Digital Commons Network^™

Connecting The Dots: Transmission Of Stony Coral Tissue Loss Disease From The Marquesas To The Dry Tortugas, Thomas Dobbelaere, Daniel M. Holstein, Erinn M. Muller, Lewis J. Gramer, Lucas Mceachron, Sara D. Williams, Emmanuel Hanert

Faculty Publications

For the last 7 years, Florida's Coral Reef (FCR) has suffered from widespread and severe coral loss caused by stony coral tissue loss disease (SCTLD). First observed off the coast of Miami-Dade county in 2014, the outbreak has since spread throughout the entirety of FCR and some areas of the Caribbean. However, the propagation of the disease through FCR seemed to slow down when it reached the western end of the Marquesas in August 2020. Despite being present about 30 km (similar to 20 miles) from the Dry Tortugas (DRTO), SCTLD was not reported in this area before May 2021. …

Strong Laser Polarization Control Of Coherent Phonon Excitation In Van Der Waals Material Fe3Gete2, Yu Gong, Ming Hu, Nico Harris, Zhonghua Yang, Ti Xie, Alem Teklu, Narayanan Kuthirummal, Jacob Koenemann, Xianghan Xu, Sang-Wook Cheong, Will Mcloud, Cheng Gong

Faculty Publications

Optical manipulation of coherent phonon frequency in two-dimensional (2D) materials could advance the development of ultrafast phononics in atomic-thin platforms. However, conventional approaches for such control are limited to doping, strain, structural or thermal engineering. Here, we report the experimental observation of strong laser-polarization control of coherent phonon frequency through time-resolved pump-probe spectroscopic study of van der Waals (vdW) materials Fe₃GeTe₂. When the polarization of the pumping laser with tilted incidence is swept between in-plane and out-of-plane orientations, the frequencies of excited phonons can be monotonically tuned by as large as 3% (~100 GHz). Our first-principles …

Hippocampal Ensembles Represent Sequential Relationships Among An Extended Sequence Of Nonspatial Events, Babak Shahbaba, Lingge Li, Forest Agostinelli, Mansi Saraf, Keiland W. Cooper, Derenik Haghverdian, Gabriel A. Elias, Pierre Baldi, Norbert J. Fortin

Faculty Publications

The hippocampus is critical to the temporal organization of our experiences. Although this fundamental capacity is conserved across modalities and species, its underlying neuronal mechanisms remain unclear. Here we recorded hippocampal activity as rats remembered an extended sequence of nonspatial events unfolding over several seconds, as in daily life episodes in humans. We then developed statistical machine learning methods to analyze the ensemble activity and discovered forms of sequential organization and coding important for order memory judgments. Specifically, we found that hippocampal ensembles provide significant temporal coding throughout nonspatial event sequences, differentiate distinct types of task-critical information sequentially within events, …

Transmodel: An R Package For Linear Transformation Model With Censored Data, Jie Zhou, Jiajia Zhang Ph.D.

Faculty Publications

Linear transformation models, including the proportional hazards model and proportional odds model, under right censoring were discussed by Chen, Jin, and Ying (2002). The asymptotic variance of the estimator they proposed has a closed form and can be obtained easily by plug-in rules, which improves the computational efficiency. We develop an R package TransModel based on Chen's approach. The detailed usage of the package is discussed, and the function is applied to the Veterans' Administration lung cancer data.

Alleviating The Challenges With Remote Learning During A Pandemic, Hani Morgan

Faculty Publications

The COVID-19 pandemic has caused many challenges that resulted from the suspension of face-to-face classes. Some of these challenges involved the problems associated with remote learning. One problem with this approach to learning is that it can be didactic. Remote learning can contribute to loneliness as well, and the lack of access to reliable technological resources that many students from low-income families experience can contribute to learning setbacks. Although the pandemic has created challenges related to providing remote learning opportunities and keeping students emotionally and physically healthy, some schools and colleges have used various methods to alleviate these concerns. This …

Search Full Text Options Here 2 Of 4 Kmt-2021-Blg-0912lb: A Microlensing Super Earth Around A K-Type Star, Cheongho Han, Ian A. Bond, Jennifer C. Yee, Weicheng Zang, Michael D. Albrow

Faculty Publications

Aims. The light curve of the microlensing event KMT-2021-BLG-0912 exhibits a very short anomaly relative to a single-lens single-source form. We investigate the light curve for the purpose of identifying the origin of the anomaly.

