Biomedical Engineering and Bioengineering Commons^™

Fmri Feature Extraction Model For Adhd Classification Using Convolutional Neural Network, Senuri De Silva, Sanuwani Udara Dayarathna, Gangani Ariyarathne, Dulani Meedeniya, Sampath Jayarathna

Computer Science Faculty Publications

Biomedical intelligence provides a predictive mechanism for the automatic diagnosis of diseases and disorders. With the advancements of computational biology, neuroimaging techniques have been used extensively in clinical data analysis. Attention deficit hyperactivity disorder (ADHD) is a psychiatric disorder, with the symptomology of inattention, impulsivity, and hyperactivity, in which early diagnosis is crucial to prevent unwelcome outcomes. This study addresses ADHD identification using functional magnetic resonance imaging (fMRI) data for the resting state brain by evaluating multiple feature extraction methods. The features of seed-based correlation (SBC), fractional amplitude of low-frequency fluctuation (fALFF), and regional homogeneity (ReHo) are comparatively applied to …

Combining Cryo-Em Density Map And Residue Contact For Protein Secondary Structure Topologies, Maytha Alshammari, Jing He

Computer Science Faculty Publications

Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. A topology of secondary structures defines the mapping between a set of sequence segments and a set of traces of secondary structures in three-dimensional space. In order to enhance accuracy in ranking secondary structure topologies, we explored a method that combines three sources of information: a set …

A Deep Learning Approach To Lncrna Subcellular Localization Using Inexact Q-Mer, Weijun Yi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Long non coding Ribonucleic Acids (lncRNAs) can be localized to different cellular components, such as the nucleus, exosome, cytoplasm, ribosome, etc. Their biological functions can be influenced by the region of the cell they are located. Many of these lncRNAs are associated with different challenging diseases. Thus, it is crucial to study their subcellular localization. However, compared to the vast number of lncRNAs, only relatively few have annotations in terms of their subcellular localization. Conventional computational methods use q-mer profiles from lncRNA sequences and then train machine learning models, such as support vector machines and logistic regression with the profiles. …

Restoration Of Bone Material And Microstructural Properties After Long-Term Remodeling Suppression, Abigail A. Coffman

Dissertations and Theses

Anti-resorptive drugs, principally bisphosphonates (BPs), are the mainstay of osteoporosis treatment. They work by inhibiting bone resorption/remodeling, thus preventing bone loss. However, long-term suppression of bone resorption adversely affects bone tissue mechanical properties, even while conserving bone mass. Lack of remodeling leads to accumulation of fatigue-induced microdamage, altered matrix mineralization and reduction in normal bone tissue heterogeneity, causing impaired strength and fracture toughness. The most severe consequence to patients, while rare, is Atypical Femur Fractures (i.e., complete fatigue fractures of the femoral shaft). To counteract the effects of long-term remodeling suppression, a temporary break in BP treatment (a "drug holiday) …

When The Brain Plays A Game: Neural Responses To Visual Dynamics During Naturalistic Visual Tasks, Jason Ki

Dissertations and Theses

Many day-to-day tasks involve processing of complex visual information in a continuous stream. While much of our knowledge on visual processing has been established from reductionist approaches in lab-controlled settings, very little is known about the processing of complex dynamic stimuli experienced in everyday scenarios. Traditional investigations employ event-related paradigms that involve presentation of simple stimuli at select locations in visual space and discrete moments in time. In contrast, visual stimuli in real-life are highly dynamic, spatially-heterogeneous, and semantically rich. Moreover, traditional experiments impose unnatural task constraints (e.g., inhibited saccades), thus, it is unclear whether theories developed under the reductionist …

Development Of Light Actuated Chemical Delivery Platform On A 2-D Array Of Micropore Structure, Hojjat Rostami Azmand, Hojjat Rostami Azmand

Dissertations and Theses

Localized chemical delivery plays an essential role in the fundamental information transfers within biological systems. Thus, the ability to mimic the natural chemical signal modulation would provide significant contributions to understand the functional signaling pathway of biological cells and develop new prosthetic devices for neurological disorders. In this paper, we demonstrate a light-controlled hydrogel platform that can be used for localized chemical delivery in a high spatial resolution. By utilizing the photothermal behavior of graphene-hydrogel composites confined within micron-sized fluidic channels, patterned light illumination creates the parallel and independent actuation of chemical release in a group of fluidic ports. The …

