Physical Sciences and Mathematics Commons^™

Probing Trapped Extracellular Vesicles By Surface-Enhanced Raman Spectroscopy, Lauren Kaufman

Electronic Thesis and Dissertation Repository

Extracellular vesicles (EVs) are released by nearly all cell types within the human body and have been found to play important biological roles including cell-to-cell communication, apoptosis and tissue repair. Lacking cellular machinery, these nano-sized vesicles carry functional proteins and nucleic acids from their parent cells, providing insight into biomarkers present in healthy, cancerous and diseased cells. EVs may be isolated from biofluids such as from blood or urine. Their detection and characterization holds extreme potential in developing less invasive disease detection and treatment methods.

In this work, we propose use of lithographic techniques to fabricate platforms to allow for …

Genetics Analysis Workshop 20: Methods And Strategies For The New Frontiers Of Epigenetics And Pharmacogenomics, Nathan L. Tintle, David W. Fardo, Mariza De Andrade, Stella Aslibekyan, Julia N. Bailey, Justo Lorenzo Bermejo, Rita M. Cantor, Saurabh Ghosh, Philip Melton, Xuexia Wang, Jean W. Maccluer, Laura Almasy

Faculty Work Comprehensive List

GAW20 provided a platform for developing and evaluating statistical methods to analyze human lipid-related phenotypes, DNA methylation, and single-nucleotide markers in a study involving a pharmaceutical intervention. In this article, we present an overview of the data sets and the contributions analyzing these data. The data, donated by the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) investigators, included data from 188 families (N = 1105) which included genome-wide DNA methylation data before and after a 3-week treatment with fenofibrate, single-nucleotide polymorphisms, metabolic syndrome components before and after treatment, and a variety of covariates. The contributions from individual …

Improved Correction For Non-Photochemical Quenching Of In Situ Chlorophyll Fluorescence Based On A Synchronous Irradiance Profile, Xiaogang Xing, Nathan Briggs, Emmanuel Boss, Hervé Claustre

Marine Sciences Faculty Scholarship

In situ chlorophyll fluorometers have been used to quantify the distribution of chlorophyll concentration in natural waters for decades. However, chlorophyll fluorescence is depressed during daylight hours due to non-photochemical quenching (NPQ). Corrections attempted to date have provided improvement but still remain unsatisfactory, often overestimating the expected value. In this study, we examine the relationship between NPQ and instantaneous Photosynthetically Active Radiation (iPAR) using field data from BGC-Argo floats equipped with Chlorophyll-a fluorometers and radiometers. This analysis leads to an improved NPQ correction that incorporates both iPAR and mixed layer depth (MLD) and is validated against data collected at sunrise …

An Outlier Detection Algorithm Based On Cross-Correlation Analysis For Time Series Dataset, Hui Lu, Yaxian Liu, Zongming Fei, Chongchong Guan

Computer Science Faculty Publications

Outlier detection is a very essential problem in a variety of application areas. Many detection methods are deficient for high-dimensional time series data sets containing both isolated and assembled outliers. In this paper, we propose an Outlier Detection method based on Cross-correlation Analysis (ODCA). ODCA consists of three key parts. They are data preprocessing, outlier analysis, and outlier rank. First, we investigate a linear interpolation method to convert assembled outliers into isolated ones. Second, a detection mechanism based on the cross-correlation analysis is proposed for translating the high-dimensional data sets into 1-D cross-correlation function, according to which the isolated outlier …

Association Analyses Of Repeated Measures On Triglyceride And High-Density Lipoprotein Levels: Insights From Gaw20, Saurabh Ghosh, David W. Fardo

Biostatistics Faculty Publications

Background: The GAW20 group formed on the theme of methods for association analyses of repeated measures comprised 4sets of investigators. The provided “real” data set included genotypes obtained from a human whole-genome association study based on longitudinal measurements of triglycerides (TGs) and high-density lipoprotein in addition to methylation levels before and after administration of fenofibrate. The simulated data set contained 200 replications of methylation levels and posttreatment TGs, mimicking the real data set.

