Engineering Commons^™

Ssaw: A New Sequence Similarity Analysis Method Based On The Stationary Discrete Wavelet Transform, Jie Lin, Donald Adjeroh, Bing-Hua Jiang, Yue Jiang

Faculty & Staff Scholarship

Background: Alignment-free sequence similarity analysis methods often lead to significant savings in computational time over alignment-based counterparts.

Results: Anewalignment-freesequencesimilarityanalysismethod,calledSSAWisproposed.SSAWstandsfor Sequence Similarity Analysis using the Stationary Discrete Wavelet Transform (SDWT). It extracts k-mers from a sequence, then maps each k-mer to a complex number field. Then, the series of complex numbers formed are transformed into feature vectors using the stationary discrete wavelet transform. After these steps, the original sequence is turned into a feature vector with numeric values, which can then be used for clustering and/or classification.

Conclusions: Usingtwodifferenttypesofapplications,namely,clusteringandclassification,wecomparedSSAW against the the-state-of-the-art alignment free sequence analysis methods. SSAW demonstrates competitive or …

Feature-Based And String-Based Models For Predicting Rna-Protein Interaction, Donald Adjeroh, Maen Allaga, Jun Tan, Jie Lin, Yue Jiang, Ahmed Abbasi, Xiaobo Zhou

Faculty & Staff Scholarship

In this work, we study two approaches for the problem of RNA-Protein Interaction (RPI). In the first approach, we use a feature-based technique by combining extracted features from both sequences and secondary structures. The feature-based approach enhanced the prediction accuracy as it included much more available information about the RNA-protein pairs. In the second approach, we apply search algorithms and data structures to extract effective string patterns for prediction of RPI, using both sequence information (protein and RNA sequences), and structure information (protein and RNA secondary structures). This led to different string-based models for predicting interacting RNA-protein pairs. We show …

Hyperspectral Imaging And K-Means Classification For Histologic Evaluation Of Ductal Carcinoma In Situ, Yasser Khouj, Jeremy Dawson, James Coad, Linda Vona-Davis

Faculty & Staff Scholarship

Hyperspectral imaging (HSI) is a non-invasive optical imaging modality that shows the potential to aid pathologists in breast cancer diagnoses cases. In this study, breast cancer tissues from different patients were imaged by a hyperspectral system to detect spectral differences between normal and breast cancer tissues. Tissue samples mounted on slides were identified from 10 different patients. Samples from each patient included both normal and ductal carcinoma tissue, both stained with hematoxylin and eosin stain and unstained. Slides were imaged using a snapshot HSI system, and the spec- tral reflectance differences were evaluated. Analysis of the spectral reflectance values indicated …

Photoluminescence Mechanism And Applications Of Zn-Doped Carbon Dots, Quan Xu, Wei Cai, Miaoran Zhang, Yingchun Ye, Yeqing Li, Lipeng Zhang, Yongjian Guo, Zhiqiang Yu, Siyu Li, Xun Lin, Yusheng Chen, Yan Lou, Jason Street, Meng Xu

Faculty & Staff Scholarship

Heteroatom-doped carbon dots (CDs) with excellent optical characteristics and negligible toxicity have emerged in many applications including bioimaging, biosensing, photocatalysis, and photothermal therapy. The metal-doping of CDs using various heteroatoms results in an enhancement of the photophysics but also imparts them with multifunctionality. However, unlike nonmetal doping, typical metal doping results in low fluorescence quantum yields (QYs), and an unclear photoluminescence mechanism. In this contribution, we detail results concerning zinc doped CDs (Zn-CDs) with QYs of up to 35%. The zinc ion charges serve as a surface passivating agent and prevent the aggregation of graphene p–p stacking, leading to an …

Development Of Low Frequency Electron Paramagnetic Resonance Methods And Instrumentation For Biological Applications, Laura A. Buchanan

Electronic Theses and Dissertations

EPR is a powerful biophysical tool that can be used to measure tumor physiology. With the addition of magnetic field gradients, the spectral properties of paramagnetic species can be mapped. To facilitate EPR imaging, methods and instrumentation at frequencies between 250 MHz and 1 GHz were developed.

