Physical Sciences and Mathematics Commons^™

Fungal Community Homogenization, Shift In Dominant Trophic Guild, And Appearance Of Novel Taxa With Biotic Invasion, Mark A. Anthony, Serita D. Frey, Kristina A. Stinson

Faculty Publications

Invasion by non-native plants may fundamentally restructure the soil fungal community. The invasive plant, Alliaria petiolata, produces secondary compounds suppressive to mycorrhizal fungi and may therefore be expected to have generally negative effects on other components of the fungal community. Here, we compared fungal biomass, diversity, community composition, and the relative abundance of fungal trophic guilds, along with edaphic properties of soils collected from uninvaded and invaded plots across six temperate forests. Invaded plots were differentiated from uninvaded plots by lower variation in fungal community composition (beta diversity) and soil properties, higher fungal richness and community evenness (alpha diversity), and …

Dietary Inflammatory Index And Colorectal Cancer Risk – A Meta-Analysis, Nitin Shivappa, Justyna Godos, James R. Hébert, Michael David Wirth, Gabriele Piuri, Attilio Speciani, Giuseppe Grosso

Faculty Publications

Diet and chronic inflammation of the colon have been suggested to be risk factors in the development of colorectal cancer (CRC). The possible link between inflammatory potential of diet, measured through the Dietary Inflammatory Index (DII®), and CRC has been investigated in several populations across the world. The aim of this study was to conduct a meta-analysis on studies exploring this association. Data from nine studies were eligible, of which five were case-control and four were cohort studies. Results from meta-analysis showed a positive association between increasing DII scores, indicating a pro-inflammatory diet, and CRC. Individuals in the highest versus …

Taming Charge Transport In Semiconducting Polymers With Branched Alkyl Side Chains, Bob C. Schroeder, Tadanori Kurosawa, Tianren Fu, Yu-Cheng Chiu, Jaewan Mun, Ging-Ji Nathan Wang, Xiaodan Gu, Leo Shaw, James Kneller, Theo Kreouzis, Michael F. Toney, Zhenan Bao

Faculty Publications

The solid-state packing and polymer orientation relative to the substrate are key properties to control in order to achieve high charge carrier mobilities in organic field effect transistors (OFET). Intuitively, shorter side chains are expected to yield higher charge carrier mobilities because of a denser solid state packing motif and a higher ratio of charge transport moieties. However our findings suggest that the polymer chain orientation plays a crucial role in high-performing diketopyrrolopyrrole-based polymers. By synthesizing a series of DPP-based polymers with different branched alkyl side chain lengths, it is shown that the polymer orientation depends on the branched alkyl …

The Sluggs Survey: Trails Of Sluggs Galaxies In A Modified Spin-Ellipticity Diagram, Sabine Bellstedt, Alister Graham, Duncan Forbes, Aaron Romanowsky, Jean Brodie, Jay Strader

Faculty Publications

We present radial tracks for four early-type galaxies with embedded intermediate-scale discs in a modified spin-ellipticity diagram. Here, each galaxy's spin and ellipticity profiles are shown as a radial track, as opposed to a single, flux-weighted aperture-dependent value as is common in the literature. The use of a single ellipticity and spin parameter is inadequate to capture the basic nature of these galaxies, which transition from fast to slow rotation as one moves to larger radii where the disc ceases to dominate. After peaking, the four galaxy's radial tracks feature a downturn in both ellipticity and spin with increasing radius, …

Automated Software Testing In The Dod: Current Practices And Opportunities For Improvement, Darryl K. Ahner, James Wisnowski, James R. Simpson

Faculty Publications

The concept of automating the testing of software-intensive systems has been around for decades, but the practice of automating testing is scarce in many industries, especially in the government defense sector. A one-year project initiated by the Office of the Secretary of Defense (OSD), Scientific Test and Analysis Techniques Center of Excellence (STAT COE) and sponsored by Navy OPNAV N94 set out to:

• study the degree to which the Department of Defense (DoD) has adopted automated software testing (AST);

• share the best software practices used by industry; and

• develop and distribute an AST implementation guide intended for program management and …

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Fatty Acid Concentration And Phase Transitions Modulate Aβ Aggregation Pathways, Pratip Rana, Dexter Dean, Edward Steen, Ashwin Vaidya, Vijayaraghavan Rangachari, Preetam Ghosh