Results: The different investigators in the group focused on the statistical challenges unique to family-based association analyses of phenotypes measured longitudinally and applied a wide spectrum of …

Estimating Dominant Runoff Modes Across The Conterminous United States, Brian Buchanan, Daniel A. Auerbach, James Knighton, Darrick Evensen, Daniel R. Fuka, Zachary Easton, Michael Wieczorek, Josephine A. Archibald, Brandon Mcwilliams, Todd Walter

United States Geological Survey: Staff Publications

Effective natural resource planning depends on understanding the prevalence of runoff generating processes. Within a specific area of interest, this demands reproducible, straightforward information that can complement available local data and can orient and guide stakeholders with diverse training and backgrounds. To address this demand within the contiguous United States (CONUS), we characterized and mapped the predominance of two primary runoff generating processes: infiltration‐excess and saturation‐excess runoff (IE vs. SE, respectively). Specifically, we constructed a gap‐filled grid of surficial saturated hydraulic conductivity using the Soil Survey Geographic and State Soil Geographic soils databases. We then compared surficial saturated hydraulic conductivity …

Using Aviris And Machine Learning To Map And Discriminate Bull Kelp And Giant Kelp Along The Pacific Coast Of The United States, Tanner Thompson, Dr. Ryan Jensen

Journal of Undergraduate Research

Kelp forests provide food and shelter for many organisms, and they are an important part of coastal ecosystems throughout the world. Along the Pacific coast of the United States, kelp forests are made up of two species of kelp: bull kelp (Nereocystis Leutkana) and giant kelp (Macrocystis Pyrifera). While similar, these two species are physiologically and structurally different.

Gaw20: Methods And Strategies For The New Frontiers Of Epigenetics And Pharmacogenomics, Nathan L. Tintle, David W. Fardo, Marzia De Andrade, Stella Aslibekyan, Julia N. Bailey, Justo Lorenzo Bermejo, Rita M. Cantor, Saurabh Ghosh, Philip Melton, Xuexua Wang, Jean W. Maccluer, Laura Almasy

Biostatistics Faculty Publications

GAW20 provided a platform for developing and evaluating statistical methods to analyze human lipid-related phenotypes, DNA methylation, and single-nucleotide markers in a study involving a pharmaceutical intervention. In this article, we present an overview of the data sets and the contributions analyzing these data. The data, donated by the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) investigators, included data from 188 families (N = 1105) which included genome-wide DNA methylation data before and after a 3-week treatment with fenofibrate, single-nucleotide polymorphisms, metabolic syndrome components before and after treatment, and a variety of covariates. The contributions from individual …

Longitudinal Data Methods For Evaluating Genome-By-Epigenome Interactions In Families, Justin C. Strickland, I-Chen Chen, Chanung Wang, David W. Fardo

Psychology Faculty Publications

Background: Longitudinal measurement is commonly employed in health research and provides numerous benefits for understanding disease and trait progression over time. More broadly, it allows for proper treatment of correlated responses within clusters. We evaluated 3 methods for analyzing genome-by-epigenome interactions with longitudinal outcomes from family data.

Results: Linear mixed-effect models, generalized estimating equations, and quadratic inference functions were used to test a pharmacoepigenetic effect in 200 simulated posttreatment replicates. Adjustment for baseline outcome provided greater power and more accurate control of Type I error rates than computation of a pre-to-post change score.

Conclusions: Comparison of all modeling approaches indicated …

Triel-Bonded Complexes Between Trr3 (Tr = B, Al, Ga; R = H, F, Cl, Br, Ch3) And Pyrazine, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Complexes between TrR3 (Tr = B, Al, Ga; R= H, F, Cl, Br, CH3)molecules and pyrazine have been characterized at the MP2 and CCSD(T) levels of theory. The adducts can be grouped according to the type of molecular arrangement. The first situation places the Tr atom in the plane of the pyrazine ring and contains a triel bond to the N lone pair. For the boron complexes the orbital interaction energy is almost equal to the electrostatic component, while the former is only half the latter for Tr= Al and Ga. The two monomers are stacked above one another in …

Tourism Review Sentiment Classification Using A Bidirectional Recurrent Neural Network With An Attention Mechanism And Topic-Enriched Word Vectors, Qin Li, Shaobo Li, Jie Hu, Sen Zhang, Jianjun Hu

Faculty Publications

Sentiment analysis of online tourist reviews is playing an increasingly important role in tourism. Accurately capturing the attitudes of tourists regarding different aspects of the scenic sites or the overall polarity of their online reviews is key to tourism analysis and application. However, the performances of current document sentiment analysis methods are not satisfactory as they either neglect the topics of the document or do not consider that not all words contribute equally to the meaning of the text. In this work, we propose a bidirectional gated recurrent unit neural network model (BiGRULA) for sentiment analysis by combining a topic …