At low spin concentrations, the rapid scan background signal is often many times larger than the EPR signal of interest. To help remove the background contribution, a data acquisition procedure that takes advantage of a cross-loop resonator and bipolar power supplies was developed at 250 MHz. In this procedure, two scans are collected. …

Studying Facial Expression Recognition And Imitation Ability Of Children With Autism Spectrum Disorder In Interaction With A Social Robot, Farzaneh Askari

Electronic Theses and Dissertations

Children with Autism Spectrum Disorder (ASD) experience limited abilities in recognizing non-verbal elements of social interactions such as facial expressions [1]. They also show deficiencies in imitating facial expressions in social situations. In this Master thesis, we focus on studying the ability of children with ASD in recognizing facial expressions and imitating the expressions using a rear-projected expressive humanoid robot, called Ryan. Recent studies show that social robots such as Ryan have great potential for autism therapy. We designed and developed three studies, first to evaluate the ability of children with ASD in recognizing facial expressions that are presented to …

Integrated Analysis Of The Value Of Wetland Services In Coastal Adaptation; Methodology And Case Study Of Hampton-Seabrook Estuary, New Hampshire, Paul Kirshen, Semra Aytur, David M. Burdick, Diane Foster, Tom Lippmann, Ellen Douglas, Sydney Nick, Chris Watson

Jackson Estuarine Laboratory

The present impacts from coastal storms and high tides grow significantly over time due to SLR even over the relatively short period to 2060. Hydrodynamic model simulations of storm surge with and without sea level rise scenarios show that although flooding and inundation increases with increasing subtidal forcing and higher sea level, dissipation of the tide and storm surge in the estuary channel somewhat limits the maximum inundation that might otherwise be expected in the back marsh areas. The estuary is dominated by high marsh, which lies high in the intertidal zone and by 2060 it will convert to mostly …

Proactive Coordination In Healthcare Service Systems Through Near Real-Time Analytics, Seung Yup Lee

Wayne State University Dissertations

The United States (U.S.) healthcare system is the most expensive in the world. To improve the quality and safety of care, health information technology (HIT) is broadly adopted in hospitals. While EHR systems form a critical data backbone for the facility, we need improved 'work-flow' coordination tools and platforms that can enhance real-time situational awareness and facilitate effective management of resources for enhanced and efficient care. Especially, these IT systems are mostly applied for reactive management of care services and are lacking when they come to improving the real-time "operational intelligence" of service networks that promote efficiency and quality of …

A Data-Driven Approach For Detecting Autism Spectrum Disorders, Manika Kapoor, David Anastasiu

Faculty Publications

No abstract provided.

Tolle Lege Works Published In 2018, Mcquade Library

Bibliographies

Compiled Tolle Lege bibliography of works published by members of the Merrimack College Community in 2018. Works include journal articles, books, book chapters, conference presentations and posters, and more.

Drughelp.Care – A Web Application For The Discovery Of Drug Addiction Treatment Facilities, Sachin Hiriyanna

ETD Archive

One of the current and biggest problems in the system of emergency care for the drug overdose epidemic, is the failure of information delivery on nearby treatment facilities. Even though some initiatives on the internet tried to solve this issue, they either failed in delivering the information or in providing ease of usability. This thesis research aims to develop a web application which, 1. Delivers a highly accurate, easy-to-understand and targeted information in a timely manner for drug abusers and their well-wishers. 2. Provides an eco-system for the treatment facilities with an easy-to-use backend to constantly update their complex information …

Data-Driven Modeling For Decision Support Systems And Treatment Management In Personalized Healthcare, Milad Zafar Nezhad

Wayne State University Dissertations

Massive amount of electronic medical records (EMRs) accumulating from patients and populations motivates clinicians and data scientists to collaborate for the advanced analytics to create knowledge that is essential to address the extensive personalized insights needed for patients, clinicians, providers, scientists, and health policy makers. Learning from large and complicated data is using extensively in marketing and commercial enterprises to generate personalized recommendations. Recently the medical research community focuses to take the benefits of big data analytic approaches and moves to personalized (precision) medicine. So, it is a significant period in healthcare and medicine for transferring to a new paradigm. …

