Physical Sciences and Mathematics Commons^™

Jessicahlawrencemastersportfolio.Pdf, Jessicah Lawrence

Jessicah Lawrence

No abstract provided.

Secure Approximation Of Edit Distance On Genomic Data, Md Momin Al Aziz, Dima Alhadidi, Noman Mohammed

All Works

© 2017 The Author(s). Background: Edit distance is a well established metric to quantify how dissimilar two strings are by counting the minimum number of operations required to transform one string into the other. It is utilized in the domain of human genomic sequence similarity as it captures the requirements and leads to a better diagnosis of diseases. However, in addition to the computational complexity due to the large genomic sequence length, the privacy of these sequences are highly important. As these genomic sequences are unique and can identify an individual, these cannot be shared in a plaintext. Methods: In …

Chelator-Free Radiolabeling Of Serrs Nanoparticles For Whole-Body Pet And Intraoperative Raman Imaging, Matthew A. Wall, Travis Shaffer, Stefan Harmsen, Darjus-Felix Tschaharganeh, Chun-Hao Huang, Scott W. Lowe, Charles Michael Drain, Moritz F. Kircher

Publications and Research

A single contrast agent that offers whole-body non-invasive imaging along with the superior sensitivity and spatial resolution of surface-enhanced resonance Raman scattering (SERRS) imaging would allow both pre-operative mapping and intraoperative imaging and thus be highly desirable. We hypothesized that labeling our recently reported ultrabright SERRS nanoparticles with a suitable radiotracer would enable pre-operative identification of regions of interest with whole body imaging that can be rapidly corroborated with a Raman imaging device or handheld Raman scanner in order to provide high precision guidance during surgical procedures. Here we present a straightforward new method that produces radiolabeled SERRS nanoparticles for …

Bacterial Communities Associated With Healthy And Diseased Acropora Cervicornis (Staghorn Coral) Using High-Throughput Sequencing, Charles Walton

HCNSO Student Theses and Dissertations

Coral diseases were first noted in the 1960s and 1970s and have had major impacts globally on coral reef community structures. In the Caribbean, a major outbreak of white band disease has been considered responsible for the drastic decline of Caribbean Acroporids since the 1970s. In addition to white band disease, another more recently described condition known as rapid tissue loss (RTL) has had major impacts on Acropora cervicornis populations, specifically offshore Broward County Southeast Florida. While these diseases have contributed to the population decline, determining their etiologies has been elusive.

Coral diseases have been characterized by shifts in their …

Socioeconomic Status, Air Quality And Geographic Variation In Emergency Room Visits For Acute Bronchitis On The California Central Coast, Sean Lang-Brown, Heather W. Starnes, Gary B. Hughes

Symposium

IMPORTANCE: Analysis of geospatial variation in acute bronchitis due to socioeconomic and environmental factors can allow the efficient delivery of resources to populations most at risk.

OBJECTIVE: We sought to determine if small scale variation in socioeconomic factors and emergency room (ER) visits for acute bronchitis are associated in small cities or rural communities. We also modeled the effects of air quality on daily rates of ER visits for acute bronchitis in the context of socioeconomic factors to investigate modifying relationships.

DESIGN, SETTING, AND PARTICIPANTS: We examined ER visits for acute bronchitis in San Luis Obispo and Santa Barbara counties …

Cellular And Molecular Targets Of Menthol Actions, Murat Oz, Eslam El Nebrisi, Keun-Hang Susan Yang, Frank Christopher Howarth, Lina T. Al Kury

Mathematics, Physics, and Computer Science Faculty Articles and Research

Menthol belongs to monoterpene class of a structurally diverse group of phytochemicals found in plant-derived essential oils. Menthol is widely used in pharmaceuticals, confectionary, oral hygiene products, pesticides, cosmetics, and as a flavoring agent. In addition, menthol is known to have antioxidant, anti-inflammatory, and analgesic effects. Recently, there has been renewed awareness in comprehending the biological and pharmacological effects of menthol. TRP channels have been demonstrated to mediate the cooling actions ofmenthol. There has been new evidence demonstrating thatmenthol can significantly influence the functional characteristics of a number of different kinds of ligand and voltage-gated ion channels, indicating that at …

Peripheral Inflammation, Apolipoprotein E4, And Amyloid-Β Interact To Induce Cognitive And Cerebrovascular Dysfunction, Felecia M. Marottoli, Yuriko Katsumata, Kevin P. Koster, Riya Thomas, David W. Fardo, Leon M. Tai