Methods. We model the light curve under various interpretations. From this, we find four solutions, in which three solutions are found under the assumption that the lens is composed of two masses (2L1S models), and the other solution is found under the assumption that the source is comprised of binary stars (1L2S model). The 1L2S model is ruled out based on the contradiction that the …

Concurrent Identification And Characterization Of Protein Structure And Continuous Internal Dynamics With Redcraft, Hanin Omar, Aaron Hein, Casey A. Cole, Homayoun Valafar

Faculty Publications

Internal dynamics of proteins can play a critical role in the biological function of some proteins. Several well documented instances have been reported such as MBP, DHFR, hTS, DGCR8, and NSP1 of the SARS-CoV family of viruses. Despite the importance of internal dynamics of proteins, there currently are very few approaches that allow for meaningful separation of internal dynamics from structural aspects using experimental data. Here we present a computational approach named REDCRAFT that allows for concurrent characterization of protein structure and dynamics. Here, we have subjected DHFR (PDB-ID 1RX2), a 159-residue protein, to a fictitious, mixed mode model of …

Comparison Of Human Urinary Exosomes Isolated Via Ultracentrifugation Alone Versus Ultracentrifugation Followed By Sec Column-Purification, Kun Huang, Sudha Garimella, Alyssa Clay-Gilmour, Lucia Vojtech, Bridget Armstrong, Madison Bessonny, Alexis Stamatikos

Faculty Publications

Chronic kidney disease is a progressive, incurable condition that involves a gradual loss of kidney function. While there are no non-invasive biomarkers available to determine whether individuals are susceptible to developing chronic kidney disease, small RNAs within urinary exosomes have recently emerged as a potential candidate to use for assessing renal function. Ultracentrifugation is the gold standard for urinary exosome isolation. However, extravesicular small RNA contamination can occur when isolating exosomes from biological fluids using ultracentrifugation, which may lead to misidentifying the presence of certain small RNA species in human urinary exosomes. Therefore, we characterized human urinary exosomal preparations isolated …

Alluvial Connectivity In Multi‐Channel Networks In Rivers And Estuaries, Willem Sonke, Maarten G. Kleinhans, Bettina Speckmann, Wout M. Dijk, Matthew Hiatt

Faculty Publications

No abstract provided.

A Bayesian Phase I/Ii Biomarker-Based Design For Identifying Subgroup-Specific Optimal Dose For Immunotherapy, Beibei Guo, Yong Zang

Faculty Publications

Immunotherapy is an innovative treatment that enlists the patient's immune system to battle tumors. The optimal dose for treating patients with an immunotherapeutic agent may differ according to their biomarker status. In this article, we propose a biomarker-based phase I/II dose-finding design for identifying subgroup-specific optimal dose for immunotherapy (BSOI) that jointly models the immune response, toxicity, and efficacy outcomes. We propose parsimonious yet flexible models to borrow information across different types of outcomes and subgroups. We quantify the desirability of the dose using a utility function and adopt a two-stage dose-finding algorithm to find the optimal dose for each …

Singing Strategies Are Linked To Perch Use On Foraging Territories In Heart-Nosed Bats, Grace C. Smarsh, Ashley M. Long, Michael Smotherman

Faculty Publications

Acoustic communication allows animals to coordinate and optimize resource utilization in space. Cardioderma cor, the heart-nosed bat, is one of the few species of bats known to sing during nighttime foraging. Previous research found that heart-nosed bats react aggressively to song playback, supporting the territorial defense hypothesis of singing in this species. We further investigated the territorial defense hypothesis from an ecological standpoint, which predicts that singing should be associated with exclusive areas containing a resource, by tracking 14 individuals nightly during the dry seasons in Tanzania. We quantified the singing behavior of individuals at all perches used throughout the …

Strict Lyapunov Functions And Feedback Controls For Sir Models With Quarantine And Vaccination, Hiroshi Ito, Michael Malisoff, Frederic Mazenc

Faculty Publications

We provide a new global strict Lyapunov function construction for a susceptible, infected, and recovered (or SIR) disease dynamics that includes quarantine of infected individuals and mass vaccination. We use the Lyapunov function to design feedback controls to asymptotically stabilize a desired endemic equilibrium, and to prove input-to-state stability for the dynamics with a suitable restriction on the disturbances. Our simulations illustrate the potential of our feedback controls to reduce peak levels of infected individuals.

