamander Courtship.” (2:50 p.m.)

10-minute break

31. Raegan Esenwein: “The Role of Topoisomerase I in Herpes Simplex Virus Infection.” (3:10 p.m.)

32. Maya Williams: “Investigation of PCNA Function During Herpes Simplex Virus Infection.” (3:20 p.m.)

36. Holly Barwatt: “Role of Topoisomerase II in Herpes Simplex Virus Infection Process.” (3:30 p.m.)

37.Taylor McClure: “Patterns of loss-of-function mutations in the human genome.” (3:40 p.m.)

40. Jessica Ghobrial: “DNA Barcoding Analysis of Fish Specimens from Duquesne University’s New Research Facility in Belize.” (3:50 p.m.)

48. Chris Farmen: Abstract Pending

https://duq.zoom.us/j/94818401418?pwd=cGk0K2lNb1V6T05YQTFucnE3T25KQT09

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Poster Session 3 - 2 p.m. to 4:15 p.m. Moderator: Dr. Ted Corcovilos, Duquesne University

Zoom Link: https://duq.zoom.us/j/97679749024?pwd=NmdpRzlUNzRSSitSZlVmSHpYVnNiZz09 Meeting ID: 976 7974 9024 Passcode: 281691 2. Lauren Rebel: “Structure Prediction and Sequence Analysis of Membrane Protein RarA.” (2 p.m.) 3. Mikayla Bayto: “Surface Water Quality in the Mingo Creek Watershed.” (2:10 p.m.)

16. Katelyn Spadavecchia: “Projective Geometric Algebra as Language for Paraxial Geometric Optics.” (2:20 p.m.)

20. Emily Matthews: “Analyzing Pion Data Using Semi-Inclusive Deep Inelastic Scattering.” (2:30 p.m.)

21. Alanna Bachtlin and Hannah Enderby: “Turbulent Mixing and Applications in Abandoned Mine Drainage.” (2:40 p.m.)

26. Peter Demjanenko: “The Fabrication of an Anti-Inflammatory Implant Surface.” (2:50 p.m.)

10-minute break

27. Aiden Boyer: “Hamamatsu H12700 Multi-Anode Photomultiplier Tube Performance Estimation.” (3:10 p.m.)

29. Taylor Teitelbaum: “Determination of Persistent Organic Pollutants (POPs) in Varying Foods.” (3:20 p.m.)

35. Kacie Cava: “Sustainable Farming Practices and Marketing Strategies for Growing and Selling Produce on a Livestock Farm.” (3:30 p.m.)

38. Thomas Aumer: “Calibration of a homemade color-based detector for water contamination.” (3:40 p.m.)

41. Hannah Weber: “Preventing Thrombus Formation on Left Ventricular Assist Device.” (3:50 p.m.)

43. Alexandra Plyler: “Extraction of Pollutants and Other Illicit Substances from Mealworms (T. molitor).” (4 p.m.)

https://duq.zoom.us/j/97679749024?pwd=NmdpRzlUNzRSSitSZlVmSHpYVnNiZz09

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Poster Session 4 - 2 p.m. to 4:15 p.m. Moderator: Dr. Lyndsie Ferrara, Duquesne University Zoom Link: https://duq.zoom.us/j/96931323753?pwd=RmFFdkFlREk2cEdCTXpsU2xLcHJGZz09 Meeting ID: 969 3132 3753 Passcode: 860962 4. Hannah Cawley: “Rapid DNA Landscape Study.” (2 p.m.)

5. Taylor Robinson: “Assessing Vulnerability in the Appalachian Region During the COVID-19 Pandemic Emergency Response.” (2:10 p.m.)

12. Yasser Morsy: “Comparing Machine Learning Models and Causal Models in Observational Data.” (2:20 p.m.)

14. Neal Krishna: “Estimating the Model Complexity of Dense FeedForward Backpropagation Neural Networks.” (2:30 p.m.)

17. Wrebekah Frederic: “Optimization of Reagent-free Mitsunobu Reactions.” (2:40 p.m.)

18. Derek Bedillion: “Understanding the Structure of a Uniquely Made Erlotinib Polymorph.” (2:50 p.m.)

10-minute break 23. Bryan Kelleher: “Computational characterization of the s2m region within mutant SARS-CoV-2 RNA.” (3:10 p.m.)

34. Sarah Coufal: “Public data consistency analysis and preliminary models of Covid-19 infection fatality rates.” (3:20 p.m.)

44. Kavya Boorgu: “The Impact of Socioeconomic Status on Neurological Outcomes in Multiple Sclerosis.” (3:30 p.m.)

45. Sofia Meléndez-Cartagena: “Dynamic Bayesian networks for analyzing and integrating longitudinal multi-omics host-microbiome dynamics in prediabetes.” (3:40 p.m.)

46. Jeffrey Onyeador: “Effective Visualization Model of EHR data to Support Physician’s Clinical Decisions.” (3:50 p.m.)

47. Yash Patel: “Finding Recurrence Associated Phenotypes in Colorectal Cancer Data Classified by an Unsupervised Learning Algorithm for Characterizing Cellular Phenotypic Heterogeneity (LEAPH).” (4 p.m.)

https://duq.zoom.us/j/96931323753?pwd=RmFFdkFlREk2cEdCTXpsU2xLcHJGZz09

2020 (Virtual) Summer Undergraduate Research Symposium Abstract Index

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1 Computational modeling of a uridylated histone

mRNA degradation intermediate bound to SLBP and 3’hExo, individually and together

Shine, Morgan1, 2; Pellegrene, Kendy1; Mihailescu, Mihaela- Rita1; Evanseck, Jeffrey1; Lackey, Patrick E.2

1 Department of Chemistry and Biochemistry, Duquesne University

2 Department of Biochemistry and Chemistry, Westminster College Histone mRNA is the only known metazoan mRNA that is not polyadenylated at its 3’ end; instead, it ends in a highly conserved stem-loop formed by Watson-Crick base pairing. During histone mRNA degradation, the stem-loop is trimmed by 3’ human exonuclease (3’hExo) and uridylated by terminal uridylyl transferase 7 (TUT7), creating uridylated intermediates. It is unknown how this trimming and uridylation affects the binding interactions between the stem-loop and its protein binding partners, the stem-loop binding protein (SLBP) and 3’hExo. In this work, we performed molecular dynamics simulations with the wild-type stem-loop and a uridylated intermediate to evaluate structural changes induced by stem-loop modification and to understand how these changes impact SLBP and 3’hExo binding. RNA-protein systems were generated by applying the AMBER force field to modified versions of the phosphorylated ternary complex (4QOZ) and unphosphorylated ternary complex (4L8R) crystal structures. At least 200 ns of production have been completed for these RNA-protein systems using NAMD. In addition to informing experimental studies, this work could yield valuable insight into the degradation mechanisms of other types of RNA.

2 Structure Prediction and Sequence Analysis of

Membrane Protein RarA Rebel, Lauren; Stolz, John

Department of Biological Sciences Duquesne University

RarA is an enzyme that has the ability to reduce a variety of oxyanion substrates, such as arsenate, selenate, nitrite, and thiosulfate. Through this transformation of toxic inorganic compounds, RarA has the potential to be valuable in the bioremediation of contaminated water. RarA is only found in select species of Sulfurospirillum, including our model organism, Sulfurospirillum barnesii SES-3. In addition, it does not have a metal center or amino acids known to participate in oxidation/reduction reactions. Previous work suggested that it had a domain indicative of a porin. The purpose of this project is to gain a greater understanding of the structure and function of RarA through the use of protein modeling and sequence alignment tools. Three-dimensional structures were generated via homology modeling, fold recognition, and ab-initio prediction using I-TASSER, SWISS-MODEL, Phyre2, and Robetta. Several 3-D models were obtained and found to have the closest homology to Occ porins such as found in Acinetobacter. These types of porins are known to transport a variety of compounds and ions including amino acids, small carbohydrates, and anions. The results have provided clues to the mechanism of RarA’s functionality.


