Physical Sciences and Mathematics Commons^™

Alternating Direction Implicit Method With Adaptive Grids For Modeling Chemotaxis In Dictyostelium Discoideum, Christopher F. Loomis

Theses and Dissertations

Dictyostelium discoideum (Dd) is a model organism, studied for reasons from cell movement to chemotaxis to human disease control. Creating a computer model of the life cycle of Dd has garnered great interest, one part of which is the Aggregation Stage, where thousands of amoeba gather together to form a slug. Chemotaxis is the mechanism through which this is accomplished. This thesis develops two- and three-dimensional alternating direction implicit code which solves the diffusion equation on an adaptive grid. The calculated values for both two and three dimensions are checked against the actual solution and error results are provided. Comparisons …

Interpolation Guided Compositional Verification, Shang-Wei Lin, Jun Sun, Truong Khanh Nguyen, Yang Liu, Jin Song Dong

Research Collection School Of Computing and Information Systems

Model checking suffers from the state space explosion problem. Compositional verification techniques such as assume-guarantee reasoning (AGR) have been proposed to alleviate the problem. However, there are at least three challenges in applying AGR. Firstly, given a system M1 M2, how do we automatically construct and refine (in the presence of spurious counterexamples) an assumption A2, which must be an abstraction of M2? Previous approaches suggest to incrementally learn and modify the assumption through multiple invocations of a model checker, which could be often time consuming. Secondly, how do we keep the state space small when checking M1 A2 |= …

Human Action Recognition In Unconstrained Videos By Explicit Motion Modeling, Yu-Gang Jiang, Qi Dai, Wei Liu, Xiangyang Xue, Chong-Wah Ngo

Research Collection School Of Computing and Information Systems

Human action recognition in unconstrained videos is a challenging problem with many applications. Most state-of-the-art approaches adopted the well-known bag-of-features representations, generated based on isolated local patches or patch trajectories, where motion patterns, such as object-object and object-background relationships are mostly discarded. In this paper, we propose a simple representation aiming at modeling these motion relationships. We adopt global and local reference points to explicitly characterize motion information, so that the final representation is more robust to camera movements, which widely exist in unconstrained videos. Our approach operates on the top of visual codewords generated on dense local patch trajectories, …

Cost-Sensitive Online Classification With Adaptive Regularization And Its Applications, Peilin Zhao, Furen Zhuang, Min Wu, Xiao-Li Li, Hoi, Steven C. H.

Research Collection School Of Computing and Information Systems

Cost-Sensitive Online Classification is recently proposed to directly online optimize two well-known cost-sensitive measures: (i) maximization of weighted sum of sensitivity and specificity, and (ii) minimization of weighted misclassification cost. However, the previous existing learning algorithms only utilized the first order information of the data stream. This is insufficient, as recent studies have proved that incorporating second order information could yield significant improvements on the prediction model. Hence, we propose a novel cost-sensitive online classification algorithm with adaptive regularization. We theoretically analyzed the proposed algorithm and empirically validated its effectiveness with extensive experiments. We also demonstrate the application of the …

Where Are The Passengers? A Grid-Based Gaussian Mixture Model For Taxi Bookings, Meng-Fen Chiang, Tuan Anh Hoang, Ee-Peng Lim

Research Collection School Of Computing and Information Systems

Taxi bookings are events where requests for taxis are made by passengers either over voice calls or mobile apps. As the demand for taxis changes with space and time, it is important to model both the space and temporal dimensions in dynamic booking data. Several applications can benefit from a good taxi booking model. These include the prediction of number of bookings at certain location and time of the day, and the detection of anomalous booking events. In this paper, we propose a Grid-based Gaussian Mixture Model (GGMM) with spatio-temporal dimensions that groups booking data into a number of spatio-temporal …

Seismic Surveys And Marine Turtles: An Underestimated Global Threat?, Sarah E. Nelms, Wendy Dow Piniak, Caroline R. Weir, Brendan J. Godley

Environmental Studies Faculty Publications

Seismic surveys are widely used in marine geophysical oil and gas exploration, employing airguns to produce sound-waves capable of penetrating the sea floor. In recent years, concerns have been raised over the biological impacts of this activity, particularly for marine mammals. While exploration occurs in the waters of at least fifty countries where marine turtles are present, the degree of threat posed by seismic surveys is almost entirely unknown. To investigate this issue, a mixed-methods approach involving a systematic review, policy comparison and stakeholder analysis was employed and recommendations for future research were identified. This study found that turtles have …

Dreissenid Mussel Research Priorities Workshop, Mark D. Sytsma, Stephen Phillips, Timothy D. Counihan

Center for Lakes and Reservoirs Publications and Presentations

Currently, dreissenid mussels have yet to be detected in the northwestern part of the United States and western Canada. Infestation of one of the jurisdictions within the mussel-free Pacific Northwest would likely have significant economic, soci­etal and environmental implications for the entire region. Understanding the biology and environmental tolerances of dreissenid mussels, and effectiveness of various man­agement strategies, is key to prevention.