Docking And Molecular Dynamic Of Microalgae Compounds As Potential Inhibitors Of Beta-Lactamase, Roberto Pestana-Nobles, Yani Aranguren-Diaz, Elwi Machado-Sierra, Juvenal Yosa, Nataly J. Galan-Freyle,, Laura X. Sepulveda-Montano, Daniel G. Kuroda, Leonardo C. Pacheco-Londono

Faculty Publications

Bacterial resistance is responsible for a wide variety of health problems, both in children and adults. The persistence of symptoms and infections are mainly treated with beta-lactam antibiotics. The increasing resistance to those antibiotics by bacterial pathogens generated the emergence of extended-spectrum beta-lactamases (ESBLs), an actual public health problem. This is due to rapid mutations of bacteria when exposed to antibiotics. In this case, beta-lactamases are enzymes used by bacteria to hydrolyze the beta-lactam rings present in the antibiotics. Therefore, it was necessary to explore novel molecules as potential beta-lactamases inhibitors to find antibacterial compounds against infection caused by ESBLs. …

Whole-Genome Sequencing And Rna-Seq Reveal Differences In Genetic Mechanism For Flowering Response Between Weedy Rice And Cultivated Rice, Richard S. Garcia, Sapphire Coronejo, Jonathan Concepcion, Prasanta K. Subudhi

Faculty Publications

Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified …

Interpretation And Inference For Altmetric Indicators Arising From Sparse Data Statistics, Lawrence Smolinsky, Bernhard Klingenberg, Brian D. Marx

Faculty Publications

In 2018 Bornmann and Haunschild (2018a) introduced a new indicator called the Mantel-Haenszel quotient (MHq) to measure alternative metrics (or altmetrics) of scientometric data. In this article we review the Mantel-Haenszel statistics, point out two errors in the literature, and introduce a new indicator. First, we correct the interpretation of MHq and mention that it is still a meaningful indicator. Second, we correct the variance formula for MHq, which leads to narrower confidence intervals. A simulation study shows the superior performance of our variance estimator and confidence intervals. Since MHq does not match its original description in the literature, we …

Deep Learning Of High-Resolution Aerial Imagery For Coastal Marsh Change Detection: A Comparative Study, Grayson R. Morgan, Cuizhen Wang, Zhenlong Li, Steven R. Schill, Daniel R. Morgan

Faculty Publications

Deep learning techniques are increasingly being recognized as effective image classifiers. Aside from their successful performance in past studies, the accuracies have varied in complex environments, in comparison with the popularly of applied machine learning classifiers. This study seeks to explore the feasibility of using a U-Net deep learning architecture to classify bi-temporal, high-resolution, county-scale aerial images to determine the spatial extent and changes of land cover classes that directly or indirectly impact tidal marsh. The image set used in the analysis is a collection of a 1-m resolution collection of National Agriculture Imagery Program (NAIP) tiles from 2009 and …

Minerals Matter: Science, Technology, And Society, Barbara L. Dutrow

Faculty Publications

The expertise of earth scientists is crucial for solving some of today's most pressing challenges, including global warming and the climate crises, natural hazard reduction, water and soil quality, exploration for critical elements for our technological society, and many others.

Search Full Text Options Here 3 Of 3 Heat-Mitigated Design And Lorentz Force-Based Steering Of An Mri-Driven Microcatheter Toward Minimally Invasive Surgery, Martin Francis Phelan Iii, Mehmet Efe Tiryaki, Jelena Lazovic, Hunter Gilbert, Metin Sitti

Faculty Publications

Catheters integrated with microcoils for electromagnetic steering under the high, uniform magnetic field within magnetic resonance (MR) scanners (3-7 Tesla) have enabled an alternative approach for active catheter operations. Achieving larger ranges of tip motion for Lorentz force-based steering have previously been dependent on using high power coupled with active cooling, bulkier catheter designs, or introducing additional microcoil sets along the catheter. This work proposes an alternative approach using a heat-mitigated design and actuation strategy for a magnetic resonance imaging (MRI)-driven microcatheter. A quad-configuration microcoil (QCM) design is introduced, allowing miniaturization of existing MRI-driven, Lorentz force-based catheters down to 1-mm …

A Survey Of Blind Modulation Classification Techniques For Ofdm Signals, Anand Kumar, Sudhan Majhi, Guan Gui, Hsiao-Chun Wu, Chau Yuen

Faculty Publications

Blind modulation classification (MC) is an integral part of designing an adaptive or intelligent transceiver for future wireless communications. Blind MC has several applications in the adaptive and automated systems of sixth generation (6G) communications to improve spectral efficiency and power efficiency, and reduce latency. It will become a integral part of intelligent software-defined radios (SDR) for future communication. In this paper, we provide various MC techniques for orthogonal frequency division multiplexing (OFDM) signals in a systematic way. We focus on the most widely used statistical and machine learning (ML) models and emphasize their advantages and limitations. The statistical-based blind …

