Physical Sciences and Mathematics Commons^™

Msspark: Implementation Of Molecular Simulation Queries Using Apache Spark, Parneet Kaur

USF Tampa Graduate Theses and Dissertations

Huge amount of data is being generated in almost every field and it cannot be avoided, rather is essential for the advancement of the field. Analysis of this data requires intensive computing power. Molecular Simulation is a powerful tool for understanding the behavior of natural systems. The simulation generates large amount data while observing the spatial and temporal relationships. The challenge is to handle the analytical queries that are often compute intensive.

Although various tools exist to tackle this problem, but in this paper we have tried an alternate approach that uses Apache Spark- a modern big data platform – …

Mineralogical Transformations And Soil Development In Shale Across A Latitudinal Climosequence, Ashlee L.D. Dere, Timothy S. White, Richard H. April, Susan L. Brantley

Geography and Geology Faculty Publications

To investigate factors controlling soil formation, we established a climosequence as part of the Susquehanna-Shale Hills Critical Zone Observatory (SSHCZO) in central Pennsylvania, USA. Sites were located on organic matter-poor, iron-rich Silurian-aged shale in Wales, Pennsylvania, Virginia, Tennessee, Alabama, and Puerto Rico, although this last site is underlain by a younger shale. Across the climosequence, mean annual temperature (MAT) increases from 7 to 24°C and mean annual precipitation (MAP) ranges from 100 to 250 cm. Variations in soil characteristics along the climosequence, including depth, morphology, particle-size distribution, geochemistry, and bulk and clay mineralogy, were characterized to investigate the role of …

Orion's Veil: Magnetic Field Strengths And Other Properties Of A Pdr In Front Of The Trapezium Cluster, Thomas H. Troland, W. M. Goss, C. L. Brogan, R. M. Crutcher, D. A. Roberts

Physics and Astronomy Faculty Publications

We present an analysis of physical conditions in the Orion Veil, an atomic photon-dominated region (PDR) that lies just in front (≈2 pc) of the Trapezium stars of Orion. This region offers an unusual opportunity to study the properties of PDRs, including the magnetic field. We have obtained 21 cm H i and 18 cm (1665 and 1667 MHz) OH Zeeman effect data that yield images of the line-of-sight magnetic field strength B _los in atomic and molecular regions of the Veil. We find B _los ≈ −50 to −75 μG in the atomic gas across much of the …

Sorting Under Forbidden Comparisons, Avah Banerjee, Dana Richards

Computer Science Faculty Research & Creative Works

In this paper we study the problem of sorting under forbidden comparisons where some pairs of elements may not be compared (forbidden pairs). Along with the set of elements V the input to our problem is a graph G(V, E), whose edges represents the pairs that we can compare in constant time. Given a graph with n vertices and m =(ⁿ₂) - q edges we propose the first non-trivial deterministic algorithm which makes O((q + n) log n) comparisons with a total complexity of O(n² + q^ω/2), where ω is the …

The Total Acquisition Number Of Random Graphs, Deepak Bal, Patrick Bennett, Andrzej Dudek, Paweł Prałat

Department of Mathematics Faculty Scholarship and Creative Works

Let G be a graph in which each vertex initially has weight 1. In each step, the weight from a vertex u to a neighbouring vertex v can be moved, provided that the weight on v is at least as large as the weight on u. The total acquisition number of G, denoted by at(G), is the minimum possible size of the set of vertices with positive weight at the end of the process. LeSaulnier, Prince, Wenger, West, and Worah asked for the minimum value of p = p(n) such that at(G(n, p)) = 1 with high probability, where G(n, …

Inquiry Of Lipid Membranes Interacting With Functional Peptides And Polyphenol Drug Molecules, Chian Sing Ho

USF Tampa Graduate Theses and Dissertations

Cellular membranes are important targets for many membrane-active peptides and drug compounds. Here we are interested in deciphering how lipid membranes are perturbed by several membrane-active molecules, including the transmembrane domain of the influenza M2 protein (M2TM), aggregates formed by a synthetic polyglutamine peptide, and three polyphenol compounds (i.e., tamoxifen, genistein, and verapamil). We employ phase-separated ternary lipid model membranes in the form of giant unilamellar vesicles (GUVs) to simulate raft-like structures that have been proposed to govern many important processes in plasma membranes (e.g., intracellular singling and trafficking). Specifically, we use fluorescent microscopy to interrogate how those membrane additives …

A Comparison Of Postural Stability In Gymnasts, Volleyball Players, And Non-Athletes, Kayla Howerton

Ursidae: The Undergraduate Research Journal at the University of Northern Colorado

Balance and postural stability are crucial elements in daily activities and the training of athletes. Volleyball requires the athlete to be capable of regaining balance after jumping and landing. Gymnastics requires the athlete to have focus on multiple aspects of balance during the execution of a skill. Current literature has examined age, comparison of certain sports to other sports, and children in athletics, all with regards to postural stability. Current literature has shown that there is a correlation between balance training and increase of performance and decrease in injuries (Oliver & Di Brezzo, 2009).

