Engineering Commons^™

Methods To Study Activity Dependent Protein Synthesis In Autism Spectrum Disorder, Megan Webb, Karin F K Ejendal, Tamara L. Kinzer-Ursem

Discovery Undergraduate Interdisciplinary Research Internship

It is estimated by the World Health Organization that 1 in 100 children have autism spectrum disorder (ASD), a condition characterized by neurological differences that may impact a person’s learning or behavior. Clinically, ASD symptoms are alleviated with behavioral or pharmacological therapies, however, not all patients respond to these interventions. Deep brain stimulation (DBS) is a promising treatment of Parkinson’s disease that could also be effective in treating ASD. SynGAP1 is a protein involved in neuronal action that is crucial for regulating synaptic plasticity. Mutations in the SYNGAP1 gene causing haploinsufficiency can result in the manifestation of ASD symptoms. This …

Designing A Computer-Vision Application: A Case Study For Hand-Hygiene Assessment In An Open-Room Environment, Chengzang Zhong, Amy R. Reibman, Hansel A. Mina, Amanda J. Deering

Department of Food Science Faculty Publications

Hand-hygiene is a critical component for safe food handling. In this paper, we apply an iterative engineering process to design a hand-hygiene action detection system to improve food- handling safety. We demonstrate the feasibility of a baseline RGB-only convolutional neural network (CNN) in the restricted case of a single scenario; however, since this baseline system performs poorly across scenarios, we also demonstrate the application of two methods to explore potential reasons for its poor performance. This leads to the development of our hierarchical system that incorporates a variety of modalities (RGB, optical flow, hand masks, and human skeleton joints) for …

On-Site And External Energy Harvesting In Underground Wireless, Usman Raza, Abdul Salam

Faculty Publications

Energy efficiency is vital for uninterrupted long-term operation of wireless underground communication nodes in the field of decision agriculture. In this paper, energy harvesting and wireless power transfer techniques are discussed with applications in underground wireless communications (UWC). Various external wireless power transfer techniques are explored. Moreover, key energy harvesting technologies are presented that utilize available energy sources in the field such as vibration, solar, and wind. In this regard, the Electromagnetic(EM)- and Magnetic Induction(MI)-based approaches are explained. Furthermore, the vibration-based energy harvesting models are reviewed as well. These energy harvesting approaches lead to design of an efficient wireless underground …

Internet Of Things In Agricultural Innovation And Security, Abdul Salam

Faculty Publications

The agricultural Internet of Things (Ag-IoT) paradigm has tremendous potential in transparent integration of underground soil sensing, farm machinery, and sensor-guided irrigation systems with the complex social network of growers, agronomists, crop consultants, and advisors. The aim of the IoT in agricultural innovation and security chapter is to present agricultural IoT research and paradigm to promote sustainable production of safe, healthy, and profitable crop and animal agricultural products. This chapter covers the IoT platform to test optimized management strategies, engage farmer and industry groups, and investigate new and traditional technology drivers that will enhance resilience of the farmers to the …

Internet Of Things In Water Management And Treatment, Abdul Salam

Faculty Publications

The goal of the water security IoT chapter is to present a comprehensive and integrated IoT based approach to environmental quality and monitoring by generating new knowledge and innovative approaches that focus on sustainable resource management. Mainly, this chapter focuses on IoT applications in wastewater and stormwater, and the human and environmental consequences of water contaminants and their treatment. The IoT applications using sensors for sewer and stormwater monitoring across networked landscapes, water quality assessment, treatment, and sustainable management are introduced. The studies of rate limitations in biophysical and geochemical processes that support the ecosystem services related to water quality …

Subsurface Mimo: A Beamforming Design In Internet Of Underground Things For Digital Agriculture Applications, Abdul Salam

Faculty Publications

In underground (UG) multiple-input and multiple-output (MIMO), the transmit beamforming is used to focus energy in the desired direction. There are three different paths in the underground soil medium through which the waves propagates to reach at the receiver. When the UG receiver receives a desired data stream only from the desired path, then the UG MIMO channel becomes three path (lateral, direct, and reflected) interference channel. Accordingly, the capacity region of the UG MIMO three path interference channel and degrees of freedom (multiplexing gain of this MIMO channel requires careful modeling). Therefore, expressions are required for the degree of …

A Theoretical Model Of Underground Dipole Antennas For Communications In Internet Of Underground Things, Abdul Salam, Mehmet C. Vuran, Xin Dong, Christos Argyropoulos, Suat Irmak

