Physical Sciences and Mathematics Commons^™

Mimicking Metabolism Of A Reversed Chloroquine Antimalarial, Kelsie Lynn Kendrick

Dissertations and Theses

The aim of this study was to elucidate the oxidation products of a candidate antimalarial drug, PL69, using a porphyrin system and to determine the accuracy of the oxidation products produced, as compared to what is expected in metabolism. PL69 is a reversed chloroquine (RCQ) that is active against chloroquine resistant malaria. Porphyrin oxidation systems have been shown to mimic in vitro enzymatic metabolism reactions. PL69 and its known metabolite, PL16, were incubated with the porphyrin system, and then the oxidation products were collected and separated by HPLC. The oxidation products were characterized by NMR and mass spectrometry and compared …

An Agile Implementation Within A Medical Device Software Organisation, Martin Mchugh, Fergal Mc Caffery, Garret Coady

Conference papers

Three surveys conducted over a 6 year period revealed that medical device software organisations have difficulties in the area of requirements management, namely accommodating changes in requirements. Medical device software is traditionally developed in accordance with a plan driven software development lifecycle (SDLC). These SDLCs are rigid and inflexible to changes once the requirements management stage has been completed. Agile methods are gaining momentum in non-regulated industries but as of yet, the adoption of these methods in regulated industries such as the medical device software domain remains low. This study presents an implementation of agile methods within a medical device …

Control Power In Perfect Controlled Teleportation Via Partially Entangled Channels, Xi-Han Li, Shohini Ghose

Physics and Computer Science Faculty Publications

We analyze and evaluate perfect controlled teleportation via three-qubit entangled channels from the point of view of the controller. The key idea in controlled teleportation is that the teleportation is performed only with the participation of the controller. We calculate a quantitative measure of the controller's power and establish a lower bound on the control power required for controlled teleportation. We show that the maximally entangled Greenberger-Horne-Zeilinger state is a suitable channel for controlled teleportation of arbitrary single qubits-the controller's power meets the bound and the teleportation fidelity without the controller's permission is no better than the fidelity of a …

Cross-Design Synthesis For Extending The Applicability Of Trial Evidence When Treatment Effect Is Heterogeneous-I. Methodology, Ravi Varadhan, Carlos Weiss

Johns Hopkins University, Dept. of Biostatistics Working Papers

Randomized controlled trials (RCTs) provide reliable evidence for approval of new treatments, informing clinical practice, and coverage decisions. The participants in RCTs are often not a representative sample of the larger at-risk population. Hence it is argued that the average treatment effect from the trial is not generalizable to the larger at-risk population. An essential premise of this argument is that there is significant heterogeneity in the treatment effect (HTE). We present a new method to extrapolate the treatment effect from a trial to a target group that is inadequately represented in the trial, when HTE is present. Our method …

Cross-Design Synthesis For Extending The Applicability Of Trial Evidence When Treatment Effect Is Heterogeneous. Part Ii. Application And External Validation, Carlos Weiss, Ravi Varadhan

Johns Hopkins University, Dept. of Biostatistics Working Papers

Randomized controlled trials (RCTs) generally provide the most reliable evidence. When participants in RCTs are selected with respect to characteristics that are potential treatment effect modifiers, the average treatment effect from the trials may not be applicable to a specific target population. We present a new method to project the treatment effect from a RCT to a target group that is inadequately represented in the trial when there is heterogeneity in the treatment effect (HTE). The method integrates RCT and observational data through cross-design synthesis. An essential component is to identify HTE and a calibration factor for unmeasured confounding for …

Cold Magnetically Trapped 2DG Scandium Atoms. I. Interaction Potential, Tijs Karman, Xi Chu, Gerrit C. Groenenboom

Chemistry and Biochemistry Faculty Publications

We present a first principles description of the interaction of two ground-state scandium atoms. Scandium has a ²D_g ground state. Thirty molecular states correlate to the lowest dissociation limit of the dimer. In the short range, potential energy curves are calculated using second-order n-electron valence state perturbation theory. The first-order long-range interaction is calculated at the complete active space self-consistent field level. We determine the second-order long-range dispersion interaction from atomic dynamic polarizabilities at imaginary frequencies. These polarizabilities are calculated using time-dependent density functional theory. We merge the short-range approach with the long-range model to obtain a physical …

Defining The Flora Family: Orbital Properties, Reflectance Properties And Age, Melissa J. Dykhuis, Lawrence Molnar, Samuel J. Van Kooten, Richard Greenberg