Assessing Midbrain Abnormalities In Parkinson’S Disease Using Magnetic Resonance Imaging, Kiarash Ghassaban

Wayne State University Dissertations

Diagnosing early-stage Parkinson’s disease (PD) and its manifestations is still a clinical challenge. Previous imaging studies using iron, neuromelanin (NM) and the Nigrosome-1 (N1) measures in the substantia nigra (SN) by themselves have been unable to provide sufficiently high diagnostic performance for these methods to be adopted clinically. In this dissertation, we start by studying idiopathic PD patients at their intermediate stages of the disease to evaluate the role of global and regional iron in the major deep gray matter nuclei. Then, we only focus on the NM complex in the midbrain and how neuronal loss interact with iron overload …

Als-Induced Excitability Changes In Individual Motorneurons And The Spinal Motorneuron Network In Sod1-G93a Mice At Symptom Onset, Christiana S.I. Draper

Browse all Theses and Dissertations

Amyotrophic lateral sclerosis (ALS) is the most common motorneuron (MN) disease in adulthood. ALS is hallmarked by the progressive loss of MNs in the brain, brainstem, and spinal cord. Many hypotheses to explain the pathogenesis of ALS have been explored, but the exact mechanisms underlying the development of this disease remain unknown. However, abnormalities in MN excitability and glutamate excitotoxicity are the most widely studied. For decades, researchers have examined MN excitability in ALS, but the current literature is inconsistent, showing evidence of hyperexcitability, hypoexcitability, or no change in excitability of MNs in ALS. Many of these studies also focus …

การพัฒนาเพื่อเพิ่มสมรรถนะของอุปกรณ์ทดสอบภูมิแพ้ทางผิวหนังประเภทพลาสติก, มุธิตา เจียระไนรุ่งโรจน์

Chulalongkorn University Theses and Dissertations (Chula ETD)

โรคภูมิแพ้ (Allergy) เป็นโรคที่พบได้บ่อยและมีผลกระทบสูงทั้งทางเศรษฐกิจและสังคม กระบวนการวินิจฉัยโรคภูมิแพ้ที่เป็นที่นิยมที่สุดในปัจจุบันคือการทดสอบที่ผิวหนังด้วยวิธี Skin prick test (SPT) อย่างไรก็ดีประสิทธิภาพของการทดสอบ SPT ขึ้นอยู่กับความเชี่ยวชาญ และ ประสบการณ์ของแพทย์ผู้ทำการทดสอบ ซึ่งพบว่ามีปัจจัยหลายประการที่ส่งผลต่อประสิทธิภาพในการทดสอบ เช่น ประเภทของอุปกรณ์ ประเภทของวัสดุ และแรงกด เป็นต้น ดังนั้นงานวิจัยจึงมีวัตถุประสงค์ในการศึกษาถึงผลกระทบของปัจจัยต่างๆ ที่ส่งผลต่อประสิทธิภาพในการทดสอบ SPT เพื่อการพัฒนาต่อยอดอุปกรณ์ทดสอบภูมิแพ้ที่มีประสิทธิภาพสูงโดยเฉพาะอย่างยิ่งที่สร้างจากพลาสติก โดยผู้วิจัยได้ทำการศึกษาเปรียบเทียบประสิทธิภาพของอุปกรณ์ทดสอบภูมิแพ้ทางผิวหนังที่มีจำหน่ายในท้องตลาดจำนวน 2 ชนิด คือ ALK lancet และ Feather Lancet และ อุปกรณ์ที่สร้างขึ้นจากการฉีดพลาสติกจำนวน 2 ชนิด (Prototype) ด้วยแรงกด 3 แรง คือ 30, 45 และ 60 กรัม กับอาสาสมัครจำนวน 12 คนโดยผู้ทดสอบเพียงคนเดียวในลักษณะสุ่มจุดเจาะ และเปรียบเทียบกับวิธีการมาตรฐานที่ใช้ ALK และ Needle ในการสะกิดโดยแพทย์ผู้เชี่ยวชาญ โดยใช้สารควบคุมบวก Histamine ความเข้มข้น 10 มก./มล และสารควบคุมลบคือ Normal Saline จากการทดลองกับผู้เข้ารับการทดสอบทั้งสิ้น 12 คน พบว่า ขนาดเฉลี่ยของตุ่มบวมโดยใช้อุปกรณ์ทั้ง 4 ประเภทมีขนาดที่เพิ่มขึ้นตามแรงกด โดยที่แรง 30, 45 และ 60 กรัม ตุ่มบวมมีขนาด 2.70 - 4.31 มม., 3.81 - 4.80 มม. และ 4.30 - 5.28 มม. ตามลำดับ และขนาดของตุ่มบวมของมีความแปรปรวนต่ำ ในขณะที่ขนาดเฉลี่ยของตุ่มบวมโดยวิธีการมาตรฐานทั้ง 2 วิธี คือ ALK และ Needle มีขนาดที่ใหญ่กว่าที่ 5.49 …