Biostatistics Faculty Publications

Cerebrovascular dysfunction is rapidly reemerging as a major process of Alzheimer’s disease (AD). It is, therefore, crucial to delineate the roles of AD risk factors in cerebrovascular dysfunction. While apolipoprotein E4 (APOE4), Amyloid-β (Aβ), and peripheral inflammation independently induce cerebrovascular damage, their collective effects remain to be elucidated. The goal of this study was to determine the interactive effect of APOE4, Aβ, and chronic repeated peripheral inflammation on cerebrovascular and cognitive dysfunction in vivo. EFAD mice are a well-characterized mouse model that express human APOE3 (E3FAD) or APOE4 (E4FAD) and overproduce human Aβ42 via expression of …

Descartes Comes Out Of The Closet, Nora E. Culik

Journal of Humanistic Mathematics

While “Descartes Comes Out of the Closet” is ostensibly about a young woman’s journey to Paris, the descriptive detail borrows language and images from Cartesian coordinate geometry, dualistic philosophy, neuroanatomy (the pineal), and projections of three dimensions onto planes. This mathematical universe is counterpointed in the natural language of the suppressed love story that locates the real in the human. Thus, at the heart of the story is the tension between competing notions of mathematics, i.e., as either an independent realm apart from history or as a culturally produced and historical set of practices. Of course, the central character proves …

Dengue Virus Ns2b/Ns3 Protease Inhibitors Exploiting The Prime Side, Kuan-Hung Lin, Akbar Ali, Linah Rusere, Djade I. Soumana, Nese Kurt Yilmaz, Celia A. Schiffer

Celia A. Schiffer

The mosquito-transmitted dengue virus (DENV) infects millions of people in tropical and subtropical regions. Maturation of DENV particles requires proper cleavage of the viral polyprotein, including processing of 8 of the 13 substrate cleavage sites by dengue virus NS2B/NS3 protease. With no available direct-acting antiviral targeting DENV, NS2/NS3 protease is a promising target for inhibitor design. Current design efforts focus on the nonprime side of the DENV protease active site, resulting in highly hydrophilic and nonspecific scaffolds. However, the prime side also significantly modulates DENV protease binding affinity, as revealed by engineering the binding loop of aprotinin, a small protein …

Depaul Discoveries Volume 6 Cover, Amanda Copeland

DePaul Discoveries

No abstract provided.

Crowdsourced Delphis: Designing Solutions To Complex Environmental Problems With Broad Stakeholder Participation, Sarah Coleman, Stephanie Hurley, Christopher Koliba, Asim Zia

College of Agriculture and Life Sciences Faculty Publications

There is a well-established need for increased stakeholder participation in the generation of adaptive management approaches and specific solutions to complex environmental problems. However, integrating participant feedback into current science, research, and decision-making processes is challenging. This paper presents a novel approach that marries a rigorous Delphi method, borrowed from policy and organizational sciences, with contemporary “crowdsourcing” to address the complex problems of water pollution exacerbated by climate change in the Lake Champlain Basin. In an online Delphi forum that occurred over a six-week period during the Spring of 2014, fifty-three participants proposed and commented on adaptive solutions to address …

A Phase Iii, Randomized, Multi-Center, Double Blind, Placebo Controlled Study Of Safety And Efficacy Of Lofexidine For Relief Of Symptoms In Individuals Undergoing Inpatient Opioid Withdrawal, Charles W. Gorodetzky, Sharon L. Walsh, Peter R. Martin, Andrew J. Saxon, Kristen L. Gullo, Kousick Biswas

Center on Drug and Alcohol Research Faculty Publications

Background: Lofexidine is an alpha-2-adrenergic receptor agonist approved in the United Kingdom (UK) for the treatment of opioid withdrawal symptoms. Lofexidine has demonstrated better efficacy than placebo for reducing opioid withdrawal symptoms in patients undergoing opioid withdrawal with less reported hypotension than clonidine.

Methods: Designed as an FDA registration trial, this 8-day, randomized, double-blind, placebo-controlled, parallel-group study in 264 patients dependent on short-acting opioids evaluated the efficacy of lofexidine hydrochloride in reducing withdrawal symptoms in patients undergoing opioid withdrawal. The primary efficacy measures were SOWS-Gossop on Day 3 and time-to-dropout. Secondary endpoints included the proportion of participants who were completers; …

Santa Clara Magazine, Volume 58 Number 2, Summer 2017, Santa Clara University

Santa Clara Magazine

18 - LISTENING IS HER SUPERPOWER The groundbreaking stage work of Anna Deavere Smith. By Jesse Hamlin.

