Digital Commons Network^™

Search For Single Top-Quark Production Via Flavour-Changing Neutral Currents At 8 Tev With The Atlas Detector (Vol 76, 55, 2016), G. Aad, B. Abbott, J. Abdallah, O. Abdinov, R. Aben, M. Abolins, O.S. Abouzeid, H. Abramowicz, H. Abreu, R. Abreu, Y. Abulaiti, B.S. Acharya, L. Adamczyk, D.L. Adams, J. Adelman, S. Adomeit, T. Adye, A. A. Affolder, T. Agatonovic-Jovin, J. Agricola, Milind Purohit

Faculty Publications

No abstract provided.

An Exploratory Study On The Microbiome Of Northern And Southern Populations Of Ixodes Scapularis Ticks Predicts Changes And Unique Bacterial Interactions, Deepak Kumar, Latoyia P. Downs, Abdulsalam Adegoke, Erika Machtinger, Kelly Oggenfuss, Richard S. Ostfeld, Monica Embers, Shahid Karim

Faculty Publications

The black-legged tick (Ixodes scapularis) is the primary vector of Borrelia burgdorferi, the causative agent of Lyme disease in North America. However, the prevalence of Lyme borreliosis is clustered around the Northern States of the United States of America. This study utilized a metagenomic sequencing approach to compare the microbial communities residing within Ix. scapularis populations from northern and southern geographic locations in the USA. Using a SparCC network construction model, we performed potential interactions between members of the microbial communities from Borrelia burgdorferi–infected tissues of unfed and blood-fed ticks. A significant difference in bacterial composition …

Surface Acoustic Wave (Saw) Sensors: Physics, Materials, And Applications, Debdyuti Mandal, Sourav Banerjee

Faculty Publications

Surface acoustic waves (SAWs) are the guided waves that propagate along the top surface of a material with wave vectors orthogonal to the normal direction to the surface. Based on these waves, SAW sensors are conceptualized by employing piezoelectric crystals where the guided elastodynamic waves are generated through an electromechanical coupling. Electromechanical coupling in both active and passive modes is achieved by integrating interdigitated electrode transducers (IDT) with the piezoelectric crystals. Innovative meta-designs of the periodic IDTs define the functionality and application of SAW sensors. This review article presents the physics of guided surface acoustic waves and the piezoelectric materials …

Development Of Advanced Machine Learning Models For Analysis Of Plutonium Surrogate Optical Emission Spectra, Ashwin P. Rao, Phillip R. Jenkins, John D. Auxier Ii, Michael B. Shattan, Anil K. Patnaik

Faculty Publications

This work investigates and applies machine learning paradigms seldom seen in analytical spectroscopy for quantification of gallium in cerium matrices via processing of laser-plasma spectra. Ensemble regressions, support vector machine regressions, Gaussian kernel regressions, and artificial neural network techniques are trained and tested on cerium-gallium pellet spectra. A thorough hyperparameter optimization experiment is conducted initially to determine the best design features for each model. The optimized models are evaluated for sensitivity and precision using the limit of detection (LoD) and root mean-squared error of prediction (RMSEP) metrics, respectively. Gaussian kernel regression yields the superlative predictive model with an RMSEP of …

Search For Continuous Gravitational Waves From 20 Accreting Millisecond X-Ray Pulsars In O3 Ligo Data, R. Abbott, T. D. Abbott, F. Acernese, K. Ackley, C. Adams

Faculty Publications

Results are presented of searches for continuous gravitational waves from 20 accreting millisecond x-ray pulsars with accurately measured spin frequencies and orbital parameters, using data from the third observing run of the Advanced LIGO and Advanced Virgo detectors. The search algorithm uses a hidden Markov model, where the transition probabilities allow the frequency to wander according to an unbiased random walk, while the J-statistic maximum-likelihood matched filter tracks the binary orbital phase. Three narrow subbands are searched for each target, centered on harmonics of the measured spin frequency. The search yields 16 candidates, consistent with a false alarm probability of …

Crop Rotational Complexity Affects Plant-Soil Nitrogen Cycling During Water Deficit, Timothy M. Bowles, Andrea Jilling, Karen Moran-Rivera, Jorg Schnecker, A. Stuart Grandy