Multi-Label Classification On Locally-Linear Data: Application To Chemical Toxicity Prediction, Xiu Huan Yap

Browse all Theses and Dissertations

Computational models may assist in identification and prioritization of large chemical libraries. Recent experimental and data curation efforts, such as from the Tox21 consortium, have contributed towards toxicological datasets of increasing numbers of chemicals and toxicity endpoints, creating a golden opportunity for the exploration of multi-label learning and deep learning approaches in this thesis. Multi-label classification (MLC) methods may improve model predictivity by accounting for label dependence. However, current measures of label dependence, such as correlation coefficient, are inappropriate for datasets with extreme class imbalance, often seen in toxicological datasets. In this thesis, we propose a novel label dependence measure …

Carbon Nanotube-Coated Scaffolds For Tissue Engineering Applications, Soham Dipakbhai Parikh

Browse all Theses and Dissertations

Carbon Nanotubes (CNTs) have beneficial properties for cell scaffolding, which has translated into effective growth of bone, muscle, and cardiac cells. However, loose carbon nanotubes can cause in vivo toxicity. To reduce this risk, our team has developed biomimetic scaffolds with multiscale hierarchy where carpet-like CNT arrays are covalently bonded to larger biocompatible substrates. In this study, we have tested such scaffolds in two distinct types of biomedical applications involving glioblastoma and keratinocyte cells. The growth of glioblastoma (GBM) cells on our CNT-coated biomimetic scaffolds was evaluated to check their suitability as a potential chemotherapy-loaded implant for GBM patient treatment. …

Two-Dimensional & Three-Dimensional Microarray Cell Culture Using Elastomeric Assembly Substrates, Angel Olivera-Torres

Honors Program: Senior Projects (Public)

Tissue engineering and regenerative medicine represent the collection of all engineering disciplines brought together for the common goal of developing novel ways of growing tissues and organs in the laboratory. Efforts have made it possible to replicate or induce growth of 2D structures in the human body like skin, but the clinical need for on-demand solid organs has yet to be met due to lack of understanding of the variables responsible for organogenesis. Cell-colony heterogeneity, 3D-cellular architecture, bioactive molecules, and crosstalk communication between parenchymal cell populations need to be further investigated, and high-throughput technologies can rapidly increase the rate at …

Using A Lubricin Reporter Cell To Test Current Vs. Optimized Media Compositions, Sean M. Kennedy

Honors Undergraduate Theses

Osteoarthritis is a joint disease characterized by the breakdown of articular cartilage. The field of tissue engineering is interested in developing methods to produce biological alternatives to current orthopedic procedures. Lubricin is a molecule which is important in the proper lubrication of articular cartilage. It is a challenge in the field of tissue engineering to produce cartilage with sufficient lubricin expression. Developing a reporter cell for lubricin allowed for a more efficient investigation of the conditions wh­­­ich may influence its expression. By comparing "optimized" and traditional media solutions, it was determined that the use of a previously reported type II …

Workspace And Kinematic Modeling And Analysis Of Semi-Robotic Laparoscopic Surgery, Immanuel E. Girgis

