Physical Sciences and Mathematics Commons^™

Npgreat: Assembly Of The Human Subtelomere Regions With The Use Of Ultralong Nanopore Reads And Linked Reads, Eleni Adam, Desh Ranjan, Harold Riethman

Computer Science Faculty Publications

Background: Human subtelomeric DNA regulates the length and stability of adjacent telomeres that are critical for cellular function, and contains many gene/pseudogene families. Large evolutionarily recent segmental duplications and associated structural variation in human subtelomeres has made complete sequencing and assembly of these regions difficult to impossible for many loci, complicating or precluding a wide range of genetic analyses to investigate their function.

Results: We present a hybrid assembly method, NanoPore Guided REgional Assembly Tool (NPGREAT), which combines Linked-Read data with mapped ultralong nanopore reads spanning subtelomeric segmental duplications to potentially overcome these difficulties. Linked-Read sets of DNA sequences identified …

Measuring The Economic Impact Of Recurrent Flooding On Workforce Productivity And Property, Joshua G. Behr, Wie Yusuf, George Mcleod, Sarah Stafford, Derek Loftis, Afi Anuar, Rafael Diaz

Presentations, Lectures, Posters, Reports

From the Executive Summary:

This research draws upon expertise across multiple disciplines and fields. Leveraged are natural systems data and social-behavioral data. The high-level objective is to advance our understanding of how very recent recurrent flooding has impacted residents within the City of Portsmouth, and then forecast these impacts under projections of sea level rise. While this research draws upon data for the City of Portsmouth, the findings may be generalized to the broader Hampton Roads region.

Applications Of Blockchain In Business Processes: A Comprehensive Review, Wattana Viriyasitavat, Li Xu, Dusit Niyato, Zhuming Bi, Danupol Hoonsopon

Information Technology & Decision Sciences Faculty Publications

Blockchain (BC), as an emerging technology, is revolutionizing Business Process Management (BPM) in multiple ways. The main adoption is to serve as a trusted infrastructure to guarantee the trust of collaborations among multiple partners in trustless environments. Especially, BC enables trust of information by using Distributed Ledger Technology (DLT). With the power of smart contracts, BC enforces the obligations of counterparties that transact in a business process (BP) by programming the contracts as transactions. This paper aims to study the state-of-the-art of BC technologies by (1) exploring its applications in BPM with the focus on how BC provides the trust …

Hydrological Drought Forecasting Using A Deep Transformer Model, Amobichukwu C. Amanambu, Joann Mossa, Yin-Hsuen Chen

University Administration Publications

Hydrological drought forecasting is essential for effective water resource management planning. Innovations in computer science and artificial intelligence (AI) have been incorporated into Earth science research domains to improve predictive performance for water resource planning and disaster management. Forecasting of future hydrological drought can assist with mitigation strategies for various stakeholders. This study uses the transformer deep learning model to forecast hydrological drought, with a benchmark comparison with the long short-term memory (LSTM) model. These models were applied to the Apalachicola River, Florida, with two gauging stations located at Chattahoochee and Blountstown. Daily stage-height data from the period 1928–2022 were …

Odu’S Storm Recovery Project Gets Boost From Dominion Energy, News @ Odu

News Items

No abstract provided.

Odu Economist Outlines Costs Resulting From Unchecked Sea Level Rise, Brendan O'Hallarn

News Items

No abstract provided.

Revisiting 228Th As A Tool For Determining Sedimentation And Mass Accumulation Rates, Joseph J. Tamborski, Pinghe Cai, Meagan Eagle, Paul Henderson, Matthew A. Charette

OES Faculty Publications

The use of ²²⁸Th has seen limited application for determining sedimentation and mass accumulation rates in coastal and marine environments. Recent analytical advances have enabled rapid, precise measurements of particle-bound ²²⁸Th using a radium delayed coincidence counting system (RaDeCC). Herein we review the ²²⁸Th cycle in the marine environment and revisit the historical use of ²²⁸Th as a tracer for determining sediment vertical accretion and mass accumulation rates in light of new measurement techniques. Case studies comparing accumulation rates from ²²⁸Th and ²¹⁰Pb are presented for a micro-tidal salt marsh and a marginal sea …

A Demonstration Of A Simple Methodology Of Flood Prediction For A Coastal City Under Threat Of Sea Level Rise: The Case Of Norfolk, Va, Usa, Tal Ezer