Faculty Publications

One of the biggest environmental challenges facing agriculture is how to both supply and retain nitrogen (N), especially as precipitation becomes more variable with climate change. We used a greenhouse experiment to assess how contrasting histories of crop rotational complexity affect plant-soil-microbe interactions that govern N processes, including during water stress. With higher levels of carbon and N cycling hydrolytic enzymes, higher mineral-associated organic matter N concentrations, and an altered microbial community, soils from the most complex rotation enabled 80% more corn N uptake under two moisture regimes, compared to soil from monoculture corn. Higher levels of plant N likely …

Gibbs–Duhem Relation For Phase-Field Models Of Polymeric Mixtures, Rami Alhasan, Douglas R. Tree

Faculty Publications

Phase-field models are relatively inexpensive field-based models capable of capturing the nonequilibrium multiphase behavior of polymers and other soft materials. With their rise in popularity over the past several years, questions have arisen concerning the thermodynamic consistency of some model formulations. In doing so, researchers have employed several different forms of the Gibbs–Duhem equation─a classical thermodynamic relationship used to assess consistency─leading to questions about the correct form of this expression for inhomogeneous mixtures. In this paper, we derive a generalized Gibbs–Duhem relation that is valid for phase-field models. The key to the derivation is the recognition that the functional derivatives …

Scanner: A Web Platform For Annotation, Visualization And Sharing Of Single Cell Rna-Seq Data, Guoshuai Cai, Xuanxuan Yu, Choonhan Youn, Jun Zhou, Feifei Xiao

Faculty Publications

In recent years, efficient scRNA-seq methods have been developed, enabling the transcriptome profiling of single cells massively in parallel. Meanwhile, its high dimensionality and complexity bring challenges to the data analysis and require extensive collaborations between biologists and bioinformaticians and/or biostatisticians. The communication between these two units demands a platform for easy data sharing and exploration. Here we developed Single-Cell Transcriptomics Annotated Viewer (SCANNER), as a public web resource for the scientific community, for sharing and analyzing scRNA-seq data in a collaborative manner. It is easy-to-use without requiring special software or extensive coding skills. Moreover, it equipped a real-time database …

Search For Continuous Gravitational Waves From 20 Accreting Millisecond X-Ray Pulsars In O3 Ligo Data, Ligo Scientific Collaboration, Virgo Collaboration, Kagra Collaboration, Tiffany Z. Summerscales

Faculty Publications

Results are presented of searches for continuous gravitational waves from 20 accreting millisecond x-ray pulsars with accurately measured spin frequencies and orbital parameters, using data from the third observing run of the Advanced LIGO and Advanced Virgo detectors. The search algorithm uses a hidden Markov model, where the transition probabilities allow the frequency to wander according to an unbiased random walk, while the J-statistic maximum-likelihood matched filter tracks the binary orbital phase. Three narrow subbands are searched for each target, centered on harmonics of the measured spin frequency. The search yields 16 candidates, consistent with a false alarm probability of …

Coupling Between Alfvén Wave And Kelvin–Helmholtz Waves In The Low Latitude Boundary Layer, Eun-Hwa Kim, Jay R. Johnson

Faculty Publications

The Kelvin–Helmholtz (KH) instability of magnetohydrodynamic surface waves at the low latitude boundary layer is examined using both an eigenfrequency analysis and a time-dependent wave simulation. The analysis includes the effects of sheared flow and Alfvén velocity gradient. When the magnetosheath flows are perpendicular to the ambient magnetic field direction, unstable KH waves that propagate obliquely to the sheared flow direction occur at the sheared flow surface when the Alfvén Mach number is higher than an instability threshold. Including a shear transition layer between the magnetosphere and magnetosheath leads to secondary KH waves (driven by the sheared flow) that are …

Reef Sediments Can Act As A Stony Coral Tissue Loss Disease Vector, Michael S. Studivan, Ashley M. Rossin, Ewelina Rubin, Nash Soderberg, Daniel M. Holstein, Ian C. Enochs