This research assessed the balance systems …

A Combined Spectroscopic And Photometric Stellar Activity Study Of Epsilon Eridani, Matthew J. Giguere, Debra A. Fischer, Cyril X. Y. Zhang, Jaymie M. Matthews, Chris Cameron, Gregory W. Henry

Information Systems and Engineering Management Research Publications

We present simultaneous ground-based radial velocity (RV) measurements and space-based photometric measurements of the young and active K dwarf Epsilon Eridani. These measurements provide a data set for exploring methods of identifying and ultimately distinguishing stellar photospheric velocities from Keplerian motion. We compare three methods we have used in exploring this data set: Dalmatian, an MCMC spot modeling code that fits photometric and RV measurements simultaneously; the FF' method, which uses photometric measurements to predict the stellar activity signal in simultaneous RV measurements; and Hα analysis. We show that our Hα measurements are strongly correlated with the Microvariability and Oscillations …

Burden Of Disease Resulting From Lead Exposure At Toxic Waste Sites In Argentina, Mexico And Uruguay, Jack Caravanos, Jonathan Carrelli, Russell Dowling, Brian Pavilonis, Bret Ericson, Richard Fuller

Publications and Research

Background: Though lead contaminated waste sites have been widely researched in many high-income countries, their prevalence and associated health outcomes have not been well documented in low- and middle-income countries.

Methods: Using the well-established health metric disability-adjusted life year (DALY) and an exposure assessment method developed by Chatham-Stephens et al., we estimated the burden of disease resulting from exposure to lead at toxic waste sites in three Latin American countries in 2012: Argentina, Mexico and Uruguay. Toxic waste sites identified through Pure Earth’s Toxic Sites Identification Program (TSIP) were screened for lead in both biological and environmental sample media. Estimates …

High-Energy Neutrino Follow-Up Search Of Gravitational Wave Event Gw150914 With Antares And Icecube, S. Adrián-Martínez, A. Albert, M. André, M. Anghinolfi, G. Anton, M. Ardid, J. J. Aubert, T. Avgitas, B. Baret, J. Barrios-Martí, S. Basa, V. Bertin, S. Biagi, R. Bormuth, M. C. Bouwhuis, R. Bruijn, J. Brunner, J. Busto, A. Capone, L. Caramete, J. Carr, S. Celli, T. Chiarusi, M. Circella, A. Coleiro, R. Coniglione, H. Costantini, P. Coyle, A. Creusot, A. Deschamps, G. De Bonis, Tiffany Z. Summerscales

Faculty Publications

© 2016 American Physical Society. We present the high-energy-neutrino follow-up observations of the first gravitational wave transient GW150914 observed by the Advanced LIGO detectors on September 14, 2015. We search for coincident neutrino candidates within the data recorded by the IceCube and Antares neutrino detectors. A possible joint detection could be used in targeted electromagnetic follow-up observations, given the significantly better angular resolution of neutrino events compared to gravitational waves. We find no neutrino candidates in both temporal and spatial coincidence with the gravitational wave event. Within ±500 s of the gravitational wave event, the number of neutrino candidates detected …

Mutation Linked To Autosomal Dominant Nocturnal Frontal Lobe Epilepsy Reduces Low-Sensitivity Α4Β2, And Increases Α5Α4Β2, Nicotinic Receptor Surface Expression, Weston A. Nichols, Brandon J. Henderson, Christopher B. Marotta, Caroline Y. Yu, Chris Richards, Dennis A. Dougherty, Henry A. Lester, Bruce N. Cohen