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3 Surface Water Quality in the Mingo Creek Watershed

Bayto, Mikayla Center for Environmental Research and Education Duquesne University

The Mingo Creek Watershed in Washington County, Southwestern Pennsylvania is comprised mainly of Mingo Creek and its tributaries. While today a large portion of the watershed lies within Mingo Creek County Park, it has been subject to drilling for natural gas and oil, and coal mining. As a result, pipelines, gas wells, oil wells, combined wells, storage wells, as well as longwall and strip coal mining operations can be found within the park. We were interested in whether these activities were affecting the water quality in the creeks. 32 of sites along Mingo Creek were monitored weekly for conductivity, dissolved oxygen, pH, temperature measurements of surface water using a YSI Multiparameter Water Quality Meter. Three sites were chosen to assay the macroinvertebrate populations and obtain additional water quality data. Anions and cations were determined using Ion Chromatography and Inductively Coupled Plasma Mass Spectrometry respectively to further determine quality of the surface water. The Hilsenhoff Biotic, Beck’s Biotic, Shannon’s H Diversity, Simpson Diversity, and Bean Biodiversity Indices were utilized for quantification of macroinvertebrate samples in relation to general water quality designations. The data collected supported that the sampled portion of Mingo Creek Watershed is of general, good water quality.

4 Rapid DNA Landscape Study Cawley, Hannah and Ferrara, Lyndsie, Ph.D. Forensic Science & Law Program Duquesne University Rapid DNA technology allows a DNA sample to be

processed in approximately 90 minutes compared to the traditional DNA analysis method that can take days to weeks in a forensic laboratory. This rapid technique requires little human intervention. Trained personnel collect the sample and insert it into the machine cartridge, then the machine produces a profile that is compared to local and national databases in order to obtain a ‘hit’ or match. Rapid DNA started as a quick screening tool to be used in police stations to compare arrestee reference samples (saliva swabs) to those DNA databases. As the technology continued to be implemented in various agencies it has evolved to process additional items including blood, bone, semen and tissue samples. The goal of this study was to compile the extensive information about rapid DNA technology spread out across various sources as well as incorporate user experiences in order to create an easily accessible resource for agencies interested in adopting rapid DNA technology. Information was sourced from interviews, webinars, websites and scientific journals. The research compiled information about the available Rapid DNA platforms, who is using the technology, and how it is being used across different agencies.


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5 Assessing Vulnerability in the Appalachian Region

During the COVID-19 Pandemic Emergency Response Robinson,Taylor Aruru, Meghana Department of Pharmacology University of Pittsburgh The COVID-19 pandemic has disproportionately affected

vulnerable, at-risk populations in the U.S. The Appalachian region is economically distressed with higher rates of chronic diseases and lower health care access than the national average. There are gaps in the literature evaluating health disparities and social vulnerability in the Appalachian region. This study aims to explore the impact of the COVID-19 pandemic on community resiliency in the Appalachian region.

Methods: We collected and transformed data to evaluate social vulnerability using the CDCs Social Vulnerability Index (SVI) and healthcare system factors to evaluate the impact of the COVID-19 pandemic in the Appalachian region.

Results: We found that the largest number of cases of the 2019 coronavirus occurred in the Southern region of Appalachia (~2m), while only ~100k cases occurred in the Central region. The largest number of deaths occurred in the Northern region (~92k) relative to ~5k deaths in the Central region. We are currently analyzing the SVI and other factors.

Conclusion: Disparities in impact of the COVID-19 pandemic exist across the regions in Appalachia and understanding social vulnerability would be critical to developing community resiliency in different communities.

6 Frictional Properties of n-Alkyl Carboxylic Acid Self-

Assembled Monolayers from an Adapted Steered Molecular Dynamics Approach

Taylor, Ethan1; Pellegrene, Kendy2; Evanseck, Jeffrey2; Lim, Min Soo1

Department of Chemistry1, Department of Chemistry and Biochemistry2

Slippery Rock University1, Duquesne University2

Miniaturization of devices, such as

microelectromechanical and nanoelectromechanical systems, requires the lubricant films to be molecularly thin. Chemical modification of such lubricant molecules could be decisive for the efficiency and life span of the devices, demanding a more complete understanding of how structural variations affect interfacial properties. Recent experimental results exhibited that the n-alkyl carboxylic acids ranging from CH3(CH2)13CO2H to CH3(CH2)16CO2H bind to the sapphire surface through the combination of monodentate and bidentate fashion. Friction force measured on the monolayer surfaces with an atomic force microscope (AFM) revealed an alternating pattern depending on an odd or even number of methylene units on the monomer backbone chains, which is called, “odd-even effect.” A Steered Molecular Dynamics method was adopted in the present research to precisely measure frictional forces on the surface of model self-assembled monolayers of the n-alkyl carboxylic acids. A two-dimensional monolayer of each n-alkyl carboxylic acid was constructed using VMD and Molefacture. A single silicon atom emulated an AFM tip and was dragged across the monolayer surfaces to measure friction force. This computational approach supported the proposed model of the odd-even effect and

provided insight on the origin of frictional properties of the monolayers.


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7 Squaramide Structure and Noncovalent Interactions

with Benzene Tressler, Serina. Evanseck, Dr. Jeffrey. Montgomery, Dr. Thomas. Bayer School of Natural and Environmental Sciences Duquesne University Since the outset of the green chemistry movement, the

development of more sustainable but equally effective catalysts has been an area of interest – often replacing metal-based systems with organocatalysts, such as dual hydrogen bond donor (DHBD) molecules. Despite the expanded use of DHBDs, the energy and structures of their interactions with aromatic systems is poorly understood. This study seeks to determine the most favorable geometries of DHBDs, specifically squaramide, thiosquaramide, and hemisquaramide, as well as determine the most favorable interaction of these molecules with benzene. We used the Truhlar M06-2X functional with Dunning’s aug-cc-pVDZ basis set and second-order Moller-Plesset perturbation theory (MP2) with Dunning’s aug-cc-pV[D,T]Z basis set for geometry optimization and energy evaluation. Squaramide and related systems possess two principal ground states with nitrogen pyramidalization yielding syn lone pairs (Cs) and anti lone pairs (C2), the C2 structures showing approximately 20-24° nonplanarity. The interactions of

squaramides with benzene have been compared energetically and structurally to known benzene-benzene interactions, such as pi-pi, lone pair-pi, and pi-H-X interactions. The findings of this study provide insight into squaramide’s structure and how squaramide-based catalysts may interact with aromatic substrates.

8 Unraveling the mysteries of dandruff and Malassezia

restricta, the dominant fungus of human scalp Roth, Talia; Santoro, Ava; Yuan, Mingyang; Mazza,

William; Kim, Wook Department of Biological Sciences Duquesne University Malassezia restricta (Mr) is a fungus found naturally on

the human skin, which numerically dominates over other fungal species particularly in the scalp. Similarly, two bacterial species, Cutibacterium acnes (Ca) and Staphylococcus epidermis (Se), dominate over all other bacteria in the scalp. Such remarkable dominance predicts that these three microbes are highly adapted to the human scalp and their symbiosis effectively displaces other competing microbes. Interestingly, scalps that suffer from dandruff consistently exhibit a conserved shift in the relative frequencies of the three dominant microbes without the appearance of a “new” pathogen. Moreover, Mr still overpowers the dandruff scalp, which contrasts with the general notion that dandruff is simply a manifestation of fungal infection, and instead predicts the disruption of Mr-Ca-Se symbiosis as the root cause. Surprisingly, little to nothing is known about Mr in general and interactions among the three microbes. Here, we combine a deep interrogation of the literature with interpretation of our recent experimental data to develop a new model for the symbiotic interactions and assess new therapeutic strategies to treat and prevent dandruff.


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9 Identification of unique genetic signatures underlying

the functional divergence of bacterial Rsm homologs Santos, Raziel; Evans, Anton; Kessler, Collin; Kim, Wook Department of Biological Sciences Duquesne University The Rsm family of proteins are a regulatory cog in

diverse physiological processes in bacteria, including metabolism, intercellular communication, motility, and biofilm formation. Rsm homologs span across the bacterial kingdom and function as a post-transcriptional regulator by repressing the translation of specific mRNA. Certain bacterial lineages possess multiple paralogs that are generalized to be functionally redundant due to high similarities in both primary sequence and predicted secondary structures. However, our recent studies in Pseudomonas fluorescens demonstrate that Rsm paralogs possess unique functions, where RsmE exclusively regulates the production of extracellular secretions that synergistically function to create space and gain optimal positioning within dense communities. We thus hypothesize that Rsm homologs possess a broad spectrum of activities that commonly and uniquely manifest across and within different species. To address this, we performed multiple bioinformatics analyses to explore the evolutionary history of Rsm homologs to discern structural rearrangements and identify unique motifs. Our results suggest that functional overlap is encoded within highly conserved sequences that comprise most of the protein, but unique functions reside within specific motifs in the C-terminus. This allows us to now categorize Rsm homologs by potentially unique functions and empirically test how the unique motifs confer specificity.