Faculty Publications

Stony coral tissue loss disease (SCTLD) was first observed in 2014 near Virginia Key in Miami-Dade County, Florida. Field sampling, lab experiments, and modeling approaches have suggested that reef sediments may play a role in SCTLD transmission, though a positive link has not been tested experimentally. We conducted an ex situ transmission assay using a statistically-independent disease apparatus to test whether reef sediments can transmit SCTLD in the absence of direct contact between diseased and healthy coral tissue. We evaluated two methods of sediment inoculation: batch inoculation of sediments collected from southeast Florida using whole colonies of diseased Montastraea cavernosa, …

Towards A Quantum Notion Of Covariance In Spherically Symmetric Loop Quantum Gravity, Rodolfo Gambini, Javier Olmedo, Jorge Pullin

Faculty Publications

The covariance of loop quantum gravity studies of spherically symmetric space-times has recently been questioned. This is a reasonable worry, given that they are formulated in terms of slicing-dependent variables. We show explicitly that the resulting space-times, obtained from Dirac observables of the quantum theory, are covariant in the usual sense of the way-they preserve the quantum line element-for any gauge that is stationary (in the exterior, if there is a horizon). The construction depends crucially on the details of the Abelianized quantization considered, the satisfaction of the quantum constraints, and the recovery of standard general relativity in the classical …

Towards A Quantum Notion Of Covariance In Spherically Symmetric Loop Quantum Gravity, Rodolfo Gambini, Javier Olmedo, Jorge Pullin

Faculty Publications

The covariance of loop quantum gravity studies of spherically symmetric space-times has recently been questioned. This is a reasonable worry, given that they are formulated in terms of slicing-dependent variables. We show explicitly that the resulting space-times, obtained from Dirac observables of the quantum theory, are covariant in the usual sense of the way-they preserve the quantum line element-for any gauge that is stationary (in the exterior, if there is a horizon). The construction depends crucially on the details of the Abelianized quantization considered, the satisfaction of the quantum constraints, and the recovery of standard general relativity in the classical …

Self-Relabeling For Noise-Tolerant Retina Vessel Segmentation Through Label Reliability Estimation, Jiacheng Li, Ruirui Li, Ruize Han, Song Wang

Faculty Publications

Background Retinal vessel segmentation benefits significantly from deep learning. Its performance relies on sufficient training images with accurate ground-truth segmentation, which are usually manually annotated in the form of binary pixel-wise label maps. Manually annotated ground-truth label maps, more or less, contain errors for part of the pixels. Due to the thin structure of retina vessels, such errors are more frequent and serious in manual annotations, which negatively affect deep learning performance.

Methods In this paper, we develop a new method to automatically and iteratively identify and correct such noisy segmentation labels in the process of network training. We consider …

Too Much Is Never Enough: Constructing Electricity Market Demand, Todd S. Aagaard, Andrew N. Kleit

Faculty Publications

Some regions of the United States have created institutions known as capacity markets in an effort to use competitive market forces to ensure adequate electricity supply at lowest cost. But capacity markets are driven more by political and bureaucratic judgments than by competition. The manner in which the capacity market is designed to determine demand exemplifies this observation. As there is no natural demand for capacity, Regional Transmission organizations (RTOs) administratively create demand in capacity markets. RTOs derive capacity demand from three components: the capacity requirement based on forecasted peak demand plus an additional margin, the net cost of new …

Electromagnetic Multi–Gaussian Speckle, Milo W. Hyde Iv, Olga Korotkova

Faculty Publications

Generalizing our prior work on scalar multi-Gaussian (MG) distributed optical fields, we introduce the two-dimensional instantaneous electric-field vector whose components are jointly MG distributed. We then derive the single-point Stokes parameter probability density functions (PDFs) of MG-distributed light having an arbitrary degree and state of polarization. We show, in particular, that the intensity contrast of such a field can be tuned to values smaller or larger than unity. We validate our analysis by generating an example partially polarized MG field with a specified single-point polarization matrix using two different Monte Carlo simulation methods. We then compute the joint PDFs of …