Chemistry Faculty Publications

A number of mutations in α4β2-containing (α4β2*) nicotinic acetylcholine (ACh) receptors (nAChRs) are linked to autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE), including one in the β2 subunit called β2V287L. Two α4β2* subtypes with different subunit stoichiometries and ACh sensitivities co-exist in the brain, a high-sensitivity subtype with (α4)₂(β2)₃ subunit stoichiometry and a low-sensitivity subtype with (α4)₃(β2)₂ stoichiometry. The α5 nicotinic subunit also co-assembles with α4β2 to form a high-sensitivity α5α4β2 nAChR. Previous studies suggest that the β2V287L mutation suppresses low-sensitivity α4β2* nAChR expression in a knock-in mouse model and also that α5 co-expression …

Predictors Of Neonatal Abstinence Syndrome In Buprenorphine Exposed Newborn: Can Cord Blood Buprenorphine Metabolite Levels Help?, Darshan Shah, Stacy Brown, Nick Hagemeier, Shimin Zheng, Amy Kyle, Jason Pryor, Nilesh Dankhara, Piyuesh Singh

ETSU Faculty Works

Background

Buprenorphine is a semi-synthetic opioid used for the treatment of opioid dependence. Opioid use, including buprenorphine, has been increasing in recent years, in the general population and in pregnant women. Consequently, there has been a rise in frequency of neonatal abstinence syndrome (NAS), associated with buprenorphine use during pregnancy. The purpose of this study was to investigate correlations between buprenorphine and buprenorphine-metabolite concentrations in cord blood and onset of NAS in buprenorphine exposed newborns.

Methods

Nineteen (19) newborns who met inclusion criteria were followed after birth until discharge in a double-blind non-intervention study, after maternal consent. Cord blood and …

Cosm News, Georgia Southern University

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

• Biology Alumnus Elected American Statistical Association Vice President

High-Energy Neutrino Follow-Up Search Of Gravitational Wave Event Gw150914 With Antares And Icecube, S. Adrián-Martínez, A. Albert, M. André, H. P. Daveloza, Joey S. Key, S. R. Morriss, Soma Mukherjee, Volker Quetschke, Malik Rakhmanov, Joseph D. Romano

Physics & Astronomy Faculty Publications

We present the high-energy-neutrino follow-up observations of the first gravitational wave transient GW150914 observed by the Advanced LIGO detectors on September 14, 2015. We search for coincident neutrino candidates within the data recorded by the IceCube and Antares neutrino detectors. A possible joint detection could be used in targeted electromagnetic follow-up observations, given the significantly better angular resolution of neutrino events compared to gravitational waves. We find no neutrino candidates in both temporal and spatial coincidence with the gravitational wave event. Within ±500 s of the gravitational wave event, the number of neutrino candidates detected by IceCube and Antares were …

A Powerful Statistical Framework For Generalization Testing In Gwas, With Application To The Hchs/Sol, Tamar Sofer, Ruth Heller, Marina Bogomolov, Christy L. Avery, Mariaelisa Graff, Kari E. North, Alex Reiner, Timothy A. Thornton, Kenneth Rice, Yoav Benjamini, Cathy C. Laurie, Kathleen F. Kerr

UW Biostatistics Working Paper Series

In GWAS, “generalization” is the replication of genotype-phenotype association in a population with different ancestry than the population in which it was first identified. The standard for reporting findings from a GWAS requires a two-stage design, in which discovered associations are replicated in an independent follow-up study. Current practices for declaring generalizations rely on testing associations while controlling the Family Wise Error Rate (FWER) in the discovery study, then separately controlling error measures in the follow-up study. While this approach limits false generalizations, we show that it does not guarantee control over the FWER or False Discovery Rate (FDR) of …

Searching For Troposphere-Mesosphere Connections Using The Alo-Usu Rayleigh-Scatter Lidar, David K. Moser, Vincent B. Wickwar, Joshua P. Herron

Posters

The paucity of whole-atmosphere data introduces significant challenges that hinder the study of atmospheric couplings. The mesosphere in particular is a low-information void between the lower and upper atmosphere, which may prevent us from a complete realization of vertical interactions. The Rayleighscatter lidar at Utah State University’s Atmospheric Lidar Observatory (ALO-USU; 41.74° N, 111.81° W), operated with little interruption from 1993 to 2004, providing a valuable temporal and spatial (45 – 90 km) resource in this realm. When studied alongside a multitude of other atmospheric data sources, possible unforeseen connections or insights may result. In this study, an adaptive fit …

Simultaneous, Collocated Rayleigh And Sodium Lidar Temperature Comparison, Leda Sox, Vincent B. Wickwar, Tao Yuan, Neal Criddle