A Survey Of Blind Modulation Classification Techniques For Ofdm Signals, Anand Kumar, Sudhan Majhi, Guan Gui, Hsiao-Chun Wu, Chau Yuen

Faculty Publications

Blind modulation classification (MC) is an integral part of designing an adaptive or intelligent transceiver for future wireless communications. Blind MC has several applications in the adaptive and automated systems of sixth generation (6G) communications to improve spectral efficiency and power efficiency, and reduce latency. It will become a integral part of intelligent software-defined radios (SDR) for future communication. In this paper, we provide various MC techniques for orthogonal frequency division multiplexing (OFDM) signals in a systematic way. We focus on the most widely used statistical and machine learning (ML) models and emphasize their advantages and limitations. The statistical-based blind …

Cu2+ And Cu3+ Acceptors In Β-Ga2O3 Crystals: A Magnetic Resonance And Optical Absorption Study, Timothy D. Gustafson, Nancy C. Giles, Brian C. Holloway, Christopher A. Lenyk, J. Jesenovec, J. S. Mccloy, M. D. Mccluskey, Larry E. Halliburton

Faculty Publications

Electron paramagnetic resonance (EPR) and optical absorption are used to characterize Cu²⁺ (3d⁹) and Cu³⁺ (3d⁸) ions in Cu-doped β-Ga₂O₃. These Cu ions are singly ionized acceptors and neutral acceptors, respectively (in semiconductor notation, they are Cu⁻ and Cu⁰ acceptors). Two distinct Cu²⁺ EPR spectra are observed in the as-grown crystals. We refer to them as Cu²⁺(A) and Cu²⁺(B). Spin-Hamiltonian parameters (a g matrix and a ^63,65Cu hyperfine matrix) are obtained from the angular dependence of each spectrum. Additional electron-nuclear double resonance …

Dominance Of Diffusive Methane Emissions From Lowland Headwater Streams Promotes Oxidation And Isotopic Enrichment, Andrew L. Robison, Wilfred M. Wollheim, Clarice R. Perryman, Annie R. Cotter, Jessica E. Mackay, Ruth K. Varner, Paige Clarizia, Jessica G. Ernakovich

Faculty Publications

Inland waters are the largest natural source of methane (CH4) to the atmosphere, yet the contribution from small streams to this flux is not clearly defined. To fully understand CH4 emissions from streams and rivers, we must consider the relative importance of CH4 emission pathways, the prominence of microbially-mediated production and oxidation of CH4, and the isotopic signature of emitted CH4. Here, we construct a complete CH4 emission budgets for four lowland headwater streams by quantifying diffusive CH4 emissions and comparing them to previously published rates of ebullitive emissions. We also examine the isotopic composition of CH4 along with the …

A New Matroid Lift Construction And An Application To Group-Labeled Graphs, Zach Walsh

Faculty Publications

A well-known result of Brylawski constructs an elementary lift of a matroid M from a linear class of circuits of M. We generalize this result by constructing a rank-k lift of M from a rank-k matroid on the set of circuits of M. We conjecture that every lift of M arises via this construction. We then apply this result to group-labeled graphs, generalizing a construction of Zaslavsky. Given a graph G with edges labeled by a group, Zaslavsky's lift matroid K is an elementary lift of the graphic matroid M(G) that respects the group-labeling; specifically, the cycles of G that …

Investigation Of Innovation In Wine Industry Via Meta-Analysis, Ali Dogru, Joseph Peyrefitte

Faculty Publications

This study provides a systematic review of 76 relevant wine business studies published in the last 30 years. Our meta-analysis investigates six commonly used variables to explain wine innovation: absorptive capacity, technology adoption, sustainable practices, export orientation, firm size, and firm age. We also investigate the association between innovation and financial performance, using the reported effect sizes in the literature. Our meta-analysis reveals that absorptive capacity, technology adoption, sustainable practices, export orientation, and firm size positively correlate with innovation efforts, and innovation is positively associated with financial performance. However, we find no correlation between firm age and innovation. In addition …

Reply To Comment: Controls On Turnover Of Marine Dissolved Organic Matter-Testing The Null Hypothesis Of Purely Concentration-Driven Uptake, Yuan Shen, Ronald Benner