Venous Thromboembolism (Vte) Harm Measurement And Risk Assessment In Real-Time Using Electronic Health Records(Ehr), Seyed Mani Marashi

Wayne State University Dissertations

Venous Thromboembolism (VTE) is a deadly disease and is considered as one of the top reasons for avoidable hospital deaths in the United States and around the world. Patients who survive this disease often must face life-long complications such as Post-thrombotic syndrome (PTS), Chronic thromboembolic pulmonary hypertension (CTPH), etc. Therefore, it is important to monitor and reduce the number of VTE instances in hospitals. This study shows how Electronic Health Records (EHRs) can be utilized to achieve this goal.

First, a new near real-time VTE harm measurement model was developed. Not only the developed model can deliver near real-time results, …

Academy Presidents And Institutional Members, Academy Editors

Journal of the Arkansas Academy of Science

No abstract provided.

Business Meeting Report (Secretary's And Treasurer's Report), Academy Editors

Journal of the Arkansas Academy of Science

No abstract provided.

Journal Acknowledgments And Editorial Board, Academy Editors

Journal of the Arkansas Academy of Science

No abstract provided.

Instructions To Authors For The Journal Of The Arkansas Academy Of Science, Academy Editors

Journal of the Arkansas Academy of Science

No abstract provided.

Chronic Risk And Disease Management Model Using Structured Query Language And Predictive Analysis, Mamata Ojha

Electronic Theses and Dissertations

Individuals with chronic conditions are the ones who use health care most frequently and more than 50% of top ten causes of death are chronic diseases in United States and these members always have health high risk scores. In the field of population health management, identifying high risk members is very important in terms of patient health care, disease management and cost management. Disease management program is very effective way of monitoring and preventing chronic disease and health related complications and risk management allows physicians and healthcare companies to reduce patient’s health risk, help identifying members for care/disease management along …

Wild-Type P53 Enhances Endothelial Barrier Function By Mediating Rac1 Signalling And Rhoa Inhibition, Nektarios Barabutis, Christiana Dimitropoulou, Betsy Gregory, John D. Catravas

Bioelectrics Publications

Inflammation is the major cause of endothelial barrier hyper-permeability, associated with acute lung injury and acute respiratory distress syndrome. This study reports that p53 "orchestrates" the defence of vascular endothelium against LPS, by mediating the opposing actions of Rac1 and RhoA in pulmonary tissues. Human lung microvascular endothelial cells treated with HSP90 inhibitors activated both Rac1- and P21-activated kinase, which is an essential element of vascular barrier function. 17AAG increased the phosphorylation of both LIMK and cofilin, in contrast to LPS which counteracted those effects. Mouse lung microvascular endothelial cells exposed to LPS exhibited decreased expression of phospho-cofilin. 17AAG treatment …

Alteration Of Metabolite Profiling By Cold Atmospheric Plasma Treatment In Human Myeloma Cells, Dehui Xu, Yujing Xu, Ning Ning, Qingjie Cui, Zhijie Liu, Xiaohua Wang, Dingxin Liu, Hailan Chen, Michael G. Kong

Bioelectrics Publications

BACKGROUND: Despite new progress of chemotherapy in multiple myeloma (MM) clinical treatment, MM is still a refractory disease and new technology is needed to improve the outcomes and prolong the survival. Cold atmospheric plasma is a rapidly developed technology in recent years, which has been widely applied in biomedicine. Although plasma could efficiently inactivate various tumor cells, the effects of plasma on tumor cell metabolism have not been studied yet.