Computational Discovery Of A New Rhombohedral Diamond Phase, Zhen-Zhen Li, Jian-Tao Wang, Hiroshi Mizuseki, Changfeng Chen

Physics & Astronomy Faculty Research

We identify by first-principles calculations a new diamond phase in R¯3c (D63d) symmetry, which has a 16-atom rhombohedral primitive cell, thus termed R16 carbon. This rhombohedral diamond comprises a characteristic all-sp3 six-membered-ring bonding network, and it is energetically more stable than previously identified diamondlike six-membered-ring bonded BC8 and BC12 carbon phases. A phonon mode analysis verifies the dynamic structural stability of R16 carbon, and electronic band calculations reveal that it is an insulator with a direct band gap of 4.45 eV. Simulated x-ray diffraction patterns provide an excellent match to recently reported distinct diffraction peaks found in milled fullerene soot, …

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Guidelines And Considerations For Designing Field Experiments Simulating Precipitation Extremes In Forest Ecosystems, Heidi Asbjornsen, John L. Campbell, Katie A. Jennings, Matthew A. Vadeboncoeur, Cameron Mcintire, Pamela H. Templer, Richard P. Phillips, Taryn L. Bauerle, Michael C. Dietze, Serita D. Frey, Peter M. Groffman, Rosella Guerrieri, Paul J. Hanson, Eric P. Kelsey, Alan K. Knapp, Nathan G. Mcdowell, Patrick Meir, Kimberly A. Novick, Scott V. Ollinger, Will T. Pockman, Paul G. Schaberg, Stan D. Wullschleger, Melinda D. Smith, Lindsey E. Rustad

Faculty Publications

Precipitation regimes are changing in response to climate change, yet understanding of how forest ecosystems respond to extreme droughts and pluvials remains incomplete. As future precipitation extremes will likely fall outside the range of historical variability, precipitation manipulation experiments (PMEs) are critical to advancing knowledge about potential ecosystem responses. However, few PMEs have been conducted in forests compared to short-statured ecosystems, and forest PMEs have unique design requirements and constraints. Moreover, past forest PMEs have lacked coordination, limiting cross-site comparisons. Here, we review and synthesize approaches, challenges, and opportunities for conducting PMEs in forests, with the goal of guiding design …

Analytical Representations For Characterizing The Global Aviation Radiation Environment Based On Model And Measurement Databases, W. Kent Tobiska, Leonid Didkovsky, Kevin Judge, Seth Weiman, Dave Bouwer, Justin Bailey, Bill Atwell, Molly Maskrey, Chris Mertens, Yihua Zheng, Margaret Shea, Don Smart, Brad Gersey, Richard Wilkins, Duane Bell, Larry Gardner, Robert Fuschino

All Physics Faculty Publications

The Nowcast of Atmospheric Ionizing Radiation for Aviation Safety climatological model and the Automated Radiation Measurements for Aerospace Safety (ARMAS) statistical database are presented as polynomial fit equations. Using equations based on altitude, L shell, and geomagnetic conditions an effective dose rate for any location from a galactic cosmic ray (GCR) environment can be calculated. A subset of the ARMAS database is represented by a second polynomial fit equation for the GCR plus probable relativistic energetic particle (REP; Van Allen belt REP) effective dose rates within a narrow band of L shells with altitudinal and geomagnetic dependency. Solar energetic particle …

Localization Effects On The Dissipation Of Gravity Wave Packets In The Upper Mesophere And Lower Thermosphere, C. J. Heale, R. L. Walterscheid, J. B. Snively

Publications

Gravity waves not subject to breaking or filtering will dissipate due to viscosity and thermal conduction in the thermosphere. However, the evolutions of wave packets, and the altitudes they reach, are highly dependent upon the spectral content. In this paper, a 2‐D numerical model is used to investigate the effect of spatial localization (and thus spectral content) of a wave packet on its dissipation, dispersion, and spectral evolution. It is found that most wave packets launched below the thermosphere evolve to smaller central vertical wavelengths as the faster, longer vertical wavelength components reach the dissipative thermosphere and are removed first, …