CCPO Publications

Many coastal cities around the world are at risk of increased flooding due to sea level rise (SLR), so here a simple flood prediction method is demonstrated for one city at risk, Norfolk, VA, on the U.S. East Coast. The probability of future flooding is estimated by extending observed hourly water level for 1927–2021 into hourly estimates until 2100. Unlike most other flood prediction methods, the approach here does not use any predetermined probability distribution function of extreme events, and instead a random sampling of past data represents tides and storm surges. The probability of flooding for 3 different flood …

Influence Of Defects On In-Plane Dynamic Properties Of Hexagonal Ligament Chiral Structures, Ning An, Xunwen Su, Dongmei Zhu, Mileta M. Tomovic

Engineering Technology Faculty Publications

Although the six-ligament chiral structure has many unique properties, due to its special structure, the stress concentration is prone to defects. In addition, additive manufacturing is also prone to defects. This paper studies the effect of defects, which is helpful for the better application of the six-ligament chiral structure. Several new six-ligament chiral structures with random and concentrated defects were designed to explore the effects of the defects on the in-plane dynamic properties. The structures were studied with the finite element ANSYS/LSDYNA numerical simulation and experimental methods. According to the defect-free six-ligament chiral structures exhibiting different deformation modes at different …

Odu Researchers Attempt To Forecast Flood Impacts In Real Dollars, News @ Odu

News Items

No abstract provided.

Perspectives On Living Shorelines: Marine Contractors And Agents In Southeast Virginia, Michelle Covi, Juita-Elena (Wie) Yusuf

Presentations, Lectures, Posters, Reports

No abstract provided.

Smart Manufacturing—Theories, Methods, And Applications, Zhuming Bi, Lida Xu, Puren Ouyang

Information Technology & Decision Sciences Faculty Publications

(First paragraph) Smart manufacturing (SM) distinguishes itself from other system paradigms by introducing ‘smartness’ as a measure to a manufacturing system; however, researchers in different domains have different expectations of system smartness from their own perspectives. In this Special Issue (SI), SM refers to a system paradigm where digital technologies are deployed to enhance system smartness by (1) empowering physical resources in production, (2) utilizing virtual and dynamic assets over the internet to expand system capabilities, (3) supporting data-driven decision making at all domains and levels of businesses, or (4) reconfiguring systems to adapt changes and uncertainties in dynamic environments. …

The History Of Air Quality In Utah: A Narrative Review, Logan E. Mitchell, Christopher Zajchowski

Human Movement Sciences & Special Education Faculty Publications

Utah has a rich history related to air pollution; however, it is not widely known or documented. This is despite air quality being a top issue of public concern for the state’s urban residents and acute episodes that feature some of the world’s worst short-term particulate matter exposure. As we discuss in this narrative review, the relationship between air pollution and the state’s residents has changed over time, as fuel sources shifted from wood to coal to petroleum and natural gas. Air pollution rose in prominence as a public issue in the 1880s as Utah’s urban areas grew. Since then, …

Estimating The Health Effects Of Adding Bicycle And Pedestrian Paths At The Census Tract Level: Multiple Model Comparison, Ross J. Gore, Christopher Lynch, Craig Jordan, Andrew Collins, R. Michael Robinson, Gabrielle Fuller, Pearson Ames, Prateek Keerthi, Yash Kandukuri

VMASC Publications

Background: Adding additional bicycle and pedestrian paths to an area can lead to improved health outcomes for residents over time. However, quantitatively determining which areas benefit more from bicycle and pedestrian paths, how many miles of bicycle and pedestrian paths are needed, and the health outcomes that may be most improved remain open questions.

Objective: Our work provides and evaluates a methodology that offers actionable insight for city-level planners, public health officials, and decision makers tasked with the question “To what extent will adding specified bicycle and pedestrian path mileage to a census tract improve residents’ health outcomes over time?” …

Contrasting Sea-Ice Algae Blooms In A Changing Arctic Documented By Autonomous Drifting Buoys, Victoria Hill, Bonnie Light, Michael Steele, Andrew Lowy Sybrandy

OES Faculty Publications

Novel observations of the seasonal evolution of an ice algal bloom on the Chukchi shelf were collected by two autonomous buoys deployed 180 km apart in first-year drifting sea ice. High attenuation of blue light in the bottom of the ice indicated considerable accumulation of ice algae biomass with derived Chlorophyll-a concentrations (Chl a) up to 184 mg m⁻². Differences in the magnitude and persistence of ice algae biomass under each buoy appear to have been driven by differences in snow thickness, as ice thickness was similar between the sites. Minimal snow cover (0.02 m) around …