Posters

There are relatively few instruments that have the capabilities to make near continuous measurements of the mesosphere-lower-thermosphere (MLT) region. Rayleigh-scatter (RS) and resonance lidars, particularly sodium (Na) resonance lidar, have been the two dominant ground-based techniques for acquiring mesosphere and MLT vertical temperature profiles, respectively, for more than two decades. With these measurements, the dynamics and long-term temperature trends of the MLT region can be studied. For the first time, we will present simultaneous, night-time averaged temperatures acquired from the same observational site, on the campus of Utah State University (USU), using these two lidar techniques. This comparison is also …

Reestablishing Observations Throughout The Mesosphere With The Alo-Usu Rayleigh-Scatter Lidar, Shayli Elliott, Bryant Ward, Benjamin Lovelady, Jessica Gardiner, Lucas Priskos, Matthew T. Emerick, Vincent B. Wickwar

Posters

In the last few years, the Rayleigh-scatter lidar at the Atmospheric Lidar Observatory at Utah State University (ALO-USU; 41.74° N, 111.81° W) has been upgraded to extend observations from 70 km up to 115 km. This project describes a student project to build and use a complementary Rayleigh-scatter lidar to go from 40 to 90 km, from the upper stratosphere to the upper mesosphere. At the upper end, this new lidar overlaps with the high-altitude lidar. This was done in a period of just over two months. This lidar shares the same lasers, but introduces a 44-cm mirror and a …

Seasonal Temperatures From The Upper Mesosphere To The Lower Thermosphere Obtained With The Large, Alo-Usu, Rayleigh Lidar, Vincent B. Wickwar, Leda Sox, Matthew T. Emerick, Joshua P. Herron

Posters

Observations have been made with the large, Rayleigh-scatter lidar at the Atmospheric Lidar Observatory at Utah State University (ALO-USU; 41.74° N, 111.81° W) from summer 2014 to summer 2015. During this first operational year, the lidar acquired nearly 100 nights of observations between 70 and 115 km altitude, i.e., from the upper mesosphere, through the mesopause, and into the lower thermosphere. This was possible because of the large 4.9 m2 collecting area of the mirrors and the 42 W of 532 nm emission at 30 Hz. These two factors produce a figure of merit, the power-aperture-product, of 206 Wm2, making …

Obtaining Continuous Observations From The Upper Stratosphere To The Lower Thermosphere Using The Alo-Usu Rayleigh-Scatter Lidar., Jonathan L. Price, Vincent B. Wickwar, Leda Sox, Matthew T. Emerick, Joshua P. Herron, Shayli Elliott, Bryant Ward, Benjamin Lovelady

Posters

The Rayleigh-scatter lidar at the Atmospheric Lidar Observatory at Utah State University (ALO-USU; 41.74° N, 111.81° W) started observations in 1993. In 2012 the original lidar system was upgraded with an array of larger mirrors and two lasers to enable observations of the upper mesosphere and lower thermosphere from 70 km to about 115 km in altitude. (Continued refinement should provide data to above 120 km.) Recently, the original system was reconfigured [Elliott et al., 2016] to again observe the lower mesosphere between 40 km and 90 km. Initial data collected by these two parts of the Rayleigh system have …

Uwrl Director, Mac Mckee, Named A 2015 Friend Of Ucowr, Utah Water Research Laboratory

News

Mac McKee, UWRL Director, was recently named a Friend of UCOWR at the Universities Council on Water Resources (UCOWR) Annual Conference awards ceremony held this year in Pensacola Beach, Florida. UCOWR recognizes no more than three individuals each year who have “made substantial contributions in time and effort toward the goals of UCOWR.” Mac held the office of UCOWR President twice and served on the board of directors for nearly a decade.

Experimental Demonstration Of The Microscopic Origin Of Circular Dichroism In Two-Dimensional Metamaterials, Alexander B. Khanikaev, N. Arju, Z. Fan, D. Purtseladze, F. Lu, J. Lee, P. Sarriugarte, M. Schnell, R. Hillenbrand, M. A. Belkin, G. Shvets

Publications and Research

Optical activity and circular dichroism are fascinating physical phenomena originating from the interaction of light with chiral molecules or other nano objects lacking mirror symmetries in three-dimensional (3D) space. While chiral optical properties are weak in most of naturally occurring materials, they can be engineered and significantly enhanced in synthetic optical media known as chiral metamaterials, where the spatial symmetry of their building blocks is broken on a nanoscale. Although originally discovered in 3D structures, circular dichroism can also emerge in a two-dimensional (2D) metasurface. The origin of the resulting circular dichroism is rather subtle, and is related to non-radiative …

Ua94/4/5 Student / Alumni Personal Papers Southern Normal School, Wku Archives

WKU Archives Collection Inventories

Small collections of personal papers relating to the Southern Normal School.