10 Epibatidine SAR Analogue Synthesis: Theoretical

Mechanistic Study of 1,3-dipolar Cylcoadditions Sobus, Michael; Montgomery, Thomas; Rohde, Jeffrey;

Evanseck, Jeffrey; Hejnosz, Sarah; Neal, Martin URP Duquesne University and Franciscan University of

Steubenville The natural product epibatidine possesses potent

analgesic bioactivity. However, existing routes towards its synthesis lack the flexibility required for a broad structure activity relationship study. Previous work in our group has shown that a [3+2] cyclization is a viable route to the core structure of epibatidine; such an approach introduces significant flexibility and superior efficiency compared to other methods. This study examined the electronic effects of different dipolarophiles on the [3+2] core formation reaction mechanism. We used Truhlar’s M06-2X functional in conjunction with Dunning’s jul-cc-pvDz basis set to optimize geometries, obtain activation barriers, and determine reaction enthalpies. Hammett sigma constants and CHELPG summed partial charges for each dipolarophile were used to select a wide range of coupling partners. Insights garnered from this work will guide future drug development research while increasing our understanding of the reaction mechanism.


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11 A Review: Theranostic Nanoemulsion Treatment of

Neuropathic Pain Alleviates Pain and May Influence Neuronal Damage Through Shifts in Transcriptome Expression and Cell Infiltration Reynolds, Laura1,2; Deal, Brooke1,2; Saleem, Muzamil1,2; Stevens, Andrea1,2; Janjic, Jelena2,3; Pollock, John A.1,2

1Department of Biological Sciences, Duquesne University 2Chronic Pain Research Consortium 3Graduate School of Pharmacy, Duquesne University Neuroinflammatory pain is a common type of chronic pain

affecting up to 18% of adults. Those affected tend to receive insufficient treatment due, in part, to the poor understanding of the underlying biology of pain. To better elucidate this, a neuroinflammatory model, chronic constriction injury (CCI), was applied to the sciatic nerve of male rats. The resulting pain-like response caused by CCI is alleviated through the administration of a single injection of a cyclooxygenase-2 (COX-2) inhibiting nanoemulsion (NSAID celecoxib), which accumulates in monocytes/macrophages. The nanoemulsion is delivered to the site of injury affecting local inflammation as well as influencing the dorsal root ganglion (DRG). Decrease in inflammation is seen via a reduction in macrophage infiltration, reduction in activation of COX-2 and reduction of PGE2. We have shown this by immunohistochemical observation as well as through transcriptomic analysis. Together, we reveal a shift in macrophage fate from pro-inflammatory to anti-inflammatory. This shift in cell fate also affects other inflammatory cells including mast cells (reducing degranulation). Furthermore, RNA expression is altered in neurons, glia, and immune cells. In conclusion, a micro-dose of NSAID targeting just COX-2 activity relieves neuroinflammatory pain and furthermore reveals the complex interplay of neurons, glia, and immune cells.

12 Comparing Machine Learning Models and Causal

Models in Observational Data Yasser Morsy Department of Biomedical Informatics University of Pittsburgh

Causal discovery focuses on identifying and quantifying causal connections based on the observational occurrences of events. This allows for a better understanding of how some variables impact and associate with others. The resulting statistical models allow us to make predictions of how the system will behave both under passive observation and intervention. However, causal discovery algorithms use relatively simple parametric models. Machine learning models are conventionally used more for predictive tasks and provide no causal insights. However, they can use non-parametric models and out-of-sample selection techniques to avoid overfitting, minimizing the assumptions they make about the data. The purpose of this project is to compare results of passive inference through predictive models based on various machine learning algorithms, to results of predictive models of causal discovery that use information from causal graphs produced by searching algorithms. Causal discovery and causal inference models are also compared through causal inference, where intervention is done on the treatment variable and the predicted treatment effects are compared to the true treatment effects of the original, generated data. With these results, the disparities between causal discovery and machine learning can be explored to determine how machine learning can help make more robust causal discovery models.


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13 Conformations that define the native fold of

bovine serum albumin by molecular dynamics and multivariate analysis

Palumbo, Rosalia; Seybert, David; Evanseck, Jeffrey; Srnec, Matthew Department of Chemistry and Biochemistry, Duquesne University Department of Chemistry and Physics, Franciscan University of Steubenville

Macromolecular crowding effects (MMCEs) have a

significant impact on cell kinetics and equilibria. However, in vitro experiments often do not implement crowding or do so without thorough consideration of the three-dimensional structure of common model crowding agents. MMCEs are frequently interpreted in terms of excluded volume effects based primarily upon theoretical geometric consequences of spheres. However, practical model crowding agents, such as bovine serum albumin (BSA), may show kinetic and equilibria deviations from predicted MMCEs. Our work uses molecular dynamics simulations and multivariate analysis to provide critical examination of the native-fold of BSA under physiological conditions, including its number of conformational substates and ellipticity.

Conformations of BSA are known to expand or contract based on pH, but are largely undefined in the pH 7-8 range. This project simulates the structural conformations of BSA at pH 7 and ionic strengths from 0 to 150 mM using NAMD and the CHARMM36 force field. The long-term project goal will implement constant pH molecular dynamics to test a broader pH range, enabling us to determine how solution conditions affect the prevalent conformational substates of BSA. This knowledge will enable more critical evaluation of excluded volume theory as it applies to spherical versus ellipsoidal crowders.

14 Estimating the Model Complexity of Dense Feed-

Forward Backpropagation Neural Networks Krishna, Neal1,2,3; Landsittel, Douglas P1,2, PhD Department of Biomedical Informatics1, Department of

Biostatistics2, Doris Duke Charitable Foundation Undergraduate Intern, Hillman Academy3

University of Pittsburgh, Hillman Cancer Center Multilayer perceptron neural networks, specifically feed-

forward backpropagation networks, are commonly utilized as a statistical tool for classifying and predicting high-dimensional and/or highly non-linear data. Such neural networks provide a more flexible methodology for modeling complex associations between interrelated data; however, because of the implicitly non-linear and flexible structure of neural network models, there is an inability to quantify their model complexity. By looking at the distribution of the likelihood ratio statistic within the context of binary classification problems, procedures for variable selection and determination of optimal model structure become better established.

We focus on resilient backpropagation networks with multiple sigmoid hidden layers of hidden units and random binomial single Bernoulli outcomes. We aim to verify via model simulations that the chi-square distribution provides an adequate approximation to the empirical test statistic distribution, and quantify how the distribution, number of covariates, and number of hidden layers and units affect model degrees of freedom. Our neural networks are trained dually using Keras with a Tensorflow backend and the neuralnet package in R, and as the number of hidden layers and units in a given model increases, our simulations validate the hypothesized correlation between parameters and model degrees of freedom.


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15 New approaches to in vitro macromolecular crowding

studies with bovine serum albumin Sipko, Emily; Seybert, David W. Department of Chemistry and Biochemistry Duquesne University

Use of model macromolecular crowding agents, including bovine serum albumin (BSA), enables in vitro enzyme kinetic studies to better mimic the in vivo cell environment. Conventionally, the kinetics of NADH-dependent enzymes are measured spectrophotometrically at 340 nm, but the UV absorbance of BSA extends into this wavelength region, yielding an unacceptably high background absorbance. Development of an alternative assay for measuring enzymatic activity at longer wavelengths would enable use of higher BSA concentrations in these studies. A viable coupled assay is a promising candidate, employing the NADH-dependent reduction of a water-soluble tetrazolium salt (WST-8) to a formazan absorbing at 450 nm. Introducing BSA into this assay, however, results in a BSA-concentration dependent decrease in the reaction rate of NADH with WST-8, and a slower NADH-independent background reaction suggesting BSA reduction of WST-8. This project focuses on investigating the cause of BSA interference with the WST-8 assay through a focus on the sulfhydryl group of the free cysteine (Cys34) on BSA. Chemical modification converting the free thiol group to a thioether is hypothesized to decrease the interference of BSA with the WST-8 assay, thus enabling higher and more physiologically relevant BSA concentrations to be used in macromolecular crowding studies.