Role Of International Research Experiences In The Development Of Women Of Color In Chemistry, R D. Davis, L Winfield, D Spivak, Z S. Wilson-Kennedy, R D. Davis

Faculty Publications

As undergraduate students cultivate their scientific knowledge and abilities, several high-impact educational practices such as undergraduate research and global experiences have proven exponentially beneficial for their development and success. Current literature on underrepresented racial and ethnic minorities has focused primarily on the impact of undergraduate research on this subpopulation. However, fewer studies have explored the impact of global research experiences and women of color in international research experiences. Grounded in the theoretical frameworks of Social Cognitive Career Theory, Intersectionality, and Community Cultural Wealth, this present study explored the impact of international undergraduate research experiences on women of color from groups …

Current Methods And Future Directions In Avian Diet Analysis, Brandon D. Hoenig, Allison M. Snider, Anna M. Forsman, Keith A. Hobson, Steven C. Latta, Eliot T. Miller, Michael J. Polito, Luke L. Powell, Samantha L. Rogers, Thomas W. Sherry, David P.L. Toews, Andreanna J. Welch, Sabrina S. Taylor, Brady A. Porter

Faculty Publications

Identifying the composition of avian diets is a critical step in characterizing the roles of birds within ecosystems. However, because birds are a diverse taxonomic group with equally diverse dietary habits, gaining an accurate and thorough understanding of avian diet can be difficult. In addition to overcoming the inherent difficulties of studying birds, the field is advancing rapidly, and researchers are challenged with a myriad of methods to study avian diet, a task that has only become more difficult with the introduction of laboratory techniques to dietary studies. Because methodology drives inference, it is important that researchers are aware of …

Search For Darkonium In E+ E− Collisions, J. P. Lees, V. Poireau, V. Tisserand, E. Grauges, A. Palano, G. Eigen, D. N. Brown, Yu. G. Kolomensky, M. Fritsch, H. Koch, T. Schroeder, R. Cheaib, C. Hearty, T. S. Mattison, J. A. Mckenna, R. Y. So, V. E. Blinov, A. R. Buzykaev, Milind Purohit, Et. Al.

Faculty Publications

Collider searches for dark sectors, new particles interacting only feebly with ordinary matter, have largely focused on identifying signatures of new mediators, leaving much of dark sector structures unexplored. In particular, the existence of dark matter bound states (darkonia) remains to be investigated. This possibility could arise in a simple model in which a dark photon (A') is light enough to generate an attractive force between dark fermions. We report herein a search for a JPC ¼ 1−− darkonium state, the ϒ_D, produced in the reaction e⁺e⁻ → γϒ_D, ϒ_D → A …

Measurements Of The Electron-Helicity Asymmetry In The Quasi-Elastic A ((E) Over Right Arrow, E' O) Process, T. Kolar, S. J. Paul, P. Achenbach, H. Arenhoevel, A. Ashkenazi, J. Beričič, R. Böhm, D. Bosnar, T. Brecelj, E. Cline, E. O. Cohen, M. O. Distler, A. Esser, I. Friščić, R. Gilman, C. Giusti, M. Heilig, M. Hoek, D, Izraeli, Steffen Strauch, Et. Al.

Faculty Publications

We present measurements of the electron helicity asymmetry in quasi-elastic proton knockout from ²H and ¹²C nuclei by polarized electrons. This asymmetry depends on the fifth structure function, is antisymmetric with respect to the scattering plane, and vanishes in the absence of final-state interactions, and thus it provides a sensitive tool for their study. Our kinematics cover the full range in off-coplanarity angle θ_pq, with a polar angle θ_pq coverage up to about 8^◦. The missing energy resolution enabled us to determine the asymmetries for knock-out resulting in different states of the residual …

The Isocaloric Substitution Of Plant-Based And Animal-Based Protein In Relation To Aging-Related Health Outcomes: A Systematic Review, Jiali Zheng, Tianren Zhu, Guanghuan Yang, Longgang Zhao, Fangyu Li, Yong-Moon Park, Fred K. Tabung, Susan E. Steck Phd, Mph, Rd, Xiaoguang Li, Hui Wang