METHODS: In this study, we investigated the metabolite profiling of He plasma treatment on myeloma tumor cells by gas-chromatography time-of-flight (GC-TOF) mass-spectrometry. Meanwhile, by bioinformatic analysis such as GO and …

Nano-Pulse Stimulation Ablates Orthotopic Rat Hepatocellular Carcinoma And Induces Innate And Adaptive Memory Immune Mechanisms That Prevent Recurrence, Brittany P. Lassiter, Siqi Guo, Stephen J. Beebe

Bioelectrics Publications

Nano-pulse stimulation (NPS), previously called nsPEFs, induced a vaccine-like effect after ablation of orthotopic N1-S1 hepatocellular carcinoma (HCC), protecting rats from subsequent challenges with N1-S1 cells. To determine immunity, immune cell phenotypes were analyzed in naïve, treated and protected rats. NPS provides a positive, post-ablation immuno-therapeutic outcome by alleviating immunosuppressive T regulatory cells (Treg) in the tumor microenvironment (TME), allowing dendritic cell influx and inducing dynamic changes in natural killer cells (NKs), NKT-cells and T-lymphocytes in blood, spleen and liver. NPS induced specific increases in NKs and NKT-cells expressing CD8 and activation receptors CD314-NKG2D and CD161 (NK1.1) in the TME …

Tumor Cell Death After Electrotransfer Of Plasmid Dna Is Associated With Cytosolic Dna Sensor Upregulation, Katarina Znidar, Masa Bosnjak, Nina Semenova, Olga N. Pakhomova, Loree Heller, Maja Cemazar

Bioelectrics Publications

Cytosolic DNA sensors are a subgroup of pattern recognition receptors (PRRs) and are activated by the abnormal presence of the DNA in the cytosol. Their activation leads to the upregulation of pro-inflammatory cytokines and chemokines and can also induce cell death. The presence of cytosolic DNA sensors and inflammatory cytokines in TS/A murine mammary adenocarcinoma and WEHI 164 fibrosarcoma cells was demonstrated using real time reverse transcription polymerase chain reaction (RT-PCR), western blotting and enzyme-linked immunosorbent assay (ELISA). After electrotransfer of plasmid DNA (pDNA) using two pulse protocols, the upregulation of DNA-depended activator of interferon regulatory factor or Z-DNA binding …

Upregulation Of Dna Sensors In B16.F10 Melanoma Spheroid Cells After Electrotransfer Of Pdna, Katarina Znidar, Masa Bosnjak, Tanja Jesenko, Loree C. Heller, Maja Cemazar

Bioelectrics Publications

Increased expression of cytosolic DNA sensors, a category of pattern recognition receptor, after control plasmid DNA electrotransfer was observed in our previous studies on B16.F10 murine melanoma cells. This expression was correlated with the upregulation of proinflammatory cytokines and chemokines and was associated with cell death. Here, we expanded our research to include the influence of features of cells in a 3-dimensional environment, which better represents the tumors’ organization in vivo. Our results show that lower number of cells were transfected in spheroids compared to 2-dimensional cultures, that growth was delayed after electroporation alone or after electrotransfer of plasmid …

Nano-Pulse Stimulation For The Treatment Of Pancreatic Cancer And The Changes In Immune Profile, Sigi Guo, Niculina I. Burcus, James Hornef, Yu Jing, Chunqi Jiang, Richard Heller, Stephen J. Beebe

Bioelectrics Publications

A Pancreatic cancer is a notorious malignant neoplasm with an extremely poor prognosis. Current standard of care is rarely effective against late-stage pancreatic cancer. In this study, we assessed nanopulse stimulation (NPS) as a local treatment for pancreatic cancer in a syngeneic mouse Pan02 pancreatic cancer model and characterized corresponding changes in the immune profile. A single NPS treatment either achieved complete tumor regression or prolonged overall survival in animals with partial tumor regression. While this is very encouraging, we also explored if this local ablation effect could also result in immune stimulation, as was observed when NPS led to …

Objectively Measuring Effects Of Electro-Acupuncture In Parkinsonian Rhesus Monkeys, Rui Zhang, Anders H. Andersen, Peter A. Hardy, Eric Forman, April Evans, Yi Ai, Jin Yue, Guihua Yue, Don M. Gash, Richard Grondin, Zhiming Zhang