16 Projective Geometric Algebra as Language for

Paraxial Geometric Optics Spadavecchia, Katelyn and Corcovilos, Theodore A. Dept. of Physics Duquesne University Geometric Algebra (GA), a subset of Clifford Algebra, is

useful in many fields of study including optics. For many decades GA was overshadowed by Gibbs’ formulation of vector algebra, but researchers are finally understanding its power. GA offers conceptual clarity by representing points, lines, and planes all as vector-like objects. As a result, geometric operations like rotations and reflections are represented by simple multiplication. GA also provides the complete framework for different types of algebras including imaginary numbers, quaternions, and differential forms.

While these newly revived math tools are gaining acceptance in computer graphics and mechanical engineering, they have sparingly been applied to optics, and for our research, paraxial geometric optics. Paraxial geometric optics uses flat surfaces and small-angle approximations to simplify calculations. In our research, we use projective geometric algebra (PGA) to show how basic optical systems like spherical mirrors and thin lenses can be described in paraxial geometric optics by simple expressions more efficiently than traditional ray tracing methods. In particular, we show how ray transfer matrices can also be used to map object points onto images. From our research, we conclude that PGA is a more natural mathematical description for paraxial geometric optics than ray tracing.


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17 Optimization of Reagent-free Mitsunobu Reactions Frederic, Wrebekah; Bloomfield, Aaron Department of Chemistry and Biochemistry Duquesne University The Mitsunobu reaction is a widely used stereoselective

nucleophilic substitution reaction in which a primary or secondary alcohol and a pronucleophile are condensed to form the desired product. A catalytic Mitsunobu reaction reported by Beddoe et al. substitutes a 2-hydroxybenzyl tertiary phosphine oxide (2-HOBTPO) catalyst for stochiometric reagents, triphenylphosphine and diethyl azodicarboxylate (DEAD). However, Beddoe’s reaction has limitations; a reaction temperature above 140°C and a pronucleophile with a pKa ≤ 3.4 is required for measurable catalysis. We propose that altering the electronics will help stabilize the high-energy phosphonium intermediate in the catalytic cycle, thus improving its efficiency. A library of 2-HOBTPOs with systematic variation of electron-donating/electron-withdrawing substituents was constructed computationally and optimized using either B3LYP hybrid functional with Pople’s 6-31+G (d, p) basis set or MP2 with Dunning’s cc-pVDZ basis set. Relative free energies and enthalpies of catalytically relevant species could then be compared. Results indicate that the electronics of substituents on the phenolic arene, and those directly bound to the phosphorus atom have significant influence on relevant intermediates. Furthermore, non-covalent intramolecular interactions, especially hydrogen bonding, appear to significantly influence the basicity of the 2-HOBTPOs. This research serves to provide a foundation for designing a more efficient catalytic Mitsunobu reaction.

18 Understanding the Structure of a Uniquely Made

Erlotinib Polymorph Bedillion A Derek, Quinones-Fernandez, Rosalynn,

Iuliucci J Robbie Washington & Jefferson College Department of

Chemistry Tarceva is a cancer drug used to treat non-small cell

lung cancer. Tarceva suffers from its active pharmaceutical ingredient’s (API) poor dissolution rate. To address the poor dissolution rate, new ways to prepare erlotinib, tarceva’s API, have been explored using surface modified metal oxides (SMMO). A novel polymorph of erlotinib has been created using a self-assembled monolayer of n-octadecylphosphonic acid on zinc oxide plates. Due to the crystallization process, crystals created by SMMO cannot be analyzed by traditional single-crystal diffraction. To solve the crystal structure of the novel form, NMR crystallography is being used. This study is to compare experimental data to predicted NMR parameters of known crystal structures for erlotinib reported in literature and theoretical crystal structures generated by crystal structure prediction (CSP). Planewave DFT with the revised Perdew, Burke, and Ernzerhof (RPBE) functional, is used to predict the chemical shift anisotropy of crystal structures with relaxed coordinates using Grimme’s D2 dispersion corrected method. Comparison to a series of crystal structures reported in the Cambridge database demonstrates that the SMMO polymorph is unique. Therefore, CSP candidate structures generated by the Materials Studio’s Polymorph module using dreiding are being screened to identify the novel crystals structures.


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19 Hybrid Quantum Mechanical-Molecular Mechanical

Computational Approach to Modeling the Water Solvated Uncatalyzed Decarboxylation of Monoanionic Malonate

Jemison, Kezia; Tamez, Angel; Evanseck, Jeffery Center for Computational Sciences, Department of

Chemistry and Biochemistry Duquesne University A multitude of factors are suspected to affect the

mechanism of enzyme catalysis. Our interest is in the impact of solvent upon the enzyme-catalyzed decarboxylation of monoanionic malonate, more specifically, how the waters directly hydrogen-bonding to malonate affect the enthalpy of activation of both enzyme-catalyzed and uncatalyzed reaction pathways. The subtractive QM/MM ONIOM method in Gaussian16 with a cluster of 10 explicit waters to satisfy all hydrogen-bonding sites and a second solvent shell to represent bulk phase water were used to reproduce and refine to the experimental enthalpy of activation of 30.0 kcal/mol for the uncatalyzed orthogonal monoanionic malonate system. The M06-2X density functional with the jul-cc-pVDZ basis set was used for geometry optimization, energy evaluation, and frequency analysis of malonate, the QM layer, while AMBER parameters were used to define the MM layer containing TIP3P waters (including Tomasi’s polarizable continuum model (PCM)). The ten explicit waters for hydrogen bonding were found to stabilize the orthogonal conformation by 2 kcal/mol over the commonly assumed pseudo-chair conformation with an intramolecular hydrogen bond and reproduced experiment. This work offers further knowledge about similar solvent-substrate interactions, and potential in describing enzyme catalyzed decarboxylation mechanisms.

20 Title: Analyzing Pion Data Using Semi-Inclusive Deep

Inelastic Scattering Matthews, Emily Physics Department Duquesne University Semi-Inclusive Deep Inelastic Scattering (SIDIS) is the

process used to crack open protons and neutrons in order to study their internal structures. This method is used at the Thomas Jefferson National Accelerator Facility in Newport News, VA. A beam of electrons is accelerated to nearly the speed of light These photons are then sent through the proton target and scattered on a proton target. Different subatomic particles can result form this reaction: pions and kaons are examples. My work consisted in studying the pion jets by understanding their energy, momentum, and angular distributions. This study is compared to Monte-Carlo calculations that will help us understand the reaction mechanism and the effects of the detector acceptance in the final Physics analysis.


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21 Turbulent Mixing and Applications in Abandoned

Mine Drainage Bachtlin, Alanna. Enderby, Hannah Center for Environmental Research and Education Duquesne University Abandoned coal mines are prevalent throughout the U.S,

particularly in the east where coal mining was most abundant. These abandoned mines contain sulfide minerals, which, when mixed with oxygen and water over time, results in polluted water known as abandoned mine drainage (AMD). Passive remediation systems such as settling ponds and wetlands can be built to remove heavy metals from the polluted AMD before it enters the local watershed. Aerobic conditions are necessary in passive systems to settle heavy metals out of the water. It’s important to study turbulent mixing in passive remediation systems to ensure oxygenation. In order to learn more about the effects of turbulent mixing on AMD, we modeled turbulent mixing of a sloped stream using the

finite element model, COMSOLⓇ, to estimate turbulent

diffusion. Our goal was to use turbulent kinetic energy (m2•s-2) to predict diffusivity (m2•s-1) and model the progression. The diffusion coefficient would tell us the following: The rate of both oxygen gas mixing into water and oxygen transport in aquatic systems and help model the remediation of heavy metals. This can inform improved passive remediation design.

22 Molecular dynamic simulations of folding and

dimerization in mutations found in the s2m motif of SARS-CoV-2

Mackenstein, Nicole; Pellegrene, Kendy; Shine, Morgan; Lackey, Patrick E.; Mihailescu, Mihaela-Rita; and Evanseck, Jeffrey D.