Faculty Publications

Plant-based and animal-based protein intake have differential effects on various aging-related health outcomes, but less is known about the health effect of isocaloric substitution of plant-based and animal-based protein. This systematic review summarized current evidence of the isocaloric substitutional effect of plant-based and animal-based protein on aging-related health outcomes. PubMed and Embase databases were searched for epidemiologic observational studies published in English up to 15 March 2021. Studies that included adults ≥18 years old; use of a nutritional substitution model to define isocaloric substitution of plant protein and animal protein; health outcomes covering mortality, aging-related diseases or indices; and reported …

Characterization Of Ti/Sno2 Interface By X-Ray Photoelectron Spectroscopy, Miranda Martinez, Chourasia R. Anil

Faculty Publications

The Ti/SnO2 interface has been investigated in situ via the technique of x-ray photoelectron spectroscopy. Thin films (in the range from 0.3 to 1.1 nm) of titanium were deposited on SnO2 substrates via the e-beam technique. The deposition was carried out at two different substrate temperatures, namely room temperature and 200 C. The photoelectron spectra of tin and titanium in the samples were found to exhibit significant differences upon comparison with the corresponding elemental and the oxide spectra. These changes result from chemical interaction between SnO2 and the titanium overlayer at the interface. The SnO2 was observed to be reduced …

Design, Construction And Operation Of The Protodune-Sp Liquid Argon Tpc, The Dune Collaboration, A. Abed Abud, B. Abi, R. Acciarri, M. A. Acero, M. R. Adames, G. Adamov, D. Adams, M. Adinolfi, A. Aduszkiewicz, J. Aguilar, Z. Ahmad, J. Ahmed, B. Ali-Mohammadzadeh, T. Alion, K. Allison, S. Alonso Monsalve, M. Alrashed, C. Alt, A. Alton, Roberto Petti, Et. Al.

Faculty Publications

The ProtoDUNE-SP detector is a single-phase liquid argon time projection chamber (LArTPC) that was constructed and operated in the CERN North Area at the end of the H4 beamline. This detector is a prototype for the first far detector module of the Deep Underground Neutrino Experiment (DUNE), which will be constructed at the Sandford Underground Research Facility (SURF) in Lead, South Dakota, U.S.A. The ProtoDUNE-SP detector incorporates full-size components as designed for DUNE and has an active volume of 7 × 6 × 7.2 m³. The H4 beam delivers incident particles with well-measured momenta and high-purity particle identification. …

Investigation Of Metastable Low Dimensional Halometallates, Navindra Keerthisinghe, Matthew S. Christian, Anna A. Berseneva, Gregory Morrison, Vladislav V. Klepov, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

The solvothermal synthesis, structure determination and optical characterization of five new metastable halometallate compounds, [1,10-phenH][Pb_3.5I₈] (1), [1,10-phenH₂][Pb₅I₁₂]·(H₂O) (2), [1,10-phen][Pb₂I₄] (3), [1,10-phen]₂[Pb₅Br₁₀] (4) and [1,10-phenH][SbI₄]·(H₂O) (5), are reported. The materials exhibit rich structural diversity and exhibit structural dimensionalities that include 1D chains, 2D sheets and 3D frameworks. The optical spectra of these materials are consistent with bandgaps ranging from 2.70 to 3.44 eV. We show …

Assessing Reproducibility Of Inherited Variants Detected With Short-Read Whole Genome Sequencing, Bohu Pan, Luyao Ren, Vitor Onuchic, Meijian Guan, Rebecca Kusko, Steve Bruinsma, Len Trigg, Andreas Scherer, Baitang Ning, Chaoyang Zhang, Christine Glidewell-Kenney, Chunlin Xiao, Eric Donaldson, Fritz J. Sedlazeck, Gary Schroth, Gokhan Yavas, Haiying Grunenwald, Haodong Chen, Heather Meinholz, Joe Meehan, Jing Wang, Jingcheng Yang, Jonathan Foox, Jun Shang, Kelci Miclaus, Lianhua Dong, Leming Shi, Marghoob Mohiyuddin, Mehdi Pirooznia, Ping Gong, Rooz Golshani, Russ Wolfinger, Samir Lababidi, Sayed Mohammed Ebrahim Sahraeian, Steve Sherry, Tao Han, Tieliu Shi, Wanwan Hou, Weigong Ge, Wen Zou, Wenjing Guo, Wenjun Bao, Wenzhong Xiao, Xiaohui Fan, Yoichi Gondo, Ying Yu, Yongmei Zhao, Zhenqiang Su, Zhichao Liu, Weida Tong, Wenming Xiao, Justin M. Zook, Yuanting Zeng, Huixiao Hong

Faculty Publications

Background: Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS.