Using Cumulative Potential Recharge For Selection Of Gcm Projections To Force Regional Groundwater Models: A Nebraska Sand Hills Example, Nathan R. Rossman, Vitaly A. Zlotnik, Clinton Rowe

Department of Earth and Atmospheric Sciences: Faculty Publications

Groundwater recharge (GR) controls vegetation, geomorphology, groundwater, wetlands and surface flow, and ultimately, the ecology and economics of semi-arid regions. Therefore, it is critical to assess hydroclimate model scenarios and the uncertainty in future GR to force regional groundwater models. We use basic statistics of downscaled Global Circulation Model (GCM)-projected cumulative potential GR (GR_p) for selecting representative projections. Cumulative GR_p is the net recharge (difference between precipitation (P) and evapotranspiration (ET) rates) over the projection period. The approach is illustrated with an example in the Nebraska Sand Hills (NSH), the largest dune …

Agroecology In Canada: Towards An Integration Of Agroecological Practice, Movement, And Science, Marney E. Isaac, S. Ryan Isakson, Bryan Dale, Charles Z. Levkoe, Sarah K. Hargreaves, V. Ernesto Méndez, Hannah Wittman, Colleen Hammelman, Jennifer C. Langill, Adam R. Martin, Erin Nelson, Michael Ekers, Kira A. Borden, Stephanie Gagliardi, Serra Buchanan, Sarah Archibald, Astrid Gálvez Ciani

College of Agriculture and Life Sciences Faculty Publications

This article surveys the current state of agroecology in Canada, giving particular attention to agroecological practices, the related social movements, and the achievements of agroecological science. In each of these realms, we find that agroecology emerges as a response to the various social and ecological problems associated with the prevailing industrial model of agricultural production that has long been promoted in the country under settler colonialism. Although the prevalence and prominence of agroecology is growing in Canada, its presence is still small and the support for its development is limited. We provide recommendations to achieve a more meaningful integration of …

A Physical Supply-Use Table Framework For Energy Analysis On The Energy Conversion Chain (2), Matthew K. Heun, Anne Owen, Paul E. Brockway

University Faculty Publications and Creative Works

In response to the oil crises of the 1970s, energy accounting experienced a revolution and became the much broader field of energy analysis, in part by expanding along the energy conversion chain from primary and final energy to useful energy and energy services, which satisfy human needs. After evolution and specialization, the field of energy analysis today addresses topics along the entire energy conversion chain, including energy conversion systems, energy resources, carbon emissions, and the role of energy services in promoting human well-being and development. And the expanded field would benefit from a common analysis framework that provides data structure …

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The Firece Green Fire: Vol. 9 Issue 2, Wofford College Environmental Studies Program

The Fierce Green Fire

No abstract provided.

A Nonlinear Systems Framework For Cyberattack Prevention For Chemical Process Control Systems, Helen Durand

Chemical Engineering and Materials Science Faculty Research Publications

Recent cyberattacks against industrial control systems highlight the criticality of preventing future attacks from disrupting plants economically or, more critically, from impacting plant safety. This work develops a nonlinear systems framework for understanding cyberattack-resilience of process and control designs and indicates through an analysis of three control designs how control laws can be inspected for this property. A chemical process example illustrates that control approaches intended for cyberattack prevention which seem intuitive are not cyberattack-resilient unless they meet the requirements of a nonlinear systems description of this property.

Shifting Echo Chambers In Us Climate Policy Networks, Lorien Jasny, Amanda M. Dewey, Anya Galli Robertson, William Yagatich, Ann H. Dubin, Joseph Mccartney Waggle, Dana R. Fisher

Sociology, Anthropology, and Social Work Faculty Publications

Although substantial attention has focused on efforts by the new Administration to block environmental policies, climate politics have been contentious in the US since well before the election of Donald Trump. In this paper, we extend previous work on empirical examinations of echo chambers in US climate politics using new data collected on the federal climate policy network in summer 2016. We test for the similarity and differences at two points in time in homophily and echo chambers using Exponential Random Graph Models (ERGM) to compare new findings from 2016 to previous work on data from 2010. We show that …

Left Ventricular Mechanical Dyssynchrony For Cad Diagnosis: Does It Have Incremental Clinical Values?, Zhixin Jiang, Weihua Zhou

Faculty Publications

No abstract provided.