University Faculty Publications and Creative Works

The Flora family resides in the densely populated inner main belt, bounded in semimajor axis by the ν6 secular resonance and the Jupiter 3:1 mean motion resonance. The presence of several large families that overlap dynamically with the Floras (e.g., the Vesta, Baptistina, and Nysa-Polana families), and the removal of a significant fraction of Floras via the nearby ν6 resonance complicates the Flora family's distinction in both proper orbital elements and reflectance properties. Here we use orbital information from the Asteroids Dynamic Site (AstDyS), color information from the Sloan Digital Sky Survey (SDSS), and albedo information from the Wide-field Infrared …

Candels/Goods-S, Cdfs, And Ecdfs: Photometric Redshifts For Normal And X-Ray-Detected Galaxies, Li-Ting Hsu, Mara Salvato, Kirpal Nandra, Marcella Brusa, Ralf Bender, Johannes Buchner, Jennifer L. Dooley, Dale D. Kocevski, Yicheng Guo, Nimish P. Hathi, Cyprian Rangel, S. P. Willner, Murray Brightman, Antonis Georgakakis, Tamás Budavári, Alexander S. Szalay, Matthew L.N. Ashby, Guillermo Barro, Tomas Dahlen, Sandra M. Faber, Henry C. Ferguson, Audrey Galametz, Andrea Grazian, Norman A. Grogin, Kuang-Han Huang, Anton M. Koekemoer, Ray A. Lucas, Elizabeth Mcgrath, Bahram Mobasher, Michael Peth, David J. Rosario, Jonathan R. Trump

Physics and Astronomy Faculty Publications

We present photometric redshifts and associated probability distributions for all detected sources in the Extended Chandra Deep Field South (ECDFS). This work makes use of the most up-to-date data from the Cosmic Assembly Near-IR Deep Legacy Survey (CANDELS) and the Taiwan ECDFS Near-Infrared Survey (TENIS) in addition to other data. We also revisit multi-wavelength counterparts for published X-ray sources from the 4 Ms CDFS and 250 ks ECDFS surveys, finding reliable counterparts for 1207 out of 1259 sources (~96%). Data used for photometric redshifts include intermediate-band photometry deblended using the TFIT method, which is used for the first time in …

Un Climate Change Report Warns Of Severe And Irreversible Effects, Lauren Carasik

Media Presence

No abstract provided.

Gwatch: A Web Platform For Automated Gene Association Discovery Analysis, Anton Svitin, Sergey Malov, Nikolay Cherkasov, Paul Geerts, Mikhail Rotkevich, Pavel Dobrynin, Andrey Shevchenko, Li Guan, Jennifer L. Troyer, Sher L. Hendrickson, Holli Hutcheson Dilks, T. K. Oleksyk, Sharyne Donfield, Edward Gomperts, Douglas A. Jabs, Efe Sezgin, Mark Van Natta, P. Richard Harrigan, Zabrina L. Brumme, Stephen J. O'Brien

Biology Faculty Articles

Background: As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations.

Findings: Here we present a dynamic web-based platform – GWATCH – that automates and facilitates four steps in genetic epidemiological discovery: 1) Rapid gene association search and discovery analysis of large genome-wide datasets; 2) Expanded visual display of gene associations for genome-wide variants (SNPs, indels, CNVs), including Manhattan plots, 2D and 3D snapshots of any gene region, and a dynamic genome browser illustrating gene association chromosomal regions; 3) Real-time validation/replication …

Verification And Comparison Of Two Commonly Used Numerical Modeling Systems In Hydrodynamic Simulation At A Dual-Inlet System, West-Central Florida, Ming Xie

USF Tampa Graduate Theses and Dissertations

Numerical modeling systems are very important tools to study tidal inlets. In order to test its capability and accuracy of solving multi-inlet system problems, this study selected two widely used numerical modeling systems: Coastal Modeling System (CMS) and Delft3D Modeling Package. The hydrodynamics modules of the two modeling systems were tested at John's Pass and Blind Pass, Florida, a dual-inlets system, based on a similar modeling scheme. Detailed bathymetric surveys and hydraulic measurements were conducted to collect water depths, tide conditions, wave and current velocities as the input data as well as verification data for the models.