22 - CASTS A SHADOW Travel bans: Four international graduate students respond. By Matt Morgan.

24 - A BIGGER STAGE Priest, social worker, CEO, and teller of stories: Jim Purcell on what drew him to Santa Clara—and what Jesuit education can be. By Steven Boyd Saum.

28 - THE GOOD, THE BAD, AND THE KID Ron Hansen M.A. ’95 talks truth and fiction and Billy the Kid—and when you can’t tell the good guys from the bad guys.

38 - DISCOVER. INNOVATE. A …

2017 Summer Research Symposium Abstract Book, Trinity College, Hartford Connecticut

Science Symposia Abstracts

2017 Summer volume of abstracts for science research projects conducted by students at Trinity College.

Crowdsourced Delphis: Designing Solutions To Complex Environmental Problems With Broad Stakeholder Participation, Sarah Coleman, Stephanie Hurley, Christopher Koliba, Asim Zia

College of Agriculture and Life Sciences Faculty Publications

There is a well-established need for increased stakeholder participation in the generation of adaptive management approaches and specific solutions to complex environmental problems. However, integrating participant feedback into current science, research, and decision-making processes is challenging. This paper presents a novel approach that marries a rigorous Delphi method, borrowed from policy and organizational sciences, with contemporary “crowdsourcing” to address the complex problems of water pollution exacerbated by climate change in the Lake Champlain Basin. In an online Delphi forum that occurred over a six-week period during the Spring of 2014, fifty-three participants proposed and commented on adaptive solutions to address …

Adults And Children In Low-Income Households That Participate In Cost-Offset Community Supported Agriculture Have High Fruit And Vegetable Consumption, Karla L. Hanson, Jane Kolodinsky, Weiwei Wang, Emily H. Morgan, Stephanie B. Jilcott Pitts, Alice S. Ammerman, Marilyn Sitaker, Rebecca A. Seguin

College of Agriculture and Life Sciences Faculty Publications

Licensee MDPI, Basel, Switzerland. This paper examines fruit and vegetable intake (FVI) in low-income households that participated in a cost-offset (CO), or 50% subsidized, community-supported agriculture (CSA) program. CSA customers paid farms upfront for a share of the harvest, and received produce weekly throughout the growing season. A cohort of adults and children 2-12 y in a summer CO-CSA were surveyed online twice: August 2015 (n = 41) and February 2016 (n = 23). FVI was measured by the National Cancer Institute’s (NCI) Fruit and Vegetable Screener (FVS) and an inventory of locally grown fruits and vegetables. FVI relative to …

Mining Non-Lattice Subgraphs For Detecting Missing Hierarchical Relations And Concepts In Snomed Ct, Licong Cui, Wei Zhu, Shiqiang Tao, James T. Case, Olivier Bodenreider, Guo-Qiang Zhang

Computer Science Faculty Publications

Objective: Quality assurance of large ontological systems such as SNOMED CT is an indispensable part of the terminology management lifecycle. We introduce a hybrid structural-lexical method for scalable and systematic discovery of missing hierarchical relations and concepts in SNOMED CT.

Material and Methods: All non-lattice subgraphs (the structural part) in SNOMED CT are exhaustively extracted using a scalable MapReduce algorithm. Four lexical patterns (the lexical part) are identified among the extracted non-lattice subgraphs. Non-lattice subgraphs exhibiting such lexical patterns are often indicative of missing hierarchical relations or concepts. Each lexical pattern is associated with a potential specific type of error. …

Abstract 4525: Hypoxia Signaling Pathway Plays A Role In Ovarian Cancer Chemoresistance, Noelle L. Cutter Ph.D., Tyler Walther Bsc, Kim Doyle, Ryan Frank

Faculty Works: BCES (1999-2023)

Hypoxia-inducible factor 1 (HIF-1) is a basic helix-loop-helix transcription factor that when induced regulates the expression of many genes involved in cytoprotective stimuli, which attenuates apoptosis and improves survival. Increased expression of HIF-1α gene (HIF1A) has been found in several carcinomas, including ovarian cancer. Ovarian cancers are generally refractory to platinum-based chemotherapy. Despite the large number of studies, molecular events that govern the emergence of aggressive therapy-resistant cells after chemotherapy are poorly defined. Genomic instabilities, such as copy number variation(CNV), may play an important role in chemoresistance and have been implicated in many complex diseases, like cancer.. We analyzed CNV …