Challenging Predictions Of Inflationary Models With Cmb Data, Richik Bhattacharya, Atanu Debnath, Esha Sajjanhar, Shravani Sardeshpande, Pablo Tenorio Hernández, José Ricardo Torres Heredia

2022 REYES Proceedings

Cosmic inflation offers the best known explanations for many of the observed features of the Universe, such as its flatness. An imprint of the qualities of this mechanism is left in the cosmic microwave background (CMB), which can be instrumental to confirm inflation. Unfortunately, there is a plethora of inflationary models, which are a priori in the same footing. It is conceivable that contrasting the predictions of the various models with the measured values of the parameters of CMB data and other cosmological observables shall allow one to single out the successful theory of inflation. In this work we provide …

A Raft To Coastal Resilience: Odu Researchers Collaborate To Help Rural Communities Combat Flooding Impacts, News @ Odu

News Items

No abstract provided.

Two-Current Transition Amplitudes With Two-Body Final States, Keegan H. Sherman, Feliipe G. Ortega-Gama, Raúl A. Briceño, Andrew W. Jackura

Physics Faculty Publications

We derive the on-shell form of amplitudes containing two external currents with a single hadron in the initial state and two hadrons in the final state, denoted as 1 + J → 2 + J . This class of amplitude is relevant in precision tests of the Standard Model as well as for exploring the structure of excited states in the QCD spectrum. We present a model-independent description of the amplitudes where we sum to all orders in the strong interaction. From this analytic form we are able to extract transition and elastic resonance form factors consistent with previous work …

Runtime Energy Savings Based On Machine Learning Models For Multicore Applications, Vaibhav Sundriyal, Masha Sosonkina

Electrical & Computer Engineering Faculty Publications

To improve the power consumption of parallel applications at the runtime, modern processors provide frequency scaling and power limiting capabilities. In this work, a runtime strategy is proposed to maximize energy savings under a given performance degradation. Machine learning techniques were utilized to develop performance models which would provide accurate performance prediction with change in operating core-uncore frequency. Experiments, performed on a node (28 cores) of a modern computing platform showed significant energy savings of as much as 26% with performance degradation of as low as 5% under the proposed strategy compared with the execution in the unlimited power case.

Future Location For Odu's Institute For Coastal Adaptation And Resilience Will Foster Research And Experiential Learning, Jonah Grinkewitz

News Items

No abstract provided.

Foundations Of Plasmas For Medical Applications, T. Von Woedtke, Mounir Laroussi, M. Gherardi

Electrical & Computer Engineering Faculty Publications

Plasma medicine refers to the application of nonequilibrium plasmas at approximately body temperature, for therapeutic purposes. Nonequilibrium plasmas are weakly ionized gases which contain charged and neutral species and electric fields, and emit radiation, particularly in the visible and ultraviolet range. Medically-relevant cold atmospheric pressure plasma (CAP) sources and devices are usually dielectric barrier discharges and nonequilibrium atmospheric pressure plasma jets. Plasma diagnostic methods and modelling approaches are used to characterize the densities and fluxes of active plasma species and their interaction with surrounding matter. In addition to the direct application of plasma onto living tissue, the treatment of liquids …

Odu Researchers Will Put Buoys In The Mediterranean Sea To Help Schools Teach Climate Change, Mindy Ayala-Diaz

News Items

No abstract provided.

A Super Fast Algorithm For Estimating Sample Entropy, Weifeng Liu, Ying Jiang, Yuesheng Xu

Mathematics & Statistics Faculty Publications

: Sample entropy, an approximation of the Kolmogorov entropy, was proposed to characterize complexity of a time series, which is essentially defined as − log(B/A), where B denotes the number of matched template pairs with length m and A denotes the number of matched template pairs with m + 1, for a predetermined positive integer m. It has been widely used to analyze physiological signals. As computing sample entropy is time consuming, the box-assisted, bucket-assisted, x-sort, assisted sliding box, and kd-tree-based algorithms were proposed to accelerate its computation. These algorithms require O(N²) or …