Faculty Publications

Aggregation of amyloid β (Aβ) peptides is a significant event that underpins Alzheimer disease (AD) pathology. Aβ aggregates, especially the low-molecular weight oligomers, are the primary toxic agents in AD and hence, there is increasing interest in understanding their formation and behavior. Aggregation is a nucleation-dependent process in which the pre-nucleation events are dominated by Aβ homotypic interactions. Dynamic flux and stochasticity during pre-nucleation renders the reactions susceptible to perturbations by other molecules. In this context, we investigate the heterotypic interactions between Aβ and fatty acids (FAs) by two independent tool-sets such as …

Synthesis Of Non-Uniformly Correlated Partially Coherent Sources Using A Deformable Mirror, Milo W. Hyde Iv, Santasri Bose-Pillai, Ryan A. Wood

Faculty Publications

The near real-time synthesis of a non-uniformly correlated partially coherent source using a low-actuator-count deformable mirror is demonstrated. The statistical optics theory underpinning the synthesis method is reviewed. The experimental results of a non-uniformly correlated source are presented and compared to theoretical predictions. A discussion on how deformable mirror characteristics such as actuator count and pitch affect source generation is also included.

Light Rare Earth Element Depletion During Deepwater Horizon Blowout Methanotrophy, Alan M. Shiller, Eric W. Chan, D.J. Joung, Molly Redmond, John D. Kessler

Faculty Publications

Rare earth elements have generally not been thought to have a biological role. However, recent work has demonstrated that the light REEs (LREEs: La, Ce, Pr, and Nd) are essential for at least some methanotrophs, being co-factors in the XoxF type of methanol dehydrogenase (MDH). We show here that dissolved LREEs were significantly removed in a submerged plume of methane-rich water during the Deepwater Horizon (DWH) well blowout. Furthermore, incubation experiments conducted with naturally methane-enriched waters from hydrocarbon seeps in the vicinity of the DWH wellhead also showed LREE removal concurrent with methane consumption. Metagenomic sequencing of incubation …

Methods For Real-Time Prediction Of The Mode Of Travel Using Smartphone-Based Gps And Accelerometer Data, Bryan D. Martin, Vittorio Addona, Julian Wolfson, Gediminas Adomavicius, Yingling Fan

Faculty Publications

We propose and compare combinations of several methods for classifying transportation activity data from smartphone GPS and accelerometer sensors. We have two main objectives. First, we aim to classify our data as accurately as possible. Second, we aim to reduce the dimensionality of the data as much as possible in order to reduce the computational burden of the classification. We combine dimension reduction and classification algorithms and compare them with a metric that balances accuracy and dimensionality. In doing so, we develop a classification algorithm that accurately classifies five different modes of transportation (i.e., walking, biking, car, bus and rail) …

Stochastic Quasilinear Evolution Equations In Umd Banach Spaces, Manil T. Mohan, Sivaguru S. Sritharan

Faculty Publications

In this work we prove the existence and uniqueness up to a stopping time for the stochastic counterpart of Tosio Kato's quasilinear evolutions in UMD Banach spaces. These class of evolutions are known to cover a large class of physically important nonlinear partial differential equations. Existence of a unique maximal solution as well as an estimate on the probability of positivity of stopping time is obtained. An example of stochastic Euler and Navier–Stokes equation is also given as an application of abstract theory to concrete models.

The Human Touch: How Non-Expert Users Perceive, Interpret, And Fix Topic Models, Tak Yeon Lee, Alison Smith, Kevin Seppi, Niklas Elmqvist, Jordan Boyd-Graber, Leah Findlater

Faculty Publications

Topic modeling is a common tool for understanding large bodies of text, but is typically provided as a “take it or leave it” proposition. Incorporating human knowledge in unsupervised learning is a promising approach to create high-quality topic models. Existing interactive systems and modeling algorithms support a wide range of refinement operations to express feedback. However, these systems’ interactions are primarily driven by algorithmic convenience, ignoring users who may lack expertise in topic modeling. To better understand how non-expert users understand, assess, and refine topics, we conducted two user studies—an in-person interview study and an online crowdsourced study. These studies …

Machine Learning Phases Of Strongly Correlated Fermions, Kelvin Ch'ng, Juan Carrasquilla, Roger Melko, Ehsan Khatami