Faculty Publications

The realization of Internet of Underground Things (IOUT) relies on the establishment of reliable communication links, where the antenna becomes a major design component due to the significant impacts of soil. In this paper, a theoretical model is developed to capture the impacts of change of soil moisture on the return loss, resonant frequency, and bandwidth of a buried dipole antenna. Experiments are conducted in silty clay loam, sandy, and silt loam soil, to characterize the effects of soil, in an indoor testbed and field testbeds. It is shown that at subsurface burial depths (0.1-0.4m), change in soil moisture impacts …

Managing Your Professional Identity: Leveraging Social Media And Emerging Metrics To Demonstrate Professional Impact, Megan R. Sapp Nelson

Libraries Faculty and Staff Presentations

This session will assist graduate students to deliberately develop an online professional identity that will uniquely identify them as an academic as well as positively highlight their personal strengths.

Students will walk away with a plan to create a unique professional identifier and an understanding of how to measure the impact of online scholarly communication.

Topics included are:

ORCID ID

social media, such as LinkedIn & ResearchGate

Alternative Metrics (Altmetrics), such has Kudos, ImpactStory, & AltMetric

Data repositories, such as GitHub & FigShare

The Relationship Between Intermittent Limit Cycles And Postural Instability Associated With Parkinson’S Disease, James R. Chagdes, Jessica E. Huber, Meredith Saletta, Meghan Darling-White, Arvind Raman, Shirley Rietdyk, Howard N. Zelaznik, Jeffrey M. Haddad

School of Mechanical Engineering Faculty Publications

Background: Many disease-specifc factors such as muscular weakness, increased muscle stiffness, varying postural strategies, and changes in postural refexes have been shown to lead to postural instability and fall risk in people with Parkinson’s disease (PD). Recently, analytical techniques, inspired by the dynamical systems perspective on movement control and coordination, have been used to examine the mechanisms underlying the dynamics of postural declines and the emergence of postural instabilities in people with PD. Methods: A wavelet-based technique was used to identify limit cycle oscillations (LCOs) in the anterior–posterior (AP) postural sway of people with mild PD (n = 10) compared …

A Study Of Alterations In Dna Epigenetic Modifications (5mc And 5hmc) And Gene Expression Influenced By Simulated Microgravity In Human Lymphoblastoid Cells, Basudev Chowdhury, Arun Seetharam, Zhiping Wang, Yunlong Liu, Amy C. Lossie, Jyothi Thimmapuram

Cyber Center Publications

Cells alter their gene expression in response to exposure to various environmental changes. Epigenetic mechanisms such as DNA methylation are believed to regulate the alterations in gene expression patterns. In vitro and in vivo studies have documented changes in cellular proliferation, cytoskeletal remodeling, signal transduction, bone mineralization and immune deficiency under the influence of microgravity conditions experienced in space. However microgravity induced changes in the epigenome have not been well characterized. In this study we have used Next-generation Sequencing (NGS) to profile ground-based “simulated” microgravity induced changes on DNA methylation (5-methylcytosine or 5mC), hydroxymethylation (5-hydroxymethylcytosine or 5hmC), and simultaneous gene …

Genome-Wide Profiling Of Histone Modifications (H3k9me2 And H4k12ac) And Gene Expression In Rust (Uromyces Appendiculatus) Inoculated Common Bean (Phaseolus Vulgaris L), Vasudevan Ayyappan, Venu Kalavacharla, Jyothi Thimmapuram, Ketaki P. Bhide, Venkateswara R. Sripathi

Cyber Center Publications

Histone modifications such as methylation and acetylation play a significant role in controlling gene expression in unstressed and stressed plants. Genome-wide analysis of such stress-responsive modifications and genes in non-model crops is limited. We report the genome-wide profiling of histone methylation (H3K9me2) and acetylation (H4K12ac) in common bean (Phaseolus vulgaris L.) under rust (Uromyces appendiculatus) stress using two high-throughput approaches, chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq). ChIP-Seq analysis revealed 1,235 and 556 histone methylation and acetylation responsive genes from common bean leaves treated with the rust pathogen at 0, 12 and 84 hour-after-inoculation (hai), while …

Ontogenetic Scaling Patterns And Functional Anatomy Of The Pelvic Limb Musculature In Emus (Dromaius Novaehollandiae), Luis P. Lamas, Russell P. Main, John R. Hutchinson

