Physical Sciences and Mathematics Commons^™

Atomistic Simulations And Network-Based Modeling Of The Hsp90-Cdc37 Chaperone Binding With Cdk4 Client Protein: A Mechanism Of Chaperoning Kinase Clients By Exploiting Weak Spots Of Intrinsically Dynamic Kinase Domains, John Czemeres, Kurt Buse, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37- Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic …

Virtual Reality As A Training Tool To Treat Physical Inactivity In Children, Adam W. Kiefer, David Pincus, Michael J. Richardson, Gregory D. Myer

Psychology Faculty Articles and Research

Lack of adequate physical activity in children is an epidemic that can result in obesity and other poor health outcomes across the lifespan. Physical activity interventions focused on motor skill competence continue to be developed, but some interventions, such as neuromuscular training (NMT), may be limited in how early they can be implemented due to dependence on the child’s level of cognitive and perceptual-motor development. Early implementation of motor-rich activities that support motor skill development in children is critical for the development of healthy levels of physical activity that carry through into adulthood. Virtual reality (VR) training may be beneficial …

A Restful Framework For Writing, Running, And Evaluating Code In Multiple Academic Settings, Christopher Ban

MS in Computer Science Project Reports

In academia, students and professors want a well-structured and implemented framework for writing and running code in both testing and learning environments. The current limitations of the paper and pencil medium have led to the creation of many different online grading systems. However, no known system provides all of the essential features our client is interested in. Our system, developed in conjunction with Doctor Halterman, offers the ability to build modules from flat files, allow code to be compiled and run in the browser, provide users with immediate feedback, support multiple languages, and offer a module designed specifically for an …

A Cluster Analysis Of Challenging Behaviors In Autism Spectrum Disorder, Elizabeth Stevens, Abigail Atchison, Laura Stevens, Esther Hong, Doreen Granpeesheh, Dennis Dixon, Erik J. Linstead

Mathematics, Physics, and Computer Science Faculty Articles and Research

We apply cluster analysis to a sample of 2,116 children with Autism Spectrum Disorder in order to identify patterns of challenging behaviors observed in home and centerbased clinical settings. The largest study of this type to date, and the first to employ machine learning, our results indicate that while the presence of multiple challenging behaviors is common, in most cases a dominant behavior emerges. Furthermore, the trend is also observed when we train our cluster models on the male and female samples separately. This work provides a basis for future studies to understand the relationship of challenging behavior profiles to …

Design And Implementation Of A Stand-Alone Tool For Metabolic Simulations, Milad Ghiasi Rad

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

In this thesis, we present the design and implementation of a stand-alone tool for metabolic simulations. This system is able to integrate custom-built SBML models along with external user’s input information and produces the estimation of any reactants participating in the chain of the reactions in the provided model, e.g., ATP, Glucose, Insulin, for the given duration using numerical analysis and simulations. This tool offers the food intake arguments in the calculations to consider the personalized metabolic characteristics in the simulations. The tool has also been generalized to take into consideration of temporal genomic information and be flexible for simulation …

Separating Markup From Text, Ronald I. Greenberg, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

As more and more online versions of Humanities texts are created, it is becoming commonplace to embed elaborate formatting, for example, through the use of HTML. But this can interfere with computerized analyses of the original text. While it may seem, at first, straightforward to simply strip markup from text, this is not the reality. Many digital texts add things that appear to be legitimate content according to the markup syntax, for example, line numbers, and even apart from this issue, existing tools for stripping markup produce inconsistent results. Apart from adopting and enforcing strict conventions for adding markup to …

Critical Digital Literacies Across Scales And Beneath The Screen, Noah Asher Golden

Education Faculty Articles and Research

Digital technologies and education scholarship tend to focus on either individual creative design or analysis of the political economy. To better understand how ideologies travel across networks, critical digital literacies must focus on enactments beneath the screen, as the linguistic constructs known as software can enact interests across scales of activity to “disembed” local actions and meaning. Investigations of these mobilities and disembedding effects challenge popular notions of digital technologies as neutral, rendering overt the ways that algorithms can naturalize manifestations of power and social arrangements. Such a framework allows for descriptive analyses of the ways hegemonic discourses are enacted …

Using Tablet Technologies To Engage And Motivate Urban High School Students, Nicol R. Howard, Keith Howard

Education Faculty Articles and Research

In this two-year study, researchers examined the impact of using tablet technologies across content areas in an urban high school setting. Class observations provided notable examples of how student motivation and learning appeared to be enhanced by use of the iPads in conjunction with opportunities to collaborate and be creative in the context of their learning. Interviews from a set of teachers with a range of classroom teaching experience provided multiple perspectives of the program’s impact. The opportunity for teachers and students to have the flexibility to select the apps they believe achieve curricular and/or learning goals supports the shift …