Honors Undergraduate Theses

Laparoscopic Surgery has been revolutionized by the world of Surgical Robotics. Robot-Assisted Surgeries have been proven to have many advantages over the fundamental, traditional "by-hand" procedures previously conducted, and still currently being done for certain operations. Robot-assisted surgery may offer benefits to patients through the use of minimally invasive techniques, which may result in reduced blood loss, reduced blood transfusion, fewer complications, reduced postoperative pain, shorter hospital stays, and reduced recovery times (Ho et al., 2011). Studies have proven that robotic surgery may lead to patients recovering faster depending on the timeframe and the type of procedure (Tang et al., …

Biom 2720: Experimental Design And Analysis For Biomedical Engineering (Syllabus), Stephen Strain

Biomedical Engineering Syllabi Archive

Course Description: Application of probability, statistics, error analysis, uncertainty in design and performance of biomedical engineering experimentation; discussion and evaluation of common experimental designs for medical device development.

Novel Tools For Analysis Of Disordered Sleep And Motor Behavior In Preclinical Models Of Disease, Dillon M. Huffman

Theses and Dissertations--Biomedical Engineering

Subtle changes in sleep architecture can accompany and be symptomatic of various diseases or disorders. Understanding the complex interactions between sleep and health requires the ability to characterize sleep, probe its underlying mechanisms through perturbation, and quantify dependent physiological outcomes. Rodent models have come to be accepted as a valuable tool for preclinical investigations. However, experimental tools to accomplish such research typically rely on laborious methods that limit throughput and flexibility. Thus, research tools that minimize workload could be of great value to the research community and expedite investigation of the underlying mechanisms of sleep and further the development of …

Changes In Cardiovascular, Respiratory, And Neural Activity By Music: Effects Of Breathing Pathway On Feeling Emotions, Mohammad Javad Mollakazemi

Theses and Dissertations--Biomedical Engineering

Listening to music can induce emotional and physiological changes. Increasing recognition of the palliative effects of music has led to its use as an adjuvant therapeutic tool in the treatment of various diseases. It is also well known that autonomic nervous activities and some cardiorespiratory rhythms change in correspondence with music. However, less is known about how these effects triggered by music come about. Listening to music affects synchronization between electroencephalograms (EEGs) and cardiac rhythmic activity. This interaction between cardiac and electrical responses led us to investigate whether EEG segments synchronized to different portions of the cardiac cycle can better …

Facilitating Analysis Of Toxoplasma Gondii Bradyzoite Metabolic Activity Via Image Processing And Multivariate Logistic Regression For High Throughput Classification Of Mitochondrial Morphologies, Brooke Place

Theses and Dissertations--Biomedical Engineering

Approximately a third of the population worldwide is chronically infected by the parasite Toxoplasma gondii. During chronic infection the parasite resides within tissue cysts as the poorly understood bradyzoite form. Observation of these bradyzoites via microscopic imaging within tissue cyst purified from infected mouse brains has shown metabolic activity with heterogeneous replication potential. With fluorescence microscopy imaging targeting the parasite’s actively respiring mitochondria, the parasite’s metabolic state can be further investigated as the morphology of mitochondria can be associated with specific physiologic states. However, manually classifying mitochondrial morphologies from these images can be tedious and prone to error as …

Tailoring Texture, Microstructure, And Shape Memory Behavior Of Niti Alloys Fabricated By L-Pbf-Am, Sayed Ehsan Saghaian N.E.

Theses and Dissertations--Mechanical and Aerospace Engineering

Laser Powder Bed Fusion (L-PBF) is one of the most promising Additive Manufacturing (AM) methods to fabricate near net-shape metallic materials for a wide range of applications such as patient-specific medical devices, functionally graded materials, and complex structures. NiTi shape memory alloys (SMAs) are of great interest due to a combination of unique features, such as superelasticity, shape memory effect, high ductility, work output, corrosion resistance, and biocompatibility that could be employed in many applications in automotive, aerospace, and biomedical industries. Due to the difficulties with traditional machining and forming of NiTi components, the ability to fabricate complex parts, tailor …

Additive Manufacturing In Personalized Medicine: Patient-Customized Solid Dose Medicines, And Patient-Customized Wound Care Device, Amir Najarzadeh