A Pilot Study Of Computerized, Tailored Intervention To Promote Hpv Vaccination In Mexican-Heritage Adolescents, Angaela Chia-Chen Chen, Michael Todd, Ashish Amresh, Usha Menon, Laura Szalacha

Ashish Amresh

Mhealth Games As Rewards: Incentive Or Distraction?, Kevin Gary, Ryan Stoll, Pooja Rallabhandi, Mandar Patwardhan, Derek Hamel, Ashish Amresh, Armando Pina, Kevin Cleary, Zenaide Quezado

Ashish Amresh

Mixture Models For Undiagnosed Prevalent Disease And Interval-Censored Incident Disease: Applications To A Cohort Assembled From Electronic Health Records., Li C Cheung, Qing Pan, Noorie Hyun, Mark Schiffman, Barbara Fetterman, Philip E Castle, Thomas Lorey, Hormuzd A Katki

Epidemiology Faculty Publications

For cost-effectiveness and efficiency, many large-scale general-purpose cohort studies are being assembled within large health-care providers who use electronic health records. Two key features of such data are that incident disease is interval-censored between irregular visits and there can be pre-existing (prevalent) disease. Because prevalent disease is not always immediately diagnosed, some disease diagnosed at later visits are actually undiagnosed prevalent disease. We consider prevalent disease as a point mass at time zero for clinical applications where there is no interest in time of prevalent disease onset. We demonstrate that the naive Kaplan-Meier cumulative risk estimator underestimates risks at early …

Numerically Solving A System Of Pdes Modeling Chronic Wounds Treated With Oxygen Therapy, Stefan Stryker

Mahurin Honors College Capstone Experience/Thesis Projects

Chronic wounds such as diabetic foot ulcers are the leading cause of non-traumatic amputations in developed countries. For researchers to better understand the physiology of these wounds, a mathematical model describing oxygen levels at the wound site can be used to help predict healing responses. The model utilizes equations that are modified from work by Guffey (2015) that consists of four variables – oxygen, bacteria, neutrophils, and chemoattractant within a system of partial differential equations. Our research focuses on numerically solving these partial differential equations using a finite volume approach. This numerical solver will be important for future research in …

Evaluation Of A Proposal For Reliable Low-Cost Grid Power With 100% Wind, Water, And Solar, Christopher T.M. Clack, Staffan A. Qvist, Jay Apt, Morgan Bazilian, Adam R. Brandt, Ken Caldeira, Steven J. Davis, Victor Diakov, Mark A. Handschy, Paul D.H. Hines, Paulina Jaramillo, Daniel M. Kammen, Jane C.S. Long, M. Granger Morgan, Adam Reed, Varun Sivaram, James Sweeney, George R. Tynan, David G. Victor, John P. Weyant, Jay F. Whitacre

College of Engineering and Mathematical Sciences Faculty Publications

A number of analyses, meta-Analyses, and assessments, including those performed by the Intergovernmental Panel on Climate Change, the National Oceanic and Atmospheric Administration, the National Renewable Energy Laboratory, and the International Energy Agency, have concluded that deployment of a diverse portfolio of clean energy technologies makes a transition to a low-carbon-emission energy system both more feasible and less costly than other pathways. In contrast, Jacobson et al. [Jacobson MZ, Delucchi MA, Cameron MA, Frew BA (2015) Proc Natl Acad Sci USA 112(49):15060-15065] argue that it is feasible to provide "low-cost solutions to the grid reliability problem with 100% penetration of …

Interdependence Of Inhibitor Recognition In Hiv-1 Protease, Janet L. Paulsen, Florian Leidner, Debra A. Ragland, Nese Kurt Yilmaz, Celia A. Schiffer

Celia A. Schiffer

Molecular recognition is a highly interdependent process. Subsite couplings within the active site of proteases are most often revealed through conditional amino acid preferences in substrate recognition. However, the potential effect of these couplings on inhibition and thus inhibitor design is largely unexplored. The present study examines the interdependency of subsites in HIV-1 protease using a focused library of protease inhibitors, to aid in future inhibitor design. Previously a series of darunavir (DRV) analogs was designed to systematically probe the S1' and S2' subsites. Co-crystal structures of these analogs with HIV-1 protease provide the ideal opportunity to probe subsite interdependency. …

Cytotoxicity Of Platinum Anticancer Drugs In Mammalian Cell Lines Of Metastatic Cancer, Hosannah Evie