On November 4-5, 2015, the Aquatic Bioinvasion Research and Policy Institute and the Center for Lakes and Reservoirs at Portland State University, the US Geological Survey, and the Pacific States Marine Fisheries Commission, convened a Dreissenid Mussel Research …

Galaxy And Mass Assembly (Gama) : The Bright Void Galaxy Population In The Optical And Mid-Ir., S. J. Penny, M. J. I. Brown, K. A. Pimbblet, M. E. Cluver, D. J. Croton, M. S. Owers, R. Lange, M. Alpaslan, I. K. Baldry, J. Bland-Hawthorn, S. Brough, S. P. Driver, Benne W. Holwerda, A. M. Hopkins, T. H. Jarrett, D. Heath Jones, L. S. Kelvin, M. A. Lara-Lopez, J. Liske, Angel R. Lopez-Sanchez, J. Loveday, M. Meyer, P. Norberg, A. S. G. Robotham, M. Rodrigues

Faculty and Staff Scholarship

We examine the properties of galaxies in the Galaxies and Mass Assembly (GAMA) survey located in voids with radii >10 h−1 Mpc. Utilizing the GAMA equatorial survey, 592 void galaxies are identified out to z ≈ 0.1 brighter than Mr = −18.4, our magnitude completeness limit. Using the WHα versus [N ii]/Hα (WHAN) line strength diagnostic diagram, we classify their spectra as star forming, AGN, or dominated by old stellar populations. For objects more massive than 5 × 109 M⊙, we identify a sample of 26 void galaxies with old stellar populations classed as passive and retired …

Why It Is Difficult To Apply Revenue Management Techniques To The Car Rental Business And What Can Be Done About It, Robert F. Gordon Ph.D.

Faculty Works: MCS (1984-2023)

Revenue management systems are used by airlines, hotels, and cruise lines to manipulate prices and availability of inventory in real-time, in order to increase profit. We discuss the reasons that the revenue management problem is more complex when applied to the car rental business. We then show how to simplify the model formulation and provide the human-computer interaction, organization, and procedures to make the problem tractable for the car rental business.

Data Selection Using Topic Adaptation For Statistical Machine Translation, Hitokazu Matsushita

Theses and Dissertations

Statistical machine translation (SMT) requires large quantities of bitexts (i.e., bilingual parallel corpora) as training data to yield good quality translations. While obtaining a large amount of training data is critical, the similarity between training and test data also has a significant impact on SMT performance. Many SMT studies define data similarity in terms of domain-overlap, and domains are defined to be synonymous with data sources. Consequently, the SMT community has focused on domain adaptation techniques that augment small (in-domain) datasets with large datasets from other sources (hence, out-of-domain, per the definition). However, many training datasets consist of topically diverse …

Building 3d-Printed Widgets To Incorporate Into Prototypes, David E. Brandt

Theses and Dissertations

Creating interactive prototypes can be a long and difficult process. It requires expertise in various fields. Prior work in developing interactive prototypes minimize time required to make a prototype, but generally sacrifice fidelity for fluidity. Advances in 3D printing create new opportunities to prototype with greater fidelity and fluidity. We investigate the use of several kinds of sensors, including IR photo interrupters, IR photo reflectors, push button switches, and potentiometers, to create interactive prototypes. We first design a library of 3D printable interaction components, buttons, sliders, and knobs using those sensors then we develop software to transform interaction events into …

Stafford County Shoreline Management Plan, C. Scott Hardaway Jr., Donna A. Milligan, Christine A. Wilcox, Marcia Berman, Tamia Rudnicky, Karinna Nunez, Sharon Kileen

Reports

With approximately 85 percent of the Chesapeake Bay shoreline privately owned, a critical need exists to increase awareness of erosion potential and the choices available for shore stabilization that maintains ecosystem services at the land-water interface. The National Academy of Science published a report that spotlights the need to develop a shoreline management framework (NRC, 2007). It suggests that improving awareness of the choices available for erosion control, considering cumulative consequences of erosion mitigation approaches, and improving shoreline management planning are key elements to minimizing adverse environmental impacts associated with mitigating shore erosion. Actions taken by waterfront property owners to …