A comparison study …

Growth Rates In Gulf Of Mexico Red Snapper, Lutjanus Campechanus, Before And After The Deepwater Horizon Blowout, Elizabeth Shea Herdter

USF Tampa Graduate Theses and Dissertations

The Deepwater Horizon blowout occurred on April 20^th, 2010 and released nearly 5 million barrels of crude oil into the northern Gulf of Mexico causing pollution of the water and sediment inhabited by many fishes for at least 87 days while the wellhead went uncapped. Populations of the Gulf of Mexico Red snapper, Lutjanus campechanus, an important fish to the ecology and economy in the region, exhibit affinity to shallow water oil infrastructure such as the Deepwater Horizon making them especially vulnerable to crude oil contamination. The objective of this study is to determine growth of Red …

Polycyclic Aromatic Hydrocarbon Metabolites As A Biomarker Of Exposure To Oil In Demersal Fishes Following The Deepwater Horizon Blowout, Susan Susan Snyder

USF Tampa Graduate Theses and Dissertations

The Deepwater Horizon blowout occurred on April 20th, 2010, releasing 4.9 million barrels of Louisiana crude oil into the Gulf of Mexico (GoM). Subsequent to the Deepwater Horizon blowout, sediment cores revealed oil on the northern GoM seafloor and abnormal skin lesions were seen in GoM fishes. Exposure to polycyclic aromatic hydrocarbons (PAHs), a component of crude oil, in fish has been associated with many sublethal effects, including cancer and population-level effects. Using a biomarker of exposure to PAHs, this thesis evaluates inter-species, temporal and spatial differences in exposure to hydrocarbon contamination between three species of fish with varying levels …

Translating Aboveground Cosmic-Ray Neutron Intensity To High-Frequency Soil Moisture Profiles At Sub-Kilometer Scale, R. Rosolem, T. Hoar, A. Arellano, J. L. Anderson, W. J. Shuttleworth, X. Zeng, Trenton E. Franz

School of Natural Resources: Faculty Publications

Above-ground cosmic-ray neutron measurements provide an opportunity to infer soil moisture at the subkilometer scale. Initial efforts to assimilate those measurements have shown promise. This study expands such analysis by investigating (1) how the information from aboveground cosmic-ray neutrons can constrain the soil moisture at distinct depths simulated by a land surface model, and (2) how changes in data availability (in terms of retrieval frequency) impact the dynamics of simulated soil moisture profiles. We employ ensemble data assimilation techniques in a “nearly-identical twin” experiment applied at semi-arid shrubland, rainfed agricultural field, and mixed forest biomes in the USA. The performance …

U.S. Drought Monitor, November 4, 2014, Matthew Rosencrans

United States Agricultural Commodities in Drought Archive

Drought map of U.S. for November 4, 2014 (11/4/14) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.

Unsupervised Learning Trojan, Arturo Geigel

CCAC Theses and Dissertations

This work presents a proof of concept of an Unsupervised Learning Trojan. The Unsupervised Learning Trojan presents new challenges over previous work on the Neural network Trojan, since the attacker does not control most of the environment. The current work will presented an analysis of how the attack can be successful by proposing new assumptions under which the attack can become a viable one. A general analysis of how the compromise can be theoretically supported is presented, providing enough background for practical implementation development. The analysis was carried out using 3 selected algorithms that can cover a wide variety of …

Prognostic Value Of Elevated Levels Of Intestinal Microbe-Generated Metabolite Trimethylamine-N-Oxide In Patients With Heart Failure: Refining The Gut Hypothesis, W.H. Wilson Tang, Zeneng Wang, Yiying Fan, Bruce Levison, Jennie E. Hazen, Lillian M. Donahue, Yuping Wu, Stanley L. Hazen

Mathematics and Statistics Faculty Publications

Background: Altered intestinal function is prevalent in patients with heart failure (HF), but its role in adverse outcomes is unclear. Objectives: This study investigated the potential pathophysiological contributions of intestinal microbiota in HF. Methods: We examined the relationship between fasting plasma trimethylamine-N-oxide (TMAO) and all-cause mortality over a 5-year follow-up in 720 patients with stable HF. Results:The median TMAO level was 5.0 μM, which was higher than in subjects without HF (3.5 μM; p < 0.001). There was modest but significant correlation between TMAO concentrations and B-type natriuretic peptide (BNP) levels (r = 0.23; p < 0.001). Higher plasma TMAO levels were associated with a 3.4-fold increased mortality risk. Following adjustments for traditional risk factors and BNP levels, elevated TMAO levels remained predictive of 5-year mortality risk (hazard ratio [HR]: 2.2; 95% CI: 1.42 to 3.43; p < 0.001), as well as following the addition of estimated glomerular filtration rate to the model (HR: 1.75; 95% CI: 1.07 to 2.86; p < 0.001). Conclusions: High TMAO levels were observed in patients with HF, and elevated TMAO levels portended higher long-term mortality risk independent of traditional risk factors and cardiorenal indexes.