Mahurin Honors College Capstone Experience/Thesis Projects

With the invention of advanced technology, focus has been put on understanding and looking for potential cures for many diseases, one of which is cancer. The difference in the leaving and non-leaving ligands of the FDA approved cancer drugs contributes to the differential cell specific cytotoxic effects. These drugs such as oxaliplatin approved for colorectal cancer, cisplatin approved for testicular cancer, and their analogs were used to treat different cancer cell lines in an MTT assay. This project aims to determine how changing the molecular shape of these compounds affects their uptake and toxicity into different cell lines. The assay …

Higher Education Capacity Building In Water Resources Engineering And Management To Support Achieving The Sustainable Development Goal For Water In Pakistan, Steven J. Burian, Mercedes Ward, Tariq Banuri, M. Aslam Chaudhry, Sajjad Ahmad, Bakhshal Lashari, Rasool Bux Mahar, Davey Stevenson, Jim Vanderslice, Kamran Ansari, Munir Babar, Abdul Latif Qureshi

Civil and Environmental Engineering and Construction Faculty Research

Achieving the Sustainable Development Goals requires a multi‐pronged approach, with a key element being the development of a trained Community of Practice to sustain the advances in the relevant sectors. The engagement of higher education as a catalyst in the development and capacity building of the next generation of professionals and citizens comprising the Community of Practice is essential to meet the challenges of poverty, climate change, and clean water and to sustain those advances past 2030. This paper describes a capacity building program funded by the United States Agency for International Development to partner the University of Utah, in …

A Microrna Signature Of Response To Erlotinib Is Descriptive Of Tgfβ Behaviour In Nsclc, Madeline J. Krentz Gober, James P. Collard, Katherine L. Thompson, Esther P. Black

Pharmaceutical Sciences Faculty Publications

Our previous work identified a 13-gene miRNA signature predictive of response to the epidermal growth factor receptor (EGFR) inhibitor, erlotinib, in Non-Small Cell Lung Cancer cell lines. Bioinformatic analysis of the signature showed a functional convergence on TGFβ canonical signalling. We hypothesized that TGFβ signalling controls expression of the miRNA genes comprising an erlotinib response signature in NSCLC. Western analysis revealed that TGFβ signalling via Smad2/3/4 occurred differently between erlotinib-resistant A549 and erlotinib- sensitive PC9 cells. We showed that TGFβ induced an interaction between Smad4 and putative Smad Binding Elements in PC9. However, qRT-PCR analysis showed that endogenous miR-140/141/200c expression …

Analysis Of A Potential A(H7n9) Influenza Pandemic Outbreak In The U.S., Walter A. Silva Sotillo

USF Tampa Graduate Theses and Dissertations

This dissertation presents a collection of manuscripts that describe development of models and model implementation to analyze impact of potential A(H7N9) pandemic influenza outbreak in the U.S. Though this virus is still only animal-to-human transmittable, it has potential to become human-to-human transmittable and trigger a pandemic. This work is motivated by the negative impact on human lives that this virus has already caused in China, and is intended to support public health officials in preparing to protect U.S. population from a potential outbreak of pandemic scale.

An agent-based (AB) simulation model is used to replicate the social dynamics of the …

Influence Of Environmental Parameters On Mold Sampling Results, Benjamin Fishman

USF Tampa Graduate Theses and Dissertations

Mold is a type of fungus present in nearly all environments. Mold thrives under several environmental parameters such as high humidity and an adequate food source. A professional, such as an industrial hygienist, can measure mold in indoor and outdoor environments. Industrial hygienists commonly use a cascade impactor with a culture plate to capture air within a sampling area. While collecting air samples, environmental parameters such as temperature, humidity, and carbon dioxide are recorded. A laboratory then cultures and analyzes the samples, identifying the types and amounts of viable mold found in the sampling area.

In this study, a data …

Treatment Pathway Of Bone Sarcoma In Children, Adolescents, And Young Adults, Damon R. Reed, Masanori Hayashi, Lars M. Wagner, Odion Binitie, Diana A. Steppan, Andrew S. Brohl, Eric T. Shinohara, Julia A. Bridge, David M. Loeb, Scott C. Borinstein, Michael S. Isakoff

Pediatrics Faculty Publications

When pediatric, adolescent, and young adult patients present with a bone sarcoma, treatment decisions, especially after relapse, are complex and require a multidisciplinary approach. This review presents scenarios commonly encountered in the therapy of bone sarcomas with the goal of objectively presenting a consensus, multidisciplinary management approach. Little variation was found in the authors' group with respect to local control or systemic therapy. Clinical trials were universally prioritized in all settings. Decisions regarding relapse therapies in the absence of a clinical trial had very minor variations initially, but a consensus was reached after a literature review and discussion. This review …