An Evaluation Of The Effects Of Intensity And Duration On Outcomes Across Treatment Domains For Children With Autism Spectrum Disorder, Erik J. Linstead, D. R. Dixon, E. Hong, C. O. Burns, Ryan French, M. N. Novack, D. Granpeesheh

Mathematics, Physics, and Computer Science Faculty Articles and Research

Applied behavior analysis (ABA) is considered an effective treatment for individuals with autism spectrum disorder (ASD), and many researchers have further investigated factors associated with treatment outcomes. However, few studies have focused on whether treatment intensity and duration have differential influences on separate skills. The aim of the current study was to investigate how treatment intensity and duration impact learning across different treatment domains, including academic, adaptive, cognitive, executive function, language, motor, play, and social. Separate multiple linear regression analyses were used to evaluate these relationships. Participants included 1468 children with ASD, ages 18 months to 12 years old, M= …

An Efficient Image Segmentation Algorithm Using Neutrosophic Graph Cut, Florentin Smarandache, Yanhui Guo, Yaman Akbulut, Abdulkadir Sengur, Rong Xia

Branch Mathematics and Statistics Faculty and Staff Publications

Segmentation is considered as an important step in image processing and computer vision applications, which divides an input image into various non-overlapping homogenous regions and helps to interpret the image more conveniently. This paper presents an efficient image segmentation algorithm using neutrosophic graph cut (NGC). An image is presented in neutrosophic set, and an indeterminacy filter is constructed using the indeterminacy value of the input image, which is defined by combining the spatial information and intensity information. The indeterminacy filter reduces the indeterminacy of the spatial and intensity information. A graph is defined on the image and the weight for …

Rating By Ranking: An Improved Scale For Judgement-Based Labels, Jack O'Neill, Sarah Jane Delany, Brian Mac Namee

Conference papers

Labels representing value judgements are commonly elicited using an interval scale of absolute values. Data collected in such a manner is not always reliable. Psychologists have long recognized a number of biases to which many human raters are prone, and which result in disagreement among raters as to the true gold standard rating of any particular object. We hypothesize that the issues arising from rater bias may be mitigated by treating the data received as an ordered set of preferences rather than a collection of absolute values. We experiment on real-world and artificially generated data, finding that treating label ratings …

Game Design & Development Curriculum: History & Future Directions, Elizabeth L. Lawley, Roger Altizer, Tracy Fullerton, Andrew Phelps, Constance Steinkuehler

Presentations and other scholarship

It has been nearly twenty years since the first undergraduate degree program in computer game development was established in 1998. Since that time, the number and size of programs in game design and development have grown at a rapid pace. While there were early efforts to establish curricular guidelines for the field, these face a number of challenges given the diverse range of academic homes for game-related programs. This panel will address the history of curricular development in the field, both in individual programs and across institutions. It will also explore the potential risks and rewards of developing curricular and/or …

Card Tricks: A Workflow For Scalability And Dynamic Content Creation Using Paper2d And Unreal Engine 4, Owen Gottlieb, Dakota Herold, Edward Amidon

Presentations and other scholarship

In this paper, we describe the design and technological methods of

our dynamic sprite system in Lost & Found, a table-top-to-mobile

card game designed to improve literacy regarding prosocial

aspects of religious legal systems, specifically, collaboration and

cooperation. Harnessing the capabilities of Unreal Engine’s

Paper2D system, we created a dynamic content creation pipeline

that empowered our game designers so that they could rapidly

iterate on the game’s systems and balance externally from the

engine. Utilizing the Unreal Blueprint component system we were

also able to modularize each actor during runtime as data may be

changed. The technological approach behind Lost …

Ancr—An Adaptive Network Coding Routing Scheme For Wsns With Different-Success-Rate Links †, Xiang Ji, Anwen Wang, Chunyu Li, Chun Ma, Yao Peng, Dajin Wang, Qingyi Hua, Feng Chen, Dingyi Fang

Department of Computer Science Faculty Scholarship and Creative Works

As the underlying infrastructure of the Internet of Things (IoT), wireless sensor networks (WSNs) have been widely used in many applications. Network coding is a technique in WSNs to combine multiple channels of data in one transmission, wherever possible, to save node’s energy as well as increase the network throughput. So far most works on network coding are based on two assumptions to determine coding opportunities: (1) All the links in the network have the same transmission success rate; (2) Each link is bidirectional, and has the same transmission success rate on both ways. However, these assumptions may not be …

A Reliable And Efficient Wireless Sensor Network System For Water Quality Monitoring, Dung Nguyen, Phu Huu Phung