Faculty Publications

Machine learning offers an unprecedented perspective for the problem of classifying phases in condensed matter physics. We employ neural network machine learning techniques to distinguish finite-temperature phases of the strongly-correlated fermions on cubic lattices. We show that a three-dimensional convolutional network trained on auxiliary field configurations produced by quantum Monte Carlo simulations of the Hubbard model can correctly predict the magnetic phase diagram of the model at the average density of one (half filling). We then use the network, trained at half filling, to explore the trend in the transition temperature as the system is doped away from half filling. …

A Brief Introduction To Equi-Chordal And Equi-Isoclinic Tight Fusion Frames, Matthew C. Fickus, John Jasper, Dustin G. Mixon, Cody E. Watson

Faculty Publications

Equi-chordal and equi-isoclinic tight fusion frames (ECTFFs and EITFFs) are both types of optimal packings of subspaces in Euclidean spaces. In the special case where these subspaces are one-dimensional, ECTFFs and EITFFs both correspond to types of optimal packings of lines known as equiangular tight frames. In this brief note, we review some of the fundamental ideas and results concerning ECTFFs and EITFFs.

A Recent Project Shows That The Microbial Carbon Pump Is A Primary Mechanism Driving Ocean Carbon Uptake, Jing M. Chen, Louis Legendre, Ronald Benner

Faculty Publications

No abstract provided.

Fresnel Spatial Filtering Of Quasihomogeneous Sources For Wave Optics Simulations, Milo W. Hyde Iv, Santasri Bose-Pillai

Faculty Publications

High-spatial-frequency optical fields or sources are often encountered when simulating directed energy, active imaging, or remote sensing systems and scenarios. These spatially broadband fields are a challenge in wave optics simulations because the sampling required to represent and then propagate these fields without aliasing is often impractical. To address this, two spatial filtering techniques are presented. The first, called Fresnel spatial filtering, finds a spatially band-limited source that, after propagation, produces the exact observation plane field as the broadband source over a user-specified region of interest. The second, called statistical or quasihomogeneous spatial filtering, finds a spatially band-limited source that, …

2d Surface Creation Using Intel Mkl, R. Steven Turley

Faculty Publications

This document illustrates how to use the Intel Math Kernel Library (MKL) to create surfaces with a given cut-off spatial frequency and rms surface height. They closely mimic typical surfaces our group has measured using atomic force microscopy (AFM).

Circular Integration Region, R. Steven Turley

Faculty Publications

This report explains how to transform a singular integration over the an arc of a circle into an integration over a unit square using various coordinate transformations include a Duffy transformation. Fortran code illustrating the algorithms is included along with unit test validations.

Temperature-Modulated Expression Of Allometric Respiration Strategies Supports A Metabolic Scaling Rule, Chet F. Rakocinski, Kelsey Burns Gillam

Faculty Publications

A model based on the mass-specific oxygen consumption rate of the tolerant polychaete, Capitella telata, related meaningfully to a novel metabolic scaling rule as applied to the infaunal size spectrum. Depending on temperature, C. telataexpressed divergent oxyregulating or oxyconforming strategies relative to oxygen availability. A non-linear response surface fitted to the allometric exponents of a family of V_O2 curves for 12 treatment combinations of DO saturation and temperature was used to project oxygen consumption rates across the infaunal size spectrum. Plasticity in respiration strategies was evident, based on four simulated dynamic 32 d oxygen-temperature exposure scenarios and …

A Lab-On-Chip Phosphate Analyzer For Long-Term In Situ Monitoring At Fixed Observatories: Optimization And Performance Evaluation In Estuarine And Oligotrophic Coastal Waters, Maxime Grand, Geraldine Clinton-Bailey, Alexander Beaton, Allison Schaap, Thomas Johengen, Mario Tamburri, Douglas Connelly, Matthew Mowlem, Eric Achterberg

Faculty Publications

The development of phosphate sensors suitable for long-term in situdeployments in natural waters, is essential to improve our understanding of the distribution, fluxes, and biogeochemical role of this key nutrient in a changing ocean. Here, we describe the optimization of the molybdenum blue method for in situ work using a lab-on-chip (LOC) analyzer and evaluate its performance in the laboratory and at two contrasting field sites. The in situ performance of the LOC sensor is evaluated using hourly time-series data from a 56-day trial in Southampton Water (UK), as well as a month-long deployment in the subtropical oligotrophic waters of …

The Relationship Of Plasma Trans Fatty Acids With Dietary Inflammatory Index Among Us Adults, Mohsen Mazidi, Hong-Kai Gao, Nitin Shivappa, Michael David Wirth, James R. Hébert, Andre Pascal Kengne

Faculty Publications

Background: It has been suggested that trans fatty acids (TFAs) play an important role in cardiovascular diseases. We investigated the association between plasma TFAs and the dietary inflammatory index (DII) ™ in US adults.