Biochemistry and Chemistry Duquesne University and Westminster College SARS-CoV-2 is the virus responsible for the COVID-19

pandemic. All coronaviruses contain a highly conserved stem-loop within the 3’ untranslated region referred to as the s2m motif. Evidence suggests that the s2m motif plays a key role in replication and recombination by facilitating dimerization. In SARS-CoV-2 we see slight differences in the s2m sequence from SARS-CoV-1, and the functional result of this is unknown. In addition to the wild-type sequence, we have also observed mutations in the s2m motif in reported coronavirus patients that were in a previously thought invariant position. To better understand dimerization in the s2m region we used MD simulations to both analyze the folding of the mutants as monomers and to study the dimerization of the mutants compared to the wildtype. Using AmberTools and NAMD, systems for each mutant were created, minimized, equilibrated, and then submitted for production. The results were analyzed and aligned to the reference sequence to allow for primary component analysis using VMD and MDTools. Changes in thermodynamics, positions of the bases, and RSMD between the reference sequence and our mutants were then observed. HNADock was then used to pin each mutant against itself to find the most thermodynamically favorable model for dimerization.


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23 Computational characterization of the s2m region

within mutant SARS-CoV-2 RNA Kelleher, Bryan; Pellegrene, Kendy; Shine, Morgan;

Lackey, Patrick E.; Evanseck, Jeffrey D.; Mihailescu, Mihaela Rita

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the virus responsible for the current COVID-19 pandemic. SARS-CoV-2 is a non-segmented positive-sense RNA virus with a highly conserved 3’ untranslated region (3’ UTR). Within the 3’ UTR lies the stem-loop II motif (s2m), a secondary structure which is believed to facilitate dimerization of the genomic RNA through interactions with the viral accessory N protein. While reviewing current SARS-CoV-2 sequence databases, multiple single point mutations were found within the s2m region despite its usual conservation. In this work, mutant sequences of the s2m region within SARS-CoV-2 RNA will be modeled computationally. Each mutation will be made from an existing protein data bank file of the previously crystallized s2m region of SARS-CoV-1 RNA. Using molecular dynamics simulations with NAMD software, comparisons between the secondary structures of each mutant sequence can be made. Then the mutant sequences will be tested using HNADOCK, an RNA-RNA docking software, to observe their differences in dimerization structures. By comparing SARS-CoV-2 with its mutant sequences, the impact that structural differences in the s2m region have on dimerization can be brought to light.

24 Optimization of MatLab Code for Analysis of Urinary

Bladder Distention for Visceromotor Response Babyok, Olivia, Gil-Silva, Mauricio, Majetic, Gabrielle,

Kolber, Benedict Department of Biological Sciences, Chronic Pain

Research Consortium Duquesne University, Pittsburgh, Pennsylvania Urologic Chronic Pelvic Pain Syndrome (UCPPS) affects

millions of people, but predominantly affects women. Symptoms of UCPPS include but are not limited to mild to severe bladder/abdominal pain, anxiety, depression, urinary incontinence, and recurring urinary tract infections. Currently, there are no known causes of UCPPS and there are no known effective treatments, which makes this a particularly important area of study. Urinary bladder distention (UBD) is a reliable and efficient way to mimic the pain and associated symptoms of UCPPS. The response measured with UBD is the visceromotor response (VMR), which is a processed electromyogram (EMG) signal. Previously, the lab used IgorPro by Wavemetrics to process the raw EMG data. However, an interest was taken in converting to MATLAB by MathWorks due to the fully customizable nature of the software. In addition, IgorPro is not well represented in neuroscience. Thus, we endeavored to create a new analysis program in MATLAB that could take in and analyze data collected from UBD trials. After completing the script for the program, a file of real experimental data that was previously collected was successfully analyzed. Looking forward, we hope to create an easy-to-use graphic user interface for more efficient and comfortable analysis.

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25 The Role of Female Behavior During Salamander

Courtship Slater, Tasia E & Woodley, Sarah K. 1Department of Biological Sciences, Duquesne University,

Pittsburgh, PA Plethodontid salamander courtship is a well-studied,

prime example of behavioral evolution over long time scales. Study of salamander courtship has focused on how males “persuade” females to engage in mating. The role of females has been largely ignored. To better understand female behavior, I will study why female mating propensity decreases for several days after insemination. I propose that with insemination, females become 1) unattractive to males, 2) energetically drained, or 3) sexually unmotivated. If females are energetically drained, I predict they will be less active and forage more. If they are sexually unmotivated, they will be uninterested in male pheromones. To test predictions, females will be paired overnight with a male, and locomotory behavior, hunger, and interest in male pheromones will be measured the next day. Females will be paired with males multiple times to compare responses after insemination versus no insemination within a female. Furthermore, if females are uninterested in male cues, I will test whether the change in female motivation is due to a change in estradiol levels. Here, females will be treated with estradiol or vehicle and mating behavior will be measured. Together, these studies will provide insight to the role of females in behavioral evolution.

26 The Fabrication of an Anti-Inflammatory Implant

Surface Demjanenko, Peter; Armen, Jennifer; Gawalt, Ellen Department of Chemistry and Biochemistry Duquesne University Total hip and total knee arthroplasties are some of the

most commonly performed surgical procedures, yet there is still a significant rate of revision surgeries; the current revision burden for total hip and knee arthroplasties are 17.5% and 8.2%, respectively. No biomaterial, alone, addresses the two largest causes of orthopedic implant failure: aseptic loosening and bacterial infection. In this work, a novel surface for orthopedic implants is being designed to address these issues. It consists of a Ti-6Al-4V coupon coated with an artificial extracellular matrix (aECM) of collagen I and high-sulfated hyaluronic acid (hsHA), further modified with vancomycin. In order to covalently immobilize the collagen and hsHA, a carboxy-terminated self-assembling monolayer will be used in conjunction with Genipin, a crosslinker. The aECM will be characterized using scanning electron microscopy (SEM), atomic force microscopy (AFM), and contact angle. The vancomycin antibiotic will be crosslinked to the matrix using a N,N’-dicyclohexylcarbodiimide (DCC)-amide coupling mechanism. The antibacterial nature of the material will be assessed using a colony forming unit analysis and LIVE/DEAD imaging with Staphylococcus epidermidis. The immunomodulatory nature of the material will be assessed with an ELISA for proinflammatory cytokines and a measurement of the M1/M2 index, using rat alveolar macrophages.


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27 Hamamatsu H12700 Multi-Anode Photomultiplier

Tube Performance Estimation Boyer, Aiden Department of Physics Duquesne University The Hamamatsu H12700 Multi-Anode Photomultiplier

Tube (MAPMT) is an amplification device that measures the intensity and spectrum of emitted light. A collection of H12700 MAPMTs are used in the two Ring Imaging Cherenkov Detectors (RICH) of the CLAS12 Spectrometer in Hall B at Jefferson Lab. The two RICH detectors use the principle of Cherenkov radiation to distinguish kaons from pions and protons resulting from high energy electron scattering experiments. One RICH was installed in 2018 and the second one is under construction. Here I report on a performance estimation done for 120 MAPMTs for the second RICH detector based on the data included on the manufacturer data sheets. The devices will be analyzed based on their gains, dark currents for different operating voltages, luminosity sensitivities of the cathode and anode, and sensitivity to blue light, which is the typical wavelength range for Cherenkov radiation. This study will be compared to the existing study of two types of older MAPMTs that were used for the first RICH.

28 CCSD(T) and DFT torsional energy scan

comparisons on 3-aryl substituted oxocarbenium ions

Rodo, Edgar; Castele, Erin; Makowski, Joseph; Woerpel, Keith; Evanseck, Jeffrey.

Department of Chemistry and Biochemistry. Duquesne University. Stereoselective reactions of five-membered-ring

oxocarbenium ions have been previously reported by experiment to proceed with high stereoselectivity dictated by C-3 substitution. To date, a stereochemical model to predict the dramatic change in stereoselectivity depending upon heteroatom or alkyl substituents does not exist. The focus of our work is to establish the expected accuracy in the structural and energetic prediction of density functional theory (DFT) on the large 3-benzyl ether five-membered-ring oxocarbenium ion. In the absence of experiment structures, the use of DFT typically relies upon the comparison with trustworthy and proven computational methods, such as the commonly referred to “golden standard” of CCSD(T). The 3-benzylether substituent has two torsional angles that dictate possible conformations. Conformations and energies were determined using Truhlar’s M06-2X functional, the second-order Moller-Plesset (MP2), and CCSD(T) methods with Dunning’s jul-cc-pvDz basis sets. The accuracy of the practical DFT method with the golden standard is discussed. A full application of DFT will allow for the development of a stereochemistry model with accuracy.