The Influence Of Floodplain Restoration On Flow And Sediment Dynamics In An Urban River, Sangaralingam Ahilan, Mingfu Guan, Andrew Sleigh, Nigel G. Wright, Heejun Chang

Geography Faculty Publications and Presentations

A study of floodplain sedimentation on a recently restored floodplain is presented. This study uses a two-dimensional hydro-morphodynamic model for predicting flow and suspended-sediment dynamics in the downstream of Johnson Creek, the East Lents reach, where the bank of the river has been reconfigured to reconnect to a restored floodplain on a 0.26 km² (26-ha) site. The simulation scenarios include 10-, 50-, 100- and 500-year event-based deposition modelling of flood events and long-term modelling using the 64 historical flood events between 1941 and 2014. Simulation results showed that the restored floodplain significantly attenuates the upstream flood peak by up …

Optimizing Methods For Extraction Of Organic Compounds From Molluscan Shells, Kaydee Jo West

USF Tampa Graduate Theses and Dissertations

Mollusk shells contain proteins within and between the crystals of calcium carbonate. These organic molecules play an important role in biomineralization and shell function, and their stable isotope ratios of carbon and nitrogen are also thought to record important ecological information about the animal's diet and nutrient sources. These proteins can be preserved for millions of years, offering potential insight into pre-anthropogenic ecological conditions. However, shell organics in older shells are typically recovered in reduced abundances due to leaching and remaining organics are often converted from insoluble proteins to soluble, free amino acids, making them difficult to detect and recover. …

Design And Validation For Fpga Trust Under Hardware Trojan Attacks, Sanchita Mal-Sarkar, Robert Karam, Seetharam Narasimhan, Anandaroop Ghosh, Aswin Krishna, Swarup Bhunia

Electrical and Computer Engineering Faculty Publications

Field programmable gate arrays (FPGAs) are being increasingly used in a wide range of critical applications, including industrial, automotive, medical, and military systems. Since FPGA vendors are typically fabless, it is more economical to outsource device production to off-shore facilities. This introduces many opportunities for the insertion of malicious alterations of FPGA devices in the foundry, referred to as hardware Trojan attacks, that can cause logical and physical malfunctions during field operation. The vulnerability of these devices to hardware attacks raises serious security concerns regarding hardware and design assurance. In this paper, we present a taxonomy of FPGA-specific hardware Trojan …

Sustainability At U.S. Urban Water Utilities: A Framework To Assess Key Attributes, Matthew Paul Ries

USF Tampa Graduate Theses and Dissertations

Urban water utilities in the United States face challenges due to a combination of external drivers. These include urbanization and population growth, which are stressing a system of aging infrastructure. Compliance with increasing regulations is also a challenge in a fiscally-constrained economic environment. A changing climate threatens infrastructure and past assumptions for water supply and quality. Urban utilities provide clean water and sanitation services to over 80% of the country’s population and its industrial centers. Therefore, the sustainability of these water utilities are crucial to the country’s and the public’s well-being.

New operating models are emerging for a “utility of …

A Spatio-Temporal Comparison Of Avian Migration Phenology Using Citizen Science Data, Ali Arab, Jason R. Courter, Jessica Zelt

United States Geological Survey: Staff Publications

The effects of climate change have wide-ranging impacts on wildlife species and recent studies indicate that birds’ spring arrival dates are advancing in response to changes in global climates. In this paper, we propose a spatio-temporal approach for comparing avian first arrival data for multiple species. As an example, we analyze spring arrival data for two long-distance migrants (Rubythroated Hummingbird Archilochus colubris; and Purple Martin Progne subis) in eastern North America from 2001–2010 using Citizen Science data. The proposed approach provides researchers with a tool to compare mean arrival dates while accounting for spatial and temporal variability. Our results show …

Species Diversification In Eriogonum Umbellatum Var. Aureum, Majus, And Umbellatum In The Colorado Rocky Mountains, Erica Arcibal

Ursidae: The Undergraduate Research Journal at the University of Northern Colorado

No abstract provided.

The Snakehead War: Administrative Rule-Making And Legislative Strategies To Minimize Destruction By The Northern Snakehead, Joshua Rice

William & Mary Environmental Law and Policy Review

No abstract provided.