Faculty Publications

Our recent bioassay experiments indicate that molecular properties are a primary control on the microbial utilization of dissolved organic matter in the ocean. This finding is questioned by Lennartz and Dittmar who modeled our experiments and concluded that our observations could be largely explained by concentration-driven uptake independent from molecular properties. We suggest the authors' models are deficient for establishing the relative roles of molecular properties and concentration-driven uptake. Our conclusion is consistent with earlier and recent experimental results and biogeochemical observations, supporting a unified theory with molecular properties as a more prominent control than concentration-driven uptake on marine organic …

Dispersed Crude Oil Induces Dysbiosis In The Red Snapper Lutjanus Campechanus External Microbiota, Andrew M. Tarnecki, Christelle Miller, Tracy A. Sherwood, Robert J. Griffitt, Ryan W. Schloesser, Dana L. Wetzel

Faculty Publications

The fish external microbiota competitively excludes primary pathogens and prevents the proliferation of opportunists. A shift from healthy microbiota composition, known as dysbiosis, may be triggered by environmental stressors and increases host susceptibility to disease. The Deepwater Horizon (DWH) oil spill was a significant stressor event in the Gulf of Mexico. Despite anecdotal reports of skin lesions on fishes following the oil spill, little information is available on the impact of dispersed oil on the fish external microbiota. In this study, juvenile red snapper (Lutjanus campechanus) were exposed to a chemically enhanced water-accommodated fraction (CEWAF) of Corexit 9500/DWH …

A Comparison Of Sporadic-E Occurrence Rates Using Gps Radio Occultation And Ionosonde Measurements, Rodney Carmona, Omar A. Nava, Eugene V. Dao, Daniel J. Emmons

Faculty Publications

Sporadic-E (E_s) occurrence rates from Global Position Satellite radio occultation (GPS-RO) measurements have shown to vary by a factor of five between studies, motivating the need for a comparison with ground-based measurements. In an attempt to find accurate GPS-RO techniques for detecting E_s formation, occurrence rates derived using five previously developed GPS-RO techniques are compared to ionosonde measurements over an eight-year period from 2010–2017. GPS-RO measurements within 170 km of a ionosonde site are used to calculate E_s occurrence rates and compared to the ground-truth ionosonde measurements. The techniques are compared individually for each ionosonde site …

Robust Error Estimation Based On Factor-Graph Models For Non-Line-Of-Sight Localization, O. Arda Vanli, Clark N. Taylor

Faculty Publications

This paper presents a method to estimate the covariances of the inputs in a factor-graph formulation for localization under non-line-of-sight conditions. A general solution based on covariance estimation and M-estimators in linear regression problems, is presented that is shown to give unbiased estimators of multiple variances and are robust against outliers. An iteratively re-weighted least squares algorithm is proposed to jointly compute the proposed variance estimators and the state estimates for the nonlinear factor graph optimization. The efficacy of the method is illustrated in a simulation study using a robot localization problem under various process and measurement models and measurement …

Connecting Ansatz Expressibility To Gradient Magnitudes And Barren Plateaus, Zoe Holmes, Kunal Sharma, M Cerezo, Patrick Coles

Faculty Publications

Parametrized quantum circuits serve as ansatze for solving variational problems and provide a flexible paradigm for the programming of near-term quantum computers. Ideally, such ansatze should be highly expressive, so that a close approximation of the desired solution can be accessed. On the other hand, the ansatz must also have sufficiently large gradients to allow for training. Here, we derive a fundamental relationship between these two essential properties: expressibility and trainability. This is done by extending the well-established barren plateau phenomenon, which holds for ansatze that form exact 2-designs, to arbitrary ansatze. Specifically, we calculate the variance in the cost …

Future Of Winter In Northeastern North America: Climate Indicators Portray Warming And Snow Loss That Will Impact Ecosystems And Communities, Elizabeth Burakowski, Alix Contosta, Danielle Grogan, Sarah Nelson, Sarah Garlick, Nora Casson

Faculty Publications

Winters in northeastern North America have warmed faster than summers, with impacts on ecosystems and society. Global climate models (GCMs) indicate that winters will continue to warm and lose snow in the future, but uncertainty remains regarding the magnitude of warming. Here, we project future trends in winter indicators under lower and higher climate-warming scenarios based on emission levels across northeastern North America at a fine spatial scale (1/16°) relevant to climate-related decision making. Under both climate scenarios, winters continue to warm with coincident increases in days above freezing, decreases in days with snow cover, and fewer nights below freezing. …