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29 Determination of Persistent Organic Pollutants

(POPs) in Varying Foods Taylor Teitelbaum1, Weier Hao 1, Tiffany Hoke1, Matt

Pamuku2, and H. M. “Skip” Kingston1 1Department of Chemistry and Biochemistry, Duquesne

University, Pittsburgh, PA 2Applied Isotope Technologies Company, Pittsburgh, PA Persistent organic pollutants (POPs) are toxic organic

molecules found at significant concentrations in the food chain with negative effects on both the human body and wildlife. POPs’ resistance to natural degrading and semi-volatility enable them to be easily dispersed throughout the environment, contaminate produce, and bioaccumulate. Some food may not be optimal for human consumption and some open for debate with accordance to laws, statutes, and toxicity health data as a result of these contaminations. These facts necessitate a robust method that will accurately quantify simultaneous POPs in foods. Stir-bar sorptive extraction (SBSE) in combination with gas chromatography mass spectrometry and isotope dilution mass spectrometry (IDMS-GC/MS) quantification will be utilized to determine the concentration of POPs in a variety of produce. SBSE is ideal for isolating trace amounts of organic compounds and is a thermal desorption method that is greener than previous extraction methods that required solutes. IDMS-GC/MS was chosen for this analysis since POPs can be separated by means of volatility and chromatography. This method is very sensitive and has a very low limit of detection and quantification. The testing of these foods via this methodology will prove the validation of labeling of foods as organic and correct some inaccurate labeling.

30 Distinguishing Between Steric and Electrostatic

Effects on Stereochemistry of Nucleophilic Addition to Five- and Six-Membered Oxocarbenium Ions

Makowski, Joseph; Rodo, Edgar; Castele, Erin; Woerpel, Keith;1 Evanseck, Jeffrey

Department of Chemistry and Biochemistry Duquesne University; 1New York University Stereoselective reactions of five- and six-membered-ring

oxocarbenium ions have been previously reported by experiment to proceed with high stereoselectivity dictated by C-3 substitution for five-membered rings and at the C-2, C-3 and C-4 positions of six-membered rings. Transition structures of nucleophilic additions to oxocarbenium ions reveal the stereochemical underpinnings of the observed selectivity and reactivity. Specifically, transition state additions of allyltrimethylsilane to the inside or outside of the envelope of oxocarbenium ions were calculated with either axially or equatorially oriented substituents (methyl, methoxy, benzyl ether) at the positions showing selectivity. The two essential noncovalent interactions involve symmetric attraction between allyl protons and the benzyl ether oxygen and silyl-methyl with the aryl face. Using the enthalpies and free energies of the most thermodynamically favored conformations for each substituent, the Curtin-Hammett principle was employed to predict the resultant stereoselectivity, which were found to be in strong agreement with experimental values (benzyl ether 98:2 compared to 94:6; methyl 90:10 compared to 93:7) where the electrostatic axial oxygen interaction at the transition structure with the vinyl protons is dominant but the silyl methyl – aryl interaction makes an important contribution. Future work will investigate stereoselectivity in additions proceeding through seven-membered ring oxocarbenium ions.


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31 The Role of Topoisomerase I in Herpes Simplex Virus

Infection Esenweina, Raegen; Packarda, Jessica; Dembowskia, Jill Department of Biological Sciencesa

Duquesne University Human topoisomerase I (TOP1) is an enzymatic protein

necessary for normal growth and development. TOP1 ensures DNA transcription and replication occur properly by relieving the topological stress of supercoiled DNA. To do so, TOP1 creates nicks in single stranded DNA, allowing for complete relaxation of the DNA. The catalytic activities of TOP1 are highly regulated by cells to prevent the negative effects which result from the accumulation of supercoiled DNA and nicks. TOP1 has been identified as a cellular protein which interacts with viral DNA during the infection cycle of herpes simplex virus type 1 (HSV1). Based on the nature of TOP1 in normal cells, the protein is thought to act near the viral replication fork of a cell infected with HSV1. It is hypothesized that by knocking out TOP1 within HSV1 infected cells, the infection process would not proceed as anticipated due to the interruption of viral DNA transcription and replication. CRISPR-Cas9 genome engineering technology was utilized to create plasmid clones which target TOP1 and initiate the knockout of the protein. The creation of these plasmids was successful, and these results will enable further study of the role of TOP1 in the HSV1 infection cycle.

32 Investigation of PCNA Function During Herpes

Simplex Virus Infection Williams, Maya, Jessica Packard, Jill Dembowski, PhD The Department of Biological Sciences Duquesne University

Proliferating cell nuclear antigen (PCNA) is a protein that

is used to stabilize DNA polymerases during DNA replication. PCNA associates with herpes simplex virus type 1 (HSV-1) replication forks, but it is not known what role it plays in this process. In order to more specifically find if and how HSV-1 uses PCNA, the CRISPR/Cas 9 technique will be utilized to knockout the PCNA protein in the host cell. To generate CRISPR/Cas9 knockout cells, we will transfect cells with a plasmid that expresses a guide RNA that guides the Cas9 enzyme to a segment of the host DNA that codes for PCNA. This plasmid also codes for Cas9, which then specifically cleaves this targeted sequence. To do this, we first designed guide RNAs to target PCNA and cloned the guide RNA sequence into the CRISPR/Cas9 plasmid. To see if the insertion of this oligo into the plasmid worked, gel electrophoresis and sequencing results are analyzed. Electrophoresis results were inconclusive, but sequencing confirmed that the insertion was successful. The next step is inserting the plasmid into a host cell then infecting the cell with HSV-1 and investigating the effect on the virus life cycle.


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33 The Structure, Flexibilities, and Energies of the

Urea/Thiourea Dual Hydrogen Bond Donor Core Moskal, Lindsay; Tressler, Serina; Cocolas, Alex; Tamez,

Angel; Montgomery, Thomas; Evanseck, Jeffrey D. Center for Computational Chemistry and Department of

Chemistry and Biochemistry Duquesne University Despite the success of ureas and thioureas as dual

hydrogen bond donor (DHBD) catalysts, the unusual structure, flexibility, and energies of the urea/thiourea core remain an enigma. Our work defines the potential energy landscape of urea and thiourea along with the tert-butyl,

phenyl, and benzyl α-substituted analogs commonly used in asymmetric catalysis. We utilized the M06-2X functional and second-order Møller-Plesset theory (MP2) with the aug-cc-pVDZ basis set. Unsubstituted DHBDs were found to adopt an anti-conformation (C2) with NH2 hydrogens pyramidalized on opposite sides of the molecule and a less stable syn-conformation (Cs) with the hydrogens pyramidalized on the same side. For the phenyl, t-butyl, and benzyl substituted thiourea anti-conformation, the core planarity about C=X (X = O or S) decreased within 2° of planarity. The twist of the α-substituent from planarity increased by up to 5°. The nonplanarity of the anti-proton for the t-butyl and benzyl substitutions increased by up to 10°. Similar analysis will be carried out for urea and its analogs. These findings have furthered our understanding of the unusual structure, flexibility, and energies of the urea/thiourea core and can be applied to other compounds with similar functional groups to design more efficient catalysts for asymmetric organic reactions.

34 Public data consistency analysis and preliminary

models of Covid-19 infection fatality rates Coufal, Sarah Biomedical Informatics University of Pittsburgh The objective of this research project is to use

epidemiological models to develop an estimate of the Covid-19 infection fatality rate (IFR) in the United States. Public data is required to inform these models. While there are many public datasets that contain information on the counts of Covid-19 deaths around the country, it is necessary to build an understanding of the quality of available data sets to ensure that data used for modeling is accurate and complete. Measuring consistency between sources identifies areas of discrepancy and determines which sources are most reliable. We identified six publicly available websites and conducted pairwise comparisons to assess the similarities in both the availability of data and the magnitude of counts. The next step will be to select a dataset using these techniques of comparison to estimate the IFR. To calculate the IFR, we will use a Bayesian approach based on SEIR models with daily death counts from one of the datasets and published probabilities of death throughout the course of an infection as inputs. A more accurate estimation of the IFR can help scientists and policymakers understand the scale of the disease and plan effective health responses.