Department of Basic Medical Sciences Faculty Publications

Emus (Dromaius novaehollandiae) are exclusively terrestrial, bipedal and cursorial ratites with some similar biomechanical characteristics to humans. Their growth rates are impressive, as their body mass increases eighty-fold from hatching to adulthood whilst maintaining the same mode of locomotion throughout life. These ontogenetic characteristics stimulate biomechanical questions about the strategies that allow emus to cope with their rapid growth and locomotion, which can be partly addressed via scaling (allometric) analysis of morphology. In this study we have collected pelvic limb anatomical data (muscle architecture, tendon length, tendon mass and bone lengths) and calculated muscle physiological cross sectional area …

Privacy-Preserving And Outsourced Multi-User K-Means Clustering, Bharath Samanthula, Fang-Yu Rao, Elisa Bertino, Xun Yi, Dangxi Liu

Cyber Center Publications

Many techniques for privacy-preserving data mining (PPDM) have been investigated over the past decade. Often, the entities involved in the data mining process are end-users or organizations with limited computing and storage resources. As a result, such entities may want to refrain from participating in the PPDM process. To overcome this issue and to take many other benefits of cloud computing, outsourcing PPDM tasks to the cloud environment has recently gained special attention. We consider the scenario where n entities outsource their databases (in encrypted format) to the cloud and ask the cloud to perform the clustering task on their …

Poster: Protecting Against Data Exfiltration Insider Attacks Through Application Programs, Asmaa Mohamed Sallama, Elisa Bertino

Cyber Center Publications

In this paper, we describe a system that distinguishes be- tween legitimate and malicious database transactions per- formed by application programs. Our system is particularly useful for protecting against code-modification attacks performed by insiders who have access to and can change the programs' source code to make them execute different queries than those they are expected to execute. Our system works with any type of DBMS and requires minimum modification to application programs.

An Efficient Certificateless Encryption For Secure Data Sharing In Public Clouds, Seung-Hyun Seo, Mohamed Yoosuf Mohamed Nabeel, Xiaoyu Ding, Elisa Bertino

Cyber Center Publications

We propose a mediated certificateless encryption scheme without pairing operations for securely sharing sensitive information in public clouds. Mediated certificateless public key encryption (mCL-PKE) solves the key escrow problem in identity based encryption and certificate revocation problem in public key cryptography. However, existing mCL-PKE schemes are either inefficient because of the use of expensive pairing operations or vulnerable against partial decryption attacks. In order to address the performance and security issues, in this paper, we first propose a mCL-PKE scheme without using pairing operations. We apply our mCL-PKE scheme to construct a practical solution to the problem of sharing sensitive …

Draft Genome Sequence Of Acetobacter Aceti Strain 1023, A Vinegar Factory Isolate, John Hung, Christopher Mill, Sandra Clifton, Vincent Magrini, Ketaki Bhide, Julie Francois, Aaron Ransome, Lucinda Fulton, Jyothi Thimmapuram, Richard Wilson, T. Joseph Kappock

Cyber Center Publications

The genome sequence of Acetobacter aceti 1023, an acetic acid bacterium adapted to traditional vinegar fermentation, comprises 3.0 Mb (chromosome plus plasmids). A. aceti 1023 is closely related to the cocoa fermenter Acetobacter pasteurianus 386B but possesses many additional insertion sequence elements.

A Practical Approach For Provenance Transmission In Wireless Sensor Networks, S.M. Iftekharul Alam, Sonia Fahmy

Cyber Center Publications

Assessing the trustworthiness of sensor data and transmitters of this data is critical for quality assurance. Trust evaluation frameworks utilize data provenance along with the sensed data values to compute the trustworthiness of each data item. However, in a sizeable multi-hop sensor network, provenance information requires a large and variable number of bits in each packet, resulting in high energy dissipation due to the extended period of radio communication. In this paper, we design energy-efficient provenance encoding and construction schemes, which we refer to as Probabilistic Provenance Flow (PPF). Our work demonstrates the feasibility of adapting the Probabilistic Packet Marking …

Security Of Graph Data: Hashing Schemes And Definitions, Muhammad U. Arshad, Ashish Kundu, Elisa Bertino, Krishna Madhavan, Arif Ghafoor

Cyber Center Publications

Use of graph-structured data models is on the rise - in graph databases, in representing biological and healthcare data as well as geographical data. In order to secure graph-structured data, and develop cryptographically secure schemes for graph databases, it is essential to formally define and develop suitable collision resistant one-way hashing schemes and show them they are efficient. The widely used Merkle hash technique is not suitable as it is, because graphs may be directed acyclic ones or cyclic ones. In this paper, we are addressing this problem. Our contributions are: (1) define the practical and formal security model of …

Randomized And Efficient Authentication In Mobile Environments, Wei Jiang, Dan Lin, Feng Li, Elisa Bertino