Crystal Structures Of Tris­[1-Oxo­Pyridine-2-Olato(1-)]Silicon(Iv) Chloride Chloro­Form-D1 Disolvate, Tris­[1-Oxo­Pyridine-2-Olato(1-)]Silicon(Iv) Chloride Aceto­Nitrile Unqu­Anti­Fied Solvate, And Fac-Tris­[1-Oxo­Pyridine-2-Thiol­Ato(1-)]Silicon(Iv) Chloride Chloro­Form-D1 Disolvate, Bradley M. Kraft, William W. Brennessel, Amy E. Ryan, Candace K. Benjamin

Chemistry Faculty/Staff Publications

The cations in the title salts, [Si(OPO)3]Cl·2CDCl3, (I), [Si(OPO)3]Cl·xCH3CN, (II), and fac-[Si(OPTO)3]Cl·2CDCl3, (III) (OPO = 1-oxo-2-pyridin­one, C5H4NO2, and OPTO = 1-oxo-2-pyridine­thione, C5H4NOS), have distorted octa­hedral coordination spheres. The first two structures contain the same cation and anion, but different solvents of crystallization led to different solvates and packing arrangements. In structures (I) and (III), the silicon complex cations and chloride anions are well separated, while in (II), there are two C-HCl distances that fall just within the sum of the van der Waals radii of the C and Cl atoms. The pyridine portions of the OPO ligands …

Galaxy And Mass Assembly (Gama) : The Wavelength Dependence Of Galaxy Structure Versus Redshift And Luminosity., Rebecca Kennedy, Steven P. Bamford, Ivan K. Baldry, Boris Haußler, Benne W. Holwerda, Andrew M. Hopkins, Lee S. Kelvin, Rebecca Lange, Amanda J. Moffett, Cristina C. Popescu, Edward N. Taylor, Richard Tuffs, Marina Vika, Benedetta Vulcani

Faculty and Staff Scholarship

We study how the sizes and radial profiles of galaxies vary with wavelength, by fitting Sersic ´ functions simultaneously to imaging in nine optical and near-infrared bands. To quantify the wavelength dependence of effective radius we use the ratio, R, of measurements in two rest-frame bands. The dependence of Sersic index on wavelength, ´ N , is computed correspondingly. Vulcani et al. have demonstrated that different galaxy populations present sharply contrasting behaviour in terms of R and N . Here we study the luminosity dependence of this result. We find that at higher luminosities, early-type galaxies display a more substantial …

A Comparative Study Of Faecal Sludge Management In Malawi And Zambia: Status, Challenges And Opportunities In Pit Latrine Emptying, Rochelle H. Holm, James Madalitso Tembo, Bernard Thole

Faculty and Staff Scholarship

This review paper covers the issues of pit latrine emptying national policies and regulations with a focus on Malawi and Zambia. With 2.4 billion people worldwide still lacking improved sanitation facilities, developing countries need to look at policy, regulation and practice for household sanitation service provision with a new lens. What happens “next,” when improved sanitation facilities eventually become full? An emphasis on faecal sludge management has multiplied this important issue in the past few years. The authors compare the pit latrine emptying situation in Malawi and Zambia with a focus on status, challenges and opportunities. To build this comparison, …

Determination Of Nanoparticle Localisation Within Subcellular Organelles In Vitro Using Raman Spectroscopy, Esen Efeoglu, Mark Keating, Jennifer Mcintyre, Alan Casey, Hugh Byrne

Articles

Ease of sample preparation, narrow spectral bandwidth and minimal influence from water are features of Raman spectroscopy which make it a powerful, label-free way to study a wide range of biological structures and phenomena. In this context, given the concerns over their toxicology arising from their increased production and use, evaluation of nanoparticle uptake and localisation in biological systems and determination of the mechanisms of subcellular interaction and trafficking can provide long-term solutions for nanotoxicology, and potential strategies for nanomedicine. In this study, Raman spectroscopy is explored to monitor the sequential trafficking of nanoparticles through subcellular organelles in-vitro and to …

Investigating The Role Of Shape On The Biological Impact Of Gold Nanoparticles In Vitro, Furong Tian, Hugh Byrne, Joao Conde, Tobias Stoeger, Martin Clift,, Alan Casey, Pablo Del Pino, Beatriz Pelaz, Barbara Rothen-Rutishauser,, Giovani Estrada, Jesús De La Fuente

Articles

Aim: To investigate the influence of gold nanoparticle (GNP) geometry on the biochemical response of Calu-3 epithelial cells.