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35 Sustainable Farming Practices and Marketing

Strategies for Growing and Selling Produce on a Livestock Farm

Center for Environmental Research and Education Duquesne University Cava, Kacie

To demonstrate that sustainable farming practices and

marketing techniques can be utilized on a livestock farm to increase yields and meet local customer demand, a field experiment was conducted to determine consumer produce needs as well as yields of zucchini, squash, cucumber, basil, and various species of peppers. These vegetables were planted in seven raised beds at the beginning of the summer and chosen based off of self-reported customer demand. Each harvest was counted and weighed over five weeks. At the end of five weeks, the total yield was divided by the total square footage allotted to each species to obtain the yield per square foot in both pounds and individual fruit. To supplement produce from the garden, produce was purchased from a local produce auction. Produce was sold to both customers of the farm as well as customers of a local ice cream stand. Results show that over five weeks, a profit was made every week. The average profit per week was $60. Both growing produce in raised beds and buying wholesale from an auction provide customers with a sustainable product while supporting the local economy and community of farmers.

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36 Role of Topoisomerase II in Herpes Simplex Virus

Infection Process Holly Barwatt, Jessica Packard, Jill Dembowski, PhD Department of Biological Sciences, Duquesne University

Topoisomerase II (TOP2B) is an essential enzyme used to unwind supercoils in DNA and relieve topological stress, primarily in DNA replication and transcription. Viruses, including the Herpes simplex virus 1 (HSV-1), utilize cellular factors such as TOP2B during the infection process. Previous studies have found that TOP2B interacts with HSV-1 genome and may aid in the DNA replication and transcription, though its exact role in still unknown. This study sought to insert a guide RNA sequence homologous to a target region of TOP2B DNA into a plasmid containing the CRIPSR-CAS9 system. By genetically modifying the DNA, the Cas9 enzyme can catalyze a knockout of the TOP2B protein. This experiment successfully cloned the plasmid to knockout the protein, and these results will be the first step of the process to help provide insight on the exact role TOP2B plays in the HSV-1 life cycle.


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37 Patterns of loss-of-function mutations in the human

genome McClure, Taylor M.1; Jensen-Seaman, Michael I.2

1Forensic Science & Law Program; 2Department of Biological Sciences

Duquesne University Natural selection acts to remove harmful variants. At the

population genetic level, this is seen in the ongoing removal of mutations that result in functionless genes (“loss-of-function” mutations). This process is rather inefficient, resulting in every human possessing several dozen loss-of-function alleles, mostly in the heterozygous state. Recent large-scale sequencing for the first time allows for an examination of the genomic patterns of loss-of-function mutations in humans. In order to test hypotheses related to gene expression, function, and mutation, the programming language Python was used to manipulate data sourced from the Genome Aggregation Database, or gnomAD – a comprehensive resource detailing variations within tens of thousands of human genomes and exomes – and the Human Protein Atlas, which provides normalized gene expression data in different tissues. We will present results regarding the frequency of loss-of-function mutations in genes that are tissue-specific vs. ubiquitously expressed and sex-biased vs. unbiased, and as a function of other genomic variables.

38 Calibration of a homemade color-based detector for

water contamination Aumer, Thomas; Corcovilos, Theodore Physics Department Duquesne University One challenge to the maintenance of safe drinking water

supplies, particularly in underdeveloped countries, is regular testing of the water for contaminants. We are developing a cost-effective handheld device that can be used to measure the concentrations of common water contaminants such as fluoride and lead. Our device works by measuring optical absorbance changes in samples of water with added appropriate chemical sensing agents. By measuring absorbance of six color bands simultaneously, our device has improved sensitivity and accuracy than traditional single-color measurements.

We present several calibration methods for our device, first comparing linear, exponential, and logistic fitting equations to the absorbance data by the maximum likelihood method. We then fit the data again using Markov Chain Monte Carlo implementation of Bayesian statistics for more accurate modeling of experimental uncertainties, including correlations between the color channels. Through extensive testing and modeling, the use of Bayesian statistics leads to an increase in sensitivity compared to the maximum likelihood method.

This work is a collaboration with Profs. David Kahler and Michael Van Stipdonk.


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39 Molecular Dynamic Simulations Reveal Allosteric

Communication Between the Androgen Receptor BF-3 Surface Binding Site and the Steroid Binding Pocket

Bravo Naila‡, Tamez Angel†, Evanseck Jeffrey†, Kotsikorou Evangelia‡.

†Center for Computational Sciences Department of Chemistry and Biochemistry, Duquesne University.

‡Department of Chemistry, University of Texas Rio Grande Valley.

Endocrine disrupting chemicals (EDCs) bind to the

androgen receptor (AR), a steroid binding receptor, and dysregulate its function, resulting in deleterious effects on humans. It is thought that EDCs bind directly to the steroid binding site and disrupt its function. However, new data indicates that EDCs may exert their effect on AR allosterically by binding to the surface site BF-3. This study investigated the effect that p,p'-DDE bound to BF-3 has on the stability of bound dihydrotestosterone (DHT). 2nd-order Møller-Plesset perturbation theory and the CHARMM General Force Field were used to develop parameters for p,p'-DDE. Molecular dynamics (MD) simulations were used to probe the effect of p,p'-DDE bound in the BF-3 site on the stability of DHT binding pocket residues. A 200-ns control MD simulation was run for the AR-steroid complex without p,p'-DDE. The parameters developed for p,p'-DDE were used to run six 200-ns simulations of the AR-steroid complex with p,p'-DDE docked in the BF-3 site. Analysis showed structural variation between the systems with p,p'-DDE and the control. The residues near DHT had increased mobility while the residues near p,p'-DDE were less mobile. Further studies will measure binding and dissociation energies of DHT via random accelerated and steered MD simulations.

40 DNA Barcoding Analysis of Fish Specimens from

Duquesne University’s New Research Facility in Belize

Ghobrial, Jessica and Porter, Brady. Department of Biological Sciences, Duquesne University

In 2019, Duquesne University established a scientific research station at Lower Dover in the Cayo District of Belize, Central America and conducted a Maymester course in Biodiversity with undergraduate students. Freshwater fishes were collected onsite from Little Barton Creek, tributary of the Belize River. Morphological samples were retained, and tissue samples were preserved in ethanol for DNA barcoding. DNA was extracted from specimens tentatively identified as the Blue-eye Cichlid (Cryptoheros spilurus), Green Swordtail (Xiphorporus helleri), and Central Tetra (Astyanax aeneus). A portion of the mitochondrial cytochrome oxidase subunit 1 (COI) gene was amplified by PCR at Duquesne’s new lab facility in Belize, and upon return to Duquesne University, the PCR products were cleaned and Sanger sequenced. The COI sequences were aligned with available sequences from GenBank. Phylogenetic analysis showed the cichlid samples were closely related to a clade that included Cryptoheros spilurus and a recently described species, Cryptoheros chetumalensis. The Green Swordtail showed a close phylogenetic relationship to Xiphoporus helleri and the Central Tetra to a clade containing Astyanax aeneus and Astyanax altior. Additional sequences and morphological analyses are required to obtain a confident identification at the species level.


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41 Preventing Thrombus Formation on Left Ventricular

Assist Device Weber, Hannah1; Armen, Jennifer M.1; Meng, Wilson

S.2,3; Gawalt, Ellen S.1,2

1Department of Chemistry and Biochemistry, 2McGowan Institute for Regenerative Medicine, 3Graduate School of Pharmaceutical Sciences, School of Pharmacy

Duquesne University Left ventricular assist devices (LVADs) made of titanium

dioxide (TiO2) can be used to assist in circulation of blood in patients in end stage heart failure. Potentially life-threatening blood clots can form on LVADs, which can prevent the motor from turning or get pumped through the heart and up to the brain, which can result in an ischemic stroke. Enoxaparin sodium and cangrelor have been used to prevent blood clots in vivo, however direct attachment to medical devices is desirable because it would allow for localized treatment. In this study, cangrelor will be attached directly to TiO2, while self-assembled monolayers (SAMs) will be utilized to immobilize enoxaparin sodium onto the surface of the metal. Modifications will be confirmed using diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy, contact angle measurement, and atomic force microscopy (AFM). In addition, the effectiveness of enoxaparin sodium and cangrelor on TiO2 in preventing blood clots will be examined using a peristaltic pump to mimic blood flow of the heart. Scanning electron microscopy (SEM) will be utilized to evaluate clot formation on samples of enoxaparin sodium, cangrelor, and combination modified TiO2.