Γ-Butyrobetaine Is A Proatherogenic Intermediate In Gut Microbial Metabolism Of L-Carnitine To Tmao, Robert A. Koeth, Bruce S. Levison, Miranda K. Culley, Jennifer A. Buffa, Zeneng Wang, Jill C. Gregory, Elin Org, Yuping Wu, Lin Li, Jonathan D. Smith, W.H. Wilson Tang, Joseph A. Didonato, Aldons J. Lusis, Stanley L. Hazen

Mathematics and Statistics Faculty Publications

L-carnitine, a nutrient in red meat, was recently reported to accelerate atherosclerosis via a metaorganismal pathway involving gut microbial trimethylamine (TMA) formation and host hepatic conversion into trimethylamine-N-oxide (TMAO). Herein, we show that following L-carnitine ingestion, γ-butyrobetaine (γBB) is produced as an intermediary metabolite by gut microbes at a site anatomically proximal to and at a rate ∼1,000-fold higher than the formation of TMA. Moreover, we show that γBB is the major gut microbial metabolite formed from dietary L-carnitine in mice, is converted into TMA and TMAO in a gut microbiota-dependent manner (like dietary L-carnitine), and accelerates atherosclerosis. Gut microbial …

Use Of A Towed Camera System For Estimating Reef Fish Populations Densities On The West Florida Shelf, Sarah Elizabeth Grasty

USF Tampa Graduate Theses and Dissertations

Reef fish species tend to reside over high relief habitat which makes them difficult to sample with traditional gears such as nets and trawls. Therefore, implementing and understanding the strengths and weaknesses of new approaches which incorporate acoustic and optical methods has become a priority for reef fish stock assessment. Beginning in June of 2013, a towed camera system known as the Camera-Based Assessment Survey System (C-BASS) has been used to visualize over 500 kilometers of transect and record more than 80 hours of video over several habitats in the Gulf of Mexico. Surveys have been completed on the West …

Cloning And Characterization Of Il-1Β, Il-8, Il-10, And Tnfα From Golden Tilefish (Lopholatilus Chamaeleonticeps) And Red Snapper (Lutjanus Campechanus), Kristina L. Deak

USF Tampa Graduate Theses and Dissertations

Cytokines are pleiotropic and redundant signaling molecules that govern the inflammatory response and immunity, a critical ecological parameter for organism success and population growth. Produced at the site of injury or pathogen intrusion by a variety of cell types, cytokines mediate cell-signaling in either an autocrine or paracrine manner. The type and magnitude of the cytokine milieu produced subsequently dictates the strength and form of immune response. As the most diverse vertebrate group, with a high sensitivity to contaminants, fish represent an important foci for the evaluation of immune system evolution, function, and alteration upon toxicant exposure. While many cytokines …

Automated Runtime Recovery For Qos-Based Service Composition, Tian Huat Tan, Manman Chen, Étienne André, Jun Sun, Yang Liu, Jin Song Dong

Research Collection School Of Computing and Information Systems

Service composition uses existing service-based applications as components to achieve a business goal. The composite service operates in a highly dynamic environment; hence, it can fail at any time due to the failure of component services. Service composition languages such as BPEL provide a compensation mechanism to rollback the error. But such a compensation mechanism has several issues. For instance, it cannot guarantee the functional properties of the composite service after compensation. In this work, we propose an automated approach based on a genetic algorithm to calculate the recovery plan that could guarantee the satisfaction of functional properties of the …

Postmodern Fuzzy System Theory: A Deconstruction Approach Based On Kabbalah, Gabriel Burstein, Constantin Virgil Negoita, Menachem Kranz

Publications and Research

Modern general system theory proposed a holistic integrative approach based on input-state-output dynamics as opposed to the traditional reductionist detail based approach. Information complexity and uncertainty required a fuzzy system theory, based on fuzzy sets and fuzzy logic. While successful in dealing with analysis, synthesis and control of technical engineering systems, general system theory and fuzzy system theory could not fully deal with humanistic and human-like intelligent systems which combine technical engineering components with human or human-like components characterized by their cognitive, emotional/motivational and behavioral/action levels of operation. Such humanistic systems are essential in artificial intelligence, cognitive and behavioral science …

Phenyl Functionalized Sol-Gel Silica Sorbent For Capillary Microextraction And Chromia-Based Sol-Gel Ucon Stationary Phase For Capillary Gas Chromatography, Michael M. Mclean

USF Tampa Graduate Theses and Dissertations

The first chapter of this thesis presents an introduction to sol-gel methodology whose usefulness as a synthetic route will be demonstrated with two applications in chromatography. The first application involves the fabrication of a capillary micro-extraction (CME) device by coating a phenyl functionalized extracting phase on the inner surface of a fused silica capillary for analyte pre-concentration. The device was coupled on-line to a RP-HPLC system and practicality was demonstrated using allergens as target analytes. The allergens chosen as model analytes are typically found in fragrance products and food. Most of the 26 fragrance allergens that are monitored by various …