Materials and Methods: Spherical, triangular and hexagonal GNPs were used. The GNP-cell interaction was assessed via atomic absorption spectroscopy (AAS) and transmission electron microscopy (TEM). The biochemical impact of GNPs was determined over 72hrs at [0.0001-1mg/mL].

Results: At 1mg/mL, hexagonal GNPs reduced Calu-3 viability below 60%, showed increased reactive oxygen species production and higher expression of pro-apoptotic markers. A cell mass burden of 1:2:12 as well as number of GNPs per cell (2:1:3) was observed for spherical:triangular:hexagonal GNPs.

Conclusion:

These findings do …

Raman Spectroscopy For Screening And Diagnosis Of Cervical Cancer, Fiona Lyng, Damien Traynor, Ines Rm Ramos, Franck Bonnier, Hugh Byrne

Articles

Cervical cancer is the fourth most common cancer in women worldwide and mainly affects younger women. The mortality associated with cervical cancer can be reduced if this disease is detected at the pre-cancer stage. Current gold standard methods include cytopathology, HPV testing and histopathology but these methods are limited in terms of subjectivity, cost and time. There is an unmet clinical need for new methods to aid clinicians in the early detection of cervical pre-cancer. These methods should be objective, rapid and require minimal sample preparation. Raman spectroscopy is a vibrational spectroscopic technique by which incident radiation is used to …

Audiovisual Processing Is Abnormal In Parkinson's Disease And Correlates With Freezing Of Gait And Disease Duration, Conor Fearon, John Butler, Louise Newman, Timothy Lynch, Richard B. Reilly

Articles

Background: Sensory and perceptual disturbances progress with disease duration in Parkinson’s disease (PD) and probably contribute to motor deficits such as bradykinesia and gait disturbances, including freezing of gait (FOG). Simple reaction time tests are ideal to explore sensory processing, as they require little cognitive processing. Multisensory integration is the ability of the brain to integrate sensory information from multiple modalities into a single coherent percept, which is crucial for complex motor tasks such as gait. 9 10 11 12 13 Objectives: The aims of this study were to: 1. Assess differences in unisensory (auditory and visual) and multisensory processing …

The Nanograv Nine-Year Data Set: Observations Arrival Time Measurements And Analysis Of 37 Millisecond Pulsars, Z. Arzoumanian, Zaven Arzoumanian, Adam Brazier, Sarah Burke-Spolaor, Sydney Chamberlin, Shami Chatterjee, Brian Christy, James M. Cordes, Neil Cornish, Fredrick A. Jenet, Jing Luo

Physics and Astronomy Faculty Publications and Presentations

We present high-precision timing observations spanning up to nine years for 37 millisecond pulsars monitored with the Green Bank and Arecibo radio telescopes as part of the North American Nanohertz Observatory for Gravitational Waves (NANOGrav) project. We describe the observational and instrumental setups used to collect the data, and methodology applied for calculating pulse times of arrival; these include novel methods for measuring instrumental offsets and characterizing low signal-to-noise ratio timing results. The time of arrival data are fit to a physical timing model for each source, including terms that characterize time-variable dispersion measure and frequency-dependent pulse shape evolution. In …

New Transitions And Feeding Of The JΠ=(8+) Isomer In 186Re, David A. Matters [*], Nikolaos Fotiades, James J. Carroll, Christopher J. Chiara, John W. Mcclory, Toshihiko Kawano, Ronald O. Nelson, Matthew Devlin

Faculty Publications

The spallation neutron source at the Los Alamos Neutron Science Center Weapons Neutron Research facility was used to populate excited states in ¹⁸⁶Re via (n,2nγ) reactions on an enriched ¹⁸⁷Re target. Gamma rays were detected with the GErmanium Array for Neutron Induced Excitations spectrometer, a Compton-suppressed array of 18 HPGe detectors. Incident neutron energies were determined by the time-of-flight technique and used to obtain γ-ray excitation functions for the purpose of identifying γ rays by reaction channel. Analysis of the singles γ-ray spectrum gated on the neutron energy range 10≤E_n≤25MeV resulted in five transitions and one …

Reversible Peg Solitaire On Graphs, John Engbers, Christopher Stocker

Mathematics, Statistics and Computer Science Faculty Research and Publications

The game of peg solitaire on graphs was introduced by Beeler and Hoilman in 2011. In this game, pegs are initially placed on all but one vertex of a graph G. If xyz forms a path in G and there are pegs on vertices x and y but not z, then a jump places a peg on z and removes the pegs from x and y. A graph is called solvable if, for some configuration of pegs occupying all but one vertex, some sequence of jumps leaves a single peg. We study the game of reversible peg …

On The Importance Of Duality And Multi-Ality In Mathematics Education, Mourat Tchoshanov, Olga Kosheleva, Vladik Kreinovich