Magnetic Resonance Imaging and Spectroscopy Center Faculty Publications

Acupuncture has increasingly been used as an alternative therapy for treatment of Parkinson’s disease (PD). However, the efficacy of acupunture for PD still remains unclear. The present study was designed to objectively and safely monitor anti-parkinsonian effects of electroacupuncture (EA) and brain activity in nonhuman primates modeling human PD. Six middle-aged rhesus monkeys were extensively studied by a computerized behavioral testing battery and by pharmacological MRI (phMRI) scans with specific dopaminergic drug stimulations. All animals were evaluated for behavior and phMRI responses under normal, parkinsonian, parkinsonian with EA treatment and parkinsonian after EA treatment conditions. Stable parkinsonian features were observed …

Exogenous Fniii 12-14 Regulates Tgf-Β1-Induced Markers, Hilmi M. Humeid

Theses and Dissertations

The extracellular matrix protein Fibronectin (FN) plays an important role in cell contractility, differentiation, growth, adhesion, and migration. The 12th -14th Type III repeats of FN (FNIII 12-14), also referred to as the Heparin-II domain, comprise a highly promiscuous growth factor (GF) binding region. This binding domain aids in cellular signaling initiated from the ECM. Additionally, FN has the ability to assemble into fibrils under certain conditions, mostly observed during cell contractile processes such as those that initiate due to upregulation of Transforming Growth Factor Beta 1 (TGF-β1) [1], [2]. Previous work from our lab has shown that self-assembly of …

Iact Undergraduate Certificate In Applied Creativity (Year 1 - 2018), Brian Laduca

IACT Certificate Program

At the Institute of Applied Creativity for Transformation (IACT) at ArtStreet, we seek to empower a creatively confident 21st-century student with the ability to discover, invent and innovate ambiguous ideas through a disruptive design process that will impact today’s ever-changing global world regardless of degree focus.

IACT is home to the nation’s first undergraduate certificate in Applied Creativity for Transformation. Open to undergraduate students of any major, the certificate is a first step in achieving the University of Dayton’s vision of innovation, applied creativity, entrepreneurship and community engagement for the common good.

Optical Coherence Tomography Application To Alopecia In The Scalp, Elizabeth Melcher

Research Opportunities for Engineering Undergraduates (ROEU) Program 2017-18

Alopecia is the loss of hair, whether it be from the scalp or other regions of the body. Current techniques used to best diagnose and track alopecia are often invasive, requiring a biopsy for results. The use of the OCT, or optical coherence tomography, could drastically improve a patient’s experience in undergoing a diagnosis while proving accurate results. The objective of this study is to develop diagnostic algorithms for the rapid, non-invasive diagnosis of alopecia with OCT. The first step is collecting OCT images of a healthy scalp to understand the anatomical structures with the imaging technique.

Design And Development Of An Emergency System For Children In A Hot Car At Risk Of Heatstroke, Nathan Kisha

Research Opportunities for Engineering Undergraduates (ROEU) Program 2017-18

Since 1998, an average of 37 children have died every year due to heat-related deaths after being stuck in a vehicle, making it the leading cause of non-crash-related fatalities among children. This creates an opportunity to create a system which will be able to detect this danger and do something in order to prevent it. There are 4 main objectives for the system to be able to accomplish: 1) determine if the temperature in the car poses a risk, 2) use an alarm to provide a warning and wake up a sleeping child, 3) determine if someone is in the …

Fatigue And Damage Of Porcine Pars Interarticularis During Asymmetric Loading, Colin Bright, Stephen Tiernan, Fiona Mcevoy, Pat Kiely

Articles

If the articular facets of the vertebra grow in an asymmetric manner, the developed bone geometry causes an asymmetry of loading. When the loading environment is altered by way of increased activity, the likelihood of acquiring a stress fracture may be increased. The combination of geometric asymmetry and increased activity is hypothesised to be the precursor to the stress fracture under investigation in this study, spondylolysis. This vertebral defect is an acquired fracture with 7% prevalence in the paediatric population. This value increases to 21% among athletes who participate in hyperextension sports. Tests were carried out on porcine lumbar vertebrae, …