Theses and Dissertations--Mechanical and Aerospace Engineering

Personalized Medicine - from a one-size fits all to a tailored approach is the future in pharmaceutical therapeutics and medical applications. The aim of this study is demonstrate additive manufacturing in two personalized medicine applications: 1. Patient- customized solid dose medicines, and 2. Patient-customized wound care device. The aim of the first application is to develop an inexpensive and accurate method to design and fabricate patient-customized tablets. Particularly this paper focuses on fabricating and dose controlling of patient-customized extended release prednisolone-poly(vinyle alcohole) PVA. Dry-Blending, Wet Granulation, Extrusion, Spherionization, Hot melt extrusion (HME) was adopted to produce drug loaded prednisolone-PVA filaments …

Electroporation Safety Factor Of 300 Nanosecond And 10 Millisecond Defibrillation In Langendorff-Perfused Rabbit Hearts, Johanna U. Neuber, Andrei G. Pakhomov, Christian W. Zemlin

Bioelectrics Publications

Aims

Recently, a new defibrillation modality using nanosecond pulses was shown to be effective at much lower energies than conventional 10 millisecond monophasic shocks in ex vivo experiments. Here we compare the safety factors of 300 nanosecond and 10 millisecond shocks to assess the safety of nanosecond defibrillation.

Methods and results

The safety factor, i.e. the ratio of median effective doses (ED50) for electroporative damage and defibrillation, was assessed for nanosecond and conventional (millisecond) defibrillation shocks in Langendorff-perfused New Zealand white rabbit hearts. In order to allow for multiple shock applications in a single heart, a pair of needle electrodes …

Bio-Inspired Materials For Electrochemical Sensors, Matthew Joseph Hummel

Electronic Theses and Dissertations

Electrochemical biosensors are a rapidly growing research area that has greatly improved its specificity, accuracy, and precision in the detection of biomolecules in contemporary literature and industry alike. Typically, these systems exist in a three-electrode conformation with a working electrode functioning as the anode, a counter electrode functioning as the cathode, and a reference electrode allowing for the control of potential in the system. The method by which these sensors work is through the sharing of electrons via redox reactions with the target molecule and the working electrode or modifications on its surface. By exploiting the function of biomaterials that …

Comparative Analysis Of Computationally Accelerated Ngs Alignment, Ada Chaeli Van Der Zijp-Tan

Honors Theses

The Smith-Waterman algorithm is the basis of most current sequence alignment technology, which can be used to identify similarities between sequences for cancer detection and treatment because it provides researchers with potential targets for early diagnosis and personalized treatment. The growing number of DNA and RNA sequences available to analyze necessitates faster alignment processes than are possible with current iterations of the Smith-Waterman (S-W) algorithm. This project aimed to identify the most effective and efficient methods for accelerating the S-W algorithm by investigating recent advances in sequence alignment. Out of a total of 22 articles considered in this project, 17 …

Sensitray: An Integrated Measuring Device For Monitoring Children’S Mealtime Dietary Intake, Hunter S. Guru, Anthony D. Weng, Santosh Pitla, Dipti Dev

Department of Child, Youth, and Family Studies: Faculty Publications

Childhood nutrition establishes consumption norms that affect an individual’s health over the course of their lives. However, early nutrition interventions to establish such norms are uncommon owing to the various inefficiencies associated with current methods of measuring childhood nutrition. Here, we present an IoT measuring device, called the SensiTray, which accurately tracks mealtime intake in a child-friendly and cost-effective fashion. Principal technologies underlying the SensiTray (including mass-sensing technologies, microcontrollers) are identified and analyzed, along with other design choices. Operation of the SensiTray is explained with special attention given to SensiTray software peripherals and algorithms. Preliminary testing consisted of static and …

Perceptually Improved Medical Image Translations Using Conditional Generative Adversarial Networks, Anurag Vaidya

Honors Theses

Magnetic resonance imaging (MRI) can help visualize various brain regions. Typical MRI sequences consist of T1-weighted sequence (favorable for observing large brain structures), T2-weighted sequence (useful for pathology), and T2-FLAIR scan (useful for pathology with suppression of signal from water). While these different scans provide complementary information, acquiring them leads to acquisition times of ~1 hour and an average cost of $2,600, presenting significant barriers. To reduce these costs associated with brain MRIs, we present pTransGAN, a generative adversarial network capable of translating both healthy and unhealthy T1 scans into T2 scans. We show that the addition of non-adversarial …