Methods: National Health and Nutrition Examination Survey (NHANES) participants with data on plasma TFAs measured from 1999 to 2010 were included. Energy-adjusted-DII ™ (E-DII ™) expressed per 1000 kcal was calculated from 24-h dietary recalls. All statistical analyses accounted for the survey design and sample weights.

Results: Of the 5446 eligible participants, 46.8% (n = 2550) were men. The mean age of the population was 47.1 …

Anomalydetection: Implementation Of Augmented Network Log Anomaly Detection Procedures, Robert J. Gutierrez, Bradley C. Boehmke, Kenneth W. Bauer, Cade M. Saie, Trevor J. Bihl

Faculty Publications

As the number of cyber-attacks continues to grow on a daily basis, so does the delay in threat detection. For instance, in 2015, the Office of Personnel Management discovered that approximately 21.5 million individual records of Federal employees and contractors had been stolen. On average, the time between an attack and its discovery is more than 200 days. In the case of the OPM breach, the attack had been going on for almost a year. Currently, cyber analysts inspect numerous potential incidents on a daily basis, but have neither the time nor the resources available to perform such a task. …

Erratum: "The Sluggs Survey: A Catalog Of Globular Cluster Radial Velocities" (2017, Aj, 153, 114), Duncan Forbes, Adebusola Alabi, Jean Brodie, Aaron Romanowsky, Jay Strader, Caroline Foster, Christopher Usher, Lee Spitler, Sabine Bellstedt, Nicola Pastorello, Sreeja Kartha, Zach Jennings, Alexa Villaume, Asher Wasserman, Vincenzo Pota

Faculty Publications

This is an erratum for the article 2017 AJ 153 114.

Typhoon Haiyan Overwash Sediments From Leyte Gulf Coastlines Show Local Spatial Variations With Hybrid Storm And Tsunami Signatures, Janneli Lea A. Soria, Adam D. Switzer, Jessica E. Pilarczyk, Fernando P. Siringan, Nicole S. Khan, Hermann M. Fritz

Faculty Publications

Marine inundation associated with the 5 to 8 m storm surge of Typhoon Haiyan in 2013 left overwash sediments inland on the coastal plains of the northwestern shores of Leyte Gulf, Philippines. The Haiyan overwash deposit provides a modern sedimentary record of storm surge deposition from a Category 5 landfalling typhoon. We studied overwash sediments at two locations that experienced similar storm surge conditions but represent contrasting sedimentological regimes, namely a siliciclastic coast and a mixed siliciclastic-carbonate coast. The contrasting local geology is significantly reflected in the differences in sediment grain size, composition and sorting at the two sites. The …

A Selection Rule For Transitions In Pt-Symmetric Quantum Theory, Lawrence R. Mead, David Garfinkle

Faculty Publications

Carl Bender and collaborators have developed a quantum theory governed by Hamiltonians that are PT-symmetric rather than Hermitian. To implement this theory, the inner product was redefined to guarantee positive norms of eigenstates of the Hamiltonian. In the general case, which includes arbitrary time-dependence in the Hamiltonian, a modification of the Schrödinger equation is necessary as shown by Gong and Wang to conserve probability. In this paper, we derive the following selection rule: transitions induced by time dependence in a PT-symmetric Hamiltonian cannot occur between normalized states of differing PT-norm. We show three examples of this selection rule in action: …

Exact And Heuristic Algorithms For Risk-Aware Stochastic Physical Search, Daniel S. Brown, Jeffrey Hudack, Nathaniel Gemelli, Bikramjit Banerjee

Faculty Publications

We consider an intelligent agent seeking to obtain an item from one of several physical locations, where the cost to obtain the item at each location is stochastic. We study risk-aware stochastic physical search (RA-SPS), where both the cost to travel and the cost to obtain the item are taken from the same budget and where the objective is to maximize the probability of success while minimizing the required budget. This type of problem models many task-planning scenarios, such as space exploration, shopping, or surveillance. In these types of scenarios, the actual cost of completing an objective at a location …