Cyber Center Publications

In a mobile environment, a number of users act as a network nodes and communicate with one another to acquire location based information and services. This emerging paradigm has opened up new business opportunities and enables numerous applications such as road safety enhancement, service recommendations and mobile entertainment. A fundamental issue that impacts the success of these applications is the security and privacy concerns raised regarding the mobile users. In that, a malicious user or service provider can track the locations of a user traveled so that other malicious act can be carried out more effectively against the user. Therefore, …

Identidroid: Android Can Finally Wear Its Anonymous Suit, Bilal Shebaro, Oyindamola Oluwatimi, Daniele Midi, Elisa Bertino

Cyber Center Publications

Because privacy today is a major concern for mobile applications, network anonymizers are widely available on smartphones, such as Android. However despite the use of such anonymizers, in many cases applications are still able to identify the user and the device by different means than the IP address. The reason is that very often applications require device services and information that go beyond the capabilities of anonymous networks in protecting users’ identity and privacy. In this paper, we propose two solutions that address this problem. The first solution is based on an approach that shadows user and application data, device …

The Palm-Tree Index: Indexing With The Crowd, Aamer Mahmood, Walid G. Aref, Eduard Dragut, Saleh Basalamah

Cyber Center Publications

Crowdsourcing services allow employing human intelligence in tasks that are difficult to accomplish with computers such as image tagging and data collection. At a relatively low monetary cost and through web interfaces such as Amazon’s Mechanical Turk (AMT), humans can act as a computational operator in large systems. Recent work has been conducted to build database management systems that can harness the crowd power in database operators, such as sort, join, count, etc. The fundamental problem of indexing within crowdsourced databases has not been studied. In this paper, we study the problem of tree-based indexing within crowd-nabled databases. We investigate …

Lonomics Atlas: A Tool To Explore Interconnected Ionomic, Genomic And Environmental Data, Eduard Dragut, Amgad Madkour, Mohamed Nabeel, Peter Baker, Mourad Ouzzani, David Salt

Cyber Center Publications

Ionomics Atlas facilitates access, analysis and interpretation of an existing large-scale heterogeneous dataset consisting of ionomic (elemental composition of an organism), ge- netic (heritable changes in the DNA of an organism) and ge- ographic information (geographic location, altitude, climate, soil properties, etc). Ionomics Atlas allows connections to be made between the genetic regulation of the ionome of plant populations and their landscape distribution, allowing scientists to investigate the role of natural ionomic variation in adaptation of populations to varied environmental conditions in the landscape. The goal of the Ionomics Atlas is twofold: (1) to allow both novice and expert users …

The Bench Scientist's Guide To Statistical Analysis Of Rna-Seq Data, Craig R. Yendrek, Elizabeth A. Ainsworth, Jyothi Thimmapuram

Cyber Center Publications

RNA sequencing (RNA-Seq) is emerging as a highly accurate method to quantify transcript abundance. However, analyses of the large data sets obtained by sequencing the entire transcriptome of organisms have generally been performed by bioinformatics specialists. Here we provide a step-by-step guide and outline a strategy using currently available statistical tools that results in a conservative list of differentially expressed genes. We also discuss potential sources of error in RNA-Seq analysis that could alter interpretation of global changes in gene expression.

Whole-Genome Resequencing Of Two Elite Sires For The Detection Of Haplotypes Under Selection In Dairy Cattle Supporting Information, Denis M. Larkin, Hans D. Daetwyler, Alvaro G. Hernandez, Chris L. Wright, Lorie A. Hetrick, Lisa Boucek, Sharon Bachman, Jyothi Thimmapuram

Cyber Center Publications

Using a combination of whole-genome resequencing and high-density genotyping arrays, genome-wide haplotypes were reconstructed for two of the most important bulls in the history of the dairy cattle industry, Pawnee Farm Arlinda Chief (“Chief”) and his son Walkway Chief Mark (“Mark”), each accounting for ∼7% of all current genomes. We aligned 20.5 Gbp (∼7.3× coverage) and 37.9 Gbp (∼13.5× coverage) of the Chief and Mark genomic sequences, respectively. More than 1.3 million high-quality SNPs were detected in Chief and Mark sequences. The genome-wide haplotypes inherited by Mark from Chief were reconstructed using ∼1 million informative SNPs. Comparison of a set …

Artl@ S And Basart: A Loose Coupling Strategy For Digital Humanities, Sorin Matei