Eddy Covariance Flux Errors Due To Random And Systematic Timing Errors During Data Acquisition, Gerardo Fratini, Simone Sabbatini, Kevin Ediger, Brad Riensche, George Burba, Giacomo Nicolini, Domenico Vitale, Dario Papale

School of Natural Resources: Faculty Publications

Modern eddy covariance (EC) systems collect high-frequency data (10–20 Hz) via digital outputs of instruments. This is an important evolution with respect to the traditional and widely used mixed analog/digital systems, as fully digital systems help overcome the traditional limitations of transmission reliability, data quality, and completeness of the datasets.

However, fully digital acquisition introduces a new problem for guaranteeing data synchronicity when the clocks of the involved devices themselves cannot be synchronized, which is often the case with instruments providing data via serial or Ethernet connectivity in a streaming mode. In this paper, we suggest that, when assembling EC …

Design And Optimization Of A 3-D Plasmonic Huygens Metasurface For Highly-Efficient Flat Optics, Bryan M. Adomanis

Theses and Dissertations

For miniaturization of future USAF unmanned aerial and space systems to become feasible, accompanying sensor components of these systems must also be reduced in size, weight and power (SWaP). Metasurfaces can act as planar equivalents to bulk optics, and thus possess a high potential to meet these low-SWaP requirements. However, functional efficiencies of plasmonic metasurface architectures have been too low for practical application in the infrared (IR) regime. Huygens-like forward-scattering inclusions may provide a solution to this deficiency, but there is no academic consensus on an optimal plasmonic architecture for obtaining efficient phase control at high frequencies. This dissertation asks …

A Framework For Detecting Injected Influence Attacks On Microblog Websites Using Change Detection Techniques, Vishnu S. Pendyala, Yuhong Liu, Silvia M. Figueira

Faculty Research, Scholarly, and Creative Activity

Presidential elections can impact world peace, global economics, and overall well-being. Recent news indicates that fraud on the Web has played a substantial role in elections, particularly in developing countries in South America and the public discourse, in general. To protect the trustworthiness of the Web, in this paper, we present a novel framework using statistical techniques to help detect veiled Web fraud attacks in Online Social Networks (OSN). Specific examples are used to demonstrate how some statistical techniques, such as the Kalman Filter and the modified CUSUM, can be applied to detect various attack scenarios. A hybrid data set, …

The Sisal Database: A Global Resource To Document Oxygen And Carbon Isotope Records From Speleothems, Kamolphat Atsawawaranunt, Laia Comas-Bru, Sahar Amirnezhad Mozhdehi, Michael Deininger, Sandy P. Harrison, Andy Baker, Meighan Boyd, Nikita Kaushal, Syed Masood Ahmad, Yassine Ait Brahim, Monica Arienzo, Petra Bajo, Kerstin Braun, Yuval Burstyn, Sakonvan Chawchai, Wuhui Duan, István Gábor Hatvani, Jun Hu, Zoltán Kern, Inga Labuhn, Matthew Lachniet, Franziska A. Lechleitner, Andrew Lorrey, Carlos Pérez-Mejías, Robyn Pickering, Nick Scroxton, Sisal Working Group Members

Geoscience Faculty Research

Stable isotope records from speleothems provide information on past climate changes, most particularly information that can be used to reconstruct past changes in precipitation and atmospheric circulation. These records are increasingly being used to provide out-of-sample evaluations of isotope-enabled climate models. SISAL (Speleothem Isotope Synthesis and Analysis) is an international working group of the Past Global Changes (PAGES) project. The working group aims to provide a comprehensive compilation of speleothem isotope records for climate reconstruction and model evaluation. The SISAL database contains data for individual speleothems, grouped by cave system. Stable isotopes of oxygen and carbon (δ18O, δ13C) measurements are …

Long-Lived Remnants From Binary Neutron Star Mergers, David Radice, Albino Perego, Sebastiano Bernuzzi, Bing Zhang

Physics & Astronomy Faculty Research

Massive neutron stars (NSs) with lifetimes of at least several seconds are expected to be the result of a sizable fraction of NS mergers. We study their formation using a large set of numerical relativity simulations. We show that they are initially endowed with angular momentum that significantly exceeds the mass-shedding limit for rigidly rotating equilibria. We find that gravitational wave (GW) emission is not able to remove this excess angular momentum within the time over which solid body rotation should be achieved. Instead, we argue that the excess angular momentum could be carried away by massive winds. Long-lived merger …