Cosm News, Georgia Southern University

College of Science & Mathematics: News & Publications (2012-2022)

• Georgia Southern professor and graduate student replicate the tide
• Scientists replicate the tide with two buckets, aquarium tubing, and a pump

Nonlinear Optimal Filter Technique For Analyzing Energy Depositions In Tes Sensors Driven Into Saturation, Benjamin Shank, Jeffrey Yen, Blas Cabrera, John Mark Kreikebaum, Robert Moffatt, Peter Redl, Betty Young, Paul Brink, Matthew Cherry, Astrid Tomada

Faculty Publications

We present a detailed thermal and electrical model of superconducting transition edge sensors(TESs) connected to quasiparticle (qp) traps, such as the W TESs connected to Al qp traps used for CDMS (Cryogenic Dark Matter Search) Ge and Si detectors. We show that this improvedmodel, together with a straightforward time-domain optimal filter, can be used to analyze pulses well into the nonlinear saturation region and reconstruct absorbed energies with optimal energyresolution.

Peptide Arrays For Detecting Naphthenic Acids In Oil Sands Process Affected Water, Kamaljit Kaur, Subir Bhattacharjee, Rajesh G. Pillai, Sahar Ahmed, Sarfuddin Azmi

Pharmacy Faculty Articles and Research

Naphthenic acids (NAs) are water-soluble components of petroleum. The characterization and quantification of NAs by analytical methods have proved quite challenging, whilst the toxic effects of these water-soluble compounds on a variety of organisms adversely affecting reproduction and steroid production is becoming apparent. In this study, we report a fluorescence-based competitive binding method for rapid sensing of the presence of NAs using cellulosic peptide array strips as sensors. The peptide array was designed from sequences derived from the estrogen receptor (ER). Several of these peptides were able to detect the presence of NAs at low micromolar (∼5 mg L^{−1 …}

Design Of Randomized Experiments In Networks, Dylan Walker, Lev Muchnik

Business Faculty Articles and Research

Over the last decade, the emergence of pervasive online and digitally enabled environments has created a rich source of detailed data on human behavior. Yet, the promise of big data has recently come under fire for its inability to separate correlation from causation-to derive actionable insights and yield effective policies. Fortunately, the same online platforms on which we interact on a day-to-day basis permit experimentation at large scales, ushering in a new movement toward big experiments. Randomized controlled trials are the heart of the scientific method and when designed correctly provide clean causal inferences that are robust and reproducible. However, …

Using Random Forest In The Field Of Metabolomics, Curtis White

Theses and Dissertations

Metabolomics is the science of comprehensive evaluation of changes in the metabolome with a goal to elucidate underlying biological mechanisms of a living system. There is an opinion in the field of metabolomics, the study of the set of metabolites present within an organism, cell, or tissue, that the future development of the field is contingent upon two factors. One of the factors is the advancement of analytical instrumentation, and the other is developing data mining methodologies for extracting meaningful and interpretable experimental results. There are many different types of data mining methodologies, but the undertaking of selecting a particular …

A Heterogeneous Compute Solution For Optimized Genomic Selection Analysis, Trevor Devore, Scott Kenneth Winkleblack, Bruce Golden, Chris Lupo

Computer Science and Software Engineering

This paper presents a heterogeneous computing solution for an optimized genetic selection analysis tool, GenSel. GenSel can be used to efficiently infer the effects of genetic markers on a desired trait or to determine the genomic estimated breeding values (GEBV) of genotyped individuals. To predict which genetic markers are informational, GenSel performs Bayesian inference using Gibbs sampling, a Markov Chain Monte Carlo (MCMC) algorithm. Parallelizing this algorithm proves to be a technically challenging problem because there exists a loop carried dependence between each iteration of the Markov chain. The approach presented in this paper exploits both task-level parallelism (TLP) and …

Discovering Perceptions In Online Social Media: A Probabilistic Approach, Derek Doran, Swapna S. Gokhale, Aldo Dagnino

Kno.e.sis Publications

People across the world habitually turn to online social media to share their experiences, thoughts, ideas, and opinions as they go about their daily lives. These posts collectively contain a wealth of insights into how masses perceive their surroundings. Therefore, extracting people’s perceptions from social media posts can provide valuable information about pertinent issues such as public transportation, emergency conditions, and even reactions to political actions or other activities. This paper proposes a novel approach to extract such perceptions from a corpus of social media posts originating from a given broad geographical region. The approach divides the broad region into …