Results: To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and …

From Balancing Redox Reactions To Determining Change Of Oxidation Numbers, Pong Kau Yuen, Cheng Man Diana Lau

Faculty Publications

Redox reaction is a core concept in teaching and learning chemistry. This article explores a new method for balancing organic redox reactions that requires the balancing of both atoms and charges. The H+, O, H2O, and e– are used as balanced vehicles in two half reactions. A non-oxidation number approach can be applied to both molecular and ionic equations. The article also provides standard operating procedures and examples. The number of transferred electrons is first determined by balancing a half redox reaction; consequently; the change of oxidation numbers can be calculated. The mathematical equation of Te– = n Te– = …

Overview Of Multi-Factor Prediction Using Deep Neural Networks, Machine Learning, And Their Open-Source Software, Richard S. Segall

Faculty Publications

This chapter first provides an overview with examples of what neural networks (NN), machine learning (ML), and artificial intelligence (AI) are and their applications in biomedical and business situations. The characteristics of 29 types of neural networks are provided including their distinctive graphical illustrations. A survey of current open-source software (OSS) for neural networks, neural network software available for free trail download for limited time use, and open-source software (OSS) for machine learning (ML) are provided. Characteristics of artificial intelligence (AI) technologies for machine learning available as open source are discussed. Illustrations of applications of neural networks, machine learning, and …

Estimating Water Transport From Short-Term Vessel-Based And Long-Term Bottom-Mounted Acoustic Doppler Current Profiler Measurements In An Arctic Lagoon Connected To The Beaufort Sea, Chunyan Li, Kevin Mershon Boswell

Faculty Publications

Acoustic Doppler current profilers (ADCP) are quasi-remote sensing instruments widely used in oceanography to measure velocity profiles continuously. One of the applications is the quantification of land–ocean exchange, which plays a key role in the global cycling of water, heat, and materials. This exchange mostly occurs through estuaries, lagoons, and bays. Studies on the subject thus require that observations of total volume or mass transport can be achieved. Alternatively, numerical modeling is needed for the computation of transport, which, however, also requires that the model is validated properly. Since flows across an estuary, lagoon, or bay are usually non-uniform and …

Multiantenna Multisource Multirelay Spectrum Sharing Networks: Buffer-Aware Direct Link Activation For Higher Reliability And Lower Overhead, Omid M. Kandelusy, Nicholas J. Kirsch

Faculty Publications

Cooperative relaying can be implemented in spectrum sharing networks to extend the range of reliable communication. In this paper, we incorporate multiple-antenna technology and buffer-aided relaying to guarantee a highly reliable connectivity for the secondary network with several source nodes. The multi-antenna configuration for the sources and destination nodes suggests that there are several potential source-to- destination channels which can be auspicious for the network in two ways. First: to balance up the buffer states. Second: to expand the link selection opportunity at each time step. Motivated by this rationale, we propose a buffer-aware communication protocol to incorporate the direct …

Guesswork With Quantum Side Information, Eric P. Hanson, Vishal Katariya, Nilanjana Datta, Mark M. Wilde

Faculty Publications

What is the minimum number of guesses needed on average to guess a realization of a random variable correctly The answer to this question led to the introduction of a quantity called guesswork by Massey in 1994, which can be viewed as an alternate security criterion to entropy. In this paper, we consider the guesswork in the presence of quantum side information, and show that a general sequential guessing strategy is equivalent to performing a single quantum measurement and choosing a guessing strategy based on the outcome. We use this result to deduce entropic one-shot and asymptotic bounds on the …