The Influence Of Particle Concentration And Bulk Characteristics On Polarized Oceanographic Lidar Measurements, Brian L. Collister, Richard C. Zimmerman, Charles I. Sukenik, William M. Balch, Victoria J. Hill

OES Faculty Publications

Oceanographic lidar measurements of the linear depolarization ratio, δ, contain information on the bulk characteristics of marine particles that could improve our ability to study ocean biogeochemistry. However, a scarcity of information on the polarized light-scattering properties of marine particles and the lack of a framework for separating single and multiple scattering effects on δ have hindered the development of polarization-based retrievals of bulk particle properties. To address these knowledge gaps, we made single scattering measurements of δ for several compositionally and morphologically distinct marine particle assemblages. We then used a bio-optical model to explore the influence of multiple …

Partial Muon Capture Rates In A = 3 And A = 6 Nuclei With Chiral Effective Field Theory, G. B. King, S. Pastore, M. Piarulli, Rocco Schiavilla

Physics Faculty Publications

Searches for neutrinoless double-β decay rates are crucial in addressing questions within fundamental symmetries and neutrino physics. The rates of these decays depend not only on unknown parameters associated with neutrinos, but also on nuclear properties. In order to reliably extract information about the neutrino, one needs an accurate treatment of the complex many-body dynamics of the nucleus. Neutrinoless double-β decays take place at momentum transfers on the order of 100MeV /c and require both nuclear electroweak vector and axial current matrix elements. Muon capture, a process in the same momentum transfer regime, has readily available experimental data to validate …

Understanding The Mechanism Of Deep Learning Frameworks In Lesion Detection For Pathological Images With Breast Cancer, Wei-Wen Hsu, Chung-Hao Chen, Chang Hao, Yu-Ling Hou, Xiang Gao, Yun Shao, Xueli Zhang, Jingjing Wang, Tao He, Yanhong Tai

Electrical & Computer Engineering Faculty Publications

With the advances of scanning sensors and deep learning algorithms, computational pathology has drawn much attention in recent years and started to play an important role in the clinical workflow. Computer-aided detection (CADe) systems have been developed to assist pathologists in slide assessment, increasing diagnosis efficiency and reducing misdetections. In this study, we conducted four experiments to demonstrate that the features learned by deep learning models are interpretable from a pathological perspective. In addition, classifiers such as the support vector machine (SVM) and random forests (RF) were used in experiments to replace the fully connected layers and decompose the end-to-end …

Climate Change Could Make Allergy Season Longer, Odu Expert Says, Amber Kennedy

News Items

No abstract provided.

Odu’S Peter Bernath Participates In Study That Reveals Damage To Ozone Layer From Extreme Wildfires, Tiffany Whitfield

News Items

No abstract provided.

Empirically Derived Thermal Thresholds Of Four Coral Species Along The Red Sea Using A Portable And Standardized Experimental Approach, Nicolas R. Evensen, Christian R. Voolstra, Maoz Fine, Gabriela Perna, Carol Buitrago-López, Anny Cárdenas, Guilhem Banc-Prandi, Katherine Rowe, Daniel J. Barshis

Biological Sciences Faculty Publications

Global warming is causing an unprecedented loss of species and habitats worldwide. This is particularly apparent for tropical coral reefs, with an increasing number of reefs experiencing mass bleaching and mortality on an annual basis. As such, there is a growing need for a standardized experimental approach to rapidly assess the thermal limits of corals and predict the survival of coral species across reefs and regions. Using a portable experimental system, the Coral Bleaching Automated Stress System (CBASS), we conducted standardized 18 h acute thermal stress assays to quantitively determine the upper thermal limits of four coral species across the …

4,6-O-Phenylethylidene Acetal Protected D-Glucosamine Carbamate-Based Gelators And Their Applications For Multi-Component Gels, Pooja Sharma, Guijun Wang

Chemistry & Biochemistry Faculty Publications

The self-assembly of carbohydrate-based low molecular weight gelators has led to useful advanced soft materials. The interactions of the gelators with various cations and anions are important in creating novel molecular architectures and expanding the scope of the small molecular gelators. In this study, a series of thirteen new C-2 carbamates of the 4,6-O-phenylethylidene acetalprotected D-glucosamine derivatives has been synthesized and characterized. These compounds are rationally designed from a common sugar template. All carbamates synthesized were found to be efficient gelators and three compounds are also hydrogelators. The resulting gels were characterized using optical microscopy, atomic force microscopy, …