Position-Scanning Peptide Libraries As Particle Immunogens For Improving Cd8+ T-Cell Responses, Michael C. Vega

Faculty Articles, Papers, and Other Scholarship

Short peptides reflecting major histocompatibility complex (MHC) class I (MHC-I) epitopes frequently lack sufficient immunogenicity to induce robust antigen (Ag)-specific CD8⁺ T cell responses. In the current work, it is demonstrated that position-scanning peptide libraries themselves can serve as improved immunogens, inducing Ag-specific CD8⁺ T cells with greater frequency and function than the wild-type epitope. The approach involves displaying the entire position-scanning library onto immunogenic nanoliposomes. Each library contains the MHC-I epitope with a single randomized position. When a recently identified MHC-I epitope in the glycoprotein gp70 envelope protein of murine leukemia virus (MuLV) is assessed, only one …

Sex-Related Differences In Murine Models Of Chemically Induced Pulmonary Fibrosis, Pavel Solopov, Ruben Manuel Luciano Colunga Biancatelli, Christiana Dimitropoulou, John D. Catravas

Bioelectrics Publications

We developed two models of chemically induced chronic lung injury and pulmonary fibrosis in mice (intratracheally administered hydrochloric acid (HCl) and intratracheally administered nitrogen mustard (NM)) and investigated male-female differences. Female mice exhibited higher 30-day survival and less weight loss than male mice. Thirty days after the instillation of either HCl or NM, bronchoalveolar lavage fluid displayed a persistent, mild inflammatory response, but with higher white blood cell numbers and total protein content in males vs. females. Furthermore, females exhibited less collagen deposition, milder pulmonary fibrosis, and lower Ashcroft scores. After instillation of either HCl or NM, all animals displayed …

Age-Dependent Chronic Lung Injury And Pulmonary Fibrosis Following Single Exposure To Hydrochloric Acid, Ruben M.L. Colunga Biancatelli, Pavel Solopov, Christiana Dimitropoulou, John D. Catravas

Bioelectrics Publications

Exposure to hydrochloric acid (HCl) represents a threat to public health. Children may inhale higher doses and develop greater injury because of their smaller airways and faster respiratory rate. We have developed a mouse model of pediatric exposure to HCl by intratracheally instilling p24 mice (mice 24 days old; 8–10 g) with 2 µL/g 0.1 N HCl, and compared the profile of lung injury to that in HCl-instilled adults (10 weeks old; 25–30 g) and their age-matched saline controls. After 30 days, alveolar inflammation was observed with increased proteinosis and mononuclear cells in the bronchoalveolar lavage fluid (BALF) in both …

Electrospinning Of Formic Acid/Acetic Acid And Nylon-6 Solutions For Wearable Hydration Sensors, Nichole Cooper, Jonathan Doak

Williams Honors College, Honors Research Projects

Students have been working on the development of wearable hydration sensors at the startup company RooSense. The goal of the company is to develop a lightweight wearable sensor that enables the user to know their hydration level, thus elevating their performance goals. To measure the hydration of the wearer, the sodium and other salt ions are collected from the user’s sweat as they exercise. This sweat is analyzed as it is collected to give the user an exact level of hydration, so they know how much fluids they need. The production of this ion sensor requires numerous steps and iteration …

Ecg Monitoring In Athletes, Jalal Jwayyed, Kelly Purgason, Joseph Linder, Annamarie Alfery, Silvia Furman

Williams Honors College, Honors Research Projects

Athletes and medical personnel need reliable methods to monitor vital signs and detect potentially life-threatening issues before they occur. Electrocardiograph (ECG) monitors are currently the best method of detecting heart-related health issues. Current ECG monitors worn by athletes are difficult to use and lack the ability to track ECGs in real time. Through research and interviews with various clinicians, further problems have been identified that include poor electrode adhesion, and a lack of compatibility with the equipment worn by athletes. Our team proposes to develop solutions that will improve performance and comfort associated with ECG monitors for athletic applications. This …