Computer Science Faculty Publications

Wireless sensor networks (WSNs) are strongly useful to monitor physical and environmental conditions to provide realtime information for improving environment quality. However, deploying a WSN in a physical environment faces several critical challenges such as high energy consumption, and data loss.In this work, we have proposed a reliable and efficient environmental monitoring system in ponds using wireless sensor network and cellular communication technologies. We have designed a hardware and software ecosystem that can limit the data loss yet save the energy consumption of nodes. A lightweight protocol acknowledges data transmission among the nodes. Data are transmitted to the cloud using …

Data Extraction From Web Tables: The Devil Is In The Details, George Nagy, Sharad C. Seth, Dongpu Jin, David W. Embley, Spencer Machado, Mukkai Krishnamoorthy

CSE Conference and Workshop Papers

We present a method based on header paths for efficient and complete extraction of labeled data from tables meant for humans. Although many table configurations yield to the proposed syntactic analysis, some require access to semantic knowledge. Clicking on one or two critical cells per table, through a simple interface, is sufficient to resolve most of these problem tables. Header paths, a purely syntactic representation of visual tables, can be transformed (“factored”) into existing representations of structured data such as category trees, relational tables, and RDF triples. From a random sample of 200 web tables from ten large statistical web …

End-To-End Conversion Of Html Tables For Populating A Relational Database, George Nagy, David W. Embley, Sharad C. Seth

CSE Conference and Workshop Papers

Automating the conversion of human-readable HTML tables into machine-readable relational tables will enable end-user query processing of the millions of data tables found on the web. Theoretically sound and experimentally successful methods for index-based segmentation, extraction of category hierarchies, and construction of a canonical table suitable for direct input to a relational database are demonstrated on 200 heterogeneous web tables. The methods are scalable: the program generates the 198 Access compatible CSV files in ~0.1s per table (two tables could not be indexed).

An Analysis Of The Application Of Simplified Silhouette To The Evaluation Of K-Means Clustering Validity, Fei Wang, Hector-Hugo Franco-Penya, John D. Kelleher, John Pugh, Robert J. Ross

Conference papers

Silhouette is one of the most popular and effective internal measures for the evaluation of clustering validity. Simplified Silhouette is a computationally simplified version of Silhouette. However, to date Simplified Silhouette has not been systematically analysed in a specific clustering algorithm. This paper analyses the application of Simplified Silhouette to the evaluation of k-means clustering validity and compares it with the k-means Cost Function and the original Silhouette from both theoretical and empirical perspectives. The theoretical analysis shows that Simplified Silhouette has a mathematical relationship with both the k-means Cost Function and the original Silhouette, while empirically, we show that …

Shortest Path Problem Under Triangular Fuzzy Neutrosophic Information, Florentin Smarandache, Said Broumi, Assia Bakali, Mohamed Talea, Luige Vladareanu

Branch Mathematics and Statistics Faculty and Staff Publications

In this paper, we develop a new approach to deal with neutrosphic shortest path problem in a network in which each edge weight (or length) is represented as triangular fuzzy neutrosophic number. The proposed algorithm also gives the shortest path length from source node to destination node using ranking function. Finally, an illustrative example is also included to demonstrate our proposed approach.

Educational Magic Tricks Based On Error-Detection Schemes, Ronald I. Greenberg

Computer Science: Faculty Publications and Other Works

Magic tricks based on computer science concepts help grab student attention and can motivate them to delve more deeply. Error detection ideas long used by computer scientists provide a rich basis for working magic; probably the most well known trick of this type is one included in the CS Unplugged activities. This paper shows that much more powerful variations of the trick can be performed, some in an unplugged environment and some with computer assistance. Some of the tricks also show off additional concepts in computer science and discrete mathematics.

P4sinc – An Execution Policy Framework For Iot Services In The Edge, Phu Huu Phung, Hong-Linh Truong, Divya Teja Yasoju

Computer Science Faculty Publications

Internet of Things (IoT) services are increasingly deployed at the edge to access and control Things. The execution of such services needs to be monitored to provide information for security, service contract, and system operation management. Although different techniques have been proposed for deploying and executing IoT services in IoT gateways and edge servers, there is a lack of generic policy frameworks for instrumentation and assurance of various types of execution policies for IoT services. In this paper, we present P4SINC as an execution policy framework that covers various functionalities for IoT services deployed in software-defined machines in IoT infrastructures. …

Hybridguard: A Principal-Based Permission And Fine-Grained Policy Enforcement Framework For Web-Based Mobile Applications, Phu Huu Phung, Abhinav Mohanty, Rahul Rachapalli, Meera Sridhar

Computer Science Faculty Publications

Web-based or hybrid mobile applications (apps) are widely used and supported by various modern hybrid app development frameworks. In this architecture, any JavaScript code, local or remote, can access available APIs, including JavaScript bridges provided by the hybrid framework, to access device resources. This JavaScript inclusion capability is dangerous, since there is no mechanism to determine the origin of the code to control access, and any JavaScript code running in the mobile app can access the device resources through the exposed APIs. Previous solutions are either limited to a particular platform (e.g., Android) or a specific hybrid framework (e.g., Cordova) …