42 The Effect of Noncovalent Interactions on Reductive

Elimination of Diaryliodoniums with Neutral Nucleophiles

Shide, Jasper; Koch, Andrew; Montgomery, Thomas; Evanseck, Jeffery

Department of Chemistry, St. Mary’s College of Maryland (In collaboration with Duquesne University)

Diaryliodoniums have seen increasing use as metal-free

‘green’ arylating agents in otherwise difficult reactions. Prior experimental and computational studies have primarily focused on reductive elimination in systems with small anionic nucleophiles. In some cases arylations with some neutral nucleophiles have given different results from reaction with anionic nucleophiles; which may indicate that they proceed through a different mechanism entirely. Characterization of the pi-pi interactions between the aromatic ring of the nucleophile and that of the target aryl group, along with the resulting transition states, will allow for a more complete understanding of the mechanism through which arylation occurs in these systems. A density functional theory (DFT) approach utilizing the MN15 functional with the cc-PVTZ basis set for atoms in rows 1-3 and the SDD effective-core potential (ECP) basis set with added d and f polarization for iodine was used for geometry optimization, transition state analysis and evaluation of energy and frequency. All calculations were performed in the gas phase. Preliminary results indicate a small but surmountable energy difference between lone-pair and pi-pi driven coordination of the nucleophile. Determination of the transition states of either conformation will indicate which reaction is more energetically favorable.


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43 Extraction of Pollutants and Other Illicit Substances

from Mealworms (T. molitor) Plyler, Alexandria; Van Stipdonk, Michael Department of Chemistry and Biochemistry Duquesne University

Insects have the ability to reflect the chemical

environment they reside in, making them a potential biological matrix for a variety of disciplines. For example, conservationists can potentially collect insects as samples for the screening of contaminants of emerging concern (CECs) in a specific ecosystem. Additionally, forensic scientists can utilize insects to detect the presence of drugs in cadavers.

This study involves the investigation of three CECs—triclosan, glyphosate, and chlorpyrifos—as well as one illicit compound of forensic interest, phenethylamine. A plan for a prospective experimental design to extract and detect these four compounds in larval mealworms (T. molitor) is laid out after a review of the relevant literature. By feeding spiked substrate to mealworms, employing a QuEChERs extraction method, and analyzing the extract using tandem mass spectrometry, we hope to provide a screening method that is applicable to both environmental and forensic science.

44 The Impact of Socioeconomic Status on

Neurological Outcomes in Multiple Sclerosis Boorgu, Devi Sai Sri Kavya1, Venkatesh, Shruthi2,

Lakani, Chirag M.3, Patel, Chirag J.3, Xia, Zongqi2

1. University of Pittsburgh School of Medicine, Pittsburgh, PA

2. Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA

3. Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA

Multiple Sclerosis (MS) is a chronic autoimmune

condition that affects the central nervous system. Unfortunately, there is significant cost associated with MS care and lower socioeconomic status (SES) is correlated with increased risk of disability progression. This study analyzes the longitudinal impact of socioeconomic status on disease progression of MS in the Pittsburgh and New York City regions. This study assesses if (1) SES status from 2011 to 2015, (2) a change in SES status from 2011 to 2018, and (3) individual versus area SES components predict neurological outcomes in 2019-2020. Patient data has been collected through clinic-based studies at the University of Pittsburgh Medical Center and Columbia University Irving Medical Center. Neurological outcomes are self-reported with Patient-Determined Disease Steps (PDDS), Multiple Sclerosis Rating Scale – Revised (MSRS-R), and Patient-Reported Outcomes Measurement Information System (PROMIS) scores. Data analysis used R software. Pearson correlations and covariate-adjusted analyses were performed using logistic regression. Results are tending toward lower SES components correlating with higher MSRS-R and PROMIS scores, indicating lower SES status may underlie higher disability in MS patients. Moreover, an increase in median household income correlates with a decrease in disability, as seen with lower associated MSRS-R and PROMIS scores.


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45 Title: Dynamic Bayesian networks for analyzing and

integrating longitudinal multi-omics host-microbiome dynamics in prediabetes

Student: Meléndez Cartagena, Sofía * Advisor: Lugo-Martinez, Jose ** *Biology Department **Computational Biology Department *Universidad de Puerto Rico Recinto de Río Piedras **Carnegie Mellon University Prediabetes and Type 2 diabetes (T2D) have been

associated with insulin resistance (IR), thus, prediabetes presents a unique opportunity to study the earliest stages of diabetes individuals at high-risk for T2D. With the purpose of gaining a deeper understanding of this prediabetes/T2D relationship, the integrative Human Microbiome Project (iHMP) has collected a multi omics time-series data set comprised of samples from 106 healthy individuals as well as individuals with prediabetes for over approximately four years. We used the iHMP data set to learn probabilistic models of the multi-omic components in the microbiome that are pivotal for the onset of T2D. From the data set, we focused on the healthy individuals whom all were classified as either insulin sensitive (IS) or IR. We used temporal alignment and dynamic bayesian networks to map out the relationships in the data, taking into consideration the final prognosis of each individual. We found that certain bacteria appear to be the source of later appearances of omics in the network more often than the rest of the possible omic sources per data sets. These bacteria have been found associated with the onset of diabetes and could provide key insight into it’s pathways.

46 Effective Visualization Model of EHR data to Support

Physician’s Clinical Decisions Onyeador, Jeffrey; Senathirajah, Yalini(mentor) Department of Biomedical Informatics University of Pittsburgh Patient Data in EHR is voluminous, complex, and hard

to digest at a glance. Exploring different visualization models can yield extrapolated information that could lead to better clinical decisions and aid the physician in understanding where a patient is at in regard to his or her health status. To address this opportunity, we employ parallel coordinate graphing model and a cluster dendrogram to provide a multidimensional representation of a patient’s individual medical history as well as establish a predictive model of the progression of a patient’s disease based of prior collected EHR data. This project focuses on applying effective visualization models to extract clinically relevant data that could improved patient health outcomes. Any insights taken from these refined visualizations model provide personalized guidance for complex decisions. .

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47 Finding Recurrence Associated Phenotypes in

Colorectal Cancer Data Classified by an Unsupervised Learning Algorithm for Characterizing Cellular Phenotypic Heterogeneity (LEAPH)

Patel, Yash; Furman, Samantha; Chennubhotla, Chakra Department of Computational and Systems Biology University of Pittsburgh

The tumor microenvironment provides a rich source of data for guiding treatment and developing individualized therapeutic strategies. Analyzing spatial relationships and cellular phenotypes within the tumor microenvironment has evolved with the introduction of multi to hyerplex (> 9 biomarkers) spatial proteomics imaging technologies. Cell DIVE (Cytiva, Inc.), one of the latest multiplex imaging technologies, is used to create the dataset used in this

study ‐ a cohort of 213 colorectal cancer (CRC) tissue samples with 50 biomarkers. Current algorithms and software used to analyze hyperplexed images are supervised, disregard the spatial component of the tumor microenvironment, and lack the ability to identify rare cell populations. In this research, we use LEAPH, an unsupervised learning algorithm for characterizing cellular phenotypic heterogeneity. The objective of this study is to use data produced from LEAPH to find phenotypes that are associated with cancer recurrence through regression models and survival analyses. We can use this information to draw more conclusions about the relationships between the tumor microenvironment and cancer progression. Ultimately, this research will give insight and guidance into immunotherapies, treatment, and the future behavior of the tumor for a better prognosis for CRC patients.

48 Chris Farmen Abstract Pending

Colleges and High Schools Represented at the 23rd Annual (Virtual) Summer Undergraduate Research Symposium

Bryn Mawr College Duquesne University Franciscan University of Steubenville Slippery Rock University St. Mary’s College of Maryland University of Connecticut University of Pittsburgh University of Pittsburgh School of Medicine University of Puerto Rico Rio Piedras University of Texas at Rio Grande Valley Vassar College Washington & Jefferson College Westminster College

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Duquesne University (Virtual) Undergraduate Research Program Vi… · (Virtual) Undergraduate Research Program 23rd Annual (Virtual) Summer Research Symposium Sponsored by The Bayer