Cyber Center Publications

The core ARTL@S digital humanities
strategy is that of loosely coupling
resources, platforms, and use scenarios.
A number of sites will feed from
the same geodatabase (BasArt),
which will be enriched by users with
new content. Inspired by the Web 2.0
design principles, ARTL@S relies on
the BasArt API, which will enable an
ecosystem of sites to use primary
data to generate their own maps,
charts, and tables. A variety of economic
models will also be used to
support the site, from free to paybased.
User-generated content will be
monitored by data management and
curation techniques that will ensure
the …

Authenticated Top-K Aggregation In Distributed And Authenticated Top-K Aggregation In Distributed And, Sunoh Choi, Hyo-Sang Lim, Elisa Bertino

Cyber Center Publications

Top-k queries have attracted interest in many different areas like network and system monitoring, information retrieval, sensor networks, and so on. Since today many applications issue top-k queries on distributed and outsourced databases,
authentication of top-k query results becomes more important. This paper addresses the problem of authenticated top-k aggregation queries (e.g. “find the k objects with the highest aggregate values”) in a distributed system. We propose a new algorithm, called Authenticated Three Phase Uniform Threshold (A-TPUT), which provides not only efficient top-k aggregation over distributed databases but also authentication on the top-k results. We also introduce several enhancements for …

Transcriptome Sequencing Of The Blind Subterranean Mole Rat, Spalax Galili: Utility And Potential For The Discovery Of Novel Evolutionary Patterns, Assaf Malik, Abraham Korol, Sariel Hubner, Aaron Avivi, Alvaro Hernandez, Jyothi Thimmapuram, Shahjahan Ali, Mark Bond, Fabian Glaser, Arnon Paz

Cyber Center Publications

The blind subterranean mole rat (Spalax ehrenbergi superspecies) is a model animal for survival under extreme environments due to its ability to live in underground habitats under severe hypoxic stress and darkness. Here we report the transcriptome sequencing of Spalax galili, a chromosomal type of S. ehrenbergi. cDNA pools from muscle and brain tissues isolated from animals exposed to hypoxic and normoxic conditions were sequenced using Sanger, GS FLX, and GS FLX Titanium technologies. Assembly of the sequences yielded over 51,000 isotigs with homology to ~12,000 mouse, rat or human genes. Based on these results, it was …

Orchardgrass (Dactylis Glomerata L.) Est And Ssr Marker Development, Annotation, And Transferability., B.S. Bushman, S.R. Larson, M Tuna, M.S. West, A.G. Hernandez, D Vullaganti, G Gong, J.G. Robbins, K. B. Jensen, Jyothi Thimmapuram

Cyber Center Publications

Orchardgrass, or cocksfoot [Dactylis glomerata (L.)], has been naturalized on nearly every continent and is a commonly used species for forage and hay production. All major cultivated varieties of orchardgrass are autotetraploid, and few tools or information are available for functional and comparative genetic analyses and improvement of the species. To improve the genetic resources for orchardgrass, we have developed an EST library and SSR markers from salt, drought, and cold stressed tissues. The ESTs were bi-directionally sequenced from clones and combined into 17,373 unigenes. Unigenes were annotated based on putative orthology to genes from rice, Triticeae grasses, other Poaceae, …

Identification And Analysis Of Common Bean (Phaseolus Vulgaris L.) Transcriptomes By Massively Parallel Pyrosequencing, Venu Kalavacharla, Zhanji Liu, Blake C. Meyers, Jyothi Thimmapuram, Kalpalatha Melmaiee

Cyber Center Publications

Common bean (Phaseolus vulgaris) is the most important food legume in the world. Although this crop is very important to both the developed and developing world as a means of dietary protein supply, resources available in common bean are limited. Global transcriptome analysis is important to better understand gene expression, genetic variation, and gene structure annotation in addition to other important features. However, the number and description of common bean sequences are very limited, which greatly inhibits genome and transcriptome research. Here we used 454 pyrosequencing to obtain a substantial transcriptome dataset for common bean.

Privacy-Preserving Assessment Of Location Data Trustworthiness, Chenyun Dai, Fang-Yu Rao, Gabriel Ghinita, Elisa Bertino

Cyber Center Publications

Assessing the trustworthiness of location data corresponding to individuals is essential in several applications, such as forensic science and epidemic control. To obtain accurate and trustworthy location data, analysts must often gather and correlate information from several independent sources, e.g., physical observation, witness testimony, surveillance footage, etc. However, such information may be fraudulent, its accuracy may be low, and its vol-
ume may be insufficient to ensure highly trustworthy data. On the other hand, recent advancements in mobile computing and positioning systems, e.g., GPS-enabled cell phones, highway sensors, etc., bring new and effective technological means to track the location of …