An Ameliorated Prediction Of Drug–Target Interactions Based On Multi-Scale Discrete Wavelet Transform And Network Features, Cong Shen, Yijie Ding, Jijun Tang, Xinying Xu, Fei Guo

Faculty Publications

The prediction of drug–target interactions (DTIs) via computational technology plays a crucial role in reducing the experimental cost. A variety of state-of-the-art methods have been proposed to improve the accuracy of DTI predictions. In this paper, we propose a kind of drug–target interactions predictor adopting multi-scale discrete wavelet transform and network features (named as DAWN) in order to solve the DTIs prediction problem. We encode the drug molecule by a substructure fingerprint with a dictionary of substructure patterns. Simultaneously, we apply the discrete wavelet transform (DWT) to extract features from target sequences. Then, we concatenate and normalize the target, drug, …

On-Chip, High-Sensitivity Temperature Sensors Based On Dye-Doped Solid-State Polymer Microring Lasers, Lei Wan, Hengky Chandrahalim, Cong Chen, Qiushu Chen, Ting Mei, Yuji Oki, Naoya Nishimura, Lingjie Jay Guo, Xudong Fan

Faculty Publications

We developed a chip-scale temperature sensor with a high sensitivity of 228.6 pm/°C based on a rhodamine 6G (R6G)-doped SU-8 whispering-gallery mode microring laser. The optical mode was largely distributed in a polymer core layer with a 30 μm height that provided detection sensitivity, and the chemically robust fused-silica microring resonator host platform guaranteed its versatility for investigating different functional polymer materials with different refractive indices. As a proof of concept, a dye-doped hyperbranched polymer (TZ-001) microring laser-based temperature sensor was simultaneously developed on the same host wafer and characterized using a free-space optics measurement setup. Compared to TZ-001, the …

Electron Paramagnetic Resonance Study Of Neutral Mg Acceptors In Β-Ga2O3 Crystals, Brant E. Kananen [*], Larry E. Halliburton, Elizabeth M. Scherrer [*], K. T. Stevens, G. K. Foundos, K. B. Chang, Nancy C. Giles

Faculty Publications

Electron paramagnetic resonance (EPR) is used to directly observe and characterize neutral Mg acceptors (Mg⁰_Ga) in a β-Ga₂O₃ crystal. These acceptors, best considered as small polarons, are produced when the Mg-doped crystal is irradiated at or near 77 K with x rays. During the irradiation, neutral acceptors are formed when holes are trapped at singly ionized Mg acceptors (Mg−Ga). Unintentionally present Fe³⁺ (3d⁵) and Cr³⁺ (3d³) transition-metal ions serve as the corresponding electron traps. The hole is localized in a nonbonding p orbital on a threefold-coordinated oxygen ion …

An Ensemble Deep Convolutional Neural Network Model With Improved D-S Evidence Fusion For Bearing Fault Diagnosis, Shaobo Li, Guoka Liu, Xianghong Tang, Jianguang Lu, Jianjun Hu

Faculty Publications

Intelligent machine health monitoring and fault diagnosis are becoming increasingly important for modern manufacturing industries. Current fault diagnosis approaches mostly depend on expert-designed features for building prediction models. In this paper, we proposed IDSCNN, a novel bearing fault diagnosis algorithm based on ensemble deep convolutional neural networks and an improved Dempster–Shafer theory based evidence fusion. The convolutional neural networks take the root mean square (RMS) maps from the FFT (Fast Fourier Transformation) features of the vibration signals from two sensors as inputs. The improved D-S evidence theory is implemented via distance matrix from evidences and modified Gini Index. Extensive evaluations …

Estimating Index Of Refraction For Specular Reflectors Using Passive Polarimetric Hyperspectral Radiance Measurements, Jacob A. Martin, Kevin C. Gross

Faculty Publications

Results of a method of estimating index of refraction from passive, polarimetric hyperspectral imaging radiance measurements are presented. As off-nadir viewing hyperspectral imaging platforms gain prominence, estimating index of refraction, which is invariant to viewing angle, may prove advantageous to estimating the emissivity, which is not. Results show that index of refraction can be retrieved to within 8% rms error for fused silica and sapphire glass targets, while simultaneously estimating object temperature. The accuracy and self-consistency of this technique for estimating index of refraction are shown to compare favorably to the maximum smoothness temperature–emissivity separation algorithm. Additionally, the results show …