Relation Algebras, Idempotent Semirings And Generalized Bunched Implication Algebras, Peter Jipsen

Mathematics, Physics, and Computer Science Faculty Articles and Research

This paper investigates connections between algebraic structures that are common in theoretical computer science and algebraic logic. Idempotent semirings are the basis of Kleene algebras, relation algebras, residuated lattices and bunched implication algebras. Extending a result of Chajda and Länger, we show that involutive residuated lattices are determined by a pair of dually isomorphic idempotent semirings on the same set, and this result also applies to relation algebras. Generalized bunched implication algebras (GBI-algebras for short) are residuated lattices expanded with a Heyting implication. We construct bounded cyclic involutive GBI-algebras from so-called weakening relations, and prove that the class of weakening …

Toward An Iot-Based Expert System For Heart Disease Diagnosis, Do Thanh Thai, Quang Tran Minh, Phu Huu Phung

Computer Science Faculty Publications

IoT technology has been recently adopted in the healthcare system to collect Electrocardiogram (ECG) signals for heart disease diagnosis and prediction. However, noises in collected ECG signals make the diagnosis and prediction system unreliable and imprecise. In this work, we have proposed a new lightweight approach to removing noises in collected ECG signals to perform precise diagnosis and prediction. First, we have used a revised Sequential Recursive (SR) algorithm to transform the signals into digital format. Then, the digital data is proceeded using a revised Discrete Wavelet Transform (DWT) algorithm to detect peaks in the data to remove noises. Finally, …

Mixed-Initiative Personal Assistants, Joshua W. Buck, Saverio Perugini

Computer Science Faculty Publications

Specification and implementation of flexible human-computer dialogs is challenging because of the complexity involved in rendering the dialog responsive to a vast number of varied paths through which users might desire to complete the dialog. To address this problem, we developed a toolkit for modeling and implementing task-based, mixed-initiative dialogs based on metaphors from lambda calculus. Our toolkit can automatically operationalize a dialog that involves multiple prompts and/or sub-dialogs, given a high-level dialog specification of it. Our current research entails incorporating the use of natural language to make the flexibility in communicating user utterances commensurate with that in dialog completion …

Infographics: A Practical Guide For Librarians, Darren Sweeper

Sprague Library Scholarship and Creative Works

No abstract provided.

Static Human Detection And Scenario Recognition Via Wearable Thermal Sensing System, Qingquan Sun, Ju Shen, Haiyan Qiao, Xinlin Huang, Chen Chen, Fei Hu

Computer Science Faculty Publications

Conventional wearable sensors are mainly used to detect the physiological and activity information of individuals who wear them, but fail to perceive the information of the surrounding environment. This paper presents a wearable thermal sensing system to detect and perceive the information of surrounding human subjects. The proposed system is developed based on a pyroelectric infrared sensor. Such a sensor system aims to provide surrounding information to blind people and people with weak visual capability to help them adapt to the environment and avoid collision. In order to achieve this goal, a low-cost, low-data-throughput binary sampling and analyzing scheme is …

Computational Analysis Of Residue Interaction Networks And Coevolutionary Relationships In The Hsp70 Chaperones: A Community- Hopping Model Of Allosteric Regulation And Communication, Gabrielle Stetz, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks …

Wireless Underground Channel Diversity Reception With Multiple Antennas For Internet Of Underground Things, Abdul Salam, Mehmet C. Vuran

CSE Conference and Workshop Papers

Internet of underground things (IOUT) is an emerging paradigm which consists of sensors and communication devices, partly or completely buried underground for real-time soil sensing and monitoring. In this paper, the performance of different modulation schemes in IOUT communications is studied through simulations and experiments. The spatial modularity of direct, lateral, and reflected components of the UG channel is exploited by using multiple antennas. First, it has been shown that bit error rates of $10^{-3}$ can be achieved with normalized delay spreads ($\tau_d$) lower than $0.05$. Evaluations are conducted through the first software-defined radio-based field experiments for UG channel. Moreover, …

Towards Internet Of Underground Things In Smart Lighting: A Statistical Model Of Wireless Underground Channel, Abdul Salam, Mehmet C. Vuran, Suat Irmak

CSE Conference and Workshop Papers

The Internet of Underground Things (IOUT) has many applications in the area of smart lighting. IOUT enables communications in smart lighting through underground (UG) and aboveground (AG) communication channels. In IOUT communications, an in-depth analysis of the wireless underground channel is important to design smart lighting solutions. In this paper, based on the empirical and the statistical analysis, a statistical channel model for the UG channel has been developed. The parameters for the statistical tapped-delay-line model are extracted from the measured power delay profiles (PDP). The PDP of the UG channel is represented by the exponential decay of the lateral, …