Departmental Technical Reports (CS)

For each mathematical object, there are usually several different equivalent representations: for example, a spatial object can be represented either in geometric terms, or by a function that describes its shape. The need for several representations comes from the fact that each of these representations is useful in solving some problems for which the use of other representations is less helpful. Thus, the more representations a student knows, the more capable this student is of solving mathematical problems. In this paper, we propose a general formal description of the corresponding notion of duality (and, more generally, "multi-ality"), and we explain …

Modelling Cascades Over Time In Microblogs, Xie Wei, Feida Zhu, Siyuan Liu, Ke Wang

Research Collection School Of Computing and Information Systems

One of the most important features of microblogging services such as Twitter is how easy it is to re-share a piece of information across the network through various user connections, forming what we call a "cascade". Business applications such as viral marketing have driven a tremendous amount of research effort predicting whether a certain cascade will go viral. Yet the rarity of viral cascades in real data poses a challenge to all existing prediction methods. One solution is to simulate cascades that well fit the real viral ones, which requires our ability to tell how a certain cascade grows over …

Genomic And Transcriptomic Evidence For Scavenging Of Diverse Organic Compounds By Widespread Deep-Sea Archaea, Meng Li, Brett J. Baker, Karthik Anantharaman, Sunit Jain, John A. Breier, Gregory J. Dick

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that …

Direct Or Indirect Match? Selecting Right Concepts For Zero-Example Case, Yi-Jie Lu, Maaike De Boer, Hao Zhang, Klamer Schutte, Wessel Kraaij, Chong-Wah Ngo

Research Collection School Of Computing and Information Systems

No abstract provided.

Challenges In Analyzing Software Documentation In Portuguese, Christoph Treude, Carlos A. Prolo, Fernando Figueira Filho

Research Collection School Of Computing and Information Systems

Many tools that automatically analyze, summarize, or transform software artifacts rely on natural language processing tooling for the interpretation of natural language text produced by software developers, such as documentation, code comments, commit messages, or bug reports. Processing natural language text produced by software developers is challenging because of unique characteristics not found in other texts, such as the presence of code terms and the systematic use of incomplete sentences. In addition, texts produced by Portuguese-speaking developers mix languages since many keywords and programming concepts are referred to by their English name. In this paper, we provide empirical insights into …

Event Detection In Wireless Sensor Networks In Random Spatial Sensors Deployments, Pengfei Zhang, Ido Nevat, Gareth W. Peters, Gaoxi Xiao, Hwee-Pink Tan

Research Collection School Of Computing and Information Systems

We develop a new class of event detection algorithms in Wireless Sensor Networks where the sensors are randomly deployed spatially. We formulate the detection problem as a binary hypothesis testing problem and design the optimal decision rules for two scenarios, namely the Poisson Point Process and Binomial Point Process random deployments. To calculate the intractable marginal likelihood density, we develop three types of series expansion methods which are based on an Askey-orthogonal polynomials. In addition, we develop a novel framework to provide guidance on which series expansion is most suitable (i.e., most accurate) to use for different system parameters. Extensive …

A Passive Testing Approach For Protocols In Wireless Sensor Networks, Xiaoping Che, Stephane Maag, Hwee Xian Tan, Hwee-Pink Tan, Zhangbing Zhou

Research Collection School Of Computing and Information Systems

Smart systems are today increasingly developed with the number of wireless sensor devices drastically increasing. They are implemented within several contexts throughout our environment. Thus, sensed data transported in ubiquitous systems are important, and the way to carry them must be efficient and reliable. For that purpose, several routing protocols have been proposed for wireless sensor networks (WSN). However, one stage that is often neglected before their deployment is the conformance testing process, a cruicial and challenging step. Compared to active testing techniques commonly used in wired networks, passive approaches are more suitable to the WSN environment. While some works …

Stack Layout Randomization With Minimal Rewriting Of Android Binaries, Yu Liang, Xinjie Ma, Daoyuan Wu, Xiaoxiao Tang, Debin Gao, Guojun Peng, Chunfu Jia, Huanguo Zhang

Research Collection School Of Computing and Information Systems

Stack-based attacks typically require that attackers have a good understanding of the stack layout of the victim program. In this paper, we leverage specific features on ARM architecture and propose a practical technique that introduces randomness to the stack layout when an Android application executes. We employ minimal binary rewriting on the Android app that produces randomized executable of the same size which can be executed on an unmodified Android operating system. Our experiments on applying this randomization on the most popular 20 free Android apps on Google Play show that the randomization coverage of functions increases from 65% (by …